| Id |
Subject |
Object |
Predicate |
Lexical cue |
| T196 |
0-28 |
Sentence |
denotes |
Molecular evolution analysis |
| T197 |
29-167 |
Sentence |
denotes |
Publicly available sequences encoding full-length GPC spike gene for SARS-CoV (3765 bp) were downloaded from GenBank and manually aligned. |
| T198 |
168-249 |
Sentence |
denotes |
For MERS-CoV, we leveraged the whole genome alignment collated by Dudas et al.69. |
| T199 |
250-376 |
Sentence |
denotes |
Specifically, the alignment corresponding to the spike gene was extracted (4059 bp), excluding sequences isolated from humans. |
| T200 |
377-468 |
Sentence |
denotes |
Final alignments for SARS- and MERS-CoV corresponded to 70 and 100 sequences, respectively. |
| T201 |
469-608 |
Sentence |
denotes |
For the dN/dS analysis, we first estimated Bayesian molecular clock phylogenies for SARS- and MERS-CoV independently using BEAST v 1.8.470. |
| T202 |
609-776 |
Sentence |
denotes |
For both viruses, we assumed an uncorrelated log-normal distributed molecular clock71, Bayesian Skyline coalescent prior72 and a codon-structured substitution model73. |
| T203 |
777-907 |
Sentence |
denotes |
Multiple independent MCMC runs of 10–20 million steps were executed to ensure that stationarity and convergence had been achieved. |
| T204 |
908-1201 |
Sentence |
denotes |
Empirical distributions of time-scaled phylogenies were obtained by combining (after the removal of burnin) the posterior tree distributions from the separate runs, which were subsequently used to estimate dN/dS ratios using the renaissance counting approach74,75 implemented in BEAST v 1.8.4. |
| T205 |
1202-1415 |
Sentence |
denotes |
We also estimated per-site amino-acid diversity, which was calculated as the average number of amino-acid difference between two sequences at an amino-acid position in all possible pairs in the sequence alignment. |
