Conserved region analysis of oncogenic human Papillomavirus genome

This study was carried out to determine the conserved regions of late genes from sequenced HPV types. HPV genome sequences were collected from the Los Alamos National Laboratory papillomavirus database. There are 74 types of HPV in the database which have completely documented genome sequences as well as their translation product. Specific types of HPV which may cause cervical cancer are grouped into high risk or low risk, according to their risk potential. This classification may differ from one research methodology to another. In order to access a representative classification, three sets of classification were studied for this research. HPV type 16 and 18 are consistently grouped as high risk, while other types of HPV varied randomly. Sequence alignment was taken and the result shows 62 conserved regions as a primer template for L1 and L2 genes. These conserved regions were then subjected to BLASTn operation in order to search the conserved region with least similarity to low risk HPV and human genome. Finally, 7 selected conserved regions were examined for secondary structures using NetPrimer program. From this operation, only region 52 (5'-ACAGGCTATGGTGCTATGGA-3') met the criteria to be used as an oligonucleotide primer.