Deletions in SARS-CoV-2 nsp6 enhance antagonism of type-I interferon signaling

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve and adapt long after it first emerged in 2019. As the causative agent of the coronavirus disease 2019 (COVID-19), a tremendous effort has been made to understand the molecular pathogenesis of SARS-CoV-2. Recent research has identified nonstructural protein 6 (nsp6) as a major contributor to SARS-CoV-2 replication through the formation of replication organelles, antagonism of interferon type I (IFN-I) responses, and NLRP3 inflammasome activation, a major factor of severe COVID-19. Here, I review the most recent published findings regarding the multiple roles of nsp6 in promoting SARS-CoV-2 replication and investigate further the effect of variant nsp6 mutations in molecular pathogenesis of SARS-CoV-2, specifically the antagonism of IFN-I pathways. I demonstrate that a mutant SARS-CoV-2 USA/WA1-2020 (WA1) containing a nsp6 mutation (ΔSGF-WA1) seen in the Alpha (B.1.1.7) and Omicron sublineages (BA.2, BA.4, BA.5) is less susceptible to IFN-α treatment in African green monkey kidney epithelial cells expressing the human co-factor TMPRSS2 (Vero E6-TMPRSS2) compared to full-length WA1. Nsp6 mutations ΔSGF and ΔLSG, a similar deletion found in BA.1 nsp6, augment the ability of nsp6 to block phosphorylation of STAT1 and STAT2 in vitro compared to WA1 nsp6, thereby suppressing the IFN-I signaling pathway. Furthermore, ΔSGF-WA1 infection of primary airway cultures secretes similar levels of infectious virus and viral RNA than WA1-infected cells but produces higher levels of intracellular viral RNA than WA1 and outcompetes parental WA1 in a competition experiment. Lastly, ΔSGF-WA1 infected mice have higher levels of viral RNA than WA1-infected mice and experience lower survival rates with a longer disease period. These data suggest that variants containing ΔSGF or ΔLSG mutations are more virulent and may cause more severe disease in COVID-19 patients.