Sasivimolrattana Thanayod, Liewchalermwong Sasiprapa, Chantratita Wasun, Sensorn Insee, Chaiwongkot Arkom, Bhattarakosol Parvapan
Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand.
Center of Excellence in Applied Medical Virology, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
Sci Prog. 2025 Apr-Jun;108(2):368504251334515. doi: 10.1177/00368504251334515. Epub 2025 Apr 15.
ObjectiveThis study aims to explore HPV genotyping in the cervical specimen using VirCapSeq by comparing the results with the reverse blot hybridization assay (REBA).MethodsA secondary cross-sectional data of HPV genotypes in 35 cervical specimens was obtained from VirCapSeq and REBA methods. The .FASTQ files were downloaded from the NCBI Sequence Read Archive (SRA) (accession number PRJNA766412) and HPV genotyping was bioinformatically analyzed by mapping the sequences to the PaVE database. HPV genotypes detected by REBA and NGS were compared. All specimens were stratified by histology into cervical intraepithelial neoplasia grades 1 (CIN1) and 2/3 (CIN2/3).ResultsNGS via VirCapSeq detected HPV DNA in 100% of the samples, whereas the REBA (hybridization-based) assay diagnosed HPV DNA in 85.71%. While the limitation of the conventional methods for HPV genotyping is the use of primers or probes, NGS detected a broader range. The results showed that mixed infections were detected in all samples by NGS, with HPV16 and HPV52 being the most abundant genotypes.ConclusionsHPV genome abundance, coverage, and diversity were associated with detection discrepancies between the methods, highlighting the enhanced sensitivity and diagnostic capabilities of NGS. These findings underscore the potential of NGS technologies for comprehensive HPV genotyping, advancing cervical cancer screening, and epidemiological studies. Future research should address cost barriers and expand cohort sizes to validate these findings.
目的
本研究旨在通过将结果与反向杂交检测法（REBA）进行比较，探索使用VirCapSeq对宫颈标本进行HPV基因分型。
方法
从VirCapSeq和REBA方法中获取35份宫颈标本中HPV基因型的二次横断面数据。.FASTQ文件从NCBI序列读取存档（SRA）（登录号PRJNA766412）下载，并通过将序列映射到PaVE数据库对HPV基因分型进行生物信息学分析。比较REBA和NGS检测到的HPV基因型。所有标本按组织学分层为宫颈上皮内瘤变1级（CIN1）和2/3级（CIN2/3）。
结果
通过VirCapSeq进行的NGS在100%的样本中检测到HPV DNA，而REBA（基于杂交）检测法诊断出HPV DNA的样本为85.71%。虽然传统HPV基因分型方法的局限性在于使用引物或探针，但NGS检测范围更广。结果显示，NGS在所有样本中均检测到混合感染，其中HPV16和HPV52是最常见的基因型。
结论
HPV基因组丰度、覆盖率和多样性与不同方法之间的检测差异相关，突出了NGS更高的灵敏度和诊断能力。这些发现强调了NGS技术在全面HPV基因分型、推进宫颈癌筛查和流行病学研究方面的潜力。未来的研究应解决成本障碍并扩大队列规模以验证这些发现。
