A random priming amplification method for whole genome sequencing of SARS-CoV-2 virus

Chrzastek, Klaudia; Tennakoon, Chandana; Bialy, Dagmara; Freimanis, Graham; Flannery, John; Shelton, Holly

doi:10.1186/s12864-022-08563-z

Table 3 Reproducibility of genome coverage and average depth for the individual viral genes of SARS-CoV-2 viruses sequenced in this study. Sequence-Independent, Single-Primer Amplification (SISPA) technique was used to recover viral RNA followed by Miseq Illumina sequencing

From: A random priming amplification method for whole genome sequencing of SARS-CoV-2 virus

SARS-CoV-2 isolate	Eng-2 (Titre)			EDB-2 (Titre)
Genes	GC^a (%)	DC^$ / bp	SD^{^}	GC^a (%)	DC^$ / bp	SD^{^}
orf1ab	100	20,330	23,576.5	100	60,851.6	62,374.8
S	100	3351.2	2153.9	100	12,865.7	10,103.3
orf3a	100	3600	1883	100	9480.8	1391.4
E	100	2510.6	565.5	100	8813.8	319.3
M	100	1675.5	394.6	100	11,363.7	3911.1
orf6	100	2155.2	144.9	100	16,381.8	2029.6
orf7a	100	5222.4	2547.5	100	13,544.9	1703.9
orf7b	100	12,817.1	726.8	100	18,326.3	356.3
orf8	100	11,888	1855.3	100	17,113.4	1333.8
N	100	30,319.9	27,469.1	100	50,962	47,834.8
orf10	100	85,634.3	13,447.4	100	175,087.4	22,253
Genome		16,935.4	22,570.4		48,758.9	58,082.7
Number of reads mapped to reference		1,708,791 (33%)			4,919,631 (79%)
Total paired reads		5,156,768			6,209,676
SARS-CoV-2 isolate	EDB- 8 (Titre)			EDB -10(Titre)
Genes	GC^a (%)	DC^$ / bp	SD^{^}	GC^a (%)	DC^$ / bp	SD^{^}
orf1ab	100	88,920.9	93,125.5	100	48,578.8	53,822.8
S	100	21,345.2	19,076.8	100	10,955.9	8806.2
orf3a	100	15,605	3046.8	100	7486.4	1778.2
E	100	13,196.2	768.9	100	7271.4	177
M	100	15,179	3580.1	100	8397.3	2216
orf6	100	15,631.4	2166.9	100	12,144	1032.1
orf7a	100	18,832.7	4354.9	100	12,510	2857.5
orf7b	100	29,776.2	703.5	100	20,697.5	541.7
orf8	100	27,124.4	2414.6	100	14,315	21,838
N	100	66,978.3	48,080.8	100	41,626.3	36,425.1
orf10	100	188,689	22,483.6	100	128,792.6	17,961.1
Genome		70,780	85,008		39,010.3	49,216.3
Number of reads mapped to reference		7,149,251 (68%)			3,934,982 (84%)
Total paired reads		10,389,994			4,676,652
SARS-CoV-2 isolate	EDB -13 (Titre)
Genes	GC^a (%)	DC^$ / bp	SD^{^}
orf1ab	100	71,457.9	77,597
S	100	15,308.9	13,398.7
orf3a	100	11,414	2831.2
E	100	9169	910.3
M	100	10,576.5	2415.9
orf6	100	10,509.1	1572.2
orf7a	100	15,260	4550.5
orf7b	100	26,180.5	571.7
orf8	100	21,716.8	3032.2
N	100	57,886.3	53,962
orf10	100	194,686	25,369.3
Genome		55,423.5	70,955.1
Number of reads mapped to reference		5,759,620 (83%)
Total paired reads		6,879,474

^a GC, genome coverage. $ DC, depth of coverage per base pair. ^ SD, Standard deviation

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