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Abstract

Background

The COVID-19 pandemic has led to an unprecedented daily use of RT-PCR tests. These tests are interpreted qualitatively for diagnosis, and the relevance of the test result intensity, i.e. the number of quantification cycles (Cq), is debated because of strong potential biases.

Aim

We explored the possibility to use Cq values from SARS-CoV-2 screening tests to better understand the spread of an epidemic and to better understand the biology of the infection.

Methods

We used linear regression models to analyse a large database of 793,479 Cq values from tests performed on more than 2 million samples between 21 January and 30 November 2020, i.e. the first two pandemic waves. We performed time series analysis using autoregressive integrated moving average (ARIMA) models to estimate whether Cq data information improves short-term predictions of epidemiological dynamics.

Results

Although we found that the Cq values varied depending on the testing laboratory or the assay used, we detected strong significant trends associated with patient age, number of days after symptoms onset or the state of the epidemic (the temporal reproduction number) at the time of the test. Furthermore, knowing the quartiles of the Cq distribution greatly reduced the error in predicting the temporal reproduction number of the COVID-19 epidemic.

Conclusion

Our results suggest that Cq values of screening tests performed in the general population generate testable hypotheses and help improve short-term predictions for epidemic surveillance.

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This work is licensed under a Creative Commons Attribution 4.0 International License.
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2022-02-10
2024-11-21
http://instance.metastore.ingenta.com/content/10.2807/1560-7917.ES.2022.27.6.2100406
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Epidemiological and clinical insights from SARS-CoV-2 RT-PCR crossing threshold values, France, January to November 2020
<p class="citation"> <span>Citation style for this article:</span> <span class="meta-value authors"> <a href="/search?value1=Samuel+Alizon&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Alizon Samuel</a>, <a href="/search?value1=Christian+Selinger&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Selinger Christian</a>, <a href="/search?value1=Mircea+T+Sofonea&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Sofonea Mircea T</a>, <a href="/search?value1=St%C3%A9phanie+Haim-Boukobza&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Haim-Boukobza Stéphanie</a>, <a href="/search?value1=Jean-Marc+Giannoli&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Giannoli Jean-Marc</a>, <a href="/search?value1=Laetitia+Ninove&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Ninove Laetitia</a>, <a href="/search?value1=Sylvie+Pillet&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Pillet Sylvie</a>, <a href="/search?value1=Vincent+Thibault&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Thibault Vincent</a>, <a href="/search?value1=Alexis+de+Rougemont&option1=author&noRedirect=true" class="nonDisambigAuthorLink">de Rougemont Alexis</a>, <a href="/search?value1=Camille+Tumiotto&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Tumiotto Camille</a>, <a href="/search?value1=Morgane+Solis&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Solis Morgane</a>, <a href="/search?value1=Robin+Stephan&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Stephan Robin</a>, <a href="/search?value1=C%C3%A9line+Bressollette-Bodin&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Bressollette-Bodin Céline</a>, <a href="/search?value1=Maud+Salmona&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Salmona Maud</a>, <a href="/search?value1=Anne-Sophie+L%E2%80%99Honneur&option1=author&noRedirect=true" class="nonDisambigAuthorLink">L’Honneur Anne-Sophie</a>, <a href="/search?value1=Sylvie+Behillil&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Behillil Sylvie</a>, <a href="/search?value1=Caroline+Lefeuvre&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Lefeuvre Caroline</a>, <a href="/search?value1=Julia+Dina&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Dina Julia</a>, <a href="/search?value1=S%C3%A9bastien+Hantz&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Hantz Sébastien</a>, <a href="/search?value1=C%C3%A9dric+Hartard&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Hartard Cédric</a>, <a href="/search?value1=David+Veyer&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Veyer David</a>, <a href="/search?value1=H%C3%A9lo%C3%AFse+M+Delagr%C3%A8verie&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Delagrèverie Héloïse M</a>, <a href="/search?value1=Slim+Fourati&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Fourati Slim</a>, <a href="/search?value1=Beno%C3%AEt+Visseaux&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Visseaux Benoît</a>, <a href="/search?value1=C%C3%A9cile+Henquell&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Henquell Cécile</a>, <a href="/search?value1=Bruno+Lina&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Lina Bruno</a>, <a href="/search?value1=Vincent+Foulongne&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Foulongne Vincent</a>, <a href="/search?value1=Sonia+Burrel&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Burrel Sonia</a>, <a href="/search?value1=on+behalf+of+the+SFM+COVID-19+study+group&option1=author&noRedirect=true" class="nonDisambigAuthorLink">on behalf of the SFM COVID-19 study group</a></span>. Epidemiological and clinical insights from SARS-CoV-2 RT-PCR crossing threshold values, France, January to November 2020. <a href="/content/ecdc">Euro Surveill.</a> 2022;27(6):pii=2100406. <a href="https://doi.org/10.2807/1560-7917.ES.2022.27.6.2100406" title="doi link" target="_blank">https://doi.org/10.2807/1560-7917.ES.2022.27.6.2100406</a> <span class="ES_Article_citation"> <span class="generated">Received</span>: 31 Mar 2021;&nbsp;&nbsp; <span class="generated">Accepted</span>: 15 Oct 2021 </span> </p>
/content/10.2807/1560-7917.ES.2022.27.6.2100406
/content/10.2807/1560-7917.ES.2022.27.6.2100406
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