Comparison of Different HIV-1 Resistance Interpretation Tools for Next-Generation Sequencing in Italy
Daniele Armenia,
Luca Carioti,
Valeria Micheli,
Isabella Bon,
Tiziano Allice,
Celestino Bonura,
Bianca Bruzzone,
Fiorenza Bracchitta,
Francesco Cerutti,
Giovanni Maurizio Giammanco,
Federica Stefanelli,
Maria Addolorata Bonifacio,
Ada Bertoli,
Marialinda Vatteroni,
Gabriele Ibba,
Federica Novazzi,
Maria Rosaria Lipsi,
Nunzia Cuomo,
Ilaria Vicenti,
Francesca Ceccherini-Silberstein,
Barbara Rossetti,
Antonia Bezenchek,
Francesco Saladini,
Maurizio Zazzi,
Maria Mercedes Santoro
Affiliations
Daniele Armenia
Departmental Faculty, UniCamillus, Saint Camillus International University of Health Sciences, 00131 Rome, Italy
Luca Carioti
Department of Experimental Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy
Valeria Micheli
Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco-University of Milan, 20157 Milan, Italy
Isabella Bon
Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
Tiziano Allice
Laboratory of Microbiology and Virology, Amedeo di Savoia Hospital, 10149 Turin, Italy
Celestino Bonura
Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro” (PROSAMI), Azienda Ospedaliera Universitaria Policlinico “P. Giaccone”-University of Palermo, 90127 Palermo, Italy
Bianca Bruzzone
Hygiene Unit, Ospedale Policlinico San Martino, 16132 Genoa, Italy
Fiorenza Bracchitta
Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco-University of Milan, 20157 Milan, Italy
Francesco Cerutti
Laboratory of Microbiology and Virology, Amedeo di Savoia Hospital, 10149 Turin, Italy
Giovanni Maurizio Giammanco
Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro” (PROSAMI), Azienda Ospedaliera Universitaria Policlinico “P. Giaccone”-University of Palermo, 90127 Palermo, Italy
Federica Stefanelli
Hygiene Unit, Ospedale Policlinico San Martino, 16132 Genoa, Italy
Maria Addolorata Bonifacio
Section of Experimental and Clinical Pathology, Department of Precision and Regenerative Medicine and Jonic Area, University of Bari, 70121 Bari, Italy
Ada Bertoli
Virology Unit, Polyclinic of “Tor Vergata”, 00133 Rome, Italy
Marialinda Vatteroni
Virology Unit, AOU Pisana, 56126 Pisa, Italy
Gabriele Ibba
Microbiology and Virology Unit, Diagnostic Department, AOU Sassari, 07100 Sassari, Italy
Federica Novazzi
Department of Medicine and Technological Innovation, University of Insubria, 21100 Varese, Italy
Maria Rosaria Lipsi
Microbiology and Virology Unit, Policlinico Riuniti Foggia Hospital, 71121 Foggia, Italy
Nunzia Cuomo
U.O.C. Microbiologia e Virologia, P.O. “D.Cotugno”-AO dei Colli, 80100 Napoli, Italy
Ilaria Vicenti
Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
Francesca Ceccherini-Silberstein
Department of Experimental Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy
Background: Next-generation sequencing (NGS) is gradually replacing Sanger sequencing for HIV genotypic drug resistance testing (GRT). This work evaluated the concordance among different NGS-GRT interpretation tools in a real-life setting. Methods: Routine NGS-GRT data were generated from viral RNA at 11 Italian laboratories with the AD4SEQ HIV-1 Solution v2 commercial kit. NGS results were interpreted by the SmartVir system provided by the kit and by two online tools (HyDRA Web and Stanford HIVdb). NGS-GRT was considered valid when the coverage was >100 reads (100×) at each PR/RT/IN resistance-associated position listed in the HIVdb 9.5.1 algorithm. Results: Among 629 NGS-GRT, 75.2%, 74.2%, and 70.9% were valid according to SmartVir, HyDRA Web, and HIVdb. Considering at least two interpretation tools, 463 (73.6%) NGS-GRT had a valid coverage for resistance analyses. The proportion of valid samples was affected by viremia 10% showed fair concordance among different interpretation tools. Conclusion: This Italian survey on NGS resistance testing suggests that viremia levels and HIV subtype affect NGS-GRT coverage. Within the current routine method for NGS-GRT, only mutations with frequency >10% seem reliably detected across different interpretation tools.
