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 language | English |
|---|---|
| Pages (from-to) | 2827-2837 |
| Number of pages | 11 |
| Journal | Journal of Clinical Microbiology |
| Volume | 55 |
| Issue number | 9 |
| DOIs | |
| Publication status | Published - 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
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 journal › Article
}
TY - JOUR
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
UR - http://www.scopus.com/inward/record.url?scp=85028324848&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85028324848&partnerID=8YFLogxK
U2 - 10.1128/JCM.00656-17
DO - 10.1128/JCM.00656-17
M3 - Article
AN - SCOPUS:85028324848
VL - 55
SP - 2827
EP - 2837
JO - Journal of Clinical Microbiology
JF - Journal of Clinical Microbiology
SN - 0095-1137
IS - 9
ER -