Dispute simmers over who first shared SARS-CoV-2’s genome | Science

When GISAID, the widely used database for influenza and SARS-CoV-2 genomes, issued a statement last week about a set of controversial sequences from the Huanan Seafood Wholesale Market in Wuhan, China, the release explained by way of background that the repository was “an essential contributor to global health” trusted by thousands of data contributors from 215 nations and territories. But GISAID also included a claim that has been puzzling and infuriating some virologists for 3 years: It was the place where the first SARS-CoV-2 genomes were publicly shared, on 10 January 2020.

That claim challenges contemporaneous news and social media accounts, the memories of many researchers contacted by Science, and non-GISAID records that all indicate the first sequence was made available through virological.org, a forum where scientists share and discuss information, early on 11 January in Europe, which was the evening of 10 January in the United States. It had been submitted by Edward Holmes, an evolutionary biologist and virologist at the University of Sydney who had received the sequence from Zhang Yong-Zhen, a virologist at Fudan University. GISAID, various information sources suggest, didn’t actually make its first genomes of the new coronavirus public until 12 January 2020.

“I am very surprised” at GISAID’s claims, Zhang wrote in an email to Science. “I could not understand why some people attempted to rewrite the history.”

GISAID Vice President and registered in-house council Ben Branda stood by its chronology in a lengthy email responding to questions from Science. He said the notion that the Zhang genome came first is “inaccurate” and based on “misinformation.”

Who exactly revealed SARS-CoV-2’s genetic code to the world may seem like a trivial issue. But the debate isn’t about scientific glory, according to Scripps Research evolutionary biologist Kristian Andersen. He calls GISAID’s version of events “deeply problematic” and says it could undermine trust in the database, which has played an essential role in charting the evolution of SARS-CoV-2 and the rise of variants.

As for Holmes, he says he would gladly credit GISAID if it was indeed first. “It’s not an ego thing,” he says. “But I have seen absolutely no evidence of their claim.”

The release of the first SARS-CoV-2 genome was the subject of an intense behind-the-scenes tussle in China, where several laboratories had sequenced the virus by early January 2020. Zhang’s lab, which had long collaborated with Holmes, received a sample from a COVID-19 patient on 3 January and had a sequence ready on 5 January, which Zhang uploaded that day to GenBank, a public database run by the U.S. National Institutes of Health (NIH). But he did so without making it immediately visible to others. China was reportedly keeping tight control on any SARS-CoV-2 information and had banned researchers there from making the sequence public.

Zhang, Holmes, and colleagues also sent a paper about the new virus to Nature on 7 January, according to the submission date on the final manuscript. On 8 January, The Wall Street Journal became the first media outlet to report that the outbreak in Wuhan was caused by a new coronavirus and that Chinese researchers had sequenced it, but the article didn’t identify which ones.

Worried by the delay in sharing the viral genome, seen as key to developing diagnostics, vaccines, and drugs, Holmes had a “series of frantic calls” with Jeremy Farrar, head of the Wellcome Trust, on 9 January, as Farrar wrote in his book Spike: The Virus vs. The People—the Inside Story. The two decided Holmes would put pressure on Zhang to go public with the sequence while Farrar would urge George Gao, head of the Chinese Center for Disease Control and Prevention (China CDC), to do the same with genomes they believed the agency had.

Zhang eventually gave Holmes the green light to make the sequence public on 11 January, while sitting on a plane about to take off from Shanghai for Beijing. Holmes says he then called virologist Andrew Rambaut of the University of Edinburgh, who runs virological.org. Rambaut posted a file with the sequence at 1:05 a.m. Greenwich Mean Time (GMT) on 11 January, before Zhang had even landed. (Zhang was reportedly punished by the Chinese government for ignoring government orders, although he disputed that in a Nature story that heralded him as one of 10 “people who helped shape science in 2020.”)

