CRISPR-Based Assays for Point-of-Need Detection and Subtyping of Influenza

Yibin B. Zhang, Jon Arizti-Sanz, A'Doriann D. Bradley, Yujia Huang, Tinna Solveig F. Kosoko-Thoroddsen, Pardis C. Sabeti, Cameron Myhrvold

Research output: Contribution to journalArticlepeer-review


The high disease burden of influenza virus poses a significant threat to human health. Optimized diagnostic technologies that combine speed, sensitivity, and specificity with minimal equipment requirements are urgently needed to detect the many circulating species, subtypes, and variants of influenza at the point of need. Here, we introduce such a method using Streamlined Highlighting of Infections to Navigate Epidemics (SHINE), a clustered regularly interspaced short palindromic repeats (CRISPR)-based RNA detection platform. Four SHINE assays were designed and validated for the detection and differentiation of clinically relevant influenza species (A and B) and subtypes (H1N1 and H3N2). When tested on clinical samples, these optimized assays achieved 100% concordance with quantitative RT-PCR. Duplex Cas12a/Cas13a SHINE assays were also developed to detect two targets simultaneously. This study demonstrates the utility of this duplex assay in discriminating two alleles of an oseltamivir resistance (H275Y) mutation as well as in simultaneously detecting influenza A and human RNAse P in patient samples. These assays have the potential to expand influenza detection outside of clinical laboratories for enhanced influenza diagnosis and surveillance.

Original languageEnglish (US)
Pages (from-to)599-612
Number of pages14
JournalJournal of Molecular Diagnostics
Issue number7
StatePublished - Jul 2024

All Science Journal Classification (ASJC) codes

  • Pathology and Forensic Medicine
  • Molecular Medicine


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