Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response

The SARS-CoV-2 virus, the causative agent of COVID-19, is undergoing constant mutation. Here, we utilized an integrative approach combining epidemiology, virus genome sequencing, clinical phenotyping, and experimental validation to locate mutations of clinical importance. We identified 35 recurrent variants, some of which are associated with clinical phenotypes related to severity. One variant, containing a deletion in the Nsp1-coding region (Δ500-532), was found in more than 20% of our sequenced samples and associates with higher RT-PCR cycle thresholds and lower serum IFN-β levels of infected patients. Deletion variants in this locus were found in 37 countries worldwide, and viruses isolated from clinical samples or engineered by reverse genetics with related deletions in Nsp1 also induce lower IFN-β responses in infected Calu-3 cells. Taken together, our virologic surveillance characterizes recurrent genetic diversity and identified mutations in Nsp1 of biological and clinical importance, which collectively may aid molecular diagnostics and drug design. [Display omitted] •SARS-CoV-2 genome sequencing and phylogenetic analyses identify 35 recurrent mutations•Association with 117 clinical phenotypes reveals potentially important mutations•Δ500-532 in Nsp1 coding region correlates with lower viral load and serum IFN-β•Viral isolates with Δ500-532 mutation induce lower IFN-I response in the infected cells Bringing together epidemiological, genetic, and clinical data, Lin et al. identify viral mutations that associate with clinical phenotypes. The 500-532 locus in the Nsp1 coding region is a deletion hotspot in the SARS-CoV-2 genome, and deletion variants lead to lower IFN-I response. Prevalence of 500-532 deletion variants is accumulating worldwide.