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SARS-CoV-2 Pops Up, Mutated, Beyond the Respiratory Tract

As if the waves of novel variants of “interest” and “concern” sweeping the planet haven’t been enough, and we find versions of SARS-CoV-2 dodging in and out of species in a complex pattern of spillovers and spillbacks, we discover that it’s even sneakier. Two new papers in Nature Communications, from a group at the Max Planck Bristol Centre of Minimal Biology, describe how the virus can differ genetically in different parts of the same host.

That may mean that if vaccines and treatments vanquish the virus in the respiratory tract, the pathogen might persist elsewhere. And the viruses in new places replicate and infect more vigorously, better able to elude our immune response. That’s not good news as protection from vaccinations or having had COVID-19 wanes.

We already knew that the virus can spew new mutations within the body of a person with compromised immunity. And it mutates rapidly in the non-vaccinated. But the new research shows that novel variants percolate into existence in different bodily niches – with an individual.

“Our results showed that one can have several different virus variants in one’s body. Some of these variants may use kidney or spleen cells as their niche to hide, while the body is busy defending against the dominant virus type. This could make it difficult for the infected patients to get rid of SARS-CoV-2 entirely,” said Kapil Gupta, lead author of one article.

The action of a virus entering a host cell centers around a pocket in the part of the virus’s spike protein that the immune system recognizes. Altering the three-dimensional shape of the pocket makes the virus like the Romulan cloaking device from Star Trek, which makes their warships dissolve into invisibility as a Federation starship nears.

The researchers studied the pocket in viruses from a single English patient that have a deletion mutation that removes 8 of the 1273 amino acids of the spike protein. This happens near a critical spot called the furin cleavage site, which is where the two parts of the spike are cut, one glomming onto a human cell while the other drags the virus inside the cell.

But instead of the missing part disabling the virus, the researchers found that the pathogen contorts so that it can still enter human cells. And that’s part of how it continually reinvents itself, in different ways in different nooks and crannies of a host’s hapless body. The English patient’s version of the virus, called BriSdelta, replicates vigorously in monkey kidney cells in culture and in human colon cancer cells, but not in human lung cancer lining cells. That could mean that the predilection for respiratory surfaces shifts to elsewhere when the virus is impaired.

The new version of the virus is also better at replicating and infecting than earlier variants. “In the heterogeneous environment of the human body, such deletion variants can emerge in suitable cell types serving as potential niches for SARS-CoV-2 to further evolve or specialize,” the researchers write.


The researchers probed how this happens using artificial versions of the virus assembled using synthetic biology techniques. The second paper describes their “synthetic minimal virions,” aka MiniVs, of wild type SARS-CoV-2 and combinations of the mutations that have peppered the parade of variants.

And they found that when fatty acids released during inflammation – the initial innate response to infection – bind the new mutant, a subtle shift in the position of the spike cloaks it from the onslaught of antibodies from the more specific adaptive arm of the immune response.

The researchers have formed a company, Halo Therapeutics, to develop pan-coronavirus antivirals based on the tango between the pocket and the ACE-2 receptors on human cells – no matter where in the body they are.

So as we take off our masks and joyously get back to some semblance of normality, let’s not forget that SARS-CoV-2 is still out there, everywhere, and ever changing. We must be ready for next time – more on that next week.

  1. Rikki Lewis cites the Kapil Gupta article ‘Structural insights in cell-type specific evolution of intra-host diversity by SARS-CoV-2’ in her posting. A single passage in Vero E6 cell revealed a NSPRRARSV deletion in Spike gene for isolate hCoV-19/England/02/2020.

    “Direct RNA sequence analysis of a virus stock of SARS-CoV-2 isolate hCoV-19/England/02/2020, produced by a single passage in Vero E6 cells, revealed the presence of the WT SARS-CoV-2 and the BriSΔ variant (Fig. 1a)…. Nanopore direct RNA sequencing confirmed that the limiting dilution yielded WT SARS-CoV-2 from Caco-2 cells. In contrast, BriSΔ was selected for in Vero E6 cells (Fig. 1a) as expected,”, by Kapil Gupta , Christine Toelzer and others

    Why the deletion occurred in Vero E6 cells, and not Cacao-2 cells, it is not clear whether the authors pursued that question. Rather, Gupta by using reverse genetics created a delta PRRA spike gene that contained a deleted PRRA

    “deleting only PRRA in S by reverse genetics resulted in a recombinant ΔPRRA SARS-CoV-2 which exhibited increased infectivity and viral titer in Vero E6 cells”,

    Gupta footnote 19 cited the Brian Johnson article, ‘Loss of furin cleavage site attenuates SARS-CoV-2 pathogenesis’, as to how the delta PRRA was created. Brian Johnson pointed to the Xuping Xie article, ‘An Infectious cDNA Clone of SARS-CoV-2’, where Xie strung together cDNA fragments using restriction sites, adding or deleting whatever fragments they wanted to.

    So the Gupta study group just by creating ΔPRRA must have had some interest in why NSPRRARSV was being deleted in Vero E6 cells. Gupta stated regarding his study’s simulations,

    “Short-range electrostatic and van der Waals interactions were truncated at 1.4 nm while long-range electrostatics were treated with the particle mesh Ewald method “

    It is not clear whether during these simulations, Gupta was testing why NSPRRARSV was being deleted in Vero E6 cells. But the possibility of electrostatic or van der Waals forces being modified in the furin cleavage site during cell passage, resulting in the deletion, may have been in the background. But rather in the foreground, Gupta studied the differences in infectivity of the wild type versus the modified.

    Michelle Vu study group authored a paper studying the furin cleavage site deletions (at the same time as Gupta), stated

    “Our prior work found that the absence of TMPRSS2 in Vero E6 cells plays a role in selection of SARS-CoV-2 strains with FCS deletions . …. Infection of untreated TMPRSS2-expressing Vero E6 revealed no difference in replication between WT and ΔQTQTN …. The presence of the FCS in SARS-CoV-2 plays a critical role in infection and pathogenesis by facilitating an increase spike processing upon nascent virion release. This FCS, unusual to SARS-like coronaviruses, has been highlighted as a potential “smoking gun” for an engineered virus. Yet, the FCS alone is insufficient to drive infection and pathogenesis. The upstream QTQTN motif adds two distinct elements that contribute to this capacity and virulence.”, in the article, ‘QTQTN motif upstream of the furin-cleavage site plays key role in SARS-CoV-2 infection and pathogenesis.’, Michelle Vu , Kumari Lokugamage, and many others

    Why NSPRRARSV is being selected for deletion during cell passage, and other parts of the Covid-19 spike gene are not being selected, may be a ‘smoking gun’ to use Vu’s terminology.

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