Discovery of three RNA viruses using ant transcriptomic datasets

Eleni Kleanthous,Andrew E Firth,Ingrida Olendraite,Nina I Lukhovitskaya

doi:10.1007/s00705-018-4093-2

Eleni Kleanthous, Andrew E Firth + Show 2 more

Open Access

https://doi.org/10.1007/s00705-018-4093-2

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Abstract

Three novel RNA viruses, named Formica fusca virus 1 (GenBank accession no. MH477287), Lasius neglectus virus 2 (MH477288) and Myrmica scabrinodis virus 2 (MH477289), were discovered in ants collected in Cambridge, UK. The proposed virus names were given based on the hosts in which they were identified. The genome sequences were obtained using de novo transcriptome assembly of high-throughput RNA sequencing reads and confirmed by Sanger sequencing. Phylogenetic analysis showed that Formica fusca virus 1 grouped within the family Nyamiviridae, Lasius neglectus virus 2 grouped within the family Rhabdoviridae and Myrmica scabrinodis virus 2 belongs to the family Dicistroviridae. All three viruses are highly divergent from previously sequenced viruses.

Highlights

Insect-infecting viruses comprise a large and diverse group, but their full diversity has as yet been poorly investigated [1]
We focused on genetically characterising three of the viral sequences with highest coverage, our analysis of Trinity assemblies revealed that further uncharacterised virus sequences were present in the Handling Editor: Ralf Georg Dietzgen
To determine the taxonomy of the three viruses, related sequences were identified within GenBank (5 Dec 2017, taxID = 10239 “viruses”), using the amino acid sequence of the entire ORF encoding the RNA-dependent RNA polymerase (RdRp) as the query in TBLASTN

Summary

Introduction

Insect-infecting viruses comprise a large and diverse group, but their full diversity has as yet been poorly investigated [1]. To determine the taxonomy of the three viruses, related sequences were identified within GenBank (5 Dec 2017, taxID = 10239 “viruses”), using the amino acid sequence of the entire ORF encoding the RNA-dependent RNA polymerase (RdRp) as the query in TBLASTN. Amino acid sequences of the RdRp-encoding ORF were aligned using MUSCLE (v3.8.31) [6], and phylogenetic trees were inferred using MRBAYES v3.2.6 [7], with one million generations and default parameters.

Results

Conclusion