Papillomaviruses have been implicated in a variety of human diseases ranging from common warts to invasive carcinoma of the anogenital mucosa. Existing assays for genotyping human papillomavirus are restricted to a small number of types. Here, we present a comprehensive, accurate microarray strategy for detection and genotyping of 102 human papillomavirus types and validate its use in a panel of 91 anal swabs. This array has equal performance to traditional dot blot analysis with the benefits of added genotype coverage and the ability to calibrate readout over a range of sensitivity or specificity values. 1. Introduction Papillomaviruses are a group of nonenveloped, epitheliotropic DNA viruses that infect the skin and mucous membranes of humans and animals. There are over 100 different human papillomaviruses (HPV), which are associated with disease of the skin, mucous membranes, and aerodigestive tract. HPV infection leads to lesions ranging from common and genital warts to laryngeal papillomatosis, to epithelial cancers, particularly cervical carcinoma and a subset of head and neck squamous cell carcinoma (HNSCC). Detection of papillomavirus is usually based on molecular assays for viral nucleic acid [1]. There is considerable sequence diversity within the family papillomaviridae. The HPVs fall into five genera: alphapapillomavirus (α-PV), betapapillomavirus (β-PV), gammapapillomavirus (γ-PV), mupapillomavirus (μ-PV), and nupapillomavirus (ν-PV). The mucosal α-PV are the best described, due to their association with genital malignancy. There are thirteen types of high-risk mucosal α-PV associated with cervical and anal intraepithelial neoplasia: 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, and 68. It has recently been recommended that HPV 66 be added to this high-risk group [2]. HPV testing is becoming increasingly important as a screening tool, in combination with cytology, for HPV-associated neoplasia [3, 4]. Most commercial assays for alphapapillomaviruses are limited to the high-risk types, which are relevant for use in the clinical setting but provide limited information in the research setting. The current FDA-approved tests for HPV are the Digene Hybrid Capture 2 (HC2) test and the Cervista HPV16/18 and HR test. HC2 combines antibody capture and chemiluminescent signal detection to detect 13 high-risk HPV types (Digene Corporation, Gaithersburg, Md, USA), while the Cervista HR uses invader chemistry to detect 14 high risk types (Hologic, Inc., Bedford, Mass, USA) [5]. While both of these assays have good sensitivity and specificity for
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