Identification of a novel human papillomavirus by metagenomic analysis of samples from patients with febrile respiratory illness

PLoS One. 2013;8(3):e58404. doi: 10.1371/journal.pone.0058404. Epub 2013 Mar 15.


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.

Publication types

  • Clinical Trial
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Base Sequence
  • Female
  • Gammapapillomavirus / genetics*
  • Genome, Viral*
  • Humans
  • Male
  • Metagenomics*
  • Molecular Sequence Data
  • Papillomavirus Infections* / genetics
  • Papillomavirus Infections* / virology
  • Respiratory Tract Diseases* / genetics
  • Respiratory Tract Diseases* / virology

Associated data

  • GENBANK/KC113191

Grants and 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),, 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.