Genomic Surveillance of SARS-Cov-2 in Iraq and In Silico Prediction of the Effect of Amino Acid Changes on the Protein Function

Abstract

    The emergence and rapid outbreak of novel coronavirus-19 show the significance of viral genomic surveillance, which provides a key insight into the tracking and pathogenicity of this infectious disease. Although data of complete genome sequences of SARS-CoV-2 is important to monitor the spreading of the ongoing pandemic, the number of genome sequences from Iraq is still limited to date. However, our efforts have been focused on establishing the first Iraqi genomic surveillance. The whole-genome sequences were uploaded from GISAID EpiCoV database to perform phylogenetic analysis and to investigate the effect of some amino acid variations on protein stability and function. The model structure of the mutant spike (A522V) was built and then used in molecular docking to assess binding affinity toward ACE-2 receptor and compared to Wuhan Spike protein sequence as wild type. The phylogenetic analysis was revealed that most of the genome sequences of the Iraqi isolates belonged to clades GH (GISAID), B.1 (Pangolin) and 20C (Nextstrain). Furthermore, the common variations D614G (spike), Q57H (NS3) and P323L (NSP12) were detected in high frequency. Moreover, there was no novel amino acid variation and most of them were found to be stabilizing the proteins of SARS-CoV-2. It has been noticed that the amino acid variation A522V has no significant effect on spike-ACE2 interactions. Finally, SARS-CoV-2 in Iraq is still virulent and has not been attenuated by the reported mutations until this time.