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journal article·2025-07Open access

A Smart Single‐Loop‐Mediated Isothermal Amplification Facilitates Flexible SNP Probe Design for On‐Site Rapid Differentiation of SARS‐CoV‐2 Omicron Variants

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

Advanced Science· Volume 12· Issue 26
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Source abstract

Abstract

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.
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Research context

OpenAlex topics: Biosensors and Analytical Detection · Advanced biosensing and bioanalysis techniques · SARS-CoV-2 detection and testing

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

Affiliations

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

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

Key Laboratory of Agricultural Information Acquisition Technology Ministry of Agriculture and Rural Affairs China Agricultural University Beijing 100083 China

Department 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 China

Department of Biological and Agricultural Engineering Center of Excellence for Poultry Science University of Arkansas Fayetteville AR 72701 USA

Changchun Veterinary Research Institute Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses Chinese Academy of Medical Sciences Changchun 130062 China

College of Animal Science and Technology Zhongkai University of Agriculture and Engineering Guangzhou 510225 China

Funding

National Key Research and Development Program of China · Fundamental Research Funds for the Central Universities

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