Complete genome analysis of one of the earliest SIVcpzPtt strains from Gabon (SIVcpzGAB2)

Abstract

Chimpanzees in west central Africa (Pan troglodytes troglodytes) are known to harbor simian immunodeficiency viruses (SIVcpzPtt) that represent the closest relatives of human immunodeficiency virus type 1 (HIV-1); however, the number of SIVcpzPtt strains that have been fully characterized is still limited. Here, we report the complete nucleotide sequence of SIVcpzGAB2, a virus originally identified in 1989 in a chimpanzee (P. t. troglodytes) from Gabon. Analysis of this sequence reveals that SIVcpzGAB2 is a member of the SIVcpzPtt group of viruses, but that it differs from other SIVcpzPtt strains by exhibiting a highly divergent Env V3 loop with an unusual crown (NLSPGTT) containing a canonical N-linked glycosylation site, an unpaired cysteine residue in Env V4, and two late (L) domain motifs (PTAP and YPSL) in Gag p6. Moreover, phylogenetic analyses indicate evidence of recombination during the early divergence of SIVcpzPtt strains; in particular, part of the pol gene sequence of SIVcpzGAB2 appears to be derived from a previously unidentified SIVcpz lineage ancestral to HIV-1 group O. These data indicate extensive diversity among naturally occurring SIVcpzPtt strains and provide new insight into the origin of HIV-1 group O.

FIG. 1

Diversity plots illustrating the extent of amino acid sequence difference between SIVcpzGAB2 and SIVcpzPtt (GAB1, CAM3), SIVcpzPts (TAN1), and representative HIV-1 group M, N, and O strains. Plots for SIVcpz strains US and CAM13 followed similar trajectories to that for GAB1; those for strains CAM5 and ANT were similar to those for CAM3 and TAN1, respectively. The HIV-1 strains used were U455 (M), YBF30 (N), and ANT70 (O). Predicted protein sequences were aligned using Clustal W with minor manual adjustment, then concatenated (C-terminal overlaps were removed); sites with ambiguous alignment, or a gap in any sequence, were excluded. Differences were calculated for windows of 200 amino acids, moved in steps of 20 amino acids along the alignment (0.1 = 10% difference); values are plotted at the midpoint of the window. The gray area shows the region within which the distance of SIVcpz GAB2 to HIV-1 group O (red line) is reduced.

FIG. 2

Phylogenetic trees depicting the relationship of SIVcpzGAB2 (boxed) to other SIVcpz and HIV-1 isolates. SIVcpz strains from P. t. troglodytes and P. t. schweinfurthii are shown in red and blue, respectively. Protein sequences were aligned using Clustal W with minor manual adjustment. Maximum likelihood trees were estimated by the Bayesian method (implemented in MRBAYES), using the JTT matrix of amino acid replacement and a gamma distribution of rates across sites, then midpoint rooted. Numbers on internal branches indicate estimated posterior probabilities (as percentages); only values of 95% or higher are shown. The scale bars indicate 5% replacement per site. Representative HIV-1 sequences used: group M subtypes A (strain U455) and B (LAI), group N strains YBF30 and YBF106, and group O strains ANT70 and MVP5180.

FIG. 3

Phylogenetic analyses of regions of the Pol protein. Region A comprised 300 residues (in the gap-stripped alignment) from the amino-terminal half of the protein (see Fig. 1); region B comprised the remaining 554 residues between region A and the carboxyl-terminus. See Figure 2 for methods and details of presentation.

FIG. 4

Comparison of gp120 V3 loop sequences among SIVcpz and representative HIV-1 strains. Sites conserved among all SIVcpz strains except SIVczpGAB2 are highlighted in the SIVcpzGAB2 sequence. Predicted N-linked glycosylation sites are underlined. The dendrogram at the left represents the phenetic similarity among sequences, inferred by the UPGMA method applied to fractional differences among pairs of sequences. SIVcpzPtt and SIVcpzPts strains are indicated by cpz/t (in red) and cpz/s (in blue), respectively. Other sequences are HIV-1 strains: for example, M/A:UG037 denotes group M, subtype A, strain UG037.