Abstract

Background: The ongoing coronavirus disease 2019 (COVID-19) pandemic has posed an unprecedented challenge to public health in Southeast Asia, a tropical region with limited resources. This study aimed to investigate the evolutionary dynamics and spatiotemporal patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the region.Materials and Methods: A total of 1491 complete SARS-CoV-2 genome sequences from 10 Southeast Asian countries were downloaded from the Global Initiative on Sharing Avian Influenza Data (GISAID) database on November 17, 2020. The evolutionary relationships were assessed using maximum likelihood (ML) and time-scaled Bayesian phylogenetic analyses, and the phylogenetic clustering was tested using principal component analysis (PCA). The spatial patterns of SARS-CoV-2 spread within Southeast Asia were inferred using the Bayesian stochastic search variable selection (BSSVS) model. The effective population size (Ne) trajectory was inferred using the Bayesian Skygrid model.Results: Four major clades (including one potentially endemic) were identified based on the maximum clade credibility (MCC) tree. Similar clustering was yielded by PCA; the first three PCs explained 46.9% of the total genomic variations among the samples. The time to the most recent common ancestor (tMRCA) and the evolutionary rate of SARS-CoV-2 circulating in Southeast Asia were estimated to be November 28, 2019 (September 7, 2019 to January 4, 2020) and 1.446 × 10−3 (1.292 × 10−3 to 1.613 × 10−3) substitutions per site per year, respectively. Singapore and Thailand were the two most probable root positions, with posterior probabilities of 0.549 and 0.413, respectively. There were high-support transmission links (Bayes factors exceeding 1,000) in Singapore, Malaysia, and Indonesia; Malaysia involved the highest number (7) of inferred transmission links within the region. A twice-accelerated viral population expansion, followed by a temporary setback, was inferred during the early stages of the pandemic in Southeast Asia.Conclusions: With available genomic data, we illustrate the phylogeography and phylodynamics of SARS-CoV-2 circulating in Southeast Asia. Continuous genomic surveillance and enhanced strategic collaboration should be listed as priorities to curb the pandemic, especially for regional communities dominated by developing countries.

Highlights

  • Coronavirus disease 2019 (COVID-19) is an infectious disease, first reported in Wuhan, China, in late December 2019 [1, 2]

  • The ML phylogenetic tree based on complete genomes showed the molecular evolution of SARS-CoV-2 isolates from Southeast Asia (Figure 1A)

  • The evolutionary rate of SARS-CoV-2 isolated from Southeast Asia was estimated to be 1.446 × 10−3 (95% highest posterior density (HPD): 1.292 × 10−3 to 1.613 × 10−3) substitutions per site per year

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Summary

Introduction

Coronavirus disease 2019 (COVID-19) is an infectious disease, first reported in Wuhan, China, in late December 2019 [1, 2]. Given the close genetic similarity, it was classified as a new member of the genus Betacoronavirus and named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [5]. The contribution of Southeast Asia, which is dominated by underdeveloped economies, to the global total of COVID-19 cases is nearly 2% at the time of writing since the first infection within the region was detected in Thailand on January 13, 2020 [9, 11]. The ongoing coronavirus disease 2019 (COVID-19) pandemic has posed an unprecedented challenge to public health in Southeast Asia, a tropical region with limited resources. This study aimed to investigate the evolutionary dynamics and spatiotemporal patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the region

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