An automated genotyping system for analysis of HIV-1 and other microbial sequences.
BACKGROUND
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.
de Oliveira
Tulio
T
Evolution Group at the Zoology Department, University of Oxford, UK. tulio.deoliveira@zoology.oxford.ac.uk
Deforche
Koen
K
Cassol
Sharon
S
Salminen
Mika
M
Paraskevis
Dimitris
D
Seebregts
Chris
C
Snoeck
Joe
J
van Rensburg
Estrelita Janse
EJ
Wensing
Annemarie M J
AM
van de Vijver
David A
DA
Boucher
Charles A
CA
Camacho
Ricardo
R
Vandamme
Anne-Mieke
AM
D000465:Algorithms; D001185:Artificial Intelligence; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D004279:DNA, Viral / Q000032:analysis / Q000235:genetics*; D005838:Genotype; D015497:HIV-1 / Q000235:genetics*; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods*; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D004279:DNA, Viral