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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)

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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.

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