Different evolutionary pathways of HIV-1 between fetus and mother perinatal transmission pairs indicate unique immune selection in fetuses

Abstract

Study of evolution and selection pressure on HIV-1 in fetuses will lead to a better understanding of the role of immune responses in shaping virus evolution and vertical transmission. Detailed genetic analyses of HIV-1 env gene from 12 in utero transmission pairs show that most infections (67%) occur within 2 months of childbirth. In addition, the env sequences from long-term-infected fetuses are highly divergent and form separate phylogenetic lineages from their cognate maternal viruses. Host-selection sites unique to neonate viruses are identified in regions frequently targeted by neutralizing antibodies and T cell immune responses. Identification of unique selection sites in the env gene of fetal viruses indicates that the immune system in fetuses is capable of exerting selection pressure on viral evolution. Studying selection and evolution of HIV-1 or other viruses in fetuses can be an alternative approach to investigate adaptive immunity in fetuses.

Keywords: HIV-1; fetus; immune selection; in utero transmission; mother to child transmission; neonate; signature.

Graphical abstract

Figure 1

Phylogenetic trees of the env sequences from each mother-neonate transmission pair Phylogenetic trees were constructed by the neighbor-joining method with the Kimura 2-parameter model, and their reliability was estimated by 1,000 bootstrap replicates. The nodes that are supported by more than 70% of bootstrap replicates are indicated by asterisks. Sequences from neonates and mothers are indicated in blue and red dots, respectively. See also Figures S1–S3.

Figure 2

Comparison of genetic diversity of the viral populations of mother and neonate from each transmission pair Genetic diversity was measured by calculating within-lineage pairwise genetic distances (p-distance) of neonate sequences at different time points and maternal sequences. P distances are plotted as black dots. The middle blue line indicates the median, the box shows 25–75 percentiles of the diversity, and whisker shows 10–90 percentiles of the diversity. Neonate versus maternal sequence diversity was statistically significant (p = 9.8 × 10⁻⁴; paired Wilcoxon test), and the diversity of sequences from the short-term-infected infants versus the long-term-infected infants are statistically significant (p = 0.006; paired Wilcoxon test). See also Figures S4 and S5.

Figure 3

Identification of unique sequence motifs in the env gene from the mother-neonate pair 10_2093 The sequences from the neonate and mother transmission pair 10_2093n are compared to the consensus sequence of the viruses in neonate (the top line). The different amino acids are indicated as they are, while identical amino acids are shown as dashes. Distinct motif sequences in the viral population in the neonate (noted as A through E) are indicated by different colors, while the identical or similar motif sequences found in the maternal virus sequences are indicated with the same colors. See also Figure S3.

Figure 4

Identification of selection sites by analyzing the accumulation of mutations across the env gene in the neonate viruses Cumulative plots of each codon average behavior for all sequences pairwise compared for the neonate and maternal viruses for synonymous (blue), non-synonymous (red) mutations, and indels (gray). Sites found under statistically significant diversifying selection by the MEME analysis are marked by arrows, where solid arrows indicate p < 0.01 and dashed arrows p = 0.01. Magenta arrows show sites under diversifying selection in both the mother and the neonate. Values of ω denote average ratios of the rate of non-synonymous substitutions per non-synonymous site (dN/dS) for each sample. See also Figure S6.

Figure 5

Selection signatures in env sequences from mother-neonate pair 9_1039 The V1V2C2 region sequences from the neonate and mother transmission pair 9_1039n are compared to the consensus sequence of the viruses in neonate (the top line). The different amino acids are indicated as they are, while identical amino acids are shown as dashes. Distinct selection signatures at different sites in the neonate and mother viruses are indicated by red boxes; similar selection in V1 for both neonate and mother viruses, unique selection in V2 for the neonate viruses, and transmission bottleneck (or purifying selection) in C2 for neonate viruses are shown. See also Figure S7 and Table S1.

Figure 6

Higher neutralization activity of placental plasma than blood plasma from the same mothers (A) Heatmap analysis of neutralizing titers of placental (PLC) plasma than systemic blood (BLD) plasma from the same mothers. The neutralization titers are color coded from dark to light, where the darker color indicates higher neutralization titers. (B) Loss of neutralization activity after IgG depletion by protein G column in both placental plasma and systemic blood plasma. The dotted line indicates the threshold for detection. (C) Similar IgG concentrations in placental plasma and blood plasma from the same mothers. HIV-1-specific IgG concentrations were determined by measuring binding of blood and placental plasma to 1086C and CON6 gp120, respectively. See also Figure S9.