Engineered RNA sensor detects and fights coronavirus inside living cells

The technology, called the Viral-Engineered RNA-based Activation System (VERAS), hijacks the virus’s own replication machinery to switch on reporter or therapeutic genes precisely in infected cells.

Coronaviruses—including strains that cause common colds and COVID-19—replicate rapidly and evolve continuously, underscoring the need for sensitive tools to monitor infection and advance antiviral development. Existing live-cell biosensors typically depend on viral protease activity, RNA editing, or engineered viral genomes, but these approaches often suffer from high background noise, limited sensitivity, or destructive readouts that require cell fixation or lysis. A key unmet challenge is the ability to dynamically sense viral transcription and replication in intact, living cells. Notably, coronaviruses rely on a specialized replication-and-transcription complex (RTC) that recognizes conserved RNA structures at the 5′ and 3′ ends of viral RNAs to generate genomic and subgenomic transcripts while evading host shut-down mechanisms. Naturally occurring defective interfering particles exploit this system, inspiring strategies that convert viral replication into a programmable biological switch.

A study (DOI: 10.1016/j.bidere.2025.100040) published in BioDesign Research on 17 July 2025 by Lei S. Qi’s team, Stanford University, enables continuous, non-destructive monitoring of viral replication while simultaneously opening the door to programmable antiviral defenses.

Using coronavirus RNA regulatory logic as a design blueprint, the researchers first engineered a synthetic RNA sensing system—VERAS—by repurposing conserved 5′ and 3′ untranslated region elements from human coronavirus 229E. The system was designed in both positive- and negative-strand formats, with negative-strand VERAS requiring transcription by the viral replication-and-transcription complex (RTC) to generate translatable positive-sense RNA. Six VERAS variants were constructed to mimic either subgenomic mRNAs or full genomic RNA, expressed in a human cell line engineered to permit 229E infection, and evaluated using reporter assays, flow cytometry, immunofluorescence, strand-specific RT-PCR, and viral reinfection experiments. These approaches revealed that only negative-strand VERAS constructs produced strong, infection-dependent reporter activation, reaching 17- to 31-fold induction, with signal intensity tightly correlated to established viral replication markers. Mechanistic analyses confirmed that viral infection drives bidirectional transcription and replication of VERAS RNAs, preserving their abundance while non-viral RNAs decayed. By incorporating transcription-regulating sequences, VERAS was further shown to support bicistronic expression, enabling virus-specific induction of a second reporter with minimal background leakage. Addition of viral packaging sequences allowed VERAS RNAs to be incorporated into progeny virions in a strain-dependent manner, facilitating transfer to newly infected cells. Extending this strategy to multiple coronaviruses demonstrated partial cross-activation, consistent with conserved cis-regulatory RNA elements. Functionally, VERAS detected infection at extremely low viral titers and was programmable to trigger antiviral responses, including apoptosis or interferon expression, only upon infection. Cells expressing interferon-encoding VERAS showed substantial reductions in viral replication and protected neighboring cells in co-culture, highlighting VERAS as a sensitive, infection-activated platform that integrates real-time viral sensing with targeted antiviral intervention.

VERAS represents a powerful new platform for virology research, enabling real-time visualization of viral replication without genetic modification of the virus. It offers a dual diagnostic-therapeutic capability: the same RNA construct can detect infection and deliver antiviral responses with high specificity. This approach could improve antiviral screening, infection imaging, and the development of inducible RNA-based medicines that activate only when and where viruses replicate.

###

References

DOI

10.1016/j.bidere.2025.100040

Original Source URL

https://doi.org/10.1016/j.bidere.2025.100040

Funding information

The project was supported by a contract grant from Bill & Melinda Gates Foundation (INV-035661) and in part by funding to L.S.Q. as a Chan Zuckerberg Biohub - San Francisco Investigator. C.O. is supported by the National Science Foundation Graduate Research Fellowship Program (Grant DGE-2146755) and the Sarafan ChEM-H Chemistry-Biological Interface Training Program. L.S.Q. is a Chan Zuckerberg Biohub - San Francisco Investigator.

About BioDesign Research

BioDesign Research is dedicated to information exchange in the interdisciplinary field of biosystems design. Its unique mission is to pave the way towards the predictable de novo design and assessment of engineered or reengineered living organisms using rational or automated methods to address global challenges in health, agriculture, and the environment.