Comparative performance of the REGA subtyping tool version 2 versus version 1

The REGA HIV-1 subtyping tool is a phylogenetic-based method for subtyping HIV-1 genomic sequences that was published in 2005 The subtyping tool combines phylogenetic approaches with recombination detection methods. Recently, version 2 was released (http://www.bioafrica net/rega-genotype/html/index.html) as an improvement of version 1 Version 2 implements a Decision-Tree-based algorithm that was not implemented in version 1 We wanted to compare the two versions on a large sequence dataset to assess the improvements of version 2 and to verify whether features lost during updating the tool needed to be recovered We analysed the results of the two versions in the genotyping of 4676 HIV-1 pol sequences. We compared those results to a manual approach, used in previous studies Our results show that version 2 has an overall better sensitivity but especially for the detection of subtypes A, B, D, F, G and CRF14_BG and CRF06_CPX For the other subtypes, no significant differences were observed in the sensitivity of versions 1 and 2. The overall increase in sensitivity was however accompanied by a decrease in the specificity for the detection of subtype B This is the main limitation of version 2 However, while the number of false negatives decreased by 53 samples, the number of false positives increased only by 5 samples from version 1 to 2 The performance of the REGA HIV-1 subtyping tool was considerably improved from one version to the other. Our results are very valuable and allow us to make suggestions for further improvement of the tool for a version 3 release (C) 2009 Elsevier B V All rights reserved.