Investigation of SARS-CoV-2 Genomic Variants in Two Patients: Insights into Initial Isolates from West Kalimantan, Indonesia

Backgrounds: The COVID-19 (coronavirus disease-2019) pandemic caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) has led to significant global health impacts. Understanding the genomic evolution and mutation dynamics of SARS-CoV-2 is crucial for devising effective control measures. This study aimed to perform genomic analysis of early 2020 SARS-CoV-2 isolates from West Kalimantan, Indonesia, focusing on the presence of the D614G mutation. 
Materials & Methods: Samples were collected from individuals whose COVID-19 was confirmed using RT-PCR at the Microbiology Laboratory of Tanjungpura University Hospital during October to November 2020. Samples were sequenced following standard protocols using GRIDION sequencer at the Genetica Science Sequencing Services Company in Jakarta. Additionally, 53.109 SARS-CoV-2 genome sequences from Indonesia (January 2020- June 2023) were retrieved from the GISAID database. A phylogenetic tree and 3D (dimensional) protein structure were constructed using MEGA X  software and I-TASSER. 

Findings: Genomic sequencing and phylogenetic analysis showed that both West Kalimantan isolates were closely related to the Wuhan Hu-1 strain and belonged to the B.1.459 lineage. Both samples exhibited the D614G mutation in the spike protein, a mutation later found in dominant variants including Delta and Omicron in Indonesia. The identification of B.1.459 in this region contributes to understanding its spread across the archipelago. 

Conclusion: This study provides genomic evidence of the first SARS-CoV-2 isolates in West Kalimantan, supporting the role of the D614G mutation in increased transmission. It also enhances understanding of the emergence and geographic distribution of the B.1.459 lineage in Indonesia, highlighting the importance of continued genomic surveillance.