The release of the novel coronavirus’ genome—which Holmes announced in a tweet 3 minutes later—was hailed as a milestone. “Potentially really important moment in global public health-must be celebrated,” Farrar tweeted after he woke up later that morning. The same day, vaccine developers started plotting how to make shots based on the SARS-CoV-2 gene coding for its spike protein.

But GISAID, now home to more than 15 million SARS-CoV-2 genomes, has a different version. Branda says China CDC submitted three genomes to GISAID at 11:29 p.m. GMT on 9 January 2020, the morning of 10 January in Beijing. The first two genomes were released after processing just over an hour later, he says, or more than 24 hours before Holmes’s post went up on virological.org. Records of the two genomes on GISAID’s database list 10 January as the date of submission, but don’t say when they went public.

GISAID also announced the news on its website right away, Branda says. A search on the Wayback Machine, which records web pages periodically, shows GISAID had a short story titled “China releases genetic sequence of newly discovered coronavirus from Wuhan” up by 13 January, but the archive did not capture GISAID’s site on 10–12 January.

GISAID’s sequence of events is at odds with the World Health Organization’s (WHO’s) version, recorded in an official timeline. A WHO spokesperson tells Science the agency received the first China CDC genomes at 6:10 p.m. GMT on 11 January. At 9:23 p.m. GMT—early in the morning of 12 January in Beijing—the agency reported the arrival of the sequences in a tweet. (For unclear reasons, WHO had not acknowledged the Zhang genome on virological.org.)

WHO tweeted that same evening that the sequences “have also been submitted by Chinese authorities to the GISAID platform,” adding: “We expect them to be made publicly available as soon as possible.” Nothing in the agency’s tweets indicated the China CDC sequences were already online—let alone that they were published almost 48 hours earlier, as GISAID says. An official timeline of China’s efforts to share pandemic information with the world, released by state news agency Xinhua in April 2020, also says the release occurred on 12 January, as does a press release by the government of Hong Kong.

And if GISAID made the announcement on 10 January, it appears to have gone completely unnoticed by the scientific community and the media. A search for references to GISAID between 10 and 12 January on Twitter—when worries that the Wuhan outbreak would spiral out of control were increasing—doesn’t turn up anything except WHO’s tweets. “It makes no sense at all” that not a single scientist spoke or tweeted about the release of SARS-CoV-2’s genome if it occurred on 10 January, Andersen says.

“The internet has memories,” Zhang adds.

Jason McLellan of the University of Texas, Austin, clearly recalls the release on virological.org as the moment when the race to produce a SARS-CoV-2 vaccine kicked off. The next morning, together with researchers at NIH, McLellan began to engineer the virus’ spike gene into the messenger RNA vaccine that Moderna later developed. At the time, “People, colleagues and others, were sort of scouring trying to find the sequence,” McLellan says. “I don’t know anybody who got the first sequence from GISAID.” He says it’s “very unlikely” that GISAID’s timeline is correct; when a colleague first told him about it, “It sort of shocked me,” McLellan says.

Branda, in GISAID’s response to Science, dismissed the Xinhua and WHO timelines as inaccurate. He shared screenshots of WhatsApp messages between GISAID and WHO officials to support his point of view, but they appear to show only that on 10 January GISAID shared with WHO the position of the novel virus in the coronavirus family tree, based on a gene called orf1b—not that its full sequence was public at that time. (WHO did not comment on the messages.)

Branda also listed as evidence four scientific papers that referenced GISAID as the source of the first genomes, including a landmark article in The New England Journal of Medicine (NEJM)in December 2020 that showed the COVID-19 vaccine produced by BioNtech and Pfizer was safe and effective. Its authors wrote that development of the vaccine “was initiated on January 10, 2020, when the SARS-CoV-2 genetic sequence was released by the Chinese Center for Disease Control and Prevention and disseminated globally” on GISAID.

“I found myself chuckling and shaking my head numerous times at the tragicomedy of the world we live in where evidence from multiple peer-reviewed scientific journal articles, including from the prestigious New England Journal of Medicine, apparently rests on the same authoritative pedestal as ‘evidence’ from questionable government sources, a timeline contradicted by its own author, and some guy on Twitter,” Branda wrote in the GISAID response.

