title: HPV Population Profiling in Healthy Men by Next-Generation Deep Sequencing Coupled with HPV-QUEST.
abstract: Multiple-type human papillomaviruses (HPV) infection presents a greater risk for persistence in asymptomatic individuals and may accelerate cancer development. To extend the scope of HPV types defined by probe-based assays, multiplexing deep sequencing of HPV L1, coupled with an HPV-QUEST genotyping server and a bioinformatic pipeline, was established and applied to survey the diversity of HPV genotypes among a subset of healthy men from the HPV in Men (HIM) Multinational Study. Twenty-one HPV genotypes (12 high-risk and 9 low-risk) were detected in the genital area from 18 asymptomatic individuals. A single HPV type, either HPV16, HPV6b or HPV83, was detected in 7 individuals, while coinfection by 2 to 5 high-risk and/or low-risk genotypes was identified in the other 11 participants. In two individuals studied for over one year, HPV16 persisted, while fluctuations of coinfecting genotypes occurred. HPV L1 regions were generally identical between query and reference sequences, although nonsynonymous and synonymous nucleotide polymorphisms of HPV16, 18, 31, 35h, 59, 70, 73, cand85, 6b, 62, 81, 83, cand89 or JEB2 L1 genotypes, mostly unidentified by linear array, were evident. Deep sequencing coupled with HPV-QUEST provides efficient and unambiguous classification of HPV genotypes in multiple-type HPV infection in host ecosystems.
authors.affiliation: Department of Pathology, Immunology &amp; Laboratory Medicine and UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA. yin@pathology.ufl.edu.
authors.forename: Li
authors.initials: L
authors.lastname: Yin
authors.affiliation: Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA. jin.yao2009@gmail.com.
authors.forename: Jin
authors.initials: J
authors.lastname: Yao
authors.affiliation: Department of Pathology, Immunology &amp; Laboratory Medicine and UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA. kaifen@pathology.ufl.edu.
authors.forename: Kaifen
authors.initials: K
authors.lastname: Chang
authors.affiliation: Department of Pathology, Immunology &amp; Laboratory Medicine and UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA. brentga@pcom.edu.
authors.forename: Brent P
authors.initials: BP
authors.lastname: Gardner
authors.affiliation: Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA. fyu@ufl.edu.
authors.forename: Fahong
authors.initials: F
authors.lastname: Yu
authors.affiliation: Center for Infection Research in Cancer at H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA. Anna.Giuliano@moffitt.org.
authors.forename: Anna R
authors.initials: AR
authors.lastname: Giuliano
authors.affiliation: Department of Pathology, Immunology &amp; Laboratory Medicine and UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA. goodenow@ufl.edu.
authors.forename: Maureen M
authors.initials: MM
authors.lastname: Goodenow
mesh_terms: D000328:Adult; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D020407:Internet; D008297:Male; D008969:Molecular Sequence Data; D027383:Papillomaviridae / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D030361:Papillomavirus Infections / Q000821:virology*; D010802:Phylogeny; D055815:Young Adult
keywords: HPV; HPV-QUEST; Linear Array; Papillomavirus Episteme; asymptomatic men; deep sequencing; multiple-type HPV infection
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