Full genome characterization of the first G3P[24] rotavirus strain detected in humans provides evidence of interspecies reassortment and mutational saturation in the VP7 gene

Abstract

During the 2008–2009 rotavirus season of the Centers for Disease Control and Prevention New Vaccine Surveillance Network, one case of paediatric acute gastroenteritis associated with a rotavirus G14P[24] strain was identified. This was the first detection of the genotype G14 and P[24] in humans, and the first detection of the G14P[24] combination. To gain an insight into the origins and the evolution of this strain, we determined the complete ORF sequences of all 11 genes. A majority of the genes identified were similar to the simian strain TUCH, except for the VP1 and VP7 genes that clustered only distantly with the bovine and equine strains, respectively. In addition, this strain carried AU-1-like NSP2 and NSP4 genes. Using codon-partitioning and protein-based phylogenetic approaches, we determined that the VP7 genotype of strain 2009727118 was actually G3; therefore, the proposed full genomic classification of the 2009727118 strain is G3-P[24]-I9-R2-C3-M3-A9-N3-T3-E3-H6. These findings indicate the possibility that the 2009727118 strain originated by interspecies transmission and multiple reassortment events involving human, bovine and equine rotaviruses, resulting in the introduction of some genes into the genome of simian rotaviruses. Additionally, we found evidence of mutational saturation in the third codon position of the VP7 ORF which presented an issue with homoplasy in phylogenetic analyses.

Analysis of a genotype G3P[9] rotavirus a strain that shows evidence of multiple reassortment events between animal and human rotaviruses

“…This type of animal is described as a reservoir for various viruses, which can cross the species barrier and infect humans, although this relationship is not yet well understood. Similarly to the present study, some studies in humans describe strains that have one or more genes that are phylogenetically related to those detected in bats, given that these strains in the G3 genotype circulating in children were associated with the P[10] (CMH079); P[14] (RCH272); and the P[24] (2009727118) genotypes . Studies conducted in chiropters describe the detection of RVH as well as the description of new RVA genotypes …”

“…In addition, humans strains RVA/Human‐wt/US/2012841174/2012/G8P[14] carrying the VP1 gene (90.8%) and RVA/Human‐wt/USA/2009727118/2009/G3P[24] carrying the NSP5 (94.3%) gene, both are related to strains of simian origin (Fig. ) …”

Rotavirus Strain Trends During the Postlicensure Vaccine Era: United States, 2008–2013

“…A G3P[24] strain from Rochester was detected during the 2009 season that appears to be a reassortant between human, equine, simian, and bovine RVAs [38, 39]. G8P[4] strains were detected in specimens from Rochester in 2009 [40] and were found to be very similar genetically to a G8P[4] strain from Germany [41].…”

Rotavirus: Genetics, pathogenesis and vaccine advances

“…A classic example is the human G9 and G12 genotypes, circulating in the population due to transfer of porcine genes into human RV genome . Reassortment is the major cause of genetic diversity; it occurs between homologous or heterologous hosts and sometimes appears with novel constellation of RV gene segments . The unusual genotypes G2P[8], G9P[8], G9P[4], G9P[6], and G12P[6] are said to be evolved by reassortment.…”

“…62 Reassortment is the major cause of genetic diversity; it occurs between homologous or heterologous hosts and sometimes appears with novel constellation of RV gene segments. 63 The unusual genotypes G2P [8], G9P [8], G9P [4], G9P [6], and G12P [6] are said to be evolved by reassortment. Similarly, G11 genotype is detected in humans because of reassortment between porcine RV and human Wa-like strain, and G8 is evolved because of reassortment between bovine and human RVs.…”