A Smart Single‐Loop‐Mediated Isothermal Amplification Facilitates Flexible SNP Probe Design for On‐Site Rapid Differentiation of SARS‐CoV‐2 Omicron Variants
Abstract Rapid on‐site typing methods for SARS‐CoV‐2 variants of concern are crucial for its effective surveillance and control. Herein, a smart single‐loop‐mediated isothermal amplification (ssLAMP) method with the absence of an inner primer but the addition of a swarm primer for differentiation of...
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| Format: | Article |
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Wiley
2025-07-01
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| Series: | Advanced Science |
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| Online Access: | https://doi.org/10.1002/advs.202502708 |
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| author | Qijie Lin Hongchao Gou Xiaoyun Qu Kaiyuan Jia Yuhui Deng Dan Li Qianyi Cai Yucen Liang Xiaozhen Xu Yanbin Li Jianhan Lin Letian Li Yuhang Jiang Shouwen Du Lingcong Deng Bailing Yan Ruidong Liu Chang Li Jianmin Zhang Ming Liao |
| author_facet | Qijie Lin Hongchao Gou Xiaoyun Qu Kaiyuan Jia Yuhui Deng Dan Li Qianyi Cai Yucen Liang Xiaozhen Xu Yanbin Li Jianhan Lin Letian Li Yuhang Jiang Shouwen Du Lingcong Deng Bailing Yan Ruidong Liu Chang Li Jianmin Zhang Ming Liao |
| author_sort | Qijie Lin |
| collection | DOAJ |
| description | Abstract Rapid on‐site typing methods for SARS‐CoV‐2 variants of concern are crucial for its effective surveillance and control. Herein, a smart single‐loop‐mediated isothermal amplification (ssLAMP) method with the absence of an inner primer but the addition of a swarm primer for differentiation of SARS‐CoV‐2 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‐CoV‐2 Omicron variants including BA.1, BA.2, BA.3, BA.4, and BA.5. A 3D‐printed portable dual fluorescence visualization device and smartphone app are developed to enable point‐of‐care testing. This assay is rapid (within 90 min), highly sensitive (100 copies/reaction), and specific (identification of SNP) for SARA‐CoV‐2 Omicron variants. The ssLAMP method identifies five BA.5‐positive 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‐site, highly specific, and rapid visualization detection of SARS‐CoV‐2 and its variants, with great application potential in pathogen genotyping, early cancer screening, and other areas of SNP mutation detection. |
| format | Article |
| id | doaj-art-6467a5031e524f5d84b2bbdd20710965 |
| institution | Kabale University |
| issn | 2198-3844 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Wiley |
| record_format | Article |
| series | Advanced Science |
| spelling | doaj-art-6467a5031e524f5d84b2bbdd207109652025-08-20T03:36:45ZengWileyAdvanced Science2198-38442025-07-011226n/an/a10.1002/advs.202502708A Smart Single‐Loop‐Mediated Isothermal Amplification Facilitates Flexible SNP Probe Design for On‐Site Rapid Differentiation of SARS‐CoV‐2 Omicron VariantsQijie Lin0Hongchao Gou1Xiaoyun Qu2Kaiyuan Jia3Yuhui Deng4Dan Li5Qianyi Cai6Yucen Liang7Xiaozhen Xu8Yanbin Li9Jianhan Lin10Letian Li11Yuhang Jiang12Shouwen Du13Lingcong Deng14Bailing Yan15Ruidong Liu16Chang Li17Jianmin Zhang18Ming Liao19National 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 ChinaGuangdong 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 ChinaNational 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 ChinaKey Laboratory of Agricultural Information Acquisition Technology Ministry of Agriculture and Rural Affairs China Agricultural University Beijing 100083 ChinaNational 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 ChinaDepartment of Respiratory Medicine Center for Infectious Diseases and Pathogen Biology Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education State Key Laboratory for Zoonotic Diseases The First Hospital of Jilin University Changchun 130021 ChinaNational 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 ChinaNational 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 ChinaNational 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 ChinaDepartment of Biological and Agricultural Engineering Center of Excellence for Poultry Science University of