Gao has supported GISAID’s version of events, saying in the 2021 CNN documentary Race to the Vaccine that “on the morning of January 10th, we published the sequences for the whole world to see.” He did not respond to questions from Science but sent references to three of the four papers.

Science asked the first and last authors of the NEJM paper whether they were sure the Pfizer-BioNTech vaccine collaboration got underway based on the GISAID genomes on 10 January, and whether the line in the paper had been suggested by GISAID officials. The authors referred the question to a Pfizer communications officer, who said the company is looking into the issue.

GISAID has argued for its timeline on multiple fronts. A March 2022 profile of Holmes in The New York Times originally reported that he and Zhang were the first to make SARS-CoV-2 genomes public, but the story was changed 6 days later to align with GISAID’s version of events. A New York Times spokesperson says the correction was made after a GISAID employee named Cheryl Bennett contacted the newspaper. Another reporter, Cat Ferguson, says she received a complaint about a story in MIT Technology Review that mentioned the virological.org post, but the magazine did not change the piece.

Andersen says GISAID is pressuring scientists to support its version as well. A January preprint co-authored by him that unveiled Outbreak.info, a platform to monitor viral mutations, credited the virological.org post as the first published SARS-CoV-2 genome. But when Outbreak.info’s creators shared the manuscript with GISAID for review (the database’s Core and Curation Team was among the authors) officials there insisted that the reference be dropped and replaced with one supporting their own timeline, Andersen says.

The team refused to do so, he says, but agreed to include a reference to the NEJM paper in the now-published version.

GISAID officials kept asking the authors to remove the offending virological.org reference even after publication, Andersen says. “They’re basically asking you to participate in their revisionist history,” he says. “I’m not willing to do that.”

Correction, 29 March, 4:45 p.m.: The timing of WHO’s first tweet about the release of the China CDC genomes has been corrected. It was sent at 9:23 p.m. GMT, not 10:23 p.m. GMT.

When GISAID, the widely used database for influenza and SARS-CoV-2 genomes, issued a statement last week about a set of controversial sequences from the Huanan Seafood Wholesale Market in Wuhan, China, the release explained by way of background that the repository was “an essential contributor to global health” trusted by thousands of data contributors from 215 nations and territories. But GISAID also included a claim that has been puzzling and infuriating some virologists for 3 years: It was the place where the first SARS-CoV-2 genomes were publicly shared, on 10 January 2020.

That claim challenges contemporaneous news and social media accounts, the memories of many researchers contacted by Science, and non-GISAID records that all indicate the first sequence was made available through virological.org, a forum where scientists share and discuss information, early on 11 January in Europe, which was the evening of 10 January in the United States. It had been submitted by Edward Holmes, an evolutionary biologist and virologist at the University of Sydney who had received the sequence from Zhang Yong-Zhen, a virologist at Fudan University. GISAID, various information sources suggest, didn’t actually make its first genomes of the new coronavirus public until 12 January 2020.

“I am very surprised” at GISAID’s claims, Zhang wrote in an email to Science. “I could not understand why some people attempted to rewrite the history.”

GISAID Vice President and registered in-house council Ben Branda stood by its chronology in a lengthy email responding to questions from Science. He said the notion that the Zhang genome came first is “inaccurate” and based on “misinformation.”

Who exactly revealed SARS-CoV-2’s genetic code to the world may seem like a trivial issue. But the debate isn’t about scientific glory, according to Scripps Research evolutionary biologist Kristian Andersen. He calls GISAID’s version of events “deeply problematic” and says it could undermine trust in the database, which has played an essential role in charting the evolution of SARS-CoV-2 and the rise of variants.

As for Holmes, he says he would gladly credit GISAID if it was indeed first. “It’s not an ego thing,” he says. “But I have seen absolutely no evidence of their claim.”

