How safe are the biolabs at Colorado State?

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draft funding proposal for the construction of a new biolab at Colorado State University raises questions about safety and security at its existing biolabs in Fort Collins, Colorado.

The draft proposal seeks funding from the National Institutes of Health to replace “aging” infrastructure within CSU’s Center for Vector-Borne Infectious Diseases, formerly known as the Arthropod-borne and Infectious Disease Laboratory (AIDL). The center rears insect and bat colonies for infectious disease experiments with dangerous pathogens such as SARS, Zika, Nipah and Hendra viruses. Live-pathogen experiments there are performed in part in BSL-3 facilities, which are air-tight laboratories with special technologies to prevent researchers from getting infected and spreading infections.

The proposal’s authors (Tony Schountz and Greg Ebel from CSU and Jonathan Epstein, a vice president at EcoHealth Alliance) write that, “several of our buildings are well past their useful lives.” They attach pictures of accumulating mold and mildew as proof of “rapidly degrading” facilities that “leak when it rains.”

The proposal also explains that the lab’s existing design requires cell samples of infected bats and insects to “be transported to different buildings prior to use.” It states that the existing autoclaves, which sterilize biohazardous materials, “frequently malfunction and there is a legitimate concern they will continue to do so.”

It is possible the troubles are overstated because they support a funding request. Here is an excerpt from the funding proposal with the images.

The proposal raises several questions: Are human lives at risk from AIDL’s faulty equipment and infrastructure? Does this decrepitude increase the likelihood of an accidental leak of dangerous pathogens? Are there other EcoHealth Alliance-affiliated facilities around the world that are similarly degraded and unsafe?  Were the conditions similarly unsafe, for example, the EcoHealth Alliance-funded Wuhan Institute of Virology? That institute has been identified as a possible source of SARS-CoV-2, the virus that causes Covid-19.

Records of CSU’s institutional biosafety committee (IBC), obtained via public records request, seem to reinforce concerns about safety of CSU biolabs. For example, meeting minutes from May 2020 indicate that a CSU researcher acquired Zika virus infection and symptoms after manipulating experimentally infected mosquitoes. The IBC noted: “Most likely this was a mosquito bite that went undetected during a chaotic time due to COVID-19 shut downs and changes.”

Ironically, increased infectious disease research on SARS-CoV-2 may have heightened the risk of biosafety lapses and mishaps at CSU. The IBC minutes express support for “concerns raised regarding the large number of research projects involving SARS-CoV-2 which has put strains on resources such as PPE, lab space, and personnel.”

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USRTK asks ODNI to declassify documents about accidents at labs that store dangerous pathogens

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U.S. Right to Know (USRTK) has asked the Office of the Director of National Intelligence (ODNI) to declassify three documents about biosafety lapses occurring in laboratories that store dangerous pathogens.

The mandatory declassification review (MDR) request responds to ODNI’s decision to withhold three classified documents responsive to a Freedom of Information Act request USRTK submitted in August 2020.

The FOIA request “sought finished intelligence produced since January 2015 about the accidental or deliberate release of biological agents, containment failures in biosafety-level (BSL)-2, BSL-3 or BSL-4 research facilities, and other incidents of concern related to dual-use biosafety research in BSL-2, BSL-3 or BSL-4 research facilities in Canada, China, Egypt, France, Germany, India, Iran, Israel, the Netherlands, Russia, former countries of the Soviet Union, South Africa, Taiwan, the United Kingdom, and Thailand.”

ODNI said in its response that it had located three documents, and determined these “must be withheld in their entirety pursuant to FOIA exemptions” regarding the protection of classified materials concerning intelligence methods and sources of national security relevance. ODNI did not describe or characterize the nature of the three documents or their contents, other than that they were responsive to the FOIA request.

In its MDR request, USRTK requested that ODNI release all reasonably segregable nonexempt portions of the three documents.

USRTK believes the public has a right to know what data exists about accidents, leaks and other mishaps at laboratories where pathogens of pandemic potential are stored and modified, and whether any such leaks are implicated in the origins of COVID-19, which has caused the deaths of more than 360,000 Americans.

For more information

U.S. Right to Know is posting documents from our public records requests for our biohazards investigation. See: FOI documents on origins of SARS-CoV-2, hazards of gain-of-function research and biosafety labs.

