Genome analyses of species A rotavirus isolated from various mammalian hosts in Northern Ireland during 2013-2016

Abstract

Rotavirus group A (RVA) is the most important cause of acute diarrhoea and severe dehydration in young mammals. Infection in livestock is associated with significant mortality and economic losses and, together with wildlife reservoirs, acts as a potential source of zoonotic transmission. Therefore, molecular surveillance of circulating RVA strains in animal species is necessary to assess the risks posed to humans and their livestock. An RVA molecular epidemiological surveillance study on clinically diseased livestock species revealed high prevalence in cattle and pigs (31 per cent and 18 per cent, respectively) with significant phylogenetic diversity including a novel and divergent ovine artiodactyl DS-1-like constellation G10-P[15]-I2-R2-C2-M2-A11-N2-T6-E2-H3. An RVA gene reassortment occurred in an RVA asymptomatic pig and identified as a G5-P[13] strain, and a non-structural protein (NSP)2 gene had intergenomically reassorted with a human RVA strain (reverse zoonosis) and possessed a novel NSP4 enterotoxin E9 which may relate to the asymptomatic RVA infection. Analysis of a novel sheep G10-P[15] strain viral protein 4 gene imparts a putative homologous intergenic and interspecies recombination event, subsequently creating the new P[15] divergent lineage. While surveillance across a wider range of wildlife and exotic species identified generally negative or low prevalence, a novel RVA interspecies transmission in a non-indigenous pudu deer (zoo origin) with the constellation of G6-P[11]12-R2-C2-M2-A3-N2-T6-E2-H3 was detected at a viral load of 11.1 log10 copies/gram. The detection of novel emerging strains, interspecies reassortment, interspecies infection, and recombination of RVA circulating in animal livestock and wildlife reservoirs is of paramount importance to the RVA epidemiology and evolution for the One Health approach and post-human vaccine introduction era where highly virulent animal RVA genotypes have the potential to be zoonotically transmitted.

Keywords: NGS; WGS; interspecies; phylogenetics; prevalence; reassortment; recombination; rotavirus group A; surveillance.

Figure 1.

Antigenic epitope region analysis of VP7 G. The amino acid colour-coding applies the RasMol properties with the threshold set to 0 per cent amino acids identical to the consensus sequence remain not colour coded and disagreements to the consensus sequence are highlighted. The RasMol properties colour codes by amino acid associated with the outer surface of a protein are given bright colours and non-polar residues are darker (Geneious, Biomatters).

Figure 2.

VP4 P genotypes. The amino acid colour applies the RasMol properties as explained in Figure 1.

Figure 3.

BOOTSCAN VP4 R2WTA65. Bootscan of the VP4 gene segment from an ovine sample R2WTA65 with breakpoints at nt 438 and 699 positions indicating an interspecies homologous recombination event.

Figure 4A.

Phylogenetic trees were inferred by using a ML with the best fit model selected as VP7 GTR +G, VP4 TN93 +G + I, and NSP4 T92 +G + I. Bootstrap values (1,000 replicates) of ≥70 per cent are shown adjacent to each branch node. The current study isolates were indicated in bold font and analysed alongside published RVA isolates. A scale bar denotes the genetic distance expressed as the number of nt substitutions per site. (A) RVA VP7 phylogenetic tree. (B) RVA VP4 phylogenetic tree. (C) RVA NSP4 enterotoxin (rooted at mid-point) phylogenetic tree.

Figure 4B.

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Figure 4C.

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