Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: Performance evaluation of the new REGA version 3 and seven other tools

Abstract

REGAv3 had an improved performance for subtype B and CRF02_AG compared to REGAv2 and is now able to also identify all epidemiologically relevant CRFs. In general the best performing tools, in alphabetical order, were COMET, jpHMM, REGAv3, and SCUEAL when analyzing pure subtypes in the pol region, and COMET and REGAv3 when analyzing most of the CRFs. Based on this study, we recommend to confirm subtyping with 2 well performing tools, and be cautious with the interpretation of short sequences.

The changing molecular epidemiology of HIV in the Philippines

“…Subtype assignments were compared with those from the Rega V3 subtyping tool and with SCUEAL (Pineda-Pena et al, 2013;Kosakovsky Pond et al, 2009).…”

A Phylogenetic Analysis of Human Immunodeficiency Virus Type 1 Sequences in Kiev: Findings Among Key Populations

“…Rega3 subtyping was performed (20). Sequences were examined for transmitted drug resistance Analysis of clusters was performed using programs written in R. Fasttree SH local branch support values of ≥80%, and a maximum genetic distance of 2.5% between all sequence pairs were used to identify clusters.…”

Co-Receptor Tropism Determined by Genotypic Assay in HIV-1 Circulating in Cuba

“…COMET version 2 (available at (http://comet.retrovirology.lu) [24], and REGA version 3 (available at http://bioafrica.mrc.ac.za:8080/ rega-genotype-3.0.2/hiv/typingtool/) [25,26] were used to do an initial subtype classification of the sequences. Since the Cuban epidemic is characterized by a high number of circulating recombinant forms (CRFs) and unique recombinant forms (URFs) [17], all assignments were confirmed with manual phylogenetic analysis.…”