Background page on U.S. Right to Know’s investigation into the origins of SARS-CoV-2.

Altered datasets raise more questions about reliability of key studies on coronavirus origins

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Revisions to genomic datasets associated with four key studies on coronavirus origins add further questions about the reliability of these studies, which provide foundational support for the hypothesis that SARS-CoV-2 originated in wildlife. The studies, Peng Zhou et al., Hong Zhou et al., Lam et al., and Xiao et al., discovered SARS-CoV-2-related coronaviruses in horseshoe bats and Malayan pangolins.

The studies’ authors deposited DNA sequence data called sequence reads, which they used to assemble bat- and pangolin-coronavirus genomes, in the National Center for Biotechnology Information (NCBI) sequence read archive (SRA). NCBI established the public database to assist independent verification of genomic analyses based on high-throughput sequencing technologies.

U.S. Right to Know obtained documents by a public records request that show revisions to these studies’ SRA data months after they were published. These revisions are odd because they occurred after publication, and without any rationale, explanation or validation.

For example, Peng Zhou et al. and Lam et al. updated their SRA data on the same two dates. The documents don’t explain why they altered their data, only that some changes were made. Xiao et al. made numerous changes to their SRA data, including the deletion of two datasets on March 10, the addition of a new dataset on June 19, a November 8 replacement of data first released on October 30, and a further data change on November 13 — two days after Nature added an Editor’s “note of concern” about the study. Hong Zhou et al. have yet to share the full SRA dataset that would enable independent verification. While journals like Nature require authors to make all data “promptly available” at the time of publication, SRA data can be released after publication; but it is unusual to make such changes months after publication.

These unusual alterations of SRA data do not automatically make the four studies and their associated datasets unreliable. However, the delays, gaps and changes in SRA data have hampered independent assembly and verification of the published genome sequences, and add to questions and concerns about the validity of the four studies, such as:

  1. What were the exact post-publication revisions to the SRA data? Why were they made? How did they affect the associated genomic analyses and results?
  2. Were these SRA revisions independently validated? If so, how? The NCBI’s only validation criterion for publishing an SRA BioProject– beyond basic information such as “organism name”– is that it cannot be a duplicate.

For more information

The National Center for Biotechnology Information (NCBI) documents can be found here: NCBI emails (63 pages)

U.S. Right to Know is posting documents from our public records requests for our biohazards investigation. See: FOI documents on origins of SARS-CoV-2, hazards of gain-of-function research and biosafety labs.

Background page on U.S. Right to Know’s investigation into the origins of SARS-CoV-2.

No peer review for addendum to prominent coronavirus origins study?

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The journal Nature did not assess the reliability of important claims made in a November 17 addendum to a study on the bat-origins of the novel coronavirus SARS-CoV-2, correspondence with Nature staff suggests.

On February 3, 2020, Wuhan Institute of Virology scientists reported discovering the closest known relative of SARS-CoV-2, a bat coronavirus called RaTG13. RaTG13 has become central to the hypothesis that SARS-CoV-2 originated in wildlife.

The addendum addresses unanswered questions about the provenance of RaTG13. The authors, Zhou et al., clarified they found RaTG13 in 2012-2013 “in an abandoned mineshaft in Mojiang County, Yunnan Province,” where six miners suffered acute respiratory distress syndrome after exposure to bat feces, and three died. Investigations of the symptoms of the sickened miners could provide important clues about the origins of SARS-CoV-2. Zhou et al. reported finding no SARS-related coronaviruses in stored serum samples of the sick miners, but they did not support their claims with data and methods about their assays and experimental controls.

The absence of key data in the addendum has raised further questions about the reliability of the Zhou et al. study. On November 27, U.S. Right to Know asked Nature questions about the addendum’s claims, and requested that Nature publish all supporting data that Zhou et al. may have provided.

On December 2, Nature Head of Communications Bex Walton replied that the original Zhou et al.  study was “accurate but unclear,” and that the addendum was an appropriate post-publication platform for clarification. She added: “With regards to your questions, we would direct you to approach the authors of the paper for answers, as these questions pertain not to the research that we have published but to other research undertaken by the authors, upon which we cannot comment” (emphasis ours). Since our questions related to research described in the addendum, the Nature representative’s statement suggests Zhou et al.’s addendum was not evaluated as research.

