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Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020.
Smith, Maureen Rebecca; Trofimova, Maria; Weber, Ariane; Duport, Yannick; Kühnert, Denise; von Kleist, Max.
  • Smith MR; Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany. smithm@rki.de.
  • Trofimova M; Bioinformatics (MF1), Robert Koch Institute, Berlin, Germany. smithm@rki.de.
  • Weber A; Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany.
  • Duport Y; Bioinformatics (MF1), Robert Koch Institute, Berlin, Germany.
  • Kühnert D; Transmission, Infection, Diversification and Evolution Group, Max-Planck Institute for the Science of Human History, Jena, Germany.
  • von Kleist M; Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany.
Nat Commun ; 12(1): 6009, 2021 10 14.
Article in English | MEDLINE | ID: covidwho-1469968
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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.
Subject(s)

Full text: Available Collection: International databases Database: MEDLINE Main subject: Genome, Viral / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Observational study / Prognostic study / Randomized controlled trials Limits: Humans Country/Region as subject: Europa / Oceania Language: English Journal: Nat Commun Journal subject: Biology / Science Year: 2021 Document Type: Article Affiliation country: S41467-021-26267-y

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Genome, Viral / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Observational study / Prognostic study / Randomized controlled trials Limits: Humans Country/Region as subject: Europa / Oceania Language: English Journal: Nat Commun Journal subject: Biology / Science Year: 2021 Document Type: Article Affiliation country: S41467-021-26267-y