New preprint: Integrated CRISPR-based detection of HIV, tuberculosis and malaria

New Preprint Alert! Ashvi Jain and Austin Si introduce HTM CARMEN, a highly multiplexed CRISPR-based molecular testing platform designed to interrogate HIV, tuberculosis (TB) and malaria within a common workflow.

HIV, TB and malaria frequently co-circulate in the same populations and can occur as coinfections, yet diagnostic testing is typically organized around individual diseases. HTM CARMEN was developed to explore a different approach: testing for these infections in parallel while also capturing additional information relevant to pathogen identity and drug resistance. The platform integrates detection of HIV-1 and HIV-2, four Plasmodium species and Mycobacterium tuberculosis, together with selected TB isoniazid-resistance-associated variants. The team evaluated the platform across analytical experiments, clinically relevant sample matrices, contrived coinfections and clinical specimens.

In the clinical cohorts tested, HTM CARMEN achieved 95% positive percent agreement for malaria, 95% for HIV-1 and 100% for Mtb, with 100% negative percent agreement for each target. The platform also simultaneously detected HIV-1 and Mtb in all nine clinical HIV-TB coinfection specimens tested. The study provides a proof of concept for organizing molecular testing around co-endemic infections and coinfections, while integrating pathogen detection, species differentiation and resistance-associated variant interrogation within a programmable platform.

The work was a collaboration with the Le Roch Lab (UC Riverside), the Yang Lab (UCLA), and the UCLA Health Clinical Microbiology Laboratory.

Congrats to all authors!

Read the preprint: https://www.medrxiv.org/content/10.64898/2026.09.26.26364094v1