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

Abstract

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.

Chronic Fatigue, Depression and Anxiety Symptoms in Long COVID Are Strongly Predicted by Neuroimmune and Neuro-Oxidative Pathways Which Are Caused by the Inflammation during Acute Infection

“…It is also possible that different variants are associated with different long COVID symptoms, with the Alpha variant possibly exhibiting more mental health and cognitive symptoms than the original variant [ 108 ]. A few months (3–4) prior to the September–December 2021 recruitment of our long COVID patients, the Alpha variant (B.1.1.7) of SARS-CoV-2 was predominant in Iraq (80.2%), while only one B.1.351 strain was detected [ 109 ]. Around 29 September 2021, the first Omicron variants appeared [ 110 ].…”

Hematological, Inflammatory, Coagulation, and Oxidative/Antioxidant Biomarkers as Predictors for Severity and Mortality in COVID-19: A Prospective Cohort-Study

“…Eventually, the data used in this investigation dated back to more than a year ago, when different SARS-CoV-2 variants were prevalent worldwide, including in Iraq. 66 However, the omega SARS-CoV-2 forms are currently the most common worldwide. 67 Despite evidence of the existence of an alteration of redox balance in COVID-19, it is still required to carry out cohort studies with a larger sample size that explain the mechanism by which the SARS-CoV-2 produces this wide range of such alterations, as well as their exact prevalence, to find effective strategies for prevention, diagnosis, treatment, and rehabilitation of these conditions.…”

A neonatal mouse model characterizes transmissibility of SARS-CoV-2 variants and reveals a role for ORF8

“…Furthermore, the poor conservation of ORF8 among related coronaviruses 61 , the appearance of a 382 nucleotide deletion in the ORF8 of SARS-CoV-2 isolates in patients during February 2020 62 , and the circulation of a SARS-CoV-2 isolate containing a truncated version of ORF8 from March through October 2020 63 suggest that ORF8 is a hotspot for SARS-CoV-2 adaptation and evolution. For example, the alpha variant, which we also characterized in our study, carries a stop codon at amino acid 27 of ORF8, resulting in the expression of a truncated ORF8 protein 64 . Interestingly, in our model, ΔORF8 and Alpha did not phenocopy in terms of URT replication, cytokine responses, or transmission.…”