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, Resistance Study Group, Manuela Colafigli, Antonio Cristaudo, Massimo Giuliani, Anna Pacifici

Research output: Contribution to journalArticlepeer-review


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
Issue number9
Publication statusPublished - Sep 2017


  • Journal Article


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