We asked a follow up question on December 2: “was this addendum subjected to any peer-review and/or editorial oversight by Nature?” Ms. Walton did not answer directly; she replied: “In general, our editors will assess comments or concerns that are raised with us in the first instance, consulting the authors, and seeking advice from peer reviewers and other external experts if we consider it necessary. Our confidentiality policy means we cannot comment on the specific handling of individual cases.”

Since Nature considers an addendum to be a post-publication update, and does not subject such post publication addenda to the same peer-review standards as original publications, it seems likely that the Zhou et al. addendum did not undergo peer-review.

Authors Zhengli Shi and Peng Zhou did not respond to our questions about their Nature addendum.

New emails show scientists’ deliberations on how to discuss SARS-CoV-2 origins 

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Newly obtained emails offer glimpses into how a narrative of certainty developed about the natural origins of the novel coronavirus SARS-CoV-2, while key scientific questions remained. The internal discussions and an early draft of a scientists’ letter show experts discussing gaps in knowledge and unanswered questions about lab origin, even as some sought to tamp down on “fringe” theories about the possibility the virus came from a lab.

Influential scientists and many news outlets have described the evidence as “overwhelming” that the virus originated in wildlife, not from a lab. However, a year after the first reported cases of SARS-CoV-2 in the Chinese city of Wuhan, little is known how or where the virus originated. Understanding the origins of SARS-CoV-2, which causes the disease COVID-19, may be crucial to preventing the next pandemic.

The emails of coronavirus expert Professor Ralph Baric — obtained through a public records request by U.S. Right to Know — show conversations between National Academy of Sciences (NAS) representatives, and experts in biosecurity and infectious diseases from U.S. universities and the EcoHealth Alliance.

On Feb. 3, the White House Office of Science and Technology Policy (OSTP) asked the National Academies of Sciences, Engineering and Medicine (NASEM) to “convene meeting of experts… to assess what data, information and samples are needed to address the unknowns, in order to understand the evolutionary origins of 2019-nCoV, and more effectively respond to both the outbreak and any resulting misinformation.”

Baric and other infectious disease experts were involved in drafting the response. The emails show the experts’ internal discussions and an early draft dated Feb. 4.

The early draft described “initial views of the experts” that “the available genomic data are consistent with natural evolution and that there is currently no evidence that the virus was engineered to spread more quickly among humans.” This draft sentence posed a question, in parentheses: “[ask experts to add specifics re binding sites?]” It also included a footnote in parentheses: “[possibly add brief explanation that this does not preclude an unintentional release from a laboratory studying the evolution of related coronaviruses].”

In one email, dated Feb. 4, infectious disease expert Trevor Bedford commented: “I wouldn’t mention binding sites here. If you start weighing evidence there’s a lot to consider for both scenarios.” By “both scenarios,” Bedford appears to refer to lab-origin and natural-origin scenarios.

The question of binding sites is important to the debate about the origins of SARS-CoV-2. Distinctive binding sites on SARS-CoV-2’s spike protein confer “near-optimal” binding and entry of the virus into human cells, and make SARS-CoV-2 more contagious than SARS-CoV. Scientists have argued that SARS-CoV-2’s unique binding sites could have originated either as a result of natural spillover in the wild or deliberate laboratory recombination of an as-yet-undisclosed natural ancestor of SARS-CoV-2.

The final letter published Feb. 6 did not mention binding sites or the possibility of a laboratory origin. It does make clear that more information is necessary to determine the origins of SARS-CoV-2. The letter states, “The experts informed us that additional genomic sequence data from geographically – and temporally – diverse viral samples are needed to determine the origin and evolution of the virus. Samples collected as early as possible in the outbreak in Wuhan and samples from wildlife would be particularly valuable.”

The emails show some experts discussing the need for clear language to counter what one described as “crackpot theories” of lab origin. Kristian Andersen, lead author of an influential Nature Medicine paper asserting a natural origin of SARS-CoV-2, said the early draft was “great, but I do wonder if we need to be more firm on the question of engineering.” He continued, “If one of the main purposes of this document is to counter those fringe theories, I think it’s very important that we do so strongly and in plain language…”

In his response, Baric aimed at conveying a scientific basis for SARS-CoV-2’s natural origin. “I do think we need to say that the closest relative to this virus (96%) was identified from bats circulating in a cave in Yunnan, China. This makes a strong statement for animal origin.”

