Genetic diversity of noroviruses and sapoviruses in children with acute sporadic gastroenteritis in New Delhi, India.
BACKGROUND
Human caliciviruses (HuCVs) cause gastroenteritis throughout the world. Limited information is available on molecular epidemiology of caliciviruses from developing countries including India.


OBJECTIVE
Standardization and evaluation of a two-step multiplex RT-PCR assay for HuCVs and characterization of strains.


METHODS
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.


CONCLUSIONS
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.
Rachakonda
Girish
G
Department of Radiation Oncology, Vanderbilt University, Nashville, TN, USA.
Choudekar
Avinash
A
Parveen
Shama
S
Bhatnagar
Shinjini
S
Patwari
Ashok
A
Broor
Shobha
S
D000208:Acute Disease; D017250:Caliciviridae Infections / Q000453:epidemiology / Q000821:virology*; D002648:Child; D002675:Child, Preschool; D005759:Gastroenteritis / Q000453:epidemiology / Q000821:virology*; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D007194:India / Q000453:epidemiology; D029322:Norovirus / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D020133:Reverse Transcriptase Polymerase Chain Reaction; D029341:Sapovirus / Q000145:classification / Q000235:genetics*