Another mechanism involves non-AUG (methionine) initiation wherein a virus targets eukaryotic initiation factor-2 (eIF2), inhibiting the host cell protein synthesis. For viral replication, the 5′ untranslated region (UTR) makes a substantial contribution by acting as the main lever that regulates various host replication initiation factors in the RNA viruses, especially in picornaviruses. A majority of ssRNA viruses contain their genome replication through 5'cap or have some secondary structures of RNA forming internal ribosomal entry sites (IRES) to recruit host replication factors. The host-pathogen interaction that follows an initial viral infection results in a struggle to survive between both the host and the pathogen and can result in counter-mechanisms that enable one to prevail and the other to perish. This family of viruses comprises the lethal viruses like SARS, MERS, and SARS-CoV-2 that causes infections in the respiratory tract. SARS-CoV-2 is a ssRNA virus belonging to the Coronaviridae family.

The results are also correlated with increased recovery rates and decreased death rates of global SARS-CoV-2 cases.ĬOVID-19 pandemic has affected over 40 million individuals globally and has been fatal for nearly 3 million people. The results obtained from molecular docking and molecular dynamics simulation indicated weaker interaction of C241T mutant stem-loops with the host transcription factor MADP1, indicating a reduced replication efficiency.

In the present study, the effect of the C241T mutation has been studied with respect to the changes in RNA structure and its interaction with the host replication factors MADP1 Zinc finger CCHC-type and RNA-binding motif 1 (hnRNP1). One of the most frequent 5’ UTR variants in the SARS-CoV-2 genome is the C241T, with a global frequency of more than 95 %. Moreover, significantly less attention has been accorded to delineate the role of the untranslated regions (UTRs) of the SARS-CoV-2 genome in the disease progression and etiology. Out of several hotspot mutations within the SARS-CoV-2 genome, recent research has focused mainly on the missense variants.

As per the GISAID database, the genomics of SARS-CoV-2 has been extensively studied, with more than 500 genome submissions per day. Novel severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has claimed more than 3.3 million lives worldwide and still counting.

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