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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

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 p...

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Autores principales: Bui, Ngoc-Niem, Lin, Yu-Tzu, Huang, Su-Hua, Lin, Cheng-Wen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Authors. Published by Elsevier B.V. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8626897/
https://www.ncbi.nlm.nih.gov/pubmed/34848355
http://dx.doi.org/10.1016/j.meegid.2021.105164
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author Bui, Ngoc-Niem
Lin, Yu-Tzu
Huang, Su-Hua
Lin, Cheng-Wen
author_facet Bui, Ngoc-Niem
Lin, Yu-Tzu
Huang, Su-Hua
Lin, Cheng-Wen
author_sort Bui, Ngoc-Niem
collection PubMed
description 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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spelling pubmed-86268972021-11-29 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 Infect Genet Evol Short Communication 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. The Authors. Published by Elsevier B.V. 2022-01 2021-11-27 /pmc/articles/PMC8626897/ /pubmed/34848355 http://dx.doi.org/10.1016/j.meegid.2021.105164 Text en © 2021 The Authors Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Short Communication
Bui, Ngoc-Niem
Lin, Yu-Tzu
Huang, Su-Hua
Lin, Cheng-Wen
Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021
title Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021
title_full Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021
title_fullStr Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021
title_full_unstemmed Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021
title_short Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021
title_sort haplotype distribution of sars-cov-2 variants in low and high vaccination rate countries during ongoing global covid-19 pandemic in early 2021
topic Short Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8626897/
https://www.ncbi.nlm.nih.gov/pubmed/34848355
http://dx.doi.org/10.1016/j.meegid.2021.105164
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