2021/12/08 by Robert Penner, Minus van Baalen, Penner, Robert +1
Biochemistry, Genetics and Molecular Biology · Environmental Science · Medicine · #Bacteriophages and microbial interactions #FOS: Biological sciences #Other Quantitative Biology (q-bio.OT) #Protein Structure and Dynamics #SARS-CoV-2 and COVID-19 Research
paper · pdf · doi:10.48550/arxiv.2201.07879
openalex publication_date 2021/12/08 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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 withoutr estriction, and a specific biophysical constraint is explored. Specifically, a nearly two- to five-fold 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.