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Chapter 38 : Molecular Detection of Human Papillomaviruses
Category: Clinical Microbiology; Bacterial Pathogenesis
The importance of human papillomaviruses (HPVs) in biology and medicine was most recently highlighted by the award of the 2008 Nobel Prize in Medicine to Harald zur Hausen in recognition of his discovery of the oncogenic role of HPV in cervical cancer. This chapter provides a brief overview of the biology and natural history of the virus and a description of current clinical applications, laboratory methods, and possible future directions. The major (L1) and minor (L2) capsid proteins make up the viral protein coat. The chapter focuses on the HPV assays that have been used in published studies, been designed to provide clinically relevant information, and are available commercially. The major limitation of targeting the E6/E7 region is the large number of variants, not all of which have been fully described for all types targeted by HPV assays. The Invader HPV16/18 reagents employ probe amplification technology for the Invader HPV screening assay. The research-use-only Linear Array HPV genotyping test is based on PGMY09/11 L1 consensus PCR followed by reverse line probe hybridization for detection of 37 HPV types. It is clear that HPV testing is evolving and many new assays are appearing on the market. Nucleic acid detection assays are often performed in molecular diagnostic or cytology laboratories and necessitate specific training of personnel. The clinical utility of HPV genotyping and implementation of guidelines for appropriate clinical follow-up based on genotype may change the paradigm for HPV testing.
Schematic diagram of genomic organization of ORF of HPV16. P97 refers to dominant promoter. All PVs are similar in their genetic organization and appearance by electron microscopy. URR, upstream regulatory region.
Phylogenetic tree containing the sequences of 118 PV types. The L1 ORF sequences were used in a modified version of the Phylip version 3.572 and based on a weighted version of the neighbor-joining analysis. The tree was constructed using the Treeview program of the University of Glasgow. The numbers at the ends of each of the branches identify an HPV type; c-numbers refer to candidate HPV types. All other abbreviations refer to animal PV types. The outermost semicircular symbols identify PV genera, e.g., the genus Alpha-papillomavirus. The number at the inner semicircular symbol refers to PV species. To give an example taken from the upper part of the figure, the HPV types 7, 40, 43, and c91 together form the HPV species 8 in the genus Alpha-papillomavirus. Reprinted from reference 13 with permission of the publisher.
Schematic representation of the locations of the different general primer sets (MY09/ 11, GP5 +/6 +, and SPF) on the HPV genome. The circular HPV DNA genome is represented by a single line, and boxes show the positions of the various early (E) and late (L) genes. Within the L1 region, the positions of the amplification targets as well as the expected amplimer sizes for each of the primer sets are indicated. Reprinted from reference 28 with permission of the publisher.
Commercially available tests for HR HPV detection a