├── webpage ├── images ├── index.html ├── manuscript.pdf └── README.md ├── content ├── individual-latex-manuscripts.txt ├── individual-docx-manuscripts.txt ├── images │ ├── FIgX1.jpg │ ├── Summary.pdf │ ├── SARS_CoV_2.png │ ├── interests.png │ ├── thumbnail.png │ ├── diagnostics.png │ ├── N000-overview.pdf │ ├── N000-overview.png │ ├── N002-Vaccines.pdf │ ├── N002-Vaccines.png │ ├── cell-lines-moi.jpg │ ├── genome-structure.png │ ├── cell-lines-moi.afdesign │ ├── N001-LifeCyclePlusDrugs.pdf │ ├── N001-LifeCyclePlusDrugs.png │ ├── cell-lines-moi-partB.afdesign │ ├── ebmdatalab-trials-original.png │ ├── 4.3-summary-R-M-biologicsDrugs.pdf │ ├── summary-M-M-Covid19Mechanism.pdf │ ├── 4.3.4.1.1-summary-L-M-DNAVaccine.pdf │ ├── 4.3.4.1.2-summary-L-L-RNAVaccine.pdf │ ├── covid-19-review-workflow-figure.pdf │ ├── covid-19-review-workflow-figure.png │ ├── 4.2-summary-R-M-smallMoleculeDrugs.pdf │ ├── 4.3.1-summary-R-M-moreTocilizumab.pdf │ ├── 4.3.2.1-summary-R-U-moreMonoclonal.pdf │ ├── covid-19-review-workflow-horizontal.pdf │ ├── covid-19-review-workflow-horizontal.png │ ├── covid-19-review-workflow-horizontal-cropped.pdf │ ├── orcid.svg │ ├── mastodon.svg │ ├── twitter.svg │ └── github.svg ├── 94-ismms-appendix-header.md ├── 90.back-matter.md ├── 70.coi-contribs.md ├── mountSinaiNames.tsv ├── available-text │ └── immune-response.md ├── previous_sections │ ├── 01.abstract.md │ └── 50.discussion.md ├── 00.front-matter.md ├── manual-references.bib └── response-to-reviews │ ├── therapeutics-v1.md │ ├── pathogenesis-v1.md │ └── methods-v1.md ├── ci ├── .gitignore ├── README.md ├── install-spellcheck.sh ├── install.sh └── deploy.sh ├── .github ├── images │ ├── 6-submit.png │ ├── 3-blue-plus.png │ ├── 1-initial-view.png │ ├── 4-click-suggest.png │ ├── 5-make-change.png │ └── 2-initial-view-files.png ├── workflows │ ├── labeler.yml │ ├── ai-revision.yaml │ ├── update-external-resources.yaml │ └── manubot.yaml ├── labeler.yml ├── ISSUE_TEMPLATE │ ├── request-for-help.md │ ├── feature_request.md │ ├── new-paper-template.md │ ├── new-diag-study-template.md │ └── new-therapy-study-template.md └── pull_request_template.md ├── .gitignore ├── output └── README.md ├── .appveyor.yml ├── CODE_OF_CONDUCT.md ├── setup.bash ├── LICENSE-CC0.md ├── CONTRIBUTING.md ├── README.md ├── INSTRUCTIONS.md ├── SETUP.md └── LICENSE.md /webpage/images: -------------------------------------------------------------------------------- 1 | v/latest/images -------------------------------------------------------------------------------- /webpage/index.html: -------------------------------------------------------------------------------- 1 | v/latest/index.html -------------------------------------------------------------------------------- /content/individual-latex-manuscripts.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /webpage/manuscript.pdf: 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-------------------------------------------------------------------------------- https://raw.githubusercontent.com/greenelab/covid19-review/HEAD/content/images/covid-19-review-workflow-horizontal-cropped.pdf -------------------------------------------------------------------------------- /.github/workflows/labeler.yml: -------------------------------------------------------------------------------- 1 | name: "Issue Labeler" 2 | on: 3 | issues: 4 | types: [opened, edited] 5 | 6 | jobs: 7 | triage: 8 | runs-on: ubuntu-latest 9 | steps: 10 | - uses: github/issue-labeler@v2.0 11 | with: 12 | repo-token: "${{ secrets.GITHUB_TOKEN }}" 13 | configuration-path: .github/labeler.yml 14 | not-before: 2020-03-23T06:00:00Z 15 | enable-versioned-regex: 0 16 | -------------------------------------------------------------------------------- /ci/README.md: -------------------------------------------------------------------------------- 1 | # Continuous integration tools 2 | 3 | This directory contains tools and files for continuous integration (CI). 4 | Specifically, [`deploy.sh`](deploy.sh) runs on successful `main` branch builds that are not pull requests. 5 | The contents of `../webpage` are committed to the `gh-pages` branch. 6 | The contents of `../output` are committed to the `output` branch. 7 | 8 | For more information on the CI implementation, see the CI setup documentation in `SETUP.md`. 9 | -------------------------------------------------------------------------------- /.github/labeler.yml: -------------------------------------------------------------------------------- 1 | virology: 2 | - '\[x\] virology' 3 | 4 | epidemiology: 5 | - '\[x\] epidemiology' 6 | 7 | biostatistics: 8 | - '\[x\] biostatistics' 9 | 10 | immunology: 11 | - '\[x\] immunology' 12 | 13 | pharmacology: 14 | - '\[x\] pharmacology' 15 | 16 | New Peer-Reviewed Paper: 17 | - '\[x\] New Peer-Reviewed Paper' 18 | 19 | Pre-print: 20 | - '\[x\] Pre-print' 21 | 22 | Peer-Reviewed Paper (Pre-2020): 23 | - '\[x\] Peer-Reviewed Paper Pre-2020' 24 | -------------------------------------------------------------------------------- /ci/install-spellcheck.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | 3 | ## install-spellcheck.sh: run during a CI build to install Pandoc spellcheck dependencies. 4 | 5 | # Set options for extra caution & debugging 6 | set -o errexit \ 7 | -o pipefail 8 | 9 | sudo apt-get update --yes 10 | sudo apt-get install --yes aspell aspell-en 11 | wget --directory-prefix=build/pandoc/filters \ 12 | https://github.com/pandoc/lua-filters/raw/13c3fa7e97206413609a48a82575cb43137e037f/spellcheck/spellcheck.lua 13 | -------------------------------------------------------------------------------- /content/images/orcid.svg: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/request-for-help.md: -------------------------------------------------------------------------------- 1 | --- 2 | name: Request for Help 3 | about: Are you trying to contribute but having difficulty? Ask for help! 4 | title: 'Help: [Add topic here]' 5 | labels: '' 6 | assignees: rando2 7 | 8 | --- 9 | 10 | 11 | ## What are you trying to do? 12 | 13 | 14 | ## What problem are you running into? 15 | 16 | 17 | ## What steps have you already taken to try to solve it? 18 | 19 | ## Is there a particular part of the [Contributor Instructions](https://github.com/greenelab/covid19-review/blob/master/Instructions.md) that has been confusing, misleading, or unhelpful? 20 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/feature_request.md: -------------------------------------------------------------------------------- 1 | --- 2 | name: Feature request 3 | about: Suggest an idea for this project 4 | title: '' 5 | labels: '' 6 | assignees: '' 7 | 8 | --- 9 | 10 | **Is your feature request related to a problem? Please describe.** 11 | A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] 12 | 13 | **Describe the solution you'd like** 14 | A clear and concise description of what you want to happen. 15 | 16 | **Describe alternatives you've considered** 17 | A clear and concise description of any alternative solutions or features you've considered. 18 | 19 | **Additional context** 20 | Add any other context or screenshots about the feature request here. 21 | -------------------------------------------------------------------------------- /content/images/mastodon.svg: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # Generated manuscript output files 2 | output/* 3 | !output/README.md 4 | 5 | webpage/v 6 | 7 | # When PDF building fails, a temporary symlink named images in the root 8 | # directory is not removed. 9 | /images 10 | 11 | # Manubot cache directory 12 | ci/cache 13 | 14 | # Pandoc filters downloaded during continuous integration setup 15 | build/pandoc/filters/spellcheck.lua 16 | 17 | # Python 18 | __pycache__/ 19 | *.pyc 20 | 21 | # Jupyter Notebook 22 | .ipynb_checkpoints 23 | 24 | # Misc temporary files 25 | *.bak 26 | 27 | # System specific files 28 | 29 | ## Linux 30 | *~ 31 | .Trash-* 32 | 33 | ## macOS 34 | .DS_Store 35 | ._* 36 | .Trashes 37 | 38 | ## Windows 39 | Thumbs.db 40 | [Dd]esktop.ini 41 | 42 | ## Text Editors 43 | .vscode 44 | .idea 45 | 46 | ## Spellcheck script 47 | spellcheck.lua 48 | -------------------------------------------------------------------------------- /ci/install.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | 3 | ## install.sh: run during an AppVeyor build to install the conda environment 4 | ## and the optional Pandoc spellcheck dependencies. 5 | 6 | # Set options for extra caution & debugging 7 | set -o errexit \ 8 | -o pipefail 9 | 10 | wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh \ 11 | --output-document miniforge.sh 12 | bash miniforge.sh -b -p $HOME/miniconda 13 | source $HOME/miniconda/etc/profile.d/conda.sh 14 | hash -r 15 | conda config \ 16 | --set always_yes yes \ 17 | --set changeps1 no 18 | mamba env create --quiet --file build/environment.yml 19 | mamba list --name manubot 20 | conda activate manubot 21 | 22 | # Install Spellcheck filter for Pandoc 23 | if [ "${SPELLCHECK:-}" = "true" ]; then 24 | bash ci/install-spellcheck.sh 25 | fi 26 | -------------------------------------------------------------------------------- /content/90.back-matter.md: -------------------------------------------------------------------------------- 1 | {% if format is not defined or format is defined and format != "tex"-%} 2 | ### References {.page_break_before} 3 | 4 | 5 |
6 | {%- endif %} 7 | 8 | 9 | [@tag:Park2020_distancing]: doi:10.3201/eid2611.201099 10 | 11 | 12 | [@individual-pathogenesis]: https://pubmed.ncbi.nlm.nih.gov/34698547/ 13 | [@individual-nutraceuticals]: https://pubmed.ncbi.nlm.nih.gov/33947804/ 14 | [@individual-pharmaceuticals]: https://pubmed.ncbi.nlm.nih.gov/34726496/ 15 | [@individual-diagnostics]: arxiv:2204.12598 16 | [@individual-vaccines-traditional]: https://pubmed.ncbi.nlm.nih.gov/36861991/ 17 | [@individual-vaccines-novel]: https://pubmed.ncbi.nlm.nih.gov/36861992/ 18 | -------------------------------------------------------------------------------- /content/images/twitter.svg: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | -------------------------------------------------------------------------------- /.github/pull_request_template.md: -------------------------------------------------------------------------------- 1 | 5 | 6 | ### Description of the proposed additions or changes 7 | 8 | 9 | 10 | ### Related issues 11 | 12 | 13 | 14 | ### Suggested reviewers (optional) 15 | 16 | 17 | 18 | ### Checklist 19 | 21 | - [ ] Text is formatted so that each sentence is on its own line. 22 | 23 | - [ ] Pre-prints cited in this pull request have a GitHub issue opened so that they can be reviewed. 24 | -------------------------------------------------------------------------------- /content/70.coi-contribs.md: -------------------------------------------------------------------------------- 1 | ## Additional Items {.page_break_before} 2 | 3 | ### Competing Interests 4 | 5 | |Author|Competing Interests|Last Reviewed| 6 | |---|---|---|{% for author in manubot.authors %} 7 | |{{author.name}}|{{author.coi.string}}|{{author.coi.lastapproved}}|{% endfor %} 8 | 9 | ### Author Contributions 10 | 11 | |Author|Contributions| 12 | |---|---|{% for author in manubot.authors %} 13 | |{{author.name}}|{% for contribution in author.contributions %}{{ contribution }}{% if not loop.last %}, {% endif %}{% endfor %}|{% endfor %} 14 | 15 | ### Acknowledgements 16 | 17 | We thank Nick DeVito for assistance with the Evidence-Based Medicine Data Lab COVID-19 TrialsTracker data. 18 | We thank Yael Evelyn Marshall who contributed writing (original draft) as well as reviewing and editing of pieces of the text but who did not formally approve the manuscript, as well as Ronnie Russell, who contributed text to and helped develop the structure of the manuscript early in the writing process and Matthias Fax who helped with writing and editing text related to diagnostics. 19 | We are also very grateful to James Fraser for suggestions about successes and limitations in the area of computational screening for drug repurposing. 20 | We are grateful to the following contributors for reviewing pieces of the text: Nadia Danilova, James Eberwine and Ipsita Krishnan. 21 | 22 | -------------------------------------------------------------------------------- /content/images/github.svg: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | -------------------------------------------------------------------------------- /content/mountSinaiNames.tsv: -------------------------------------------------------------------------------- 1 | Alessandra Soares Schanoski 2 | Alfonso Rodriguez 3 | Alvaro Moreira 4 | Andrew Chan 5 | Andrew Charap 6 | Andrew Leader 7 | Assaf Magen 8 | Bérengère Salomé 9 | Cansu Cimen Bozkus 10 | Chang Moon 11 | Conor Gruber 12 | Dan Fu Ruan 13 | Daniel Lozano-Ojalvo 14 | Divya Jha 15 | Elliot Meritt 16 | Emma Risson 17 | Erica Dalla 18 | Etienne Humblin 19 | Evan Cody 20 | Francesca Cossarini 21 | Gabrielle Lubitz 22 | Graham Britton 23 | Gustavo Martinez-Delgado 24 | Ivan Reyes Torres 25 | Jaime Mateus-Tique 26 | Jamie Redes 27 | Jessica Tan 28 | Joan Shang 29 | Joel Kim 30 | John Grout 31 | Jonathan Chung 32 | Jovani Catalan 33 | Julia Kodysh 34 | Justine Noel 35 | Katherine Lindblad 36 | Louise Malle 37 | Luisanna Pia 38 | Manasi Agrawal 39 | Maria Casanova-Acebes 40 | Maria Kuksin 41 | Maria Suprun 42 | Mark Aleynick 43 | Mark Roberto 44 | Matthew Brown 45 | Matthew Lin 46 | Matthew Park 47 | Matthew Spindler 48 | Matthias Wilk 49 | Meriem Belabed 50 | Miriam Saffern 51 | Miyo Ota 52 | Monica Centa 53 | Natalie Vaninov 54 | Nicolas Fernandez 55 | Pauline Hamon 56 | Rachel Levantovsky 57 | Samarth Hegde 58 | Steven Chen 59 | Tamar Plitt 60 | Tim O’Donnell 61 | Venu Pothula 62 | Verena Van Der Heide 63 | Zafar Mahmood 64 | Alice Khamporst 65 | Amir Horowitz 66 | Brian Brown 67 | Dirk Homann 68 | Dusan Bogunovic 69 | Emilie Grasset 70 | Ephraim Kenigsberg 71 | Jeremiah Faith 72 | Konstantina Alexandropoulos 73 | Maria Lafaille 74 | Miriam Merad 75 | Nicolas Vabret 76 | Nina Bhardwaj 77 | Peter Heeger 78 | Robert Samstein 79 | Saurabh Mehandru 80 | Uri Laserson 81 | -------------------------------------------------------------------------------- /content/available-text/immune-response.md: -------------------------------------------------------------------------------- 1 | Infection also induces other immune responses. 2 | The development of memory B cells and memory T cells has also been assessed in several studies. 3 | Dan et al. (2021) showed that SARS-CoV-2 S-specific memory B cell levels rose steadily over the first 120 days following symptom onset [@doi:10.1126/science.abf4063]. 4 | Receptor binding domain (RBD)-specific memory B cells had been detected in COVID-19 patients 90 days post-symptom onset in previous studies [@doi:10.1016/j.cell.2020.11.029; @pmid:33443036], and this study confirms these finding and shows that levels of these cells increased over the 4-5 months post-symptom onset [@doi:10.1126/science.abf4063]. 5 | Gaebler et al. have shown that memory B cells specific to the RBD remain unaltered and exhibit clonal turnover and antibody sequence evolution 6 months post infection, indicative of prolonged germinal cell reactions [@doi:10.1038/s41586-021-03207-w]. 6 | The same study showed that antibodies expressed by these memory B cells have resistance to RBD mutations, greater somatic hypermutations, and increased potency, which the authors suggest might be evidence of continued evolution of humoral immunity [@doi:10.1038/s41586-021-03207-w]. 7 | Indeed, Wheatley et al. showed that S-specific IgG^+^ memory B cells consistently increase over time and by 4 months comprise approximately 0.8% of all IgG^+^ memory B cells, which may indicate cellular immune memory to even mild-to-moderate COVID-19 infection [@doi:10.1038/s41467-021-21444-5]. 8 | Dan et al. (2021) showed that N-specific memory B cells steadily increased up to 4-5 months post-symptom onset [@doi:10.1126/science.abf4063]. 9 | SARS-CoV-2 memory CD8^+^ T cells were also detected in 70% of 169 COVID-19 patients after 1 month [@doi:10.1126/science.abf4063], which is consistent with previous research [@doi:10.1016/j.cell.2020.05.015]. 10 | These approaches all evaluated indicators that can be used to gain insight into prior infection. 11 | 12 | 13 | -------------------------------------------------------------------------------- /output/README.md: -------------------------------------------------------------------------------- 1 | # Generated citation / reference files 2 | 3 | The `output` branch contains files automatically generated by the manuscript build process. 4 | It consists of the contents of the `output` directory of the `main` branch. 5 | These files are not tracked in `main`, but instead written to the `output` branch by continuous integration builds. 6 | 7 | ## Files 8 | 9 | This directory contains the following files: 10 | 11 | + [`citations.tsv`](citations.tsv) is a table of citations extracted from the manuscript and the corresponding standard citations and citation IDs. 12 | + [`manuscript.md`](manuscript.md) is a markdown document of all manuscript sections, with citation strings replaced by citation IDs. 13 | + [`manuscript.pdf`](manuscript.pdf) is a pdf document of all manuscript sections, with citation strings replaced by citation IDs. 14 | + [`references.json`](references.json) is CSL-JSON file of bibliographic item metadata ([see specification](https://github.com/citation-style-language/schema/blob/master/csl-data.json)) for all references. 15 | + [`variables.json`](variables.json) contains variables that were passed to the jinja2 templater. These variables contain those automatically generated by the manubot as well as those provided by the user via the `--template-variables-path` option. 16 | 17 | Additionally, individual sections specified in [`content/individual-manuscripts.txt`](content/individual-manuscripts.txt) are output in docx format with citation strings replaced by citation IDs. 18 | Their names are formatted as `sectionName-manuscript.docx` where `sectionName`is a line from [`content/individual-docx-manuscripts.txt`](../content/individual-docx-manuscripts.txt). 19 | Similarity, tex outputs for individual manuscripts are provided based on the section names in [`content/individual-latex-manuscripts.txt`](../content/individual-latex-manuscripts.txt) 20 | 21 | Pandoc consumes `manuscript.md` and `references.json` to create the formatted manuscript, which is exported to `manuscript.html`, `manuscript.pdf`, and optionally `manuscript.docx`. 