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Title: | Cycle Threshold Probability Score for Immediate and Sensitive Detection of B.1.351 SARS-CoV-2 Lineage | Authors: | DE SMET, Dieter Vanhee, Merijn MAES, Brigitte Swaerts, Koen De Jaeger, Peter Maelegheer, Karel Van Hoecke, Frederik Martens, Geert Antoine |
Issue Date: | 2022 | Publisher: | OXFORD UNIV PRESS INC | Source: | AMERICAN JOURNAL OF CLINICAL PATHOLOGY, 157 (5) , p. 731 -741 | Abstract: | Background Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern associated with immune escape is important to safeguard vaccination efficacy. We describe the potential of delayed N gene amplification in the Allplex SARS-CoV-2 Assay (Seegene) for screening of the B.1.351 (20H/501.V2, variant of concern 2 [VOC.V2], South African SARS-CoV-2 variant) lineage. Methods In a study cohort of 397 consecutive polymerase chain reaction-positive samples genotyped by whole-genome sequencing, amplification curves of E/N/S-RdRP targets indicated delayed N vs E gene amplification characteristic of B.1.351. Logistic regression was used to calculate a VOC.V2 probability score that was evaluated as a separate screening test in an independent validation cohort vs sequencing. Results B.1.351 showed a proportionally delayed amplification of the N vs E gene. In logistic regression, only N and E gene cycle thresholds independently contributed to B.1.351 prediction, allowing calculation of a VOC.V2 probability score with an area under the curve of 0.94. At an optimal dichotomous cutoff point of 0.12, the VOC.V2 probability score achieved 98.7% sensitivity at 79.9% specificity, resulting in a negative predictive value (NPV) of 99.6% and a positive predictive value of 54.6%. The probability of B.1.351 increased with an increasing VOC.V2 probability score, achieving a likelihood ratio of 12.01 above 0.5. A near-maximal NPV was confirmed in 153 consecutive validation samples. Conclusions Delayed N vs E gene amplification in the Allplex SARS-CoV-2 Assay can be used for fast and highly sensitive screening of B.1.351. | Notes: | Martens, GA (corresponding author), AZ Delta Gen Hosp, Dept Lab Med, Roeselare, Belgium.; Martens, GA (corresponding author), Univ Ghent, Dept Biomol Med, Ghent, Belgium. geert.martens@azdelta.be |
Keywords: | PCR;Cycle threshold value;Modeling;Data analysis;SARS-CoV-2;Secondary data analysis | Document URI: | http://hdl.handle.net/1942/37379 | ISSN: | 0002-9173 | e-ISSN: | 1943-7722 | DOI: | 10.1093/ajcp/aqab186 | ISI #: | WOS:000789196800001 | Rights: | The Author(s) 2021. Published by Oxford University Press on behalf of American Society for Clinical Pathology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com | Category: | A1 | Type: | Journal Contribution |
Appears in Collections: | Research publications |
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