CONICET | Buscador de Institutos y Recursos Humanos

IntroductionBats are natural reservoirs of a large variety of viruses, including many important zoonotic viruses that cause severe diseases in humans and domestic animals, such as severe acute respiratory syndrome (SARS)-related coronavirus, Ebola virus, Nipah virus, and Hendra virus. Cross-species spillover events, as scientific evidence suggests for SARS-CoV-2 coronavirus, highlight the need to further characterize bat viruses inhabiting different geographical regions to help identifying those with the highest cross-species transmission. As most bat-borne viruses are transmitted by four routes (airborne, droplet, oral?fecal and contact transmission) to other hosts, it is particularly important to determine the viral communities present at oral/anal cavities or enteric canals of these animals.ObjectiveThe objective of this study is to investigate viral diversity on fecal samples from bats species from Argentina using Next Generation Sequencing technology and a metagenomic approach. Material and MethodsBats fecal samples were collected from two different sites: the Tadarida brasiliensis colony located in downtown Rosario city, Argentina, and Villarino Park at Zavalla city, Argentina. Selected fecal samples from 29 individuals from six different bat species (T. brasiliensis, Eumops patagonicus, Eptesicus diminutus, Molossus molossus, Molossus sp. And Eumops bonariensis) were prepared and pooled by species, sex and collection site. To concentrate viral particles, samples were filtered, centrifuged at high speed and nuclease-treated, subsequently viral DNA was enriched using whole genome amplification. The paired-end libraries were prepared and sequenced on Illumina MiSeq platform. Reads obtained were trimmed and filtered using the bbduk program (BBTools v38.42). Host, human and bacterial reads were subtracted by mapping reference genomes using Bowtie2 (v2.2.4). Sequences were further subjected to viral taxonomic classification using the centrifuge sequence classification system (Centrifuge version 1.0.3-beta) with a reference-index viral data base. ResultsA total of 4,520,370 read pairs were sequestered from the enriched pooled samples and 3,750,093 of them passed the quality filtering and trimming procedures. The taxonomic classification approach revealed that a total of 740,774 read pairs (20% of the filtered-clean reads) mapped to viral taxa. Sequences from Parvoviridae, Circoviridae, Genomoviridae, Papillomaviridae, Herpesviridae, Poxviridae and Arteriviridae were the most prevalent among vertebrate viral families and identified in all bats species included in this study. Higher diversity of vertebrate viral families was identified in fecal pooled samples from bats inhabiting Villarino Park (individual bats) in comparison to fecal pooled samples collected at T. brasiliensis colony. In addition a large number of phage-related sequences were detected, reflecting the bacteria present in the bat digestive system. ConclusionCharacterizing the bat virome is important for understanding viral diversity and detecting viral spillover between animal species. Our findings provide new insights on viruses present in different bats species of our region and living in close contact with humans and contribute to determine their possible role as pathogen reservoirs.