Unsupervised explainable AI for molecular evolutionary study of forty thousand SARS-CoV-2 genomes

BMC Microbiology

Table 1 Mutations analyzed in this study. The numbering of the first seven mutation (M1-M7) is according to the previous study [14]

Mutation	Gene	Protein	AA change	Nucleotide change	Relation	L	S	V	G	GH	GR	1^st appear
M1	5’UTR			5’UTR, -25C > U	C241U				Ga	GHa	GRa	Sichuan, 1/24
M2	ORF1ab	Nsp3	F106	UAC > UAU	C3037U				Ga	GHa	GRa	Sichuan & Zhejiang, 1/24
M3	ORF1ab	RNA-dependent RNA polymerase	P323L	CCU > CUU	C14408U				Ga	GHa	GRa	Zhejiang, 1/24
M4	S	Surface glycoprotein	D614G	GAU > GGU	A23403G				Ga	GHa	GRa	Sichuan & Zhejiang, 1/24
M5	ORF3a	ORF3a protein	Q57H	CAG > CAU	G25563U					GHa		USA, 2/4
M6	ORF1ab	Nsp2	T85I	ACC > AUC	C1059U					GHi		USA, 2/4
M7	N	Nucleocapsid phosphoprotein	RG203_204KR	AGGGGA > AAACGA	GGG28881AAC						GRa	England, 2/16
M8	ORF1ab	3’-to-5’ exonuclease	L280L	CUA > UUA	C18877U					GHiip		Canada, 2/28
M9	ORF1ab	Nsp6	L37F	UUG > UUU	G11083U			Va				Yuuan, 1/17
M10	ORF8	ORF8 protein	L84S	UUA > UCA	U28144C		Sa					Wuhan, 1/5
M11	ORF1ab	Nsp4	S76S	AGC > AGU	C8782U		Sa					Wuhan, 1/5
M12	ORF1ab	RNA-dependent RNA polymerase	Y55Y	UAC > UAU	C14805U		Sp	Vi				England, 2/9
M13	N	Nucleocapsid phosphoprotein	S194L	UCA > UUA	C28854U	Liip			Gp	GHiip		Hong Kong, 2/2
N1	S	Surface glycoprotein	P1140	CT24981NN	CCUU > CNNU				Gp		GRp	USA, 3/7
M0	ORF3a	ORF3a protein	G251V	GGU > GUU	(G26144U)

ISSN: 1471-2180