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.

The rapid emergence and spread of SARS-CoV-2 has caused an unprecedented global emergency. The first case in the Philippines was detected January 30th and the country recorded the first COVID-19 death outside China. From mid-March the Philippines implemented one of the world's strictest and longest lockdowns. However, over 300,000 cases and 5,000 deaths have since been reported and the Philippines has the most cases per capita in Southeast Asia(1).
Genomic surveillance is a powerful component of the pandemic response, characterising circulating virus diversity to pinpoint sources of introductions, to identify and quantify community transmission, geographic spread, and the extent of importations and health-care associated infections. Yet, there has been limited application of these technologies in low- and middle-income countries (LMICs); only ~7% of 60,000+ genomes contributed globally are from LMICs.
This project will operationalize genomic surveillance and inform responses across the Philippines, in collaboration with the national laboratory network, the Epidemiology Bureau and its surveillance units within the DOH and the provincial health offices. Our approach embeds large-scale real-time sequencing capacity at the national reference laboratory and builds local sequencing capacity at Sub-National Laboratories (SNLs). Resources, training and accessible workflows will fast-track interpretation of real-time sequencing and results will directly inform stakeholders and national, regional, and local-scale responses. The research will further enable evaluation of control measures across settings, from
infection controls to prevent hospital-acquired infections, lockdowns to interrupt community transmission, and quarantining and movement restrictions to contain introductions, whilst increasing our understanding of SARS-CoV-2 transmission and control.
(1)WHO Coronavirus Disease Dashboard, https://COVID-1919.who.int/, accessed 07/10/2020