Two preprint studies posted this past weekend (26 February) offer further evidence that the coronavirus originated in animals and spread to humans in late 2019 at the Huanan Seafood Market in Wuhan, China, reports Kaiser Health News.
One of the studies, neither of which has been peer-reviewed or published in a professional journal, used spatial analysis to show that the earliest known COVID-19 cases, diagnosed in December 2019, were centred on the market. The researchers also report that environmental samples that tested positive for the virus, SARS-CoV-2, were strongly associated with live-animal vendors, according to CNN.
The other study says the two major viral lineages were the result of at least two events in which the virus crossed species into humans. The first transmission probably happened in late November or early December 2019, the researchers say, and the other lineage was probably introduced within weeks of the first event.
Study 1 details
The Huanan market was the epicenter of SARS-CoV-2 emergence
Michael Worobey, Joshua Levy, Lorena Malpica Serrano, Alexander Crits-Christoph, Jonathan Pekar, Stephen Goldstein, Angela Rasmussen, Moritz Kraemer, Chris Newman; Marion Koopmans, Marc Suchard, Joel Wertheim, Philippe Lemey, David Robertson, Robert Garry, Edward Holmes, Andrew Rambaut, Kristian Andersen.
Pre-print on Zenodo on 26 February 2022
Abstract
Despite strong epidemiological links and the documented presence of SARS-CoV-2 susceptible animals, the role of the Huanan Seafood Wholesale Market in the COVID-19 pandemic remains controversial. Using spatial analyses we show that the earliest known COVID-19 cases diagnosed in December 2019 were geographically distributed near to, and centered on, this market. This distribution cannot be explained by high densities of elderly people at greater risk of symptomatic COVID-19. This pattern was stronger in cases without, rather than with, identified epidemiological links to the Huanan market, consistent with SARS-CoV-2 community transmission starting in the surrounding area. By combining spatial and genomic data, we show that both the two early lineages of SARS-CoV-2 have a clear association with the Huanan market.
We also report that live mammals, including raccoon dogs, were sold at the market in late 2019 and geospatial analyses within the market show that SARS-CoV-2-positive environmental samples were strongly associated with vendors selling live animals. Together, these analyses provide dispositive evidence for the emergence of SARS-CoV-2 via the live wildlife trade and identify the Huanan market as the unambiguous epicenter of the COVID-19 pandemic.
One sentence summary: geographical clustering of the earliest known COVID-19 cases and the proximity of positive environmental samples to live-animal vendors suggest that the Huanan Seafood Wholesale Market in Wuhan was the site of origin of the COVID-19 pandemic
Study 2 details
SARS-CoV-2 emergence very likely resulted from at least two zoonotic events
Jonathan Pekar, Andrew Magee, Edyth Parker, Niema Moshiri, Katherine Izhikevich, Jennifer Havens, Karthik Gangavarapu, Lorena Malpica, Alexander Crits-Christoph, Nathaniel Matteson, Mark Zeller, Joshua Levy, Jade Wang, Scott Hughes, Jungmin Lee, Heedo Park, Man-Seong Park, Katherine Ching Zi Yan, Raymond Tzer Pin Lin, Mohd Noor Mat Isa, Yusuf Muhammad Noor, Tetyana Vasylyeva, Robert Garry, Edward Holmes, Andrew Rambaut, Marc Suchard, Kristian Andersen, Michael Worobey, Joel Wertheim.
Pre-print published on Zenodo on 26 February 2022
Abstract
Understanding the circumstances that lead to pandemics is critical to their prevention. Here, we analyse the pattern and origin of genomic diversity of SARS-CoV-2 early in the COVID-19 pandemic. We show that the SARS-CoV-2 genomic diversity prior to February 2020 comprised only two distinct viral lineages—denoted A and B—with no transitional haplotypes. Novel phylodynamic rooting methods, coupled with epidemic simulations, indicate that these two lineages were the result of at least two separate cross-species transmission events into humans.
The first zoonotic transmission likely involved lineage B viruses and occurred in late-November/early-December 2019 and no earlier than the beginning of November 2019, while the introduction of lineage A likely occurred within weeks of the first event. These findings define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported. Hence, as with SARS-CoV-1 in 2002 and 2003, SARS-CoV-2 emergence likely resulted from multiple zoonotic events.
Zenodo pre-print – The Huanan market was the epicenter of SARS-CoV-2 emergence (Open access)
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‘Strong evidence’ of COVID-19’s origin in Wuhan live-animal market
Wuhan scientists planned to release coronavirus into bat caves: Leaked papers
COVID-19 Wuhan lab escape theory gets a second look
WHO report on COVID-19's Wuhan origins 'raises more questions than answers'
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