Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak

Abstract Background We report a genomic surveillance of SARS-CoV-2 lineages circulating in Paraná, southern Brazil, from March 2020 to April 2021. Our analysis, based on 333 genomes, revealed that the first variants detected in the state of Paraná in March 2020 were the B.1.1.33 and B.1.1.28 variant...

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Autores principales:	Mauro M. Oliveira, Michelle O. Schemberger, Andreia A. Suzukawa, Irina N. Riediger, Maria do Carmo Debur, Guilherme Becker, Paola Cristina Resende, Tiago Gräf, Eduardo Balsanelli, Valter Antônio de Baura, Emanuel M. de Souza, Fábio O. Pedrosa, Lysangela R. Alves, Lucas Blanes, Sheila Cristina Nardelli, Alessandra M. Aguiar, Letusa Albrecht, Dalila Zanette, Andréa R. Ávila, Luis Gustavo Morello, Fabricio K. Marchini, Hellen G. dos Santos, Fabio Passetti, Bruno Dallagiovanna, Helisson Faoro
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Phylogenetic analyses of SARS-CoV-2 VOC Gamma Gamma-like-II and new mutations Infectious and parasitic diseases RC109-216
Acceso en línea:	https://doaj.org/article/f11cacfe52e3448d9fa0fb6c8567f91e
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spelling	oai:doaj.org-article:f11cacfe52e3448d9fa0fb6c8567f91e2021-11-21T12:02:09ZRe-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak10.1186/s12985-021-01690-11743-422Xhttps://doaj.org/article/f11cacfe52e3448d9fa0fb6c8567f91e2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12985-021-01690-1https://doaj.org/toc/1743-422XAbstract Background We report a genomic surveillance of SARS-CoV-2 lineages circulating in Paraná, southern Brazil, from March 2020 to April 2021. Our analysis, based on 333 genomes, revealed that the first variants detected in the state of Paraná in March 2020 were the B.1.1.33 and B.1.1.28 variants. The variants B.1.1.28 and B.1.1.33 were predominant throughout 2020 until the introduction of the variant P.2 in August 2020 and a variant of concern (VOC), Gamma (P.1), in January 2021. The VOC Gamma, a ramification of the B.1.1.28 lineage first detected in Manaus (northern Brazil), has grown rapidly since December 2020 and was thought to be responsible for the deadly second wave of COVID-19 throughout Brazil. Methods The 333 genomic sequences of SARS-CoV-2 from March 2020 to April 2021 were generated as part of the genomic surveillance carried out by Fiocruz in Brazil Genomahcov Fiocruz. SARS-CoV-2 sequencing was performed using representative samples from all geographic areas of Paraná. Phylogenetic analyses were performed using the 333 genomes also included other SARS-CoV-2 genomes from the state of Paraná and other states in Brazil that were deposited in the GISAID. In addition, the time-scaled phylogenetic tree was constructed with up to 3 random sequences of the Gamma variant from each state in Brazil in each month of 2021. In this analysis we also added the sequences identified as the B.1.1.28 lineage of the Amazonas state and and the Gamma-like-II (P.1-like-II) lineage identified in different regions of Brazil. Results Phylogenetic analyses of the SARS-CoV-2 genomes that were previously classified as the VOC Gamma lineage by WHO/PANGO showed that some genomes from February to April 2021 branched in a monophyletic clade and that these samples grouped together with genomes recently described with the lineage Gamma-like-II. Additionally, a new mutation (E661D) in the spike (S) protein has been identified in nearly 10% of the genomes classified as the VOC Gamma from Paraná in March and April 2021.Finally, we analyzed the correlation between the lineage and the Gamma variant frequency, age group (patients younger or older than 60 years old) and the clinical data of 86 cases from the state of Paraná. Conclusions Our results provided a reliable picture of the evolution of the SARS-CoV-2 pandemic in the state of Paraná characterized by the dominance of the Gamma strain, as well as a high frequencies of the Gamma-like-II lineage and the S:E661D mutation. Epidemiological and genomic surveillance efforts should be continued to unveil the biological relevance of the novel mutations detected in the VOC Gamma in Paraná.Mauro M. OliveiraMichelle O. SchembergerAndreia A. SuzukawaIrina N. RiedigerMaria do Carmo DeburGuilherme BeckerPaola Cristina ResendeTiago GräfEduardo BalsanelliValter Antônio de BauraEmanuel M. de SouzaFábio O. PedrosaLysangela R. AlvesLucas BlanesSheila Cristina NardelliAlessandra M. AguiarLetusa AlbrechtDalila ZanetteAndréa R. ÁvilaLuis Gustavo MorelloFabricio K. MarchiniHellen G. dos SantosFabio PassettiBruno DallagiovannaHelisson FaoroBMCarticlePhylogenetic analyses of SARS-CoV-2VOC GammaGamma-like-II and new mutationsInfectious and parasitic diseasesRC109-216ENVirology Journal, Vol 18, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Phylogenetic analyses of SARS-CoV-2 VOC Gamma Gamma-like-II and new mutations Infectious and parasitic diseases RC109-216
