In a pair of related studies, published July 26, 2022 online via First Release in Science, researchers at University of California San Diego, with colleagues on four continents, show that the origin of the COVID-19 pandemic in 2019 was at the Huanan Seafood Wholesale Market in Wuhan, China, and resulted from at least two instances of the SARS-CoV-2 virus jumping from live animal hosts to humans working or shopping there.
The findings, first reported in February after the papers were posted online as preprints awaiting peer review, garnered international attention, primarily focusing on identifying the market as the early epicenter of the COVID-19 pandemic. The World Health Organization estimates that there have been more than 566 million confirmed cases of COVID-19 worldwide and 6.3 million deaths since the pandemic was declared in early 2020.
“It’s vital that we know as much about the origin of COVID-19 as possible because only by understanding how pandemics get started can we hope to prevent them in the future,” said Joel O. Wertheim, PhD, associate professor in the Division of Infectious Diseases and Global Public Health at UC San Diego School of Medicine, and a co-author on both papers.
But elemental to understanding pandemic origins is pinpointing not just where, but how, a pathogen successfully jumps from a non-human animal host to human, known as a zoonotic event.
“I think there’s been consensus that this virus did in fact come from the Huanan Market, but a strong case for multiple introductions hasn’t been made by anyone else yet,” said Wertheim, senior author of the study that posits the SARS-CoV-2 virus, which causes COVID-19, jumped from animals to humans at least twice and perhaps as many as two dozen times.
According to researchers, two evolutionary branches of the virus were present early in the pandemic, differentiated only by two differences in nucleotides — the basic building blocks of DNA and RNA.
Lineage B, which included samples from people who worked at and visited the market, became globally dominant. Lineage A spread within China, and included samples from people pinpointed only to the vicinity the market. If the viruses in lineage A evolved from those in lineage B, or vice versa, Wertheim said this would suggest SARS-CoV-2 jumped only once from animals to humans.
But work by Wertheim and collaborators found that the earliest SARS-CoV-2 genomes were inconsistent with a single zoonotic jump into humans. Rather, the first zoonotic transmission likely occurred with lineage B viruses in late-November 2019 while the introduction of lineage A into humans likely occurred within weeks of the first event. Both strains were present at the market simultaneously.
Researchers arrived at this conclusion by deciphering the evolutionary rate of viral genomes to deduce whether or not the two lineages diverged from a single common ancestor in humans. They used a technique called molecular clock analysis and an epidemic simulation tool called FAVITES, invented by Wertheim team member Niema Moshiri, PhD, an assistant professor of computer science at Jacobs School of Engineering at UC San Diego and study co-author.
“None of this could have been done without FAVITES,” said Wertheim.
Validation
In February 2022, researchers at the Chinese Center for Disease Control and Prevention published a long-delayed analysis of genetic traces of the earliest environmental samples collected at the market two years earlier.
The samples were obtained after the first reports of a new, mysterious illness and after the market had already been shut down. The Huanan Seafood Wholesale Market in Wuhan is a so-called “wet market” where live animals are often slaughtered and sold for human consumption, including in some cases, wildlife.
However, no live wild mammals were left at the market after it was shut down. Instead, Chinese researchers swabbed walls, floors and other surfaces, tested meat still in freezers, sampled sewers and caught mice and stray cats and dogs around the market.
Their findings confirmed the not-yet-published predictions of Wertheim’s team that Lineage A was also at the market.
“We felt validated, but what we felt more was immense pressure because they beat our preprint to the punch by about 12 hours, and we could only discuss their findings in light of ours,” Wertheim said. “We were also shocked that they had been sitting on evidence for lineage A at the market for over a year without realizing its importance.”
The newly published data, said study authors, are powerful evidence that the two viral lineages evolved separately and that multiple spillover events occurred. The Wuhan market reportedly contained a robust live wild animal business, with snakes, badgers, muskrats, birds and raccoon dogs (a canid indigenous to Asia) and other species sold for food. Wertheim said he believes there were likely many viral introductions. At least two successfully made the animal-human leap; other viral strains went extinct.
