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.
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).
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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 | Isolate | Accession number | RefSeq number | Available sequence | Virus Abbrev. | |
---|---|---|---|---|---|---|---|
Alphapapillomavirus 1 | human papillomavirus 32 | X74475 | NC_001586 | Complete genome | HPV32 | ||
Alphapapillomavirus 1 | human papillomavirus 42 | M73236 | Complete genome | HPV42 | |||
Alphapapillomavirus 2 | human papillomavirus 10 | X74465 | NC_001576 | Complete genome | HPV10 | ||
Alphapapillomavirus 2 | human papillomavirus 160 | TM | AB745694 | Complete genome | HPV160 | ||
Alphapapillomavirus 2 | human papillomavirus 94 | AJ620211 | Complete genome | HPV94 | |||
Alphapapillomavirus 2 | human papillomavirus 125 | SIBX9 | FN547152 | Complete genome | HPV125 | ||
Alphapapillomavirus 2 | human papillomavirus 117 | a_wart10 | GQ246950 | Complete genome | HPV117 | ||
Alphapapillomavirus 2 | human papillomavirus 78 | XS2 | KC138720 | Complete genome | HPV78 | ||
Alphapapillomavirus 2 | human papillomavirus 28 | U31783 | Complete genome | HPV28 | |||
Alphapapillomavirus 2 | human papillomavirus 29 | U31784 | Complete genome | HPV29 | |||
Alphapapillomavirus 2 | human papillomavirus 3 | X74462 | Complete genome | HPV3 | |||
Alphapapillomavirus 2 | human papillomavirus 77 | Y15175 | Complete genome | HPV77 | |||
Alphapapillomavirus 3 | human papillomavirus 61 | U31793 | NC_001694 | Complete genome | HPV61 | ||
Alphapapillomavirus 3 | human papillomavirus 83 | AF151983 | Complete genome | HPV83 | |||
Alphapapillomavirus 3 | human papillomavirus 84 | CY10-452 | AF293960 | Complete genome | HPV84 | ||
Alphapapillomavirus 3 | human papillomavirus 86 | AF349909 | Complete genome | HPV86 | |||
Alphapapillomavirus 3 | human papillomavirus 89 | AF436128 | Complete genome | HPV89 | |||
Alphapapillomavirus 3 | human papillomavirus 87 | AJ400628 | Complete genome | HPV87 | |||
Alphapapillomavirus 3 | human papillomavirus 81 | AJ620209 | Complete genome | HPV81 | |||
Alphapapillomavirus 3 | human papillomavirus 62 | Qv18091 | AY395706 | Complete genome | HPV62 | ||
Alphapapillomavirus 3 | human papillomavirus 102 | Qv34077 | DQ080083 | Complete genome | HPV102 | ||
Alphapapillomavirus 3 | human papillomavirus 114 | GQ244463 | Complete genome | HPV114 | |||
Alphapapillomavirus 3 | human papillomavirus 72 | X94164 | Complete genome | HPV72 | |||
Alphapapillomavirus 4 | human papillomavirus 2 | X55964 | NC_001352 | Complete genome | HPV2 | ||
Alphapapillomavirus 4 | human papillomavirus 57 | X55965 | Complete genome | HPV57 | |||
Alphapapillomavirus 4 | human papillomavirus 27 | X74473 | Complete genome | HPV27 | |||
Alphapapillomavirus 5 | human papillomavirus 26 | X74472 | NC_001583 | Complete genome | HPV26 | ||
Alphapapillomavirus 5 | human papillomavirus 69 | AB027020 | Complete genome | HPV69 | |||
Alphapapillomavirus 5 | human papillomavirus 82 | AB027021 | Complete genome | HPV82 | |||
Alphapapillomavirus 5 | human papillomavirus 51 | M62877 | Complete genome | HPV51 | |||
Alphapapillomavirus 6 | human papillomavirus 30 | X74474 | NC_038889 | Complete genome | HPV30 | ||
Alphapapillomavirus 6 | human papillomavirus 66 | U31794 | Complete genome | HPV66 | |||
Alphapapillomavirus 6 | human papillomavirus 53 | X74482 | Complete genome | HPV53 | |||
Alphapapillomavirus 6 | human papillomavirus 56 | X74483 | Complete genome | HPV56 | |||
Alphapapillomavirus 7 | human papillomavirus 18 | X05015 | NC_001357 | Complete genome | HPV18 | ||
Alphapapillomavirus 7 | human papillomavirus 85 | AF131950 | Complete genome | HPV85 | |||
Alphapapillomavirus 7 | human papillomavirus 68 | Plasmid 952 | DQ080079 | Complete genome | HPV68 | ||
