SARS-CoV-2 variant evolution in the United States: High accumulation of viral mutations over time likely through serial Founder Events and mutational bursts.

Since the first case of COVID-19 in December 2019 in Wuhan, China, SARS-CoV-2 has spread worldwide and within a year and a half has caused 3.56 million deaths globally. With dramatically increasing infection numbers, and the arrival of new variants with increased infectivity, tracking the evolution...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Rafail Nikolaos Tasakis, Georgios Samaras, Anna Jamison, Michelle Lee, Alexandra Paulus, Gabrielle Whitehouse, Laurent Verkoczy, F Nina Papavasiliou, Marilyn Diaz
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/20d9691c69244f98842dd8b3ab74a933
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:20d9691c69244f98842dd8b3ab74a933
record_format	dspace
spelling	oai:doaj.org-article:20d9691c69244f98842dd8b3ab74a9332021-12-02T20:18:55ZSARS-CoV-2 variant evolution in the United States: High accumulation of viral mutations over time likely through serial Founder Events and mutational bursts.1932-620310.1371/journal.pone.0255169https://doaj.org/article/20d9691c69244f98842dd8b3ab74a9332021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0255169https://doaj.org/toc/1932-6203Since the first case of COVID-19 in December 2019 in Wuhan, China, SARS-CoV-2 has spread worldwide and within a year and a half has caused 3.56 million deaths globally. With dramatically increasing infection numbers, and the arrival of new variants with increased infectivity, tracking the evolution of its genome is crucial for effectively controlling the pandemic and informing vaccine platform development. Our study explores evolution of SARS-CoV-2 in a representative cohort of sequences covering the entire genome in the United States, through all of 2020 and early 2021. Strikingly, we detected many accumulating Single Nucleotide Variations (SNVs) encoding amino acid changes in the SARS-CoV-2 genome, with a pattern indicative of RNA editing enzymes as major mutators of SARS-CoV-2 genomes. We report three major variants through October of 2020. These revealed 14 key mutations that were found in various combinations among 14 distinct predominant signatures. These signatures likely represent evolutionary lineages of SARS-CoV-2 in the U.S. and reveal clues to its evolution such as a mutational burst in the summer of 2020 likely leading to a homegrown new variant, and a trend towards higher mutational load among viral isolates, but with occasional mutation loss. The last quartile of 2020 revealed a concerning accumulation of mostly novel low frequency replacement mutations in the Spike protein, and a hypermutable glutamine residue near the putative furin cleavage site. Finally, end of the year data and 2021 revealed the gradual increase to prevalence of known variants of concern, particularly B.1.1.7, that have acquired additional Spike mutations. Overall, our results suggest that predominant viral genomes are dynamically evolving over time, with periods of mutational bursts and unabated mutation accumulation. This high level of existing variation, even at low frequencies and especially in the Spike-encoding region may become problematic when super-spreader events, akin to serial Founder Events in evolution, drive these rare mutations to prominence.Rafail Nikolaos TasakisGeorgios SamarasAnna JamisonMichelle LeeAlexandra PaulusGabrielle WhitehouseLaurent VerkoczyF Nina PapavasiliouMarilyn DiazPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 7, p e0255169 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Rafail Nikolaos Tasakis Georgios Samaras Anna Jamison Michelle Lee Alexandra Paulus Gabrielle Whitehouse Laurent Verkoczy F Nina Papavasiliou Marilyn Diaz SARS-CoV-2 variant evolution in the United States: High accumulation of viral mutations over time likely through serial Founder Events and mutational bursts.
