Comparison of Two Commercial Molecular Tests and a Laboratory-Developed Modification of the CDC 2019-nCoV Reverse Transcriptase PCR Assay for the Detection of SARS-CoV-2

Nicholas M Moore, Haiying Li, Debra Schejbal, Jennifer Lindsley, Mary K Hayden, Nicholas M Moore, Haiying Li, Debra Schejbal, Jennifer Lindsley, Mary K Hayden

Abstract

We compared the ability of 2 commercial molecular amplification assays (RealTime SARS-CoV-2 on the m2000 [abbreviated ACOV; Abbott] and ID Now COVID-19 [abbreviated IDNOW; Abbott]) and a laboratory-developed test (modified CDC 2019-nCoV reverse transcriptase PCR [RT-PCR] assay with RNA extraction by eMag [bioMérieux] and amplification on QuantStudio 6 or ABI 7500 real-time PCR system [abbreviated CDC COV]) to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in upper respiratory tract specimens. Discrepant results were adjudicated by medical record review. A total of 200 nasopharyngeal swab specimens in viral transport medium (VTM) were collected from symptomatic patients between 27 March and 9 April 2020. Results were concordant for 167 specimens (83.5% overall agreement), including 94 positive and 73 negative specimens. The ACOV assay yielded 33 additional positive results, 25 of which were also positive by the CDC COV assay but not by the IDNOW assay. In a follow-up evaluation, 97 patients for whom a dry nasal swab specimen yielded negative results by IDNOW had a paired nasopharyngeal swab specimen collected in VTM and tested by the ACOV assay; SARS-CoV-2 RNA was detected in 13 (13.4%) of these specimens. Medical record review deemed all discrepant results to be true positives. The IDNOW test was the easiest to perform and provided a result in the shortest time but detected fewer cases of COVID-19. The ACOV assay detected more cases of COVID-19 than the CDC COV or IDNOW assays.

Keywords: COVID-19; RT-PCR; SARS-CoV-2; coronavirus; novel coronavirus.

Copyright © 2020 American Society for Microbiology.

Figures

FIG 1
FIG 1
SARS-CoV-2 standard curves for CDC COV and ACOV assays. Values shown represent results of testing independent replicates in triplicate. Trend line equations: CDC COV assay (N1), y = −2.054ln(x) + 40.585, R2 = 1.0; CDC assay (N2), y = −1.966ln(x) + 40.022, R2 = 0.99; ACOV assay, y = −1.729ln(x) + 25.899, R2 = 0.99.
FIG 2
FIG 2
Comparison of CT values among samples detected by each of the three assays as measured by the ACOV assay. Median CT value differences were compared using the Kruskal-Wallis test and Dunn’s correction for multiple comparisons. CDC COV, modified CDC 2019-nCoV RT-PCR assay; ACOV, RealTime SARS-CoV-2 assay; IDNOW, ID Now COVID-19 assay; +, positive; −, negative.

