Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil.

The sharp increase of COVID-19 cases in late 2020 has made Brazil the new epicenter of the ongoing SARS-CoV-2 pandemic. The novel viral lineages P.1 (Variant of Concern Gamma) and P.2, respectively identified in the Brazilian states of Amazonas and Rio de Janeiro, have been associated with potential...

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Autores principales:	Alessandra P Lamarca, Luiz G P de Almeida, Ronaldo da Silva Francisco, Lucymara Fassarella Agnez Lima, Kátia Castanho Scortecci, Vinícius Pietta Perez, Otavio J Brustolini, Eduardo Sérgio Soares Sousa, Danielle Angst Secco, Angela Maria Guimarães Santos, George Rego Albuquerque, Ana Paula Melo Mariano, Bianca Mendes Maciel, Alexandra L Gerber, Ana Paula de C Guimarães, Paulo Ricardo Nascimento, Francisco Paulo Freire Neto, Sandra Rocha Gadelha, Luís Cristóvão Porto, Eloiza Helena Campana, Selma Maria Bezerra Jeronimo, Ana Tereza R Vasconcelos
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270
Acceso en línea:	https://doaj.org/article/5e180e4cbe264088acf63130e070529d
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spelling	oai:doaj.org-article:5e180e4cbe264088acf63130e070529d2021-12-02T20:23:35ZGenomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil.1935-27271935-273510.1371/journal.pntd.0009835https://doaj.org/article/5e180e4cbe264088acf63130e070529d2021-10-01T00:00:00Zhttps://doi.org/10.1371/journal.pntd.0009835https://doaj.org/toc/1935-2727https://doaj.org/toc/1935-2735The sharp increase of COVID-19 cases in late 2020 has made Brazil the new epicenter of the ongoing SARS-CoV-2 pandemic. The novel viral lineages P.1 (Variant of Concern Gamma) and P.2, respectively identified in the Brazilian states of Amazonas and Rio de Janeiro, have been associated with potentially higher transmission rates and antibody neutralization escape. In this study, we performed the whole-genome sequencing of 185 samples isolated from three out of the five Brazilian regions, including Amazonas (North region), Rio Grande do Norte, Paraíba and Bahia (Northeast region), and Rio de Janeiro (Southeast region) in order to monitor the spread of SARS-CoV-2 lineages in Brazil in the first months of 2021. Here, we showed a widespread dispersal of P.1 and P.2 across Brazilian regions and, except for Amazonas, P.2 was the predominant lineage identified in the sampled states. We estimated the origin of P.2 lineage to have happened in February, 2020 and identified that it has differentiated into new clades. Interstate transmission of P.2 was detected since March, but reached its peak in December, 2020 and January, 2021. Transmission of P.1 was also high in December and its origin was inferred to have happened in August 2020. We also confirmed the presence of lineage P.7, recently described in the southernmost region of Brazil, to have spread across the Northeastern states. P.1, P.2 and P.7 are descended from the ancient B.1.1.28 strain, which co-dominated the first phase of the pandemic in Brazil with the B.1.1.33 strain. We also identified the occurrence of a new lineage descending from B.1.1.33 that convergently carries the E484K mutation, N.9. Indeed, the recurrent report of many novel SARS-CoV-2 genetic variants in Brazil could be due to the absence of effective control measures resulting in high SARS-CoV2 transmission rates. Altogether, our findings provided a landscape of the critical state of SARS-CoV-2 across Brazil and confirm the need to sustain continuous sequencing of the SARS-CoV-2 isolates worldwide in order to identify novel variants of interest and monitor for vaccine effectiveness.Alessandra P LamarcaLuiz G P de AlmeidaRonaldo da Silva FranciscoLucymara Fassarella Agnez LimaKátia Castanho ScortecciVinícius Pietta PerezOtavio J BrustoliniEduardo Sérgio Soares SousaDanielle Angst SeccoAngela Maria Guimarães SantosGeorge Rego AlbuquerqueAna Paula Melo MarianoBianca Mendes MacielAlexandra L GerberAna Paula de C GuimarãesPaulo Ricardo NascimentoFrancisco Paulo Freire NetoSandra Rocha GadelhaLuís Cristóvão PortoEloiza Helena CampanaSelma Maria Bezerra JeronimoAna Tereza R VasconcelosPublic Library of Science (PLoS)articleArctic medicine. Tropical medicineRC955-962Public aspects of medicineRA1-1270ENPLoS Neglected Tropical Diseases, Vol 15, Iss 10, p e0009835 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270
