Skip directly to page options Skip directly to A-Z link
Volume 19, Number 5—May 2013
Research

Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus

Matthew Cotten, Tommy T. Lam, Simon J. Watson, Anne L. Palser, Velislava Petrova, Paul Grant, Oliver G. Pybus, Andrew Rambaut, Yi Guan, Deenan Pillay, Paul KellamComments to Author , and Eleni Nastouli
Author affiliations: Wellcome Trust Sanger Institute, Hinxton, UK (M. Cotten, S.J. Watson, A.L. Palser, V. Petrova, P. Kellam); University of Oxford, Oxford, UK (T.T. Lam, O.G. Pybus); University College London, London, UK (D. Pillay, P. Kellam); University College London Hospitals,; London (P.Grant, E. Nastouli); University of Edinburgh, Edinburgh, Scotland, UK (A. Rambaut); Fogarty International Center–National Institutes for Health, Bethesda, Maryland, USA (A. Rambaut); The University of Hong Kong, Hong Kong (Y. Guan)

Main Article

Table 2

Nonconsensus variants detected in the sequence of a novel human betacoronavirus

Name* Start† End >0.01–0.05‡ >0.05–0.1 >0.1 Total§ Length %¶#
NSP9 12659 12988 3 0 0 3 329 0.91
NSP10 12989 13408 3 0 0 3 419 0.72
NSP14 18001 19572 6 1 1 8 1571 0.51
NSP6 10937 11812 4 0 0 4 875 0.46
NSP3 2837 8497 25 0 0 25 5660 0.44
NSP12 13432 16206 11 1 0 12 2774 0.43
NSP7 11813 12061 1 0 0 1 248 0.40
NSP5 10019 10936 3 0 0 3 917 0.33
N 28565 29806 4 0 0 4 1241 0.32
S 21455 25516 12 0 1 13 4061 0.32
ORF 4a 25851 26180 1 0 0 1 329 0.30
M 27852 28511 2 0 0 2 659 0.30
ORF 8b 28761 29099 1 0 0 1 338 0.30
NSP13 16307 18000 5 0 0 5 1693 0.30
NSP4 8498 10018 4 0 0 4 1520 0.26
NSP2 857 2836 4 0 0 4 1979 0.20
NSP8 12062 12658 1 0 0 1 596 0.17
ORF 4b 26092 26832 0 1 0 1 740 0.14
NSP15 19573 20601 1 0 0 1 1028 0.10
NSP1 278 856 0 0 0 0 578 0.00
NSP11 13409 13453 0 0 0 0 44 0.00
NSP16 20602 21513 0 0 0 0 911 0.00
ORF 3 25531 25842 0 0 0 0 311 0.00
ORF 5 26839 27513 0 0 0 0 674 0.00
E 27589 27837 0 0 0 0 248 0.00

*ORF nomenclature is from van Boheemen et al. (3). ORF, open reading frame; NSP, nonstructural protein.
†Nucleotide position in England/Qatar/2012 genome.
‡No. nucleotide positions showing the indicated fraction of nonconsensus nucleotides. Only positions with a minimum of 1,000-fold coverage and a Phred quality score of 30 were included.
§No. nucleotide positions with >0.01 (1%) nonconsensus nucleotides.
¶Total no. positions with variation divided by length of ORF) × 100.
#ORFs were sorted by decreasing amino acid percentage change.

