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Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have been emerging and circulating globally since the start of the COVID-19 pandemic, of which B.1.617 lineage that was first reported in India at the end of 2020, soon became predominant. Tracing genomic variations and understand...

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Autores principales: Fan, Lin-qian, Hu, Xiao-yun, Chen, Yi-yue, Peng, Xiang-lei, Fu, Yuan-hui, Zheng, Yan-peng, Yu, Jie-mei, He, Jin-sheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8529246/
https://www.ncbi.nlm.nih.gov/pubmed/34691002
http://dx.doi.org/10.3389/fmicb.2021.750725
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author Fan, Lin-qian
Hu, Xiao-yun
Chen, Yi-yue
Peng, Xiang-lei
Fu, Yuan-hui
Zheng, Yan-peng
Yu, Jie-mei
He, Jin-sheng
author_facet Fan, Lin-qian
Hu, Xiao-yun
Chen, Yi-yue
Peng, Xiang-lei
Fu, Yuan-hui
Zheng, Yan-peng
Yu, Jie-mei
He, Jin-sheng
author_sort Fan, Lin-qian
collection PubMed
description Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have been emerging and circulating globally since the start of the COVID-19 pandemic, of which B.1.617 lineage that was first reported in India at the end of 2020, soon became predominant. Tracing genomic variations and understanding their impact on the viral properties are the foundations for the vaccine and drug development and for the mitigation measures to be taken or lifted. In this study, 1,051 near-complete genomes and 1,559 spike (S) sequences belonging to the B.1.617 were analyzed. A genome-wide spread of single nucleotide polymorphisms (SNPs) was identified. Of the high frequency mutations identified, 61% (11/18) involved structural proteins, despite two third of the viral genome encoding nonstructural proteins. There were 22 positive selection sites, mostly distributed across the S protein, of which 16 were led by non-C to U transition and should be of a special attention. Haplotype network revealed that a large number of daughter haplotypes were continually derived throughout the pandemic, of which H177, H181 H219 and H286 from the ancestor haplotype H176 of B.1.617.2 were widely prevalent. Besides the well known substitutions of L452R, P681R and deletions of E156 and F157, as well as the potential biological significance, structural analysis in this study still indicated that new amino acid changes in B.1.617, such as E484Q and N501Y, had reshaped the viral bonding network, and increasingly sequenced N501Y mutant with a potential enhanced binding ability was detected in many other countries in the follow-up monitoring. Although we can’t conclude the properties of all the mutants including N501Y thoroughly, it merits focusing on their spread epidemically and biologically.
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spelling pubmed-85292462021-10-22 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617 Fan, Lin-qian Hu, Xiao-yun Chen, Yi-yue Peng, Xiang-lei Fu, Yuan-hui Zheng, Yan-peng Yu, Jie-mei He, Jin-sheng Front Microbiol Microbiology Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have been emerging and circulating globally since the start of the COVID-19 pandemic, of which B.1.617 lineage that was first reported in India at the end of 2020, soon became predominant. Tracing genomic variations and understanding their impact on the viral properties are the foundations for the vaccine and drug development and for the mitigation measures to be taken or lifted. In this study, 1,051 near-complete genomes and 1,559 spike (S) sequences belonging to the B.1.617 were analyzed. A genome-wide spread of single nucleotide polymorphisms (SNPs) was identified. Of the high frequency mutations identified, 61% (11/18) involved structural proteins, despite two third of the viral genome encoding nonstructural proteins. There were 22 positive selection sites, mostly distributed across the S protein, of which 16 were led by non-C to U transition and should be of a special attention. Haplotype network revealed that a large number of daughter haplotypes were continually derived throughout the pandemic, of which H177, H181 H219 and H286 from the ancestor haplotype H176 of B.1.617.2 were widely prevalent. Besides the well known substitutions of L452R, P681R and deletions of E156 and F157, as well as the potential biological significance, structural analysis in this study still indicated that new amino acid changes in B.1.617, such as E484Q and N501Y, had reshaped the viral bonding network, and increasingly sequenced N501Y mutant with a potential enhanced binding ability was detected in many other countries in the follow-up monitoring. Although we can’t conclude the properties of all the mutants including N501Y thoroughly, it merits focusing on their spread epidemically and biologically. Frontiers Media S.A. 2021-10-07 /pmc/articles/PMC8529246/ /pubmed/34691002 http://dx.doi.org/10.3389/fmicb.2021.750725 Text en Copyright © 2021 Fan, Hu, Chen, Peng, Fu, Zheng, Yu and He. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Fan, Lin-qian
Hu, Xiao-yun
Chen, Yi-yue
Peng, Xiang-lei
Fu, Yuan-hui
Zheng, Yan-peng
Yu, Jie-mei
He, Jin-sheng
Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617
title Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617
title_full Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617
title_fullStr Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617
title_full_unstemmed Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617
title_short Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617
title_sort biological significance of the genomic variation and structural dynamics of sars-cov-2 b.1.617
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8529246/
https://www.ncbi.nlm.nih.gov/pubmed/34691002
http://dx.doi.org/10.3389/fmicb.2021.750725
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