References

    1. Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, Zhao X, Huang B, Shi W, Lu R, Niu P, Zhan F, Ma X, Wang D, Xu W, Wu G, Gao GF, Tan W, China Novel Coronavirus Investigating and Research Team. 2020. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med 382:727–733. doi:10.1056/NEJMoa2001017.
    1. Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, Hu Y, Tao ZW, Tian JH, Pei YY, Yuan ML, Zhang YL, Dai FH, Liu Y, Wang QM, Zheng JJ, Xu L, Holmes EC, Zhang YZ. 2020. A new coronavirus associated with human respiratory disease in China. Nature 579:265–269. doi:10.1038/s41586-020-2008-3.
    1. Young BE, Ong SWX, Kalimuddin S, Low JG, Tan SY, Loh J, Ng OT, Marimuthu K, Ang LW, Mak TM, Lau SK, Anderson DE, Chan KS, Tan TY, Ng TY, Cui L, Said Z, Kurupatham L, Chen MI, Chan M, Vasoo S, Wang LF, Tan BH, Lin RTP, Lee VJM, Leo YS, Lye DC, Singapore Novel Coronavirus Outbreak Research Team. 2020. Epidemiologic features and clinical course of patients infected with SARS-CoV-2 in Singapore. JAMA 323:1488–1494. doi:10.1001/jama.2020.3204.
    1. Bernard Stoecklin S, Rolland P, Silue Y, Mailles A, Campese C, Simondon A, Mechain M, Meurice L, Nguyen M, Bassi C, Yamani E, Behillil S, Ismael S, Nguyen D, Malvy D, Lescure FX, Georges S, Lazarus C, Tabai A, Stempfelet M, Enouf V, Coignard B, Levy-Bruhl D, Investigation T. 2020. First cases of coronavirus disease 2019 (COVID-19) in France: surveillance, investigations and control measures, January 2020. Euro Surveill 25:pii=2000094. doi:10.2807/1560-7917.ES.2020.25.6.2000094.
    1. Spiteri G, Fielding J, Diercke M, Campese C, Enouf V, Gaymard A, Bella A, Sognamiglio P, Sierra Moros MJ, Riutort AN, Demina YV, Mahieu R, Broas M, Bengner M, Buda S, Schilling J, Filleul L, Lepoutre A, Saura C, Mailles A, Levy-Bruhl D, Coignard B, Bernard-Stoecklin S, Behillil S, van der Werf S, Valette M, Lina B, Riccardo F, Nicastri E, Casas I, Larrauri A, Salom Castell M, Pozo F, Maksyutov RA, Martin C, Van Ranst M, Bossuyt N, Siira L, Sane J, Tegmark-Wisell K, Palmerus M, Broberg EK, Beaute J, Jorgensen P, Bundle N, Pereyaslov D, Adlhoch C, Pukkila J, Pebody R, Olsen S, et al. . 2020. First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020. Euro Surveill 25:2000178. doi:10.2807/1560-7917.ES.2020.25.9.2000178.
    1. Mousavi SH, Shah J, Giang HTN, Al-Ahdal TMA, Zahid SU, Temory F, Paikan FM, Karimzadeh S, Huy NT. 2020. The first COVID-19 case in Afghanistan acquired from Iran. Lancet Infect Dis 20:657–658. doi:10.1016/S1473-3099(20)30231-0.
    1. Silverstein WK, Stroud L, Cleghorn GE, Leis JA. 2020. First imported case of 2019 novel coronavirus in Canada, presenting as mild pneumonia. Lancet 395:734. doi:10.1016/S0140-6736(20)30370-6.
    1. Holshue ML, DeBolt C, Lindquist S, Lofy KH, Wiesman J, Bruce H, Spitters C, Ericson K, Wilkerson S, Tural A, Diaz G, Cohn A, Fox L, Patel A, Gerber SI, Kim L, Tong S, Lu X, Lindstrom S, Pallansch MA, Weldon WC, Biggs HM, Uyeki TM, Pillai SK, Washington State 2019-nCoV Case Investigation Team. 2020. First case of 2019 novel coronavirus in the United States. N Engl J Med 382:929–936. doi:10.1056/NEJMoa2001191.
    1. Kim JY, Choe PG, Oh Y, Oh KJ, Kim J, Park SJ, Park JH, Na HK, Oh MD. 2020. The first case of 2019 novel coronavirus pneumonia imported into Korea from Wuhan, China: implication for infection prevention and control measures. J Korean Med Sci 35:e61. doi:10.3346/jkms.2020.35.e61.
    1. Ghinai I, McPherson TD, Hunter JC, Kirking HL, Christiansen D, Joshi K, Rubin R, Morales-Estrada S, Black SR, Pacilli M, Fricchione MJ, Chugh RK, Walblay KA, Ahmed NS, Stoecker WC, Hasan NF, Burdsall DP, Reese HE, Wallace M, Wang C, Moeller D, Korpics J, Novosad SA, Benowitz I, Jacobs MW, Dasari VS, Patel MT, Kauerauf J, Charles EM, Ezike NO, Chu V, Midgley CM, Rolfes MA, Gerber SI, Lu X, Lindstrom S, Verani JR, Layden JE, Illinois COVID-19 Investigation Team. 2020. First known person-to-person transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the USA. Lancet 395:1137–1144. doi:10.1016/S0140-6736(20)30607-3.
    1. Abbott Laboratories. Abbott RealTime SARS-CoV-2 assay package insert. Abbott Laboratories, Chicago, IL: .
    1. Centers for Disease Control and Prevention. 2020. CDC 2019-novel coronavirus (2019-nCoV) real-time RT-PCR diagnostic panel services. Centers for Disease Control and Prevention, Atlanta, GA: .
    1. Abbott Laboratories. ID Now COVID-19 package insert. Abbott Laboratories, Chicago, IL: .
    1. Food and Drug Administration. Policy for diagnostics tests for coronavirus disease-2019 during the public health emergency. Food and Drug Administration, Washington, DC: . Accessed 17 March 2020.
    1. Harrington A, Cox B, Snowdon J, Bakst J, Ley E, Grajales P, Maggiore J, Kahn S. 23 April 2020. Comparison of Abbott ID Now and Abbott m2000 methods for the detection of SARS-CoV-2 from nasopharyngeal and nasal swabs from symptomatic patients. J Clin Microbiol doi:10.1128/JCM.00798-20.
    1. Clinical and Laboratory Standards Institute. 2008. User protocol for evaluation of qualitative test performance; approved guideline—2nd ed CLSI document EP12-A2 Clinical and Laboratory Standards Institute, Wayne, PA.
    1. McAdam AJ. 2000. Discrepant analysis: how can we test a test? J Clin Microbiol 38:2027–2029. doi:10.1128/.38.6.2027-2029.2000.
    1. Druce J, Garcia K, Tran T, Papadakis G, Birch C. 2012. Evaluation of swabs, transport media, and specimen transport conditions for optimal detection of viruses by PCR. J Clin Microbiol 50:1064–1065. doi:10.1128/JCM.06551-11.

Source: PubMed

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