Papillomaviridae - v201911


Papillomaviridae - v201911

Papillomaviridae

Koenraad Van Doorslaer​, Zigui Chen​, Hans-Ulrich Bernard, Paul K. S. Chan​, Rob DeSalle​, Joakim Dillner, Ola Forslund, Takeshi Haga, Alison A. McBride8, Luisa L. Villa and Robert D. Burk

Chapter contents

Posted June 2018

Papillomaviridae: The family

Member taxa

Supporting information

  • Authors - corresponding author: Koenraad Van Doorslaer (vandoorslaer@email.arizona.edu)
  • Resources - web resources, sequence alignments and tree files
  • Further reading - reviews and additional information
  • References

Citation 

A summary of this ICTV Report chapter has been published as an ICTV Virus Taxonomy Profile article in the Journal of General Virology, and should be cited when referencing this online chapter as follows:

Van Doorslaer, K., Chen, Z., Bernard, H., Chan, P.K.S, DeSalle, R., Dillner, J., Forslund, O., Haga, T., McBride, A.A., Villa, L.L., Burk, R.D., and ICTV Report Consortium. 2018, ICTV Virus Taxonomy Profile: Papillomaviridae, Journal of General Virology, 99, 989–990.

Summary

The Papillomaviridae is a family of small, non-enveloped viruses with double stranded DNA genomes of 5,748 bp to 8,607 bp. Their classification is based on pairwise nucleotide sequence identity across the L1 open reading frame. Members of the Papillomaviridae primarily infect mucosal and keratinized epithelia, and have been isolated from fish, reptiles, birds and mammals. Despite a long co-evolutionary history with their hosts, some papillomaviruses are pathogens of their natural host species.

Table 1.Papillomaviridae. Characteristics of the family Papillomaviridae.

Characteristic

Description

Typical member

human papillomavirus 16 (K02718), species Alphapapillomavirus 9,  genus Alphapapillomavirus, subfamily Firstpapillomavirinae

Virion

Non-enveloped, 55 nm, icosahedral

Genome

Circular dsDNA. Genome varies from 5,748 bp to 8,607 bp.

Replication

Bidirectional theta replication

Translation

Early and late transcripts, alternative splicing, alternative open reading frames

Host Range

Mammals, reptiles, birds, and fish

Taxonomy

Two subfamilies include >50 genera and >130 species

Virion

Morphology

Papillomavirus virions are non-enveloped. The viral capsid is ~600 Å in diameter and consists of 360 copies (arranged as 72 pentamers) of the major capsid protein, L1, and ~12 molecules of the L2 minor capsid protein (Figure 1.Papillomaviridae; (Finnen et al., 2003)). Expression of recombinant L1 with or without L2 allows for self-assembly of virus-like particles (VLPs). Each capsid packages a single copy of the viral circular dsDNA. The packaged viral DNA is associated with core histone proteins (Larsen et al., 1987).

Figure 1.Papillomaviridae. (Left) Atomic rendering of a papillomavirus capsid. Derived from an image reconstruction from Cryo-electron microscopy of human papillomavirus type 16 at 4.5 Å resolution and colored according to the radial coloring scheme shown (PDB: 5KEP; (Guan et al., 2017)). (Center) Schematic diagram representing the 72 capsomers in a T=7 arrangement of a papillomavirus capsid. The icosahedral structure is composed solely of pentameric capsomeres for a total of 360 capsid proteins. (Right) Negative-contrast electron micrograph of human papillomavirus 1 (HPV1) virions. The bar represents 100 nm.

Physicochemical and physical properties

The virion Mr is 47×106. Buoyant density of virions in sucrose and CsCl gradients is 1.20 and 1.34–1.35 g cm−3, respectively. Virion S20,W is 300. Virions are resistant to a wide array of environmental and chemical treatments (Meyers et al., 2014).

Nucleic acid

The papillomavirus genome is approximately 7,500 bp. Viral genomes vary from 5,748 bp (Sparus aurata papillomavirus type 1; SaPV1) to 8,607 bp (canine papillomavirus type 1; CPV1). The genomes have an average GC content of about 42% (36–59%).

Proteins

Papillomavirus gene expression is tightly regulated at the level of transcription and RNA processing, including alternative mRNA polyadenylation and splicing (Schwartz 2013). A typical papillomavirus encodes six to nine proteins (Figure 2.Papillomaviridae). However, the ancestral papillomavirus may have only contained a core set of four proteins (E1, E2, L1, and L2). Temporal expression of the viral genome is associated with tissue differentiation (Figure 3.Papillomaviridae). The viral DNA helicase (E1) is the only viral enzyme, and is essential for replication and amplification of the viral chromosome in the nucleus of infected cells. (Bergvall et al., 2013). The viral E2 protein is the master regulator of the viral life cycle, and plays key roles in transcriptional regulation, initiation of DNA replication and partitioning the viral genome (McBride 2013). The E1^E4 gene product is typically translated from a spliced mRNA fusing approximately the first four E1 codons to the E4 ORF, present in an alternative reading frame to the E2 ORF (Doorbar 2013). A subset of viral mRNA encodes a short, hydrophobic, transmembrane protein, E5. Other than hydrophobicity, there is low sequence similarity among different E5 proteins (DiMaio and Petti 2013). The E5 proteins can be further divided into different classes based on phylogeny and hydrophobic profiles (Bravo and Alonso 2004). E5 proteins are typically encoded in the 3ʹ-end of the early coding region. However, hydrophobic proteins, located in other parts of the viral genome have also been described. Designated as E10, these non-E5 hydrophobic proteins either overprint the E6 ORF, or are located in this region in the absence of an E6 gene (Van Doorslaer and McBride 2016). The productive phase of the viral life cycle occurs in differentiated cells that have exited the cell cycle. In order to complete the viral life cycle, the virus needs to uncouple replication from differentiation (Figure 3). The E6 and E7 proteins have been shown to play key roles in usurping the cellular environment to allow for replication. The E6 protein contains two zinc-binding motifs essential for its function (Vande Pol and Klingelhutz 2013). The E7 amino terminus contains regions of similarity to conserved regions (CR) 1 and CR2 of the mastadenovirus E1A protein, and the polyomavirus large T antigen (Roman and Munger 2013). The E7 C-terminus contains a single zinc-binding motif homologous to the E6 motifs (Van Doorslaer 2013). The E6 and E7 proteins appear to be essential for members of the genus Alphapapillomavirus. Remarkably, the E6 and E7 proteins are not encoded by all papillomaviruses (Van Doorslaer 2013). The E8 exon is embedded within E1, and utilizes the same splice acceptor site as E1^E4 mRNA, generating mRNA for the E8^E2 protein. The E8^E2 viral repressor protein is present in essentially every known papillomavirus. E8^E2 inhibits viral replication and gene expression. Upon cellular differentiation, the viral capsid proteins L1 and L2 are expressed. The major capsid protein L1 is the structural component of the viral capsid (Buck et al., 2013). The minor capsid protein L2 plays an active role in viral assembly and throughout the infectious process (Wang and Roden 2013).

Figure 2.Papillomaviridae. (B) Diagram of the human papillomavirus 16 genome. The viral dsDNA is indicated. The outer boxes indicate the protein-coding open reading frames. Dotted lines represent intron sequences. The black circle represents the viral origin of replication (ori). 

Figure 3.Papillomaviridae. Organization of the viral lifecycle. The different layers of the epithelium are shown on the left. The timing of expression and associated protein levels are summarized using triangles. Viral genome maintenance is facilitated by the expression of E6 and E7 together with E1 and E2. Increased levels of the viral replication proteins facilitate viral genome amplification. The expression of L1 and L2 allows for the formation of infectious virions (virus assembly). 

Genome organization and replication

Transcription of the circular virus genome occurs from only one DNA strand. The viral genome can be divided into three functional regions. The early region encodes viral proteins involved in transcription, replication, and manipulation of the cellular milieu. The late region encodes the capsid proteins L1, and L2. The upstream regulatory region (URR or LCR) is located between the L1 and E6 ORFs and contains the viral origin of replication as well as binding sites for viral and cellular transcription factors.

The viral replication cycle consists of three distinct phases of replication. Initial limited viral DNA amplification is supported by the viral E1 and E2 replication proteins. The viral E2 protein binds to its binding sites in the viral origin of replication, recruiting the viral E1 helicase allowing for replication. This initial burst of replication is followed by maintenance replication, during which the viral genome is maintained at a relatively low, but constant copy number in the proliferating cells of a clonally expanded population of infected cells. Finally, as an infected cell completes cellular differentiation, there is a switch towards differentiation-dependent genome amplification and eventual generation of progeny virions (McBride 2008). During maintenance replication, the virus needs to establish an S-phase like state in differentiated cells. Through a plethora of protein-protein interactions, the viral E6 and E7 proteins usurp the cellular environment, allowing for viral replication in differentiated cells. Remarkably, recent work has highlighted that different genera may induce this pseudo-S-phase through different mechanisms (White et al., 2012, Meyers et al., 2017, Brimer et al., 2017). The maintenance phase of the viral life cycle can last for months to years. In addition to regulating replication, the viral E2 protein plays a key role during maintenance by ensuring that the viral genomes are faithfully partitioned into the daughter cells. In the top layers of the differentiated epithelia, the viral DNA is amplified to a high copy number. The vegetative phase of the viral life-cycle requires the cellular DNA Damage Response (Bristol et al., 2017). The viral capsid proteins self-assemble into particles encapsidating the viral DNA. As the cells slough off into the environment, infectious virions are released, completing the viral life cycle.

Antigenicity 

Antigenicity is primarily determined by the major capsid protein, L1. Following vaccination, neutralizing epitopes typically map to a single variable loop (Ludmerer et al., 1997), or more commonly two non-contiguous loops (McClements et al., 2001, Christensen et al., 2001). Viral immunity appears to be highly species-specific, and there is only limited cross-protection, even to types within the same viral species. Furthermore, following natural infection, only approximately half of women seroconvert within 18 months following exposure (Carter et al., 2000). Prophylactic vaccines induce high-titer neutralizing antibodies restricted to a subset of (oncogenic) types within the genus Alphapapillomavirus. The current vaccines do not protect against types belonging to different genera. Vaccination with L2 (minor capsid protein) derived vaccines induces low-titer, yet broadly cross-neutralizing antibodies to heterologous PV types. These vaccines provide cross-protection in animal challenge models (Schellenbacher et al., 2017). Efforts to broaden the human papillomavirus (HPVvaccines using L2 (poly)-peptides are currently underway (Schellenbacher et al., 2017).

Biology

Epidemiological and biological data is primarily available for the viral types belonging to the genus Alphapapillomavirus, and specifically those viruses associated with (cervical) cancer. An estimated 79 million Americans are infected, with an additional 14 million new HPV infections occurring every year (CDC 2017). HPV is spread by skin-to-skin contact, and infections with genital human papillomaviruses are the most common sexually transmitted infection (STI).