Alphapapillomavirus 7 | human papillomavirus 97 | Qv28597 | DQ080080 | Complete genome | HPV97 | ||
Alphapapillomavirus 7 | human papillomavirus 39 | M62849 | Complete genome | HPV39 | |||
Alphapapillomavirus 7 | human papillomavirus 70 | U21941 | Complete genome | HPV70 | |||
Alphapapillomavirus 7 | human papillomavirus 45 | X74479 | Complete genome | HPV45 | |||
Alphapapillomavirus 7 | human papillomavirus 59 | X77858 | Complete genome | HPV59 | |||
Alphapapillomavirus 8 | human papillomavirus 7 | X74463 | NC_001595 | Complete genome | HPV7 | ||
Alphapapillomavirus 8 | human papillomavirus 91 | AF419318 | Complete genome | HPV91 | |||
Alphapapillomavirus 8 | human papillomavirus 43 | AJ620205 | Complete genome | HPV43 | |||
Alphapapillomavirus 8 | human papillomavirus 40 | X74478 | Complete genome | HPV40 | |||
Alphapapillomavirus 9 | human papillomavirus 16 | K02718 | NC_001526 | Complete genome | HPV16 | ||
Alphapapillomavirus 9 | human papillomavirus 67 | D21208 | Complete genome | HPV67 | |||
Alphapapillomavirus 9 | human papillomavirus 58 | GN479 | D90400 | Complete genome | HPV58 | ||
Alphapapillomavirus 9 | human papillomavirus 31 | J04353 | Complete genome | HPV31 | |||
Alphapapillomavirus 9 | human papillomavirus 33 | M12732 | Complete genome | HPV33 | |||
Alphapapillomavirus 9 | human papillomavirus 35 | X74477 | Complete genome | HPV35 | |||
Alphapapillomavirus 9 | human papillomavirus 52 | X74481 | Complete genome | HPV52 | |||
Alphapapillomavirus 10 | human papillomavirus 6 | X00203 | NC_001355 | Complete genome | HPV6 | ||
Alphapapillomavirus 10 | human papillomavirus 74 | AE10 | AF436130 | Complete genome | HPV74 | ||
Alphapapillomavirus 10 | human papillomavirus 11 | M14119 | Complete genome | HPV11 | |||
Alphapapillomavirus 10 | human papillomavirus 44 | U31788 | Complete genome | HPV44 | |||
Alphapapillomavirus 10 | human papillomavirus 13 | X62843 | Complete genome | HPV13 | |||
Alphapapillomavirus 10 | Pan paniscus papillomavirus 1 | X62844 | Complete genome | PpPV1 | |||
Alphapapillomavirus 11 | human papillomavirus 34 | X74476 | NC_001587 | Complete genome | HPV34 | ||
Alphapapillomavirus 11 | human papillomavirus 73 | X94165 | Complete genome | HPV73 | |||
Alphapapillomavirus 12 | Macaca mulata papillomavirus 1 | M60184 | NC_001678 | Complete genome | MmPV1 | ||
Alphapapillomavirus 12 | Macaca fascicularis papillomavirus 7 | Mac18 | EF558838 | Complete genome | MfPV7 | ||
Alphapapillomavirus 12 | Macaca fascicularis papillomavirus 3 | Mac26 | EF558839 | Complete genome | MfPV3 | ||
Alphapapillomavirus 12 | Macaca fascicularis papillomavirus 6 | Mac39 | EF558840 | Complete genome | MfPV6 | ||
Alphapapillomavirus 12 | Macaca fascicularis papillomavirus 4 | Mac54 | EF558841 | Complete genome | MfPV4 | ||
Alphapapillomavirus 12 | Macaca fascicularis papillomavirus 8 | Mac70 | EF558842 | Complete genome | MfPV8 | ||
Alphapapillomavirus 12 | Macaca fascicularis papillomavirus 5 | Mac76 | EF558843 | Complete genome | MfPV5 | ||
Alphapapillomavirus 12 | Macaca fascicularis papillomavirus 10 | Mac616 | EU490515 | Complete genome | MfPV10 | ||
Alphapapillomavirus 12 | Macaca fascicularis papillomavirus 9 | Mac592 | EU490516 | Complete genome | MfPV9 | ||
Alphapapillomavirus 12 | Macaca fascicularis papillomavirus 11 | Mac1637 | GQ227670 | Complete genome | MfPV11 | ||
Alphapapillomavirus 12 | Papio hamadryas papillomavirus 1 | Mac2085 | JF304764 | Complete genome | PhPV1 | ||
Alphapapillomavirus 12 | Macaca fuscata papillomavirus 1 | OSCC1 | KT944080 | Complete genome | 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 | Complete genome | HPV90 | |||
Alphapapillomavirus 14 | human papillomavirus 106 | Qv28897 | DQ080082 | Complete genome | HPV106 | ||
Alphapapillomavirus 14 | Colobus guereza papillomavirus 1 | GU014532 | Complete genome | 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 |
HPV-mEV06c12b |