The Influence of the Omicron Variant on RNA Extraction and RT-qPCR Detection of SARS-CoV-2 in a Laboratory in Brazil

The emergence of SARS-CoV-2 variants can affect their detection via RT-qPCR. The Omicron variant has a greater affinity for the upper respiratory system and causes clinical conditions similar to bronchitis, as opposed to the pneumonitis-like conditions caused by other SARS-CoV-2 variants. This chara...

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Bibliographic Details
Published in:Viruses 2023-08, Vol.15 (8), p.1690
Main Authors: Silva, Lívia Mara, Riani, Lorena Rodrigues, Leite, Juliana Brovini, de Assis Chagas, Jessica Mara, Fernandes, Laura Silva, Fochat, Romário Costa, Perches, Carmen Gomide Pinto, Nascimento, Thiago César, Jaeger, Lauren Hubert, Silvério, Marcelo Silva, dos Santos Pereira-Júnior, Olavo, Pittella, Frederico
Format: Article
Language:English
Subjects:
Amino acids
Bronchitis
Communication
Cooling
COVID-19
diagnostics
Enzymes
Extraction (Chemistry)
Gene amplification
Gene expression
Laboratories
Methods
Mutation
Nucleic acids
Omicron variant
Pneumonitis
Polymerase chain reaction
Proteins
Reagents
Respiratory system
RT-qPCR
SARS-CoV-2
Separation
Severe acute respiratory syndrome coronavirus 2
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Summary:The emergence of SARS-CoV-2 variants can affect their detection via RT-qPCR. The Omicron variant has a greater affinity for the upper respiratory system and causes clinical conditions similar to bronchitis, as opposed to the pneumonitis-like conditions caused by other SARS-CoV-2 variants. This characteristic increases the viscosity of clinical samples collected for diagnosis. Coinciding with the arrival of the Omicron variant, we observed a failure in control gene expression in our laboratory. In this report, we have optimized a rapid nucleic acid extraction step to restore gene expression and detect the presence of the SARS-CoV-2 virus. We reevaluated 3000 samples, compared variant types occurring in different time periods, and confirmed that the presence of the Omicron variant was responsible for changes observed in the characteristics of these clinical samples. For samples with large amounts of mucus, such as those containing the Omicron variant, a modification to the nucleic acid extraction step was sufficient to restore the quality of RT-qPCR results.
ISSN:1999-4915
1999-4915
DOI:10.3390/v15081690