21
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Identification of a Novel Human Papillomavirus by Metagenomic Analysis of Samples from Patients with Febrile Respiratory Illness

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          As part of a virus discovery investigation using a metagenomic approach, a highly divergent novel Human papillomavirus type was identified in pooled convenience nasal/oropharyngeal swab samples collected from patients with febrile respiratory illness. Phylogenetic analysis of the whole genome and the L1 gene reveals that the new HPV identified in this study clusters with previously described gamma papillomaviruses, sharing only 61.1% (whole genome) and 63.1% (L1) sequence identity with its closest relative in the Papillomavirus episteme (PAVE) database. This new virus was named HPV_SD2 pending official classification. The complete genome of HPV-SD2 is 7,299 bp long (36.3% G/C) and contains 7 open reading frames (L2, L1, E6, E7, E1, E2 and E4) and a non-coding long control region (LCR) between L1 and E6. The metagenomic procedures, coupled with the bioinformatic methods described herein are well suited to detect small circular genomes such as those of human papillomaviruses.

          Related collections

          Author and article information

          Contributors
          Role: Editor
          Journal
          PLoS One
          PLoS ONE
          plos
          plosone
          PLoS ONE
          Public Library of Science (San Francisco, USA )
          1932-6203
          2013
          15 March 2013
          : 8
          : 3
          : e58404
          Affiliations
          [1 ]Department of Biology, San Diego State University, San Diego, California, United States of America
          [2 ]Global Viral Forecasting (now known as Metabiota), San Francisco, California, United States of America
          [3 ]Centre for Molecular and Biomolecular Informatics/Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
          [4 ]Naval Health Research Center, U.S. Navy, San Diego, California, United States of America
          [5 ]Center for Microbial Sciences, San Diego State University, San Diego, California, United States of America
          Albert Einstein College of Medicine, United States of America
          Author notes

          Competing Interests: JLM, YWL, BSS and TT were associated with the Global Viral Forecasting Initiative, now known as Metabiota, during the time of the execution of the study. These authors have declared that no competing interests exist. DM was associated with the Naval Health Research Center, U.S. Navy, San Diego, CA, USA, during the study period. DM has moved to Ibis Biosciences, Carlsbad, CA. DM has declared that no competing interests exist. These authors fully adhere to all the PLOS ONE policies on sharing data and materials.

          Collected samples, obtained IRB clearance: PJB DM CAM. Read, edited and approved the manuscript: JLM BED YWL BSS TT MRH DM CAM PJB BN NDW FLR. Conceived and designed the experiments: JLM FLR NDW PJB DM. Performed the experiments: JLM YWL MRH. Analyzed the data: JLM BED TT BN. Contributed reagents/materials/analysis tools: NDW BSS FLR. Wrote the paper: JLM.

          [¤a]

          Current address: Ibis Biosciences, Carlsbad, California, United States of America

          [¤b]

          Current address: Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America

          Article
          PONE-D-12-33549
          10.1371/journal.pone.0058404
          3600855
          23554892
          757b6bed-0615-42e6-9cd0-c102ec104b7c
          Copyright @ 2013

          This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

          History
          : 27 October 2012
          : 4 February 2013
          Page count
          Pages: 12
          Funding
          BED is supported by the Dutch Science Foundation (NWO) Veni grant (016.111.075). Global Viral Forecasting (JLM, BSS and NDW) was graciously supported by the U.S. Department of Defense Global Emerging Infections, Surveillance and Response Systems (DoD GEIS) and the Defense Threat Reduction Agency (DTRA), Cooperative Biological Engagement Program (CBEP), Google.org, the Skoll Foundation, and the U.S. Agency for International Development (USAID) Emerging Pandemic Threats Program, PREDICT project, under the terms of Cooperative Agreement Number GHN-A-OO-09-00010-00. The Surveillance conducted by Naval Health Research Center (NHRC) was supported by the Global Emerging Infections System division of the Armed Forces Health Surveillance Center. The views expressed in this work are those of the authors and do not reflect the official policy of the Department of the Navy, Department of Defense, or the US Government. Approved for public releases; distribution is unlimited. This research has been conducted in compliance with all applicable federal regulations governing the protection of human subjects in research. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
          Categories
          Research Article
          Biology
          Genomics
          Metagenomics
          Microbiology
          Virology

          Uncategorized
          Uncategorized

          Comments

          Comment on this article