Here’s the full analysis of newly uncovered genetic data on COVID’s origins

Security guards stand in front of the closed Huanan Seafood Wholesale Market in the city of Wuhan, in the Hubei Province, on January 11, 2020, where the Wuhan health commission said that the man who died from a respiratory illness had purchased goods.
Enlarge / Security guards stand in front of the closed Huanan Seafood Wholesale Market in the city of Wuhan, in the Hubei Province, on January 11, 2020, where the Wuhan health commission said that the man who died from a respiratory illness had purchased goods.

A group of independent international researchers has released its full analysis of newly uncovered metagenomic data collected by the Chinese Centers for Disease Control and Prevention in January and February of 2020. The data closely links SARS-CoV-2 to the genetic tracks of wild animals, particularly raccoon dogs sold at the Huanan Wholesale Seafood Market in Wuhan, China, the early epicenter of the COVID-19 pandemic, the group’s analysis says.

The full analysis provides additional compelling evidence that the pandemic coronavirus made its leap to humans through a natural spillover, with a wild animal at the market acting as an intermediate host between the virus’s natural reservoir in horseshoe bats and humans. It was authored by 19 scientists, led by Michael Worobey, an evolutionary biologist at the University of Arizona; Kristian Andersen, a virologist at the Scripps Research Institute in California; and Florence Débarre, a theoretician who specializes in evolutionary biology at France’s national research agency, CNRS.

Prior to the release of the full analysis late Monday, information on the findings was only made public through media reports and statements from the World Health Organization, which was briefed on the analysis last week. But, the raw metagenomic data behind the analysis is still not publicly available. It was briefly posted on a public genetic database called the Global Initiative on Sharing Avian Influenza Data (GISAID) as recently as earlier this month, and the international researchers were able to download it during that window of availability. But, administrators for the database quickly removed the data after its discovery, saying the removal was at the request of the submitter, a researcher at China CDC.

Dark data

Researchers at China CDC have since indicated to the international researchers and the WHO that they intend to share the data, which supports a scientific manuscript currently undergoing peer review at a scientific journal. But the international researchers note that there is no timeline for the release of the data or stated plans if their manuscript is not accepted for publication.

Throughout the pandemic, efforts to investigate SARS-CoV-2’s origins have been thwarted by stonewalling from China, which holds to an unsupported hypothesis that the virus originated outside its borders.

In introductory remarks to the newly released analysis, the researchers argue that, while they’re honoring GISAID’s terms of use, it is long past due for this data to be available to the public and scientific community. They called on both GISAID and colleagues in China to make it available.

“The GISAID terms of use do not preclude the public discussion of data as long as the data generators are acknowledged and best efforts have been made to collaborate with the contributors,” they wrote in defense of releasing their full analysis. “CCDC [China CDC] has thus far declined to collaborate on this. We respect our CCDC colleagues’ right to be first to publish a manuscript on their own data and do not plan to submit a paper that would compete with their manuscript currently undergoing review.” Still, they argued that by GISAID allowing China CDC to remove the genetic data from public view amid peer review, the database is essentially granting China CDC an embargo, which is a departure from GISAID’s stated mission to rapidly overcome such hurdles for sharing virological data.

“Samples from the Huanan Market were collected in January and February 2020 and, given their importance to understanding the origin of the pandemic, we feel this is an unreasonable amount of time to have passed,” the researchers wrote.

Data context

They also highlighted that the metagenomic data briefly posted on GISAID is not the full extent of genetic data China CDC has, which it has not shared with the international community. Metagenomic data from other market sampling remains to be seen publicly, they note.

The data the group has been able to get its hands on so far, however, paints a nearly complete picture of how the devastating pandemic began. The metagenomic data came from around 50 data files, which are listed in the analysis’ appendix B, but are currently not publicly available. The data is metagenomic sequences from some of the swabs and wastewater sampling that China CDC collected around the Huanan market after it was shut down on January 1, 2020. These swabs were previously reported; In February 2022, China CDC researchers released a preprint study on 1,380 environmental and animal samples taken from the market.

The preprint study was led by George Gao, then-director of China CDC. It indicated that environmental swabs were positive for SARS-CoV-2 and contained human genetic material but that the swabs of animals in the market—including mostly rabbits, stray cats, snakes, and hedgehogs—were all negative. Given those findings, Gao and colleagues concluded that humans—not animals—brought the virus into the large market, which then acted as an amplifier of infection due to the large number of people who visited the market daily. China previously suggested that the virus was introduced to the country on imported frozen foods sold at the market.

Still, that preprint data indicated that SARS-CoV-2-positive samples were predominantly in the southwestern zone of the market, where live mammals were sold. Other investigations have since found the same, including the Joint WHO-China study and an analysis published last July in Science by Worobey and colleagues. In Figure 4 of the Science article, Worobey and his co-authors showed that the southwest corner of the market had the highest density of SARS-CoV-2-positive environmental samples and was also where illegally sold wild mammals were held. That includes raccoon dogs, one of which was photographed in 2014 by one of the study authors, Edward Holmes, a biologist at the University of Sydney. The study also found that some of the earliest human cases of COVID-19 clustered in the western portion of the market, around where the live animals were housed.

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