Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020

Maureen Rebecca Smith (), Maria Trofimova, Ariane Weber, Yannick Duport, Denise Kühnert and Max von Kleist ()
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Maureen Rebecca Smith: Robert Koch Institute
Maria Trofimova: Robert Koch Institute
Ariane Weber: Max-Planck Institute for the Science of Human History
Yannick Duport: Robert Koch Institute
Denise Kühnert: Max-Planck Institute for the Science of Human History
Max von Kleist: Robert Koch Institute

Nature Communications, 2021, vol. 12, issue 1, 1-13

Abstract: Abstract By October 2021, 230 million SARS-CoV-2 diagnoses have been reported. Yet, a considerable proportion of cases remains undetected. Here, we propose GInPipe, a method that rapidly reconstructs SARS-CoV-2 incidence profiles solely from publicly available, time-stamped viral genomes. We validate GInPipe against simulated outbreaks and elaborate phylodynamic analyses. Using available sequence data, we reconstruct incidence histories for Denmark, Scotland, Switzerland, and Victoria (Australia) and demonstrate, how to use the method to investigate the effects of changing testing policies on case ascertainment. Specifically, we find that under-reporting was highest during summer 2020 in Europe, coinciding with more liberal testing policies at times of low testing capacities. Due to the increased use of real-time sequencing, it is envisaged that GInPipe can complement established surveillance tools to monitor the SARS-CoV-2 pandemic. In post-pandemic times, when diagnostic efforts are decreasing, GInPipe may facilitate the detection of hidden infection dynamics.

Date: 2021
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DOI: 10.1038/s41467-021-26267-y

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