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

Mohammad Saeid Emadi; Saber Soltani; Bezhan  Noori; milad zandi; Zainab Shateri; Alireza Tabibzadeh; Emad Behboudi; Yousef Erfani; Seidamir Pasha Tabaeian; Behzad Pourhossein; Mojtaba Didehdar

doi:10.22037/jcma.v7i2.36963

Journal of Cellular & Molecular Anesthesia

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https://doi.org/10.22037/jcma.v7i2.36963

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(s):

Mohammad Saeid Emadi

^1,*,

Saber Soltani

²,

Bezhan Noori³,

milad zandi³,

Zainab Shateri⁴,

Alireza Tabibzadeh

²,

Emad Behboudi⁵,

Yousef Erfani¹,

Seidamir Pasha Tabaeian⁶,

Behzad Pourhossein⁷,

Mojtaba Didehdar

⁸

1Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Tehran University Medical Sciences, Tehran, Iran

2Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran

3Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran

4Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran

5Department of Microbiology, Golestan University of Medical Sciences, Gorgan, Iran

6Department of Internal Medicine, School of Medicine, Iran University of Medical Sciences, Tehran, Iran

7Core Fasility, Deputy of Research & Technology, Hamadan University of Medical Sciences, Hamadan, Iran

8Department of Medical Parasitology and Mycology, Arak University of Medical Sciences, Arak, Iran

Journal of Cellular & Molecular Anesthesia:Vol. 7, issue 2; e149707

Published online:Feb 10, 2022

Article type:Original Articles

How to Cite:Mohammad Saeid EmadiSaber SoltaniBezhan Noorimilad zandiZainab ShateriAlireza TabibzadehEmad BehboudiYousef ErfaniSeidamir Pasha TabaeianBehzad PourhosseinMojtaba Didehdaret al.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.J Cell Mol Anesth.7(2):e149707.https://doi.org/10.22037/jcma.v7i2.36963.

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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Author(s):

Mohammad Saeid Emadi:[PubMed][Scholar]
Saber Soltani:[PubMed][Scholar]
Bezhan Noori:[PubMed][Scholar]
milad zandi:[PubMed][Scholar]
Zainab Shateri:[PubMed][Scholar]
Alireza Tabibzadeh:[PubMed][Scholar]
Emad Behboudi:[PubMed][Scholar]
Yousef Erfani:[PubMed][Scholar]
Seidamir Pasha Tabaeian:[PubMed][Scholar]
Behzad Pourhossein:[PubMed][Scholar]
Mojtaba Didehdar:[PubMed][Scholar]