A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern

Detalhes bibliográficos
Autor(a) principal: Bezerra, Matheus Filgueira
Data de Publicação: 2021
Outros Autores: Machado, Lais Ceschini, Carvalho, Viviane do Carmo Vasconcelos de, Docena, Cássia, Brandão-Filho, Sinval Pinto, Ayres, Constância Flávia Junqueira, Paiva, Marcelo Henrique Santos, Wallau, Gabriel Luz
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/52140
Resumo: Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
id CRUZ_8e7c398419cf1c00f324316d5173dea8
oai_identifier_str oai:www.arca.fiocruz.br:icict/52140
network_acronym_str CRUZ
network_name_str Repositório Institucional da FIOCRUZ (ARCA)
repository_id_str 2135
spelling Bezerra, Matheus FilgueiraMachado, Lais CeschiniCarvalho, Viviane do Carmo Vasconcelos deDocena, CássiaBrandão-Filho, Sinval PintoAyres, Constância Flávia JunqueiraPaiva, Marcelo Henrique SantosWallau, Gabriel Luz2022-04-10T22:25:23Z2022-04-10T22:25:23Z2021BEZERRA, Matheus Filgueira et al. A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern. Infection, Genetics and Evolution, v. 92, p. 1-5, 8 May 2021.1567-1348https://www.arca.fiocruz.br/handle/icict/5214010.1016/j.meegid.2021.104910Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.Fundação Oswaldo Cruz. Instituto Aggeu Magalhães. Departamento de Microbiologia. Recife, PE, Brasil.Fundação Oswaldo Cruz. Instituto Aggeu Magalhães. Departamento de Entomologia e Núcleo de Bioinformática. Recife, PE, Brasil.Fundação Oswaldo Cruz. Instituto Aggeu Magalhães. Núcleo de Plataforma Tecnológica. Recife, PE, Brasil.Fundação Oswaldo Cruz. Instituto Aggeu Magalhães. Núcleo de Plataforma Tecnológica. Recife, PE, Brasil.Fundação Oswaldo Cruz. Instituto Aggeu Magalhães. Departamento de Parasitologia. Recife, PE, Brasil.Fundação Oswaldo Cruz. Instituto Aggeu Magalhães. Departamento de Entomologia e Núcleo de Bioinformática. Recife, PE, Brasil.Fundação Oswaldo Cruz. Instituto Aggeu Magalhães. Departamento de Entomologia e Núcleo de Bioinformática. Recife, PE, Brasil / Universidade Federal de Pernambuco. Centro Acadêmico do Agreste. Núcleo de Ciências da Vida. Caruaru, PE, Brasil.Fundação Oswaldo Cruz. Instituto Aggeu Magalhães. Departamento de Entomologia e Núcleo de Bioinformática. Recife, PE, Brasil.The global spread of new SARS-CoV-2 variants of concern underscore an urgent need of simple deployed molecular tools that can differentiate these lineages. Several tools and protocols have been shared since the beginning of the COVID-19 pandemic, but they need to be timely adapted to cope with SARS-CoV-2 evolution. Although whole-genome sequencing (WGS) of the virus genetic material has been widely used, it still presents practical difficulties such as high cost, shortage of available reagents in the global market, need of a specialized laboratorial infrastructure and well-trained staff. These limitations result in SARS-CoV-2 surveillance blackouts across several countries. Here we propose a rapid and accessible protocol based on Sanger sequencing of a single PCR fragment that is able to identify and discriminate all SARS-CoV-2 variants of concern (VOCs) identified so far, according to each characteristic mutational profile at the Spike-RBD region (K417N/T, E484K, N501Y, A570D). Twelve COVID-19 samples from Brazilian patients were evaluated for both WGS and Sanger sequencing: three P.2, two P.1, six B.1.1 and one B.1.1.117 lineage. All results from the Sanger sequencing method perfectly matched the mutational profile of VOCs and non-VOCs RBD’s characterized by WGS. In summary, this approach allows a much broader network of laboratories to perform molecular surveillance of SARS-CoV-2 VOCs and report results within a shorter time frame, which is of utmost importance in the context of rapid public health decisions in a fast evolving worldwide pandemic.engElsevierhttps://www.arca.fiocruz.br/handle/icict/47064Variantes preocupantesSequenciamento SangerVigilância molecularCOVID-19SARS-CoV-2Variants of concernSanger sequencingMolecular