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J Gen Virol 89 (2008), 2467-2474; DOI 10.1099/vir.0.2008/001925-0

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Four novel human betapapillomaviruses of species 2 preferentially found in actinic keratosis

Natasa Vasiljevic, Kristina Hazard, Joakim Dillner and Ola Forslund

Department of Laboratory Medicine, Division of Medical Microbiology, Lund University, University Hospital, Malmö, Sweden

Correspondence
Ola Forslund
Ola.forslund{at}med.lu.se


   ABSTRACT
TOP
ABSTRACT
INTRODUCTION
METHODS
RESULTS
DISCUSSION
REFERENCES
 
Recent studies have suggested an association between human papillomaviruses (HPVs), particularly species 2 members of the genus Betapapillomavirus, and squamous cell carcinoma (SCC) of the skin. As most of these viruses are uncharacterized, molecular characterization and epidemiology are needed to advance our understanding of their significance in carcinogenesis. This study determined the complete genomes of four betapapillomaviruses of species 2 from skin lesions designated HPV-107, -110 and -111 and FA75[KI88-03], an isolate of an unpublished HPV type, and analysed their prevalence and viral loads in biopsies from SCC, actinic keratosis (AK), basal cell carcinoma, seborrhoeic keratosis and the healthy skin of 263 immunocompetent patients by HPV type-specific real-time PCR assays. Seventeen patients (6.5 %) harboured at least one of the four HPV types in their lesion, whereas seven patients (2.7 %) harboured one or more of the HPV types in healthy skin. Overall, the four viruses were more common in AK than in healthy skin (odds ratio 5.0, 95 % confidence interval 1.4–17.5), but the prevalence and viral loads were low. This characterization of HPV-107, -110 and -111 and FA75[KI88-03] expands the heterogeneity of members of species 2 of the genus Betapapillomavirus. However, as these types were found in only a few samples and in low amounts, a possible role in carcinogenesis remains elusive.

The GenBank/EMBL/DDBJ accession numbers for the sequences of isolates HPV-107 (FA85), HPV-110 (FA5), HPV-111 (FA51) and FA75[KI88-03] determined in this work are EF422221, EU410348, EU410349 and EU410347, respectively.


   INTRODUCTION
TOP
ABSTRACT
INTRODUCTION
METHODS
RESULTS
DISCUSSION
REFERENCES
 
Papillomaviruses (PVs) infect a large number of different species, including humans, cattle, rabbits, and non-human primates (Antonsson et al., 2003aDown; Shadan & Villarreal, 1993Down). In general, they are highly species specific, but occasional interspecies transmission has been observed between closely related species (Chambers et al., 2003Down; Martens et al., 2001Down). PVs have a tissue tropism for epithelial cells, either cutaneous or mucosal, and can cause infections in the skin or mucosal epithelium of the genital tract, oral pharynx and oesophagus (Doorbar, 2005Down). Among human PVs (HPVs) infecting the mucosal epithelium, 15 types are known as high-risk types and are important carcinogens in the development of anogenital and oral cancers (Woodman et al., 2007Down). The different PV genotypes have less than 90 % nucleotide sequence similarity in the open reading frame (ORF) of the major capsid protein L1 (de Villiers et al., 2004Down). To date, well over 100 different PV types have been characterized and classified phylogenetically into 16 genera (de Villiers et al., 2004Down). In addition, about 100 additional putative HPV types appear to exist, with sequence information so far available only from PCR amplimers (Berkhout et al., 1995Down; Forslund, 2007Down; Shamanin et al., 1994Down).

Non-melanoma skin cancers (NMSCs), comprising basal cell carcinoma (BCC) and squamous cell carcinoma (SCC), are the most prevalent malignancies in the Caucasian population (Oberyszyn, 2008Down; Stern, 1999Down). SCC accounts for up to 20 % of all deaths from skin cancer, whereas BCC has a relatively good prognosis (Ramos et al., 2004Down). Epidemiological studies have established a causal association between UV radiation and NMSC, as well as that fair skin and the immune status of the host are important risk factors (Boukamp, 2005Down; Preston & Stern, 1992Down; Reichrath, 2006Down). In addition, as cutaneous HPV infection is more prevalent at sun-exposed sites and, as the viral proteins affect the apoptotic pathway of the cell, infection is proposed to be a co-factor to UV irradiation in the development of NMSC (Forslund et al., 2007Down; Jackson et al., 2000Down).

