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expert reaction to study looking at the evolutionary origins of the SARS-CoV-2 virus lineage responsible for the COVID-19 pandemic

A study, published in Nature Microbiology, looked at he evolutionary origins of the SARS-CoV-2 virus lineage responsible for the COVID-19 pandemic.


Prof Mark Pagel, Professor of Evolutionary Biology, University of Reading, said:

Has this study been done well; is it robust?


Does the press release accurately reflect the paper?


Is this a surprise / is it a significant finding?

“Less a surprise than a careful analysis of a lingering question.

Is this the first study to put a specific data on the evolution of Sars-Cov-2 and the divergence from bat viruses?

“No, but it is probably the best estimate yet.

“The new Nature Microbiology paper is important for providing evidence that the SARS-CoV-2 (hereafter covid-19) jumped directly into humans from the horseshoe bats rather than via an intermediate host, suspected by many to be the pangolins.  The authors’ analyses, if correct, suggest that coronaviruses capable of infecting humans have been present in bats for perhaps 40 to 70 years but have gone undetected.  This is significant in pointing to the scale and nature of the problems that zoonotic transmission presents to humans — there may be numerous and as yet undetected viruses capable of infecting humans that reside in animal hosts.

“Pangolins have been suspected as the possible source of covid-19 because of their prevalence in live animal markets and their use in traditional medicines, but also because a key part of the pangolin coronavirus that is implicated in human infectivity – the variable loop region of the important spike protein – is more closely related to covid-19 than is the variable loop region of the most closely related horseshoe bat coronavirus, known as RaTG13.

“The spike protein is the region of the covid-19 virus that allows it to gain access to human cells, and is the part of the virus that vaccine developers are targeting.  Superficially this new result might suggest that the pangolin is the intermediate host from which the virus jumped to humans.  But the authors’ analysis shows that the difference between RaTG13 and covid-19 in the critical variable loop region probably arose in RaTG13 after it separated from the common ancestor it shares with covid-19.  This then points to the conclusion that there are as yet undetected horseshoe bat viruses that are the likely source of covid-19 — ones that have not been altered like RaTG13 has.

“To achieve these new results the authors removed regions of the bat, human and pangolin coronavirus sequences that are thought to exchange information with each other when they are found in the same host, a phenomenon known as recombination.  Previous studies have not done this.  Removing these regions leaves a clearer signal of ancestry and improves dating.  The authors’ work is robust, but unlikely to be the final word.  If they are correct, there will be coronaviruses circulating in horseshoe or other closely related bats that will prove to be closer to covid-19 than is RaTG13.  In an earlier epidemic – that of the original SARS – researchers searched for over 14 years before finding the probable source, also in horseshoe bats.”



‘Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic’ by Maciej F. Boni et al. was published in Nature Microbiology on Tuesday 28 July 2020.

DOI: 10.1038/s41564-020-0771-4


All our previous output on this subject can be seen at this weblink:


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None received.

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