22 | -------------------------------------------------------------------------------- /webpage/README.md: -------------------------------------------------------------------------------- 1 | # Output directory containing the formatted manuscript 2 | 3 | The [`gh-pages`](https://github.com/$REPO_SLUG/tree/gh-pages) branch hosts the contents of this directory at . 4 | The permalink for this webpage version is . 5 | To redirect to the permalink for the latest manuscript version at anytime, use the link . 6 | 7 | ## Files 8 | 9 | This directory contains the following files, which are mostly ignored on the `main` branch: 10 | 11 | + [`index.html`](index.html) is an HTML manuscript. 12 | + [`manuscript.pdf`](manuscript.pdf) is a PDF manuscript. 13 | 14 | The `v` directory contains directories for each manuscript version. 15 | In general, a version is identified by the commit hash of the source content that created it. 16 | 17 | ### Timestamps 18 | 19 | The `*.ots` files in version directories are OpenTimestamps which can be used to verify manuscript existence at or before a given time. 20 | [OpenTimestamps](https://opentimestamps.org/) uses the Bitcoin blockchain to attest to file hash existence. 21 | The `deploy.sh` script run during continuous deployment creates the `.ots` files through its `manubot webpage` call. 22 | There is a delay before timestamps get confirmed by a Bitcoin block. 23 | Therefore, `.ots` files are initially incomplete and should be upgraded at a later time, so that they no longer rely on the availability of a calendar server to verify. 24 | The `manubot webpage` call during continuous deployment identifies files matched by `webpage/v/**/*.ots` and attempts to upgrade them. 25 | You can also manually upgrade timestamps, by running the following in the `gh-pages` branch: 26 | 27 | ```shell 28 | ots upgrade v/*/*.ots 29 | rm v/*/*.ots.bak 30 | git add v/*/*.ots 31 | ``` 32 | 33 | Verifying timestamps with the `ots verify` command requires running a local bitcoin node with JSON-RPC configured, at this time. 34 | 35 | ## Source 36 | 37 | The manuscripts in this directory were built from 38 | [`$COMMIT`](https://github.com/$REPO_SLUG/commit/$COMMIT). 39 | -------------------------------------------------------------------------------- /content/previous_sections/01.abstract.md: -------------------------------------------------------------------------------- 1 | ## Abstract {.page_break_before .unnumbered} 2 | Since late 2019, Coronavirus disease 2019 (COVID-19) has spread around the world, resulting in the declaration of a pandemic by the World Health Organization (WHO). 3 | This infectious disease is caused by the newly identified _Severe acute respiratory syndrome-related coronavirus 2_ (SARS-CoV-2). 4 | Research on the SARS-CoV-2 virus and the disease it causes is emerging rapidly through global scientific efforts. 5 | Short-term mitigation of viral impacts will require public health interventions, and long-term mitigation will require new diagnostic and therapeutic technologies. 6 | The urgency of the pandemic has led to a rapidly emerging scientific literature on SARS-CoV-2 and COVID-19. 7 | This manuscript represents a collaborative effort to organize and consolidate this body of literature. 8 | We present information about the virus in the context of what is known about related viruses, describe the pathogenesis of COVID-19, and synthesize studies emerging about the diagnosis and treatment of COVID-19 alongside literature about related illnesses. 9 | We summarize this emerging literature with an eye towards discussing elements of the disease that will be fundamental to efforts to develop interventions. 10 | Our review is a collaboratively-authored, evolving document into which we seek to incorporate the ever-expanding body of information on the topic. 11 | This document provides a snapshot as of October, 2020. 12 | We continue to accept new contributions and anticipate future snapshots until technologies to mitigate the pandemic are widely deployed. 13 | 14 | ## How to Contribute {.unnumbered} 15 | 16 | We invite potential contributors to introduce themselves through GitHub: [https://github.com/greenelab/covid19-review/issues/17](https://github.com/greenelab/covid19-review/issues/17) 17 | 18 | We have established a community chat room on a service called Gitter: [https://gitter.im/covid19-review/community](https://gitter.im/covid19-review/community) 19 | 20 | More information about how to contribute is available in a README document on GitHub: [https://github.com/greenelab/covid19-review#sars-cov-2-and-covid-19-an-evolving-review-of-diagnostics-and-therapeutics](https://github.com/greenelab/covid19-review#sars-cov-2-and-covid-19-an-evolving-review-of-diagnostics-and-therapeutics) 21 | -------------------------------------------------------------------------------- /.github/workflows/ai-revision.yaml: -------------------------------------------------------------------------------- 1 | name: ai-revision 2 | on: 3 | workflow_dispatch: 4 | inputs: 5 | branch: 6 | description: 'Branch to revise' 7 | required: true 8 | type: string 9 | default: 'main' 10 | file_names: 11 | description: 'File names to revise' 12 | required: false 13 | type: string 14 | default: '' 15 | model: 16 | description: 'Language model' 17 | required: true 18 | type: string 19 | default: 'text-davinci-003' 20 | custom_prompt: 21 | description: 'Custom prompt' 22 | required: false 23 | type: string 24 | default: '' 25 | branch_name: 26 | description: 'Output branch' 27 | required: true 28 | type: string 29 | default: 'ai-revision-davinci' 30 | 31 | jobs: 32 | ai-revise: 33 | name: AI Revise 34 | runs-on: ubuntu-latest 35 | permissions: 36 | contents: write 37 | pull-requests: write 38 | defaults: 39 | run: 40 | shell: bash --login {0} 41 | steps: 42 | - name: Checkout Repo 43 | uses: actions/checkout@v3 44 | with: 45 | ref: ${{ inputs.branch }} 46 | - name: Install environment 47 | uses: actions/setup-python@v4 48 | with: 49 | python-version: '3.11' 50 | - name: Install Manubot AI revision dependencies 51 | run: | 52 | # install using the same URL used for manubot in build/environment.yml 53 | manubot_line=$(grep "github.com/manubot/manubot" build/environment.yml) 54 | manubot_url=$(echo "$manubot_line" | awk -F"- " '{print $2}') 55 | 56 | pip install ${manubot_url}#egg=manubot[ai-rev] 57 | - name: Revise manuscript 58 | env: 59 | OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }} 60 | AI_EDITOR_LANGUAGE_MODEL: ${{ inputs.model }} 61 | AI_EDITOR_FILENAMES_TO_REVISE: ${{ inputs.file_names }} 62 | AI_EDITOR_CUSTOM_PROMPT: ${{ inputs.custom_prompt }} 63 | # More variables can be specified to control the behavior of the model: 64 | # https://github.com/manubot/manubot-ai-editor/blob/main/libs/manubot_ai_editor/env_vars.py 65 | run: manubot ai-revision --content-directory content/ 66 | - name: Create Pull Request 67 | uses: peter-evans/create-pull-request@v4 68 | with: 69 | commit-message: 'revise using AI model\n\nUsing the OpenAI model ${{ inputs.model }}' 70 | title: 'AI-based revision using ${{ inputs.model }}' 71 | author: OpenAI model ${{ inputs.model }} 72 | add-paths: | 73 | content/*.md 74 | branch: ${{ inputs.branch_name }} 75 | draft: true 76 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/new-paper-template.md: -------------------------------------------------------------------------------- 1 | --- 2 | name: New Paper Template (Other) 3 | about: Note papers to read and organize information and summaries 4 | title: 'New Paper (Other): [Title]' 5 | labels: New Paper 6 | assignees: '' 7 | 8 | --- 9 | 10 | 11 | 12 | Title: Please edit the title to add the name of the paper after the colon. 13 | 14 | # General Information 15 | ## Please paste a link to the paper or a citation here: 16 | 17 | Link: 18 | 19 | ## What is the paper's [Manubot-style citation](https://github.com/greenelab/covid19-review/blob/master/USAGE.md#citations)? 20 | 21 | 22 | Citation: 23 | 24 | ### Is this paper primarily relevant to Background or Pathogenesis? 25 | 27 | 28 | - [ ] Background 29 | - [ ] Pathogenesis 30 | - [ ] Methods 31 | 32 | ## Please list some keywords (3-10) that help identify the relevance of this paper to COVID-19 33 | 34 | * keyword 1 (replace me, copy and paste more than three if needed) 35 | * keyword 2 (replace me, copy and paste more than three if needed) 36 | * keyword 3 (replace me, copy and paste more than three if needed) 37 | 38 | ## Please note the publication / review status 39 | 40 | 41 | - [ ] Pre-print 42 | - [ ] New Peer-Reviewed Paper 43 | - [ ] Peer-Reviewed Paper Pre-2020 44 | 45 | ## Which areas of expertise are particularly relevant to the paper? 46 | 47 | 48 | - [ ] virology 49 | - [ ] epidemiology 50 | - [ ] biostatistics 51 | - [ ] immunology 52 | - [ ] pharmacology 53 | - [ ] other: 54 | 55 | 61 | # Summary 62 | 63 | ### Suggested questions to answer about each paper: 64 | - What did they analyze? 65 | - What methods did they use? 66 | - Does this paper study COVID-19, SARS-CoV-2, or a related disease and/or virus? 67 | - What is the main finding (or a few main takeaways)? 68 | - What does this paper tell us about the background and/or diagnostics/therapeutics for COVID-19 / SARS-CoV-2? 69 | - Do you have any concerns about methodology or the interpretation of these results beyond this analysis? 70 | 71 | ### Any comments or notes? 72 | -------------------------------------------------------------------------------- /.github/workflows/update-external-resources.yaml: -------------------------------------------------------------------------------- 1 | name: Update external resources 2 | on: 3 | schedule: 4 | # Run every day at 00:00 5 | - cron: '0 0 * * *' 6 | # Enable manually updating the external resources 7 | workflow_dispatch: 8 | 9 | jobs: 10 | update_external_resources: 11 | name: Update external resources 12 | runs-on: ubuntu-latest 13 | steps: 14 | # Scheduled workflows run on the default branch 15 | - name: Checkout external-resources branch 16 | uses: actions/checkout@v2 17 | with: 18 | ref: external-resources 19 | - name: Install environment # Use mamba as in https://github.com/conda-incubator/setup-miniconda/issues/274 and https://github.com/conda-incubator/setup-miniconda#example-10-miniforge 20 | uses: conda-incubator/setup-miniconda@v2 21 | with: 22 | activate-environment: covid19 23 | environment-file: environment.yml 24 | auto-activate-base: false 25 | miniforge-variant: Mambaforge 26 | channels: conda-forge 27 | channel-priority: true 28 | use-mamba: true 29 | - name: List information about mamba and environment 30 | shell: bash --login {0} 31 | run: | 32 | mamba info 33 | mamba list 34 | mamba config --show-sources 35 | mamba config --show 36 | printenv | sort 37 | - name: Update JHU CSSE data 38 | shell: bash --login {0} 39 | run: bash csse/generate-csse-stats.sh 40 | - name: Update EBM Data Lab data 41 | shell: bash --login {0} 42 | run: bash ebmdatalab/generate-ebmdatalab-stats.sh 43 | - name: Update OWID data 44 | shell: bash --login {0} 45 | run: bash owiddata/generate-owiddata-stats.sh 46 | - name: Update CORD-19 data 47 | shell: bash --login {0} 48 | run: bash CORD-19/generate-cord19-stats.sh 49 | # - name: Update manuscript statistics data 50 | # shell: bash --login {0} 51 | # run: bash analyze-ms-stats/calc-manuscript-stats.sh 52 | - name: Commit JHU CSSE, EBM Data Lab, OWID, CORD-19, and manuscript growth figures 53 | uses: EndBug/add-and-commit@v4 54 | with: 55 | add: '*/*.png */*.svg */*/*.png */*/*.svg' 56 | author_name: GitHub Actions 57 | author_email: actions@github.com 58 | message: 'Update JHU CSSE, EBM Data Lab, OWID, CORD-19, and manuscript growth figures' 59 | ref: external-resources 60 | env: 61 | GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} 62 | - name: Update figure versions 63 | shell: bash --login {0} 64 | run: bash version-figures.sh 65 | - name: Commit JHU CSSE, EBM Data Lab, OWID, CORD-19, and manuscript growth statistics 66 | uses: EndBug/add-and-commit@v4 67 | with: 68 | add: '*/*.json' 69 | author_name: GitHub Actions 70 | author_email: actions@github.com 71 | message: 'Update JHU CSSE, EBM Data Lab, OWID, CORD-19, and manuscript growth statistics' 72 | ref: external-resources 73 | env: 74 | GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} 75 | -------------------------------------------------------------------------------- /ci/deploy.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | 3 | ## deploy.sh: run during a CI build to deploy manuscript outputs to the output and gh-pages branches on GitHub. 4 | 5 | # Set options for extra caution & debugging 6 | set -o errexit \ 7 | -o nounset \ 8 | -o pipefail 9 | 10 | # set environment variables for GitHub Actions 11 | REPO_SLUG=${GITHUB_REPOSITORY} 12 | COMMIT=${GITHUB_SHA} 13 | BRANCH=${DEFAULT_BRANCH:-main} 14 | 15 | # Add commit hash to the README 16 | OWNER_NAME="$(dirname "$REPO_SLUG")" 17 | REPO_NAME="$(basename "$REPO_SLUG")" 18 | export REPO_SLUG COMMIT OWNER_NAME REPO_NAME 19 | envsubst < webpage/README.md > webpage/README-complete.md 20 | mv webpage/README-complete.md webpage/README.md 21 | 22 | # Configure git 23 | git config --global push.default simple 24 | git config --global user.email "$(git log --max-count=1 --format='%ae')" 25 | git config --global user.name "$(git log --max-count=1 --format='%an')" 26 | git checkout "$BRANCH" 27 | 28 | # Configure deployment credentials 29 | MANUBOT_DEPLOY_VIA_SSH=true 30 | git remote set-url origin "git@github.com:$REPO_SLUG.git" 31 | if [ -v MANUBOT_SSH_PRIVATE_KEY ] && [ "$MANUBOT_SSH_PRIVATE_KEY" != "" ]; then 32 | echo >&2 "[INFO] Detected MANUBOT_SSH_PRIVATE_KEY. Will deploy via SSH." 33 | elif [ -v MANUBOT_ACCESS_TOKEN ] && [ "$MANUBOT_ACCESS_TOKEN" != "" ]; then 34 | echo >&2 "[INFO] Detected MANUBOT_ACCESS_TOKEN. Will deploy via HTTPS." 35 | MANUBOT_DEPLOY_VIA_SSH=false 36 | git remote set-url origin "https://$MANUBOT_ACCESS_TOKEN@github.com/$REPO_SLUG.git" 37 | else 38 | echo >&2 "[INFO] Missing MANUBOT_SSH_PRIVATE_KEY and MANUBOT_ACCESS_TOKEN. Will deploy via SSH." 39 | fi 40 | 41 | if [ $MANUBOT_DEPLOY_VIA_SSH = "true" ]; then 42 | # Decrypt and add SSH key 43 | eval "$(ssh-agent -s)" 44 | ( 45 | set +o xtrace # disable xtrace in subshell for private key operations 46 | if [ -v MANUBOT_SSH_PRIVATE_KEY ]; then 47 | base64 --decode <<< "$MANUBOT_SSH_PRIVATE_KEY" | ssh-add - 48 | else 49 | echo >&2 "Deployment will fail since neither of the following environment variables are set: MANUBOT_ACCESS_TOKEN or MANUBOT_SSH_PRIVATE_KEY." 50 | fi 51 | ) 52 | fi 53 | 54 | # Fetch and create gh-pages and output branches 55 | git remote set-branches --add origin gh-pages output 56 | git fetch origin gh-pages:gh-pages output:output || \ 57 | echo >&2 "[INFO] could not fetch gh-pages or output from origin." 58 | 59 | # Configure versioned webpage and timestamp 60 | manubot webpage \ 61 | --timestamp \ 62 | --no-ots-cache \ 63 | --checkout=gh-pages \ 64 | --version="$COMMIT" 65 | 66 | # Commit message 67 | MESSAGE="\ 68 | $(git log --max-count=1 --format='%s') 69 | [ci skip] 70 | 71 | This build is based on 72 | https://github.com/$REPO_SLUG/commit/$COMMIT. 73 | 74 | This commit was created by the following CI build and job: 75 | $CI_BUILD_WEB_URL 76 | $CI_JOB_WEB_URL 77 | " 78 | 79 | # Deploy the manubot outputs to output 80 | ghp-import \ 81 | --push \ 82 | --branch=output \ 83 | --message="$MESSAGE" \ 84 | output 85 | 86 | # Deploy the webpage directory to gh-pages 87 | ghp-import \ 88 | --no-jekyll \ 89 | --follow-links \ 90 | --push \ 91 | --branch=gh-pages \ 92 | --message="$MESSAGE" \ 93 | webpage 94 | 95 | if [ $MANUBOT_DEPLOY_VIA_SSH = "true" ]; then 96 | # Workaround https://github.com/travis-ci/travis-ci/issues/8082 97 | ssh-agent -k 98 | fi 99 | -------------------------------------------------------------------------------- /.appveyor.yml: -------------------------------------------------------------------------------- 1 | # See https://www.appveyor.com/docs/getting-started-with-appveyor-for-linux/ 2 | # Don't build branches with a PR, since their build will be created with the PR itself. 3 | # Otherwise there would be two builds -- one for the PR and one for the branch. 4 | # If you're having issues with getting your PR to build, make sure there are no merge conflicts. 5 | skip_branch_with_pr: true 6 | 7 | # Enable 'Do not build on "Push" events' in the AppVeyor project settings 8 | # to only build commits from pull requests 9 | branches: 10 | only: 11 | - main 12 | - master 13 | 14 | # Only run AppVeyor on commits that modify at least one of the following files 15 | # Delete these lines to run AppVeyor on all main/master branch commits 16 | only_commits: 17 | files: 18 | - .appveyor.yml 19 | - build/ 20 | - ci/install.sh 21 | - content/ 22 | 23 | image: ubuntu2204 24 | services: 25 | - docker 26 | 27 | # Set SPELLCHECK to true to enable Pandoc spellchecking 28 | environment: 29 | SPELLCHECK: true 30 | 31 | install: 32 | # Create the message with the triggering commit before install so it is 33 | # available if the build fails 34 | - TRIGGERING_COMMIT=${APPVEYOR_PULL_REQUEST_HEAD_COMMIT:-APPVEYOR_REPO_COMMIT} 35 | - JOB_MESSAGE=" for commit $TRIGGERING_COMMIT " 36 | - source ci/install.sh 37 | 38 | test_script: 39 | - bash build/build.sh 40 | - MANUSCRIPT_FILENAME=manuscript-$APPVEYOR_BUILD_VERSION-${TRIGGERING_COMMIT:0:7} 41 | - cp output/manuscript.html $MANUSCRIPT_FILENAME.html 42 | - cp output/manuscript.pdf $MANUSCRIPT_FILENAME.pdf 43 | - appveyor PushArtifact $MANUSCRIPT_FILENAME.html 44 | - appveyor PushArtifact $MANUSCRIPT_FILENAME.pdf 45 | - | 46 | if [ "${SPELLCHECK:-}" = "true" ]; then 47 | SPELLING_ERRORS_FILENAME=spelling-errors-$APPVEYOR_BUILD_VERSION-${TRIGGERING_COMMIT:0:7}.txt 48 | cp output/spelling-errors.txt $SPELLING_ERRORS_FILENAME 49 | appveyor PushArtifact $SPELLING_ERRORS_FILENAME 50 | SPELLING_ERROR_LOCATIONS_FILENAME=spelling-error-locations-$APPVEYOR_BUILD_VERSION-${TRIGGERING_COMMIT:0:7}.txt 51 | cp output/spelling-error-locations.txt $SPELLING_ERROR_LOCATIONS_FILENAME 52 | appveyor PushArtifact $SPELLING_ERROR_LOCATIONS_FILENAME 53 | fi 54 | 55 | build: off 56 | 57 | cache: 58 | - ci/cache 59 | 60 | on_success: 61 | - echo "Artifacts available from $APPVEYOR_URL/project/$APPVEYOR_ACCOUNT_NAME/$APPVEYOR_PROJECT_SLUG/builds/$APPVEYOR_BUILD_ID/artifacts" 62 | - echo "Updated PDF available from $APPVEYOR_URL/api/buildjobs/$APPVEYOR_JOB_ID/artifacts/$MANUSCRIPT_FILENAME.pdf" 63 | - appveyor AddMessage "$JOB_MESSAGE is now complete." 64 | - | 65 | if [ "${SPELLCHECK:-}" = "true" ]; then 66 | SPELLING_ERROR_COUNT=($(wc -l $SPELLING_ERROR_LOCATIONS_FILENAME)) 67 | appveyor AddMessage "
Found $SPELLING_ERROR_COUNT potential spelling error(s). Preview:$(head -n 100 $SPELLING_ERROR_LOCATIONS_FILENAME)" 68 | appveyor AddMessage "...