“While I'm hesitant to call it proof, what we presented is the most comprehensive explanation for the SARS-CoV-2 genomic diversity at the outset of the pandemic,” Wertheim said. “There are really no other good explanations for both of these strains being at the market except for multiple jumps into humans.”
(The findings undercut a circulating and persistent theory that the SARS-CoV-2 virus escaped from the Wuhan Institute of Virology, located a few miles from the market.)
Jonathan E. Pekar, a doctoral student in Bioinformatics and Systems Biology who co-led the project with Wertheim and is lead author, said the pandemic was likely looming for years, awaiting only for the opportunity when humans would come into contact with an animal host capable of transmitting the virus.
“Everything complicated happened before that introduction,” Pekar said. “The last step is just extended contact and transmission from hosts to humans. At that point, it would actually be unusual to only have one introduction. We've seen this before with MERS-CoV (a similar zoonotic virus). We’ve seen it with humans giving SARS-CoV-2 to minks on farms and then minks giving it back to humans.
“This has happened before, and it's going to keep happening. Nature is a better lab than humans will ever be.”
The latest study continues a series of published papers by Wertheim and colleagues investigating and chronicling the origin and spread of COVID-19.
In September 2020, they published data explaining how the first, few cases of novel coronavirus in North America and Europe quickly spread due to insufficient testing and contact tracing. In March 2021, Wertheim, Pekar and colleagues characterized the brief time-period during which SARS-CoV-2 could have circulated undetected before the first human cases in Wuhan.
Co-authors of “The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2” include: Andrew Magee, Karthik Gangavarapu and Marc A. Suchard, all at UCLA; Edyth Parker, Nathaniel L. Matteson, Mark Zeller, Joshua I. Levy and Kristian G. Andersen, all at The Scripps Research Institute; Katherine Izhikevich, Jennifer L. Havens and Tetyana I.Vasylyeva, all at UC San Diego; Lorena Mariana Malpica Serrano and Michael Worobey, both at University of Arizona; Alexander Crits-Christoph, Johns Hopkins Bloomberg School of Public Health; Jade C. Wang and Scott Hughes, both at New York City Department of Health; Jungmin Lee, Heedo Park, Man-Seong Park, Korea University; Katherine Ching Zi Yan and Raymond Tzer Pin Lin, all at National Centre for Infectious Diseases, Singapore; Mohd Noor Mat Isa and Yusuf Muhammad Noor, both at Malaysia Genome and Vaccine Institute; Robert F. Garry, Tulane University; Edward C. Holmes, University of Sydney, Australia; and Andrew Rambaut, University of Edinburgh.
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ARTICLE PUBLICATION DATE
26-Jul-2022
An international team of 18 researchers, including a scientist at University of Utah Health, have determined that the earliest cases of COVID-19 in humans arose at a wholesale fish market in Wuhan China in December, 2019. They linked these cases to bats, foxes and other live mammals infected with the virus sold in the market either for consumption as meat or for their fur.
The finding, published in the July 26, 2022, issue of Science, confirms early reports, later dismissed by senior Chinese officials, that live animals sold at the Huanan Seafood Wholesale Market were the likely source of the pandemic that has claimed at least 6.4 million lives since it first emerged in China nearly three years ago.
“These are the most compelling and most detailed studies of what happened in Wuhan in the earliest stages of what would become the COVID-19 pandemic,” says Stephen Goidstein. Ph.D., a co-author of the study led by senior author Kristian Anderson, Ph.D., from the Scripps Research Institute in La Jolla and first author Michael Worobey, Ph.D., from the University of Arizona. Goldstein is a post-doctoral researcher in the department of Human Genetics at U of U Health. “We have convincingly shown that the wild animal sales at the Huanan Market in Wuhan are implicated in the first human cases of the disease.”
Among the study’s key findings:
- The emergence of the SARS-CoV-2, the virus that causes COVID-19, can likely be traced to one or more of the 10 to 15 stalls in the market that sold live dogs, rats, porcupines, badgers, hares, foxes, hedgehogs, marmots, and Chinese Muntjac (a small deer). Health officials and researchers detected SARS-CoV-2 on animal cages, carts, and drainage grates in these venues.
