Variability in V1V2 and PNGs in Pediatric HIV-1 Viral Variants Transmitted Through Vertical Route

Characteristic features in the fraternal twin, V1V2 and its kindred, potential N-linked glycosylation sites (PNGs) have been reported to correlate with mucosal transmission of majority of HIV-1 subtypes. The changes in length of V1V2 often involve the addition or loss of PNGs and play a key role in viral infectivity, antigen conformation, and immune escape. In addition, loss of PNGs in the V1V2 regions of HIV is reported to enhance macrophage tropism and infection of cells expressing low levels of CD4. The mechanisms that generate shifting sites and tolerance of such shifting PNGs in viral proteins provide a unique evolutionary avenue for immune evasion. ¹

This study involved sequencing of envelope gene from HIV-1-infected babies (n = 16) aged between 2 and 18 months, whose mothers were HIV positive at the time of pregnancy. Whole blood samples were subjected to proviral DNA extraction, amplification of HIV-1 envelope, followed by DNA sequencing using 3100 Avant Genetic Analyzer (Applied Biosystems). The envelope sequences were analyzed to characterize the viral variants at the sequence level.

Sequences generated in this study formed a tight monophyletic cluster with other Indian and Chinese clade C isolates and were predicted to use CCR5 as the coreceptor. Amino acids (59–75) showed maximal variation among the sequences in V1V2 region (Fig. 1). Significant difference in number (3–6) and position of PNGs within the variable region sequence was also identified. The infecting potential of a virus is influenced by the length of the variable region; it has been reported that viruses encoding Env glycoproteins with shorter V1V2 regions are transmitted more effectively. Changes in V1V2 PNGs often influence antigenic domains in other regions, for example, they can alter antibody recognition of both the V3 loop and CD4 binding site. ¹ In horizontal nonsubtype C transmission, significantly shorter V1V2 and fewer number of PNGs were noticed in subtypes A and B viral variants ² and circulating recombinant forms CRF01_AE-CN and CRF01_AE-non-CN ³ with improved neutralization sensitivities of the virus; Whereas minimal impact of neutralization sensitivity was observed with respect to shorter V1V2 and reduced degree of PNGs in subtype C isolates. ⁴ Interestingly, in vertical transmission we did find both the extremes of shorter V1V2 (60 amino acids) with reduced degree of PNGs (3 PNGs) and longer V1V2 (75 amino acids) with increased degree of PNGs (6 PNGs) with the average being 65 amino acids and 5 PNGs. Deletion in V1V2 alone can result in a more open conformation of the envelope, with better exposure of the V3 loop. Even relatively small changes in the V1V2 loop could result in a more open envelope conformation. A large deletion was identified in NIRT_0195 and it is believed to make the virus more susceptible to anti-V3 antibodies.

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FIG. 1.

Representation of distinct features of V1V2 and PNGs in HIV-1 subtype C isolates obtained from children recently infected through mother-to-child transmission. Potential N-linked glycosylation sites are boxed in red. The shadow with blue indicates consensus sequences; the high intensity of color denotes more conservation and less intensity denotes less conservation. Reference sequence, HXB2, and the consensus sequence are shown at the top and bottom of the image and are highlighted in green and violet, respectively. (.) indicates identity to the consensus sequence and (+/−) indicates insertion/deletion at particular position. PNGs, potential N-linked glycosylation sites.

We summarize that the vertically transmitted viral variants are unique with respect to the length of V1V2 and the number and pattern of PNGs in contrast to HIV-1 strains transmitted recently through horizontal route. In future, additional studies need to be undertaken to address the characteristics of variable loops in founder virus sequences transmitted through vertical route.