Full genome characterization of feline and porcine origin G3P[9] rotavirus A strain in a child with acute gastroenteritis in Japan

Abstract

The group A rotavirus (RVA) G3P[9] is a rare genotype isolated in humans and cats. We isolated only one G3P[9] strain RVA/Human-wt/JPN/R11-035/2014/G3P[9] among 487 stool samples in our rotavirus surveillance of children with gastroenteritis in Japan, during 2014–2015. The R11-035 strain was isolated from a 2 year old girl presenting with vomiting and diarrhea who had daily contact with cats. She had type A histo-blood group antigen, which is reported to be related to rare human P[9] rotavirus infection. Full genome sequencing revealed that the R11-035 strain had AU-1-like constellations, except for the NSP3 (T) gene, G3-P[9]-I3-R3-C3-M3-A3-N3-T1-E3-H6. Phylogenetic analysis of all genome segments, except for the NSP3 gene, showed that the R11-035 strain formed distinct clusters and had high nucleotide sequence identity with human/feline-like strains. We postulate that the R11-035 strain was directly transmitted from a cat to the patient. Interestingly, the NSP3 gene of R11-035 was found to cluster closely with Taiwanese porcine strains. Since the remaining genes of R11-035 were closely related to those of human/feline-like human strains, it is likely that R11-035 acquired its NSP3 gene through intergenotype reassortment events with porcine strains before being transmitted to humans. The CAU14-1-262 strain, isolated from a 2 year old girl in South Korea in 2014, is the only reported strain having the same genome constellations as R11-035. These two strains had extremely high nucleotide sequence identity in all 11 gene segments (99.3–99.9%). It is therefore likely that strains with these genome sequences are circulating in East Asia.