Consensus-level substitution rates are distinct from the virion-level rate
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arXiv
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| Format: | Preprint |
| Publié: |
2026
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| _version_ | 1866911733108441088 |
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| author | Pascall, David J |
| author_facet | Pascall, David J |
| contents | 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. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2605_31305 |
| institution | arXiv |
| publishDate | 2026 |
| record_format | arxiv |
| spellingShingle | Consensus-level substitution rates are distinct from the virion-level rate Pascall, David J Populations and Evolution Methodology 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. |
| title | Consensus-level substitution rates are distinct from the virion-level rate |
| topic | Populations and Evolution Methodology |
| url | https://arxiv.org/abs/2605.31305 |