Background:  While studies focus on viral genetic characteristics of mother-to-child transmission (MTCT), little is known about the genetic evolution of HIV-1 during the course of pregnancy. The aim of this study was to explore potential interactions between maternal immune responses, Env sequence evolution and co-receptor usage during pregnancy.

Methods:  A longitudinal study of Env sequences was performed in pregnant women infected with HIV-1 of B (n = 16) or non-B subtypes (n = 9). Polymerase chain reaction amplification of env V1-V3 region was performed on plasma viral RNA followed by subcloning and sequencing (20 clones/trimester). Tropism was inferred using 4 prediction algorithms. Intra-host viral phylogenies were constructed. Sequence diversity (P distances) and selective pressure (dN/dS) were computed. Numbers of potential N-glycosylation sites and the net charge of V3 were determined.

Results:  Viral load decreased progressively during the course of pregnancy. Nucleic acid p distances were negatively correlated with CD4⁺ T cell counts at study entry (P = 0.02). R5 phenotype was uniformly predicted in all subtype B variants. In contrast, X4 variants were detected in 4 of 9 subjects infected with non-B subtypes, including 4 of 6 subjects who exhibited CD4⁺ T cell counts <200 cells/mm³. Evolution of tropism from R5 to X4 was observed in 2 subjects and evolution from dual tropism to exclusive X4 was seen in 1 subject between 2 consecutive pregnancies. Presence of X4 variants was associated with increases in the net charge of V3 throughout pregnancy, as opposed to R5 variants (+0.36 versus –0.1 charge units/trimester; P = 0.03). In 2 subjects infected with subtype C, X4 variants showed significantly longer V1 regions than R5 variants (P <0.0001), corresponding to addition of potential N-glycosylation sites. Finally, greater P distances were observed in the V2 region of non-B variants as compared with B variants. Selective pressure exerted on V2 declined with progression of pregnancy in subjects infected with non-B subtypes but remained constant in subtype B carriers.

Conclusions:  These results inform the possible interplay between Env sequence evolution, co-receptor tropism, and selective pressures exerted by HIV-specific immune responses during pregnancy, and highlight the differential involvement of HIV subtype-specific components. This study provides insights into viral population dynamics and maternal immunity that could lead to a better understanding of HIV pathogenesis and MTCT.