A comparison study of GeneXpert and In-House N1N2 CDC Real-Time RT-PCR for detection of SARS-CoV-2 infection


Andi Yasmon(1*), Lola Febriana Dewi(2), Fithriyah Fithriyah(3), Ariyani Kiranasari(4), Andriansjah Rukmana(5), Yulia Rosa Saharman(6), Fera Ibrahim(7), Pratiwi Sudarmono(8)

(1) Department of Microbiology, Faculty of Medicine Universitas Indonesia/Cipto Mangunkusumo Hospital, Jakarta
(2) Department of Microbiology, Faculty of Medicine Universitas Indonesia/Cipto Mangunkusumo Hospital, Jakarta
(3) Department of Microbiology, Faculty of Medicine Universitas Indonesia/Cipto Mangunkusumo Hospital, Jakarta
(4) Department of Clinical Microbiology, Faculty of Medicine, Krida Wacana Christian University, Jakarta
(5) Department of Microbiology, Faculty of Medicine Universitas Indonesia/Cipto Mangunkusumo Hospital, Jakarta
(6) Department of Biology, Faculty of Information Technology and Science, Hindu University of Indonesia, East Denpasar, Bali
(7) Department of Biology, Faculty of Information Technology and Science, Hindu University of Indonesia, East Denpasar, Bali
(8) Department of Biology, Faculty of Information Technology and Science, Hindu University of Indonesia, East Denpasar, Bali
(*) Corresponding Author


COVID-19 is a disease caused by SARS-CoV-2, a new virus from genus β-coronaviruses. This disease has been declared a pandemic by WHO on 11 March 2020 until now. The nucleic acid tests are the most frequently used assays because of their high sensitivity and specificity. One of the tests is the GeneXpert, a real-time reverse transcription polymerase chain reaction (rRT-PCR)-based assay platform. The use of the GeneXpert shows great public health interest because of the rapid (50 min), the minimum number of trained staff, and less infrastructure and equipment. However, there are limited data on the application of the GeneXpert for the detection of SARS-CoV-2. Therefore, we conducted a comparative study between the GeneXpert and in-house N1N2 CDC rRT-PCR assay. Of 86 samples, 17 were rRT-PCR positive while 13 were GeneXpert positive. Of rRT-PCR positive 17 samples, 7 were GeneXpert negative [58.82% (10/17] sensitivity]. We also found that 3 GeneXpert positive samples showed rRT-PCR negative (95.65% [66/69] specificity). It is concluded that negative results by the GeneXpert can not rule out the possibility of SARS-CoV-2 infection, particularly in close-contact individuals and the interpretation of the positive result should be analyzed carefully, particularly amplification with Ct>40.


