Rapid real time PCR to distinguish between high risk human papillomavirus types 16 and 18

H A Cubie¹, A L Seagar¹, E McGoogan², J Whitehead¹, A Brass², M J Arends² and M W Whitley³

¹ Regional Clinical Virology Laboratory, Lothian University Hospitals NHS Trust, City Hospital, Greenbank Drive, Edinburgh EH10 5SB, UK
² Department of Pathology, University of Edinburgh Medical School, Teviot Place, Edinburgh EH8 9AG, UK
³ St Triduana's Medical Practice, Moira Park, Edinburgh EH7 6RU, UK

Correspondence to:
Dr Cubie heather.cubie{at}luht.scot.nhs.uk

Aims—To assess the validity and practicality of real time polymerase chain reaction (PCR) for human papillomavirus (HPV) testing in combination with liquid based cytology samples for cervical screening.

Methods—Real time PCR using consensus (GP5+/6+) and type specific primers was developed to detect genital HPV types. This provides rapid, efficient amplification followed by denaturation of the product and computer analysis of the kinetics data that are generated. Liquid based cytology samples were obtained from patients attending routine cervical screening clinics. DNA was extracted from the residual cellular suspension after cytology using spin columns.

Results—Real time PCR successfully distinguished between HPV-16 and HPV-18 on the basis of amplification with consensus primers followed by DNA melting temperature (T_m) analysis. Sensitivities of one to 10 copies of HPV-16 (mean T_m = 79.4°C; 2 SD, 0.8) and four to 40 copies of HPV-18 (mean T_m = 80.4°C; 2 SD, 0.4) were obtained. In a mixed population of SiHa and HeLa cells containing known copy numbers of HPV-16 and HPV-18 genomes, HPV-16 and HPV-18 products were clearly separated by T_m analysis in mixtures varying from equivalence to 1/1000. Together with detailed melt analysis, type specific primers from the same region of the L1 gene confirmed the differential ability of this system. The method was applied to 100 liquid based cytology samples where HPV status using conventional GP5+/6+ PCR was already known. There was 95% agreement between the methods, with 55 positives detected by conventional PCR and 59 with real time PCR. The method was then tested on 200 routine liquid based cytology samples. Approximately 10% were positive by real time PCR, most of which were classified as HPV-16 by detailed melt analysis. Thirteen (6.8%) HPV positives were identified in 189 samples showing no evidence of cervical cytological abnormality.

Conclusions—Real time PCR is a rapid, efficient method for the detection of HPV with the separation of HPV-16 and HPV-18 on the basis of differential T_m. Preliminary results suggest it could prove useful if HPV testing is added to cervical screening programmes.

Key Words: real time polymerase chain reaction • cervical screening • human papillomavirus types 16 and 18

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