- The only areas where the virus was spreading in December, 2019, was in neighborhoods within a half-mile of the market. Previously, some researchers had suggested that the virus was brought into the market from elsewhere in the city and spread among its patrons. Instead, the new findings strongly suggest that the virus originated in the market via live animal sales, and slowly spread from there into nearby neighborhoods and then the city at large.
- Two variants of the SARS-CoV-2 virus were detected at the market. That suggests both variants originated independently at the market and helps confirm the researchers’ hypothesis that early spread of the infection began there. If the virus originated elsewhere, it’s more likely that only a single variant would have been found.
Moving forward, the researchers say public officials should seek better understanding of the wildlife trade in China and elsewhere and promote more comprehensive testing of live animals sold in markets to lower the risk of future pandemics.
####
The research published as “The Huanan Seafood Wholesale Market in Wuhan Was the Early Epicenter of the COVID-19 Pandemic” in Science on July 26, 2022.
METHOD OF RESEARCH
Observational study
SUBJECT OF RESEARCH
Not applicable
ARTICLE TITLE
The Huanan Seafood Wholesale Market in Wuhan Was the Early Epicenter of the COVID-19 Pandemic
ARTICLE PUBLICATION DATE
26-Jul-2022
An international team of researchers has confirmed that live animals sold at the Huanan Seafood Wholesale Market were the likely source of the COVID-19 pandemic that has claimed 6.4 million lives since it began nearly three years ago.
Led by University of Arizona virus evolution expert Michael Worobey, international teams of researchers have traced the start of the pandemic to the market in Wuhan, China, where foxes, raccoon dogs and other live mammals susceptible to the virus were sold live immediately before the pandemic began. Their findings were published Tuesday in two papers in the journal Science, after being previously released in pre-print versions in February.
The publications, which have since gone through peer review and include additional analyses and conclusions, virtually eliminate alternative scenarios that have been suggested as origins of the pandemic. Moreover, the authors conclude that the first spread to humans from animals likely occurred in two separate transmission events in the Huanan market in late November 2019.
One study scrutinized the locations of the first known COVID-19 cases, as well as swab samples taken from surfaces at various locations at the market. The other focused on genomic sequences of SARS-CoV-2 from samples collected from COVID-19 patients during the first weeks of the pandemic in China.
The first paper, led by Worobey and Kristian Andersen at Scripps Research Institute in San Diego, California, examined the geographic pattern of COVID-19 cases in the first month of the outbreak, December 2019. The team was able to determine the locations of almost all of the 174 COVID-19 cases identified by the World Health Organization that month, 155 of which were in Wuhan.
Analyses showed that these cases were clustered tightly around the Huanan market, whereas later cases were dispersed widely throughout Wuhan – a city of 11 million people. Notably, the researchers found that a striking percentage of early COVID patients with no known connection to the market – meaning they neither worked there nor shopped there – turned out to live near the market. This supports the idea that the market was the epicenter of the epidemic, Worobey said, with vendors getting infected first and setting off a chain of infections among community members in the surrounding area.
"In a city covering more than 3,000 square miles, the area with the highest probability of containing the home of someone who had one of the earliest COVID-19 cases in the world was an area of a few city blocks, with the Huanan market smack dab inside it," said Worobey, who heads UArizona Department of Ecology and Evolutionary Biology.
This conclusion was supported by another finding: When the authors looked at the geographical distribution of later COVID cases, from January and February 2020, they found a "polar opposite" pattern, Worobey said. While the cases from December 2019 mapped "like a bullseye" on the market, the later cases coincided with areas of the highest population density in Wuhan.
"This tells us the virus was not circulating cryptically," Worobey said. "It really originated at that market and spread out from there."
In an important addition to their earlier findings, Worobey and his collaborators addressed the question of whether health authorities found cases around the market simply because that's where they looked.
