Ullah Mohammad Fahad, Alnour Tarig M S, Elssaig Elmutuz H, Ahmed-Abakur Eltayib H
Department of Medical Laboratory Technology (FAMS), University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia.
Prince Fahad Research Chair, University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia.
Saudi J Biol Sci. 2021 Dec;28(12):6803-6807. doi: 10.1016/j.sjbs.2021.07.054. Epub 2021 Jul 22.
SARS-CoV-2 has become one of the unprecedented global health challenge for human population. Genomic signature studies of SARS-CoV-2 reveals relation between geographical location of the isolates and genetic diversity. The present work is an , cross sectional study aimed to determine the genetic heterogeneity of SARS-CoV-2 variants isolated in Saudi Arabia compared to the first isolated strain NC_045512 (reference sequence). Each sequence was aligned against the reference sequence using local alignment search tool (NCBI) Nucleotide-BLAST. A total of 58 SARS-CoV-2 genomes were isolated in KSA and retrieved from NCBI. Our study shows that KSA variants demonstrated homology ranging between 99.96 and 99.98 % compared to the reference strain. There are 89 nucleotide changes that have been identified among the KSA variants; the most common nucleotide change was C: T accounting for 50.6% (45/89). These nucleotides changes resulted in 53.9% (48/89) missense mutations and 42.7% (38/89) silent mutations; while the majority of mutations- 48.3% (43/89) occurred in ORF1ab gene. All structural genes displayed mutations; N gene harbored 16.9% (15/89) mutations, S gene displayed 15.7% (14/89) mutations, M gene exhibited 2.2% (2/89) mutations and E gene showed only 1 mutation which was silent. The most frequently changed nucleotide was C3037T (silent mutation) and A23403G (D614G), each of which occurred in 57 variants out of 58 followed by C14408T (P4715L) and C241T (5'UTR) which were found in 56 and 55 variants respectively. The Phylogenetic trees showed that SARS-CoV-2 variants isolated in Saudi Arabia clustered together closely.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）已成为人类面临的前所未有的全球健康挑战之一。SARS-CoV-2的基因组特征研究揭示了分离株的地理位置与遗传多样性之间的关系。本研究为横断面研究，旨在确定沙特阿拉伯分离的SARS-CoV-2变体与首个分离株NC_045512（参考序列）相比的遗传异质性。使用局部比对搜索工具（NCBI）核苷酸BLAST将每个序列与参考序列进行比对。在沙特阿拉伯共分离出58个SARS-CoV-2基因组，并从NCBI中检索到。我们的研究表明，与参考菌株相比，沙特阿拉伯的变体显示出99.96%至99.98%的同源性。在沙特阿拉伯的变体中鉴定出89个核苷酸变化；最常见的核苷酸变化是C：T，占50.6%（45/89）。这些核苷酸变化导致53.9%（48/89）的错义突变和42.7%（38/89）的沉默突变；而大多数突变——48.3%（43/89）发生在ORF1ab基因中。所有结构基因均显示出突变；N基因有16.9%（15/89）的突变，S基因有15.7%（14/89）的突变，M基因有2.2%（2/89）的突变，E基因仅显示1个沉默突变。最常发生变化的核苷酸是C3037T（沉默突变）和A23403G（D614G），在58个变体中的57个中出现，其次是C14408T（P4715L）和C241T（5'UTR），分别在56个和55个变体中发现。系统发育树显示，在沙特阿拉伯分离的SARS-CoV-2变体紧密聚集在一起。
