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3دورية أكاديمية
المؤلفون: Bruningk, Sarah C., Klatt, Juliane, Stange, Madlen, Mari, Alfredo, Brunner, Myrta, Roloff, Tim-Christoph, Seth-Smith, Helena M. B., Schweitzer, Michael, Leuzinger, Karoline, Sogaard, Kirstine K., Torres, Diana Albertos, Gensch, Alexander, Schlotterbeck, Ann-Kathrin, Nickel, Christian H., Ritz, Nicole, Heininger, Ulrich, Bielicki, Julia, Rentsch, Katharina, Fuchs, Simon, Bingisser, Roland, Siegemund, Martin, Pargger, Hans, Ciardo, Diana, Dubuis, Olivier, Buser, Andreas, Tschudin-Sutter, Sarah, Battegay, Manuel, Schneider-Sliwa, Rita, Borgwardt, Karsten M., Hirsch, Hans H., Egli, Adrian
الوصف: Transmission chains within small urban areas (accommodating similar to 30 per cent of the European population) greatly contribute to case burden and economic impact during the ongoing coronavirus pandemic and should be a focus for preventive measures to achieve containment. Here, at very high spatio-temporal resolution, we analysed determinants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission in a European urban area, Basel-City (Switzerland). We combined detailed epidemiological, intra-city mobility and socio-economic data sets with whole-genome sequencing during the first SARS-CoV-2 wave. For this, we succeeded in sequencing 44 per cent of all reported cases from Basel-City and performed phylogenetic clustering and compartmental modelling based on the dominating viral variant (B.1-C15324T; 60 per cent of cases) to identify drivers and patterns of transmission. Based on these results we simulated vaccination scenarios and corresponding healthcare system burden (intensive care unit (ICU) occupancy). Transmissions were driven by socio-economically weaker and highly mobile population groups with mostly cryptic transmissions which lacked genetic and identifiable epidemiological links. Amongst more senior population transmission was clustered. Simulated vaccination scenarios assuming 60-90 per cent transmission reduction and 70-90 per cent reduction of severe cases showed that prioritising mobile, socio-economically weaker populations for vaccination would effectively reduce case numbers. However, long-term ICU occupation would also be effectively reduced if senior population groups were prioritised, provided there were no changes in testing and prevention strategies. Reducing SARS-CoV-2 transmission through vaccination strongly depends on the efficacy of the deployed vaccine. A combined strategy of protecting risk groups by extensive testing coupled with vaccination of the drivers of transmission (i.e. highly mobile groups) would be most effective at reducing the spread of SARS-CoV-2 ...
وصف الملف: application/pdf
العلاقة: https://edoc.unibas.ch/95288/1/Determinants%20of%20SARS-CoV-2%20transmission%20to%20guide%20vaccination%20strategy%20in%20an%20urban%20area.pdfTest; Bruningk, Sarah C. and Klatt, Juliane and Stange, Madlen and Mari, Alfredo and Brunner, Myrta and Roloff, Tim-Christoph and Seth-Smith, Helena M. B. and Schweitzer, Michael and Leuzinger, Karoline and Sogaard, Kirstine K. and Torres, Diana Albertos and Gensch, Alexander and Schlotterbeck, Ann-Kathrin and Nickel, Christian H. and Ritz, Nicole and Heininger, Ulrich and Bielicki, Julia and Rentsch, Katharina and Fuchs, Simon and Bingisser, Roland and Siegemund, Martin and Pargger, Hans and Ciardo, Diana and Dubuis, Olivier and Buser, Andreas and Tschudin-Sutter, Sarah and Battegay, Manuel and Schneider-Sliwa, Rita and Borgwardt, Karsten M. and Hirsch, Hans H. and Egli, Adrian. (2022) Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area. Virus Evolution, 8 (1). ARTN veac002.; info:isi/000770096600001; info:pmid/35310621; urn:ISSN:2057-1577
الإتاحة: https://doi.org/10.1093/ve/veac002Test
https://edoc.unibas.ch/95288Test/
https://edoc.unibas.ch/95288/1/Determinants%20of%20SARS-CoV-2%20transmission%20to%20guide%20vaccination%20strategy%20in%20an%20urban%20area.pdfTest -
4دورية أكاديمية
المؤلفون: Stange, Madlen, Mari, Alfredo, Roloff, Tim, Seth-Smith, Helena M. B., Schweitzer, Michael, Brunner, Myrta, Leuzinger, Karoline, Sogaard, Kirstine K., Gensch, Alexander, Tschudin-Sutter, Sarah, Fuchs, Simon, Bielicki, Julia, Pargger, Hans, Siegemund, Martin, Nickel, Christian H., Bingisser, Roland, Osthoff, Michael, Bassetti, Stefano, Schneider-Sliwa, Rita, Battegay, Manuel, Hirsch, Hans H., Egli, Adrian
