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Human Papilloma Virus Genotyping, Variants and Viral Load in Tumors, Squamous Intraepithelial Lesions, and Controls in a North Indian Population Subset
  1. Archna Singh, MD, PhD, MPH*,
  2. Palika Datta, MSc*,
  3. Sunesh Kumar Jain, MD,
  4. Neeraja Bhatla, MD,
  5. Siddhartha Dutta Gupta, MD,
  6. Bindu Dey, PhD§ and
  7. Neeta Singh, PhD*
  1. * Department of Biochemistry,
  2. Department of Obstetrics and Gynecology,
  3. Department of Pathology, All India Institute of Medical Sciences,
  4. § Department of Biotechnology, Ministry of Science and Technology, New Delhi, India.
  1. Address correspondence and reprint requests to Neeta Singh, PhD, Department of Biochemistry, All India Institute of Medical Sciences, Room No.3027A, New Delhi, India. E-mail: singh_neeta{at}


A study of human papilloma virus (HPV) types and variants is important for developing preventive protocols and appropriate intervention targets. The presence of HPV types, their variants, and viral load in a population subset from North India was studied. Polymerase chain reaction (PCR) and line blots were used for HPV genotyping; HPV 16 and 18 viral loads were measured using real-time PCR. Variant analysis was done by sequencing of the PCR-amplified E6/E7regions of HPV 16 and the long control region and E6/E7 regions of HPV 18. The 93.6%, 78.6%, and 10% of tumors, squamous intraepithelial lesions (SILs), and controls were HPV-positive, respectively. The most commonly observed type was HPV 16. Human papilloma virus 73 which is uncommonly observed was seen in 2 tumors. Multiple infections were more common in controls and SILs than tumors. The majority (86.4%) of the HPV 16-positive and all of the HPV 18-positive samples belonged to the European variant class. Five novel nonsynonymous changes were seen in the HPV 16-positive and 2 in HPV 18-positive samples. There was a significant increase in viral loads from controls through SILs to tumors, but no significant differences in viral loads were observed between different stages of cancer. In tumors, a significant increase in HPV 16 viral loads was seen with increasing age. The study shows a similar HPV type and variant distribution to European studies, with some differences in type distribution. Viral load does not appear to be good marker for stage wise progression and intralesional variability may affect its use as a differentiating parameter between high-grade squamous intraepithelial lesion and low-grade squamous intraepithelial lesions.

  • HPV genotypes
  • Variants
  • Viral load

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