Metagenomic detection of a wide variety of viruses from Vietnamese bats

Abstract

Introduction: The species richness of tropical bats is astonishing, such as the diversity of bat-borne viruses. As bats are important reservoirs of zoonotic pathogens, we investigated the viruses found in Vietnamese bats. Methods: Overall, sixty-one bats of 16 species were sampled in Southern Vietnam (Dak Nong and Ho Chi Minh Provinces) and sixty-six samples (11 lung and 55 faeces) were investigated. Individual samples were subjected to viral enrichment and unbiased metagenomic sequencing on Illumina platform. Viral contigs were aligned against a custom-made bat viral database based on DBatVir and against the NCBI-nr database. Results: A wide variety of bat-borne viruses were found in the samples. According to sample type, individual faeces samples contained more viruses than lung samples from the same (Macroglossus cf. minimus) individuals. Viruses from the following viral families were represented in our study: Orthoherpesviridae, Genomoviridae, Circoviridae, Parvoviridae, Coronaviridae, Picornaviridae, Astroviridae, Adenoviridae, Hepeviridae, and Hepadnaviridae.We have found a new recombinant Sarbecovirus from a Rhinolophus thomasi, two new Hepevirus from a Kerivoula titania and a Scotomanes ornatus, as well as several viruses from Circovirus, Adenovirus, Alphacoronavirus and other genera.Several faeces samples contained different bat viruses, providing evidence for co-infection. Interestingly, the faeces of the bat infected with the Sarbecovirus contained a cyclovirus, a parvovirus, and a Hepatitis B virus as well. Discussion: As our metagenomic results show, bats harbour a great diversity of viruses. Our samples were not pooled, hence we could study the viral diversity of single bats, describe co-infections, and de novo assembly complete genomes without the problem caused by the co-infection of specimens with nearly identical viruses. Drawback of the method is the limitation of samples that could be investigated from the same number of Illumina runs. Conclusion: Metagenomic approach is an effective way to find and characterize new viruses. NGS sequencing of individual samples has trade-offs but can provide interesting and important results. New viruses were found from the families Orthoherpesviridae, Genomoviridae, Circoviridae, Parvoviridae, Coronaviridae, Picornaviridae, Astroviridae, Adenoviridae, Hepeviridae, and Hepadnaviridae in Vietnamese bats.