In silico detection of SARS-CoV-2 specific B-cell epitopes and validation in ELISA for serological diagnosis of COVID-19.
In silico detection of SARS-CoV-2 specific B-cell epitopes and validation in ELISA for serological diagnosis of COVID-19.
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DOI：
10.1038/s41598-021-83730-y
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发表时间：
2021-02-22
影响因子：
4.6
通讯作者：
Van Voorhis WC
中科院分区：
文献类型：
--
作者：
Phan IQ;Subramanian S;Kim D;Murphy M;Pettie D;Carter L;Anishchenko I;Barrett LK;Craig J;Tillery L;Shek R;Harrington WE;Koelle DM;Wald A;Veesler D;King N;Boonyaratanakornkit J;Isoherranen N;Greninger AL;Jerome KR;Chu H;Staker B;Stewart L;Myler PJ;Van Voorhis WC
快速生成诊断方法对于了解流行病学和控制新冠肺炎等新兴传染病的传播至关重要。预测病原体特异性血清诊断表位的计算方法可能有助于加快新诊断技术的发展。对27个SARS-CoV-2蛋白进行了系统的调查，以评估现有的B细胞表位预测方法，结合对序列数据库和结构数据的全面挖掘，是否能够预测特定蛋白是否适合用于血清诊断。使用SARS-CoV-2感染患者的血浆和血清，用重组SARS-CoV-2蛋白以ELISA法验证了其中9项预测，另外11项预测与最近的文献进行了比较。结果似乎与12项预测一致，与3项不一致，另有5项被认为是不确定的。我们发现，在我们的前五个候选序列中，有两个，即核蛋白的N端片段和Spike蛋白的受体结合域，在用ELISA法检测新冠肺炎血清/血浆方面具有最高的敏感性、特异性和信噪比。将两种抗原混合用于包被酶标板，敏感性为94%(来自RT- = 确诊为SARS-CoV-2感染者的80份样本)，特异性为97.2%(N- = 10 6对照样本)。
Rapid generation of diagnostics is paramount to understand epidemiology and to control the spread of emerging infectious diseases such as COVID-19. Computational methods to predict serodiagnostic epitopes that are specific for the pathogen could help accelerate the development of new diagnostics. A systematic survey of 27 SARS-CoV-2 proteins was conducted to assess whether existing B-cell epitope prediction methods, combined with comprehensive mining of sequence databases and structural data, could predict whether a particular protein would be suitable for serodiagnosis. Nine of the predictions were validated with recombinant SARS-CoV-2 proteins in the ELISA format using plasma and sera from patients with SARS-CoV-2 infection, and a further 11 predictions were compared to the recent literature. Results appeared to be in agreement with 12 of the predictions, in disagreement with 3, while a further 5 were deemed inconclusive. We showed that two of our top five candidates, the N-terminal fragment of the nucleoprotein and the receptor-binding domain of the spike protein, have the highest sensitivity and specificity and signal-to-noise ratio for detecting COVID-19 sera/plasma by ELISA. Mixing the two antigens together for coating ELISA plates led to a sensitivity of 94% (N = 80 samples from persons with RT-PCR confirmed SARS-CoV-2 infection), and a specificity of 97.2% (N = 106 control samples).
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DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Fu L;Niu B;Zhu Z;Wu S;Li W
通讯作者：
Li W
影响因子：
2.9
作者：
Park, Hahnbeom;Lee, Gyu Rie;Baker, David
通讯作者：
Baker, David
影响因子：
--
作者：
SHANNON, CE
通讯作者：
SHANNON, CE
影响因子：
82.9
作者：
Amanat F;Stadlbauer D;Strohmeier S;Nguyen THO;Chromikova V;McMahon M;Jiang K;Arunkumar GA;Jurczyszak D;Polanco J;Bermudez-Gonzalez M;Kleiner G;Aydillo T;Miorin L;Fierer DS;Lugo LA;Kojic EM;Stoever J;Liu STH;Cunningham-Rundles C;Felgner PL;Moran T;García-Sastre A;Caplivski D;Cheng AC;Kedzierska K;Vapalahti O;Hepojoki JM;Simon V;Krammer F
通讯作者：
Krammer F
影响因子：
10.7
作者：
Katoh K;Standley DM
通讯作者：
Standley DM