Papillomavirus subtypes are natural and old taxa: phylogeny of human papillomavirus types 44 and 55 and 68a and -b.
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.
Calleja-Macias
Itzel E
IE
Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA.
Kalantari
Mina
M
Allan
Bruce
B
Williamson
Anna-Lise
AL
Chung
Lap-Ping
LP
Collins
Robert J
RJ
Zuna
Rosemary E
RE
Dunn
S Terence
ST
Ortiz-Lopez
Rocio
R
Barrera-Saldaña
Hugo A
HA
Cubie
Heather A
HA
Cuschieri
Kate
K
Villa
Luisa L
LL
Bernard
Hans-Ulrich
HU
D008969:Molecular Sequence Data; D027383:Papillomaviridae / Q000145:classification / Q000235:genetics*; D010802:Phylogeny