Utilization of the E6 gene as a target for detection of Human Papillomavirus type 11 using the Polymerase Chain Reaction method

The Human Papillomavirus (HPV) type 11 infection, potentially triggers condyloma acuminate, which is a risk factor of anogenital cancer. Recently, the low risk HPV groups, particularly type 11, were detected on the L1 gene by polymerase chain reaction (PCR) method. Meanwhile, the weakness of using the L1 sequence includes its high mutation rate and the facts that the gene was not inserted into the human genome during infection. Therefore, this study aims to design a primary pair, based on the nucleotide sequence of the E6 gene for type 11 HPV, and to conduct their implementation using the cervical swabs samples from RSUD Bangil, East Java, Indonesia. The Primer3 Plus software was used to design the primers and further analyzed them using both Oligoanalyzer 3.1 and BLASTn from NCBI. The annealing temperature of PCR was optimized at the gradient ranging from 44–63°C. The pilot implementation of the primer was conducted approximately a month for new outpatients suspected of being infected with HPV. The primers pair, such as E11(+)/E11(-), designed into the following sequences: 5'-GTA AAG ATG CCT CCA CGT CT-3' and 5'-CTA CTG TAG GTG CAT ATG CAG C-3' were presented in the 8 to 288 E6 gene. These were the ideal primers for type 11 HPV in terms of various parameters. Meanwhile, only one band of ~260- bp size appeared at the end of PCR on the annealing gradient temperature between 44–63°C using the total DNA obtained from patients infected with type 11 HPV as a template. A total of four patients were referred by doctors during the data collection period to test for the possibility of HPV infection. However, one of them (code B1) was detected positively for having the L1 gene on PCR using the GP5(+)/GP6(+) primers. Based on the detection of E6 gene using E11(+)/E11(-) primer, all the patients' samples contained type 11 HPV. In conclusion, the E6 gene based-primers, such as E11(+)/E11(-), detected the presence of type 11 HPV more accurately compared to the L1 sequence.