Intelligent Criminology Research Lab (ICRL), National Center of Artificial Intelligence (NCAI), Al-Khawarizmi Institute of Computer Science (KICS), University of Engineering and Technology (UET), Lahore, Pakistan.
Department of Computer Science, University of Engineering and Technology (UET), Lahore, Pakistan.
J Med Virol. 2021 Jul;93(7):4382-4391. doi: 10.1002/jmv.26974. Epub 2021 Apr 8.
The coronavirus disease 2019 (COVID-19) pandemic has spread around the globe very rapidly. Previously, the evolution pattern and similarity among the COVID-19 causative organism severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and causative organisms of other similar infections have been determined using a single type of genetic marker in different studies. Herein, the SARS-CoV-2 and related β coronaviruses Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV, bat coronavirus (BAT-CoV) were comprehensively analyzed using a custom-built pipeline that employed phylogenetic approaches based on multiple types of genetic markers including the whole genome sequences, mutations in nucleotide sequences, mutations in protein sequences, and microsatellites. The whole-genome sequence-based phylogeny revealed that the strains of SARS-CoV-2 are more similar to the BAT-CoV strains. The mutational analysis showed that on average MERS-CoV and BAT-CoV genomes differed at 134.21 and 136.72 sites, respectively, whereas the SARS-CoV genome differed at 26.64 sites from the reference genome of SARS-CoV-2. Furthermore, the microsatellite analysis highlighted a relatively higher number of average microsatellites for MERS-CoV and SARS-CoV-2 (106.8 and 107, respectively), and a lower number for SARS-CoV and BAT-CoV (95.8 and 98.5, respectively). Collectively, the analysis of multiple genetic markers of selected β viral genomes revealed that the newly born SARS-COV-2 is closely related to BAT-CoV, whereas, MERS-CoV is more distinct from the SARS-CoV-2 than BAT-CoV and SARS-CoV.
2019 年冠状病毒病（COVID-19）大流行在全球迅速蔓延。此前，不同研究中使用单一类型的遗传标记来确定 COVID-19 病原体严重急性呼吸综合征冠状病毒 2（SARS-CoV-2）和其他类似感染病原体的进化模式和相似性。在此，使用基于多种遗传标记（包括全基因组序列、核苷酸序列突变、蛋白质序列突变和微卫星）的基于系统发育的方法，综合分析了 SARS-CoV-2 和相关的β冠状病毒中东呼吸综合征冠状病毒（MERS-CoV）、SARS-CoV、蝙蝠冠状病毒（BAT-CoV）。基于全基因组序列的系统发育树表明，SARS-CoV-2 株与 BAT-CoV 株更为相似。突变分析显示，平均而言，MERS-CoV 和 BAT-CoV 基因组分别在 134.21 和 136.72 个位点上存在差异，而 SARS-CoV 基因组与 SARS-CoV-2 的参考基因组在 26.64 个位点上存在差异。此外，微卫星分析突出显示了 MERS-CoV 和 SARS-CoV-2 的平均微卫星数相对较高（分别为 106.8 和 107），而 SARS-CoV 和 BAT-CoV 的平均微卫星数较低（分别为 95.8 和 98.5）。综上所述，对选定的β病毒基因组的多种遗传标记的分析表明，新出现的 SARS-COV-2 与 BAT-CoV 密切相关，而 MERS-CoV 与 SARS-CoV-2 的关系比 BAT-CoV 和 SARS-CoV 更为明显。
