SARS-CoV-2 and COVID-19: An Evolving Review of Diagnostics and Therapeutics

Project Status:

Section	Title	Status Issue	Submission Status	Venue	Links
Pathogenesis	Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure	✔️	Published 🎉	mSystems	Release; Preprint
Evolution	Evolutionary Perspectives on SARS-CoV-2	#867	Suspended	Manubot only
Diagnostics	Molecular and Serologic Diagnostic Technologies for SARS-CoV-2	#1156	Reviewed, not revised	mSystems	Release; Preprint
Pharmaceuticals	Identification and Development of Therapeutics for COVID-19	✔️	Published 🎉	mSystems	Release; Preprint
Vaccines- Established Platforms	Application of Traditional Vaccine Development Strategies to SARS-CoV-2	✔️	Published 🎉	mSystems	Release; Preprint
Vaccines- Novel Platforms	The Coming of Age of Nucleic Acid Vaccines during COVID-19	✔️	Published 🎉	mSystems	Release; Preprint
Nutraceuticals	Dietary Supplements and Nutraceuticals Under Investigation for COVID-19 Prevention and Treatment	✔️	Published 🎉	mSystems	Release; Preprint
Social Determinants of Health	Social Factors Influencing COVID-19 Exposure and Outcomes	#868	Suspended	Manubot only
Methods (Cyberinfrastructure)	An Open-Publishing Response to the COVID-19 Infodemic	✔️	Published 🎉	DISCO 2021	Release; Preprint

This project was most active from March 2020 through February 2023 and is not currently receiving major updates.

Code of Conduct

This project operates under a code of conduct. 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. We take this very seriously. 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).

Project Description

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. This repository is an online, collaborative review paper written with manubot. We are seeking input from scientists at all levels anywhere in the world.

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. 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). 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.

Contributions

You'll need to make a free GitHub account.

Instructions and procedures for contributing are outlined here.

We will follow the ICMJE Guidelines for determining authorship.

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. 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.

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).

Pull Requests

If you are not familiar with git and GitHub, you can use these directions to start contributing.

Please feel encouraged to ask questions by opening a Request for Help issue

This project is a collaborative effort that will benefit from the expertise of scientists across a wide range of disciplines!

Manubot

Manubot is a system for writing scholarly manuscripts via GitHub. Manubot automates citations and references, versions manuscripts using git, and enables collaborative writing via GitHub. An overview manuscript presents the benefits of collaborative writing with Manubot and its unique features. The rootstock repository is a general purpose template for creating new Manubot instances, as detailed in SETUP.md. See USAGE.md for documentation how to write a manuscript.

Please open an issue for questions related to Manubot usage, bug reports, or general inquiries.

Repository directories & files

• This file is called README.md It is the centralized document for the repository and will help direct users to other relevant information.
• CONTRIBUTING.md contains procedures and directions for contributing to this effort.
• INSTRUCTIONS.md contains instructions for new GitHub users for how to navigate GitHub in the browser as well as GitHub vocabulary. It also includes some instructions for more experienced users about the procedures we recommend and how to run manubot on the command line.
• USAGE.md describes formatting instructions for formatting text, citing references, adding figures and tables, etc.
• SETUP.md includes information about setting up manubot
• LICENSE.md and 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.

The directories are as follows:

• content contains the manuscript source, which includes markdown files as well as inputs for citations and references. These are the files that most contributors will be editing. See USAGE.md for more information.
• output contains the outputs (generated files) from Manubot including the resulting manuscripts. You should not edit these files manually, because they will get overwritten.
• webpage is a directory meant to be rendered as a static webpage for viewing the HTML manuscript.
• build contains commands and tools for building the manuscript.
• ci contains files necessary for deployment via continuous integration.

License

Except when noted otherwise, the entirety of this repository is licensed under a CC BY 4.0 License (LICENSE.md), which allows reuse with attribution. Please attribute by linking to https://github.com/manubot/rootstock.

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). All files matched by the following glob patterns are dual licensed under CC BY 4.0 and CC0 1.0:

• *.sh
• *.py
• *.yml / *.yaml
• *.json
• *.bib
• *.tsv
• .gitignore

All other files are only available under CC BY 4.0, including:

• *.md
• *.html
• *.pdf
• *.docx

Please open an issue for any question related to licensing.