HPV16-Genotyper: A Computational Tool for Risk-Assessment, Lineage Genotyping and Recombination Detection in HPV16 Sequences, Based on a Large-Scale Evolutionary Analysis
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...
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MDPI AG
2021-10-01
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| author | Marios Nikolaidis Dimitris Tsakogiannis Garyfalia Bletsa Dimitris Mossialos Christine Kottaridi Ioannis Iliopoulos Panayotis Markoulatos Grigoris D. Amoutzias |
| author_facet | Marios Nikolaidis Dimitris Tsakogiannis Garyfalia Bletsa Dimitris Mossialos Christine Kottaridi Ioannis Iliopoulos Panayotis Markoulatos Grigoris D. Amoutzias |
| author_sort | Marios Nikolaidis |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T06:37:02Z |
| format | Article |
| id | doaj.art-d7043e9f61bf48cabd1c835a6146f82c |
| institution | Directory Open Access Journal |
| issn | 1424-2818 |
| language | English |
| last_indexed | 2024-03-10T06:37:02Z |
| publishDate | 2021-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Diversity |
| spelling | doaj.art-d7043e9f61bf48cabd1c835a6146f82c2023-11-22T17:59:46ZengMDPI AGDiversity1424-28182021-10-01131049710.3390/d13100497HPV16-Genotyper: A Computational Tool for Risk-Assessment, Lineage Genotyping and Recombination Detection in HPV16 Sequences, Based on a Large-Scale Evolutionary AnalysisMarios Nikolaidis0Dimitris Tsakogiannis1Garyfalia Bletsa2Dimitris Mossialos3Christine Kottaridi4Ioannis Iliopoulos5Panayotis Markoulatos6Grigoris D. Amoutzias7Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, GreeceResearch Center, Hellenic Anticancer Institute, 10680 Athens, GreeceResearch Center, Hellenic Anticancer Institute, 10680 Athens, GreeceMicrobial Biotechnology-Molecular Bacteriology-Virology Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, GreeceMicrobiology Laboratory, Department of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, GreeceSchool of Medicine, University of Crete, 71003 Heraklion, GreeceMicrobial Biotechnology-Molecular Bacteriology-Virology Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, GreeceBioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, GreecePrevious 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.https://www.mdpi.com/1424-2818/13/10/497HPV16evolutionphylogeneticsbioinformatics toolcancer riskSNPs |
| spellingShingle | Marios Nikolaidis Dimitris Tsakogiannis Garyfalia Bletsa Dimitris Mossialos Christine Kottaridi Ioannis Iliopoulos Panayotis Markoulatos Grigoris D. Amoutzias HPV16-Genotyper: A Computational Tool for Risk-Assessment, Lineage Genotyping and Recombination Detection in HPV16 Sequences, Based on a Large-Scale Evolutionary Analysis Diversity HPV16 evolution phylogenetics bioinformatics tool cancer risk SNPs |
| title | HPV16-Genotyper: A Computational Tool for Risk-Assessment, Lineage Genotyping and Recombination Detection in HPV16 Sequences, Based on a Large-Scale Evolutionary Analysis |
| title_full | HPV16-Genotyper: A Computational Tool for Risk-Assessment, Lineage Genotyping and Recombination Detection in HPV16 Sequences, Based on a Large-Scale Evolutionary Analysis |
| title_fullStr | HPV16-Genotyper: A Computational Tool for Risk-Assessment, Lineage Genotyping and Recombination Detection in HPV16 Sequences, Based on a Large-Scale Evolutionary Analysis |
| title_full_unstemmed | HPV16-Genotyper: A Computational Tool for Risk-Assessment, Lineage Genotyping and Recombination Detection in HPV16 Sequences, Based on a Large-Scale Evolutionary Analysis |
| title_short | HPV16-Genotyper: A Computational Tool for Risk-Assessment, Lineage Genotyping and Recombination Detection in HPV16 Sequences, Based on a Large-Scale Evolutionary Analysis |
| title_sort | hpv16 genotyper a computational tool for risk assessment lineage genotyping and recombination detection in hpv16 sequences based on a large scale evolutionary analysis |
| topic | HPV16 evolution phylogenetics bioinformatics tool cancer risk SNPs |
| url | https://www.mdpi.com/1424-2818/13/10/497 |
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