| Literature DB >> 32723432 |
Heungsup Sung, Myung-Guk Han, Cheon-Kwon Yoo, Sang-Won Lee, Yoon-Seok Chung, Jae-Sun Park, Mi-Na Kim, Hyukmin Lee, Ki Ho Hong, Moon-Woo Seong, Kyunghoon Lee, Sail Chun, Wee Gyo Lee, Gye-Cheol Kwon, Won-Ki Min.
Abstract
External quality assessment (EQA) is essential for ensuring reliable test results, especially when laboratories are using assays authorized for emergency use for newly emerging pathogens. We developed an EQA panel to assess the quality of real-time reverse transcription PCR assays being used in South Korea to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With the participation of 23 public health organization laboratories and 95 nongovernmental laboratories involved in SARS-CoV-2 testing, we conducted qualitative and semiquantitative performance assessments by using pooled respiratory samples containing different viral loads of SARS-CoV-2 or human coronavirus OC43. A total of 110 (93.2%) laboratories reported correct results for all qualitative tests; 29 (24.6%) laboratories had >1 outliers according to cycle threshold values. Our EQA panel identified the potential weaknesses of currently available commercial reagent kits. The methodology we used can provide practical experience for those planning to conduct evaluations for testing of SARS-CoV-2 and other emerging pathogens in the future.Entities:
Keywords: COVID-19; SARS-CoV-2; South Korea; coronavirus disease; external quality assessment; respiratory infections; severe acute respiratory syndrome coronavirus 2; viruses; zoonoses
Mesh:
Substances:
Year: 2020 PMID: 32723432 PMCID: PMC7510727 DOI: 10.3201/eid2610.202551
Source DB: PubMed Journal: Emerg Infect Dis ISSN: 1080-6040 Impact factor: 6.883
Figure 1Protocols used for real-time RT-PCR in 118 laboratories participating in an external quality assessment of severe acute respiratory syndrome coronavirus 2 testing, South Korea, March 23–27, 2020. The flow diagram shows the variations in specimens tested, RNA extraction platforms, PCR reagents and amplification platforms, and sample volume equivalent RNA input used in the PCR reaction. The weight of the lines reflects the number of laboratories using a particular step. Numbers in the circles indicate number of laboratories. RT-PCR, reverse transcription PCR.
Figure 2Protocols used for laboratories that reported >1 outliers in results of real-time RT-PCR tests for severe acute respiratory syndrome coronavirus 2, South Korea, March 23–27, 2020. The flow diagram shows the variations in specimens tested, RNA extraction platforms, PCR reagents and amplification platforms, and sample volume equivalent RNA input used in the PCR reaction. The weight of the lines reflects the number of laboratories using a particular step. Numbers in the circles indicate number of laboratories. RT-PCR, reverse transcription PCR.
