Review describes scalable testing workflow for emerging infectious diseases

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medRxiv Published April 18, 2026 Medically reviewed April 25, 2026 Study authors: Dekens, M. P. S.; Neumann, T.; Micheler, T.; Gandhi, V.; Kellner, M. J.; Rocha-Hasler, M.; Weissenbo… DOI ↗ By Dr. Amelia Tan, PhD · Internal Medicine & Chronic Disease

Key Takeaway

Consider scalable testing workflows for emerging diseases, but note observational evidence.

This publication is an after-action report review that synthesizes experiences from a scalable workflow for specimen collection, analysis, and reporting during the COVID-19 pandemic, covering conditions like SARS-CoV-2, influenza, AIDS, SARS, Ebola, and Zika. The review focuses on repurposing non-medical, nonprofit laboratory infrastructure with qPCR assays and frequent testing with same-day notification, applied to patients worldwide, local staff, caregivers, and the general population, involving 4,295,664 viral genomes, 476,502 specimens, and 2,475 systematically monitored caregivers between September 2020 and December 2021.

Key findings include a significant reduction in incidence among the 2,475 systematically monitored caregivers compared with the general population, with an effect size of d=4.54 and P=0.007. The workflow demonstrated high analytical sensitivity, enabled detection of SARS-CoV-2 below the infectious viral load, and achieved inclusive specificity of >99.99%. Effective control of viral transmission was associated with frequent testing with same-day notification, though the review notes that causality is not reported and the evidence is observational.

Limitations are not explicitly detailed in the source, but the review does not report on safety outcomes such as adverse events, serious adverse events, discontinuations, or tolerability. Funding or conflicts of interest are also not reported. The practice relevance is framed as an operationally grounded framework for responding to emerging infectious diseases, but clinicians should interpret these findings cautiously due to the lack of randomized trial data and potential biases in observational settings.

Study Details

EvidenceLevel 5

PublishedApr 2026

View Original Abstract ↓

Background Recent epidemics of influenza, AIDS, SARS, Ebola, Zika, and COVID-19 highlight the persistent threat of RNA viruses to public health. COVID-19 exposed major gaps in monitoring capabilities, leaving lockdowns as the only means to reduce transmission. Moreover, their effectiveness was limited by economic pressures that forced early relaxation. Methods To strengthen monitoring capabilities, we designed a scalable workflow for specimen collection, analysis, and reporting. Rapid implementation was achieved by repurposing non medical, nonprofit, laboratory infrastructure. We analyzed the variation in 4,295,664 viral genomes collected from patients worldwide using software developed in-house. qPCR assays targeting stable regions of the pathogen's genome were developed and then validated in a clinical performance study. Between September 2020 and December 2021, 476,502 specimens from local staff and caregivers were analyzed, 177,756 of which were processed in batches. Results The effectiveness of this response model is demonstrated by the significant reduction in incidence (P=0.007, d=4.54) among 2,475 systematically monitored caregivers compared with the general population. Performance validation of the assays showed high analytical sensitivity, enabling scaling up while detecting SARS-CoV-2 below the infectious viral load. Frequent testing with same-day notification was associated with effective control of viral transmission, comparing favorably with lockdowns. The high inclusive specificity (>99.99%) of the diagnostic panel further minimized outbreak risk. Interpretation Timely identification and isolation of cases is essential to protect health systems, inform policy decisions, and support economic stability. Infectious diseases with pre- or asymptomatic transmission necessitate molecular diagnostic testing. Effective deployment requires dedicated workflows that integrate supply and information systems, combining high-throughput with fast, affordable results. This after-action report presents an operationally grounded framework for responding to emerging infectious diseases.