" 69 | fi 70 | 71 | on_failure: 72 | - appveyor AddMessage "$JOB_MESSAGE failed." 73 | 74 | # The following lines can be safely deleted, which will disable AppVeyorBot 75 | # notifications in GitHub pull requests 76 | # Notifications use Mustache templates http://mustache.github.io/mustache.5.html 77 | # See https://www.appveyor.com/docs/notifications/#customizing-message-template 78 | # for available variables 79 | notifications: 80 | - provider: GitHubPullRequest 81 | template: "AppVeyor [build {{buildVersion}}]({{buildUrl}}) 82 | {{#jobs}}{{#messages}}{{{message}}}{{/messages}}{{/jobs}} 83 | {{#passed}}The rendered manuscript from this build is temporarily available for download at:\n\n 84 | {{#jobs}}{{#artifacts}}- [`{{fileName}}`]({{permalink}})\n{{/artifacts}}{{/jobs}}{{/passed}}" 85 | -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- 1 | # Contributor Covenant Code of Conduct 2 | 3 | ## Our Values 4 | 5 | In this project, we seek to provide an environment for researchers from all backgrounds and disciplines to contribute to the consolidation and synthesis of scientific information related to COVID-19. 6 | Our project will be most successful when we create a space where a diverse group of people can collaboratively approach emerging information with curiosity and creativity. 7 | As a result, one of our primary goals is to make the online community associated with the repository welcoming to all members of the scientific community. 8 | Creativity thrives when people feel supported, accepted, and encouraged. 9 | As a result, inclusivity is one of the central tenents of this project. 10 | 11 | ## Our Pledge 12 | 13 | In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to make participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation. 14 | 15 | ## Our Standards 16 | 17 | Examples of behavior that contributes to creating a positive environment include: 18 | 19 | * Using welcoming and inclusive language 20 | * Being respectful of differing viewpoints and experiences 21 | * Gracefully accepting constructive criticism 22 | * Focusing on what is best for the community 23 | * Showing empathy towards other community members 24 | 25 | Examples of unacceptable behavior by participants include: 26 | 27 | * The use of sexualized language or imagery and unwelcome sexual attention or advances 28 | * Trolling, insulting/derogatory comments, and personal or political attacks 29 | * Public or private harassment 30 | * Publishing others' private information, such as a physical or electronic address, without explicit permission 31 | * Other conduct which could reasonably be considered inappropriate in a professional setting 32 | 33 | ## Our Responsibilities 34 | 35 | Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior. 36 | 37 | Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. 38 | 39 | ## Scope 40 | 41 | This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. 42 | Examples of representing a project or community include acting as an appointed representative at an online or offline event, such as for media coverage or for conferences or other presentations. 43 | 44 | ## Enforcement 45 | 46 | Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at halie.rando@pennmedicine.upenn.edu or greenescientist@gmail.com. 47 | All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. 48 | The project team is obligated to maintain confidentiality with regard to the reporter of an incident. 49 | Further details of specific enforcement policies may be posted separately. 50 | 51 | Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership. 52 | Only contributors in good standing with respect to the code of conduct will be offered the opportunity to review the approve the final manuscript, which is required for authorship through the ICMJE criteria. 53 | 54 | ## Attribution 55 | 56 | This Code of Conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org), [version 1.4](https://www.contributor-covenant.org/version/1/4/code-of-conduct.html). 57 | 58 | For answers to common questions about this code of conduct, see https://www.contributor-covenant.org/faq 59 | -------------------------------------------------------------------------------- /content/00.front-matter.md: -------------------------------------------------------------------------------- 1 | {## 2 | This file contains a Jinja2 front-matter template that adds version and authorship information. 3 | Changing the Jinja2 templates in this file may cause incompatibility with Manubot updates. 4 | Pandoc automatically inserts title from metadata.yaml, so it is not included in this template. 5 | ##} 6 | 7 | {## Uncomment & edit the following line to reference to a preprinted or published version of the manuscript. 8 | _A DOI-citable version of this manuscript is available at _. 9 | ##} 10 | 11 | {## Template to insert build date, source, and cross-references to merged or individual reviews ##} 12 | 13 | This manuscript 14 | {% if manubot.ci_source is defined and manubot.ci_source.provider == "appveyor" -%} 15 | ([permalink]({{manubot.ci_source.artifact_url}})) 16 | {% elif manubot.html_url_versioned is defined -%} 17 | ([permalink]({{manubot.html_url_versioned}})) 18 | {% endif -%} 19 | was automatically generated 20 | {% if manubot.ci_source is defined -%} 21 | from [{{manubot.ci_source.repo_slug}}@{{manubot.ci_source.commit | truncate(length=7, end='', leeway=0)}}](https://github.com/{{manubot.ci_source.repo_slug}}/tree/{{manubot.ci_source.commit}}) 22 | {% endif -%} 23 | on {{manubot.generated_date_long}}. 24 | {% if manubot.pdf_url_versioned is defined -%} 25 | It is also available as a [PDF]({{manubot.pdf_url_versioned}}). 26 | {% endif -%} 27 | {% if individual is defined -%} 28 | It represents one section of a larger evolving review on SARS-CoV-2 and COVID-19 available at 29 | {% else -%} 30 | Snapshots of individual sections have been published [@individual-pathogenesis; @individual-nutraceuticals; @individual-pharmaceuticals; @individual-methods; @individual-vaccines-traditional; @individual-vaccines-novel] or posted as preprints [@individual-diagnostics]. 31 | {% endif -%} 32 | 33 | 34 | {## 35 | {% if manubot.date_long != manubot.generated_date_long -%} 36 | Published: {{manubot.date_long}} 37 | {% endif %} 38 | ##} 39 | 40 | 41 | 42 | [ 43 | []{.fas .fa-info-circle .fa-lg} **This in progress manuscript is not intended for the general public.**
44 | This is a review paper that is authored by scientists for an audience of scientists to discuss research that is in progress. 45 | If you are interested in guidelines on testing, therapies, or other issues related to your health, you should not use this document. 46 | Instead, you should collect information from your local health department, the [CDC's guidance](https://www.cdc.gov/coronavirus/2019-ncov/index.html), or your own government. 47 | This project was most active from March 2020 through February 2023 and is not currently receiving major updates. 48 | ]{.banner .lightred} 49 | 50 | ## Authors {.unnumbered} 51 | 52 | {## Template for listing authors, simplified for the individual manuscripts ##} 53 | {% for author in manubot.authors %} 54 | + **{{author.name}}**
55 | {%- if author.orcid is defined and author.orcid is not none %} 56 | {%- if individual is not defined %} ![ORCID icon](images/orcid.svg){.inline_icon width=16 height=16} {%- endif %} 57 | [{{author.orcid}}](https://orcid.org/{{author.orcid}}) 58 | {%- endif %} 59 | {%- if author.github is defined and author.github is not none %} 60 | {%- if individual is not defined %} · ![GitHub icon](images/github.svg){.inline_icon width=16 height=16} {%- endif %} 61 | [{{author.github}}](https://github.com/{{author.github}}) 62 | {%- endif %} 63 | {%- if author.twitter is defined and author.twitter is not none %} 64 | {%- if individual is not defined %} · ![Twitter icon](images/twitter.svg){.inline_icon width=16 height=16} {%- endif %} 65 | [{{author.twitter}}](https://twitter.com/{{author.twitter}}) 66 | {%- endif %}
67 | 68 | {%- if author.affiliations is defined and author.affiliations|length %} 69 | {{author.affiliations | join('; ')}} 70 | {%- endif %} 71 | {%- if author.funders is defined and author.funders|length %} 72 | · Funded by {{author.funders | join('; ')}} 73 | {%- endif %} 74 | 75 | {% endfor %} 76 | 77 | {## Template for listing consortium members ##} 78 | **COVID-19 Review Consortium:** 79 | {% for member in consortiummembers %}{{ member }}{% if not loop.last %}, {% endif %}{% endfor %} 80 | 81 | {## Author order note ##} 82 | {%- if individual is defined %} 83 | Authors with similar contributions are ordered alphabetically. 84 | {% else %} 85 | Authors are ordered arbitrarily. 86 | {%- endif %} 87 | -------------------------------------------------------------------------------- /.github/workflows/manubot.yaml: -------------------------------------------------------------------------------- 1 | name: Manubot 2 | on: 3 | push: 4 | branches: 5 | - main 6 | - master 7 | pull_request: 8 | branches: 9 | - main 10 | - master 11 | # NOTE: scheduled workflows are supported as of 2022-09-27 (example commented below) 12 | # https://github.com/community/community/discussions/12269#discussioncomment-3747667 13 | # scheduled: 14 | # - cron: '40 10 1 * *' # https://crontab.guru/#40_10_1_*_* 15 | workflow_dispatch: 16 | inputs: 17 | BUILD_HTML: 18 | type: boolean 19 | description: generate HTML output 20 | default: true 21 | BUILD_PDF: 22 | type: boolean 23 | description: generate PDF output 24 | default: true 25 | BUILD_DOCX: 26 | type: boolean 27 | description: generate DOCX output 28 | default: false 29 | BUILD_LATEX: 30 | type: boolean 31 | description: generate LaTeX output 32 | default: false 33 | SPELLCHECK: 34 | type: boolean 35 | description: Check spelling 36 | default: true 37 | MANUBOT_USE_DOCKER: 38 | type: boolean 39 | description: Use Docker to generate PDF 40 | default: true 41 | jobs: 42 | manubot: 43 | name: Manubot 44 | runs-on: ubuntu-latest 45 | permissions: 46 | contents: write 47 | env: 48 | GITHUB_PULL_REQUEST_SHA: ${{ github.event.pull_request.head.sha }} 49 | LITSEARCH: false 50 | # Set SPELLCHECK to true/false for whether to check spelling in this action. 51 | # For workflow dispatch jobs, this SPELLCHECK setting will be overridden by the user input. 52 | SPELLCHECK: true 53 | BUILD_HTML: true 54 | BUILD_PDF: true 55 | BUILD_DOCX: false 56 | BUILD_INDIVIDUAL: true 57 | defaults: 58 | run: 59 | shell: bash --login {0} 60 | steps: 61 | - name: Checkout Repository 62 | uses: actions/checkout@v3 63 | with: 64 | # fetch entire commit history to support get_rootstock_commit 65 | fetch-depth: 0 66 | - name: Set Environment Variables (Workflow Dispatch) 67 | if: github.event_name == 'workflow_dispatch' 68 | run: | 69 | echo "BUILD_PDF=${{ github.event.inputs.BUILD_PDF }}" >> $GITHUB_ENV 70 | echo "BUILD_DOCX=${{ github.event.inputs.BUILD_DOCX }}" >> $GITHUB_ENV 71 | echo "BUILD_LATEX=${{ github.event.inputs.BUILD_LATEX }}" >> $GITHUB_ENV 72 | echo "SPELLCHECK=${{ github.event.inputs.SPELLCHECK }}" >> $GITHUB_ENV 73 | echo "MANUBOT_USE_DOCKER=${{ github.event.inputs.MANUBOT_USE_DOCKER }}" >> $GITHUB_ENV 74 | - name: Set Environment Variables 75 | run: | 76 | TRIGGERING_SHA=${GITHUB_PULL_REQUEST_SHA:-$GITHUB_SHA} 77 | echo "TRIGGERING_SHA_7=${TRIGGERING_SHA::7}" >> $GITHUB_ENV 78 | echo "TRIGGERING_SHA: $TRIGGERING_SHA" 79 | DEFAULT_BRANCH=${{ github.event.repository.default_branch }} 80 | echo "DEFAULT_BRANCH=${DEFAULT_BRANCH}" >> $GITHUB_ENV 81 | echo "DEFAULT_BRANCH_REF=refs/heads/$DEFAULT_BRANCH" >> $GITHUB_ENV 82 | echo "DEFAULT_BRANCH=$DEFAULT_BRANCH" 83 | - name: Cache 84 | uses: actions/cache@v3 85 | with: 86 | path: ci/cache 87 | key: ci-cache-${{ github.ref }} 88 | restore-keys: | 89 | ci-cache-${{ env.DEFAULT_BRANCH_REF }} 90 | - name: Install Environment 91 | uses: conda-incubator/setup-miniconda@v2 92 | with: 93 | activate-environment: manubot 94 | environment-file: build/environment.yml 95 | auto-activate-base: false 96 | miniforge-variant: Mambaforge 97 | miniforge-version: 'latest' 98 | use-mamba: true 99 | - name: Install Spellcheck 100 | if: env.SPELLCHECK == 'true' 101 | run: bash ci/install-spellcheck.sh 102 | - name: Build Manuscript 103 | run: bash build/build.sh 104 | - name: Upload Artifacts 105 | uses: actions/upload-artifact@v3 106 | with: 107 | name: manuscript-${{ github.run_id }}-${{ env.TRIGGERING_SHA_7 }} 108 | path: output 109 | - name: Deploy Manuscript 110 | if: github.ref == env.DEFAULT_BRANCH_REF && github.event_name != 'pull_request' && !github.event.repository.fork 111 | env: 112 | MANUBOT_ACCESS_TOKEN: ${{ secrets.GITHUB_TOKEN }} 113 | MANUBOT_SSH_PRIVATE_KEY: ${{ secrets.MANUBOT_SSH_PRIVATE_KEY }} 114 | CI_BUILD_WEB_URL: https://github.com/${{ github.repository }}/commit/${{ github.sha }}/checks 115 | CI_JOB_WEB_URL: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }} 116 | run: bash ci/deploy.sh 117 | -------------------------------------------------------------------------------- /content/manual-references.bib: -------------------------------------------------------------------------------- 1 | @article{doi:10/drbx, 2 | title = {A pilot study of hydroxychloroquine in treatment of patients with common coronavirus disease-19 ({COVID}-19)}, 3 | volume = {49}, 4 | issn = {1008-9292}, 5 | url = {https://doi.org/10.3785/j.issn.1008-9292.2020.03.03}, 6 | doi = {10.3785/j.issn.1008-9292.2020.03.03}, 7 | language = {cn}, 8 | number = {1}, 9 | urldate = {2020-04-06}, 10 | journal = {Journal of Zhejiang University (Medical Sciences)}, 11 | author = {{CHEN Jun} and {LIU Danping} and {LIU Li} and {LIU Ping} and {XU Qingnian} and {XIA Lu} and {LING Yun} and {HUANG Dan} and {SONG Shuli} and {ZHANG Dandan} and {QIAN Zhiping} and {LI Tao} and {SHEN Yinzhong} and {LU Hongzhou}}, 12 | month = mar, 13 | year = {2020} 14 | } 15 | 16 | @article{doi:10.1101/2020.01.27.20018952, 17 | title = {Estimating the effective reproduction number of the 2019-{nCoV} in {China}}, 18 | copyright = {{\textcopyright} 2020, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NoDerivs 4.0 International), CC BY-ND 4.0, as described at http://creativecommons.org/licenses/by-nd/4.0/}, 19 | url = {https://www.medrxiv.org/content/10.1101/2020.01.27.20018952v1}, 20 | doi = {10.1101/2020.01.27.20018952}, 21 | abstract = {{\textless}p{\textgreater}We estimate the effective reproduction number for 2019-nCoV based on the daily reported cases from China CDC. The results indicate that 2019-nCoV has a higher effective reproduction number than SARS with a comparable fatality rate.{\textless}/p{\textgreater}}, 22 | language = {en}, 23 | urldate = {2020-04-15}, 24 | journal = {medRxiv}, 25 | author = {Cao, Zhidong and Zhang, Qingpeng and Lu, Xin and Pfeiffer, Dirk and Jia, Zhongwei and Song, Hongbing and Zeng, Daniel Dajun}, 26 | month = jan, 27 | year = {2020}, 28 | pages = {2020.01.27.20018952} 29 | } 30 | 31 | @article{https://doi.org/10.1098/rspa.1927.0118, 32 | title = {A contribution to the mathematical theory of epidemics}, 33 | volume = {115}, 34 | url = {https://doi.org/10.1098/rspa.1927.0118}, 35 | doi = {10.1098/rspa.1927.0118}, 36 | abstract = {(1) One of the most striking features in the study of epidemics is the difficulty of finding a causal factor which appears to be adequate to account for the magnitude of the frequent epidemics of disease which visit almost every population. It was with a view to obtaining more insight regarding the effects of the various factors which govern the spread of contagious epidemics that the present investigation was undertaken. Reference may here be made to the work of Ross and Hudson (1915-17) in which the same problem is attacked. The problem is here carried to a further stage, and it is considered from a point of view which is in one sense more general. The problem may be summarised as follows: One (or more) infected person is introduced into a community of individuals, more or less susceptible to the disease in question. The disease spreads from the affected to the unaffected by contact infection. Each infected person runs through the course of his sickness, and finally is removed from the number of those who are sick, by recovery or by death. The chances of recovery or death vary from day to day during the course of his illness. The chances that the affected may convey infection to the unaffected are likewise dependent upon the stage of the sickness. As the epidemic spreads, the number of unaffected members of the community becomes reduced. Since the course of an epidemic is short compared with the life of an individual, the population may be considered as remaining constant, except in as far as it is modified by deaths due to the epidemic disease itself. In the course of time the epidemic may come to an end. One of the most important probems in epidemiology is to ascertain whether this termination occurs only when no susceptible individuals are left, or whether the interplay of the various factors of infectivity, recovery and mortality, may result in termination, whilst many susceptible individuals are still present in the unaffected population. It is difficult to treat this problem in its most general aspect. In the present communication discussion will be limited to the case in which all members of the community are initially equally susceptible to the disease, and it will be further assumed that complete immunity is conferred by a single infection.}, 37 | number = {772}, 38 | urldate = {2020-05-29}, 39 | journal = {Proceedings of the Royal Society of London. Series A, Containing Papers of a Mathematical and Physical Character}, 40 | author = {Kermack, William Ogilvy and McKendrick, A. G.}, 41 | month = aug, 42 | year = {1927}, 43 | pages = {700--721} 44 | } 45 | 46 | @article{owidcoronavirus, 47 | author = {Roser, Max and Ritchie, Hannah and Ortiz-Ospina, Esteban and Hasell, Joe}, 48 | title = {Coronavirus Pandemic {(COVID-19)}}, 49 | journal = {Our World in Data}, 50 | year = {2020}, 51 | url = {https://ourworldindata.org/coronavirus} 52 | } 53 | 54 | @incollection{timetree, 55 | title = {Placental mammals ({Eutheria})}, 56 | url = {http://www.timetree.org/public/data/pdf/Murphy2009Chap71.pdf}, 57 | booktitle = {The {Timetree} of {Life}}, 58 | publisher = {Oxford University Press}, 59 | author = {Murphy, William J and Eizirik, Eduardo}, 60 | year = {2009}, 61 | pages = {471--474}, 62 | } 63 | -------------------------------------------------------------------------------- /setup.bash: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # Setup Manubot 3 | # Based on https://github.com/manubot/rootstock/blob/main/SETUP.md 4 | # This is designed to be run from the bash terminal 5 | 6 | # Stop on first error. 7 | set -e 8 | 9 | usage() { 10 | echo "Usage: $0 [--owner text] [--repo text] [--yes]" 11 | echo "Guides the user through the creation of a new Manubot repository for their manuscript." 12 | echo 13 | echo "If no options are supplied a fully interactive process is used." 14 | echo "OWNER and REPO refer to the details of your manuscript repo location:" 15 | echo "i.e. https://github.com/OWNER/REPO." 16 | echo 17 | echo "Options:" 18 | echo " -o --owner GitHub user or organization name." 19 | echo " -r --repo Name of the repository for your new manuscript." 20 | echo " -y --yes Non-interactive mode. Continue script without asking for confirmation that the repo exists." 21 | echo " -s --ssh Use SSH to authenticate GitHub account. HTTPS is used by default." 22 | echo " Option only effective if --yes is also set, otherwise answer given in user interaction takes precedence." 23 | echo " -h --help Display usage information." 24 | 1>&2; exit 1; } 25 | 26 | # Check if to continue 27 | check(){ 28 | while true 29 | do 30 | echo "Once you have created your repo press enter to continue setup," 31 | read -r -p "or type exit to quit now: " input 32 | 33 | case $input in 34 | "") 35 | echo 36 | echo "Continuing Setup..." 37 | echo 38 | break 39 | ;; 40 | [eE][xX][iI][tT]) 41 | exit 1 42 | ;; 43 | *) 44 | echo 45 | echo "Invalid input, try again..." 46 | echo 47 | ;; 48 | esac 49 | done 50 | } 51 | 52 | # Option strings 53 | SHORT=o:r:hys 54 | LONG=owner:,repo:,help,yes,ssh 55 | 56 | YES=0 # continue when prompted 57 | AUTH=0 # used https or ssh auth 58 | 59 | # read the options 60 | OPTS=$(getopt --options $SHORT --long $LONG --name "$0" -- "$@") 61 | 62 | if [ $? != 0 ] ; then echo "Failed to parse options...exiting." >&2 ; exit 1 ; fi 63 | 64 | eval set -- "$OPTS" 65 | 66 | # extract options and their arguments into variables. 67 | while true ; do 68 | case "$1" in 69 | -o | --owner ) 70 | shift; 71 | OWNER=$1 72 | shift 73 | ;; 74 | -r | --repo ) 75 | REPO="$2" 76 | shift 2 77 | ;; 78 | -y | --yes ) 79 | YES=1 80 | shift 81 | ;; 82 | -s | --ssh ) 83 | AUTH=1; 84 | shift 85 | ;; 86 | -- ) 87 | shift 88 | break 89 | ;; 90 | -h | --help ) 91 | shift 92 | usage 93 | exit 1 94 | ;; 95 | *) 96 | echo "Internal error!" 97 | exit 1 98 | ;; 99 | esac 100 | done 101 | 102 | if [ -z "${OWNER}" ] || [ -z "${REPO}" ]; then 103 | echo "This script will take you through the setup process for Manubot." 104 | echo "First, we need to specify where to create the GitHub repo for your manuscript." 105 | echo 106 | echo "The URL will take this format: https://github.com/OWNER/REPO." 107 | echo "OWNER is your username or organization" 108 | echo "REPO is the name of your repository" 109 | echo 110 | read -r -p "Type in the OWNER now:" input 111 | OWNER=$input 112 | read -r -p "Type in the REPO now:" input 113 | REPO=$input 114 | fi 115 | 116 | # If using interactive mode, check remote repo exists. 117 | if [[ "$YES" == '0' ]]; then 118 | while true 119 | do 120 | echo 121 | read -r -p "Have you manually created https://github.com/${OWNER}/${REPO}? [y/n] " input 122 | 123 | case $input in 124 | [yY][eE][sS]|[yY]) 125 | 126 | echo 127 | echo "Continuing Setup..." 128 | echo 129 | break 130 | ;; 131 | [nN][oO]|[nN]) 132 | echo 133 | echo "Go to https://github.com/new and create https://github.com/${OWNER}/${REPO}" 134 | echo "Note: the new repo must be completely empty or the script will fail." 135 | echo 136 | check 137 | break 138 | ;; 139 | *) 140 | echo 141 | echo "Invalid input, try again..." 142 | echo 143 | ;; 144 | esac 145 | done 146 | else 147 | echo "Setting up https://github.com/${OWNER}/${REPO}" 148 | fi 149 | 150 | # Clone manubot/rootstock 151 | echo 152 | echo "Cloning Rootstock..." 153 | echo 154 | git clone --single-branch https://github.com/manubot/rootstock.git ${REPO} 155 | cd ${REPO} 156 | 157 | echo 158 | echo "Setup tracking of remote..." 159 | 160 | # Configure remotes 161 | git remote add rootstock https://github.com/manubot/rootstock.git 162 | 163 | # Check auth method 164 | if [[ "$YES" == '0' ]]; then 165 | while true 166 | do 167 | echo 168 | read -r -p "Would you like to use SSH to authenticate your GitHub account? [y/n] " input 169 | 170 | case $input in 171 | [yY][eE][sS]|[yY]) 172 | AUTH=1 173 | break 174 | ;; 175 | [nN][oO]|[nN]) 176 | AUTH=0 177 | break 178 | ;; 179 | *) 180 | echo 181 | echo "Invalid input, try again..." 182 | echo 183 | ;; 184 | esac 185 | done 186 | fi 187 | 188 | case $AUTH in 189 | 0) 190 | echo 191 | echo "Setting origin URL using its https web address" 192 | echo 193 | git remote set-url origin https://github.com/${OWNER}/${REPO}.git 194 | ;; 195 | 1) 196 | echo 197 | echo "Setting origin URL using SSH" 198 | echo 199 | git remote set-url origin git@github.com:$OWNER/$REPO.git 200 | ;; 201 | esac 202 | 203 | git push --set-upstream origin main 204 | 205 | # To use GitHub Actions only: 206 | echo "Setup for GitHub Actions ONLY..." 207 | # remove AppVeyor config 208 | git rm .appveyor.yml 209 | # remove ci/install.sh (only used by AppVeyor) 210 | git rm ci/install.sh 211 | 212 | # Update README 213 | echo "Updating README..." 214 | # Perform substitutions 215 | sed "s/manubot\/rootstock/${OWNER}\/${REPO}/g" README.md > tmp && mv -f tmp README.md 216 | sed "s/manubot\.github\.io\/rootstock/${OWNER}\.github\.io\/${REPO}/g" README.md > tmp && mv -f tmp README.md 217 | 218 | echo "Committing rebrand..." 219 | git add --update 220 | git commit --message "Brand repo to $OWNER/$REPO" 221 | git push origin main 222 | echo 223 | echo "Setup complete" 224 | echo 225 | echo "The new repo has been created at $(pwd)" 226 | echo 227 | echo "A good first step is to modify content/metadata.yaml with the relevant information for your manuscript." 228 | echo 229 | -------------------------------------------------------------------------------- /LICENSE-CC0.md: -------------------------------------------------------------------------------- 1 | # CC0 1.0 Universal 2 | 3 | ``` 4 | CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS INFORMATION ON AN "AS-IS" BASIS. CREATIVE COMMONS MAKES NO WARRANTIES REGARDING THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED HEREUNDER, AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED HEREUNDER. 5 | ``` 6 | 7 | ### Statement of Purpose 8 | 9 | The laws of most jurisdictions throughout the world automatically confer exclusive Copyright and Related Rights (defined below) upon the creator and subsequent owner(s) (each and all, an "owner") of an original work of authorship and/or a database (each, a "Work"). 10 | 11 | Certain owners wish to permanently relinquish those rights to a Work for the purpose of contributing to a commons of creative, cultural and scientific works ("Commons") that the public can reliably and without fear of later claims of infringement build upon, modify, incorporate in other works, reuse and redistribute as freely as possible in any form whatsoever and for any purposes, including without limitation commercial purposes. These owners may contribute to the Commons to promote the ideal of a free culture and the further production of creative, cultural and scientific works, or to gain reputation or greater distribution for their Work in part through the use and efforts of others. 