An article in Science explores the evidence for the animal origin of COVID, which was first detected in December 2019, but inferred to be present in Hubei province, China, for about a month beforehand.
The current COVID epidemic can be better understood by examining the severe acute respiratory syndrome coronavirus (SARS-CoV) outbreak which began in 2002. Investigations later found that horseshoe bats (Rhinolophus) in China harboured related coronaviruses. It was inferred that a sarbecovirus circulating in horseshoe bats seeded the progenitor of SARS-CoV in an intermediate animal host, most probably civet cats Although other possible intermediate hosts for SARS-CoV were identified, it is a population of civet cats within markets that appear to have acted as the conduits of transmission to humans from the horseshoe bat reservoir of SARS-CoV. Presumably a captive civet cat initially became infected by direct contact with bats or was infected before capture.
SARS-CoV-2 first emerged in Wuhan city, over 1500 km from the closest known naturally occurring sarbecovirus collected from horseshoe bats in Yunnan province. Coronaviruses genetically close to SARS-CoV-2 are circulating in horseshoe bats with wide geographic ranges indicate that the singular focus on Yunnan is misplaced. Confirming this assertion, the evolutionarily closest bat sarbecoviruses are estimated to share a common ancestor with SARS-CoV-2 at least 40 years ago, showing that these Yunnan-collected viruses are highly divergent from the SARS-CoV-2 progenitor.
Though the virus may have jumped to humans from direct horseshoe bat–to–human contact, a known risk for SARSr-CoVs, the first detected SARS-CoV-2 cases in December 2019 are associated with Wuhan wet markets. This is consistent with multiple animal-market–associated spillover events in November and December (9). It is currently not possible to be certain of the animal source of SARS-CoV-2, but it is notable that live animals, including civet cats, foxes, minks, and raccoon dogs, all susceptible to sarbecoviruses, were for sale in Wuhan markets, including the Huanan market (identified as an epicenter of the outbreak in Wuhan) throughout 2019.
Together, this suggests a central role for SARSr-CoV–susceptible live intermediate host animals as the primary source of the SARS-CoV-2 progenitor that humans were exposed to, as was the case with the origin of SARS.
Spillover events are not so rare, indicated by evidence of SARSr-CoV–specific antibodies in people living in rural areas, and even higher rates recorded in people living near bat caves. When exposed a densely packed human population, such as in Wuhan city, these spillover events have a much higher chance of resulting in substantial onward spread
Interestingly, the proximity of humans to wildlife may have been increased by demand for alternative meat sources caused by reduced availability of pork in 2019. This was caused by the African swine fever virus (ASFV) pandemic, which led to ∼150 million pigs being culled in China, resulting in a pork supply reduction of ∼11.5 million tonnes in 2019, and from which the country is still recovering. Increased use of cold-chain logistics in the wake of the ASFV pandemic means that frozen animal carcasses carrying SARS-CoV-2 may have been brought from much farther afield.
Once crossed over, SARS-CoV-2 readily established itself in humans by being a generalist, as opposed to being specialised for humans. Ironically, since humans are now the largest reservoir of the virus, animals in contact with humans are at risk of virus spillover. The article authors closed by stressing the need for much greater viral surveillance to spot emerging threats, as current coverage is extremely spotty.