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Comparative evaluation of subtyping tools for surveillance of newly emerging HIV-1 strains
- Publication Year :
- 2017
- Publisher :
- American Society for Microbiology, 2017.
-
Abstract
- HIV-1 non-B subtypes/circulating recombinant forms (CRFs) are increasing worldwide. Since subtype identification can be clinically relevant, we assessed the added value in HIV-1 subtyping using updated molecular phylogeny (Mphy) and the performance of routinely used automated tools. Updated Mphy (2015 updated reference sequences), used as a gold standard, was performed to subtype 13,116 HIV-1 protease/reverse transcriptase sequences and then compared with previous Mphy (reference sequences until 2014) and with COMET, REGA, SCUEAL, and Stanford subtyping tools. Updated Mphy classified subtype B as the most prevalent (73.4%), followed by CRF02_AG (7.9%), C (4.6%), F1 (3.4%), A1 (2.2%), G (1.6%), CRF12_BF (1.2%), and other subtypes (5.7%). A 2.3% proportion of sequences were reassigned as different subtypes or CRFs because of misclassification by previous Mphy. Overall, the tool most concordant with updated Mphy was Stanford-v8.1 (95.4%), followed by COMET (93.8%), REGA-v3 (92.5%), Stanford-old (91.1%), and SCUEAL (85.9%). All the tools had a high sensitivity (≥98.0%) and specificity (≥95.7%) for subtype B. Regarding non-B subtypes, Stanford-v8.1 was the best tool for C, D, and F subtypes and for CRFs 01, 02, 06, 11, and 36 (sensitivity, ≥92.6%; specificity, ≥99.1%). A1 and G subtypes were better classified by COMET (92.3%) and REGA-v3 (98.6%), respectively. Our findings confirm Mphy as the gold standard for accurate HIV-1 subtyping, although Stanford-v8.1, occasionally combined with COMET or REGA-v3, represents an effective subtyping approach in clinical settings. Periodic updating of HIV-1 reference sequences is fundamental to improving subtype characterization in the context of an effective epidemiological surveillance of non-B strains.
- Subjects :
- 0301 basic medicine
Microbiology (medical)
Settore MED/17 - Malattie Infettive
Human immunodeficiency virus (HIV)
Context (language use)
HIV Infections
Biology
medicine.disease_cause
Sensitivity and Specificity
Genetic diversity
Comparative evaluation
03 medical and health sciences
HIV Protease
Virology
Genotype
Circulating recombinant forms
HIV-1
Phylogeny
Subtypes
Subtyping automated tools
Databases, Genetic
medicine
Humans
CRFS
Automation, Laboratory
Base Sequence
Sequence Analysis, RNA
circulating recombinant forms
genetic diversity
phylogeny
subtypes
subtyping automated tools
microbiology
Gold standard (test)
Subtyping
HIV Reverse Transcriptase
Molecular Typing
030104 developmental biology
Epidemiological surveillance
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Accession number :
- edsair.doi.dedup.....412d8a78738e32e68c081959183e683a