12 | 13 | For these and/or other purposes and motivations, and without any expectation of additional consideration or compensation, the person associating CC0 with a Work (the "Affirmer"), to the extent that he or she is an owner of Copyright and Related Rights in the Work, voluntarily elects to apply CC0 to the Work and publicly distribute the Work under its terms, with knowledge of his or her Copyright and Related Rights in the Work and the meaning and intended legal effect of CC0 on those rights. 14 | 15 | 1. __Copyright and Related Rights.__ A Work made available under CC0 may be protected by copyright and related or neighboring rights ("Copyright and Related Rights"). Copyright and Related Rights include, but are not limited to, the following: 16 | 17 | i. the right to reproduce, adapt, distribute, perform, display, communicate, and translate a Work; 18 | 19 | ii. moral rights retained by the original author(s) and/or performer(s); 20 | 21 | iii. publicity and privacy rights pertaining to a person's image or likeness depicted in a Work; 22 | 23 | iv. rights protecting against unfair competition in regards to a Work, subject to the limitations in paragraph 4(a), below; 24 | 25 | v. rights protecting the extraction, dissemination, use and reuse of data in a Work; 26 | 27 | vi. database rights (such as those arising under Directive 96/9/EC of the European Parliament and of the Council of 11 March 1996 on the legal protection of databases, and under any national implementation thereof, including any amended or successor version of such directive); and 28 | 29 | vii. other similar, equivalent or corresponding rights throughout the world based on applicable law or treaty, and any national implementations thereof. 30 | 31 | 2. __Waiver.__ To the greatest extent permitted by, but not in contravention of, applicable law, Affirmer hereby overtly, fully, permanently, irrevocably and unconditionally waives, abandons, and surrenders all of Affirmer's Copyright and Related Rights and associated claims and causes of action, whether now known or unknown (including existing as well as future claims and causes of action), in the Work (i) in all territories worldwide, (ii) for the maximum duration provided by applicable law or treaty (including future time extensions), (iii) in any current or future medium and for any number of copies, and (iv) for any purpose whatsoever, including without limitation commercial, advertising or promotional purposes (the "Waiver"). Affirmer makes the Waiver for the benefit of each member of the public at large and to the detriment of Affirmer's heirs and successors, fully intending that such Waiver shall not be subject to revocation, rescission, cancellation, termination, or any other legal or equitable action to disrupt the quiet enjoyment of the Work by the public as contemplated by Affirmer's express Statement of Purpose. 32 | 33 | 3. __Public License Fallback.__ Should any part of the Waiver for any reason be judged legally invalid or ineffective under applicable law, then the Waiver shall be preserved to the maximum extent permitted taking into account Affirmer's express Statement of Purpose. In addition, to the extent the Waiver is so judged Affirmer hereby grants to each affected person a royalty-free, non transferable, non sublicensable, non exclusive, irrevocable and unconditional license to exercise Affirmer's Copyright and Related Rights in the Work (i) in all territories worldwide, (ii) for the maximum duration provided by applicable law or treaty (including future time extensions), (iii) in any current or future medium and for any number of copies, and (iv) for any purpose whatsoever, including without limitation commercial, advertising or promotional purposes (the "License"). The License shall be deemed effective as of the date CC0 was applied by Affirmer to the Work. Should any part of the License for any reason be judged legally invalid or ineffective under applicable law, such partial invalidity or ineffectiveness shall not invalidate the remainder of the License, and in such case Affirmer hereby affirms that he or she will not (i) exercise any of his or her remaining Copyright and Related Rights in the Work or (ii) assert any associated claims and causes of action with respect to the Work, in either case contrary to Affirmer's express Statement of Purpose. 34 | 35 | 4. __Limitations and Disclaimers.__ 36 | 37 | a. No trademark or patent rights held by Affirmer are waived, abandoned, surrendered, licensed or otherwise affected by this document. 38 | 39 | b. Affirmer offers the Work as-is and makes no representations or warranties of any kind concerning the Work, express, implied, statutory or otherwise, including without limitation warranties of title, merchantability, fitness for a particular purpose, non infringement, or the absence of latent or other defects, accuracy, or the present or absence of errors, whether or not discoverable, all to the greatest extent permissible under applicable law. 40 | 41 | c. Affirmer disclaims responsibility for clearing rights of other persons that may apply to the Work or any use thereof, including without limitation any person's Copyright and Related Rights in the Work. Further, Affirmer disclaims responsibility for obtaining any necessary consents, permissions or other rights required for any use of the Work. 42 | 43 | d. Affirmer understands and acknowledges that Creative Commons is not a party to this document and has no duty or obligation with respect to this CC0 or use of the Work. 44 | -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- 1 | # How to Contribute 2 | 3 | ## What to Contribute 4 | 5 | We're looking for contributors from a variety of backgrounds -- not just biologists and other scientists interested in reading and synthesizing the literature, but people with experience running collaborative literature reviews or managing large projects in GitHub have also been extremely helpful. 6 | 7 | To look for ideas of what is currently needed, check [here](https://github.com/greenelab/covid19-review/issues/34) or look through the open [Issues](https://github.com/greenelab/covid19-review/issues) until you find a topic that interests you. 8 | 9 | ## First Step 10 | 11 | First, go [here](https://github.com/greenelab/covid19-review/issues/17) and tell us a bit about yourself per the questions at the top. 12 | 13 | ## Suggesting a Paper 14 | 15 | One of the best things you can do is suggest a paper for review (even if it's outside of your own field but you think it seems interesting). 16 | To suggest a paper, choose the appropriate [New Paper Template](https://github.com/greenelab/covid19-review/issues/new/choose), depending on whether the paper pertains to therapeutics, diagnostics, or another category, and fill in as many sections as you feel comfortable responding to. 17 | 18 | ## Summarizing a Paper 19 | 20 | If you find a [suggested paper](https://github.com/greenelab/covid19-review/labels/New%20Paper) you feel comfortable evaluating, copy the questions from the template and fill them out as best you can. 21 | Ideally we'd like two people to look at each paper. 22 | It's OK if you can't evaluate everything. 23 | Feel free to mention what expertise you think would complement yours. 24 | 25 | ## How to Contribute Text 26 | 27 | 1. First, go [here](https://github.com/greenelab/covid19-review/issues/17) and tell us a bit about yourself. 28 | 2. Then, you can look through [current document](https://greenelab.github.io/covid19-review/) or at each section in the [content](https://github.com/greenelab/covid19-review/tree/master/content) folder. 29 | 3. To contribute suggestions or changes, beginners should follow [these instructions](INSTRUCTIONS.md). 30 | Experienced git users can find a suggested workflow and manubot build instructions [here](INSTRUCTIONS.md#command-line-users). 31 | 32 | [Click here](https://github.com/greenelab/covid19-review/blob/master/USAGE.md#manuscript-metadata) for formatting instructions. 33 | 34 | Once the answer to the question "did you change the contents of the repository in some way that was meaningful (i.e., not just adding an apostrophe or fixing typos)?" is yes, please add yourself to the author list by following the Authorship Guidelines below. 35 | 36 | ## Reviewing Someone's Pull Request 37 | 38 | Reviewing text that other contributors submit is one of the most important ways you can help. 39 | Because we are all coming from different fields, there is value in having as many people as possible look at each submission to help new ideas percolate. 40 | Right now, we are asking for at least two people to look at each new piece of text. 41 | Some things you can check for when you review someone's pull request: 42 | - Does it pass all manubot checks? ([See here for more information](https://github.com/greenelab/covid19-review/blob/master/INSTRUCTIONS.md#how-can-i-see-my-change)) 43 | - Is there an issue opened for every paper cited? 44 | - To the extent that the text overlaps with your own area of expertise, is it correct? 45 | Are there any ambiguities, oversimplifications, or topics you think should be clarified? 46 | - Do you have questions about any of the scientific content inside or outside of your field? 47 | - Will the text be easy for someone from a different scientific discipline to understand? 48 | 49 | If you have questions about the topic broadly, or want to discuss theory, how it may relate to other sections of the paper or to other fields, etc., you are encouraged to open an issue and start this discussion! 50 | One of the goals of this project is to get scientists from different disciplines working together and thinking creatively about the problems related to COVID-19. 51 | You can tag a PR in an issue by typing "\#" and the number of the PR (beside the title). 52 | (For example, #100 will call up the PR that added a code of conduct). 53 | 54 | ### The How-To of Review 55 | 56 | When you open someone's pull request, there are a few ways you can propose suggestions or changes. 57 | ![Looking at a pull request](.github/images/1-initial-view.png "Looking at a pull request") 58 | 59 | Here we will walk you through our preferred method. 60 | 61 | **Step One:** Navigate to the "Files" tab so that you can see the changes the user is proposing. 62 | ![Files tab](.github/images/2-initial-view-files.png "Looking at a pull request") 63 | 64 | In the picture above, you can see the text of the document. 65 | Green highlights the content that this pull request (PR) changes or adds. 66 | These lines also begin with a plus sign (`+`). 67 | Red highlights the content that they have deleted. 68 | These lines also begin with a minus sign (`-`). 69 | 70 | **Step Two:** Locate a line where you'd like to suggest a change, hover over it so that a blue "+" appears, and then click the "+" 71 | ![Blue plus](.github/images/3-blue-plus.png "Click the blue plus") 72 | 73 | **Step Three:** Click the page symbol (in blue here) to insert a suggestion 74 | ![Insert a suggestion](.github/images/4-click-suggest.png "Insert a suggestion") 75 | 76 | **Step Four:** Propose in-line edits 77 | ![Propose in-line edits](.github/images/5-make-change.png "Propose an in-line edit") 78 | 79 | Anything typed within the code formating block (the section sandwiched between \`\`\`), as in the picture above, will be considered an inline change. 80 | You can also type a separate comment outside of the code for block (i.e., before the first \`\`\` or after the second \`\`\`). 81 | 82 | **Step Five:** Click the green "Start a Review" button below the comment box to finalize your suggestion (although you can go back and edit it by clicking the three dots next the smiley face that you'll see beside the proposed change in the image for step 6). 83 | Starting a Review means that all of your suggestions will be grouped together for easier viewing -- we encourage this! 84 | Now repeat steps 2-4 for all of the changes you'd like to propose. 85 | 86 | **Step Six:** When you're finished proposing changes, click the large green "Finish Your Review" in the upper right corner 87 | ![Submit review](.github/images/6-submit.png "Submit Review") 88 | 89 | Thank you for reviewing a submission! 90 | If you have questions about this tutorial, please open an issue to let us know what's confusing, or ask for help on the [project gitter](https://gitter.im/covid19-review/community). 91 | 92 | 93 | ## Authorship Guidelines 94 | 95 | We're using the [ICMJE Guidelines](http://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authors-and-contributors.html) for determining authorship. 96 | To add yourself to the author list following a meaningful contribution to the repository, please: 97 | 1. Look up the [CRediT Taxonomy](https://casrai.org/credit/) and determine which Contributor Role(s) best characterizes your contribution. 98 | (You can always update this later if you take on more responsibilities) 99 | 2. Fill in your [author information](USAGE.md#manuscript-metadata) by initiating a [pull request](INSTRUCTIONS.md#how-to-contribute) on [this file](content/metadata.yaml) 100 | 101 | ## Chat Platform 102 | 103 | We're using [gitter](https://gitter.im) for informal conversations. 104 | Our group is called [covid19-review](https://gitter.im/covid19-review/community). 105 | It is linked to your GitHub credentials, so you won't need to make a new account. 106 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/new-diag-study-template.md: -------------------------------------------------------------------------------- 1 | --- 2 | name: New Paper Template (Diagnostic) 3 | about: If the paper or preprint primarily reports a diagnostic, use this template. 4 | title: 'New Paper (Diagnostic): [Title]' 5 | labels: New Paper, diagnostic 6 | assignees: '' 7 | 8 | --- 9 | 10 | 11 | 12 | Title: Please edit the title to add the name of the paper after the colon 13 | 14 | ## Please paste a link to the paper or a citation here: 15 | 16 | Link: 17 | 18 | ## What is the paper's [Manubot-style citation](https://github.com/greenelab/covid19-review/blob/master/USAGE.md#citations)? 19 | 20 | 21 | Citation: 22 | 23 | ## Please list some keywords (3-10) that help identify the relevance of this paper to COVID-19 24 | 25 | * keyword 1 (replace me, copy and paste more than three if needed) 26 | * keyword 2 (replace me, copy and paste more than three if needed) 27 | * keyword 3 (replace me, copy and paste more than three if needed) 28 | 29 | ## Please note the publication / review status 30 | 31 | 32 | - [ ] Pre-print 33 | - [ ] New Peer-Reviewed Paper 34 | - [ ] Peer-Reviewed Paper Pre-2020 35 | 36 | ## Which areas of expertise are particularly relevant to the paper? 37 | 38 | 39 | - [ ] virology 40 | - [ ] epidemiology 41 | - [ ] biostatistics 42 | - [ ] immunology 43 | - [ ] pharmacology 44 | 45 | 46 | 47 | ## Questions to answer about each paper: 48 | 49 | ### Please provide 1-2 sentences introducing the study and its main findings 50 | 51 | 52 | 53 | ### Study question(s) being investigated: 54 | 55 | #### What type of testing scenario is being considered? 56 | 57 | Is it a screening test (used for individuals with no symptoms), diagnostic test (used for individuals with symptoms), or definitive test (used for individuals who have had previous positive test results on diagnostic or screening tests)? 58 | 59 | ### Study population: 60 | 61 | #### What is the model system (e.g., human study, animal model, cell line study)? 62 | 63 | #### What is the sample size? 64 | 65 | #### What is the "pre-test" probability of disease in the study population (i.e., what is the anticipated prevalence of the disease?) 66 | 67 | #### For human studies, the following are related to the pre-test probability: 68 | 69 | ##### What countries/regions are considered? 70 | 71 | ##### What is the age range, gender, other relevant characteristics? 72 | 73 | ##### What is the setting of the study (e.g., random sample of school children, retirement communities, etc.)? 74 | 75 | ##### What other specific inclusion-exclusion criteria are considered? 76 | 77 | ### Reference test: 78 | 79 | #### What reference test is considered as a "gold standard" comparator for the test under investigation? 80 | 81 | #### Test assignment: 82 | 83 | ##### How are the new and reference tests assigned? 84 | 85 | Examples of assignment could include: Recruited individuals have initially undergone neither the new nor the reference test; individuals tested as positive or negative by the reference test undergo the new test; individuals who have undertaken the new test are assessed by the standard test. 86 | 87 | ##### Are there any other relevant details about the study design? 88 | 89 | Depending on how individuals are chosen, the test may be biasing towards more sick or less sick individuals or very clear-cut positive/negative cases. 90 | Any factors that would influence this bias should be included here. 91 | 92 | ### Test conduct: 93 | 94 | #### How were tests performed? 95 | 96 | Describe technical details of assays used, when measurements were taken and by whom, etc. for both the new and standard tests. 97 | 98 | ### Test Assessment 99 | 100 | #### Describe how individuals are classified as positive or negative, e.g. if a threshold is used. 101 | 102 | #### Is there evidence that the test is precise/reproducible when repeated more than once? 103 | 104 | #### Are measurements complete? 105 | 106 | For example: Do some participants undergo just one test (the new or the reference test)? 107 | Are there individuals with inconclusive results? 108 | 109 | ### Results summary: 110 | 111 | #### What are the estimated sensitivity, specificity, positive predictive value (PPV), and negative predicted value (NPV)? 112 | 113 | Note that the PPV and NPV represent "post-test" probabilities of disease and are generally more meaningful than sensitivity and specificity. 114 | Sometimes the post-test odds will be given instead. 115 | 116 | #### What are the confidence bounds around these intervals? 117 | 118 | ### Interpretation of results for study population: 119 | 120 | #### How good is the test at ruling in or ruling out a disease based on the post-test probabilities? 121 | 122 | #### Are there identified side affects of the test? 123 | 124 | #### Is patient adherence to the test likely to be an issue? 125 | 126 | ### Extrapolation of conclusions to other groups of individuals 127 | 128 | #### How well is the test likely to work in populations with different pretest odds? 129 | 130 | For example, if the prevalence is lower, then the PPV will also be lower, but the NPV will be higher. 131 | 132 | #### How costly is the test? 133 | 134 | #### How difficult is it to perform the test in different settings? 135 | 136 | #### Could the test be combined with other existing tests? 137 | 138 | ### Summary of reliability 139 | 140 | 1-2 sentences on concluding remarks, including summary of strengths, weaknesses, limitations. 141 | 142 | ### Progress 143 | 144 | _Check off the components as they are completed. If the component is not applicable, check the box as well._ 145 | 146 | 147 | 148 | - [ ] 1-2 sentences introducing the study and its main findings 149 | - [ ] Describe testing scenario 150 | - [ ] Describe model system 151 | - [ ] Sample size 152 | - [ ] Describe prevalnce of disease 153 | - [ ] Describe countries/regions are considered 154 | - [ ] Describe age range, gender, other relevant characteristics 155 | - [ ] Describe setting of the study 156 | - [ ] Describe other specific inclusion-exclusion criteria 157 | - [ ] Describe "gold standard" 158 | - [ ] Describe how the new and reference tests assigned 159 | - [ ] Describe other relevant details about the study design 160 | - [ ] Describe how the tests were performed 161 | - [ ] Describe how individuals are classified as positive or negative 162 | - [ ] Describe if test is precise/reproducible 163 | - [ ] Describe whether measurements are complete 164 | - [ ] What are the estimated sensitivity, specificity, positive predictive value (PPV), and negative predicted value (NPV)? 165 | - [ ] What are the confidence bounds around these intervals? 166 | - [ ] Describe post-test probabilities 167 | - [ ] Describe side affects of the test 168 | - [ ] Describe patient adherence 169 | - [ ] Describe how it will extrapolate 170 | - [ ] How costly is the test? 171 | - [ ] How difficult is it to perform the test in different settings? 172 | - [ ] Could the test be combined with other existing tests? 173 | - [ ] Summary of reliability 174 | -------------------------------------------------------------------------------- /content/response-to-reviews/therapeutics-v1.md: -------------------------------------------------------------------------------- 1 | This review article is an excerpt from a comprehensive COVID-19 encyclopedia available online at https://greenelab.github.io/covid19-review/. The section on therapeutics has been submitted, which is a topic of broad interest. The strengths of this review are its scope and detail, including many useful citations. However, multiple major weaknesses were noted: 2 | 3 | ** 4 | We are grateful for the reviewer's feedback and have made substantial changes to the manuscript in order to address their concerns. 5 | ** 6 | 7 | 1.1 Lack of conceptual organization. The review is organized by type of drug. While I could see the value in this as a resource it does not translate well to a review article that can be read in one sitting. What is the intended audience of this piece? If it is clinicians, it may make more sense to organize the sections based on how promising the therapeutic is. If it is basic scientists, it would help to group the interventions by mechanism of action or some other biological question. 8 | 9 | ** 10 | The intended audience is basic scientists, and we appreciate the reviewer's suggestions for how to improve usefulness for this audience. 11 | We absolutely understand the reviewer's concerns about the organization of the original text. 12 | In order to make the content more navigable, the new version of the text is divided into two sections. 13 | The article itself provides an overview of therapeutic development for COVID-19, emphasizing the differences between drug development versus repurposing, therapeutics targeting the host versus the virus, and small molecules versus biologics. 14 | Much of the original text, where individual papers are critiqued, has been moved to an appendix. 15 | We hope this will provide a broad view of the current state of therapeutic development for most readers, with in-depth critique available for readers who would like to investigate a particular therapeutic further. 16 | ** 17 | 18 | 1.2 Too much text discussing failed approaches and limitations of clinical trials. A considerable amount of text is spent on chloroquine, despite the wide consensus that it does not have an effect. In contrast, promising approaches like monoclonal antibodies are given just a few short paragraphs. I also felt that the in-depth criticisms of clinical trial design were unnecessary and distracted from the main message of each section. They are certainly valid points, but it would be great to get the conclusion across in a more concise manner, while providing references that enable interested readers to dive deeper into each study's strengths and weaknesses. 19 | 20 | ** 21 | We hope that the new structure serves to address most of these concerns. 22 | The detailed critiques have been moved to the appendix, and the narratives surrounding failed approaches has been streamlined so as not to over-emphasize them. 23 | ** 24 | 25 | It also seems dangerous to infer researcher biases like p-hacking without more definitive data that support these potentially damaging claims. 26 | 27 | ** 28 | The sentence in question has been modified to read: "Additionally, disparities between the pre-registered and published protocols raises concerns about experimental design." 29 | ** 30 | 31 | 1.3 This article as presented seems premature. I was especially confused by the statement in the abstract that "this review will be updated as progress is made." Is that even possible at mSystems? 32 | 33 | ** 34 | The project is built on Manubot, a relatively new resource for collaborative writing that allow for version control and continual editing. 35 | An up-to-date version of the manuscript is available online at all times at , but _mSystems_ has agreed to review a version of record and to allow the submission of updates as more evidence becomes available over time, in the style of a living review. 36 | However, we understand this could confuse readers and have removed the text from the abstract and body that referred to updating the manuscript. 37 | ** 38 | 39 | More importantly, the conclusion for all but 1-2 therapeutics is that more data is needed, leaving me wondering what the value of this review is at time present. One useful contribution would be to rank the promise of each approach. Each has issues, but which ones are worth investing more resources in? 40 | 41 | ** 42 | We hope that the recontextualization of the content serves to address the concerns related to the usefulness of the project -- the goal is to organize the available evidence to allow scientists to get or stay up to speed on the status of these therapeutics without needing to dive independently into the exceptionally large body of literature. 43 | We also took your recommendation to integrate grades for each therapeutic. 44 | We drew the grades from https://cdcn.org/corona-data-viewer/. 45 | These are now listed in Table 1 and used to color-code the therapeutics in the illustration of their mechanisms. 46 | ** 47 | 48 | 1.4 Figure 1 - I'm not sure this adds much to the current topic. 49 | 50 | ** 51 | Figure 1 has been modified to show the relative trajectories of the SARS-CoV-1 and SARS-CoV-2 viral outbreaks (data were not available for MERS). 52 | The goal of this figure is to show why pharmacology plays such a bigger role in the present pandemic than it has in the past, as well as to emphasize how much more feasible clinical trials are based on the differences in caseload. 