Table 5.
Phylogenetic position of carnivore and swine relative to human SARS‐CoV isolates in trees calculated under various edit costs under direct optimization for the 157 isolate data set
| Indel cost | TV cost | TS cost | Tree length | Position of SARS CoV isolated from carnivores and swine in tree | Position of SARS CoV isolated from Chiroptera in tree |
|---|---|---|---|---|---|
| 1 | 1 | 1 | 60614 | Terminal, nested within SARS‐ CoV isolated from humans | Basal to SARS‐CoV isolated from humans, carnivores and swine |
| 2 | 2 | 1 | 98057 | Terminal, nested within SARS‐ CoV isolated from humans | Basal to SARS‐CoV isolated from humans, carnivores and swine |
| 2 | 1 | 1 | 74521 | Terminal, nested within SARS‐ CoV isolated from humans | Basal to SARS‐CoV isolated from humans, carnivores, and swine |
| 4 | 2 | 1 | 123885 | Terminal, nested within SARS‐ CoV isolated from humans | Basal to SARS‐CoV isolated from humans, carnivores, and swine |
| 8 | 2 | 1 | 154549 | Terminal, nested within SARS‐ CoV isolated from humans | Most basal to SARS‐CoV isolated from humans, carnivores, and swine. Two isolates from Chiroptera are terminal |