Full-length genome analyses of two new simian immunodeficiency virus (SIV) strains from mustached monkeys (C. Cephus) in Gabon illustrate a complex evolutionary history among the SIVmus/mon/gsn lineage

Abstract

The Simian Immunodeficiency Virus (SIV) mus/mon/gsn lineage is a descendant of one of the precursor viruses to the HIV-1/SIVcpz/gor viral lineage. SIVmus and SIVgsn were sequenced from mustached and greater spot nosed monkeys in Cameroon and SIVmon from mona monkeys in Cameroon and Nigeria. In order to further document the genetic diversity of SIVmus, we analyzed two full-length genomes of new strains identified in Gabon. The whole genomes obtained showed the expected reading frames for gag, pol, vif, vpr, tat, rev, env, nef, and also for a vpu gene. Analyses showed that the Gabonese SIVmus strains were closely related and formed a monophyletic clade within the SIVmus/mon/gsn lineage. Nonetheless, within this lineage, the position of both new SIVmus differed according to the gene analyzed. In pol and nef gene, phylogenetic topologies suggested different evolutions for each of the two new SIVmus strains whereas in the other nucleic fragments studied, their positions fluctuated between SIVmon, SIVmus-1, and SIVgsn. In addition, in C1 domain of env, we identified an insertion of seven amino acids characteristic for the SIVmus/mon/gsn and HIV‑1/SIVcpz/SIVgor lineages. Our results show a high genetic diversity of SIVmus in mustached monkeys and suggest cross-species transmission events and recombination within SIVmus/mon/gsn lineage. Additionally, in Central Africa, hunters continue to be exposed to these simian viruses, and this represents a potential threat to humans.

Figure 1

Geographical distribution of samples from moustached monkeys in Gabon. Haut-Ogooué (HO) n = 6, Moyen Ogooué (MO) n = 10, Ngounié (NG) n = 12, Nyanga (NY) n = 1, Ogooué Ivindo (OI) n = 27, Ogooué Lolo (OL) n = 4, Ogooué Maritime (OM) n = 7, Woleu-Ntem (WN) n = 4. Red points show the two sites where SIVmus positive animals were identified.

Figure 2

Comparison of C1 domain, between the first and second conserved cysteine residues for different Simian Immunodeficiency Virus (SIV) lineages, Human Immunodeficiency Virus (HIV)-1 and HIV-2. The insertion of seven amino acids present in the SIVmus/mon/gsn lineage, SIVcpz, SIVgor and HIV-1 M, N, O, P is shown in red letters. In SIVs from guenons (Cercopithecus species), this domains ends in a glycine (highlighted in green box), while in all hominoid lineages the last amino acid residue of this domain is a highly conserved histidine (highlighted in yellow box). Dots indicate amino acid identity and dashes indicate gaps introduced to optimize the alignment.

Figure 3

Phylogenetic relationships of the newly derived SIVmus sequences to other SIV lineages in the three major genes. gag (1228 nt) (a), pol (2772 nt) (b), and env (1953) (c). Only sequences of interest are shown. Phylogenies were inferred using both Bayesian and Maximum Likelihood methods implemented in Mr Bayes and PhyML, respectively, under the GTR + Γ₄ + I model of evolution. Stars and crosses at nodes represent posterior probability (≥90%) and bootstrap values (≥80%), respectively. Scale bars indicate substitution per site. In env, the tree topologies differed according the phylogenetic method used. In the figure, (c) represents the topology done for env by using the bayesian method whereas (c’) represents the topology done by using PhyML method.

Figure 4

Similarity plots of nucleotide sequences illustrating the extent of genetic diversity between the new SIVmus and other SIV lineages. Similarity plots of gag, pol, vif, env, and nef non-concatenated nucleic acid sequences showing similarities between SIVmus-09Gab-0I81 and SIVmus-11Gab-Pts02 and other SIVs representative for the different SIV lineages (sliding window of 500 na moved in steps of 50 na). Only SIV lineages of interest are retained in the figure for clarity.

Figure 5

Bootscan analyses of the new SIVmus whole genome sequences versus other SIV lineages infecting arboreal cercopithecus. Bootscan analyses were performed using the same full-length nucleic acid alignment of SIVs infecting only arboreal Cercopithecus. monkeys with the SIMPLOT package version 2.5 [27]. (a) showed the bootscan result for SIVmus-09Gab-OI81 versus other SIV lineages, (b) showed the bootscan result for SIVmus-11Gab-Pts02 versus other SIV lineages. Hatched blue rectangles and green rectangle showed the divergent fragments between the two new SIVmus strains (fragments B, D, E, H and d).

Figure 6

Phylogenetic relationships between SIVmus-09Gab-OI81 and SIVmus-11Gab-Pts02 with other representative SIV lineages infecting arboreal cercopithecus along the full-length genome. Phylogenetic analyses were done according to the bootscan analyses (Figure 5). We defined eight fragments (A to H) for SIVmus-09Gab-OI81 and seven fragments (A–C, d, F–H) for SIVmus-11Gab-Pts02. Phylogenies were inferred using both Bayesian (run for 1,000,000 generations) and Maximum Likelihood methods implemented in Mr Bayes and PhyML, respectively, under the GTR + Γ₄ + I model of evolution. Stars and crosses at nodes represent posterior probability (≥90%) and bootstrap (≥70%) values, respectively. Scale bars indicate substitution per site. The new SIVmus strains are highlighted in red.