spellingShingle	Phylogenetic analyses of SARS-CoV-2 VOC Gamma Gamma-like-II and new mutations Infectious and parasitic diseases RC109-216 Mauro M. Oliveira Michelle O. Schemberger Andreia A. Suzukawa Irina N. Riediger Maria do Carmo Debur Guilherme Becker Paola Cristina Resende Tiago Gräf Eduardo Balsanelli Valter Antônio de Baura Emanuel M. de Souza Fábio O. Pedrosa Lysangela R. Alves Lucas Blanes Sheila Cristina Nardelli Alessandra M. Aguiar Letusa Albrecht Dalila Zanette Andréa R. Ávila Luis Gustavo Morello Fabricio K. Marchini Hellen G. dos Santos Fabio Passetti Bruno Dallagiovanna Helisson Faoro Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak
description	Abstract Background We report a genomic surveillance of SARS-CoV-2 lineages circulating in Paraná, southern Brazil, from March 2020 to April 2021. Our analysis, based on 333 genomes, revealed that the first variants detected in the state of Paraná in March 2020 were the B.1.1.33 and B.1.1.28 variants. The variants B.1.1.28 and B.1.1.33 were predominant throughout 2020 until the introduction of the variant P.2 in August 2020 and a variant of concern (VOC), Gamma (P.1), in January 2021. The VOC Gamma, a ramification of the B.1.1.28 lineage first detected in Manaus (northern Brazil), has grown rapidly since December 2020 and was thought to be responsible for the deadly second wave of COVID-19 throughout Brazil. Methods The 333 genomic sequences of SARS-CoV-2 from March 2020 to April 2021 were generated as part of the genomic surveillance carried out by Fiocruz in Brazil Genomahcov Fiocruz. SARS-CoV-2 sequencing was performed using representative samples from all geographic areas of Paraná. Phylogenetic analyses were performed using the 333 genomes also included other SARS-CoV-2 genomes from the state of Paraná and other states in Brazil that were deposited in the GISAID. In addition, the time-scaled phylogenetic tree was constructed with up to 3 random sequences of the Gamma variant from each state in Brazil in each month of 2021. In this analysis we also added the sequences identified as the B.1.1.28 lineage of the Amazonas state and and the Gamma-like-II (P.1-like-II) lineage identified in different regions of Brazil. Results Phylogenetic analyses of the SARS-CoV-2 genomes that were previously classified as the VOC Gamma lineage by WHO/PANGO showed that some genomes from February to April 2021 branched in a monophyletic clade and that these samples grouped together with genomes recently described with the lineage Gamma-like-II. Additionally, a new mutation (E661D) in the spike (S) protein has been identified in nearly 10% of the genomes classified as the VOC Gamma from Paraná in March and April 2021.Finally, we analyzed the correlation between the lineage and the Gamma variant frequency, age group (patients younger or older than 60 years old) and the clinical data of 86 cases from the state of Paraná. Conclusions Our results provided a reliable picture of the evolution of the SARS-CoV-2 pandemic in the state of Paraná characterized by the dominance of the Gamma strain, as well as a high frequencies of the Gamma-like-II lineage and the S:E661D mutation. Epidemiological and genomic surveillance efforts should be continued to unveil the biological relevance of the novel mutations detected in the VOC Gamma in Paraná.
format	article
author	Mauro M. Oliveira Michelle O. Schemberger Andreia A. Suzukawa Irina N. Riediger Maria do Carmo Debur Guilherme Becker Paola Cristina Resende Tiago Gräf Eduardo Balsanelli Valter Antônio de Baura Emanuel M. de Souza Fábio O. Pedrosa Lysangela R. Alves Lucas Blanes Sheila Cristina Nardelli Alessandra M. Aguiar Letusa Albrecht Dalila Zanette Andréa R. Ávila Luis Gustavo Morello Fabricio K. Marchini Hellen G. dos Santos Fabio Passetti Bruno Dallagiovanna Helisson Faoro
author_facet	Mauro M. Oliveira Michelle O. Schemberger Andreia A. Suzukawa Irina N. Riediger Maria do Carmo Debur Guilherme Becker Paola Cristina Resende Tiago Gräf Eduardo Balsanelli Valter Antônio de Baura Emanuel M. de Souza Fábio O. Pedrosa Lysangela R. Alves Lucas Blanes Sheila Cristina Nardelli Alessandra M. Aguiar Letusa Albrecht Dalila Zanette Andréa R. Ávila Luis Gustavo Morello Fabricio K. Marchini Hellen G. dos Santos Fabio Passetti Bruno Dallagiovanna Helisson Faoro
author_sort	Mauro M. Oliveira
title	Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak
title_short	Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak
title_full	Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak
title_fullStr	Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak
title_full_unstemmed	Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak
title_sort	re-emergence of gamma-like-ii and emergence of gamma-s:e661d sars-cov-2 lineages in the south of brazil after the 2021 outbreak
publisher	BMC
publishDate	2021
url	https://doaj.org/article/f11cacfe52e3448d9fa0fb6c8567f91e
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Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak

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