Journal of Clinical Virology 43 (2008) 42–48 Genetic diversity of noroviruses and sapoviruses in children with acute sporadic gastroenteritis in New Delhi, India Girish Rachakonda a , Avinash Choudekar b , Shama Parveen c , Shinjini Bhatnagar d , Ashok Patwari e , Shobha Broor b,∗ a Department of Radiation Oncology, Vanderbilt University, Nashville, TN, USA b Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110029, India c Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India d Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India e Department of Pediatrics, Kalawati Saran Children’s Hospital, Lady Harding Medical College, New Delhi, India Received 13 February 2008; received in revised form 8 May 2008; accepted 13 May 2008 Abstract Background: Human caliciviruses (HuCVs) cause gastroenteritis throughout the world. Limited information is available on molecular epidemiology of caliciviruses from developing countries including India. Objectives: Standardization and evaluation of a two-step multiplex RT-PCR assay for HuCVs and characterization of strains. Study design: Two hundred and twenty-six stool samples were collected from children with acute gastroenteritis (AGE) over a one and half year to study the prevalence and diversity of HuCVs in children with AGE in New Delhi, India. A multiplex two-step RT-PCR using 3 sets of external and 4 sets of internal primers from the RdRp gene was standardized for detection of NoVs and SaVs. Molecular characterization of some HuCV strains was done by sequencing followed by phylogenetic analysis. Results: Fifty-nine HuCVs strains were detected in 54 (24%) of the samples; 5 samples had mixed infections. Of these 59 HuCVs, 36 (61%) were norovirus (34 were GGII; 2 were GGI) and 23 (39%) were sapovirus (22 were GGI; 1 was GGII). Phylogenetic analysis of partial RdRp gene of 12 HuCV strains identified three genotypes (GGI/4, GGII/3 and a newly identified GIIb/Hilversum cluster) in NoVs and one genotype (GGI/1) in SaVs. Conclusion: This is one of the few reports from India on detection and characterization of HuCVs by multiplex RT-PCR assay. This assay can be a useful tool for epidemiological studies of HuCV infections. © 2008 Elsevier B.V. All rights reserved. Keywords: Norovirus; Sapovirus; Multiplex PCR assay; Gastroenteritis; Genetic diversity 1. Introduction Human caliciviruses (HuCVs) are one of the leading eti- ological agents of acute gastroenteritis in all age groups and are responsible for majority of non-bacterial food- borne outbreaks of gastroenteritis (Noel et al., 1999). They belong to family Caliciviridae having single stranded pos- itive sense RNA genome of approximately 7.5kb. HuCVs have been classified into two genera, noroviruses (NoVs) and ∗ Corresponding author. Tel.: +91 11 2659 4926; fax: +91 11 2658 8663. E-mail address: shobha.broor@gmail.com (S. Broor). sapoviruses (SaVs), based on the morphology and genome organization (Green et al., 1995). RT-PCR and sequencing, followed by phylogenetic anal- ysis, are major tools for detection and characterization of HuCVs. Of the four genogroups in NoVs, three genogroup (GGI, GGII, and GGIV) cause infections in humans. Each genogroup is further classified into genetic clusters or geno- types: there are 14 clusters in GGI, 17 in GGII and 1 in GGIV (Kageyama et al., 2004). SaVs are also classified into five genogroups (GI–GV), of which GI, GII, GIV and GV cause human infections. SaV clusters or genotypes within the genogroups have also been described (Hansman et al., 2007). 1386-6532/$ – see front matter © 2008 Elsevier B.V. All rights reserved. doi:10.1016/j.jcv.2008.05.006