FROM THE MARKET NOT THE LAB
Genetic evidence from a new report suggests the coronavirus pandemic most likely spilled over from animals in the Wuhan market.
By Joel Achenbach
September 19, 2024
An international team of scientists published a peer-reviewed paper Thursday saying genetic evidence indicates the coronavirus pandemic most likely originated with a natural spillover from an animal or animals sold in a market in Wuhan, China, where many of the first human cases of covid-19 were identified.
The paper, which appears in the journal Cell, does not claim to prove conclusively that the pandemic began in the Huanan Seafood Wholesale Market, and it is unlikely to end the acrimonious and politicized debate over the coronavirus’s origin.
For more than four years, researchers, intelligence agencies, journalists and amateur sleuths have tussled over the two main scenarios for the pandemic’s origin: a natural spillover from animals or some kind of leak from a laboratory experimenting on coronaviruses.
The new report bolsters the natural spillover theory, but it does not rule out other origins. A key limitation of the research is that the genetic data, obtained by Chinese investigators in the early days of the pandemic after the market was closed, cannot reveal whether any animal was actually infected with the virus.
“The results we see are consistent with infected animals, but we cannot prove that they were,” said Florence Débarre, an evolutionary biologist at the French National Center for Scientific Research and a co-author of the new paper.
Much of the report is familiar territory. Many of the 23 authors of the paper are known to have long supported a market origin for the virus. In an informal report in March 2023, they presented a central feature of the genetic data — the confirmation that animals potentially capable of triggering a pandemic were in the market.
That early report, which was not peer-reviewed or published in a journal, had a scientifically awkward provenance. It was written over the course of about 10 days, Débarre said, after she noticed that Chinese researchers had posted some of their genetic data from the market on GISAID, a public database regularly scanned by pandemic researchers.
The Chinese researchers had submitted a report to the journal Nature, and, after peer review, it was published in April 2023. The Nature paper from the Chinese scientists describes the genetic data as inconclusive about the origin of the pandemic, including that there is no proof any animals were infected with the virus.
“Furthermore, even if the animals were infected, our study does not rule out human-to-animal transmission, as the sampling was carried out after the human infection within the market,” the Nature paper states. “Thus, the possibility of potential introduction of the virus to the market through infected humans, or cold-chain products, cannot yet be ruled out.”
The new paper in Cell is longer, more comprehensive, probes a broader range of questions, and includes more data from the market and early-patient cases than the international team’s informal 2023 report, Débarre said.
Both the earlier and the new reports document that traces of the virus were found clustered in a section of the Huanan Seafood Wholesale Market where genetic traces of animals were also found. Several of those species — raccoon dogs, rabbits and dogs — are known to be susceptible to infection with SARS-CoV-2, the virus that causes covid. Raccoon dogs have also been shown experimentally to be capable of transmitting the virus.
A significant element of the new paper is an analysis of when the pandemic began. Scientists can study mutations of the coronavirus, which evolves at a relatively steady rate, to estimate when the millions of genomes deposited in databases had the most recent common ancestor. That genetic evidence points to mid-November 2019 as the most likely time the virus spilled into humans and began spreading, and there could have been two or more spillover events, the researchers said.
“The timing of the origin of the market outbreak is genetically indistinguishable from the timing of the origin of the pandemic as a whole,” the report states.
There are many independent lines of evidence pointing to the market as the epicenter of the pandemic, said Kristian Andersen, an infectious-disease researcher at Scripps Research in La Jolla, Calif., and a co-author of the report in Cell. No previous virus spillover has been so well-documented, he said.
“Of any previous outbreak, pandemic, you name it, we don’t have this level of granularity,” he said. “We can narrow it down to a single market, and narrow it down to a section in that market, and maybe even narrow it down to a single stall in that market. That is mind-boggling.”
Early in the outbreak, as word spread of an unusual respiratory illness in Wuhan, officials closed the Huanan market. It was cleaned and all animals were removed.
Finding the specific animals that could have caused a spillover of the virus may be impossible, said Michael Worobey, a University of Arizona evolutionary biologist and co-author of the report.
“Immediately, you have a needle-in-a-haystack situation, but then you incinerate all the haystacks and burn up all the needles,” Worobey said.
