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Herein, a smart single\u2010loop\u2010mediated isothermal amplification (ssLAMP) method with the absence of an inner primer but the addition of a swarm primer for differentiation of SARS\u2010CoV\u20102 Omicron variants is developed. This unique primer design strategy offers greater flexibility in introducing single nucleotide polymorphism (SNP) identification probes and enables multiple detection assays for SARS\u2010CoV\u20102 Omicron variants including BA.1, BA.2, BA.3, BA.4, and BA.5. A 3D\u2010printed portable dual fluorescence visualization device and smartphone app are developed to enable point\u2010of\u2010care testing. This assay is rapid (within 90\u00a0min), highly sensitive (100 copies\/reaction), and specific (identification of SNP) for SARA\u2010CoV\u20102 Omicron variants. The ssLAMP method identifies five BA.5\u2010positive samples among 97 nasopharyngeal swab samples from the clinic, with a 100% concordance rate with Sanger sequencing. The ssLAMP assay system is expected to be utilized for on\u2010site, highly specific, and rapid visualization detection of SARS\u2010CoV\u20102 and its variants, with great application potential in pathogen genotyping, early cancer screening, and other areas of SNP mutation detection.<\/jats:p>","DOI":"10.1002\/advs.202502708","type":"journal-article","created":{"date-parts":[[2025,4,2]],"date-time":"2025-04-02T11:06:09Z","timestamp":1743591969000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["A Smart Single\u2010Loop\u2010Mediated Isothermal Amplification Facilitates Flexible SNP Probe Design for On\u2010Site Rapid Differentiation of SARS\u2010CoV\u20102 Omicron Variants"],"prefix":"10.1002","volume":"12","author":[{"given":"Qijie","family":"Lin","sequence":"first","affiliation":[{"name":"National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control Key Laboratory of Zoonoses Ministry of Agriculture Key Laboratory of Zoonoses Prevention and Control of Guangdong Province Animal Infectious Diseases Laboratory College of Veterinary Medicine South China Agricultural University  Guangzhou 510642 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongchao","family":"Gou","sequence":"additional","affiliation":[{"name":"Guangdong Provincial Key Laboratory of Livestock Disease Prevention Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province Institute of Animal Health Guangdong Academy of Agricultural Sciences  Guangzhou 510640 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoyun","family":"Qu","sequence":"additional","affiliation":[{"name":"National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control Key Laboratory of Zoonoses Ministry of Agriculture Key Laboratory of Zoonoses Prevention and Control of Guangdong 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