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Why viral mutation rates depend on how you measure them

David J Pascall

May 29, 2026

Viral mutation rates can be measured two ways: by counting actual mutations in individual virions, or by tracking changes in consensus sequences across a population. These give different answers because the consensus rule you choose—majority vote, most common, etc.—shapes what you measure. The distinction matters for accurately dating viral outbreaks and understanding within-host evolution.
Published as Consensus-level substitution rates are distinct from the virion-level rate arXiv:2605.31305
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