title: Hospital based surveillance and genetic characterization of rotavirus strains in children (<5 years) with acute gastroenteritis in Kolkata, India, revealed resurgence of G9 and G2 genotypes during 2011-2013.
abstract: BACKGROUND
  India accounts for an estimated 457,000-884,000 hospitalizations and 2 million outpatient visits for diarrhea. In spite of the huge burden of rotavirus (RV) disease, RV vaccines have not been introduced in national immunization programme of India. Therefore, continuous surveillance for prevalence and monitoring of the circulating genotypes is needed to assess the disease burden prior to introduction of vaccines in this region.
  
  
  METHODS
  During January 2011 through December 2013, 830 and 1000 stool samples were collected from hospitalized and out-patient department (OPD) patients, respectively, in two hospitals in Kolkata, Eastern India. After primary screening, the G-P typing was done by multiplex semi-nested PCR using type specific primers followed by sequencing. Phylogenetic analysis for the VP7 gene of 25 representative strains was done.
  
  
  RESULTS
  Among hospitalized and OPD patients, 53.4% and 47.5% cases were positive for rotaviruses, respectively. Unlike previous studies where G1 was predominant, in hospitalized cases G9 rotavirus strains were most prevalent (40%), followed by G2 (39.6%) whereas G1 and G12 occurred at 16.4% and 5.6% frequency. In OPD cases, the most prevalent strain was G2 (40.3%), followed by G1, G9 and G12 at 25.5%, 22.8%, 9.3%, respectively. Phylogenetically the G1, G2 and G9 strains from Kolkata did not cluster with corresponding genotypes of Rotarix, RotaTeq and Rotavac (116E) vaccine strains.
  
  
  CONCLUSIONS
  The study highlights the high prevalence of RV in children with gastroenteritis in Kolkata. The circulating genotypes have changed over the time with predominance of G9 and G2 strains during 2011-2013. The current G2, G9 and G1 Kolkata strains shared low amino acid homologies with current vaccine strains. Although there is substantial evidence for cross protection of vaccines against a variety of strains, still the strain variation should be monitored post vaccine introduction to determine if it has any impact on vaccine effectiveness.
authors.affiliation: National Institute of Cholera and Enteric Diseases, Kolkata, India.
authors.forename: Satarupa
authors.initials: S
authors.lastname: Mullick
authors.affiliation: National Institute of Cholera and Enteric Diseases, Kolkata, India.
authors.forename: Paulami
authors.initials: P
authors.lastname: Mandal
authors.affiliation: National Institute of Cholera and Enteric Diseases, Kolkata, India.
authors.forename: Mukti Kant
authors.initials: MK
authors.lastname: Nayak
authors.affiliation: Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan.
authors.forename: Souvik
authors.initials: S
authors.lastname: Ghosh
authors.affiliation: National Institute of Cholera and Enteric Diseases, Kolkata, India.
authors.forename: Papiya
authors.initials: P
authors.lastname: De
authors.affiliation: National Institute of Cholera and Enteric Diseases, Kolkata, India.
authors.forename: K
authors.initials: K
authors.lastname: Rajendran
authors.affiliation: National Institute of Cholera and Enteric Diseases, Kolkata, India.
authors.forename: Mihir K
authors.initials: MK
authors.lastname: Bhattacharya
authors.affiliation: National Institute of Cholera and Enteric Diseases, Kolkata, India.
authors.forename: Utpala
authors.initials: U
authors.lastname: Mitra
authors.affiliation: National Institute of Cholera and Enteric Diseases, Kolkata, India.
authors.forename: Thandavarayan
authors.initials: T
authors.lastname: Ramamurthy
authors.affiliation: Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan.
authors.forename: Nobumichi
authors.initials: N
authors.lastname: Kobayashi
authors.affiliation: National Institute of Cholera and Enteric Diseases, Kolkata, India. Electronic address: chawlam70@gmail.com.
authors.forename: Mamta
authors.initials: M
authors.lastname: Chawla-Sarkar
mesh_terms: D000956:Antigens, Viral / Q000235:genetics; D036022:Capsid Proteins / Q000235:genetics; D002675:Child, Preschool; D003967:Diarrhea / Q000453:epidemiology / Q000821:virology; D005759:Gastroenteritis / Q000453:epidemiology* / Q000821:virology; D005838:Genotype; D006760:Hospitalization; D006801:Humans; D007194:India / Q000453:epidemiology; D007223:Infant; D017720:Molecular Epidemiology; D010802:Phylogeny; D012401:Rotavirus / Q000235:genetics*; D012400:Rotavirus Infections / Q000453:epidemiology* / Q000821:virology
chemical_list: D000956:Antigens, Viral; D036022:Capsid Proteins; C050779:VP7 protein, Rotavirus
keywords: Diarrhea; G2 strains; G9 strains; India; Kolkata; Rotavirus