Phylogenetic analyses of severe acute respiratory syndrome coronavirus 2 reveals multiple routes of introduction into Taiwan, the United States, Japan, and other countries
Supplemental Table 1. Genome sequences used in this study. Supplemental Figure 1. Variable sites found from SARS-CoV-2 ORF sequences After alignment, the SARS-CoV-2 sequences had 112 variable sites from 29,148 bps aligned ORF sequences from 76 samples isolated from humans. Dots indicate the identical bases with the reference bases on the top of the alignment. A, C, G or T indicate the differences in the sequences. Nucleotide position numbers in the reference genome are shown above the alignment. All sites containing gaps were removed from the analysis. Supplemental Figure 2. Topological phylogeny of SARS-CoV-2 Maximum-likelihood phylogenetic analyses under each condition below. Blue, green, and yellow branches indicate group TCT, TCC, and CTC respectively. Bootstrap values (≧30%) based on 1,000 replications are indicated at nodes. Branch length was meaningless. (A) No separate condition. Final log-likelihood was −59284.685031. BIC score was 120234.752998. (B) Separating 1st/2nd and 3rd codon position condition. Final log-likelihood was − 56877.337100. BIC score was 115522.858552. (C) Separating each ORF condition. Final log-likelihood was −59849.040154. BIC score was 121764.388766. (D) Separating each ORF and also 1st/2nd and 3rd codon position condition. Final log-likelihood was − 56521.449588. BIC score was 115530.693437. (E) Separating each ORF and each codon position condition. Final log-likelihood was −56149.612346. BIC score was 115074.862919. Supplemental File 1. Parsimony informative sites found in SARS-CoV genomes. Supplemental File 2. Parsimony informative sites found in Ebola virus genomes. Supplemental File 3. Parsimony informative sites found in Zika virus genomes.