Molecular benchmarks of a SARS-CoV-2 epidemic

Hakon Jonsson, Olafur T. Magnusson, Pall Melsted, Jonas Berglund, Arna B. Agustsdottir, Berglind Eiríksdottir, Run Fridriksdottir, Elisabet Eir Garðarsdottir, Gudmundur Georgsson, Olafia S. Gretarsdottir, Kjartan R. Guðmundsson, Thora Rosa Gunnarsdottir, Hannes Eggertsson, Arnaldur Gylfason, Hilma Holm, Brynjar O. Jensson, Aslaug Jonasdottir, Frosti Jonsson, Kamilla S. Josefsdottir, Marianna Thordardottir, Karl G. Kristinsson, Þórður Kristjánsson, Droplaug N. Magnusdottir, Louise le Roux, Jona Saemundsdottir, Asgeir Sigurdsson, Gudrun Sigmundsdottir, Gardar Sveinbjornsson, Solvi Rognvaldsson, Ogmundur Eiriksson, Magnus Karl Magnusson, Kristin Eva Sveinsdottir, Maney Sveinsdottir, Emil Aron Thorarensen, Bjarni Thorbjornsson, Arthur Löve, Gudmundur L. Norddahl, Ingileif Jonsdottir, Patrick Sulem, Gisli Masson, Alma Moller, Thorolfur Gudnason, Mar Kristjansson, Agnar Helgason, Daniel F. Gudbjartsson, Unnur Thorsteinsdottir and Kari Stefansson ()
Additional contact information
Hakon Jonsson: deCODE genetics/Amgen, Inc.
Olafur T. Magnusson: deCODE genetics/Amgen, Inc.
Pall Melsted: deCODE genetics/Amgen, Inc.
Jonas Berglund: deCODE genetics/Amgen, Inc.
Arna B. Agustsdottir: deCODE genetics/Amgen, Inc.
Berglind Eiríksdottir: deCODE genetics/Amgen, Inc.
Run Fridriksdottir: deCODE genetics/Amgen, Inc.
Elisabet Eir Garðarsdottir: deCODE genetics/Amgen, Inc.
Gudmundur Georgsson: deCODE genetics/Amgen, Inc.
Olafia S. Gretarsdottir: Landspitali University Hospital
Kjartan R. Guðmundsson: deCODE genetics/Amgen, Inc.
Thora Rosa Gunnarsdottir: Landspitali University Hospital
Hannes Eggertsson: deCODE genetics/Amgen, Inc.
Arnaldur Gylfason: deCODE genetics/Amgen, Inc.
Hilma Holm: deCODE genetics/Amgen, Inc.
Brynjar O. Jensson: deCODE genetics/Amgen, Inc.
Aslaug Jonasdottir: deCODE genetics/Amgen, Inc.
Frosti Jonsson: deCODE genetics/Amgen, Inc.
Kamilla S. Josefsdottir: Directorate of health
Marianna Thordardottir: Directorate of health
Karl G. Kristinsson: Landspitali University Hospital
Þórður Kristjánsson: deCODE genetics/Amgen, Inc.
Droplaug N. Magnusdottir: deCODE genetics/Amgen, Inc.
Louise le Roux: deCODE genetics/Amgen, Inc.
Jona Saemundsdottir: deCODE genetics/Amgen, Inc.
Asgeir Sigurdsson: deCODE genetics/Amgen, Inc.
Gudrun Sigmundsdottir: Directorate of health
Gardar Sveinbjornsson: deCODE genetics/Amgen, Inc.
Solvi Rognvaldsson: deCODE genetics/Amgen, Inc.
Ogmundur Eiriksson: deCODE genetics/Amgen, Inc.
Magnus Karl Magnusson: deCODE genetics/Amgen, Inc.
Kristin Eva Sveinsdottir: deCODE genetics/Amgen, Inc.
Maney Sveinsdottir: Landspitali University Hospital
Emil Aron Thorarensen: deCODE genetics/Amgen, Inc.
Bjarni Thorbjornsson: deCODE genetics/Amgen, Inc.
Arthur Löve: Landspitali University Hospital
Gudmundur L. Norddahl: deCODE genetics/Amgen, Inc.
Ingileif Jonsdottir: deCODE genetics/Amgen, Inc.
Patrick Sulem: deCODE genetics/Amgen, Inc.
Gisli Masson: deCODE genetics/Amgen, Inc.
Alma Moller: Directorate of health
Thorolfur Gudnason: Directorate of health
Mar Kristjansson: Landspitali University Hospital
Agnar Helgason: deCODE genetics/Amgen, Inc.
Daniel F. Gudbjartsson: deCODE genetics/Amgen, Inc.
Unnur Thorsteinsdottir: deCODE genetics/Amgen, Inc.
Kari Stefansson: deCODE genetics/Amgen, Inc.

Nature Communications, 2021, vol. 12, issue 1, 1-8

Abstract: Abstract A pressing concern in the SARS-CoV-2 epidemic and other viral outbreaks, is the extent to which the containment measures are halting the viral spread. A straightforward way to assess this is to tally the active cases and the recovered ones throughout the epidemic. Here, we show how epidemic control can be assessed with molecular information during a well characterized epidemic in Iceland. We demonstrate how the viral concentration decreased in those newly diagnosed as the epidemic transitioned from exponential growth phase to containment phase. The viral concentration in the cases identified in population screening decreased faster than in those symptomatic and considered at high risk and that were targeted by the healthcare system. The viral concentration persists in recovering individuals as we found that half of the cases are still positive after two weeks. We demonstrate that accumulation of mutations in SARS-CoV-2 genome can be exploited to track the rate of new viral generations throughout the different phases of the epidemic, where the accumulation of mutations decreases as the transmission rate decreases in the containment phase. Overall, the molecular signatures of SARS-CoV-2 infections contain valuable epidemiological information that can be used to assess the effectiveness of containment measures.

Date: 2021
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-23883-6

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DOI: 10.1038/s41467-021-23883-6

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