The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread

Ngoc-Niem Bui; Yu-Tzu Lin; Su-Hua Huang; Cheng-Wen Lin

doi:10.1016/j.meegid.2021.104800

The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread

Infect Genet Evol. 2021 Jul:91:104800. doi: 10.1016/j.meegid.2021.104800. Epub 2021 Mar 5.

Authors

Ngoc-Niem Bui¹, Yu-Tzu Lin¹, Su-Hua Huang², Cheng-Wen Lin³

Affiliations

¹ Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 40402, Taiwan.
² Department of Biotechnology, Asia University, Taichung 41354, Taiwan.
³ Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 40402, Taiwan; Department of Biotechnology, Asia University, Taichung 41354, Taiwan. Electronic address: cwlin@mail.cmu.edu.tw.

Abstract

The pandemic spread of Coronavirus Disease 2019 (COVID-19) is still ongoing since severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is identified as the etiologic pathogen late December 2019. After over six-month spread of COVID-19, SARS-CoV-2 causes critical threats to global public health and economy. The investigations on evolution and genotyping on genetic variations are of great importance, therefore, the present study characterized the molecular variation of SARS-CoV-2 by analyzing 4230 complete genome sequences from the worldwide samples collected during the first 6-month pandemic. Phylogenetic tree analysis with Neighbor-Joining and Maximum-Parsimony methods indicated that the haplotypes of SARS-CoV-2 genome sequences were classified into four clades with the unique nucleotide and amino acid changes: T27879C (ORF8 L84S) in clade 1 (25.34%), A23138G (spike D614G) in clade 2 (63.54%), G10818T (nsp6 L37F), C14540T (nsp12 T442I), and G25879T (ORF3a V251F) in clade 3 (2.58%), and miscellaneous changes in clade 4 (8.54%). Interestingly, subclade 2B with the amino acid changes at nsp2 T85I, Spike D614G, and ORF3a Q57H was firstly reported on March 4, 2020 in United States of America, becoming the most frequent sub-haplogroup in the world (36.21%) and America (45.81%). Subclade 1C with the amino acid changes at nsp13 P504L and ORF8 L84S was becoming the second most frequent sub-haplogroup in the world (19.91%) and America (26.29%). Subclade 2A with the amino acid changes in Spike D614G and Nucleocapsid R203K and G204R was highly prevalent in Asia (18.82%) and Europe (29.72%). The study highlights the notable clades and sub-clades with unique mutations, revealing the genetic and geographical relevant post the six-month outbreak of COVID-19. This study thoroughly observed the genetic feature of SARS-CoV-2 haplotyping, providing an epidemiological trend of COVID-19.

Keywords: COVID-19; Clade; Epidemiological trend; Genetic variation; Phylogenetic tree; SARS-CoV-2.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Americas / epidemiology
Amino Acid Substitution
Asia / epidemiology
COVID-19 / epidemiology*
COVID-19 / transmission
COVID-19 / virology
Europe / epidemiology
Evolution, Molecular
Gene Expression Regulation, Viral
Genetic Variation*
Genome, Viral*
Haplotypes
Humans
Mutation Rate
Nucleocapsid Proteins / genetics*
Open Reading Frames
Phylogeny
SARS-CoV-2 / classification
SARS-CoV-2 / genetics*
Selection, Genetic
Spike Glycoprotein, Coronavirus / genetics*

Substances

Nucleocapsid Proteins
Spike Glycoprotein, Coronavirus
spike protein, SARS-CoV-2