期刊
JOURNAL OF VIROLOGICAL METHODS
卷 168, 期 1-2, 页码 114-120出版社
ELSEVIER
DOI: 10.1016/j.jviromet.2010.04.030
关键词
HIV; Single genome sequencing (SGS); pro-pol diversity; Cloning and sequencing; Treatment naive
资金
- National institute for Allergy and Infectious Disease [T32 AI07389, CFAAR 1P30A142853-10, K24 A1055293-06A1, K23 AI074423-03]
- Center for Drug Abuse and AIDS Research [P30 DA013868]
- George Kirby Foundation
- NATIONAL CANCER INSTITUTE [ZIABC010819] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES [T32AI007389, K23AI074423] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE ON DRUG ABUSE [P30DA013868] Funding Source: NIH RePORTER
To compare standard PCR/cloning and single genome sequencing (SGS) in their ability to reflect actual intra-patient polymorphism of HIV-1 populations, a total of 530 HIV-1 pro-pol sequences obtained by both sequencing techniques from a set of 17 ART naive patient specimens was analyzed. For each specimen, 12 and 15 sequences, on average, were characterized by the two techniques. Using phylogenetic analysis, tests for panmixia and entropy, and Bland-Altman plots, no difference in population structure or genetic diversity was shown in 14 of the 17 subjects. Evidence of sampling bias by the presence of subsets of identical sequences was found by either method. Overall, the study shows that neither method was more biased than the other, and providing that an adequate number of PCR templates is analyzed, and that the bulk sequencing captures the diversity of the viral population, either method is likely to provide a similar measure of population diversity. (C) 2010 Elsevier B.V. All rights reserved.
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