Hungarian scientists claim that samples of Antarctic soil sent to a Shanghai firm in 2019 became contaminated with an unknown variant

By Sarah Knapton

An early version of Covid-19 that appears to have been grown in a laboratory has been discovered in samples from a Chinese biotechnology firm.

The finding lends weight to claims that the virus may have started life as a lab experiment that accidentally leaked out.

Bioinformatics experts from the University of Veterinary Medicine and Lorand University in Budapest, Hungary, made the discovery by accident while examining genetic data from soil samples collected from Antarctica in late 2018 and early 2019.

The samples were sent to Sangon Biotech in Shanghai for sequencing in Dec 2019, where they became contaminated with a previously unknown variant of Covid-19.

The variant has mutations that bridge the gap between bat coronavirus and the earliest Wuhan strain, so it may be an ancestral version of the virus.

The samples also contain DNA from hamsters and monkeys, suggesting that the early virus may have been grown in animal cell lines.

Viscount Ridley, author of Viral: The Search for the Origin of Covid-19, said: “The unique mutations hint at it being an ancestral variant. So if it was sequenced in say mid-December, before anybody had identified the virus in people and started trying to grow it in labs, then it points to secret samples in labs in 2019.”

Commenting on the animal DNA discovered, he said: “These are not from seals or penguins but from African green monkeys and Chinese hamsters. Both species are the source of commonly used laboratory cell lines.”

Sangon Biotech in the spotlight
Sangon Biotech is frequently used by Chinese scientists for sequencing, including the Wuhan Institute of Virology, which some experts think is the most likely location for a leak.

The exact date at which the DNA extraction took place is uncertain. However, researchers say that if it took place in December 2019, the virus could be the ancestor of the original human Wuhan strain.

If it was sequenced in early 2020, it may have been contaminated from experiments carried out by researchers trying to learn more about the emerging virus.

Dr Jesse Bloom, a virologist from the Fred Hutchinson Cancer Research Centre in Seattle, re-ran the data and confirmed that the Antarctic samples did contain Covid-19 which had three key mutations which brought bat coronaviruses closer to the first human Wuhan strain, Wuhan-Hu-1.

Currently, the closest natural relatives to Covid-19 have been found in bats. One such bat coronavirus, named RaTG13, was found in caves in Yunnan Province, in south-western China, while several others, named Banal 20 to 52, were discovered in Laos, which shares a border with Yunnan.

Both areas were being studied by “virus hunters” with samples sent to researchers at the Wuhan Institute of Virology.

Covid virus origins
Describing the significance of the discovery, Dr Bloom said: “Those three mutations are intriguing because they are all ancestral mutations that move the sequence ‘closer’ to the bat coronavirus relatives RaTG13 and Banal 20-52 relative to first reported Wuhan-Hu-1 sequence from the Huanan Seafood Market.”

In May 2021, a team of US evolutionary biologists published research on what an ancestor to Covid-19 should look like, and came up with two options. One had the same three mutations found in the samples.

“A virus with those three mutations relative to Wuhan-Hu-1 is one of the two plausible progenitors for all currently known human SarsCov2s,” added Dr Bloom.

“The timeline matters a lot here. If they were sequenced in Dec 2019 then it’s exceptionally important, because [China] holds SarsCov2s not discovered until December 30 to 31.

“On other hand, if sequenced in early 2020 then they could be contaminated with some early patient samples and still concord with Chinese government timeline. Right now, it doesn’t seem there is enough info to narrow down timeline to distinguish between these.

“All we can say is that these samples were contaminated at Sangon Biotech with some early SarsCov2 viruses, some of which appear to have been from lab-grown samples.”

The Hungarian team say that when it first pointed out the discrepancy in the sequencing data, the samples were immediately removed from the genetic database by the Chinese, although have since been restored.

Sangon Biotech has been approached for comment.

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