Puzzles, challenges, and information reservoir of SARS-CoV-2 quasispecies

J Virol. 2023 Dec 21;97(12):e0151123. doi: 10.1128/jvi.01511-23. Epub 2023 Nov 21.

Abstract

Upon the emergence of SARS-CoV-2 in the human population, it was conjectured that for this coronavirus the dynamic intra-host heterogeneity typical of RNA viruses would be toned down. Nothing of this sort is observed. Here we review the main observations on the complexity and diverse composition of SARS-CoV-2 mutant spectra sampled from infected patients, within the framework of quasispecies dynamics. The analyses suggest that the information provided by myriads of genomic sequences within infected individuals may have a predictive value of the genomic sequences that acquire epidemiological relevance. Possibilities to reconcile the presence of broad mutant spectra in the large RNA coronavirus genome with its encoding a 3' to 5' exonuclease proofreading-repair activity are considered. Indeterminations in the behavior of individual viral genomes provide a benefit for the survival of the ensemble. We propose that this concept falls in the domain of "stochastic thinking," a notion that applies also to cellular processes, as a means for biological systems to face unexpected needs.

Keywords: cancer heterogeneity; coronavirus; deletion; error threshold; mutant spectrum; mutation; prion; ultra-deep sequencing; viral disease control; virus complexity.

Publication types

  • Review

MeSH terms

  • COVID-19* / virology
  • Genome, Viral
  • Humans
  • Quasispecies
  • RNA Viruses* / genetics
  • SARS-CoV-2* / genetics
  • SARS-CoV-2* / physiology