Whole Genome Analysis of African G12P[6] and G12P[8] Rotaviruses Provides Evidence of Porcine-Human Reassortment at NSP2, NSP3, and NSP4

Abstract

Group A rotaviruses (RVA) represent the most common cause of pediatric gastroenteritis in children <5 years, worldwide. There has been an increase in global detection and reported cases of acute gastroenteritis caused by RVA genotype G12 strains, particularly in Africa. This study sought to characterize the genomic relationship between African G12 strains and determine the possible origin of these strains. Whole genome sequencing of 34 RVA G12P[6] and G12P[8] strains detected from the continent including southern (South Africa, Zambia, Zimbabwe), eastern (Ethiopia, Uganda), central (Cameroon), and western (Togo) African regions, were sequenced using the Ion Torrent PGM method. The majority of the strains possessed a Wa-like backbone with consensus genotype constellation of G12-P[6]/P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1, while a single strain from Ethiopia displayed a DS-1-like genetic constellation of G12-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2. In addition, three Ethiopian and one South African strains exhibited a genotype 2 reassortment of the NSP3 gene, with genetic constellation of G12-P[8]-I1-R1-C1-M1-A1-N1-T2-E1-H1. Overall, 10 gene segments (VP1–VP4, VP6, and NSP1–NSP5) of African G12 strains were determined to be genetically related to cognate gene sequences from globally circulating human Wa-like G12, G9, and G1 strains with nucleotide (amino acid) identities in the range of 94.1–99.9% (96.5–100%), 88.5–98.5% (93–99.1%), and 89.8–99.0% (88.7–100%), respectively. Phylogenetic analysis showed that the Ethiopian G12P[6] possessing a DS-1-like backbone consistently clustered with G2P[4] strains from Senegal and G3P[6] from Ethiopia with the VP1, VP2, VP6, and NSP1–NSP4 genes. Notably, the NSP2, NSP3, and NSP4 of most of the study strains exhibited the closest relationship with porcine strains suggesting the occurrence of reassortment between human and porcine strains. Our results add to the understanding of potential roles that interspecies transmission play in generating human rotavirus diversity through reassortment events and provide insights into the evolutionary dynamics of G12 strains spreading across selected sub-Saharan Africa regions.

Prevalence and genomic characterization of rotavirus group A genotypes in piglets from southern highlands and eastern Tanzania

“…The whole genome has been reported to reveal the common origin of human Wa-like rotavirus and porcine rotaviruses, DS-1-like and bovine rotavirus in Belgium ( Matthijnssens et al., 2008a , b ). The reassortment and interspecies transmission were also reported between human, porcine and bovine rotaviruses in South Korea, Uganda, Cameroon, Ethiopia, South Africa, Togo, Uganda, Zambia, Zimbabwe Nigeria, Thailand and Italy ( Bwogi et al., 2017 ; Komoto et al., 2016 ; Medici et al., 2015 ; Mokoena et al., 2021 ; Tacharoenmuang et al., 2018 ). The aim of this study was to investigate genetic diversity of pigs RVA in southern highland and eastern Tanzania to comprehend the rotavirus epidemiology, improve biosecurity and to document the zoonotic threats and the phylogenetic relationship to global RVA strains.…”

The Evolution of Post-Vaccine G8P[4] Group a Rotavirus Strains in Rwanda; Notable Variance at the Neutralization Epitope Sites

“…Notably, one strain exhibited inter-genogroup reassortment at the NSP2 genome segment, and this reassortment phenomenon has also been reported in another G8P[4] study [ 54 ]. Reassortment of rotavirus genome segments is a relatively frequent phenomenon that generates reassortant rotavirus strains [ 11 , 12 , 15 , 55 , 56 , 57 , 58 ]. These findings underscore the genotype constellation diversity of G8P[4] strains.…”

Prevalence and Genomic Characterization of Rotavirus A from Domestic Pigs in Zambia: Evidence for Possible Porcine–Human Interspecies Transmission

“…These findings implied that the possible origin of G4P [6] would be porcine and bovine, respectively [18,20]. Also, whole genome analysis of a human G12 from Zambia, South Africa, Ethiopia, and Cameroon revealed a porcine-human reassortment [14]. However, in Zambia, G2 was the most common genotype in humans' post-rotavirus vaccine introduction, and G1 and G9 were predominant during the pre-vaccination period [37].…”

“…Through these events, novel RVA strains emerge with the capacity to affect the effectiveness of current vaccines in pigs and humans [11][12][13]. Recent reports have shown that strains known to cause infections only in pigs are now being detected in humans with evidence of porcine-human reassortment [9,13,14]. Evidence also indicates that direct transmission of RVA from pigs to humans does occur [15,16].…”