Whole-Genomic Analysis of Rotavirus Strains: Current Status and Future Prospects

Abstract

Studies on genetic diversity of rotaviruses have been primarily based on the genes encoding the antigenically significant VP7 and VP4 proteins. Since the rotavirus genome has 11 segments of RNA that are vulnerable to reassortment events, analyses of the VP7 and VP4 genes may not be sufficient to obtain conclusive data on the overall genetic diversity, or true origin of strains. In the last few years following the advent of the whole-genome-based genotype classification system, the whole genomes of at least 167 human group A rotavirus strains have been analyzed, providing a plethora of new and important information on the complex origin of strains, inter- and intra-genogroup reassortment events, animal-human reassortment events, zoonosis, and genetic linkages involving different group A rotavirus gene segments. In addition, the whole genomes of a limited number of human group B, C and novel group rotavirus strains have been analyzed. This article briefly reviews the available data on whole-genomic analysis of human rotavirus strains. The significance and future prospects of whole-genome-based studies are also discussed.

A bovine G8P[1] group A rotavirus isolated from an asymptomatically infected dog

“…This finding is in accordance with previously published data that G8P[1] strains are typical bovine isolates (Papp et al, 2013), and that they are able to cross species barriers and also infect humans (Ghosh & Kobayashi, 2011). For phylogenetic analysis of the canine RVA, we calculated genetic distances employing the Tamura-Nei model at the nucleotide level.…”

“…Interestingly, rotavirus infections of human patients with strains of G8P[1] genotypes have been described (Ghosh et al, 2011). Therefore, the zoonotic potential needs to be further assessed.…”

Evolution of a G6P[6] rotavirus strain isolated from a child with acute gastroenteritis in Ghana, 2012

“…Human rotaviruses of uncommon G and P type combinations are largely classified into two categories; one comprises strains suggestive of reassortants between the Wa-like and the DS-l-like genotype constellations (Ghosh & Kobayashi, 2011, 2014Iturriza-Gó mara et al, 2001;Matthijnssens & Van Ranst, 2012), such as G1P [6] (Ghosh et al, 2013), G1P[4] (Sasaki et al, 2015) and G3P[4] (Tran et al, 2013). The other comprises rotavirus strains possessing either G or P genotype suggestive of animal rotavirus origin (Ghosh & Kobayashi, 2011, 2014Matthijnssens & Van Ranst, 2012;Steyer et al, 2008), such as G3P [9], of probable feline rotavirus origin (Nakagomi & Nakagomi, 1989), G4P [6], of probable porcine rotavirus origin (Martinez et al, 2014), G5P [6] (Ahmed et al, 2007), G6P [1] (Doan et al, 2013), G6P[11] (Steyer et al, 2013), G6P[14] (Cooney et al, 2001) and G8P[1] (Adah et al, 2001), of probable bovine rotavirus origin.…”

Whole genomic analysis of a porcine-like human G5P[6] rotavirus strain isolated from a child with diarrhoea and encephalopathy in Japan

“…Whole genomic analysis is a reliable method for obtaining conclusive data on the origin of an RVA strain and for tracing its evolutionary pattern (Matthijnssens et al, 2008(Matthijnssens et al, , 2011Ghosh & Kobayashi, 2011). To date, all 11 gene segments of only one human G5P [6] strain, Bulgarian BG620, have been analysed, providing evidence of its porcine origin (Mladenova et al, 2012).…”