NMSCs are common on sun-exposed sites in patients with the rare inherited genetic disease epidermodysplasia verruciformis (Jablonska & Majewski, 1994Down). These patients are highly susceptible to HPV infections (Kremsdorf et al., 1984Down; Orth et al., 1978Down), predominantly HPV-5 and -8, which belong to the genus Betapapillomavirus (Pfister, 2003Down; Pfister & Ter Schegget, 1997Down). These viruses are detectable both in skin cancers and in specimens of healthy skin from the general population (Antonsson et al., 2003aDown; Astori et al., 1998Down; Harwood & Proby, 2002Down), but a recent study has found that betapapillomaviruses of species 1 tend to be associated with benign skin lesions, whilst betapapillomaviruses of species 2 are more commonly found in skin cancers (Forslund et al., 2007Down). Four viruses of species 2 that were found in SCC samples in this recent study were the isolates FA5, FA51, FA7 and FA85, which had previously also been detected in samples from healthy skin (Antonsson et al., 2003aDown, bDown; Forslund et al., 1999Down).

The fact that many putative HPVs remain uncharacterized significantly impairs our ability to study the biological significance of the cutaneous viruses in more detail. Therefore, we characterized the four betapapillomavirus isolates previously found in skin cancers (Forslund et al., 2007Down) and investigated whether these viruses were medically significant by assaying their prevalence and viral load among patients with skin lesions.


   METHODS
TOP
ABSTRACT
INTRODUCTION
METHODS
RESULTS
DISCUSSION
REFERENCES
 
Cloning of novel types.
HPV-107 (isolate FA85), HPV-110 (isolate FA5) and HPV-111 (isolate FA51) were isolated from stripped punch biopsies and FA75[KI88-03] (isolate FA75) from a swab sample from immunocompetent patients included in the ‘Viraskin’ European case–control study of NMSC (Forslund et al., 2007Down). Isolate FA75[KI88-03] was collected from an SCC lesion on the ear of a 93-year-old male, HPV-107 was cloned from an actinic keratosis (AK) on the temple of a 76-year-old male, HPV-110 was isolated from the cheek of an 88-year-old female diagnosed with SCC in situ and HPV-111 was isolated from the ear of a 79-year-old female with the same diagnosis. These samples were used as templates in an Expand Long Template PCR System (Roche). The 25 µl PCR solution contained 2.5 µl extracted DNA, 0.5 µM each forward and reverse primer, 0.35 mM each dNTP (Roche Diagnostics), 1x Buffer I and 1.875 U Expand Long Template Enzyme mix. Primer pairs (Cybergene) used for complete genome amplification are listed in Table 1Down. PCRs were performed in a Hybaid PCR Express machine with simulated tube control using the following cycling conditions: 2 min at 94 °C; 10 cycles of 10 s at 94 °C, 30 s at 49 °C (FA75[KI88-03]), 58 °C (HPV-107), 55 °C (HPV-110) or 53 °C (HPV-111), and 10 min at 68 °C; 30 cycles of 15 s at 94 °C, 30 s at the same temperature as in the previous annealing step and 10 min at 68 °C with an extra 20 s per cycle; and a final incubation at 68 °C for 10 min.


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Table 1. Primers for long-range PCR amplification and probes for real-time PCR detection of HPV-107, -110 and -111 and FA75[KI88-03]

Primers and probes were designed from the L1 ORF.

 
The amplified DNA of HPV-107 and -110 was separated by electrophoresis in a 1 % IBI Agarose gel (Kodak) in TBE buffer and a band of approximately 8 kb was excised and purified using a QIAquick Gel Extraction kit (Qiagen). The amplicons of HPV-111 and FA75[KI88-03] were separated on E-Gel CloneWell agarose gels (Invitrogen) using an E-Gel iBase Power system (Invitrogen) and the DNA was collected in 20 µl water. The samples were concentrated by overnight evaporation and dissolved in 5 µl water. All the amplicons were cloned using a TOPO TA Cloning kit (Invitrogen).

