title: Genetic diversity of cosaviruses in nonpolio acute flaccid paralysis cases of undefined etiology, Northern India, 2010-2011.
abstract: BACKGROUND
  No cases of wild poliovirus have been reported for more than one and a half years from India. Cases of acute flaccid paralysis (AFP) of undefined etiology continue to occur in the region. Despite the recent discovery of the human Cosavirus (HCoSV) in the feces of children from developing countries, there have been no studies of cosavirus infection in India.
  
  
  OBJECTIVE
  To detect and characterize HCoSVs in stool specimens of nonpolio AFP cases by RT-PCR followed by sequencing.
  
  
  METHODS
  A total of 387 fecal samples collected from AFP cases in Uttar Pradesh, India, between May 2010 and April 2011, tested negative on cell culture according to WHO algorithm, were subjected to 5'-UTR region specific RT-PCR followed by sequencing to detect HCoSV. Molecular characterization of HCoSV strains was done by sequencing followed by phylogenetic analysis.
  
  
  RESULTS
  123 (32%) samples tested positive for cosaviruses and 87 (70.7%) were identified for genetic variants by sequencing a 316-nucleotide interval in the partial 5'-UTR region. Cosavirus strains were characterized as putative species HCoSV-A (n=70; 82%), HCoSV-B (n=7; 8%), HCoSV-C (n=1; 1.1) and HCoSV-D (n=4; 4.5%) while 5 (5%) strains remain uncharacterized. The cosavirus infection appeared highest (63.5%) in younger children, and showed a distinct seasonality, with a late summer peak and winter low.
  
  
  CONCLUSIONS
  This study demonstrates a diversity of cosavirus strains in circulation, and reports the first investigation of HCoSV infection in children with nonpolio acute flaccid paralysis in India. Currently, this study provides baseline data for further studies of HCoSV infections in children with common enteric infections in India.
authors.affiliation: Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow 226014, India.
authors.forename: Harjeet Singh
authors.initials: HS
authors.lastname: Maan
authors.forename: Rashmi
authors.initials: R
authors.lastname: Chowdhary
authors.forename: Akhalesh Kumar
authors.initials: AK
authors.lastname: Shakya
authors.forename: Tapan N
authors.initials: TN
authors.lastname: Dhole
mesh_terms: D000293:Adolescent; D002648:Child; D002675:Child, Preschool; D016000:Cluster Analysis; D005243:Feces / Q000821:virology; D005260:Female; D014644:Genetic Variation; D006801:Humans; D007194:India / Q000453:epidemiology; D007223:Infant; D008297:Male; D008969:Molecular Sequence Data; D010243:Paralysis / Q000453:epidemiology / Q000209:etiology*; D010802:Phylogeny; D010849:Picornaviridae / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D010850:Picornaviridae Infections / Q000150:complications* / Q000453:epidemiology / Q000821:virology*; D012367:RNA, Viral / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA
chemical_list: D012367:RNA, Viral
keywords: AFP; Acute flaccid paralysis; CPE; Cosavirus; Emerging viruses; HCoSV; India; NPEV's; Novel picornaviruses; RD; RT-PCR; UP; UTR; Uttar Pradesh; WHO; World Health Organization; acute flaccid paralysis; cytopathic effect; human cosavirus; human rhabdomyosarcoma cells; nonpolio enteroviruses; reverse-transcriptase-polymerase chain reaction; untranslated region