Jon Arizti Sanz

All Publications

• Bead-based approaches for increased sensitivity and multiplexing of CRISPR diagnostics NATURE BIOMEDICAL ENGINEERING Siddiqui, S. M., Welch, N. L., Nguyen, T. G., Razmi, A., Chang, T., Senft, R., Arizti-Sanz, J., Mirhashemi, M. E., Stirling, D. R., Ackerman, C. M., Cimini, B. A., Blainey, P. C., Sabeti, P. C., Myhrvold, C. 2025

  Abstract

  CRISPR-based diagnostics have emerged as a promising tool for fast, accurate and portable pathogen detection. There has been rapid progress in pre-amplification processes and CRISPR-related enzymes used in these approaches, but the development of reporter systems and reaction platforms has lagged behind. In this paper, we develop bead-based techniques to address these gaps. First, we develop a novel bead-based split-luciferase reporter system with up to 20× sensitivity compared with standard fluorescence-based reporter design in CRISPR diagnostics. Second, we develop a highly deployable, bead-based platform capable of detecting nine distinct viral targets in parallelized, droplet-based reactions, with sensitivity reaching as low as 2.5 copies per µl of input RNA. We demonstrate the enhanced performance of both approaches on synthetic and clinical sample sensitivity, speed, multiplexing and deployability.

  View details for DOI 10.1038/s41551-025-01498-2

  View details for Web of Science ID 001575793800001

  View details for PubMedID 40983646

  View details for PubMedCentralID 10184463

• Establishing Methods to Monitor Influenza (A)H5N1 Virus in Dairy Cattle Milk, Massachusetts, USA. Emerging infectious diseases Stachler, E., Gnirke, A., McMahon, K., Gomez, M., Stenson, L., Guevara-Reyes, C., Knoll, H., Hill, T., Hill, S., Messer, K. S., Arizti-Sanz, J., Albeez, F., Curtis, E., Samani, P., Wewior, N., O'Connor, D. H., Vuyk, W., Khoury, S. E., Schnizlein, M. K., Rockey, N. C., Broemmel, Z., Mina, M., Madoff, L. C., Wohl, S., O'Connor, L., Brown, C. M., Ozonoff, A., Park, D. J., MacInnis, B. L., Sabeti, P. C. 2025; 31 (13): 70-75

  Abstract

  Highly pathogenic avian influenza A(H5N1) virus has caused a multistate outbreak among US dairy cattle, spreading across 16 states and infecting hundreds of herds since its onset. We rapidly developed and optimized PCR-based detection assays and sequencing protocols to support H5N1 molecular surveillance. Using 214 retail milk samples from 20 states for methods development, we found that H5N1 virus concentrations by digital PCR strongly correlated with quantitative PCR cycle threshold values; digital PCR exhibited greater sensitivity. Metagenomic sequencing after hybrid selection was best for higher concentration samples, whereas amplicon sequencing performed best for lower concentrations. By establishing these methods, we were able to support the creation of a statewide surveillance program to perform monthly testing of bulk milk samples from all dairy cattle farms in Massachusetts, USA, which remain negative to date. The methods, workflow, and recommendations described provide a framework for others aiming to conduct H5N1 surveillance efforts.

  View details for DOI 10.3201/eid3113.250087

  View details for PubMedID 40138725

  View details for PubMedCentralID PMC12078538

• Ensuring Biosecurity and Research Agility for Outbreak Response: A Researcher's Perspective on the Federal Nucleic Acid Screening Framework APPLIED BIOSAFETY Siddiqui, S. M., Arizti-Sanz, J., Rao, A. S., Ozonoff, A., Sabeti, P. C. 2025; 30 (3): 211-216

  Abstract

  The Framework for Nucleic Acid Synthesis Screening (FNASS), introduced by the U.S. White House Office of Science and Technology Policy, establishes new biosecurity measures to address emerging concerns about the potential misuse of synthetic nucleic acid sequences. While these measures are crucial for preventing misuse, they could potentially impede rapid response during infectious disease outbreaks, where swift access to synthetic nucleic acids is essential for developing diagnostics and therapeutics. This paper analyzes the framework's implications for outbreak response capabilities and proposes six practical solutions to maintain research agility without compromising biosecurity: pre-verification of outbreak first responders, priority emergency processing channels, pre-approval of standard countermeasure sequences, optimized computational screening, proactive training programs, and establishment of evaluation metrics. We recommend implementing these solutions through a hybrid approach combining federal support and public-private partnerships, ensuring both robust security measures and rapid emergency response capabilities as the framework's April 2025 implementation approaches.

