Thread by @ZhouLabUCR

A paper just published today in Cell: "A Genomic Perspective on the Origin and Emergence of #SARSCoV2". The lead author Dr. Zhang published the world's first genome sequence of #SARSCoV2 on an open-access site, virological.org on January 10, 2020. cell.com/cell/fulltext/…

Dr. Zhang's laboratory at the Shanghai Public Health Clinical Center was ordered to shut down a day after his team first shared the genome sequence of #SARSCoV2 with the world 🤔 scmp.com/news/china/soc…

3/ Now back to science: "While this again suggests that the market played an important role in virus emergence, it is not clear whether the samples were derived from people who inadvertently deposited infectious material or from animals or animal matter present at that location."

4/ "... the bat viruses most closely related to #SARSCoV2 were sampled from animals in Yunnan province, over 1,500 km from Wuhan. There are relatively few bat coronaviruses from Hubei province, and those that have been sequenced are relatively distant to #SARSCoV2..."

5/ "although sequence similarity values of 96%–97% make it sound like the available bat viruses are very closely related to #SARSCoV2, in reality this likely represents more than 20 years of sequence evolution..."

6/ "...#SARSCoV2 and RaTG13 differ in a number of key genomic features, arguably the most important of which is that #SARSCoV2 contains a polybasic (furin) cleavage site insertion (residues PRRA) at the junction of the S1 and S2 subunits of the S protein"

7/ "...an independent insertion(s) of the amino acids PAA at the S1/S2 cleavage site was recently observed in a virus (RmYN02) sampled in mid-2019 from another Rhinolophus bat..., indicating that these insertion events reflect a natural part of ongoing coronavirus evolution."

8/"...more sampling will identify additional bat viruses that are even closer relatives of #SARSCoV2. A key issue is whether these viruses, or those from any other animal species, contain the key RBD mutations and the same furin-like cleavage site insertion as found in #SARSCoV2"

9/"Another issue that has received...attention is whether #SARSCoV2 is a recombinant virus...whether such recombination might have facilitated its emergence." "...distinguishing recombination that assisted virus emergence from “background” recombination events is not trivial."

10/"...trying to determine the exact pattern and genomic ancestry of recombination events is difficult, particularly as many of the recombinant regions may be small and are likely to change as we sample more viruses related to #SARSCoV2."

11/"...it is difficult to determine using genomic comparisons alone whether the virus is fixing phenotypically important mutations as it spreads through the global population, and any such claims require careful experimental verification."

12/"...It seems inevitable that SARS-CoV-2 will become the fifth endemic coronavirus in the human population (along with HKU1, NL63, OC43, and 229E) and one that is currently spreading in a totally susceptible population."

13/ "Given the enormous diversity of viruses in wildlife and their ongoing evolution, arguably the simplest and most cost-effective way to reduce the risk of future outbreaks is to limit our exposure to animal pathogens as much as possible."

14/14 A nice article! The authors are very cautious to not draw firm conclusions without strong evidence (not like some other papers I recently read on this topic). More questions to be answered and more research to be done!