Emerging Infectious Disease ISSN: 1080-6059

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)

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Figure 3

Phylogenetic analyses of coronaviruses. A–F) Maximum-likelihood phylogenies of combined and each individual open reading frame (ORF), including ORF 1ab, S, E, M, and N. Previously defined viral lineages (group 1, 2a, 2b, 2c, 2d, 3, and 4) are highlighted by color blocks and described in (A). G) Phylogenetic analyses on the partial RNA-dependent RNA polymerase sequence region (396 bp) of coronaviruses (CoVs). Partial gene sequences from other CoVs that are closely related to the novel human betaC

Figure 3. . . . Phylogenetic analyses of coronaviruses. A–F) Maximum-likelihood phylogenies of combined and each individual open reading frame (ORF), including ORF 1ab, S, E, M, and N. Previously defined viral lineages (group 1, 2a, 2b, 2c, 2d, 3, and 4) are highlighted by color blocks and described in (A). G) Phylogenetic analyses on the partial RNA-dependent RNA polymerase sequence region (396 bp) of coronaviruses (CoVs). Partial gene sequences from other CoVs that are closely related to the novel human betaCoVs are included and marked with asterisks. Bootstrap analysis of 1,000 replicates was performed for each phylogeny. The novel human betaCoVs studied here are shown in red. Scale bar indicates nucleotide substitutions per site.

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