Obstacles and Possibilities in Pathogen Agnostic Sequencing for Public Health Monitoring: Insights from the Worldwide Emerging Infections Monitoring Program

Abstract

Given its use in infectious disease monitoring and detection, pathogen agnostic sequencing has been recognized as a biodefense and public health tool. Since Sanger sequencing, next-generation sequencing (NGS) technologies higher throughput genome sequencing methods that can be used for pathogen agnostic sequencing—have become more accessible and widely used in public health and biomedical labs. Additionally, the price per genome or sample sequenced has dropped significantly, hastening the shift of NGS from a research endeavor to a necessary part of routine public health monitoring. Conclusion:The GEIS program has made investments in surveillance and advanced characterization infrastructure in accordance with the biosurveillance landscape. Over time, the DOD has maintained and expanded these capabilities for broader public health surveillance, and these investments have continued to support the need for timely information on emerging infectious threats. In our opinion, these technologies will have a greater long-term impact when used in a strong and well- coordinated laboratory network for infectious disease response and surveillance.