Desta, Kassu(PhD candidate, associate professor)Araya, Shambel (MSc)Woldesemayat, Belete2021-10-292023-11-062021-10-292023-11-062021-09http://etd.aau.edu.et/handle/123456789/28420Abstract Background: Laboratory has a key role for the management of coronavirus disease-2019 (COVID-19). Since the outbreak reported, many commercial Nucleic Acid Testing (NAT) assays have been developed all over the world, and real-time PCR detection has been the routine and standard method. However, due to a number of NAATs were rapidly developed and quickly applied to clinical testing, diagnostic performance testing for different detection assays and PCR platforms should be considered. Objective: To assess the diagnostic performance of SARS-CoV-2 real time polymerase chain reaction (RT-PCR) testing assays and some platforms available in Ethiopia for the diagnosis of COVID-19 in Ethiopian public health institute from December 1 to December 30/2020. Methods: Comparative experimental study was conducted to assess the performance of four PCR testing assays and platforms by using Composite reference standard (CRS) as a reference method in Ethiopian Public Health Institute at National HIV Reference laboratory from December 1 to 30/2020. Sample size was determined based on WHO recommendation for method evaluation, 164 samples were selected by systematic random Sampling technique. Selected samples were extracted manually by using QIAamp® viral RNA mini kit (QIAGEN GmbH, Hilden, Germany) and Abbott DNA sample preparation system (Abbott Molecular Inc. des Plaines, IL, USA) for automated extraction. Amplification and detection was done on Abbott m2000, Roche 4800 and ABI 7500 RT-PCR platforms. Finally, the data was entered, cleared and analyzed by using SPSS version 23. Sensitivity, specificity, positive and negative percent agreement was analyzed and kappa Estimator was employed to determine the strength of agreement of each method with CRS. Results: A total of 164 samples included in the study, out of these the rate of positive and negative COVID-19 test was 59.1% (97) and 40.9% (67) respectively in the CRS. Rate of positivity/negativity assays with respective platforms were comparatively similar with CRS (p>0.05). However, Sansure Biotech result was comparatively different with CRS (p <0.05). Sensitivity, specificity, Positive Percent Agreement (PPA), Negative percent agreement (NPA) and overall percent agreement (OPA) for four assays and three platforms lied in ≥93.8%, ≥ 98.5 %, ≥ 93.8%, 98.5 %, ≥96.3 % respectively. The Cohen’s Kappa strength of agreement of assays and platforms lied in 0.925 – 1.000. The study also showed N gene sensitivity was more than ORF1a/b sensitivity based on their CT value. Conclusion: The performance of four SARS-CoV-2 assays and three platforms had almost comparable diagnostic performance. However Sansure Biotech had low rate of positivity compared with CRS. On the other hand N gene sensitivity was better than ORF1a/b gene. Finally, Sansure Biotech assay (RUO) needs further verification on its use in Ethiopia and additional study should be important for the evaluation of respective manufacturers claim.en-USSARS-CoV-2; RT-PCR; detection kit; PCR platform; COVID-19; EthiopiaThesis