Respiratory Treatment and Prevention (Advances in Experimental Medicine and Biology)

Table 1

Bioinformatic analysis of next-generation sequencing (NGS) data from samples containing serial dilutions of herpes simplex virus (HSV-1) and huma

n immunodefi-

ciency virus (HIV)Virus

HIV

HSV-1

Viral copy number (per reaction)

10

1

10

2

10

3

10

4

10

1

10

2

10

3

10

4

All reads

28,061,486 25,451,203 38,824,869 38,445,871

29,427,549 35,563,729 37,265,053

33,590,050

Reads after trimming

27,521,179 25,130,211 38,030,780 38,059,038

28,167,940 34,159,264 35,710,638

32,195,105

Human

26,790,866 23,491,647 37,058,865 36,195,659

26,490,780 33,227,773 32,660,536

31,208,000

(97.35 %)

(93.48 %)

(97.44 %)

(95.10 %)

(94.05 %)

(97.27 %)

(91.46 %)

(96.93 %)

Viral

2452

2035

9860

235,243

113,081

14,679

908,566

34,657

(0.01 %)

(0.01 %)

(0.03 %)

(0.62 %)

(0.40 %)

(0.04 %)

(2.54 %)

(0.11)

Bacterial

285,519

1,039,411

409,000

574,836

1,040,489

552,050

1,123,961

294,172

(1.04 %)

(4.14 %)

(1.08 %)

(1.51 %)

(3.69 %)

(1.62 %)

(3.15 %)

(0.91 %)

Fungal

41,242

111,571

92,310

118,438

48,506

26,304

141,358

52,367

(0.15 %)

(0.26 %)

(0.24 %)

(0.31 %)

(0.17 %)

(0.08 %)

(0.40 %)

(0.16 %)

Archeal

155

13

55

501

35

18

192

52

(0.00 %)

(0.00 %)

(0.00 %)

(0.00 %)

(0.00 %)

(0.00 %)

(0.00 %)

(0.00 %)

Protozoan

27,373

38,223

37,608

60,627

22,476

14,057

102,683

94,557

(0.10 %)

(0.15 %)

(0.10 %)

(0.16 %)

(0.08 %)

(0.04 %)

(0.29 %)

(0.29 %)

Other

a

155,230

188,205

183,186

385,748

194,950

143,329

453,406

270,508

(0.56 %)

(0.75 %)

(0.48 %)

(1.01 %)

(0.69 %)

(0.42 %)

(1.27 %)

(0.84 %)

No match

218,342

259,106

239,896

487,986

257,623

181,054

319,936

240,792

(0.79 %)

(1.03 %)

(0.63 %)

(1.28 %)

(0.91 %)

(0.53 %)

(0.90 %)

(0.75 %)

Identified viruses (number of reads)

0

HIV (1501) HIV (8731) HIV (226,290) 0

0

HSV-1 (1151) HSV-1 (8989)

0.006 %

b

0.022 %

b

0.590 %

b

0.003 %

b

0.028 %

b

Viral genome coverage

0

30.0 %

90.2 %

97.0 %

0

0

3.6 %

13.0 %

Sequences were compared to the NCBI-nt databaseaSequences related to plants, plant viruses, and synthetic constructsbPercentage of all reads after trimming

Sensitivity of Next-Generation Sequencing Metagenomic Analysis for Detection... 57