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Molecular detection of omicron SARS-CoV-2 variant is achieved by RT-LAMP despite genomic mutations
Almeida, Letícia Trindade; Gonçalves, Amanda Bonoto; Franco-Luiz, Ana Paula Moreira; Silva, Thais Bárbara de Souza; Alves, Pedro Augusto; Monte-Neto, Rubens Lima do.
  • Almeida, Letícia Trindade; Fundação Oswaldo Cruz-Fiocruz. Instituto René Rachou. Biotecnologia Aplicada a Patógenos. Belo Horizonte. BR
  • Gonçalves, Amanda Bonoto; Fundação Oswaldo Cruz-Fiocruz. Instituto René Rachou. Biotecnologia Aplicada a Patógenos. Belo Horizonte. BR
  • Franco-Luiz, Ana Paula Moreira; Fundação Oswaldo Cruz-Fiocruz. Instituto René Rachou. Biotecnologia Aplicada a Patógenos. Belo Horizonte. BR
  • Silva, Thais Bárbara de Souza; Fundação Oswaldo Cruz-Fiocruz. Instituto René Rachou. Imunologia de Doenças Virais. Belo Horizonte. BR
  • Alves, Pedro Augusto; Fundação Oswaldo Cruz-Fiocruz. Instituto René Rachou. Imunologia de Doenças Virais. Belo Horizonte. BR
  • Monte-Neto, Rubens Lima do; Fundação Oswaldo Cruz-Fiocruz. Instituto René Rachou. Biotecnologia Aplicada a Patógenos. Belo Horizonte. BR
Mem. Inst. Oswaldo Cruz ; 117: e220050, 2022. graf
Article in English | LILACS-Express | LILACS | ID: biblio-1386350
ABSTRACT
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.


Full text: Available Index: LILACS (Americas) Type of study: Diagnostic study / Prognostic study Language: English Journal: Mem. Inst. Oswaldo Cruz Journal subject: Tropical Medicine / Parasitology Year: 2022 Type: Article / Project document Affiliation country: Brazil Institution/Affiliation country: Fundação Oswaldo Cruz-Fiocruz/BR

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Full text: Available Index: LILACS (Americas) Type of study: Diagnostic study / Prognostic study Language: English Journal: Mem. Inst. Oswaldo Cruz Journal subject: Tropical Medicine / Parasitology Year: 2022 Type: Article / Project document Affiliation country: Brazil Institution/Affiliation country: Fundação Oswaldo Cruz-Fiocruz/BR