Global impact of COVID-19 pandemic has heightened the urgency for efficient virus detection and identification of variants such as the Q57H mutation. Early and efficient detection of SARS-CoV-2 among densely populated developing countries is paramount objective. Although RT-PCR assays offer accuracy, however, dependence on expansive kits and availability of allied health resources pose an immense challenge for developing countries. In the current study, RT-LAMP based detection of SARS-Cov-2 with subsequent confirmation of Q57H variant through ARMS-PCR was performed. Among the 212 collected samples, 134 yielded positive results, while 78 tested negative using RT-LAMP. Oropharyngeal swabs of suspected individuals were collected and processed for viral RNA isolation. Isolated viral RNA was processed further by using either commercially available WarmStart Master Mix or our in house developed LAMP master mix separately. Subsequently, the end results of each specimen were evaluated by colorimetry. For LAMP assays, primers targeting three genes (ORF1ab, N and S) were designed using PrimerExplorer software. Interestingly, pooling of these three genes in single reaction tube increased sensitivity (95.5%) and specificity (93.5%) of LAMP assay. SARS-CoV-2 positive specimens were screened further for Q57H mutation using ARMS-PCR. Based on amplicon size variation, later confirmed by sequencing, our data showed 18.5% samples positive for Q57H mutation. Hence, these findings strongly advocate use of RT-LAMP-based assay for SARS-CoV-2 screening within suspected general population. Furthermore, ARMS-PCR also provides an efficient mean to detect prevalent mutations against SARS-Cov-2.

Centre of Medical and Bio Allied Health Sciences Research Ajman University Ajman 13306 United Arab Emirates

Department of Biosciences COMSATS University Islamabad Islamabad Pakistan

Department of Microbiology Faculty of Medicine Umm Al Qura University Makkah Saudi Arabia

Department of Molecular Biology Shaheed Zulfiqar Ali Bhutto Medical University Islamabad Pakistan

Department of Virology National Institute of Health Islamabad Pakistan

Gilbert and Rose Marie Chagoury School of Medicine Lebanese American University Beirut 1102 2801 Lebanon

Laboratory Medicine Department Faculty of Applied Medical Sciences Umm Al Qura University PO Box 7607 Makkah Al Abdeyah Saudi Arabia

Laboratory of Animal Immunology and Biotechnology Department of Animal Morphology Physiology and Genetics Faculty of AgriSciences Mendel University in Brno Brno 61300 Czech Republic

Master Program on Clinical Epidemiology and Biostatistics Faculty of Health Sciences Universidad Científica del Sur Lima 15046 Peru

Molecular Diagnostic Unit Clinical Pathology Department PAEC General Hospital Islamabad Pakistan

Research and Scientific Studies Unit College of Nursing and Health Sciences Jazan University Jazan 45142 Saudi Arabia

Research Unit Universidad Continental Huancayo 12000 Peru

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