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Bioinformatics Advance Access originally published online on August 2, 2005
Bioinformatics 2005 21(19):3797-3800; doi:10.1093/bioinformatics/bti607
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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, Joe Snoeck 2, Estrelita Janse van Rensburg 3, Annemarie M. J. Wensing 6,7, David A. van de Vijver 6, Charles A. Boucher 6, Ricardo Camacho 8 and Anne-Mieke Vandamme 2

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

*To whom correspondence should be addressed.

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.

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 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/html/

Contact: tulio.deoliveira{at}zoology.oxford.ac.uk

Received on March 28, 2005; revised on June 23, 2005; accepted on July 28, 2005

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