description	Since the first case of COVID-19 in December 2019 in Wuhan, China, SARS-CoV-2 has spread worldwide and within a year and a half has caused 3.56 million deaths globally. With dramatically increasing infection numbers, and the arrival of new variants with increased infectivity, tracking the evolution of its genome is crucial for effectively controlling the pandemic and informing vaccine platform development. Our study explores evolution of SARS-CoV-2 in a representative cohort of sequences covering the entire genome in the United States, through all of 2020 and early 2021. Strikingly, we detected many accumulating Single Nucleotide Variations (SNVs) encoding amino acid changes in the SARS-CoV-2 genome, with a pattern indicative of RNA editing enzymes as major mutators of SARS-CoV-2 genomes. We report three major variants through October of 2020. These revealed 14 key mutations that were found in various combinations among 14 distinct predominant signatures. These signatures likely represent evolutionary lineages of SARS-CoV-2 in the U.S. and reveal clues to its evolution such as a mutational burst in the summer of 2020 likely leading to a homegrown new variant, and a trend towards higher mutational load among viral isolates, but with occasional mutation loss. The last quartile of 2020 revealed a concerning accumulation of mostly novel low frequency replacement mutations in the Spike protein, and a hypermutable glutamine residue near the putative furin cleavage site. Finally, end of the year data and 2021 revealed the gradual increase to prevalence of known variants of concern, particularly B.1.1.7, that have acquired additional Spike mutations. Overall, our results suggest that predominant viral genomes are dynamically evolving over time, with periods of mutational bursts and unabated mutation accumulation. This high level of existing variation, even at low frequencies and especially in the Spike-encoding region may become problematic when super-spreader events, akin to serial Founder Events in evolution, drive these rare mutations to prominence.
format	article
author	Rafail Nikolaos Tasakis Georgios Samaras Anna Jamison Michelle Lee Alexandra Paulus Gabrielle Whitehouse Laurent Verkoczy F Nina Papavasiliou Marilyn Diaz
author_facet	Rafail Nikolaos Tasakis Georgios Samaras Anna Jamison Michelle Lee Alexandra Paulus Gabrielle Whitehouse Laurent Verkoczy F Nina Papavasiliou Marilyn Diaz
author_sort	Rafail Nikolaos Tasakis
title	SARS-CoV-2 variant evolution in the United States: High accumulation of viral mutations over time likely through serial Founder Events and mutational bursts.
title_short	SARS-CoV-2 variant evolution in the United States: High accumulation of viral mutations over time likely through serial Founder Events and mutational bursts.
title_full	SARS-CoV-2 variant evolution in the United States: High accumulation of viral mutations over time likely through serial Founder Events and mutational bursts.
title_fullStr	SARS-CoV-2 variant evolution in the United States: High accumulation of viral mutations over time likely through serial Founder Events and mutational bursts.
title_full_unstemmed	SARS-CoV-2 variant evolution in the United States: High accumulation of viral mutations over time likely through serial Founder Events and mutational bursts.
title_sort	sars-cov-2 variant evolution in the united states: high accumulation of viral mutations over time likely through serial founder events and mutational bursts.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/20d9691c69244f98842dd8b3ab74a933
work_keys_str_mv	AT rafailnikolaostasakis sarscov2variantevolutionintheunitedstateshighaccumulationofviralmutationsovertimelikelythroughserialfoundereventsandmutationalbursts AT georgiossamaras sarscov2variantevolutionintheunitedstateshighaccumulationofviralmutationsovertimelikelythroughserialfoundereventsandmutationalbursts AT annajamison sarscov2variantevolutionintheunitedstateshighaccumulationofviralmutationsovertimelikelythroughserialfoundereventsandmutationalbursts AT michellelee sarscov2variantevolutionintheunitedstateshighaccumulationofviralmutationsovertimelikelythroughserialfoundereventsandmutationalbursts AT alexandrapaulus sarscov2variantevolutionintheunitedstateshighaccumulationofviralmutationsovertimelikelythroughserialfoundereventsandmutationalbursts AT gabriellewhitehouse sarscov2variantevolutionintheunitedstateshighaccumulationofviralmutationsovertimelikelythroughserialfoundereventsandmutationalbursts AT laurentverkoczy sarscov2variantevolutionintheunitedstateshighaccumulationofviralmutationsovertimelikelythroughserialfoundereventsandmutationalbursts AT fninapapavasiliou sarscov2variantevolutionintheunitedstateshighaccumulationofviralmutationsovertimelikelythroughserialfoundereventsandmutationalbursts AT marilyndiaz sarscov2variantevolutionintheunitedstateshighaccumulationofviralmutationsovertimelikelythroughserialfoundereventsandmutationalbursts
_version_	1718374212731666432

SARS-CoV-2 variant evolution in the United States: High accumulation of viral mutations over time likely through serial Founder Events and mutational bursts.

Ejemplares similares