title: Prevalence of human papillomavirus types and phylogenetic analysis of HPV-16 L1 variants from Southern India.
abstract: BACKGROUND
  The human papillomavirus (HPV) and its variants show wide geographical distribution and have been reported to cause cervical lesions. With cervical neoplasia as the leading cancer in Indian women, the aim of the present study was to evaluate the multiple infection HPV type distribution and variant genotypes in cervical samples from the coastal Karnataka region, India.
  
  
  METHODS
  A total of 212 samples were screened by nested polymerase chain reaction using PGMY9/11 and GP5+/6+ primers. HPV positive samples were sequenced to identify the types and a phylogenetic tree was constructed using the neighbor-joining method.
  
  
  RESULTS
  Sequence analysis identified a total of 14 HPV types distributed in 20%, 73.3% and 82.5% of non-malignant, pre-malignant [low grade squamous intraepithelial lesion (LSIL) and high grade squamous intraepithelial lesion (HSIL)] and cervical cancer samples. The distribution of high risk HPV in cancer samples was HPV 16, 76.4%, HPV18, 11.7%, HPV81, 2.9%, HPV31, 1.4%, HPV35, 1.4% and HPV 45, 1.4%. Multiple infections were observed in 11.8% of tumor samples with HPV 16 contributing to 62.5% of cases. In non-malignant samples, 20% of HPV positive samples were detected with HPV16, 82.3%, HPV33, 5.8% and HPV58, 5.8% and very low incidence of multiple infections. Comparative phylogenetic analysis of HPV variants identified 9 HPV sequences as new papillomavirus species, predominantly classified as European lineage type.
  
  
  CONCLUSIONS
  The findings for HPV infections associated with progression of cervical cancer in coastal Karnataka region and HPV variant analysis provide baseline data for prevention and HPV vaccination programs.
authors.affiliation: Division of Biotechnology, School of Life Sciences, Manipal University, Karnataka, India E-mail : ksatyamoorthy@manipal.edu.
authors.forename: Shama Prasada
authors.initials: SP
authors.lastname: Kabekkodu
authors.forename: Samatha
authors.initials: S
authors.lastname: Bhat
authors.forename: Deeksha
authors.initials: D
authors.lastname: Pandey
authors.forename: Vinay Koshy
authors.initials: VK
authors.lastname: Varghese
authors.forename: Vaibhav
authors.initials: V
authors.lastname: Shukla
authors.forename: Supriti
authors.initials: S
authors.lastname: Ghosh
authors.forename: Pralhad
authors.initials: P
authors.lastname: Kushtagi
authors.forename: Parvati
authors.initials: P
authors.lastname: Bhat
authors.forename: Puthiya Mundayat
authors.initials: PM
authors.lastname: Gopinath
authors.forename: Kapaettu
authors.initials: K
authors.lastname: Satyamoorthy
mesh_terms: D000328:Adult; D004279:DNA, Viral / Q000235:genetics; D005260:Female; D005838:Genotype; D052162:Human papillomavirus 16 / Q000235:genetics* / Q000276:immunology; D006801:Humans; D007194:India / Q000453:epidemiology; D008875:Middle Aged; D030361:Papillomavirus Infections / Q000453:epidemiology* / Q000276:immunology / Q000473:pathology / Q000821:virology; D053918:Papillomavirus Vaccines / Q000276:immunology; D010802:Phylogeny; D015995:Prevalence; D002583:Uterine Cervical Neoplasms / Q000276:immunology / Q000473:pathology / Q000821:virology
chemical_list: D004279:DNA, Viral; D053918:Papillomavirus Vaccines