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Viruses 2016, 8(2), 28; doi:10.3390/v8020028

HPV Population Profiling in Healthy Men by Next-Generation Deep Sequencing Coupled with HPV-QUEST

1
Department of Pathology, Immunology & Laboratory Medicine and UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
2
Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA
3
Center for Infection Research in Cancer at H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
*
Author to whom correspondence should be addressed.
Academic Editors: Johnson Mak, Peter Walker and Marcus Thomas Gilbert
Received: 6 October 2015 / Revised: 11 December 2015 / Accepted: 11 January 2016 / Published: 25 January 2016
View Full-Text   |   Download PDF [1816 KB, uploaded 26 January 2016]   |  

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. View Full-Text
Keywords: HPV; multiple-type HPV infection; asymptomatic men; deep sequencing; HPV-QUEST; Linear Array; Papillomavirus Episteme HPV; multiple-type HPV infection; asymptomatic men; deep sequencing; HPV-QUEST; Linear Array; Papillomavirus Episteme
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Yin, L.; Yao, J.; Chang, K.; Gardner, B.P.; Yu, F.; Giuliano, A.R.; Goodenow, M.M. HPV Population Profiling in Healthy Men by Next-Generation Deep Sequencing Coupled with HPV-QUEST. Viruses 2016, 8, 28.

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