Mary Wilson
Well-known member
Crits-Christoph, Alex; 
Gangavarapu, Karthik; Pekar, Jonathan E.; Moshiri, Niema; Singh, Reema; Levy , Joshua I.; Goldstein, Stephen A.; Suchard, Marc A.; Popescu, Saskia; Robertson, David L.; Lemey, Philippe; Wertheim, Joel O.; Garry, Robert F.; Rasmussen, Angela L.; Andersen, Kristian G.; Holmes, Edward C.; Rambaut, Andrew; Worobey, Michael; Débarre, Florence
Report:
Genetic evidence of susceptible wildlife in SARS-CoV-2 positive samples at the Huanan Wholesale Seafood Market, Wuhan:
Analysis and interpretation of data released by the Chinese Center for Disease Control
In an attempt to ensure transparency and engagement towards global partnership, we would like to provide further context regarding the timeline of work and efforts to collaborate on the research presented in the report below.
On 4 March 2023 (dates in UTC), we discovered accessions posted publicly on the GISAID database corresponding to sequences from environmental samples collected at the Huanan Seafood Wholesale Market, Wuhan. On 9 March, we realized that those accessions were associated with raw metagenomic sequence read data files. We further recognised that it was the data underlying the preprint posted on Research Square by Gaoet al. at the Chinese Center for Disease Control and Prevention (CCDC) on 25 February 2022 (DOI: 10.21203/rs.3.rs-1370392). The metadata on GISAID indicated these sequencing data had been uploaded in June 2022, however, they evidently had not been released at that time. We downloaded the public data to search for genetic sequences from non-human animals, which the CCDC did not identify in their February 2022 preprint. The preprint also posited that all SARS-CoV-2-positive samples in the market were the result of human infections, claiming that the market was a site of amplification of an already widespread epidemic. We and others therefore had urgently requested release of the data. The potential for analysis of samples for animal DNA had also been recommended in the mission report of the World Health Organization (WHO)-convened global study of origins of SARS-CoV-2: China Part, released March 20211.
Once the data were identified on GISAID, it became possible to test the veracity of these claims. We found information that was critical to understanding the nature of the origins of the human infections at the Huanan market, as this was the early epicenter of SARS-CoV-2 spread and was likely where spillover occurred and sustained human-to-human transmission was established.
Our analysis of these data found that genetic evidence of multiple animal species was present in locations of the market where SARS-CoV-2 positive environmental samples had been collected. This includes raccoon dogs, which are susceptible to SARS-CoV-2 infection and shed sufficient virus to transmit to other species. However, this also included ...
1 https://www.who.int/publications/i/i...v-2-china-part
** Download to read**
https://zenodo.org/record/7754299#.ZBj5oC2ZORs
Gangavarapu, Karthik; Pekar, Jonathan E.; Moshiri, Niema; Singh, Reema; Levy , Joshua I.; Goldstein, Stephen A.; Suchard, Marc A.; Popescu, Saskia; Robertson, David L.; Lemey, Philippe; Wertheim, Joel O.; Garry, Robert F.; Rasmussen, Angela L.; Andersen, Kristian G.; Holmes, Edward C.; Rambaut, Andrew; Worobey, Michael; Débarre, FlorenceReport:
Genetic evidence of susceptible wildlife in SARS-CoV-2 positive samples at the Huanan Wholesale Seafood Market, Wuhan:
Analysis and interpretation of data released by the Chinese Center for Disease Control
In an attempt to ensure transparency and engagement towards global partnership, we would like to provide further context regarding the timeline of work and efforts to collaborate on the research presented in the report below.
On 4 March 2023 (dates in UTC), we discovered accessions posted publicly on the GISAID database corresponding to sequences from environmental samples collected at the Huanan Seafood Wholesale Market, Wuhan. On 9 March, we realized that those accessions were associated with raw metagenomic sequence read data files. We further recognised that it was the data underlying the preprint posted on Research Square by Gaoet al. at the Chinese Center for Disease Control and Prevention (CCDC) on 25 February 2022 (DOI: 10.21203/rs.3.rs-1370392). The metadata on GISAID indicated these sequencing data had been uploaded in June 2022, however, they evidently had not been released at that time. We downloaded the public data to search for genetic sequences from non-human animals, which the CCDC did not identify in their February 2022 preprint. The preprint also posited that all SARS-CoV-2-positive samples in the market were the result of human infections, claiming that the market was a site of amplification of an already widespread epidemic. We and others therefore had urgently requested release of the data. The potential for analysis of samples for animal DNA had also been recommended in the mission report of the World Health Organization (WHO)-convened global study of origins of SARS-CoV-2: China Part, released March 20211.
Once the data were identified on GISAID, it became possible to test the veracity of these claims. We found information that was critical to understanding the nature of the origins of the human infections at the Huanan market, as this was the early epicenter of SARS-CoV-2 spread and was likely where spillover occurred and sustained human-to-human transmission was established.
Our analysis of these data found that genetic evidence of multiple animal species was present in locations of the market where SARS-CoV-2 positive environmental samples had been collected. This includes raccoon dogs, which are susceptible to SARS-CoV-2 infection and shed sufficient virus to transmit to other species. However, this also included ...
1 https://www.who.int/publications/i/i...v-2-china-part
** Download to read**
https://zenodo.org/record/7754299#.ZBj5oC2ZORs