Year: 2026
Type: preprint
Abstract: Estimating viral substitution rates is central to evolutionary epidemiology, and recent interest in within-host evolution has sharpened the question of what such rates measure. I distinguish two classes of evolutionary rate estimand that are rarely separated in phylogenetic analysis: the virion-level substitution rate (VLSR), a molecular quantity counting mutational events along lineages, and consensus-level substitution rates (CLSRs), population-summary quantities counting allele frequency threshold crossings from below. CLSRs are indexed by the consensus-generation rule. The VLSR and CLSRs are both biologically meaningful, but not interchangeable. Because the consensus-generation rule defines a given CLSR, it should be reported routinely. This reflection should help analysts make more informed methodological choices when working with sets of virus sequences.
Source: arXiv (Cornell University)
Author: Pascall, David J
Institutions: University of Cambridge, MRC Biostatistics Unit
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: green
Awards: G2493601830, G2537968379
OpenAlex ID: W7162998796