Metagenomic Study of Enteric Viruses in Proboscis Monkey (Nasalis larvatus)

• Main Author: Ng, Kar Hon
• Format: Thesis
• Language: English
• Published: Universiti Malaysia Sarawak (UNIMAS) 2019
• Subjects: Q Science (General); QL Zoology; QR355 Virology
• Online Access: http://ir.unimas.my/id/eprint/25741/3/Metagenomic%20Study%20of%20Enteric%20Viruses%20in%20Proboscis%20Monkey%20%28Nasalis%20lavartus%29.pdf; http://ir.unimas.my/id/eprint/25741/

Proboscis monkey (Nasalis larvatus), endemic to Borneo, is listed as “Endangered” species by the International Union for Conservation of Nature (IUCN). Non-human primates are known to be the natural hosts for a variety of virus and bacteria, which some have zoonotic potential. To date, no studies were done to reveal the preference diets and the enteric virome of proboscis monkey. This study aimed to determine the diets, feeding preference and enteric virome of proboscis monkeys, as well as to correlate the enteric viral composition of proboscis monkeys with their diets. For the past few decades, Bocaparvoviruses (BoVs) were reported detected in both the human and other non-human primates. This BoVs were known to cause gastrointestinal and respiratory diseases in both human and non-human primates. Cross-species transmission of BoVs between human with non-human primates was also previously reported. Hence, this study also aimed to assemble the novel proboscis monkey Bocaparvovirus (PMBoV) and reconstruct the BoV phylogenetic trees to infer the genetic relatedness of PMBoV with other BoVs. Vegetation plot and feeding data were collected from the feeding sites of these animals. Fresh fecal samples were collected and processed for viral RNA extraction, reverse transcription and high-throughput sequencing. This study shows that proboscis monkeys fed mainly on leaves and fruits, and their diets depended on the availability of foods within their habitat with selective preference on six species of plants, namely Vitex sp., Talipariti tilliaceus, Calophyllum inophyllum, Avicennia sp., Rhizophora sp. and Sonneratia sp.. The dietary diversity of proboscis monkey showed significant difference between two different sampling sites of BNP beach forest and SWS mangrove forest, rather than between fruiting and non-fruiting seasons. A total of 819,779,634 reads from proboscis monkey fecal samples were sequenced with 2,090,455 reads (~ 3%) were identified as viruses reads. The enteric virome of proboscis monkeys was composed of 34 virus families with the most prevalence enteric virus families were the bacteriophage, Microviridae (52%) followed by plant infecting virus family, Virgaviridae (38%) and pathogenic virus family, Parvoviridae (3%). The Pearson correlation showed that there is correlation between the diets and the enteric virus families of proboscis monkey only when under the least influence of bias resulted from the enrichment process during sequencing. A novel PMBoV was assembled and four BoV phylogenetic trees of full genome, NS1, NP1 and VP1 were reconstructed. This study revealed the possibility of cross-species transmission of BoV between proboscis monkeys and other non-primate hosts. As proboscis monkey is an endangered species, this study is important by providing food reference data for the captive conservation of proboscis monkey and facilitate future disease diagnoses based on the known reservoirs of viruses discovered in this non-human primate. Keywords: Enteric virus, Metagenomics, Proboscis monkeys, Bocaparvovirus