Characterization of HIV-1 envelope gp41 genetic diversity and functional domains following perinatal transmission

Abstract

Background: HIV-1 envelope gp41 is a transmembrane protein that promotes fusion of the virus with the plasma membrane of the host cells required for virus entry. In addition, gp41 is an important target for the immune response and development of antiviral and vaccine strategies, especially when targeting the highly variable envelope gp120 has not met with resounding success. Mutations in gp41 may affect HIV-1 entry, replication, pathogenesis, and transmission. We, therefore, characterized the molecular properties of gp41, including genetic diversity, functional motifs, and evolutionary dynamics from five mother-infant pairs following perinatal transmission.

Results: The gp41 open reading frame (ORF) was maintained with a frequency of 84.17% in five mother-infant pairs' sequences following perinatal transmission. There was a low degree of viral heterogeneity and estimates of genetic diversity in gp41 sequences. Both mother and infant gp41 sequences were under positive selection pressure, as determined by ratios of non-synonymous to synonymous substitutions. Phylogenetic analysis of 157 mother-infant gp41 sequences revealed distinct clusters for each mother-infant pair, suggesting that the epidemiologically linked mother-infant pairs were evolutionarily closer to each other as compared with epidemiologically unlinked sequences. The functional domains of gp41, including fusion peptide, heptad repeats, glycosylation sites and lentiviral lytic peptides were mostly conserved in gp41 sequences analyzed in this study. The CTL recognition epitopes and motifs recognized by fusion inhibitors were also conserved in the five mother-infant pairs.

Conclusion: The maintenance of an intact envelope gp41 ORF with conserved functional domains and a low degree of genetic variability as well as positive selection pressure for adaptive evolution following perinatal transmission is consistent with an indispensable role of envelope gp41 in HIV-1 replication and pathogenesis.

Figure 1

Phylogenetic analysis of 157 envelope gp41 sequences from five mother-infant pairs following perinatal transmission. The neighbor-joining tree is based on the distances calculated between the nucleotide sequences from the five mother-infant pairs. Each terminal node represents one gp41 sequence. The numbers on the branch points indicate the percent occurrences of the branches over 1000 bootstrap resamplings of the data set. The sequences from each mother formed distinct clusters and are well discriminated and in confined subtrees, indicating that variants from the same mother are closer to each other than to other mothers' sequences and that there was no PCR cross contamination. These data were strongly supported by the high bootstrap values indicated on the branch points.

Figure 2

Multiple sequence alignment of the deduced amino acids encoded by envelope gp41 gene of HIV-1 from mother-infant pair B following perinatal transmission. The sequences of pair B are aligned to consensus B (cons B) on top. Each line refers to a clone identified by a clone number preceded by MB (for mother B sequences) and IB (for infant B sequences). Dots indicate amino acid agreement with cons B, dashes represent gaps, and asterisks represent stop codons. The functional motifs of gp41 are indicated above the alignment.

Figure 3

Multiple sequence alignment of the deduced amino acids encoded by envelope gp41 gene of HIV-1 from mother-infant pair D following perinatal transmission. Each line refers to a clone identified by a clone number preceded by MD (for mother D sequences) and ID (for infant D sequences). The sequences of pair D are aligned to consensus B (cons B) on top. Dots indicate amino acid agreement with cons B, dashes represent gaps, and asterisks represent stop codons. The functional motifs of gp41 are indicated above the alignment.

Figure 4

Multiple sequence alignment of the deduced amino acids encoded by envelope gp41 gene of HIV-1 from mother-infant pair E after perinatal transmission. Each line refers to a clone identified by a clone number preceded by ME (for mother E sequences) and IE (for infant E sequences). The sequences of pair E are aligned to consensus B (cons B) on top. Dots indicate amino acid agreement with cons B, dashes represent gaps, and asterisks represent stop codons. The functional motifs of gp41 are indicated above the alignment.

Figure 5

Multiple sequence alignment of the deduced amino acids encoded by envelope gp41 gene of HIV-1 from mother-infant pair F after perinatal transmission. Each line refers to a clone identified by a clone number preceded by MF (for mother F sequences) and IF (for infant F sequences). The sequences of pair F are aligned to consensus B (cons B) on top. Dots indicate amino acid agreement with cons B, dashes represent gaps, and asterisks represent stop codons. The functional motifs of gp41 are indicated above the alignment.

Figure 6

Multiple sequence alignment of the deduced amino acids encoded by envelope gp41 gene of HIV-1 from mother-infant pair G after perinatal transmission. Each line refers to a clone identified by a clone number preceded by MG (for mother G sequences) and IG (for infant G sequences). The sequences of pair G are aligned to consensus B (cons B) on top. Dots indicate amino acid agreement with cons B, dashes represent gaps, and asterisks represent stop codons. The functional motifs of gp41 are indicated above the alignment.