Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area
By
Sarah C. Brueningk,
Juliane Klatt,
Madlen Stange,
Alfredo Mari,
Myrta Brunner,
Tim-Christoph Roloff,
Helena Seth-Smith,
Michael Schweitzer,
Karoline Leuzinger,
Kirstine Kobberoee Soegaard,
Diana Albertos Torres,
Alexander Gensch,
Ann-Kathrin Schlotterbeck,
Christian Nickel,
Nicole Ritz,
Ulrich Heininger,
Julia Bielicki,
Katharina Rentsch,
Simon Fuchs,
Roland Bingisser,
Martin Siegemund,
Hans Pargger,
Diana Ciardo,
Olivier Dubuis,
Andreas Buser,
Sarah Tschudin-Sutter,
Manuel Battegay,
Rita Schneider-Sliwa,
Karsten Borgwardt,
Hans H. Hirsch,
Adrian Egli
Posted 17 Dec 2020
medRxiv DOI: 10.1101/2020.12.15.20248130
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 socio economically 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, socio economically 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.
Download data
- Downloaded 1,274 times
- Download rankings, all-time:
- Site-wide: 18,377
- In public and global health: 377
- Year to date:
- Site-wide: 6,302
- Since beginning of last month:
- Site-wide: 26,801
Altmetric data
Downloads over time
Distribution of downloads per paper, site-wide
PanLingua
News
- 27 Nov 2020: The website and API now include results pulled from medRxiv as well as bioRxiv.
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!