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

Year 2022, , 139 - 147, 15.12.2022

Oktaviani Naulita Turnıp Chairunnisa Fadhillah Anwar Rovık Ayu Rahayu

https://doi.org/10.5799/jmid.1218631

Abstract

Objectives: This study aims to understand the epidemiological 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 regions with various mutations in the spike protein.
Conclusion: During the early pandemic, all countries in the Southeast Asia regions 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.

Keywords

Epidemiology, Phylogeny, SARS-Cov-2, Pandemic

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