SAGO Statement on Newly Published SARS-CoV-2 Metagenomic Data from Chinese CDC at GISAID

On 12 March 2023, WHO was notified of new SARS-CoV-2 sequences and metagenomic data associated with samples collected from the Huanan Seafood Wholesale Market, Wuhan, China, since January 2020, which became available on GISAID for a short time time. The data was later downloaded by numerous researchers from several countries. Access was restricted shortly thereafter, apparently to allow further data updates by the Chinese CDC. WHO then immediately contacted the Chinese CDC and the President and Vice President of SAGO. After discussions between WHO and Chinese colleagues, it was explained that the genomic data is the basis for the expected update of the existing one Liu et al. Reprint 2022 (1), which is in the process of being resubmitted for publication to Nature by the Chinese CDC.

After discussions with the WHO Secretariat and the Chair and Vice-Chair of SAGO, an invitation was arranged on March 12 to the involved scientists from the Chinese CDC and some of those who accessed the data from GISAID, to assess the significance of these data and analyses. of this data. WHO subsequently organized a meeting on 14 March 2023 with all SAGO members and invited researchers from the Chinese CDC to present an updated analysis of their data. WHO and SAGO also invited researchers who informed WHO that they had accessed data from GISAID to present their analysis of provisionally published sequences.

Presentations by the Chinese CDC and invited international researchers highlighted newly available data from the Huanan Seafood Wholesale Market. This included metagenomic data of environmental samples from various stands and wastewater collection sites collected as far back as January 2020. Analyzes of these data suggested that in addition to SARS-CoV-2 sequences, some samples also contained human DNA, as well as the mitochondrial DNA of several animal species. species, including some known to be susceptible to SARS-CoV-2. These include DNA from wild raccoon dogs, Malaysian porcupines, and bamboo rats, among others, in SARS-CoV-2 positive environmental samples.

The findings suggest that the animals were present at the market shortly before the market was cleared on January 1, 2020, as part of public health measures by the Chinese authorities. These results provide potential clues for the identification of intermediate hosts of SARS-CoV-2 and potential sources of human infections in the marketplace.

According to a reprint by Chinese authors (Liu et al 2022), of 1380 samples collected from the environment and animals in the market in early 2020, 73/923 environmental samples were positive for RT-qPCR specific for SARS-CoV-2, from various stalls and sewage systems in the market and around her. , but the virus was not detected in 457 animal samples tested. The animal samples included animal carcasses, frozen animal carcasses and animal products, as well as stray animals around the market, and included 18 species. According to the preprint, raccoon dogs were not among the animals tested. However, the presence of high levels of raccoon mitochondrial DNA in metagenomic data from environmental samples identified in the new analysis suggests that raccoon dogs and other animals may have been present before the market was cleared as part of a public health intervention.

Historical photographic evidence has been provided to show that raccoon dogs and other animals were sold at these special stands in the past. Although this does not provide definitive proof of the intermediate host or origin of the virus, the data provide additional evidence of the presence of susceptible animals on the market that may have been the source of human infection.

SAGO will continue to evaluate all scientific data shared by Chinese and other researchers from anywhere in the world. SAGO encourages all data related to the study of the origin of SARS-CoV-2 to be immediately available for a robust and comprehensive review.

As mentioned in SAGO preliminary report (2), SAGO strongly recommends that researchers in China investigate the upstream sources of animals and animal products present in Huanan Market just before its closure and removal of all animal products on January 1, 2020.

Furthermore, SAGO would like to encourage that all available sequencing and metagenomics data be published in GISAID or any other sequence database, and that manuscripts under review be shared as soon as possible so that the scientific community has an opportunity for their further review. analysis. In addition, SAGO encourages researchers using this data to collaborate and engage with Chinese researchers. WHO and SAGO are happy to support this collaboration.

(1) Liu et al, 2022 Surveillance of SARS-CoV-2 in the environment and animal samples 2 Huanan Seafood Market, Available: https://www.researchsquare.com/article/rs-1370392/v1

(2) Preliminary report for the Scientific Advisory Group on the Origin of Emerging Pathogens (SAGO) June 2022, available: https://www.who.int/publications/m/item/scientific-advisory-group-on-the- report on the origin of new pathogens