title: Genetic characterization of norovirus strains in hospitalized children from Pakistan.
abstract: Norovirus is one of the most common causes of acute gastroenteritis among children in developing countries. No data on the prevalence and genetic variability of norovirus are available for Pakistan, where early childhood mortality due to acute gastroenteritis is common. We tested 255 fecal specimens from children under 5 years of age hospitalized between April 2006 and March 2008 with severe acute gastroenteritis in five hospitals in the four largest cities in Pakistan for norovirus by real-time RT-PCR. Positive samples were further genotyped by conventional RT-PCR targeting the 5'-end of the capsid gene followed by sequencing of the positive PCR products. Overall, 41 (16.1%) samples tested positive for norovirus with an equal frequency in rotavirus-positive and rotavirus-negative samples. Nine (22%) samples were genogroup (G)I positive, 30 (73%) GII positive and two (5%) samples contained a mixture of GI and GII viruses. Sequence analyses demonstrated co-circulation of 14 norovirus genotypes including four GI genotypes (GI.3, GI.5, GI.7, GI.8) and 10 GII genotypes (GII.2, GII.3, GII.4, GII.5, GII.6, GII.7, GII.9, GII.13, GII.16, and GII.21). The most prevalent genotypes were GI.7 and GII.4 both causing 12.2% of the infections. This report confirms the presence of multiple norovirus genotypes in hospitalized children with acute gastroenteritis in Pakistan and a lack of clear predominance of GII.4 viruses.
authors.affiliation: Department of Pediatrics and Child Health, The Aga Khan University Hospital, Karachi, Pakistan.
authors.forename: Amna
authors.initials: A
authors.lastname: Alam
authors.affiliation: Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan.
authors.forename: Sohail A
authors.initials: SA
authors.lastname: Qureshi
authors.affiliation: Division of Viral Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia.
authors.forename: Jan
authors.initials: J
authors.lastname: Vinjé
authors.affiliation: Department of Pediatrics and Child Health, The Aga Khan University Hospital, Karachi, Pakistan.|Enteric and Diarrheal Diseases, Global Health, Bill and Melinda Gates Foundation, North Seattle, Washington.
authors.forename: Anita
authors.initials: A
authors.lastname: Zaidi
mesh_terms: D017250:Caliciviridae Infections / Q000453:epidemiology / Q000821:virology*; D002673:Child, Hospitalized; D002675:Child, Preschool; D002947:Cities / Q000453:epidemiology; D005243:Feces / Q000821:virology; D005260:Female; D005759:Gastroenteritis / Q000453:epidemiology / Q000821:virology*; D014644:Genetic Variation; D005838:Genotype; D006761:Hospitals; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D008297:Male; D017720:Molecular Epidemiology; D029322:Norovirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D010154:Pakistan / Q000453:epidemiology; D015995:Prevalence; D060888:Real-Time Polymerase Chain Reaction; D012401:Rotavirus / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D012400:Rotavirus Infections / Q000453:epidemiology / Q000821:virology; D017422:Sequence Analysis, DNA
keywords: Pakistan; acute gastroenteritis; co-infection; genogroup I and II; norovirus