The origin of the SARS-CoV-2 virus, which has triggered the COVID-19 pandemic, has been hotly debated.
This debate has triggered substantial difficulties within the Australia-China relationship, with a name by Overseas Minister Marise Payne for one more inquiry into its origin being thought of by China as a hostile act.
What’s not unsure is the closest kin of the virus are present in bats. How, the place and when the virus spilled over into people is the contentious challenge.
One broadly supported speculation is the spillover occurred within the “moist markets” of Wuhan, the place many species of wildlife from throughout China are held in crowded circumstances.
Nevertheless, there’s no proof the species of bats during which the closest kin of SARS-CoV-2 are discovered have been offered by means of the Wuhan moist markets at any time within the two years earlier than the pandemic. This speculation requires the existence of a “bridge host”, one other species that turns into contaminated by way of spillover from the unique bat hosts, after which passes the virus onto people.
Bridge hosts are well-known in lots of rising human illnesses. For instance, Hendra virus, which my group research, has flying foxes as its reservoir. Hendra spills over to horses with some frequency. Horses then amplify the virus as a bridge host and might infect people.
Luckily, that is extraordinarily uncommon, with solely seven identified circumstances. Tragically, 4 of these individuals died. Hendra has by no means been identified to unfold instantly from flying foxes to people.
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Extra proof a lab leak may be very unlikely
A second, rather more contentious speculation is the origin of the pandemic was the results of a “lab leak”.
Wuhan has one of the vital refined virological laboratories in China, and the laboratory does work on bat viruses. The suggestion is the virus might have inadvertently been launched into the overall neighborhood by way of one of many employees. No direct proof helps this speculation.
A brand new pre-print research, launched on-line this month, gives sturdy proof to assist the “pure spillover” speculation, with outcomes which can be onerous to reconcile with the “lab leak” speculation.
The research is but to be peer reviewed. Nevertheless it’s based mostly on an in depth examination of the genetic sequences of two early lineages obtained from individuals contaminated in late 2019 and early 2020.
For comfort, these two lineages are referred to as A and B. The 2 lineages differ by simply two nucleotides (letters within the genetic code) at two completely different key websites within the genetic sequence.
If there was a single lab escape occasion, the separation into lineages A and B will need to have occurred after the lab escape. We might subsequently anticipate to see a considerable variety of intermediate lineages, with the lineage A nucleotide at one web site, and the lineage B nucleotide on the different web site.
Nevertheless, if nearly all the genetic sequences obtained from people are “pure” lineage A or pure lineage B, this means there have been not less than two completely different spillover occasions, both instantly from bats or by way of bridge hosts.
And the evolution of the 2 lineages occurred earlier than people have been contaminated.
The researchers downloaded all full genetic sequences for SARS-CoV-2 that had been lodged in a broadly used genomic database. Of those sequences, 369 have been lineage A, 1,297 have been lineage B and simply 38 have been intermediates.
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Genetic sequencing isn’t excellent. Shut examination of the 38 intermediates strongly prompt they have been extra prone to be sequencing errors of pure lineage A or lineage B than to be true intermediates.
The genetic proof, subsequently, suggests very strongly there have been not less than two separate spillover occasions into human populations, one being from lineage A and one other being from lineage B.
Did a human convey SARS-CoV-2 to the moist markets?
The information don’t inform us there have been solely two spillover occasions — there might have been extra. Nor do they inform us whether or not these spillovers occurred instantly from bats, or whether or not some or all occurred by way of an intermediate bridge host.
A Nature information article suggests this proof factors to the spillover having occurred by way of the wildlife commerce, however I believe that is taking it a step too far.
Whereas a few of the wildlife species offered by means of the Wuhan moist market can certainly turn out to be contaminated with SARS-CoV-2 (for instance raccoon canines and mink), there’s no proof any offered by means of the market have been contaminated.
Lots of the earliest human viral sequences (all lineage B) have been recovered from the Wuhan seafood market, however moist markets and abattoirs are well-known to be locations the place the SARS-CoV-2 virus spreads very nicely from human to human.
So, it might have been a human who introduced the virus to the Wuhan seafood market, relatively than a species of wildlife.
One factor we do know is that this pandemic originated by means of a human coming involved with one other species contaminated with the virus.
It’s unknown whether or not this was a bat or a bridge host, and whether or not this contact occurred in a wildlife market, or in a bat cave, or some other place solely completely different.
Nonetheless, as people encroach increasingly on the habitats of untamed animals and as wild animals are introduced extra often into shut contact with people, we are able to anticipate additional spillovers and pandemics to happen.
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Hamish McCallum receives funding from the Australian Reserch Council and from the US companies NSF, NIH and DARPA