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Volume 26, Number 8—August 2020
Synopsis

US CDC Real-Time Reverse Transcription PCR Panel for Detection of Severe Acute Respiratory Syndrome Coronavirus 2

Xiaoyan Lu, Lijuan Wang, Senthilkumar K. Sakthivel, Brett Whitaker, Janna Murray, Shifaq Kamili, Brian Lynch, Lakshmi Malapati, Stephen A. Burke, Jennifer Harcourt, Azaibi Tamin, Natalie J. Thornburg, Julie M. Villanueva, and Stephen LindstromComments to Author 
Author affiliations: Centers for Disease Control and Prevention, Atlanta, Georgia, USA (X. Lu, B. Whitaker, S.A. Burke, J. Harcourt, A. Tamin, N.J. Thornburg, J.M. Villanueva, S. Lindstrom); Synergy America, Inc., Atlanta (L. Wang, S. Kamili); Eagle Contracting, Atlanta (S.K. Sakthivel, J. Murray, B. Lynch); Leidos, Atlanta (L. Malapati); Battelle, Atlanta (S.A. Burke)

Main Article

Table 4

Performance of the US CDC rRT-PCR panel for detection of SARS-CoV-2 with various specimen matrices spiked with SARS-CoV-2*

Virus titer, TCID50† N1 Ct
 N2 Ct
 N3 Ct
 RP Ct
Test
1 Test
2 Test
3 Call rate Test
1 Test
2 Test
3 Call rate Test
1 Test
2 Test
3 Call rate Test
1 Test
2 Test
3 Call rate
1 × 100.5
NP 30.4 29.9 29.9 3/3 30.3 30.5 30.5 3/3 30.0 29.6 29.7 3/3 26.0 26.1 26.1 3/3
OP 30.1 29.7 29.7 3/3 30.7 30.8 30.5 3/3 29.6 29.5 29.5 3/3 30.0 30.3 30.2 3/3
Sputum 30.3 30.1 30.4 3/3 31.2 31.5 31.7 3/3 30.5 30.0 30.4 3/3 24.9 24.8 25.1 3/3
Serum 30.1 29.7 29.8 3/3 31.1 31.0 31.1 3/3 29.8 29.8 29.6 3/3 29.1 28.6 28.3 3/3
Stool
 30.7
 30.5
 30.7
 3/3
31.7
 31.9
 31.7
 3/3
30.7
 29.9
 30.2
 3/3
34.9
 35.1
 35.7
 3/3
1 × 100
NP 32.1 30.8 30.4 3/3 32.3 32.0 31.6 3/3 31.3 30.7 30.9 3/3 24.5 24.2 25.0 3/3
OP 31.6 31.3 31.4 3/3 32.8 32.3 32.2 3/3 30.8 31.3 31.1 3/3 29.3 29.2 29.5 3/3
Sputum 32.0 32.0 31.8 3/3 33.1 32.9 32.7 3/3 31.7 31.4 32.1 3/3 24.3 24.3 24.6 3/3
Serum 32.2 30.8 31.4 3/3 32.4 32.6 33.1 3/3 31.2 31.3 31.3 3/3 28.1 28.2 27.5 3/3
Stool
 32.1
 32.3
 32.0
 3/3
33.6
 33.9
 33.5
 3/3
32.1
 32.0
 32.1
 3/3
34.6
 35.1
 34.5
 3/3
1 × 10–0.5
NP 33.7 32.5 33.9 3/3 34.1 33.9 35.5 3/3 33.2 32.6 33.5 3/3 25.3 25.4 25.5 3/3
OP 33.6 33.6 33.1 3/3 34.4 34.4 34.6 3/3 33.5 33.0 32.0 3/3 29.2 29.4 29.6 3/3
Sputum 35.1 33.4 33.0 3/3 35.0 34.2 34.8 3/3 33.5 33.4 33.2 3/3 24.0 24.2 24.3 3/3
Serum 33.4 32.2 33.3 3/3 35.2 34.1 33.9 3/3 32.7 32.7 33.1 3/3 28.3 28.2 29.3 3/3
Stool
 35.0
 35.3
 35.3
 3/3
36.2
 36.4
 35.3
 3/3
34.2
 34.6
 34.0
 3/3
33.4
 36.2
 35.0
 3/3
1 × 10–1
NP 33.9 34.0 34.6 3/3 36.0 36.2 36.5 3/3 34.1 34.3 35.1 3/3 25.6 25.6 25.9 3/3
OP 33.4 33.3 33.6 3/3 35.9 36.7 35.3 3/3 34.5 34.3 35.1 3/3 29.2 29.3 29.3 3/3
Sputum 35.2 35.0 36.2 3/3 36.8 36.8 35.3 3/3 35.3 35.2 35.1 3/3 24.1 24.1 24.3 3/3
