Genomic surveillance is transforming public health action by providing a deeper understanding of
pathogens, their evolution and circulation. Used with clinical, epidemiological and other multi-source
data, genomic data for pathogens with pandemic and epidemic potential inform risk assessments and can support development of vaccines, therapeutics, diagnostic assays, and decisions on public health social measures. New technologies in sequencing and bioinformatics have emerged in recent years, and some countries have made major strides in establishing capabilities and capacities.
The COVID-19 pandemic has exposed challenges for genomics in public health surveillance systems.
Laboratories and networks dedicated to specific disease threats such as influenza, tuberculosis,
measles/rubella and polio, were mobilized to support SARS-CoV-2 genomic surveillance efforts. In some contexts, repurposing capacities came at a cost to the disease programs and their own surveillance and diagnostic needs. In addition, the scale, geographic representativeness, timeliness, quality, comparability and integration of genomic surveillance outputs with epidemiological and clinical surveillance findings remain weak.