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Emerging Microbes & Infections Volume 9, 2020 - Issue 1
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Articles

SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East

Yu-Nong Gonga Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan;b Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, TaiwanORCID Iconhttps://orcid.org/0000-0002-6799-1561View further author information
ORCID Icon,
Kuo-Chien Tsaoa Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan;b Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan;c Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, TaiwanView further author information
,
Mei-Jen Hsiaob Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, TaiwanView further author information
,
Chung-Guei Huangb Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan;c Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, TaiwanView further author information
,
Peng-Nien Huanga Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan;d Division of Infectious Diseases, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, TaiwanView further author information
,
Po-Wei Huangb Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, TaiwanView further author information
,
Kuo-Ming Leea Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, TaiwanORCID Iconhttps://orcid.org/0000-0002-3215-8342View further author information
ORCID Icon,
Yi-Chun Liub Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, TaiwanView further author information
,
Shu-Li Yangb Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan;c Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, TaiwanView further author information
,
Rei-Lin Kuoa Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan;c Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan;e Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan;f Division of Asthma, Allergy, and Rheumatology, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, TaiwanView further author information
,
Kuan-Fu Cheng Department of Emergency Medicine, Chang Gung Memorial Hospital, Keelung, Taiwan;h Clinical Informatics and Medical Statistics Research Center, Chang Gung University, Taoyuan, Taiwan;i Community Medicine Research Center, Chang Gung Memorial Hospital, Keelung, TaiwanView further author information
,
Yen-Chin Liua Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, TaiwanView further author information
,
Sheng-Yu Huanga Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, TaiwanView further author information
,
Hsing-I. Huanga Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan;c Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan;e Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan;j Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, TaiwanView further author information
,
Ming-Tsan Liuk Centers for Disease Control, Taipei, TaiwanView further author information
,
Ji-Rong Yangk Centers for Disease Control, Taipei, TaiwanView further author information
,
Cheng-Hsun Chiul Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan;m Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, TaiwanView further author information
,
Cheng-Ta Yangn Department of Respiratory Therapy, College of Medicine, Chang Gung University, Taoyuan, Taiwan;o Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, TaiwanView further author information
,
Guang-Wu Chena Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan;b Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan;p Department of Computer Science and Information Engineering, School of Electrical and Computer Engineering, College of Engineering, Chang Gung University, Taoyuan, TaiwanCorrespondence[email protected]
ORCID Iconhttps://orcid.org/0000-0002-5322-4839View further author information
ORCID Icon &
Shin-Ru Shiha Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan;b Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan;c Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan;q Research Center for Chinese Herbal Medicine, Research Center for Food and Cosmetic Safety, and Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, TaiwanCorrespondence[email protected]
ORCID Iconhttps://orcid.org/0000-0003-4874-401XView further author information
ORCID Icon show all
Pages 1457-1466 | Received 30 Apr 2020, Accepted 09 Jun 2020, Published online: 03 Jul 2020