53 | We hope the relevance is improved with these changes. 54 | ** 55 | 56 | 1.5 Figure 2 - panel labels (letters) are needed. 57 | 58 | ** 59 | This change has been made. 60 | ** 61 | 62 | The y-axis of panel 4 is difficult to read - the panel should either be stretched or some of the less common approaches could be trimmed off. The "other" category could also be removed. 63 | 64 | ** 65 | These changes have been made. 66 | ** 67 | 68 | More importantly, I worry that this figure is immediately out of date, is there any indication that these trends will be stable over time? If not, why is it important to know what fraction of trials are in Phase 2 right now? 69 | 70 | ** 71 | As part of this project, we developed software to pull data from the web and update these figures every night. 72 | See https://greenelab.github.io/covid19-review/ for the most recent version of this figure. 73 | While the version of record will be locked at a certain time point, this approach does allow us to keep the version online continually updated. 74 | The stability of these trends over time is an interesting question that it would be possible to address using these data sources. 75 | The main purpose of the figure in the context of the manuscript is to show what research is in progress and therefore what evidence is expected to eventually become available. 76 | The question of whether trends remain stable over time is an interesting one. 77 | It seems to have been evaluated by Bugin & Woodcock (2021) in _Nature Reviews Drug Discovery_ as a Biobusiness brief (DOI:10.1038/d41573-021-00037-3). 78 | They reported that trends have changed over time, with antivirals and immunomodulators very popular at the beginning of 2020 but dipping as the year went on, while neutralizing antibodies and other avenues of investigation increased by October 2020. 79 | Our efforts were primarily to visualize the distribution of research across different categories, and adding a temporal component to evaluating the specific therapeutics under investigation (rather than categories as in Bugin & Woodcock (2021)) would be an interesting future direction related to this project. 80 | 81 | ** 82 | 83 | 1.6 Figure 3 - I really liked this figure and would like to see it earlier in the review. One concern I have is that all of the drugs are equivalent on this diagram, which could lead the reader to think that HCQ/CQ are effective. Perhaps it would be safer to remove the drug names and indicate the various mechanisms that could be theoretically targeted. Or alternatively, the thickness of the arrows could be used to indicate current data on efficacy. 84 | 85 | ** 86 | Thank you for your positive feedback and thoughtful critique of this figure. 87 | The figure has been moved up in the manuscript to correspond to a new section focusing on virological insights into drug repurposing. 88 | 89 | ** 90 | 91 | 1.7 typo on Line 1288 - "reduce accelerate" 92 | 93 | ** 94 | This typo has been corrected. 95 | The sentence now reads: "The interim analysis of the phase 2 portion suggested that bamlanivimab alone was able to accelerate the reduction in viral load." 96 | ** 97 | 98 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/new-therapy-study-template.md: -------------------------------------------------------------------------------- 1 | --- 2 | name: New Paper Template (Therapeutic) 3 | about: If the paper or preprint primarily reports a therapeutic, use this template. 4 | title: 'New Paper (Therapeutic): [Title]' 5 | labels: New Paper, therapeutic 6 | assignees: '' 7 | 8 | --- 9 | 10 | 11 | 12 | Title: Please edit the title to add the name of the paper after the colon 13 | 14 | ## Please paste a link to the paper or a citation here: 15 | 16 | Link: 17 | 18 | ## What is the paper's [Manubot-style citation](https://github.com/greenelab/covid19-review/blob/master/USAGE.md#citations)? 19 | 20 | 21 | Citation: 22 | 23 | ## Please list some keywords (3-10) that help identify the relevance of this paper to COVID-19 24 | 25 | * keyword 1 (replace me, copy and paste more than three if needed) 26 | * keyword 2 (replace me, copy and paste more than three if needed) 27 | * keyword 3 (replace me, copy and paste more than three if needed) 28 | 29 | ## Please note the publication / review status 30 | 31 | 32 | - [ ] Pre-print 33 | - [ ] New Peer-Reviewed Paper 34 | - [ ] Peer-Reviewed Paper Pre-2020 35 | 36 | ## Which areas of expertise are particularly relevant to the paper? 37 | 38 | 39 | - [ ] virology 40 | - [ ] epidemiology 41 | - [ ] biostatistics 42 | - [ ] immunology 43 | - [ ] pharmacology 44 | 45 | 46 | 47 | ## Questions to answer about each paper: 48 | 49 | ### Please provide 1-2 sentences introducing the study and its main findings 50 | 51 | 52 | ### Study question(s) being investigated: 53 | 54 | #### How many/what drugs/combinations are being considered? 55 | 56 | 57 | #### What are the main hypotheses being tested? 58 | 59 | 60 | ### Study population: 61 | 62 | #### What is the model system (e.g., human study, animal model, cell line study)? 63 | 64 | 65 | #### What is the sample size? If multiple groups are considered, give sample size for each group (including controls). 66 | 67 | * number treated with treatment A 68 | * number treated with treatment B 69 | 70 | #### For human studies: 71 | 72 | ##### What countries/regions are considered? 73 | 74 | ##### What is the age range, gender, other relevant characteristics? 75 | 76 | ##### What is the setting of the study (random sample of school children, inpatient, outpatient, etc)? 77 | 78 | ##### What other specific inclusion-exclusion criteria are considered? 79 | 80 | For example, do the investigators exclude patients with diagnosed neoplasms or patients over/under a certain age? 81 | 82 | 83 | ### Treatment assignment: 84 | 85 | #### How are treatments assigned? 86 | 87 | For example, is it an interventional or an observational study? 88 | 89 | #### Is the study randomized? 90 | 91 | A study can be interventional but not randomized (e.g., a phase I or II clinical trial is interventional but often not randomized). 92 | 93 | #### Provide other relevant details about the design. 94 | 95 | This includes possible treatment stratification (e.g., within litters for animal studies, within hospitals for human studies), possible confounding variables (e.g., having a large age range of individuals), possible risks of bias and how they are addressed (e.g., is there masking in a clinical trial? how are individuals chosen in an observational study?). 96 | 97 | 98 | ### Outcome Assessment: 99 | 100 | #### Describe the outcome that is assessed and whether it is appropriate. 101 | 102 | For example: Is the outcome assessed by a clinician or is it self-reported? 103 | Is the outcome based on viral load or a functional measurement (e.g., respiratory function, discharge from hospital)? 104 | What method is used to measure the outcome? 105 | How long after a treatment is the outcome measured? 106 | 107 | #### Are outcome measurements complete? 108 | 109 | For example, are there individuals lost to follow up? 110 | 111 | #### Are outcome measurements subject to various kinds of bias? 112 | 113 | For example, a lack of masking in randomized clinical trials. 114 | 115 | 116 | ### Statistical Methods Assessment: 117 | 118 | #### What methods are used for inference? 119 | 120 | For example, logistic regression, nonparametric methods. 121 | 122 | #### Are the methods appropriate for the study? 123 | 124 | For example, are clustered data treated independently or are clusters adjusted for, such as different hospitals or litters? 125 | 126 | #### Are adjustments made for possible confounders? 127 | 128 | For example, adjustment for age, sex, or comorbidities. 129 | 130 | 131 | ### Results Summary: 132 | 133 | #### What is the estimated association? 134 | 135 | For example, is it an estimated odds ratio, a median difference in detected cases, etc? 136 | 137 | #### What measures of confidence or statistical significance are provided? 138 | 139 | For example, confidence intervals, p-values, and/or Bayes factors. 140 | 141 | 142 | ### Interpretation of results for study population: 143 | 144 | #### Can we make a causal interpretation for the individuals in the study of drug -> outcome, such as "taking drug A improves likelihood of survival twofold over taking drug B." 145 | 146 | For example, with a well-performed animal study or randomized trial it is often possible to infer causality. 147 | If is an observational study, does it match up with some of the Bradford Hill criteria? https://www.edwardtufte.com/tufte/hill https://en.wikipedia.org/wiki/Bradford_Hill_criteria 148 | 149 | #### Are there identified side effects or interactions with other drugs? 150 | 151 | For example, is the treatment known to cause liver damage or to not be prescribed for individuals with certain comorbities? 152 | 153 | #### Are there specific subgroups with different findings? 154 | 155 | For example, do individuals with a specific baseline seem to do particularly well? Be particularly cautious with respect to multiple testing here. 156 | 157 | 158 | ### Extrapolation of conclusions to other groups of individuals not specifically included in the study: 159 | 160 | #### If the study is an animal study, which animal and how relevant is that model? 161 | 162 | Is the model system appropriate? Is there evidence from past use that it's highly-relevant to therapeutic design in this context? 163 | 164 | #### If it is a human study, what characteristics of the study population may support/limit extrapolation? 165 | 166 | * Can results extrapolate easily to other similar groups? (e.g., same country, similar age groups) 167 | * What would happen if conditions are extended in terms of dose or duration? 168 | * Can results be extrapolated to other populations or in very different settings? (e.g., different age group, primary care setting vs emergency department etc) 169 | 170 | 171 | ### Summary of reliability 172 | 173 | 1-2 sentences on concluding remarks, including summary of strengths, weaknesses, limitations. 174 | 175 | ### Progress 176 | 177 | _Check off the components as they are completed. If the component is not applicable, check the box as well._ 178 | 179 | 180 | 181 | - [ ] 1-2 sentences introducing the study and its main findings 182 | - [ ] Describe How many/what drugs/combinations are being considered 183 | - [ ] Describe the model system 184 | - [ ] What is the sample size? 185 | - [ ] What countries/regions are considered 186 | - [ ] What is the age range, gender, other relevant characteristics 187 | - [ ] Describe study setting 188 | - [ ] Describe other specific inclusion-exclusion criteria 189 | - [ ] Describe how treatments are assigned 190 | - [ ] Describe randomization (or not) and other relavent details about the design 191 | - [ ] Describe the outcome that is assessed and whether it is appropriate. 192 | - [ ] Describe whether the outcome measurements are complete 193 | - [ ] Are outcome measurements subject to various kinds of bias? 194 | - [ ] Describe methods used for inference 195 | - [ ] Describe whether the methods are appropriate for the study 196 | - [ ] Are adjustments made for possible confounders? 197 | - [ ] Describe the estimated association 198 | - [ ] What measures of confidence or statistical significance are provided? 199 | - [ ] Describe whether a causal interpretation can be made 200 | - [ ] Are there identified side effects or interactions with other drugs? 201 | - [ ] Are there specific subgroups with different findings? 202 | - [ ] If the study is an animal study, which animal and how relevant is that model? 203 | - [ ] If it is a human study, what characteristics of the study population may support/limit extrapolation? 204 | - [ ] Summary of reliability 205 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # SARS-CoV-2 and COVID-19: An Evolving Review of Diagnostics and Therapeutics 2 | 3 | 4 | 5 | [![HTML Manuscript](https://img.shields.io/badge/manuscript-HTML-blue.svg)](https://greenelab.github.io/covid19-review/) 6 | [![PDF Manuscript](https://img.shields.io/badge/manuscript-PDF-blue.svg)](https://greenelab.github.io/covid19-review/manuscript.pdf) 7 | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5532921.svg)](https://doi.org/10.5281/zenodo.5532921) 8 | [![GitHub Actions Status](https://github.com/greenelab/covid19-review/workflows/Manubot/badge.svg)](https://github.com/greenelab/covid19-review/actions) 9 | [![Gitter](https://badges.gitter.im/covid19-review/community.svg)](https://gitter.im/covid19-review/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge) 10 | 11 | 12 | Project Status: 13 | | Section | Title | Status Issue | Submission Status | Venue | Links 14 | | -- | -- | -- | -- |-- | -- | 15 | | [Pathogenesis](https://greenelab.github.io/covid19-review/#pathogenesis-symptomatology-and-transmission-of-sars-cov-2-through-analysis-of-viral-genomics-and-structure) | Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure | ✔️ | [Published](https://doi.org/10.1128/mSystems.00095-21) 🎉 | _mSystems_ | [Release](https://github.com/greenelab/covid19-review/releases/tag/pathogenesis-v3); [Preprint](http://arxiv.org/abs/2102.01521) 16 | | [Evolution](https://greenelab.github.io/covid19-review/#evolutionary-perspectives-on-sars-cov-2) | Evolutionary Perspectives on SARS-CoV-2 | #867 | Suspended | Manubot only 17 | | [Diagnostics](https://greenelab.github.io/covid19-review/#molecular-and-serologic-diagnostic-technologies-for-sars-cov-2) | Molecular and Serologic Diagnostic Technologies for SARS-CoV-2| #1156 | Reviewed, not revised | _mSystems_ | [Release](https://github.com/greenelab/covid19-review/releases/tag/diagnostics-v1); [Preprint](https://arxiv.org/abs/2204.12598) | 18 | | [Pharmaceuticals](https://greenelab.github.io/covid19-review/#identification-and-development-of-therapeutics-for-covid-19) | Identification and Development of Therapeutics for COVID-19 | ✔️ | [Published](https://doi.org/10.1128/mSystems.00233-21) 🎉 | _mSystems_ | [Release](https://github.com/greenelab/covid19-review/releases/tag/pharmaceuticals-v3); [Preprint](http://arxiv.org/abs/2103.02723) | 19 | | [Vaccines- Established Platforms](https://greenelab.github.io/covid19-review/#application-of-traditional-vaccine-development-strategies-to-sars-cov-2) | Application of Traditional Vaccine Development Strategies to SARS-CoV-2 | ✔️ | [Published](https://doi.org/10.1128/msystems.00927-22) 🎉 | _mSystems_ | [Release](https://github.com/greenelab/covid19-review/releases/tag/vaccines-trad-v2.1); [Preprint](https://arxiv.org/abs/2208.08907) | 20 | | [Vaccines- Novel Platforms](https://greenelab.github.io/covid19-review/#the-coming-of-age-of-nucleic-acid-vaccines-during-covid-19) | The Coming of Age of Nucleic Acid Vaccines during COVID-19 | ✔️ | [Published](https://doi.org/10.1128/msystems.00928-22) 🎉 | _mSystems_ | [Release](https://github.com/greenelab/covid19-review/releases/tag/vaccines-novel-v2); [Preprint](https://arxiv.org/abs/2210.07247) | 21 | | [Nutraceuticals](https://greenelab.github.io/covid19-review/#dietary-supplements-and-nutraceuticals-under-investigation-for-covid-19-prevention-and-treatment) | Dietary Supplements and Nutraceuticals Under Investigation for COVID-19 Prevention and Treatment | ✔️ | [Published](https://doi.org/10.1128/mSystems.00122-21) 🎉 | _mSystems_ | [Release](https://github.com/greenelab/covid19-review/releases/tag/nutraceuticals-v2); [Preprint](http://arxiv.org/abs/2102.02250) | 22 | | [Social Determinants of Health](https://greenelab.github.io/covid19-review/#social-factors-influencing-covid-19-exposure-and-outcomes) | Social Factors Influencing COVID-19 Exposure and Outcomes | #868 | Suspended | Manubot only 23 | | [Methods (Cyberinfrastructure)](https://greenelab.github.io/covid19-review/#an-open-publishing-response-to-the-covid-19-infodemic) | An Open-Publishing Response to the COVID-19 Infodemic | ✔️ | [Published](http://ceur-ws.org/Vol-2976/paper-2.pdf) 🎉 | [DISCO 2021](https://infoqualitylab.org/events/disco2021/) | [Release](https://github.com/greenelab/covid19-review/releases/tag/methods-v4); [Preprint](https://arxiv.org/abs/2109.08633) 24 | 25 | This project was most active from March 2020 through February 2023 and is not currently receiving major updates. 26 | 27 | ## Code of Conduct 28 | 29 | This project operates under a code of conduct. 30 | Participating in the project in any way (issues, pull requests, gitter, or other media) indicates that you agree that you will follow the [code of conduct](CODE_OF_CONDUCT.md). 31 | We take this very seriously. 32 | If you experience harassment or notice violations of the code of conduct, please raise the issue to one of the project organizers (@rando2 or @cgreene). 33 | 34 | ## Project Description 35 | 36 | 37 | With the rapidly evolving global situation related to COVID-19, the infectious disease caused by the SARS-CoV-2 virus, there is a need to centralize scientific knowledge relevant to the development of diagnostics and therapeutics. 38 | This repository is an online, collaborative review paper written with [manubot](https://manubot.org/). 39 | We are seeking input from scientists at all levels anywhere in the world. 40 | 41 | Our goal is to quickly and accurately summarize and synthesize the papers that are coming out in order to develop a broader picture of what's being attempted and the status of those efforts. 42 | We hope to contextualize elements of this virus and infectious disease with respect to better understood viruses and diseases (e.g., to identify shared mechanisms). 43 | This repository is also a living document that aims to consolidate and integrate helpful information about diagnostics and therapeutics that is circulating in decentralized spaces (e.g., Twitter threads) into a more permanent and unified format. 44 | 45 | ## Contributions 46 | 47 | You'll need to make a free [GitHub account](https://github.com/join?source=header-home). 48 | 49 | Instructions and procedures for contributing are [outlined here](CONTRIBUTING.md). 50 | 51 | We will follow the [ICMJE Guidelines](http://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authors-and-contributors.html) for determining authorship. 52 | 53 | Please note that, while reading scientific literature is a particular skill, we know that people outside of science are also invested in this topic and there is a lot of information circulating about the virus and about possible therapies. 54 | Non-scientists are welcome to contribute by opening New Paper issues to let us know about topics or papers they're concerned about or would like to see addressed. 55 | 56 | Undergraduate students who are interested are encouraged to take part in discussions, ask questions, post interesting papers, and contribute paper summaries (just please note in your summary that you're a student). 57 | 58 | ## Pull Requests 59 | 60 | If you are not familiar with git and GitHub, you can use [these directions](INSTRUCTIONS.md) to start contributing. 61 | 62 | Please feel encouraged to ask questions by opening a [Request for Help issue](https://github.com/greenelab/covid19-review/issues/new?assignees=rando2&labels=&template=request-for-help.md&title=Help%3A+%5BAdd+topic+here%5D) 63 | [![GitHub issues](https://img.shields.io/github/issues-raw/greenelab/covid19-review?label=Open%20Issue&style=social)](https://github.com/greenelab/covid19-review/issues/new/choose) 64 | 65 | This project is a collaborative effort that will benefit from the expertise of scientists across a wide range of disciplines! 66 | 67 | ## Manubot 68 | 69 | 70 | Manubot is a system for writing scholarly manuscripts via GitHub. 71 | Manubot automates citations and references, versions manuscripts using git, and enables collaborative writing via GitHub. 72 | An [overview manuscript](https://greenelab.github.io/meta-review/ "Open collaborative writing with Manubot") presents the benefits of collaborative writing with Manubot and its unique features. 73 | The [rootstock repository](https://git.io/fhQH1) is a general purpose template for creating new Manubot instances, as detailed in [`SETUP.md`](SETUP.md). 74 | See [`USAGE.md`](USAGE.md) for documentation how to write a manuscript. 75 | 76 | Please open [an issue](https://git.io/fhQHM) for questions related to Manubot usage, bug reports, or general inquiries. 77 | 78 | ### Repository directories & files 79 | 80 | + This file is called [`README.md`](README.md) 81 | It is the centralized document for the repository and will help direct users to other relevant information. 82 | + [`CONTRIBUTING.md`](CONTRIBUTING.md) contains procedures and directions for contributing to this effort. 83 | + [`INSTRUCTIONS.md`](INSTRUCTIONS.md) contains instructions for new GitHub users for how to navigate GitHub in the browser as well as GitHub vocabulary. 84 | It also includes some instructions for more experienced users about the procedures we recommend and how to run manubot on the command line. 85 | + [`USAGE.md`](USAGE.md) describes formatting instructions for formatting text, citing references, adding figures and tables, etc. 86 | + [`SETUP.md`](SETUP.md) includes information about setting up manubot 87 | + [`LICENSE.md`](LICENSE.md) and [`LICENSE-CC0.md`](LICENSE-CC0.md) contain the licenses associated with manubot and with the content we are developing in this project. Please see the "License" section below. 88 | 89 | The directories are as follows: 90 | 91 | + [`content`](content) contains the manuscript source, which includes markdown files as well as inputs for citations and references. 92 | These are the files that most contributors will be editing. 93 | See [`USAGE.md`](USAGE.md) for more information. 94 | + [`output`](output) contains the outputs (generated files) from Manubot including the resulting manuscripts. 95 | You should not edit these files manually, because they will get overwritten. 96 | + [`webpage`](webpage) is a directory meant to be rendered as a static webpage for viewing the HTML manuscript. 97 | + [`build`](build) contains commands and tools for building the manuscript. 98 | + [`ci`](ci) contains files necessary for deployment via continuous integration. 99 | 100 | ## License 101 | 102 | 106 | 107 | [![License: CC BY 4.0](https://img.shields.io/badge/License%20All-CC%20BY%204.0-lightgrey.svg)](http://creativecommons.org/licenses/by/4.0/) 108 | [![License: CC0 1.0](https://img.shields.io/badge/License%20Parts-CC0%201.0-lightgrey.svg)](https://creativecommons.org/publicdomain/zero/1.0/) 109 | 110 | Except when noted otherwise, the entirety of this repository is licensed under a CC BY 4.0 License ([`LICENSE.md`](LICENSE.md)), which allows reuse with attribution. 111 | Please attribute by linking to https://github.com/manubot/rootstock. 112 | 113 | Since CC BY is not ideal for code and data, certain repository components are also released under the CC0 1.0 public domain dedication ([`LICENSE-CC0.md`](LICENSE-CC0.md)). 114 | All files matched by the following glob patterns are dual licensed under CC BY 4.0 and CC0 1.0: 115 | 116 | + `*.sh` 117 | + `*.py` 118 | + `*.yml` / `*.yaml` 119 | + `*.json` 120 | + `*.bib` 121 | + `*.tsv` 122 | + `.gitignore` 123 | 124 | All other files are only available under CC BY 4.0, including: 125 | 126 | + `*.md` 127 | + `*.html` 128 | + `*.pdf` 129 | + `*.docx` 130 | 131 | Please open [an issue](https://github.com/manubot/rootstock/issues) for any question related to licensing. 132 | -------------------------------------------------------------------------------- /INSTRUCTIONS.md: -------------------------------------------------------------------------------- 1 | # Instructions for Contributing with GitHub 2 | 3 | ## Instructions for New Users 4 | 5 | If you are new to GitHub or would prefer to work in your browser, please follow the directions in this section. 6 | 7 | ### What is Git? 8 | 9 | Have you ever frantically edited a paper, then realized you liked your original version better? 10 | Git is a tool that allows you to track all the changes made to a document over time. 11 | Have you ever been writing something as a team and found that someone was editing an old version of the document? 12 | Git tracks different people's contributions and manages how they get merged together to avoid the headache of figuring out what changed when. 13 | 14 | We are managing this project through GitHub with the goal of a) allowing for the manuscript to evolve rapidly as new information comes out, and b) give everyone credit for their contributions. 15 | While we believe this is a great tool, we know it can sometimes be intimidating to get started. 16 | We don't want the medium to turn anyone away from contributing, so please let us know if you're having problems. 17 | 18 | ### Most Important: Make a GitHub account 19 | 20 | GitHub is an online platform that visualizes changes made with git (think of a really elegant "Track Changes"). 21 | You can make an account [here](https://github.com/). 22 | As long as you do this first step of making a GitHub account, you will always be able to open an issue to ask us for help! 23 | 24 | ### GitHub Vocabulary 25 | 26 | - [Repository](http://github.com/greenelab/covid19-review): 27 | The set of files, issue tracker issues, etc. related to this manuscript. 28 | - [Issue](https://github.com/greenelab/covid19-review/issues): 29 | The ticketing system for GitHub. 30 | A ticket can be a question, concern, problem, bug, or anything else you want to bring to the attention of the people working on a repository. 31 | Here, we will use tickets not only for problems or questions, but also to gather papers and preprints that come out about diagnostics and therapeutics related to COVID-19. 32 | - Issue Template: 33 | A way of pre-specifying what an "issue" should look like to be useful. 34 | There might be a template that fits your needs (e.g., New Paper, or asking for help with GitHub). 