Speaker
Description
The unprecedented number of PCR tests and viral genomic sequences generated during the COVID-19 pandemic offers an unprecedented amount of data to follow the dynamics and evolution of a pathogen. While largely used during the pandemic, in particular to follow potential changes in vaccine efficacy, the full potential these community data remains to be exploited. For this project, building on a previous collaboration, we teamed up with a French group of private laboratories, Biogroup, to analyze SARS-CoV-2 PCR test results from over 6.5 million tests from over 4 million individuals between July 2021 and March 2022. The dataset covers the spread of the Delta variant in France, and the arrival and spread of Omicron. Included in the datasets – but then missing in the data shared in France’s national repository, and therefore unique information – is the interval since symptoms onset, as estimated by the tested symptomatic individuals, as well as Ct values – used proxies for viral load. These data, combined, can therefore provide a better understanding of the within-host dynamics of SARS-CoV-2, and how they are affected by vaccination, and by different variants of concern. These data are however imperfect, sparse, and were not produced in the context of a cohort study; they therefore pose specific challenges. We develop mathematical models of different complexity to reconstruct individual viral dynamics, benchmark them with simulated data, and use them with the real data. From these models, we assess incubation time, maximal viral load, and time to an undetectable viral load, and explore the effects of vaccination and of the infecting variant on these quantities.
| Expedited Notification | No thanks, I do not require Expedited Notification |
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