title: Identification of a novel human papillomavirus by metagenomic analysis of samples from patients with febrile respiratory illness.
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.
authors.affiliation: Department of Biology, San Diego State University, San Diego, California, USA. jmokili@gmail.com
authors.forename: John L
authors.initials: JL
authors.lastname: Mokili
authors.forename: Bas E
authors.initials: BE
authors.lastname: Dutilh
authors.forename: Yan Wei
authors.initials: YW
authors.lastname: Lim
authors.forename: Bradley S
authors.initials: BS
authors.lastname: Schneider
authors.forename: Travis
authors.initials: T
authors.lastname: Taylor
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Haynes
authors.forename: David
authors.initials: D
authors.lastname: Metzgar
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Myers
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Blair
authors.forename: Bahador
authors.initials: B
authors.lastname: Nosrat
authors.forename: Nathan D
authors.initials: ND
authors.lastname: Wolfe
authors.forename: Forest
authors.initials: F
authors.lastname: Rohwer
mesh_terms: D001483:Base Sequence; D005260:Female; D052689:Gammapapillomavirus / Q000235:genetics*; D016679:Genome, Viral; D006801:Humans; D008297:Male; D056186:Metagenomics; D008969:Molecular Sequence Data; D030361:Papillomavirus Infections / Q000235:genetics / Q000821:virology; D012140:Respiratory Tract Diseases / Q000235:genetics / Q000821:virology
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