Kimmy T. Pham

TL;DR: A mathematical model of random viral evolution and phylogenetic tree construction is developed and used to analyze 3,449 complete env sequences derived by single genome amplification from 102 subjects with acute HIV-1 (clade B) infection, suggesting a finite window of potential vulnerability of HIV- 1 to vaccine-elicited immune responses, although phenotypic properties of transmitted Envs pose a formidable defense.

TL;DR: It is shown 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.

TL;DR: A mathematical model and Monte Carlo simulation of viral evolution during acute infection is described and detailed comparisons of the model and simulations results to 306 envelope sequences obtained from eight newly infected subjects at a single time point are provided.