"It is important to realize that all these cases were people who were identified because they were hospitalized," Worobey said. "None were mild cases that might have been identified by knocking on doors of people who lived near the market and asking if they felt ill. In other words, these patients were recorded because they were in the hospital, not because of where they lived."
To rule out any potentially lingering possibility of bias, Worobey's team took one further step: Starting at the market, they began removing cases from their analyses, going farther in distance from the market as they went, and ran the stats again. The result: Even when two-thirds of cases were removed, the findings were the same.
"Even in that scenario, with the majority of cases, removed, we found that the remaining ones lived closer to the market than what would be expected if there was no geographical correlation between these earliest COVID cases and the market," Worobey said.
The study also looked at swab samples taken from market surfaces like floors and cages after Huanan market was shuttered. Samples that tested positive for SARS-CoV-2 were significantly associated with stalls selling live wildlife.
The researchers determined that mammals now known to be susceptible to SARS-CoV-2, including red foxes, hog badgers and raccoon dogs, were sold live at the Huanan market in the weeks preceding the first recorded COVID-19 cases. The scientists developed a detailed map of the market and showed that SARS-CoV-2-positive samples reported by Chinese researchers in early 2020 showed a clear association with the western portion of the market, where live or freshly butchered animals were sold in late 2019.
"Upstream events are still obscure, but our analyses of available evidence clearly suggest that the pandemic arose from initial human infections from animals for sale at the Huanan Seafood Wholesale Market in late November 2019," said Andersen, who was a co-senior author of both studies and is a professor in the Department of Immunology and Microbiology at Scripps Research.
Virus likely jumped from animals to humans more than once
The second study, an analysis of SARS-CoV-2 genomic data from early cases, was co-led by Jonathan Pekar and Joel Wertheim at the University of California, San Diego and Marc Suchard of the University of California Los Angeles, as well as Andersen and Worobey.
The researchers combined epidemic modeling with analyses of the virus's early evolution based on the earliest sampled genomes. They determined that the pandemic, which initially involved two subtly distinct lineages of SARS-CoV-2, likely arose from at least two separate infections of humans from animals at the Huanan market in November 2019 and perhaps in December 2019. The analyses also suggested that, in this period, there were many other animal-to-human transmissions of the virus at the market that failed to manifest in recorded COVID-19 cases.
The authors used a technique known as molecular clock analysis, which relies on the natural pace with which genetic mutations occur over time, to establish a framework for the evolution of the SARS-CoV-2 virus lineages. They found that a scenario of a singular introduction of the virus into humans rather than multiple introductions would be inconsistent with molecular clock data. Earlier studies had suggested that one lineage of the virus – named A and closely related to viral relatives in bats – gave rise to a second lineage, named B. More likely, according to the new data, is a scenario in which the two lineages jumped from animals into humans on separate occasions, both at the Huanan market, Worobey said.
"Otherwise, lineage A would have had to have been evolving in slow motion compared to the lineage B virus, which just doesn't make biological sense," said Worobey.
The two studies provide evidence that COVID-19 originated via jumps from animals to humans at the Huanan market, likely following transmission to those animals from coronavirus-carrying bats in the wild or on farms in China. Moving forward, the researchers say scientists and public officials should seek better understanding of the wildlife trade in China and elsewhere and promote more comprehensive testing of live animals sold in markets to lower the risk of future pandemics.
Funding for the research was provided by the National Institutes of Health and the National Science Foundation.
METHOD OF RESEARCH
Data/statistical analysis
SUBJECT OF RESEARCH
People
ARTICLE TITLE
The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic
ARTICLE PUBLICATION DATE
26-Jul-2022
Two studies published in Science by Michael Worobey et al. and Jonathan Pekar et al. use complementary approaches – involving spatial and environmental analyses, as well as molecular analyses – to provide evidence that the Huanan market in Wuhan, China, was the early epicenter for the COVID-19 pandemic. The scientists concluded that SARS-CoV-2 was very likely present in live mammals sold at this market in late 2019 and suggest the virus spilled over into people working or shopping there from two separate zoonotic transmissions, in which lineage A and B progenitor viruses were both circulating in non-human mammals prior to their introduction into humans. Future work, say the authors of both studies, should be focused on better understanding events upstream of the introduction of SARS-CoV-2 to the market, including where the wild mammals for sale at Huanan came from, to lower the risk of future pandemics.