Sequence analysis.
The cloned DNA of HPV-107 was used as template in primer-walking sequencing reactions. Clones containing the complete genomes of HPV-110 and -111 and FA75[KI88-03] were used in an EZ-Tn <TET-1> (Epicentre Biotechnologies) insertion reaction according to the kit manual. Briefly, 10 µl mix containing 0.2 µg plasmid, 0.025 pmol EZ-Tn5 <TET-1> transposon, 1 µl buffer and 1 µl transposase was incubated for 2 h at 37 °C. One microlitre of stop solution was added and the mix was incubated at 70 °C for 10 min. Two microlitres of the mix was used for transformation of One Shot TOP10 chemically competent Escherichia coli (Invitrogen). At least 30 colonies were picked and the plasmids sequenced using transposon-specific primers. Sequencing was carried out using an ABI Prism Big Dye Terminator Cycle Sequencing Ready Reaction kit (Applied Biosystems) and analysed on a 3730 automated sequencer (Applied Biosystems). The sequences were overlapped using BioEdit version 7.0.1 (Hall, 1999Down). The ORF of each protein was identified using BioEdit and proteins were compared with available amino acid sequences in GenBank using the BLAST server.

The clones and corresponding complete sequences were submitted to the International Reference Centre for Papillomaviruses at the German Cancer Research Centre, Heidelberg, Germany, where they were labelled: HPV-107 (FA85) (GenBank accession no. EF422221 [GenBank] ), HPV-110 (FA5) (GenBank accession no. EU410348 [GenBank] ) and HPV-111 (FA51) (GenBank accession no. EU410349 [GenBank] ). The sequence of FA75[KI88-03] was identical to an unpublished HPV type previously submitted to the Reference Center and was therefore deposited as isolate FA75[KI88-03] (GenBank accession no. EU410347 [GenBank] ).

Phylogenetic analysis.
Phylogenetic analysis was based on an L1 ORF alignment made using the CLUSTAL W multiple alignment in BioEdit of HPV-107, -110 and -111 and FA75[KI88-03] and all other betapapillomavirus types from species 2, as well as HPV-5, -49, -92 and -96. A neighbour-joining tree was generated using MEGA version 4 (Tamura et al., 2007Down) using 500 bootstrap replications and the Kimura two-parameter model.

Patient panel.
Stripped (Forslund et al., 2004Down) lesions and healthy skin biopsies from patients with the diagnoses AK (n=50), seborrhoeic keratosis (SK) (n=45), BCC (n=118) and SCC (n=50) were collected from 263 immunocompetent patients attending dermatology clinics in Sweden. Healthy skin biopsies were collected 10–15 cm from the lesion or proximally to the ear, depending on the location of the lesion. The samples were selected from a larger series of 489 patients (Forslund et al., 2007Down) and all four skin-lesion groups were matched for age and sex. All four groups had a mean age of 76±1 years. The distribution between men and women was 56±1 and 44±1 %, respectively, within each group.

The DNA from each biopsy was extracted using a phenol-free method (Forslund et al., 1999Down). To ensure the quality of the extracted DNA, all samples were checked for the presence of the β-globin gene (Hazard et al., 2006Down). Swab samples from the tops of the lesions (before stripping) were collected in 1 ml saline (Forslund et al., 2004Down).

Real-time PCR.
Primers and probes for quantitative PCR (Table 1Up) were designed in the L1 region, using Primer Express version 2.0 (Applied Biosystems).

Calculations of virus copy numbers for standard curves were based on spectrophotometric measurement of a plasmid containing the L1 ORF of HPV-107 and plasmids containing the FA fragments (the FA fragment constitutes about 30 % of the L1 ORF and is generated by primers FAP59 and FAP64; Forslund et al., 1999Down) of HPV-110 and -111 and FA75[KI88-03]. For the establishment of standard curves, serial logarithmic dilutions covering a range of 6 logs (from 105 copies to one copy per reaction) were employed using a solution of human placental DNA (10 ng µl–1) as diluent.

