Highly Conserve Sequences in Envelope, Nucleoprotein and RNA-Dependent RNA Polymerase of SARS-CoV-2 in Nasopharyngeal Samples of the COVID-19 Patients; a Diagnostic Target for Further Studies
| Author | Mohammad Saeid Emadi | en |
| Author | Saber Soltani | en |
| Author | Bezhan Noori | en |
| Author | milad zandi | en |
| Author | Zainab Shateri | en |
| Author | Alireza Tabibzadeh | en |
| Author | Emad Behboudi | en |
| Author | Yousef Erfani | en |
| Author | Seidamir Pasha Tabaeian | en |
| Author | Behzad Pourhossein | en |
| Author | Mojtaba Didehdar | en |
| Orcid | Mohammad Saeid Emadi [0000-0001-6920-3162] | en |
| Orcid | Saber Soltani [0000-0003-3369-0856] | en |
| Orcid | Alireza Tabibzadeh [0000-0003-0070-2208] | en |
| Orcid | Mojtaba Didehdar [0000-0003-4677-4768] | en |
| Issued Date | 2022-06-30 | en |
| 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. | en |
| DOI | https://doi.org/10.22037/jcma.v7i2.36963 | en |
| Keyword | SARS-CoV-2 | en |
| Keyword | COVID-19 | en |
| Keyword | Mutation | en |
| Keyword | Phylogenetic | en |
| Publisher | Brieflands | en |
| Title | Highly Conserve Sequences in Envelope, Nucleoprotein and RNA-Dependent RNA Polymerase of SARS-CoV-2 in Nasopharyngeal Samples of the COVID-19 Patients; a Diagnostic Target for Further Studies | en |
| Type | Original Articles | en |
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