Adaptation of a diverse simian immunodeficiency virus population to a new host is revealed through a systematic approach to identify amino acid sites under selection

Abstract

Simian immunodeficiency viruses (SIV) have had considerable success at crossing species barriers; both human immunodeficiency virus (HIV)-1 and HIV-2 have been transmitted on multiple occasions from SIV-infected natural host species. However, the precise evolutionary and ecological mechanisms characterizing a successful cross-species transmission event remain to be elucidated. Here, in addition to expanding and clarifying our previous description of the adaptation of a diverse, naturally occurring SIVsm inoculum to a new rhesus macaque host, we present an analytical framework for understanding the selective forces driving viral adaptation to a new host. A preliminary analysis of large-scale changes in virus population structure revealed that viruses replicating in the macaques were subject to increasing levels of selection through day 70 postinfection (p.i.), whereas contemporaneous viruses in the mangabeys remained similar to the source inoculum. Three different site-by-site methods were employed to identify the amino acid sites responsible for this macaque-specific selection. Of 124 amino acid sites analyzed, 3 codons in V2, a 2-amino acid shift in an N-linked glycosylation site, and variation at 2 sites in the highly charged region were consistently evolving under either directional or diversifying selection at days 40 and 70 p.i. This strong macaque-specific selection on the V2 loop underscores the importance of this region in the adaptation of SIVsm to rhesus macaques. Due to the extreme viral diversity already extant in the naturally occurring viral inoculum, we employed a broad range of phylogenetic and numerical tools in order to distinguish the signatures of past episodes of selection in viral sequences from more recent selection pressures.

FIG. 1.—

SIVsm env V1V2 is highly diverse in the plasma of the naturally infected SM used for experimental inoculation of SMs and RMs. All 29 SI sequences were aligned and summarized using WebLogo (http://weblogo.berkeley.edu). The relative height of each amino acid letter designation at any given site represents their frequency, whereas the overall height of the column indicates the amount of information contained at that site. Unnumbered amino acid sites were excluded from all analyses due to the presence of gaps. Putative N-linked glycosylation motifs (NXS/T) are represented in gray. Underlined N-linked glycosylation motifs were not present in the majority of sequences sampled from the RMs at day 14 p.i. Sites labeled with a filled star were found to be under selection in both the RMs and the SMs. Sites labeled with an open star were found to under RM-specific selection pressures.

FIG. 2.—

SIVsm undergoes multiple adaptive events in RMs but not SMs during the early postacute phase of infection. (A) The number of adaptations occurring in SIVsm populations infecting both RMs and SMs through day 100 p.i. (B) The rate of increase in adaptive events over time occurring in RM-specific SIVsm populations between days 14 and 70 p.i. is significantly greater than 0, whereas the slight decrease in adaptive events among SMs is indistinguishable from 0 (Spearman's rank correlation, P < 0.05).

FIG. 3.—

SIVsm populations adapting to RMs are distinct from those in SMs. Bayesian phylogenetic trees of all variants sampled from each individual animal and the SI. FCo, FGu, and FLn are the SMs, and RHt and RZw are the RMs. Time points sampled from individually inoculated animals are represented by colored squares. The SI is represented by green triangles, and each variant is numbered. The clade containing the 6 SI variants from which most of the day 14 RM variants are descended is outlined in red. The node on which trees were rooted to determine the ancestral sequence for inferring substitutions is indicated with a light green circle.

FIG. 4.—

Summary of the amino acid sites found to be under selection for all 3 site-by-site analyses. Analyses are partitioned by analysis then by species and then by time point. Gray boxes indicate selection at that site and time point. “+” or “−” symbols indicate the presence of positive or purifying selection, respectively, as determined by the maximum likelihood analysis of dN and dS (P < 0.25, likelihood ratio test). Sites with gray forward hatching indicate the sites in V2 found to be under selection in a majority of the analyses. Sites with gray backward hatching are the sites in V2 found to be under positive selection by only the likelihood method.

FIG. 5.—

SIVsm V2 sequences at day 70 in RMs are more similar to V2 sequences from several major macaque-adapted SIV clones than to the contemporaneous SM V2 sequences. The 3 sites under significant RM-specific selection are indicated by stars, and N-glyc sites are backed in gray. The V2 sequences of RM-adapted clones were found at Los Alamos National Laboratories HIV Sequence Database (http://www.hiv.lanl.gov) and aligned by hand to maximize amino acid and codon usage similarity.