Arkansas Fayetteville AR 72701 USAKey Laboratory of Agricultural Information Acquisition Technology Ministry of Agriculture and Rural Affairs China Agricultural University Beijing 100083 ChinaChangchun Veterinary Research Institute Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses Chinese Academy of Medical Sciences Changchun 130062 ChinaChangchun Veterinary Research Institute Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses Chinese Academy of Medical Sciences Changchun 130062 ChinaGuangdong 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 ChinaChangchun Veterinary Research Institute Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses Chinese Academy of Medical Sciences Changchun 130062 ChinaDepartment of Respiratory Medicine Center for Infectious Diseases and Pathogen Biology Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education State Key Laboratory for Zoonotic Diseases The First Hospital of Jilin University Changchun 130021 ChinaNational 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 ChinaChangchun Veterinary Research Institute Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses Chinese Academy of Medical Sciences Changchun 130062 ChinaNational 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 ChinaNational 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 ChinaAbstract Rapid on‐site typing methods for SARS‐CoV‐2 variants of concern are crucial for its effective surveillance and control. Herein, a smart single‐loop‐mediated isothermal amplification (ssLAMP) method with the absence of an inner primer but the addition of a swarm primer for differentiation of SARS‐CoV‐2 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‐CoV‐2 Omicron variants including BA.1, BA.2, BA.3, BA.4, and BA.5. A 3D‐printed portable dual fluorescence visualization device and smartphone app are developed to enable point‐of‐care testing. This assay is rapid (within 90 min), highly sensitive (100 copies/reaction), and specific (identification of SNP) for SARA‐CoV‐2 Omicron variants. The ssLAMP method identifies five BA.5‐positive 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‐site, highly specific, and rapid visualization detection of SARS‐CoV‐2 and its variants, with great application potential in pathogen genotyping, early cancer screening, and other areas of SNP mutation detection.https://doi.org/10.1002/advs.202502708nucleic acid amplificationSARS‐CoV‐2 variants of concernSNP detectionssLAMP |
| spellingShingle | Qijie Lin Hongchao Gou Xiaoyun Qu Kaiyuan Jia Yuhui Deng Dan Li Qianyi Cai Yucen Liang Xiaozhen Xu Yanbin Li Jianhan Lin Letian Li Yuhang Jiang Shouwen Du Lingcong Deng Bailing Yan Ruidong Liu Chang Li Jianmin Zhang Ming Liao A Smart Single‐Loop‐Mediated Isothermal Amplification Facilitates Flexible SNP Probe Design for On‐Site Rapid Differentiation of SARS‐CoV‐2 Omicron Variants Advanced Science nucleic acid amplification SARS‐CoV‐2 variants of concern SNP detection ssLAMP |
| title | A Smart Single‐Loop‐Mediated Isothermal Amplification Facilitates Flexible SNP Probe Design for On‐Site Rapid Differentiation of SARS‐CoV‐2 Omicron Variants |
| title_full | A Smart Single‐Loop‐Mediated Isothermal Amplification Facilitates Flexible SNP Probe Design for On‐Site Rapid Differentiation of SARS‐CoV‐2 Omicron Variants |
| title_fullStr | A Smart Single‐Loop‐Mediated Isothermal Amplification Facilitates Flexible SNP Probe Design for On‐Site Rapid Differentiation of SARS‐CoV‐2 Omicron Variants |
| title_full_unstemmed | A Smart Single‐Loop‐Mediated Isothermal Amplification Facilitates Flexible SNP Probe Design for On‐Site Rapid Differentiation of SARS‐CoV‐2 Omicron Variants |
| title_short | A Smart Single‐Loop‐Mediated Isothermal Amplification Facilitates Flexible SNP Probe Design for On‐Site Rapid Differentiation of SARS‐CoV‐2 Omicron Variants |
| title_sort | smart single loop mediated isothermal amplification facilitates flexible snp probe design for on site rapid differentiation of sars cov 2 omicron variants |
| topic | nucleic acid amplification SARS‐CoV‐2 variants of concern SNP detection ssLAMP |
| url | https://doi.org/10.1002/advs.202502708 |
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