Speaker
Description
The accrual of nucleotide substitutions in virus genomes accompanies transmission of those viruses through their host populations. Because lineages with higher fitness tend to transmit rapidly to new hosts before incurring very many substitutions, large numbers of related sequences are usually interpreted as evidence of transmission success. Quantities like the local branching index (LBI) aim to identify successful lineages in this way, essentially by scoring sequences according to the number of close relatives captured in the dataset. While calculating measures like LBI from a given phylogenetic tree (or a distribution of trees) is easy, it can be difficult to judge whether apparent lineage success is affected by sampling bias. Epidemiologic characteristics, such as the distribution of incubation times, as well as the probability of being asymptomatic, also seem likely to shape the distribution of LBI in ways that might confound interpretations of successful transmission. To disentangle the contribution of these factors to LBI, we use compartmental models to simulate outbreaks and generate distributions of phylogenies. We find that LBI can be sensitive to noise if, for example, incubation times are long and sampling is both rare and unequal across the host population. We describe other situations where LBI fails to reflect viral fitness and identify situations where it is the most useful.
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