A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19

SIMPLE SUMMARY: The pathogenicity and transmissibility of the COVID-19 pandemic causative agent, the SARS-CoV-2 virus, is related to the functions of the proteins synthesized intracellularly, as guided by viral RNA. It is vitally important to accurately pinpoint novel variants of concern of the SARS-CoV-2 virus, in order to understand the molecular features of novel mutations and manage the on-going battle against the COVID-19 pandemic. We focused on A105V mutation in the ORF7a accessory protein. Sequencing and clinical data showed that this mutation is associated with increased severity and lethality in a group of Romanian patients, despite a lower viral copy number and a lower number of associated comorbidities. This effect is primarily due to increased protein stability through allosteric effects as shown by molecular dynamics analyses. This behavior manifests especially among residues 39–56, and the ones adjacent to 26–30 loop, placed in direct contact with potential interaction partners. Together, the results provide novel insights into the role of ORF7a in the pathogenicity of SARS-CoV-2. ABSTRACT: The ongoing COVID-19 pandemic follows an unpredictable evolution, driven by both host-related factors such as mobility, vaccination status, and comorbidities and by pathogen-related ones. The pathogenicity of its causative agent, SARS-CoV-2 virus, relates to the functions of the proteins synthesized intracellularly, as guided by viral RNA. These functions are constantly altered through mutations resulting in increased virulence, infectivity, and antibody-evasion abilities. Well-characterized mutations in the spike protein, such as D614G, N439K, Δ69–70, E484K, or N501Y, are currently defining specific variants; however, some less studied mutations outside the spike region, such as p. 3691 in NSP6, p. 9659 in ORF-10, 8782C > T in ORF-1ab, or 28144T > C in ORF-8, have been proposed for altering SARS-CoV-2 virulence and pathogenicity. Therefore, in this study, we focused on A105V mutation of SARS-CoV-2 ORF7a accessory protein, which has been associated with severe COVID-19 clinical manifestation. Molecular dynamics and computational structural analyses revealed that this mutation differentially alters ORF7a dynamics, suggesting a gain-of-function role that may explain its role in the severe form of COVID-19 disease.