  View details for DOI 10.1089/apb.2024.0063

  View details for Web of Science ID 001423431400001

  View details for PubMedID 40927142

  View details for PubMedCentralID PMC12415158

• CRISPR-Based Assays for Point-of-Need Detection and Subtyping of Influenza. The Journal of molecular diagnostics : JMD Zhang, Y. B., Arizti-Sanz, J., Bradley, A., Huang, Y., Kosoko-Thoroddsen, T. F., Sabeti, P. C., Myhrvold, C. 2024; 26 (7): 599-612

  Abstract

  The high disease burden of influenza virus poses a significant threat to human health. Optimized diagnostic technologies that combine speed, sensitivity, and specificity with minimal equipment requirements are urgently needed to detect the many circulating species, subtypes, and variants of influenza at the point of need. Here, we introduce such a method using Streamlined Highlighting of Infections to Navigate Epidemics (SHINE), a clustered regularly interspaced short palindromic repeats (CRISPR)-based RNA detection platform. Four SHINE assays were designed and validated for the detection and differentiation of clinically relevant influenza species (A and B) and subtypes (H1N1 and H3N2). When tested on clinical samples, these optimized assays achieved 100% concordance with quantitative RT-PCR. Duplex Cas12a/Cas13a SHINE assays were also developed to detect two targets simultaneously. This study demonstrates the utility of this duplex assay in discriminating two alleles of an oseltamivir resistance (H275Y) mutation as well as in simultaneously detecting influenza A and human RNAse P in patient samples. These assays have the potential to expand influenza detection outside of clinical laboratories for enhanced influenza diagnosis and surveillance.

  View details for DOI 10.1016/j.jmoldx.2024.04.004

  View details for PubMedID 38901927

  View details for PubMedCentralID PMC12178390

• Simplified Cas13-based assays for the fast identification of SARS-CoV-2 and its variants. Nature biomedical engineering Arizti-Sanz, J., Bradley, A., Zhang, Y. B., Boehm, C. K., Freije, C. A., Grunberg, M. E., Kosoko-Thoroddsen, T. F., Welch, N. L., Pillai, P. P., Mantena, S., Kim, G., Uwanibe, J. N., John, O. G., Eromon, P. E., Kocher, G., Gross, R., Lee, J. S., Hensley, L. E., MacInnis, B. L., Johnson, J., Springer, M., Happi, C. T., Sabeti, P. C., Myhrvold, C. 2022; 6 (8): 932-943

  Abstract

  The widespread transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) call for rapid nucleic acid diagnostics that are easy to use outside of centralized clinical laboratories. Here we report the development and performance benchmarking of Cas13-based nucleic acid assays leveraging lyophilised reagents and fast sample inactivation at ambient temperature. The assays, which we named SHINEv.2 (for 'streamlined highlighting of infections to navigate epidemics, version 2'), simplify the previously reported RNA-extraction-free SHINEv.1 technology by eliminating heating steps and the need for cold storage of the reagents. SHINEv.2 detected SARS-CoV-2 in nasopharyngeal samples with 90.5% sensitivity and 100% specificity (benchmarked against the reverse transcription quantitative polymerase chain reaction) in less than 90 min, using lateral-flow technology and incubation in a heat block at 37 °C. SHINEv.2 also allows for the visual discrimination of the Alpha, Beta, Gamma, Delta and Omicron SARS-CoV-2 variants, and can be run without performance losses by using body heat. Accurate, easy-to-use and equipment-free nucleic acid assays could facilitate wider testing for SARS-CoV-2 and other pathogens in point-of-care and at-home settings.

  View details for DOI 10.1038/s41551-022-00889-z

  View details for PubMedID 35637389

  View details for PubMedCentralID PMC9398993

• Biosecurity risks and governance in the age of synthetic biology MIT Science Policy Review Arizti Sanz, J., Dunlap, G., Nolan, N., O'Leary, C. 2022

  View details for DOI 10.38105/spr.x3nlyr0fkc

• Streamlined inactivation, amplification, and Cas13-based detection of SARS-CoV-2. Nature communications Arizti-Sanz, J., Freije, C. A., Stanton, A. C., Petros, B. A., Boehm, C. K., Siddiqui, S., Shaw, B. M., Adams, G., Kosoko-Thoroddsen, T. F., Kemball, M. E., Uwanibe, J. N., Ajogbasile, F. V., Eromon, P. E., Gross, R., Wronka, L., Caviness, K., Hensley, L. E., Bergman, N. H., MacInnis, B. L., Happi, C. T., Lemieux, J. E., Sabeti, P. C., Myhrvold, C. 2020; 11 (1): 5921

  Abstract

  The COVID-19 pandemic has highlighted that new diagnostic technologies are essential for controlling disease transmission. Here, we develop SHINE (Streamlined Highlighting of Infections to Navigate Epidemics), a sensitive and specific diagnostic tool that can detect SARS-CoV-2 RNA from unextracted samples. We identify the optimal conditions to allow RPA-based amplification and Cas13-based detection to occur in a single step, simplifying assay preparation and reducing run-time. We improve HUDSON to rapidly inactivate viruses in nasopharyngeal swabs and saliva in 10 min. SHINE's results can be visualized with an in-tube fluorescent readout - reducing contamination risk as amplification reaction tubes remain sealed - and interpreted by a companion smartphone application. We validate SHINE on 50 nasopharyngeal patient samples, demonstrating 90% sensitivity and 100% specificity compared to RT-qPCR with a sample-to-answer time of 50 min. SHINE has the potential to be used outside of hospitals and clinical laboratories, greatly enhancing diagnostic capabilities.

  View details for DOI 10.1038/s41467-020-19097-x

  View details for PubMedID 33219225

  View details for PubMedCentralID PMC7680145