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.