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

doi:10.1016/j.heliyon.2023.e23029

Genomic epidemiology reveals early transmission of SARS-CoV-2 and mutational dynamics in Nanning, China

Heliyon. 2023 Nov 29;9(12):e23029. doi: 10.1016/j.heliyon.2023.e23029. eCollection 2023 Dec.

Authors

DeWu Bi^{1

2

3}, XiaoLu Luo^{1

2

3}, ZhenCheng Chen⁴, ZhouHua Xie^{5

3}, Ning Zang⁶, LiDa Mo^{1

3}, ZeDuan Liu^{1

3}, YanRong Lin^{7

3}, YaQin Qin^{7

3}, XiKe Tang^{7

3}, Lü Lin^{8

3}, YuanLi Wang⁴, LiangLi Cao⁴, FeiJun Zhao⁴, JinAi Zhou⁶, ShanQiu Wei^{1

3}, ShaoYong Xi^{1

3}, QiuYing Ma^{1

3}, JianYan Lin^{2

3}

Affiliations

¹ Department of Clinical Laboratory, The Fourth People's Hospital of Nanning, Nanning, China.
² Key Laboratory of Infectious Diseases, The Fourth People's Hospital of Nanning, Nanning, China.
³ Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China.
⁴ School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, China.
⁵ Department of Respiratory Medicine, The Fourth People's Hospital of Nanning, Nanning, China.
⁶ Guangxi Medical Research Center, Guangxi Medical University, Nanning, China.
⁷ Department of Critical Care Medicine, The Fourth People's Hospital of Nanning, Nanning, China.
⁸ Emergency Department, The Fourth People's Hospital of Nanning, Nanning, China.

Abstract

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.

Keywords: COVID-19; Evolution; Mutation; SARS-CoV-2; Variant.