Background: Dynamic changes in Human Immunodeficiency Virus 1 (HIV-1) sequence diversity and divergence are
associated with immune control during primary infection and progression to AIDS. Consensus sequencing or single
genome amplification sequencing of the HIV-1 envelope (env) gene, in particular the variable (V) regions, is used as
a marker for HIV-1 genome diversity, but population diversity is only minimally, or semi-quantitatively sampled
using these methods.
Results: Here we use second generation deep sequencing to determine inter-and intra-patient sequence
heterogeneity and to quantify minor variants in a cohort of individuals either receiving or not receiving
antiretroviral treatment following seroconversion; the SPARTAC trial. We show, through a cross-sectional study of
sequence diversity of the env V3 in 30 antiretroviral-naive patients during primary infection that considerable
population structure diversity exists, with some individuals exhibiting highly constrained plasma virus diversity.
Diversity was independent of clinical markers (viral load, time from seroconversion, CD4 cell count) of infection.
Serial sampling over 60 weeks of non-treated individuals that define three initially different diversity profiles showed
that complex patterns of continuing HIV-1 sequence diversification and divergence could be readily detected.
Evidence for minor sequence turnover, emergence of new variants and re-emergence of archived variants could be
inferred from this analysis. Analysis of viral divergence over the same time period in patients who received short
(12 weeks, ART12) or long course antiretroviral therapy (48 weeks, ART48) and a non-treated control group revealed
that ART48 successfully suppressed viral divergence while ART12 did not have a significant effect.
Conclusions: Deep sequencing is a sensitive and reliable method for investigating the diversity of the env V3 as an
important component of HIV-1 genome diversity. Detailed insights into the complex early intra-patient dynamics of
env V3 diversity and divergence were explored in antiretroviral-naïve recent seroconverters. Long course
antiretroviral therapy, initiated soon after seroconversion and administered for 48 weeks, restricts HIV-1 divergence
significantly. The effect of ART12 and ART48 on clinical markers of HIV infection and progression is currently
investigated in the SPARTAC trial.