The final letter from the NASEM presidents does not take a position on the virus origin. It states that, “Research studies to better understand the origin of 2019-nCoV and how it relates to viruses found in bats and other species are already underway. The closest known relative of 2019-nCoV appears to be a coronavirus identified from bat-derived samples collected in China.” The letter referenced two studies that were conducted by EcoHealth Alliance and Wuhan Institute of Virology. Both posit a natural origin for SARS-CoV-2.

A few weeks later, the NASEM presidents’ letter appeared as an authoritative source for an influential scientists’ statement published in The Lancet that conveyed far more certainty about the origins of SARS-CoV-2. USRTK previously reported that EcoHealth Alliance President Peter Daszak drafted that statement, which asserted that “scientists from multiple countries…overwhelmingly conclude that this coronavirus originated in wildlife.” This position, the statement notes, is “further supported by a letter from the presidents of the US National Academies of Science, Engineering, and Medicine.”

The subsequent appointments of Peter Daszak and other EcoHealth Alliance allies to The Lancet COVID19 Commission and Daszak to the World Health Organization’s investigations of SARS-CoV-2’s origins means the credibility of these efforts are undermined by conflicts of interest, and by the appearance that they have already pre-judged the matter at hand.

——–

“issues we should probably avoid”

The Baric emails also show a NAS representative suggesting to U.S. scientists they should “probably avoid” questions about SARS-CoV-2’s origin in bilateral meetings they were planning with Chinese COVID-19 experts. The emails in May and June 2020 discussed plans for the meetings. Participating American scientists, many of whom are members of the NAS Standing Committee on emerging infectious diseases and 21st-century health threats, included Ralph Baric, Peter Daszak, David Franz, James Le Duc, Stanley Perlman, David Relman, Linda Saif, and Peiyong Shi.

The participating Chinese scientists included George Gao, Zhengli Shi, and Zhiming Yuan. George Gao is Director of China CDC. Zhengli Shi leads the coronavirus research at Wuhan Institute of Virology, and Zhiming Yuan is Director of WIV.

In an email to American participants about a planning session, NAS Senior Program Officer Benjamin Rusek described the purpose of the meeting: “to fill you in on the dialogue background, discuss the topics/questions (list in your invitation letter and attached) and issues we should probably avoid (origin questions, politics)…”

For more information

Link to University of North Carolina Professor Ralph Baric’s emails can be found here: Baric emails (83,416 pages)

U.S. Right to Know is posting documents from our public records requests for our biohazards investigation. See: FOI documents on origins of SARS-CoV-2, hazards of gain-of-function research and biosafety labs.

Items from coronavirus expert Ralph Baric‘s emails 

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This page lists documents in Professor Ralph Baric’s emails, which U.S. Right to Know obtained via a public records request. Dr. Baric is a coronavirus expert at the University of North Carolina, Chapel Hill (UNC). He has developed genetic techniques to enhance the pandemic potential of existing bat coronaviruses in collaboration with Dr. Zhengli Shi at the Wuhan Institute of Virology and with EcoHealth Alliance.

The emails show internal discussions and an early draft of a key scientists’ letter about coronavirus origins, and shed some light on relationships between U.S. and Chinese experts in biodefense and infectious diseases, and the roles of organizations such as EcoHealth Alliance and National Academy of Sciences (NAS).

Please email anything of interest we may have missed to sainath@usrtk.org, so that we can include them below.

