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

2 Citations (Scopus)

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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Phylogeny
HIV-1
Sensitivity and Specificity

Keywords

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

ASJC Scopus subject areas

  • Microbiology (medical)

Cite this

Comparative evaluation of subtyping tools for surveillance of newly emerging HIV-1 strains. / Fabeni, Lavinia; Berno, Giulia; Fokam, Joseph; Bertoli, Ada; Alteri, Claudia; Gori, Caterina; Forbici, Federica; Takou, Desiré; 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; Torimiro, Judith N.

In: Journal of Clinical Microbiology, Vol. 55, No. 9, 01.09.2017, p. 2827-2837.

Research output: Contribution to journalArticle

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, CM, Montella, F, Mussini, C, Andreoni, M, Antinori, A, Perno, CF, Santoro, MM, Armenia, D, Bellocchi, MC, Biddittu, A, Bruni, M, Buonomini, AR, Carioti, L, Ceccherini-Silberstein, F, Cerva, C, Cesta, N, Di Carlo, D, Dori, L, Foroghi, L, Gentilotti, E, Giannella, S, Guenci, T, Malagnino, V, Ricciardi, A, Romani, M, Salpini, O, Sarmati, L, Scutari, R, Serafini, V, Sordillo, P, Stazi, F, Stingone, C, Svicher, V, Teti, E, Viscione, M, Abbate, I, Acinapura, R, Alba, L, Ammassari, A, Baldini, F, Bellagamba, R, Boumis, E, Capobianchi, MR, Carta, S, Cicalini, S, Continenza, F, De Carli, G, D'Arrigo, R, D'Offizi, G, Fedele, V, Galati, V, Giannetti, A, Girardi, E, Grisetti, S, Libertone, R, Liuzzi, G, Lorenzini, P, Maddaluno, R, Mariano, A, Navarra, A, Nicastri, E, Nurra, G, Orchi, N, Palummieri, A, Pinnetti, C, Pittalis, S, Pizzi, D, Puro, V, Sampaolesi, A, Sciarrone, MR, Scognamiglio, P, Sias, C, Visco-Comandini, U, Colafigli, M, Cristaudo, A, Giuliani, M, Pacifici, A, Di Sora, F, Iebba, F, Lichtner, M, Marocco, R, Bernardi, S, Anzalone, E, Bonaventura, ME, Marchili, M, Pitorri, A, Di Francesco, LF, Di Giammartino, D, Caterini, A, Armignacco, O, Mariani, R, Paoloni, M, Parruti, G, Pieri, A, Sozio, F, Cellini, A, Grimaldi, A, Mariani, M, Picchi, G, Gennari, W, Nanfack, AJ, Ndjolo, A & Torimiro, JN 2017, 'Comparative evaluation of subtyping tools for surveillance of newly emerging HIV-1 strains', Journal of Clinical Microbiology, vol. 55, no. 9, pp. 2827-2837. https://doi.org/10.1128/JCM.00656-17
Fabeni, Lavinia ; Berno, Giulia ; Fokam, Joseph ; Bertoli, Ada ; Alteri, Claudia ; Gori, Caterina ; Forbici, Federica ; Takou, Desiré ; 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 ; Torimiro, Judith N. / Comparative evaluation of subtyping tools for surveillance of newly emerging HIV-1 strains. In: Journal of Clinical Microbiology. 2017 ; Vol. 55, No. 9. pp. 2827-2837.
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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.",
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author = "Lavinia Fabeni and Giulia Berno and Joseph Fokam and Ada Bertoli and Claudia Alteri and Caterina Gori and Federica Forbici and Desir{\'e} Takou and Alessandra Vergori and Mauro Zaccarelli and Gaetano Maffongelli and Vanni Borghi and Alessandra Latini and Alfredo Pennica and Mastroianni, {Claudio Maria} and Francesco Montella and Cristina Mussini and Massimo Andreoni and Andrea Antinori and Perno, {Carlo Federico} and Santoro, {Maria Mercedes} and Daniele Armenia and Bellocchi, {Maria Concetta} and Andrea Biddittu and Massimiliano Bruni and Buonomini, {Anna Rita} and Luca Carioti and Francesca Ceccherini-Silberstein and Carlotta Cerva and Novella Cesta and {Di Carlo}, Domenico and Luca Dori and Luca Foroghi and Elisa Gentilotti and Sara Giannella and Tania Guenci and Vincenzo Malagnino and Alessandra Ricciardi and Marzia Romani and Omina Salpini and Loredana Sarmati and Rossana Scutari and Valentina Serafini and Pasquale Sordillo and Francesca Stazi and Cristof Stingone and Valentina Svicher and Elisabetta Teti and Magdalena Viscione and Isabella Abbate and Rosa Acinapura and Lucia Alba and Adriana Ammassari and Franco Baldini and Rita Bellagamba and Evangelo Boumis and Capobianchi, {Maria Rosaria} and Stefania Carta and Stefania Cicalini and Fabio Continenza and {De Carli}, Gabriella and Roberta D'Arrigo and Gianpiero D'Offizi and Valentina Fedele and Vincenzo Galati and Alberto Giannetti and Enrico Girardi and Susanna Grisetti and Raffaella Libertone and Giuseppina Liuzzi and Patrizia Lorenzini and Rita Maddaluno and Andrea Mariano and Assunta Navarra and Emanuele Nicastri and Giuseppina Nurra and Nicoletta Orchi and Antonio Palummieri and Carmela Pinnetti and Silvia Pittalis and Daniele Pizzi and Vincenzo Puro and Alessandro Sampaolesi and Sciarrone, {Maria Rosaria} and Paola Scognamiglio and Catia Sias and Ubaldo Visco-Comandini and Manuela Colafigli and Antonio Cristaudo and Massimo Giuliani and Anna Pacifici and {Di Sora}, Fiorella and Filippo Iebba and Miriam Lichtner and Raffaella Marocco and Stefania Bernardi and Enza Anzalone and Bonaventura, {Maria Elena} and Mauro Marchili and Antonella Pitorri and {Di Francesco}, {Luigi Falconi} and {Di Giammartino}, Dante and Antonio Caterini and Orlando Armignacco and Rinalda Mariani and Maurizio Paoloni and Giustino Parruti and Alessandro Pieri and Federica Sozio and Antonio Cellini and Alessandro Grimaldi and Maurizio Mariani and Giovanna Picchi and William Gennari and Nanfack, {Aubin J.} and Alexis Ndjolo and Torimiro, {Judith N.}",
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T1 - Comparative evaluation of subtyping tools for surveillance of newly emerging HIV-1 strains

