SARS-COV-2 RBD (Receptor binding domain) mutations and variants (A sectional-analytical study)

Hajazadeh, Faezeh and Khanizadeh, Sayyad and Khodadadi, Hamidreza and Mokhayeri, Yaser and Ajorloo, Mehdi and Malekshahi, Asra and Heydari, Ezatoallah (2022) SARS-COV-2 RBD (Receptor binding domain) mutations and variants (A sectional-analytical study). Microb Pathog.

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Abstract

An essential step in SARS-CoV-2 infection is binding the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein to the ACE2 receptor on the surface of host cells. Therefore, variation in this region can have crucial effects on clinical outcomes and the emergence of variants of concern (VOCs) and variants of interest (VOIs). In this cross-sectional descriptive study, 54 patients with SARS-COV-2 infection were enrolled. After collecting samples and identifying the virus using the One-Step Real-Time qRT-PCR technique and confirming the viral infection, the region containing the RBD region for detection of any mutations was amplified using the Nested-PCR method. Finally, to identify probable mutations, the Nested-PCR product was sequenced. Our data show that the most mutant strains in circulation in our population are the delta variant (90.74%), alpha variant (5.56%), and omicron variant (3.70%), respectively. Pangolin Lineages strains were B.1.1.7(Alpha variant), B.1.617.2(Delta variant) and B.1.1.529(Omicron variant). Also, the mutation profile of variants suggests that N501Y, T478K, and D614G amino acid substitutions, are the significant mutations in the alpha and delta variants that are common with the Omicron variant. The highest frequency of clinical signs in the patients were: lung involvement (42.59%); fever, chills (40.74%); body pain (15%), and other signs (1.67%). Our data revealed that SARS-COV-2 RBD region variation results in substituting essential amino acids and the emergence of the new variant. We can consider it as a predictor for monitoring the emergence of variants of concerns and viral outcomes.

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