A new paper in Science (click on screenshot below, pdf here, reference at bottom) suggests that Covid-19—referred to in this study as SARS-CoV-2—likely originated in horseshoe bats that were collected in Yunnan in southern China, were not contaminations from the Wuhan Institute of Viriology (WIV), but were transferred to humans via an intermediate animal vector (probably a civet cat) in a wet market. Note that two of the authors are Chinese, and one might think that they have an interest in exculpating the WIV, but that opens up a whole can of worms that I’d prefer to avoid.
Here’s a phylogeny (family tree) of the “sarbecoviruses” that are evolutionarily closest to the Covid-19 virus, with the caption from the Science paper. Click on photo twice to make it really big.
Note that the three viruses closet to human coronavirus in sequence are all from areas close together in Yunnan, and all in species of horseshoe bats ( genus Rhinolophus, variants RpYN06, RmYN02, and PRC31). Viruses in pangolins (Manis javanica), also presumably derived from bats, are much less closely related, and thus unlikely as a source of human infection. The virus RaTG13, sequenced and kept at WIV, seems too distant from the human coronavirus to have been the source, and horseshoe bats are found not just in Yunnan, but are widely dispersed throughout China.
The authors posit that, since bats were not sold in Wuhan markets, another animal—they think the civet cat—is the likely transmitter of the virus to humans in a wet market, and this happened in about December of 2019. The bat virus may have gotten into a civet (or a raccoon dog, or a fox, or a mink) on one of the many farms where these animals are raised for sale as meat, and then transported to wet markets in other places in China.
As an interesting sidelight, the authors suggest that the spread of the coronavirus was promoted by a shortage of pork in China in 2019, which itself was due to swine flu that led to 150 million pigs being killed. They posit that other animals, like civet, could have replaced pork in the diet, and those animals would be intermediate vectors that led to the interspecies leap in late 2019. (Our own species is now considered the main vector for Covid-19!). They suggest, alternatively, that the virus could have survived in frozen wild meat rather than in live animals sold in wet markets.
Finally, now that we’re the main host of the virus, the authors worry that we ourselves could infect other wildlife, which would then become reservoirs for evolution and re-infection (this is called “reverse zoonoisis”)
There are several questions that are unanswered in this short paper, but may be common knowledge. How do the authors manage to discount a lab strain as a source of the human infection? Were the closest Yunnan viruses not kept in the Wuhan Institute? Did anybody sample civets or other animals sold in the Wuhan market for coronavirus? (The market, of course, is closed, so this may be impossible.) Why do the authors consider the civet cat (palm civet) the most likely intermediate host of the virus? They cite this paper, showing a near-identity of the human and palm civet virus, but do they have similar data from other mammals?
I am not an expert on the various theories of transmission of cornavirus from bats (the most likely origin) to humans, but offer this for your delectation.
Lytras, S., W. Xia, J. Hughes, X. Jiang, and D. L. Robertson. 2021. The animal origin of SARS-CoV-2. Science: DOI: 10.1126/science.abh0117