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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)

Main Article

Table 1

Nucleotide and amino acid differences between novel human betacoronaviruses EMC/2012 and England/Qatar/2012 major ORFs

ORF* Nucleotide
Amino acid
Difference† Change, %‡ Difference† Change, %‡§
ORF 3 4 1.28 2 1.92
N 11 0.86 4 0.94
ORF 8b 2 0.59 1 0.88
ORF 4a 3 0.88 1 0.88
NSP13 4 0.24 4 0.71
NSP2 7 0.35 4 0.61
NSP15 3 0.29 2 0.58
ORF 5 3 0.44 1 0.44
NSP3 21 0.37 8 0.42
NSP4 3 0.20 2 0.39
ORF 4b 4 0.46 1 0.34
ORF 1a 45 0.34 14 0.32
S 10 0.24 2 0.15
ORF 1b 15 0.19 3 0.11
E 0 0.00 0 0.00
M 0 0.00 0 0.00
NSP1 2 0.35 0 0.00
NSP5 2 0.22 0 0.00
NSP6 4 0.46 0 0.00
NSP7 1 0.40 0 0.00
NSP8 1 0.17 0 0.00
NSP9 3 0.91 0 0.00
NSP10 1 0.24 0 0.00
NSP11 0 0.00 0 0.00
NSP12 4 0.14 0 0.00
NSP14 3 0.19 0 0.00
NSP16 1 0.11 0 0.00

*ORF nomenclature is from van Boheemen et al. (3). ORF, open reading frame; NSP, nonstructural protein.
†No. nucleotide or amino acid differences between aligned ORF or their predicted protein products.
‡No. differences (nucleotide or amino acid) divided by the length of the ORF or the predicted protein.
§ORFs were sorted by decreasing amino acid percentage change.

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