{"id":64,"date":"2025-04-07T13:01:35","date_gmt":"2025-04-07T13:01:35","guid":{"rendered":"https:\/\/c29ugbqilr.preview.infomaniak.website\/?page_id=64"},"modified":"2025-05-09T14:53:10","modified_gmt":"2025-05-09T12:53:10","slug":"explore-publications","status":"publish","type":"page","link":"https:\/\/spsp.ch\/fr\/explore-publications\/","title":{"rendered":"Explore – Publications"},"content":{"rendered":"

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We list below publications from the SPSP Consortium or related to SPSP activities.<\/p>\n

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2024<\/h3>
1.<\/div>

Wegner, Fanny; Cabrera-Gil, Blanca; Tanguy, Araud; Beckmann, Christiane; Beerenwinkel, Niko; Bertelli, Claire; Carrara, Matteo; Cerutti, Lorenzo; Chen, Chaoran; Cordey, Samuel; Dumoulin, Alexis; du Plessis, Louis; Friedli, Marc; Gerth, Yannick; Greub, Gilbert; H\u00e4rri, Adrian; Hirsch, Hans; Howald, Cedric; Huber, Michael; Imhof, Alexander; Kaiser, Laurent; Kufner, Verena; Leib, Stephen L.; Leuzinger, Karoline; Lleshi, Etleva; Martinetti, Gladys; M\u00e4usezahl, Mirjam; Moraz, Milo; Neher, Richard; Nolte, Oliver; Ramette, Alban; Redondo, Maurice; Risch, Lorenz; Rohner, Lionel; Roloff, Tim; Schl\u00e4epfer, Pascal; Schneider, Katrin; Singer, Franziska; Spina, Valeria; Stadler, Tanja; Studer, Erik; Topolsky, Ivan; Trkola, Alexandra; Walther, Daniel; Wohlwend, Nadia; Zehnder, Cinzia; Neves, Aitana; and, Adrian Egli<\/p>

How much should we sequence? An analysis of the Swiss SARS-CoV-2 surveillance effort<\/a> Article de journal<\/span> <\/p>

Dans: <\/span>Microbiol Spectr, <\/span>vol. 12, <\/span>no. 5, <\/span>2024<\/span>, ISSN: 2165-0497<\/span>.<\/p>

R\u00e9sum\u00e9<\/a><\/span> | Liens<\/a><\/span> | BibTeX<\/a><\/span><\/p>

@article{Wegner2024,
\r\ntitle = {How much should we sequence? An analysis of the Swiss SARS-CoV-2 surveillance effort},
\r\nauthor = {Fanny Wegner and Blanca Cabrera-Gil and Araud Tanguy and Christiane Beckmann and Niko Beerenwinkel and Claire Bertelli and Matteo Carrara and Lorenzo Cerutti and Chaoran Chen and Samuel Cordey and Alexis Dumoulin and Louis du Plessis and Marc Friedli and Yannick Gerth and Gilbert Greub and Adrian H\u00e4rri and Hans Hirsch and Cedric Howald and Michael Huber and Alexander Imhof and Laurent Kaiser and Verena Kufner and Stephen L. Leib and Karoline Leuzinger and Etleva Lleshi and Gladys Martinetti and Mirjam M\u00e4usezahl and Milo Moraz and Richard Neher and Oliver Nolte and Alban Ramette and Maurice Redondo and Lorenz Risch and Lionel Rohner and Tim Roloff and Pascal Schl\u00e4epfer and Katrin Schneider and Franziska Singer and Valeria Spina and Tanja Stadler and Erik Studer and Ivan Topolsky and Alexandra Trkola and Daniel Walther and Nadia Wohlwend and Cinzia Zehnder and Aitana Neves and Adrian Egli and },
\r\neditor = {Sophia B. Georghiou},
\r\ndoi = {10.1128\/spectrum.03628-23},
\r\nissn = {2165-0497},
\r\nyear  = {2024},
\r\ndate = {2024-05-02},
\r\njournal = {Microbiol Spectr},
\r\nvolume = {12},
\r\nnumber = {5},
\r\npublisher = {American Society for Microbiology},
\r\nabstract = {ABSTRACT<\/jats:title>
\n          
\n            
\n            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\u2014something that is unknown at the time of sequencing\u2014and comes at the cost of accuracy, in particular for tracking the emergence of potential VOCs.<\/jats:p>
\n            
\n              IMPORTANCE<\/jats:title>
\n              Switzerland 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.<\/jats:p>
\n            <\/jats:sec>
\n          <\/jats:sec>},
\r\nkeywords = {},
\r\npubstate = {published},
\r\ntppubtype = {article}
\r\n}
\r\n<\/pre><\/div>
Fermer<\/a><\/p><\/div>
ABSTRACT<\/jats:title>
\n          
\n            
\n            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\u2014something that is unknown at the time of sequencing\u2014and comes at the cost of accuracy, in particular for tracking the emergence of potential VOCs.<\/jats:p>
\n            
\n              IMPORTANCE<\/jats:title>
\n              Switzerland 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.<\/jats:p>
\n            <\/jats:sec>
\n          <\/jats:sec><\/div>
Fermer<\/a><\/p><\/div>