Discovery and Characterization of Distinct Simian Pegiviruses in Three Wild African Old World Monkey Species

Abstract

Within the Flaviviridae, the recently designated genus Pegivirus has expanded greatly due to new discoveries in bats, horses, and rodents. Here we report the discovery and characterization of three simian pegiviruses (SPgV) that resemble human pegivirus (HPgV) and infect red colobus monkeys (Procolobus tephrosceles), red-tailed guenons (Cercopithecus ascanius) and an olive baboon (Papio anubis). We have designated these viruses SPgVkrc, SPgVkrtg and SPgVkbab, reflecting their host species’ common names, which include reference to their location of origin in Kibale National Park, Uganda. SPgVkrc and SPgVkrtg were detected in 47% (28/60) of red colobus and 42% (5/12) red-tailed guenons, respectively, while SPgVkbab infection was observed in 1 of 23 olive baboons tested. Infections were not associated with any apparent disease, despite the generally high viral loads observed for each variant. These viruses were monophyletic and equally divergent from HPgV and pegiviruses previously identified in chimpanzees (SPgVcpz). Overall, the high degree of conservation of genetic features among the novel SPgVs, HPgV and SPgVcpz suggests conservation of function among these closely related viruses. Our study describes the first primate pegiviruses detected in Old World monkeys, expanding the known genetic diversity and host range of pegiviruses and providing insight into the natural history of this genus.

Local Virus Extinctions following a Host Population Bottleneck

“…Persistent HPgV infections have not been shown to be pathogenic and may reduce mortality in HIV-coinfected subjects (43,51). We report here the detection of a pegivirus in AGMs whose closest relatives were recently described in Old World monkeys from Uganda, although from different genera in the Cercopithecidae family (29,52). Evidence of recombination with the pegiviruses of other Old World monkeys may reflect an ancient association between these viruses' ancestors within coinfected hosts.…”

“…Based on its level of genomic nucleotide identity to SPgVkrtg_RT11 (GenBank accession no. KF234529) and recently adopted nomenclature (27,29), we identified it as a novel viral species from African green monkeys and designated it simian pegivirus in African green monkey (SPgVagm).…”

GB Virus C Coinfections in West African Ebola Patients

“…We believe that this is unlikely because (i) we detected GBV-C in patients with EBOV plasma loads of Ͼ10 8 (see supplemental Fig. S2 in reference 2) and (ii) in previous studies, we have detected multiple viruses from a single sample using a similar methodology, even in samples where at least one virus was highly concentrated (17)(18)(19)(20). Recovery of unique reads targeting the majority of the viral genome provide unequivocal evidence for GBV-C infection in all but one of the samples; however, in the one sample where less than half of the genome is covered, verification of GBV-C status using an independent assay (e.g., reverse transcription-quantitative PCR [RT-qPCR]) would be ideal but is not currently possible.…”

Arteriviruses, Pegiviruses, and Lentiviruses Are Common among Wild African Monkeys

“…1A). These viruses were more closely related to simian pegiviruses from baboons (genus Papio) sampled in Zambia and Uganda than to simian pegiviruses from the more closely related but geographically distant sabaeus monkeys (Chlorocebus sabaeus) sampled in Gambia (9,16,22). We also discovered two novel simian arteriviruses, which we named Drakensberg Mountain vervet virus (DMVV-1) and Zambian malbrouck virus (ZMbV-1).…”

“…Previously, we used unbiased deep sequencing, a technique that utilizes random hexamers to prime cDNA synthesis from RNA in combination with next-generation sequencing, to discover and characterize blood-borne RNA viruses in wild monkeys from several cercopithecoid (i.e., Old World monkey [OWM]) species in Uganda, Tanzania, and Zambia (9)(10)(11)(12)(13)(14)(15)(16). We consistently detected viruses from three genera: lentiviruses (i.e., SIV, Retroviridae family), pegiviruses (i.e., simian pegivirus [SPgV], Flaviviridae family), and simian arteriviruses (i.e., viruses distantly related to simian hemorrhagic fever virus [SHFV], Arteriviridae family).…”