Full Genome Sequencing and Genetic Characterization of Eubenangee Viruses Identify Pata Virus as a Distinct Species within the Genus Orbivirus

Abstract

Eubenangee virus has previously been identified as the cause of Tammar sudden death syndrome (TSDS). Eubenangee virus (EUBV), Tilligery virus (TILV), Pata virus (PATAV) and Ngoupe virus (NGOV) are currently all classified within the Eubenangee virus species of the genus Orbivirus , family Reoviridae . Full genome sequencing confirmed that EUBV and TILV (both of which are from Australia) show high levels of aa sequence identity (>92%) in the conserved polymerase VP1(Pol), sub-core VP3(T2) and outer core VP7(T13) proteins, and are therefore appropriately classified within the same virus species. However, they show much lower amino acid (aa) identity levels in their larger outer-capsid protein VP2 (<53%), consistent with membership of two different serotypes - EUBV-1 and EUBV-2 (respectively). In contrast PATAV showed significantly lower levels of aa sequence identity with either EUBV or TILV (with <71% in VP1(Pol) and VP3(T2), and <57% aa identity in VP7(T13)) consistent with membership of a distinct virus species. A proposal has therefore been sent to the Reoviridae Study Group of ICTV to recognise ‘Pata virus’ as a new Orbivirus species, with the PATAV isolate as serotype 1 (PATAV-1). Amongst the other orbiviruses, PATAV shows closest relationships to Epizootic Haemorrhagic Disease virus (EHDV), with 80.7%, 72.4% and 66.9% aa identity in VP3(T2), VP1(Pol), and VP7(T13) respectively. Although Ngoupe virus was not available for these studies, like PATAV it was isolated in Central Africa, and therefore seems likely to also belong to the new species, possibly as a distinct ‘type’. The data presented will facilitate diagnostic assay design and the identification of additional isolates of these viruses.

Mobuck virus genome sequence and phylogenetic analysis: identification of a novel Orbivirus isolated from a white-tailed deer in Missouri, USA

“…The 59 NCRs of all mobuck virus segments contain six conserved nucleotides, with three conserved nucleotides at their 39 end (59-GUUAAA----UAC-39). The two nucleotides proximal to the 59 and 39 ends are also inverted complements of each other and are identical to those of other orbiviruses (Attoui et al, , 2009Belaganahalli et al, 2011Belaganahalli et al, , 2012. Similar to most orbiviruses, the 59 NCR of mobuck virus is shorter than the corresponding 39 NCR (Mertens et al, 2005;Maan et al, 2008).…”

“…The viral RNA-dependent RNA polymerase VP1 protein, T2 protein [designated either VP2(T2) or VP3(T2)], and VP7(T13) are highly conserved among all orbiviruses and have consequently been used for taxonomic classification and phylogenetic comparisons (Attoui et al, 2009;Belaganahalli et al, 2011Belaganahalli et al, , 2012Dilcher & Weidmann, 2012;Gouet et al, 1999;Grimes, et al, 1998). VP1 amino acid sequence identities of at least 20 % are classified to a single genus within the family Reoviridae (Attoui et al, 2000).…”

Full Genome Sequencing of Corriparta Virus, Identifies California Mosquito Pool Virus as a Member of the Corriparta virus Species

“…However, this is in the +2 reading-frame (at 143–598 bp), encoding the 152 aa NS4 protein. NS4 has previously been identified in several other orbiviruses and has been characterised in BTV and GIV [24], [37], [38]. The downstream Seg-9 ORF of CORV has a strong Kozak context ( A GG AUG G ) and is expected to produce a protein in infected cells.…”

“…Comparisons of nucleotide (nt) and amino acid (aa) sequence data also provide a basis for grouping of orbivirus isolates into topotypes and for molecular epidemiology studies [23], [25], [32], [33]. However, full-genome sequence data are currently available for representatives of only 11 of the recognized Orbivirus species [24] (accession numbers given in Table S1). Additional partial-sequences are available for the highly conserved genome-segment encoding the subcore ‘T2’ protein (VP3 of BTV) of some Orbivirus species, including Warrego virus (WARV), Wallal virus (WALV), Wongorr virus (WGRV) and CORV [32] (Table S1).…”

A Review of Knowledge Gaps and Tools for Orbivirus Research

“…The genomes of over 300 BTV strains have already been fully sequenced. This is rapidly becoming the accepted standard for the characterization of novel outbreak strains (Maan et al 2008, Maan et al 2010 and has helped to identify new BTV serotypes and new Orbivirus species (Hofmann et al 2008, Maan et al 2011a, Belaganahalli et al 2012). Further developments have included the generation of representative sequence data for each of the different recognized orbivirus species.…”