HPV16-Genotyper: A Computational Tool for Risk-Assessment, Lineage Genotyping and Recombination Detection in HPV16 Sequences, Based on a Large-Scale Evolutionary Analysis
| Autor: | Ioannis Iliopoulos, Christine Kottaridi, D. Tsakogiannis, Garyfalia Bletsa, Marios Nikolaidis, Panayotis Markoulatos, Dimitris Mossialos, Grigoris D. Amoutzias |
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| Rok vydání: | 2021 |
| Předmět: |
HPV16
Ecology Phylogenetic tree QH301-705.5 Ecological Modeling Lineage (evolution) Single-nucleotide polymorphism cancer risk Biology Agricultural and Biological Sciences (miscellaneous) Genome recombination phylogenetics Phylogenetics Evolutionary biology evolution Genotype bioinformatics tool Biology (General) Clade Genotyping SNPs Nature and Landscape Conservation |
| Zdroj: | Diversity, Vol 13, Iss 497, p 497 (2021) Diversity Volume 13 Issue 10 |
| ISSN: | 1424-2818 |
| DOI: | 10.3390/d13100497 |
| Popis: | Previous analyses have identified certain but limited evidence of recombination among HPV16 genomes, in accordance with a general perception that DNA viruses do not frequently recombine. In this evolutionary/bioinformatics study we have analyzed more than 3600 publicly available complete and partial HPV16 genomes. By studying the phylogenetic incongruence, similarity plots and the distribution patterns of lineage-specific SNPs, we identify several potential recombination events between the two major HPV16 evolutionary clades. These two clades comprise the (widely considered) phenotypically more benign (lower risk) lineage A and the (widely considered) phenotypically more aggressive (higher risk) non-European lineages B, C and D. We observe a frequency of potential recombinant sequences ranging between 0.3 and 1.2% which is low, but nevertheless considerable. Our findings have clinical implications and highlight that HPV16 genotyping and risk assessment based only on certain genomic regions and not the entire genome may provide a false genotype and, therefore, its associated risk estimate. Finally, based on this analysis, we have developed a bioinformatics tool that automates the entire process of HPV16 lineage genotyping, recombination detection and further identifies, within the submitted sequences, SNPs that have been reported in the literature to increase the risk of cancer. |
| Databáze: | OpenAIRE |
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