전체메뉴
검색
Article Search

JMB Journal of Microbiolog and Biotechnology

QR Code QR Code

Articles Service

Supplementary
Share this article on :
Metrics

Related articles in JMB

More Related Articles

Minireview

Molecular and Cellular Microbiology (MCM)  |  Microbial Genomes and Metagenomics

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

Polly Soo Xi Yap1,*, Tse Siang Tan2, Yoke Fun Chan1, Kok Keng Tee1, Adeeba Kamarulzaman3, Cindy Shuan Ju Teh1,*

1Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia 2Department of Anaesthesiology and Intensive Care, UKM Medical Centre, 56000 Kuala Lumpur, Malaysia 3Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia

Correspondence to:
Cindy Shuan Ju Teh,
E-mail : cindysjteh@um.edu.my
Received: June 6, 2020; Revised: June 17, 2020; Accepted: June 21, 2020

J. Microbiol. Biotechnol. 2020; 30(7): 962-966

Published July 28, 2020 https://doi.org/10.4014/jmb.2006.06009

Copyright © The Korean Society for Microbiology and Biotechnology.

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, COVID-19, mutation, Southeast Asia

Graphical Abstract

References

  1. Sirkeci I, Yüceşahin MM. 2020. Coronavirus and migration: Analysis of human mobility and the spread of COVID-19. Migrat. Lett. 17: 379-398.
  2. Southeast Asia Covid-19 Tracker. 2020. Available from: https://www.csis.org/programs/southeast-asia-program/southeast-asiacovid-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-responsecapacities-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. 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-tostay-amid-outbreak.html. Accessed 23 April, 2020.
  7. The Center for Migration Studies. The Stateless Rohingya in Thailand. Available from: https://cmsny.org/the-stateless-rohingya-inthailand/.Accessed May 20, 2020
  8. 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.
  9. Moya A, Holmes EC, Gonzalez-Candelas F. 2004. The population genetics and evolutionary epidemiology of RNA viruses. Nat. Rev. Microbiol. 2: 279-288.
    Pubmed PMC
  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.
    Pubmed PMC
  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.
    Pubmed PMC
  12. GISAID. 2020. GISAID_hCoV-19_Analysis_Update_2020-06-12_1900UTC. Available from: https://www.gisaid.org/. AccessedJune 16, 2020.
  13. Khailany RA, Safdar M, Ozaslan M. 2020. Genomic characterization of a novel SARS-CoV-2. Gene Rep. 19: 100682.
    Pubmed PMC
  14. 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.
    Pubmed PMC
  15. 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.
    Pubmed PMC
  16. 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.
    Pubmed PMC
  17. 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.
    Pubmed PMC
  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.
    Pubmed PMC
  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.
    Pubmed PMC
  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-healthdg.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.
    Pubmed PMC
  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.
    Pubmed PMC
  23. 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.
  24. 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.
  25. Holmes EC, Dudas G, Rambaut A, Andersen KG. 2016. The evolution of Ebola virus: Insights from the 2013-2016 epidemic. Nature 538: 193-200.
    Pubmed PMC