{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T06:08:59Z","timestamp":1775628539002,"version":"3.50.1"},"reference-count":23,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T00:00:00Z","timestamp":1775606400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>The recurrent threat of respiratory infectious disease outbreaks creates an urgent need for diagnostic tests that are rapid, portable, and user-friendly, applicable across diverse settings\u2014from central laboratories and hospitals to field deployments, resource-limited regions, and home use.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>In response, we developed three novel nucleic acid detection platforms\u2014RT-RAA-MPs, RT-RAA-F-PfAgo, and RT-RAA-L-PfAgo\u2014that integrate reverse transcription-recombinase-aided amplification (RT-RAA) with distinct instrument-free readout mechanisms. These systems utilize custom-designed primers and guide DNA (gDNA) targeting the SARS-CoV-2\u202fN and ORF genes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Performance evaluation demonstrated high analytical sensitivity, with detection limits of 10\n                      <jats:sup>2<\/jats:sup>\n                      copies\/\u03bcL for RT-RAA-MPs and 5 copies\/\u03bcL for both RT-RAA-F-PfAgo and RT-RAA-L-PfAgo. All assays exhibited excellent specificity, showing no cross-reactivity with nine common respiratory pathogens. Clinical validation using 23 patient samples revealed perfect agreement with RT-qPCR (100% concordance), supported by a Kappa value of 1.00, indicating outstanding diagnostic consistency and statistical robustness.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>With lyophilized reagent compatibility and minimal equipment requirements, these platforms are readily adaptable for a wide range of applications, including clinical diagnosis at all hospital levels, point-of-care screening, border control inspection, and environmental monitoring. This work establishes a versatile, reliable, and deployable toolkit for effective outbreak response and decentralized molecular diagnostics.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmicb.2026.1792924","type":"journal-article","created":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T05:32:08Z","timestamp":1775626328000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrating isothermal amplification with magnetic flocculation and DNA-guided PfAgo for SARS-CoV-2 detection"],"prefix":"10.3389","volume":"17","author":[{"given":"Xiaoxing","family":"Zhou","sequence":"first","affiliation":[{"name":"School of Clinical Medicine, Guilin Medical University","place":["Guilin, Guangxi, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mengru","family":"Xie","sequence":"additional","affiliation":[{"name":"The First Clinical Medical College, Guangxi Medicine University","place":["Nanning, Guangxi, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xia","family":"Yu","sequence":"additional","affiliation":[{"name":"Joint Inspection Center of Precision Medicine, The People\u2019s Hospital of Guangxi Zhuangzu Autonomous Region and Guangxi Academic of Medical Sciences","place":["Nanning, Guangxi, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leping","family":"Ning","sequence":"additional","affiliation":[{"name":"Clinical Laboratory, The People\u2019s Hospital of Guangxi Zhuangzu Autonomous Region and Guangxi Academic of Medical Sciences","place":["Nanning, Guangxi, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chao","family":"Ye","sequence":"additional","affiliation":[{"name":"Joint Inspection Center of Precision Medicine, The People\u2019s Hospital of Guangxi Zhuangzu Autonomous Region and Guangxi Academic of Medical Sciences","place":["Nanning, Guangxi, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yilian","family":"Zhao","sequence":"additional","affiliation":[{"name":"Joint Inspection Center of Precision Medicine, The People\u2019s Hospital of Guangxi Zhuangzu Autonomous Region and Guangxi Academic of Medical Sciences","place":["Nanning, Guangxi, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yan","family":"Wei","sequence":"additional","affiliation":[{"name":"Clinical Laboratory, The People\u2019s Hospital of Fengjie","place":["Chongqing, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinchu","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Clinical Medicine, Guilin Medical University","place":["Guilin, Guangxi, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinghui","family":"Ma","sequence":"additional","affiliation":[{"name":"The First Clinical Medical College, Guangxi Medicine University","place":["Nanning, Guangxi, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jilin","family":"Qing","sequence":"additional","affiliation":[{"name":"Center for Reproductive Medicine and Genetics, The People\u2019s Hospital of Guangxi Zhuangzu Autonomous Region and Guangxi Academic of Medical Sciences","place":["Nanning, Guangxi, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhencheng","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Electronic Engineering and Automation, Guilin University of Electronic Technology","place":["Guilin, Guangxi, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhizhong","family":"Chen","sequence":"additional","affiliation":[{"name":"Joint Inspection Center of Precision Medicine, The People\u2019s Hospital of Guangxi Zhuangzu Autonomous Region and Guangxi Academic of Medical Sciences","place":["Nanning, Guangxi, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2026,4,8]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"1187","DOI":"10.1039\/d4an01526f","article-title":"A steam-mediated isothermal amplification and flocculation-based detection platform for electricity-free point of care diagnostics","volume":"150","author":"Achary","year":"2025","journal-title":"Analyst"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"103465","DOI":"10.1016\/j.sjbs.2022.103465","article-title":"SARS-CoV-2 detection methods: a comprehensive review","volume":"29","author":"Alhamid","year":"2022","journal-title":"Saudi J. 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(Camb.)"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"608","DOI":"10.1016\/j.watres.2018.07.029","article-title":"Coagulation\/flocculation in dewatering of sludge: a review","volume":"143","author":"Wei","year":"2018","journal-title":"Water Res."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"120526","DOI":"10.1016\/j.cca.2025.120526","article-title":"Viral detection using clustered regularly interspaced short palindromic repeats\/CRISPR-associated protein and Argonaute nucleases","volume":"578","author":"Xu","year":"2026","journal-title":"Clin. Chim. Acta Int. J. Clin. Chem."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"2905","DOI":"10.1038\/s41467-021-23185-x","article-title":"A rapid, accurate, scalable, and portable testing system for COVID-19 diagnosis","volume":"12","author":"Xun","year":"2021","journal-title":"Nat. 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