Menasria Taha, Aguilera Margarita
Department of Applied Biology, Faculty of Exact Sciences and Natural and Life Sciences, University of Larbi Tebessi, Tebessa 12002, Algeria.
Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain.
Microorganisms. 2022 Feb 18;10(2):467. doi: 10.3390/microorganisms10020467.
Here, we report a first comprehensive genomic analysis of SARS-CoV-2 variants circulating in North African countries, including Algeria, Egypt, Libya, Morocco, Sudan and Tunisia, with respect to genomic clades and mutational patterns. As of December 2021, a total of 1669 high-coverage whole-genome sequences submitted to EpiCoV GISAID database were analyzed to infer clades and mutation annotation compared with the wild-type variant Wuhan-Hu-1. Phylogenetic analysis of SARS-CoV-2 genomes revealed the existence of eleven GISAID clades with GR (variant of the spike protein S-D614G and nucleocapsid protein N-G204R), GH (variant of the ORF3a coding protein ORF3a-Q57H) and GK (variant S-T478K) being the most common with 25.9%, 19.9%, and 19.6%, respectively, followed by their parent clade G (variant S-D614G) (10.3%). Lower prevalence was noted for GRY (variant S-N501Y) (5.1%), S (variant ORF8-L84S) (3.1%) and GV (variant of the ORF3a coding protein NS3-G251V) (2.0%). Interestingly, 1.5% of total genomes were assigned as GRA (Omicron), the newly emerged clade. Across the North African countries, 108 SARS-CoV-2 lineages using the Pangolin assignment were identified, whereby most genomes fell within six major lineages and variants of concern (VOC) including B.1, the Delta variants (AY.X, B.1.617.2), C.36, B.1.1.7 and B.1.1. The effect of mutations in SAR-CoV-2 genomes highlighted similar profiles with D614G spike (S) and ORF1b-P314L variants as the most changes found in 95.3% and 87.9% of total sequences, respectively. In addition, mutations affecting other viral proteins appeared frequently including; N:RG203KR, N:G212V, NSP3:T428I, ORF3a:Q57H, S:N501Y, M:I82T and E:V5F. These findings highlight the importance of genomic surveillance for understanding the SARS-CoV-2 genetic diversity and its spread patterns, leading to a better guiding of public health intervention measures. The know-how analysis of the present work could be implemented worldwide in order to overcome this health crisis through harmonized approaches.
在此，我们报告了对在阿尔及利亚、埃及、利比亚、摩洛哥、苏丹和突尼斯等北非国家传播的新冠病毒（SARS-CoV-2）变体进行的首次全面基因组分析，内容涉及基因组进化枝和突变模式。截至2021年12月，我们分析了提交至EpiCoV GISAID数据库的1669条高覆盖度全基因组序列，以推断进化枝并与野生型变体武汉-胡-1进行突变注释比较。对SARS-CoV-2基因组的系统发育分析揭示了11个GISAID进化枝的存在，其中GR（刺突蛋白S-D614G和核衣壳蛋白N-G204R变体）、GH（ORF3a编码蛋白ORF3a-Q57H变体）和GK（变体S-T478K）最为常见，分别占25.9%、19.9%和19.6%，其次是它们的亲本进化枝G（变体S-D614G）（10.3%）。GRY（变体S-N501Y）（5.1%）、S（变体ORF8-L84S）（3.1%）和GV（ORF3a编码蛋白NS3-G251V变体）（2.0%）的流行率较低。有趣的是，在全部基因组中，1.5%被归类为GRA（奥密克戎），即新出现的进化枝。在北非各国，共鉴定出108个使用穿山甲分类法的SARS-CoV-2谱系，其中大多数基因组属于六个主要谱系和关注变体（VOC），包括B.1、德尔塔变体（AY.X、B.1.617.2）、C.36、B.1.1.7和B.1.1。SARS-CoV-2基因组中突变的影响突出显示了相似的特征，D614G刺突（S）和ORF1b-P314L变体分别在95.3%和87.9%的总序列中出现的变化最多。此外，影响其他病毒蛋白的突变也频繁出现，包括：N:RG203KR、N:G212V、NSP3:T428I、ORF3a:Q57H、S:N501Y、M:I82T和E:V5F。这些发现凸显了基因组监测对于了解SARS-CoV-2遗传多样性及其传播模式的重要性，有助于更好地指导公共卫生干预措施。本研究的技术分析可在全球范围内实施，以便通过统一的方法克服这一健康危机。
