Three recent studies give a detailed picture of how the coronavirus pandemic began and strengthen the case that the virus came from animals at the Huanan seafood market
28 February 2022
The SARS-CoV-2 virus appears to have jumped from animals to humans at the Huanan seafood market in Wuhan, China, at least twice in late 2019, according to three preliminary studies that give a remarkably detailed insight into how the covid-19 pandemic began.
The picture depicted by these studies is as follows. At some point before 2020, the ancestor of the SARS-CoV-2 coronavirus jumped from bats into other mammals. We don’t know when or where this happened or which mammals were involved.
But we do know that by November 2019, the coronavirus was spreading among mammals kept in cages at the Huanan seafood market. The evidence for this comes from nearly 600 swabs of objects at the market taken in January 2020. Of these, 33 tested positive for the virus, according to a report by the Chinese Center for Disease Prevention and Control.
An international group of coronavirus researchers led by Michael Worobey at the University of Arizona has now mapped the precise locations of these positive objects. The team found that 31 out of the 33 objects were in the western part of the market where live mammals were kept.
Five positive samples were found in just one market stall. The objects that tested positive at this stall included a metal cage in a back room, two carts used to move cages and a hair/feather remover – all objects directly associated with animals.
Documents and photographs show that the live mammals present at the Huanan market in November 2019 included raccoon dogs (Nyctereutes procyonoides), hog badgers (Arctonyx albogularis), Chinese bamboo rats (Rhizomys sinensis) and red foxes (Vulpes vulpes). All these animals can be infected by SARS-CoV-2, and we know that raccoon dogs are capable of spreading it.
Around 25 November 2019, the SARS-CoV-2 virus jumped from one of these infected mammals to a person. Then, around 2 December, it happened again, but this time with a slightly different version of the virus.
The evidence that the Huanan market was the source of the virus comes from multiple sources. For starters, the early covid-19 cases in December 2019 were clustered around the market, and many were directly linked to it. The first confirmed case of covid-19 was in a seafood vendor there who became ill on 10 December and went into hospital on 16 December, for instance.
Even if you only map those cases in December with no known link to Huanan market, they still cluster around the market, Worobey and his colleagues have shown.
Two distinct jumps
What’s more, it has long been known that there were two variants of SARS-CoV-2 right from the start, known as lineage A and B. They differ by two mutations: lineage A is more like related bat viruses, but lineage B was the first to infect people and became far more common.
There have previously been reports of intermediate forms, suggesting that one lineage arose from another after the jump to humans. But now a study by Jonathan Pekar at the University of California, San Diego, and his colleagues, including Worobey, suggests these intermediate forms are a result of sequencing errors or later mutations, and that the two early lineages were the result of two distinct jumps of the virus from animals to humans.
A third, separate study by George Gao at the Chinese Center for Disease Control and Prevention has provided more details on the object and animal tests done at the market. Most significantly, this research reveals for the first time that one object tested positive for lineage A.
All the other viruses found on objects at the market were lineage B, so this is the first evidence that both variants were present there. That further strengthens the case for the market being the place where the jumps to people took place.
The clincher would be direct evidence that some mammals at the market were infected with the SARS-CoV-2 virus, but that almost certainly doesn’t exist any more.
Health authorities in China did test some live and frozen animals at the market, including stray cats, dogs, snakes, rabbits and mice. No raccoon dogs at the market or from the farms and wild areas that supplied the market were ever tested, as far as Worobey’s team is aware.
But put together, the multiple lines of evidence described in these three studies add up to a strong case. “[It is] deep detective work… providing very convincing evidence for the Huanan market as [the] epicentre for the pandemic,” tweeted Marion Koopmans at the Erasmus University Medical Center in Rotterdam.
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