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Analysis of SARS-CoV-2 Genomes from West Java, Indonesia.
Azzania Fibriani1, Rebecca Stephanie1, Afifah Alifia Alfiantie1
1Bandung Institute of Technology, Bandung, West Java 40132, Indonesia.
Viruses
|October 26, 2021
Summary
This study analyzed SARS-CoV-2 genome sequences from West Java, Indonesia, revealing dominant variants like Delta and identifying key mutations impacting protein stability. Further research is needed to understand functional consequences.
Area of Science:
- Virology
- Genomics
- Molecular Biology
Background:
- West Java Health Laboratory (WJHL) has sequenced numerous SARS-CoV-2 genomes but lacked advanced analyses.
- Genomic surveillance is crucial for understanding viral evolution and public health responses.
Purpose of the Study:
- To analyze SARS-CoV-2 variant distribution, hotspot mutations, and their impact on protein structure and function.
- To investigate mutation patterns in sequences collected from West Java, Indonesia between September 2020 and June 2021.
Main Methods:
- Retrieved 163 SARS-CoV-2 genome sequences from GISAID.
- Analyzed frequency and distribution of non-synonymous mutations.
- Examined the effect of prevalent mutations on protein stability.
Main Results:
- West Bandung samples exhibited the highest genomic diversity.
- Dominant variants included B.1.617.2 (Delta), B.1.466.2, and B.1.470.
- Spike, NSP3, nucleocapsid, NSP12, and ORF3a proteins had the most mutations.
- Mutations may increase structural protein stability but decrease non-structural protein stability.
Conclusions:
- SARS-CoV-2 evolution in West Java is characterized by specific dominant variants and mutation hotspots.
- Observed mutations potentially alter protein stability, necessitating further investigation into functional impacts.
- Advanced genomic analysis is vital for effective SARS-CoV-2 surveillance and control strategies.
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