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Analyses of Long-Term Epidemic Trends and Evolution Characteristics of Haplotype Subtypes Reveal the Dynamic Selection on SARS-CoV-2

The scale of SARS-CoV-2 infection and death is so enormous that further study of the molecular and evolutionary characteristics of SARS-CoV-2 will help us better understand and respond to SARS-CoV-2 outbreaks. The present study analyzed the epidemic and evolutionary characteristics of haplotype subt...

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Autores principales: Xi, Binbin, Meng, Yuhuan, Jiang, Dawei, Bai, Yunmeng, Chen, Zixi, Qu, Yimo, Li, Shuhua, Wei, Jinfen, Huang, Lizhen, Du, Hongli
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8954678/
https://www.ncbi.nlm.nih.gov/pubmed/35336862
http://dx.doi.org/10.3390/v14030454
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author Xi, Binbin
Meng, Yuhuan
Jiang, Dawei
Bai, Yunmeng
Chen, Zixi
Qu, Yimo
Li, Shuhua
Wei, Jinfen
Huang, Lizhen
Du, Hongli
author_facet Xi, Binbin
Meng, Yuhuan
Jiang, Dawei
Bai, Yunmeng
Chen, Zixi
Qu, Yimo
Li, Shuhua
Wei, Jinfen
Huang, Lizhen
Du, Hongli
author_sort Xi, Binbin
collection PubMed
description The scale of SARS-CoV-2 infection and death is so enormous that further study of the molecular and evolutionary characteristics of SARS-CoV-2 will help us better understand and respond to SARS-CoV-2 outbreaks. The present study analyzed the epidemic and evolutionary characteristics of haplotype subtypes or regions based on 1.8 million high-quality SARS-CoV-2 genomic data. The estimated ratio of the rates of non-synonymous to synonymous changes (Ka/Ks) in North America and the United States were always more than 1.0, while the Ka/Ks in other continents and countries showed a sharp decline, then a slow increase to 1.0, and a dramatic increase over time. H1 (B.1) with the highest substitution rate has become the most dominant haplotype subtype since March 2020 and has evolved into multiple haplotype subtypes with smaller substitution rates. Many evolutionary characteristics of early SARS-CoV-2, such as H3 being the only early haplotype subtype that existed for the shortest time, the global prevalence of H1 and H1-5 (B.1.1) within a month after being detected, and many high divergent genome sequences early in February 2020, indicate the missing of early SARS-CoV-2 genomic data. SARS-CoV-2 experienced dynamic selection from December 2019 to August 2021 and has been under strong positive selection since May 2021. Its transmissibility and the ability of immune escape may be greatly enhanced over time. This will bring greater challenges to the control of the pandemic.
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spelling pubmed-89546782022-03-26 Analyses of Long-Term Epidemic Trends and Evolution Characteristics of Haplotype Subtypes Reveal the Dynamic Selection on SARS-CoV-2 Xi, Binbin Meng, Yuhuan Jiang, Dawei Bai, Yunmeng Chen, Zixi Qu, Yimo Li, Shuhua Wei, Jinfen Huang, Lizhen Du, Hongli Viruses Article The scale of SARS-CoV-2 infection and death is so enormous that further study of the molecular and evolutionary characteristics of SARS-CoV-2 will help us better understand and respond to SARS-CoV-2 outbreaks. The present study analyzed the epidemic and evolutionary characteristics of haplotype subtypes or regions based on 1.8 million high-quality SARS-CoV-2 genomic data. The estimated ratio of the rates of non-synonymous to synonymous changes (Ka/Ks) in North America and the United States were always more than 1.0, while the Ka/Ks in other continents and countries showed a sharp decline, then a slow increase to 1.0, and a dramatic increase over time. H1 (B.1) with the highest substitution rate has become the most dominant haplotype subtype since March 2020 and has evolved into multiple haplotype subtypes with smaller substitution rates. Many evolutionary characteristics of early SARS-CoV-2, such as H3 being the only early haplotype subtype that existed for the shortest time, the global prevalence of H1 and H1-5 (B.1.1) within a month after being detected, and many high divergent genome sequences early in February 2020, indicate the missing of early SARS-CoV-2 genomic data. SARS-CoV-2 experienced dynamic selection from December 2019 to August 2021 and has been under strong positive selection since May 2021. Its transmissibility and the ability of immune escape may be greatly enhanced over time. This will bring greater challenges to the control of the pandemic. MDPI 2022-02-23 /pmc/articles/PMC8954678/ /pubmed/35336862 http://dx.doi.org/10.3390/v14030454 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Xi, Binbin
Meng, Yuhuan
Jiang, Dawei
Bai, Yunmeng
Chen, Zixi
Qu, Yimo
Li, Shuhua
Wei, Jinfen
Huang, Lizhen
Du, Hongli
Analyses of Long-Term Epidemic Trends and Evolution Characteristics of Haplotype Subtypes Reveal the Dynamic Selection on SARS-CoV-2
title Analyses of Long-Term Epidemic Trends and Evolution Characteristics of Haplotype Subtypes Reveal the Dynamic Selection on SARS-CoV-2
title_full Analyses of Long-Term Epidemic Trends and Evolution Characteristics of Haplotype Subtypes Reveal the Dynamic Selection on SARS-CoV-2
title_fullStr Analyses of Long-Term Epidemic Trends and Evolution Characteristics of Haplotype Subtypes Reveal the Dynamic Selection on SARS-CoV-2
title_full_unstemmed Analyses of Long-Term Epidemic Trends and Evolution Characteristics of Haplotype Subtypes Reveal the Dynamic Selection on SARS-CoV-2
title_short Analyses of Long-Term Epidemic Trends and Evolution Characteristics of Haplotype Subtypes Reveal the Dynamic Selection on SARS-CoV-2
title_sort analyses of long-term epidemic trends and evolution characteristics of haplotype subtypes reveal the dynamic selection on sars-cov-2
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8954678/
https://www.ncbi.nlm.nih.gov/pubmed/35336862
http://dx.doi.org/10.3390/v14030454
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