意大利下一代测序中不同 HIV-1 耐药性解读工具的比较。
Comparison of Different HIV-1 Resistance Interpretation Tools for Next-Generation Sequencing in Italy.
机构信息
Departmental Faculty, UniCamillus, Saint Camillus International University of Health Sciences, 00131 Rome, Italy.
Department of Experimental Medicine, University of Rome "Tor Vergata", 00133 Rome, Italy.
出版信息
Viruses. 2024 Sep 6;16(9):1422. doi: 10.3390/v16091422.
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.
背景
下一代测序（NGS）正逐渐取代 Sanger 测序，用于 HIV 基因型耐药性检测（GRT）。本研究评估了不同 NGS-GRT 解释工具在实际环境中的一致性。
方法
使用 AD4SEQ HIV-1 Solution v2 商业试剂盒，11 家意大利实验室从病毒 RNA 中生成常规 NGS-GRT 数据。NGS 结果由试剂盒提供的 SmartVir 系统和两个在线工具（HyDRA Web 和斯坦福 HIVdb）进行解释。当每个 PR/RT/IN 耐药相关位置的覆盖率>100 个读（100×）时，NGS-GRT 被认为是有效的，这些位置列在 HIVdb 9.5.1 算法中。
结果
在 629 份 NGS-GRT 中，根据 SmartVir、HyDRA Web 和 HIVdb，分别有 75.2%、74.2%和 70.9%是有效的。考虑到至少两种解释工具，463 份（73.6%）NGS-GRT 对耐药分析具有有效的覆盖率。有效样本的比例受到病毒载量<10,000-1000 拷贝/mL 和非 B 亚型的影响。在 NGS 频率>10%的突变在不同的解释工具之间具有良好的一致性。
结论
这项关于 NGS 耐药检测的意大利研究表明，病毒载量水平和 HIV 亚型会影响 NGS-GRT 的覆盖率。在当前 NGS-GRT 的常规方法中，只有频率>10%的突变似乎可以在不同的解释工具中可靠地检测到。
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