Sensitivity of seven HIV subtyping tools differs among subtypes/recombinants in the Spanish cohort of naïve HIV-infected patients (CoRIS)

• Published in: Antiviral research Vol. 89; no. 1; pp. 19 - 25
• Main Authors: Yebra, Gonzalo, de Mulder, Miguel, Martín, Leticia, Pérez-Cachafeiro, Santiago, Rodríguez, Carmen, Labarga, Pablo, García, Federico, Tural, Cristina, Jaén, Àngels, Navarro, Gemma, Holguín, Á.
• Format: Journal Article
• Language: English
• Published: Kidlington Elsevier B.V 2011; Elsevier
• Subjects: Automation - methods; Biological and medical sciences; Fundamental and applied biological sciences. Psychology; Genotype; HIV Infections - virology; HIV-1 - classification; HIV-1 - genetics; HIV-1 - isolation & purification; HIV-1 non-B subtypes; Human immunodeficiency virus 1; Human viral diseases; Humans; Immunodeficiencies; Immunodeficiencies. Immunoglobulinopathies; Immunopathology; Infectious diseases; Medical sciences; Microbiology; Molecular Typing; Phylogenetic analysis; Phylogeny; pol Gene Products, Human Immunodeficiency Virus - genetics; Recombinants; Replicative cycle, interference, host-virus relations, pathogenicity, miscellaneous strains; Sensitivity and Specificity; Spain; Subtyping tools; Viral diseases; Viral diseases of the lymphoid tissue and the blood. Aids; Virology; Virology - methods; Europe; Spain; Phylogenetic analysis; Subtyping tools; Recombinants; HIV-1 non-B subtypes; HIV-1 virus; Recombinant virus; Phylogeny; Microbiological investigation; Classification; Clinical isolate; Human; Immunopathology; Typing; Phylogenetic tree; Genetic variant; Retroviridae; AIDS; Immune deficiency; Lentivirus; Infection; Virus; Analysis method; Viral disease; Human immunodeficiency virus; Subtype
• ISSN: 0166-3542; 1872-9096
• DOI: 10.1016/j.antiviral.2010.10.008

HIV-1 group M is classified into 9 subtypes and recombinants (CRFs/URFs). Variants other than subtype B (non-B) cause 90% of infections worldwide. HIV is often subtyped using automated tools instead of the gold-standard phylogenetic analysis. We evaluated the reliability of subtyping tools vs. phylogeny in a panel of HIV-1 pol sequences from the cohort of naïve patients of the HIV/AIDS Spanish Research Network (CoRIS). HIV-1 subtyping was performed using seven automated subtyping tools (Stanford, Geno2pheno, Rega, NCBI, EuResist, STAR, TherapyEdge) in HIV-1 pol sequences from 670 CoRIS patients previously subtyped by phylogeny (587 subtype B/83 non-B). Sensitivity with respect to phylogeny was assessed. Most tools correctly classified subtype B, although up to 15% of non-B sequences were wrongly identified as B depending on the tool. For subtype B and CRF02_AG identification, Stanford/NCBI and Geno2pheno/Rega presented the highest/lowest sensitivities, respectively. EuResist and Geno2pheno correctly classified all 13 non-B “pure”subtypes at pol. The efficacy of all subtyping tools dropped clearly when identifying recombinants different from CRF02_AG. Only NCBI05, Rega and STAR identified URF, but with very low sensitivities. NCBI classified the highest number of subtypes B as non-B, and overestimated recombinants, especially when including references of 2009. Automated tools are useful for subtype B identification, although they present serious limitations in classifying variants uncommon in developed regions, especially recombinants. Their sensitivity depends on the prevalence of non-B variants in the population, and decreases drastically when the frequency of recombinants increases. Furthermore, HIV-1 variant distribution differs according to the tool used.