Evaluation of the clinical and analytical performance of the Seegene allplex™ SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI).
Evaluation of the clinical and analytical performance of the Seegene allplex™ SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI).
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DOI：
10.1016/j.jcv.2021.104996
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发表时间：
2021-11
期刊：
影响因子：
--
通讯作者：
Wilmer A
中科院分区：
文献类型：
--
作者：
Caza M;Hogan CA;Jassem A;Prystajecky N;Hadzic A;Wilmer A
当全基因组测序(WGS)不可用或有限时，用于检测SARS-CoV-2关注变种(VOC)和感兴趣变种(VOI)的高通量分析是一种诊断替代方法。本研究评价了Seegene Allplex™-CoV-2变异体I检测S基因HV69/70缺失、N501Y和E484K突变的临床和分析性能。以WGS为参考标准，对871份SARS-CoV-2RNA阳性标本、408份鼻咽拭子和463份盐水漱口标本进行基因分型。对分析性能进行了评估，包括稳定性、重现性、检出限(LOD)、交叉反应性和对各种呼吸道微生物的干扰。HV 69/70缺失的敏感性(95%CI 99.27%~100%)和特异性(95%CI 98.99%~100%)；N501Y的敏感性(95%CI 99.55%~100%)和特异性(95%CI 93.73%~100%)；E484K突变的敏感性(95%CI 98.94%~100%)和特异性(95%CI 96.53%~99.08%)。在10例Kappa变异(B.1.627.1)标本中检测到E484Q突变。分析性能在7天内表现出稳定性和重现性，计算出NP拭子样本的LOD为698亿cp/mL，SG样本的LOD为968亿cp/mL。没有注意到与其他微生物的干扰或交叉反应。Allplex™-CoV-2变异体I试验可用于临床检测关注的变异体和感兴趣的变异体。
High-throughput assays for the detection of SARS-CoV-2 variants of concern (VOC) and interest (VOI) are a diagnostic alternative when whole genome sequencing (WGS) is unavailable or limited. This study evaluated the clinical and analytical performance of the Seegene Allplex™ SARS-CoV-2 Variants I assay, which detects the HV69/70 deletion, N501Y and E484K mutations of the S gene. Genotyping was evaluated on -871 SARS-CoV-2 RNA positive specimens, 408 nasopharyngeal (NP) swabs and 463 saline gargle (SG) specimens, with WGS used as the reference standard. Analytical performance was assessed including stability, reproducibility, limit of detection (LOD), cross-reactivity and interference with various respiratory microorganisms. The clinical study revealed sensitivity of 100% (95% CI 99.27%–100%) and specificity of 100% (95% CI 98.99%–100%) for HV69/70 deletion, sensitivity of 100% (95% CI 99.55%–100%) and specificity of 100% (95% CI 93.73% – 100%) for N501Y, and sensitivity of 100% (95% CI 98.94% – 100%) and specificity of 98.10% (95% CI 96.53% – 99.08%) for E484K mutation. The E484Q mutation was detected in 10 specimens of the Kappa variant (B.1.627.1). Analytical performance demonstrated stability and reproducibility over 7 days, and LOD was calculated at 698 cp/mL for NP swab specimens, and 968 cp/mL for SG specimens. No interference or cross-reactivity with other microorganisms was noted. The Allplex™ SARS-CoV-2 Variants I assay is acceptable for clinical use for the detection of variant of concern and variant of interest.
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SARS-COV-2血统的估计可传播和影响B.1.1.7在英国。
DOI：
10.1126/science.abg3055
发表时间：
2021-04-09
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Davies NG;Abbott S;Barnard RC;Jarvis CI;Kucharski AJ;Munday JD;Pearson CAB;Russell TW;Tully DC;Washburne AD;Wenseleers T;Gimma A;Waites W;Wong KLM;van Zandvoort K;Silverman JD;CMMID COVID-19 Working Group;COVID-19 Genomics UK (COG-UK) Consortium;Diaz-Ordaz K;Keogh R;Eggo RM;Funk S;Jit M;Atkins KE;Edmunds WJ
通讯作者：
Edmunds WJ
影响因子：
64.8
作者：
Plante JA;Liu Y;Liu J;Xia H;Johnson BA;Lokugamage KG;Zhang X;Muruato AE;Zou J;Fontes-Garfias CR;Mirchandani D;Scharton D;Bilello JP;Ku Z;An Z;Kalveram B;Freiberg AN;Menachery VD;Xie X;Plante KS;Weaver SC;Shi PY
通讯作者：
Shi PY
影响因子：
4.7
作者：
Socher E;Conrad M;Heger L;Paulsen F;Sticht H;Zunke F;Arnold P
通讯作者：
Arnold P
影响因子：
64.5
作者：
Hoffmann M;Arora P;Groß R;Seidel A;Hörnich BF;Hahn AS;Krüger N;Graichen L;Hofmann-Winkler H;Kempf A;Winkler MS;Schulz S;Jäck HM;Jahrsdörfer B;Schrezenmeier H;Müller M;Kleger A;Münch J;Pöhlmann S
通讯作者：
Pöhlmann S
影响因子：
--
作者：
O'Toole, Aine;Hill, Verity;Kraemer, Moritz U G
通讯作者：
Kraemer, Moritz U G