{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T20:51:10Z","timestamp":1790628670328,"version":"4.1.0"},"reference-count":167,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2025,8,15]],"date-time":"2025-08-15T00:00:00Z","timestamp":1755216000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Intramural Research Program of the NIH, National Institute of Environmental Health Sciences","award":["1ZIAES103310"],"award-info":[{"award-number":["1ZIAES103310"]}]},{"name":"Intramural Research Program of the NIH, National Institute of Environmental Health Sciences","award":["1ZICES102506"],"award-info":[{"award-number":["1ZICES102506"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>The COVID-19 pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), catalyzed unprecedented innovation in molecular diagnostics to address critical gaps in rapid pathogen detection. Over the past five years, CRISPR-based systems, isothermal amplification techniques, and portable biosensors have emerged as transformative tools for nucleic acid detection, offering improvements in speed, sensitivity, and point-of-care applicability compared to conventional PCR. While numerous reviews have cataloged the technical specifications of these platforms, a critical gap remains in understanding the strategic and economic hurdles to their real-world implementation. This review provides a forward-looking analysis of the feasibility, scalability, and economic benefits of integrating these next-generation technologies into future pandemic-response pipelines. We synthesize advances in coronavirus-specific diagnostic platforms and attempt to highlight the need for their implementation as a cost-saving measure during surges in clinical demand. We evaluate the feasibility of translating these technologies\u2014particularly CRISPR-Cas integration with recombinase polymerase amplification (RPA)\u2014into robust first-line diagnostic pipelines for novel viral threats. By analyzing the evolution of diagnostic strategies during the COVID-19 era, we aim to provide strategic insights and new directions for developing and deploying effective detection platforms to better confront future viral pandemics.<\/jats:p>","DOI":"10.3390\/microorganisms13081905","type":"journal-article","created":{"date-parts":[[2025,8,15]],"date-time":"2025-08-15T14:24:28Z","timestamp":1755267868000},"page":"1905","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Next-Generation Nucleic Acid-Based Diagnostics for Viral Pathogens: Lessons Learned from the SARS-CoV-2 Pandemic"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2144-2441","authenticated-orcid":false,"given":"Amy","family":"Papaneri","sequence":"first","affiliation":[{"name":"In Vivo Neurobiology Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC 27709, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4555-028X","authenticated-orcid":false,"given":"Guohong","family":"Cui","sequence":"additional","affiliation":[{"name":"In Vivo Neurobiology Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC 27709, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5853-6903","authenticated-orcid":false,"given":"Shih-Heng","family":"Chen","sequence":"additional","affiliation":[{"name":"Viral Vector Core Facility, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC 27709, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,8,15]]},"reference":[{"key":"ref_1","unstructured":"Mathieu, E., Ritchie, H., Rod\u00e9s-Guirao, L., Appel, C., Gavrilov, D., Giattino, C., Hasell, J., Macdonald, B., Dattani, S., and Beltekian, D. 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