Epidemiological Features and Phylogeny of SARS-CoV-2 Circulating in the Southeast Asia in Early Pandemic

Oktaviani Naulita Turnip¹, Chairunisa Fadhilah², Anwar Rovik³, Ayu Rahayu^3,4

¹Department of Microbiology, Faculty of Medicine, Universitas Palangka Raya, Indonesia

²Biomedical Science, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia

³Center of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia

Department of Microbiology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta,

Indonesia

ABSTRACT

Objectives: This study aims to understand the epidemiological features and level of genetic similarity in the SARS-CoV-2 from different geographical areas in The Southeast Asia Region during an early pandemic.

Methods: The data on COVID-19 cases in Southeast Asia was collected from https://worldometer.info/ and extracted independently. Complete genome SARS-CoV-2 nucleotide sequence data was obtained from GISAID and NCBI online platforms. The sequences were aligned using MEGA X software and identified RdRp and Spike genes using UGENE software. The phylogenetic was constructed using MEGA X software to know the similarity of these genes among isolates in the Southeast Asia region.

Results: The result showed that the first case in Southeast Asia was reported in January 2020. The highest number of COVID-19 cases and death were reported from populous and suffering countries. The phylogenetic results showed an identical solid (100%) among isolates, except for the Philippines-5 isolate. The Wuhan-Hu-1 (China) SARS-CoV-2 isolate (Acc. NC_045512) was transmitted to other countries in Southeast Asia region with various mutations in the spike protein.

Conclusion: During the early pandemic, all countries in the Southeast Asia region reported COVID-19 cases. Indonesia became the country with the highest number of COVID-19 cases and deaths. The level of similarity of the RdRp gene in the SARS-CoV-2 in Southeast Asia is higher than the Spike genes.  J Microbiol Infect Dis 2022; 12(4):139-148.