Reassortment of Human and Animal Rotavirus Gene Segments in Emerging DS-1-Like G1P[8] Rotavirus Strains

Abstract

The emergence and rapid spread of novel DS-1-like G1P[8] human rotaviruses in Japan were recently reported. More recently, such intergenogroup reassortant strains were identified in Thailand, implying the ongoing spread of unusual rotavirus strains in Asia. During rotavirus surveillance in Thailand, three DS-1-like intergenogroup reassortant strains having G3P[8] (RVA/Human-wt/THA/SKT-281/2013/G3P[8] and RVA/Human-wt/THA/SKT-289/2013/G3P[8]) and G2P[8] (RVA/Human-wt/THA/LS-04/2013/G2P[8]) genotypes were identified in fecal samples from hospitalized children with acute gastroenteritis. In this study, we sequenced and characterized the complete genomes of strains SKT-281, SKT-289, and LS-04. On whole genomic analysis, all three strains exhibited unique genotype constellations including both genogroup 1 and 2 genes: G3-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2 for strains SKT-281 and SKT-289, and G2-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2 for strain LS-04. Except for the G genotype, the unique genotype constellation of the three strains (P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2) is commonly shared with DS-1-like G1P[8] strains. On phylogenetic analysis, nine of the 11 genes of strains SKT-281 and SKT-289 (VP4, VP6, VP1-3, NSP1-3, and NSP5) appeared to have originated from DS-1-like G1P[8] strains, while the remaining VP7 and NSP4 genes appeared to be of equine and bovine origin, respectively. Thus, strains SKT-281 and SKT-289 appeared to be reassortant strains as to DS-1-like G1P[8], animal-derived human, and/or animal rotaviruses. On the other hand, seven of the 11 genes of strain LS-04 (VP7, VP6, VP1, VP3, and NSP3-5) appeared to have originated from locally circulating DS-1-like G2P[4] human rotaviruses, while three genes (VP4, VP2, and NSP1) were assumed to be derived from DS-1-like G1P[8] strains. Notably, the remaining NSP2 gene of strain LS-04 appeared to be of bovine origin. Thus, strain LS-04 was assumed to be a multiple reassortment strain as to DS-1-like G1P[8], locally circulating DS-1-like G2P[4], bovine-like human, and/or bovine rotaviruses. Overall, the great genomic diversity among the DS-1-like G1P[8] strains seemed to have been generated through reassortment involving human and animal strains. To our knowledge, this is the first report on whole genome-based characterization of DS-1-like intergenogroup reassortant strains having G3P[8] and G2P[8] genotypes that have emerged in Thailand. Our observations will provide important insights into the evolutionary dynamics of emerging DS-1-like G1P[8] strains and related reassortant ones.

Equine-like G3 rotavirus in Hungary, 2015 – Is it a novel intergenogroup reassortant pandemic strain?

“…One minor difference was a distinct genotype E2 NSP4 variant in the 2013-2014 strains, suggesting that the European equine-like G3 strains could have acquired the NSP4 gene through reassortment from another genotype 2 constellation strain and then the new reassortant strain spread within the continent (Figures 2 and 3). Of note is that the backbone genes showed close relatedness with other intergenogroup reassortant strains, including contemporary Philippine, Thai, and Japanese G1P [8] rotaviruses [17,18] (Figure 2). …”

Whole genomic analysis of human and bovine G8P[1] rotavirus strains isolated in Nigeria provides evidence for direct bovine-to-human interspecies transmission

“…We next constructed phylogenetic trees using the full-genome sequence for each of the 11 gene segments because phylogenetic analysis of RVA nucleotide sequences furnishes direct evidence of their relatedness to those of other strains, even within the same genotype (Matthijnssens et al, 2008a;Komoto et al, 2014bKomoto et al, , 2016.…”

Full Genome Characterization of Novel DS-1-Like G8P[8] Rotavirus Strains that Have Emerged in Thailand: Reassortment of Bovine and Human Rotavirus Gene Segments in Emerging DS-1-Like Intergenogroup Reassortant Strains

“…Although intergenogroup reassortant strains can be generated, it is believed that such RVA strains possessing both genogroup 1 and 2 genes may have decreased evolutionary fitness compared to that of the parental strains and thus would be selected against in the context of human infections [18–20]. However, the emergence of novel human intergenogroup reassortant strains, DS-1-like G1P[8] strains and reassortant ones derived from them possessing a DS-1-like non-G/P genotype constellation (I2-R2-C2-M2-A2-N2-T2-E2-H2) together with G/P genotypes G1P[8], G2P[8], G3P[8], and G8P[8]: G1/2/3/8-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2, were recently reported in Japan, Thailand, Vietnam, Australia, Hungary, and Spain [19, 21–27]. …”

“…In 2013, DS-1-like intergenogroup reassortant strains having G2P[8] and G3P[8] genotypes were also detected in Thailand (including strains LS-04 (G2P[8]) and SKT-281 (G3P[8])) and Australia (including strain D388 (G3P[8])) [19, 22]. Furthermore, in 2013–2014, we identified DS-1-like intergenogroup reassortant strains having G8P[8] genotypes (including strains KKL-17, PCB-79, PCB-84, PCB-85, PCB-103, SKT-107, SWL-12, NP-130, PCB-656, SKT-457, SSKT-269, and SSL-55) in Thailand as major strains [29].…”