Papillomaviruses primarily infect epithelial cells. Following a micro-abrasion, the incoming virion complexes with extracellular heparin sulfate proteoglycans on the basement membrane. This interaction results in conformational changes in the L1 and L2 capsid proteins, in turn allowing for the transfer of the virion to an unknown entry receptor. Following furin cleavage of L2, the virion becomes internalized using a process that shares similarities with macropinocytosis (Campos 2017). Early trafficking events involve transporting virions from early endosomes into acidic late endosome and multivesicular bodies. This allows for capsid disassembly and uncoating. During this process, the viral DNA is believed to remain bound to L2. The L2-DNA complex traffics to the trans-Golgi network, remaining there until the onset of mitosis. During mitosis, the trans-Golgi network naturally vesiculates, and the vesicle-bound viral DNA finds its way into the nucleus. By metaphase, the viral DNA is associated with host chromosomes. Following mitosis, the viral DNA can be seen to be associated with nuclear ND10 bodies (Campos 2017).

As the life cycle is completed in cells already destined for cell death, papillomaviruses are not viremic and are hidden from the immune system. In addition, papillomaviruses have evolved a plethora of mechanisms actively limiting the interferon response, a key antiviral defense mechanism (Kanodia et al., 2007). Overall, papillomaviruses appear to effectively evade the innate immune response, thereby delaying the activation of adaptive immunity. In turn, this likely plays an important role in persistence of the virus for months or even years.

Pathogenicity 

Healthy skin harbors a large spectrum of different papillomavirus types belonging to different genera. While the majority of viral infections are subclinical, certain viral types cause (cervical, anal and/or oral pharyngeal) cancers, and have been associated with an increasing number of squamous cell carcinomas at specific sites. Based on their tropism, papillomaviruses can be roughly divided into cutaneous or mucocutaneous. Epidemiologically, the mucocutaneous HPV types can be further subdivided based on whether they are associated with benign or malignant lesions (Cubie 2013). Importantly, even in the case of viral types associated with specific pathologies, the majority of infections still present as subclinical. In the cervical environment, approximately 90% of HPV infections are cleared within two years post infection. Where clearance depends on an effective cell-mediated immune response, it is not clear why some infections are able to persist. Importantly, in the case of the oncogenic alphapapillomavirus types, persistent infection, not an incident infection is the main risk factor for progression towards cancer (Burk et al., 2009). Indeed, cellular transformation and viral replication are mutually exclusive, suggesting that oncogenic progression is not a typical outcome of infection. 

Subfamily demarcation criteria

The current taxonomic classification of papillomaviruses is based on the nucleotide sequence of the L1 ORF. The L1 ORF of members of different subfamilies shares less than 45% sequence identity.

Genus demarcation criteria 

The original criteria distinguishing genera stated: “Most types within a PV genus show less than 60% sequence identity to types of other genera based on global multiple sequence or pairwise alignments of the L1 genes. Nevertheless, the suggested percentage identities that define PV genera have to be taken as general, but not absolute criteria as curation is necessary” (de Villiers et al., 2004). Practically, papillomavirus genera are primarily delineated by visual inspection of phylogenetic trees derived from concatenated E1, E2, L1, and L2 nucleotide sequences. Efforts are underway to refine the papillomavirus classification scheme.

Derivation of names

Papilloma: from Latin papilla, “nipple, pustule”, and Greek suffix -oma, used to form nouns denoting “tumors”. Viral genera belonging to the subfamily of the Firstpapillomavirinae are named according to the Greek alphabet (e.g., Alphapapillomavirus). The prefixes “Dyo-” and “Treis-” are used to accommodate the growing list of viral genera within this subfamily. The names Alphapapillomavirus, Betapapillomavirus, and Gammapapillomavirus have been used for the genera containing papillomaviruses that infect humans and are not used in combination with the Dyo- or Treis- prefixes. Genera within the Secondpapillomavirinae are named according to the Semitic abjads. Currently, the Secondpapillomavirinae contain a single genus, bearing the first letter of this alphabet (transcribed as “A” in Latin): Alefpapillomavirus.

Phylogenetic relationships

Phylogenetic analysis of papillomaviruses based on the concatenated alignment of four coding sequences (E1, E2, L2, and L1) from isolates from the type species of each of the  53 genera (Figure 4. Papillomaviridae) supports the existence of at least two distinct subfamilies (Firstpapillomavirinae and Secondpapillomavirinae). Likewise, this phylogeny, and that of an analysis of all 133 species (tree available in Resources), corroborates many genera and species within the Firstpapillomavirinae. However, not all genera or species are equally supported. There may be a need in the near future to base the taxonomy of the Papillomaviridae on the phylogenetic tree.

Figure 4.Papillomaviridae. Phylogenetic analysis of isolates from the type species of each papillomavirus genus. The E1, E2, L2, and L1 nucleotide sequences were translated into amino acids and aligned using MUSCLE v7.221 (Edgar 2004). A maximium likelihood tree of concatenated nucleotide sequences was produced using the optimal model of evolution (GTR + G) as determined within MEGA 7 (Kumar et al., 2016). Nodes supported by >70% of bootstrap replicates are indicated.This phylogenetic tree and corresponding sequence alignment are available to download from the Resources page, along with a complete tree including an additional 290 isolates.

Similarity with other taxa 

There is evidence of recombination between a polyomavirus and a papillomavirus. The unclassified bandicoot papillomatosis carcinomatosis virus types 1 and 2 (BPCV1 and BPCV2) have circular dsDNA genomes encoding large and small T antigens related to avian polyomaviruses and capsid proteins (L1 and L2) of a putative marsupial papillomavirus.


Subfamily: Firstpapillomavirinae


Genus: Alphapapillomavirus

Distinguishing features

Members of this genus preferentially infect the oral or anogenital mucosa in humans and primates. Members of certain species (e.g. Alphapapillomavirus 2 and Alphapapillomavirus 4) are also found in lesions of cutaneous sites. Specific members of certain species (e.g. Alphapapillomavirus 7 and Alphapapillomavirus 9) are considered as oncogenic in view of their regular presence in malignant tissue. All members of this genus code for a hydrophobic E5 protein, located at the 3′-end of the early region.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% nucleotide identity across the L1 ORF to papillomaviruses within the genus (Figure 1.Alphapapillomavirus).

Figure 1.Alphapapillomavirus. Phylogenetic tree of members of the genus Alphapapillomavirus. The E1, E2, L2, and L1 nucleotide sequences of 343 papillomavirus isolates including representatives of all species and genera within the Papillomaviridae family were aligned as amino acid sequences using MUSCLE v7.221 (Edgar 2004). JModeltest2 (Darriba et al., 2012) was used to determine the optimal model of evolution (GTR + I + G) for the concatenated nucleotide sequences. Maximum likelihood (ML) trees were constructed using RAxML MPI v8.2.9 (Stamatakis 2006) implementing the GTR substitution model. ML bootstrap analysis used the autoMRE-based stopping criterion in RAxML. Following tree construction (tree available in the Resources section of the Papillomaviridae Report), the subtree corresponding to the genus Alphapapillomavirus was isolated. Tips are labelled with virus names and accession numbers; nodes are labelled with bootstrap support values.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Alphapapillomavirus 1 human papillomavirus 32 X74475 NC_001586 Complete genome HPV32
Alphapapillomavirus 1 human papillomavirus 42 M73236 HPV42
Alphapapillomavirus 2 human papillomavirus 10 X74465 NC_001576 Complete genome HPV10
Alphapapillomavirus 2 human papillomavirus 160 TM AB745694 HPV160
Alphapapillomavirus 2 human papillomavirus 94 AJ620211 HPV94
Alphapapillomavirus 2 human papillomavirus 125 SIBX9 FN547152 HPV125
Alphapapillomavirus 2 human papillomavirus 117 a_wart10 GQ246950 HPV117
Alphapapillomavirus 2 human papillomavirus 78 XS2 KC138720 HPV78
Alphapapillomavirus 2 human papillomavirus 28 U31783 HPV28
Alphapapillomavirus 2 human papillomavirus 29 U31784 HPV29
Alphapapillomavirus 2 human papillomavirus 3 X74462 HPV3
Alphapapillomavirus 2 human papillomavirus 77 Y15175 HPV77
Alphapapillomavirus 3 human papillomavirus 61 U31793 NC_001694 Complete genome HPV61
Alphapapillomavirus 3 human papillomavirus 83 AF151983 HPV83
Alphapapillomavirus 3 human papillomavirus 84 CY10-452 AF293960 HPV84
Alphapapillomavirus 3 human papillomavirus 86 AF349909 HPV86
Alphapapillomavirus 3 human papillomavirus 89 AF436128 HPV89
Alphapapillomavirus 3 human papillomavirus 87 AJ400628 HPV87
Alphapapillomavirus 3 human papillomavirus 81 AJ620209 HPV81
Alphapapillomavirus 3 human papillomavirus 62 Qv18091 AY395706 HPV62
Alphapapillomavirus 3 human papillomavirus 102 Qv34077 DQ080083 HPV102
Alphapapillomavirus 3 human papillomavirus 114 GQ244463 HPV114
Alphapapillomavirus 3 human papillomavirus 72 X94164 HPV72
Alphapapillomavirus 4 human papillomavirus 2 X55964 NC_001352 Complete genome HPV2
Alphapapillomavirus 4 human papillomavirus 57 X55965 HPV57
Alphapapillomavirus 4 human papillomavirus 27 X74473 HPV27
Alphapapillomavirus 5 human papillomavirus 26 X74472 NC_001583 Complete genome HPV26
Alphapapillomavirus 5 human papillomavirus 69 AB027020 HPV69
Alphapapillomavirus 5 human papillomavirus 82 AB027021 HPV82
Alphapapillomavirus 5 human papillomavirus 51 M62877 HPV51
Alphapapillomavirus 6 human papillomavirus 30 X74474 NC_038889 Complete genome HPV30
Alphapapillomavirus 6 human papillomavirus 66 U31794 HPV66
Alphapapillomavirus 6 human papillomavirus 53 X74482 HPV53
Alphapapillomavirus 6 human papillomavirus 56 X74483 HPV56
Alphapapillomavirus 7 human papillomavirus 18 X05015 NC_001357 Complete genome HPV18
Alphapapillomavirus 7 human papillomavirus 85 AF131950 HPV85
Alphapapillomavirus 7 human papillomavirus 68 Plasmid 952 DQ080079 HPV68
Alphapapillomavirus 7 human papillomavirus 97 Qv28597 DQ080080 HPV97
Alphapapillomavirus 7 human papillomavirus 39 M62849 HPV39
Alphapapillomavirus 7 human papillomavirus 70 U21941 HPV70
Alphapapillomavirus 7 human papillomavirus 45 X74479 HPV45
Alphapapillomavirus 7 human papillomavirus 59 X77858 HPV59
Alphapapillomavirus 8 human papillomavirus 7 X74463 NC_001595 Complete genome HPV7
Alphapapillomavirus 8 human papillomavirus 91 AF419318 HPV91
Alphapapillomavirus 8 human papillomavirus 43 AJ620205 HPV43
Alphapapillomavirus 8 human papillomavirus 40 X74478 HPV40
Alphapapillomavirus 9 human papillomavirus 16 K02718 NC_001526 Complete genome HPV16
Alphapapillomavirus 9 human papillomavirus 67 D21208 HPV67
Alphapapillomavirus 9 human papillomavirus 58 GN479 D90400 HPV58
Alphapapillomavirus 9 human papillomavirus 31 J04353 HPV31
Alphapapillomavirus 9 human papillomavirus 33 M12732 HPV33
Alphapapillomavirus 9 human papillomavirus 35 X74477 HPV35
Alphapapillomavirus 9 human papillomavirus 52 X74481 HPV52
Alphapapillomavirus 10 human papillomavirus 6 X00203 NC_001355 Complete genome HPV6
Alphapapillomavirus 10 human papillomavirus 74 AE10 AF436130 HPV74
Alphapapillomavirus 10 human papillomavirus 11 M14119 HPV11
Alphapapillomavirus 10 human papillomavirus 44 U31788 HPV44
Alphapapillomavirus 10 human papillomavirus 13 X62843 HPV13
Alphapapillomavirus 10 Pan paniscus papillomavirus 1 X62844 PpPV1
Alphapapillomavirus 11 human papillomavirus 34 X74476 NC_001587 Complete genome HPV34
Alphapapillomavirus 11 human papillomavirus 73 X94165 HPV73
Alphapapillomavirus 12 Macaca mulata papillomavirus 1 M60184 NC_001678 Complete genome MmPV1
Alphapapillomavirus 12 Macaca fascicularis papillomavirus 7 Mac18 EF558838 MfPV7
Alphapapillomavirus 12 Macaca fascicularis papillomavirus 3 Mac26 EF558839 MfPV3
Alphapapillomavirus 12 Macaca fascicularis papillomavirus 6 Mac39 EF558840 MfPV6
Alphapapillomavirus 12 Macaca fascicularis papillomavirus 4 Mac54 EF558841 MfPV4
Alphapapillomavirus 12 Macaca fascicularis papillomavirus 8 Mac70 EF558842 MfPV8
Alphapapillomavirus 12 Macaca fascicularis papillomavirus 5 Mac76 EF558843 MfPV5
Alphapapillomavirus 12 Macaca fascicularis papillomavirus 10 Mac616 EU490515 MfPV10
Alphapapillomavirus 12 Macaca fascicularis papillomavirus 9 Mac592 EU490516 MfPV9
Alphapapillomavirus 12 Macaca fascicularis papillomavirus 11 Mac1637 GQ227670 MfPV11
Alphapapillomavirus 12 Papio hamadryas papillomavirus 1 Mac2085 JF304764 PhPV1
Alphapapillomavirus 12 Macaca fuscata papillomavirus 1 OSCC1 KT944080 MfuPV1
Alphapapillomavirus 13 human papillomavirus 54 U37488 NC_001676 Complete genome HPV54
Alphapapillomavirus 14 human papillomavirus 71 AB040456 NC_039089 Complete genome HPV71
Alphapapillomavirus 14 human papillomavirus 90 AY057438 HPV90
Alphapapillomavirus 14 human papillomavirus 106 Qv28897 DQ080082 HPV106
Alphapapillomavirus 14 Colobus guereza papillomavirus 1 GU014532 CgPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Related, unclassified viruses

