OPEN READING FRAME 8 GENE SEQUENCE VARIATION OF CORONA VIRUS IN PATIENTS FROM ERBIL CITY, IRAQ

Abdulla Kamil Abdulla; Ruqaya Muammed  Gharib AL-Barzinji; Chato A. Taher

doi:10.46903/gjms/22.01.1499

OPEN READING FRAME 8 GENE SEQUENCE VARIATION OF CORONA VIRUS IN PATIENTS FROM ERBIL CITY, IRAQ

Abdulla Kamil Abdulla, Ruqaya Muammed Gharib AL-Barzinji, Chato A. Taher

Abstract

Background: The rapid rate of mutation of corona virus, which is a significant characteristic, suggests that as it moves across various habitats, the viral genome undergoes new alterations. The objective of this study was to analyze SARS-COV2 ORF8 gene sequence variation among patients in Erbil city.

Materials & Methods: During the period of January to December 2022, ten SARS-CoV-2 positive patients (4 female and 6 male), who were detected during the pandemic at Erbil central Laboratory aged (20-70) years enrolled in this cross-sectional study. The single strand RNA extracted from patients and transformed to double stranded complementary DNA. The primers (forward and reveres)- were designed by Bioinformatics program, (Primer3 Plus). Polymerase chain reaction amplification for ORF8 gene was carried out. The products ran on gel electrophoresis to visualize the DNA products. Each species was bi-directionally sequenced to get sequence of DNA strand according to forward primer. The sequence editing was analyzed using BLAST NCBI to indicate the homology from closest species. Phylogenetic tree was constructed.

Results: In comparing to the wild type that stated by NCBI (Genbank Reference accession number: OP732758.1) sequencing of our samples showed mutations at different position in which codon number 35 nucleotide A changed to C which results in replacement of an amino acid Aspartic Acid by Alanine, in addition to that in codon 69 nucleotide T changed to C as a consequence amino acid Serine change to Proline..

Conclusions: Sequence variation in viral ORF8 gene is regarded as the primary hotspot for genetic recombination and mutation of spike protein of SARS-CoV-2. Monitoring frequent nucleotide substitutions in ORF8 gene could be extremely helpful in understanding how the virus evolved in the community. Formation of new clades in Erbil city may have impact on vaccination program or the infectivity of the virus.

Keywords

SARS-CoV-2; ORF8; Spike protein; Mutation; Phylogenetic tree.

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DOI: https://doi.org/10.46903/gjms/22.01.1499