A rapidly deployable CRISPR-Cas3 diagnostic platform for emerging RNA viruses

Nakamura, J.; Miyazaki, K.; Torii, S.; Kitajima, M.; Mikamo, K.; Kimihira, T.; Morimoto, L.; Ashayqa, H.; Ito, J.; Takeshita, K.; Kosugi, S.; Minegishi, Y.; Ito, M.; Hirano, R.; Ishida, S.; Yoshimi, K.; Halfmann, P. J.; Kawaoka, Y.; Mashimo, T.

doi:10.64898/2026.08.25.746999

bioRxiv · 10.64898/2026.08.25.746999

A rapidly deployable CRISPR-Cas3 diagnostic platform for emerging RNA viruses

Nakamura, J.·Miyazaki, K.·Torii, S.·Kitajima, M.·Mikamo, K.·Kimihira, T.·Morimoto, L.·Ashayqa, H.·Ito, J.·Takeshita, K.·Kosugi, S.·Minegishi, Y.·Ito, M.·Hirano, R.·Ishida, S.·Yoshimi, K.·Halfmann, P. J.·Kawaoka, Y.·Mashimo, T.

View original source ↗Export metadata ↓

Abstract

Rapidly converting viral genome information into deployable molecular tests remains a major challenge in outbreak preparedness. We developed CONAN-SWIFT (Simple Workflow for Isothermal Field Testing), a sequence-to-test platform that integrates computational assay design, reverse-transcription loop-mediated isothermal amplification, CRISPR-Cas3 detection, reagent lyophilization and lateral-flow readout. Sequence-guided assays for Andes virus and Bundibugyo virus were established within approximately three weeks and extended to four additional filoviruses. A web-based designer supported crRNA selection, and systematic RT-LAMP primer optimization improved amplification performance. Recombinant Escherichia coli-expressed Cascade enabled standardized preparation of lyophilized Cas3-detection reagents, which were combined with a battery-operated isothermal device. The portable system detected as few as 10 input RNA copies per reaction within approximately 40 min. It also detected viral RNA and biologically contained, replication-incompetent Ebola virus in spiked human blood and concentrated wastewater. These findings establish the analytical feasibility of a rapidly adaptable CRISPR-Cas3 engineering framework for decentralized detection of emerging RNA viruses.

Explore related subjects

bioengineering Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Nakamura, J., Miyazaki, K., Torii, S., Kitajima, M., Mikamo, K., Kimihira, T., Morimoto, L., Ashayqa, H., Ito, J., Takeshita, K., Kosugi, S., Minegishi, Y., Ito, M., Hirano, R., Ishida, S., Yoshimi, K., Halfmann, P. J., Kawaoka, Y., Mashimo, T.. 2026-08-26. A rapidly deployable CRISPR-Cas3 diagnostic platform for emerging RNA viruses. https://doi.org/10.64898/2026.08.25.746999

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Impact of Adipogenic Differentiation on the Nutrition and Sensory Profile of Cultivated Pork Fat Tissue

Adipose tissue is a principal source of texture, flavor, and aroma in meat products. Higher fat content corresponds to higher juiciness, tenderness and overall palatability of meat products, making it a key component of cultivated meat. Our previous study investigated the aromatic characteristics of cultivated pork fat tissue, finding comparable consumer panel hedonic scores between conventional livestock derived and cultivated pork fats. Further research was pursued to characterize if adipogenic differentiation of the cells is required to enhance the flavor of cultivated fat. While differentiation of cultivated cells results in tissues that more closely resemble the morphology of livestock-derived tissue, the process substantially increases production timelines and material costs associated with cultivated meat production. As a result, we observed changes in organoleptic and nutritional properties of cultivated pork fat cells associated with differentiation of porcine dedifferentiated fat (PDFAT) cells. We assessed the effect of varying degrees of adipogenesis with soybean oil supplementation on fat content, composition, and volatile compound formation. Notably, we observed the concentrations of 2-pentylfuran, 2-heptanone, hexanal and (E)-2-octenal increased compared to the undifferentiated preadipocytes. These compounds, along with other ketones, aldehydes, alcohol and lactone molecules, contribute to fruity, herbal, and fatty aromas. Additionally, these results were achieved without requiring the maximum differentiation time frame of 12 days in culture. These findings emphasize the importance of adipocyte differentiation in cultivated fat production and highlight its potential as a strategy for optimizing both flavor and nutritional attributes of cultivated meat.

