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Complete HIV-1 Sequences in Acute and Early Infection Reveal the Genetic Identity, Biological Phenotype, and Precise Evolutionary Pathways of Transmitted/Founder Viruses and Their Progeny
Jesus Salazar-Gonzalez*1, M Salazar1, B Keele1, G Learn1, E Hunter2, M Markowitz3, B Haynes4, B Korber5,6, B Hahn1, and G Shaw1
1Univ of Alabama at Birmingham, US; 2Emory Univ, Atlanta, GA, US; 3Aaron Diamond AIDS Res Ctr, The Rockefellar Univ, New York, NY, US; 4Duke Univ Med Ctr, Durham, NC, US; 5Los Alamos Natl Lab, NM, US; and 6Santa Fe Inst, NM, US
Background: Sexual transmission of HIV-1 generally
results from virus exposure at mucosal surfaces. Because of the inaccessibility
of these anatomical sites, the molecular details of HIV-1 transmission and
early replication are largely unknown.
Methods: Full-length HIV-1 genomes representing the
early progeny of transmitted viruses were polymerase chain reaction (PCR)
amplified by single genome amplification (SGA) and sequenced directly from
plasma vRNA of 12 acutely infected subjects (9 clade B; 3 clade C). Molecular
clones of transmitted viruses were generated by chemical synthesis or PCR
cloning, and tested for in vitro infectivity in primary human T cells
and macrophages. In 3 patients, half genomes were amplified and sequenced from
sequential plasma samples 4 to 12 months after infection.
Results: Complete genomic sequences of
transmitted/founder viruses were determined in each of 12 subjects. Molecular
clones representing transmitted full-length 10-Kb genomes allowed for a
biological analysis of viruses responsible for productive clinical infection
and for a comprehensive mapping of the evolving viral quasispecies for
mutations that are necessary, sufficient, or incidental to the establishment of
viral persistence. Surprisingly, transmitted/founder viruses, which were CD4
and CCR5 tropic, replicated efficiently in activated normal human CD4+
T lymphocytes but not in monocyte-derived macrophages from the same donors.
Transmitted/founder viruses exhibited sensitivity to broadly neutralizing human
monoclonal antibodies and to peptidic fusion inhibitors but not to antibodies
targeting CD4-induced bridging sheet or V3 epitopes, all features typical of
primary virus strains. In 3 subjects whom we studied serially between peak
viremia (pre-seroconversion; Fiebig stage II) and viral load setpoint 3 to 6
months later, the evolving viral quasispecies showed evidence of rapid
selection at 4 to 14 discreet loci across the proteome.
Conclusions: Identification of transmitted/founder
virus genomes and their progeny by SGA-direct sequencing is a novel strategy
for probing the molecular basis of HIV-1 (and simian immunodeficiency virus)
transmission and for evaluating the genetic imprint of host factors that act to
constrain or facilitate virus replication.
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