35 | If not, just try to explain why you're opening the issue (e.g., "I was doing X and ran into problem Y", or "I saw the paper linked here and thought it might be interesting for X reason"). 36 | - [Manuscript Source](content): 37 | The files that comprise the manuscript. 38 | These are located in the "content" folder that you see. 39 | These are written in a language called ["markdown"](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet#lists) which is essentially plain text (thankfully!) 40 | We have separate a file for each section of the manuscript (Introduction, Pathogenesis, Diagnostics, and Therapeutics right now). 41 | - [Pull Request](https://github.com/greenelab/covid19-review/pulls) or PR: 42 | A request to change the content of the repository in some way. 43 | Here, this will usually mean you are adding or editing text. 44 | 45 | ### How to Make a Pull Request 46 | 47 | 1. Look in the [Manuscript Source](content) for the file you want to edit (for example, the [Abstract](content/01.abstract.md)). 48 | 2. Click the "Edit" button, which looks like a pencil in the upper right corner. 49 | 3. Make any desired changes. 50 | 4. Scroll down to the bottom; there you will see a section that says "Commit changes" 51 | Give your submission a title in the top box and briefly summarize your changes in the bottom box. 52 | 5. Click the box that says "Create a new branch for this commit and start a pull request" 53 | This will submit a request to add your changes to the underlying document and will notify us to integrate your text into the document! 54 | 6. Don't forget to [add your information to the author list](CONTRIBUTING.md). 55 | If you don't have an ORCID, you can make one [here](https://orcid.org/). 56 | 57 | ### How can I see my change? 58 | 59 | If you've made a pull request, congratulations! 60 | This is a huge step in getting your contributions into the review. 61 | It's possible to see what the document will look like with your changes incorporated. 62 | The first thing that Manubot does is rebuild the document with your changes included. 63 | You'll know this is completed when you can scroll down to the bottom of your pull request and see "All checks have passed." 64 | At this point, you can click "Show all checks". 65 | 66 | 67 | ![show all checks](https://user-images.githubusercontent.com/542643/77359590-2ed13680-6d22-11ea-9cd5-26df2549e546.png "Show all checks link") 68 | 69 | 70 | Next, you'll see the various checks that have completed. 71 | There might be a few of these, and the one you want will be the one from Manubot. 72 | Click the details link to the right of Manubot. 73 | 74 | 75 | ![Manubot Details](https://user-images.githubusercontent.com/542643/77359602-35f84480-6d22-11ea-84b3-2b3cf869d43c.png "Manubot details link") 76 | 77 | 78 | This will take you to a screen describing what was run. 79 | You should see a dropdown titled "Artifacts" 80 | Clicking on that dropdown should reveal something that says "manuscript-..." 81 | 82 | 83 | ![Artifacts Dropdown](https://user-images.githubusercontent.com/542643/77359613-3abcf880-6d22-11ea-96c2-3ccdbd9b0836.png "Artifacts Dropdown") 84 | 85 | 86 | Clicking on the manuscript link will download a zip file to your computer containing the manuscript. 87 | You should be able to open the PDF in your favorite PDF reader. 88 | 89 | 90 | ### Questions 91 | 92 | If you are new to GitHub and struggling to follow these directions, we want to know how to help you and how to improve them. 93 | If you find something confusing, please open an [issue](https://github.com/greenelab/covid19-review/issues) and tell us what you're trying to do, what's going on wrong, or where you're stuck. 94 | We want this review to be a collaborative effort that brings scientists of all skillsets together -- not just people who already know how to use tools like GitHub. 95 | Opening an issue means your question will be available for others to learn from in the future! 96 | It will also us help continually update this document to provide the information people really need as they start contributing. 97 | 98 | ### A Word of Encouragement 99 | 100 | Thanks to GitHub, you won't be able to change anything we can't change back-- so you can't really make a mistake! 101 | 102 | ## Command Line Users 103 | 104 | ### Pull Request Instructions 105 | 106 | If you're already someone who uses Git, you can instead: 107 | 1. Fork the repository [greenelab/covid19-review](https://github.com/greenelab/covid19-review) 108 | [![GitHub forks](https://img.shields.io/github/forks/greenelab/covid19-review?label=Fork&style=social)](https://github.com/greenelab/covid19-review/fork) 109 | 2. Push your modifications. 110 | If writing full paragraphs, please put one sentence per line. 111 | 3. Submit a pull request to add your changes to [greenelab/covid19-review](https://github.com/greenelab/covid19-review) 112 | 4. Submit a second pull request to add your information to the bottom of the [metadata file](content/metadata.yaml) using the format outlined [here](content/metadata.yaml) 113 | 114 | ### Local execution 115 | 116 | The easiest way to run Manubot is to use [continuous integration](#continuous-integration) to rebuild the manuscript when the content changes. 117 | If you want to build a Manubot manuscript locally, install the [conda](https://conda.io) environment as described in [`build`](build). 118 | Then, you can build the manuscript on POSIX systems by running the following commands from this root directory. 119 | 120 | ```sh 121 | # Activate the manubot conda environment (assumes conda version >= 4.4) 122 | conda activate manubot 123 | 124 | # Build the manuscript, saving outputs to the output directory 125 | bash build/build.sh 126 | 127 | # At this point, the HTML & PDF outputs will have been created. The remaining 128 | # commands are for serving the webpage to view the HTML manuscript locally. 129 | # This is required to view local images in the HTML output. 130 | 131 | # Configure the webpage directory 132 | manubot webpage 133 | 134 | # You can now open the manuscript webpage/index.html in a web browser. 135 | # Alternatively, open a local webserver at http://localhost:8000/ with the 136 | # following commands. 137 | cd webpage 138 | python -m http.server 139 | ``` 140 | 141 | Sometimes it's helpful to monitor the content directory and automatically rebuild the manuscript when a change is detected. 142 | The following command, while running, will trigger both the `build.sh` script and `manubot webpage` command upon content changes: 143 | 144 | ```sh 145 | bash build/autobuild.sh 146 | ``` 147 | 148 | ### Continuous Integration 149 | 150 | Whenever a pull request is opened, CI (continuous integration) will test whether the changes break the build process to generate a formatted manuscript. 151 | The build process aims to detect common errors, such as invalid citations. 152 | If your pull request build fails, see the CI logs for the cause of failure and revise your pull request accordingly. 153 | 154 | When a commit to the `master` branch occurs (for example, when a pull request is merged), CI builds the manuscript and writes the results to the [`gh-pages`](https://github.com/manubot/rootstock/tree/gh-pages) and [`output`](https://github.com/manubot/rootstock/tree/output) branches. 155 | The `gh-pages` branch uses [GitHub Pages](https://pages.github.com/) to host the following URLs: 156 | 157 | + **HTML manuscript** at https://greenelab.github.io/covid19-review/ 158 | + **PDF manuscript** at https://greenelab.github.io/covid19-review/manuscript.pdf 159 | 160 | For continuous integration configuration details, see [`.github/workflows/manubot.yaml`](.github/workflows/manubot.yaml) if using GitHub Actions or [`.travis.yml`](.travis.yml) if using Travis CI. 161 | See the [`.github/workflows/update-external-resources.yaml`](.github/workflows/update-external-resources.yaml) for more information about the scheduled workflow that updates the contents of the `external-resources` branch. 162 | 163 | ### Updating Appendix 1 164 | 165 | Only maintainers need to update Appendix 1, which contains reviews from , referred to below as the "upstream" repository. 166 | (Maintainers have been explicitly invited to take on this role. 167 | Very few contributors are acting as maintainers.) 168 | The appendix content `content/95-ismms-himc-appendix.md` is automatically generated from the upstream repository. 169 | Therefore, it should not to be manually edited. 170 | Any errors in the appendix are corrected by submitting a pull request in the upstream repository. 171 | 172 | To manually edit a review, fork the repository at . 173 | Files in the [ISMMS markdown_files directory](https://github.com/ismms-himc/covid-19_sinai_reviews/tree/master/markdown_files) are labeled by DOI, with the `/` character replaced by a `-`. 174 | Create a PR to request changes to these files. 175 | Edits made in these files will propagate to the appendix once you follow the directions below. 176 | 177 | When the upstream repository is updated, a maintainer can run the following commands from the base directory of this repository: 178 | ```sh 179 | # checkout a new branch, named using the current date, e.g. ismms-2020-04-09 180 | git checkout -b ismms-$(date '+%Y-%m-%d') 181 | # download the latest reviews from the upstream repository and re-write content/95-ismms-himc-appendix.md 182 | bash build/mssm-jc.sh 183 | ``` 184 | Then, they can proceed to add and commit `content/95-ismms-himc-appendix.md` in the new branch and make a pull request. 185 | 186 | The script `build/mssm-jc.sh` will add a comment to the top of the appendix that contains the SHA-1 hash of the upstream repository. 187 | For example, 188 | ``` 189 | 190 | ``` 191 | This can be used to track which version of the reviews appear in this manuscript. 192 | -------------------------------------------------------------------------------- /content/previous_sections/50.discussion.md: -------------------------------------------------------------------------------- 1 | ## Discussion 2 | 3 | As of October 2020 the SARS-CoV-2 virus remains a serious worldwide threat. 4 | The scientific community has responded by rapidly collecting and disseminating information about the SARS-CoV-2 virus and the associated illness, COVID-19. 5 | The rapid identification of the genomic sequence of the virus allowed for early contextualization of SARS-CoV-2 among other known respiratory viruses. 6 | The pathogen is a coronavirus that is closely related to SARS-CoV-1, which caused the SARS pandemics of the early 2000s. 7 | Knowing the phylogenetic context and genomic sequence of the virus then allowed for rapid insights into its structure and pathogenesis. 8 | As with other HCoV, the immune response to SARS-CoV-2 is likely driven by detection of its spike protein, which allows it to enter cells through the ACE2 receptor. 9 | Epithelial cells have also emerged as the major cellular target of the virus, contextualizing the respiratory and gastrointestinal symptoms that are frequently observed in COVID-19. 10 | However, as COVID-19 cases have been more widely characterized, it has become clear that the disease presentation is highly heterogeneous. 11 | Many cases, especially in younger adults, present with mild symptoms or even asymptomatically, while others, especially in older adults, can be severe or fatal. 12 | In children, the SARS-CoV-2 virus can present as two distinct diseases, COVID-19 or MIS-C. 13 | While the overall infection fatality rate remains unknown, estimates suggest that it is not more than 1%; however, the severity of many non-lethal cases makes COVID-19 an ongoing, significant concern. 14 | 15 | Characterizing the rate of infection and fatality rates hinges on the availability of rapid and accurate diagnostic testing. 16 | Major advancements have been made in identifying diagnostic approaches. 17 | The development of diagnostic technologies have been rapid, beginning with the release of the SARS-CoV-2 viral genome sequence in January. 18 | As of October 2020, a range of diagnostic tests have become available. 19 | One class of tests uses PCR (RT-PCR or qRT-PCR) to assess the presence of SARS-CoV-2 RNA, while another typically uses ELISA to test for the presence of antibodies to SARS-CoV-2. 20 | The former approach is useful for identifying active infections, while the latter measures hallmarks of the immune response and therefore can detect either active infections or immunity gained from prior infection. 21 | Combining these tests leads to extremely accurate detection of SARS-CoV-2 infection (98.6%), but when used alone, PCR-based tests are recommended before 5.5 days after the onset of the illness and antibody tests after 5.5 days [@doi:10.1001/jama.2020.8259]. 22 | Other strategies for testing can also influence the tests' accuracy, such as the use of nasopharyngeal swabs versus BALF [@doi:10.1001/jama.2020.8259], which allow for trade-offs between patient's comfort and test sensitivity. 23 | Additionally, technologies such as digital PCR may allow for scale-up in the throughput of diagnostic testing, facilitating widespread testing. 24 | One major question that remains is whether people who recover from SARS-CoV-2 develop sustained immunity, and over what period this immunity is expected to last. 25 | Some reports have suggested that some patients may develop COVID-19 reinfections (e.g., [@doi:10/ghfgkt]), but the rates of reinfection are currently unknown. 26 | Serologic testing combined with PCR testing will be critical to confirming purported cases of reinfection and to identifying the duration over which immunity is retained and to understanding reinfection risks. 27 | 28 | One of the goals of characterizing the immune response is to identify strategies for the prophylactic enhancements of immunity. 29 | Though some concerns remain about the duration of sustained immunity for convalescents, vaccine development efforts are ongoing and show initial promising results. 30 | The Moderna trial, for example, reported that the neutralizing activity in participants who received two doses of the vaccine was similar to that observed in convalescent plasma. 31 | Vaccine development for COVID-19 is progressing rapidly compared to typical timelines, but vaccine development is still a lengthy process. 32 | In the meantime, some advances have also been made in the treatment of patients with COVID-19. 33 | As cases have become better characterized, it has become evident that many patients experience an initial immune response to the virus that is typically characterized by fever, cough, dyspnea, and related symptoms. 34 | However, the most serious concern is cytokine release syndrome, when the body's immune response becomes dysregulated, resulting in an extreme inflammatory response. 35 | The RECOVERY trial, a large-scale, multi-arm trial enrolling about 15% of all COVID-19 patients in the United Kingdom, was the first to identify that the widely available steroid dexamethasone seems to be beneficial for patients suffering from this immune dysregulation [@doi:10.1101/2020.06.22.20137273]. 36 | Efforts to identify therapeutic treatments to treat patients early in the course of infection have been more ambiguous. 37 | Early interest in the drugs hydroxychloroquine and chloroquine yielded no promising results from studies with robust experimental designs. 38 | The experimental drug remdesivir, which was developed for Ebola, has received enough support from early analyses to receive FDA approval, but results have been mixed. 39 | The potential for other drugs, such as tocilizumab, to reduce recovery time remains unclear, but some early results were promising. 40 | 41 | ### Additional Therapeutics of Interest 42 | 43 | Given what is currently known about these therapeutics for COVID-19, a number of related therapies beyond those explored above may also prove to be of interest. 44 | For example, the demonstrated benefit of dexamethasone and the ongoing potential of tocilizumab for treatment of COVID-19 suggests that other anti-inflammatory agents might also hold value for the treatment of COVID-19. 45 | Given that current evidence about treating COVID-19 with dexamethasone suggests that the need to curtail the cytokine storm inflammatory response to the virus can transcend the risks of immunosuppression, exploration of more anti-inflammatory agents may be warranted. 46 | While dexamethasone is considered widely available and generally affordable, the high costs of biologics such as tocilizumab therapy may present obstacles to wide-scale distribution of this drug if it proves of value. 47 | At the doses used for rheumatoid arthritis patients, the cost for tocilizumab ranges from $179.20 to $896 per dose for the IV form and $355 for the pre-filled syringe [@url:https://www.ncbi.nlm.nih.gov/books/NBK349513/table/T43/]. 48 | There are several anti-inflammatory agents used for the treatment of autoimmune diseases that may also be able to counter the effects of the cytokine storm induced by the virus, some of which, such as cyclosporine, are likely to be more cost-effective and readily available than biologics [@url:https://escholarship.umassmed.edu/meyers_pp/385]. 49 | While tocilizumab targets IL-6, several other inflammatory markers could be potential targets, including TNF-alpha. 50 | Inhibition of TNF-alpha by an inhibitor such as Etanercept has been previously suggested for treatment of SARS-CoV-1 [@doi:10.1185/030079903125002757] and may be relevant for SARS-CoV-2 as well. 51 | Another anti-IL-6 antibody, sarilumab, is also being investigated [@url:http://www.news.sanofi.us/2020-03-16-Sanofi-and-Regeneron-begin-global-Kevzara-R-sarilumab-clinical-trial-program-in-patients-with-severe-COVID-19; @clinicaltrials:NCT04327388]. 52 | Baricitinib and other small molecule inhibitors of the Janus-activated kinase pathway also curtail the inflammatory response and have been suggested as potential options for SARS-CoV-2 infections [@doi:10/dph5]. 53 | Baricitinib in particular may be able to reduce the ability of SARS-CoV-2 to infect lung cells [@doi:10/ggnrsx]. 54 | Clinical trials studying baricitinib in COVID-19 have already begun in the US and in Italy [@url:https://investor.lilly.com/news-releases/news-release-details/lilly-begins-clinical-testing-therapies-covid-19; @clinicaltrials:NCT04320277]. 55 | Identification and targeting of further inflammatory markers that are relevant in SARS-CoV-2 infection may be of value for curtailing the inflammatory response and lung damage. 56 | 57 | In addition to immunosuppressive treatments that are most beneficial late in disease progression, much research is focused on identifying treatments would be likely to benefit early-stage patients. 58 | For example, although studies of hydroxychloroquine have not supported the early theory-driven interest in this antiviral treatment, alternative compounds with related mechanisms may still have potential. 59 | Hydroxyferroquine derivatives of HCQ have been described as a class of bioorganometallic compounds that exert antiviral effects with some selectivity for SARS-CoV-1 _in vitro_ [@doi:10.1021/jm0601856]. 60 | Future work could explore whether such compounds exert antiviral effects against SARS-CoV-2 and whether they would be safer for use in COVID-19. 61 | Another potential approach is the development of antivirals, which could be broad-spectrum, specific to coronaviruses, or targeted to SARS-CoV-2. 62 | Development of new antivirals is complicated by the fact that none have yet been approved for human coronaviruses. 63 | Intriguing new options are emerging, however. 64 | Beta-D-N4-hydroxycytidine (NHC) is an orally bioavailable ribonucleotide analog showing broad-spectrum activity against RNA viruses, which may inhibit SARS-CoV-2 replication _in vitro_ and _in vivo_ in mouse models of HCoVs [@doi:10.1126/scitranslmed.abb5883]. 65 | A range of other antivirals are also in development. 66 | Development of antivirals will be further facilitated as research reveals more information about the interaction of SARS-CoV-2 with the host cell and host cell genome, mechanisms of viral replication, mechanisms of viral assembly, and mechanisms of viral release to other cells; this can allow researchers to target specific stages and structures of the viral life cycle. 67 | Many researchers have also focused their attention to the potential use of dietary supplements and nutraceuticals. 68 | Indeed, there has been recent interest for the potential use of vitamin D as a prophylactic and therapeutic agent against COVID-19 as several observational studies have linked low vitamin D status to its incidence [@doi:10.1111/joim.13149; @doi:10.1001/jamanetworkopen.2020.19722]. 69 | These associations have yet to be confirmed and rigorous trials are required before considering supplementation recommendations. 70 | However, the nutritional status and general health of a patient can affect their outcomes in various diseases, thus it would be pertinent to advise people to follow a healthy diet and life style to the best of their ability to prevent nutrient deficiencies and insufficiencies and to maintain a healthy immune system [@doi:10.1093/advances/nmaa125]. 71 | Finally, antibodies against viruses, also known as antiviral monoclonal antibodies, could be an alternative as well and are described in detail in an above section. 72 | The goal of antiviral antibodies is to neutralize viruses through either cell-killing activity or blocking of viral replication [@doi:10.1016/j.tim.2015.07.005]. 73 | They may also engage the host immune response, encouraging the immune system to hone in on the virus. 74 | Given the cytokine storm that results from immune system activation in response to the virus, which has been implicated in worsening of the disease, a neutralizing antibody (nAb) may be preferable. 75 | Upcoming work may explore the specificity of nAbs for their target, mechanisms by which the nAbs impede the virus, and improvements to antibody structure that may enhance the ability of the antibody to block viral activity. 76 | 77 | Some research is also investigating potential therapeutics and prophylactics that would interact with components of the innate immune response. 78 | For example, there are a variety of TLRs, PRRs that recognize PAMPs and DAMPs. 79 | TLRs form a part of innate immune recognition and can more generally contribute to promoting both innate and adaptive responses [@ISBN:9780815332183]. 80 | In mouse models, poly(I:C) and CpG, which are agonists of toll-like receptors TLR3 and TLR9, respectively, showed protective effects when administered prior to SARS-CoV-1 infection [@doi:10.1128/JVI.01410-12]. 81 | Therefore, TLR agonists hold some potential for broad-spectrum prophylaxis. 82 | 83 | Given that a large number of clinical trials are currently in progress, more information about the potential of these and other therapeutics should become available over time. 84 | This information, combined with advances in understanding the molecular structure and viral pathogenesis of SARS-CoV-2, may lead to a more complete understanding of how the virus affects the human host and what strategies can improve outcomes. 85 | To date, investigations of potential therapeutics for COVID-19 have focused primarily on repurposing existing drugs. 86 | This approach is necessary given the urgency of the situation as well as the extensive time required for developing and testing new therapies. 87 | However, in the long-term, new drugs specific for treatment of COVID-19 may also enter development. 88 | Development of novel drugs is likely to be guided by what is known about the pathogenesis and molecular structure of SARS-CoV-2. 89 | For example, understanding the various structural components of SARS-CoV-2 may allow for the development of small molecule inhibitors of those components. 90 | Currently, crystal structures of the SARS-CoV-2 main protease have recently been resolved [@doi:10.1038/s41586-020-2223-y; @url:https://www.diamond.ac.uk/covid-19/for-scientists/Main-protease-structure-and-XChem.html], and efforts are already in place to perform screens for small molecule inhibitors of the main protease, which have yielded potential hits [@doi:10.1038/s41586-020-2223-y]. 91 | Much work remains to be done to determine further crystal structures of other viral components, understand the relative utility of targeting different viral components, perform additional small molecule inhibitor screens, and determine the safety and efficacy of the potential inhibitors. 92 | While still nascent, work in this area is promising. 93 | Over the longer term, this approach and others may lead to the development of novel therapeutics specifically for COVID-19 and SARS-CoV-2. 94 | 95 | -------------------------------------------------------------------------------- /SETUP.md: -------------------------------------------------------------------------------- 1 | # Table of contents 2 | 3 | - [Creating a new manuscript](#creating-a-new-manuscript) 4 | * [Using setup script](#using-setup-script) 5 | * [Manual configuration](#manual-configuration) 6 | * [Create repository](#create-repository) 7 | * [Continuous integration](#continuous-integration) 8 | + [GitHub Actions](#github-actions) 9 | + [SSH Deploy Key](#ssh-deploy-key) 10 | - [Add the public key to GitHub](#add-the-public-key-to-github) 11 | - [Add the private key to GitHub](#add-the-private-key-to-github) 12 | + [Previewing pull request builds with AppVeyor](#previewing-pull-request-builds-with-appveyor) 13 | * [README updates](#readme-updates) 14 | * [Finalize](#finalize) 15 | - [Merging upstream rootstock changes](#merging-upstream-rootstock-changes) 16 | * [Default branch](#default-branch) 17 | 18 | _generated with [markdown-toc](https://ecotrust-canada.github.io/markdown-toc/)_ 19 | 20 | # Creating a new manuscript 21 | 22 | These instructions detail how to create a new manuscript based off of the [`manubot/rootstock`](https://github.com/manubot/rootstock/) repository. 