SARS-CoV-2 related viruses from bats in Laos

Various SARS-CoV-2 like viruses have been isolated from bats in China, Thailand, and Japan, but none have a spike protein that can bind ACE2 and allow entry into human cells. Sampling of bats in Laos has now revealed the presence of such viruses.

The genome of a virus called RaTG13, from Rhinolophus affinis bats in China, is the closest to SARS-CoV-2 (although infectious RaTG13 has never been isolated). However the spike receptor binding domain (RBD) encoded in this genome has low sequence similarity with that of SARS-CoV-2 and its affinity for ACE2 is very limited. RaTG13 is clearly not the proximal ancestor of SARS-CoV-2.

Sampling of 645 bats from limestone caves in Northern Laos (see map) yielded three Sarbecovirus genomes, called BANAL-52, -103, and -236, with high sequence similarity to SARS-CoV-2 and RaTG13. These three viral genomes were obtained from three different Rhinolophus species. Of the 17 amino acids that interact with the receptor binding domain of ACE2, 16 are conserved between SARS-CoV-2 and BANAL-52 or -103, and 15/17 conserved with BANAL-236. In contrast, only 11/17 RBD amino acids are conserved among SARS-CoV-2 and RaTG13. In other words, the RBD encoded in these BANAL genomes are closer to SARS-CoV-2 than that of any other known bat virus.

Binding affinity assays done with purified proteins revealed that the BANAL-52/103 and -236 spikes bind ACE2 with affinities in the low nanomolar range, comparable to reported values for the SARS-CoV-2 spike.

Lentiviral particles with the spike protein from BANAL-236 were able to bind and enter human cells producing ACE2. Entry of this virus was blocked by human sera containing antibodies to SARS-CoV-2 but not by control sera.

Infectious BANAL-236 virus was recovered from a bat fecal swab after inoculation of Vero cells, providing a rare virus isolate for a bat SARS-CoV-2 like virus. The virus will be useful for studying the biology of infection.

Recombination analysis demonstrated that the SARS-CoV-2 genome is a mosaic of at least five different genomes, including BANAL-52, -103, and -236, and the previously published RmYN02, RpYN06, and RaTG13, the latter all discovered in China. The implication of these observations is clear: SARS-CoV-2 likely arose from recombination of viruses circulating in different species of Rhinolophus bats in the limestone caves of South China and Southeast Asia. Because the RBD of the BANAL isolates can mediate binding to and entry into cells that produce ACE2, no host to host passage need be hypothesized to explain increased RBD affinity in an intermediate host before spillover into humans.

The spike proteins encoded in the BANAL isolates do not have the furin cleavage site found in the protein from SARS-CoV-2. Such sites might be present in viruses within these bat communities, but were missed due to insufficient sampling. Alternatively, it is possible that selection for the furin cleavage site occurred after spillover into humans or another intermediate host.

These findings further emphasize and demonstrate that SARS-CoV-2 came from Nature, not from a lab.

7 thoughts on “SARS-CoV-2 related viruses from bats in Laos”

  1. Dr Aidan P Cooney

    Vincent. Would it be possible to splice a part of a genome and recombined inorder that a polypeptide is produced with a primary structure; which after folding produced a secondary structure in which the hydrogen bonding brought cationic amino acids in close proximity. Thus producing a ” strained system” which was under constant electrostatic repulsion .
    If you like ” force directed”.
    So that mutation is no longer random but in fact deterministically chaotic?
    This ” force directed mutation” would increase the mutation rate because the virus constantly wants to produce a variant that is ” under less electrostatic repulsion .
    Could this lead to a mutation rate that was now exponential?
    What if the altered original genome was tailored to code for a a polypeptide with a “genetic hook” to hold the stained polypeptide in a constant state of strain.
    In which the structure with the cationic amino acids was stabilised.
    If all of this could force direct variants with increased mutation rate in which the rate continually increased. Thereby making a variant with increased human transmission more likeky”.
    If SARS(COV)-2 was such a deterministically chaotic system it would be virtually impossible to stop! It would be completely unpredictable with infection numbers not following any particular pattern under a normal plot.
    If however you stuck the data on a poincare plot perhaps you could self-similarity I.e. a repeating pattern.

  2. Here is my comment on the Lin-Fa Wang paper back in February:

    Great paper. The Lancang River in Yunnan province becomes the Mekong in South East Asia. Yunnan’s capital city of Kunming is a transportation hub connected to Wuhan and other major Chinese cities. I suspect that the bats and nocturnal arboreal mammals (palm civets, pangolins, and racoon dogs) can be found in the same trees at night throughout this region/ecosystem. In addition to China and northern Thailand, Laos and Vietnam (along the Mekong) should be considered ground-zero for these SC2r-CoVs, in my opinion.

