Avinash Choudekar1, Rajesh1, Shama Parveen2, V.L.N. S. Raghuram1, Shinjini Bhatnager3, Lalit Dar1, Shobha Broor1
1Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India.
2Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India.
3Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India.
Noroviruses (NoVs) are an important cause of acute gastroenteritis in humans worldwide. NoVs are genetically diverse and are divided into five genogroups (GI-V) of which two genogroups NoVs, GI and GII are responsible for most of the human infections and are further subdivided into at least 29 genotypes based on genetic differences in the capsid gene. The RNA recombination is a significant driving force in viral evolution. The increased awareness of recombination in NoVs has led to a rise in the identification of NoV recombinants and they are now reported at high frequency from different parts of the world. Along withsmall-scale mutations, recombination events seem to contribute to the genetic variability between NoVs. This phenomenon was identified by incongruent clustering of different regions of the genome in phylogenetic analyses for NoVs from all the 5 genogroups. Based upon predictive models, the majority of NoV recombinants have breakpoints located either within or close to the ORF1-ORF2 junction. Consequently, this region has been suggested to constitute recombination hotspot in NoVs recombinants. Fifty stool samples positive for NoVs by RT-PCR collected from patients with acute gastroenteritis during different studies at the Microbiology Department, All India Institute of Medical Sciences selected for this study. The published primers were used for amplification and sequencing of 3′ of the RNA dependent polymerase (RdRp) and capsid gene which includes region A in ORF1 for GII, region B in ORF1 for GI and ORF1-ORF2 overlapping region including structural and non-structural (N/S) domain of capsid gene. The nucleotide sequences were aligned in Genedoc, Bioedit, Clustal X and phylogenetic trees were constructed using the Neighbour Joining method in MEGA 4.0. Dendograms of partial RdRp and capsid gene were compared for the branching pattern of NoVs genotypes to identify recombinants. Based on phylogenetic grouping for partial RdRp gene of 16 NoVs GI strains compared with the phylogenetic grouping based on partial capsid gene, 12 strains were identified as recombinants. Of these 12 novel intergenotype recombinants strains, 10 were GI.d/GI.3 recombinant type and 1 each was GI.c/GI.5, GI.f/GI.7 and GII.e/NA recombinant types. Read more…