Characterization and Diversity of 243 Complete Human Papillomavirus Genomes in Cervical Swabs Using Next Generation Sequencing

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.

HPV DeepSeq: An Ultra-Fast Method of NGS Data Analysis and Visualization Using Automated Workflows and a Customized Papillomavirus Database in CLC Genomics Workbench

“…Furthermore, testing the workflows on a portable notebook computer endorses software performance efficiency for benchtop or fieldwork, as well as, in austere clinical settings. In contradistinction, a recent publication used nine bioinformatics software for HPV de novo assembly, genotyping, phylogenetic analysis, and visualization (Bowtie2, SPAdes, VAPiD, MAFFT, RAxML, MEGA7, iTOL5.3, Dendroscope3, and R) [ 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 ]. In recent years, the list of superb bioinformatics software has lengthened considerably and is welcomed by the research community [ 18 , 37 ].…”

HPV DeepSeq: Ultra-Fast Method of NGS Data Analysis and Visualization Using Automated Workflows and a Customized Papillomavirus Database in CLC Genomics Workbench

“…Furthermore, testing the workflows on a portable notebook computer endorses software performance efficiency for benchtop or fieldwork, as well as, in austere clinical settings. In contradistinction, a recent publication used nine bioinformatics software for HPV de novo assembly, genotyping, phylogenetic analysis, and visualization (Bowtie2, SPAdes, VAPiD, MAFFT, RAxML, MEGA7, iTOL5.3, Dendro-scope3, and R) [23]. In recent years, the list of superb bioinformatics software has lengthened considerably and is welcomed by the research community [18,24].…”

Human papillomavirus genotype concordance between Anyplex II HPV28 and linear array HPV genotyping test in anogenital samples

“…HPV-28 has been widely used for HPV genotyping in clinical and epidemiological studies [10][11][12][13][14][15] and has been evaluated in comparative studies against various genotyping assays. 12,[16][17][18][19][20][21] Anyplex HPV II HR detection assay has been validated using the international Valgent framework 8 and was shown to meet the international consensus guideline for HPV test requirements. 22 HPV-28 has been previously compared with LA-HPV using cervical samples, [18][19][20] but to our knowledge, these assays have not been compared using other specimens from the anogenital tract nor among people living with HIV.…”

“…HPV‐28 is thus a suitable alternative to LA‐HPV for HPV genotyping. HPV‐28 has been widely used for HPV genotyping in clinical and epidemiological studies 10–15 and has been evaluated in comparative studies against various genotyping assays 12,16–21 . Anyplex HPV II HR detection assay has been validated using the international Valgent framework 8 and was shown to meet the international consensus guideline for HPV test requirements 22 …”