Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2.

ABSTRACT: Public health researchers and practitioners commonly infer phylogenies from viral genome sequences to understand transmission dynamics and identify clusters of genetically-related samples. However, viruses that reassort or recombine violate phylogenetic assumptions and require more sophisticated methods. Even when phylogenies are appropriate, they can be unnecessary or difficult to interpret without specialty knowledge. For example, pairwise distances between sequences can be enough to identify clusters of related samples or assign new samples to existing phylogenetic clusters. In this work, we tested whether dimensionality reduction methods could capture known genetic groups within two human pathogenic viruses that cause substantial human morbidity and mortality and frequently reassort or

SUBMITTER: Nanduri S 

PROVIDER: S-EPMC11383015 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature