Geographic Information Systems and Genotyping in Identification of Rotavirus G12 Infections in Residents of an Urban Slum with Subsequent Detection in Hospitalized Children: Emergence of G12 Genotype in South India

Abstract

Rotavirus infections by G12 strains in several countries have recently been described. In this study, we report the emergence of G12 strains in south India. Fourteen cases of G12 infection were identified between June and September 2005. G12 was seen in combination with P[6], P[8], or nontypeable P type. Nine cases, including five symptomatic infections and four asymptomatic infections, were identified as part of routine surveillance for rotavirus infections in a birth cohort in the community between June and July 2005. Significant temporal and time-space clustering of eight of these cases represents a possible recent introduction of a new rotavirus VP7 genotype. Previous rotavirus infections had been documented for six of the nine children in the community. In the following 2 months, five cases of G12 infection were identified among children presenting to a referral hospital with diarrhea. This is the first description of symptomatic and asymptomatic G12 infections in children in the community. The detection of G12 strains from different parts of the world in recent years suggests the possibility of its emergence as an important global genotype. Monitoring of cocirculating rotavirus strains and detection of emerging strains is important in the context of the availability of rotavirus vaccines.

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

“…Multiple sequence alignment and phylogenetic analysis of the partial VP7 gene sequence of 13 untyped strains identified them as G12 HRV strains, as reported [Ramani et al, 2007]. Further characterization by analysis of the partial nucleotide sequence of all 13 strains (CRI 32215, CRI 32442, CRI 32548, CRI 32608, CRI 32609, CRI 32742, CRI 32920, CRI 33015, RV 404, RV 412, RV 413, RV 417, and RV 430) showed maximum homology with the Indian ISO-5 G12 strain (97-99% at the nucleotide level and 97-99% at the deduced amino acid level).…”

“…All G12 strains analyzed in this study clustered in lineage III. P types determined in 12 of the 13 G12 strains from Vellore as reported separately [Ramani et al, 2007], were P[6] in 9 strains (69.2%) and, P[8] in 3 strains (23.1%), with one sample remaining untyped for VP4 (Table I). Since a first round amplification product of the VP4 gene could not be obtained for the untyped sample, sequence analysis was not possible.…”

“…A total of 13 samples from which the G type was not determined after the second round of G-typing multiplex PCR using type specific primers , but which had a fragment of 881 bp of the VP7 gene amplified in the first round PCR using VP7 consensus primers were sequenced as described [Ramani et al, 2007]. The PCR amplicons obtained in the first round of the VP7 specific RT-PCR were purified and sequenced in both directions with the ABI PRISM Big Dye Terminator Cycle Sequencing Ready Reaction Kit (Applied Biosystems, Foster City, CA) using the same primer pairs as in the VP7 first round PCR reaction.…”

“…In this study, the recently reported G12 strains [Ramani et al, 2007] from children in South India have been characterized by VP4 typing by PCR and partial sequence analysis of the genes encoding VP7, VP6, and NSP4. The evaluation of a modified multiplex G-typing PCR incorporating a newly designed G12-specific primer is also described.…”

Prevalence and Molecular Genotyping of Group A Rotaviruses in Iranian Children

“…Use of newly optimised molecular techniques has increased sensitivity of detection and characterisation of unusual rotavirus strains apart from commonly described genotypes [9]. Results of earlier studies in Iran have shown that rotavirus is a major aetiological agent of acute diarrhoea in infants and young children [10].…”