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 Kellam , 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)
Figure 2. . . . A) Sequence differences among EMC/2012, England/Qatar/2012 and England1. The sequences of the 3 genomes were aligned, and differences between the sequence of England/Qatar/2012 and England1 (upper row) or EMC/2012 and England1 (lower row) were tabulated. The colored vertical ticks indicate nucleotide differences (change to A: red, change to T: dark red, change to G: indigo, change to C: medium blue, gap: gray). B) Non-consensus variants detected in the virus sample. The Illumina readset (Illumina, San Diego, CA, USA) for England/Qatar/2012 was mapped to the England/Qatar/2012 genome. Nucleotide positions showing nucleotides that differed from the consensus were tabulated. Colored dots indicate nucleotide positions with >1%–5% (gray), >5%–10% (orange), and >10% (red) nonconsensus variants. Positions with >5% variation and observed nucleotides are as follows: 14311: T, 92.07; G, 7.81; C, 0.12. 18460: C, 94.03; T, 5.97. 18692: G, 85.35; T, 14.65. 22385: G, 83.59; A, 16.41; C, 0.01. 26554: A, 90.85; G, 9.00; T, 0.15. C) Open reading frame (ORF) analysis of England/Qatar/2012. The positions of stop codons in each of the 3 forward ORFs are indicated by vertical black lines; the presence of ORFs of >75 aa are indicated by a closed box. ORF nomenclature is from Van Boheemen et al. (3).
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