Virus name

Accession number

Virus abbreviation

human papillomavirus mEV06c12b

MF588676

HPV-mEV06c12b

Virus names and virus abbreviations are not official ICTV designations.

Genus: Betapapillomavirus

Distinguishing features

Members of this genus typically cause latent infections. However, in patients with specific (immune) disorders, members of this genus can cause warts or progress to cutaneous squamous cell carcinomas (SCC). Patients suffering from the rare disease epidermodysplasia verruciformis (EV) are at a higher risk of developing SCC, and certain members of the genus Betapapillomavirus have been implicated (Arnold and Hofbauer 2012). Recent evidence suggests that, in the general population, certain betapapillomavirus types may be a co-factor in the development of SCC. Remarkably, these betapapillomavirus types are not detected in most SSC, suggesting that viral proteins may not be required to maintain the malignant SCC lesions. Members of the genus Betapapillomavirus are also the most common human papillomavirus (HPV) types found in the human oral cavity and some have been prospectively associated with oropharyngeal cancer development (Agalliu et al., 2016).

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus (Figure 1.Betapapillomavirus). 

Figure 1.Betapapillomavirus. Phylogenetic tree of members of the genus Betapapillomavirus. The E1, E2, L2, and L1 nucleotide sequences of 343 papillomavirus isolates including representatives of all species and genera within the Papillomaviridae family were aligned as amino acid sequences using MUSCLE v7.221 (Edgar 2004). JModeltest2 (Darriba et al., 2012) was used to determine the optimal model of evolution (GTR + I + G) for the concatenated nucleotide sequences. Maximum likelihood (ML) trees were constructed using RAxML MPI v8.2.9 (Stamatakis 2006) implementing the GTR substitution model. ML bootstrap analysis used the autoMRE-based stopping criterion in RAxML. Following tree construction (tree available in the Resources section of the Papillomaviridae Report), the subtree corresponding to the genus Betapapillomavirus was isolated. Tips are labelled with virus names and accession numbers; nodes are labelled with bootstrap support values.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Betapapillomavirus 1 human papillomavirus 5 M17463 NC_001531 Complete genome HPV5
Betapapillomavirus 1 human papillomavirus 93 AY382778 HPV93
Betapapillomavirus 1 Macaca fascicularis papillomavirus 1 EF028290 MfPV1
Betapapillomavirus 1 human papillomavirus 98 GA1-3 FM955837 HPV98
Betapapillomavirus 1 human papillomavirus 99 GA3-1 FM955838 HPV99
Betapapillomavirus 1 human papillomavirus 105 DL294 FM955841 HPV105
Betapapillomavirus 1 human papillomavirus 118 b_wart3 GQ246951 HPV118
Betapapillomavirus 1 human papillomavirus 124 NJ3900 GQ845446 HPV124
Betapapillomavirus 1 Colobus guereza papillomavirus 2 GU014533 CgPV2
Betapapillomavirus 1 human papillomavirus 143 CL3220 HM999995 HPV143
Betapapillomavirus 1 human papillomavirus 152 Muc17.1 JF304768 HPV152
Betapapillomavirus 1 human papillomavirus 8 M12737 HPV8
Betapapillomavirus 1 human papillomavirus 47 M32305 HPV47
Betapapillomavirus 1 human papillomavirus 20 U31778 HPV20
Betapapillomavirus 1 human papillomavirus 21 U31779 HPV21
Betapapillomavirus 1 human papillomavirus 24 U31782 HPV24
Betapapillomavirus 1 human papillomavirus 36 U31785 HPV36
Betapapillomavirus 1 human papillomavirus 12 X74466 HPV12
Betapapillomavirus 1 human papillomavirus 14 X74467 HPV14
Betapapillomavirus 1 human papillomavirus 19 X74470 HPV19
Betapapillomavirus 1 human papillomavirus 25 X74471 HPV25
Betapapillomavirus 2 human papillomavirus 9 X74464 NC_001596 Complete genome HPV9
Betapapillomavirus 2 human papillomavirus 107 FA85 EF422221 HPV107
Betapapillomavirus 2 human papillomavirus 110 EU410348 HPV110
Betapapillomavirus 2 human papillomavirus 111 EU410349 HPV111
Betapapillomavirus 2 human papillomavirus 100 DL267 FM955839 HPV100
Betapapillomavirus 2 human papillomavirus 104 DL253 FM955840 HPV104
Betapapillomavirus 2 human papillomavirus 113 DL250 FM955842 HPV113
Betapapillomavirus 2 human papillomavirus 151 SIBX2 FN677756 HPV151
Betapapillomavirus 2 human papillomavirus 120 CL3857 GQ845442 HPV120
Betapapillomavirus 2 human papillomavirus 122 CL3802 GQ845444 HPV122
Betapapillomavirus 2 human papillomavirus 159 SIBX8 HE963025 HPV159
Betapapillomavirus 2 human papillomavirus 174 V001 HF930491 HPV174
Betapapillomavirus 2 human papillomavirus 145 CL4112 HM999997 HPV145
Betapapillomavirus 2 human papillomavirus 22 U31780 HPV22
Betapapillomavirus 2 human papillomavirus 23 U31781 HPV23
Betapapillomavirus 2 human papillomavirus 37 U31786 HPV37
Betapapillomavirus 2 human papillomavirus 38 U31787 HPV38
Betapapillomavirus 2 human papillomavirus 15 X74468 HPV15
Betapapillomavirus 2 human papillomavirus 17 X74469 HPV17
Betapapillomavirus 2 human papillomavirus 80 Y15176 HPV80
Betapapillomavirus 3 human papillomavirus 49 X74480 NC_001591 Complete genome HPV49
Betapapillomavirus 3 human papillomavirus 115 GC02 FJ947080 HPV115
Betapapillomavirus 3 human papillomavirus 75 Y15173 HPV75
Betapapillomavirus 3 human papillomavirus 76 Y15174 HPV76
Betapapillomavirus 4 human papillomavirus 92 AF531420 NC_004500 Complete genome HPV92
Betapapillomavirus 5 human papillomavirus 96 AY382779 NC_005134 Complete genome HPV96
Betapapillomavirus 5 human papillomavirus 150 SIBX1 FN677755 HPV150
Betapapillomavirus 6 Macaca fascicularis papillomavirus 2 Mac191 GU014531 NC_015691 Complete genome MfPV2
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Related, unclassified viruses

Virus name

Accession number

Virus abbreviation

human papillomavirus mEV03c09

MF588687

HPV-mEV03c09

human papillomavirus mHIVGc36

MF588677

HPV-mHIVGc36

human papillomavirus mMTS1

KY349817

HPV-mMTS1

human papillomavirus mRTRX7

U85660

HPV-mRTRX7

human papillomavirus mTVMBSFc09

MF588684

HPV-mTVMBSFc09

human papillomavirus mTVMBSGc2024

MF588686

HPV-mTVMBSGc2024

human papillomavirus mm090c09

MF588681

HPV-mm090c09

human papillomavirus mm292c10

MF588678

HPV-mm292c10

human papillomavirus mm292c100

MF588685

HPV-mm292c100

human papillomavirus mm292c14

MF588682

HPV-mm292c14

human papillomavirus mm292c88

MF588683

HPV-mm292c88

human papillomavirus mw15c111

MF588679

HPV-mw15c111

Virus names and virus abbreviations are not official ICTV designations.

Genus: Chipapillomavirus

Distinguishing features

Members of this genus are associated with skin plaques in carnivore hosts.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus (Figure 1.Chipapillomavirus).