Test results for severe acute respiratory syndrome coronavirus 2 RdRp gene obtained from the proficiency test provider (expected value), Asan Medical Center, Seoul, and from participating laboratories according to the reagent used, South Korea, March 23–27, 2020*
| Sample no. | Dilution | PowerChek | Allplex | Standard M, N = 6 | Laboratory-developed test, N = 5 | Real-Q, N = 1 | |||
|---|---|---|---|---|---|---|---|---|---|
| Expected value | Participating laboratories, N = 67 | Expected value | Participating laboratories, N = 38† | ||||||
| 41 | 1:2 × 105 | 33.60 | 33.64 | 34.37 | 34.64 | 30.38 (29.44–35.46)§ | 34.32 (32.57–34.62) | 38.27 | |
| 42 | 1:2 × 102 | 24.62 | 24.16 | 25.67 | 26.29 | 21.28 (19.98–27.54) | 25.94 (23.28–28.07) | 24.06 | |
| 43 | 1:2 × 104 | 30.73 | 30.60 | 31.34 | 32.05 | 27.49 (26.79–33.39) | 31.66 (30.01–32.83) | 30.54 | |
| 45 | 1:2 × 103 | 27.69 | 27.71 | 28.73 | 29.40 | 24.67 (23.51–31·21) | 28.12 (26.77–29.05) | 27.31 | |
| 46 | 1:2 × 103 | 24.82 | 25.61 | 26.12 | 26.07 | 22.18 (21.50–23.46) | 27.78 (25.74–28.49) | 26.61 | |
| 48 | 1:2 × 102 | 21.27 | 22.06 | 22.49 | 22.41 | 19.06 (17.20–19.86) | 24.07 (22.04–25.02) | 22.96 | |
| 49 | 1:2 × 105 | 32.14 | 32.57 | 32.55 | 32.35 | 29.36 (27.49–30.02) | 34.39 (32.18–35.42) | 33.36 | |
| 50 | 1:2 × 104 | 28.58 | 29.19 | 29.45 | 29.32 | 25.82 (24.20–27.01) | 31.29 (29.38–32.40) | 29.21 | |
*Cycle threshold values are shown. Mean + SD is shown for the results obtained by using the PowerChek 2019-nCoV and Allplex 2019-nCoV kits. Median and range are shown for the results obtained by using the Standard M nCoV-Detection and laboratory-developed tests. †For nCoV-20–41−45, the number of laboratories was 37. ‡Calculated after exclusion of negative results from 9 laboratories. §Calculated after exclusion of negative results from 1 laboratory. ¶Calculated after exclusion of negative results from 3 laboratories. #Calculated after exclusion of negative results from 1 laboratory.
Figure 3Semiquantitative real-time reverse transcription PCR Ct values for severe acute respiratory syndrome coronavirus 2 proficiency panel samples tested by PowerChek and Allplex 2019-nCoV kits, South Korea, March 23–27, 2020. Horizontal line within each box denotes the median value; x indicates the mean; top and bottom of box indicate third and first quartiles, respectively; error bars indicate minimum and maximum values; dots indicate outlier results. E gene (A) and RdRp gene (B) Ct values were from 67 laboratories using the PowerChek 2019-nCoV reagents; E gene (C), RdRp gene (D), and N gene (E) Ct values were from 38 laboratories using the Allplex 2019-nCoV reagents. Ct, cycle threshold.
Severe acute respiratory syndrome coronavirus 2 external quality assessment panel homogeneity tests of triplicate test results of 3 samples using the NucliSENS easyMAG extraction and Allplex nCoV-2019 kits performed at the Asan Medical Center, Seoul, South Korea, as a proficiency test provider, March 23, 2020*
| Sample no. | ||||||||
|---|---|---|---|---|---|---|---|---|
| Mean Ct | %CV | Mean Ct | %CV | Mean Ct | %CV | |||
| 41 | 33.82 | 4.5 | 34.37 | 1.6 | 34.38 | 0.5 | ||
| 42 | 25.15 | 1.4 | 25.67 | 1.8 | 26.67 | 0.5 | ||
| 43 | 30.33 | 1.5 | 31.34 | 1.5 | 31.55 | 0.7 | ||
| 44 | ND | ND | ND | ND | ND | ND | ||
| 45 | 27.52 | 2.2 | 28.73 | 0.3 | 29.05 | 0.7 | ||
| 46 | 24.47 | 0.7 | 26.12 | 0.3 | 27.05 | 0.2 | ||
| 47 | ND | ND | ND | ND | ND | ND | ||
| 48 | 20.68 | 2.5 | 22.49 | 0.6 | 23.49 | 0.3 | ||
| 49 | 31.07 | 0.8 | 32.55 | 0.6 | 33.32 | 0.9 | ||
| 50 | 27.89 | 0.9 | 29.45 | 0.2 | 30.35 | 0.6 | ||
*Ct, cycle threshold; EQA, external quality assessment; %CV, percentage coefficient of variation; ND, not detected.