Two novel simian arteriviruses in captive and wild baboons (Papio spp.)

Abstract

Since the 1960s, simian hemorrhagic fever virus (SHFV; Nidovirales, Arteriviridae) has caused highly fatal outbreaks of viral hemorrhagic fever in captive Asian macaque colonies. However, the source(s) of these outbreaks and the natural reservoir(s) of this virus remain obscure. Here we report the identification of two novel, highly divergent simian arteriviruses related to SHFV, Mikumi yellow baboon virus 1 (MYBV-1) and Southwest baboon virus 1 (SWBV-1), in wild and captive baboons, respectively, and demonstrate the recent transmission of SWBV-1 among captive baboons. These findings extend our knowledge of the genetic and geographic diversity of the simian arteriviruses, identify baboons as a natural host of these viruses, and provide further evidence that baboons may have played a role in previous outbreaks of simian hemorrhagic fever in macaques, as has long been suspected. This knowledge should aid in the prevention of disease outbreaks in captive macaques and supports the growing body of evidence that suggests that simian arterivirus infections are common in Old World monkeys of many different species throughout Africa.

Importance: Historically, the emergence of primate viruses both in humans and in other primate species has caused devastating outbreaks of disease. One strategy for preventing the emergence of novel primate pathogens is to identify microbes with the potential for cross-species transmission in their natural state within reservoir species from which they might emerge. Here, we detail the discovery and characterization of two related simian members of the Arteriviridae family that have a history of disease emergence and host switching. Our results expand the phylogenetic and geographic range of the simian arteriviruses and define baboons as a natural host for these viruses. Our findings also identify a potential threat to captive macaque colonies by showing that simian arteriviruses are actively circulating in captive baboons.

FIG 1

Prevalence of simian arteriviruses in wild and captive baboon populations. Unbiased deep sequencing and qRT-PCR specific for MYBV-1 and SWBV-1 were used to determine the percentage of each baboon species that was viremic (black) or aviremic (white) at the time of sampling. Simian arterivirus prevalences were 18/43 (41.9%, 95% confidence interval [CI] = 28.4% to 56.7%) in Mikumi yellow baboons, 0/23 (0.0%, 95% CI = 0.0% to 16.9%) in Kibale olive baboons, 2/21 (9.5%, 95% CI = 1.5% to 30.1%) in SNPRC olive baboons, and 0/10 (0.0%, 95% CI = 0.0% to 32.1%) in SNPRC hybrid olive/yellow baboons. The prevalence of simian arterivirus infections was significantly higher in Mikumi baboons than in baboons from Kibale or SNPRC (Fisher's exact test, P < 0.01 in both cases). Maps and animal silhouettes are not to scale.

FIG 2

Plasma viral loads of simian arterivirus and longitudinal sampling of SWBV-1. RNA was isolated from plasma, and qRT-PCR was performed using primers and probes designed from deep sequencing data. (A) The difference in viral loads between MYBV-1 (circles) and SWBV-1 (squares) was not significant (n.s.; two-tailed t test performed on log-transformed 95% confidence interval values). Baboon identifiers and sample collection dates are indicated for SWBV-1-infected baboons. (B) Collection dates and results of testing of banked samples from SNPRC olive baboons 16986 and 19466: not tested (nt), SWBV-1 positive (+), and SWBV-1 negative (−).

FIG 3

Genome organization and plot of the similarity of SWBV-1 and MYBV-1 sequences to those of other simian arteriviruses. (A) The genome organization of SWBV-1 and MYBV-1 is shown in comparison to that of SHFV, the prototype simian arterivirus. Boxes represent open reading frames and are drawn to scale. ORFs unique to the simian arteriviruses are shown in gray. For ORFs that produce a defined protein homologue in other arteriviruses, the name of the putative protein product is given in bold. (B) Sliding-window similarity plots of percent amino acid identity among select SHFV variants across aligned coding genomes. The analysis was performed with a window size of 300 and a step size of 25. Dashed vertical lines, the start positions of each ORF.

FIG 4

Simian arterivirus phylogeny based on ORF1b nucleotide sequence alignment. The simian arterivirus phylogenetic history was inferred using the maximum likelihood method (1,000 bootstrap replicates) with a best-fit substitution model of the form GTR+Γ (with five rate categories, +Γ parameter = 1.1092). All positions containing gaps and missing data were eliminated, resulting in a final data set of 4,380 positions. Bootstrap values greater than 70% are shown. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. Analyses were conducted using MEGA6 (22).

FIG 5

Comparison of SWBV-1 sequences. Consensus nucleotide sequences were extracted from deep sequencing read mappings and aligned using the MUSCLE algorithm in CLC Genomics Workbench (version 6.5). Pairwise comparisons were used to calculate percent nucleotide similarity (A), nucleotide differences (B), and amino acid differences (C). For amino acid comparisons, consensus sequences were annotated and each ORF was translated, aligned, and concatenated. Baboon identifiers and sample collection dates are indicated. (D) Alignment showing the region of SWBV-1 ORF5 with a high density of amino acid changes (red) relative to the sequence collected from baboon 16986 on 4 November 2013. (E) Frequencies of minor nucleotide variants (gray, baboon 16986; white, baboon 19466) at the 33 sites that differentiate SWBV-1 consensus sequences from baboon 16986 (white) and baboon 19466 (gray) collected in 2014.