New RNA Detection Tool Shows Promise for HIV and Other Viral Testing

RNA viruses such as human immunodeficiency virus (HIV) require assays that can detect very low levels of viral genetic material. Clinical and environmental testing can also expose enzymes to harsh assay conditions, including high temperatures. This creates a need for detection components that combine sensitivity with stability. New research demonstrates an engineered Cas13a enzyme optimized to meet both requirements in RNA detection assays.

Rice University (Houston, TX, USA) scientists developed an improved version of Cas13a, a CRISPR-associated enzyme that targets RNA rather than DNA. In a detection assay, Cas13a binds to a target RNA sequence, such as RNA from HIV or SARS-CoV-2, and generates a signal that a person or instrument can read. To develop the improved enzyme, the team began with a stable Cas13a variant that could tolerate harsh assay conditions but lacked the sensitivity needed to detect very small quantities of target RNA.

To understand how to improve sensitivity while preserving stability, the researchers first resolved the protein’s structure. This required overcoming a technical challenge: Cas13a moves substantially as it binds RNA. The team therefore devised a way to hold the CRISPR/Cas13a system and its target RNA in place while collecting structural information. The resulting structure revealed two regions of the enzyme that the researchers believed could be modified to increase sensitivity.

Guided by these structural findings, the team engineered the two regions and tested the modified enzymes in the laboratory. Altering both regions made the enzyme overly sensitive, triggering signals even when target RNA was absent. Modifying just one region, however, increased sensitivity 100-fold without compromising stability. This engineered Cas13a variant also demonstrated a 100-fold performance improvement in a detection assay using a synthetic, noninfectious HIV sample.

The study was published in Cell Chemical Biology on October 13, 2026. The same Cas13a enzyme can be paired with a programmable guide designed to target different RNA sequences. According to the source, the guide could be reprogrammed for SARS-CoV-2, influenza virus, Ebola virus, Zika virus, respiratory syncytial virus or hepatitis C virus, and the enzyme could potentially be used in commercial assays such as reverse transcription quantitative PCR (RT-qPCR) and lateral flow testing.

“Any enzyme used in an assay needs to be both sensitive and stable. It needs to be able to detect very small amounts of RNA while enduring harsh conditions, like high temperatures. Here, we took a stable Cas13a and engineered it to have the desired sensitivity,” said Yang Gao, associate professor of biosciences at Rice University and corresponding author.

“In a CRISPR system, the enzyme is paired with a guide that targets a particular sequence of RNA. The guide is easy to program, so the critical part of the system is having an enzyme that’s compatible with your assays. Our version of Cas13a is optimized for sensitive and stable RNA detection assays and could potentially be used in commercial assays like RT-qPCR and lateral flow,” added Gao.

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