Primers and probes were tested for cross-hybridization with closely related types within species 2 of the genus Betapapillomavirus. The 25 µl PCR mixture contained 3.5 mM MgCl2 (Applied Biosystems), 1x Reaction buffer (Applied Biosystems), 0.2 mM each dNTP (Roche Diagnostics), 0.2 µM each primer (Cybergene; Table 1Up), 0.04 µM Taqman probe (Cybergene; Table 1Up), 0.625 U AmpliTaq Gold polymerase (Applied Biosystems) and 2.5 µl sample. Real-time PCR was carried out in a GeneAmp 5700 SDS (Applied Biosystems), using the following parameters: 2 min at 50 °C and 10 min at 95 °C, followed by 40 cycles of 15 s at 95 °C and 1 min at 60 °C. Human placental DNA (10 ng µl–1) and water (both from Sigma) were used as non-template controls in each run. The same parameters were used for the patient samples, which were diluted 1 : 2 in TE buffer before analysis. All samples positive for HPV-107, -110 or -111 or FA75[KI88-03] in the real-time PCRs were verified in triplicate using undiluted samples. The coefficient of variation (CV) for each sample was based on these verification runs. In addition, these amplicons were cloned and sequenced.

In order to determine the viral load, the number of cells in each sample was determined by quantification of the β-globin gene as described previously (Hazard et al., 2006Down). For all lesion biopsies found to be positive for any of the novel types, a swab sample taken from the top of the lesion before stripping was also analysed.

Statistical analysis.
Odds ratios (ORs) and 95 % confidence intervals (CIs) were estimated by comparing proportions using StatCalc within Epi Info version 3.4.3 (CDC, Atlanta, GA, USA). A two-sided Mann–Whitney U-test was used to test differences in viral load (SPSS version 16.0).

Study approval.
This study was approved by the ethics committees of Karolinska Institute and Lund University, Sweden. All patients gave informed consent.


   RESULTS
TOP
ABSTRACT
INTRODUCTION
METHODS
RESULTS
DISCUSSION
REFERENCES
 
Characteristics of the novel HPV types
The characteristics of the genomes of HPV-107 (FA85), HPV-110 (FA5), HPV-111(FA51) and isolate FA75[KI88-03] (FA75) are shown in Table 2Down. The complete genome of HPV-107 comprised 7562 bp with a G+C content of 41.1 mol% and was most closely related to HPV-80 with 74.3 % sequence identity in the L1 ORF. The complete genome of HPV-110 was 7423 bp with a G+C content of 40.0 mol% and was also most closely related to HPV-80 with 80.3 % sequence identity in the L1 ORF. The complete genome of HPV-111 comprised 7384 bp with a G+C content of 40.2 mol% and was most closely related to HPV-9 with 78.1 % sequence identity in the L1 ORF. The complete genome of isolate FA75[KI88-03] was 7401 bp with a G+C content of 39.4 mol%. The L1 ORF had two possible start sites, and alignments of the L1 ORF with other HPV types suggested that the second ATG was the most likely start codon. The L1 ORF, starting from the second ATG, showed the closest sequence identity to HPV-80 (75.8 %).


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Table 2. Sizes of putative proteins and nucleotide positions of the ORFs of HPV-107, -110 and -111 and FA75[KI88-03]

 
As HPV-107 and -110 and FA75[KI88-03] were all most closely related to HPV-80 but showed only 72 % (HPV-107 and -110), 77 % (HPV-107 and FA75[KI88-03]) and 74 % (FA75[KI88-03] and HPV-110) sequence similarity to each other in the L1 ORF, they constitute three separate genotypes. Phylogenetic analyses of the novel types classified them as betapapillomaviruses within species 2 (Fig. 1Down). Pairwise comparison of the novel L1 ORFs with types representative of each species showed that L1 shared the highest identity with the species 2 types (Table 3Down).