Items from Baric emails

  1. Tracy McNamara, Professor of Pathology at Western University of Health Sciences in Pomona, California wrote on March 25, 2020: : “The Federal govt has spent over $1 billion dollars in support of the Global Health Security Agenda to help developing nations create the capacity to detect/report/respond to pandemic threats. An additional $200 million was spent on the PREDICT project via USAID looking for emerging viruses in bats, rats and monkeys overseas. And now the Global Virome Project wants $1.5 billion dollars to run around the world hunting down every virus on the face of the earth. They will probably get funding. But none of these programs have made taxpayers safer right here at home.” (emphasis in the original)
  2. Dr. Jonathan Epstein, Vice President for Science and Outreach at EcoHealth Alliance, sought guidance for a request from the U.S. Defense Advanced Research Projects Agency (DARPA) about communicating “potentially sensitive dual-use information” (March 2018).
  3. EcoHealth Alliance paid Dr. Baric an undisclosed sum as honorarium (January 2018).
  4. Invitation to U.S. National Academy of Sciences, Engineering and Medicine (NASEM) and the Chinese Academy of Agricultural Sciences (CAAS) U.S. China Dialogue and Workshop on the Challenges of Emerging Infections, Laboratory Safety, Global Health Security and Responsible Conduct in the Use of Gene Editing in Viral Infectious Disease Research, Harbin, China, Jan 8-10, 2019 (November 2018-January 2019). Preparatory emails and a travel memorandum indicate the identities of the American participants.
  5. NAS invitation to a meeting of U.S. and Chinese experts working to counter infectious disease and improve global health (November 2017). The meeting was convened by the NAS and the Galveston National Laboratory. It took place on January 16-18, 2018, in Galveston, Texas. A travel memorandum indicates the identities of the American participants. Subsequent emails show that the WIV’s Dr. Zhengli Shi is present at the meeting.
  6. On February 27, 2020, Baric wrote, “at this moment the most likely origins are bats, and I note that it is a mistake to assume that an intermediate host is needed.”
  7. On March 5, 2020, Baric wrote, “there is absolutely no evidence that this virus is bioengineered.”

For more information

A link to Professor Ralph Baric’s emails can be found here: Baric emails (~83,416 pages)

U.S. Right to Know is posting documents from our Biohazards investigation. See: FOI documents on origins of SARS-CoV-2, hazards of gain-of-function research and biosafety labs.

Scientist with conflict of interest leading Lancet COVID-19 Commission task force on virus origins

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Last week, U.S. Right to Know reported that an influential statement in The Lancet signed by 27 prominent public health scientists about the origins of SARS-CoV-2 was organized by employees of EcoHealth Alliance, a non-profit group that has received millions of dollars of U.S. taxpayer funding to genetically manipulate coronaviruses with scientists at the Wuhan Institute of Virology (WIV). 

The Feb. 18 statement condemned “conspiracy theories” suggesting COVID-19 may have come from a lab, and said scientists “overwhelmingly conclude” the virus originated in wildlife. Emails obtained by USRTK revealed that EcoHealth Alliance President Peter Daszak drafted the letter and orchestrated it to “avoid the appearance of a political statement.” 

The Lancet failed to disclose that four other signers of the statement also have positions with EcoHealth Alliance, which has a financial stake in deflecting questions away from the possibility that the virus could have originated in a lab.

Now, The Lancet is handing even more influence to the group that has conflicts of interest on the important public health question of the pandemic origins. On Nov. 23, The Lancet named a new 12-member panel to the The Lancet COVID 19 Commission. The chairman of the new task force to investigate the “Origins, Early Spread of the Pandemic, and One Health Solutions to Future Pandemic Threats” is none other than the EcoHealth Alliance’s Peter Daszak. 

Half the task force members — including Daszak, Hume Field, Gerald Keusch, Sai Kit Lam, Stanley Perlman and Linda Saif — were also signatories to the Feb. 18 statement that claimed to know the origins of the virus barely a week after the World Health Organization announced that the disease caused by the novel coronavirus would be named COVID-19. 

In other words, at least half The Lancet’s COVID Commission task force on the origins of SARS-CoV-2 appear to have already pre-judged the outcome before the investigation has even begun. This undermines the credibility and authority of the task force.

The origins of SARS-CoV-2 are still a mystery and a thorough and credible investigation may well be crucial to preventing the next pandemic. The public deserves an investigation that is not tainted by such conflicts of interest.

Update (November 25, 2020): Peter Daszak has also been appointed to the World Health Organization’s 10-person team researching the origins of SARS-CoV-2.

EcoHealth Alliance orchestrated key scientists’ statement on “natural origin” of SARS-CoV-2

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Update 2.15.21 – Newly surfaced Daszak email: “No need for you to sign the ‘Statement’ Ralph!!” 

Emails obtained by U.S. Right to Know show that a statement in The Lancet authored by 27 prominent public health scientists condemning “conspiracy theories suggesting that COVID-19 does not have a natural origin” was organized by employees of EcoHealth Alliance, a non-profit group that has received millions of dollars of U.S. taxpayer funding to genetically manipulate coronaviruses with scientists at the Wuhan Institute of Virology.

The emails obtained via public records requests show that EcoHealth Alliance President Peter Daszak drafted the Lancet statement, and that he intended it to “not be identifiable as coming from any one organization or person” but rather to be seen as “simply a letter from leading scientists”. Daszak wrote that he wanted “to avoid the appearance of a political statement”.

The scientists’ letter appeared in The Lancet on February 18, just one week after the World Health Organization announced that the disease caused by the novel coronavirus would be named COVID-19.

The 27 authors “strongly condemn[ed] conspiracy theories suggesting that COVID-19 does not have a natural origin,” and reported that scientists from multiple countries “overwhelmingly conclude that this coronavirus originated in wildlife.” The letter included no scientific references to refute a lab-origin theory of the virus. One scientist, Linda Saif, asked via email whether it would be useful “to add just one or 2 statements in support of why nCOV is not a lab generated virus and is naturally occuring? Seems critical to scientifically refute such claims!” Daszak responded, “I think we should probably stick to a broad statement.”

Growing calls to investigate the Wuhan Institute of Virology as a potential source of SARS-CoV-2 have led to increased scrutiny of EcoHealth Alliance. The emails show how members of EcoHealth Alliance played an early role in framing questions about possible lab origin of SARS-CoV-2 as “crackpot theories that need to be addressed,” as Daszak told The Guardian.

Although the phrase “EcoHealth Alliance” appeared only once in The Lancet statement, in association with co-author Daszak, several other co-authors also have direct ties to the group that were not disclosed as conflicts of interest. Rita Colwell and James Hughes are members of the Board of Directors of EcoHealth Alliance, William Karesh is the group’s Executive Vice President for Health and Policy, and Hume Field is Science and Policy Advisor.

The statement’s authors also claimed that the “rapid, open, and transparent sharing of data on this outbreak is now being threatened by rumours and misinformation around its origins.” Today, however, little is known about the origins of SARS-CoV-2, and investigations into its origins by the World Health Organization and The Lancet COVID-19 commission have been shrouded in secrecy and mired by conflicts of interests.

Peter Daszak, Rita Colwell, and The Lancet Editor Richard Horton did not provide comments in response to our requests for this story.

For more information

A link to the entire batch of EcoHealth Alliance emails can be found here: EcoHealth Alliance emails: University of Maryland (466 pages)

U.S. Right to Know is posting documents obtained through public freedom of information (FOI) requests for our Biohazards investigation in our post: FOI documents on origins of SARS-CoV-2, hazards of gain-of-function research and biosafety labs.

Related posts

Nature journal adds “Editor’s note” highlighting concerns about the reliability of study linking pangolin coronaviruses to origin of SARS-CoV-2

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On November 9, 2020, U.S. Right to Know released emails with senior authors of Liu et al. and Xiao et al., and staff and editors at PLoS Pathogens and Nature journals. These studies have provided scientific credence to the zoonotic hypothesis that coronaviruses closely related to SARS-CoV-2 circulate in the wild, and that SARS-CoV-2 has a wild animal source. On November 11, 2020, Nature added the following note to Xiao et al.’s paper: “Editor’s Note: Readers are alerted that concerns have been raised about the identity of the pangolin samples reported in this paper and their relationship to previously published pangolin samples. Appropriate editorial action will be taken once this matter is resolved.”

