Mutations in SARS-CoV-2 surface glycoprotein are clustered
The mutations were mapped onto the surface glycoprotein sequence to determine clusters around specific domains (Figure 1). Interestingly, the mutations were found to cluster around the N-terminal domain (NTD), the receptor-binding domain (RBD), and the N-terminal of the S2 fragment.
The N-terminal domain (NTD) showed 14 substitutions and a single deletion mutation which were identified from 28 different isolates. H49Y was identified in six isolates originating from China (5) and the United States of America (1) (Figure 2A). Furthermore, Q239K was found in six isolates from the Netherlands (5) and Finland (1). While M153T (2 isolates from China) and S254F (Isolates from Germany and Netherlands) were identified in 2 isolates each.
The receptor-binding domain (RBD) showed 12 substitution mutations that were identified from 19 different isolates. V367F was found in six isolates that originated from France (5) and Hong Kong (1). Also, V483A was identified in three isolates from the United States of America.
Analysis of mutations in the C-terminal of the S1 fragment revealed that the SARS-CoV-2 virus is spreading in two forms around the globe. Specifically, 481 isolates showed an aspartic acid (D) at residue 615 accounting for 68.5% of the total isolates analyzed (Figure 2B). Nearly all isolates from China, including the first reported SARS-CoV-2 genome, contained this amino acid substitution except for two isolates. Furthermore, D614 was found in multiple isolates from America, Europe, Asia, and Australasia. However, G614 was found in 221 isolates accounting for 31.5% of all sequences (Figure 2B). Interestingly, nearly all the isolates G164 were from outside of China (G614 was found in Wuhan_HBCDC-HB-06_2020 and China_Shanghai_SH0025). The G614 variant first emerged in China on the 6th of February 2020 in isolate China_Shanghai_SH0025. In fact, both the D614 and G614 variants emerged in China and subsequently have spread throughout the world.