Infant transmitted/founder HIV-1 viruses from peripartum transmission are neutralization resistant to paired maternal plasma

Abstract

Despite extensive genetic diversity of HIV-1 in chronic infection, a single or few maternal virus variants become the founders of an infant's infection. These transmitted/founder (T/F) variants are of particular interest, as a maternal or infant HIV vaccine should raise envelope (Env) specific IgG responses capable of blocking this group of viruses. However, the maternal or infant factors that contribute to selection of infant T/F viruses are not well understood. In this study, we amplified HIV-1 env genes by single genome amplification from 16 mother-infant transmitting pairs from the U.S. pre-antiretroviral era Women Infant Transmission Study (WITS). Infant T/F and representative maternal non-transmitted Env variants from plasma were identified and used to generate pseudoviruses for paired maternal plasma neutralization sensitivity analysis. Eighteen out of 21 (85%) infant T/F Env pseudoviruses were neutralization resistant to paired maternal plasma. Yet, all infant T/F viruses were neutralization sensitive to a panel of HIV-1 broadly neutralizing antibodies and variably sensitive to heterologous plasma neutralizing antibodies. Also, these infant T/F pseudoviruses were overall more neutralization resistant to paired maternal plasma in comparison to pseudoviruses from maternal non-transmitted variants (p = 0.012). Altogether, our findings suggest that autologous neutralization of circulating viruses by maternal plasma antibodies select for neutralization-resistant viruses that initiate peripartum transmission, raising the speculation that enhancement of this response at the end of pregnancy could further reduce infant HIV-1 infection risk.

Fig 1. Highlighter plots of maternal and infant env sequences.

An example of a mother-infant pair where the infant was infected by a single T/F virus with no evidence of evolutionary selection in the infant (3/16 infants) (A). An example of a mother infant with evidence of evolutionary selection in the infant (B). An example of a mother infant pair where the infant was infected by two distinct T/F viruses (C). Individual infant and maternal viruses are represented by red dots and blue squares, respectively, on the tree. Colored hash marks on each highlighter plot represent nucleotide differences as compared with the infant consensus sequence at the top and are color-coded according to nucleotide.

Fig 2. Tier phenotyping and neutralization sensitivity of infant T/F pseudoviruses to paired maternal plasma.

Dark colors represent viruses that were easily neutralized. The second T/F viruses are marked with asterisks.

Fig 3. Neutralization sensitivity of infant T/F pseudoviruses to a panel of bNAbs.

The potency of the responses is color coded from dark to light where darker colors indicate stronger responses. Shades of red are used for infant responses, shades of green for potency, and shades of blue for breadth (% neutralization). Gray boxes indicate absence of response. The potency (geometric mean of responses) and breadth (% neutralized) of the infant viruses to each bNAb were compared with the geometric means of the bNAb’s potency and breadth obtained from published studies using the LANL repository CATNAP (columns on the right). The most potent neutralization against infant viruses was mediated by V3 glycan bNAbs and CD4 binding site specific NIH45-46.

Fig 4. Neutralization sensitivity of non-transmitted maternal variants and infant T/F pseudoviruses to paired maternal plasma.

(A) Neutralization sensitivity of infant T/F viruses were compared to non transmitted maternal viruses for each mother-infant pair and (B) neutralization sensitivity were compared between all infant T/F viruses and all non-transmitted maternal variants together. Maternal non-transmitted variants are shown by black dots and infant T/F viruses are represented by blue triangles (1st T/F) and blue dots (2nd T/F). Maternal variant sequences were selected following an algorithm to represent different motifs that diverge from the infant T/F (see Methods). Black horizontal lines represent the median of the ID₅₀ of maternal and infant sequences. The P value was determined by one sided permutation test.

Fig 5. Neutralization sensitivity of maternal and infant viruses to bNAbs DH512 and VRC-01.

IC₅₀ was determined for maternal non-transmitted variants (black dots) and infant T/F variants (triangles and circles in blue) as neutralized by VRC-01 and DH512. Black horizontal lines represent the median of the IC₅₀ bNAbs. Dashed lines represent the highest Ab concentration (5μg/ml) used in the experiment.

Fig 6. Comparison of neutralization sensitivity of maternal and infant viruses to DH512.

Comparison of paired maternal plasma and MPER specific bNAb DH512 maternal non-transmitted sequences (black dots) and infant T/F sequences (blue triangles) between sequences that carry the wild type amino acid at HXB2 positions 662, 676, 676, and 683, compared with those that carry a mutant. These four positions were chosen because they yielded a significant association with either maternal plasma responses (i.e. sequences carrying the mutant were statistically significantly more resistant to maternal plasma) or with DH512 responses (i.e. sequences carrying the mutant were statistically significantly more resistant to DH 512) in the MPER epitope. P-values were obtained using a 1-sided permutation test (see Methods). Gray boxes represent median and quartiles of the responses.

Fig 7. Frequency plot of the V3 region sequences of mother and infant T/F viruses.

Weblogo plot showing frequency of amino acids in the V3 region was made using the AnalyzAlign tool from the LANL website. Positions were numbered based on HXB2 amino acid sequence. Amino acid positions identified in the signature sequence analysis are marked at the top of the plot.