Confusions in orbivirus protein classification

Abstract

An extensive comparative analysis of orbivirus genomes revealed four cases of unclear numeration and protein designation, due to confused reference to protein size or segment size by which they are encoded. A concise nomenclature based on type species, sequence homology and functional characteristics independent of segment or protein size is suggested.

Background

The genus Orbivirus is one of 15 in the family of Reoviridae containing 22 serogroups (species) and at least 160 different serotypes (strains) [1]. Orbiviruses are transmitted by insects (midges, flies, mosquitoes) or by ticks. Their double-stranded RNA (dsRNA) genomes consist of 10 segments coding for seven structural and at least three non-structural proteins. Orbiviruses have no envelope but a double-shelled icosahedral capsid [2] and include pathogenic agents of wild animals (Epizootic hemorrhagic disease virus (EHDV)), domestic animals (Bluetongue virus (BTV) and African horse sickness virus (AHSV)), and of man (Kemerovo virus (KEMV)) [3]. Type species of the genus is the Culicoides midge transmitted BTV. Insect-borne orbiviruses are much better characterized than tick-transmitted orbiviruses for which few sequences have been described: Broadhaven virus (BRDV, partial) [4], Sandy Bay virus (SBaV, partial (formerly Nugget virus)) [5–8], St Croix River virus (SCRV, complete genome) [9], Great Island virus (GIV, complete genome) [7].

Recently we determined the complete genomes of Tribeč virus (TRBV) and KEMV in a pyrosequencing approach [10] complementing available partial information on segments 1, 2 and 6 of these viruses and of Lipovnik virus (LIPV) [7].

During our extensive comparative analysis of orbivirus genomes we noticed four cases of unclear numeration and protein designation (see Tables 1 and 2). Some laboratories classify orbivirus proteins according to the size of the proteins whereas others use the size of genome segments from which they are encoded.

• (i) The inner shell protein T2 for example can be encoded by segment 2 (tick- and mosquito-borne orbiviruses) or segment 3 (Culicoides-borne orbiviruses). This leads to some laboratories labeling this protein VP2(T2) (e.g. GIV), while others designate it VP3(T2) as in the type species BTV. For Peruvian horse sickness virus (PHSV) however, the segment 2 encoded protein is designated VP3(T2) although it is larger (925 amino acids) than the segment 3 encoded VP2 protein (881 amino acids) [11]. To avoid confusion with the outer shell protein VP2 we suggest to exclusively use VP3(T2) for all T2 proteins.

• (ii) VP2 and VP2 homologous proteins can be encoded by segments 2, 3, 4 and 5 and are designated VP2, VP3 (YUOV, SCRV) or VP4 (BRDV segment 4 ( [12, 13], sequence entry to GenBank missing)), GIV segment 5). Because of the location on the outer capsid and the described sequence similarity with other VP2 proteins, we suggest that the VP4 proteins (BRDV, GIV) as well as the VP3 proteins (YUOV, SCRV) should be uniformly termed VP2, even though tick-borne VP2 proteins have only half the size of insect-borne VP2 proteins [13].

• (iii) The capping enzyme VP4(CaP) can be encoded by segment 4 (BTV, YUOV, SCRV etc.) or segment 3 (TRBV, KEMV). In GIV this protein is designated VP3(CaP) [7] and should be renamed VP4(CaP) to avoid confusions with VP3(T2).

• (iv) In most cases VP5 is encoded by segment 6 and comprises a component of the outer shell that might be involved in membrane fusion and penetration [14]. TRBV and KEMV also encode VP5 on segment 6. The highest similarity of TRBV VP5 is to LIPV VP5 (95.6%), again encoded by segment 6 [7]. However, VP5 of BRDV is described as encoded by segment 5 [15]. Since in the classification of the viral genome segments bigger segments have smaller segment numbers, and the size of BRDV segment 6 (1714 bp) encoding the NS1(TuP) [16] is larger than the size of BRDV segment 5 (1658 bp) encoding VP5, a reassignment of BRDV segment 5 and 6 (a vice versa switch) seems necessary.

Table 1 Comparison of the genome segments and encoded proteins of BTV, YUOV, TRBV, KEMV and GIV

Table 2 Comparison of the genome segments and encoded proteins of SCRV, PHSV, BRDV and LIPV

To summarize, it would be much more helpful if the nomenclature of the viral proteins in orbiviruses would reflect the sequence homology and functional relationship rather than protein size or encoding segment size, since the sizes of the orbivirus genome segments sometimes only differ slightly, which leads to even closely related viruses such as TRBV and KEMV encoding VP2 and NS1(TuP) on different genome segments. We therefore suggest the following concise nomenclature based on the type species BTV and on sequence homology and functional characteristics independent of segment or protein size: VP1(Pol), VP2, VP3(T2), VP4(CaP), VP5, VP6(Hel), VP7(T13), NS1(TuP), NS2(ViP), NS3.

Author’s contributions

MD and MW wrote the paper. Both authors read and approved the final manuscript.