Modification of rotavirus multiplex RT‐PCR for the detection of G12 strains based on characterization of emerging G12 rotavirus strains from South India

Abstract

Rotaviruses are the major etiological agents of diarrhea in children less than 5 years of age. The commonest G types in humans are G1-4 and G9. G12 is a rare human rotavirus (HRV) strain first reported in the Philippines. In this study, 13 G12 strains obtained from a community-based cohort and a hospital-based surveillance system in 2005 were characterized by phylogenetic analysis of partial nucleotide sequences of VP7, VP6, and NSP4 genes. Sequence and phylogenetic analysis of VP7 gene sequences showed that these southern Indian strains had the greatest homology with G12 strains recently reported from eastern India (97-99% identity both at the nucleotide level and deduced amino acid level) and less homology with the prototype G12 strain, L26 (89-90% identity at the nucleotide level and 90-94% at the deduced amino acid level). Phylogenetic analysis of the VP6 and the NSP4 genes revealed that the Vellore G12 strains belonged to VP6 subgroup II and NSP4 genotype B. The P types associated with these strains were P[6] and P [8]. A G12 typespecific primer was designed for inclusion in an established VP7 G-typing multiplex RT PCR, and tested against a panel of known G types and untyped samples and was found to detect G12 strains in the multiplex-PCR. Close homology of the South Indian G12 strains to those from Kolkata suggests that G12 HRV strains are emerging in India. Methods for characterization of rotaviruses in epidemiological studies need to be updated frequently, particularly in developing countries.

Rotavirus Infection: A Perspective on Epidemiology, Genomic Diversity and Vaccine Strategies

“…In a study from Kolkata (1998Kolkata ( -2000, the most predominant genotype was G1P [8], followed by G2P [4] and G4P [8]. A number of uncommon genotypes, G1P [4], G2P [8], G2P [6], G4P [4], and G4P [6] were also observed [29]. A novel rotavirus strain G4P [8] was also reported from children with acute diarrhea during that study.…”

“…In a study by IturrizaGomara et al [45], a collection of over 3000 rotavirus isolates collected during 1995-1998 indicated the presence of four common types, G1P [8], G2P [4], G3P [8] and G4P [8], that constituted over 94% of typed isolates [45]. However, uncommon strains like G1P [4], G2P [8], G4P [4], G9P [6] and G9P [8] were found in smaller frequencies. In contrast, an epidemiological survey conducted in India from 1986 to 1988, showed that 70% of strains belonged to the unusual combination of G9P [11] [29,74].…”

“…In contrast, an epidemiological survey conducted in India from 1986 to 1988, showed that 70% of strains belonged to the unusual combination of G9P [11] [29,74]. A survey conducted in 1993 showed equal distribution of the common strain G2P [4] and the unusual strain G9P [6], which were found in 21 and 24% of isolates, respectively in India [4,74]. In two European studies, 38% of isolates belonged to G1P [8], 52% to G4P [8] and 3% to the unusual combination of G9P [8] [4,83].…”

“…In two European studies, 38% of isolates belonged to G1P [8], 52% to G4P [8] and 3% to the unusual combination of G9P [8] [4,83]. In a North and central American study carried out in 1990-1992, 71% of isolates were of type G1P [8], with 20% of isolates belonging to either G3P [8] or the unusual type G1P [6] [75,83]. In a similar study carried out a few years later (1996-1997) the emergence of G9P [6] was observed, increasing from 0% (in 1990) to 6% [75].…”

“…In a North and central American study carried out in 1990-1992, 71% of isolates were of type G1P [8], with 20% of isolates belonging to either G3P [8] or the unusual type G1P [6] [75,83]. In a similar study carried out a few years later (1996-1997) the emergence of G9P [6] was observed, increasing from 0% (in 1990) to 6% [75]. In Brazil, serotype G5 is commonly isolated in greater numbers, [10% as reported in many studies [39,51].…”