ANALYSIS OF THE SARS-COV-2 GENOME SEQUENCES FROM INDONESIA IN MARCH 2020 â FEBRUARY 2021
Since the first case was reported in March 2020, the Covid-19 pandemic in Indonesia has been going on for one year. In handling the Covid-19 pandemic, it is important to analyse the SARS-CoV-2 genome to provide an overview of the virus, so that the appropriate policy can be taken. However, until now...
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| Format: | Final Project |
| Language: | Indonesia |
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| Online Access: | https://digilib.itb.ac.id/gdl/view/55492 |
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| Institution: | Institut Teknologi Bandung |
| Language: | Indonesia |
| Summary: | Since the first case was reported in March 2020, the Covid-19 pandemic in Indonesia has been going on for one year. In handling the Covid-19 pandemic, it is important to analyse the SARS-CoV-2 genome to provide an overview of the virus, so that the appropriate policy can be taken. However, until now, the SARS-CoV-2 genome analysis of Indonesian isolates has not been carried out. Therefore, this study analyses the SARS-CoV-2 genome of Indonesian isolates which were recorded in the GISAID database. Statistical analysis was carried out to see the distribution of samples, variants and mutations. Furthermore, the hotspot mutations in Indonesian SARS-CoV-2 isolates were identified. Three-dimensional protein structure model was obtained from C-I-TASSER. The effect of hotspot mutations on protein structure stability was predicted by FoldX, I-Mutant 3.0, and mCSM, while the effect of the mutations on protein function was predicted by PROVEAN, PhD-SNP, and SIFT. Until March 4, 2021, there were 502 Indonesian SARS-CoV-2 genome sequences and 404 sequences met the criteria for further analysis. More than 86% of the samples came from Java Island. The profile of the SARS-CoV-2 variant circulating in Indonesia has shifted over time. At the early of the pandemic, L clade variant was dominant, but currently the GH clade is dominating in Indonesia. There were 8 mutation hotspots (occurring frequency>10%) found at S, N, NSP3, NSP12, and ORF3a genes. Among the hotspot mutations, 5 mutations are predicted to have a significant effect on the protein structure stability (??G>0,05 kcal/mol) and two of them, Q57H (ORF3a) and P227L (NSP12) mutations, are also predicted to affect protein function significantly. In addition, the hotspot mutations combinations R203K/G204R (N) and P227L/P323L (NSP12) are predicted to significantly affect the protein structure stability and function. Overall, this study shows the distribution of SARS-CoV-2 in Indonesia over the past year and the effect of the mutation hotspots found. The information obtained from this study is expected to be a reference for the stakeholders in handling the Covid-19 pandemic in Indonesia.
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