Identification of a Target Region for Specific Molecular Diagnosis of Human Papillomavirus Subtype 16

Abstract

Objective: To identify a target region for molecular diagnosis from the E6 region of the Human papillomavirus (HPV). Method: This was a quantitative data research. The sample was composed of sequences from the National Center for Biotechnology Information (NCBI), HPV subtype 16, E6 region, using the following search filters: viruses, genomic DNA/RNA. 3227 sequences were obtained, which were separated according to the country of origin. After selection, the total number of samples consisted of 22 sequences that were aligned in the Clustal/o program, available on the online platform at: https://www.ebi.ac.uk/Tools/msa/clustalo/ and reading it through the Jalview program to identify consensus regions. For the primer design, the FastPCR program was used and the data were attached to a spreadsheet in Microsoft Excel 2010. Results: The consensus sequence among the countries was selected according to the consensus region for the primer design, called the target region, with 95 nucleotides. FastPCR analyzed the sequence and defined 10 pairs of primers, 5 forward and 5 reverse. The primers were selected according to the percentage CG/AT ratio (50%-60%) and the specific temperature of 58 °C, resulting in 3 primer pairs. The pairs were analyzed in the BLAST program, obtaining a 100% identification and query score, identifying other sequences of HPV 16, region E6. Conclusion: The use of a primer with greater specificity will lead to the specific diagnosis of the virus, making possible the early diagnosis and the most effective treatment.