Mutational hotspots and conserved domains of SARS-CoV-2 genome in African population

Beni-Suef University Journal of Basic and Applied Sciences

Table 1 Recurrent mutation distribution in the SARS-CoV-2 genome in African population

		S protein		N protein			ORF3	ORF8	nsp2	nsp5	nsp6	nsp12
Country	Viral samples	N501Y	D614G	S194L	R203K	G204R	Q57H	L84S	T265I	G3278S	L3606F	P4715L
Global	230,845	607	214,571	13,479	77,609	76,904	49,109	6142	31,802	4923	15,027	214,154
Africa	3045	103	2881	188	1539	1516	383	169	197	191	152	2787
Algeria	3		3				3		3			3
Benin	12		8				5	4	5			7
Botswana	1		1				1		1			1
Burkina Faso	50		38		13	13	3	32				18
Congo	8		8				7					8
Côte D’Ivoire	43		41				10	28	3		5	15
DR Congo	186		178		16	16	14	4		7	35	178
Egypt	150		143	3	24	3	94	6	2	12		94
Equatorial Guinea	45		45	1							2	45
Gabon	4		2				1	2	1			2
Gambia	235		234		83	83	16		12		3	234
Ghana	15		7		3	3	2	8				7
Kenya	25		19		2	2	1	3	1		3	19
Madagascar	6		4		2	2	2				2	4
Mali	22		7				6	13	3		2	8
Morocco	59		59		22	22	14		10		1	59
Mozambique	2		2		1	1	1		1			2
Nigeria	140		120		66	65	41	11	9	2	13	121
Reunion	4		4				1		1			4
Rwanda	5		5	1			1					5
Senegal	83		77		14	14	16	4	12		5	77
Sierra Leone	10		5		2	2	2	4	2		1	5
South Africa	1735	103	1730	177	1241	1240	111	1	111	160	60	1730
Tunisia	43		39	1	8	8	20	2	9	2	5	39
Uganda	121		64	1	14	14	5	47	5	8	13	64
Zambia	1		1		1	1						1
Zimbabwe	37		37	4	27	27	6		6		2	37
Total	3045	103	2881	188	1539	1516	383	169	197	191	152	2787

3045 complete SARS-CoV-2 sequences from 27 African countries were mined and analyzed (all recurrent mutations observed are presented as Supplementary file S2)
*Highly recurrent mutations were observed in ORF1ab polyprotein (nsp 5, 6, and 12), S protein (S1 domain), ORF3, and N protein, flagging these regions as SARS-CoV-2 mutational hotspots