Real-time monitoring of COVID-19 transmission through phylodynamics
- Funded by Swiss National Science Foundation (SNSF)
- Total publications:9 publications
Grant number: 196267
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Key facts
Disease
COVID-19Start & end year
20202022Known Financial Commitments (USD)
$303,513.25Funder
Swiss National Science Foundation (SNSF)Principal Investigator
Stadler TanjaResearch Location
SwitzerlandLead Research Institution
Computational Systems Biology Department of Biosystems, D-BSSE ETH ZürichResearch Priority Alignment
N/A
Research Category
Epidemiological studies
Research Subcategory
Disease transmission dynamics
Special Interest Tags
N/A
Study Type
Non-Clinical
Clinical Trial Details
N/A
Broad Policy Alignment
Pending
Age Group
Not Applicable
Vulnerable Population
Not applicable
Occupations of Interest
Not applicable
Abstract
I propose to analyse genomic sequencing and confirmed case data from the COVID-19 pandemic in order to quantify, in real-time, transmission dynamics as well as the total number of infections, including `hidden' infections from untested and asymptomatic individuals. The results will allow me to rapidly evaluate the effectiveness of public health responses, and to suggest changes to strategies if need be. I have three main objectives.My first objective is to quantify transmission rates and the effective reproductive number of COVID-19 across geographic regions in real-time. In particular, I will determine which public health interventions and which environmental factors such as population density, temperature, or humidity have an impact on the reproductive number within outbreaks. Second, I will quantify transmission between geographic regions, providing insight into the importance of cross-border transmission and the impact of closing borders on the pandemic. The third objective is to estimate the overall number of COVID-19 cases through time and across regions. These estimates are required to evaluate the number of people with immunity against Sars-CoV-2 and, in combination with the estimated reproductive number, to forecast future spread. Further, the estimates of the overall number of COVID-19 cases enable a refinement of estimates of the case fatality rate of the disease.I will employ phylodynamic tools which were developed in my group over the past years for doing this quantification. The quantification will be done on a country level, meaning information regarding transmission rates and effectiveness of public health interventions will be available on a country level. For Switzerland, I will focus both on the country-level as well as the Cantons of Basel-Stadt and Basel-Landschaft. The Basel results will in particular be directly communicated to the Vorstand Ärztegesellschaft Baselland, Ressortchef 'Public Health'.For Basel-Landschaft, as part of a different project, I am leading efforts to generate COVID-19 sequencing data. Further, my group is involved in curating and releasing the confirmed case data on a Cantonal level. All other data will be accessed through publicly available databases.
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