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

Autor:	Almeida LT; Fundação Oswaldo Cruz-Fiocruz, Instituto René Rachou, Biotecnologia Aplicada a Patógenos, Belo Horizonte, MG, Brasil., Gonçalves AB; Fundação Oswaldo Cruz-Fiocruz, Instituto René Rachou, Biotecnologia Aplicada a Patógenos, Belo Horizonte, MG, Brasil., Franco-Luiz APM; Fundação Oswaldo Cruz-Fiocruz, Instituto René Rachou, Biotecnologia Aplicada a Patógenos, Belo Horizonte, MG, Brasil., Silva TBS; Fundação Oswaldo Cruz-Fiocruz, Instituto René Rachou, Imunologia de Doenças Virais, Belo Horizonte, MG, Brasil., Alves PA; Fundação Oswaldo Cruz-Fiocruz, Instituto René Rachou, Imunologia de Doenças Virais, Belo Horizonte, MG, Brasil., Monte-Neto RLD; Fundação Oswaldo Cruz-Fiocruz, Instituto René Rachou, Biotecnologia Aplicada a Patógenos, Belo Horizonte, MG, Brasil.
Jazyk:	angličtina
Zdroj:	Memorias do Instituto Oswaldo Cruz [Mem Inst Oswaldo Cruz] 2022 Jun 22; Vol. 117, pp. e220050. Date of Electronic Publication: 2022 Jun 22 (Print Publication: 2022).
DOI:	10.1590/0074-02760220050
Abstrakt:	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.
Databáze:	MEDLINE
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