The release of the first SARS-CoV-2 genome was the subject of an intense behind-the-scenes tussle in China, where several laboratories had sequenced the virus by early January 2020. Zhang’s lab, which had long collaborated with Holmes, received a sample from a COVID-19 patient on 3 January and had a sequence ready on 5 January, which Zhang uploaded that day to GenBank, a public database run by the U.S. National Institutes of Health (NIH). But he did so without making it immediately visible to others. China was reportedly keeping tight control on any SARS-CoV-2 information and had banned researchers there from making the sequence public.

Zhang, Holmes, and colleagues also sent a paper about the new virus to Nature on 7 January, according to the submission date on the final manuscript. On 8 January, The Wall Street Journal became the first media outlet to report that the outbreak in Wuhan was caused by a new coronavirus and that Chinese researchers had sequenced it, but the article didn’t identify which ones.

Worried by the delay in sharing the viral genome, seen as key to developing diagnostics, vaccines, and drugs, Holmes had a “series of frantic calls” with Jeremy Farrar, head of the Wellcome Trust, on 9 January, as Farrar wrote in his book Spike: The Virus vs. The People—the Inside Story. The two decided Holmes would put pressure on Zhang to go public with the sequence while Farrar would urge George Gao, head of the Chinese Center for Disease Control and Prevention (China CDC), to do the same with genomes they believed the agency had.

The internet has memories.

• Zhang Yong-Zhen
• Fudan University

Zhang eventually gave Holmes the green light to make the sequence public on 11 January, while sitting on a plane about to take off from Shanghai for Beijing. Holmes says he then called virologist Andrew Rambaut of the University of Edinburgh, who runs virological.org. Rambaut posted a file with the sequence at 1:05 a.m. Greenwich Mean Time (GMT) on 11 January, before Zhang had even landed. (Zhang was reportedly punished by the Chinese government for ignoring government orders, although he disputed that in a Nature story that heralded him as one of 10 “people who helped shape science in 2020.”)

The release of the novel coronavirus’ genome—which Holmes announced in a tweet 3 minutes later—was hailed as a milestone. “Potentially really important moment in global public health-must be celebrated,” Farrar tweeted after he woke up later that morning. The same day, vaccine developers started plotting how to make shots based on the SARS-CoV-2 gene coding for its spike protein.

But GISAID, now home to more than 15 million SARS-CoV-2 genomes, has a different version. Branda says China CDC submitted three genomes to GISAID at 11:29 p.m. GMT on 9 January 2020, the morning of 10 January in Beijing. The first two genomes were released after processing just over an hour later, he says, or more than 24 hours before Holmes’s post went up on virological.org. Records of the two genomes on GISAID’s database list 10 January as the date of submission, but don’t say when they went public.

GISAID also announced the news on its website right away, Branda says. A search on the Wayback Machine, which records web pages periodically, shows GISAID had a short story titled “China releases genetic sequence of newly discovered coronavirus from Wuhan” up by 13 January, but the archive did not capture GISAID’s site on 10–12 January.

GISAID’s sequence of events is at odds with the World Health Organization’s (WHO’s) version, recorded in an official timeline. A WHO spokesperson tells Science the agency received the first China CDC genomes at 6:10 p.m. GMT on 11 January. At 9:23 p.m. GMT—early in the morning of 12 January in Beijing—the agency reported the arrival of the sequences in a tweet. (For unclear reasons, WHO had not acknowledged the Zhang genome on virological.org.)

WHO tweeted that same evening that the sequences “have also been submitted by Chinese authorities to the GISAID platform,” adding: “We expect them to be made publicly available as soon as possible.” Nothing in the agency’s tweets indicated the China CDC sequences were already online—let alone that they were published almost 48 hours earlier, as GISAID says. An official timeline of China’s efforts to share pandemic information with the world, released by state news agency Xinhua in April 2020, also says the release occurred on 12 January, as does a press release by the government of Hong Kong.