الوصف: COVID-19 was first reported in December 2019 in Wuhan, China, and has spread around the globe since. The most common tool for tracking and containing the spread of the disease-causing virus-SARS-CoV-2 -are classical epidemiology and contact tracing, which collapse under too high case burdens as seen in this pandemic. However, whole-genome sequencing and phylogenetic analyses of the viral genomes will be crucial to understand the virus evolution and outbreak dynamics to ultimately stop the spread of the disease. Here we combined epidemiological data and whole-genome sequences originating from the time of the arrival of the virus in early 2020 in a typical medium-sized European city, namely Basel-City, Switzerland. On one hand, we identified limited community spread of very distinct viral variants originating from travel returners, which is possibly due to the heightened attention and restrictions imposed on international travellers. On the other hand, we find evidence for large cryptic community spread of a single virus variant in the city, which we infer to have originated around mid-February 2020 in the larger tri-national area around Basel, and which has epidemiological links to a mass gathering event in the region of Alsace, France. The first case of SARS-CoV-2 in Basel, Switzerland was detected on February 26(th) 2020. We present a phylogenetic study to explore viral introduction and evolution during the exponential early phase of the local COVID-19 outbreak from February 26(th) until March 23(rd). We sequenced SARS-CoV-2 naso-oropharyngeal swabs from 746 positive tests that were performed at the University Hospital Basel during the study period. We successfully generated 468 high quality genomes from unique patients and called variants with our COVID-19 Pipeline (COVGAP), and analysed viral genetic diversity using PANGOLIN taxonomic lineages. To identify introduction and dissemination events we incorporated global SARS-CoV-2 genomes and inferred a time-calibrated phylogeny. Epidemiological data from patient ...
وصف الملف: application/pdf
العلاقة: https://edoc.unibas.ch/95290/1/20230711131936_64ad3ac8801c9.pdfTest; Stange, Madlen and Mari, Alfredo and Roloff, Tim and Seth-Smith, Helena M. B. and Schweitzer, Michael and Brunner, Myrta and Leuzinger, Karoline and Sogaard, Kirstine K. and Gensch, Alexander and Tschudin-Sutter, Sarah and Fuchs, Simon and Bielicki, Julia and Pargger, Hans and Siegemund, Martin and Nickel, Christian H. and Bingisser, Roland and Osthoff, Michael and Bassetti, Stefano and Schneider-Sliwa, Rita and Battegay, Manuel and Hirsch, Hans H. and Egli, Adrian. (2021) SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. PLoS Pathogens, 17 (3). ARTN e1009374.; info:isi/000631028400004; info:pmid/33740028; urn:ISSN:1553-7366; urn:ISSN:1553-7374
الإتاحة: https://doi.org/10.1371/journal.ppat.1009374Test
https://edoc.unibas.ch/95290Test/
https://edoc.unibas.ch/95290/1/20230711131936_64ad3ac8801c9.pdfTest -
5دورية أكاديمية
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6دورية أكاديمية
المؤلفون: Müller, Nicola F., Wüthrich, Daniel, Goldman, Nina, Sailer, Nadine, Saalfrank, Claudia, Brunner, Myrta, Augustin, Noémi, Seth-Smith, Helena Mb, Hollenstein, Yvonne, Syedbasha, Mohammedyaseen, Lang, Daniela, Neher, Richard A., Dubuis, Olivier, Naegele, Michael, Buser, Andreas, Nickel, Christian H., Ritz, Nicole, Zeller, Andreas, Lang, Brian M., Hadfield, James, Bedford, Trevor, Battegay, Manuel, Schneider-Sliwa, Rita, Egli, Adrian, Stadler, Tanja
الوصف: Infecting large portions of the global population, seasonal influenza is a major burden on societies around the globe. While the global source sink dynamics of the different seasonal influenza viruses have been studied intensively, its local spread remains less clear. In order to improve our understanding of how influenza is transmitted on a city scale, we collected an extremely densely sampled set of influenza sequences alongside patient metadata. To do so, we sequenced influenza viruses isolated from patients of two different hospitals, as well as private practitioners in Basel, Switzerland during the 2016/2017 influenza season. The genetic sequences reveal that repeated introductions into the city drove the influenza season. We then reconstruct how the effective reproduction number changed over the course of the season. While we did not find that transmission dynamics in Basel correlate with humidity or school closures, we did find some evidence that it may positively correlated with temperature. Alongside the genetic sequence data that allows us to see how individual cases are connected, we gathered patient information, such as the age or household status. Zooming into the local transmission outbreaks suggests that the elderly were to a large extent infected within their own transmission network. In the remaining transmission network, our analyses suggest that school-aged children likely play a more central role than pre-school aged children. These patterns will be valuable to plan interventions combating the spread of respiratory diseases within cities given that similar patterns are observed for other influenza seasons and cities.
