Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India.
Abstracts of the papers presented at the XVIII National Conference of Indian Virological Society at Post Graduate Institute of Medical Education and Research, Chandigarh, India, December 11–13, 2008.
Rotaviruses are the most important aetiological agent of severe dehydrating diarrhea in children claiming approximately 611,000 lives annually. Two major surface proteins, a glycoprotein (G type) and Protease cleaved (P type) form the basis of classification system of Group A rotaviruses. To date 18 G (VP7) types and 27 P (VP4) types have been identified. A recent study from India reported high prevalence of G12 genotype along with a considerable percentage of G/P nontypeables. Therefore, the present study aimed to characterize these partially/completely nontypeable clinical rotavirus isolates. Six clinical isolates were characterized by sequencing for VP7 gene alone, 5 for VP4 gene and 4 for both VP7 and VP4 genes. The amplification product obtained using consensus primers was purified by GeneClean purification method and sequenced on an automated sequencer. Phylogenetic analysis was performed with Mega software (version 3.1). Out of the 6 G nontypeables sequenced, 3 were G1 and 1 each comprised of G2, G9 and G12 genotypes. The VP4 gene sequencing data of 5 P nontypeables revealed 3 with P[8] and 2 with P[4] genotype specificity. However, among the 4 completely nontypeable (for both G and P) RV strains, 3 were G1P[8] and 1 G9P[8] specific. The nucleotide sequence alignment of the 6 G1 RV strains showed three consistent mismatches at nt 14 (C:A), 17 (T:T) and 19 (C:A) from the primers 3’ end. Additionally, a fourth mismatch at nt 11 (A:C) was observed in 5 of these 6 G1 samples while the sixth one had a mismatch at nt 3(A:C). Similarly, lone G2 strain and 2 G9 strains also had single nucleotide mismatch at nt 19 (T:G) and 5 (T:G) respectively (data not shown). Four out of seven partially typed VP4 nontypeables with P[8] primer had nucleotide mismatches at nt 7 (A:C), 9 (A:A), 10 (G:T) and 12 (T:C). Additionally, 3 of these samples also had a mismatch at nt 8 (T:G) and one at nt 1 (C:A). The present study involved characterization of partially/completely nontypeable rotavirus isolates and demonstrated majority of them to have G1(54.5%) or P[8] (77.8%) genotype specificity, with consistent mismatches within type specific primers. This highlights the need to regularly update our typing method with addition of new genotype specific primers.
