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Bioinformatics Advance Access published online on August 2, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti607
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received March 28, 2005
Revised June 23, 2005
Accepted July 28, 2005

Applications note

An automated genotyping system for analysis of HIV-1 and other microbial sequences

Tulio de Oliveira 1*, Koen Deforche 2, Sharon Cassol 3, Mika Salminen 4, Dimitris Paraskevis 2, Chris Seebregts 5, Joke Snoeck 2, Estrelita Janse van Rensburg 3, Annemarie M. J. Wensing 6, David A. van de Vijver 7, Charles A. Boucher 7, Ricardo Camacho 8, and Anne-Mieke Vandamme 2

1 Evolution Group at the Zoology Department, University of Oxford, UK
2 Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
3 HIV-1 Immunopathogenesis and Therapeutics Research Program, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
4 Department of Infectious Disease Epidemiology, HIV-Laboratory, National Public Health Institute, Helsinki, Finland
5 Research Information Systems Division, South African Medical Research Council, Cape Town, South Africa
6 Eijkman Winkler Institute, Department of Medical Microbiology, Sub department of Virology, University Medical Center Utrecht, Utrecht, the Netherlands; Division of Internal Medicine and Dermatology, Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht, the Netherlands
7 Eijkman Winkler Institute, Department of Medical Microbiology, Sub department of Virology, University Medical Center Utrecht, Utrecht, the Netherlands
8 Virology Laboratory, Hospital Egas Moniz, Lisbon, Portugal

* To whom correspondence should be addressed.
Tulio de Oliveira, E-mail: tulio.deoliveira{at}zoo.oxford.ac.uk


  Abstract

Motivation: Genetic analysis of HIV-1 is important not only for vaccine development, but also to guide treatment strategies, track the emergence of new viral variants and ensure that diagnostic assays are contemporary and fully optimized. However, most genotyping methods are laborious and complex, and involve the use of multiple software applications. Here, we describe the development of an automated genotyping system that can be easily applied to HIV-1, and other rapidly evolving viral pathogens.

Design and Results: The new REGA subtyping tool, developed using Java programming and PERL scripts, combines phylogenetic analyses with bootscanning methods for the genetic subtyping of full-length and subgenomic fragments of HIV-1. When used to investigate the subtype of previously published reference datasets that were analysed using manual phylogenetic methods, the automated method correctly identified 97.5%-100% of non-recombinant and circulating recombinant forms (CRFs) of HIV-1, including 108 full-length, 108 gag and 221 env sequences downloaded from the Los Alamos database.

Availability: The tool, which can be easily downloaded and installed on either a UNIX or Linux-based computer system, is available at http//www.bioafrica.net/subtypetool/.


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