And if GISAID made the announcement on 10 January, it appears to have gone completely unnoticed by the scientific community and the media. A search for references to GISAID between 10 and 12 January on Twitter—when worries that the Wuhan outbreak would spiral out of control were increasing—doesn’t turn up anything except WHO’s tweets. “It makes no sense at all” that not a single scientist spoke or tweeted about the release of SARS-CoV-2’s genome if it occurred on 10 January, Andersen says.

“The internet has memories,” Zhang adds.

Jason McLellan of the University of Texas, Austin, clearly recalls the release on virological.org as the moment when the race to produce a SARS-CoV-2 vaccine kicked off. The next morning, together with researchers at NIH, McLellan began to engineer the virus’ spike gene into the messenger RNA vaccine that Moderna later developed. At the time, “People, colleagues and others, were sort of scouring trying to find the sequence,” McLellan says. “I don’t know anybody who got the first sequence from GISAID.” He says it’s “very unlikely” that GISAID’s timeline is correct; when a colleague first told him about it, “It sort of shocked me,” McLellan says.

Branda, in GISAID’s response to Science, dismissed the Xinhua and WHO timelines as inaccurate. He shared screenshots of WhatsApp messages between GISAID and WHO officials to support his point of view, but they appear to show only that on 10 January GISAID shared with WHO the position of the novel virus in the coronavirus family tree, based on a gene called orf1b—not that its full sequence was public at that time. (WHO did not comment on the messages.)

Branda also listed as evidence four scientific papers that referenced GISAID as the source of the first genomes, including a landmark article in The New England Journal of Medicine (NEJM)in December 2020 that showed the COVID-19 vaccine produced by BioNtech and Pfizer was safe and effective. Its authors wrote that development of the vaccine “was initiated on January 10, 2020, when the SARS-CoV-2 genetic sequence was released by the Chinese Center for Disease Control and Prevention and disseminated globally” on GISAID.

“I found myself chuckling and shaking my head numerous times at the tragicomedy of the world we live in where evidence from multiple peer-reviewed scientific journal articles, including from the prestigious New England Journal of Medicine, apparently rests on the same authoritative pedestal as ‘evidence’ from questionable government sources, a timeline contradicted by its own author, and some guy on Twitter,” Branda wrote in the GISAID response.

Gao has supported GISAID’s version of events, saying in the 2021 CNN documentary Race to the Vaccine that “on the morning of January 10th, we published the sequences for the whole world to see.” He did not respond to questions from Science but sent references to three of the four papers.

Science asked the first and last authors of the NEJM paper whether they were sure the Pfizer-BioNTech vaccine collaboration got underway based on the GISAID genomes on 10 January, and whether the line in the paper had been suggested by GISAID officials. The authors referred the question to a Pfizer communications officer, who said the company is looking into the issue.

GISAID has argued for its timeline on multiple fronts. A March 2022 profile of Holmes in The New York Times originally reported that he and Zhang were the first to make SARS-CoV-2 genomes public, but the story was changed 6 days later to align with GISAID’s version of events. A New York Times spokesperson says the correction was made after a GISAID employee named Cheryl Bennett contacted the newspaper. Another reporter, Cat Ferguson, says she received a complaint about a story in MIT Technology Review that mentioned the virological.org post, but the magazine did not change the piece.

Andersen says GISAID is pressuring scientists to support its version as well. A January preprint co-authored by him that unveiled Outbreak.info, a platform to monitor viral mutations, credited the virological.org post as the first published SARS-CoV-2 genome. But when Outbreak.info’s creators shared the manuscript with GISAID for review (the database’s Core and Curation Team was among the authors) officials there insisted that the reference be dropped and replaced with one supporting their own timeline, Andersen says.

The team refused to do so, he says, but agreed to include a reference to the NEJM paper in the now-published version.

GISAID officials kept asking the authors to remove the offending virological.org reference even after publication, Andersen says. “They’re basically asking you to participate in their revisionist history,” he says. “I’m not willing to do that.”

Correction, 29 March, 4:45 p.m.: The timing of WHO’s first tweet about the release of the China CDC genomes has been corrected. It was sent at 9:23 p.m. GMT, not 10:23 p.m. GMT.