Molecular characterization of VP4, VP6, VP7, NSP4, and NSP5/6 genes identifies an unusual G3P[10] human rotavirus strain

Abstract

An unusual strain of human rotavirus G3P [10] (CMH079/05) was detected in a stool sample of a 2-year-old child admitted to the hospital with severe diarrhea in Chiang Mai, Thailand. Analysis of the VP7 gene sequence revealed highest identities with unusual human rotavirus G3 strain CMH222 at 98.7% on the nucleotide and 99.6% on the amino acid levels. Phylogenetic analysis of the VP7 sequence confirmed that the CMH079/05 strain formed a cluster with G3 rotavirus reference strains and showed the closest lineage with the CMH222 strain. Analysis of partial VP4 gene of CMH079/05 revealed highest degree of sequence identities with P[10] rotavirus prototype strain 69M at nucleotide and amino acid levels of 92.9% and 94.6%, respectively. Phylogenetic analysis of the VP4 sequence revealed that CMH079/05 and 69M clustered closely together in a monophyletic branch separated from other rotavirus genotypes. To our knowledge, this is a novel G-P combination of G3 and P[10] genotypes. In addition, analyses of VP6, NSP4, and NSP5/6 genes revealed these uncommon genetic characteristics: (i) the VP6 gene differed from the four other known subgroups; (ii) the NSP4 gene was identified as NSP4 genetic group C, an uncommon group in humans; and (iii) the NSP5/6 gene was most closely related with T152, a G12P[9] rotavirus previously isolated in Thailand. The finding of uncommon G3P [10] rotavirus in this pediatric patient provided additional evidence of the genetic diversity of human group A rotaviruses in Chiang Mai, Thailand.

Predominance of Porcine P[23] Genotype Rotaviruses in Piglets with Diarrhea in Northern Thailand

“…Previous epidemiological studies demonstrated that the combination of G3, G4, and G5 genotypes with P [6] and P [7] were the most common genotypes of porcine rotaviruses in the same geographical area of northern Thailand. An epidemiological surveillance from 2000 to 2001 revealed that 17 (43.6%) isolates were genotype G4P [6] and 13 (33.3%) were G3P [19] (11).…”

“…An epidemiological surveillance from 2000 to 2001 revealed that 17 (43.6%) isolates were genotype G4P [6] and 13 (33.3%) were G3P [19] (11). In addition, one rare G2P[27] strain, three G3P [6] strains, one G4P [13] strain, two G5P [13] strains, and one G9P [7] strain were isolated (6,11). From 2002 to 2003, a multiple combination of the P [13] genotype with G3, G4, and G5 was detected, with the appearance of G3P [6] as a major genotype (2).…”

“…Among these strains, the VP8* gene of the Hokkaido-14 strain in Japan bore the greatest resemblance to that of the CMP48/08 strain in this study. Previously, the P[23] rotavirus was seen as an unusual genotype in pigs, while P [6], P [7], P [13], P [19], and P[26] were known to be common genotypes. However, the emergence of the P[23] genotype in a major epidemic rotavirus was identified first in this study.…”

“…Furthermore, some uncommon human rotavirus strains, G3P [10] and G3P [3], which were considered animal-like rotaviruses, had been identified previously in this area (5,7). Therefore, the continuous monitoring of human and animal rotaviruses in this area is required for the investigation of emerging novel rotavirus strains.…”

Sequence analysis of human rotavirus strains: comparison of clinical isolates from Northern and Southern Italy

“…Thus far, few P [10] RV strains have been reported [23]. However, each of these P [10] RV strains carried different G-P genotype combinations.…”