Secondary structure of the SARS-CoV-2 genome is predictive of nucleotide substitution frequency.

ABSTRACT: Accurate estimation of the effects of mutations on SARS-CoV-2 viral fitness can inform public-health responses such as vaccine development and predicting the impact of a new variant; it can also illuminate biological mechanisms including those underlying the emergence of variants of concern. Recently, Lan et al. reported a model of SARS-CoV-2 secondary structure and its underlying dimethyl sulfate reactivity data (Lan et al., 2022). I investigated whether base reactivities and secondary structure models derived from them can explain some variability in the frequency of observing different nucleotide substitutions across millions of patient sequences in the SARS-CoV-2 phylogenetic tree. Nucleotide basepairing was compared to the estimated 'mutational fitness' of substitutions, a measurement

SUBMITTER: Hensel Z 

PROVIDER: S-EPMC11870649 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature