title: Papillomavirus subtypes are natural and old taxa: phylogeny of human papillomavirus types 44 and 55 and 68a and -b.
abstract: A human papillomavirus (HPV) type is defined as an HPV isolate whose L1 gene sequence is at least 10% different from that of any other type, while a subtype is 2 to 10% different from any HPV type. In order to analyze the phylogeny behind the subtype definition, we compared 49 isolates of HPV type 44 (HPV-44) and its subtype HPV-55, previously misclassified as a separate type, and 41 isolates of the subtype pair HPV-68a and -b, sampled from cohorts in four continents. The subtypes of each pair are separated by deep dichotomic branching, and three of the four subtypes have evolved large phylogenetic clusters of genomic variants forming a "star" phylogeny, with some branches specific for ethnically defined cohorts. We conclude that subtypes of HPV types are natural and old taxa, equivalent to types, which either diverged more recently than types or evolved more slowly.
authors.affiliation: Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA.
authors.forename: Itzel E
authors.initials: IE
authors.lastname: Calleja-Macias
authors.forename: Mina
authors.initials: M
authors.lastname: Kalantari
authors.forename: Bruce
authors.initials: B
authors.lastname: Allan
authors.forename: Anna-Lise
authors.initials: AL
authors.lastname: Williamson
authors.forename: Lap-Ping
authors.initials: LP
authors.lastname: Chung
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Collins
authors.forename: Rosemary E
authors.initials: RE
authors.lastname: Zuna
authors.forename: S Terence
authors.initials: ST
authors.lastname: Dunn
authors.forename: Rocio
authors.initials: R
authors.lastname: Ortiz-Lopez
authors.forename: Hugo A
authors.initials: HA
authors.lastname: Barrera-Saldaña
authors.forename: Heather A
authors.initials: HA
authors.lastname: Cubie
authors.forename: Kate
authors.initials: K
authors.lastname: Cuschieri
authors.forename: Luisa L
authors.initials: LL
authors.lastname: Villa
authors.forename: Hans-Ulrich
authors.initials: HU
authors.lastname: Bernard
mesh_terms: D008969:Molecular Sequence Data; D027383:Papillomaviridae / Q000145:classification / Q000235:genetics*; D010802:Phylogeny