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The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread.
Infect Genet Evol. 2021 07; 91:104800.IG

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.

Authors+Show Affiliations

Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 40402, Taiwan.Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 40402, Taiwan.Department of Biotechnology, Asia University, Taichung 41354, Taiwan.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.

Pub Type(s)

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

Language

eng

PubMed ID

33677109

Citation

Bui, Ngoc-Niem, et al. "The Extent of Molecular Variation in Novel SARS-CoV-2 After the Six-month Global Spread." Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, vol. 91, 2021, p. 104800.
Bui NN, Lin YT, Huang SH, et al. The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Infect Genet Evol. 2021;91:104800.
Bui, N. N., Lin, Y. T., Huang, S. H., & Lin, C. W. (2021). The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 91, 104800. https://doi.org/10.1016/j.meegid.2021.104800
Bui NN, et al. The Extent of Molecular Variation in Novel SARS-CoV-2 After the Six-month Global Spread. Infect Genet Evol. 2021;91:104800. PubMed PMID: 33677109.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. AU - Bui,Ngoc-Niem, AU - Lin,Yu-Tzu, AU - Huang,Su-Hua, AU - Lin,Cheng-Wen, Y1 - 2021/03/05/ PY - 2020/09/03/received PY - 2021/02/28/revised PY - 2021/03/02/accepted PY - 2021/3/8/pubmed PY - 2021/6/1/medline PY - 2021/3/7/entrez KW - COVID-19 KW - Clade KW - Epidemiological trend KW - Genetic variation KW - Phylogenetic tree KW - SARS-CoV-2 SP - 104800 EP - 104800 JF - Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases JO - Infect Genet Evol VL - 91 N2 - 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. SN - 1567-7257 UR - https://www.unboundmedicine.com/medline/citation/33677109/The_extent_of_molecular_variation_in_novel_SARS_CoV_2_after_the_six_month_global_spread_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1567-1348(21)00097-6 DB - PRIME DP - Unbound Medicine ER -