Early response model for containing newly emerging infectious diseases

Global interconnectedness has heightened the risk of rapidly spreading pathogens. The recent epidemics of influenza, AIDS, SARS, Ebola, Zika, and COVID suggest that RNA viruses will drive future threats. During COVID, the lack of monitoring capabilities left lockdowns as the only measure to reduce virus transmission, though these had to be cut short to prevent an economic collapse. By contrast, early identification and isolation of cases can protect health systems, inform policy decisions, and maintain economic stability. Molecular diagnostics are critical for detecting pathogens that spread pre- and asymptomatically, but must shift from medical to epidemiological applications. Minimizing outbreak risk requires purpose-built workflows with integrated supply and information systems, combining high frequency testing with fast, reliable and affordable results. We implemented monitoring by repurposing nonprofit research infrastructure, which validated the diagnostic process for containing outbreaks. Additionally, we developed qPCR assays that can detect circulating and newly emerging SARS-CoV-2 variants, preventing detection evasion and minimizing outbreak size. Here we present an after-action report and propose an early response model for containing newly emerging infectious diseases.