High throughput HPV genotyping by next generation sequencing for detection of 28 HPV types and 13 sexually transmitted infections: A first community-based cervical cancer screening study from India.

BACKGROUND

High-risk human papillomavirus (HR-HPV) infection is the primary cause of cervical cancer. However, conventional PCR-based assays provide limited HPV genotyping, and cytology alone has low sensitivity for detecting subclinical infections. Comprehensive molecular approaches are needed to better characterize HPV genotypes and co-infections in community screening settings.

METHODS

This study evaluated the analytical performance of a next-generation sequencing (NGS)-based HPV-STI assay in comparison with the clinically validated Roche CobasⓇ 4800 platform in a community screening cohort from South India. Cervical exfoliated cell samples from 96 asymptomatic, married women previously tested by CobasⓇ 4800 with partial HR-HPV genotyping (HPV16, HPV18, and a pooled group of 12 other high-risk types) were analyzed using NGS. The NGS assay enabled comprehensive detection of 28 HPV genotypes and 13 sexually transmitted infections (STIs) on the Illumina NextSeq 550 platform. Liquid-based cytology with RAPID-Pap staining was performed for all sequenced samples.

RESULTS

The NGS assay showed high agreement with the CobasⓇ 4800 platform, with an overall concordance of 95.8% (92/96). Concordance was 94.4% (17/18) for HPV16 detection, 100% (3/3) for HPV18, 96.7% (58/60) for pooled other high-risk HPV types (non-HPV16/18), and 85.7% (7/8) for mixed infections, including co-infections of HPV16 or HPV18 with non-HPV16/18 high-risk types as well as HPV16/18 dual infections. Among women with abnormal cytology (ASCUS and HSIL), non-HPV16/18 infections were identified in 58.3% (7/12) of cases. Concurrent non-HPV STIs were detected in 52.1% (50/96) of participants, with Ureaplasma parvum and Mycoplasma hominis being the most prevalent.

CONCLUSION

A substantial proportion of women with abnormal cytology in this community cohort harboured non-HPV16 and HPV18 high-risk infections, highlighting the importance of extended HPV genotyping. NGS-based HPV genotyping was concordant with the comparator assay used and had simultaneous STI identification, supporting its potential utility as a comprehensive tool for community-based cervical cancer screening and risk stratification.