Defining the analytical and clinical sensitivity of the ARTIC method for the detection of SARS-CoV-2
Defining the analytical and clinical sensitivity of the ARTIC method for the detection of SARS-CoV-2
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定义 ARTIC 方法检测 SARS-CoV-2 的分析和临床敏感性
DOI：
10.1101/2021.10.09.21264695
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发表时间：
2021
期刊：
影响因子：
--
通讯作者：
Alikhan N
中科院分区：
文献类型：
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作者：
Alikhan N
SARS-CoV-2 ARTIC扩增子方案是SARS-CoV-2最广泛使用的基因组测序方法，占公众可用基因组序列的43%以上。该方案利用98个引物扩增SARS-CoV-2基因组的约400 bp片段，覆盖所有30，000个碱基。了解本方案的分析性能指标将改善数据的使用和解释方式。使用不同浓度的SARS-CoV-2对照材料确定ARTIC方案的检测限（LoD）。结果证明LoD至少为25-50个病毒颗粒/mL。ARTIC的灵敏度与已发表的商业诊断检测试剂的灵敏度相当，因此可用于确认诊断检测结果。然后对来自英国三个地区的一组超过3，600份临床样本进行评价，以比较方案与临床诊断检测试剂盒（Roche Lightcycler 480 II、AusDiagnostics、Roche Cobas、Hologic Panther、Corman RdRp、Roche Flow、ABI QuantStudio 5、Seegene Nimbus、Qiagen Rotorgene、Abbott M2000、Thermo TaqPath、Xpert）的性能。我们开发了一个Python工具RonaLDO来执行此验证（在GNU GPL 3开源许可下可从https：//github.com/quadram-institute-bioscience/ronaldo获得）。通过诊断平台检测到的阳性通常得到测序数据的支持;使用RT-qPCR的平台是样本随后是否成功测序的最佳预测因子。为了最大限度地成功进行系统发育分析的样品测序，应选择Ct <31的样品。对于无法提供可定量Ct值的诊断检测，建议添加定量步骤。ARTIC SARS-CoV-2测序方案具有高度灵敏度，能够在Ct值高达30 s的样本中检测到SARS-CoV-2。然而，为了常规获得全基因组覆盖率，推荐Ct <31的样品。比较接近其LoD的不同病毒检测方法具有挑战性，并观察到显著不一致性。
The SARS-CoV-2 ARTIC amplicon protocol is the most widely used genome sequencing method for SARS-CoV-2, accounting for over 43% of publicly-available genome sequences. The protocol utilises 98 primers to amplify ∼400bp fragments of the SARS-CoV-2 genome covering all 30,000 bases. Understanding the analytical performance metrics of this protocol will improve how the data is used and interpreted. Different concentrations of SARS-CoV-2 control material were used to establish the limit of detection (LoD) of the ARTIC protocol. Results demonstrated the LoD was a minimum of 25-50 virus particles per mL. The sensitivity of ARTIC was comparable to the published sensitivities of commercial diagnostics assays and could therefore be used to confirm diagnostic testing results. A set of over 3,600 clinical samples from three UK regions were then evaluated to compare the protocols performance to clinical diagnostic assays (Roche Lightcycler 480 II, AusDiagnostics, Roche Cobas, Hologic Panther, Corman RdRp, Roche Flow, ABI QuantStudio 5, Seegene Nimbus, Qiagen Rotorgene, Abbott M2000, Thermo TaqPath, Xpert). We developed a Python tool, RonaLDO, to perform this validation (available under the GNU GPL3 open-source licence from https://github.com/quadram-institute-bioscience/ronaldo). Positives detected by diagnostic platforms were generally supported by sequencing data; platforms that used RT-qPCR were the best predictors of whether the sample would subsequently sequence successfully. To maximise success of sample sequencing for phylogenetic analysis, samples with Ct <31 should be chosen. For diagnostic tests that do not provide a quantifiable Ct value, adding a quantification step is recommended. The ARTIC SARS-CoV-2 sequencing protocol is highly sensitive, capable of detecting SARS-CoV-2 in samples with Cts in the high 30s. However, to routinely obtain whole genome coverage, samples with Ct <31 are recommended. Comparing different virus detection methods close to their LoD was challenging and significant discordance was observed.
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DOI：
10.3760/cma.j.cn112338-20200427-00659
发表时间：
2020-12
影响因子：
--
作者：
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通讯作者：
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DOI：
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发表时间：
2020
期刊：
影响因子：
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作者：
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DOI：
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发表时间：
2017
期刊：
Cerveau & Psycho
影响因子：
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作者：
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DOI：
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发表时间：
2020
期刊：
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