Rapid Response to Emerging Threats

Source: Elisha Are

The COVID-19 pandemic has highlighted the need for modelling and analysis that can respond quickly to emerging situations. SACEMA’s Rapid Response to Emerging Threats research theme focuses on rapidly producing analyses to increase situational awareness and aid decision making.

Work in this theme has included assessing the effectiveness of a reactive vaccination campaign during a measles outbreak in Stellenbosch, projecting the impact of a product recall on the national Listeriosis outbreak, and developing models of the potential impact of COVID-19 in South Africa and beyond.

In 2020, the spread of SARS-CoV-2, the virus that causes COVID-19 disease, became a global crisis. Modelling has taken on a more urgent character, as many agencies need to plan rapidly for an evolving situation with little certainty even about the present state of affairs, much less the future. SACEMA has supported the South African response in a number of ways, including early modelling to show the urgency of intervention, projection updates to support resource management, and development of metrics to monitor for epidemic resurgences and the emergence of new waves.

In 2017-2018, South Africa experienced a listeriosis outbreak of unprecedented scale, with more than 1000 laboratory-confirmed cases. In Week 8 of 2018, the national Department of Health issued a nationwide recall of the processed meat products implicated in the outbreak. To help set expectations about the decline of the outbreak, SACEMA developed a model-based forecast for how case numbers would respond to the product recall. The model took into account the anticipated change in the risky exposures through time and the distribution of the incubation period, using these to project the weekly incidence of new cases. Subsequent comparison of model projections and the actual number of cases showed that the model adequately captured the key features of the decline. These projections helped set and communicate expectations for the outbreak’s decline, increasing situational awareness and providing a benchmark against which incoming data could be assessed. Use of the projections during the South African listeriosis outbreak demonstrated that model-based forecasting can be a useful operational tool for outbreak surveillance and response.

At the beginning of, 2017, there was a measles outbreak at a school in Stellenbosch. SACEMA responded by using model-based counterfactual scenarios to assess the impact of a reactive vaccination campaign during the outbreak. We also developed an information sheet that was shared with students and their families, and an app that allowed students to explore the model used in the assessment.

A key initiative under this research theme is SACEMA’s Modelling and Analysis Response Team (SMART), which provides a platform for researchers to develop familiarity with outbreak responses and skills in outbreak analytics and modelling. SACEMA is also a member of the World Health Organization’s Global Outbreak Alert and Response Network (GOARN).