Figure 1
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Fig. 1. Neighbour-joining tree based on the alignment of the complete L1 ORFs of HPV-107, -110 and -111 and FA75[KI88-03] and closely related HPV types within species 2 of the genus Betapapillomavirus. HPV-5, -49, -92, -96 and -16 were added for orientation. The novel types are indicated by an asterisk.

 

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Table 3. Identity (%) between the L1 ORFs of the novel HPV types and types representing different Betapapillomavirus species

 
As expected, the genomes of the four characterized types contained seven ORFs (Table 2Up), potentially encoding five early genes (E6, E7, E1, E2 and E4) and two late genes (L2 and L1). The putative proteins of the novel HPV types also showed typical domains. The E6 and E7 proteins contained two and one conserved zinc-binding domains, CXXC(X)29CXXC (Ullman et al., 1996Down), respectively, separated by 36 aa. The E7 ORFs also contained a pRb-binding motif (LXCXE) (Radulescu et al., 1995Down). The ATP-binding site of the ATP-dependent helicase (GPPDTGKS) (Wilson et al., 2002Down) was conserved in the carboxyl-terminal region of E1 of HPV-110 and -111, whilst this binding site contained one mutation in HPV-107 and FA75[KI88-03] (GPPDSGKS; mutation indicated in bold). The E4 ORF contained a start codon and overlapped with the E2 ORF. Within the upstream regulatory region of all types, a TATA box (TATAA) was identified as well as putative binding sites for E2 (ACCN6GGT, four sites in HPV-107 and -111 and FA75[KI88-03], and three in HPV-110), NF-1 (TTGGC, four in HPV-110 and -111 and FA75[KI88-03], and nine in HPV-107) and AP-1 (TGACTAA, one in each type).

Real-time PCR
In order to verify the specificity of primers and probes, plasmid titration series ranging from 105 copies down to one copy per sample of plasmids containing HPV-9, -15, -17, -22, -23, -37 and -38 were all tested in real-time PCRs using the specific primers and probes for HPV-107, -110 and -111 and FA75[KI88-03]. No cross-reactivity was detected. Plasmid titration series with HPV-107, -110 and -111 and FA75[KI88-03] showed that the PCR assays had sensitivities of one viral copy per reaction (data not shown).

The presence and quantity of each HPV type are described in Table 4Down. A total of 19 patients (7.2 %) were positive for one or more of the investigated types in their healthy or lesion biopsy. Seventeen patients (6.5 %) harboured at least one HPV type in the lesion, whereas seven patients (2.7 %) harboured HPV in healthy skin (Table 4Down) (OR 2.53, 95 % CI 0.97–6.84). Viral load was investigated in biopsies from the HPV-positive lesions and corresponding swabs from the top of lesions, as well as in biopsies from HPV-positive healthy skin. Twelve out of 20 swab samples were HPV positive for the same virus as the lesion, and overall the viral loads were higher on top of the lesions (P<0.001) (Table 4Down). Furthermore, the viral loads did not differ between healthy skin and tumour biopsies (P=0.42). Amongst the lesions, the highest viral load was detected in an SK with three copies per cell, and the viral loads were significantly higher than in AK lesions (SK vs AK: P=0.03; SK vs BCC: P=0.10; SK vs SCC: P=0.25). No other differences in viral load were detected (AK vs BCC: P=0.72; AK vs SCC: P=0.41; BCC vs SCC: P=0.80).


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Table 4. Prevalence and viral loads of HPV-107, -110 and -111 and FA75[KI88-03] in skin lesions

 
In total, three (15.8 %) of the HPV-positive patients harboured multiple infections either in the lesion or in healthy skin. One AK was positive for all four HPV types tested. Three of the patients harboured different types in the lesion and the healthy skin biopsy (Table 4Up).

Considering the four viruses together, they were most frequently detected in AK lesions (6/50), which was significantly more often than in all healthy skin samples (7/263) (OR 5.0, 95 % CI 1.4–17.5). The prevalences in the other lesions were not significantly different from the prevalence in healthy skin: SK: OR 1.7, 95 % CI 0.3–8.5; BCC: OR 1.6, 95 % CI 0.4–5.8; SCC: OR 2.3, 95 % CI 0.5–10.5.


