Khan Kashif Aziz, Cheung Peter
Department of Biology, York University, Toronto, Canada.
Bio Protoc. 2020 Dec 20;10(24):e3871. doi: 10.21769/BioProtoc.3871.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; initially named 2019-nCoV) is responsible for the recent coronavirus disease (COVID-19) pandemic, and polymerase chain reaction (PCR) is the current standard method for diagnosis from patient samples. As PCR assays are prone to sequence mismatches due to mutations in the viral genome, it is important to verify the genomic variability at primer/probe binding regions periodically. This step-by-step protocol describes a bioinformatics approach for an extensive evaluation of the sequence variability within the primer/probe target regions of the SARS-CoV-2 genome. The protocol can be applied to any molecular diagnostic assay of choice using freely available software programs and the ready-to-use multiple sequence alignment (MSA) file provided. Graphic abstract The figure was created using the Library of Science and Medical Illustrations from somersault18:24 licensed under a CC BY-NC-SA 4.0 license (https://creativecommons.org/licenses/by-nc-sa/4.0/). https://youtu.be/M1lV1liWE9k.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2；最初命名为2019-nCoV）是近期冠状病毒病（COVID-19）大流行的病原体，聚合酶链反应（PCR）是目前用于从患者样本中进行诊断的标准方法。由于PCR检测容易因病毒基因组突变而出现序列错配，因此定期验证引物/探针结合区域的基因组变异性很重要。本分步方案描述了一种生物信息学方法，用于广泛评估SARS-CoV-2基因组引物/探针靶区域内的序列变异性。该方案可应用于任何选择的分子诊断检测，使用免费的软件程序和提供的即用型多序列比对（MSA）文件。图形摘要 该图使用了来自somersault18:24的科学与医学插图库创建，根据CC BY-NC-SA 4.0许可（https://creativecommons.org/licenses/by-nc-sa/4.0/）授权。https://youtu.be/M1lV1liWE9k。
