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

Lu Chen

Lu Chen, West China Medical School, Sichuan University, China


SARS-CoV-2 virus that causes COVID-19 is undergoing constant mutation. We utilized epidemiology, virus genome sequencing, clinical phenotyping, and validation to locate virus mutations of clinical importance. We identified one variant, Δ500-532 deletion in Nsp1, in ~20% of samples, which was associated with higher Ct value and lower serum IFN-β levels in patients. Deletion variants in this locus were found in 37 countries worldwide, and isolated viruses or viruses engineered by reverse genetics with related deletions were also found to induce lower IFN-β response in infected Calu-3 cells. Thus, our virologic surveillance characterized recurrent genetic diversity and identified mutations in Nsp1 of biological and clinical importance.


Dr. Lu Chen is a researcher at Sichuan University in China, pursuing a career on human health by integrating bioinformatics and experiments in genetics. He obtained his Ph.D. at the University of Bath in 2012, and received his post-doc training at the Wellcome Trust Sanger Institute and the University of Cambridge from 2011 to 2016.