Massi Muhammad Nasrum, Sjahril Rizalinda, Halik Handayani, Soraya Gita Vita, Hidayah Najdah, Pratama Muhammad Yogi, Faruk Muhammad, Handayani Irda, Gazali Faris Muhammad, Hakim Mohamad Saifudin, Wibawa Tri
Department of Clinical Microbiology, Faculty of Medicine, Universitas Hasanuddin, Makassar, Indonesia.
Hasanuddin University Medical Research Center (HUM-RC) Laboratory, Faculty of Medicine, Universitas Hasanuddin, Makassar, Indonesia.
Heliyon. 2023 Feb;9(2):e13382. doi: 10.1016/j.heliyon.2023.e13382. Epub 2023 Jan 31.
This study aimed to perform mutation and phylogenetic analyses of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Delta variants and analyze the characteristic signs and symptoms of patients infected with SARS-CoV-2 Delta variant originated from Makassar during the Delta outbreak.Methods: We collected samples from patients who were infected with coronavirus disease 2019 (COVID-19) between June and October 2021. We selected the Quantitative Reverse Transcription-Polymerase Chain Reaction (PCR)-positive samples with a cycle threshold value of <30 for whole genome sequencing. Total viral ribonucleic acid (RNA) was isolated from 34 PCR-positive nasopharyngeal swab samples, and whole genome sequencing was performed using the Oxford Nanopore GridlON sequencer. Phylogenetic and maximum clade credibility analyses were performed using the Bayesian Markov chain Monte Carlo method.
It was found that 33 patients were infected with the SARS-CoV-2 Delta variant in this cohort study, among whom 63.6% (21) patients were female. According to the clinical data, 24 (72.7%), 7 (21.2%), and 2 (6.1%) patients had mild, moderate, and severe COVID-19 infections. Phylogenetic analysis based on the spike and RNA-dependent RNA polymerase (RdRp) genes showed that the collected samples were clustered in the main lineage of B.1.617.2 (Delta variant). The Delta variants had a high frequency of distinct mutations in the spike protein region, including T19R (94.12%), L452R (88.23%), T478K (91.17%), D614G (97%), P681R (97%), and D950 N (97%). Other unique mutations found in a smaller frequency in our samples were present in the N-terminal domain, including A27T (2.94%) and A222V (14.70%), and in the receptor-binding domain, including Q414K (5.88%), G446V (2.94%), and T470 N (2.94%).
This study revealed the unique mutations in the S protein region of Delta variants. T19R, L452R, T478K/T478R, D614G, P681R, and D950 N were the most common substitutions in Makassar's Delta variant.
本研究旨在对严重急性呼吸综合征冠状病毒2（SARS-CoV-2）德尔塔变异株进行突变和系统发育分析，并分析在德尔塔疫情期间源自望加锡的感染SARS-CoV-2德尔塔变异株患者的特征性体征和症状。
我们收集了2021年6月至10月期间感染2019冠状病毒病（COVID-19）患者的样本。我们选择循环阈值<30的定量逆转录-聚合酶链反应（PCR）阳性样本进行全基因组测序。从34份PCR阳性鼻咽拭子样本中分离出总病毒核糖核酸（RNA），并使用牛津纳米孔GridlON测序仪进行全基因组测序。使用贝叶斯马尔可夫链蒙特卡罗方法进行系统发育和最大分支可信度分析。
在这项队列研究中发现33名患者感染了SARS-CoV-2德尔塔变异株，其中63.6%（21名）为女性。根据临床数据，24名（72.7%）、7名（21.2%）和2名（6.1%）患者分别患有轻度、中度和重度COVID-19感染。基于刺突蛋白和RNA依赖性RNA聚合酶（RdRp）基因的系统发育分析表明，收集的样本聚集在B.1.617.2（德尔塔变异株）的主要谱系中。德尔塔变异株在刺突蛋白区域有高频率的独特突变，包括T19R（94.12%）、L452R（88.23%）、T478K（91.17%）、D614G（97%）、P681R（97%）和D950N（97%）。在我们样本中以较低频率发现的其他独特突变存在于N端结构域，包括A27T（2.94%）和A22V（14.70%），以及受体结合结构域，包括Q414K（5.88%）、G446V（2.94%）和T470N（2.94%）。
本研究揭示了德尔塔变异株S蛋白区域的独特突变。T19R、L452R、T478K/T478R、D614G、P681R和D950N是望加锡德尔塔变异株中最常见的替代突变。