23 | The process can be a bit challenging, because it requires a few steps that are difficult to automate. 24 | However, you will only have to perform these steps once for each manuscript. 25 | 26 | These steps should be performed in a command-line shell (terminal), starting in the directory where you want the manuscript folder be created. 27 | Setup is supported on Linux, macOS, and Windows. 28 | Windows setup requires [Git Bash](https://gitforwindows.org/) or [Windows Subsystem for Linux](https://docs.microsoft.com/en-us/windows/wsl/faq). 29 | 30 | ## Using setup script 31 | Creating a new manuscript using GitHub actions, the recommended default CI service (see below), can be achieved easily using the [setup script](https://github.com/manubot/rootstock/blob/main/setup.bash). 32 | This simply runs the steps detailed below in the manual configuration. 33 | 34 | Use the command below to copy `setup.bash` and run it. 35 | You can check the code that will be executed [here](https://github.com/manubot/rootstock/blob/main/setup.bash). 36 | 37 | ````sh 38 | bash <( curl --location https://github.com/manubot/rootstock/raw/main/setup.bash ) 39 | ```` 40 | The script will then take you through the process of cloning the rootstock repo, make the changes required to use GitHub actions, edit the README to point to your repo and commit the changes. 41 | Your new manuscript repo is then ready for you to start adding your own content. 42 | 43 | This script does not create the remote repo for you, so you will be prompted to manually create an empty GitHub repository at . 44 | Do not initialize the repository, other than optionally adding a description. 45 | 46 | ### CLI 47 | There is also a command line interface for users who want to create manuscripts at scale and in an automated way. 48 | See the help for details. 49 | 50 | ````sh 51 | bash setup.bash --help 52 | ```` 53 | 54 | ## Manual configuration 55 | 56 | If you do not wish to use the above setup script to configure your new manuscript repository, you can instead execute the steps manually. 57 | First, you must configure two environment variables (`OWNER` and `REPO`). 58 | These variables specify the GitHub repository for the manuscript (i.e. `https://github.com/OWNER/REPO`). 59 | Make sure that the case of `OWNER` matches how your username is displayed on GitHub. 60 | In general, assume that all commands in this setup are case-sensitive. 61 | **Edit the following commands with your manuscript's information:** 62 | 63 | ```sh 64 | # GitHub username or organization name (change from manubot) 65 | OWNER=manubot 66 | # Repository name (change from rootstock) 67 | REPO=rootstock 68 | ``` 69 | 70 | ## Create repository 71 | 72 | **Execute the remaining commands verbatim.** 73 | They do not need to be edited (if the setup works as intended). 74 | 75 | Next you must clone `manubot/rootstock` and reconfigure the remote repositories: 76 | 77 | ```sh 78 | # Clone manubot/rootstock 79 | git clone --single-branch https://github.com/manubot/rootstock.git $REPO 80 | cd $REPO 81 | 82 | # Configure remotes 83 | git remote add rootstock https://github.com/manubot/rootstock.git 84 | 85 | # Option A: Set origin URL using its web address 86 | git remote set-url origin https://github.com/$OWNER/$REPO.git 87 | # Option B: If GitHub SSH key access is enabled for OWNER, run the following command instead 88 | git remote set-url origin git@github.com:$OWNER/$REPO.git 89 | ``` 90 | 91 | Then create an empty repository on GitHub. 92 | You can do this at or via the [GitHub command line interface](https://github.com/cli/cli) (if installed) with `gh repo create`. 93 | Make sure to use the same "Owner" and "Repository name" specified above. 94 | Do not initialize the repository, other than optionally adding a Description. 95 | Next, push your cloned manuscript: 96 | 97 | ```sh 98 | git push --set-upstream origin main 99 | ``` 100 | 101 | ## Continuous integration 102 | 103 | Manubot integrates with cloud services to perform continuous integration (CI). 104 | For Manubot that means automatically building and deploying your manuscript. 105 | Manubot supports the following CI services: 106 | 107 | | Service | Default | Artifacts | Deployment | Config | Private Repos | 108 | |---------|---------|-----------|---------|--------|---------------| 109 | | [GitHub Actions](https://github.com/features/actions) | ✔️ | ✔️ | ✔️ | [`manubot.yaml`](.github/workflows/manubot.yaml) | 2,000 minutes per month | 110 | | [AppVeyor](https://www.appveyor.com/) | ❌ | ✔️ with PR comments | ❌ | [`.appveyor.yml`](.appveyor.yml) | 14 day trial | 111 | 112 | Notes on table fields: 113 | 114 | - **Default**: Whether the following uncollapsed setup instructions enable the service by default. 115 | - **Artifacts**: Manuscript outputs that are saved alongside the CI build logs. 116 | This is especially helpful for previewing changes that are under development in a pull request. 117 | Both GitHub Actions and AppVeyor upload the rendered manuscript as an artifact for pull request builds. 118 | However, only AppVeyor comments on pull requests with a download link to the artifacts ([example](https://github.com/manubot/rootstock/pull/262#issuecomment-519944731)). 119 | - **Deployment**: Whether the CI service can write outputs back to the GitHub repository (to the `output` and `gh-pages` branches). 120 | Deployment provides GitHub Pages with the latest manuscript version to serve to the manuscript's URL. 121 | GitHub Actions will deploy by default without any additional setup. 122 | - **Config**: File configuring what operations CI will perform. 123 | Removing this file is one method to disable the CI service. 124 | - **Private Repos**: Quota for private repos. 125 | Only GitHub Actions supports cost-free builds of private repositories beyond a trial period. 126 | All services are cost-free for public repos. 127 | 128 | Manubot was originally designed to use Travis CI, 129 | but later switched to primarily use GitHub Actions. 130 | Support for Travis was [removed](https://github.com/manubot/rootstock/issues/446) in 2021. 131 | 132 | ### GitHub Actions 133 | 134 | GitHub Actions is the recommended default CI service because it requires no additional setup. 135 | To use GitHub Actions only, remove configuration files for other CI services: 136 | 137 | ```shell 138 | # remove AppVeyor config 139 | git rm .appveyor.yml 140 | # remove ci/install.sh (only used by AppVeyor) 141 | git rm ci/install.sh 142 | ``` 143 | 144 | GitHub Actions is _usually_ able to deploy without any additional setup using the [`GITHUB_TOKEN`](https://help.github.com/en/actions/configuring-and-managing-workflows/authenticating-with-the-github_token) for authentication. 145 | GitHub Pages deployment using `GITHUB_TOKEN` recently started working on GitHub without an official announcement. 146 | If it does not work for you after completing this setup, try reselecting "gh-pages branch" as the Source for GitHub Pages in the repository Settings. 147 | GitHub Pages should now trigger on the next commit. 148 | If not, [let us know](https://github.com/manubot/rootstock/issues/new). 149 | 150 | For an alternative deployment method on GitHub, 151 | you can use an SSH Deploy Key instead. 152 | However, the setup is more complex. 153 | The following sections, collapsed by default, detail how to generate an SSH Deploy Key. 154 | 155 |
156 | Expand for SSH Deploy Key setup 157 | 158 | ### SSH Deploy Key 159 | 160 | Previously, GitHub Actions required an SSH Deploy Key, 161 | but now GitHub can deploy using the `GITHUB_TOKEN` secret. 162 | Therefore, users following the default configuration can skip these steps. 163 | Otherwise, generate a deploy key so CI can write to the repository. 164 | 165 | ```sh 166 | # Generate deploy.key.pub (public) and deploy.key (private) 167 | ssh-keygen \ 168 | -t rsa -b 4096 -N "" \ 169 | -C "deploy@manubot.org" \ 170 | -f ci/deploy.key 171 | 172 | # Encode deploy.key to remove newlines, writing encoded text to deploy.key.txt. 173 | # This was required for entry into the Travis settings. 174 | openssl base64 -A -in ci/deploy.key > ci/deploy.key.txt 175 | ``` 176 | 177 | #### Add the public key to GitHub 178 | 179 | ```sh 180 | # Print the URL for adding the public key to GitHub 181 | echo "https://github.com/$OWNER/$REPO/settings/keys/new" 182 | 183 | # Print the public key for copy-pasting to GitHub 184 | cat ci/deploy.key.pub 185 | ``` 186 | 187 | Go to the GitHub settings URL echoed above in a browser, and click "Add deploy key". 188 | For "Title", add a description like "Manubot Deploy Key". 189 | Copy-paste the contents of the `ci/deploy.key.pub` text file (printed above by `cat`) into the "Key" text box. 190 | Check the "Allow write access" box below. 191 | Finally, click "Add key". 192 | 193 | #### Add the private key to GitHub 194 | 195 | If you would like GitHub Actions to use SSH for deployment, rather than via HTTPS using `GITHUB_TOKEN`, perform the steps in this section. 196 | 197 | ```sh 198 | # Print the URL for adding the private key to GitHub 199 | echo "https://github.com/$OWNER/$REPO/settings/secrets" 200 | 201 | # Print the encoded private key for copy-pasting to GitHub 202 | cat ci/deploy.key.txt && echo 203 | ``` 204 | 205 | Next, go to the GitHub repository settings page (URL echoed above). 206 | Click "Add a new secret". 207 | For "Name", enter `MANUBOT_SSH_PRIVATE_KEY`. 208 | Next, copy-paste the content of `ci/deploy.key.txt` into "Value" 209 | (printed above by `cat`, including any trailing `=` characters if present). 210 |
211 | 212 | 213 |
214 | Expand for AppVeyor setup 215 | 216 | ### Previewing pull request builds with AppVeyor 217 | 218 | You can optionally enable AppVeyor continuous integration to view pull request builds. 219 | AppVeyor supports storing manuscripts generated during pull request builds as artifacts. 220 | These can be previewed to facilitate pull request review and ensure formatting and reference changes render as expected. 221 | When a pull request build runs successfully, **@AppVeyorBot** will comment on the pull request with a download link to the manuscript PDF. 222 | 223 | To enable AppVeyor, follow steps 1 and 2 of the [AppVeyor welcome](https://www.appveyor.com/docs/) to sign in to AppVeyor and add your manuscript repository as an AppVeyor project. 224 | The repository already contains an `.appveyor.yml` build configuration file, so no other setup is required. 225 | AppVeyor only runs when it detects changes that are likely to affect the manuscript. 226 |
227 | 228 | ## README updates 229 | 230 | The continuous integration configuration should now be complete. 231 | Now update `README.md` files to reference your new repository: 232 | 233 | ```shell 234 | # Perform substitutions 235 | sed "s/manubot\/rootstock/$OWNER\/$REPO/g" README.md > tmp && mv -f tmp README.md 236 | sed "s/manubot\.github\.io\/rootstock/$OWNER\.github\.io\/$REPO/g" README.md > tmp && mv -f tmp README.md 237 | ``` 238 | 239 | ## Finalize 240 | 241 | The `content/02.delete-me.md` file details the Markdown syntax and formatting options available with Manubot. 242 | Remove it to reduce the content to a blank manuscript: 243 | 244 | ```shell 245 | # Remove deletable content file 246 | git rm content/02.delete-me.md 247 | ``` 248 | 249 | Run `git status` or `git diff --color-words` to double check the changes thus far. 250 | If the changes look okay, commit and push: 251 | 252 | ```shell 253 | git add --update 254 | git commit --message "Brand repo to $OWNER/$REPO" 255 | git push origin main 256 | ``` 257 | 258 | You should be good to go now. 259 | A good first step is to modify [`content/metadata.yaml`](content/metadata.yaml) with the relevant information for your manuscript. 260 | 261 | # Merging upstream rootstock changes 262 | 263 | This section will describe how to incorporate changes to rootstock that occurred since initializing your manuscript. 264 | You will want to do this if there are new enhancements or bugfixes that you want to incorporate. 265 | This process can be difficult, especially if conflicts have arisen, and is recommended only for advanced git users. 266 | 267 | It is recommended to do rootstock upgrades via a pull request to help you view the proposed changes and to ensure the build uses the updated environment. 268 | First, checkout a new branch to use as the pull request head branch: 269 | 270 | ```shell 271 | # checkout a new branch, named using the current date, i.e. rootstock-2018-11-16 272 | git checkout -b rootstock-$(date '+%Y-%m-%d') 273 | ``` 274 | 275 | Second, pull the new commits from rootstock, but do not automerge: 276 | 277 | ```shell 278 | # if rootstock remote is not set, add it 279 | git config remote.rootstock.url || git remote add rootstock https://github.com/manubot/rootstock.git 280 | 281 | # pull the new commits from rootstock 282 | git pull --no-ff --no-rebase --no-commit rootstock main 283 | ``` 284 | 285 | If all goes well, there won't be any conflicts. 286 | However, if there are conflicts, follow the suggested commands to resolve them. 287 | 288 | You can add the changes incrementally using `git add --patch`. 289 | This is helpful to see each upstream change. 290 | You may notice changes that affect how items in `content` are processed. 291 | If so, you should edit and stage `content` files as needed. 292 | When there are no longer any unstaged changes, then do `git commit`. 293 | 294 | If updating your default branch (i.e. `main` or `master`) via a pull request, proceed to push the commit to GitHub and open a pull request. 295 | Once the pull request is ready to merge, use GitHub's "Create a merge commit" option rather than "Squash and merge" or "Rebase and merge" to preserve the rootstock commit hashes. 296 | 297 | The environment for local builds does not automatically update when [`build/environment.yml`](build/environment.yml) changes. 298 | To update your local conda `manubot` environment with new changes, run: 299 | 300 | ```shell 301 | # update a local conda environment 302 | conda env update --file build/environment.yml 303 | ``` 304 | 305 | ## Default branch 306 | 307 | On 2020-10-01, GitHub [changed](https://github.blog/changelog/2020-10-01-the-default-branch-for-newly-created-repositories-is-now-main/) the default branch name for new repositories from `master` to `main`. 308 | More information on GitHub's migration is available at [github/renaming](https://github.com/github/renaming). 309 | 310 | On 2020-12-10, Manubot [updated](https://github.com/manubot/rootstock/pull/399) the Rootstock default branch to `main`. 311 | For existing manuscripts, the default branch will remain `master`, 312 | unless manually switched to `main`. 313 | Rootstock has been configured to run continuous integration on both `main` and `master`, 314 | so existing manuscripts can, but are not required, to switch their default branch to `main`. 315 | 316 | Upgrading to the latest Rootstock will change several READMEs links to `main`. 317 | For manuscripts that do not plan to switch their default branch, 318 | do not include these changes in the upgrade merge commit. 319 | -------------------------------------------------------------------------------- /content/response-to-reviews/pathogenesis-v1.md: -------------------------------------------------------------------------------- 1 | Reviewer 1 2 | 3 | Rando et al., provide a thoughtful and comprehensive review of the scientific literature relevant to the COVID-19 pandemic. This review will provide a useful resource for the scientific community but is missing some crucial information and would be improved by a more clear description of how this virus is detected and the limitations of these methods. 4 | 5 | ** 6 | We are very grateful for your supportive words about this project and for your guidance in making our review of these topics more complete. 7 | ** 8 | 9 | Major: 10 | 1.1 Heparin sulfate dependency: The 'Pathogenic mechanisms' section is lacking any reference to the dependence of SARS-Cov-2 binding to heparin sulfate which has been cited over 100 times since its publication in November and has been supported by work from numerous labs: 11 | https://www.sciencedirect.com/science/article/abs/pii/S0092867420312307 12 | 13 | ** 14 | This oversight has been corrected. 15 | A discussion of heparan sulfate has now been added to the section "Pathogenic Mechanisms of Coronaviruses." 16 | ** 17 | 18 | 1.2 Furin discussion: The description of furin in this manuscript is confusing; it is highlighted in the conclusion as a mutation that has allowed for increased virulence, but is not mentioned in the opening paragraphs of the paper where host proteases are described (e.g. lines 229-235, line 279), or the section describing the hinge-like movement of the spike protein which is induced by furin (lines 591-603) and only mentioned fleetingly in the middle of a the next paragraph. A more thorough discussion of the furin-site insertion in the SARS-CoV-2 genome (and what information is still missing) earlier or more prominently in the paper is warranted. 19 | 20 | ** 21 | Thank you for catching this oversight. 22 | Several additions have been made to the text to address the role of furin. 23 | The paragraph that introduces proteolytic priming (previously lines 229-235) has been expanded to discuss the furin injection site insertion and the fact that _in vitro_ studies suggest it increases pathogenesis. 24 | The following line was added to the section on Host Cell Susceptibility (previously beginning at 279): 25 | "Additionally, the addition of the furin site insertion at the S1/S2 boundary means that SARS-CoV-2 does not require TMPRSS-2 when furin, an ubiquitously expressed endoprotease [@doi:10.1038/nrm934], is present, enabling cell-cell fusion independent of TMPRSS-2 availability [@doi:10.1016/j.molcel.2020.04.022]." 26 | The section about the hinge-like movement of the spike protein (previously 591-603) has been expanded to include: 27 | "Spike proteins cleaved at the furin-like binding site are substantially more likely to take an open conformation (66%) than those that are uncleaved (17%) [@doi:10.1038/s41594-020-0468-7]." 28 | In the following paragraph, the discussion of the acquisition of the furin insertion site has been moved to the beginning of the paragraph and modified to read: 29 | "The furin recognition site at the S1/S2 junction is likely to increase pathogenicity via destabilization of the spike protein during fusion to ACE2 and the facilitation of cell-cell adhesion [@doi:10.1016/j.cell.2020.02.058; @doi:10.1126/science.abb2507; @doi:10.1038/s41594-020-0468-7; @doi:10/bvgh5b; @doi:10.1006/viro.1999.9716; @doi:10.1016/j.isci.2020.101212]." 30 | ** 31 | 32 | 1.3 Detected versus infectious: The distinction between RT-qPCR detection and viral infection assays in cell culture models should be more clear. Although this point is acknowledged (e.g. lines 713-714) it is not clear whether viral RNA or infectious virus is being described at certain points in the review (i.e. line 663) and a brief description of the advantages and limitations of these methods would be useful for the reader. 33 | 34 | ** 35 | This is a very important point, so to emphasize it we have added a section entitled "Quantifying Viral Presence" that outlines the different information conveyed by RT-PCR and _in vitro_ cultivation. 36 | We have also expanded the review of aerosol transmission to more adequately contextualize the study mentioned in the above comment. 37 | ** 38 | 39 | Minor: 40 | 1.4 Typos 41 | 42 | Lines 205; The legend of Figure 1 incorrectly states that RNA polymerase is a protease 43 | 44 | ** 45 | The word "protease" has been changed to "enzyme." 46 | ** 47 | 48 | Line 709; typo -> 'either typical or atypical' 49 | 50 | ** 51 | This change has been made. 52 | ** 53 | 54 | Line 755; 'content level' should be 'continental level'? 55 | 56 | ** 57 | This change has been made. 58 | ** 59 | 60 | Line 788; what does adding the 'exposed' variable in this model mean and why is that important for SARS-CoV-2 61 | 62 | ** 63 | This sentence has been modified to read: 64 | "To capture the dynamics of SARS-CoV-2 accurately, the addition of a fourth compartment, i.e. a susceptible-exposed-infectious-recovered model, may be appropriate because such models account for the relative lengths of incubation and infectious periods [@doi:10.1038/s41598-020-76563-8]." 65 | ** 66 | 67 | Line 852; typo, duplicate 'has coordinated' 68 | 69 | ** 70 | This typo has been corrected. 71 | ** 72 | 73 | Line 874; typo, "as in the current pandemic" 74 | 75 | ** 76 | This change has been made. 77 | ** 78 | 79 | 1.5 This work is important not only for the current moment, but for contextualizing this virus for response to future outbreaks; in my opinion it would be nice to have a sentence in the discussion to this effect (this review represents a ton of work - the effort is worthwhile!) 80 | 81 | ** 82 | Thank you for pointing this out. 83 | We have added two sentences to the first paragraph of the conclusion that read: 84 | "With the emergence of three devestating HCoV over the past twenty years, emergent viruses are likely to represent an ongoing threat. 85 | Contextualizing SARS-CoV-2 alongside other viruses serves not only to provide insights that can be immediately useful for combatting this v 86 | irus itself, but may also prove valuable in the face of future viral threats." 87 | Additionally, the last sentence of the manuscript is now: "In the future, interdisciplinary work on SARS-CoV-2 and COVID-19 may guide a response to a new viral threat." 88 | The potential for SARS-CoV-2 research to contribute to the handling of future emerging HCoV was also added to the "Importance" section of the abstract. 89 | ** 90 | 91 | Reviewer 2 92 | 93 | Overall, this was a very comprehensive, thorough review of the current state of knowledge of SARS-CoV2. The manuscript is well written and extensively researched, with great attention to the details of the outbreak with regards to data from various regions of the world, providing an extremely useful resource for the scientific community. The manuscript is well researched and well written for a general scientific audience. I only had a handful of minor concerns, mostly for word choice/organization for clarity but I would leave these changes at the discretion of the authors as they do not detract from the overall narrative of the manuscript. 94 | 95 | ** 96 | Thank you very much for your encouraging feedback. 97 | ** 98 | 99 | Minor Points 100 | 101 | 2.1 Line 196 - insert "the" prior to replication. 102 | 103 | ** 104 | This change has been made. 105 | ** 106 | 107 | 2.2 Lines 213-214 - wording was a bit odd, might suggest adding "a process conserved among coronaviruses" to the previous sentence. 108 | 109 | ** 110 | This change has been made. 111 | ** 112 | 113 | 2.3 Line 250-252 - might suggest excluding skin and just keeping mucus, the way this reads suggests the respiratory mucosa provides no protection at all- is this true? 114 | 115 | ** 116 | The question you raised is interesting -- the Liu et al. (2016) reference, which investigated viral dissemination of SARS-CoV-1 in rhesus macaques, states, "Many viruses, including SARS-CoV, breach this mucosal barrier by infecting the epithelium directly." 117 | This conclusion cites two articles, one of which (Richt et al., 2012 in PLoS One) examined swine influenza A virus (H2N3) in macaques and found higher replication of swine H2N3 than human H2N2 in the nasal mucosa and lung tissue. 118 | The other (Nicholls et al., 2006 in PLoS Medicine) reported the cellular localization of the SARS-CoV-1 virus in deceased SARS patients using a monoclonal antibody, concluding that the virus's "chief target" is the pulmonary alveolar epithelium. 119 | Based on these citations, it doesn't seem appropriate to conclude that the respiratory mucosa does not provide protection at all, but rather that viruses vary in their ability to bypass its protection. 120 | Therefore, the sentence has been rephrased to read: "Infecting the epithelium can help viruses such as SARS-CoV-1 bypass the physical barriers, such as mucus, that comprise the immune system's first line of defense." 121 | ** 122 | 123 | 2.4 Line 275 - suggest changing "can facilitate" to "may facilitate" 124 | 125 | ** 126 | This change has been made. 127 | ** 128 | 129 | 2.5 Line 311 - reference was not highlighted in blue- not sure if this was a formatting issue but may want to check to make sure this reference is correct. 130 | 131 | ** 132 | Thank you for catching this error. 133 | The correct reference is a June 2020 letter to the editor in the New England Journal of Medicine (doi:10.1056/NEJMc2010419). 134 | This line has been corrected to refer to the correct article. 135 | ** 136 | 137 | 2.6 Might suggest moving up the Pediatric Presentation (Lines 428-454) to immediately before cytokine release syndrome as it follows the clinical presentation and directly leads into the cytokine release syndrome. 138 | 139 | ** 140 | This change has been made. 141 | ** 142 | 143 | 2.7 The intro paragraph for the cytokine release syndrome is quite long and could be readily shortened (or even eliminated) without sacrificing the relevant information pertaining to COVID-19 (which is primarily the second 2 paragraphs). 144 | 145 | ** 146 | This section has been shortened and reorganized to remove extraneous information. 147 | ** 148 | 149 | 2.8 Might suggest moving the cytokine section to be under the Systems-Level Effects rather than Clinical Presentation section, but it could fit in either. 150 | 151 | ** 152 | The modified section has been left under the Clinical Presentation section, but the Systems-Level Effects section has been renamed to "Insights from Systems Biology" to indicate that it focuses on research in omics rather than systems-level analyses more broadly. 153 | ** 154 | 155 | 2.9 Line 505 - statement regarding other respiratory viruses encoding antagonists to IFN response should reference the relevant studies. 