title: E2 sequence variations of HPV 16 among patients with cervical neoplasia seen in the Indian subcontinent.
abstract: OBJECTIVE
  Specific nucleotide variations in the E2 DNA sequence were looked for in samples with an intact human papillomavirus (HPV) 16 episomal E2 DNA.
  
  
  METHODS
  Ninety-two women, 76 with invasive cervical carcinoma and 16 with cervical intraepithelial neoplasia (CIN) were recruited. HPV DNA typing was performed by polymerase chain reaction (PCR) based restriction fragment length polymorphism (RFLP). Intact episomal E2 DNA of HPV 16 was detected by PCR. Important nucleotide variations in samples with amplifiable E2 DNA were detected by RFLP. Nucleotide sequencing was performed on representative samples to confirm RFLP findings.
  
  
  RESULTS
  A total of 89 (96.7%) women were positive for HPV DNA. Of these, 56 (63%) were positive for HPV 16, and of these, 38 (68%) were positive for intact episomal HPV 16 E2 DNA while 18 (32%) were negative. Samples with intact episomal HPV 16 E2 DNA sequences were grouped into four different digestion profiles I to IV based on RFLP patterns. Digestion patterns revealed absence of any sequence variations in samples with digestion profile I and presence of a 2983 A-G variation in those with profile II. Samples with digestion profiles III and IV revealed three variations in the hinge region (3516 C-A, 3538 A-C, 3566 T-G) and two in the DNA binding domain (3684 C-A, 3694 T-A) of the E2 sequence. Sequencing performed on representative samples confirmed RFLP findings.
  
  
  CONCLUSIONS
  PCR-RFLP helped in the identification of important HPV 16 E2 sequence variations, circumventing the need for sequencing. The presence of the nucleotide variations in positions that could alter the biological and immunological functions of the E2 protein combined with its increased occurrence in this study bring out the importance of these variations.
authors.affiliation: Department of Clinical Virology, Christian Medical College, Vellore, India.
authors.forename: Narayanan
authors.initials: N
authors.lastname: Sathish
authors.forename: Priya
authors.initials: P
authors.lastname: Abraham
authors.forename: Abraham
authors.initials: A
authors.lastname: Peedicayil
authors.forename: Gopalan
authors.initials: G
authors.lastname: Sridharan
authors.forename: R V
authors.initials: RV
authors.lastname: Shaji
authors.forename: George
authors.initials: G
authors.lastname: Chandy
mesh_terms: D001483:Base Sequence; D004279:DNA, Viral / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000276:immunology; D005260:Female; D006801:Humans; D009856:Oncogene Proteins, Viral / Q000235:genetics* / Q000276:immunology; D027383:Papillomaviridae / Q000235:genetics* / Q000276:immunology; D030361:Papillomavirus Infections / Q000150:complications / Q000821:virology*; D010957:Plasmids / Q000235:genetics; D012150:Polymorphism, Restriction Fragment Length; D002583:Uterine Cervical Neoplasms / Q000473:pathology / Q000821:virology*; D002578:Uterine Cervical Dysplasia / Q000473:pathology / Q000821:virology
chemical_list: D004279:DNA, Viral; D004268:DNA-Binding Proteins; C054855:E2 protein, Human papillomavirus type 16; D009856:Oncogene Proteins, Viral