Evidence-based public health decision-making in the COVID-19 pandemic
The World Health Organization received notification of a new and infectious respiratory disease in Wuhan, China at the end of December 2019, and issued the first outbreak report about the ‘pneumonia of unknown cause’ in January 20201. These were subsequently identified as COVID-19 cases arising from infection with the novel SARS-CoV-2 virus. With the pandemic potential of the new disease quickly becoming clear, countries around the world moved to plan their own control measures against this new threat to public health.
Drawing upon world-leading expertise in virology, exemplified by the Department of Viroscience at Erasmus MC in Rotterdam, the Netherlands, opted to use genomic epidemiology from the onset — introducing rapid sequencing and analysis of all patients with suspected diseases. The first cases were identified in late February 2020 as introductions of the virus from Italy. Cases increased rapidly among non-travellers, including healthcare workers; it was not clear how big a problem disease transmission in healthcare settings was. This was already a sensitive political issue, given an expected shortage of personal protective equipment to reduce risks to health professionals.
Rapid sequencing continued for all suspected cases in travellers and healthcare workers, plus local surveillance, and by mid-March, the genomes of 189 SARS-CoV-2 viruses from the Netherlands had been sequenced — over a quarter of the sequences available worldwide at that point. The data revealed that multiple virus sub-types were circulating in the population; ongoing local transmission was creating the local and regional clusters of disease, but there was little infection of healthcare workers taking place in medical settings. This meant that community transmission was the main mode of spread within the Netherlands at this point; there were also indications that mass gatherings such as festivals could be acting as super-spreading events.
The combination of real-time whole genome sequencing with the data from the National Public Health response team has provided information that helped decide on the next steps in the decision-making. Oude Munnink et al. Nature Medicine2
This information prompted an immediate change in approach to targeted public health interventions to control the outbreaks, including the introduction of restrictions on movement and the closure of schools, catering, and sports clubs, as well as physical distancing measures at regional (and subsequently national) levels4.
The Netherlands continued to use genomic epidemiological surveillance and were able to spot transmission of SARS-CoV-2 variants between humans and minks on fur farms as early as April 2020, warning correctly that this could pose a further public health risk5; in November 2020, Danish authorities enacted a cull of all mink after a new viral variant transmissible to humans and with the potential to reduce the effectiveness of new vaccines emerged6.Download genomic epidemiology white paper
1. World Health Organization. Pneumonia of unknown cause — China. 2020. Available at: https://www.who.int/emergencies/disease-outbreak-news/item/2020-DON229 [Accessed: 01 February 2021]
2. Oude Munnink, B. B., Nieuwenhuijse, D. F., Stein, M., et al. Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands. Nat Med. 26(9):1405-1410 (2020)
3. BBC. Call for coronavirus screening at mink farms. Available at: https://www.bbc.co.uk/news/science-environment-55048418. [Accessed 02 February 2021]
4. Sikkema, R. S., Pas, S. D., Nieuwenhuijse, D. F., et al. COVID-19 in health-care workers in three hospitals in the south of the Netherlands: a cross-sectional study. Lancet Infect Dis. 20(11): 1273-1280 (2020).
5. Oreshkova, N., Molenaar, R. J., Vreman, S., et al. SARSCoV-2 infection in farmed minks, the Netherlands, April and May 2020. Eurosurveillance. 25(23):2001005 (2020).
6. Koopmans, M. SARS-CoV-2 and the human-animal interface: outbreaks on mink farms. Lancet Infect Dis. 21(1):18-19 (2020).