Figure 1.Chipapillomavirus. Phylogenetic tree of members of the genus Chipapillomavirus. The E1, E2, L2, and L1 nucleotide sequences of 343 papillomavirus isolates including representatives of all species and genera within the Papillomaviridae family were aligned as amino acid sequences using MUSCLE v7.221 (Edgar 2004). JModeltest2 (Darriba et al., 2012) was used to determine the optimal model of evolution (GTR + I + G) for the concatenated nucleotide sequences. Maximum likelihood (ML) trees were constructed using RAxML MPI v8.2.9 (Stamatakis 2006) implementing the GTR substitution model. ML bootstrap analysis used the autoMRE-based stopping criterion in RAxML. Following tree construction (tree available in the Resources section of the Papillomaviridae Report), the subtree corresponding to the genus Chipapillomavirus was isolated. Tips are labelled with virus names and accession numbers; nodes are labelled with bootstrap support values.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Chipapillomavirus 1 Canis familiaris papillomavirus 3 DQ295066 NC_008297 Complete genome CPV3
Chipapillomavirus 1 Canis familiaris papillomavirus 5 Birkenfeld FJ492743 CPV5
Chipapillomavirus 1 Canis familiaris papillomavirus 9 JF800656 CPV9
Chipapillomavirus 1 Canis familiaris papillomavirus 11 JF800658 CPV11
Chipapillomavirus 1 Canis familiaris papillomavirus 12 Deacon C JQ754321 CPV12
Chipapillomavirus 1 Canis familiaris papillomavirus 18 Boston 2015 KT326919 CPV18
Chipapillomavirus 1 Canis familiaris papillomavirus 20 Ada KT901797 CPV20
Chipapillomavirus 2 Canis familiaris papillomavirus 4 pug2006 EF584537 NC_010226 Complete genome CPV4
Chipapillomavirus 2 Canis familiaris papillomavirus 16 Chana KP099966 CPV16
Chipapillomavirus 3 Canis familiaris papillomavirus 8 Charlotte HQ262536 NC_016014 Complete genome CPV8
Chipapillomavirus 3 Canis familiaris papillomavirus 10 JF800657 CPV10
Chipapillomavirus 3 Canis familiaris papillomavirus 14 JQ701802 CPV14
Chipapillomavirus 3 Canis familiaris papillomavirus 15 Hercules2012 JX899359 CPV15
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Deltapapillomavirus

Distinguishing features

These viruses are associated with fibropapillomas in their respective ungulate hosts. Trans-species transmission occurs, where it induces non-productive sarcoids. The E5 protein, located in the region between the early and late genes, has transforming properties.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus (Figure 1.Deltapapillomavirus).

Figure 1.Deltapapillomavirus. Phylogenetic tree of members of the genus Deltapapillomavirus. The E1, E2, L2, and L1 nucleotide sequences of 343 papillomavirus isolates including representatives of all species and genera within the Papillomaviridae family were aligned as amino acid sequences using MUSCLE v7.221 (Edgar 2004). JModeltest2 (Darriba et al., 2012) was used to determine the optimal model of evolution (GTR + I + G) for the concatenated nucleotide sequences. Maximum likelihood (ML) trees were constructed using RAxML MPI v8.2.9 (Stamatakis 2006) implementing the GTR substitution model. ML bootstrap analysis used the autoMRE-based stopping criterion in RAxML. Following tree construction (tree available in the Resources section of the Papillomaviridae Report), the subtree corresponding to the genus Deltapapillomavirus was isolated. Tips are labelled with virus names and accession numbers; nodes are labelled with bootstrap support values.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Deltapapillomavirus 1 Alces alces papillomavirus 1 M15953 NC_001524 Complete genome AaPV1
Deltapapillomavirus 1 Rangifer tarandus papillomavirus 1 AF443292 RtPV1
Deltapapillomavirus 2 Odocoileus virginianus papillomavirus 1 M11910 NC_001523 Complete genome OvPV1
Deltapapillomavirus 3 Ovis aries papillomavirus 1 U83594 NC_001789 Complete genome OaPV1
Deltapapillomavirus 3 Ovis aries papillomavirus 2 U83595 OaPV2
Deltapapillomavirus 4 Bos taurus papillomavirus 1 X02346 NC_001522 Complete genome BPV1
Deltapapillomavirus 4 Bos taurus papillomavirus 13 JQ798171 BPV13
Deltapapillomavirus 4 Bos grunniens papillomavirus 1 QH-1 JX174437 BgPV1
Deltapapillomavirus 4 Bos taurus papillomavirus 14 CGKnose1 KP276343 BPV14
Deltapapillomavirus 4 Bos taurus papillomavirus 2 M20219 BPV2
Deltapapillomavirus 5 Capreolus capreolus papillomavirus 1 EF680235 NC_011051 Complete genome CcaPV1
Deltapapillomavirus 5 Rusa alfredi papillomavirus 1 DE1641-14 KT626573 RalPV1
Deltapapillomavirus 6 Camelus dromedarius papillomavirus 1 HQ912790 NC_015267 Complete genome CdPV1
Deltapapillomavirus 6 Camelus dromedarius papillomavirus 2 HQ912791 CdPCV2
Deltapapillomavirus 7 Giraffa camelopardalis papillomavirus 1 GC2011 KX954132 NC_039036 Complete genome GcPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Dyochipapillomavirus

Distinguishing features

The sole member of this genus was isolated from the skin of a donkey (Equus asinus).

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Dyochipapillomavirus 1 Equus asinus papillomavirus Asinara KF741371 NC_023882 Complete genome EaPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Dyodeltapapillomavirus

Distinguishing features

Members of this genus are associated with genital lesions in pigs (Sus scrofa). Members of this genus lack an E7 ORF.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

 Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Dyodeltapapillomavirus 1 Sus scrofa papillomavirus 1 variant a EF395818 NC_011280 Complete genome SsPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Dyoepsilonpapillomavirus

Distinguishing features

Members of this genus are associated with the healthy skin of yellow-necked spurfowl or yellow-necked francolin (Pternistis leucoscepus) living in Africa, a species of bird in the family Phasianidae. The E6 protein contains a single zinc-binding domain. The genome also encodes for a unique E9 protein (Van Doorslaer et al., 2017b).

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Dyoepsilonpapillomavirus 1 Francolinus leucoscepus papillomavirus 1 EU188799 NC_013117 Complete genome FlPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Dyoetapapillomavirus

Distinguishing features

Members of this genus are associated with hair follicles of the European hedgehog (Erinaceus europaeus).

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Dyoetapapillomavirus 1 Erinaceus europaeus papillomavirus 1 FJ379293 NC_011765 Complete genome EePV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Dyoiotapapillomavirus

Distinguishing features

Members of this genus are associated with mucosal lesions in horses (Equus caballus).

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Dyoiotapapillomavirus 1 Equus caballus papillomavirus 3 Haflinger GU384895 NC_017862 Complete genome EcPV3
Dyoiotapapillomavirus 1 Equus caballus papillomavirus 2 EU503122 EcPV2
Dyoiotapapillomavirus 2 Equus caballus papillomavirus 4 JQ031032 NC_020085 Complete genome EcPV4
Dyoiotapapillomavirus 2 Equus caballus papillomavirus 5 JQ031033 EcPV5
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Dyokappapapillomavirus

Distinguishing features

Members of this genus are associated with the skin lesions of ungulates.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus (Figure 1.Dyokappapapillomavirus).

Figure 1.Dyokappapapillomavirus. Phylogenetic tree of members of the genus Dyokappapapillomavirus. The E1, E2, L2, and L1 nucleotide sequences of 343 papillomavirus isolates including representatives of all species and genera within the Papillomaviridae family were aligned as amino acid sequences using MUSCLE v7.221 (Edgar 2004). JModeltest2 (Darriba et al., 2012) was used to determine the optimal model of evolution (GTR + I + G) for the concatenated nucleotide sequences. Maximum likelihood (ML) trees were constructed using RAxML MPI v8.2.9 (Stamatakis 2006) implementing the GTR substitution model. ML bootstrap analysis used the autoMRE-based stopping criterion in RAxML. Following tree construction (tree available in the Resources section of the Papillomaviridae Report), the subtree corresponding to the genus Dyokappapapillomavirus was isolated. Tips are labelled with virus names and accession numbers; nodes are labelled with bootstrap support values. 

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Dyokappapapillomavirus 1 Ovis aries papillomavirus 3 Sar1 FJ796965 NC_038516 Complete genome OaPV3
Dyokappapapillomavirus 2 Rupicapra rupicapra papillomavirus 1 KC876045 NC_023895 Complete genome RrPV1
Dyokappapapillomavirus 3 Bos taurus papillomavirus 16 KU519391 NC_030796 Complete genome BPV16
Dyokappapapillomavirus 4 Bos taurus papillomavirus 18 KU519393 NC_030798 Complete genome BPV18
Dyokappapapillomavirus 5 Pudu puda papillomavirus 1 ILAT 93802 KT932713 NC_039037 Complete genome PpuPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Dyolambdapapillomavirus

Distinguishing features

Members of this genus are associated with a lesion on an extremely rare marsupial, woylie or brush-tailed bettong (Bettongia penicillata).

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Dyolambdapapillomavirus 1 Bettongia penicillata papillomavirus 1 GU220391 NC_014143 Complete genome BpPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Dyomupapillomavirus

Distinguishing features

Members of this genus are associated with skin lesions on carpet python or diamond python (Morelia spilota).

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Dyomupapillomavirus 1 Morelia spilota papillomavirus 1 Zurich 2009 HQ262535 NC_016013 Complete genome MsPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Dyonupapillomavirus

Distinguishing features

Members of this genus are associated with skin lesions of sea lions (Zalophus californianus).

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Dyonupapillomavirus 1 Zalophus californianus papillomavirus 1 2008 HQ293213 NC_015325 Complete genome ZcPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Dyoomegapapillomavirus

Distinguishing features

Members of this genus were isolated from the oral mucosa of bats.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Dyoomegapapillomavirus 1 Eptesicus serotinus papillomavirus 2 KC858264 NC_038517 Complete genome EsPV2
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Dyoomikronpapillomavirus

Distinguishing features

Members of this genus are associated with oral lesions in a New World monkey, brown howler (Alouatta guaribaand common squirrel monkey (Saimiri sciureus).

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Dyoomikronpapillomavirus 1 Saimiri sciureus papillomavirus 1 Mac2066 JF304765 NC_023496 Complete genome SscPV1
Dyoomikronpapillomavirus 1 Saimiri sciureus papillomavirus 2 Mac2067.1 JF304766 SscPV2
Dyoomikronpapillomavirus 1 Saimiri sciureus papillomavirus 3 Mac2167.2 JF304767 SscPV3
Dyoomikronpapillomavirus 1 Alouatta guariba papillomavirus 1 PPV03_SP KP861980 AgPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Dyophipapillomavirus

Distinguishing features

Members of this genus were isolated from the healthy skin of a European mole (Talpa europaea).

