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 boot-scanning 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.
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 boot-scanning 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.
Authors: Ziad El-Khatib; Anna Mia Ekstrom; Johanna Ledwaba; Lerato Mohapi; Fatima Laher; Alan Karstaedt; Salome Charalambous; Max Petzold; David Katzenstein; Lynn Morris Journal: AIDS Date: 2010-07-17 Impact factor: 4.177
Authors: Nellie Wadonda-Kabondo; Richard Banda; Kundai Moyo; Maurice M'bang'ombe; Mabvuto Chiwaula; Carol Porter; Michael R Jordan Journal: Clin Infect Dis Date: 2012-05 Impact factor: 9.079
Authors: Gustavo H Kijak; Sodsai Tovanabutra; Chris Beyrer; Eric E Sanders-Buell; Miguel A Arroyo; Merlin L Robb; Nelson L Michael; Francine E McCutchan; Jerome H Kim Journal: AIDS Res Hum Retroviruses Date: 2010-10-21 Impact factor: 2.205
Authors: Íris M Santos; Elis A da Rosa; Tiago Gräf; Luiz G E Ferreira; Andrea Petry; Fernanda Cavalheiro; Edna M Reiche; Carlos R Zanetti; Aguinaldo R Pinto Journal: AIDS Res Hum Retroviruses Date: 2015-09-21 Impact factor: 2.205