Open AccessA Robust Measure of HIV-1 Population Turnover Within Chronically Infected Individuals
Author(s) -
Guillaume Achaz
Publication year - 2004
Publication title -
molecular biology and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 6.637
H-Index - 218
eISSN - 1537-1719
pISSN - 0737-4038
DOI - 10.1093/molbev/msh196
Subject(s) - biology , coalescent theory , mutation rate , population , human immunodeficiency virus (hiv) , measure (data warehouse) , effective population size , population structure , evolutionary biology , mutation , statistics , sequence (biology) , genetics , genetic variation , mathematics , phylogenetics , demography , virology , gene , computer science , database , sociology
A simple nonparameteric test for population structure was applied to temporally spaced samples of HIV-1 sequences from the gag-pol region within two chronically infected individuals. The results show that temporal structure can be detected for samples separated by about 22 months or more. The performance of the method, which was originally proposed to detect geographic structure, was tested for temporally spaced samples using neutral coalescent simulations. Simulations showed that the method is robust to variation in samples sizes and mutation rates, to the presence/absence of recombination, and that the power to detect temporal structure is high. By comparing levels of temporal structure in simulations to the levels observed in real data, we estimate the effective intra-individual population size of HIV-1 to be between 10(3) and 10(4) viruses, which is in agreement with some previous estimates. Using this estimate and a simple measure of sequence diversity, we estimate an effective neutral mutation rate of about 5 x 10(-6) per site per generation in the gag-pol region. The definition and interpretation of estimates of such "effective" population parameters are discussed.