Phylogenetic prioritization of HIV-1 transmission clusters with viral lineage-level diversification rates.

ABSTRACT:

Background and objectives

Public health officials faced with a large number of transmission clusters require a rapid, scalable and unbiased way to prioritize distribution of limited resources to maximize benefits. We hypothesize that transmission cluster prioritization based on phylogenetically derived lineage-level diversification rates will perform as well as or better than commonly used growth-based prioritization measures, without need for historical data or subjective interpretation.

Methodology

9822 HIV pol sequences collected during routine drug resistance genotyping were used alongside simulated sequence data to infer sets of phylogenetic transmission clusters via patristic distance threshold. Prioritized clusters inferred from empirical data were compared to those p

SUBMITTER: Miller RL 

PROVIDER: S-EPMC9311310 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature