BACKGROUND HIV-1 DNA genotypic drug resistance testing is increasingly performed to guide treatment switching or simplification in controlled patients. The Sentosa NGS platform is a fully automated system marketed for drug resistance testing on HIV-1 RNA samples. OBJECTIVES The aim of this study was to evaluate this automated NGS solution for routine resistance genotypic resistance testing in proviral HIV-1 DNA. STUDY DESIGN Sanger sequencing (SS) of the reverse transcriptase (RT), protease (PR) and integrase (IN) genes was performed using the French ANRS protocol. NGS was performed retrospectively on frozen samples, using the Sentosa platform combined with the Sentosa SQ HIV genotyping Assay. RESULTS A total of 77 samples were run once using NGS. A successful sequencing of the three HIV-1 genes (RT, PR, IN) was obtained for 45 samples. The number of cumulated RAMs was 179, 185 and 219 with SS, NGS 20% and NGS 10% respectively; however most of them were minor mutations in the PR region. The mutation detection rate was similar between SS and NGS 20%. Several discordances were observed between both methods in the RT and PR regions, mainly due to the use of different DNA extracts, and hypermutation. CONCLUSIONS HIV-1 DNA genotypic resistance testing can be performed with the Sentosa platform. Few technical optimizations are still needed to include the extraction step and to improve the sequencing efficiency.

中文翻译：

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使用自动下一代测序测定法对HIV-1前病毒DNA进行常规耐药性测试。

背景技术越来越多地进行HIV-1 DNA基因型耐药性测试，以指导受控患者中的治疗切换或简化。圣淘沙NGS平台是一个用于对HIV-1 RNA样品进行耐药性测试的全自动系统。目的本研究的目的是评估该自动NGS解决方案，以对原病毒HIV-1 DNA中的常规抗性基因型抗性进行测试。研究设计使用French ANRS方案对逆转录酶（RT），蛋白酶（PR）和整合酶（IN）基因进行Sanger测序（SS）。使用Sentosa平台结合Sentosa SQ HIV基因分型分析，对冷冻样品进行NGS回顾性研究。结果使用NGS总共运行了77个样品。对于45个样本，成功获得了三个HIV-1基因（RT，PR，IN）的测序。RAM的累积数量分别为179、185和219，其中SS，NGS 20％和NGS 10％；然而，大多数是在PR地区的微小突变。SS和NGS 20％之间的突变检测率相似。在RT和PR区域，两种方法之间都存在一些不一致之处，这主要是由于使用了不同的DNA提取物以及超突变。结论可以使用Sentosa平台进行HIV-1 DNA基因型耐药性测试。仍然需要很少的技术优化来包括提取步骤并提高测序效率。在RT和PR区域，两种方法之间都存在一些不一致之处，这主要是由于使用了不同的DNA提取物以及超突变。结论可以使用Sentosa平台进行HIV-1 DNA基因型耐药性测试。仍然需要很少的技术优化来包括提取步骤并提高测序效率。在RT和PR区域，两种方法之间都存在一些不一致之处，这主要是由于使用了不同的DNA提取物以及超突变。结论可以使用Sentosa平台进行HIV-1 DNA基因型耐药性测试。仍然需要很少的技术优化来包括提取步骤并提高测序效率。