(via @Agent K)
U.S. Confirms Removal of Wuhan Virus Sequences from DatabaseDetails of the genetic makeup of some of the earliest samples of coronavirus in China were removed from an American database where they were initially stored, at the request of Chinese researchers, U.S. officials confirmed, adding to concerns over secrecy surrounding the outbreak and its origins.
The data, first submitted to the U.S.-based Sequence Read Archive in March 2020, were “requested to be withdrawn” by the same researcher three months later in June, the U.S. National Institutes of Health said in a statement Wednesday. The genetic sequences came from the Chinese city of Wuhan where the Covid-19 outbreak was initially concentrated.
(via @Lu Ann Lewellen)About a year ago, more than 200 data entries from the genetic sequencing of early cases of Covid-19 in Wuhan disappeared from an online scientific database.
Now, by rooting through files stored on Google Cloud, a researcher in Seattle reports that he has recovered 13 of those original sequences — intriguing new information for discerning when and how the virus may have spilled over from a bat or another animal into humans.
The new analysis, released on Tuesday, bolsters earlier suggestions that a variety of coronaviruses may have been circulating in Wuhan before the initial outbreaks linked to animal and seafood markets in December 2019.
The story began in early 2020, when researchers at Wuhan University investigated a new way to test for the deadly coronavirus sweeping the country. They sequenced a short stretch of genetic material from virus samples taken from 34 patients at a Wuhan hospital.
The researchers posted their findings online in March 2020. That month, they also uploaded the sequences to an online database called the Sequence Read Archive, which is maintained by the National Institutes of Health, and submitted a paper describing their results to a scientific journal called Small. The paper was published in June 2020. [...]
At the time, a spokeswoman for the N.I.H. said that the authors of the study had requested in June 2020 that the sequences be withdrawn from the database. The authors informed the agency that the sequences were being updated and would be added to a different database. (The authors did not respond to inquiries from The Times.)
On July 5, more than a year after the researchers withdrew the sequences from the Sequence Read Archive and two weeks after Dr. Bloom’s report was published online, the sequences were quietly uploaded to a database maintained by China National Center for Bioinformation by Ben Hu, a researcher at Wuhan University and a co-author of the Small paper.
On July 21, the disappearance of the sequences was brought up during a news conference in Beijing, where Chinese officials rejected claims that the pandemic started as a lab leak.
According to a translation of the news conference by a journalist at the state-controlled Xinhua News Agency, the vice minister of China’s National Health Commission, Dr. Zeng Yixin, said that the trouble arose when editors at Small deleted a paragraph in which the scientists described the sequences in the Sequence Read Archive.
“Therefore, the researchers thought it was no longer necessary to store the data in the N.C.B.I. database,” Dr. Zeng said, referring to the Sequence Read Archive, which is run by the N.I.H.
An editor at Small, which specializes in science at the micro and nano scale and is based in Germany, confirmed his account. “The data availability statement was mistakenly deleted,” the editor, Plamena Dogandzhiyski, wrote in an email. “We will issue a correction very shortly, which will clarify the error and include a link to the depository where the data is now hosted.”
The journal posted a formal correction to that effect on Thursday.
On their own, these sequences can’t resolve the open questions about how the pandemic originated, whether through a contact with a wild animal, a leak from a lab or some other route.
But the sequence of that bat virus found in 2013 differs from SARS-CoV-2 by about 1100 nucleotides, which means decades must have passed before it evolved into the pandemic coronavirus—and other species may well have been infected with the bat virus before it made the final jump into people. This great difference in sequences, says evolutionary biologist Andrew Rambaut at the University of Edinburgh, means researchers cannot use a few mutations like the ones Bloom highlights to look back in time to see the "roots" of the family tree of SARS-CoV-2 tree.
Rambaut notes that the Chinese researchers submitted their Small paper before requesting that the SRA remove the data. "The idea that the group was trying to hide something is farcical," Rambaut says. "If they were covering something [up] they surely would have not submitted the paper. … I don't like the insinuations about malfeasance where [Bloom] has zero knowledge of the reasons the authors of the paper had for removing their data."
Others are underwhelmed. "Jesse is resurfacing info that's been online for over a year and claiming it proves a cover-up," says Stephen Goldstein, an evolutionary virologist at the University of Utah. "I don't understand [his reasoning]." The Small paper is simply a good study that "unfortunately flew below the radar," he adds.
Bloom acknowledges that researchers can piece together the coronavirus sequences from the data found in the Small paper.
• it wasn't really a cover-up,
• the data is back online,
• there were no bombshell revelations = there was no reason to cover anything up.