On this page we are linking to various material that have to do with our investigations of the origin and evolution of SARS-CoV-2, the virus responsible for the COVID-19 pandemic.
Paper - The Proximal Origin of SARS-CoV-2
This short peer-reviewed article in Nature Medicine summarizes our scientific investigations into the proximal origins of SARS-CoV-2. Due to constraints on article format, many references could not be included, and experimental details were limited. We deeply investigated both natural and artificial scenarios for the proximal origin of SARS-CoV-2. Our analyses strongly support a natural origin of the virus and all the data are fully consistent with evolutionary processes having led to the emergence of SARS-CoV-2 in the human population.
You can access the paper here.
Earlier version also on Virological.
Very relevant (and technical) Virological post by Bill Gallaher about the molecular mechanism of how SARS-CoV-2 gained its furin/polybasic cleavage site.
Another very relevant Virological post by Spyros Lytras about the evolution of the furin/polybasic cleavage site.
Refuting the "Yan Report"
A report from Dr. Li-Meng Yan and colleagues came out in September 2020 proposing that SARS-CoV-2 had been created in the lab. This report is one of many examples of conspiracy theories circulating about lab-based scenarios for the proximal origin of SARS-CoV-2. While such scenarios should not be dismissed without inquiry and deserve careful scientific inquiry (as we did in our "Proximal" paper), this particular report is entirely unsupported, non-scientific, and appear to have been created to support baseless conspiracy theories.
Twitter thread outlining the issues with the Yan Report.
Authenticity of recent SARS-like coronavirus genomes
We downloaded raw data and reassembled relevant genomes from recently discovered SARS-like coronaviruses from bats and pangolins to assess their authenticity. The analyses show that all the genomes are authentic and as reported in the relevant manuscripts describing their sequencing and assembly.
Data available via Google Cloud.
Summary of the findings with further discussion on Virological.
Snakes not the reservoir of SARS-CoV-2
Early on in the pandemic it was suggested that snakes served as the reservoir of SARS-CoV-2. This conclusion was based on very naive and entirely wrong analyses. More in-depth analyses clearly show that snakes are unlikely to be the reservoir for the virus.
Post with analyses and discussion on Virological.
Also very relevant post by David Robertson on Virological.
Early evolutionary estimates of SARS-CoV-2 molecular clock and the timing of the COVID-19 pandemic
In January 2020, we performed one of the earliest estimates of the evolutionary rate and timing of SARS-CoV-2 based on 27 sequences shared publicly on GISAID from Chinese investigators. The clock of ~1E-3 s/s/y and timing of mid-November / early-December have both remained remarkably stable as more genomes have been produced (more than 100k as of this writing).
Post on Virological describing the findings, including important caveats and criticism of our analyses, etc.
The Scripps Research Institute
La Jolla, CA, USA