MinION nanopore sequencing and assembly of a complete human papillomavirus genome

• Published in: Journal of virological methods Vol. 294; p. 114180
• Main Authors: Brancaccio, Rosario N., Robitaille, Alexis, Dutta, Sankhadeep, Rollison, Dana E., Tommasino, Massimo, Gheit, Tarik
• Format: Journal Article Web Resource
• Language: English
• Published: Netherlands Elsevier B.V 01.08.2021; Elsevier; Elsevier/North-Holland Biomedical Press
• Subjects: Alphapapillomavirus; High-Throughput Nucleotide Sequencing; Human health sciences; Humans; Immunologie & maladie infectieuse; Immunology & infectious disease; MinION sequencer; Nanopore Sequencing; Oxford Nanopore Technologies; Papillomaviridae - genetics; Papillomavirus; Sciences de la santé humaine; Sequence Analysis, DNA; Whole-genome sequencing; Papillomavirus; RCA; MinION sequencer; ONT; Whole-genome sequencing; NGS; Oxford Nanopore Technologies; HPV
• ISSN: 0166-0934; 1879-0984; 1879-0984
• DOI: 10.1016/j.jviromet.2021.114180

•The MinION sequencer allows whole HPV genome sequencing.•The proposed bioinformatics pipeline enables the reconstruction of whole HPV genome.•Rapid whole-genome characterization of HPV genomes with a minimal error rate. The MinION sequencer belongs to the third generation of sequencing technology that allows for the generation of ultra-long reads, representing a potentially more effective approach to characterize entire viral genome sequences than other time-consuming and low-throughput methodologies. We report the use of the MinION nanopore sequencer to sequence the full-length genome of human papillomavirus (HPV)-ICB2 (7441 bp), which was previously characterized in our laboratory. Three independent MinION libraries were prepared and sequenced using either three consecutive 12 -h runs (Protocol A) or a single run of 48 h starting from a pool of three barcoded DNA libraries (Protocol B). A fully automated bioinformatics pipeline was developed for the reconstruction of the viral genome. Protocols A and B generated 9,354,933 and 3,255,879 reads, respectively. Read length N50 values ranged between 6976 and 7360 nucleotides over the four sequencing runs. Bioinformatics analysis showed that both protocols allowed for the reconstruction of the whole viral genome, with pairwise percentages of identity to HPV-ICB2 of 100 % for protocol A and 99.98 % for protocol B. Our results show that the use of the MinION nanopore sequencer represents an effective strategy for whole-genome sequencing of HPVs with a minimal error rate.