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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
agricultural and biological sciences
Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing
Journal of Virology, Volume 82, No. 8, Year 2008
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Description
Accurate identification of the transmitted virus and sequences evolving from it could be instrumental in elucidating the transmission of human immunodeficiency virus type 1 (HIV-1) and in developing vaccines, drugs, or microbicides to prevent infection. Here we describe an experimental approach to analyze HIV-1 env genes as intact genetic units amplified from plasma virion RNA by single-genome amplification (SGA), followed by direct sequencing of uncloned DNA amplicons. We show that this strategy precludes in vitro artifacts caused by Taq-induced nucleotide substitutions and template switching, provides an accurate representation of the env quasispecies in vivo, and has an overall error rate (including nucleotide misincorporation, insertion, and deletion) of less than 8 × 10-5. Applying this method to the analysis of virus in plasma from 12 Zambian subjects from whom samples were obtained within 3 months of seroconversion, we show that transmitted or early founder viruses can be identified and that molecular pathways and rates of early env diversification can be defined. Specifically, we show that 8 of the 12 subjects were each infected by a single virus, while 4 others acquired more than one virus; that the rate of virus evolution in one subject during an 80-day period spanning seroconversion was 1.7 × 10-5 substitutions per site per day; and that evidence of strong immunologic selection can be seen in Env and overlapping Rev sequences based on nonrandom accumulation of nonsynonymous mutations. We also compared the results of the SGA approach with those of more-conventional bulk PCR amplification methods performed on the same patient samples and found that the latter is associated with excessive rates of Taq-induced recombination, nucleotide misincorporation, template resampling, and cloning bias. These findings indicate that HIV-1 env genes, other viral genes, and even full-length viral genomes responsible for productive clinical infection can be identified by SGA analysis of plasma virus sampled at intervals typical in large-scale vaccine trials and that pathways of viral diversification and immune escape can be determined accurately. Copyright © 2008, American Society for Microbiology. All Rights Reserved.
Authors & Co-Authors
Salazar-González, Jesús Fidel
United States, Birmingham
The University of Alabama at Birmingham
Bailes, Elizabeth
United Kingdom, Nottingham
University of Nottingham
Pham, Kimmy T.
United States, Birmingham
The University of Alabama at Birmingham
Salazar, Maria G.
United States, Birmingham
The University of Alabama at Birmingham
Guffey, M. B.
United States, Birmingham
The University of Alabama at Birmingham
Keele, Brandon F.
United States, Birmingham
The University of Alabama at Birmingham
Derdeyn, Cynthia A.
United States, Atlanta
Emory University
Farmer, Paul K.
United States, Atlanta
Emory University
Hunter, Eric
United States, Atlanta
Emory University
Allen, Susan A.
Zambia, Lusaka
Zambia-emory Hiv Research Project
Manigart, Olivier
Zambia, Lusaka
Zambia-emory Hiv Research Project
Mulenga, Joseph
Zambia, Lusaka
Zambia-emory Hiv Research Project
Anderson, Jeffrey A.
United States, Chapel Hill
The University of North Carolina at Chapel Hill
Swanstrom, Ronald I.
United States, Chapel Hill
The University of North Carolina at Chapel Hill
Haynes, Barton F.
United States, Durham
Duke University Medical Center
Athreya, Gayathri S.
United States, Los Alamos
Los Alamos National Laboratory
Korber, Bette T.
United States, Los Alamos
Los Alamos National Laboratory
Sharp, Paul M.
United Kingdom, Edinburgh
The University of Edinburgh
Shaw, George M.
United States, Birmingham
The University of Alabama at Birmingham
Hahn, Beatrice H.
United States, Birmingham
The University of Alabama at Birmingham
Statistics
Citations: 20
Authors: 20
Affiliations: 8
Identifiers
Doi:
10.1128/JVI.02660-07
ISSN:
0022538X
Research Areas
Genetics And Genomics
Health System And Policy
Infectious Diseases