156 | 157 | ** 158 | This line has been amended to include references to some broad discussions of this feature of viruses, as well as specific instances within betacoronaviruses. 159 | It now reads: "Other respiratory viruses have been found to encode antagonists to the IFN response [@doi:10.1016/j.mib.2010.05.009; @doi:10.1371/journal.pone.0112014], including SARS-CoV-1 [@doi:10.1128/JVI.01782-06] and MERS-CoV [@doi:10.1128/JVI.01845-13]." 160 | ** 161 | 162 | 2.10 Line 513 - word choice- replace extent with magnitude. 163 | 164 | ** 165 | This change has been made. 166 | ** 167 | 168 | 2.11 Lines 557-559 - this was a really intriguing statement- can the authors provide an additional sentence or two to provide additional context to why this might be the case? 169 | 170 | ** 171 | The authors of the study described in this passage state the following: "We compared our SARS-CoV-2 interaction map with those of ten other pathogens (Fig. 2e) and found that West Nile virus and _Mycobacterium tuberculosis_ had the most similar host-protein interaction partners. The association with _M. tuberculosis_ is of particular interest as it also infects lung tissue." 172 | 173 | On a proximal level, the apparent similarity between the protein-protein interaction networks of SARS-CoV-2 and _M. tuberculosis_ could be an artifact of the pathogens selected for comparison: as the authors themselves point out, both pathogens are known to affect the lungs, while the other pathogens used for comparison are not known for respiratory symptoms (hepatitis C, human immunodeficiency virus, human papillomavirus, Kaposi's sarcoma-associated herpesvirus, and West Nile virus). 174 | Therefore, the original study seems to suggest that altered regulation in the lungs might be driving this similarity. 175 | The sentence here has been rephrased to make this clearer and now reads: 176 | "The fact that the host-pathogen interactome of the bacterium *Mycobacterium tuberculosis* was found to be similar to that of SARS-CoV-2 suggests that changes related to lung pathology might comprise a significant contributor to these expression profiles." 177 | ** 178 | 179 | 2.12 I understand that this field moves ridiculously fast, but in the transmission section it might be worth including the most recent variants that are predicted to have increased transmission. 180 | 181 | ** 182 | Thank you for this suggestion. 183 | A discussion of variants of concern has been added to the section "Molecular Signatures and Transmission," which has been renamed to "Molecular Signatures, Transmission, and Variants of Concern" and moved earlier in the text. 184 | We have also made additional updates to reflect changes in the field since the paper was first reviewed (e.g., pediatric hospitalizations, reproduction number estimates). 185 | ** 186 | 187 | Reviewer 3 188 | 189 | Overall, the manuscript by Rando et al seeks to review and condense the current corpus of knowledge for SARS-CoV-2. The authors do a great job of making the findings of various studies easy to understand. Overall, this reviewer believes that it will be an excellent resource to the scientific community. This reviewer recommends that the author incorporates a handful of suggested changes (below) to improve the already impressive state of this manuscript. 190 | 191 | ** 192 | Thank you very much for your kind words and helpful suggestions. 193 | ** 194 | 195 | 3.1 Structure of Coronaviruses, paragraph 1: Please modify the definition of “non-segmented”. It refers more to the fact that it is a single molecule of ssRNA, than to whether it is contained in a capsid. 196 | 197 | ** 198 | This error has been correct. 199 | The text now reads: 200 | "They are non-segmented, which means the viral genome is a single continuous strand of DNA, and are enveloped, which means that the genome and capsid are encased by a lipid bilayer." 201 | ** 202 | 203 | 3.2 Cytokine release syndrome, paragraph 1: Please modify the wording from “dysregulated systemic inflammation can cause sepsis…” to something similar to “dysregulated systemic inflammation can contribute to pathogenesis associated with sepsis”. The reviewer is unsure about the relevance of this sentence since sepsis is associated with bacterial infection rather than viral infection. 204 | 205 | ** 206 | The section "Cytokine release syndrome" has been rewritten in line with comments from reviewer 2 above (comment 2.7). 207 | While most sepsis cases are attributed to bacteria, concerns have been raised that viral sepsis may be underidentified broadly [@doi:10.1183/16000617.0038-2020] and that it may be particularly relevant to SARS-CoV-2 [@doi:10/ggsps7]. 208 | The relationship between viruses and sepsis is an oversight in the current manuscript, so the paragraph indicated here has been modified to include background on viral sepsis. 209 | It now reads: "A dysregulated immune response can cause significant damage to the host [@isbn:9780815332183; @isbn:9780071283663; @doi:10.1016/j.chom.2020.05.009] including pathogenesis associated with sepsis. 210 | Sepsis, which can lead to multi-organ failure and death [@doi:10.1128/MMBR.05015-11; @pmid:22142805], is traditionally associated with bacterial infections, but sepsis associated with viral infections may be underidentified [@doi:10.1183/16000617.0038-2020], and sepsis has emerged as a major concern associated with SARS-CoV-2 infection [@doi:10/ggsps7]." 211 | ** 212 | 213 | 3.3 Cytokine release syndrome, paragraph 2: The relevance of sepsis to this paragraph is also unclear, unless the authors are comparing SARS-CoV-2 infection to other respiratory diseases caused by bacteria. Specifying the relevance of this comparison would be helpful. 214 | 215 | ** 216 | As with 3.2 above, this paragraph has been restructured. 217 | We hope the changes serve to emphasize the concerns about sepsis in the context of SARS-CoV-2. 218 | ** 219 | 220 | 3.4 Molecular signatures and transmission: It may be helpful to the readers if the authors included a brief synopsis of viral comparative genomics analyses that have been performed including: 221 | 222 | https://www.sciencedirect.com/science/article/abs/pii/S0140673620317578 223 | https://www.sciencedirect.com/science/article/pii/S0092867421000805 224 | https://jvi.asm.org/content/94/17/e00790-20.abstract 225 | https://www.sciencedirect.com/science/article/pii/S0092867420304864 226 | 227 | ** 228 | This section of the paper has been expanded based on this suggestion and based on Reviewer 2's comment 2.12. 229 | The four references suggested have been incorporated into this paper and into the separate Evolution manuscript associated with this project. 230 | Additionally, we have included analyses of variants of concern. 231 | ** 232 | 233 | 3.5 Conclusions, paragraph 3: The same reference (222) is included twice for the same statement. 234 | 235 | ** 236 | This duplication has been removed. 237 | ** 238 | -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- 1 | # Creative Commons Attribution 4.0 International 2 | 3 | Creative Commons Corporation (“Creative Commons”) is not a law firm and does not provide legal services or legal advice. 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Many concern the front-end. 7 | 8 | Regretfully, their live review https://greenelab.github.io/covid19-review/ could deter possible readers, as – at least within the first ~5 minutes – it did not render robustly on two different computers of mine after scrolling (tried one M1 mac, and one i7/64GB mac). 9 | 10 | Further the linked repository https://github.com/greenelab/covid19-review/tree/e5a4e3ce43f493c0c913ae647951488b89345106/output did not contain manuscript.pdf which would have allowed for a possibly smooth read (or more specifically: the link in the readme file would point to a file that would not be publicly visible) ; I thus strongly recommend prior acceptance that https://greenelab.github.io/covid19-review/ will be extended to allow users a download of the composite pdf without any need to scroll or recompile (and wait seconds/minutes for text to appear when advancing the screen at https://greenelab.github.io/covid19-review). 11 | 12 | ** 13 | References to the .pdf location have been added to the manuscript and the README. 14 | We are also exploring ways to collapse the references and appendices so that the HTML rendering is faster. 15 | ** 16 | 17 | The main contributors to the automated review seem to have been people that also contribute as authors to the current submission, or are otherwise affiliated with them. For others planning community efforts, it could be useful if the authors shared an extended discussion on where they faced obstacles - and success - in the recruitment of contributors, and how they see their mobilization efforts to compare to other groups which try to build and promote community around COVID-19 literature (e.g.: subdivision of preLights). Additionally, none of the most frequent contributors appear to include a medical doctor from pulmonary medicine – suggesting that some interesting potential community members have not been attracted. 18 | 19 | ** 20 | The challenges associated with this project fall into two three groups: content contribution, technical or methodological contribution, and project management. 21 | The first set of tasks primarily attracted individuals from a variety of biological fields who have contributed content on their specific areas of expertise. 22 | Some of these contributors have been involved only in a single section of a single manuscript, while others have brought their perspective to many sections across many manuscripts. 23 | This contribution is dependent on the individual's interest in and availability for this project over the past 1.5 years. 24 | The second category applies to most of the named authors of the current manuscript, who have worked mainly behind the scenes to promote rigorous evaluation of the literature and to develop the computational infrastructure needed to support the project. 25 | The task of project management has fallen mainly to the first and last authors of the current manuscript. 26 | These authors are biological data scientists, and thus they contribute content or techncial additions as needed. 27 | 28 | The COVID-19 pandemic presented unique challenges -- we had the most engagement during the initial phase of lockdown, when many biologists were unable to access their labs. 29 | As labs have opened back up, we have seen a smaller set of regular contributors. 30 | Additionally, it has been very difficult (as the reviewer notes) to recruit MDs, likely in part due to the fact that this effort is taking place at a time when the medical field is in an "all hands on deck" mode of operation. 31 | A review of these limitations has been added to the discussion. 32 | ** 33 | 34 | Presently the user-interface for the construction of the review is provided by git/github. As the authors note, this could deter some contributors. Would there be ways to create a simple user interface that appeals to target contributors? 35 | 36 | ** 37 | Increasing the accessibility of this tool is a long-term goal of the authors, and this is a comment we will take into consideration as we continue to develop resources for Manubot. 38 | ** 39 | 40 | Reading the automated review, it seems to aggregate information, rather than to synthesize and condense the literature – which is a role of reviews that has been noted by others before (e.g.: in “Laboratory Life” by Latour and Woolgar). Therefore, it would be interesting to learn more about the author’s intended target audience and usage scenarios – and whether the work that they created would be even something new aside from “reviews” or “literature surveys”. 41 | 42 | ** 43 | While originally the review read as a series of summaries/critiques of individual papers, the second phase of the project (during 2021) has focused on consolidating each topic into a more traditional synthesis. 44 | This shift is apparent in the difference between the pharmaceuticals appendix (content/21.pharmaceuticals-app.md) compared to the primary pharmaceuticals text (content/20.pharmaceuticals.md), which offers a more zoomed-out view of ongoing research in therapeutics. 45 | ** 46 | 47 | Though thinkable given their technical solution for the back-end, the option for personalized reviews appears absent in the discussion. 48 | 49 | ** 50 | The following sentence has been added to the discussion: "The licensing and infrastructure also provide an opportunity for individuals to adapt from this project to create their own snapshots of the COVID-19 literature that derive from, but are not wholly identical to, the primary versions of these reviews." 51 | ** 52 | 53 | For their data-integration on clinical trials, they could possibly use the integration provided by dimensions.ai to save redundant work on their end. 54 | 55 | ** 56 | Thank you for pointing us to this resource. 57 | In the present case, we used a resource that had already aggregated information from COVID-19 clinical trials, reducing the need for data cleaning on our end, but this is a very interesting resource to consider for future developments. 58 | ** 59 | 60 | # Review 2 61 | 62 | This paper falls well into the scope of this workshop. It introduced a novel publishing platform, “Manubot,” which also acts as an infrastructure for collaboration and knowledge synthesis. In particular, it discussed the application of Manubot in producing a “living review” of covid-19, challenges that emerged with such a task, and how they dealt with the challenges. The paper is overall well written, and I only have a few minor suggestions. 63 | 64 | (1) Section 2.1 didn’t give me a clear picture of the team structure that produces the review. What is the relation between recruited participants (“recruited by word of mouth and on Twitter”) and the consortium? 65 | 66 | ** 67 | Thank you for catching this oversight. 68 | Section 2.1 now contains the sentence: "Given the permeability of feedback, ideas, and suggestions among contributors of different topics throughout the development of these reviews, contributors to a specific manuscript were recognized with masthead authorship, while all contributors to the project were recognized with consortium authorship on all papers (including this one)." 69 | ** 70 | 71 | I am asking this also because, later on, you wrote: “We collaborated with the Immunology Institute at the Mount Sinai School of Medicine to incorporate summaries written by their students, post-docs, and faculty [49, 15]. Additionally, two of the consortium authors were undergraduate students recruited through the American Physician Scientist Association’s Virtual Summer Research Program.” It left me with the impression that there were two ways to recruit contributors. One is of relatively low barrier and informal (“recruited by word of mouth and on Twitter”). The other is of high barrier and formal (e.g., through organizations). 72 | 73 | ** 74 | Thank you for alerting us to this confusing presentation of the recruitment process. 75 | The sentence reference above in section 2.1 was amended to read, "Contributors were recruited primarily by word of mouth and on Twitter, though we also collaborated with existing efforts to train early-career researchers." 76 | We also added a description of the established programs as "more formal" approaches to recruitment. 77 | ** 78 | 79 | (2) Figure 3 has no associated narratives in the paper. 80 | 81 | ** 82 | We now note how this figure demonstrates how some contributors remained engaged in the project for the long term. 83 | "Though only a fraction of potential contributors contributed to the text included in the manuscripts (Figure 2), many contributors remained engaged over the long term (Figure 3)." 84 | ** 85 | 86 | (3) It is not very clear to me how the knowledge synthesis and updating process take place. I only know how the summary statistics and figures were handled (“To address this concern, Manubot and GitHub’s CI features were used to create figures that integrated online data sources to respond to changes in the COVID-19 pandemic over time.”). How about the narratives? 87 | 88 | ** 89 | Thank you for pointing this out. 90 | This is a limitation of this approach to the infodemic. 91 | It requires that contributors remain engaged and provide updates as needed. 92 | This is a recognized challenge in massively open online papers [@doi:10.5334/kula.63]. 93 | In our case, some contributors returned to update their text, while others did not. 94 | Each paper had 2-3 leads who would review the text periodically to ensure it was up-to-date. 95 | Ideally in the future, an integration with a resource such as CoronaCentral might make it easier to keep a running list of the sections most likely to require additions, given that CoronaCentral can detect the topics of new papers as well as their impact. 96 | A paragraph describing this limitation has been added to the discussion. 97 | ** 98 | 99 | (4) If you need more space to address the previous comments, I suggest the following to help you find some space. 100 | 101 | The spelling checking function (page 4-5) is not particularly interesting and doesn’t worth so much space. 102 | The emphasis that researchers in the biomedical domain are not particularly familiar with Git/GitHub. I understand it’s a major concern for the authors. Still, I don’t think this factor should take a front seat (e.g., mentioned at the very beginning of section 2.1) over other matters and be mentioned in several different places of the paper. I suggest pulling all materials about familiarizing users with GitHub into one section, including the concerns and solutions (e.g., training materials, easy tasks such as pull requests for beginners, using Gitter.im). 103 | 104 | ** 105 | We retained some of the technical detail in order to properly credit the third-party software that Manubot uses for these steps. 106 | We removed the clinical trials figure and word cloud figure to create additional space. 107 | ** 108 | 109 | # Review 3 110 | 111 | Summary 112 | This paper addresses the COVID-19 infodemic by proposing a collaborative manuscript writing approach, using Manubot. Researchers from a variety of domains were asked to contribute to a review article that organizes the large quantity of COVID-19 related research. To this end, Manubot has been extended to add functionalities specifically needed for this use case. 113 | 114 | General remarks 115 | The paper is well written and relevant for this workshop, as it proposes a novel approach to collaborative sciences, in the form of version controlled living documents. 116 | 117 | As the authors mention, the approach does require technical skills of researchers in order to contribute to a manuscript. Although instructions are provided, this is a major weakness of the approach. Although claimed differently by the authors, I do not think this approach will work for most researchers without the required technical skills. Even when they are willing to invest time in learning how to contribute to a manuscript, technical issues could arise and more complex git commands might be needed to solve this. What this paper is lacking, is a proper user evaluation that focuses on the question whether this approach is indeed suitable for non-technical users. For example, evaluating the usability of the whole process (e.g., with a SUS evaluation), and the participants’ attitudes towards the approach, ! 118 | or task load (via TLX assessment). At the current state, one cannot make claims on whether this approach is suitable for non-technical users. 119 | 120 | ** 121 | Based on your suggestions, the phrasing in the discussion has been modified to make it clear that this is an example of a project that included non-technical authors, rather than evidence that Manubot is appropriate for non-technical authors. 122 | The potential for a formal evaluation has also been added to the future directions section of the discussion. 123 | In our case, the structure of our consortium made it so that hurdles such as merge conflicts could be managed by someone in a project management role who had git experience. 124 | However, this would certainly be a limitation for projects run by and for biologists, as it would still require someone with experience managing large git-based collaborations be involved. 125 | We have expanded the discussion to point out these limitations. 126 | We hope to expand Manubot in the future to make it more accessible to wider audiences. 127 | ** 128 | 129 | In the introduction, the current challenges of scholarly communication (and in particular related to COVID-19 research) are listed. Although this paper does propose several solutions to mentioned issues (lacking collaboration, static review articles etc.), it does not directly address the most critical challenge: the "infodemic". The proposed approach still relies on document-based scholarly communication, and publications of the articles created with this approach will also contribute to the infodemic. A possible solution could be to integrate machine actionable descriptions of the results in the review articles, possibly by including semantic annotation to the text (I understand this might be out of scope for this research, but it is an interesting approach that would address the infodemic at its core). 130 | 131 | ** 132 | Thank you for pointing out this limitation. 133 | Based on comments from you and Reviewer #2, a paragraph describing this limitation has been added to the discussion. 134 | ** 135 | 136 | Other remarks and questions 137 | 138 | A comparison with other manuscript authoring approaches and tools would be interesting. Why was Manubot selected in the first place? Are there any alternatives available that do not require technical skills, but still have support for versioning and collaborative authoring? How would this approach compare to using a Wiki system for authoring? Using Manubot was taken for granted without a justification. 139 | 140 | ** 141 | An analysis of the advantages of Manubot for this project has been added to the introduction. 142 | It reads: We selected Manubot because it offers several advantages over comparable collaborative writing platforms such as Authorea, Overleaf, Google Docs, Word Online, or wikis [@doi:10.1371/journal.pcbi.1007128]. 143 | Citation-by-identifier ensures consistent reference metadata standards that would be difficult to maintain manually in a manuscript with dozens of authors and over 1,500 citations. 144 | Manubot's pull request-based contribution model balances the goals of making the project open to everyone and maintaining scientific accuracy. 145 | All contributions are reviewed, discussed, and formally approved on GitHub before text updates appear in the public-facing manuscript^[https://greenelab.github.io/covid19-review]. 146 | Continuous integration (CI) seamlessly combines author-produced text and figures with automatically generated and updated statistics and figures from external data sources and the manuscript's own content. 147 | In addition, the authors who initially launched this project included Manubot developers who had prior successes using Manubot for massively open and traditional manuscript, such as a large-scale collaborative efforts such as a review of developments in deep learning [@doi:10.1098/rsif.2017.0387] and a re-evaluation of the role of authorship in modern collaborations [@doi:10.1080/08989621.2020.1779591]. 148 | ** 149 | An itemized list of changes made to Manubot would be helpful (this is explained in the text already, but a list provides a better overview). 150 | 151 | ** 152 | The suggested list is now included as Table 1. 153 | ** 154 | The selection of participants could be biased towards people that are interested in technology already, otherwise they would not have participated in the first place. This should be mentioned as limitation. 155 | 156 | ** 157 | This limitation is now noted in the discussion. 158 | ** 159 | 160 | As mentioned in the paper, the manuscript grew too large for a single document. Why didn't the authors create multiple repositories for each of the articles? 161 | 162 | ** 163 | Because of the evolving nature of the pandemic, the number of manuscripts has changed throughout the past year and a half. 164 | For example, one section was originally covered therapeutics and prophylactics broadly. 165 | It was then subdivided into pharmaceuticals and nutraceuticals. 166 | The pharmaceuticals section was then further subdivided into pharmaceutical therapeutics and vaccines. 167 | Keeping all of the text in a single repository has allowed for the flexibility to split and lump sections as more information becomes available. 168 | It also cuts down on potential confusion for both project managers and contributors by keeping everything centralized (e.g., all of the issues are in one place, a single search can reveal merged PRs that touched on a topic of interest, etc.) 169 | We added a sentence to the text to note the desire to keep all GitHub discussion centralized in a single repository. 170 | ** 171 | 172 | When does a contributor become an author of a paper? For example, fixing a typo is presumably not enough to be considered a paper author? 173 | 174 | ** 175 | The following sentence has been added to the section "Contributor Recruitment and Roles": "Authorship was determined based on Contributor Roles Taxonomy ()." 176 | ** 177 | 178 | Figure 5 does not seem to visualize the interests that are mention in the text and figure caption. Maybe the wrong figure is used here? 179 | 180 | ** 181 | Given constraints on space, Figure 5 has been removed, as it did not provide much additional background on the authors. 182 | ** 183 | 184 | Consider using footnotes for URLs. 185 | 186 | ** 187 | This change has been made. 188 | ** 189 | 190 | --------------------------------------------------------------------------------