{"id":2973,"date":"2023-03-22T06:49:31","date_gmt":"2023-03-22T11:49:31","guid":{"rendered":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/?p=2973"},"modified":"2023-03-22T06:56:47","modified_gmt":"2023-03-22T11:56:47","slug":"analysis-and-interpretation-of-metagenomic-data-from-the-huanan-market","status":"publish","type":"post","link":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/2023\/03\/22\/analysis-and-interpretation-of-metagenomic-data-from-the-huanan-market\/","title":{"rendered":"Analysis and interpretation of metagenomic data from the Huanan market."},"content":{"rendered":"
\n

Link to full text PDF<\/a><\/p>\n\n\n\n

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.<\/p>\n\n\n\n

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 Gao
et 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.<\/p>\n\n\n\n

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 other mammalian species that require consideration as possible intermediate hosts of
SARS-CoV-2. Although live mammals had previously been observed at Huanan market in
late 2019, their exact locations were not conclusively known, and some of the animal
species we identify in the report below were not included in the list of live or dead animals
tested at the Huanan market, as reported in the 2021 WHO-China joint report on the origin
of the COVID-19 pandemic. Our results show that they were present. In some cases, the
amount of animal genetic material was greater than the amount of human genetic material,
consistent with the presence of SARS-CoV-2 in these samples being due to animal
infections.<\/p>\n\n\n\n

We contacted an author of the Gao et al. preprint on 9 March 2023 to inquire about the
data, and were told that we could conduct an independent analysis. On 10 March we
advised the same author that we had discovered the presence of animal genetic material
in the samples. On 11 March 2023, we discovered that the data had been made
unavailable (at the request of the submitter according to a statement on GISAID). <\/p>\n\n\n\n

On the same day we contacted both the corresponding author of the preprint as well as the
author who had contributed the raw data to GISAID and asked if they would like to
collaborate with us on analyses of these data. On 13 March 2023, those of us who had
either downloaded the data, or associated metadata, or contacted the corresponding
author of the preprint, received emails from the GISAID Secretariat admonishing us to
comply with the GISAID terms of use or in some cases falsely accusing us of having
breached the GISAID terms of use. We are well aware of these terms of use, have not
breached them, and have no intention of breaching them.<\/p>\n\n\n\n

We informed WHO of our preliminary findings on 11 March 2023. On 12 March 2023,
some of us met with WHO and some members of SAGO (the WHO-convened Scientific
Advisory Group for the Origins of Novel pathogens) to discuss our observations. On
March 2023, the WHO convened a meeting with SAGO where some of us and
representatives from CCDC presented our respective results. <\/p>\n\n\n\n

We cannot comment on the CCDC team\u2019s findings, as those are theirs to share, but some findings from our analyses have already been shared in the media and in public statements by the WHO
This meeting constituted one of several efforts to establish a collaborative relationship with our
colleagues at CCDC to share data and findings as rapidly as possible.<\/p>\n\n\n\n

We acknowledge that these circumstances are unusual. We are proponents of open data
sharing, and ensuring that data from our analyses are broadly accessible in public
repositories is our standard practice. Although our colleagues at the CCDC have stated
their intention to share these raw sequence data to support the publication currently
undergoing review, they remain inaccessible through GISAID at the time of writing. There is <\/p>\n\n\n\n

no clear timeline for data availability, nor any indication of when data may become available
if the manuscript is not recommended for publication after peer review. We have also
encouraged our Chinese colleagues to seek to immediately share as a preprint their
manuscript. At the time of writing, we are not aware that that has happened.<\/p>\n\n\n\n

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. CCDC has thus far declined to collaborate on this. We respect our CCDC
colleagues\u2019 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. We
note, however, that by providing a data generator with the ability to embargo data (for
nearly 8 months \u2013 the CCDC\u2019s data is recorded as having been uploaded on 2 June
2022), GISAID has deviated from its stated mission to overcome \u201cdisincentive hurdles and
restrictions, which discourage or prevented sharing of virological data prior to formal
publication\u201d. 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.<\/p>\n<\/div><\/div>","protected":false},"excerpt":{"rendered":"

Link to full text PDF In an attempt to ensure transparency and engagement towards global partnership, wewould like to provide further context regarding the timeline of work and efforts tocollaborate on the research presented in the report below. On 4 March 2023 (dates in UTC), we discovered accessions posted publicly on the GISAIDdatabase corresponding to […]<\/p>\n","protected":false},"author":11,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"Analysis and interpretation of metagenomic data from the #Huananseafood market #wuhan #china #covid #raccoondog @gisaid","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[1],"tags":[],"class_list":["post-2973","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/posts\/2973","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/users\/11"}],"replies":[{"embeddable":true,"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/comments?post=2973"}],"version-history":[{"count":3,"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/posts\/2973\/revisions"}],"predecessor-version":[{"id":2977,"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/posts\/2973\/revisions\/2977"}],"wp:attachment":[{"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/media?parent=2973"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/categories?post=2973"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.unmc.edu\/healthsecurity\/transmission\/wp-json\/wp\/v2\/tags?post=2973"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}