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http://dx.doi.org/10.4014/jmb.2006.06009

An Overview of the Genetic Variations of the SARS-CoV-2 Genomes Isolated in Southeast Asian Countries  

Yap, Polly Soo Xi (Department of Medical Microbiology, Faculty of Medicine, University of Malaya)
Tan, Tse Siang (Department of Anaesthesiology and Intensive Care, UKM Medical Centre)
Chan, Yoke Fun (Department of Medical Microbiology, Faculty of Medicine, University of Malaya)
Tee, Kok Keng (Department of Medical Microbiology, Faculty of Medicine, University of Malaya)
Kamarulzaman, Adeeba (Department of Medicine, Faculty of Medicine, University of Malaya)
Teh, Cindy Shuan Ju (Department of Medical Microbiology, Faculty of Medicine, University of Malaya)
Publication Information
Journal of Microbiology and Biotechnology / v.30, no.7, 2020 , pp. 962-966 More about this Journal
Abstract
Monitoring the mutation dynamics of human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical in understanding its infectivity, virulence and pathogenicity for development of a vaccine. In an "age of mobility," the pandemic highlights the importance and vulnerability of regionalization and labor market interdependence in Southeast Asia. We intend to characterize the genetic variability of viral populations within the region to provide preliminary information for regional surveillance in the future. By analyzing 142 complete genomes from South East Asian (SEA) countries, we identified three central variants distinguished by nucleotide and amino acid changes.
Keywords
Coronavirus; SARS-CoV-2; genetic variation; mutation; COVID-19; Southeast Asia;
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1 Sirkeci I, Yüceşahin MM. 2020. Coronavirus and migration: Analysis of human mobility and the spread of COVID-19. Migrat. Lett. 17: 379-398.   DOI
2 Southeast Asia Covid-19 Tracker. 2020. Available from: https://www.csis.org/programs/southeast-asia-program/southeast-asia-covid-19-tracker-0. Accesed May 12, 2020.
3 World Health Organisation. 2020. WHO emphasizes on agile response capacities, as South-East Asia Region confirms more COVID-19 cases. Available from: https://www.who.int/southeastasia/news/detail/04-03-2020-who-emphasizes-on-agile-response-capacities-as-south-east-asia-region-confirms-more-covid-19-cases. Accessed May 18, 2020.
4 TRIANGLE in ASEAN International Labour Organisation. Available from: https://www.ilo.org/asia/projects/WCMS_428584/lang--en/index.htm. Accessed May 20, 2020.
5 Today Online. 2018. Amid cross border tensions, Malaysians working in Singapore hope rice bowls unaffected. Available from: https://www.todayonline.com/world/amid-cross-border-tensions-malaysians-working-singapore-hope-rice-bowls-unaffected. Accessed May 20, 2020.
6 Moya A, Holmes EC, Gonzalez-Candelas F. 2004. The population genetics and evolutionary epidemiology of RNA viruses. Nat. Rev. Microbiol. 2: 279-288.   DOI
7 The Jakarta Post. 2020. High influx of Indonesian migrant workers from Malaysia, despite call to stay amid outbreak. Available from: https://www.thejakartapost.com/news/2020/04/23/high-influx-of-indonesian-migrant-workers-from-malaysia-despite-call-to-stay-amid-outbreak.html. Accessed 23 April, 2020.
8 The Center for Migration Studies. The Stateless Rohingya in Thailand. Available from: https://cmsny.org/the-stateless-rohingya-in-thailand/. Accessed May 20, 2020
9 The Guardian. 2020. Malaysia cites Covid-19 for rounding up hundreds of migrants. Available from: https://www.theguardian.com/global-development/2020/may/02/malaysia-cites-covid-19-for-rounding-up-hundreds-of-migrants. Accessed May 2, 2020.
10 Chong YM, Sam IC, Ponnampalavanar S, Syed Omar SF, Kamarulzaman A, Munusamy V, et al. 2020. Complete Genome Sequences of SARS-CoV-2 Strains Detected in Malaysia. Microbiol. Resour. Announc. 9: e00383-20.
11 van Dorp L, Acman M, Richard D, Shaw LP, Ford CE, Ormond L, et al. 2020. Emergence of genomic diversity and recurrent mutations in SARS-CoV-2. Infect. Genet. Ecol. 83: 104351.   DOI
12 GISAID. 2020. GISAID_hCoV-19_Analysis_Update_2020-06-12_1900UTC. Available from: https://www.gisaid.org/. Accessed June 16, 2020.
13 Khailany RA, Safdar M, Ozaslan M. 2020. Genomic characterization of a novel SARS-CoV-2. Gene Rep. 19: 100682.   DOI
14 Forster P, Forster L, Renfrew C, Forster M. 2020. Phylogenetic network analysis of SARS-CoV-2 genomes. Proc. Natl. Acad. Sci. USA 117: 9241-9243.   DOI
15 Wang C, Liu Z, Chen Z, Huang X, Xu M, He T, et al. 2020. The establishment of reference sequence for SARS-CoV-2 and variation analysis. J. Med. Virol. 92: 667-674.   DOI
16 Lau SK, Woo PC, Li KS, Huang Y, Tsoi HW, Wong BH, et al. 2005. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proc. Natl. Acad. Sci. USA 102: 14040-14045.   DOI
17 Kim JI, Kim YJ, Lemey P, Lee I, Park S, Bae JY, et al. 2016. The recent ancestry of Middle East respiratory syndrome coronavirus in Korea has been shaped by recombination. Sci. Rep. 6: 18825.   DOI
18 Muth D, Corman VM, Roth H, Binger T, Dijkman R, Gottula LT, et al. 2018. Attenuation of replication by a 29 nucleotide deletion in SARS-coronavirus acquired during the early stages of human-to-human transmission. Sci. Rep. 8: 15177.   DOI
19 Lau SK, Feng Y, Chen H, Luk HK, Yang WH, Li KS, et al. 2015. Severe Acute Respiratory Syndrome (SARS) coronavirus ORF8 protein is acquired from SARS-Related coronavirus from greater horseshoe bats through recombination. J. Virol. 9: 10532-10547.
20 The Star. 2020. New Covid-19 cluster emerges from students returning from Indonesia, says Health DG. Available from: https://www.thestar.com.my/news/nation/2020/04/19/new-covid-19-cluster-emerges-from-students-returning-from-indonesia-says-health-dg. Accessed April 19, 2020.
21 Du L, He Y, Zhou Y, Liu S, Zheng BJ, Jiang S. 2009. The spike protein of SARS-CoV--a target for vaccine and therapeutic development. Nat. Rev. Microbiol. 7: 226-236.   DOI
22 Choi Y, Chan AP. 2015. PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics 31: 2745-2747.   DOI
23 Holmes EC, Dudas G, Rambaut A, Andersen KG. 2016. The evolution of Ebola virus: Insights from the 2013-2016 epidemic. Nature 538: 193-200.   DOI
24 Jin X, Lian JS, Hu JH, Gao J, Zheng L, Zhang YM, et al. 2020. Epidemiological, clinical and virological characteristics of 74 cases of coronavirus-infected disease 2019 (COVID-19) with gastrointestinal symptoms. Gut 69: 1002-1009.   DOI
25 Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, et al. 2014. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 345: 1369-1372.   DOI