Incorporating Within-Host Diversity in Phylogenetic Analyses for Detecting Clusters of New HIV Diagnoses

Incorporating Within-Host Diversity in Phylogenetic Analyses for Detecting Clusters of New HIV Diagnoses

BackgroundPhylogenetic analyses of HIV sequences are used to detect clusters and inform public health interventions. Conventional approaches summarize within-host HIV diversity with a single consensus sequence per host of the pol gene, obtained from Sanger or next-generation sequencing (NGS). There...

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Bibliographic Details
Main Authors: August Guang, Mark Howison, Lauren Ledingham, Matthew D’Antuono, Philip A. Chan, Charles Lawrence, Casey W. Dunn, Rami Kantor
Format: Article
Language:English
Published: Frontiers Media S.A. 2022-02-01
Series:Frontiers in Microbiology
Subjects:
HIV
cluster inference
profile sampling
phylogenetics
next generation sequencing (NGS)
near-whole-genome
Online Access:https://www.frontiersin.org/articles/10.3389/fmicb.2021.803190/full

Internet

https://www.frontiersin.org/articles/10.3389/fmicb.2021.803190/full

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