The note can be seen here: https://www.nature.com/articles/s41586-020-2313-x

Nature and PLoS Pathogens probe scientific veracity of key studies linking pangolin coronaviruses to origin of SARS-CoV-2

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By Sainath Suryanarayanan, PhD 

Here, we provide our emails with senior authors of Liu et al. and Xiao et al., and the editors of PLoS Pathogens and Nature. We also present an in-depth discussion of the questions and concerns raised by these emails, which put in doubt the validity of these key studies on the origin of the novel coronavirus SARS-CoV-2 that causes COVID-19. See our reporting on these emails, Validity of key studies on origin of coronavirus in doubt; science journals investigating (11.9.20)


Email communications with Dr. Jinping Chen, senior author of Liu et al:


Dr. Jinping Chen’s emails raise a number of concerns and questions: 

1– Liu et al. (2020) assembled their published pangolin coronavirus genome sequence based on coronaviruses sampled from three pangolins, two samples from a smuggled batch in March 2019, and one sample from a different batch intercepted in July 2019. The National Center for Biotechnology Information (NCBI) database, where scientists are required to deposit sequence data to ensure independent verification and reproducibility of published results, contains the sequence read archive (SRA) data for the two March 2019 samples but is missing data for the July 2019 sample. Upon being asked about this missing sample, which Dr. Jinping Chen identifies as F9, Dr. Jinping Chen stated: “The raw data of these three samples could be found under NCBI accession number PRJNA573298, and the BioSample ID were SAMN12809952, SAMN12809953, and SAMN12809954, moreover, individual (F9) from different batch was also positive, the raw data can be seen in NCBI SRA SUB 7661929, which will be released soon for we have another MS (under review)” (our emphasis).

It is concerning that Liu et al. have not published data corresponding to 1 of the 3 pangolins samples that they used to assemble their pangolin coronavirus genome sequence. Dr. Jinping Chen also did not share this data upon being asked. The norm in science is to publish and/or share all data that would allow others to independently verify and reproduce the results. How did PLoS Pathogens let Liu et al. evade publishing crucial sample data? Why is Dr. Jinping Chen not sharing data pertaining to this third pangolin sample? Why would Liu et al. want to release unpublished data pertaining to this third pangolin sample as part of another study that has been submitted to a different journal? The concern here is that scientists would misattribute the missing pangolin sample from Liu et al. to a different study, making it difficult for others to subsequently trace important details about this pangolin sample, such as the context in which the pangolin sample was collected.

2– Dr. Jinping Chen denied that Liu et al. have had any relationship with Xiao et al.’s (2020) Nature study. He wrote: “We submitted our PLOS Pathogens paper on Feb.14, 2020 before the Nature paper (the Reference 12 in our PLOS pathogens paper, they submitted on Feb.16, 2020 from their submit date in Nature), our PLOS pathogens paper explain that SARS-Cov-2 is not from pangolin coronavirus directly and pangolin not as intermediate host. We knew their work after their news briefing on Feb. 7, 2020, and we have different opinions with them, the other two papers (Viruses and Nature) have been listed in the PLOS Pathogen paper as reference papers (reference number 10 and 12), we are different research groups from Nature paper authors, and there is no relationship with each other, and we took samples with detail sample information from the Guangdong wildlife rescue center with helps from Jiejian Zou and Fanghui Hou as our co-authors and we don’t know where the samples of the Nature paper from.” (our emphases)

The following points raise doubts about Dr. Chen’s claims above: 

a– Liu et al. (2020), Xiao et al (2020) and Liu et al. (2019) shared the following authors: Ping Liu and Jinping Chen were authors on the 2019 Viruses paper and the 2020 PLoS Pathogens paper, senior author Wu Chen on Xiao et al. (2020) was a co-author of the 2019 Viruses paper, and Jiejian Zhou and Fanghui Hou were authors on both Xiao et al. and Liu et al. 

b– Both manuscripts were deposited to the public preprint server bioRxiv on the same date: February 20, 2020. 

c– Xiao et al. “renamed pangolin samples first published by Liu et al. [2019] Viruses without citing their study as the original article that described these samples, and used the metagenomic data from these samples in their analysis” (Chan and Zhan). 

d– Liu et al.’s full pangolin coronavirus genome is 99.95% identical at the nucleotide level to the full pangolin coronavirus genome published by Xiao et al. How could Liu et al. have produced a whole genome that is 99.95% identical (only ~15 nucleotides difference) to Xiao et al. without sharing datasets and analyses?

When different research groups independently arrive at similar sets of conclusions about a given research question, it significantly increases the likelihood of truth of the involved claims. The concern here is that Liu et al. and Xiao et al. were not independently conducted studies as claimed by Dr. Chen. Was there any coordination between Liu et al. and Xiao et al. regarding their analysis and publications? If so, what was the extent and nature of that coordination? 

