Implementing genomic surveillance to support SARS-CoV-2 control and mitigation strategies in the Philippines

As scientists and public health practitioners battle to understand and control the COVID-19 pandemic, the application of genomic surveillance i.e. tracking changes in the virus' genetic footprint, has become an invaluable tool. Genome sequences provide unique insights into how the virus is evolving and spreading and how it can be more effectively controlled. This information enhances traditional surveillance methods like contact tracing to resolve transmission scenarios e.g. providing evidence to determine the most likely route of transmission if an infected hospital worker has had multiple patient and community contacts, guiding improved infection control. It simultaneously provides a means to monitor the impact of control efforts, such as lockdown, by tracking the local extinction or re-introduction of virus lineages. We propose to build genomic surveillance and response capacity in the Philippines, where it can inform infection control at local and regional scales, e.g within healthcare settings and between different islands or provinces. We will deploy the latest sequencing and analytical technologies to characterize virus circulation from archived samples and enable rapid interpretation of genomic data from new case investigations to directly inform responses. This approach will provide crucial and transferrable insights into SARS-CoV-2 dynamics across the island archipelago and globally. Moreover, this project will build surveillance and response capacity against future viral threats and for the control and elimination of diseases that continue to pose a major burden.