
Characterization and diversity of 243 complete human papillomavirus genomes in cervical swabs using next generation sequencing
- Author
- Ardashel Latsuzbaia, Anke Wienecke-Baldacchino, Jessica Tapp, Marc Arbyn (UGent) , Irma Karabegovic, Zigui Chen, Marc Fischer, Friedrich Muhlschlegel, Steven Weyers (UGent) , Pascale Pesch and Joel Mossong
- Organization
- Abstract
- In recent years, next generation sequencing (NGS) technology has been widely used for the discovery of novel human papillomavirus (HPV) genotypes, variant characterization and genotyping. Here, we compared the analytical performance of NGS with a commercial PCR-based assay (Anyplex II HPV28) in cervical samples of 744 women. Overall, HPV positivity was 50.2% by the Anyplex and 45.5% by the NGS. With the NGS, we detected 25 genotypes covered by Anyplex and 41 additional genotypes. Agreement between the two methods for HPV positivity was 80.8% (kappa = 0.616) and 84.8% (kappa = 0.652) for 28 HPV genotypes and 14 high-risk genotypes, respectively. We recovered and characterized 243 complete HPV genomes from 153 samples spanning 40 different genotypes. According to phylogenetic analysis and pairwise distance, we identified novel lineages and sublineages of four high-risk and 16 low-risk genotypes. In total, 17 novel lineages and 14 novel sublineages were proposed, including novel lineages of HPV45, HPV52, HPV66 and a novel sublineage of HPV59. Our study provides important genomic insights on HPV types and lineages, where few complete genomes were publicly available.
- Keywords
- HPV HR DETECTION, CLINICAL VALIDATION, VARIANTS, CANCER, RISK, E6, CLASSIFICATION, ASSOCIATION, PERFORMANCE, ALIGNMENT, Anyplex II HPV28, cervical cancer, human papillomavirus, next generation, sequencing, rolling-circle amplification
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-8697670
- MLA
- Latsuzbaia, Ardashel, et al. “Characterization and Diversity of 243 Complete Human Papillomavirus Genomes in Cervical Swabs Using next Generation Sequencing.” VIRUSES-BASEL, vol. 12, no. 12, 2020, doi:10.3390/v12121437.
- APA
- Latsuzbaia, A., Wienecke-Baldacchino, A., Tapp, J., Arbyn, M., Karabegovic, I., Chen, Z., … Mossong, J. (2020). Characterization and diversity of 243 complete human papillomavirus genomes in cervical swabs using next generation sequencing. VIRUSES-BASEL, 12(12). https://doi.org/10.3390/v12121437
- Chicago author-date
- Latsuzbaia, Ardashel, Anke Wienecke-Baldacchino, Jessica Tapp, Marc Arbyn, Irma Karabegovic, Zigui Chen, Marc Fischer, et al. 2020. “Characterization and Diversity of 243 Complete Human Papillomavirus Genomes in Cervical Swabs Using next Generation Sequencing.” VIRUSES-BASEL 12 (12). https://doi.org/10.3390/v12121437.
- Chicago author-date (all authors)
- Latsuzbaia, Ardashel, Anke Wienecke-Baldacchino, Jessica Tapp, Marc Arbyn, Irma Karabegovic, Zigui Chen, Marc Fischer, Friedrich Muhlschlegel, Steven Weyers, Pascale Pesch, and Joel Mossong. 2020. “Characterization and Diversity of 243 Complete Human Papillomavirus Genomes in Cervical Swabs Using next Generation Sequencing.” VIRUSES-BASEL 12 (12). doi:10.3390/v12121437.
- Vancouver
- 1.Latsuzbaia A, Wienecke-Baldacchino A, Tapp J, Arbyn M, Karabegovic I, Chen Z, et al. Characterization and diversity of 243 complete human papillomavirus genomes in cervical swabs using next generation sequencing. VIRUSES-BASEL. 2020;12(12).
- IEEE
- [1]A. Latsuzbaia et al., “Characterization and diversity of 243 complete human papillomavirus genomes in cervical swabs using next generation sequencing,” VIRUSES-BASEL, vol. 12, no. 12, 2020.
@article{8697670, abstract = {{In recent years, next generation sequencing (NGS) technology has been widely used for the discovery of novel human papillomavirus (HPV) genotypes, variant characterization and genotyping. Here, we compared the analytical performance of NGS with a commercial PCR-based assay (Anyplex II HPV28) in cervical samples of 744 women. Overall, HPV positivity was 50.2% by the Anyplex and 45.5% by the NGS. With the NGS, we detected 25 genotypes covered by Anyplex and 41 additional genotypes. Agreement between the two methods for HPV positivity was 80.8% (kappa = 0.616) and 84.8% (kappa = 0.652) for 28 HPV genotypes and 14 high-risk genotypes, respectively. We recovered and characterized 243 complete HPV genomes from 153 samples spanning 40 different genotypes. According to phylogenetic analysis and pairwise distance, we identified novel lineages and sublineages of four high-risk and 16 low-risk genotypes. In total, 17 novel lineages and 14 novel sublineages were proposed, including novel lineages of HPV45, HPV52, HPV66 and a novel sublineage of HPV59. Our study provides important genomic insights on HPV types and lineages, where few complete genomes were publicly available.}}, articleno = {{1437}}, author = {{Latsuzbaia, Ardashel and Wienecke-Baldacchino, Anke and Tapp, Jessica and Arbyn, Marc and Karabegovic, Irma and Chen, Zigui and Fischer, Marc and Muhlschlegel, Friedrich and Weyers, Steven and Pesch, Pascale and Mossong, Joel}}, issn = {{1999-4915}}, journal = {{VIRUSES-BASEL}}, keywords = {{HPV HR DETECTION,CLINICAL VALIDATION,VARIANTS,CANCER,RISK,E6,CLASSIFICATION,ASSOCIATION,PERFORMANCE,ALIGNMENT,Anyplex II HPV28,cervical cancer,human papillomavirus,next generation,sequencing,rolling-circle amplification}}, language = {{eng}}, number = {{12}}, pages = {{15}}, title = {{Characterization and diversity of 243 complete human papillomavirus genomes in cervical swabs using next generation sequencing}}, url = {{http://doi.org/10.3390/v12121437}}, volume = {{12}}, year = {{2020}}, }
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