Table 1 The comparison of performance of four different random priming amplification methods to recover RNA viral genetic material of SARS-CoV-2 genome. SARS-CoV-2 was quantified by plaque assay titration on Vero E6 cells (pfu/ml) and qRT-PCR (CT value). For metagenomics, three independent methods were used to detect the presence of the virus in the samples. Kraken, each read was inspected using Kraken and its database to build a report containing the possible organisms the sequences originated from and the number of reads supporting their presence. Blast, if the contig assembled by SPAdes using inhouse pipeline was larger than 150 bases, a random 100 bp segment of that contig was sampled. These samples were aligned with BLAST to the nt-database. The final method, Align is the alignment of sequencing reads to customised reference database

1

2.6 × 10⁶

1,399,928

4502

0.32

97.68

29.10

23.8

1,395,426

N

Y

Y

H-P

2.6 × 10⁵

1,120,143

1757

0.16

93.99

10.22

12.76

1,118,386

N

Y

Y

2.6 × 10⁴

1,535,429

1729

0.11

72.79

8.62

24.28

1,533,700

N

Y

Y

2.6 × 10³

635,446

142

0.02

27.22

0.74

1.66

635,304

N

N

N

2.6 × 10²

1,100,547

794

0.07

48.81

4.82

8.91

1,099,753

N

N

N

26

966,273

45

0

10.22

0.27

0.97

966,228

N

N

N

2.6

973,044

3

0

0.75

0.01

0.14

973,041

N

N

N

0

739,156

1

0

0.12

0.00

0.03

739,155

N

N

N

2

2.6 × 10⁶

1,414,247

10,798

0.76

99.36

72.83

68.41

1,403,449

Y

Y

Y

K-P

2.6 × 10⁵

1,137,392

6183

0.54

98.06

40.41

54.51

1,131,209

Y

Y

Y

2.6 × 10⁴

1,307,167

4073

0.31

96.43

24.11

29.18

1,303,094

N

Y

Y

2.6 × 10³

1,452,489

3391

0.23

91.19

21.16

46.71

1,449,098

N

Y

Y

2.6 × 10²

1,313,739

827

0.06

67.8

4.91

10.02

1,312,912

N

Y

Y

26

779,997

484

0.06

38.92

2.32

5.40

779,513

N

N

Y

2.6

621,358

8

0

2.42

0.04

0.25

621,350

N

N

N

0

579,159

8

0

0.47

0.01

0.20

579,151

N

N

N

3

2.6 × 10⁶

3,760,214

1,780,362

47.35

100

13,486

15,324

1,979,852

Y

Y

Y

SISPA

2.6 × 10⁵

1,318,547

825,545

62.61

100

5620

7583

493,002

Y

Y

Y

2.6 × 10⁴

1,074,343

502,065

46.73

100

3716

4323

572,278

Y

Y

Y

2.6 × 10³

320,287

86,097

26.88

100

628

809

234,190

Y

Y

Y

2.6 × 10²

62,371

6666

10.69

84.36

44.85

86.80

55,705

N

Y

Y

26

54,312

438

0.81

23.63

2.88

10.34

53,874

N

Y

Y

2.6

28,572

53

0.19

16.19

0.28

0.7

28,519

N

N

N

0

1,251,455

177

0.01

19

1.00

2.12

1,251,278

N

N

N

4

2.6 × 10⁶

880,977

130,315

14.79

100

835

1334

750,662

Y

Y

Y

S-P

2.6 × 10⁵

688,161

109,020

13.76

100

705

1020

579,141

Y

Y

Y

2.6 × 10⁴

1,175,085

105,719

9.00

100

668

973

1,069,366

Y

Y

Y

2.6 × 10³

80,352

6901

8.59

100

43.84

58.94

73,451

N

Y

Y

2.6 × 10²

344,436

9026

2.62

89.22

56.69

73.17

335,410

N

Y

Y

26

105,886

384

0.36

14.28

2.22

9.71

105,502

N

Y

Y

2.6

151,936

41

0.03

9.17

0.21

0.76

151,895

N

N

N

0

734,944

18

0

4.52

0

0.48

734,926

N

N

N