References

  • Lefkowitz EJ, Dempsey DM, Hendrickson RC, et al. Virus taxonomy: the database of the International Committee on Taxonomy of viruses (ICTV). Nucleic Acids Res. 2018 Jan 4;46(D1):D708–D717. doi: 10.1093/nar/gkx932
  • Drosten C, Gunther S, Preiser W, et al. Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N Engl J Med. 2003 May 15;348(20):1967–1976. doi: 10.1056/NEJMoa030747
  • van der Hoek L, Pyrc K, Jebbink MF, et al. Identification of a new human coronavirus. Nat Med. 2004 Apr;10(4):368–373. doi: 10.1038/nm1024
  • Woo PC, Lau SK, Chu CM, et al. Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J Virol. 2005 Jan;79(2):884–895. doi: 10.1128/JVI.79.2.884-895.2005
  • de Groot RJ, Baker SC, Baric RS, et al. Middle East respiratory syndrome coronavirus (MERS-CoV): announcement of the Coronavirus study Group. J Virol. 2013 Jul;87(14):7790–7792. doi: 10.1128/JVI.01244-13
  • Zhu N, Zhang D, Wang W, et al. A novel Coronavirus from patients with Pneumonia in China, 2019. N Engl J Med. 2020 Feb 20;382(8):727–733. doi: 10.1056/NEJMoa2001017
  • Coronaviridae Study Group of the International Committee on Taxonomy of V. The species severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol. 2020 Apr;5(4):536–544. doi: 10.1038/s41564-020-0695-z
  • Coronavirus disease 2019 (COVID-19) situation reports: World Health Organization; [cited 2020 April 14]. Available from: https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports.
  • Number of Confirmed Cases of COVID-19 in Taiwan: Taiwan Centers for Disease Control; [cited 2020 April 14]. Available from: https://sites.google.com/cdc.gov.tw/2019-ncov/taiwan.
  • Shu Y, McCauley J. GISAID: global initiative on sharing all influenza data - from vision to reality. Euro Surveill. 2017 Mar 30;22(13):30494. doi: 10.2807/1560-7917.ES.2017.22.13.30494
  • Corman VM, Landt O, Kaiser M, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 2020 Jan;25(3):2000045. doi: 10.2807/1560-7917.ES.2020.25.3.2000045
  • Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014 Aug 1;30(15):2114–2120. doi: 10.1093/bioinformatics/btu170
  • Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015 Apr;12(4):357–360. doi: 10.1038/nmeth.3317
  • Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012 May;19(5):455–477. doi: 10.1089/cmb.2012.0021
  • Gong YN, Chen GW, Yang SL, et al. A next-generation sequencing data analysis pipeline for detecting unknown pathogens from mixed clinical samples and revealing their genetic diversity. PLoS One. 2016;11(3):e0151495. doi: 10.1371/journal.pone.0151495
  • Wickham H. Ggplot2: Elegant graphics for data analysis. New York: Springer-Verlag; 2016.
  • Kuraku S, Zmasek CM, Nishimura O, et al. Aleaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity. Nucleic Acids Res. 2013 Jul;41 (Web Server issue):W22–W28. doi: 10.1093/nar/gkt389
  • Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014 May 1;30(9):1312–1313. doi: 10.1093/bioinformatics/btu033
  • Eden JS, Rockett R, Carter I, et al. An emergent clade of SARS-CoV-2 linked to returned travellers from Iran. Virus Evol. 2020 Jan;6(1):veaa027. doi: 10.1093/ve/veaa027
  • Su YCF, Anderson DE, Young BE, et al. Discovery of a 382-nt deletion during the early evolution of SARS-CoV-2. bioRxiv. 2020;2020.03.11.987222.
  • Muth D, Corman VM, Roth H, et al. Attenuation of replication by a 29 nucleotide deletion in SARS-coronavirus acquired during the early stages of humanto-human transmission. Sci Rep. 2018 Oct 11;8(1):15177. doi: 10.1038/s41598-018-33487-8
  • Walls AC, Park YJ, Tortorici MA, et al. Structure, function, and antigenicity of the SARS-CoV-2 spike Glycoprotein. Cell. 2020 Apr 16;181(2):281–292.e6. doi: 10.1016/j.cell.2020.02.058
  • Shang J, Ye G, Shi K, et al. Structural basis of receptor recognition by SARS-CoV-2. Nature. 2020 May;581(7807):221–224. doi: 10.1038/s41586-020-2179-y
  • Letko M, Marzi A, Munster V. Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses. Nat Microbiol. 2020 Apr;5(4):562–569. doi: 10.1038/s41564-020-0688-y
  • Lan J, Ge J, Yu J, et al. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature. 2020 May;581(7807):215–220. doi: 10.1038/s41586-020-2180-5
  • Wrapp D, Wang N, Corbett KS, et al. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science. 2020 Mar 13;367(6483):1260–1263. doi: 10.1126/science.abb2507
  • Lau SY, Wang P, Mok BW, et al. Attenuated SARS-CoV-2 variants with deletions at the S1/S2 junction. Emerg Microbes Infect. 2020 Dec;9(1):837–842. doi: 10.1080/22221751.2020.1756700
  • Vankadari N, Wilce JA. Emerging WuHan (COVID-19) coronavirus: glycan shield and structure prediction of spike glycoprotein and its interaction with human CD26. Emerg Microbes Infect. 2020;9(1):601–604. doi: 10.1080/22221751.2020.1739565
  • Hanada K, Suzuki Y, Gojobori T. A large variation in the rates of synonymous substitution for RNA viruses and its relationship to a diversity of viral infection and transmission modes. Mol Biol Evol. 2004 Jun;21(6):1074–1080. doi: 10.1093/molbev/msh109
  • Eckerle LD, Lu X, Sperry SM, et al. High fidelity of murine hepatitis virus replication is decreased in nsp14 exoribonuclease mutants. J Virol. 2007 Nov;81(22):12135–12144. doi: 10.1128/JVI.01296-07
  • Denison MR, Graham RL, Donaldson EF, et al. Coronaviruses: an RNA proofreading machine regulates replication fidelity and diversity. RNA Biol. 2011 Mar-Apr;8(2):270–279. doi: 10.4161/rna.8.2.15013
  • Dickson RP, Huang YJ, Martinez FJ, et al. The lung microbiome and viral-induced exacerbations of chronic obstructive pulmonary disease: new observations, novel approaches. Am J Respir Crit Care Med. 2013 Nov 15;188(10):1185–1186. doi: 10.1164/rccm.201309-1573ED
  • Norskov-Lauritsen N. Classification, identification, and clinical significance of Haemophilus and Aggregatibacter species with host specificity for humans. Clin Microbiol Rev. 2014 Apr;27(2):214–240. doi: 10.1128/CMR.00103-13
  • Molyneaux PL, Mallia P, Cox MJ, et al. Outgrowth of the bacterial airway microbiome after rhinovirus exacerbation of chronic obstructive pulmonary disease. Am J Respir Crit Care Med. 2013 Nov 15;188(10):1224–1231. doi: 10.1164/rccm.201302-0341OC
  • Hofstra JJ, Matamoros S, van de Pol MA, et al. Changes in microbiota during experimental human Rhinovirus infection. BMC Infect Dis. 2015 Aug 14;15:336. doi: 10.1186/s12879-015-1081-y
  • Kosikowska U, Biernasiuk A, Rybojad P, et al. Haemophilus parainfluenzae as a marker of the upper respiratory tract microbiota changes under the influence of preoperative prophylaxis with or without postoperative treatment in patients with lung cancer. BMC Microbiol. 2016 Apr 6;16:62. doi: 10.1186/s12866-016-0679-6
  • Ou X, Zhou L, Huang H, et al. A severe case with co-infection of SARS-CoV-2 and common respiratory pathogens. Travel Med Infect Dis. 2020 Apr 16;35:101672. doi: 10.1016/j.tmaid.2020.101672

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