Background: The precise identification of the HIV-1 envelope glycoprotein (Env) responsible for productive clinical infection could be instrumental in elucidating the molecular basis of HIV-1 transmission and in designing effective vaccines, drugs, or microbicides to prevent infection.

Methods: We developed a mathematical model of random viral evolution, and together with phylogenetic tree construction, used it to analyze 3476 complete env sequences derived by single genome amplification (SGA) of plasma viral RNA from 102 subjects with acute HIV-1 (clade B) infection.

Results: Viral env genes evolving from individual transmitted or founder viruses generally exhibited a Poisson distribution of mutations and star-like phylogeny, which coalesced to an inferred consensus sequence at or near the estimated time of virus transmission. Overall, 78 of 102 subjects had evidence of productive clinical infection by a single virus, and 24 others by a minimum of 2 to 5 viruses. Phenotypic analysis of transmitted or early founder Env revealed a consistent pattern of CCR5 dependence, masking of co-receptor binding regions, and modestly enhanced resistance to the fusion inhibitor T1249 and to certain broadly neutralizing antibodies. We extended this work to the identification of transmitted/early founder clade C virus env and complete (9-kb) transmitted/early founder HIV-1 clade B and C genomes. Low multiplicity infection and limited viral evolution preceding peak viremia suggest a finite window of potential vulnerability of HIV-1 to vaccine-elicited immune responses, although phenotypic properties of transmitted Env and subsequent evolution of neutralizing antibody and cytotoxic T lymphocyte epitopes pose a formidable viral defense.

Conclusions: SGA and sequencing of HIV-1 RNA in acute and early infection represents a powerful experimental strategy for identifying transmitted and early founder viruses and for characterizing molecular mechanisms responsible for immune evasion by HIV-1 in naïve individuals and in vaccinated.