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