Complete genotyping of unusual species A rotavirus G12P[11] and G10P[14] isolates and evidence of frequent in vivo reassortment among the rotaviruses detected in children with diarrhea in Kolkata, India, during 2014

Abstract

Species A rotaviruses (RVA) are the most important cause of acute gastroenteritis in the young of humans and many animal species globally. G1P[8], G2P[4], G3P[8], G4P[8], G9P[6/8] and G12P[6/8] are the predominantly isolated genotypes throughout the world including India. Unusual genotypes from different host species such as G5, G6, G8, G10 and G11 have also been reported in humans with low frequency. In the present study, among >650 RVA positive stool samples collected from children with diarrhea in Kolkata, India, during 2014, two isolates each of the genotype G12P[11] and G10P[14] were obtained and their genomes completely sequenced. The full genotype constellations were G12-P[11]-I1-R1-C1-M2-A1-N1-T2-E1-H1 and G12-P[11]-I1-R1-C1-M1-A5-N1-T1-E1-H1 for G12P[11] viruses, suggesting several reassortments between Wa- and DS-1-like human RVA strains, including possible reassortment of a simian NSP1 gene. The G10P[14] viruses (G10-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3) were found to contain multiple genes closely related to RVAs of artiodactyl origin, highlighting the role of inter-host species transmissions of RVAs. From the G/P constellation of all RVA isolates, it could be concluded that approximately one quarter had likely arisen from reassortment events in vivo among RVAs of 'usual' genotypes.

Molecular epidemiology of group A rotavirus in outpatient diarrhea infants and children in Chongqing, China, 2011‐2015

“…The frequency of untypable G or P‐genotype specimens was 13.07% and 8.66%, respectively. On one hand, it may be the result of a mismatch between primers and target sequences, as new G and P genotypes appeared in recent years . Some mismatches were observed after alignment of the primers and the VP7 and VP4 sequences of recently appeared genotypes.…”

“…On one hand, it may be the result of a mismatch between primers and target sequences, as new G and P genotypes appeared in recent years. [41][42][43][44][45] Some mismatches were observed after alignment of the primers and the VP7 and VP4 sequences of recently appeared genotypes. The corresponding sequences of these untypable rotavirus strains can be obtained by optimizing primer sequences or by Sequence-Independent-Single-Primer-Amplification for genotyping in the future.…”

Molecular characterization of unusual G10P[33], G6P[14] genomic constellations and evidence of zooanthroponosis in bovines

“…The G6P[14] and G6P[4] strains shared identity in range of 93.3-98.8% (nucleotide) and 99.3% (amino acid) with other strains in cluster 1. Interestingly, this cluster comprised of unusual Indian bovine strain BRV133 (G3P[11]) as well as Indian porcine-bovine like strains (HP113 and HP140, G6P[13]), and human-bovine like strains [(MCS-KOL-383 (G10P[14]), N-1(G6P[14])] whose VP6 gene is believed to be derived from Indian bovine strain (Ghosh and Kobayashi, 2014; Mandal et al, 2016). The G10P[11] study strains exhibited 94.9-95.6% (nucleotide) and >99.3% (amino acid) similarity with cluster 2.…”

“…In VP4 phylogeny, previously reported Indian bovine G8P[14] strains (BRV68, BRV79, BRV86) from Pune region and G10P[14] strains (RUBV 81) occupied Lineage-1 with Indian human-bovine like strain N-1 (G6P[14]) (Chitambar et al, 2011; Mullick et al, 2013). In contrast the study strains grouped in proposed Lineage-8 along with Indian human-bovine like GXP[14] strain (CMC-00022), and G10P[14] strains (MCS-KOL-383 and KOL-29), earlier considered in Lineage-4 (only VP8* region sequence available) (Mandal et al, 2016). The higher sequence identities of VP6, VP7 and VP4 genes and grouping in same lineages with strains previously known for interspecies transmission hypothesize zoonotic potential of bovine G6P[14] strains detected in the present study.…”

“…The combination of interspecies transmission and reassortment between RVAs of different species lead to the emergence and spread of zoonotic rotavirus strains (Desselberger, 2014). The worldwide detection including India of bovine rotavirus genomic constellations, G10P[11] and G6P[14], in neonates have raised concerns about zoonotic transmission (Iturriza-Gomara et al 2004; Matthijnssens et al, 2009; Desselberger, 2014, Mandal et al, 2016). Besides this zooanthraponotic transmission reported in bovine (G2P[4], G1P[11] and G9P[X]) and ovine (G2P[4] and G1P[8]) species suggest complex epidemiology of rotavirus in India (Rajendran and Kang, 2014; Choudhary et al, 2017; Kumar et al, 2018).…”