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Comparison of Different HIV-1 Resistance Interpretation Tools for Next-Generation Sequencing in Italy.
Armenia, Daniele; Carioti, Luca; Micheli, Valeria; Bon, Isabella; Allice, Tiziano; Bonura, Celestino; Bruzzone, Bianca; Bracchitta, Fiorenza; Cerutti, Francesco; Giammanco, Giovanni Maurizio; Stefanelli, Federica; Bonifacio, Maria Addolorata; Bertoli, Ada; Vatteroni, Marialinda; Ibba, Gabriele; Novazzi, Federica; Lipsi, Maria Rosaria; Cuomo, Nunzia; Vicenti, Ilaria; Ceccherini-Silberstein, Francesca; Rossetti, Barbara; Bezenchek, Antonia; Saladini, Francesco; Zazzi, Maurizio; Santoro, Maria Mercedes.
Afiliação
  • Armenia D; Departmental Faculty, UniCamillus, Saint Camillus International University of Health Sciences, 00131 Rome, Italy.
  • Carioti L; Department of Experimental Medicine, University of Rome "Tor Vergata", 00133 Rome, Italy.
  • Micheli V; Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco-University of Milan, 20157 Milan, Italy.
  • Bon I; Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy.
  • Allice T; Laboratory of Microbiology and Virology, Amedeo di Savoia Hospital, 10149 Turin, Italy.
  • Bonura C; 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.
  • Bruzzone B; Hygiene Unit, Ospedale Policlinico San Martino, 16132 Genoa, Italy.
  • Bracchitta F; Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco-University of Milan, 20157 Milan, Italy.
  • Cerutti F; Laboratory of Microbiology and Virology, Amedeo di Savoia Hospital, 10149 Turin, Italy.
  • Giammanco GM; 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.
  • Stefanelli F; Hygiene Unit, Ospedale Policlinico San Martino, 16132 Genoa, Italy.
  • Bonifacio MA; Section of Experimental and Clinical Pathology, Department of Precision and Regenerative Medicine and Jonic Area, University of Bari, 70121 Bari, Italy.
  • Bertoli A; Virology Unit, Polyclinic of "Tor Vergata", 00133 Rome, Italy.
  • Vatteroni M; Virology Unit, AOU Pisana, 56126 Pisa, Italy.
  • Ibba G; Microbiology and Virology Unit, Diagnostic Department, AOU Sassari, 07100 Sassari, Italy.
  • Novazzi F; Department of Medicine and Technological Innovation, University of Insubria, 21100 Varese, Italy.
  • Lipsi MR; Microbiology and Virology Unit, Policlinico Riuniti Foggia Hospital, 71121 Foggia, Italy.
  • Cuomo N; U.O.C. Microbiologia e Virologia, P.O. "D.Cotugno"-AO dei Colli, 80100 Napoli, Italy.
  • Vicenti I; Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy.
  • Ceccherini-Silberstein F; Department of Experimental Medicine, University of Rome "Tor Vergata", 00133 Rome, Italy.
  • Rossetti B; Infectious Disease Department, USL SUDEST, Toscana, Misericordia Hospital, 58100 Grosseto, Italy.
  • Bezenchek A; IPRO-InformaPRO S.r.l., 00152 Rome, Italy.
  • Saladini F; EuResist Network GEIE, 00152 Rome, Italy.
  • Zazzi M; Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy.
  • Santoro MM; Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy.
Viruses ; 16(9)2024 Sep 06.
Article em En | MEDLINE | ID: mdl-39339898
ABSTRACT

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 <10,000-1000 copies/mL and non-B subtypes. Mutations at an NGS frequency >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.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Infecções por HIV / HIV-1 / Farmacorresistência Viral / Sequenciamento de Nucleotídeos em Larga Escala Limite: Humans País/Região como assunto: Europa Idioma: En Revista: Viruses Ano de publicação: 2024 Tipo de documento: Article País de afiliação: Itália País de publicação: Suíça
Texto completo
Adicionar na Minha BVS
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Infecções por HIV / HIV-1 / Farmacorresistência Viral / Sequenciamento de Nucleotídeos em Larga Escala Limite: Humans País/Região como assunto: Europa Idioma: En Revista: Viruses Ano de publicação: 2024 Tipo de documento: Article País de afiliação: Itália País de publicação: Suíça