Novel Human Gammapapillomavirus Species in a Nasal Swab
Tung Gia Phan,a,bNguyen P. Vo,a,cMatti Aronen,dLaura Jartti,dTuomas Jartti,d,eEric Delwarta,b
Blood Systems Research Institute, San Francisco, California, USAa; Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California,
USAb; Pharmacology Department, School of Pharmacy, Ho Chi Minh City University of Medicine and Pharmacy, Ho Chi Minh City, Vietnamc; Department of Geriatrics,
Turku City Hospital, Turku, Finlandd; Department of Pediatrics, Turku University Hospital, Turku, Finlande
symptomswasgeneticallycharacterized.TheL1geneofHPV-Fin864shared <70%nucleotideidentitytootherreported ?-HPV
genomes,provisionallyqualifyingitasanewspeciesinthe Gammapapillomavirus genus.
Received 8 January 2013 Accepted 6 February 2013 Published 7 March 2013
Citation Phan TG, Vo NP, Aronen M, Jartti L, Jartti T, Delwart E. 2013. Novel human gammapapillomavirus species in a nasal swab. Genome Announc. 1(2):e00022-13.
Copyright © 2013 Phan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Address correspondence to Eric Delwart, firstname.lastname@example.org.
(HPVs) are highly diverse and have been classified into five gen-
era, each made of multiple species that are further divided into
types (1). A subset of HPVs cause anogenital or head and neck
cancers (2–4), while others cause noncancerous skin growths.
Other HPVs are commonly found on healthy human skin (5).
Here, we describe a novel papillomavirus genome from a viral
metagenomic analysis of a nasal swab from an elderly Finnish
patient who was hospitalized due to a respiratory infection of un-
known origin (negative for metapneumovirus, adenovirus, coro-
virus, rhinovirus, and bocavirus 1) (6). A complete circular DNA
viral genome was amplified using PCR and inverse PCR with
primers designed from 454 pyrosequences showing significant
BLASTn matches to HPVs. The circular genome (HPV-Fin864)
was 7,247 bp, with a G?C content of 37%. Seven distinct open
including the early genes E6, E7, E1, E2, and E4 and the late genes
L2 and L1. The long control region (LCR) between the L1 and E6
ORFs was 413 bp long, containing the TATA box (TATAAA) and
four consensus E2-binding sites (ACC-AGAAGC-GGT [ACC-
X6-GGT]) (7). Two characteristic zinc-binding domains (C-X2-
and one was identified in E7 (8). The E1 protein contained the
nucleotide-binding domain of the helicase (GPPGTGKS [G-X4-
GKT/S]) (9). The E1 protein contained a cyclin interaction RXL
motif required for viral replication (10).
The L1 gene of HPV-Fin864 showed a best BLASTn match to
HPV-156, a recently described ?-HPV species found in skin sam-
ples from immunocompetent patients (11). The Gammapapillo-
mavirus genus currently consists of 10 viral species known to in-
fect humans (1). Recently published genomes are expected to
increase that number (11, 13). According to the International
Committee on Taxonomy of Viruses (ICTV), the members of a
papillomavirus species should share at least 70% nucleotide iden-
showed that the L1 genes of HPV-156 and HPV-Fin864 shared
embers of the Papillomaviridae family are small double-
stranded circular DNA viruses. Human papillomaviruses
67% nucleotide identity. HPV-Fin864 therefore qualifies as a
novel species in the Gammapapillomavirus genus, pending ICTV
review. Given the association of human papillomaviruses with
benign or malignant proliferative diseases of cutaneous and mu-
cosal epithelia, the detection of HPV-Fin864 in the respiratory
fluid of a patient with respiratory symptoms may have been coin-
Nucleotide sequence accession number. The complete ge-
accession no. KC311731.
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