Table 4.

South Africa.

(A)			09/01–12/07/2020
Position	Location	Mutation	Count	Incidence
174nt	5´UTR	GT → TT	12/95	DE,US
		noneffective
241nt		CG → TG	95/95	Prevalent
		noneffective
1,059nt	nsp2	CC → TC	10/95	Prevalent
		ACC (Threonine) → ATC (Isoleucine)
2,164nt		GA → CA	11/95	IN
		GAGAAG (Glutamic Acid Lysine) → GACAAG (Aspartic Acid Lysine)
3,037nt	nsp3	CT → TT	95/95	Prevalent
		noneffective
5,230nt		GT → TT	12/95	DE
		AAGTGG (Lysine Tryptophan) → AATTGG (Asparagine Tryptophan)
6,762nt		CT → TT	13/95	Unique
		ACT (Threonine) → ATT (Isoleucine)
10,323nt	3C‐like proteinase	AG → GG	11/95	Unique
		AAG (Lysine) → AGG (Arginine)
11,230nt	nsp6	GC → TC	11/95	Unique
		ATGCCT (Methionine Proline) → ATTCCT (Isoleucine Proline)
12,503nt	nsp8	TA → CA	26/95	Unique
		TAT (Tyrosine) → CAT (Histidine)
14,408nt	RNA‐dependent RNA polymerase	CT → TT	95/95	Prevalent
		CCT (Proline) → CTT (Leucine)
20,268nt	endoRNAse	AG → GG	21/95	FR,ES,RU
		noneffective
21,801nt	Spike glycoprotein	AT → CT	10/95	Unique
		GAT (Aspartic Acid) → GCT (Alanine)
22,675nt		CG → TG	10/95	Unique
		noneffective
22,813nt		GA → TA	10/95	DE
		noneffective
23,012nt		GA → AA	12/95	IN
		GAA (Glutamic Acid) → AAA (Lysine)
23,403nt		AT → GT	95/95	Prevalent
		GAT (Aspartic Acid) → GGT (Glycine)
23,664nt		CA → TA	14/95	ES,IN
		GCA (Alanine) → GTA (Valine)
25,563nt	ORF3a protein	GA → TA	10/95	Prevalent
		CAGAGC (Glutamine Serine) → CATAGC (Histidine Serine)
25,770nt		GC → TC	20/95	RU
		AGGCTT (Arginine Leucine) → AGTCTT (Serine Leucine)
25,904nt		CA → TA	10/95	BR,DE
		TCA (Serine) → TTA (Leucine)
26,456nt	Envelope protein	CT → TT	10/95	Unique
		CCT (Proline) → CTT (Leucine)
28,253nt	ORF8 protein	CA → TA	14/95	BR,DE,ES,FR,US
		noneffective
28,854nt	Nucleocapsid phosphoprotein	CA → TA	23/95	CN,DE,ES,FR,IN,RU
		TCA (Serine) → TTA (Leucine)
28,881nt		GGG → AAC	61/95	Prevalent
		AGGGGA (Arginine Glycine) → AAACGA (Lysine Arginine)
28,887nt		CT → TT	11/95	BR,CN,FR,IN,RU
		ACT (Threonine) → ATT (Isoleucine)
29,721nt	3´UTR	CC → TC	26/95	Unique
		noneffective

(B)			01/19/2020–01/20/2021
Position	Location	Mutation	Total Count	Percentage
174nt	5´UTR	G → T	181	10.17
241nt		C → T	1,772	99.61
355nt	ORF1ab polyprotein → leader protein	C → T	59	3.32
1,059nt	nsp2	C → T	149	8.38
2,094nt		C → T	38	2.14
2,164nt		G → C	84	4.72
2,692nt		A → T	41	2.3
3,037nt	nsp3	C → T	1,746	98.15
4,002nt		C → T	165	9.27
4,093nt		C → T	48	2.7
5,230nt		G → T	147	8.26
6,027nt		C → T	46	2.59
6,762nt		C → T	178	10.01
7,064nt		A → G	124	6.97
8,660nt	nsp4	C → T	69	3.88
8,964nt		C → T	69	3.88
9,498nt		T → C	36	2.02
10,097nt	3C‐like proteinase	G → A	163	9.16
10,323nt		A → G	169	9.5
11,083nt	nsp6	G → T	60	3.37
11,230nt		G → T	75	4.22
11,447nt		G → A	129	7.25
12,503nt	nsp8	T → C	389	21.87
13,536nt	RNA‐dependent RNA polymerase	C → T	170	9.56
14,408nt		C → T	1,773	99.66
14,925nt		C → T	71	3.99
16,376nt	Helicase	C → T	54	3.04
16,490nt		C → T	39	2.19
16,853nt		G → T	47	2.64
16,946nt		C → T	43	2.42
18,747nt	3'‐to‐5' exonuclease	C → T	115	6.46
20,234nt	endoRNAse	C → T	42	2.36
20,268nt		A → G	209	11.75
21,801nt	Spike glycoprotein	A → C	142	7.98
22,206nt		A → G	71	3.99
22,287nt		T → A	86	4.83
22,299nt		G → T	69	3.88
22,675nt		C → T	290	16.3
22,813nt		G → T	139	7.81
23,012nt		G → A	146	8.21
23,063nt		A → T	140	7.87
23,403nt		A → G	1,772	99.61
23,625nt		C → T	53	2.98
23,664nt		C → T	154	8.66
23,731nt		C → T	161	9.05
25,455nt	ORF3a	G → T	65	3.65
25,521nt		C → T	66	3.71
25,563nt		G → T	148	8.32
25,770nt		G → T	285	16.02
25,904nt		C → T	143	8.04
26,456nt	Envelope protein	C → T	140	7.87
26,586nt	Membrane glycoprotein	C → T	62	3.49
27,384nt	ORF6	T → C	120	6.75
27,504nt	ORF7a	T → C	50	2.81
28,077nt	ORF8	G → T	74	4.16
28,253nt		C → T	178	10.01
28,854nt	Nucleocapsid phosphoprotein	C → T	173	9.72
28,881nt		G → A	1,238	69.59
28,882nt		G → A	1,238	69.59
28,883nt		G → C	1,238	69.59
28,887nt		C → T	152	8.54
29,425nt		G → T	117	6.58
29,721nt	3´UTR	C → T	388	21.81

The Table presents characteristics of SARS‐CoV‐2 mutants from South African isolates. For Table design, see legend to Table 5.