How much should we sequence? An analysis of the Swiss SARS-CoV-2 surveillance effort.

Autor:	Wegner F; Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland., Cabrera-Gil B; Clinical Bioinformatics, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland., Tanguy A; Genesupport, Geneva, Switzerland., Beckmann C; Viollier AG, Allschwil, Switzerland., Beerenwinkel N; Department of Biosystems Science and Engineering, ETH Zurich, Switzerland & SIB Swiss Institute of Bioinformatics, Basel, Switzerland., Bertelli C; Clinical Microbiology, University Hospital, Lausanne, Switzerland., Carrara M; NEXUS Personalized Health Technologies, ETH Zurich, Switzerland & SIB Swiss Institute of Bioinformatics, Basel, Switzerland., Cerutti L; Health2030 Genome Center, Geneva, Switzerland., Chen C; Department of Biosystems Science and Engineering, ETH Zurich, Switzerland & SIB Swiss Institute of Bioinformatics, Basel, Switzerland., Cordey S; Laboratory of Virology, Geneva University Hospitals, Geneva, Switzerland., Dumoulin A; Valais Hospital, Central Institute, Sion, Switzerland., du Plessis L; Department of Biosystems Science and Engineering, ETH Zurich, Switzerland & SIB Swiss Institute of Bioinformatics, Basel, Switzerland., Friedli M; Health2030 Genome Center, Geneva, Switzerland., Gerth Y; Humanmedizinische Mikrobiologie, Zentrum für Labormedizin, St. Gallen, Switzerland., Greub G; Clinical Microbiology, University Hospital, Lausanne, Switzerland., Härri A; Biolytix, Witterswil, Switzerland., Hirsch H; Clinical Virology, University Hospital, Basel, Switzerland., Howald C; Health2030 Genome Center, Geneva, Switzerland., Huber M; Institute of Medical Virology, University of Zurich, Zurich, Switzerland., Imhof A; Spitalregion Oberaargau, Langenthal, Switzerland., Kaiser L; Laboratory of Virology, Geneva University Hospitals, Geneva, Switzerland., Kufner V; Institute of Medical Virology, University of Zurich, Zurich, Switzerland., Leib SL; Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland., Leuzinger K; Clinical Virology, University Hospital, Basel, Switzerland., Lleshi E; Microbiology Department, Synlab, Bioggio, Switzerland., Martinetti G; Department of Laboratory Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland., Mäusezahl M; Federal Office of Public Health, Bern, Switzerland., Moraz M; Valais Hospital, Central Institute, Sion, Switzerland., Neher R; Biozentrum, University of Basel, Switzerland & SIB Swiss Institute of Bioinformatics, Basel, Switzerland., Nolte O; Humanmedizinische Mikrobiologie, Zentrum für Labormedizin, St. Gallen, Switzerland., Ramette A; Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland., Redondo M; Viollier AG, Allschwil, Switzerland., Risch L; Labor Dr. Risch, Buchs, Switzerland., Rohner L; Federal Office of Public Health, Bern, Switzerland., Roloff T; Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland., Schläepfer P; Clinical Microbiology, University Hospital, Basel, Switzerland., Schneider K; Federal Office of Public Health, Bern, Switzerland., Singer F; NEXUS Personalized Health Technologies, ETH Zurich, Switzerland & SIB Swiss Institute of Bioinformatics, Basel, Switzerland., Spina V; Department of Laboratory Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland., Stadler T; Department of Biosystems Science and Engineering, ETH Zurich, Switzerland & SIB Swiss Institute of Bioinformatics, Basel, Switzerland., Studer E; Federal Office of Public Health, Bern, Switzerland., Topolsky I; Department of Biosystems Science and Engineering, ETH Zurich, Switzerland & SIB Swiss Institute of Bioinformatics, Basel, Switzerland., Trkola A; Institute of Medical Virology, University of Zurich, Zurich, Switzerland., Walther D; Clinical Bioinformatics, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland., Wohlwend N; Labor Dr. Risch, Buchs, Switzerland., Zehnder C; Microbiology Department, Synlab, Bioggio, Switzerland., Neves A; Clinical Bioinformatics, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland., Egli A; Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
Jazyk:	angličtina
Zdroj:	Microbiology spectrum [Microbiol Spectr] 2024 May 02; Vol. 12 (5), pp. e0362823. Date of Electronic Publication: 2024 Mar 18.
DOI:	10.1128/spectrum.03628-23
Abstrakt:	During the SARS-CoV-2 pandemic, many countries directed substantial resources toward genomic surveillance to detect and track viral variants. There is a debate over how much sequencing effort is necessary in national surveillance programs for SARS-CoV-2 and future pandemic threats. We aimed to investigate the effect of reduced sequencing on surveillance outcomes in a large genomic data set from Switzerland, comprising more than 143k sequences. We employed a uniform downsampling strategy using 100 iterations each to investigate the effects of fewer available sequences on the surveillance outcomes: (i) first detection of variants of concern (VOCs), (ii) speed of introduction of VOCs, (iii) diversity of lineages, (iv) first cluster detection of VOCs, (v) density of active clusters, and (vi) geographic spread of clusters. The impact of downsampling on VOC detection is disparate for the three VOC lineages, but many outcomes including introduction and cluster detection could be recapitulated even with only 35% of the original sequencing effort. The effect on the observed speed of introduction and first detection of clusters was more sensitive to reduced sequencing effort for some VOCs, in particular Omicron and Delta, respectively. A genomic surveillance program needs a balance between societal benefits and costs. While the overall national dynamics of the pandemic could be recapitulated by a reduced sequencing effort, the effect is strongly lineage-dependent-something that is unknown at the time of sequencing-and comes at the cost of accuracy, in particular for tracking the emergence of potential VOCs.IMPORTANCESwitzerland had one of the most comprehensive genomic surveillance systems during the COVID-19 pandemic. Such programs need to strike a balance between societal benefits and program costs. Our study aims to answer the question: How would surveillance outcomes have changed had we sequenced less? We find that some outcomes but also certain viral lineages are more affected than others by sequencing less. However, sequencing to around a third of the original effort still captured many important outcomes for the variants of concern such as their first detection but affected more strongly other measures like the detection of first transmission clusters for some lineages. Our work highlights the importance of setting predefined targets for a national genomic surveillance program based on which sequencing effort should be determined. Additionally, the use of a centralized surveillance platform facilitates aggregating data on a national level for rapid public health responses as well as post-analyses. Competing Interests: The authors declare no conflict of interest.
Databáze:	MEDLINE
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