|
1
|
Silva LM, Riani LR, Leite JB, de Assis Chagas JM, Fernandes LS, Fochat RC, Perches CGP, Nascimento TC, Jaeger LH, Silvério MS, dos Santos Pereira-Júnior O, Pittella F. The Influence of the Omicron Variant on RNA Extraction and RT-qPCR Detection of SARS-CoV-2 in a Laboratory in Brazil. Viruses 2023; 15:1690. [PMID: 37632032 PMCID: PMC10458054 DOI: 10.3390/v15081690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/19/2023] [Accepted: 07/30/2023] [Indexed: 08/27/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- Lívia Mara Silva
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Lorena Rodrigues Riani
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Juliana Brovini Leite
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Jessica Mara de Assis Chagas
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Laura Silva Fernandes
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Romário Costa Fochat
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Carmen Gomide Pinto Perches
- Hospital Universitário, Universidade Federal de Juiz de Fora, Av. Eugênio do Nascimento, s/n, Juiz de Fora 36038-330, MG, Brazil;
| | - Thiago César Nascimento
- Faculdade de Enfermagem, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil;
| | - Lauren Hubert Jaeger
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Marcelo Silva Silvério
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Olavo dos Santos Pereira-Júnior
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Frederico Pittella
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| |
Collapse
|
|
2
|
Wang Y, Wang C, Zhou Z, Si J, Li S, Zeng Y, Deng Y, Chen Z. Advances in Simple, Rapid, and Contamination-Free Instantaneous Nucleic Acid Devices for Pathogen Detection. BIOSENSORS 2023; 13:732. [PMID: 37504131 PMCID: PMC10377012 DOI: 10.3390/bios13070732] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 07/29/2023]
Abstract
Pathogenic pathogens invade the human body through various pathways, causing damage to host cells, tissues, and their functions, ultimately leading to the development of diseases and posing a threat to human health. The rapid and accurate detection of pathogenic pathogens in humans is crucial and pressing. Nucleic acid detection offers advantages such as higher sensitivity, accuracy, and specificity compared to antibody and antigen detection methods. However, conventional nucleic acid testing is time-consuming, labor-intensive, and requires sophisticated equipment and specialized medical personnel. Therefore, this review focuses on advanced nucleic acid testing systems that aim to address the issues of testing time, portability, degree of automation, and cross-contamination. These systems include extraction-free rapid nucleic acid testing, fully automated extraction, amplification, and detection, as well as fully enclosed testing and commercial nucleic acid testing equipment. Additionally, the biochemical methods used for extraction, amplification, and detection in nucleic acid testing are briefly described. We hope that this review will inspire further research and the development of more suitable extraction-free reagents and fully automated testing devices for rapid, point-of-care diagnostics.
Collapse
Affiliation(s)
- Yue Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Chengming Wang
- Department of Cardiovascular Medicine, The Affiliated Zhuzhou Hospital Xiangya Medical College, Central South University, Zhuzhou 412000, China
| | - Zepeng Zhou
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Jiajia Si
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yezhan Zeng
- School of Electrical and Information Engineering, Hunan University of Technology, Zhuzhou 412007, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| |
Collapse
|
|
3
|
Bogožalec Košir A, Lužnik D, Tomič V, Milavec M. Evaluation of DNA Extraction Methods for Reliable Quantification of Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa. BIOSENSORS 2023; 13:bios13040463. [PMID: 37185538 PMCID: PMC10136035 DOI: 10.3390/bios13040463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/25/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023]
Abstract
Detection and quantification of DNA biomarkers relies heavily on the yield and quality of DNA obtained by extraction from different matrices. Although a large number of studies have compared the yields of different extraction methods, the repeatability and intermediate precision of these methods have been largely overlooked. In the present study, five extraction methods were evaluated, using digital PCR, to determine their efficiency in extracting DNA from three different Gram-negative bacteria in sputum samples. The performance of two automated methods (GXT NA and QuickPick genomic DNA extraction kit, using Arrow and KingFisher Duo automated systems, respectively), two manual kit-based methods (QIAamp DNA mini kit; DNeasy UltraClean microbial kit), and one manual non-kit method (CTAB), was assessed. While GXT NA extraction kit and the CTAB method have the highest DNA yield, they did not meet the strict criteria for repeatability, intermediate precision, and measurement uncertainty for all three studied bacteria. However, due to limited clinical samples, a compromise is necessary, and the GXT NA extraction kit was found to be the method of choice. The study also showed that dPCR allowed for accurate determination of extraction method repeatability, which can help standardize molecular diagnostic approaches. Additionally, the determination of absolute copy numbers facilitated the calculation of measurement uncertainty, which was found to be influenced by the DNA extraction method used.
Collapse
Affiliation(s)
- Alexandra Bogožalec Košir
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000 Ljubljana, Slovenia
| | - Dane Lužnik
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik 36, 4204 Golnik, Slovenia
| | - Viktorija Tomič
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik 36, 4204 Golnik, Slovenia
| | - Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000 Ljubljana, Slovenia
| |
Collapse
|
|
4
|
Comparison of Two RNA Extraction Methods for the Molecular Detection of SARS-CoV-2 from Nasopharyngeal Swab Samples. Diagnostics (Basel) 2022; 12:diagnostics12071561. [PMID: 35885467 PMCID: PMC9317615 DOI: 10.3390/diagnostics12071561] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 11/23/2022] Open
Abstract
Background: Rapid diagnosis of COVID-19 is essential in order to restrict the spread of the pandemic, and different approaches for SARS-CoV-2 testing have been proposed as cost-effective and less time-consuming alternatives. For virus detection, the real-time reverse transcriptase–polymerase chain reaction (RT-PCR) technique is still the “gold standard” for accuracy and reliability, but its performance is affected by the efficiency of nucleic acid extraction methods. Objective: In order to improve the SARS-CoV-2 diagnostic workflow, we compared a “standard” commercially available kit, based on viral RNA extraction from human swab samples by magnetic beads, with its technological evolution. The two methods differ mainly in their time consumption (9 vs. 35 min). Methods: We adopted the MAGABIO PLUS VIRUS DNA/RNA PURIFICATION KIT II (BIOER), defined as “standard”, with the automatic extractor BIOER (GenePure Pro fully automatic nucleic acid purification system) to isolate RNA from nasopharyngeal swabs for the detection of SARS-CoV-2 by RT-PCR. We tested this kit with a new faster version of the first one, defined as “rapid” (MAGABIO PLUS VIRUS RNA PURIFICATION KIT II). Results and Conclusion: The two evaluated procedures provided similar analytical results, but the faster method proved to be a more suitable tool for the detection of SARS-CoV-2 from nasopharyngeal swabs, due to a more rapid availability of results, which may contribute to improving both clinical decision making and patient safety.
Collapse
|