Restricted genetic diversity of HIV-1 subtype C envelope glycoprotein from perinatally infected Zambian infants

Abstract

Background: Mother-to-child transmission of HIV-1 remains a significant problem in the resource-constrained settings where anti-retroviral therapy is still not widely available. Understanding the earliest events during HIV-1 transmission and characterizing the newly transmitted or founder virus is central to intervention efforts. In this study, we analyzed the viral env quasispecies of six mother-infant transmission pairs (MIPs) and characterized the genetic features of envelope glycoprotein that could influence HIV-1 subtype C perinatal transmission.

Methodology and findings: The V1-V5 region of env was amplified from 6 MIPs baseline samples and 334 DNA sequences in total were analyzed. A comparison of the viral population derived from the mother and infant revealed a severe genetic bottleneck occurring during perinatal transmission, which was characterized by low sequence diversity in the infant. Phylogenetic analysis indicates that most likely in all our infant subjects a single founder virus was responsible for establishing infection. Furthermore, the newly transmitted viruses from the infant had significantly fewer potential N-linked glycosylation sites in Env V1-V5 region and showed a propensity to encode shorter variable loops compared to the nontransmitted viruses. In addition, a similar intensity of selection was seen between mothers and infants with a higher rate of synonymous (dS) compared to nonsynonymous (dN) substitutions evident (dN/dS<1).

Conclusions: Our results indicate that a strong genetic bottleneck occurs during perinatal transmission of HIV-1 subtype C. This is evident through population diversity and phylogenetic patterns where a single viral variant appears to be responsible for infection in the infants. As a result the newly transmitted viruses are less diverse and harbored significantly less glycosylated envelope. This suggests that viruses with the restricted glycosylation in envelope glycoprotein appeared to be preferentially transmitted during HIV-1 subtype C perinatal transmission. In addition, our findings also indicated that purifying selection appears to predominate in shaping the early intrahost evolution of HIV-1 subtype C envelope sequences.

Figure 1. Neighbor-joining phylogenetic tree showing V1-V5 envelope gene sequences from all patients of the cohort with bootstrap values calculated from 1000 bootstrap replicates shown for each major branch.

Each transmission pair is labeled with nucleotide sequences from mothers (green) and infants (blue). The tree was constructed using MEGA version 4.

Figure 2. Rooted maximum-likelihood trees illustrating the epidemiologic linkage between sequences from mother (green) and infant (blue) subjects within each transmission pair.

The nucleotide sequences of env V1-V5 region from each pair were aligned with two unrelated outgroup HIV-1 subtype C sequences obtained from the Los Alamos HIV Sequence Database. The branch containing unrelated outgroup sequences are not shown for space considerations. Only bootstrap support values greater than 75 are shown for the major nodes segregating mother and infant subjects.

Figure 3. Comparison of Env V1-V5 length between mother and infant variants.

(A) Comparison of Env V1-V5 length for each transmission pair. The P value for each comparison between the mother and infant are shown. The horizontal bars indicate the mean value for each individual. (B) Comparison of Env V1-V5 length of the aggregate sequences from mothers and infants. The P value for the comparison between the mother and infant is shown. The box and whiskers plot denotes the median, minimum and maximum values.

Figure 4. Comparison of PNGS in Env V1-V5 region between mother and infant variants.

(A) Comparison of PNGS in Env V1-V5 region for each transmission pair. The P value for each comparison between the mother and infant are shown. The horizontal bars indicate the mean value for each individual. (B) Comparison of PNGS in Env V1-V5 region of the aggregate sequences from mothers and infants. The P value for the comparison between the mother and infant is shown. The box and whiskers plot denotes the median, minimum and maximum values.