Abstract
Background: The etiological agent of COVID-19 is SARS-CoV-2. Conversional molecular methods used for detection of virus in COVID-19 infected patient. This study aimed to investigate the presence of escape mutations from molecular detection on SARS-CoV-2 targeted genes, which indicates importance of mutations in false negative PCR test results in detection of virus in clinical specimens of patients with COVID-19. Material and Method: The 20 nasopharyngeal swabs samples collected from COVID-19 confirmed patients. The SARS-CoV-2 E, nsp12 and N genetic regions Amplified by RT-PCR assay. PCR products sequenced using the Sanger sequencing method and Multiple sequence alignment for the assessment of the polymorphism and mutations preformed using MEGA X software and Maximum likelihood method for the phylogenetic assessment. Result: Among all COVID-19 cases 60% and 40% were male and female, respectively. The MSA showed high conservation between all of the evaluated samples and VOCs in all N, E and nsp12 genes. Also, the phylogenetic evaluation by Maximum likelihood method reported high similarity between all SARS-CoV-2 sequenced samples, VOCs and Wuhan reference sequence in evaluated region. Conclusion: Our study results approved the relatively conserved suitability of the E, N and RdRp-gene regions without any diversity, therefore, making them perfect candidates for first-line screening.
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Copyright
© 2022, Author(s). This open-access article is available under the Creative Commons Attribution 4.0 (CC BY 4.0) International License (https://creativecommons.org/licenses/by/4.0/), which allows for unrestricted use, distribution, and reproduction in any medium, provided that the original work is properly cited.