Human papillomavirus (HPV) is a double-stranded circular DNA virus with a genome of approximately 7–8 kb. This study aimed to establish an overlapping extension polymerase chain reaction method for the amplification of the entire genome of HPV16.
Methods
The HPV16 genome was divided into two larger fragments (with lengths of 3.9 kilobases and 5.3 kilobases, respectively), each of which had overlapping regions of more than 500 base pairs. A nested primer (outer primer: Fout/Rout; inner primer: Fin/Rin) was used to amplify each fragment. The key reaction parameters were optimized, including the selection of two highly accurate DNA polymerases; and a series of diluted samples (initial concentration of 2,000 copies/microliter, diluted to 2, 20, 200, and 2,000 copies/microliter) were used for amplification tests to evaluate the sensitivity of this method.
Results
This study demonstrated high sensitivity for HPV16 detection, with effective amplification of samples as low as 2 copies/µL. For low-concentration samples (<200 copies/µL), the Thermo Fisher enzyme showed 50% and 75% effective amplification success rates at 2 copies/µL and 20 copies/µL, respectively, while the Vazyme enzyme achieved 0% success at both concentrations. Both enzymes enabled stable amplification of high-concentration samples (≥200 copies/µL). The amplified products matched the theoretical size, and Illumina sequencing confirmed Q30 ≥ 96% and >98% identity with the HPV16 reference sequence (K02718.1).
Conclusions
The overlapping extension PCR method established in this study demonstrates high sensitivity and specificity for amplifying HPV16 in cervical exfoliated cells. This method provides a robust technical foundation for genomic research, with potential applications in whole-genome sequencing and variation analysis. Additionally, this study provides insights for the optimization of nested PCR amplification systems and serves as a reference for other studies involving the amplification of long DNA fragments.
Full text
https://www.xiahepublishing.com/2996-3427/OnA-2025-00025
The study was recently published in the Oncology Advances .
Oncology Advances is dedicated to improving the diagnosis and treatment of human malignancies, advancing the understanding of molecular mechanisms underlying oncogenesis, and promoting translation from bench to bedside of oncological sciences. The aim of Oncology Advances is to publish peer-reviewed, high-quality articles in all aspects of translational and clinical studies on human cancers, as well as cutting-edge preclinical and clinical research of novel cancer therapies.