bioengineering↗

bioRxiv2026

Acoustic Masking of Electric Stimulation at Basal and Extra-Cochlear Sites

Cochlear implant (CI) candidates with residual low frequency hearing increasingly receive hearing preserving electrode arrays to enable electric acoustic stimulation (EAS). However, assessing very low frequency hearing in newborns and young children remains difficult. Previous work has shown that acoustic stimulation can mask electrically evoked auditory percepts when stimulation sites are spatially separated. Whether such masking also occurs when electric stimulation is delivered near the round window (RW), prior to cochlear insertion, remains unclear. This study investigated ipsilateral acoustic masking of electric stimulation delivered at apical, basal, and near RW sites in 12 EAS users with residual low frequency hearing implanted with short or partially inserted electrode arrays. Using a psychophysical paradigm, threshold elevations of electric pulse trains were measured during simultaneous acoustic stimulation. Electric stimulation was applied at extra cochlear RW locations and intra cochlear basal and apical electrodes, while stimulation parameters were systematically varied. Electric stimulation near the RW reliably evoked auditory percepts without side effects, though optimal stimulation parameters and masking strength varied across participants. Strong acoustic masking was consistently observed for apical stimulation, whereas weaker but measurable masking occurred for basal and RW stimulation. A cochlear lumped parameter model indicated that approximately 5% of current delivered at the RW can reach apical regions, explaining the observed masking by low frequency acoustic tones. Masking strength correlated with residual hearing for apical stimulation only. These findings indicate that acoustic masking of apical electric stimulation, which correlated with residual hearing, holds potential as a diagnostic tool for assessing low frequency hearing post operatively. The detection of masking during both RW and basal stimulation represents a promising result, indicating that these stimulation paradigms can produce quantifiable effects. Given the considerable variability observed among participants, further investigation is required to establish the extent to which masking measures reflect residual hearing or hearing loss. Nonetheless, these results provide novel insight into auditory perception and side effects associated with basal and extra cochlear electric stimulation, informing future efforts to optimize this approach for low-frequency hearing assessment.

bioengineering↗

bioRxiv2026

Electrophysiological and neuroimmune responses of a cortical tissue model to chronic gamma radiation exposure

Exposure to chronic space radiation is a major health concern for long-duration missions beyond low Earth orbit. While most experimental studies simulate mission-relevant doses using acute irradiation, astronauts will experience persistent low-dose-rate exposure over months. Here, we used engineered three-dimensional (3D) mouse cortical tissue models and two-dimensional (2D) primary cortical cultures to investigate the effects of radiation dose rate on neuroglial function, inflammatory responses, and neuronal network activity. Cultures were exposed to a cumulative 0.5 Gy dose of {gamma}-radiation delivered either acutely (1 h) or chronically (166 h), with or without pretreatment using the radioprotective agent amifostine. In 3D cortical tissue models, we quantified DNA damage, astrocyte and microglia reactivity, neuronal survival, neurite morphology, and secretion of pro-inflammatory cytokines. In parallel, microelectrode array recordings were used to assess electrophysiological function in 2D neuronal networks following {gamma}-radiation or treatment with the radiomimetic drug bleomycin. Acute gamma radiation induced modest astrocyte activation, whereas chronic exposure caused limited neuroimmune alterations. Neither exposure paradigm impaired neuronal network activity, despite measurable DNA damage responses. Together, these findings indicate that neuronal function is preserved following low-dose-rate gamma irradiation while glial populations display selective sensitivity to radiation exposure.

bioengineering↗