Molecular investigation of SARS-CoV-2 among participants in the 2021 Arbaeen March

Molecular epidemiology techniques played a crucial role during the COVID-19 pandemic, as the genotyping of emerging variants was essential for effective surveillance, predicting transmission rates, and understanding the evolutionary dynamics of the virus. In Iraq, the epidemiological status before and after the 4th wave of Omicron emerging variant is unknown as it was preceded by a mass gathering event of Arbaeen pilgrimage. In this study, TaqPath RT-PCR assay was exploited along with epidemiological approaches to monitor and track dominant mutation and to identify hot spot region in Iraq through analyzing 3,748 SARS-CoV-2 positive specimens collected from different Iraqi governorates from September 5th, 2021, to March 28th, 2022. Current analysis showed that Karbala province represents a hot spot region of infection rather than the capital, Baghdad. Furthermore, the results showed high prevalence of histidine/valine deletion at codon 69/70 (H69/70V) of SARS-CoV-2 spike gene. This genetic signature is a basic characteristic of Alpha and Omicron variants. In silico analysis of genomic data retrieved from Global Initiative on Sharing All Influenza Data (GISAID) repository showed high prevalence of Delta variants and descended sublineages and confirmed the existence of Alpha variants during the studied period. The current study demonstrated that mass gathering events contribute to an increased transmission rate, elevating the prevalence of the H69/70 deletion found in local viral isolates, and offering a thorough epidemiological perspective on the factors that led to the rapid surge of the Omicron fourth wave in Iraq.