Epidemiology of the COVID-19 pandemic using open-source data

Research program: 
Currently recruiting: 
The challenge: 

The unprecedented COVID-19 pandemic makes it important to consider the epidemiologic risk factors for spread under different conditions so that appropriate policies can be developed to prevent or respond to future outbreaks. Throughout the pandemic, data on individual cases of COVID-19 around the world have been collected and is now available as an open-source database for researchers to access and analyse. In the absence of formal reporting in many countries early in the pandemic, open-source data is a valuable epidemiological tool that can enable researchers to fill in gaps in research and make recommendations for public health policy. The aim of this study will be to examine the epidemiological and genetic factors linked to the COVID-19 pandemic using open source data both in Australia and globally.

The project: 

Using an open-source epidemiologic database of COVID-19 cases, we will link SARS-CoV-2 genetic sequence data from open-source data such as GISAID and analyse the genetic epidemiology of COVID-19. The effects of COVID-19 on various public health settings such as aged care and health care using open-source data will be investigated. The burden of COVID-19 on the travel industry will also be evaluated during this study.

The method: 

Data from the Open COVID-19 Data Curation Group will be used for selected countries and linked to open-source genetic sequence data where possible, using a matching algorithm already developed by the Biosecurity Program. Epidemiologic and GIS analysis (using Arc GIS) will be done. A line list of COVID-19 cases in select countries will be created using open-source data and matched to COVID-19 outbreaks using a matching criteria developed by the Biosecurity Program. Outbreaks in the travel industry will be tracked and matched to COVID-19 cases using the same matching criteria.

The results: 

Epidemiologic analysis will then be done on data sets obtained and used in publications to highlight the importance of open-source data early on in pandemics and to advise on public health policies. 

The impact: 

The principle of open-source epidemic data is to allow many different groups to apply critical thinking and analysis to help mitigate the epidemic. Our research will provide additional analysis and insights on COVID-19 epidemiology both nationally and globally. This project will address the current COVID-19 global outbreak in geographic hot spots as well as evaluate Australia’s preparedness for likely future coronaviral disease outbreaks.

Project contact: 
Head, Biosecurity Program, and Professor of Global Biosecurity, Kirby Institute and NHMRC Principal Research Fellow
Project collaborators: 
  • Samsung Lim
  • Phi Yen Nguyen 
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