Prevalence of Human Papillomavirus Types and Phylogenetic Analysis of HPV-16 L1 Variants from Southern India

Background: The human papillomavirus (HPV) and its variants show wide geographical distribution andhave 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 genotypesin cervical samples from the coastal Karnataka region, India. Materials and
Methods: A total of 212 sampleswere screened by nested polymerase chain reaction using PGMY9/11 and GP5+/6+ primers. HPV positivesamples were sequenced to identify the types and a phylogenetic tree was constructed using the neighbor-joiningmethod.
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 squamousintraepithelial lesion (HSIL)] and cervical cancer samples. The distribution of high risk HPV in cancer sampleswas HPV 16, 76.4%, HPV18, 11.7%, HPV81, 2.9%, HPV31, 1.4%, HPV35, 1.4% and HPV 45, 1.4%. Multipleinfections were observed in 11.8% of tumor samples with HPV 16 contributing to 62.5% of cases. In non-malignantsamples, 20% of HPV positive samples were detected with HPV16, 82.3%, HPV33, 5.8% and HPV58, 5.8% andvery low incidence of multiple infections. Comparative phylogenetic analysis of HPV variants identified 9 HPVsequences as new papillomavirus species, predominantly classified as European lineage type.
Conclusions: Thefindings for HPV infections associated with progression of cervical cancer in coastal Karnataka region and HPVvariant analysis provide baseline data for prevention and HPV vaccination programs.