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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.
Bui, Ngoc-Niem; Lin, Yu-Tzu; Huang, Su-Hua; Lin, Cheng-Wen.
  • 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.
Infect Genet Evol ; 97: 105164, 2022 01.
Article in English | MEDLINE | ID: covidwho-1536954
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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Full text: Available Collection: International databases Database: MEDLINE Main subject: Spike Glycoprotein, Coronavirus / COVID-19 Vaccines / SARS-CoV-2 / COVID-19 / Mutation Type of study: Experimental Studies / Observational study / Randomized controlled trials Topics: Vaccines / Variants Limits: Humans Country/Region as subject: Asia / Europa Language: English Journal: Infect Genet Evol Journal subject: Biology / Communicable Diseases / Genetics Year: 2022 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Spike Glycoprotein, Coronavirus / COVID-19 Vaccines / SARS-CoV-2 / COVID-19 / Mutation Type of study: Experimental Studies / Observational study / Randomized controlled trials Topics: Vaccines / Variants Limits: Humans Country/Region as subject: Asia / Europa Language: English Journal: Infect Genet Evol Journal subject: Biology / Communicable Diseases / Genetics Year: 2022 Document Type: Article