S protein sequence-based phylogenetic analyses of alphacoronaviruses.

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S protein sequence-based phylogenetic analyses of alphacoronaviruses. S protein sequence-based phylogenetic analyses of alphacoronaviruses. (A to C) Protein sequences of the complete S protein (A), S1 domain (B), and S2 domain (C) were aligned using MAFFT within the Geneious 10 software package, and maximum-likelihood phylogenetic trees were generated with PhyML. The trees were rooted using MHV-A59. Numbers at nodes indicate the bootstrap support on 100 replicates. Scale bars indicate estimated numbers of substitutions per site. (D) The sequences corresponding to the S protein region around the S1/S2 cleavage site of Alphacoronavirus 1 strains and closely related viruses were aligned with MAFFT using the Geneious 10 software package. For all panels, accession numbers for spike (S) protein sequences used are found in Materials and Methods. NTD, N-terminal domain; C-domain, C-terminal domain; FP, fusion peptide; TM, transmembrane domain. Gary R. Whittaker et al. mSphere 2018; doi:10.1128/mSphereDirect.00463-17