Early response model for containing newly emerging infectious diseases

Abstract Recent epidemics of influenza, AIDS, SARS, Ebola, Zika, and COVID-19 suggest that RNA viruses will drive future threats. COVID-19 exposed major gaps in monitoring capabilities, leaving lockdowns as the only means to reduce transmission. However, their effectiveness was limited by economic pressures that forced early relaxation. Identification and isolation of cases can protect health systems, inform policy decisions, and support economic stability. Infectious diseases with pre- or asymptomatic transmission necessitate molecular diagnostic testing. Unlike routine clinical diagnostics, outbreak containment requires prioritizing frequent testing and rapid test results over maximal analytical sensitivity. To strengthen monitoring capabilities, we designed a scalable workflow for specimen collection, analysis, and reporting. Rapid implementation was achieved by reallocating nonmedical, nonprofit, molecular biology research infrastructure. Vigilance is crucial, as the robustness of diagnostic assays can be compromised by emerging mutants. We developed software to analyze genomic variation and applied it to 4,295,664 SARS-CoV-2 genomes collected from patients worldwide. To minimize outbreak size, we developed and validated variant-inclusive qPCR assays that target stable regions. Between September 2020 and December 2021, 476,502 specimens from local staff and caregivers were analyzed, 177,756 of which were processed in batches. This after-action report presents a framework grounded in operational objectives, aiming to provide guidance on containing newly emerging infectious diseases.