    Normally I’d be proud of my well reasoned predictions but, given all the geopolitical madness involved, this discovery feels more like salt in a festering wound.

    Vincent: you might want to search for the e-mail I sent TWiV on May 8th, 2020. Festering indeed. I, Cassandra.

  3. How are those findings incompatible with the hypothesis a natural virus escaped from a lab where it was kept after having been sampled, or result from in lab recombination, even accidental? The Indochine peninsula is not exactly close to Wuhan. The question of how it ended up there is still unresolved.

  4. A few words in reply to “ALEX” ( 28.September 2021 @ 7:17pm):

    1. it is important to understand that the Wuhan Lab did not have “a natural virus”, the widely maligned RaTg13 was never isolated, i.e. they never had an infectious virus and were never able to grow it in cells.
    2. a proposed “in-lab-recombination” would require to have not only this but also all the other relevant donor viruses at hand – and infect an animal with all of them and then to be able to isolate, identify and grow the result of the recombination.
    3. the geographic distance between a limestone cave in Laos and any metropolis in China is woefully irrelevant. Or did the Marburg virus originate in Germany? HIV in LA? Zika in New York City?

  5. A few words in reply to “Holm Bussler”
    1) It is important to understand that we don’t know what the Wuhan Lab did or did not have. It is also important to note that it likely only matters what is sequenced, not what is isolated, as grant application docs clearly show the WIV was interested in synthesizing infectious genomes based on sequence data.

    2) No, in one scenario, the natural recombination could have occurred before sampling, then all that is needed is the sequence data from a fecal swab (or isolation of the virus).

    In a scenario in which the recombination did not happen in the wild, a super-infection scenario with multiple strains still isn’t needed.
    A possible scenario would require that the database in Wuhan had similar virus genome data. Given that they also expressed interest in synthesizing “consensus genomes” from viruses with 95% sequence identity or greater, It would just require a set of genomes 95% similar or more to SARS-CoV-2 (we know they had at least one), that when combined make a consensus genome very similar to SARS-CoV-2

    3) “did the Marburg virus originate in Germany?” The 1967 oubreak did come from a German lab, yes. The virus crossed the geographic distance because of lab-associated activities. Generally speaking, we see lots of diversity in the Marburg virus with an MRCA estimated to be nearly 200 years ago. This is not comparable to SARS-CoV-2 with an estimated MRCA in November 2019, and phylogenetics pointing back to the MRCA being in Wuhan, not Africa (as is the case for Marburg).
    Similar arguments are made for Zika and HIV – not analagous to the SARS-CoV-2 situation.

    I know that 1) and 2) involve speculation and appeal to a gap in evidence, rather than actual evidence.
    At the same time, there is no evidence of any infected animals at the wetmarkets in Wuhan, phylogenetics shows that SARS-CoV-2 was spreading (and split into lineages A and B) before it reached the Huanana seafood market. Lineage A doesn’t have any real link to any wildlife market, and clinically diagnosed cases in November show up right around the estimated MRCA (rendering a multiple spillover hypothesis highly unlikely)…
    The natural spillover hypothesis at this point also involves speculation and appeals to gaps in evidence.
    “We didn’t sample nature enough” vs “We can’t check the WIV” database.

    Both hypotheses remain viable, with the natural spillover preferred just because that was assumed to have a higher prior probability.

  6. We have absolutely NO idea of what the Wuhan lab had or didn’t have. We have to trust the Chinese government, which is known to be very transparent right?

    If you think distance is irrelevant, you are going to have to explain how a virus can teleport itself thousands of miles away. I am waiting for the answer.

    Now, I am NOT saying there was a conspiracy or that the virus was engineered in a lab. What I am saying is that finding a related strain THOUSANDS of miles away doesn’t tell us anything about the lab leak hypothesis.

    The total lack of transparency of the authorities, including funding bodies in the US and the UK are not really helping the case, either. And we have the documents, see here:

    I don’t get the comparison with Marburg virus since, YES, it was named so after leaking from a lab in Germany. Which is the kind of scenario that is possible with the sars-cov2.

    I honestly don’t know what is true but I find the rejection of the lab leak hypothesis relies on Chinese reports, which no one in his right mind would believe are trustworthy sources.

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