Complete molecular genome analyses of equine rotavirus A strains from different continents reveal several novel genotypes and a largely conserved genotype constellation

Abstract

In this study, the complete genome sequences of seven equine group A rotavirus (RVA) strains (RVA/Horse-tc/GBR/L338/1991/G13P [18] [12] from South Africa) were determined. Multiple novel genotypes were identified and genotype numbers were assigned by the Rotavirus Classification Working Group: R9 (VP1), C9 (VP2), N9 (NSP2), T12 (NSP3), E14 (NSP4), and H7 and H11 (NSP5). The genotype constellation of L338 was unique: G13-P[18]-I6-R9-C9-M6-A6-N9-T12-E14-H11. The six remaining equine RVA strains showed a largely conserved genotype constellation: G3/G14-P[12]-I2/I6-R2-C2-M3-A10-N2-T3-E2/E12-H7, which is highly divergent from other known non-equine RVA genotype constellations. Phylogenetic analyses revealed that the sequences of these equine RVA strains are related distantly to nonequine RVA strains, and that at least three lineages exist within equine RVA strains. A small number of reassortment events were observed. Interestingly, the three RVA strains from Argentina possessed the E12 genotype, whereas the three RVA strains from Ireland and South Africa possessed the E2 genotype. The unusual E12 genotype has until now only been described in Argentina among RVA strains collected from guanaco, cattle and horses, suggesting geographical isolation of this NSP4 genotype. This conserved genetic configuration of equine RVA strains could be useful for future vaccine development or improvement of currently used equine RVA vaccines. INTRODUCTIONEquine group A rotavirus (RVA) strains were first detected in diarrhoeic foals in England in 1975(Flewett et al., 1975 and are a major cause of dehydrating diarrhoea in young 3Present address: Deltamune (Pty) Ltd, 248 Jean Avenue, Lyttelton, Centurion, 0140, South Africa.The GenBank/EMBL/DDBJ accession numbers for the equine rotavirus strains described in this study are JF712555-JF712565, JF712566-JF712576, JF712577-JF712587, JN872865-JN872875, JQ345489-JQ345499 and JN903507-JN903528. foals (Browning & Begg, 1996;Frederick et al., 2009; Imagawa et al., 1991;Saif et al., 1994). Serological data from Japan, the USA and France suggest that RVA is a ubiquitous pathogen in horse populations (Conner & Darlington, 1980;Imagawa et al., 1982;Pearson et al., 1982;Takahashi et al., 1979).RVA strains are icosahedral, non-enveloped viruses possessing a genome of 11 segments of dsRNA. The two outer capsid proteins, VP7 and VP4, elicit neutralizing antibodies independently and are used to differentiate RVA strains into G-types (glycoprotein) and P-types (proteasesensitive), respectively (Ciarlet & Estes, 2002 (Browning et al., 1991a). L338 was shown to possess the unique G13 and P[18] genotypes and a highly divergent NSP1 gene sequence, and to be distinct from other human and animal RVA strains by using RNA-RNA hybridization assays (Browning et al., 1991a; Iša & Snodgrass, 1994;Kojima et al., 1996;Taniguchi et al., 1994;Wu et al., 1993). In addition, a limited number of porcine-, bovineand feline-like RVA strains have been detected in horses. Examples include the G5P [7] RVA strain RVA/Horse-tc/ ...

Genetic linkage of capsid protein-encoding RNA segments in group A equine rotaviruses

“…dConsensus sequences from equine complete genome sequences. rotaviruses tend to present constellations of genes that remain stable over time (Heiman et al, 2008;Matthijnssens et al, 2012;McDonald et al, 2009). Human RVA can be divided into three major genome constellations (GI-GIII), being the Wa strain as the prototype for GI, DS-1 for GII and AU-1 for GIII.…”

“…Equine RVAs have also been shown to present a high level of conservation in their genome constellations, with the VP7, VP6 and NSP4 gene segments being distinguished into two different genotypes, i.e. G3/G14, I2/I6 and E2/E12, respectively (Ghosh et al, 2013;Matthijnssens et al, 2012;Nemoto et al, 2015). Importantly, only one P type (P[12]) has been found in RVAs infecting horses, which indicates a high restriction at the species level.…”

“…All the equine RVA strains sequenced to date present the same genotype for the VP2 gene (C2) (Ghosh et al, 2013;Matthijnssens et al, 2012;Nemoto et al, 2015). As only two amino acid substitutions (I38V and V39I) were found in the VP6 : VP2 interacting region, which seem to compensate for each other (Ile for Val and vice versa), no major differences can be expected with the VP2 interaction, and therefore the same VP2 protein could be shared by the equine strains showing G3P [12] and G14P[12] genotypes.…”

“…Based on differences within RVA, a number of genotypes have been described for the VP4 (P[1]-P[37]), VP6 (I1-I16) and VP7 (G1-G27) gene (Estes & Greenberg, 2013;Matthijnssens et al, 2012;Trojnar et al, 2013 (Browning et al, 1991;Ciarlet et al, 2001;Isa et al, 1996;Miño et al, 2013;Taniguchi et al, 1994), G3P[12] and G14P[12] are the most prevalent strains associated with diarrhoea in foals worldwide. Rotavirus strains carrying the G3 genotype have been found in a wide range of host species (Estes & Greenberg, 2013;Martella et al, 2010), but the equine-like G3, G14 and P[12] genotypes have never been found producing outbreaks in any other host species than equines (Bailey et al, 2013;Garaicoechea et al, 2011;Matthijnssens et al, 2015;Weinberg et al, 2013).…”

“…Genomes of equine RVA G3P [12] and G14P[12] are highly conserved, and only three gene segments have shown different genotypes (i.e. VP7: G3 and G14; VP6: I2 and I6; and NSP4: E2 and E12) in all complete genomes available currently (Ma et al, 2015;Matthijnssens et al, 2012;Nemoto et al, 2015).…”