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Dyophipapillomavirus 1 Talpa europaea papillomavirus 1 Bruges/2009/22 KC460987 NC_039038 Complete genome TePV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Dyopipapillomavirus

Distinguishing features

Members of this genus are associated with genital lesions in cetaceans. There is evidence for (intra-genus) recombination. Members of this genus lack an E7 ORF.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel PV genome with complete genome sequence data available and being <70% related to PV’s within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Dyopipapillomavirus 1 Phocoena phocoena papillomavirus GU117623 NC_018076 Complete genome PphPV4
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Dyopsipapillomavirus

Distinguishing features

Members of this genus were isolated from the oral mucosa of bats.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Dyopsipapillomavirus 1 Eptesicus serotinus papillomavirus 1 KC858263 NC_038518 Complete genome EsPV1
Dyopsipapillomavirus 1 Eptesicus serotinus papillomavirus 3 KC858265 EsPV3
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Dyorhopapillomavirus

Distinguishing features

Members of this genus are associated with mucosal lesions in horses.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel PV genome with complete genome sequence data available and being <70% related to PV’s within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Dyorhopapillomavirus 1 Equus caballus papillomavirus 6 Sirkar_2011 JQ965698 NC_020500 Complete genome EcPV6
Dyorhopapillomavirus 1 Equus caballus papillomavirus 7 JX035935 EcPV7
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Dyosigmapapillomavirus

Distinguishing features

Members of this genus are associated with a cutaneous exophytic lesion in beavers (Castor canadensis).

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Dyosigmapapillomavirus 1 Castor canadensis papillomavirus 1 KC020689 NC_023178 Complete genome CcanPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Dyotaupapillomavirus

Distinguishing features

Members of this genus are associated with lesions from insectivorous bats.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Dyotaupapillomavirus 1 Miniopterus schreibersii papillomavirus 2 TT20F JQ692938 NC_038519 Complete genome MscPV2
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Dyothetapapillomavirus

Distinguishing features

Members of this genus are associated with a papillomavirus isolated from feline Bowenoid in situ carcinomas.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Dyothetapapillomavirus 1 Felis domesticus papillomavirus 2 Main Coon 2007 EU796884 NC_038520 Complete genome FcaPV2
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Dyoupsilonpapillomavirus

Distinguishing features

Members of this genus are associated with lesions from bats.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Dyoupsilonpapillomavirus 1 Eidolon helvum papillomavirus 1 JX123128 NC_038521 Complete genome EhPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Dyoxipapillomavirus

Distinguishing features

Members of this genus are associated with skin and teat lesions of cattle.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Dyoxipapillomavirus 1 Bos taurus papillomavirus 7 DQ217793 NC_007612 Complete genome BPV7
Dyoxipapillomavirus 2 Bos taurus papillomavirus 19 KU519394 NC_030799 Complete genome BPV19
Dyoxipapillomavirus 2 Bos taurus papillomavirus 21 KU519396 BPV21
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Dyozetapapillomavirus

Distinguishing features

Members of this genus are associated with the skin lesions of marine turtles. The E6 protein contains a single zinc-binding domain.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Dyozetapapillomavirus 1 Caretta caretta papillomavirus 1 EU493092 NC_011530 Complete genome CcPV1
Dyozetapapillomavirus 1 Chelonia mydas papillomavirus 1 EU493091 CmPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Epsilonpapillomavirus

Distinguishing features

Infections are associated with cutaneous papillomas in ungulates.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Epsilonpapillomavirus 1 Bos taurus papillomavirus 5 AF457465 NC_004195 Complete genome BPV5
Epsilonpapillomavirus 1 Bos taurus papillomavirus 8 BAPV1 DQ098913 BPV8
Epsilonpapillomavirus 2 Cervus elaphus papillomavirus 1 BernieDPV KU350625 NC_030151 Complete genome CePV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Etapapillomavirus

Distinguishing features

Members of this genus are associated with cutaneous lesions in birds. Unlike the prototypical E6 protein which contains two zinc-binding motifs, the etapapillomavirus E6 protein contains a single zinc-binding motif. These papillomaviruses contain an E9 protein of unknown function. No E8^E2 or E1^E4 proteins have been identified.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Etapapillomavirus 1 Fringilla coelebs papillomavirus AY057109 NC_004068 Complete genome FcPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Gammapapillomavirus

Distinguishing features

Members of this genus are typically found on the skin and oral mucosa of primates. Infections are usually asymptomatic. However, some infections cause cutaneous lesions in their host and are histologically distinguishable by intracytoplasmic inclusion bodies. The members of the species Gammapapillomavirus 6 do not contain an E6 ORF, but encode a putative E10 protein in the same location.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus (Figure 1.Gammapapillomavirus).

Figure 1.Gammapapillomavirus. Phylogenetic tree of members of the genus Gammapapillomavirus. The E1, E2, L2, and L1 nucleotide sequences of 343 papillomavirus isolates including representatives of all species and genera within the Papillomaviridae family were aligned as amino acid sequences using MUSCLE v7.221 (Edgar 2004). JModeltest2 (Darriba et al., 2012) was used to determine the optimal model of evolution (GTR + I + G) for the concatenated nucleotide sequences. Maximum likelihood (ML) trees were constructed using RAxML MPI v8.2.9 (Stamatakis 2006) implementing the GTR substitution model. ML bootstrap analysis used the autoMRE-based stopping criterion in RAxML. Following tree construction (tree available in the Resources section of the Papillomaviridae Report), the subtree corresponding to the genus Gammapapillomavirus was isolated. Tips are labelled with virus names and accession numbers; nodes are labelled with bootstrap support values.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Gammapapillomavirus 1 human papillomavirus 4 X70827 NC_001457 Complete genome HPV4
Gammapapillomavirus 1 human papillomavirus 95 AJ620210 HPV95
Gammapapillomavirus 1 human papillomavirus 173 KF006400 HPV173
Gammapapillomavirus 1 human papillomavirus 205 EP01 KT698167 HPV205
Gammapapillomavirus 1 human papillomavirus 65 X70829 HPV65
Gammapapillomavirus 2 human papillomavirus 48 U31789 NC_001690 Complete genome HPV48
Gammapapillomavirus 2 human papillomavirus 200 KP692114 HPV200
Gammapapillomavirus 3 human papillomavirus 50 U31790 NC_001691 Complete genome HPV50
Gammapapillomavirus 4 human papillomavirus 60 U31792 NC_001693 Complete genome HPV60
Gammapapillomavirus 5 human papillomavirus 88 EF467176 NC_010329 Complete genome HPV88
Gammapapillomavirus 6 human papillomavirus 101 Qv23954 DQ080081 NC_008189 Complete genome HPV101
Gammapapillomavirus 6 human papillomavirus 103 QV33725 DQ080078 HPV103
Gammapapillomavirus 6 human papillomavirus 108 FM212639 HPV108
Gammapapillomavirus 7 human papillomavirus 109 EU541441 NC_012485 Complete genome HPV109
Gammapapillomavirus 7 human papillomavirus 123 NJ2501 GQ845445 HPV123
Gammapapillomavirus 7 human papillomavirus 149 10-18 GU117629 HPV149
Gammapapillomavirus 7 human papillomavirus 134 39-65 GU117634 HPV134
Gammapapillomavirus 7 human papillomavirus 138 GH13 HM999990 HPV138
Gammapapillomavirus 7 human papillomavirus 139 GH1646 HM999991 HPV139
Gammapapillomavirus 7 human papillomavirus 155 SE42 JF906559 HPV155
Gammapapillomavirus 7 human papillomavirus 170 KC8 JX413110 HPV170
Gammapapillomavirus 8 human papillomavirus 112 EU541442 NC_012486 Complete genome HPV112
Gammapapillomavirus 8 human papillomavirus 119 CL3647 GQ845441 HPV119
Gammapapillomavirus 8 human papillomavirus 147 GH659 HM999999 HPV147
Gammapapillomavirus 8 human papillomavirus 164 KC4 JX413106 HPV164
Gammapapillomavirus 8 human papillomavirus 168 KC15 KC862317 HPV168
Gammapapillomavirus 9 human papillomavirus 116 FJ804072 NC_013035 Complete genome HPV116
Gammapapillomavirus 9 human papillomavirus 129 GU233853 HPV129
Gammapapillomavirus 10 human papillomavirus 121 NJ3301 GQ845443 NC_014185 Complete genome HPV121
Gammapapillomavirus 10 human papillomavirus 130 24-43 GU117630 HPV130
Gammapapillomavirus 10 human papillomavirus 133 28-52 GU117633 HPV133
Gammapapillomavirus 10 human papillomavirus 142 GH1302 HM999994 HPV142
Gammapapillomavirus 10 human papillomavirus 180 FA69 KC108722 HPV180
Gammapapillomavirus 11 human papillomavirus 126 AB646346 NC_016157 Complete genome HPV126
Gammapapillomavirus 11 human papillomavirus 136 CL3865 HM999988 HPV136
Gammapapillomavirus 11 human papillomavirus 140 NJ2801C1 HM999992 HPV140
Gammapapillomavirus 11 human papillomavirus 141 NJ2801Cn HM999993 HPV141
Gammapapillomavirus 11 human papillomavirus 154 PV77 JN211193 HPV154
Gammapapillomavirus 11 human papillomavirus 169 KC6 JX413105 HPV169
Gammapapillomavirus 11 human papillomavirus 171 KF006398 HPV171
Gammapapillomavirus 11 human papillomavirus 202 KP692116 HPV202
Gammapapillomavirus 12 human papillomavirus 127 R3a HM011570 NC_014469 Complete genome HPV127
Gammapapillomavirus 12 human papillomavirus 157 GC08 KT698166 HPV157
Gammapapillomavirus 12 human papillomavirus 132 27-50 GU117632 HPV132
Gammapapillomavirus 12 human papillomavirus 148 34-60 GU129016 HPV148
Gammapapillomavirus 12 human papillomavirus 165 KC7 JX444072 HPV165
Gammapapillomavirus 12 human papillomavirus 199 KC82-SLO KJ913662 HPV199
Gammapapillomavirus 12 human papillomavirus 158 GC23 KT698168 HPV158
Gammapapillomavirus 13 human papillomavirus 128 GU225708 NC_014952 Complete genome HPV128
Gammapapillomavirus 13 human papillomavirus 153 JN171845 HPV153
Gammapapillomavirus 14 human papillomavirus 131 27-49 GU117631 NC_014954 Complete genome HPV131
Gammapapillomavirus 15 human papillomavirus 135 NJ3500 HM999987 NC_017993 Complete genome HPV135
Gammapapillomavirus 15 human papillomavirus 179 SIBX16 HG421739 HPV179
Gammapapillomavirus 15 human papillomavirus 146 GH1677 HM999998 HPV146
Gammapapillomavirus 16 human papillomavirus 137 NJ2801H HM999989 NC_017995 Complete genome HPV137
Gammapapillomavirus 17 human papillomavirus 144 CL3740 HM999996 NC_017997 Complete genome HPV144
Gammapapillomavirus 18 human papillomavirus 156 GC01 JX429973 NC_033781 Complete genome HPV156
Gammapapillomavirus 19 human papillomavirus 161 KC1 JX413109 NC_038522 Complete genome HPV161
Gammapapillomavirus 19 human papillomavirus 166 KC9 JX413104 HPV166
Gammapapillomavirus 19 human papillomavirus 162 KC2 JX413108 HPV162
Gammapapillomavirus 20 human papillomavirus 163 KC3 JX413107 NC_028125 Complete genome HPV163
Gammapapillomavirus 21 human papillomavirus 167 KC10 KC862318 NC_022892 Complete genome HPV167
Gammapapillomavirus 22 human papillomavirus 172 KF006399 NC_038523 Complete genome HPV172
Gammapapillomavirus 23 human papillomavirus 175 SE87 KC108721 NC_038524 Complete genome HPV175
Gammapapillomavirus 24 human papillomavirus 178 KJ130020 NC_023891 Complete genome HPV178
Gammapapillomavirus 24 human papillomavirus 197 SE46 KM085343 HPV197
Gammapapillomavirus 25 human papillomavirus 184 SIBX17 HG530535 NC_038914 Complete genome HPV184
Gammapapillomavirus 26 human papillomavirus 187 ACS447 KR816174 NC_039086 Complete genome HPV187
Gammapapillomavirus 27 human papillomavirus 201 KP692115 NC_027528 Complete genome HPV201
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Related, unclassified viruses

