ON THE ORIGINS OF THE OMICRON VARIANT OF THE SARS-COV-2 VIRUS
Abstract
A possible explanation based on first principles for the appearance of the Omicron variant of the SARS-CoV-2 virus is proposed
involving coinfection with HIV. The gist is that the resultant HIV-induced immunocompromise
allows SARS-CoV-2 greater latitude to explore its own mutational space. This latitude is not without
restriction, and a specific biophysical constraint is
explored. Specifically, a nearly two - to fivefold discrepancy in backbone hydrogen bonding is observed
between sub-molecules in Protein Data Bank files of the spike glycoprotein yielding two conclusions: mutagenic residues in the
receptor-binding subunit of the spike much more frequently do not participate in backbone hydrogen bonds;
and a technique of viral escape is therefore to remove such bonds within physico-chemical and functional constraints.
Earlier work, from which the previous discussion is entirely independent, explains these phenomena
from general principles of free energy, namely, the metastability of the glycoprotein. The conclusions therefore likely hold more generally as principles in virology.
Origin : Files produced by the author(s)