Leveraging of SARS-CoV-2 PCR Cycle Thresholds Values to Forecast COVID-19 Trends.

Nicolas Yin,Niel Hens,Olivier Vandenberg,Magali Wautier,Liv Nymark,Nicolas Franco,Simon Dellicour,Marius Gilbert,Dieter Van Cauteren,Marie Hallin,Valery Daubie,Christel Faes

doi:10.3389/fmed.2021.743988

Abstract

Introduction: We assessed the usefulness of SARS-CoV-2 RT-PCR cycle thresholds (Ct) values trends produced by the LHUB-ULB (a consolidated microbiology laboratory located in Brussels, Belgium) for monitoring the epidemic's dynamics at local and national levels and for improving forecasting models.Methods: SARS-CoV-2 RT-PCR Ct values produced from April 1, 2020, to May 15, 2021, were compared with national COVID-19 confirmed cases notifications according to their geographical and time distribution. These Ct values were evaluated against both a phase diagram predicting the number of COVID-19 patients requiring intensive care and an age-structured model estimating COVID-19 prevalence in Belgium.Results: Over 155,811 RT-PCR performed, 12,799 were positive and 7,910 Ct values were available for analysis. The 14-day median Ct values were negatively correlated with the 14-day mean daily positive tests with a lag of 17 days. In addition, the 14-day mean daily positive tests in LHUB-ULB were strongly correlated with the 14-day mean confirmed cases in the Brussels-Capital and in Belgium with coinciding start, peak, and end of the different waves of the epidemic. Ct values decreased concurrently with the forecasted phase-shifts of the diagram. Similarly, the evolution of 14-day median Ct values was negatively correlated with daily estimated prevalence for all age-classes.Conclusion: We provide preliminary evidence that trends of Ct values can help to both follow and predict the epidemic's trajectory at local and national levels, underlining that consolidated microbiology laboratories can act as epidemic sensors as they gather data that are representative of the geographical area they serve.

Highlights

We assessed the usefulness of SARS-CoV-2 RT-PCR cycle thresholds (Ct) values trends produced by the LHUB-ULB for monitoring the epidemic’s dynamics at local and national levels and for improving forecasting models
The objectives of this study were: [1] to verify the accuracy of using of SARS-CoV-2 PCR Ct values trends in a single clinical microbiology laboratories (CMLs) to monitor the dynamics of the epidemic; [2] to determine the added-value of using these data as an additional advanced information for scenario analysis, in relation to a phase diagram and an age-structured compartmental model, both developed to follow the path of the Belgian COVID-19 epidemic [14, 15]
From April 1, 2020, to May 15, 2021, a total of 155,049 SARSCoV-2 RT-PCR were performed in the LHUB-ULB and resulted in 12,771 positive results of which 7,906 Cts were analysed

Summary

Introduction

We assessed the usefulness of SARS-CoV-2 RT-PCR cycle thresholds (Ct) values trends produced by the LHUB-ULB (a consolidated microbiology laboratory located in Brussels, Belgium) for monitoring the epidemic’s dynamics at local and national levels and for improving forecasting models. Since the start of the COVID-19 pandemic, several authors have demonstrated that CMLs could represent the first step toward a global set of sensor networks for infectious diseases surveillance, where each one of the CMLs can be seen as a real-time sensor in its area within an interconnected, complex network [1, 3, 4] In this perspective, CMLs have become a cornerstone in the fight against SARSCoV-2 infections due to their ability to process large amounts of samples in large geographic areas while using highly specialised diagnostic tests [1, 5]. The semi-quantitative dimension of positive test results is not used by surveillance systems yet

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