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 changes in the consensus sequences. 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 a routine reporting requirement. This reflection should help analysts make more informed methodological choices when working with sets of virus sequences.

翻译：估算病毒替代速率是进化流行病学的核心问题，近年来对宿主内进化的关注进一步深化了这类速率测量对象的内涵。本文将两类进化速率估计量加以区分——这两类估计量在系统发育分析中鲜有明确分离：病毒颗粒级替代速率（VLSR）是统计谱系间突变事件的分子量；共识级替代速率（CLSR）是统计共识序列变化的群体汇总量。CLSR由共识生成规则进行索引。VLSR与CLSR均具有生物学意义，但不可相互替代。由于共识生成规则定义了特定的CLSR，因此应将其列为常规报告要求。这一思考有助于分析人员在使用病毒序列数据集时做出更明智的方法学选择。