3– Why did Liu et al. not make publicly available the raw amplicon sequencing data that they used to assemble their pangolin coronavirus genome? Without this raw data, the pangolin coronavirus genome assembled by Liu et al., others cannot independently verify and reproduce the results of Liu et al. As mentioned earlier, the norm in science is to publish and/or share all data that would allow others to independently verify and reproduce the results. We asked Dr. Jingping Chen to share Liu et al.’s raw amplicon sequence data. He responded by sharing Liu et al.’s RT-PCR product sequence results, which are not the raw amplicon data used to assemble the pangolin coronavirus genome. Why is Dr. Jinping Chen reluctant to release the raw data that would allow others to independently verify Liu et al.’s analysis.

4– Liu et al. Viruses (2019) was published in October 2019 and its authors had deposited their pangolin coronavirus (sequence read archive) SRA data with NCBI on September 23, 2019, but waited until January 22, 2020 to make this data publicly accessible. Scientists typically release raw genomic sequence data on publicly accessible databases as soon as possible after the publication of their studies. This practice ensures that others can independently access, verify and utilize such data. Why did Liu et al. 2019 wait 4 months to make their SRA data publicly accessible? Dr. Jinping Chen chose not to directly answer this question of ours in his response on November 9, 2020.

We also got in touch with Dr. Stanley Perlman, PLoS Pathogens Editor of Liu et al. and this is what he had to say.

Notably, Dr. Perlman acknowledged that:

  • “PLoS Pathogens is investigating this paper in more detail” 
  • He “did not verify the veracity of the July 2019 sample during pre-publication peer review”
  • “[c]oncerns about similarity between the two studies [Liu et al. and Xiao et al.] came to light only after both studies had been published.”
  • He “did not see any amplicon data during peer review. The authors provided an accession number for the assembled genome…although after publication it came to light that the accession number listed in the article’s Data Availability Statement is incorrect. This error and questions around the raw contig sequencing data are currently being addressed as part of the post-publication case.”

When we contacted PLoS Pathogens with our concerns about Liu et al. we got the following response from the Senior Editor of the PLoS Publication Ethics team:

Emails from Xiao et al.

On October 28, the Chief Biological Sciences Editor of Nature replied (below) with the key phrase “we take these issues very seriously and will look into the matter you raise below very carefully.” 

On October 30, Xiao et al. finally publicly released their raw amplicon sequence data. However, as of the publication of this piece, the amplicon sequence data submitted by Xiao et al. is missing the actual raw data files that would allow for others to assemble and verify their pangolin coronavirus genome sequence.

Important questions remain that need to be addressed: 

  1. Are the pangolin coronaviruses real? The caption for Figure 1e in Xiao et al. states: “Viral particles are seen in double-membrane vesicles in the transmission electron microscopy image taken from Vero E6 cell culture inoculated with supernatant of homogenized lung tissue from one pangolin, with morphology indicative of coronavirus.” If Xiao et al. isolated the pangolin coronavirus, would they share the isolated virus sample with researchers outside of China? This could go a long way toward verifying that this virus actually exists and came from pangolin tissue.
  2. How early in 2020, or even 2019, were Liu et al., Xiao et al., Lam et al. and Zhang et al. aware that they would be publishing results based on the same dataset?
    a. Was there any coordination considering that one was preprinted on February 18 and three were preprinted on February 20?
    b. Why did Liu et al. (2019) not make their sequence read archive data publicly accessible on the date they deposited it on NCBI’s database? Why did they wait until January 22, 2020 to make this pangolin coronavirus sequence data public.
    c. Before the Liu et al. 2019 Viruses data was released on NCBI on January 22, 2020, was this data accessible to other researchers in China? If so, what database was the pangolin coronavirus sequencing data stored on, who had access, and when was the data deposited and made accessible?
  3. Will the authors cooperate in an independent investigation to track the source of these pangolin samples to see if more SARS-CoV-2-like viruses can be found in the March to July 2019 batches of smuggled animals—which could exist as frozen samples or be still alive in the Guangdong Wildlife Rescue Center?
  4. And will the authors cooperate in an independent investigation to see if the smugglers (were they imprisoned? or fined and let go?) have SARS virus antibodies from regular exposure to these viruses?