Immune pressure is key to understanding observed patterns of respiratory virus evolution in prolonged infections.

ABSTRACT: Analyses of viral samples from prolonged SARS-CoV-2 infections as well as from prolonged infections with other respiratory viruses have indicated that there are several consistent patterns of evolution observed across these infections. These patterns include accelerated rates of nonsynonymous substitution, viral genetic diversification into distinct lineages, parallel substitutions across infected individuals, and heterogeneity in rates of antigenic evolution. Here, we use within-host model simulations to explore the drivers of these intrahost evolutionary patterns. Our simulations build on a tunably rugged fitness landscape model to first assess the role that mutations that impact only viral replicative fitness have in driving these patterns. We then further incorporate pleiotropic sites

SUBMITTER: Coats A 

PROVIDER: S-EPMC12360705 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature