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Maung Myint T, Chong CH, von Huben A, Attia J, Webster AC, Blosser CD, Craig JC, Teixeira-Pinto A, Wong G. Serum and urine nucleic acid screening tests for BK polyomavirus-associated nephropathy in kidney and kidney-pancreas transplant recipients. Cochrane Database Syst Rev 2024; 11:CD014839. [PMID: 39606952 PMCID: PMC11603539 DOI: 10.1002/14651858.cd014839.pub2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
Abstract
BACKGROUND BK polyomavirus-associated nephropathy (BKPyVAN) occurs when BK polyomavirus (BKPyV) affects a transplanted kidney, leading to an initial injury characterised by cytopathic damage, inflammation, and fibrosis. BKPyVAN may cause permanent loss of graft function and premature graft loss. Early detection gives clinicians an opportunity to intervene by timely reduction in immunosuppression to reduce adverse graft outcomes. Quantitative nucleic acid testing (QNAT) for detection of BKPyV DNA in blood and urine is increasingly used as a screening test as diagnosis of BKPyVAN by kidney biopsy is invasive and associated with procedural risks. In this review, we assessed the sensitivity and specificity of QNAT tests in patients with BKPyVAN. OBJECTIVES We assessed the diagnostic test accuracy of blood/plasma/serum BKPyV QNAT and urine BKPyV QNAT for the diagnosis of BKPyVAN after transplantation. We also investigated the following sources of heterogeneity: types and quality of studies, era of publication, various thresholds of BKPyV-DNAemia/BKPyV viruria and variability between assays as secondary objectives. SEARCH METHODS We searched MEDLINE (OvidSP), EMBASE (OvidSP), and BIOSIS, and requested a search of the Cochrane Register of diagnostic test accuracy studies from inception to 13 June 2023. We also searched ClinicalTrials.com and the WHO International Clinical Trials Registry Platform for ongoing trials. SELECTION CRITERIA We included cross-sectional or cohort studies assessing the diagnostic accuracy of two index tests (blood/plasma/serum BKPyV QNAT or urine BKPyV QNAT) for the diagnosis of BKPyVAN, as verified by the reference standard (histopathology). Both retrospective and prospective cohort studies were included. We did not include case reports and case control studies. DATA COLLECTION AND ANALYSIS Two authors independently carried out data extraction from each study. We assessed the methodological quality of the included studies by using Quality Assessment of Diagnostic-Accuracy Studies (QUADAS-2) assessment criteria. We used the bivariate random-effects model to obtain summary estimates of sensitivity and specificity for the QNAT test with one positivity threshold. In cases where meta-analyses were not possible due to the small number of studies available, we detailed the descriptive evidence and used a summative approach. We explored possible sources of heterogeneity by adding covariates to meta-regression models. MAIN RESULTS We included 31 relevant studies with a total of 6559 participants in this review. Twenty-six studies included kidney transplant recipients, four studies included kidney and kidney-pancreas transplant recipients, and one study included kidney, kidney-pancreas and kidney-liver transplant recipients. Studies were carried out in South Asia and the Asia-Pacific region (12 studies), North America (9 studies), Europe (8 studies), and South America (2 studies). INDEX TEST blood/serum/plasma BKPyV QNAT The diagnostic performance of blood BKPyV QNAT using a common viral load threshold of 10,000 copies/mL was reported in 18 studies (3434 participants). Summary estimates at 10,000 copies/mL as a cut-off indicated that the pooled sensitivity was 0.86 (95% confidence interval (CI) 0.78 to 0.93) while the pooled specificity was 0.95 (95% CI 0.91 to 0.97). A limited number of studies were available to analyse the summary estimates for individual viral load thresholds other than 10,000 copies/mL. Indirect comparison of thresholds of the three different cut-off values of 1000 copies/mL (9 studies), 5000 copies/mL (6 studies), and 10,000 copies/mL (18 studies), the higher cut-off value at 10,000 copies/mL corresponded to higher specificity with lower sensitivity. The summary estimates of indirect comparison of thresholds above 10,000 copies/mL were uncertain, primarily due to a limited number of studies with wide CIs contributed to the analysis. Nonetheless, these indirect comparisons should be interpreted cautiously since differences in study design, patient populations, and methodological variations among the included studies can introduce biases. Analysis of all blood BKPyV QNAT studies, including various blood viral load thresholds (30 studies, 5658 participants, 7 thresholds), indicated that test performance remains robust, pooled sensitivity 0.90 (95% CI 0.85 to 0.94) and specificity 0.93 (95% CI 0.91 to 0.95). In the multiple cut-off model, including the various thresholds generating a single curve, the optimal cut-off was around 2000 copies/mL, sensitivity of 0.89 (95% CI 0.66 to 0.97) and specificity of 0.88 (95% CI 0.80 to 0.93). However, as most of the included studies were retrospective, and not all participants underwent the reference standard tests, this may result in a high risk of selection and verification bias. INDEX TEST urine BKPyV QNAT There was insufficient data to thoroughly investigate both accuracy and thresholds of urine BKPyV QNAT resulting in an imprecise estimation of its accuracy based on the available evidence. AUTHORS' CONCLUSIONS There is insufficient evidence to suggest the use of urine BKPyV QNAT as the primary screening tool for BKPyVAN. The summary estimates of the test sensitivity and specificity of blood/serum/plasma BKPyV QNAT test at a threshold of 10,000 copies/mL for BKPyVAN were 0.86 (95% CI 0.78 to 0.93) and 0.95 (95% CI 0.91 to 0.97), respectively. The multiple cut-off model showed that the optimal cut-off was around 2000 copies/mL, with test sensitivity of 0.89 (95% CI 0.66 to 0.97) and specificity of 0.88 (95% CI 0.80 to 0.93). While 10,000 copies/mL is the most commonly used cut-off, with good test performance characteristics and supports the current recommendations, it is important to interpret the results with caution because of low-certainty evidence.
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Affiliation(s)
- Thida Maung Myint
- John Hunter Hospital, Newcastle, Australia
- Sydney School of Public Health, University of Sydney, Sydney, Australia
| | - Chanel H Chong
- Sydney School of Public Health, University of Sydney, Sydney, Australia
| | - Amy von Huben
- Sydney School of Public Health, University of Sydney, Sydney, Australia
| | - John Attia
- University of Newcastle, Newcastle, Australia
| | - Angela C Webster
- Sydney School of Public Health, University of Sydney, Sydney, Australia
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Westmead Applied Research Centre, The University of Sydney at Westmead, Westmead, Australia
- Centre for Transplant and Renal Research, Westmead Hospital, Westmead, Australia
| | - Christopher D Blosser
- Department of Medicine, Nephrology, University of Washington & Seattle Children's Hospital, Seattle, WA, USA
| | - Jonathan C Craig
- College of Medicine and Public Health, Flinders University, Adelaide, Australia
- Cochrane Kidney and Transplant, Centre for Kidney Research, The Children's Hospital at Westmead, Westmead, Australia
| | | | - Germaine Wong
- Sydney School of Public Health, University of Sydney, Sydney, Australia
- Centre for Transplant and Renal Research, Westmead Hospital, Westmead, Australia
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Shrewsbury JV, Vitus ES, Koziol AL, Nenarokova A, Jess T, Elmahdi R. Comprehensive phage display viral antibody profiling using VirScan: potential applications in chronic immune-mediated disease. J Virol 2024; 98:e0110224. [PMID: 39431820 PMCID: PMC11575288 DOI: 10.1128/jvi.01102-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2024] Open
Abstract
Phage immunoprecipitation sequencing (PhIP-Seq) is a high-throughput platform that uses programmable phage display for serology. VirScan, a specific PhIP-Seq library encoding viral peptides from all known human viruses, enables comprehensive quantification of past viral exposures. We review its use in immune-mediated diseases (IMDs), highlighting its utility in identifying viral exposures in the context of IMD development. Finally, we evaluate its potential for precision medicine by integrating it with other large-scale omics data sets.
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Affiliation(s)
- Jed Valentiner Shrewsbury
- Faculty of Medicine, Imperial College London, London, United Kingdom
- Ashford and St. Peter's Hospitals NHS Foundation Trust, Chertsey, United Kingdom
| | - Evangelin Shaloom Vitus
- Centre for Molecular Prediction of Inflammatory Bowel Disease (PREDICT), Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
| | - Adam Leslie Koziol
- Centre for Molecular Prediction of Inflammatory Bowel Disease (PREDICT), Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
| | | | - Tine Jess
- Centre for Molecular Prediction of Inflammatory Bowel Disease (PREDICT), Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Department of Gastroenterology and Hepatology, Aalborg University Hospital, Aalborg, Denmark
| | - Rahma Elmahdi
- Centre for Molecular Prediction of Inflammatory Bowel Disease (PREDICT), Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Department of Gastroenterology and Hepatology, Aalborg University Hospital, Aalborg, Denmark
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3
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Sajal SSA, Islam DZ, Khandker SS, Solórzano-Ortiz E, Fardoun M, Ahmed MF, Jamiruddin MR, Azmuda N, Mehta M, Kumar S, Haque M, Adnan N. Strategies to Overcome Erroneous Outcomes in Reverse Transcription-Polymerase Chain Reaction (RT-PCR) Testing: Insights From the COVID-19 Pandemic. Cureus 2024; 16:e72954. [PMID: 39498425 PMCID: PMC11532724 DOI: 10.7759/cureus.72954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2024] [Accepted: 11/03/2024] [Indexed: 11/07/2024] Open
Abstract
The reverse transcription-polymerase chain reaction (RT-PCR) test to detect SARS-CoV-2, the virus causing COVID-19, has been regarded as the diagnostic gold standard. However, the excessive sensitivity of RT-PCR may cause false-positive outcomes from contamination. Again, its technical complexity increases the chances of false-negatives due to pre-analytical and analytical errors. This narrative review explores the elements contributing to inaccurate results during the COVID-19 pandemic and offers strategies to minimize these errors. False-positive results may occur due to specimen contamination, non-specific primer binding, residual viral RNA, and false-negatives, which may arise from improper sampling, timing, labeling, storage, low viral loads, mutations, and faulty test kits. Proposed mitigation strategies to enhance the accuracy of RT-PCR testing include comprehensive staff training in specimen collection, optimizing the timing of tests, analyzing multiple gene targets, incorporating clinical findings, workflow automation, and implementing stringent contamination control measures. Identifying and rectifying sources of error in RT-PCR diagnosis through quality control and standardized protocols is imperative for ensuring quality patient care and effective epidemic control.
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Affiliation(s)
- Sm Shafiul Alam Sajal
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Dhaka, BGD
| | | | - Shahad Saif Khandker
- Department of Microbiology, Gonoshasthaya Samaj Vittik Medical College, Dhaka, BGD
| | - Elizabeth Solórzano-Ortiz
- Department of Chemical, Biological, Biomedical and Biophysical Research, Mariano Gálvez University, Guatemala City, GTM
| | - Manal Fardoun
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, LBN
| | - Md Firoz Ahmed
- Department of Microbiology, Jahangirnagar University, Dhaka, BGD
| | - Mohd Raeed Jamiruddin
- Department of Pharmacy, Bangladesh Rural Advancement Committee (BRAC) University, Dhaka, BGD
| | - Nafisa Azmuda
- Department of Microbiology, Jahangirnagar University, Dhaka, BGD
| | - Miral Mehta
- Department of Pedodontics and Preventive Dentistry, Karnavati School of Dentistry, Karnavati University, Gandhinagar, IND
| | - Santosh Kumar
- Department of Periodontology and Implantology, Karnavati School of Dentistry, Karnavati University, Gandhinagar, IND
| | - Mainul Haque
- Department of Pharmacology and Therapeutics, National Defence University of Malaysia, Kuala Lumpur, MYS
| | - Nihad Adnan
- Department of Microbiology, Jahangirnagar University, Dhaka, BGD
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4
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Feng W, Chen Y, Han Y, Diao Z, Zhao Z, Zhang Y, Huang T, Ma Y, Li Z, Jiang J, Li J, Li J, Zhang R. Key performance evaluation of commercialized multiplex rRT-PCR kits for respiratory viruses: implications for application and optimization. Microbiol Spectr 2024; 12:e0164124. [PMID: 39470276 PMCID: PMC11619282 DOI: 10.1128/spectrum.01641-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 10/06/2024] [Indexed: 10/30/2024] Open
Abstract
Respiratory tract infections (RTIs) caused by viruses are prevalent and significant conditions in clinical settings. Accurate and effective detection is of paramount importance in the diagnosis, treatment, and prevention of viral RTIs. With technological advancements, multiplex real-time reverse transcription polymerase chain reaction (rRT-PCR) assays have been developed and extensively adopted for the diagnosis of viral RTIs. Given the potential challenges in the detection performance of multiplex assays, this study evaluated the analytical sensitivity and competitive interference of the six most commonly used multiplex rRT-PCR kits for detection of respiratory viruses in China. The results revealed that the limits of detection were variable across the viruses and kits. Most of the evaluated multiplex kits demonstrated comparable or enhanced analytical sensitivity compared with singleplex kits for clinically significant viruses, including human adenovirus (HAdV)-3, HAdV-7, Omicron BA.5, H1N1pdm09, H3N2, B/Victoria, respiratory syncytial virus subtype A, and respiratory syncytial virus subtype B, whereas multiplex kits showed relatively less analytical sensitivity for human rhinovirus-B72, human metapneumovirus-A2, parainfluenza virus (PIV)-1, and PIV-3. In addition, most multiplex kits successfully identified co-infections when one analyte was present at a low concentration and another analyte was present at a high concentration. IMPORTANCE The complexity and severity of viral respiratory tract infections (RTIs) emphasize the pivotal role of precise diagnosis for viral RTIs in guiding effective public health responses and ensuring appropriate medical interventions, given the substantial population at risk. This study highlights the necessity and importance of evaluating the analytical validity of multiplex real-time reverse transcription polymerase chain reaction assays, offering valuable insights into their optimization and application.
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Affiliation(s)
- Wanyu Feng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Yuqing Chen
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Yanxi Han
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Zhenli Diao
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Zihong Zhao
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Yuanfeng Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Tao Huang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Yu Ma
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Ziqiang Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jian Jiang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jing Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
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5
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Drori P, Mouhadeb O, Moya Muñoz GG, Razvag Y, Alcalay R, Klocke P, Cordes T, Zahavy E, Lerner E. Rapid and specific detection of nanoparticles and viruses one at a time using microfluidic laminar flow and confocal fluorescence microscopy. iScience 2024; 27:110982. [PMID: 39391727 PMCID: PMC11466642 DOI: 10.1016/j.isci.2024.110982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 07/24/2024] [Accepted: 09/13/2024] [Indexed: 10/12/2024] Open
Abstract
Mainstream virus detection relies on the specific amplification of nucleic acids via polymerase chain reaction, a process that is slow and requires extensive laboratory expertise and equipment. Other modalities, such as antigen-based tests, allow much faster virus detection but have reduced sensitivity. In this study, we introduce an approach for rapid and specific detection of single nanoparticles using a confocal-based flow virometer. The combination of laminar flow in a microfluidic channel and correlated fluorescence signals emerging from both free dyes and fluorescently labeled primary antibodies provide insights into nanoparticle volumes and specificities. We evaluate and validate the assay using fluorescent beads and viruses, including SARS-CoV-2 with fluorescently labeled primary antibodies. Additionally, we demonstrate how hydrodynamic focusing enhances the assay sensitivity for detecting viruses at relevant loads. Based on our results, we envision the future use of this technology for clinically relevant bio-nanoparticles, supported by the implementation of the assay in a portable and user-friendly setup.
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Affiliation(s)
- Paz Drori
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Odelia Mouhadeb
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Gabriel G. Moya Muñoz
- Physical and Synthetic Biology. Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
- Biophysical Chemistry, Department of Chemistry and Chemical Biology, Technische Universität Dortmund, Dortmund, Germany
| | - Yair Razvag
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ron Alcalay
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Philipp Klocke
- Physical and Synthetic Biology. Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology. Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
- Biophysical Chemistry, Department of Chemistry and Chemical Biology, Technische Universität Dortmund, Dortmund, Germany
| | - Eran Zahavy
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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6
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van Gent-Pelzer MPE, Dullemans AM, Verbeek M, Bonants PJM, van der Lee TAJ. Development and evaluation of one-step RT-qPCR TaqMan multiplex panels applied to six viruses occurring in lily and tulip bulbs. J Virol Methods 2024; 329:114987. [PMID: 38901647 DOI: 10.1016/j.jviromet.2024.114987] [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: 02/01/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/22/2024]
Abstract
One-step RT-qPCR TaqMan assays have been developed for six plant viruses with considerable economic impact in the growing of tulip and lily bulbs: lily mottle virus, lily symptomless virus, lily virus X, Plantago asiatica mosaic virus, tulip breaking virus and tulip virus X. To enhance efficacy and cost-efficiency these assays were combined into multiplex panels. Four different multiplex panels were designed, each consisting of three virus assays and an adapted assay for the housekeeping gene nad5 of lilies and tulips, that acts as an internal amplification control. To eliminate false negative results due to variation in the viral genome sequences, for each target virus two assays were developed on distinct conserved genomic regions. Specificity, PCR efficiency and compatibility of primers and probes were tested using gBlock constructions. Diagnostic samples were used to evaluate the strategy. High Throughput Sequencing of a set of the diagnostic samples, further verified the presence or absence of the viruses in the RNA samples and sequence variations in the target genes. This interchangeable multiplex panel strategy may be a valuable tool for the detection of viruses in certification, surveys and virus diagnostics.
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Affiliation(s)
- M P E van Gent-Pelzer
- Wageningen Plant Research, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen 6700 AA, the Netherlands.
| | - A M Dullemans
- Wageningen Plant Research, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen 6700 AA, the Netherlands.
| | - M Verbeek
- Wageningen Plant Research, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen 6700 AA, the Netherlands
| | - P J M Bonants
- Wageningen Plant Research, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen 6700 AA, the Netherlands
| | - T A J van der Lee
- Wageningen Plant Research, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen 6700 AA, the Netherlands
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7
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Kim MG, Yoo B, Min AY, Seo DW, Choi C, Kim SH, Kim SH. Comparative analysis of reverse-transcription-polymerase chain reaction for Aichivirus detection. Food Sci Biotechnol 2024; 33:2807-2814. [PMID: 39184978 PMCID: PMC11339220 DOI: 10.1007/s10068-024-01537-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/17/2024] [Accepted: 01/29/2024] [Indexed: 08/27/2024] Open
Abstract
Aichivirus-A (AiV-A), a member of the Kobuvirus genus of the family Picornaviridae, was first reported in stool samples of patients with non-bacterial gastroenteritis in Aichi Prefecture, Japan, in 1989. AiV has been reported from in various aquatic environments, such as surface water and sewage, can be transmitted via the fecal-oral route through contaminated water. As AiV is known to acute gastroenteritis worldwide, developing methods for AiV detection from contaminated environments and food is required. In the present study, we established an effective polymerase chain reaction (PCR) method to detect AiV. Various real-time reverse transcription (RT)-PCR and conventional PCR methods for AiV detection were compared, and the limit of detection was confirmed by comparing the sensitivity at varied primer concentrations and PCR conditions. The final detection limits were 102 copy/μL in conventional PCR, and 101 copy/μL in the real-time RT-PCR. The optimized method used in this study might aid in detecting AiV contamination.
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Affiliation(s)
- Mi-Gyeong Kim
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do 28159 Republic of Korea
| | - Boeun Yoo
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do 28159 Republic of Korea
| | - A Young Min
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do 28159 Republic of Korea
| | - Doo Won Seo
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do 28159 Republic of Korea
| | - Changsun Choi
- School of Food Science and Technology, Chung-Ang University, Ansung, 456-756 South Korea
| | - Seung Hwan Kim
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do 28159 Republic of Korea
| | - Soon Han Kim
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do 28159 Republic of Korea
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8
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Roy SD, Ramasamy S, Obbineni JM. An evaluation of nucleic acid-based molecular methods for the detection of plant viruses: a systematic review. Virusdisease 2024; 35:357-376. [PMID: 39071869 PMCID: PMC11269559 DOI: 10.1007/s13337-024-00863-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/15/2024] [Indexed: 07/30/2024] Open
Abstract
Precise and timely diagnosis of plant viruses is a prerequisite for the implementation of efficient management strategies, considering factors like globalization of trade and climate change facilitating the spread of viruses that lead to agriculture yield losses of billions yearly worldwide. Symptomatic diagnosis alone may not be reliable due to the diverse symptoms and confusion with plant abiotic stresses. It is crucial to detect plant viruses accurately and reliably and do so with little time. A complete understanding of the various detection methods is necessary to achieve this. Enzyme-linked immunosorbent assay (ELISA), has become more popular as a method for detecting viruses but faces limitations such as antibody availability, cost, sample volume, and time. Advanced techniques like polymerase chain reaction (PCR) have surpassed ELISA with its various sensitive variants. Over the last decade, nucleic acid-based molecular methods have gained popularity and have quickly replaced other techniques, such as serological techniques for detecting plant viruses due to their specificity and accuracy. Hence, this review enables the reader to understand the strengths and weaknesses of each molecular technique starting with PCR and its variations, along with various isothermal amplification followed by DNA microarrays, and next-generation sequencing (NGS). As a result of the development of new technologies, NGS is becoming more and more accessible and cheaper, and it looks possible that this approach will replace others as a favoured approach for carrying out regular diagnosis. NGS is also becoming the method of choice for identifying novel viruses. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-024-00863-0.
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Affiliation(s)
- Subha Deep Roy
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu India
- School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, Tamil Nadu India
| | | | - Jagan M. Obbineni
- School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, Tamil Nadu India
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9
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Sun A, Vopařilová P, Liu X, Kou B, Řezníček T, Lednický T, Ni S, Kudr J, Zítka O, Fohlerová Z, Pajer P, Zhang H, Neužil P. An integrated microfluidic platform for nucleic acid testing. MICROSYSTEMS & NANOENGINEERING 2024; 10:66. [PMID: 38784376 PMCID: PMC11111744 DOI: 10.1038/s41378-024-00677-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 11/30/2023] [Accepted: 01/07/2024] [Indexed: 05/25/2024]
Abstract
This study presents a rapid and versatile low-cost sample-to-answer system for SARS-CoV-2 diagnostics. The system integrates the extraction and purification of nucleic acids, followed by amplification via either reverse transcription-quantitative polymerase chain reaction (RT-qPCR) or reverse transcription loop-mediated isothermal amplification (RT-LAMP). By meeting diverse diagnostic and reagent needs, the platform yields testing results that closely align with those of commercial RT-LAMP and RT‒qPCR systems. Notable advantages of our system include its speed and cost-effectiveness. The assay is completed within 28 min, including sample loading (5 min), ribonucleic acid (RNA) extraction (3 min), and RT-LAMP (20 min). The cost of each assay is ≈ $9.5, and this pricing is competitive against that of Food and Drug Administration (FDA)-approved commercial alternatives. Although some RNA loss during on-chip extraction is observed, the platform maintains a potential limit of detection lower than 297 copies. Portability makes the system particularly useful in environments where centralized laboratories are either unavailable or inconveniently located. Another key feature is the platform's versatility, allowing users to choose between RT‒qPCR or RT‒LAMP tests based on specific requirements.
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Affiliation(s)
- Antao Sun
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace; School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072 P. R. China
| | - Petra Vopařilová
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1, 61300 Brno, Czech Republic
| | - Xiaocheng Liu
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace; School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072 P. R. China
| | - Bingqian Kou
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace; School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072 P. R. China
| | - Tomáš Řezníček
- ITD Tech s.r.o, Osvoboditelů 1005, 735 81 Bohumín, Czech Republic
| | - Tomáš Lednický
- Central European Institute of Technology, Brno University of Technology, Purkyňova 123, Brno, 61200 Czech Republic
| | - Sheng Ni
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Jiří Kudr
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1, 61300 Brno, Czech Republic
| | - Ondřej Zítka
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1, 61300 Brno, Czech Republic
| | - Zdenka Fohlerová
- Department of Microelectronics, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technická 3058/10, Brno, 61600 Czech Republic
| | - Petr Pajer
- Military Health Institute, U Vojenské nemocnice 1200, 16200 Praha 6, Czech Republic
| | - Haoqing Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049 P. R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an, 710049 P. R. China
| | - Pavel Neužil
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace; School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072 P. R. China
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10
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Sampad MJN, Saiduzzaman SM, Walker ZJ, Wells TN, Wayment JX, Ong EM, Mdaki SD, Tamhankar MA, Yuzvinsky TD, Patterson JL, Hawkins AR, Schmidt H. Label-free and amplification-free viral RNA quantification from primate biofluids using a trapping-assisted optofluidic nanopore platform. Proc Natl Acad Sci U S A 2024; 121:e2400203121. [PMID: 38598338 PMCID: PMC11032468 DOI: 10.1073/pnas.2400203121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/07/2024] [Indexed: 04/12/2024] Open
Abstract
Viral outbreaks can cause widespread disruption, creating the need for diagnostic tools that provide high performance and sample versatility at the point of use with moderate complexity. Current gold standards such as PCR and rapid antigen tests fall short in one or more of these aspects. Here, we report a label-free and amplification-free nanopore sensor platform that overcomes these challenges via direct detection and quantification of viral RNA in clinical samples from a variety of biological fluids. The assay uses an optofluidic chip that combines optical waveguides with a fluidic channel and integrates a solid-state nanopore for sensing of individual biomolecules upon translocation through the pore. High specificity and low limit of detection are ensured by capturing RNA targets on microbeads and collecting them by optical trapping at the nanopore location where targets are released and rapidly detected. We use this device for longitudinal studies of the viral load progression for Zika and Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infections in marmoset and baboon animal models, respectively. The up to million-fold trapping-based target concentration enhancement enables amplification-free RNA quantification across the clinically relevant concentration range down to the assay limit of RT-qPCR as well as cases in which PCR failed. The assay operates across all relevant biofluids, including semen, urine, and whole blood for Zika and nasopharyngeal and throat swab, rectal swab, and bronchoalveolar lavage for SARS-CoV-2. The versatility, performance, simplicity, and potential for full microfluidic integration of the amplification-free nanopore assay points toward a unique approach to molecular diagnostics for nucleic acids, proteins, and other targets.
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Affiliation(s)
| | - S. M. Saiduzzaman
- School of Engineering, University of California, Santa Cruz, CA95064
| | - Zach J. Walker
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT84602
| | - Tanner N. Wells
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT84602
| | - Jesse X. Wayment
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT84602
| | - Ephraim M. Ong
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT84602
| | | | | | | | | | - Aaron R. Hawkins
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT84602
| | - Holger Schmidt
- School of Engineering, University of California, Santa Cruz, CA95064
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11
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Torres-Salvador F, Ojeda J, Castro C, Gerasimova Y, Chumbimuni-Torres K. A Single Electrochemical Biosensor Designed to Detect Any Virus. Anal Chem 2024; 96:5752-5756. [PMID: 38560822 PMCID: PMC11459061 DOI: 10.1021/acs.analchem.3c05962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Viruses are the primary cause of many infectious diseases in both humans and animals. Various testing methods require an amplification step of the viral RNA sample before detection, with quantitative reverse transcription polymerase chain reaction (RT-qPCR) being one of the most widely used along with lesser-known methods like Nucleic Acid Sequence-Based Amplification (NASBA). NASBA offers several advantages, such as isothermal amplification and high selectivity for specific sequences, making it an attractive option for low-income facilities. In this research, we employed a single electrochemical biosensor (E-Biosensor) designed for potentially detecting any virus by modifying the NASBA protocol. In this modified protocol, a reverse primer is designed with an additional 22-nucleotide sequence (tag region) at the 5'-end, which is added to the NASBA process. This tag region becomes part of the final amplicon generated by NASBA. It can hybridize with a single specific E-Biosensor probe set, enabling subsequent virus detection. Using this approach, we successfully detected three different viruses with a single E-Biosensor design, demonstrating the platform's potential for virus detection.
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Affiliation(s)
| | - Julio Ojeda
- Department of Chemistry, University of Central Florida, Orlando, FL 32816, US
| | - Cynthia Castro
- Department of Chemistry, University of Central Florida, Orlando, FL 32816, US
| | - Yulia Gerasimova
- Department of Chemistry, University of Central Florida, Orlando, FL 32816, US
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12
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Drori P, Mouhadeb O, Moya Muñoz GG, Razvag Y, Alcalay R, Klocke P, Cordes T, Zahavy E, Lerner E. Rapid and specific detection of single nanoparticles and viruses in microfluidic laminar flow via confocal fluorescence microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.31.573251. [PMID: 38260394 PMCID: PMC10802330 DOI: 10.1101/2023.12.31.573251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Mainstream virus detection relies on the specific amplification of nucleic acids via polymerase chain reaction, a process that is slow and requires extensive laboratory expertise and equipment. Other modalities, such as antigen-based tests, allow much faster virus detection but have reduced sensitivity. In this study, we report the development of a flow virometer for the specific and rapid detection of single nanoparticles based on confocal microscopy. The combination of laminar flow and multiple dyes enable the detection of correlated fluorescence signals, providing information on nanoparticle volumes and specific chemical composition properties, such as viral envelope proteins. We evaluated and validated the assay using fluorescent beads and viruses, including SARS-CoV-2. Additionally, we demonstrate how hydrodynamic focusing enhances the assay sensitivity for detecting clinically-relevant virus loads. Based on our results, we envision the use of this technology for clinically relevant bio-nanoparticles, supported by the implementation of the assay in a portable and user-friendly setup.
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Affiliation(s)
- Paz Drori
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Odelia Mouhadeb
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Gabriel G Moya Muñoz
- Physical and Synthetic Biology. Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Yair Razvag
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ron Alcalay
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Philipp Klocke
- Physical and Synthetic Biology. Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology. Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Eran Zahavy
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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13
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Harthan JS, Than T, Shorter E, Hartwick ATE, Morettin CE, Huecker JB, Johnson SD, Migneco MK, Whiteside M, Olson CK, Alferez CS, van Zyl T, Gordon MO. Natural history of adenoviral conjunctivitis in a US-based population: Viral load, signs, and symptoms. Cont Lens Anterior Eye 2024; 47:102110. [PMID: 38171995 PMCID: PMC10960668 DOI: 10.1016/j.clae.2023.102110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024]
Abstract
PURPOSE To report the clinical signs, symptoms, and viral clearance in individuals in the United States with adenoviral conjunctivitis (Ad-Cs). METHODS Individuals ≥ 18 years presenting within 4 days of symptoms of Ad-Cs who met eligibility criteria and tested positive with both point-of-care immunoassay antigen and quantitative polymerase chain reaction (qPCR) testing were enrolled. Patient-reported symptoms, clinician-graded signs, and qPCR viral titers were collected at baseline, days 1-2, 4 (days 3-5), 7 (days 6-10), 14 (days 11-17) and 21 (days 18-21). RESULTS There was no detectable viral titers by the day 14 visit in 6/8 patients. By day 21, there was no detectable viral titers in the 7 participants who completed the visit; however, signs and symptoms persisted including: blurry vision (5/7), discomfort (2/7) or redness (1/7). Masked clinicians also noted conjunctival redness (4/7), follicular conjunctivitis (4/7) and bulbar edema (3/7). CONCLUSION Many patient-reported symptoms and clinical signs persist after viral titers are no longer detectable by qPCR. Using clinical signs and symptoms to determine quarantine duration may result in patients being furloughed longer than the time that the patient is infectious.
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Affiliation(s)
| | - Tammy Than
- Carl Vinson VA Medical Center, United States
| | - Ellen Shorter
- Illinois Eye and Ear Infirmary University of Illinois at Chicago, United States
| | | | | | | | | | | | | | | | | | | | - Mae O Gordon
- Washington University School of Medicine, United States
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14
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Nwe MK, Jangpromma N, Taemaitree L. Evaluation of molecular inhibitors of loop-mediated isothermal amplification (LAMP). Sci Rep 2024; 14:5916. [PMID: 38467647 PMCID: PMC10928092 DOI: 10.1038/s41598-024-55241-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 02/21/2024] [Indexed: 03/13/2024] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is a cost-effective and easy-to-perform assay that enables the direct detection of DNA. Its use in point-of-care diagnostic tests is growing, while it has the potential to be used in presumptive on-the-field forensic tests. Samples are often collected from complex matrices that contain high levels of contaminants. Herein, we evaluate the effect of seven common DNA amplification inhibitors on LAMP - bile salts, calcium chloride, hematin, humic acid, immunoglobulin G, tannic acid and urea. We study the effect of each inhibitor individually in real-time detection systems coupled with end-point measurements to delineate their inhibitory effects from the matrix in which they may be found. Our studies show LAMP inhibitors generally delay the onset of amplicon formation and quench fluorescence at similar or higher concentrations compared to PCR, but that end-point measurements of LAMP amplicons are unaffected. This is important as LAMP amplicons can be detected in non-fluorometric ways thus contributing to the assertions that LAMP is more robust to inhibitors than PCR.
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Affiliation(s)
- May Khat Nwe
- Department of Integrated Science, Forensic Science Program, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Nisachon Jangpromma
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Lapatrada Taemaitree
- Department of Integrated Science, Forensic Science Program, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand.
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15
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Azizan A, Alfaro AC, Venter L, Jaramillo D, Bestbier M, Bennett P, Foxwell J, Young T. Quantification of Photobacterium swingsii and characterisation of disease progression in the New Zealand Greenshell™ mussel, Perna canaliculus. J Invertebr Pathol 2024; 203:108065. [PMID: 38246322 DOI: 10.1016/j.jip.2024.108065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/23/2024]
Abstract
Greenshell™ mussels (Perna canaliculus) are endemic to New Zealand and support the largest aquaculture industry in the country. Photobacterium swingsii was isolated and identified from moribund P. canaliculus mussels following a mass mortality event. In this study, a challenge experiment was used to characterise, detect, and quantify P. swingsii in adult P. canaliculus following pathogen exposure via injection into the adductor muscle. A positive control (heat-killed P. swingsii injection) was included to account for the effects of injection and inactive bacterial exposure. Survival of control and infected mussels remained 100% during 72-hour monitoring period. Haemolymph was sampled for bacterial colony counts and haemocyte flow cytometry analyses; histology sections were obtained and processed for histopathological assessments; and adductor muscle, gill, digestive gland were sampled for quantitative polymerase chain reaction (PCR) analyses, all conducted at 12, 24, 48 h post-challenge (hpc). The most profound effects of bacterial injection on mussels were seen at 48 hpc, where mussel mortality, haemocyte counts and haemolymph bacterial colony forming were the highest. The quantification of P. swingsii via qPCR showed highest levels of bacterial DNA at 12 hpc in the adductor muscle, gill, and digestive gland. Histopathological observations suggested a non-specific inflammatory response in all mussels associated with a general stress response. This study highlights the physiological effects of P. swingsii infection in P. canaliculus mussels and provides histopathological insight into the tissue injury caused by the action of injection into the adductor muscle. The multi-technique methods used in this study can be applied for use in early surveillance programs of bacterial infection on mussel farms.
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Affiliation(s)
- Awanis Azizan
- Aquaculture Biotechnology Research Group, Department of Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | - Andrea C Alfaro
- Aquaculture Biotechnology Research Group, Department of Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand.
| | - Leonie Venter
- Aquaculture Biotechnology Research Group, Department of Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | - Diana Jaramillo
- Animal Health Laboratory, Ministry for Primary Industries, PO Box 2526, Wellington 6140, New Zealand
| | - Mark Bestbier
- Animal Health Laboratory, Ministry for Primary Industries, PO Box 2526, Wellington 6140, New Zealand
| | - Peter Bennett
- Animal Health Laboratory, Ministry for Primary Industries, PO Box 2526, Wellington 6140, New Zealand
| | - Jonathan Foxwell
- Animal Health Laboratory, Ministry for Primary Industries, PO Box 2526, Wellington 6140, New Zealand
| | - Tim Young
- Aquaculture Biotechnology Research Group, Department of Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand; Centre for Biomedical & Chemical Sciences, School of Science, Auckland University of Technology, Auckland, New Zealand
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16
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Geletu US, Musa AA, Usmael MA, Keno MS. Molecular Detection and Isolation of Lumpy Skin Disease Virus during an Outbreak in West Hararghe Zone, Eastern Ethiopia. Vet Med Int 2024; 2024:9487970. [PMID: 38455362 PMCID: PMC10919987 DOI: 10.1155/2024/9487970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 01/21/2024] [Accepted: 02/19/2024] [Indexed: 03/09/2024] Open
Abstract
Lumpy skin disease (LSD) is a highly contagious viral disease that causes significant economic losses in cattle populations globally. This study aimed to isolate and detect the LSD virus responsible for an outbreak in selected areas (Daaroo Labuu, Hawwii Guddina, and Gumbi Bordede district) of the West Hararghe Zone in Ethiopia between January 2020 and December 2021. Out of the 625 animals examined for the presence of LSD, only 73 animals showed clinical signs, and skin scrapes were collected from these animals for further analysis. Among those, 12 animals (1.9%) succumbed to the disease. Skin biopsy samples from 45 animals displaying clinical signs of LSD were inoculated in Vero cell lines because of limited equipment. After three blind passages, all samples developed cytopathic effects (CPEs). The presence of the LSD virus was confirmed using real-time PCR. Conventional PCR detected LSDV in 47 (64.4%) of the skin scrap samples, while high-resolution melt qPCR detected it in 49 (67.1%) samples. The study revealed a morbidity rate of 11.68%, a mortality rate of 1.92%, and a case fatality rate of 16.44% based on clinical data. The findings suggest that LSD causes significant economic losses, even in vaccinated animals prior to an outbreak. To effectively control and eradicate LSD, the government should develop new strategic policies. Community awareness campaigns are necessary to improve vector control measures and drainage systems. In addition, the present vaccination policy and strategy should be re-evaluated for effectiveness. This study focused on a specific region and timeframe, limiting generalizability. Factors such as environmental conditions and management practices were not extensively explored. Similar studies should be conducted in different regions to assess the prevalence and genetic diversity of LSDV. The effectiveness of control measures and vaccination strategies should be investigated. The impact of environmental factors and management practices on LSD transmission and disease severity warrants further exploration. This study provides insights into the detection and isolation of the LSD virus during an outbreak in the West Hararghe Zone of Ethiopia. The results highlight the need for continued surveillance and monitoring of emerging infectious diseases in the region. Furthermore, the importance of using molecular methods for detecting and characterizing viral outbreaks in livestock populations is emphasized.
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Affiliation(s)
- Umer Seid Geletu
- Department of Animal Science, College of Agriculture, Oda Bultum University, P.O. Box 226, Chiro, Ethiopia
| | - Ahmedin Abdurehman Musa
- Department of Animal Science, College of Agriculture, Oda Bultum University, P.O. Box 226, Chiro, Ethiopia
| | - Munera Ahmednur Usmael
- Oromia Bureau Livestock and Fishery Resources, West Hararghe Zone, P.O. Box 226, Wereda, Chiro, Ethiopia
| | - Melaku Sombo Keno
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
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Olaimat AN, Taybeh AO, Al-Nabulsi A, Al-Holy M, Hatmal MM, Alzyoud J, Aolymat I, Abughoush MH, Shahbaz H, Alzyoud A, Osaili T, Ayyash M, Coombs KM, Holley R. Common and Potential Emerging Foodborne Viruses: A Comprehensive Review. Life (Basel) 2024; 14:190. [PMID: 38398699 PMCID: PMC10890126 DOI: 10.3390/life14020190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/17/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Human viruses and viruses from animals can cause illnesses in humans after the consumption of contaminated food or water. Contamination may occur during preparation by infected food handlers, during food production because of unsuitably controlled working conditions, or following the consumption of animal-based foods contaminated by a zoonotic virus. This review discussed the recent information available on the general and clinical characteristics of viruses, viral foodborne outbreaks and control strategies to prevent the viral contamination of food products and water. Viruses are responsible for the greatest number of illnesses from outbreaks caused by food, and risk assessment experts regard them as a high food safety priority. This concern is well founded, since a significant increase in viral foodborne outbreaks has occurred over the past 20 years. Norovirus, hepatitis A and E viruses, rotavirus, astrovirus, adenovirus, and sapovirus are the major common viruses associated with water or foodborne illness outbreaks. It is also suspected that many human viruses including Aichi virus, Nipah virus, tick-borne encephalitis virus, H5N1 avian influenza viruses, and coronaviruses (SARS-CoV-1, SARS-CoV-2 and MERS-CoV) also have the potential to be transmitted via food products. It is evident that the adoption of strict hygienic food processing measures from farm to table is required to prevent viruses from contaminating our food.
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Affiliation(s)
- Amin N. Olaimat
- Department of Clinical Nutrition and Dietetics, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan; (M.A.-H.); (M.H.A.)
| | - Asma’ O. Taybeh
- Department of Nutrition and Food Technology, Faculty of Agriculture, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan; (A.O.T.); (A.A.-N.); (T.O.)
| | - Anas Al-Nabulsi
- Department of Nutrition and Food Technology, Faculty of Agriculture, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan; (A.O.T.); (A.A.-N.); (T.O.)
| | - Murad Al-Holy
- Department of Clinical Nutrition and Dietetics, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan; (M.A.-H.); (M.H.A.)
| | - Ma’mon M. Hatmal
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan;
| | - Jihad Alzyoud
- Department of Anatomy, Physiology and Biochemistry, Faculty of Medicine, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan; (J.A.); (I.A.)
| | - Iman Aolymat
- Department of Anatomy, Physiology and Biochemistry, Faculty of Medicine, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan; (J.A.); (I.A.)
| | - Mahmoud H. Abughoush
- Department of Clinical Nutrition and Dietetics, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan; (M.A.-H.); (M.H.A.)
- Science of Nutrition and Dietetics Program, College of Pharmacy, Al Ain University, Abu Dhabi P.O. Box 64141, United Arab Emirates
| | - Hafiz Shahbaz
- Department of Food Science and Human Nutrition, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan;
| | - Anas Alzyoud
- Faculty of Medicine, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan;
| | - Tareq Osaili
- Department of Nutrition and Food Technology, Faculty of Agriculture, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan; (A.O.T.); (A.A.-N.); (T.O.)
- Department of Clinical Nutrition and Dietetics, College of Health Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
| | - Mutamed Ayyash
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University, P.O. Box 15551, Al Ain 53000, United Arab Emirates;
| | - Kevin M. Coombs
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada;
| | - Richard Holley
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada;
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18
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Nazli A, Qiu J, Tang Z, He Y. Recent Advances and Techniques for Identifying Novel Antibacterial Targets. Curr Med Chem 2024; 31:464-501. [PMID: 36734893 DOI: 10.2174/0929867330666230123143458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/30/2022] [Accepted: 11/11/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND With the emergence of drug-resistant bacteria, the development of new antibiotics is urgently required. Target-based drug discovery is the most frequently employed approach for the drug development process. However, traditional drug target identification techniques are costly and time-consuming. As research continues, innovative approaches for antibacterial target identification have been developed which enabled us to discover drug targets more easily and quickly. METHODS In this review, methods for finding drug targets from omics databases have been discussed in detail including principles, procedures, advantages, and potential limitations. The role of phage-driven and bacterial cytological profiling approaches is also discussed. Moreover, current article demonstrates the advancements being made in the establishment of computational tools, machine learning algorithms, and databases for antibacterial target identification. RESULTS Bacterial drug targets successfully identified by employing these aforementioned techniques are described as well. CONCLUSION The goal of this review is to attract the interest of synthetic chemists, biologists, and computational researchers to discuss and improve these methods for easier and quicker development of new drugs.
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Affiliation(s)
- Adila Nazli
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Jingyi Qiu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Chongqing, 400714, P. R. China
| | - Ziyi Tang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Chongqing, 400714, P. R. China
| | - Yun He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
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19
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Lee YJ, Jun LJ, Kim YJ, Han JE, Ko YJ, Oh YE, Lee EJ, Lee J, Jeong JB. Comparison of specificity and sensitivity of diagnostic methods for Enteromyxum leei and Enteromyxum fugu detected from cultured tiger puffer, Takifugu rubripes in Korea. JOURNAL OF FISH DISEASES 2024; 47:e13865. [PMID: 37731267 DOI: 10.1111/jfd.13865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/03/2023] [Accepted: 09/07/2023] [Indexed: 09/22/2023]
Abstract
Enteromyxum leei and Enteromyxum fugu, which are myxosporean parasites, were first found in cultured tiger puffer Takifugu rubripes in Korea. We collected four tiger puffers that showed severe emaciation signs for our experiments. DNA sequencing was confirmed that the tiger puffers were coinfected with E. leei and E. fugu. Furthermore, similar amounts of E. leei and E. fugu were confirmed using real-time PCR in the intestine. To the best of our knowledge, there have been no reports of E. fugu infection in the olive flounder Paralichthys olivaceus. However, the diagnosis of inflowing water, discharged water and olive flounder samples using highly sensitive diagnostic methods confirmed the presence of E. fugu in water and fish samples from olive flounder farms near the tiger puffer farm. Therefore, the present study aimed to develop highly sensitive diagnostic methods such as real-time and two-step PCR for early diagnosis and follow-up of the emaciation disease and multiplex PCR for rapid diagnosis. The multiplex PCR method exhibited the same sensitivity as the one-step PCR method developed in this study, demonstrating its efficacy for rapid diagnosis. Therefore, the suggested methods can be utilized for the early diagnosis and rapid diagnosis of emaciation diseases and reduction of economic losses through rapid disease control.
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Affiliation(s)
- Young Juhn Lee
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| | - Lyu Jin Jun
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| | - Ye Ji Kim
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| | - Ji Eun Han
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| | - Ye Jin Ko
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| | - Yeong Eun Oh
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| | - Eung Joon Lee
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| | - Jehee Lee
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| | - Joon Bum Jeong
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
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20
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Yoo B, Kim MG, Min AY, Seo DW, Kim SH, Kim SH. Optimization of RT-PCR methods for enterovirus detection in groundwater. Heliyon 2023; 9:e23028. [PMID: 38149210 PMCID: PMC10750030 DOI: 10.1016/j.heliyon.2023.e23028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/16/2023] [Accepted: 11/24/2023] [Indexed: 12/28/2023] Open
Abstract
Enteroviruses (EVs), which belong to the Picornaviridae family, infect individuals asymptomatically or cause mild symptoms (fever, runny nose, cough, skin rash, sneezing, mouth blister). Severe cases can cause various diseases, such as acute hemorrhagic conjunctivitis, aseptic meningitis, or myocarditis, especially in infants. These viruses can be transmitted via the fecal-oral route via contaminated water. In this study, we established a polymerase chain reaction (PCR) method for detecting EVs in water sample using Coxsackievirus B5 (CV-B5) and Echovirus 30 (E-30), which belong to species B of the four species of EVs (EV-A to D). Several methods have been investigated and compared for the detection of EVs, including real-time reverse transcription (RT) polymerase chain reaction and conventional RT-PCR. The most sensitive primer sets were selected, and the PCR conditions were modified to increase sensitivity. We also quantified the detection limits of real-time and conventional RT-PCR. The detection limits of conventional RT-PCR were detected in 105-106 copy/mL for CV-B5 and 106-107 copy/mL for E-30, respectively. This optimized method for detecting EVs is expected to contribute substantially to the investigation of EV outbreaks in water samples.
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Affiliation(s)
- Boeun Yoo
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 28159, Republic of Korea
| | - Mi-Gyeong Kim
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 28159, Republic of Korea
| | - A Young Min
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 28159, Republic of Korea
| | - Doo Won Seo
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 28159, Republic of Korea
| | - Seung Hwan Kim
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 28159, Republic of Korea
| | - Soon Han Kim
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 28159, Republic of Korea
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21
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Cui H, Xu S, Xu X, Ji J, Kan Y, Yao L, Bi Y, Xie Q. Multienzyme isothermal rapid amplification and lateral flow dipstick combination assay for visible detection of chicken chaphamaparvovirus. Poult Sci 2023; 102:103144. [PMID: 37839164 PMCID: PMC10589884 DOI: 10.1016/j.psj.2023.103144] [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: 08/18/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 10/17/2023] Open
Abstract
Chicken chaphamaparvovirus (CkChpV) is a newly emerging pathogen that is currently prevalent in chickens with diarrhea symptoms. To diagnose CkChpV more conveniently and rapidly, this study established a multienzyme isothermal rapid amplification (MIRA) assay, with a reaction time of only 15 min and optimal reaction temperature of 38°C. In combination with the lateral flow dipstick assay, the CkChpV-MIRA assay can be completed within 20 min. We revealed that the detection limit of the MIRA assay using standard plasmids as templates was as low as 21.3 copies, and its sensitivity was 100 times higher than that of nested PCR. Moreover, the designed primer set and probe could only detect CkChpV specifically, and there was no cross reaction with avian nephritis virus, rotavirus, chicken parvovirus virus, Newcastle disease virus, and infectious bronchitis virus, which may cause diarrhea. These findings demonstrated that the CkChpV-MIRA assay established in this study is convenient, sensitive, and specific and does not require sophisticated equipment. It is more suitable for the detection of CkChpV in clinical samples.
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Affiliation(s)
- Hao Cui
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, PR China; Chifeng Municipal Hospital, Chifeng, Inner Mongolia 024000, PR China
| | - Shuqi Xu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, PR China
| | - Xin Xu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, PR China
| | - Jun Ji
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, PR China.
| | - Yunchao Kan
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, PR China
| | - Lunguang Yao
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, PR China
| | - Yingzuo Bi
- College of Animal Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Qingmei Xie
- College of Animal Science, South China Agricultural University, Guangzhou 510642, PR China
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22
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Harris DT, Ingraham N, Badowski M. Comparison of Manual versus Automated SARS-CoV-2 Rapid Antigen Testing in Asymptomatic Individuals. J Clin Med 2023; 12:7146. [PMID: 38002757 PMCID: PMC10672191 DOI: 10.3390/jcm12227146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
The SARS-CoV-2 pandemic has infected more than 770 M people and killed more than 6.9 M persons worldwide. In the USA, as of August 2023, it has infected more than 103 M people while causing more than 1.1 M deaths. During a pandemic, it is necessary to rapidly identify those individuals infected with the virus so that disease transmission can be stopped. We examined the sensitivity of the Quidel Rapid Antigen test on the manual Sofia 2 platform and the Beckman-Coulter antigen test on the automated DxI-800 system for use in screening asymptomatic individuals at the University of Arizona from March through May 2021. A total of 378 asymptomatic subjects along with 176 validation sets of samples in 23 independent experiments were assessed in side-by-side antigen testing using both assays. Nasal swabs and saliva were used as viral sources. Manual testing (Quidel) was compared with automated testing (Beckman) methods for cost and efficiency. Limit dilution of viral antigen spiked samples was performed to determine sensitivity to antigen load by the tests. The results between the two tests were found to be concordant. Both tests were comparable in terms of detecting low numbers of positive subjects in the asymptomatic population. A concordance of 98% was observed between the two tests. Experiments also demonstrated that saliva specimens were an acceptable viral source and produced comparable results for each test. Overall, the two methods were interchangeable.
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Affiliation(s)
- David T. Harris
- University of Arizona Health Sciences Biorepository, Tucson, AZ 85724, USA; (N.I.); (M.B.)
- Department of Immunobiology & Medicine, The University of Arizona, Tucson, AZ 85724, USA
- Biorepository, The University of Arizona, AHSC 6122, 1501 N Campbell Ave, P.O. Box 245221, Tucson, AZ 85724, USA
| | - Nicole Ingraham
- University of Arizona Health Sciences Biorepository, Tucson, AZ 85724, USA; (N.I.); (M.B.)
| | - Michael Badowski
- University of Arizona Health Sciences Biorepository, Tucson, AZ 85724, USA; (N.I.); (M.B.)
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23
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Alex-Sanders N, Woodhall N, Farkas K, Scott G, Jones DL, Walker DI. Development and validation of a duplex RT-qPCR assay for norovirus quantification in wastewater samples. J Virol Methods 2023; 321:114804. [PMID: 37643662 DOI: 10.1016/j.jviromet.2023.114804] [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: 06/15/2023] [Revised: 08/21/2023] [Accepted: 08/26/2023] [Indexed: 08/31/2023]
Abstract
Norovirus (NoV) is a highly contagious enteric virus that causes widespread outbreaks and a substantial number of deaths across communities. As clinical surveillance is often insufficient, wastewater-based epidemiology (WBE) may provide novel pathways of tracking outbreaks. To utilise WBE, it is important to use accurate and sensitive methods for viral quantification. In this study, we developed a one-step duplex RT-qPCR assay to simultaneously test the two main human pathogenic NoV genogroups, GI and GII, in wastewater samples. The assay had low limits of detection (LOD), namely 0.52 genome copies (gc)/µl for NoVGI and 1.37 gc/µl for NoVGII. No significant concentration-dependent interactions were noted for both NoVGI and for NoVGII when the two targets were mixed at different concentrations in the samples. When tested on wastewater-derived RNA eluents, no significant difference between duplex and singleplex concentrations were found for either target. Low levels of inhibition (up to 32 %) were noted due to organic matter present in the wastewater extracts. From these results we argue that the duplex RT-qPCR assay developed enables the sensitive detection of both NoVGI and NoVGII in wastewater-derived RNA eluents, in a time and cost-effective way and may be used for surveillance to monitor public and environmental health.
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Affiliation(s)
| | - Nick Woodhall
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Kata Farkas
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - George Scott
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - Davey L Jones
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - David I Walker
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
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24
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Shigemori H, Fujita S, Tamiya E, Wakida SI, Nagai H. Solid-Phase Collateral Cleavage System Based on CRISPR/Cas12 and Its Application toward Facile One-Pot Multiplex Double-Stranded DNA Detection. Bioconjug Chem 2023; 34:1754-1765. [PMID: 37782626 PMCID: PMC10587867 DOI: 10.1021/acs.bioconjchem.3c00294] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/31/2023] [Indexed: 10/04/2023]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 12 (Cas12) system is attracting interest for its potential as a next-generation nucleic acid detection tool. The system can recognize double-stranded DNA (dsDNA) based on Cas12-CRISPR RNA (crRNA) and induce signal transduction by collateral cleavage. This property is expected to simplify comprehensive genotyping. Here, we report a solid-phase collateral cleavage (SPCC) reaction by CRISPR/Cas12 and its application toward one-pot multiplex dsDNA detection with minimal operational steps. In the sensor, Cas12-crRNA and single-stranded DNA (ssDNA) are immobilized on the sensing surface and act as enzyme and reporter substrates, respectively. We also report a dual-target dsDNA sensor prepared by immobilizing Cas12-crRNA and a fluorophore-labeled ssDNA reporter on separate spots. When a spot captures a target dsDNA sequence, it cleaves the ssDNA reporter on the same spot and reduces its fluorescence by 42.1-57.3%. Crucially, spots targeting different sequences do not show a reduction in fluorescence, thus confirming the one-pot multiplex dsDNA detection by SPCC. Furthermore, the sequence specificity has a two-base resolution, and the detectable concentration for the target dsDNA is at least 10-9 M. In the future, the SPCC-based sensor array could achieve one-pot comprehensive genotyping by using an array spotter as a reagent-immobilizing method.
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Affiliation(s)
- Hiroki Shigemori
- Advanced
Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL),
National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita, Osaka 565-0871, Japan
- Graduate
School of Human Development and Environment, Kobe University, 3-11
Tsurukabuto, Nada-ku, Kobe, Hyogo 657-0011, Japan
| | - Satoshi Fujita
- Advanced
Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL),
National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Eiichi Tamiya
- Advanced
Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL),
National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita, Osaka 565-0871, Japan
- Institute
of Scientific and Industrial Research (SANKEN), Osaka University, 8-1
Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Shin-ichi Wakida
- Advanced
Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL),
National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita, Osaka 565-0871, Japan
- Institute
of Scientific and Industrial Research (SANKEN), Osaka University, 8-1
Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Hidenori Nagai
- Advanced
Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL),
National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita, Osaka 565-0871, Japan
- Graduate
School of Human Development and Environment, Kobe University, 3-11
Tsurukabuto, Nada-ku, Kobe, Hyogo 657-0011, Japan
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25
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Nieves O, Ortiz de Zárate D, Aznar E, Caballos I, Garrido E, Martínez-Máñez R, Dortu F, Bernier D, Mengual-Chuliá B, López-Labrador FX, Sloth JJ, Loeschner K, Duedahl-Olesen L, Prado N, Hervello M, Menéndez A, Gransee R, Klotzbuecher T, Gonçalves MC, Zare F, Fuentes López A, Fernández Segovia I, Baviera JMB, Salcedo J, Recuero S, Simón S, Fernández Blanco A, Peransi S, Gómez-Gómez M, Griol A. Development of Photonic Multi-Sensing Systems Based on Molecular Gates Biorecognition and Plasmonic Sensors: The PHOTONGATE Project. SENSORS (BASEL, SWITZERLAND) 2023; 23:8548. [PMID: 37896641 PMCID: PMC10611383 DOI: 10.3390/s23208548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023]
Abstract
This paper presents the concept of a novel adaptable sensing solution currently being developed under the EU Commission-founded PHOTONGATE project. This concept will allow for the quantification of multiple analytes of the same or different nature (chemicals, metals, bacteria, etc.) in a single test with levels of sensitivity and selectivity at/or over those offered by current solutions. PHOTONGATE relies on two core technologies: a biochemical technology (molecular gates), which will confer the specificity and, therefore, the capability to be adaptable to the analyte of interest, and which, combined with porous substrates, will increase the sensitivity, and a photonic technology based on localized surface plasmonic resonance (LSPR) structures that serve as transducers for light interaction. Both technologies are in the micron range, facilitating the integration of multiple sensors within a small area (mm2). The concept will be developed for its application in health diagnosis and food safety sectors. It is thought of as an easy-to-use modular concept, which will consist of the sensing module, mainly of a microfluidics cartridge that will house the photonic sensor, and a platform for fluidic handling, optical interrogation, and signal processing. The platform will include a new optical concept, which is fully European Union Made, avoiding optical fibers and expensive optical components.
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Affiliation(s)
- Oscar Nieves
- Nanophotonics Technology Center, Universitat Politècnica de València, Camí de Vera s/n, 46022 Valencia, Spain; (O.N.); (D.O.d.Z.)
| | - David Ortiz de Zárate
- Nanophotonics Technology Center, Universitat Politècnica de València, Camí de Vera s/n, 46022 Valencia, Spain; (O.N.); (D.O.d.Z.)
| | - Elena Aznar
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain; (E.A.); (I.C.); (E.G.); (R.M.-M.)
- Unidad Mixta de Investigación en Nanomedicina y Sensores, Instituto de Investigación Sanitaria La Fe (IISLAFE) Avenida Fernando Abril Martorell 106, 46026 Valencia, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 46022 Valencia, Spain
| | - Isabel Caballos
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain; (E.A.); (I.C.); (E.G.); (R.M.-M.)
- Unidad Mixta de Investigación en Nanomedicina y Sensores, Instituto de Investigación Sanitaria La Fe (IISLAFE) Avenida Fernando Abril Martorell 106, 46026 Valencia, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 46022 Valencia, Spain
| | - Eva Garrido
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain; (E.A.); (I.C.); (E.G.); (R.M.-M.)
- Unidad Mixta de Investigación en Nanomedicina y Sensores, Instituto de Investigación Sanitaria La Fe (IISLAFE) Avenida Fernando Abril Martorell 106, 46026 Valencia, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 46022 Valencia, Spain
| | - Ramón Martínez-Máñez
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain; (E.A.); (I.C.); (E.G.); (R.M.-M.)
- Unidad Mixta de Investigación en Nanomedicina y Sensores, Instituto de Investigación Sanitaria La Fe (IISLAFE) Avenida Fernando Abril Martorell 106, 46026 Valencia, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 46022 Valencia, Spain
| | - Fabian Dortu
- Multitel, Parc Initialis 2, Rue Pierre et Marie Curie, 7000 Mons, Belgium; (F.D.); (D.B.)
| | - Damien Bernier
- Multitel, Parc Initialis 2, Rue Pierre et Marie Curie, 7000 Mons, Belgium; (F.D.); (D.B.)
| | - Beatriz Mengual-Chuliá
- Virology Laboratory, Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, FISABIO-Public Health, Generalitat Valenciana, 46020 Valencia, Spain; (B.M.-C.); (F.X.L.-L.)
| | - F. Xavier López-Labrador
- Virology Laboratory, Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, FISABIO-Public Health, Generalitat Valenciana, 46020 Valencia, Spain; (B.M.-C.); (F.X.L.-L.)
