Typing of human papillomaviruses by polymerase chain reaction amplification with L1 consensus primers and RFLP analysis

Abstract

Human papillomaviruses (HPV) cause benign and malignant lesions of the epithelial and mucosal surfaces. Certain virus types are associated with cervical carcinomas, while others are associated with benign condylomata. We have developed a rapid method for determining HPV type that is based on restriction fragment length polymorphism (RFLP) analysis within the L1 region of HPVs that is amplified by PCR using the consensus primers described by Manos et al. Analysis of the product generated by PCR amplification of plasmids containing cloned HPV genomes and of 88 clinical specimens, known to contain HPV viral DNA by previous hybridization analysis, revealed that this method is useful for typing HPV sequences amplified from a variety of sources including cervical lavages, fresh tissue, and paraffin-embedded formalin-fixed biopsy material. The method can differentiate between most known types of HPV and discriminate between infections with single, multiple or novel HPV types. A high correlation (86%) was obtained when this method was compared with PCR amplification and Southern blot hybridization analysis of PCR product, or Southern blot hybridization analysis of total genomic DNA. Differences in typing occurred mostly for specimens that contained multiple or new/unknown HPV types. However, RFLP typing easily identified repeated patterns for new HPV types that were not detected by the other methods. In summary, PCR-RFLP typing is a sensitive and specific method to identify and characterize rapidly HPV DNA in clinical specimens from a variety of sources.