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Amino acid variation analysis of surface spike glycoprotein at 614 in SARS-CoV-2
strains
#MMPMID32837981
Canhui Cao
; Huang L
; Liu K
; Ma K
; Tian Y
; Qin Y
; Sun H
; Ding W
; Gui L
; Wu P
Genes Dis
2020[Dec]; 7
(4
): 567-577
PMID32837981
show ga
As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to
disperse globally with worrisome speed, identifying amino acid variations in the
virus could help to understand the characteristics of it. Here, we studied 489
SARS-CoV-2 genomes obtained from 32 countries from the Nextstrain database and
performed phylogenetic tree analysis by clade, country, and genotype of the
surface spike glycoprotein (S protein) at site 614. We found that virus strains
from mainland China were mostly distributed in Clade B and Clade undefined in the
phylogenetic tree, with very few found in Clade A. In contrast, Clades A2 (one
case) and A2a (112 cases) predominantly contained strains from European regions.
Moreover, Clades A2 and A2a differed significantly from those of mainland China
in age of infected population (P = 0.0071, mean age 40.24 to 46.66), although
such differences did not exist between the US and mainland China. Further
analysis demonstrated that the variation of the S protein at site 614
(QHD43416.1: p.614D>G) was a characteristic of stains in Clades A2 and A2a.
Importantly, this variation was predicted to have neutral or benign effects on
the function of the S protein. In addition, global quality estimates and 3D
protein structures tended to be different between the two S proteins. In summary,
we identified different genomic epidemiology among SARS-CoV-2 strains in
different clades, especially in an amino acid variation of the S protein at 614,
revealing potential viral genome divergence in SARS-CoV-2 strains.