The genetic evidence, the new report contends, supports the hypothesis that SARS-CoV-2 emerged in the same way that SARS-CoV-1 — which sickened people in 2002-2003 but was extinguished before it could cause a full-blown pandemic — is widely believed to have started, from animals sold in a market. The authors contend the world needs to take more aggressive action to shut down the illegal trade in wildlife to lower the risk of another catastrophic pandemic.
“All the data [on the origin of the pandemic] currently available point in the same direction, which is the wildlife trade in the Huanan market. Will it put the debate to an end? I’m afraid it’s unlikely,” Débarre said.
The natural spillover hypothesis has been challenged by proponents of the “lab leak theory,” an umbrella term for a suite of scenarios, many of them involving the Wuhan Institute of Virology. The sprawling institute conducted extensive research on coronaviruses, including SARS-CoV-1. Proponents of the lab leak theory argue the institute conducted research with lax biosafety protocols.
The debate over covid’s origins continues to be contentious and politicized. It is also entangled with geopolitical tensions and with a broader debate about biosafety practices and the regulatory oversight of laboratory experiments that seek to assess and understand the threat pathogens could pose.
The lab leak theory emerged early in 2020 and was embraced by President Donald Trump. It gained momentum in May 2021 when 18 scientists, including Worobey, wrote a letter to the journal Science saying all possible origins of the pandemic, including a lab leak, deserve investigation. President Joe Biden then asked his intelligence agencies to investigate.
They were unable to reach a consensus. Most favored a natural origin, but two agencies favored a lab origin. None claimed high confidence in their conclusions.
A report from Senate Republicans in 2022 said a “research-related accident” was the “most likely” origin of the pandemic, although it did not rule out a natural origin. “Critical corroborating evidence of a natural zoonotic spillover is missing,” the report said.
There is no evidence that the virus, or its progenitor, was inside a laboratory before the outbreak. Chinese officials have denied the virus came from a lab. But the Chinese government has limited outside investigations, and the lack of transparency has been an obstacle in the search to understand the origin of the virus.
Chinese officials have also dismissed the market origin, instead floating conjectures, generally dismissed by the global scientific community, that the virus came from outside China, possibly via packages of frozen seafood or from a military research facility in Maryland.
“To the question — Did it come from a lab or come from a market? — I think we already knew the answer to that,” Andersen said. “Yep, it’s the market. It’s natural, as we’ve previously seen happen.”
September 19, 2024
An international team of scientists published a peer-reviewed paper Thursday saying genetic evidence indicates the coronavirus pandemic most likely originated with a natural spillover from an animal or animals sold in a market in Wuhan, China, where many of the first human cases of covid-19 were identified.
The paper, which appears in the journal Cell, does not claim to prove conclusively that the pandemic began in the Huanan Seafood Wholesale Market, and it is unlikely to end the acrimonious and politicized debate over the coronavirus’s origin.
For more than four years, researchers, intelligence agencies, journalists and amateur sleuths have tussled over the two main scenarios for the pandemic’s origin: a natural spillover from animals or some kind of leak from a laboratory experimenting on coronaviruses.
The new report bolsters the natural spillover theory, but it does not rule out other origins. A key limitation of the research is that the genetic data, obtained by Chinese investigators in the early days of the pandemic after the market was closed, cannot reveal whether any animal was actually infected with the virus.
“The results we see are consistent with infected animals, but we cannot prove that they were,” said Florence Débarre, an evolutionary biologist at the French National Center for Scientific Research and a co-author of the new paper.
Much of the report is familiar territory. Many of the 23 authors of the paper are known to have long supported a market origin for the virus. In an informal report in March 2023, they presented a central feature of the genetic data — the confirmation that animals potentially capable of triggering a pandemic were in the market.
That early report, which was not peer-reviewed or published in a journal, had a scientifically awkward provenance. It was written over the course of about 10 days, Débarre said, after she noticed that Chinese researchers had posted some of their genetic data from the market on GISAID, a public database regularly scanned by pandemic researchers.
The Chinese researchers had submitted a report to the journal Nature, and, after peer review, it was published in April 2023. The Nature paper from the Chinese scientists describes the genetic data as inconclusive about the origin of the pandemic, including that there is no proof any animals were infected with the virus.
“Furthermore, even if the animals were infected, our study does not rule out human-to-animal transmission, as the sampling was carried out after the human infection within the market,” the Nature paper states. “Thus, the possibility of potential introduction of the virus to the market through infected humans, or cold-chain products, cannot yet be ruled out.”
