Evolution of HIV-1 subtype C gp120 envelope sequences in the female genital tract and blood plasma during acute and chronic infection
Heterosexual transmission of HIV-1 via the female genital tract is the leading route of HIV infection in sub-Saharan Africa. Viruses then traffic between the cervical compartment and blood ensuring pervasive infection. Previous studies have however reported the existence of genetically diverse viral populations in various tissue types, each evolving under separate selective pressures within a single individual, though it is still unclear how compartmentalization dynamics change over acute and chronic infection in the absence of ARVs. To better characterize intrahost evolution and the movement of viruses between different anatomical tissue types, statistical and phylogenetic methods were used to reconstruct temporal dynamics between blood plasma and cervico-vaginal lavage (CVL) derived HIV-1 subtype C gp120 envelope sequences. A total of 206 cervical and 253 blood plasma sequences obtained from four treatment naïve women enrolled in the CAPRISA Acute Infection study cohort in South Africa were evaluated for evidence of genotypic and phenotypic differences between viral populations from each tissue type up to 3.6 years post-infection. Evidence for tissue-specific differences in genetic diversity, V-loop length variation, codon-based selection, co-receptor usage, hypermutation, recombination and potential N-linked glycosylation (PNLG) site accumulation were investigated. Of the four participants studied, two anonymously identified as CAP270 and CAP217 showed evidence of infection with a single HIV-1 variant, whereas CAP177 and CAP261 showed evidence of infection by more than one variant. As a result, genetic diversity, PNLGs accumulation and the number of detectable recombination events along the gp120 env region were lowest in the former patients and highest in the latter. Overall, genetic diversity increased over the course of infection in all participants and correlated significantly with viral load measurements from the blood plasma in one of the four participants tested (i.e. CAP177). Employing a structured coalescent model approach, rates of viral migration between anatomical tissue types on time-measured genealogies were also estimated. No persistent evidence for the existence of separate viral populations in the cervix and blood plasma was found in any of the participants and instead, sequences generally clustered together by time point on Bayesian Maximum Clade Credibility (MCC) trees. Clades that were monophyletic by tissue type comprised mostly of low diversity or monotypic sequences from the same time point, consistent with bursts of viral replication. Tissue-specific monophyletic clades also generally contained few sequences and were interspersed among sequences from both tissue-types. Tree and distance-based statistical tests were employed to further evaluate the degree to which cervical and blood plasma viruses clustered together on Bayesian MCC trees using the Slatkin-Maddison (S-M), Simmonds Association index (AI), Monophyletic Clade (MC), Wright’s measure of population subdivision (FST) and Hudson’s Nearest Neighbour (Snn) statistics, in the presence and absence of monotypic and low diversity sequences. Statistical evidence for the presence of tissue-specific population structure disappeared or was greatly reduced after the removal of monotypic and low diversity sequences, except in CAP177 and CAP217, in 3/5 of longitudinal tree and distance-based tests. Analysis of phenotypic differences between viral populations from the blood plasma and cervix revealed inconsistent tissue-specific patterns in genetic diversity, codon-based selection, co-receptor usage, hypermutation, recombination, V-loop length variation and PNLG site accumulation during acute and chronic infection among all participants. There is therefore no evidence to support the existence of distinct viral populations within the blood plasma and cervical compartments longitudinally, however slightly constrained populations may exist within the female genital tract at isolated time points, based on the statistical findings presented in this study.