Table 1 Targeted HTS analysis showing patterns of virus detection at different virus spiked levels for each participating laboratory

From: Virus detection by short read high throughput sequencing in a high virus low cellular background

Spiked level of reference virus genome (SL)a

Lab ID

Reference Virus

Additional Virus

PCV1

EBV

FeLV

RSV

Reo1

PERVb

SMRVc

SL-6

2, 3

+

+

+

+

+

+ ( ≈ 4)

+ ( ≈ 7)

SL-5

5

+

+

+

+

+

+ ( ≈ 3)

+ ( ≈ 6)

SL-4

1–3, 5–7

+

+

+

+

+

+ ( ≈ 2)

+ ( ≈ 5)

4

+

+

+

+

+

− ( ≈ 2)

+ ( ≈ 5)

SL-3

1, 3, 5

+

+

+

+

+

+ ( ≈ 1)

+ ( ≈ 4)

4, 6

+

+

+

+

+

− ( ≈ 1)

+ ( ≈ 4)

SL-2

2

+

+

+

− ( ≈ 0)

+ ( ≈ 3)

3

+

+

+

+ ( ≈ 0)

+ ( ≈ 3)

4

+

− ( ≈ 0)

+ ( ≈ 3)

5

+

+

+

+

+

− ( ≈ 0)

+ ( ≈ 3)

7

+

+

+

+

+ ( ≈ 0)

+ ( ≈ 3)

SL-1

5

+

+

+

− (≈ -1)

+ ( ≈ 2)

  1. aThe five reference viruses were spiked together at 1 × 10x GC/mL into 1 × 109 GC/mL of Ad5, except that two laboratories spiked the final virus genome copies into the final volume used for their extractions so the reference viruses and Ad5 GC/mL were calculated as 2.5 × 10x for Laboratory 3 and 5 × 10x for Laboratory 4. Exponent × indicates the spike level. The same applies to the additional viruses. For simplicity, the spiked viruses are indicated as spike level (SL) 2 to 6 with GC/mL ranging from SL-2 = 1 × 102 to 5 × 102 to SL-6 = 1 × 106 to 2.5 × 106, respectively. SL-1 (tested only by one laboratory) = 1 × 101.
  2. bThe concentration of PERV in SL-4 (tested by all laboratories) was 1.4 × 102 GC/mL, except for Laboratories 3 and 4, where PERV was 3.5 × 102 GC/mL and 7 × 102 GC/mL, respectively (as explained in footnote a). The spiked level of PERV (GC/mL) corresponding to that of the reference viruses is indicated in the parenthesis as the exponent of base 10.
  3. cSMRV corresponding to the reference virus SL-6 was 3.0 × 107 GC/mL, which was calculated for Laboratories 3 and 4 as 7.5 × 107 GC/mL and 1.5 × 108 GC/mL, respectively. The spiked level of SMRV (GC/mL) corresponding to that of the reference viruses is indicated in the parenthesis as the exponent of base 10.