Genomic epidemiology reveals early transmission of SARS-CoV-2 and mutational dynamics in Nanning, China
DeWu Bi,
XiaoLu Luo,
ZhenCheng Chen,
ZhouHua Xie,
Ning Zang,
LiDa Mo,
ZeDuan Liu,
YanRong Lin,
YaQin Qin,
XiKe Tang,
Lü Lin,
YuanLi Wang,
LiangLi Cao,
FeiJun Zhao,
JinAi Zhou,
ShanQiu Wei,
ShaoYong Xi,
QiuYing Ma,
JianYan Lin
Affiliations
DeWu Bi
Department of Clinical Laboratory, The Fourth People's Hospital of Nanning, Nanning, China; Key Laboratory of Infectious Diseases, The Fourth People's Hospital of Nanning, Nanning, China; Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China; Corresponding author. The Fourth People's Hospital of Nanning, No.1, Erli, Changgang Road, Xingning District, 530023, Nanning, Guangxi, China.
XiaoLu Luo
Department of Clinical Laboratory, The Fourth People's Hospital of Nanning, Nanning, China; Key Laboratory of Infectious Diseases, The Fourth People's Hospital of Nanning, Nanning, China; Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China
ZhenCheng Chen
School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, China
ZhouHua Xie
Department of Respiratory Medicine, The Fourth People's Hospital of Nanning, Nanning, China; Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China
Ning Zang
Guangxi Medical Research Center, Guangxi Medical University, Nanning, China
LiDa Mo
Department of Clinical Laboratory, The Fourth People's Hospital of Nanning, Nanning, China; Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China
ZeDuan Liu
Department of Clinical Laboratory, The Fourth People's Hospital of Nanning, Nanning, China; Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China
YanRong Lin
Department of Critical Care Medicine, The Fourth People's Hospital of Nanning, Nanning, China; Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China
YaQin Qin
Department of Critical Care Medicine, The Fourth People's Hospital of Nanning, Nanning, China; Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China
XiKe Tang
Department of Critical Care Medicine, The Fourth People's Hospital of Nanning, Nanning, China; Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China
Lü Lin
Emergency Department, The Fourth People's Hospital of Nanning, Nanning, China; Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China
YuanLi Wang
School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, China
LiangLi Cao
School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, China
FeiJun Zhao
School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, China
JinAi Zhou
Guangxi Medical Research Center, Guangxi Medical University, Nanning, China
ShanQiu Wei
Department of Clinical Laboratory, The Fourth People's Hospital of Nanning, Nanning, China; Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China
ShaoYong Xi
Department of Clinical Laboratory, The Fourth People's Hospital of Nanning, Nanning, China; Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China
QiuYing Ma
Department of Clinical Laboratory, The Fourth People's Hospital of Nanning, Nanning, China; Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China
JianYan Lin
Key Laboratory of Infectious Diseases, The Fourth People's Hospital of Nanning, Nanning, China; Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China; Corresponding author. Key Laboratory of Infectious Diseases, The Fourth People's Hospital of Nanning, Nanning, China.
Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are a fatal pathogen resulting in substantial morbidity and mortality, and posing a great threat to human health with epidemics and pandemics. Methods: Next-generation sequencing (NGS) was performed to investigate the SARS-CoV-2 genomic characterization. Phylogenetic analysis of SARS-CoV-2 genomes was used to probe the evolutionary. Homology protein structure modelling was done to explore potential effect of the mutations. Results: The eighty genome sequences of SARS-CoV-2 obtained from the thirty-nine patients with COVID-19. A novel variant with mutation H625R concomitant with S50L in spike glycoprotein had been identified. Phylogenetic analysis revealed that SARS-CoV-2 variants belong to several distinct lineages. Homology modelling indicated that variant with mutation H625R and S50L increases flexibility of S1 subunit. Conclusions: SARS-CoV-2 genomes are constantly evolving by accumulation of point mutations. The amino acid H625R in combination with S50L may have a significant impact on the interaction between spike glycoprotein and ACE2.
