RE: New York Times "Bracing for the BA.2 Wave"24 Mar 2022 08:37
Variants are driving the Covid-19 pandemic. New variants, mutated to improve transmissibility, immune evasion, and pathogenicity, have emerged to fuel wave after wave of new infections. These new strains, to date, have almost exclusively mutated via point mutations, small deletions, or insertions.
There is a new class of SARS-CoV-2 that the scientific community has long contended may soon become a problem. These are SARS-CoV-2 recombinants. Recombinants are the result of exchanging one part of a virus for another. Recombination is possible with SARS-CoV-2 if a host cell is infected with two different variants at the same time. For SARS-CoV-2, this may occur when one variant displaces another over time, such as the current displacement of BA.1 by BA.2 or the recent overtaking of Delta by Omicron.
The New York Times reports 463 million confirmed global Covid cases since the pandemic's start. This number is likely much higher, perhaps in the billions, with asymptomatic and unreported cases. Millions of cases extrapolated into dozens of significant strains throughout the past two years yield the ideal breeding ground for new recombinant strains.
Coronaviruses are particularly prone to recombination as template switching, that is polymerase jumping from one strand to another, is required for messenger RNA synthesis. Although most of these jumps occur at sequences called transcription regulatory sequences (TRS), other sites have also been documented as template switching sequences, albeit at a lower frequency. The SARS-CoV-2 replication transcription machinery may also switch templates at transcription pause sites when they encounter stable secondary structures.
Although these recombinants have been identified, their significance remains to be determined. To date, none of these seem to show a propensity for displacing current variants. The concern comes chiefly from the fact that recombination of existing SARS-CoV-2 viruses actually occurs and they are not so rare as to remain undetected. New recombinants that arise may be able to enhance the three critical virological variables: transmissibility, immune evasion, and virulence.
Recombinants may also appear not only by coinfection in humans, but infection in the large reservoir of animal populations SARS-CoV-2 is capable of infecting, namely housepets, mice, deer, and others.
We also note detection of highly mutated reverse zoonosis variants in New York City sewers containing nearly sixty amino acid changes, posing another risk of recombination. There is a chance that SARS-CoV-2 could coinfect an animal with another coronavirus, resulting in a recombinant that makes its way back to humans. This is of particular concern as some animal viruses have an extensive set of mutations in the Spike protein and larger genome, for example, deer viruses in Ontario were found with 76 nucleotide mutations throughout the virus.
These are the early days in our detection and understanding of recombinan
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