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REGA HPV Alignment & Subtyping Process

The subtyping process consists of three steps:

The initiat steps involves the identification of the genomic region at the HPV1 reference sequence. This process uses BLAST software.

The second step involves the alignment of the query sequences with complete L1 reference sequences for HPV..  More information on the alignment is found below.

The final step involves construction of a phylogenetic tree using HKY distance method with gamma distribution in PAUP* software. The HHV8 subtypes and sub-groups are identified using JAVA software.

Papillomavirus classification system


Taxonomic level




Less than 60% nt identity in entire L1 ORF

18 genera (alpha to sigma)



2 additional new genera, yet unnamed (containing TtPV2 and RaPV1 respectively)


Between 60% and 70% nt identity in L1

From 1 species (in most genera) up to 15 species (in genus alpha)


Between 71 and 89 % nt identity in L1

Currently 120 papillomavirus genotypes completely genomically characterized and available in Genbank (98 human: HPV; 32 non-human)


Between 90 and 98 % identity in L1

Very rare


More than 98 % identity in L1



- For a novel papillomavirus sequence to be classified as a new genotype, the complete genome has to be cloned and the L1 ORF has to differ by more than 10% from the closest known PV type.


Genetic regions suitable for classification:

Current classification is based on sequence identity in the L1 ORF because:

- The L1 ORF is the most conserved gene within the genome, and has been used for identification of new PV genotypes over past decades.

- Almost all subgenomic PCR amplicons that are generated with the currently available consensus or degenerate primer sets are located within the L1 ORF.


Reasons why other genomic regions are not used for classification:

- Some ORFs are not present in all papillomaviruses: E4, E5, E6 and E7 are lacking in some PVs.

- The E1, E2, E4, E4, E5, E6, E7 and L2 ORFs are all less conserved than L1, making reliable alignment of these ORFs difficult for PVs belonging to different genera, and only short conserved parts of these ORFs can be reliably aligned.



de Villiers EM, Fauquet C, Broker TR, Bernard HU, zur Hausen H. Classification of papillomaviruses. Virology. 2004 Jun 20;324(1):17-27.


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Developed by: Annabel Rector, Marc Van Ranst, Andrew Rambaut, and Tulio de Oliveira.

Developed in cooperation with the Evolutionary Biology Group at University of Oxford, UK, the REGA Institute at the Katholieke Universiteit Leuven, Belgium.

Funded by the Marie Curie Fellowship, Flemish Fund for Scientific Research (Fonds voor Wetenschappelijk Onderzoek, FWO) grant G.0513.06 and by a postdoctoral fellowship of the Research Fund K.U.Leuven

For HPV subtyping questions please contact Dr Tulio de Oliveira.