Document Type : Original Article
Authors
1
Department of Medical Techniques, Faculty of Health and Medical Techniques, Middle Technical University, Baghdad, Iraq
2
Otolaryngologist, ENT department, Al-Furat General Hospital, Iraq
3
community medicine, Public health department , Al-Furat General Hospital, Iraq
Abstract
Background: COVID-19 is caused by the novel virus SARS-CoV-2, which led to an unexpected worldwide pandemic. Numerous researchers worldwide have strived to achieve genome sequencing of the virus and share highly conservative data about Covid-19 genome with very few mutations and no recombination. Methods: Tthis study was carried out to align eleven genomes sequence (29000) of SARS-CoV-2 from different countries (Iraq, Turkey, Iran, Jordan, Egypt, Morocco, India and china) and (Basra, Erbil) with a reference genome called Covid virus in NCBI by using many software (MAFFT, Genome detective, Next clade, Neighbor joining for all existing alignments and estimate a relationship between them. Results: Results of MAFFT alignment for the sequence of SARS-CoV-2 genome found that the 11 sample had a nucleotide identity comparable to 99 with reference genome. While the results of mutation rate indicated that many variations between these sequences and indicated high rate of mutation for Egypt, china, Iraq, Erbil, Iran, India, Morocco, Basra, Turkey and Jordan, with most frequent mutation 23403A>G. While the phylogenic tree found the all “SARS-CoV-2” sequences accumulated in a different clade, Sequences from a variety of nations were found in some big clades. Although there were some mutation in low frequencies, with common mutation D614G found in most sequence (Iraq, Erbil, Turkey, Jordan, Egypt, Morocco, India and china). This mutation makes a virus transmit more efficiently and 10-fold higher aggressive than the original Chinese strain. Followed by the second most frequent mutation L452R indicates that the binding to the selected monoclonal antibody (mAb) is reduced and may affect their neutralization potential. Conclusion: The S protein of the delta and kappa variants demonstrated improved viral replication kinetics when compared to the wild-type virus.All these data should be considered for developing vaccines and antiviral treatment strategies and tracking the diversity of viruses around the world. The initial candidates for the COVID-19 vaccine were developed to specifically target the D614 sequence position of the SARS-CoV-2 virus, the efficacy of the existing antibodies and vaccines may be carefully tested with the G614 variant, immunogenicity and protective efficacy of a DNA vaccine encoding spike protein with D614G mutation were tested. A segment of nucleic acid-based, vectored, protein subunit vaccines was developed utilizing the S protein of SARS-CoV-2, incorporating these specific mutations.
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