COVID-19; SARS-CoV-2; GeneXpert; PCR; nucleic acid tests

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Chen W, Xiao Q, Fang Z, Lv X, Yao M, Deng M. Correlation analysis between the viral load and the progression of COVID-19. Comput Math Methods Medi 2021; 2021:9926249.
2.Jalandra R, Yadav AK, Verma D, Dalal N, Sharma M, Singh R, et al. Strategies and perspectives to develop SARS-CoV-2 detection methods and diagnostics. Biomed Pharmacother 2020; 129:110446.
3.Afzal A. Molecular diagnostic technologies for COVID-19: Limitations and challenges. J Adv Res 2020; 26:149-59.
4.Uhteg K, Jarrett J, Richards M, Howard C, Morehead E, Geahr M, et al. Comparing the analytical performance of three SARS-CoV-2 molecular diagnostic assays. J Clin Virol 2020; 127:104384.
5.Goldenberger D, Leuzinger K, Sogaard KK, Gosert R, Roloff T, Naegele K, et al. Brief validation of the novel GeneXpert Xpress SARS-CoV-2 PCR assay. J Virol Methods 2020; 284:113925.
6.WHO. COVID-19: epidemiology, virology, and prevention. UpToDate; 2022.
7.WHO. Novel Coronavirus; 2022.
8.Vaz SN, de Santana DS, Netto EM, Wang WK, Brites C. Validation of the GeneXpert Xpress SARS-CoV-2 PCR assay using saliva as biological specimen. Braz J Infect Dis 2021; 25(2):101543.
9.Eftekhari A, Alipour M, Chodari L, Maleki Dizaj S, Ardalan M, Samiei M, et al. A comprehensive review of detection methods for SARS-CoV-2. Microorganisms 2021; 9(2):232.
10.CDC. Research use only 2019-novel coronavirus (2019-nCoV) real-time RT-PCR primers and probes. 2021. Available at https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html). Accessed December , 14, 2021,
11.US Food and Drug Administration. Xpert Xpress SARS-CoV-2. (Package insert.) US Food and Drug Administration, Silver Spring, MD. 2021. Available at https://www.cepheid.com/en/coronavirus. Accessed December, 14, 2021.
12.Vogels CBF, Brito AF, Wyllie AL, Fauver JR, Ott IM, Kalinich CC, et al. Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT–qPCR primer–probe sets. Nat Microbiol 2020; 5(10):1299-305.
13.Nalla AK, Casto AM, Huang MLW, Perchetti GA, Sampoleo R, Shrestha L, et al. Comparative performance of SARS-CoV-2 detection assays using seven different primer-probe sets and one assay kit. J Clin Microbiol 2020; 58(6):e00557-20.
14.Chu DKW, Pan Y, Cheng SMS, Hui KPY, Krishnan P, Liu Y, et al. Molecular diagnosis of a novel coronavirus (2019-nCoV) causing an outbreak of pneumonia. Clin Chem 2020; 66(4):549-55.
15.Moreno JL, Zúñiga S, Enjuanes L, Sola I. Identification of a coronavirus transcription enhancer. J Virol 2008; 82(8):3882-93.
16.Huang Y, Johnston L, Parra A, Sweeney C, Hayes E, Hansen LT, et al. Detection of SARS-CoV-2 in wastewater in Halifax, Nova Scotia, Canada, using four RT-qPCR assays. FACETS 2021; 6:959-65.
17.Etievant S, Bal A, Escuret V, Brengel-Pesce K, Bouscambert M, Cheynet V, et al. Performance assessment of SARS-CoV-2 PCR assays developed by WHO referral laboratories. J Clin Med 2020; 9(6):1871.
18.Coryell MP, Iakiviak M, Pereira N, Murugkar PP, Rippe J, Williams DB, et al. A method for detection of SARS-CoV-2 RNA in healthy human stool: a validation study. Lancet Microbe 2021; 2(6):e259-e66.
19.Hong PY, Rachmadi AT, Mantilla-Calderon D, Alkahtani M, Bashawri YM, Al Qarni H, et al. Estimating the minimum number of SARS-CoV-2 infected cases needed to detect viral RNA in wastewater: To what extent of the outbreak can surveillance of wastewater tell us? Environ Res 2021; 195:110748.
20.Procop GW, Brock JE, Reineks EZ, Shrestha NK, Demkowicz R, Cook E, et al. A Comparison of five SARS-CoV-2 molecular assays with clinical correlations. Am J Clin Pathol 2021; 155(1):69-78.
21.Das R, Joshi S, Pednekar S, Karyakarte R. Comparison of Xpert Xpress SARS-CoV-2 assay and RT-PCR test in diagnosis of COVID-19. IOSR-JDMS 2021; 20(6):12-7.
22.La Scola B, Le Bideau M, Andreani J, Hoang VT, Grimaldier C, Colson P, et al. Viral RNA load as determined by cell culture as a management tool for discharge of SARS-CoV-2 patients from infectious disease wards. Eur J Clin Microbiol Infect Dis 2020; 39(6):1059-61.
23.Glenet M, Lebreil AL, Heng L, N’Guyen Y, Meyer I, Andreoletti L. Asymptomatic COVID-19 adult outpatients identified as significant viable SARS-CoV-2 shedders. Sci Rep 2021; 11(1):20615.
24.Arons MM, Hatfield KM, Reddy SC, Kimball A, James A, Jacobs JR, et al. Presymptomatic SARS-CoV-2 infections and transmission in a skilled nursing facility. N Engl J Med 2020; 382(22):2081-90.
25.Kujawski SA, Wong KK, Collins JP, Epstein L, Killerby ME, Midgley CM, et al. Clinical and virologic characteristics of the first 12 patients with coronavirus disease 2019 (COVID-19) in the United States. Nat Med 2020; 26(6):861-8.
26.Singanayagam A, Patel M, Charlett A, Lopez Bernal J, Saliba V, Ellis J, et al. Duration of infectiousness and correlation with RT-PCR cycle threshold values in cases of COVID-19, England, January to May 2020. Euro Surveill 2020; 25(32):2001483.
27.Platten M, Hoffmann D, Grosser R, Wisplinghoff F, Wisplinghoff H, Wiesmüller G, et al. SARS-CoV-2, CT-values, and infectivity-conclusions to be drawn from side observations. Viruses 2021; 13(8):1459.
28.Rakotosamimanana N, Randrianirina F, Randremanana R, Raherison MS, Rasolofo V, Solofomalala GD, et al. GeneXpert for the diagnosis of COVID-19 in LMICs. Lancet Glob Health 2020; 8(12):e1457-e8.
29.Moran A, Beavis KG, Matushek SM, Ciaglia C, Francois N, Tesic V, et al. Detection of SARS-CoV-2 by use of the cepheid Xpert Xpress SARS-CoV-2 and roche cobas SARS-CoV-2 assays. J Clin Microbiol 2020; 58(8):e00772-20.

DOI: https://doi.org/10.19106/JMedSci005403202203

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Journal of the Medical Sciences (Berkala Ilmu Kedokteran) by  Universitas Gadjah Mada is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
Based on a work at http://jurnal.ugm.ac.id/bik/.