Serum 37.5 35.3 34.8 3/3 36.4 37.2 36.3 3/3 35.2 33.7 34.3 3/3 28.3 28.3 28.6 3/3
Stool
 36.1
 35.8
 36.0
 3/3
37.3
 37.9
 38.1
 3/3
35.8
 35.6
 34.7
 3/3
34.1
 33.9
 34.2
 3/3
1 × 10–1.5
NP 35.6 36.8 35.9 3/3 39.9 36.8 37.6 3/3 36.7 35.1 35.7 3/3 26.1 26.3 26.6 3/3
OP 36.2 35.2 Neg 2/3 36.8 38.0 Neg 2/3 Neg Neg Neg 0/3 29.3 29.3 29.6 3/3
Sputum 36.9 36.3 Neg 2/3 39.1 39.5 38.4 3/3 35.8 38.2 Neg 2/3 23.9 24.2 24.2 3/3
Serum 36.8 36.5 36.4 3/3 38.4 39.1 36.9 3/3 35.6 36.2 Neg 2/3 27.9 28.2 27.4 3/3
Stool
 Neg
 Neg
 Neg
 0/3
39.2
 38.1
 37.5
 3/3
35.5
 38.1
 38.0
 3/3
34.2
 33.3
 35.6
 3/3
1 × 10–2
NP Neg Neg Neg 0/3 39.4 Neg Neg 1/3 Neg Neg Neg 0/3 25.5 25.7 25.8 3/3
OP Neg Neg Neg 0/3 38.5 38.0 Neg 2/3 37.1 Neg Neg 1/3 29.4 29.3 29.4 3/3
Sputum 36.1 Neg Neg 1/3 38.2 38.5 Neg 2/3 37.1 37.5 Neg 2/3 24.0 24.0 24.1 3/3
Serum 37.5 Neg Neg 1/3 39.9 Neg Neg 1/3 38.9 Neg Neg 1/3 28.2 27.9 27.2 3/3
Stool
 Neg
 Neg
 Neg
 0/3
39.1
 Neg
 Neg
 1/3
38.1
 Neg
 Neg
 1/3
33.5
 35.1
 34.6
 3/3
1 × 10–2.5
NP 36.2 Neg Neg 1/3 38.9 Neg Neg 1/3 Neg Neg Neg 0/3 26.3 26.5 26.6 3/3
OP Neg Neg Neg 0/3 Neg Neg Neg 0/3 Neg Neg Neg 0/3 29.0 29.2 29.2 3/3
Sputum 37.4 Neg Neg 1/3 Neg Neg Neg 0/3 36.7 Neg Neg 1/3 24.0 24.2 24.4 3/3
Serum 36.4 Neg Neg 1/3 38.4 Neg Neg 1/3 Neg Neg Neg 0/3 28.1 28.2 27.2 3/3
Stool
 37.6
 Neg
 Neg
 1/3
Neg
 Neg
 Neg
 0/3
Neg
 Neg
 Neg
 0/3
33.4
 34.1
 35.5
 3/3
1 × 10–3
NP Neg Neg Neg 0/3 Neg Neg Neg 0/3 Neg Neg Neg 0/3 26.8 26.7 27.0 3/3
OP Neg Neg Neg 0/3 Neg Neg Neg 0/3 Neg Neg Neg 0/3 29.2 29.4 29.1 3/3
Sputum Neg Neg Neg 0/3 Neg Neg Neg 0/3 Neg Neg Neg 0/3 23.9 24.1 24.3 3/3
Serum Neg Neg Neg 0/3 Neg Neg Neg 0/3 Neg Neg Neg 0/3 28.2 28.3 27.9 3/3
Stool
 Neg
 Neg
 Neg
 0/3
Neg
 Neg
 Neg
 0/3
Neg
 Neg
 Neg
 0/3
34.1
 35.0
 35.0
 3/3
0
NP Neg Neg Neg 0/3 Neg Neg Neg 0/3 Neg Neg Neg 0/3 25.0 25.2 24.8 3/3
OP Neg Neg Neg 0/3 Neg Neg Neg 0/3 Neg Neg Neg 0/3 28.6 28.3 28.5 3/3
Sputum Neg Neg Neg 0/3 Neg Neg Neg 0/3 Neg Neg Neg 0/3 23.1 23.0 23.1 3/3
Serum Neg Neg Neg 0/3 Neg Neg Neg 0/3 Neg Neg Neg 0/3 27.6 27.8 27.7 3/3
Stool Neg Neg Neg 0/3 Neg Neg Neg 0/3 Neg Neg Neg 0/3 33.5 33.8 33.2 3/3

*Call rate indicates each assay performed in triplicate. CDC, Centers for Disease Control and Prevention; Ct, cycle threshold; N, nucleocapsid protein gene; neg, negative; NP, nasopharyngeal; OP, oropharyngeal; RP, ribonuclease P gene; rRT-PCR, real-time reverse transcription PCR; SARS-CoV-2, severe acute respiratory coronavirus 2; TCID50, 50% tissue culture infectious dose.
†50% tissue culture infectious dose/mL.

Main Article

Page created: May 14, 2020
Page updated: July 17, 2020
Page reviewed: July 17, 2020
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
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