Main Article

References
  1. Haagmans  BL, Andeweg  AC, Osterhaus  AD. The application of genomics to emerging zoonotic viral diseases. PLoS Pathog. 2009;5:e1000557. DOIPubMedGoogle Scholar
  2. Bolles  M, Donaldson  E, Baric  R. SARS-CoV and emergent coronaviruses: viral determinants of interspecies transmission. Curr Opin Virol. 2011;1:624–34.
  3. van Boheemen  S, de Graaf  M, Lauber  C, Bestebroer  TM, Raj  VS, Zaki  AM, Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans. MBio. 2012;3:e00473-12.
  4. Bermingham  A, Chand  M, Brown  C, Aarons  E, Tong  C, Langrish  C, Severe respiratory illness caused by a novel coronavirus in a patient transferred to the United Kingdom from the Middle East, September 2012. Euro Surveill. 2012;17:20290 .PubMedGoogle Scholar
  5. Zaki  AM, van Boheemen  S, Bestebroer  TM, Osterhaus  AD, Fouchier  RA. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N Engl J Med. 2012;367:1814–20. DOIPubMedGoogle Scholar
  6. Corman  VM, Eckerle  I, Bleicker  T, Zaki  A, Landt  O, Eschbach-Bludau  M, Detection of a novel human coronavirus by real-time reverse-transcription polymerase chain reaction. Euro Surveill. 2012;17:20285 .PubMedGoogle Scholar
  7. World Health Organization. Novel coronavirus infection–update 21 February 2013 [cited 2013 Feb 21]. http://www.who.int/csr/don/2013_02_21/en/index.html
  8. Watson  SJ, Welkers  MR, Depledge  DP, Coulter  E, Breuer  JM, de Jong  MD, Viral population analysis and minority-variant detection using short read next-generation sequencing. Philos Trans R Soc Lond B Biol Sci. 2013;368:20120205. DOIPubMedGoogle Scholar
  9. Li  H, Durbin  R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–60. DOIPubMedGoogle Scholar
  10. Zerbino  DR, Birney  E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821–9. DOIPubMedGoogle Scholar
  11. Zerbino  DR. Using the Velvet de novo assembler for short-read sequencing technologies. Curr Protoc Bioinformatics. 2010;Chapter 11:Unit 11.5.
  12. Gladman  S, Seemann  T. VelvetOptimiser [cited 2012 Oct 22]. http://www.vicbioinformatics.com/software.velvetoptimiser.shtml
  13. Edgar  RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7. DOIPubMedGoogle Scholar
  14. Tamura  K, Peterson  D, Peterson  N, Stecher  G, Nei  M, Kumar  S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;28:2731–9. DOIPubMedGoogle Scholar
  15. Guindon  S, Dufayard  JF, Lefort  V, Anisimova  M, Hordijk  W, Gascuel  O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59:307–21. DOIPubMedGoogle Scholar
  16. Drummond  AJ, Suchard  MA, Xie  D, Rambaut  A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012;29:1969–73. DOIPubMedGoogle Scholar
  17. Health Protection Agency. Genetic sequence information for scientists about the novel coronavirus 2012 [2013 Feb 18]. http://www.hpa.org.uk/webw/HPAweb&HPAwebStandard/HPAweb_C/1317136246479
  18. Reusken  CB, Lina  PH, Pielaat  A, de Vries  A, Dam-Deisz  C, Adema  J, Circulation of group 2 coronaviruses in a bat species common to urban areas in Western Europe. Vector Borne Zoonotic Dis. 2010;10:785–91. DOIPubMedGoogle Scholar
  19. Falcón  A, Vázquez-Morón  S, Casas  I, Aznar  C, Ruiz  G, Pozo  F, Detection of alpha and betacoronaviruses in multiple Iberian bat species. Arch Virol. 2011;156:1883–90. DOIPubMedGoogle Scholar
  20. Zhao  Z, Li  H, Wu  X, Zhong  Y, Zhang  K, Zhang  YP, Moderate mutation rate in the SARS coronavirus genome and its implications. BMC Evol Biol. 2004;4:21. DOIPubMedGoogle Scholar
  21. Salemi  M, Fitch  WM, Ciccozzi  M, Ruiz-Alvarez  MJ, Rezza  G, Lewis  MJ. Severe acute respiratory syndrome coronavirus sequence characteristics and evolutionary rate estimate from maximum likelihood analysis. J Virol. 2004;78:1602–3. DOIPubMedGoogle Scholar
  22. Pyrc  K, Dijkman  R, Deng  L, Jebbink  MF, Ross  HA, Berkhout  B, Mosaic structure of human coronavirus NL63, one thousand years of evolution. J Mol Biol. 2006;364:964–73. DOIPubMedGoogle Scholar
  23. Lau  SK, Lee  P, Tsang  AK, Yip  CC, Tse  H, Lee  RA, Molecular epidemiology of human coronavirus OC43 reveals evolution of different genotypes over time and recent emergence of a novel genotype due to natural recombination. J Virol. 2011;85:11325–37. DOIPubMedGoogle Scholar
  24. Guan  Y, Zheng  BJ, He  YQ, Liu  XL, Zhuang  ZX, Cheung  CL, Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science. 2003;302:276–8. DOIPubMedGoogle Scholar
  25. Vijgen  L, Keyaerts  E, Moes  E, Thoelen  I, Wollants  E, Lemey  P, Complete genomic sequence of human coronavirus OC43: molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission event. J Virol. 2005;79:1595–604. DOIPubMedGoogle Scholar
  26. Lau  SK, Woo  PC, Li  KS, Huang  Y, Wang  M, Lam  CS, Complete genome sequence of bat coronavirus HKU2 from Chinese horseshoe bats revealed a much smaller spike gene with a different evolutionary lineage from the rest of the genome. Virology. 2007;367:428–39. DOIPubMedGoogle Scholar
  27. Huynh  J, Li  S, Yount  B, Smith  A, Sturges  L, Olsen  JC, Evidence supporting a zoonotic origin of human coronavirus strain NL63. J Virol. 2012;86:12816–25. DOIPubMedGoogle Scholar
  28. Woo  PC, Lau  SK, Li  KS, Poon  RW, Wong  BH, Tsoi  HW, Molecular diversity of coronaviruses in bats. Virology. 2006;351:180–7. DOIPubMedGoogle Scholar
  29. Tang  XC, Zhang  JX, Zhang  SY, Wang  P, Fan  XH, Li  LF, Prevalence and genetic diversity of coronaviruses in bats from China. J Virol. 2006;80:7481–90. DOIPubMedGoogle Scholar
  30. Yip  CW, Hon  CC, Shi  M, Lam  TT, Chow  KY, Zeng  F, Phylogenetic perspectives on the epidemiology and origins of SARS and SARS-like coronaviruses. Infect Genet Evol. 2009;9:1185–96. DOIPubMedGoogle Scholar
  31. Müller  MA, Raj  VS, Muth  D, Meyer  B, Kallies  S, Smits  SL, Human coronavirus EMC does not require the SARS-coronavirus receptor and maintains broad replicative capability in mammalian cell lines. MBio. 2012;3:e00515-12.

Main Article

Page created: April 23, 2013
Page updated: April 23, 2013
Page reviewed: April 23, 2013
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
file_external