Molecular detection of omicron SARS-CoV-2 variant is achieved by RT-LAMP despite genomic mutations

Detalhes bibliográficos
Autor(a) principal: Almeida, Letícia Trindade
Data de Publicação: 2022
Outros Autores: Gonçalves, Amanda Bonoto, Luiz, Ana Paula Moreira Franco, Silva, Thais Bárbara de Souza, Alves, Pedro Augusto, Monte Neto, Rubens Lima do
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/55708
Resumo: Fundação Oswaldo Cruz. Instituto René Rachou. Biotecnologia Aplicada a Patógenos. Belo Horizonte, MG, Brasil.
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spelling Almeida, Letícia TrindadeGonçalves, Amanda BonotoLuiz, Ana Paula Moreira FrancoSilva, Thais Bárbara de SouzaAlves, Pedro AugustoMonte Neto, Rubens Lima do2022-11-18T18:41:23Z2022-11-18T18:41:23Z2022ALMEIDA, Letícia Trindade et al. Molecular detection of omicron SARS-CoV-2 variant is achieved by RT-LAMP despite genomic mutations. Memórias do Instituto Oswaldo Cruz, Rio de Janeiro, v. 117, e220050, p. 1-5, 2022.0074-0276https://www.arca.fiocruz.br/handle/icict/5570810.1590/0074-02760220050engInstituto Oswaldo CruzMolecular detection of omicron SARS-CoV-2 variant is achieved by RT-LAMP despite genomic mutationsinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Instituto René Rachou. Biotecnologia Aplicada a Patógenos. Belo Horizonte, MG, Brasil.Fundação Oswaldo Cruz. Instituto René Rachou. Biotecnologia Aplicada a Patógenos. Belo Horizonte, MG, Brasil.Fundação Oswaldo Cruz. Instituto René Rachou. Biotecnologia Aplicada a Patógenos. Belo Horizonte, MG, Brasil.Fundação Oswaldo Cruz. Instituto René Rachou. Imunologia de Doenças Virais. Belo Horizonte, MG, Brasil.Fundação Oswaldo Cruz. Instituto René Rachou. Imunologia de Doenças Virais. Belo Horizonte, MG, Brasil.Fundação Oswaldo Cruz. Instituto René Rachou. Biotecnologia Aplicada a Patógenos. Belo Horizonte, MG, Brasil.BACKGROUND Severe acute respiratory syndrome coronavirus (SARS-CoV-2) omicron variant was first detected in South Africa in November 2021. Since then, the number of cases due to this variant increases enormously every day in different parts of the world. Mutations within omicron genome may impair the molecular detection resulting in false negative results during Coronavirus disease 19 (COVID-19) diagnosis. OBJECTIVES To verify if colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) targeting N and E genes would work efficiently to detect omicron SARS-CoV-2 variant and its sub-lineages. METHODS SARS-CoV-2 reverse transcription quantitative polymerase chain reaction (RT-qPCR) positive samples were sequenced by next generation DNA sequencing. The consensus sequences generated were submitted to Pangolin tool for SARS-CoV-2 lineage identification. RT-LAMP reactions were performed at 65ºC/30 min targeting N and E. FINDINGS SARS-CoV-2 omicron can be detected by RT-LAMP targeting N and E genes despite the genomic mutation of this more transmissible lineage. Omicron SARS-CoV-2 sub-lineages were tested and efficiently detected by RT-LAMP. We demonstrated that this test is very sensitive in detecting omicron variant, with LoD as low as 0.4 copies/µL. MAIN CONCLUSIONS Molecular detection of omicron SARS-CoV-2 variant and its sub-lineages can be achieved by RT-LAMP despite the genomic mutations as a very sensitive surveillance tool for COVID-19 molecular diagnosis.SARS-CoV-2RT-LAMPomicron Ngenes mutationsCOVID-19info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/55708/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALMolecular detection of omicron SARS-CoV-2 variant is achieved by RT-LAMP despite genomic mutations.pdfMolecular detection of omicron SARS-CoV-2 variant is achieved by RT-LAMP despite genomic 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dc.title.en_US.fl_str_mv Molecular detection of omicron SARS-CoV-2 variant is achieved by RT-LAMP despite genomic mutations
title Molecular detection of omicron SARS-CoV-2 variant is achieved by RT-LAMP despite genomic mutations
spellingShingle Molecular detection of omicron SARS-CoV-2 variant is achieved by RT-LAMP despite genomic mutations
Almeida, Letícia Trindade
SARS-CoV-2
RT-LAMP
omicron N
genes mutations
COVID-19
title_short Molecular detection of omicron SARS-CoV-2 variant is achieved by RT-LAMP despite genomic mutations
title_full Molecular detection of omicron SARS-CoV-2 variant is achieved by RT-LAMP despite genomic mutations
title_fullStr Molecular detection of omicron SARS-CoV-2 variant is achieved by RT-LAMP despite genomic mutations
title_full_unstemmed Molecular detection of omicron SARS-CoV-2 variant is achieved by RT-LAMP despite genomic mutations
title_sort Molecular detection of omicron SARS-CoV-2 variant is achieved by RT-LAMP despite genomic mutations
author Almeida, Letícia Trindade
author_facet Almeida, Letícia Trindade
Gonçalves, Amanda Bonoto
Luiz, Ana Paula Moreira Franco
Silva, Thais Bárbara de Souza
Alves, Pedro Augusto
Monte Neto, Rubens Lima do
author_role author
author2 Gonçalves, Amanda Bonoto
Luiz, Ana Paula Moreira Franco
Silva, Thais Bárbara de Souza
Alves, Pedro Augusto
Monte Neto, Rubens Lima do
author2_role author
author
author
author
author
dc.contributor.author.fl_str_mv Almeida, Letícia Trindade
Gonçalves, Amanda Bonoto
Luiz, Ana Paula Moreira Franco
Silva, Thais Bárbara de Souza
Alves, Pedro Augusto
Monte Neto, Rubens Lima do
dc.subject.en.en_US.fl_str_mv SARS-CoV-2
RT-LAMP
omicron N
genes mutations
topic SARS-CoV-2
RT-LAMP
omicron N
genes mutations
COVID-19
dc.subject.en.none.fl_str_mv COVID-19
description Fundação Oswaldo Cruz. Instituto René Rachou. Biotecnologia Aplicada a Patógenos. Belo Horizonte, MG, Brasil.
publishDate 2022
dc.date.accessioned.fl_str_mv 2022-11-18T18:41:23Z
dc.date.available.fl_str_mv 2022-11-18T18:41:23Z
dc.date.issued.fl_str_mv 2022
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 ALMEIDA, Letícia Trindade et al. Molecular detection of omicron SARS-CoV-2 variant is achieved by RT-LAMP despite genomic mutations. Memórias do Instituto Oswaldo Cruz, Rio de Janeiro, v. 117, e220050, p. 1-5, 2022.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/55708
dc.identifier.issn.en_US.fl_str_mv 0074-0276
dc.identifier.doi.none.fl_str_mv 10.1590/0074-02760220050
identifier_str_mv ALMEIDA, Letícia Trindade et al. Molecular detection of omicron SARS-CoV-2 variant is achieved by RT-LAMP despite genomic mutations. Memórias do Instituto Oswaldo Cruz, Rio de Janeiro, v. 117, e220050, p. 1-5, 2022.
0074-0276
10.1590/0074-02760220050
url https://www.arca.fiocruz.br/handle/icict/55708
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Instituto Oswaldo Cruz
publisher.none.fl_str_mv Instituto Oswaldo Cruz
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
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bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/55708/1/license.txt
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