Characterization of Pipistrellus pygmaeus Bat Virome from Sweden

Abstract

Increasing amounts of data indicate that bats harbor a higher viral diversity relative to other mammalian orders, and they have been recognized as potential reservoirs for pathogenic viruses, such as the Hendra, Nipah, Marburg, and SARS-CoV viruses. Here, we present the first viral metagenomic analysis of Pipistrellus pygmaeus from Uppsala, Sweden. Total RNA was extracted from the saliva and feces of individual bats and analyzed using Illumina sequencing. The results identified sequences related to 51 different viral families, including vertebrate, invertebrate, and plant viruses. These viral families include Coronaviridae, Picornaviridae, Dicistroviridae, Astroviridae, Hepeviridae, Reoviridae, Botourmiaviridae, Lispviridae, Totiviridae, Botoumiaviridae, Parvoviridae, Retroviridae, Adenoviridae, and Partitiviridae, as well as different unclassified viruses. We further characterized three near full-length genome sequences of bat coronaviruses. A phylogenetic analysis showed that these belonged to alphacoronaviruses with the closest similarity (78–99% at the protein level) to Danish and Finnish bat coronaviruses detected in Pipistrellus and Myotis bats. In addition, the full-length and the near full-length genomes of picornavirus were characterized. These showed the closest similarity (88–94% at the protein level) to bat picornaviruses identified in Chinese bats. Altogether, the results of this study show that Swedish Pipistrellus bats harbor a great diversity of viruses, some of which are closely related to mammalian viruses. This study expands our knowledge on the bat population virome and improves our understanding of the evolution and transmission of viruses among bats and to other species.

Investigation of the Virome and Characterization of Issyk-Kul Virus from Swedish Myotis brandtii Bats

“…However, the comparison of viral diversity between different studies is complex and may be attributed to different factors, for example, bat species, sampling location, season, year, sample size, sample type, sample preparation and sequence analysis [ 38 , 39 , 40 , 41 ]. This is further highlighted by the fact that the viruses from this study that were genetically characterized were not detected in our previous metagenomic study investigating Pipistrellus pygmaeus bats in Uppland [ 23 ]. Furthermore, in the Pipistrellus pygmaeus bats, a majority of the viral reads were coronaviruses, while in these M. brandtii , no coronaviruses were detected.…”

“…Bats have also been shown to harbor viruses related to the Tymoviridae family, and these have also been linked to the bat feed [ 11 , 23 , 38 ]. Members of this family consist of positive-sense, single-stranded RNA with a genome size ranging from 6 to 7.5 kb, and they have one to four ORFs depending on the genus.…”

“…The individual samples were processed, sequenced and bioinformatically analyzed as previously described by Cholleti et al [ 23 ]. Briefly, RNA was extracted from 200 µL swab solution using a combination of TRIzol TM LS reagent (Invitrogen, Carlsbad, CA, USA) and Genejet RNA extraction kit (Thermo Fisher Scientific, Waltham, MA, USA).…”

“…For example, Myotis daubentonii bats from the southern part of Sweden have been shown to carry antibodies for European bat lyssavirus [ 21 ] and, through a metagenomic study, been shown to carry alphacoronavirus [ 22 ]. In addition, we have recently characterized the virome from feces of Pipistrellus pygmaeus bats collected in the Uppland region of Sweden [ 23 ]. In that study, three near-full length genomes of bat coronaviruses and two picornaviruses were characterized.…”