Full-Genome Sequences of Alphacoronaviruses and Astroviruses from Myotis and Pipistrelle Bats in Denmark.

Christina M Lazov,Graham J Belsham,Thomas Bruun Rasmussen,Anette Bøtner

doi:10.3390/v13061073

Christina M Lazov, Graham J Belsham + Show 2 more

Open Access

https://doi.org/10.3390/v13061073

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Abstract

Bat species worldwide are receiving increased attention for the discovery of emerging viruses, cross-species transmission, and zoonoses, as well as for characterizing virus infections specific to bats. In a previous study, we investigated the presence of coronaviruses in faecal samples from bats at different locations in Denmark, and made phylogenies based on short, partial ORF1b sequences. In this study, selected samples containing bat coronaviruses from three different bat species were analysed, using a non-targeted approach of next-generation sequencing. From the resulting metagenomics data, we assembled full-genome sequences of seven distinct alphacoronaviruses, three astroviruses, and a polyomavirus, as well as partial genome sequences of rotavirus H and caliciviruses, from the different bat species. Comparisons to published sequences indicate that the bat alphacoronaviruses belong to three different subgenera—i.e., Pedacovirus, Nyctacovirus, and Myotacovirus—that the astroviruses may be new species in the genus Mamastrovirus, and that the polyomavirus could also be a new species, but unassigned to a genus. Furthermore, several viruses of invertebrates—including two Rhopalosiphum padi (aphid) viruses and a Kadipiro virus—present in the faecal material were assembled. Interestingly, this is the first detection in Europe of a Kadipiro virus.

Highlights

The bat coronavirus (BtCoV) genomes from M. daubentonii and M. dasycneme were assembled de novo using SPAdes, which, with one exception, produced a single contig covering the entire genome
The alphacoronaviruses detected in these samples from different bat species were compared using phylogenetic analysis based on short regions (130 or 208 nt) of the ORF1ab coding sequence
This enabled the generation of 7 full-length BtCoV genome sequences of 27,943–28,192 nucleotides—two of which were from the same sample

Summary

Introduction

Studies of bat viruses typically focus on those that have emerged as human pathogens, including coronaviruses, lyssaviruses, paramyxoviruses, filoviruses, and reoviruses [7,8]; this is reflected in the distribution of known virus sequences from bats [9]. Another approach has been to sequence and taxonomically assign the entire bat virome, e.g., all nucleic acids present in faecal samples [10,11,12,13,14,15]. These studies discover many viruses, but have low coverage of individual viruses, and mammalian, invertebrate, fungal, and bacterial viruses will all be present in the data

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