Rapid Differentiation of Vaccine and Wild-Type Measles Virus During an Ongoing Outbreak using a new molecular assay

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ID: 332518
2026
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Abstract
Abstract Background Differentiating wild and vaccine measles virus (MeV) strains is critical for appropriate healthcare response during outbreak vaccination campaigns. Sequencing, the current standard, is expensive, time-consuming, and limited to specialized laboratories. We developed and implemented a novel differential MeV RT-qPCR assay to address these challenges, which we describe herein. Methods We designed a differential two-step assay; the first step, termed MRRV, distinguishes between rubella, wild MeV, and vaccine MeV. The second, termed “MeV differential”, differentiates between genotypes A (vaccine), B and D. Results The assay detects 10-50 copies per reaction and accurately classifies weak clinical samples (Cq > 32), with 100% accuracy, compared with the N gene sequencing gold standard. Evaluated on over 4,000 clinical samples retrospectively and during the 2025-2026MeV outbreak in Israel, the assay revealed that ∼9% of tested originated from vaccine strain. Among tested municipalities, those running active vaccination campaigns had significantly higher vaccine strain detections (>10 cases each) than those with routine vaccination (1-2 cases). Retrospective analysis of samples from 2018-2024 identified a mix of B and D strains. The novel assay successfully identified double infection cases (exposure to a wild strain shortly before or after vaccination). Conclusion The novel assay proved useful both as a diagnostic tool that enables focused, efficient healthcare response, and as an epidemiological tool that provides valuable information in real-time. This assay is faster, cheaper and more amendable for high throughput testing, compared with the gold-standard sequencing classification.
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Authors Efrat Dahan Bucris, Tal Levin, Roberto Azar, Batya Mannasse, Hadar Assraf, Vardit Moshayoff, Roaa Shatrubi, Yara Kanaaneh, Victoria Indenbaum, Neta S. Zuckerman, Yaniv Lustig, Oran Erster
Journal The Journal of infectious diseases
Year 2026
DOI
10.1093/infdis/jiag518
URL
https://doi.org/10.1093/infdis/jiag518
Keywords Keywords not found

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