Phylogenetic measures of indel rate variation among the HIV-1 group M subtypes

Abstract

The transmission fitness and pathogenesis of HIV-1 is disproportionately influenced by evolution in the five variable regions (V1–V5) of the surface envelope glycoprotein (gp120). Insertions and deletions (indels) are a significant source of evolutionary change in these regions. However, the rate and composition of indels has not yet been quantified through a large-scale comparative analysis of HIV-1 sequences. Here, we develop and report results from a phylogenetic method to estimate indel rates for the gp120 variable regions across five major subtypes and two circulating recombinant forms (CRFs) of HIV-1 group M. We processed over 26,000 published HIV-1 gp120 sequences, from which we extracted 6,605 sequences for phylogenetic analysis. We reconstructed time-scaled phylogenies by maximum likelihood and fit a binomial-Poisson model to the observed distribution of indels between closely related pairs of sequences in each tree (cherries). By focusing on cherries in each tree, we obtained phylogenetically independent indel reconstructions, and the shorter time scales in cherries reduced the bias due to purifying selection. Rate estimates ranged from 3.0×10−5 to 1.5×10−3 indels/nt/year and varied significantly among variable regions and subtypes. Indel rates were significantly lower in V3 relative to V1, and were also lower in HIV-1 subtype B relative to the 01_AE reference. We also found that V1, V2, and V4 tended to accumulate significantly longer indels. Furthermore, we observed that the nucleotide composition of indels was distinct from the flanking sequence, with higher frequencies of G and lower frequencies of T. Indels affected N-linked glycosylation sites more often in V1 and V2 than expected by chance, consistent with positive selection on glycosylation patterns within these regions. These results represent the first comprehensive measures of indel rates in HIV-1 gp120 across multiple subtypes and CRFs, and identifies novel and unexpected patterns for further research in the molecular evolution of HIV-1.

On the stability of sequences inserted into viral genomes

“…When introducing GFP into the five variable regions of HIV-1, certain regions (V4 and V5) were more tolerant to foreign gene insertions than the other variable regions (V1, V2, and V3) (Nakane, Iwamoto, and Matsuda 2015). In particular, GFP insertions into the V3 region showed lower levels of expression (Nakane, Iwamoto, and Matsuda 2015), which is consistent with V3 having the lowest indel rate (Palmer and Poon 2018), thus having a lower stability after gene insertions. This piece of empirical evidence again shows that the site of insertion plays an important role in determining expression levels and stability.…”

“…The HIV-1 surface envelope glycoprotein contains five variable regions (V1–V5) that can tolerate a higher rate of indels than the rest of the genome. Interestingly, indel rate estimates vary significantly among variable regions and subtypes (from different hosts) (Palmer and Poon 2018).…”

Large Evolutionary Rate Heterogeneity among and within HIV-1 Subtypes and CRFs

“…These coordinates were chosen to ensure both a broader sampling across subtypes and CRFs ( Figures S1 and S2 ) and keeping in mind their clinical and historical significance. Moreover, the choice of the C2-V3-C3 env region was partly inspired by a recent analysis by Palmer and Poon (2019) who calculated indel rates in env across major HIV-1 subtypes and CRFs [ 14 ], and partly by this region’s demonstrated epidemiological accuracy and popularity in past phylogenetic studies [ 17 ]. The HIV-1 M surface envelope glycoprotein (gp120) is notorious for accumulating indels, especially in the regions around the so-called variable loops (V1–V5).…”

“…The HIV-1 M surface envelope glycoprotein (gp120) is notorious for accumulating indels, especially in the regions around the so-called variable loops (V1–V5). Palmer and Poon (2019) showed that V3 accumulates the least and shortest indels, relative to other variable regions [ 14 ]. The V3 mediates HIV entry by binding to the host co-receptors.…”

“…In theory, the evolutionary rate should encompass the rate of mutations, substitutions (mutations that become fixed in a population), insertions and deletions (indels), recombination, inversions, and duplications, among other evolutionary events. However, calculation of all these processes is not straightforward, though some success has been achieved in estimating indel rate variation in the hypervariable env loop regions [ 14 ]. Therefore, while we use the terms evolutionary and substitution rate interchangeably throughout this manuscript, in reality, the analysis describes substitution rate heterogeneity in the HIV-1 M group.…”