Research Article | Open Access

Volume 2025 |Article ID 100040 | https://doi.org/10.1016/j.bidere.2025.100040

Engineered RNA-based activation system for coronavirus sensing in live cells

Leiping Zeng,^1,5 Christian Otero,^2,3,5 Lei S. Qi ^1,3,4

¹Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
²Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
³Sarafan ChEM-H, Stanford University, Stanford, CA, 94305, USA
⁴Chan Zuckerberg Biohub – San Francisco, San Francisco, CA, 94158, USA
⁵These authors contributed equally

Abstract

Real-time sensing of viral infection in live cells is crucial for virology research and antiviral development. However, existing methods face challenges of low signal sensitivity and the necessity for viral manipulation and cell fixation. Here, we develop a Viral-Engineered RNA-based Activation System (VERAS) that harnesses the viral replicase to induce transgene expression upon viral infection. VERAS is designed to detect real-time viral transcription and replication in live cells, which can trigger the translation of reporter and therapeutic genes. By integrating a viral packaging sequence, VERAS can also be transmitted to neighboring cells through progeny virions, effectively acting as a ‘Trojan Horse’. The negative-stranded VERAS elements demonstrated effective detection of several coronaviruses, including 229E and OC43, due to the conservation of cis-acting RNA structures across coronaviruses. Notably, VERAS functions as a dual-purpose system, acting both as an infection detector and inducible antiviral system. VERAS has the potential for basic virology research applications and can be adopted in improving the inducible expression of mRNA medicines for future coronaviruses.