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

By a genetic and phylogenetic surveillance of SARS-CoV-2 in southwest China revealed the presence of Nsp1 deletion mutants (Δ500-532), where is considered to be the hotspot of deletion within the Nsp1 molecule. These mutations were correlated with the lower viral load and serum interferon-β level. A molecular study using plasmid-expressing Nsp1 with these deletions indicates these mutations are involved in the reduction of interferon response. Moreover, a reverse genetics enginering of recombinat SARS-CoV-2 using Nsp1 deletions showed that these mutants are directly involed in the induction of the lower interferon response in the viral infection stage.