Saturday, April 25, 2020

COVID-19: Whose Virus Is It Anyway? Possible origins of SARS-CoV-2

It's only reasonable you may want to know about the origins of the COVID-19 pandemic. After all, our lives have been affected, one way or the other. But was it the bat? Was it the pangolin? Or was it a lab experiment gone wrong? Let's look at the two most definitive evidence we have at hand: virus genomics and structure.

Evidence #1

The receptor binding domain (RBD) in the spike protein is the most variable part of the coronavirus family genome. SARS-CoV-2 seems to have an RBD that binds with high affinity to ACE2 from humans, and other species with high receptor homology. This RBD has six key amino acid residues.

Evidence #2

The second notable feature of SARS-CoV-2 is a polybasic cleavage site at the junction of S1 and S2, the two subunits of the spike. This allows effective cleavage by furin and other proteases and has a role in determining viral infectivity and host range. Insertion of proline to this site and subsequent addition of O-linked glycans are unique to SARS-CoV-2.

Keeping these in mind, we have:

Theory #1
Natural selection in animal before zoonotic transfer

As many early cases of COVID-19 were linked to the Huanan market in Wuhan, it is possible that an animal source was present at this location.

Given the similarity of SARS-CoV-2 to bat SARS-CoV-like coronaviruses, it is likely that bats serve as reservoir hosts for its progenitor. This "bat virus" or more formally, RaTG13 is nearly 96% identical to SARS-CoV-2. Its spike diverges in the RBD, which suggests that it may not bind efficiently to human ACE2. 

Malayan pangolins illegally imported into Guangdong province contain coronaviruses similar to SARS-CoV-2. Some "pangolin coronavirus" exhibit strong similarity to SARS-CoV-2 in the RBD, including all six key RBD residues. This clearly shows that the SARS-CoV-2 spike protein optimised for binding to human-like ACE2 is the result of natural selection.

Neither the bat nor the pangolin coronavirus, however, has polybasic cleavage sites. This means, no animal coronavirus has been identified that is sufficiently similar to be the direct progenitor of SARS-CoV-2. That said, the diversity of coronaviruses in bats and other species is massively undersampled. Mutations, insertions and deletions can occur near the S1–S2 junction of coronaviruses, which shows that the polybasic cleavage site can arise by a natural evolutionary process. This perfectly sets us up for our next theory.

Theory #2
Natural selection in human after zoonotic transfer

It is possible that a progenitor of SARS-CoV-2 jumped into humans to acquire the genomic features described above through adaptation, during undetected human-to-human transmission. Once acquired, these adaptations would enable the pandemic to take off.

All SARS-CoV-2 genomes sequenced so far have the genomic features described above and are thus derived from a common ancestor that had them too. The "pangolin coronavirus" has an RBD very similar to that of SARS-CoV-2, by the process of natural selection. From this, we can infer the same happened with the virus that jumped to humans. So we can say, with some degree of confidence, the insertion of polybasic cleavage site occured during human-to-human transmission.

From what we know the first case of COVID-19 has been traced back to November 2019. This presumes a period of unrecognised human-to-human transmission, between the initial zoonotic event and the acquisition of the polybasic cleavage site.

Theory #3
Lab experiment gone wrong

Basic research involving passage of bat SARS-CoV-like coronaviruses in cell culture and animal models has been ongoing for many years in biosafety level 2 laboratories across the world, and there are documented instances of laboratory escapes of SARS-CoV. In theory, it is possible that SARS-CoV-2 acquired RBD mutations during adaptation to passage in cell culture.

Having said that, the "pangolin coronavirus" with nearly identical RBDs, provides a much stronger explanation of how SARS-CoV-2 acquired these via recombination or mutation. The high-affinity binding of the SARS-CoV-2 spike protein to human ACE2 is most likely the result of natural selection on a human or human-like ACE2.

The acquisition of both the polybasic cleavage site and predicted O-linked glycans also argues against culture-based scenarios. New polygenic cleavage sites have only been observed after prolonged in-vivo passage whereas generating O-linked glycans likely involves an immune system.

Furthermore, if genetic manipulation had been performed, one of the several reverse-genetic systems available for coronaviruses would probably have been used. However, the genetic data irrefutably show that SARS-CoV-2 is not derived from any previously used virus backbone.

These are strong arguments that SARS-CoV-2 is not the product of purposeful manipulation.

Theory #2 seems most likely, given the information currently available, but more scientific data could swing the balance of evidence to favour one hypothesis over another. What's important is to further study the possible origins, not just for understanding the current zoonotic pandemic but also to prevent the potential future ones.

1. 'The proximal origin of SARS-CoV-2' by Andersen et al:
2. 'A pneumonia outbreak associated with a new coronavirus of probable bat origin' by Zhou et al:
3. 'A new coronavirus associated with human respiratory disease in China' by Wu et al:

Ashish Singh

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