COVID-19 resources for bioinformaticians and data scientists
COVID-19 case data
Coronavirus case data is reported by the following sources:
| Source | Provider |
|---|---|
| 2019 Novel Coronavirus COVID-19 (2019-nCoV) Data Repository | Johns Hopkins CSSE |
| Geographic distribution of COVID-19 cases worldwide | European Centre for Disease Prevention and Control |
| Coronavirus (COVID-19) map | |
| 2019–20 coronavirus pandemic by country and territory | Wikipedia |
SARS-CoV-2 genome analysis
The first genome sequence of the virus was published on February 3 and is available in GenBank (MN908947).
This has been followed by a number of papers further analyzing the genomic data. In The proximal origin of SARS-CoV-2, Andersen et al. show that the new virus arose naturally and was not engineered in a lab and deliberately released to make people sick.
In NCBI's Taxonomy Database, the virus is assigned the ID 2697049 (NCBI:txid2697049). The taxonomy page contains links to all NCBI data related to the virus.
There are about 500 SARS-CoV-2 sequences currently available in GenBank and 300 in the Sequence Read Archive (SRA). The live list is published by NCBI here and is available in the YAML format here.
Structural biology of SARS-CoV-2
The structure of the spike protein through which the virus binds to human cells was published on March 13. This glycoprotein is a key target for vaccines, therapeutic antibodies, and diagnostics.
COVID-19 clinical trials data
ClinicalTrails.gov indicates that there are over 300 COVID-19 clinical trials that are under way around the world.
The first clinical trial (NCT04280705) in the U.S. aims to evaluate the safety and efficacy of the drug remdesivir.
Additional resources
- https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/
- https://www.nih.gov/health-information/coronavirus
- https://www.coronavirus.gov/
- https://www.cdc.gov/coronavirus/2019-nCoV/index.html
- https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/cases-in-us.html
- https://www.whitehouse.gov/briefings-statements/call-action-tech-community-new-machine-readable-covid-19-dataset/
- LitCovid, a feed of relevant articles about the 2019 novel Coronavirus in PubMed
- WHO database of publications on coronavirus disease (COVID-19)
- COVID-19 Open Research Dataset (CORD-19), a dataset of 47,000 scholarly articles about COVID-19, SARS-CoV-2, and related coronaviruses
- Collection of relevant articles curated by Nature Research's editorial teams