Incorporating temporal distribution of population-level viral load enables real-time estimation of COVID-19 transmissibility

Lin, Yun; Yang, Bingyi; Cobey, Sarah; Lau, Eric H. Y.; Adam, Dillon C.; Wong, Jessica Y.; Bond, Helen S.; Cheung, Justin; Ho, Faith C. S.; Gao, Huizhi; Ali, Sheikh Taslim; Leung, Nancy; Tsang, Tim K.; Wu, Peng; Leung, Gabriel M.; Cowling, Benjamin J.

doi:10.21203/rs.3.rs-841953/v1

2021

DOI: 10.21203/rs.3.rs-841953/v1

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Incorporating temporal distribution of population-level viral load enables real-time estimation of COVID-19 transmissibility

Yun Lin

Bingyi Yang

Sarah Cobey

et al.

Abstract: Many locations around the world have used real-time estimates of the time-varying effective reproductive number (\({R}_{t}\)) of COVID-19 to provide evidence of transmission intensity to inform control strategies. Estimates of \({R}_{t}\) are typically based on statistical models applied to case counts and typically suffer lags of more than a week because of the incubation period and reporting delays. Noting that viral loads tend to decline over time since illness onset, analysis of the distribution of viral l… Show more

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Cycle threshold values in symptomatic COVID-19 cases in England

Funk

Abbott

2022

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## Introduction Since the start of the pandemic SARS-CoV-2 infection has most commonly been confirmed using reverse transcriptase polymerase chain reaction (RT-PCR), with results translated into a binary positive/negative outcomes. Previous studies have found that there is additional useful information in the level of the Cycle threshold (Ct value) of positive cases. Here we characterise variation in Ct values as a proxy for viral loads in more than 3 million test-positive COVID-19 cases in England with the aim of better quantifying the utility of such data. ## Methods We used individual N gene Ct values from symptomatic PCR positive (with Ct value less than 30) Pillar 2 cases in England who self-reported the date of symptom onset, and for whom age, reinfection status, variant status, and the number of vaccines received was available. Those with a positive test result more than 6 days after their reported symptom onset were excluded to mitigate the potential impact of recall bias. We used a generalised additive model, to estimate Ct values empirical mean Ct values for each strata of interest independently as well as to predict Ct values using a model that adjusted for a range of demographic and epidemiological covariates jointly. We present empirical Ct values and compare them to predicted mean Ct values. ## Results We found that mean Ct values varied by vaccine status, and reinfection status with the number of vaccine doses having little apparent effect. Modelling Ct values as a smooth function of time since onset and other variables struggled to reproduce the individual variation in the data but did match the population-level variation over time relatively well with this being apparently dominated by large differences between variants. Other variation over time was also captured to some degree though their remained several periods where the model could not capture the empirical means with a potential explanation being epidemic phase bias. ## Conclusions Analysing a large dataset of routine Ct values from symptomatic COVID-19 cases in England we found variation based on time since symptom onset, vaccine status, age, and variant. Ct values were highest 1-3 days after symptom onset and differed most due to variant status. We found no clear correlation between previously estimated differences in intrinsic transmissibility and Ct values indicating that this is potentially mediated at least partly by factors other than viral load as estimated using Ct values. We found evidence that a model adjusting for a range of covariates could explain some of the population-level variation over time but systematically underestimated Ct values when incidence was increasing, and overestimated them when incidence was decreasing. This indicates the utility of Ct values from this data source as a tool for surveillance, potentially avoiding some of the biases of aggregated positive counts.

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Cycle threshold values in symptomatic COVID-19 cases in England

Funk

Abbott

2022

Preprint

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Incorporating temporal distribution of population-level viral load enables real-time estimation of COVID-19 transmissibility

Cited by 1 publication

References 23 publications

Cycle threshold values in symptomatic COVID-19 cases in England

Cycle threshold values in symptomatic COVID-19 cases in England

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