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
{"title":"意大利下一代测序中不同 HIV-1 抗药性解读工具的比较","authors":"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","doi":"10.3390/v16091422","DOIUrl":null,"url":null,"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.","PeriodicalId":501326,"journal":{"name":"Viruses","volume":"3 1","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Comparison of Different HIV-1 Resistance Interpretation Tools for Next-Generation Sequencing in Italy\",\"authors\":\"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\",\"doi\":\"10.3390/v16091422\",\"DOIUrl\":null,\"url\":null,\"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.\",\"PeriodicalId\":501326,\"journal\":{\"name\":\"Viruses\",\"volume\":\"3 1\",\"pages\":\"\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2024-09-06\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Viruses\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.3390/v16091422\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Viruses","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.3390/v16091422","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
Comparison of Different HIV-1 Resistance Interpretation Tools for Next-Generation Sequencing in 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 <10,000–1000 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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