1. A rapid point-of-care population-scale dipstick assay to identify and differentiate SARS-CoV-2 variants in COVID-19-positive patients
- Author
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Deepjyoti Paul, Jyoti Verma, Shakti Kumar, Daizee Talukdar, Pradipta Jana, Lekshmi Narendrakumar, Roshan Kumar, Subhash Tanwar, Mudita Gosain, Sonali Porey Karmakar, Madhu Pareek, Shailendra Mani, Susmita Chaudhuri, Pallavi Kshetrapal, Nitya Wadhwa, Shinjini Bhatnagar, Pramod Kumar Garg, and Bhabatosh Das
- Subjects
SARS-CoV-2 ,COVID-19 ,next-generation sequencing ,multiplex-PCR ,dipstick assay ,rapid detection ,Microbiology ,QR1-502 - Abstract
Delta and Omicron variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) are remarkably contagious, and have been recognized as variants of concern (VOC). The acquisition of spontaneous substitutions or insertion–deletion mutations (indels) in the spike protein-encoding gene substantially increases the binding affinity of the receptor binding domain (RBD)-hACE2 complex and upsurges the transmission of both variants. In this study, we analyzed thousands of genome sequences from 30 distinct SARS-CoV-2 variants, focusing on the unique nucleic acid signatures in the spike gene specific to the Delta and Omicron variants. Using these variant-specific sequences, we synthesized a range of oligonucleotides and optimized a multiplex PCR (mPCR) assay capable of accurately identifying and differentiating between the Delta and Omicron variants. Building on this mPCR assay, we developed a dipstick format by incorporating a tag linker sequence at the 5′ end of the forward primer and adding biotin to the 3′ end of the oligonucleotides, enhancing the assay’s usability and accessibility. Streptavidin-coated latex beads and the dipstick imprinted with a probe for the tag linker sequence in the test strips were used for the detection assay. Our dipstick-based assay, developed as a rapid point-of-care test for identifying and differentiating SARS-CoV-2 variants has the potential to be used in low-resource settings and scaled up to the population level.
- Published
- 2024
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