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Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021.
Infect Genet Evol. 2022 01; 97:105164.IG

Abstract

The widespread severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continuously impacts our economic and public health. The potential of emerging variants to increase transmissibility and evade vaccine-induced immunity lets us put more effort to research on viral mutations and explore the pathogenic haplotypes. In this study, we characterized the haplotype and sub-haplotype diversity of SARS-CoV-2 global variants in January-March and the areas with low and high COVID19 vaccination rates in May 2021 by analyzing viral proteome of complete genome sequences published. Phylogenetic tree analysis of the proteomes of SARS-CoV-2 variants with Neighbor-Joining and Maximum Parsimony methods indicated that haplotype 2 variant with nsp12 P323L and Spike D614G was dominant (98.81%), including new sub-haplotypes 2A_1 to 2A_3, 2B_1 to 2B_3, and 2C_1 to 2C_2 emerged post-one-year COVID-19 outbreak. In addition, the profiling of sub-haplotypes indicated that sub-haplotype 2A_1 with the mutations at N501Y, A570D, D614G, P681H, T716I, S982A, and D118H in Spike was over 58% in May 2021 in the high partly vaccinated rate group (US, Canada, and Germany). Meanwhile, the new haplotype 2C_3 bearing the mutations at EFR156-158del, T19R, A222V, L452R, T478K, and D614G in Spike occupied over 54.8% in May 2021 in the low partly vaccinated rate group (India, Malaysia, Taiwan, and Vietnam). Sub-haplotypes 2A_1 and 2C_3 had a meaningful alternation of ACE2-specific recognition site, neutralization epitopes, and furin cleavage site in SARS-CoV-2 Spike protein. The results discovered the haplotype diversity and new sub-haplotypes of SARS-CoV-2 variants post one-year pandemic in January-March 2021, showing the profiles of sub-haplotypes in the groups with low and high partly vaccinated rates in May 2021. The study reports the emergence of new SARS-CoV-2 sub-haplotypes during ongoing pandemic and vaccination in early 2021, which might help inform the response to vaccination strategies.

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Authors+Show Affiliations

Bui NN
Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 40402, Taiwan; Faculty of Medicine, Can Tho University of Medicine and Pharmacy, Can Tho 94117, Viet Nam.
Lin YT
Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 40402, Taiwan.
Huang SH
Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 41354, Taiwan.
Lin CW
Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 40402, Taiwan; Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 41354, Taiwan. Electronic address: cwlin@mail.cmu.edu.tw.

MeSH

AmericasAmino Acid SubstitutionAsiaCOVID-19COVID-19 VaccinesEpidemiological MonitoringEuropeGene ExpressionGenome, ViralHaplotypesHumansImmune EvasionModels, MolecularMutationPhylogenyProtein Interaction Domains and MotifsSARS-CoV-2Spike Glycoprotein, CoronavirusVaccination Coverage

Pub Type(s)

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

Language

eng

PubMed ID

34848355

Citation

Bui, Ngoc-Niem, et al. "Haplotype Distribution of SARS-CoV-2 Variants in Low and High Vaccination Rate Countries During Ongoing Global COVID-19 Pandemic in Early 2021." Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, vol. 97, 2022, p. 105164.
Bui NN, Lin YT, Huang SH, et al. Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. Infect Genet Evol. 2022;97:105164.
Bui, N. N., Lin, Y. T., Huang, S. H., & Lin, C. W. (2022). Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 97, 105164. https://doi.org/10.1016/j.meegid.2021.105164
Bui NN, et al. Haplotype Distribution of SARS-CoV-2 Variants in Low and High Vaccination Rate Countries During Ongoing Global COVID-19 Pandemic in Early 2021. Infect Genet Evol. 2022;97:105164. PubMed PMID: 34848355.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. AU - Bui,Ngoc-Niem, AU - Lin,Yu-Tzu, AU - Huang,Su-Hua, AU - Lin,Cheng-Wen, Y1 - 2021/11/27/ PY - 2021/09/03/received PY - 2021/11/23/revised PY - 2021/11/25/accepted PY - 2021/12/2/pubmed PY - 2022/1/28/medline PY - 2021/12/1/entrez KW - Haplotype KW - Ongoing pandemic KW - Partly vaccinated rate KW - Severe acute respiratory syndrome coronavirus 2 KW - Variant SP - 105164 EP - 105164 JF - Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases JO - Infect Genet Evol VL - 97 N2 - The widespread severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continuously impacts our economic and public health. The potential of emerging variants to increase transmissibility and evade vaccine-induced immunity lets us put more effort to research on viral mutations and explore the pathogenic haplotypes. In this study, we characterized the haplotype and sub-haplotype diversity of SARS-CoV-2 global variants in January-March and the areas with low and high COVID19 vaccination rates in May 2021 by analyzing viral proteome of complete genome sequences published. Phylogenetic tree analysis of the proteomes of SARS-CoV-2 variants with Neighbor-Joining and Maximum Parsimony methods indicated that haplotype 2 variant with nsp12 P323L and Spike D614G was dominant (98.81%), including new sub-haplotypes 2A_1 to 2A_3, 2B_1 to 2B_3, and 2C_1 to 2C_2 emerged post-one-year COVID-19 outbreak. In addition, the profiling of sub-haplotypes indicated that sub-haplotype 2A_1 with the mutations at N501Y, A570D, D614G, P681H, T716I, S982A, and D118H in Spike was over 58% in May 2021 in the high partly vaccinated rate group (US, Canada, and Germany). Meanwhile, the new haplotype 2C_3 bearing the mutations at EFR156-158del, T19R, A222V, L452R, T478K, and D614G in Spike occupied over 54.8% in May 2021 in the low partly vaccinated rate group (India, Malaysia, Taiwan, and Vietnam). Sub-haplotypes 2A_1 and 2C_3 had a meaningful alternation of ACE2-specific recognition site, neutralization epitopes, and furin cleavage site in SARS-CoV-2 Spike protein. The results discovered the haplotype diversity and new sub-haplotypes of SARS-CoV-2 variants post one-year pandemic in January-March 2021, showing the profiles of sub-haplotypes in the groups with low and high partly vaccinated rates in May 2021. The study reports the emergence of new SARS-CoV-2 sub-haplotypes during ongoing pandemic and vaccination in early 2021, which might help inform the response to vaccination strategies. SN - 1567-7257 UR - https://www.unboundmedicine.com/medline/citation/34848355/Haplotype_distribution_of_SARS_CoV_2_variants_in_low_and_high_vaccination_rate_countries_during_ongoing_global_COVID_19_pandemic_in_early_2021_ DB - PRIME DP - Unbound Medicine ER -