Hotspot Mutations in SARS-CoV-2

Since its emergence in Wuhan, China, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has spread very rapidly around the world, resulting in a global pandemic. Though the vaccination process has started, the number of COVID-affected patients is still quite large. Hence, an analysis of ho...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Indrajit Saha, Nimisha Ghosh, Nikhil Sharma , Suman Nandi
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	COVID-19 deletions entropy hotspot mutations SARS-CoV-2 genomes substitution Genetics QH426-470
Acceso en línea:	https://doaj.org/article/6ccfbb26cbb94677a77bcbb6e9bed147
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:6ccfbb26cbb94677a77bcbb6e9bed147
record_format	dspace
spelling	oai:doaj.org-article:6ccfbb26cbb94677a77bcbb6e9bed1472021-12-01T13:44:26ZHotspot Mutations in SARS-CoV-21664-802110.3389/fgene.2021.753440https://doaj.org/article/6ccfbb26cbb94677a77bcbb6e9bed1472021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fgene.2021.753440/fullhttps://doaj.org/toc/1664-8021Since its emergence in Wuhan, China, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has spread very rapidly around the world, resulting in a global pandemic. Though the vaccination process has started, the number of COVID-affected patients is still quite large. Hence, an analysis of hotspot mutations of the different evolving virus strains needs to be carried out. In this regard, multiple sequence alignment of 71,038 SARS-CoV-2 genomes of 98 countries over the period from January 2020 to June 2021 is performed using MAFFT followed by phylogenetic analysis in order to visualize the virus evolution. These steps resulted in the identification of hotspot mutations as deletions and substitutions in the coding regions based on entropy greater than or equal to 0.3, leading to a total of 45 unique hotspot mutations. Moreover, 10,286 Indian sequences are considered from 71,038 global SARS-CoV-2 sequences as a demonstrative example that gives 52 unique hotspot mutations. Furthermore, the evolution of the hotspot mutations along with the mutations in variants of concern is visualized, and their characteristics are discussed as well. Also, for all the non-synonymous substitutions (missense mutations), the functional consequences of amino acid changes in the respective protein structures are calculated using PolyPhen-2 and I-Mutant 2.0. In addition to this, SSIPe is used to report the binding affinity between the receptor-binding domain of Spike protein and human ACE2 protein by considering L452R, T478K, E484Q, and N501Y hotspot mutations in that region.Indrajit SahaNimisha GhoshNikhil Sharma Suman NandiFrontiers Media S.A.articleCOVID-19deletionsentropyhotspot mutationsSARS-CoV-2 genomessubstitutionGeneticsQH426-470ENFrontiers in Genetics, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	COVID-19 deletions entropy hotspot mutations SARS-CoV-2 genomes substitution Genetics QH426-470
spellingShingle	COVID-19 deletions entropy hotspot mutations SARS-CoV-2 genomes substitution Genetics QH426-470 Indrajit Saha Nimisha Ghosh Nikhil Sharma Suman Nandi Hotspot Mutations in SARS-CoV-2
description	Since its emergence in Wuhan, China, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has spread very rapidly around the world, resulting in a global pandemic. Though the vaccination process has started, the number of COVID-affected patients is still quite large. Hence, an analysis of hotspot mutations of the different evolving virus strains needs to be carried out. In this regard, multiple sequence alignment of 71,038 SARS-CoV-2 genomes of 98 countries over the period from January 2020 to June 2021 is performed using MAFFT followed by phylogenetic analysis in order to visualize the virus evolution. These steps resulted in the identification of hotspot mutations as deletions and substitutions in the coding regions based on entropy greater than or equal to 0.3, leading to a total of 45 unique hotspot mutations. Moreover, 10,286 Indian sequences are considered from 71,038 global SARS-CoV-2 sequences as a demonstrative example that gives 52 unique hotspot mutations. Furthermore, the evolution of the hotspot mutations along with the mutations in variants of concern is visualized, and their characteristics are discussed as well. Also, for all the non-synonymous substitutions (missense mutations), the functional consequences of amino acid changes in the respective protein structures are calculated using PolyPhen-2 and I-Mutant 2.0. In addition to this, SSIPe is used to report the binding affinity between the receptor-binding domain of Spike protein and human ACE2 protein by considering L452R, T478K, E484Q, and N501Y hotspot mutations in that region.
format	article
author	Indrajit Saha Nimisha Ghosh Nikhil Sharma Suman Nandi
author_facet	Indrajit Saha Nimisha Ghosh Nikhil Sharma Suman Nandi
author_sort	Indrajit Saha
title	Hotspot Mutations in SARS-CoV-2
title_short	Hotspot Mutations in SARS-CoV-2
title_full	Hotspot Mutations in SARS-CoV-2
title_fullStr	Hotspot Mutations in SARS-CoV-2
title_full_unstemmed	Hotspot Mutations in SARS-CoV-2
title_sort	hotspot mutations in sars-cov-2
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/6ccfbb26cbb94677a77bcbb6e9bed147
work_keys_str_mv	AT indrajitsaha hotspotmutationsinsarscov2 AT nimishaghosh hotspotmutationsinsarscov2 AT nikhilsharma hotspotmutationsinsarscov2 AT sumannandi hotspotmutationsinsarscov2
_version_	1718405123170893824

Hotspot Mutations in SARS-CoV-2

Ejemplares similares