Identification by high-throughput sequencing of HPV variants and quasispecies that are untypeable by linear reverse blotting assay in cervical specimens

• Published in: Papillomavirus research Vol. 8; p. 100169
• Main Authors: Molet, Lucie, Girlich, Delphine, Bonnin, Rémy A., Proust, Alexis, Bouligand, Jérôme, Bachelerie, Françoise, Hantz, Sébastien, Deback, Claire
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.12.2019; Elsevier
• Subjects: Base Sequence; Cervix Uteri - virology; DNA, Viral; Female; Genetic Variation; Genotype; Genotyping; High-Throughput Nucleotide Sequencing; High-throughput sequencing; Human papillomavirus; Humans; Life Sciences; Molecular Typing; Papillomaviridae - classification; Papillomaviridae - genetics; Papillomavirus Infections - complications; Papillomavirus Infections - virology; Phylogeny; Quasispecies; Quasispecies - genetics; Sequence Analysis, DNA; Uterine Cervical Neoplasms - diagnosis; Uterine Cervical Neoplasms - etiology; Variants; Quasispecies; Variants; Human papillomavirus; Genotyping; High-throughput sequencing
• ISSN: 2405-8521; 2405-8521
• DOI: 10.1016/j.pvr.2019.100169

The linear reverse blotting assays are valid methods for accurate human papillomavirus (HPV) typing required to manage women at risk of developing cervical cancer. However, some samples showed a positive signal in HPV lines but failed to display a positive signal in subsequent typing lines (designated as HPV-X), which indicate that certain types were not available on the respective typing blots. The aim of this study is to elucidate the types or variants of HPV through the high-throughput sequencing (HTS) of 54 ASCUS cervical samples in which the viruses remained untypeable with INNO LiPA HPV® assays. Low-risk (LR)-HPV types (HPV6, 30, 42, 62, 67, 72, 74, 81, 83, 84, 87, 89, 90 and 114), high-risk (HR)-HPV35 and possibly (p)HR-HPV73 were detected among HPV-X. Individual multiple infections (two to seven types) were detected in 40.7% of samples. Twenty-two specimens contained variants characterised by 2–10 changes. HPV30 reached the maximal number of 17 variants with relative abundance inferior or equal to 2.7%. The presence of L1 quasispecies explains why linear reverse blotting assays fail when variants compete or do not match the specific probes. Further studies are needed to measure the LR-HPV quasispecies dynamics and its role during persistent infection. •Types which linear reverse blotting assays are unable to identify are mainly multiple LR-HPV.•Deep sequencing of L1 permits to identify minority variants in 41% of these samples.•Understanding of LR-HPV quasispecies dynamics during infection is awaited.