Comparative evaluation of subtyping tools for surveillance of newly emerging HIV-1 strains

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

Research output: Contribution to journalArticle

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.

Original languageEnglish
Pages (from-to)2827-2837
Number of pages11
JournalJournal of Clinical Microbiology
Volume55
Issue number9
DOIs
Publication statusPublished - Sep 1 2017

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Keywords

  • Circulating recombinant forms
  • Genetic diversity
  • HIV-1
  • Phylogeny
  • Subtypes
  • Subtyping automated tools

ASJC Scopus subject areas

  • Microbiology (medical)

Cite this

Fabeni, L., Berno, G., Fokam, J., Bertoli, A., Alteri, C., Gori, C., Forbici, F., Takou, D., Vergori, A., Zaccarelli, M., Maffongelli, G., Borghi, V., Latini, A., Pennica, A., Mastroianni, C. M., Montella, F., Mussini, C., Andreoni, M., Antinori, A., ... Torimiro, J. N. (2017). Comparative evaluation of subtyping tools for surveillance of newly emerging HIV-1 strains. Journal of Clinical Microbiology, 55(9), 2827-2837. https://doi.org/10.1128/JCM.00656-17