The new paper in Cell is longer, more comprehensive, probes a broader range of questions, and includes more data from the market and early-patient cases than the international team’s informal 2023 report, Débarre said.
Both the earlier and the new reports document that traces of the virus were found clustered in a section of the Huanan Seafood Wholesale Market where genetic traces of animals were also found. Several of those species — raccoon dogs, rabbits and dogs — are known to be susceptible to infection with SARS-CoV-2, the virus that causes covid. Raccoon dogs have also been shown experimentally to be capable of transmitting the virus.
A significant element of the new paper is an analysis of when the pandemic began. Scientists can study mutations of the coronavirus, which evolves at a relatively steady rate, to estimate when the millions of genomes deposited in databases had the most recent common ancestor. That genetic evidence points to mid-November 2019 as the most likely time the virus spilled into humans and began spreading, and there could have been two or more spillover events, the researchers said.
“The timing of the origin of the market outbreak is genetically indistinguishable from the timing of the origin of the pandemic as a whole,” the report states.
There are many independent lines of evidence pointing to the market as the epicenter of the pandemic, said Kristian Andersen, an infectious-disease researcher at Scripps Research in La Jolla, Calif., and a co-author of the report in Cell. No previous virus spillover has been so well-documented, he said.
“Of any previous outbreak, pandemic, you name it, we don’t have this level of granularity,” he said. “We can narrow it down to a single market, and narrow it down to a section in that market, and maybe even narrow it down to a single stall in that market. That is mind-boggling.”
Early in the outbreak, as word spread of an unusual respiratory illness in Wuhan, officials closed the Huanan market. It was cleaned and all animals were removed.
Finding the specific animals that could have caused a spillover of the virus may be impossible, said Michael Worobey, a University of Arizona evolutionary biologist and co-author of the report.
“Immediately, you have a needle-in-a-haystack situation, but then you incinerate all the haystacks and burn up all the needles,” Worobey said.
The genetic evidence, the new report contends, supports the hypothesis that SARS-CoV-2 emerged in the same way that SARS-CoV-1 — which sickened people in 2002-2003 but was extinguished before it could cause a full-blown pandemic — is widely believed to have started, from animals sold in a market. The authors contend the world needs to take more aggressive action to shut down the illegal trade in wildlife to lower the risk of another catastrophic pandemic.
“All the data [on the origin of the pandemic] currently available point in the same direction, which is the wildlife trade in the Huanan market. Will it put the debate to an end? I’m afraid it’s unlikely,” Débarre said.
The natural spillover hypothesis has been challenged by proponents of the “lab leak theory,” an umbrella term for a suite of scenarios, many of them involving the Wuhan Institute of Virology. The sprawling institute conducted extensive research on coronaviruses, including SARS-CoV-1. Proponents of the lab leak theory argue the institute conducted research with lax biosafety protocols.
The debate over covid’s origins continues to be contentious and politicized. It is also entangled with geopolitical tensions and with a broader debate about biosafety practices and the regulatory oversight of laboratory experiments that seek to assess and understand the threat pathogens could pose.
The lab leak theory emerged early in 2020 and was embraced by President Donald Trump. It gained momentum in May 2021 when 18 scientists, including Worobey, wrote a letter to the journal Science saying all possible origins of the pandemic, including a lab leak, deserve investigation. President Joe Biden then asked his intelligence agencies to investigate.
They were unable to reach a consensus. Most favored a natural origin, but two agencies favored a lab origin. None claimed high confidence in their conclusions.
A report from Senate Republicans in 2022 said a “research-related accident” was the “most likely” origin of the pandemic, although it did not rule out a natural origin. “Critical corroborating evidence of a natural zoonotic spillover is missing,” the report said.
There is no evidence that the virus, or its progenitor, was inside a laboratory before the outbreak. Chinese officials have denied the virus came from a lab. But the Chinese government has limited outside investigations, and the lack of transparency has been an obstacle in the search to understand the origin of the virus.
Chinese officials have also dismissed the market origin, instead floating conjectures, generally dismissed by the global scientific community, that the virus came from outside China, possibly via packages of frozen seafood or from a military research facility in Maryland.
“To the question — Did it come from a lab or come from a market? — I think we already knew the answer to that,” Andersen said. “Yep, it’s the market. It’s natural, as we’ve previously seen happen.”
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