An evaluation of phylogenetic methods for reconstructing transmitted HIV variants using longitudinal clonal HIV sequence data.

ABSTRACT:

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A population of human immunodeficiency virus (HIV) within a host often descends from a single transmitted/founder virus. The high mutation rate of HIV, coupled with long delays between infection and diagnosis, make isolating and characterizing this strain a challenge. In theory, ancestral reconstruction could be used to recover this strain from sequences sampled in chronic infection; however, the accuracy of phylogenetic techniques in this context is unknown. To evaluate the accuracy of these methods, we applied ancestral reconstruction to a large panel of published longitudinal clonal and/or single-genome-amplification HIV sequence data sets with at least one intrapatient sequence set sampled within 6 months of infection or seroconversion (n = 19,486 sequences, median [

SUBMITTER: McCloskey RM 

PROVIDER: S-EPMC4093844 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature