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, email@example.com.
(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.
1. Bernard HU, Burk RD, Chen Z, van Doorslaer K, Hausen Hz, de
Villiers EM. 2010. Classification of papillomaviruses (PVs) based on 189
PV types and proposal of taxonomic amendments. Virology 401:70–79.
2. O’Rorke MA, Ellison MV, Murray LJ, Moran M, James J, Anderson LA.
2012. Human papillomavirus related head and neck cancer survival: a
systematic review and meta-analysis. Oral Oncol. 48:1191–1201.
3. Chelimo C, Wouldes TA, Cameron LD, Elwood JM. 2013. Risk factors
for and prevention of human papillomaviruses (HPV), genital warts and
cervical cancer. J. Infect. 66:207–17.
4. Gillison ML, Alemany L, Snijders PJ, Chaturvedi A, Steinberg BM,
Schwartz S, Castellsagué X. 2012. Human papillomavirus and diseases of
the upper airway: head and neck cancer and respiratory papillomatosis.
Vaccine 30(Suppl 5):F34–F54.
5. Antonsson A, Erfurt C, Hazard K, Holmgren V, Simon M, Kataoka A,
Hossain S, Håkangård C, Hansson BG. 2003. Prevalence and type spec-
continents. J. Gen. Virol. 84:1881–1886.
6. Allander T, Jartti T, Gupta S, Niesters HG, Lehtinen P, Osterback R,
Vuorinen T, Waris M, Bjerkner A, Tiveljung-Lindell A, van den Hoo-
gen BG, Hyypiä T, Ruuskanen O. 2007. Human bocavirus and acute
wheezing in children. Clin. Infect. Dis. 44:904–910.
7. McBride AA, Romanczuk H, Howley PM. 1991. The papillomavirus E2
regulatory proteins. J. Biol. Chem. 266:18411–18414.
8. Mavromatis KO, Jones DL, Mukherjee R, Yee C, Grace M, Münger K.
1997. The carboxyl-terminal zinc-binding domain of the human papillo-
mavirus E7 protein can be functionally replaced by the homologous se-
quences of the E6 protein. Virus Res. 52:109–118.
Genome Announcements March/April 2013 Volume 1 Issue 2 e00022-13genomea.asm.org 1
9. Titolo S, Pelletier A, Sauvé F, Brault K, Wardrop E, White PW, Amin
A, Cordingley MG, Archambault J. 1999. Role of the ATP-binding do-
main of the human papillomavirus type 11 E1 helicase in E2-dependent
binding to the origin. J. Virol. 73:5282–5293.
10. Ding Q, Li L, Whyte P. 2013. Human papillomavirus 18 E1^E4 protein
11. Chouhy D, Bolatti EM, Piccirilli G, Sanchez A, Fernandez Bussy R, Giri
AA. 7 November 2012. Identification of HPV-156, the prototype of a new
human gammapapillomavirus species, by a generic and highly sensitive
PCR strategy for long DNA fragments. J. Gen. Virol. [Epub ahead of
12. de Villiers EM, Fauquet C, Broker TR, Bernard HU, zur Hausen H.
2004. Classification of papillomaviruses. Virology 324:17–27.
13. Li J, Cai H, Xu Z, Wang Q, Hang D, Shen N, Liu M, Zhang C, Abliz A,
Ke Y. 2012. Nine complete genome sequences of cutaneous human pap-
illomavirus genotypes isolated from healthy skin of individuals living in
rural He Nan province, China. J. Virol. 86:11936.
Phan et al.
2 genomea.asm.orgMarch/April 2013 Volume 1 Issue 2 e00022-13