Despite the observation that the preponderance of earliest known COVID-19 cases – flagged by hospitals in Wuhan in December 2019 – were linked to the Huanan market, this did not establish activities at the Huanan market as the trigger for the pandemic. But, as Worobey and colleagues note, determining the epicenter of the COVID-19 pandemic at the neighborhood- rather than city-level could help resolve if SARS-CoV-2 had a zoonotic origin. To test the hypothesis of the market as the pandemic’s epicenter, Worobey et al. obtained data from a range of sources. First, they used mapping tools to estimate the longitude and latitude locations of more than 150 of the earliest reported virus cases from December 2019, including those without reported direct links to the market. The highest density of these cases centered around the Huanan market, they say. By mapping cases from January and February of 2020 using data from Weibo, a social media app that created a channel for people with Covid to seek medical help, the researchers identified cases in other parts of central Wuhan radiating from the market as the pandemic progressed. Using social media "check-in" data, the researchers performed analyses to rule out the many other locations in Wuhan, a city of 11 million, that would have been equally or more likely than the market to sustain the first cluster of a new respiratory pathogen. In further analyses, they report that multiple plausible intermediate wildlife hosts of SARS-CoV-2 progenitor viruses were sold live at the Huanan market until at least November of 2019. Using and extending a data set on samples from surfaces in the Huanan market, they identified five stalls that were likely selling live or freshly butchered mammals; the proximity to such live mammal vendors was predictive of human virus cases, their analyses show.
To further understand the circumstances that led to the pandemic's origin, Pekar and colleagues analyzed the genomic diversity of SARS-CoV-2 early in the pandemic. While the diversity of SARS-CoV-2 increased as the pandemic spread from China to other countries, two lineages of SARS-CoV-2 – designated A and B – marked the beginning of the COVID-19 pandemic in Wuhan. Only lineage B was represented in the eleven sequenced genomes from humans directly associated with the Huanan market. The earliest lineage A genomes from humans lacked any known contact to the market but were sampled from humans who lived or stayed close by. It has been hypothesized that the two lineages emerged separately. To test this hypothesis, Pekar and colleagues analyzed genomic and epidemiological data from early in the COVID-19 pandemic with models and simulations. Through their analyses, they provide support for two separate introductions of lineages A and B into humans, both circulating in non-human mammals prior, with lineage B first appearing in humans no earlier than late October 2019 and likely in mid-November 2019 and lineage A being introduced within days to weeks of this event. Their simulations do not support a single introduction of the virus giving rise to the observed patterns of virus lineage spread. Further, the results from the study of Worobey et al., they say, are consistent with the idea of a separate and subsequent origin of lineage A at the Huanan market in late-November 2019. These findings, say the authors, indicate that it is unlikely that SARS-CoV-2 circulated widely in humans prior to November 2019 and define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported. The authors report several limitations to their studies, in both cases.
***AAAS/Science will host a Zoom Webinar briefing on these papers TODAY, 26 June 2022, at 2:00 p.m. U.S. ET. Reporters interested in joining should please pre-register here as soon as possible. The briefing speakers are listed below - they will have limited availability and encourage reporters to reach them during the briefing, rather than via email.
• Joel O. Wertheim
• Jonathan E. Pekar
• Michael Worobey
• Kristian G. Andersen
ARTICLE TITLE
The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic
ARTICLE PUBLICATION DATE
26-Jul-2022
Pair of studies illuminates COVID-19 pandemic origins
Analyses based on locations and viral sequencing of early cases suggest pandemic started in Wuhan’s Huanan market, with two separate jumps from animals to humans
Peer-Reviewed PublicationSCRIPPS RESEARCH INSTITUTE
LA JOLLA, CA—The COVID-19-causing coronavirus, SARS-CoV-2, likely first spread to humans from animals in two separate transmission events in a Wuhan market in late November 2019, according to a pair of analyses by international teams co-led by Scripps Research scientists.
