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KMID : 0364820200560030241
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Korean Journal of Microbiology
2020 Volume.56 No. 3 p.241 ~ p.253
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A phylodynamic analysis of epidemiological situation of East Asia due to the coronavirus disease of 2019
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Choi Sang-Chul
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Abstract
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The coronavirus disease of 2019, COVID-19, has been causing devastating economic losses and mental health stress to societies around the world. An outbreak in the central region of China proceeded to spread to the rest of mainland China and its neighboring regions. Three locales of Japan, South Korea, and Taiwan, mainland China’s neighbors to the east, each reported their index cases of COVID-19 around mid-January 2020. The etiological agent of the severe pneumonic disease is a humaninfecting coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 genome sequences that are collected at a high rate are available at the Global Initiative on Sharing All Influenza Data (GISAID) to help the fight against COVID-19. Here, we detect phylogenetic and epidemiological signals in viral genomes sampled from COVID-19 patients in the three locales of East Asia using phylodynamic models implemented in a Bayesian statistical method of BEAST2 software. We estimate and compare the dates of epidemic origin and the basic reproductive number in the three locales. Because the phylodynamic sample from East Asia was small, the sensitivity of the phylodynamic analysis to random sampling from the data was evaluated. Consistent with the early surge of the COVID-19 cases in South Korea, we analyzed viral genomes isolated before February 27, 2020 and found that, during the early period of the pandemic, the basic reproductive number for South Korea was greater than one.
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KEYWORD
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Bayesian inference, COVID-19, genomic epidemiology, Markov chain Monte Carlo, SARS-CoV-2
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