spellingShingle	Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 Alessandra P Lamarca Luiz G P de Almeida Ronaldo da Silva Francisco Lucymara Fassarella Agnez Lima Kátia Castanho Scortecci Vinícius Pietta Perez Otavio J Brustolini Eduardo Sérgio Soares Sousa Danielle Angst Secco Angela Maria Guimarães Santos George Rego Albuquerque Ana Paula Melo Mariano Bianca Mendes Maciel Alexandra L Gerber Ana Paula de C Guimarães Paulo Ricardo Nascimento Francisco Paulo Freire Neto Sandra Rocha Gadelha Luís Cristóvão Porto Eloiza Helena Campana Selma Maria Bezerra Jeronimo Ana Tereza R Vasconcelos Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil.
description	The sharp increase of COVID-19 cases in late 2020 has made Brazil the new epicenter of the ongoing SARS-CoV-2 pandemic. The novel viral lineages P.1 (Variant of Concern Gamma) and P.2, respectively identified in the Brazilian states of Amazonas and Rio de Janeiro, have been associated with potentially higher transmission rates and antibody neutralization escape. In this study, we performed the whole-genome sequencing of 185 samples isolated from three out of the five Brazilian regions, including Amazonas (North region), Rio Grande do Norte, Paraíba and Bahia (Northeast region), and Rio de Janeiro (Southeast region) in order to monitor the spread of SARS-CoV-2 lineages in Brazil in the first months of 2021. Here, we showed a widespread dispersal of P.1 and P.2 across Brazilian regions and, except for Amazonas, P.2 was the predominant lineage identified in the sampled states. We estimated the origin of P.2 lineage to have happened in February, 2020 and identified that it has differentiated into new clades. Interstate transmission of P.2 was detected since March, but reached its peak in December, 2020 and January, 2021. Transmission of P.1 was also high in December and its origin was inferred to have happened in August 2020. We also confirmed the presence of lineage P.7, recently described in the southernmost region of Brazil, to have spread across the Northeastern states. P.1, P.2 and P.7 are descended from the ancient B.1.1.28 strain, which co-dominated the first phase of the pandemic in Brazil with the B.1.1.33 strain. We also identified the occurrence of a new lineage descending from B.1.1.33 that convergently carries the E484K mutation, N.9. Indeed, the recurrent report of many novel SARS-CoV-2 genetic variants in Brazil could be due to the absence of effective control measures resulting in high SARS-CoV2 transmission rates. Altogether, our findings provided a landscape of the critical state of SARS-CoV-2 across Brazil and confirm the need to sustain continuous sequencing of the SARS-CoV-2 isolates worldwide in order to identify novel variants of interest and monitor for vaccine effectiveness.
format	article
author	Alessandra P Lamarca Luiz G P de Almeida Ronaldo da Silva Francisco Lucymara Fassarella Agnez Lima Kátia Castanho Scortecci Vinícius Pietta Perez Otavio J Brustolini Eduardo Sérgio Soares Sousa Danielle Angst Secco Angela Maria Guimarães Santos George Rego Albuquerque Ana Paula Melo Mariano Bianca Mendes Maciel Alexandra L Gerber Ana Paula de C Guimarães Paulo Ricardo Nascimento Francisco Paulo Freire Neto Sandra Rocha Gadelha Luís Cristóvão Porto Eloiza Helena Campana Selma Maria Bezerra Jeronimo Ana Tereza R Vasconcelos
author_facet	Alessandra P Lamarca Luiz G P de Almeida Ronaldo da Silva Francisco Lucymara Fassarella Agnez Lima Kátia Castanho Scortecci Vinícius Pietta Perez Otavio J Brustolini Eduardo Sérgio Soares Sousa Danielle Angst Secco Angela Maria Guimarães Santos George Rego Albuquerque Ana Paula Melo Mariano Bianca Mendes Maciel Alexandra L Gerber Ana Paula de C Guimarães Paulo Ricardo Nascimento Francisco Paulo Freire Neto Sandra Rocha Gadelha Luís Cristóvão Porto Eloiza Helena Campana Selma Maria Bezerra Jeronimo Ana Tereza R Vasconcelos
author_sort	Alessandra P Lamarca
title	Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil.
title_short	Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil.
title_full	Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil.
title_fullStr	Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil.
title_full_unstemmed	Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil.
title_sort	genomic surveillance of sars-cov-2 tracks early interstate transmission of p.1 lineage and diversification within p.2 clade in brazil.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/5e180e4cbe264088acf63130e070529d
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Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil.

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