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Journal of Virology, May 2005, p. 6565-6569, Vol. 79, No. 10
0022-538X/05/$08.00+0     doi:10.1128/JVI.79.10.6565-6569.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Papillomavirus Subtypes Are Natural and Old Taxa: Phylogeny of Human Papillomavirus Types 44 and 55 and 68a and -b

Itzel E. Calleja-Macias,¹ Mina Kalantari,¹ Bruce Allan,² Anna-Lise Williamson,^2,3 Lap-Ping Chung,⁴ Robert J. Collins,⁴ Rosemary E. Zuna,⁵ S. Terence Dunn,⁵ Rocio Ortiz-Lopez,⁶ Hugo A. Barrera-Saldaña,⁶ Heather A. Cubie,⁷ Kate Cuschieri,⁷ Luisa L. Villa,⁸ and Hans-Ulrich Bernard^1*

Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California 92697,¹ Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences,² National Health Laboratory Service, University of Cape Town, Cape Town, South Africa,³ Queen Mary Hospital and the University of Hong Kong, Hong Kong,⁴ Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104,⁵ Departamento de Bioquimica, Facultad de Medicina, Universidad Autonoma de Nueva Leon, Monterrey, Mexico,⁶ Royal Infirmary of Edinburgh, Edinburgh, Scotland,⁷ Ludwig Institute for Cancer Research, Sao Paulo, Brazil⁸

Received 16 November 2004/ Accepted 18 January 2005

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.

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* Corresponding author. Mailing address: Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900. Phone: (949) 824-5162. Fax: (949) 824-8551. E-mail: hbernard{at}uci.edu.

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Journal of Virology, May 2005, p. 6565-6569, Vol. 79, No. 10
0022-538X/05/$08.00+0     doi:10.1128/JVI.79.10.6565-6569.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

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