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Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT-qPCR primer-probe sets.
Nat Microbiol. 2020 10; 5(10):1299-1305.NM

Abstract

The recent spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exemplifies the critical need for accurate and rapid diagnostic assays to prompt clinical and public health interventions. Currently, several quantitative reverse transcription-PCR (RT-qPCR) assays are being used by clinical, research and public health laboratories. However, it is currently unclear whether results from different tests are comparable. Our goal was to make independent evaluations of primer-probe sets used in four common SARS-CoV-2 diagnostic assays. From our comparisons of RT-qPCR analytical efficiency and sensitivity, we show that all primer-probe sets can be used to detect SARS-CoV-2 at 500 viral RNA copies per reaction. The exception for this is the RdRp-SARSr (Charité) confirmatory primer-probe set which has low sensitivity, probably due to a mismatch to circulating SARS-CoV-2 in the reverse primer. We did not find evidence for background amplification with pre-COVID-19 samples or recent SARS-CoV-2 evolution decreasing sensitivity. Our recommendation for SARS-CoV-2 diagnostic testing is to select an assay with high sensitivity and that is regionally used, to ease comparability between outcomes.

Authors+Show Affiliations

Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA. chantal.vogels@yale.edu.Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA.Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA.Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA.Department of Medicine, Northeast Medical Group, Yale-New Haven Health, New Haven, CT, USA.Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA.Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA.Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA.Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA.Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA. Howard Hughes Medical Institute, Chevy Chase, MD, USA.Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA. Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA. Clinical Virology Laboratory, Yale-New Haven Hospital, New Haven, CT, USA.Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA. Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA.Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA. nathan.grubaugh@yale.edu.

Pub Type(s)

Comparative Study
Evaluation Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

32651556

Citation

Vogels, Chantal B F., et al. "Analytical Sensitivity and Efficiency Comparisons of SARS-CoV-2 RT-qPCR Primer-probe Sets." Nature Microbiology, vol. 5, no. 10, 2020, pp. 1299-1305.
Vogels CBF, Brito AF, Wyllie AL, et al. Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT-qPCR primer-probe sets. Nat Microbiol. 2020;5(10):1299-1305.
Vogels, C. B. F., Brito, A. F., Wyllie, A. L., Fauver, J. R., Ott, I. M., Kalinich, C. C., Petrone, M. E., Casanovas-Massana, A., Catherine Muenker, M., Moore, A. J., Klein, J., Lu, P., Lu-Culligan, A., Jiang, X., Kim, D. J., Kudo, E., Mao, T., Moriyama, M., Oh, J. E., ... Grubaugh, N. D. (2020). Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT-qPCR primer-probe sets. Nature Microbiology, 5(10), 1299-1305. https://doi.org/10.1038/s41564-020-0761-6
Vogels CBF, et al. Analytical Sensitivity and Efficiency Comparisons of SARS-CoV-2 RT-qPCR Primer-probe Sets. Nat Microbiol. 2020;5(10):1299-1305. PubMed PMID: 32651556.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT-qPCR primer-probe sets. AU - Vogels,Chantal B F, AU - Brito,Anderson F, AU - Wyllie,Anne L, AU - Fauver,Joseph R, AU - Ott,Isabel M, AU - Kalinich,Chaney C, AU - Petrone,Mary E, AU - Casanovas-Massana,Arnau, AU - Catherine Muenker,M, AU - Moore,Adam J, AU - Klein,Jonathan, AU - Lu,Peiwen, AU - Lu-Culligan,Alice, AU - Jiang,Xiaodong, AU - Kim,Daniel J, AU - Kudo,Eriko, AU - Mao,Tianyang, AU - Moriyama,Miyu, AU - Oh,Ji Eun, AU - Park,Annsea, AU - Silva,Julio, AU - Song,Eric, AU - Takahashi,Takehiro, AU - Taura,Manabu, AU - Tokuyama,Maria, AU - Venkataraman,Arvind, AU - Weizman,Orr-El, AU - Wong,Patrick, AU - Yang,Yexin, AU - Cheemarla,Nagarjuna R, AU - White,Elizabeth B, AU - Lapidus,Sarah, AU - Earnest,Rebecca, AU - Geng,Bertie, AU - Vijayakumar,Pavithra, AU - Odio,Camila, AU - Fournier,John, AU - Bermejo,Santos, AU - Farhadian,Shelli, AU - Dela Cruz,Charles S, AU - Iwasaki,Akiko, AU - Ko,Albert I, AU - Landry,Marie L, AU - Foxman,Ellen F, AU - Grubaugh,Nathan D, Y1 - 2020/07/10/ PY - 2020/04/06/received PY - 2020/06/25/accepted PY - 2020/7/12/pubmed PY - 2020/10/2/medline PY - 2020/7/12/entrez SP - 1299 EP - 1305 JF - Nature microbiology JO - Nat Microbiol VL - 5 IS - 10 N2 - The recent spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exemplifies the critical need for accurate and rapid diagnostic assays to prompt clinical and public health interventions. Currently, several quantitative reverse transcription-PCR (RT-qPCR) assays are being used by clinical, research and public health laboratories. However, it is currently unclear whether results from different tests are comparable. Our goal was to make independent evaluations of primer-probe sets used in four common SARS-CoV-2 diagnostic assays. From our comparisons of RT-qPCR analytical efficiency and sensitivity, we show that all primer-probe sets can be used to detect SARS-CoV-2 at 500 viral RNA copies per reaction. The exception for this is the RdRp-SARSr (Charité) confirmatory primer-probe set which has low sensitivity, probably due to a mismatch to circulating SARS-CoV-2 in the reverse primer. We did not find evidence for background amplification with pre-COVID-19 samples or recent SARS-CoV-2 evolution decreasing sensitivity. Our recommendation for SARS-CoV-2 diagnostic testing is to select an assay with high sensitivity and that is regionally used, to ease comparability between outcomes. SN - 2058-5276 UR - https://www.unboundmedicine.com/medline/citation/32651556/Analytical_sensitivity_and_efficiency_comparisons_of_SARS_CoV_2_RT_qPCR_primer_probe_sets_ L2 - https://doi.org/10.1038/s41564-020-0761-6 DB - PRIME DP - Unbound Medicine ER -