Ulfah Maria, Helianti Is
Department of Biocatalyst, Centre for Bioindustrial Technology, Agency for Assessment and Application of Technology (BPPT), Laboratorium of Bioindustrial Technology, LAPTIAB BPPT, Puspiptek-Serpong, Tangerang Selatan, Indonesia.
Iran J Microbiol. 2021 Apr;13(2):145-155. doi: 10.18502/ijm.v13i2.5973.
In first May 2020, Indonesia has been successfully submitted the first three full-length sequence of SARS-CoV-2 to GISAID database. Until September 10, 2020, Indonesia had submitted 54 WGS. In this study, we have analyzed and annotated SARS-CoV-2 mutations in spike protein and main proteases.
The Whole Genome Sequence (WGS) of Indonesia were obtained from GISAID data base. The 54 data were taken from March to September 10, 2020. The sequences corresponded to Spike Protein (SP), 3-chymotrypsin like protease (3CLpro), and papain like protease (PLpro) were selected. The Wuhan genome was used as reference.
In total WGS from Indonesia, we found 5 major clades, which dominated as G clade, where the mutation of D614G was found. This D614G was identified as much as 59%, which mostly reported in late samples submitted. Beside D614G mutation, we report three unique mutations: A352S, S477I, and Q677H. Besides, some mutations were also detected in two domains that were expected to be conserved region, the main viral proteases: PLpro (P77L and V205I), 3CLpro (M49I and L50F).
The analysis of SARS-CoV-2 from WGS Indonesia showed a high genetic variation. The diversity in SARS-CoV-2 may epidemiologically enhance virulence and transmission of this virus. The prevalence of D614G over the time in different locations, indicating that changes in this mutation may related to host infection and the viral transmission. However, some mutations that have been reported in this study were not eligible for the most stable conformation.
2020年5月1日，印度尼西亚成功向全球共享流感数据倡议组织（GISAID）数据库提交了首批三个严重急性呼吸综合征冠状病毒2（SARS-CoV-2）全长序列。截至2020年9月10日，印度尼西亚已提交了54个全基因组测序（WGS）数据。在本研究中，我们对SARS-CoV-2刺突蛋白和主要蛋白酶中的突变进行了分析和注释。
印度尼西亚的全基因组序列（WGS）数据来自GISAID数据库。这54个数据取自2020年3月至9月10日。选择了与刺突蛋白（SP）、3-胰凝乳蛋白酶样蛋白酶（3CLpro）和木瓜蛋白酶样蛋白酶（PLpro）对应的序列。以武汉基因组作为参考。
在印度尼西亚的全部WGS数据中，我们发现了5个主要分支，其中以G分支为主，该分支存在D614G突变。该D614G突变的占比达59%，大多出现在后期提交的样本中。除了D614G突变外，我们还报告了三个独特的突变：A352S、S477I和Q677H。此外，在病毒主要蛋白酶这两个预期为保守区域中也检测到了一些突变：PLpro（P77L和V205I）、3CLpro（M49I和L50F）。
对来自印度尼西亚WGS的SARS-CoV-2分析显示出高度的基因变异。SARS-CoV-2的这种多样性在流行病学上可能会增强该病毒的毒力和传播力。D614G突变在不同时间和地点的流行情况表明，该突变的变化可能与宿主感染及病毒传播有关。然而，本研究中报告的一些突变不符合最稳定构象的条件。
