期刊
JOURNAL OF VIROLOGY
卷 81, 期 12, 页码 6643-6651出版社
AMER SOC MICROBIOLOGY
DOI: 10.1128/JVI.02268-06
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资金
- NIAID NIH HHS [R01 AI057167, AI47745, AI43638, AI57167, P30 AI036214, R56 AI047745, U01 AI043638, R01 AI047745, AI36214, R21 AI047745] Funding Source: Medline
- NIDA NIH HHS [DA14533, R21 DA014533, R01 DA012580, DA12580] Funding Source: Medline
- NIGMS NIH HHS [GM056529, R01 GM056529] Funding Source: Medline
- NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES [R01AI047745, R01AI057167, P30AI036214, R56AI047745, R21AI047745, U01AI043638] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM056529] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE ON DRUG ABUSE [R21DA014533, R01DA012580] Funding Source: NIH RePORTER
Human immunodeficiency virus (HIV) infects different organs and tissues. During these infection events, subpopulations of HIV type 1 (HIV-1) develop and, if viral trafficking is restricted between subpopulations, the viruses can follow independent evolutionary histories, i.e., become compartmentalized. This phenomenon is usually detected via comparative sequence analysis and has been reported for viruses isolated from the central nervous system (CNS) and the genital tract. Several approaches have been proposed to study the compartmentalization of HIV sequences, but to date, no rigorous comparison of the most commonly employed methods has been made. In this study, we systematically compared inferences made by six different methods for detecting compartmentalization based on three data sets: (i) a sample of 45 patients with sequences gathered from the CNS, (ii) sequences from the female genital tract of 18 patients, and (iii) a set of simulated sequences. We found that different methods often reached contradictory conclusions. Methods based on the topology of a phylogenetic tree derived from clonal sequences were generally more sensitive in detecting compartmentalization than those that relied solely upon pairwise genetic distances between sequences. However, as the branching structure in a phylogenetic tree is often uncertain, especially for short, low-diversity, or recombinant sequences, tree-based approaches may need to be modified to take phylogenetic uncertainty into account. Given the frequently discordant predictions of different methods and the strengths and weaknesses of each particular methodology, we recommend that a suite of several approaches be used for reliable inference of compartmentalized population structure.
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