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.

Comparative evaluation of subtyping tools for surveillance of newly emerging HIV-1 strains / L. Fabeni, G. Berno, J. Fokam, A. Bertoli, C. Alteri, C. Gori, F. Forbici, D. Takou, A. Vergori, M. Zaccarelli, G. Maffongelli, V. Borghi, A. Latini, A. Pennica, C.M. Mastroianni, F. Montella, C. Mussini, M. Andreoni, A. Antinori, C.F. Perno, M.M. Santoro. - In: JOURNAL OF CLINICAL MICROBIOLOGY. - ISSN 0095-1137. - 55:9(2017), pp. 2827-2837.

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

C. Alteri;C.F. Perno;
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.
English
Circulating recombinant forms; Genetic diversity; HIV-1; Phylogeny; Subtypes; Subtyping automated tools; Microbiology (medical)
Settore MED/07 - Microbiologia e Microbiologia Clinica
Articolo
Esperti anonimi
Pubblicazione scientifica
2017
American Society for Microbiology
55
9
2827
2837
11
Pubblicato
Periodico con rilevanza internazionale
Aderisco
info:eu-repo/semantics/article
Comparative evaluation of subtyping tools for surveillance of newly emerging HIV-1 strains / L. Fabeni, G. Berno, J. Fokam, A. Bertoli, C. Alteri, C. Gori, F. Forbici, D. Takou, A. Vergori, M. Zaccarelli, G. Maffongelli, V. Borghi, A. Latini, A. Pennica, C.M. Mastroianni, F. Montella, C. Mussini, M. Andreoni, A. Antinori, C.F. Perno, M.M. Santoro. - In: JOURNAL OF CLINICAL MICROBIOLOGY. - ISSN 0095-1137. - 55:9(2017), pp. 2827-2837.
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Prodotti della ricerca::01 - Articolo su periodico
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Article (author)
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L. Fabeni, G. Berno, J. Fokam, A. Bertoli, C. Alteri, C. Gori, F. Forbici, D. Takou, A. Vergori, M. Zaccarelli, G. Maffongelli, V. Borghi, A. Latini, ...espandi
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/623143
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