Virus name

Accession number

Virus abbreviation

human papillomavirus mCG2

JF966378

HPV-mCG2

human papillomavirus mCG3

JF966379

HPV-mCG3

human papillomavirus mCH2

KF791917

HPV-mCH2

human papillomavirus mDysk1

KX781280

HPV-mDysk1

human papillomavirus mDysk2

KX781281

HPV-mDysk2

human papillomavirus mDysk3

KX781282

HPV-mDysk3

human papillomavirus mDysk5

KX781284

HPV-mDysk5

human papillomavirus mDysk6

KX781285

HPV-mDysk6

human papillomavirus mEV03c05

MF588698

HPV-mEV03c05

human papillomavirus mEV03c104

MF588724

HPV-mEV03c104

human papillomavirus mEV03c188

MF588729

HPV-mEV03c188

human papillomavirus mEV03c212

MF588735

HPV-mEV03c212

human papillomavirus mEV03c40

MF588746

HPV-mEV03c40

human papillomavirus mEV03c434

MF588755

HPV-mEV03c434

human papillomavirus mEV03c45

MF588721

HPV-mEV03c45

human papillomavirus mEV03c60

MF588699

HPV-mEV03c60

human papillomavirus mEV06c107

MF588747

HPV-mEV06c107

human papillomavirus mEV06c118

MF588736

HPV-mEV06c118

human papillomavirus mEV07c367

MF588716

HPV-mEV07c367

human papillomavirus mEV07c382

MF588723

HPV-mEV07c382

human papillomavirus mEV07c390

MF588705

HPV-mEV07c390

human papillomavirus mFD1

JF966375

HPV-mFD1

human papillomavirus mFD2

JF966376

HPV-mFD2

human papillomavirus mFS1

JF966373

HPV-mFS1

human papillomavirus mFi864

KC311731

HPV-mFi864

human papillomavirus mHIVGc70

MF588713

HPV-mHIVGc70

human papillomavirus mICB1

MF356498

HPV-mICB1

human papillomavirus mKC5

JX444073

HPV-mKC5

human papillomavirus mKN1

JF966371

HPV-mKN1

human papillomavirus mKN2

JF966372

HPV-mKN2

human papillomavirus mKN3

JF966374

HPV-mKN3

human papillomavirus mL55

KF482069

HPV-mL55

human papillomavirus mLCOSOc196

MF588688

HPV-mLCOSOc196

human papillomavirus mMTS2

KY780961

HPV-mMTS2

human papillomavirus mSD2

KC113191

HPV-mSD2

human papillomavirus mSE355

KJ506870

HPV-mSE355

human papillomavirus mSE379

KP692117

HPV-mSE379

human papillomavirus mSE383

KP692118

HPV-mSE383

human papillomavirus mTVMBSGc529

MF588706

HPV-mTVMBSGc529

human papillomavirus mTVMBSGc2450

MF588732

HPV-mTVMBSGc2450

human papillomavirus mTVMBSHc13

MF588738

HPV-mTVMBSHc13

human papillomavirus mTVMBSHc33

MF588707

HPV-mTVMBSHc33

human papillomavirus mTVMBSWc141

MF588739

HPV-mTVMBSWc141

human papillomavirus mZJ01

KX082661

HPV-mZJ01

human papillomavirus mdo1c02

MF588734

HPV-mdo1c02

human papillomavirus mdo1c232

MF588704

HPV-mdo1c232

human papillomavirus mga2c01

MF588744

HPV-mga2c01

human papillomavirus mga2c70

MF588754

HPV-mga2c70

human papillomavirus mm090c10

MF588745

HPV-mm090c10

human papillomavirus mm090c145

MF588737

HPV-mm090c145

human papillomavirus mm090c66

MF588748

HPV-mm090c66

human papillomavirus mw02c24a

MF588696

HPV-mw02c24a

human papillomavirus mw03c65

MF588697

HPV-mw03c65

human papillomavirus mw07c34d

MF588753

HPV-mw07c34d

human papillomavirus mw07c68b

MF588717

HPV-mw07c68b

human papillomavirus mw07c74b

MF588749

HPV-mw07c74b

human papillomavirus mw11C24

MF588709

HPV-mw11C24

human papillomavirus mw11C39

MF588710

HPV-mw11C39

human papillomavirus mw11C51

MF588689

HPV-mw11C51

human papillomavirus mw11c13

MF588718

HPV-mw11c13

human papillomavirus mw18c07

MF588740

HPV-mw18c07

human papillomavirus mw18c11d

MF588733

HPV-mw18c11d

human papillomavirus mw18c134

MF588725

HPV-mw18c134

human papillomavirus mw18c25

MF588714

HPV-mw18c25

human papillomavirus mw18c39

MF588741

HPV-mw18c39

human papillomavirus mw20c01a

MF588701

HPV-mw20c01a

human papillomavirus mw20c01b

MF588708

HPV-mw20c01b

human papillomavirus mw20c02c

MF588702

HPV-mw20c02c

human papillomavirus mw20c03a

MF588715

HPV-mw20c03a

human papillomavirus mw20c04

MF588695

HPV-mw20c04

human papillomavirus mw20c08a

MF588742

HPV-mw20c08a

human papillomavirus mw20c09

MF588703

HPV-mw20c09

human papillomavirus mw20c10a

MF588726

HPV-mw20c10a

human papillomavirus mw21c693

MF588743

HPV-mw21c693

human papillomavirus mw22c09

MF588750

HPV-mw22c09

human papillomavirus mw23c08c

MF588690

HPV-mw23c08c

human papillomavirus mw23c101c

MF588711

HPV-mw23c101c

human papillomavirus mw23c77

MF588719

HPV-mw23c77

human papillomavirus mw27c04c

MF588728

HPV-mw27c04c

human papillomavirus mw27c157c

MF588692

HPV-mw27c157c

human papillomavirus mw27c39c

MF588712

HPV-mw27c39c

human papillomavirus mw27c52c

MF588691

HPV-mw27c52c

human papillomavirus mw34c04a

MF588693

HPV-mw34c04a

human papillomavirus mw34c11a

MF588720

HPV-mw34c11a

human papillomavirus mw34c14a

MF588694

HPV-mw34c14a

human papillomavirus mw34c28a

MF588751

HPV-mw34c28a

human papillomavirus mw34c34a

MF588731

HPV-mw34c34a

human papillomavirus mwg1c05

MF588756

HPV-mwg1c05

human papillomavirus mwg1c09

MF588727

HPV-mwg1c09

Virus names and virus abbreviations are not official ICTV designations.

Genus: Iotapapillomavirus

Distinguishing features

These papillomaviruses are associated with cutaneous lesions in rodents.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Iotapapillomavirus 1 Mastomys natalensis papillomavirus 1 U01834 NC_001605 Complete genome MnPV1
Iotapapillomavirus 1 Rattus norvegicus papillomavirus 2 HQ625441 RnPV2
Iotapapillomavirus 1 Rattus norvegicus papillomavirus 3 Rat_60S KT945134 RnPV3
Iotapapillomavirus 2 Peromyscus papillomavirus 1 M-14 JF755418 NC_039039 Complete genome PmPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Kappapapillomavirus

Distinguishing features

Members of this genus cause cutaneous and mucosal lesions in rabbits. The E6 ORF is larger than in other genera. The viral genomes contain an E5 and an E10 ORF in the early region.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Kappapapillomavirus 1 Oryctolagus cuniculus papillomavirus 1 AF227240 NC_002232 Complete genome OcPV1
Kappapapillomavirus 2 Sylvilagus floridanus papillomavirus 1 K02708 NC_001541 Complete genome SfPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Lambdapapillomavirus

Distinguishing features

Members of this genus infect carnivores. The region between the early and late coding regions is exceptionally large.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus (Figure 1.Lambdapapillomavirus).

Figure 1.Lambdapapillomavirus. Phylogenetic tree of members of the genus Lambdapapillomavirus. The E1, E2, L2, and L1 nucleotide sequences of 343 papillomavirus isolates including representatives of all species and genera within the Papillomaviridae family were aligned as amino acid sequences using MUSCLE v7.221 (Edgar 2004). JModeltest2 (Darriba et al., 2012) was used to determine the optimal model of evolution (GTR + I + G) for the concatenated nucleotide sequences. Maximum likelihood (ML) trees were constructed using RAxML MPI v8.2.9 (Stamatakis 2006) implementing the GTR substitution model. ML bootstrap analysis used the autoMRE-based stopping criterion in RAxML. Following tree construction (tree available in the Resources section of the Papillomaviridae Report), the subtree corresponding to the genus Lambdapapillomavirus was isolated. Tips are labelled with virus names and accession numbers; nodes are labelled with bootstrap support values.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Lambdapapillomavirus 1 Felis domesticus papillomavirus 1 AF480454 NC_004765 Complete genome FcaPV1
Lambdapapillomavirus 1 Lynx rufus papillomavirus 1 AY904722 LrPV1
Lambdapapillomavirus 1 Puma concolor papillomavirus 1 AY904723 PcPV1
Lambdapapillomavirus 1 Panthera leo persica papillomavirus 1 AY904724 PlpPV1
Lambdapapillomavirus 1 Uncia uncia papillomavirus 1 DQ180494 UuPV1
Lambdapapillomavirus 2 Canis familiaris oral papillomavirus 1 Y62 D55633 NC_001619 Complete genome CPV1
Lambdapapillomavirus 3 Canis familiaris papillomavirus 6 Zurich FJ492744 NC_013237 Complete genome CPV6
Lambdapapillomavirus 4 Procyon lotor papillomavirus 1 Z146-02 AY763115 NC_007150 Complete genome PlPV1
Lambdapapillomavirus 4 Enhydra lutris papillomavirus 1 6898-13 KJ410351 ElPV1
Lambdapapillomavirus 5 Crocuta crocuta papillomavirus 1 HQ585856 NC_018575 Complete genome CcrPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Mupapillomavirus

Distinguishing features

Primate papillomaviruses associated with cutaneous lesions

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus(Figure 1.Mupapillomavirus). 

