New Delhi: The debate on the origin of the coronavirus is back on social media platforms. A paper — published in August 2020 — on bat sequences from China and pertaining to the natural origins of COVID-19 was retracted this month from the Nature journal. The reason cited was that 41 of the 1,246 bat sequences studied came from bats from the Laos border region, not China, and 27 sequences had been duplicated.
A revised paper on the remaining sequences was published on 19 December after an independent peer review soon after the retraction. However, the retraction notice and subsequent standard publishing of a fresh paper has spurred a flurry of commentary online, alleging that these latest developments support the so-called ‘lab-leak’ theory, which gained traction in 2021.
In 2021, a flurry of news reports revealed email exchanges between the then-US infectious diseases head, Anthony Fauci, and scientists during the first few weeks of COVID-19, discussing the nature and possible ‘engineering’ of coronaviruses while talking about their origin. This fuelled speculations about a ‘lab leak’ during experiments at the Wuhan Institute of Virology, China, on samples sent from EcoHealth Alliance.
According to Peter Daszak, a corresponding author of the republished paper, which has brought back the ‘lab leak’ theory into online discussions, and president of EcoHealth, bats co-mingle across borders and the inclusion and subsequent exclusion of some bat sequences in the paper did not change the results substantially.
He added that it is just that since the paper focussed on China, as reflected in the title, the authors decided to remove the foreign sequences and repeat the entire analysis. In effect, the abstract and conclusion of the fresh paper are the same after peer review but with the number of sequences updated.
“This study is like many others in the field, employing well-established methods in phylogenetics and evolutionary biology to explore the relationships among coronaviruses identified in bats,” said B.R. Ansil, a postdoctoral fellow at the University of Oklahoma and bat genetics researcher with an experience of working on with bats in Asia.
“The author’s decision to retract the whole manuscript and upload the new one seems courageous and ethical, especially since such a step is bound to provoke controversy. I think It shows their commitment to accurate representation of findings,” he said.
Details of the paper
The paper, ‘Origin and cross-species transmission of bat coronaviruses in China’, was originally published in Nature Communications in August 2020. The authors are primarily affiliated with two institutes — the Wuhan Institute of Virology and the New York-based non-profit EcoHealth Alliance — which have been in the eye of a storm for the ‘lab leak’.
Peter Daszak is the president of EcoHealth Alliance. Other authors are from the Guangdong Academy of Sciences, China, and Duke-NUS Medical School, Singapore. Their paper was cited 154 times in other papers and, at times, in international policy documents.
The subsequent paper was submitted to the journal in August this year and published this month after peer review.
“The sequences from Laos are not identical to those from China, though some similarities are there — which is expected. The key question is how these Laos sequences got handled in the previous analyses and representations,” explained Ansil.
Supplementary data in the two papers show that Laos bats belong to a family that overlaps with another that could be the ancestral hosts for the SARS-CoV viruses.
“This paper specifically focuses on investigating the sharing of alpha and beta CoVs among different bat families and genera within China (hence, it is an error to have Laos sequences). They also included human CoV (SARS-CoV1 and 2) and Pangolin CoV sequences into the analyses to draw conclusions about the potential evolutionary origins of these viruses,” he added. “It is important to note that evolutionary origin here does not mean a direct spillover event from bats to humans but, instead, it means there is significant similarity between sequences found in these bats and SARS-CoV2.”
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Implications of retraction
While the retraction and publishing of a fresh paper after an independent peer review is a common procedure, several online commentators have latched on to the former.
Refuting speculations, EcoHealth previously denied that it submitted samples or bat sequences to Wuhan laboratory. However, some commentators pointed out that such sequences existed in the data set. Commentators also questioned the delay in the retraction of the paper.
However, neither the retracted nor the new paper, nor including or excluding the Laos sequences in the analysis, have any connection to the “engineering” of the virus in a lab or “leaking it”.
“This paper specifically focuses on investigating the sharing of alpha and beta CoVs among different bat families and genera within China (hence, it’s an error to have Laos sequences). There is not even a remote connection I see between the Laos sequences and the lab leak theory,” said Ansil.
Online commentators, however, questioned why the paper was retracted instead of being amended when the genetic differences between the sequences from China and Laos were insignificant. However, Ansil explained that since duplicates existed despite removing the Laos sequences, a reanalysis, and hence fresh paper, was necessary.
He said retractions generally receive negative attention while pointing out that the amount of COVID-19 literature published during the pandemic was overwhelming.
“As a researcher, I found it challenging to keep up with all the studies that came out at that time. This fast turnaround time implies a faster peer review process, which may or may not be as rigorous as at other times — which could have increased the chances of minor errors in the literature published at that time. I am not saying literature published at other times is error-free, but we expect the rigorous peer review process to identify such errors.”
Some have alleged the retraction of the “phoney conclusion” on the natural origins of coronavirus precedes Trump’s ascendency to the US presidency and could likely be a legal manoeuvre to evade imminent “proper scrutiny”.
ThePrint has contacted Peter Daszak for a comment, and the report will be updated upon receiving a response.
(Edited by Madhurita Goswami)
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