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Journal of Virology, April 2008, p. 3952-3970, Vol. 82, No. 8
0022-538X/08/$08.00+0     doi:10.1128/JVI.02660-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Deciphering Human Immunodeficiency Virus Type 1 Transmission and Early Envelope Diversification by Single-Genome Amplification and Sequencing

Departments of Medicine,¹ Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294,¹⁰ Institute of Genetics, University of Nottingham, Nottingham NG7 2UH, United Kingdom,² Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia 30329,³ Zambia-Emory HIV Research Group (ZEHRG) and Zambia Blood Transfusion Service, Lusaka, Zambia,⁴ Department of Internal Medicine,⁵ UNC Center for AIDS Research, University of North Carolina, Chapel Hill, North Carolina 27599,⁶ Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina 27710,⁷ Los Alamos National Laboratory, Los Alamos, New Mexico 87545,⁸ Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom⁹

Received 14 December 2007/ Accepted 29 January 2008

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 x 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 x 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.

Published ahead of print on 6 February 2008.

^# These authors contributed equally to the work.

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