Department of Mathematics, Statistics, and Computer Science, University of Illinois at Chicago, Chicago, IL 60607, USA.
Genomics. 2020 Sep;112(5):3588-3596. doi: 10.1016/j.ygeno.2020.04.016. Epub 2020 Apr 27.
The emerging global infectious COVID-19 disease by novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) presents critical threats to global public health and the economy since it was identified in late December 2019 in China. The virus has gone through various pathways of evolution. To understand the evolution and transmission of SARS-CoV-2, genotyping of virus isolates is of great importance. This study presents an accurate method for effectively genotyping SARS-CoV-2 viruses using complete genomes. The method employs the multiple sequence alignments of the genome isolates with the SARS-CoV-2 reference genome. The single-nucleotide polymorphism (SNP) genotypes are then measured by Jaccard distances to track the relationship of virus isolates. The genotyping analysis of SARS-CoV-2 isolates from the globe reveals that specific multiple mutations are the predominated mutation type during the current epidemic. The proposed method serves an effective tool for monitoring and tracking the epidemic of pathogenic viruses in their global and local genetic variations. The genotyping analysis shows that the genes encoding the S proteins and RNA polymerase, RNA primase, and nucleoprotein, undergo frequent mutations. These mutations are critical for vaccine development in disease control.
新型严重急性呼吸系统综合症冠状病毒 2 (SARS-CoV-2) 引发的全球传染性 COVID-19 疾病自 2019 年 12 月在中国被发现以来，对全球公共卫生和经济构成了重大威胁。该病毒经历了各种进化途径。为了了解 SARS-CoV-2 的进化和传播，对病毒分离株进行基因分型非常重要。本研究提出了一种利用完整基因组有效对 SARS-CoV-2 病毒进行基因分型的精确方法。该方法采用基因组分离物与 SARS-CoV-2 参考基因组的多重序列比对。然后通过杰卡德距离测量单核苷酸多态性 (SNP) 基因型，以跟踪病毒分离物的关系。对来自全球的 SARS-CoV-2 分离物的基因分型分析表明，在当前疫情中，特定的多种突变是主要的突变类型。该方法为监测和跟踪全球和本地遗传变异中致病病毒的流行提供了有效的工具。基因分型分析表明，编码 S 蛋白和 RNA 聚合酶、RNA 引物酶和核蛋白的基因经常发生突变。这些突变对于疾病控制中的疫苗开发至关重要。