Figure 1.Mupapillomavirus. Phylogenetic tree of members of the genus Mupapillomavirus. The E1, E2, L2, and L1 nucleotide sequences of 343 papillomavirus isolates including representatives of all species and genera within the Papillomaviridae family were aligned as amino acid sequences using MUSCLE v7.221 (Edgar 2004). JModeltest2 (Darriba et al., 2012) was used to determine the optimal model of evolution (GTR + I + G) for the concatenated nucleotide sequences. Maximum likelihood (ML) trees were constructed using RAxML MPI v8.2.9 (Stamatakis 2006) implementing the GTR substitution model. ML bootstrap analysis used the autoMRE-based stopping criterion in RAxML. Following tree construction (tree available in the Resources section of the Papillomaviridae Report), the subtree corresponding to the genus Mupapillomavirus was isolated. Tips are labelled with virus names and accession numbers; nodes are labelled with bootstrap support values.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Mupapillomavirus 1 human papillomavirus 1 V01116 NC_001356 Complete genome HPV1
Mupapillomavirus 2 human papillomavirus 63 X70828 NC_001458 Complete genome HPV63
Mupapillomavirus 3 human papillomavirus 204 A342 KP769769 NC_038525 Complete genome HPV204
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Related, unclassified viruses 

Virus name

Accession number

Virus abbreviation

human papillomavirus md01c06

MF588757

HPV-md01c06

Virus names and virus abbreviations are not official ICTV designations.

Genus: Nupapillomavirus

Distinguishing features

Members of this genus are human papillomaviruses causing benign and malignant cutaneous lesions.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Nupapillomavirus 1 human papillomavirus 41 X56147 NC_001354 Complete genome HPV41
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Omegapapillomavirus

Distinguishing features

Members of this genus are associated with polar bears (Ursus maritimus)Members of this genus lack an E7 ORF.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Omegapapillomavirus 1 Ursus maritimus papillomavirus 1 EF536349 NC_010739 Complete genome UmPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Omikronpapillomavirus

Distinguishing features

Members are associated with genital lesions of cetaceans. No E7 protein is present.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Omikronpapillomavirus 1 Phocoena spinipinnis papillomavirus AJ238373 NC_003348 Complete genome PsPV1
Omikronpapillomavirus 1 Phocoena phocoena papillomavirus 1 GU117621 PphPV1
Omikronpapillomavirus 1 Tursiops truncatus papillomavirus 5 Tt08-09-5 JN709470 TtPV5
Omikronpapillomavirus 1 Tursiops truncatus papillomavirus 6 Tt08-305 JN709471 TtPV6
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Phipapillomavirus

Distinguishing features

Members of this genus are associated with the healthy skin of goats (Capra hircus).

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Phipapillomavirus 1 Capra hircus papillomavirus 1 DQ091200 NC_008032 Complete genome ChPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Pipapillomavirus

Distinguishing features

Members of this genus are associated with cutaneous lesions in rodents.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Pipapillomavirus 1 Mesocricetus auratus papillomavirus 1 APV10 HG530538 NC_022647 Complete genome MaPV1
Pipapillomavirus 1 Phodopus sungorus papillomavirus 1 HG939559 PsuPV1
Pipapillomavirus 2 Mastomys coucha papillomavirus 2 DQ664501 NC_008519 Complete genome McPV2
Pipapillomavirus 2 Micromys minutus papillomavirus 1 DQ269468 MmiPV1
Pipapillomavirus 2 Rattus norvegicus papillomavirus 1 EES-2009 GQ180114 RnPV1
Pipapillomavirus 2 Mus musculus papillomavirus 1 MusPV GU808564 MmuPV1
Pipapillomavirus 2 Apodemus sylvaticus papillomavirus 1 HQ625440 AsPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Psipapillomavirus

Distinguishing features

Members of this genus are associated with cutaneous lesions in bats.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus (Figure 1.Psipapillomavirus).

Figure 1.Psipapillomavirus. Phylogenetic tree of members of the genus Psipapillomavirus. The E1, E2, L2, and L1 nucleotide sequences of 343 papillomavirus isolates including representatives of all species and genera within the Papillomaviridae family were aligned as amino acid sequences using MUSCLE v7.221 (Edgar 2004). JModeltest2 (Darriba et al., 2012) was used to determine the optimal model of evolution (GTR + I + G) for the concatenated nucleotide sequences. Maximum likelihood (ML) trees were constructed using RAxML MPI v8.2.9 (Stamatakis 2006) implementing the GTR substitution model. ML bootstrap analysis used the autoMRE-based stopping criterion in RAxML. Following tree construction (tree available in the Resources section of the Papillomaviridae Report), the subtree corresponding to the genus Psipapillomavirus was isolated. Tips are labelled with virus names and accession numbers; nodes are labelled with bootstrap support values.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Psipapillomavirus 1 Rousettus aegyptiacus papillomavirus 1 DQ366842 NC_008298 Complete genome RaPV1
Psipapillomavirus 2 Eidolon helvum papillomavirus 2 KX276957 NC_033740 Complete genome EhPV2
Psipapillomavirus 3 Eidolon helvum papillomavirus 3 KX276956 NC_033745 Complete genome EhPV3
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Rhopapillomavirus

Distinguishing features

Members of this genus are associated with skin lesions on manatees (Trichechus manatus).

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Rhopapillomavirus 1 Trichechus manatus latirostris papillomavirus 1 AY609301 NC_006563 Complete genome TmPV1
Rhopapillomavirus 1 Trichechus manatus latirostris papillomavirus 2 M09-20 JN709473 TmPV2
Rhopapillomavirus 2 Trichechus manatus latirostris papillomavirus 3 KP205502 NC_038526 Complete genome TmPV3
Rhopapillomavirus 2 Trichechus manatus latirostris papillomavirus 4 KP205503 TmPV4
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Sigmapapillomavirus

Distinguishing features

Members of this genus are associated with cutaneous lesions of a North American porcupine (Erethizon dorsatum).

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Sigmapapillomavirus 1 Erethizon dorsatum papillomavirus 1 AY684126 NC_006951 Complete genome EdPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Taupapillomavirus

Distinguishing features

Members of this genus are clinically associated with viral plaques in carnivores.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus (Figure 1.Taupapillomavirus).

Figure 1.Taupapillomavirus. Phylogenetic tree of members of the genus Taupapillomavirus. The E1, E2, L2, and L1 nucleotide sequences of 343 papillomavirus isolates including representatives of all species and genera within the Papillomaviridae family were aligned as amino acid sequences using MUSCLE v7.221 (Edgar 2004). JModeltest2 (Darriba et al., 2012) was used to determine the optimal model of evolution (GTR + I + G) for the concatenated nucleotide sequences. Maximum likelihood (ML) trees were constructed using RAxML MPI v8.2.9 (Stamatakis 2006) implementing the GTR substitution model. ML bootstrap analysis used the autoMRE-based stopping criterion in RAxML. Following tree construction (tree available in the Resources section of the Papillomaviridae Report), the subtree corresponding to the genus Taupapillomavirus was isolated. Tips are labelled with virus names and accession numbers; nodes are labelled with bootstrap support values.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Taupapillomavirus 1 Canis familiaris papillomavirus 2 AY722648 NC_006564 Complete genome CPV2
Taupapillomavirus 1 Canis familiaris papillomavirus 7 Edinburgh FJ492742 CPV7
Taupapillomavirus 1 Canis familiaris papillomavirus 17 OralSCCPV KT272399 CPV17
Taupapillomavirus 1 Canis familiaris papillomavirus 19 tvmb1 KX599536 CPV19
Taupapillomavirus 2 Canis familiaris papillomavirus 13 Zurich/2011 JX141478 NC_023852 Complete genome CPV13
Taupapillomavirus 3 Felis catus papillomavirus 3 MyDave JX972168 NC_021472 Complete genome FcaPV3
Taupapillomavirus 3 Felis catus papillomavirus 4 My-3 KF147892 FcaPV4
Taupapillomavirus 4 Mustela putorius papillomavirus 1 KF006988 NC_022253 Complete genome MpPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Thetapapillomavirus

Distinguishing features

Members of the only species in this genus are associated with cutaneous lesions in birds and does not contain an E6 ORF, but contains an E9 protein of unknown function. No E8^E2 or E1^E4 proteins have been identified.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Thetapapillomavirus 1 Psittacus erithacus papillomavirus 1 AF502599 NC_003973 Complete genome PePV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Treisdeltapapillomavirus

Distinguishing features

Members of this genus were isolated from the oral mucosa of bats.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Treisdeltapapillomavirus 1 Rhinolophus ferrumequinum papillomavirus 1 KC858266 NC_038527 Complete genome RfPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Treisepsilonpapillomavirus

Distinguishing features

The sole member of this genus was isolated from the healthy skin of an Adélie penguin (Pygoscelis adeliae). The E6 protein contains a single zinc-binding E6 motif. The genome also encodes a unique E9 protein (Van Doorslaer et al., 2017b).

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Treisepsilonpapillomavirus 1 Pygoscelis adeliae papillomavirus Crozier_2013 KJ173785 NC_023894 Complete genome PaPV1
Treisepsilonpapillomavirus 1 Pygoscelis adeliae papillomavirus 1 MF168943 PaPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Treisetapapillomavirus

Distinguishing features

The sole member of this genus is associated with the red fox (Vulpes vulpes).

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Treisetapapillomavirus 1 Vulpes vulpes papillomavirus 1 ILAT 93957 KF857586 NC_038531 Complete genome VvPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Treisiotapapillomavirus

Distinguishing features

Members of this genus are associated with insectivorous bats.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Treisiotapapillomavirus 1 Myotis ricketti papillomavirus 1 JQ814847 NC_039040 Complete genome MrPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Treiskappapapillomavirus

Distinguishing features

Members of this genus are associated with lesions from horses.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Treiskappapapillomavirus 1 Equus caballus papillomavirus 8 NCSU KU963288 NC_031756 Complete genome EcPV8
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Treisthetapapillomavirus

Distinguishing features

The sole member of this genus is associated with the Javan rusa deer (Rusa timorensis).

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Treisthetapapillomavirus 1 Rusa timorensis papillomavirus 1 IZW 39/08 KP757765 NC_039041 Complete genome RtiPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Treiszetapapillomavirus

Distinguishing features

The sole member of this genus is associated with a cartilaginous lesion of a bird, a northern fulmar (Fulmarus glacialis). The E6 protein contains a single zinc-binding E6 motif.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Treiszetapapillomavirus 1 Fulmarus glacialis papillomavirus 1 KJ452243 NC_024300 Complete genome FgPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Upsilonpapillomavirus

Distinguishing features

Members of this genus are associated with genital lesions in cetaceans. There is evidence for (intra-genus) recombination. Members of this genus lack an E7 ORF.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus (Figure 1.Upsilonpapillomavirus).

