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ORIGINAL RESEARCH article

Front. Microbiol.
Sec. Virology
Volume 15 - 2024 | doi: 10.3389/fmicb.2024.1459644

A rapid point-of-care population-scale dipstick assay to identify and differentiate SARS-CoV-2 variants in COVID-19-positive patients

Provisionally accepted
Dr. Deepjyoti Paul Dr. Deepjyoti Paul 1Jyoti Verma Jyoti Verma 1Shakti Kumar Shakti Kumar 1Daizee Talukdar Daizee Talukdar 1Pradipta Jana Pradipta Jana 1Lekshmi Narendrakumar Lekshmi Narendrakumar 1Roshan Kumar Roshan Kumar 1Subhash Tanwar Subhash Tanwar 1Mudita Gosain Mudita Gosain 1Sonali Porey Karmakar Sonali Porey Karmakar 1Madhu Pareek Madhu Pareek 1Shailendra Mani Shailendra Mani 1Susmita Chaudhuri Susmita Chaudhuri 1Pallavi Kshetrapal Pallavi Kshetrapal 1Nitya Wadhwa Nitya Wadhwa 1Shinjini Bhatnagar Shinjini Bhatnagar 1Pramod K. Garg Pramod K. Garg 2Bhabatosh Das Bhabatosh Das 1*
  • 1 Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India
  • 2 All India Institute of Medical Sciences, New Delhi, National Capital Territory of Delhi, India

The final, formatted version of the article will be published soon.

    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.

    Keywords: SARS-CoV-2, COVID-19, Next-generation sequencing, Multiplex-PCR, Dipstick assay, Rapid detection

    Received: 04 Jul 2024; Accepted: 09 Oct 2024.

    Copyright: © 2024 Paul, Verma, Kumar, Talukdar, Jana, Narendrakumar, Kumar, Tanwar, Gosain, Porey Karmakar, Pareek, Mani, Chaudhuri, Kshetrapal, Wadhwa, Bhatnagar, Garg and Das. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Bhabatosh Das, Translational Health Science and Technology Institute (THSTI), Faridabad, 122016, Haryana, India

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.