Rational Primer and Probe Construction in PCR-Based Assays for the Efficient Diagnosis of Drifting Variants of SARS-CoV-2

Table 3

Number of prevalent (3A) and unique (3B) SNPs in various target genes of SARS-CoV-2 genomes.

3A				3B
Genomic regions	Total SNP counts	Region size	Total SNP counts per Nt per 10000 genomes	Genomic region	Unique SNP counts	Region size	Unique SNP counts per Nt per 10000 genomes
NSP10	718	417	0.35	NSP10	158	417	0.078
NSP8	1238	594	0.43	NSP5	365	918	0.082
NSP16	2050	894	0.47	NSP8	239	594	0.083
NSP9	1179	339	0.72	NSP16	361	894	0.083
E	837	228	0.75	NSP12 (RdRp)	1140	2795	0.084
ORF7b	574	132	0.89	NSP13	756	1803	0.086
NSP7	1112	249	0.92	NSP9	143	339	0.087
ORF7a	1664	366	0.93	NSP14	706	1581	0.092
ORF6	904	186	0.99	NSP4	679	1500	0.093
NSP14	8351	1581	1.09	NSP6	418	870	0.099
NSP13	10084	1803	1.15	NSP3	2818	5835	0.099
NSP5	5176	918	1.16	NSP7	122	249	0.1
NSP1	3056	540	1.16	S	1897	3811	0.1
NSP4	8696	1500	1.19	M	340	669	0.1
M	4059	669	1.25	NSP15	543	1038	0.11
ORF10	710	117	1.25	ORF10	64	117	0.11
NSP15	6470	1038	1.28	E	125	228	0.11
NSP3	56466	5835	1.99	ORF6	111	186	0.12
NSP6	8697	870	2.06	NSP2	1157	1914	0.12
NSP2	22135	1914	2.38	ORF7b	85	132	0.13
S	51998	3811	2.81	NSP1	351	540	0.13
ORF8	6514	366	3.66	ORF8	256	366	0.14
NSP12 (RdRp)	50441	2795	3.71	N	930	1260	0.15
3′ UTR	4738	229	4.25	ORF7a	277	366	0.16
N	27209	1260	4.44	ORF3a	631	828	0.16
ORF3a	22717	828	5.64	5′ UTR	334	265	0.26
5′ UTR	37872	265	29.38	3′ UTR	433	229	0.39