AU - Fabeni, Lavinia

AU - Berno, Giulia

AU - Fokam, Joseph

AU - Bertoli, Ada

AU - Alteri, Claudia

AU - Gori, Caterina

AU - Forbici, Federica

AU - Takou, Desiré

AU - Vergori, Alessandra

AU - Zaccarelli, Mauro

AU - Maffongelli, Gaetano

AU - Borghi, Vanni

AU - Latini, Alessandra

AU - Pennica, Alfredo

AU - Mastroianni, Claudio Maria

AU - Montella, Francesco

AU - Mussini, Cristina

AU - Andreoni, Massimo

AU - Antinori, Andrea

AU - Perno, Carlo Federico

AU - Santoro, Maria Mercedes

AU - Armenia, Daniele

AU - Bellocchi, Maria Concetta

AU - Biddittu, Andrea

AU - Bruni, Massimiliano

AU - Buonomini, Anna Rita

AU - Carioti, Luca

AU - Ceccherini-Silberstein, Francesca

AU - Cerva, Carlotta

AU - Cesta, Novella

AU - Di Carlo, Domenico

AU - Dori, Luca

AU - Foroghi, Luca

AU - Gentilotti, Elisa

AU - Giannella, Sara

AU - Guenci, Tania

AU - Malagnino, Vincenzo

AU - Ricciardi, Alessandra

AU - Romani, Marzia

AU - Salpini, Omina

AU - Sarmati, Loredana

AU - Scutari, Rossana

AU - Serafini, Valentina

AU - Sordillo, Pasquale

AU - Stazi, Francesca

AU - Stingone, Cristof

AU - Svicher, Valentina

AU - Teti, Elisabetta

AU - Viscione, Magdalena

AU - Abbate, Isabella

AU - Acinapura, Rosa

AU - Alba, Lucia

AU - Ammassari, Adriana

AU - Baldini, Franco

AU - Bellagamba, Rita

AU - Boumis, Evangelo

AU - Capobianchi, Maria Rosaria

AU - Carta, Stefania

AU - Cicalini, Stefania

AU - Continenza, Fabio

AU - De Carli, Gabriella

AU - D'Arrigo, Roberta

AU - D'Offizi, Gianpiero

AU - Fedele, Valentina

AU - Galati, Vincenzo

AU - Giannetti, Alberto

AU - Girardi, Enrico

AU - Grisetti, Susanna

AU - Libertone, Raffaella

AU - Liuzzi, Giuseppina

AU - Lorenzini, Patrizia

AU - Maddaluno, Rita

AU - Mariano, Andrea

AU - Navarra, Assunta

AU - Nicastri, Emanuele

AU - Nurra, Giuseppina

AU - Orchi, Nicoletta

AU - Palummieri, Antonio

AU - Pinnetti, Carmela

AU - Pittalis, Silvia

AU - Pizzi, Daniele

AU - Puro, Vincenzo

AU - Sampaolesi, Alessandro

AU - Sciarrone, Maria Rosaria

AU - Scognamiglio, Paola

AU - Sias, Catia

AU - Visco-Comandini, Ubaldo

AU - Colafigli, Manuela

AU - Cristaudo, Antonio

AU - Giuliani, Massimo

AU - Pacifici, Anna

AU - Di Sora, Fiorella

AU - Iebba, Filippo

AU - Lichtner, Miriam

AU - Marocco, Raffaella

AU - Bernardi, Stefania

AU - Anzalone, Enza

AU - Bonaventura, Maria Elena

AU - Marchili, Mauro

AU - Pitorri, Antonella

AU - Di Francesco, Luigi Falconi

AU - Di Giammartino, Dante

AU - Caterini, Antonio

AU - Armignacco, Orlando

AU - Mariani, Rinalda

AU - Paoloni, Maurizio

AU - Parruti, Giustino

AU - Pieri, Alessandro

AU - Sozio, Federica

AU - Cellini, Antonio

AU - Grimaldi, Alessandro

AU - Mariani, Maurizio

AU - Picchi, Giovanna

AU - Gennari, William

AU - Nanfack, Aubin J.

AU - Ndjolo, Alexis

AU - Torimiro, Judith N.

PY - 2017/9/1

Y1 - 2017/9/1

N2 - 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.

AB - 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.

KW - Circulating recombinant forms

KW - Genetic diversity

KW - HIV-1

KW - Phylogeny

KW - Subtypes

KW - Subtyping automated tools

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