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].