وصف الملف: application/pdf
العلاقة: https://edoc.unibas.ch/80930/1/file%20%281%29.pdfTest; Müller, Nicola F. and Wüthrich, Daniel and Goldman, Nina and Sailer, Nadine and Saalfrank, Claudia and Brunner, Myrta and Augustin, Noémi and Seth-Smith, Helena Mb and Hollenstein, Yvonne and Syedbasha, Mohammedyaseen and Lang, Daniela and Neher, Richard A. and Dubuis, Olivier and Naegele, Michael and Buser, Andreas and Nickel, Christian H. and Ritz, Nicole and Zeller, Andreas and Lang, Brian M. and Hadfield, James and Bedford, Trevor and Battegay, Manuel and Schneider-Sliwa, Rita and Egli, Adrian and Stadler, Tanja. (2020) Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics. PLoS Pathogens, 16 (11). e1008984.; info:pmid/33211775; urn:ISSN:1553-7366; urn:ISSN:1553-7374
الإتاحة: https://doi.org/10.1371/journal.ppat.1008984Test
https://edoc.unibas.ch/80930Test/
https://edoc.unibas.ch/80930/1/file%20%281%29.pdfTest -
7تقرير
المؤلفون: Brüningk, Sarah, id_orcid:0 000-0003-3176-1032, Klatt, Juliane, id_orcid:0 000-0003-4096-566X, Stange, Madlen, Mari, Alfredo, Brunner, Myrta, Roloff, Tim-Christoph, Seth-Smith, Helena M.B., Schweitzer, Michael, Leuzinger, Karoline, Søgaard, Kirstine K., Albertos Torres, Diana, Gensch, Alexander, Schlotterbeck, Ann-Kathrin, Nickel, Christian H., Ritz, Nicole, Heininger, Ulrich, Bielicki, Julia, Rentsch, Katharina, Fuchs, Simon, Bingisser, Roland, Siegemund, Martin, Pargger, Hans, Ciardo, Diana, Dubuis, Olivier, Buser, Andreas, Tschudin-Sutter, Sarah, Battegay, Manuel, Schneider-Sliwa, Rita, Borgwardt, Karsten, Hirsch, Hans H., Egli, Adrian
المصدر: medRxiv
الوصف: Background Transmission chains within small urban areas (accommodating∼30% of the European population) greatly contribute to case burden and economic impact during the ongoing COVID-19 pandemic, and should be a focus for preventive measures to achieve containment. Here, at very high spatio-temporal resolution, we analysed determinants of SARS-CoV-2 transmission in a European urban area, Basel-City (Switzerland). Methodology. We combined detailed epidemiological, intra-city mobility, and socioeconomic data-sets with whole-genome-sequencing during the first SARS-CoV-2 wave. For this, we succeeded in sequencing 44% of all reported cases from Basel-City and performed phylogenetic clustering and compartmental modelling based on the dominating viral variant (B.1-C15324T; 60% of cases) to identify drivers and patterns of transmission. Based on these results we simulated vaccination scenarios and corresponding healthcare-system burden (intensive-care-unit occupancy). Principal Findings. Transmissions were driven by socioeconomically weaker and highly mobile population groups with mostly cryptic transmissions, whereas amongst more senior population transmission was clustered. Simulated vaccination scenarios assuming 60-90% transmission reduction, and 70-90% reduction of severe cases showed that prioritizing mobile, socioeconomically weaker populations for vaccination would effectively reduce case numbers. However, long-term intensive-care-unit occupation would also be effectively reduced if senior population groups were prioritized, provided there were no changes in testing and prevention strategies. Conclusions. Reducing SARS-CoV-2 transmission through vaccination strongly depends on the efficacy of the deployed vaccine. A combined strategy of protecting risk groups by extensive testing coupled with vaccination of the drivers of transmission (i.e. highly mobile groups) would be most effective at reducing the spread of SARS-CoV-2 within an urban area.
وصف الملف: application/application/pdf
الإتاحة: https://doi.org/20.500.11850/525249Test
https://doi.org/10.3929/ethz-b-000525249Test
https://doi.org/10.1101/2020.12.15.20248130Test
https://hdl.handle.net/20.500.11850/525249Test -
8دورية أكاديمية
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9دورية أكاديمية
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10دورية أكاديمية
النص الكامل