Pamukkale University, Faculty of Medicine, Department of Medical Genetics, Denizli, Turkey.
Pamukkale University, Faculty of Medicine, Department of Medical Microbiology, Denizli, Turkey.
J Infect Dev Ctries. 2021 Apr 30;15(4):470-477. doi: 10.3855/jidc.14560.
Coronaviruses which are single-stranded RNAs, are members of a large family of viruses that may be important pathogens for humans. SARS-CoV-2 was found to cause the severe respiratory syndrome, and on January 22, 2020 first human-to-human transmission was reported. We aimed to reveal the complete genomes of 19 SARS-CoV-2 isolates from Denizli province and identify Turkish patients' genetic similarities.
15 samples with the highest viral loads resulting from RT-PCR were selected for NGS analysis. Fifteen SARS-CoV-2 complete genome sequences were then subjected to phylogenetic analysis and uploaded to the GISAID database. Phylogenetic trees were constructed by the Neighbor-Joining method using MEGAX software.
Whole-genome sequencing of the viral RNA samples revealed 32 missense, 21 synonymous, and 4 non-coding alleles. In all samples c.1-25C>T (5'UTR), c.14144C>T (ORF1ab), c.2772C>T (ORF1ab) and c.1841A>G(S) mutations were detected. Phylogenetic analysis revealed that most of the present study's genomes are in 20B clade while the two are in 20A. The phylogenetic tree constructed with all complete SARS-CoV-2 genomes of Turkey showed that the viruses were spread nearly homogenous on eastern (around Kars) and western (around Istanbul) sides.
Here, we reported the viral genomes in Denizli comprehensively for the first time. We identified 11 rare missense mutations in the virus compared to the reference genome. Phylogenetic analysis revealed that while most of our isolates were similar to European sequences, some had different sublineages depending on their genomic variants.
冠状病毒为单链 RNA 病毒，是一大类病毒的成员，可能是人类的重要病原体。SARS-CoV-2 被发现可引起严重呼吸道综合征，2020 年 1 月 22 日首次报告了人与人之间的传播。我们旨在揭示来自代尼兹利省的 19 种 SARS-CoV-2 分离株的完整基因组，并确定土耳其患者的遗传相似性。
从 RT-PCR 结果中病毒载量最高的 15 个样本中选择用于 NGS 分析。然后对 15 个 SARS-CoV-2 全基因组序列进行系统发育分析，并上传至 GISAID 数据库。使用 MEGAX 软件通过邻接法构建系统发育树。
对病毒 RNA 样本的全基因组测序显示有 32 个错义突变、21 个同义突变和 4 个非编码突变。在所有样本中都检测到 c.1-25C>T（5'UTR）、c.14144C>T（ORF1ab）、c.2772C>T（ORF1ab）和 c.1841A>G(S) 突变。系统发育分析显示，本研究的大部分基因组属于 20B 分支，而其余两个属于 20A 分支。与土耳其所有完整 SARS-CoV-2 基因组构建的系统发育树显示，病毒在东部（靠近卡尔斯）和西部（靠近伊斯坦布尔）几乎均匀分布。
我们首次全面报道了代尼兹利的病毒基因组。与参考基因组相比，我们在病毒中发现了 11 种罕见的错义突变。系统发育分析显示，虽然我们的大多数分离株与欧洲序列相似，但有些分离株由于其基因组变异而具有不同的亚谱系。
