1. Comparative evaluation of subtyping tools for surveillance of newly emerging HIV-1 strains
- Author
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Fabeni, Lavinia, Berno, Giulia, Fokam, Joseph, Bertoli, Ada, Alteri, Claudia, Gori, Caterina, Forbici, Federica, Takou, Desirã, Vergori, Alessandra, Zaccarelli, Mauro, Maffongelli, Gaetano, Borghi, Vanni, Latini, Alessandra, Pennica, Alfredo, Mastroianni, Claudio Maria, Montella, Francesco, Mussini, Cristina, Andreoni, Massimo, Antinori, Andrea, Perno, Carlo Federico, Santoro, Maria Mercedes, Armenia, Daniele, Bellocchi, Maria Concetta, Biddittu, Andrea, Bruni, Massimiliano, Buonomini, Anna Rita, Carioti, Luca, Ceccherini Silberstein, Francesca, Cerva, Carlotta, Cesta, Novella, Di Carlo, Domenico, Dori, Luca, Foroghi, Luca, Gentilotti, Elisa, Giannella, Sara, Guenci, Tania, Malagnino, Vincenzo, Ricciardi, Alessandra, Romani, Marzia, Salpini, Omina, Sarmati, Loredana, Scutari, Rossana, Serafini, Valentina, Sordillo, Pasquale, Stazi, Francesca, Stingone, Cristof, Svicher, Valentina, Teti, Elisabetta, Viscione, Magdalena, Abbate, Isabella, Acinapura, Rosa, Alba, Lucia, Ammassari, Adriana, Baldini, Franco, Bellagamba, Rita, Boumis, Evangelo, Capobianchi, Maria Rosaria, Carta, Stefania, Cicalini, Stefania, Continenza, Fabio, De Carli, Gabriella, D'Arrigo, Roberta, D'Offizi, Gianpiero, Fedele, Valentina, Galati, Vincenzo, Giannetti, Alberto, Girardi, Enrico, Grisetti, Susanna, Libertone, Raffaella, Liuzzi, Giuseppina, Lorenzini, Patrizia, Maddaluno, Rita, Mariano, Andrea, Navarra, Assunta, Nicastri, Emanuele, Nurra, Giuseppina, Orchi, Nicoletta, Palummieri, Antonio, Pinnetti, Carmela, Pittalis, Silvia, Pizzi, Daniele, Puro, Vincenzo, Sampaolesi, Alessandro, Sciarrone, Maria Rosaria, Scognamiglio, Paola, Sias, Catia, Visco Comandini, Ubaldo, Colafigli, Manuela, Cristaudo, Antonio, Giuliani, Massimo, Pacifici, Anna, Di Sora, Fiorella, Iebba, Filippo, Lichtner, Miriam, Marocco, Raffaella, Bernardi, Stefania, Anzalone, Enza, Bonaventura, Maria Elena, Marchili, Mauro, Pitorri, Antonella, Di Francesco, Luigi Falconi, Di Giammartino, Dante, Caterini, Antonio, Armignacco, Orlando, Mariani, Rinalda, Paoloni, Maurizio, Parruti, Giustino, Pieri, Alessandro, Sozio, Federica, Cellini, Antonio, Grimaldi, Alessandro, Mariani, Maurizio, Picchi, Giovanna, Gennari, William, Nanfack, Aubin J., Ndjolo, Alexis, and Torimiro, Judith N.
- 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 - 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.
- Published
- 2017