surveillanceCOVID-19SARS-CoV-2A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concerninfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-83134https://www.arca.fiocruz.br/bitstream/icict/52140/1/license.txt0ab46789d568c4ba27c7b5d29a9fe9c4MD51ORIGINALBezerra_Matheus Filgueira_etal_IAM_2021_COVID-19_ARTIGO_FINAL.pdfBezerra_Matheus Filgueira_etal_IAM_2021_COVID-19_ARTIGO_FINAL.pdfapplication/pdf877126https://www.arca.fiocruz.br/bitstream/icict/52140/2/Bezerra_Matheus%20Filgueira_etal_IAM_2021_COVID-19_ARTIGO_FINAL.pdf7cd88967894b95837c53d0094d7c5753MD52icict/521402022-04-10 19:53:05.665oai:www.arca.fiocruz.br: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Repositório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352022-04-10T22:53:05Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false
dc.title.pt_BR.fl_str_mv A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern
title A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern
spellingShingle A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern
Bezerra, Matheus Filgueira
Variantes preocupantes
Sequenciamento Sanger
Vigilância molecular
COVID-19
SARS-CoV-2
Variants of concern
Sanger sequencing
Molecular surveillance
COVID-19
SARS-CoV-2
title_short A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern
title_full A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern
title_fullStr A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern
title_full_unstemmed A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern
title_sort A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern
author Bezerra, Matheus Filgueira
author_facet Bezerra, Matheus Filgueira
Machado, Lais Ceschini
Carvalho, Viviane do Carmo Vasconcelos de
Docena, Cássia
Brandão-Filho, Sinval Pinto
Ayres, Constância Flávia Junqueira
Paiva, Marcelo Henrique Santos
Wallau, Gabriel Luz
author_role author
author2 Machado, Lais Ceschini
Carvalho, Viviane do Carmo Vasconcelos de
Docena, Cássia
Brandão-Filho, Sinval Pinto
Ayres, Constância Flávia Junqueira
Paiva, Marcelo Henrique Santos
Wallau, Gabriel Luz
author2_role author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Bezerra, Matheus Filgueira
Machado, Lais Ceschini
Carvalho, Viviane do Carmo Vasconcelos de
Docena, Cássia
Brandão-Filho, Sinval Pinto
Ayres, Constância Flávia Junqueira
Paiva, Marcelo Henrique Santos
Wallau, Gabriel Luz
dc.subject.other.pt_BR.fl_str_mv Variantes preocupantes
Sequenciamento Sanger
Vigilância molecular
COVID-19
SARS-CoV-2
topic Variantes preocupantes
Sequenciamento Sanger
Vigilância molecular
COVID-19
SARS-CoV-2
Variants of concern
Sanger sequencing
Molecular surveillance
COVID-19
SARS-CoV-2
dc.subject.en.pt_BR.fl_str_mv Variants of concern
Sanger sequencing
Molecular surveillance
COVID-19
SARS-CoV-2
description Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
publishDate 2021
dc.date.issued.fl_str_mv 2021
dc.date.accessioned.fl_str_mv 2022-04-10T22:25:23Z
dc.date.available.fl_str_mv 2022-04-10T22:25:23Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv BEZERRA, Matheus Filgueira et al. A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern. Infection, Genetics and Evolution, v. 92, p. 1-5, 8 May 2021.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/52140
dc.identifier.issn.pt_BR.fl_str_mv 1567-1348
dc.identifier.doi.none.fl_str_mv 10.1016/j.meegid.2021.104910
identifier_str_mv BEZERRA, Matheus Filgueira et al. A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern. Infection, Genetics and Evolution, v. 92, p. 1-5, 8 May 2021.
1567-1348
10.1016/j.meegid.2021.104910
url https://www.arca.fiocruz.br/handle/icict/52140
dc.language.iso.fl_str_mv eng
language eng
dc.relation.isversionof.pt_BR.fl_str_mv https://www.arca.fiocruz.br/handle/icict/47064
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/52140/1/license.txt
https://www.arca.fiocruz.br/bitstream/icict/52140/2/Bezerra_Matheus%20Filgueira_etal_IAM_2021_COVID-19_ARTIGO_FINAL.pdf
bitstream.checksum.fl_str_mv 0ab46789d568c4ba27c7b5d29a9fe9c4
7cd88967894b95837c53d0094d7c5753
bitstream.checksumAlgorithm.fl_str_mv MD5
MD5
repository.name.fl_str_mv Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)
repository.mail.fl_str_mv repositorio.arca@fiocruz.br
_version_ 1798324886122266624

Registros relacionados