Figure 1.Upsilonpapillomavirus. Phylogenetic tree of members of the genus Upsilonpapillomavirus. The E1, E2, L2, and L1 nucleotide sequences of 343 papillomavirus isolates including representatives of all species and genera within the Papillomaviridae family were aligned as amino acid sequences using MUSCLE v7.221 (Edgar 2004). JModeltest2 (Darriba et al., 2012) was used to determine the optimal model of evolution (GTR + I + G) for the concatenated nucleotide sequences. Maximum likelihood (ML) trees were constructed using RAxML MPI v8.2.9 (Stamatakis 2006) implementing the GTR substitution model. ML bootstrap analysis used the autoMRE-based stopping criterion in RAxML. Following tree construction (tree available in the Resources section of the Papillomaviridae Report), the subtree corresponding to the genus Upsilonpapillomavirus was isolated. Tips are labelled with virus names and accession numbers; nodes are labelled with bootstrap support values.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Upsilonpapillomavirus 1 Tursiops truncatus papillomavirus 1 EU240894 NC_011109 Complete genome TtPV1
Upsilonpapillomavirus 1 Tursiops truncatus papillomavirus 3 EU240895 TtPV3
Upsilonpapillomavirus 1 Delphinus delphis papillomavirus 1 GU117620 DdPV1
Upsilonpapillomavirus 1 Tursiops truncatus papillomavirus 4 Tt08-09-4 JN709469 TtPV4
Upsilonpapillomavirus 1 Tursiops truncatus papillomavirus 7 Tt09-43 JN709472 TtPV7
Upsilonpapillomavirus 2 Tursiops truncatus papillomavirus 2 AY956402 NC_008184 Complete genome TtPV2
Upsilonpapillomavirus 3 Phocoena phocoena papillomavirus 2 GU117622 NC_018075 Complete genome PphPV2
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Xipapillomavirus

Distinguishing features

Infections by members of this genus cause true papillomas on the cutaneous or mucosal surfaces of ungulates. Most members of this genus do not encode an E6 protein. All viruses in this genus express an E10 protein from part of the genome typically occupied by E6. The E10 protein displays transforming properties.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus (Figure 1.Xipapillomavirus).

Figure 1.Xipapillomavirus. Phylogenetic tree of members of the genus Xipapillomavirus. The E1, E2, L2, and L1 nucleotide sequences of 343 papillomavirus isolates including representatives of all species and genera within the Papillomaviridae family were aligned as amino acid sequences using MUSCLE v7.221 (Edgar 2004). JModeltest2 (Darriba et al., 2012) was used to determine the optimal model of evolution (GTR + I + G) for the concatenated nucleotide sequences. Maximum likelihood (ML) trees were constructed using RAxML MPI v8.2.9 (Stamatakis 2006) implementing the GTR substitution model. ML bootstrap analysis used the autoMRE-based stopping criterion in RAxML. Following tree construction (tree available in the Resources section of the Papillomaviridae Report), the subtree corresponding to the genus Xipapillomavirus was isolated. Tips are labelled with virus names and accession numbers; nodes are labelled with bootstrap support values.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Xipapillomavirus 1 Bos taurus papillomavirus 3 AF486184 NC_004197 Complete genome BPV3
Xipapillomavirus 1 Bos taurus papillomavirus 9 AB331650 BPV9
Xipapillomavirus 1 Bos taurus papillomavirus 10 AB331651 BPV10
Xipapillomavirus 1 Bos taurus papillomavirus 11 AB543507 BPV11
Xipapillomavirus 1 Bos taurus papillomavirus 6 AJ620208 BPV6
Xipapillomavirus 1 Bos taurus papillomavirus 15 Aks-02 KM983393 BPV15
Xipapillomavirus 1 Bos taurus papillomavirus 23 04Ac14 KX098515 BPV23
Xipapillomavirus 1 Bos taurus papillomavirus 4 X05817 BPV4
Xipapillomavirus 2 Bos taurus papillomavirus 12 PR000001 JF834523 NC_028126 Complete genome BPV12
Xipapillomavirus 3 Rangifer tarandus papillomavirus 2 KC810012 NC_021930 Complete genome RtPV2
Xipapillomavirus 4 Bos taurus papillomavirus 17 KU519392 NC_030797 Complete genome BPV17
Xipapillomavirus 5 Cervus elaphus papillomavirus 2 S129/08.1 KT932712 NC_039042 Complete genome CePV2
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Genus: Zetapapillomavirus

Distinguishing features

Members of this genus produce cutaneous infections in horses.

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Zetapapillomavirus 1 Equus caballus papillomavirus 1 AF498323 NC_003748 Complete genome EcPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Subfamily: Secondpapillomavirinae

Distinguishing features

The exemplar isolate of the single species in the single genus in the Secondpapillomavirinae was isolated from a fish and has the smallest papillomavirus genome known. The genome consists of the core viral proteins (E1, E2, L1, and L2).

Member taxa


Genus: Alefpapillomavirus

Distinguishing features

The exemplar isolate of the single species in this genus was associated with skin lesions of fish, gilt-head (sea) bream (Sparus aurata).

Virion

See discussion under family description

Genome organization and replication

See discussion under family description.

Antigenicity

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

Putative novel papillomavirus genome with complete genome sequence data available and that is <70% related to papillomaviruses within the genus.

Member species

Species Virus name(s) Exemplar isolate Exemplar accession number Exemplar RefSeq number Available sequence Other isolates Other isolate accession numbers Virus abbreviation Isolate abbreviation
Alefpapillomavirus 1 Sparus aurata papillomavirus 1 SA9pv KX643372 NC_030839 Complete genome SaPV1
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Authors: Papillomaviridae

Koenraad Van Doorslaer*
Papillomaviridae Study Group Chair
School of Animal and Comparative Biomedical Sciences
Cancer Biology Graduate Interdisciplinary Program
Genetics Graduate Interdisciplinary Program
BIO5 Institute, and the University of Arizona Cancer Center
University of Arizona,
Tucson, AZ, USA
E-mail: vandoorslaer@email.arizona.edu

Zigui Chen
Department of Microbiology
The Chinese University of Hong Kong
Hong Kong SAR, China
E-mail: zigui.chen@cuhk.edu.hk

Hans-Ulrich Bernard
Department of Molecular Biology and Biochemistry
School of Biological Sciences
University of California Irvine
Irvine, CA, USA
E-mail: hbernard@uci.edu

Chan, Paul
Department of Microbiology
The Chinese University of Hong Kong
Hong Kong SAR, China
E-mail: paulkschan@cuhk.edu.hk

Rob Desalle
Sackler Institute for Comparative Genomics
American Museum of Natural History
Central Park West and 79th St.
New York, NY, USA
E-mail: desalle@amnh.org

Joakim Dillner
International HPV Reference Center
Department of Laboratory Medicine
Karolinska Institutet
14186 Stockholm, Sweden
E-mail: joakim.dillner@ki.se

Ola Forslund
Department of Medical Microbiology
Laboratory Medicine, Lund University
Sölvegatan 23, Sjukhusområdet,
221 85 Lund, Sweden
E-mail: ola.forslund@med.lu.se

Takeshi Haga
The University of Tokyo
Division of Infection Control and Disease Prevention,
Department of Veterinary Medical Science,
1-1-1, Yayoi, Bunkyo-ku,
Tokyo, 113-8657, Japan
E-mail: ahaga@mail.ecc.u-tokyo.ac.jp

Alison A. McBride   
Laboratory of Viral Diseases
National Institute of Allergy and Infectious Diseases
National Institutes of Health
Bethesda, MD 20892, USA
E-mail: AMCBRIDE@niaid.nih.gov

Luisa L. Villa
Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo
Instituto do Câncer do Estado de São Paulo
Centro de Investigação Translacional em Oncologia
Universidade de São Paulo
São Paulo, SP, Brazil
E-mail: llvilla@incthpv.org.br

Robert D. Burk
Departments of Epidemiology and Population Health, Pediatrics, Microbiology and Immunology, and Obstetrics & Gynecology and Women’s Health
Albert Einstein College of Medicine
Bronx, NY, USA
E-mail: robert.burk@einstein.yu.edu

* to whom correspondence should be addressed

The chapter in the Ninth ICTV Report, which served as the template for this chapter, was contributed by Bernard, H.-U., Burk, R.D., deVilliers, E.-M. and zur Hausen, H.


Resources: Papillomaviridae

Websites:

Sequence alignments and tree files:

Figure 4.Papillomaviridae

Concatenated E1, E2, L1, L2 alignment – for 53 isolates (one from each type species)

Tree file (newick format)

Alignment file (FASTA format)

Extended Figure 4.Papillomaviridae 

Concatenated E1, E2, L1, L2 alignment for 343 isolates

Image (pdf format)

Tree file (tre format)

Alignment file (FASTA format)

Genera phylogenetic trees:

Figure 1.Alphapapillomavirus

Figure 1.Betapapillomavirus

Figure 1.Chipapillomavirus

Figure 1.Deltapapillomavirus

Figure 1.Dyokappapapillomavirus

Figure 1.Gammapapillomavirus

Figure 1.Lambdapapillomavirus

Figure 1.Mupapillomavirus

Figure 1.Psipapillomavirus

Figure 1.Taupapillomavirus

Figure 1.Upsilonpapillomavirus

Figure 1.Xipapillomavirus


    Further reading: Papillomaviridae

    The Papillomavirus Episteme (PaVE; pave.niaid.nih.gov (Van Doorslaer et al., 2017; Van Doorslaer et al., 2013)) provides centralized access to a special edition of the journal ‘Virology’ (Lambert PF et al., 2013). This special edition combined expert reviews of various papillomavirus-associated topics.

    Lambert PF, McBride A & HU, B. (2013).Editorial: Special issue: The Papillomavirus Episteme. Virology 445, 1.

    Van Doorslaer, K., Li, Z., Xirasagar, S., Maes, P., Kaminsky, D., Liou, D., Sun, Q., Kaur, R., Huyen, Y. & McBride, A. A. (2017).The Papillomavirus Episteme: a major update to the papillomavirus sequence database. Nucleic Acids Res 45, D499-D506. [PubMed]

    Van Doorslaer, K., Tan, Q., Xirasagar, S., Bandaru, S., Gopalan, V., Mohamoud, Y., Huyen, Y. & McBride, A. A. (2013).The Papillomavirus Episteme: a central resource for papillomavirus sequence data and analysis. Nucleic Acids Res 41, D571-D578. [PubMed]


    References: Papillomaviridae

    Agalliu, I., Gapstur, S., Chen, Z., Wang, T., Anderson, R. L., Teras, L., Kreimer, A. R., Hayes, R. B., Freedman, N. D. & Burk, R. D. (2016).Associations of oral α-, β-, and γ-human papillomavirus types with risk of incident head and neck cancer. JAMA Oncology 2, 599-606. [PubMed]

    Arnold, A. W. & Hofbauer, G. F. (2012).Human papillomavirus and squamous cell cancer of the skin--epidermodysplasia verruciformis-associated human papillomavirus revisited. Curr Probl Dermatol 43, 49-56. [PubMed]

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    Citation: Papillomaviridae

    A summary of this ICTV Report chapter has been published as an ICTV Virus Taxonomy Profile article in the Journal of General Virology, and should be cited when referencing this online chapter as follows:

    Van Doorslaer, K., Chen, Z., Bernard, H., Chan, P.K.S, DeSalle, R., Dillner, J., Forslund, O., Haga, T., McBride, A.A., Villa, L.L., Burk, R.D., and ICTV Report Consortium. 2018, ICTV Virus Taxonomy Profile: Papillomaviridae, Journal of General Virology, 99, 989–990.