   DISCUSSION
TOP
ABSTRACT
INTRODUCTION
METHODS
RESULTS
DISCUSSION
REFERENCES
 
We found low prevalences and viral loads of four betapapillomaviruses of species 2 using highly sensitive and type-specific quantitative PCRs. Interestingly, an association of the four HPV types with AK was observed. This is in agreement with epidemiological reports linking this pre-cancerous stage to HPV infection (Boxman et al., 2001Down; Pfister et al., 2003Down). However, contrary to a previous report (Weissenborn et al., 2005Down), the viral loads were not higher in AK compared with the other lesion types investigated. The viral loads in the present study might be lower due to the tape stripping method used, which reduces superficial layers harbouring HPV DNA from the lesions (Cazzaniga et al., 2008Down; Forslund et al., 2004Down). Three (15.8 %) of the HPV-positive patients harboured multiple HPV infections with any of the four novel types. Of note, one patient with AK was positive for HPV-38 (Hazard et al., 2006Down) as well as HPV-107, -110 and -111 and FA75[KI88-03] in the lesion and in the swab sample taken from the top of the lesion, but not in the healthy skin biopsy, exemplifying that skin lesions may contain numerous HPV types. In the case of multiple infections, competing HPV types may distort the ability to detect all HPVs when using a general PCR method. Therefore, the use of type-specific primers should generate a more accurate result concerning the actual prevalence of a certain HPV type. As all four of the type-specific PCR systems developed were able to detect as few as one viral copy per reaction, the results of the present study provide more exact and sensitive results regarding the presence of these viruses in skin lesions. Nevertheless, only a low prevalence of the four novel types was observed, in line with other reports studying HPV in skin lesions (Asgari et al., 2008Down; Forslund et al., 2003Down).

The viral loads in the HPV-positive patients were low, ranging from one viral copy per ~35 000 cells to three copies per cell, a trend also observed by other groups (Bens et al., 1998Down; Meyer et al., 2001Down; Weissenborn et al., 2005Down). We found that SK lesions harboured higher amounts of virus than AK; however, due to the small number of observations, this finding requires further investigation. Also, when only minute amounts of virus are present, the possibility that results may reflect contamination rather than actual infection needs to be considered, in particular with regard to the remarkable viral loads of cutaneous HPV-88 described recently (Kullander et al., 2008Down). We found that many HPV-positive lesions contained higher amounts of virus on top of the lesion than in the lesion itself, in line with previous reports (Forslund et al., 2004Down). Surprisingly, in our study we also found lesions that contained significant amounts of virus even though HPV DNA was not detected on top of the lesion. Speculatively, the lack of detectable superficial HPV DNA might be due to an impaired productive life cycle in these lesions. In addition, a possible reason for the absence of HPV in the SK samples from the top of the lesion could be that the irregular anatomy of this lesion type makes it difficult to swab its entire surface, consequently leading to failure in detection.

In conclusion, the characterization of HPV-107, HPV-110, HPV-111 and HPV isolate FA75[KI88-03] expands our knowledge of the heterogeneity of members of species 2 of the genus Betapapillomavirus. However, a large number of additional putative types exist within this species and much more effort will be required to elucidate fully the medical implications of these viruses.


   ACKNOWLEDGEMENTS
 
HPV plasmids were kindly provided by Dr E.-M. de Villiers (HPV-37 and -38), Deutsches Krebsforschungszentrum, Heidelberg, Germany, and Dr G. Orth (HPV-9, -15, -17, -22 and -23), Institut Pasteur, Paris, France. This study was supported by grants from the European Commission (‘Viraskin’ QLK2-CT-2002-01500), the Science Council of Sweden, the Swedish Cancer Society, Scania Regional Council and the Cancer Foundation of the University Hospital, Malmö.


   REFERENCES
TOP
ABSTRACT
INTRODUCTION
METHODS
RESULTS
DISCUSSION
REFERENCES
 
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Received 7 March 2008; accepted 15 June 2008.


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