High prevalence of an alpha variant lineage with a premature stop codon in ORF7a in Iraq, winter 2020-2021

Since the first reported case of coronavirus disease 2019 (COVID-19) in China, SARS-CoV-2 has been spreading worldwide. Genomic surveillance of SARS-CoV-2 has had a critical role in tracking the emergence, introduction, and spread of new variants, which may affect transmissibility, pathogenicity, and escape from infection or vaccine-induced immunity. As anticipated, the rapid increase in COVID-19 infections in Iraq in February 2021 is due to the introduction of variants of concern during the second wave of the COVID-19 pandemic. To understand the molecular epidemiology of SARS-CoV-2 during the second wave in Iraq (2021), we sequenced 76 complete SARS-CoV-2 genomes using NGS technology and identified genomic mutations and proportions of circulating variants among these. Also, we performed an in silico study to predict the effect of the truncation of NS7a protein (ORF7a) on its function. We detected nine different lineages of SARS-CoV-2. The B.1.1.7 lineage was predominant (80.20%) from February to May 2021, while only one B.1.351 strain was detected. Interestingly, the phylogenetic analysis showed that multiple strains of the B.1.1.7 lineage clustered closely with those from European countries. A notable frequency (43.33%) of stop codon mutation (NS7a Q62stop) was detected among the B.1.1.7 lineage sequences. In silico analysis of NS7a with Q62stop found that this stop codon had no considerable effect on the function of NS7a. This work provides molecular epidemiological insights into the spread variants of SARS-CoV-2 in Iraq, which are most likely imported from Europe.

Automated summary

Since the first reported case of COVID-19 in China, SARS-CoV-2 has been spreading globally. Genomic surveillance plays a crucial role in tracking the emergence, introduction, and spread of new variants. The rapid increase in COVID-19 infections in Iraq during the second wave is attributed to the introduction of concern variants, likely imported from Europe. Molecular epidemiological analysis revealed the dominance of the B.1.1.7 lineage in Iraq, with multiple strains closely related to those from European countries. A notable frequency of stop codon mutation was observed among the B.1.1.7 lineage sequences, but it didn't significantly affect the function of NS7a protein.