The analyses, published July 26, 2022 in Science and released in earlier, pre-print versions in February, were based mainly on the locations of cases and environmental samples, as well as genomic sequences of SARS-CoV-2 isolates, from the first weeks of the pandemic in China.
“Upstream events are still obscure, but our analyses of available evidence clearly suggest that the pandemic arose from initial human infections from animals for sale at the Huanan Seafood Wholesale Market in late November 2019,” says Kristian Andersen, PhD, who was a co-senior author of both studies and is a professor in the Department of Immunology and Microbiology at Scripps Research.
In the first analysis, co-senior authored by Michael Worobey, DPhil, of the University of Arizona, the researchers examined the geographic pattern of COVID-19 cases in the first month of the outbreak, December 2019.
"In a city covering more than 3,000 square miles, the area with the highest probability of containing the home of someone who had one of the earliest COVID-19 cases in the world was an area of a few city blocks, with the Huanan market smack dab inside it," says Worobey.
They were able to determine the locations of 155 of the 174 COVID-19 cases identified by the World Health Organization for that month. Their statistical analysis showed that these cases clustered tightly around the Huanan Market, whereas later cases were dispersed widely throughout Wuhan—a sprawling megacity of 11 million people. One striking finding was that early COVID-19 patients with no history of having recently visited the market resided significantly closer to it, on average, than patients who had visited the market, showing the close association between early cases and the market.
The researchers also determined that mammals now known to be infectable by SARS-CoV-2, including red foxes, hog badgers and raccoon dogs, were sold live at the Huanan market in the weeks preceding the first recorded COVID-19 cases. The scientists developed a detailed map of the market, and showed that SARS-CoV-2-positive samples reported by Chinese researchers in early 2020 showed a clear association with the western portion of the market, where live or freshly butchered animals were sold in late 2019.
“There has been broad agreement that the Huanan market was a place where early spread of the virus was amplified, but what our data show is that the market was also the early epicenter and very likely the place of emergence,” says co-author Joshua Levy, PhD, a postdoctoral researcher in the Andersen lab.
The second study, an analysis of SARS-CoV-2 genomic data from early cases, was co-led by Andersen and Worobey, along with Jonathan Pekar and Joel Wertheim, PhD, of UC San Diego, and Marc Suchard, MD, PhD, of UCLA.
Here the researchers combined epidemic modeling with analyses of the virus’s early evolution based on the earliest sampled genomes. They determined that the pandemic, which initially involved two subtly distinct lineages of SARS-CoV-2, likely arose from at least two separate infections of humans from animals at the Huanan market in late November 2019. The analyses also suggested that, in this period, there were many other animal-to-human transmissions at the market that nevertheless failed to manifest in recorded COVID-19 cases.
According to the authors, the two studies collectively show that SARS-CoV-2, like SARS-CoV-1 before it, originated via jumps from animals to humans—in this case from animals being sold at a specific market in Wuhan, likely following transmission to those animals from coronavirus-carrying bats in the wild or on farms in China.
“To more fully understand the origin of SARS-CoV-2, we need to more fully understand events upstream of the Huanan market, which will require close international collaboration and cooperation,” Andersen says.
Funding for the research was provided principally by the National Institutes of Health and the National Science Foundation.
About Scripps Research
Scripps Research is an independent, nonprofit biomedical institute ranked the most influential in the world for its impact on innovation by Nature Index. We are advancing human health through profound discoveries that address pressing medical concerns around the globe. Our drug discovery and development division, Calibr, works hand-in-hand with scientists across disciplines to bring new medicines to patients as quickly and efficiently as possible, while teams at Scripps Research Translational Institute harness genomics, digital medicine and cutting-edge informatics to understand individual health and render more effective healthcare. Scripps Research also trains the next generation of leading scientists at our Skaggs Graduate School, consistently named among the top 10 US programs for chemistry and biological sciences. Learn more at www.scripps.edu.
ARTICLE PUBLICATION DATE
26-Jul-2022
