Viruses in sanctuary chimpanzees across Africa

Abstract

Infectious disease is a major concern for both wild and captive primate populations. Primate sanctuaries in Africa provide critical protection to thousands of wild‐born, orphan primates confiscated from the bushmeat and pet trades. However, uncertainty about the infectious agents these individuals potentially harbor has important implications for their individual care and long‐term conservation strategies. We used metagenomic next‐generation sequencing to identify viruses in blood samples from chimpanzees (Pan troglodytes) in three sanctuaries in West, Central, and East Africa. Our goal was to evaluate whether viruses of human origin or other “atypical” or unknown viruses might infect these chimpanzees. We identified viruses from eight families: Anelloviridae, Flaviviridae, Genomoviridae, Hepadnaviridae, Parvoviridae, Picobirnaviridae, Picornaviridae, and Rhabdoviridae. The majority (15/26) of viruses identified were members of the family Anelloviridae and represent the genera Alphatorquevirus (torque teno viruses) and Betatorquevirus (torque teno mini viruses), which are common in chimpanzees and apathogenic. Of the remaining 11 viruses, 9 were typical constituents of the chimpanzee virome that have been identified in previous studies and are also thought to be apathogenic. One virus, a novel tibrovirus (Rhabdoviridae: Tibrovirus) is related to Bas‐Congo virus, which was originally thought to be a human pathogen but is currently thought to be apathogenic, incidental, and vector‐borne. The only virus associated with disease was rhinovirus C (Picornaviridae: Enterovirus) infecting one chimpanzee subsequent to an outbreak of respiratory illness at that sanctuary. Our results suggest that the blood‐borne virome of African sanctuary chimpanzees does not differ appreciably from that of their wild counterparts, and that persistent infection with exogenous viruses may be less common than often assumed.

Five Species of Wild Freshwater Sport Fish in Wisconsin, USA, Reveal Highly Diverse Viromes

“…Metagenomic next-generation sequencing was performed as previously described [ 6 , 18 , 25 , 26 ]. In brief, samples were centrifuged at 10,000× g (4 °C) for 10 min to remove debris, then supernatants were transferred to a new tube and centrifuged further at 25,000× g (4 °C) for 3 h to pellet viruses.…”

“…A virus was considered present if a fish had ≥2 overlapping viral reads of 50 bp or more. Reads that mapped to each virus, or any of the viruses examined (total viral load), were then normalized for sequencing depth and viral sequence length and log-transformed to become log10 viral reads per million per kilobase of target sequence (Log10vRPM/kb) [ 6 , 25 , 26 ].…”

Mapping glycoprotein structure reveals defining events in the evolution of theFlaviviridae

“…The search was complemented by referencing sequences from Mifsud et al 2022 42 and supplemented with sequences from the NCBI nucleotide database using the search phrase "flavi[All Fields] OR pesti[All Fields] OR hepaci[All Fields] OR pegi[All Fields] AND viruses[filter]" on the same date. Additional sequences were later retrieved from publications that had sequences not available in GenBank at the time 9,33,[44][45][46][47][48][49] .…”

Observational approaches to chimpanzee behavior in an African sanctuary: Implications for research, welfare, and capacity‐building

“…Prior work integrating data on the chimpanzees' real‐life social relationships with their performance on cooperative tasks (Engelmann & Herrmann, 2016; Engelmann et al, 2019) shows the power of combining these approaches, something that is much more feasible in sanctuaries than in the wild. Similarly, it is also feasible to collect a variety of biological samples from sanctuary populations (Cole et al, 2020; Dunay et al, 2023; Rosati et al, 2023; Standley et al, 2011; Wobber et al, 2013; Wobber, Hare, et al, 2010), some of which—such as saliva, or blood collected in the context of routine health checks for the animal's own well‐being—are difficult or impossible in the wild. This kind of observational data can also be linked to detailed information on individual's heath status.…”