Protein mutation analysis
The proteins encoded by each SARS-CoV-2 genomes were retrieved with
Biopython [21]. The Multiple sequence
alignments (MSA) were done with MUSCLE v3.8.31 for each kind of protein
respectively and the the mutations were called based on each reference
protein sequence.
The cryo-EM structure of SARS-CoV-2 spike glycoprotein was downloaded
from PDB (http://www.rcsb.org/) with the ID of 6vsb. The structure
and frequently mutated amino acids of the spike protein were displayed
with MOLMOL [22].