Melting curve-based assay as an alternative technique for the accurate detection of SARS-CoV-2

Shima Aboutalebian; Somaye Mirzaaghaei; Hamed Fakhim; Sama Faramarzi; Somayeh Mousavi; Safiyeh Ghafel; Sahar Gholipour; Armin Farhang; Hossein Mirhendi; Mahnaz Nikaeen

doi:10.4103/abr.abr_87_21

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ORIGINAL ARTICLE

Year : 2022 | Volume : 11 | Issue : 1 | Page : 37

Melting curve-based assay as an alternative technique for the accurate detection of SARS-CoV-2

Shima Aboutalebian¹, Somaye Mirzaaghaei¹, Hamed Fakhim², Sama Faramarzi¹, Somayeh Mousavi¹, Safiyeh Ghafel³, Sahar Gholipour⁴, Armin Farhang⁵, Hossein Mirhendi⁶, Mahnaz Nikaeen⁷
¹ Department of Medical Parasitology and Mycology, School of Medicine, & Research Core Facilities Laboratory, Isfahan University of Medical Sciences, Isfahan, Iran
² Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
³ Department of Medical Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
⁴ Department of Environmental Health Engineering, Faculty of Health, Kashan University of Medical Sciences, Isfahan, Iran
⁵ Department of Pharmaceutical Biotechnology, School of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
⁶ Department of Medical Parasitology and Mycology, School of Medicine, & Research Core Facilities Laboratory, Isfahan University of Medical Sciences, Isfahan, Iran
⁷ Department of Environmental Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran

Correspondence Address:
Prof. Hossein Mirhendi
Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan
Iran

Source of Support: None, Conflict of Interest: None

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DOI: 10.4103/abr.abr_87_21

Background: Early and cost-effective diagnosis and monitoring of the infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are critically important to anticipate and control the disease. We aimed to set up a SYBR Green-based one-step real-time polymerase chain reaction (PCR) as a lower-cost alternative method to detect the virus. Materials and Methods: An in-house SYBR Green-based PCR assay targeting the envelope (E) and RNA-dependent RNA polymerase (RdRp) genes, was set up to diagnose the infection, and was compared with the reference probe-based PCR method. Results: When the commercial probe-based assay was considered as the reference method, SYBR Green-based PCR had a slightly lower sensitivity (81.98% and 86.25% for E and RdRp targets, respectively) and a good specificity (100% and 94.44% for E and RdRp targets, respectively). For both gene targets, three different melting temperature (Tm) patterns were found in the PCRs of the nasopharyngeal/oropharyngeal swab samples, but no size polymorphism was seen in agarose gel electrophoresis. Conclusion: Further studies to improvement of the assay are needed to make it an inexpensive and reliable tool for the diagnosis of COVID-19.

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