In a recent study posted to the bioRxiv* pre-print server, researchers characterized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) isolates extracted from the samples of two individuals infected with the virus in Peru (ΔN25) and Brazil (ΔN135) in January 2021.
The S variants had dramatically large and rare deletions in a small beta-sheet on top of the N-terminal domain (NTD) galectin fold (βN3N5). Additionally, the ΔN135 isolate had a signal peptide P9L mutation in the receptor-binding domain (RBD) of its S that disrupted the formation of 15-136 disulfide bonds (DS15-136) and consequently impacted the structural architecture of NTD.
The S1 subunit of SARS-CoV-2 S glycoprotein houses the NTD and RBD which are targets of SARS-CoV-2 neutralizing antibodies (nAbs) and escape mutations. Interestingly, many SARS-CoV-2 variants have small deletions in the exposed protruding NTD loops.