Detection and complete genome characterization of a novel RNA virus related to members of the Hepe-Virga clade in bird species, hoopoe (Upupa epops)

Abstract

Using viral metagenomics, next-generation sequencing and RT-PCR techniques a genetically divergent hepevirus-like RNA virus was identified and characterized from a faecal sample of wild bird species, hoopoe (Upupa epops) in Hungary. The complete viral genome sequence of hoopoe/BBanka01/2015/HUN (GenBank accession number MN852439) is 7052 nt long including a 54-nt 5′ and an 18-nt 3′ non-coding region without poly(A)-tail. Sequence analysis indicated that the hoopoe/BBanka01/2015/HUN genome has potentially three overlapping open reading frames (ORFs). The ORF1 (6558 nt/2185aa) encodes a long, non-structural polyprotein (replicase) including putative functional domains and conserved aa motifs of methyltransferase with domain Y, RNA helicase and RdRp and has <33% aa identity to the known hepe- and hepe-like viruses. The ORF2 (1446 nt/481aa) encodes a putative structural (capsid) protein overlapping with ORF1 but translated in different coding frame. The functions of the short ORF3 (426 nt/141aa) were not predictable. Similar virus sequences were not detected from samples from 21 further bird species. The taxonomic position of this novel virus is presently unknown.