Comparison of four different human papillomavirus genotyping methods in cervical samples: Addressing method-specific advantages and limitations

• Published in: Heliyon Vol. 10; no. 3; p. e25474
• Main Authors: Siqueira, Juliana D., Alves, Brunna M., Castelo Branco, Adriana B.C., Duque, Kristiane C.D., Bustamante-Teixeira, Maria Teresa, Soares, Esmeralda A., Levi, José Eduardo, Azevedo e Silva, Gulnar, Soares, Marcelo A.
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 15.02.2024; Elsevier
• Subjects: HPV genotyping; HPV multiple infections; Next-generation sequencing; Real-time PCR; Reverse hybridization; Sanger sequencing; HPV multiple infections; Reverse hybridization; Next-generation sequencing; Sanger sequencing; Real-time PCR; HPV genotyping
• ISSN: 2405-8440; 2405-8440
• DOI: 10.1016/j.heliyon.2024.e25474

Since human papillomavirus (HPV) is recognized as the causative agent of cervical cancer and associated with anogenital non-cervical and oropharyngeal cancers, the characterization of the HPV types circulating in different geographic regions is an important tool in screening and prevention. In this context, this study compared four methodologies for HPV detection and genotyping: real-time PCR (Cobas® HPV test), nested PCR followed by conventional Sanger sequencing, reverse hybridization (High + Low PapillomaStrip® kit) and next-generation sequencing (NGS) at an Illumina HiSeq2500 platform. Cervical samples from patients followed at the Family Health Strategy from Juiz de Fora, Minas Gerais, Brazil, were collected and subjected to the real-time PCR. Of those, 114 were included in this study according to the results obtained with the real-time PCR, considered herein as the gold standard method. For the 110 samples tested by at least one methodology in addition to real-time PCR, NGS showed the lowest concordance rates of HPV and high-risk HPV identification compared to the other three methods (67–75 %). Real-time PCR and Sanger sequencing showed the highest rates of concordance (97–100 %). All methods differed in their sensitivity and specificity. HPV genotyping contributes to individual risk stratification, therapeutic decisions, epidemiological studies and vaccine development, supporting approaches in prevention, healthcare and management of HPV infection. •Different HPV genotyping methods have specific characteristics and applications.•Reverse hybridization and real-time PCR are limited regarding HPV types identified.•Rolling circle amplification followed by NGS recovers HPV complete genomes.•L1 PCR followed by Sanger sequencing is limited in detecting multiple infections.•Sanger sequencing and NGS are valuable for HPV prevalence and genotyping studies.