Exceptional Simian Hemorrhagic Fever Virus Diversity in a Wild African Primate Community

Abstract

h Simian hemorrhagic fever virus (SHFV) is an arterivirus that causes severe disease in captive macaques. We describe two new SHFV variants subclinically infecting wild African red-tailed guenons (Cercopithecus ascanius). Both variants are highly divergent from the prototype virus and variants infecting sympatric red colobus (Procolobus rufomitratus). All known SHFV variants are monophyletic and share three open reading frames not present in other arteriviruses. Our data suggest a need to modify the current arterivirus classification. Simian hemorrhagic fever virus (SHFV) is a member of the family Arteriviridae, together with equine arteritis virus (EAV), lactate dehydrogenase elevating virus (LDV), and porcine reproductive and respiratory syndrome virus (PRRSV) (1). SHFV was first isolated from captive macaques (Macaca sp.) in 1964 after nearly simultaneous outbreaks in Soviet and American primate centers (2-4), possibly having originated from subclinically infected wild-caught patas monkeys (Erythrocebus patas), green monkeys (Chlorocebus aethiops), or guinea baboons (Papio papio) (5,6). Much of what is known about SHFV comes from prototype variants LVR 42-0/M6941 and Sukhumi, isolated during the original two outbreaks, and their derivatives (4, 7).We recently discovered two novel SHFV variants infecting a male red colobus monkey (Procolobus rufomitratus) from Kibale National Park, Uganda (8). These viruses are highly divergent from each other and the prototype variants but, like the prototype variants, contain three unique open reading frames (ORFs) (2a, 2b, and 3) downstream from the replicase-encoding ORFs (8,9). This genomic architecture may be characteristic of the SHFV taxon.Here, we report the discovery of two novel SHFV variants in red-tailed guenons (Cercopithecus ascanius) from the same location where we previously reported SHFV in a red colobus (8). In 2010, we sampled 13 Kibale red-tailed guenons as part of a larger study of primate ecology, conservation, and health (10). Animals were anesthetized and samples were collected as previously described (8). Viral RNA was prepared from blood plasma for direct sequencing as previously described (8), with minor modifications for sequencing on an Illumina MiSeq instrument. De novo assembly of sequence reads yielded complete SHFV coding genomes from three individuals (two females, RT05 and RT11, and one male, RT10). A fourth nearly complete SHFV coding genome was recovered from another male individual, RT09, and small gaps were filled by PCR and 3= rapid amplification of cDNA ends (RACE) followed by Sanger sequencing (8).Viral genomes were annotated with CLC Genomics Workbench version 5.5 (CLC Bio, Aarhus, Denmark), and putative ORFs were confirmed by querying the NCBI GenBank database (11). Open reading frames were individually aligned with prototype variant LVR 42-0/M6941 and red colobus variants SHFV-krc1 and SHFV-krc2 using a codon-based version of the MAFFT algorithm (12) implemented in Translator X (13). Individual ORF alignments were then concatenated...

Competing pressures on populations: long-term dynamics of food availability, food quality, disease, stress and animal abundance

“…There is recently an abundance of data on the viruses of red colobus [17,73]. Unfortunately, no long-term comparative data are available, so we cannot evaluate if there has been a change in the nature of the viral infections in this population of red colobus.…”

A Novel Hepacivirus with an Unusually Long and Intrinsically Disordered NS5A Protein in a Wild Old World Primate

“…After DNase treatment, RNA was random hexamer primed, subjected to double-stranded cDNA synthesis, and prepared for sequencing on the Illumina MiSeq using the Nextera DNA sample preparation kit (Illumina, San Diego, CA) as previously described (19). Sequence data were analyzed using CLC Genomics Workbench 5.5 (CLC bio, Aarhus, Denmark).…”

Two Novel Simian Arteriviruses in Captive and Wild Baboons (Papio spp.)

“…Samples were processed for sequencing in a biosafety level 3 laboratory as described previously (13,14), with slight modifications. Briefly, for each animal, viral RNA was isolated from approximately 200 l of plasma using a Qiagen QIAamp MinElute virus spin kit (Qiagen, Hilden, Germany), omitting carrier RNA.…”

“…Importantly, simian arterivirus infection has never been demonstrated in a free-living patas monkey, and monkeys from the two species known to harbor simian arteriviruses in nature, the red colobus (Procolobus rufomitratus tephrosceles) and the red-tailed guenon (Cercopithecus ascanius schmidti), were not associated with past outbreaks of SHF in macaques (2,13,14). Grivets (Chlorocebus aethiops) and baboons (genus Papio) have long been suspected of harboring simian arteriviruses in captivity, but empirical evidence demonstrating infection of these hosts, either in the wild or in captivity, has, to our knowledge, never been presented (6,15).…”