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2021-10-14Zeitschriftenartikel
Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020
dc.contributor.authorSmith, Maureen Rebecca
dc.contributor.authorTrofimova, Maria
dc.contributor.authorWeber, Ariane
dc.contributor.authorDuport, Yannick
dc.contributor.authorKühnert, Denise
dc.contributor.authorvon Kleist, Max
dc.date.accessioned2024-08-26T11:58:25Z
dc.date.available2024-08-26T11:58:25Z
dc.date.issued2021-10-14none
dc.identifier.other10.1038/s41467-021-26267-y
dc.identifier.urihttp://edoc.rki.de/176904/11965
dc.description.abstractBy 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.eng
dc.language.isoengnone
dc.publisherRobert Koch-Institut
dc.rights(CC BY 3.0 DE) Namensnennung 3.0 Deutschlandger
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/de/
dc.subjectdata processingeng
dc.subjectepidemiologyeng
dc.subjectphylogenyeng
dc.subjectpopulation geneticseng
dc.subjectstochastic modellingeng
dc.subject.ddc610 Medizin und Gesundheitnone
dc.titleRapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020none
dc.typearticle
dc.identifier.urnurn:nbn:de:0257-176904/11965-1
dc.type.versionpublishedVersionnone
local.edoc.container-titleNature Communicationsnone
local.edoc.container-issn2041-1723none
local.edoc.pages13none
local.edoc.type-nameZeitschriftenartikel
local.edoc.container-typeperiodical
local.edoc.container-type-nameZeitschrift
local.edoc.container-urlhttps://www.nature.com/ncomms/none
local.edoc.container-publisher-nameSpringer Naturenone
local.edoc.container-volume12none
local.edoc.container-reportyear2021none
dc.description.versionPeer Reviewednone

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