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Departament de Microbiologia i Ecologia, Facultat de Medicina, Universitat de València, 46010 Valencia, Spain
| | - Jens J. Sloth
- National Food Institute, Technical University of Denmark, Kemitorvet B201, DK-2800 KGS. Lyngby, Denmark; (J.J.S.); (K.L.); (L.D.-O.)
| | - Katrin Loeschner
- National Food Institute, Technical University of Denmark, Kemitorvet B201, DK-2800 KGS. Lyngby, Denmark; (J.J.S.); (K.L.); (L.D.-O.)
| | - Lene Duedahl-Olesen
- National Food Institute, Technical University of Denmark, Kemitorvet B201, DK-2800 KGS. Lyngby, Denmark; (J.J.S.); (K.L.); (L.D.-O.)
| | - Natalia Prado
- Asociación de Investigación de Industrias Cárnicas del Principado de Asturias (ASINCAR), Polígono La Barreda, Calle Solelleros 5, 33180 Noreña, Spain; (N.P.); (M.H.); (A.M.)
| | - Martín Hervello
- Asociación de Investigación de Industrias Cárnicas del Principado de Asturias (ASINCAR), Polígono La Barreda, Calle Solelleros 5, 33180 Noreña, Spain; (N.P.); (M.H.); (A.M.)
| | - Armando Menéndez
- Asociación de Investigación de Industrias Cárnicas del Principado de Asturias (ASINCAR), Polígono La Barreda, Calle Solelleros 5, 33180 Noreña, Spain; (N.P.); (M.H.); (A.M.)
| | - Rainer Gransee
- Fraunhofer IMM, Carl-Zeiss-Str. 18-20, 55129 Mainz, Germany; (R.G.); (T.K.)
| | | | - M. Clara Gonçalves
- Instituto Superior Técnico, CQE, Avenida Rovisco País 1, 1049 001 Lisboa, Portugal; (M.C.G.); (F.Z.)
| | - Fahimeh Zare
- Instituto Superior Técnico, CQE, Avenida Rovisco País 1, 1049 001 Lisboa, Portugal; (M.C.G.); (F.Z.)
| | - Ana Fuentes López
- Departamento de Tecnología de Alimentos, Escuela Técnica Superior de Ingeniería Agronómica y del Medio Natural, Universitat Politècnica de València, 46022 Valencia, Spain; (A.F.L.); (J.M.B.B.)
| | - Isabel Fernández Segovia
- Departamento de Tecnología de Alimentos, Escuela Técnica Superior de Ingeniería Agronómica y del Medio Natural, Universitat Politècnica de València, 46022 Valencia, Spain; (A.F.L.); (J.M.B.B.)
| | - Jose M. Barat Baviera
- Departamento de Tecnología de Alimentos, Escuela Técnica Superior de Ingeniería Agronómica y del Medio Natural, Universitat Politècnica de València, 46022 Valencia, Spain; (A.F.L.); (J.M.B.B.)
| | - Jaime Salcedo
- Lumensia Sensors S.L., Camí de Vera s/n, 46020 Valencia, Spain; (J.S.); (S.R.); (A.F.B.)
| | - Sara Recuero
- Lumensia Sensors S.L., Camí de Vera s/n, 46020 Valencia, Spain; (J.S.); (S.R.); (A.F.B.)
| | - Santiago Simón
- Lumensia Sensors S.L., Camí de Vera s/n, 46020 Valencia, Spain; (J.S.); (S.R.); (A.F.B.)
| | - Ana Fernández Blanco
- Lumensia Sensors S.L., Camí de Vera s/n, 46020 Valencia, Spain; (J.S.); (S.R.); (A.F.B.)
| | - Sergio Peransi
- Lumensia Sensors S.L., Camí de Vera s/n, 46020 Valencia, Spain; (J.S.); (S.R.); (A.F.B.)
| | - Maribel Gómez-Gómez
- Nanophotonics Technology Center, Universitat Politècnica de València, Camí de Vera s/n, 46022 Valencia, Spain; (O.N.); (D.O.d.Z.)
| | - Amadeu Griol
- Nanophotonics Technology Center, Universitat Politècnica de València, Camí de Vera s/n, 46022 Valencia, Spain; (O.N.); (D.O.d.Z.)
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Pichler I, Schmutz S, Ziltener G, Zaheri M, Kufner V, Trkola A, Huber M. Rapid and sensitive single-sample viral metagenomics using Nanopore Flongle sequencing. J Virol Methods 2023; 320:114784. [PMID: 37516367 DOI: 10.1016/j.jviromet.2023.114784] [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: 04/21/2023] [Revised: 07/11/2023] [Accepted: 07/25/2023] [Indexed: 07/31/2023]
Abstract
The ability of viral metagenomic Next-Generation Sequencing (mNGS) to unbiasedly detect nucleic acids in a clinical sample is a powerful tool for advanced diagnosis of viral infections. When clinical symptoms do not provide a clear differential diagnosis, extensive laboratory testing with virus-specific PCR and serology can be replaced by a single viral mNGS analysis. However, widespread diagnostic use of viral mNGS is thus far limited by long sample-to-result times, as most protocols rely on Illumina sequencing, which provides high and accurate sequencing output but is time-consuming and expensive. Here, we describe the development of an mNGS protocol based on the more cost-effective Nanopore Flongle sequencing with decreased turnaround time and lower, yet sufficient sequencing output to provide sensitive virus detection. Sample preparation (6 h) and sequencing (2 h) times are substantially reduced compared to Illumina mNGS and allow detection of DNA/RNA viruses at low input (up to 33-38 cycle threshold of specific qPCR). Although Flongles yield lower sequencing output, direct comparison with Illumina mNGS on diverse clinical samples showed similar results. Collectively, the novel Nanopore mNGS approach is specifically tailored for use in clinical diagnostics and provides a rapid and cost-effective mNGS strategy for individual testing of severe cases.
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Affiliation(s)
- Ian Pichler
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Gabriela Ziltener
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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Botto MM, Borsellini A, Lamers MH. A four-point molecular handover during Okazaki maturation. Nat Struct Mol Biol 2023; 30:1505-1515. [PMID: 37620586 DOI: 10.1038/s41594-023-01071-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 07/17/2023] [Indexed: 08/26/2023]
Abstract
DNA replication introduces thousands of RNA primers into the lagging strand that need to be removed for replication to be completed. In Escherichia coli when the replicative DNA polymerase Pol IIIα terminates at a previously synthesized RNA primer, DNA Pol I takes over and continues DNA synthesis while displacing the downstream RNA primer. The displaced primer is subsequently excised by an endonuclease, followed by the sealing of the nick by a DNA ligase. Yet how the sequential actions of Pol IIIα, Pol I polymerase, Pol I endonuclease and DNA ligase are coordinated is poorly defined. Here we show that each enzymatic activity prepares the DNA substrate for the next activity, creating an efficient four-point molecular handover. The cryogenic-electron microscopy structure of Pol I bound to a DNA substrate with both an upstream and downstream primer reveals how it displaces the primer in a manner analogous to the monomeric helicases. Moreover, we find that in addition to its flap-directed nuclease activity, the endonuclease domain of Pol I also specifically cuts at the RNA-DNA junction, thus marking the end of the RNA primer and creating a 5' end that is a suitable substrate for the ligase activity of LigA once all RNA has been removed.
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Affiliation(s)
- Margherita M Botto
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, the Netherlands
- Department of Molecular and Cellular Biology, Geneva University, Geneva, Switzerland
| | - Alessandro Borsellini
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, the Netherlands
- Department of Structural Biology, Human Technopole, Milan, Italy
| | - Meindert H Lamers
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, the Netherlands.
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Werbajh S, Larocca L, Carrillo C, Stolowicz F, Ogas L, Pallotto S, Cassará S, Mammana L, Zapiola I, Bouzas MB, Vojnov AA. Colorimetric RT-LAMP Detection of Multiple SARS-CoV-2 Variants and Lineages of Concern Direct from Nasopharyngeal Swab Samples without RNA Isolation. Viruses 2023; 15:1910. [PMID: 37766315 PMCID: PMC10537693 DOI: 10.3390/v15091910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/31/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Since, during the Coronavirus disease 19 (COVID-19) pandemic, a large part of the human population has become infected, a rapid and simple diagnostic method has been necessary to detect its causative agent, the Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2), and control its spread. Thus, in the present study, we developed a colorimetric reverse transcription-loop-mediated isothermal amplification (RT-LAMP) kit that allows the detection of SARS-CoV-2 from nasopharyngeal swab samples without the need for RNA extraction. The kit utilizes three sets of LAMP primers targeting two regions of ORF1ab and one region in the E gene. The results are based on the colorimetric change of hydroxynaphthol blue, which allows visual interpretation without needing an expensive instrument. The kit demonstrated sensitivity to detect between 50 and 100 copies of the viral genome per reaction. The kit was authorized by the National Administration of Drugs, Food and Technology (ANMAT) of Argentina after validation using samples previously analyzed by the gold standard RT-qPCR. The results showed a sensitivity of 90.6% and specificity of 100%, consistent with conventional RT-qPCR. In silico analysis confirmed the recognition of SARS-CoV-2 variants of concern (B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.427, and B.1.429), and lineages of the Omicron variant (B.1.1.529) with 100% homology. This rapid, simple, and sensitive RT-LAMP method paves the way for a large screening strategy to be carried out at locations lacking sophisticated instrumental and trained staff, as it particularly happens in regional hospitals and medical centers from rural areas.
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Affiliation(s)
- Santiago Werbajh
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
| | - Luciana Larocca
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
| | - Carolina Carrillo
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
| | - Fabiana Stolowicz
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
| | - Lorena Ogas
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
| | - Sergio Pallotto
- Laboratorio Pablo Cassará S.R.L. Saladillo 2452, Buenos Aires C1440FFX, Argentina
| | - Solange Cassará
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
| | - Liliana Mammana
- Sección Virología, Hospital de Enfermedades Infecciosas Francisco Javier Muñiz Uspallata 2272, Buenos Aires C1282AEN, Argentina (I.Z.); (M.B.B.)
| | - Inés Zapiola
- Sección Virología, Hospital de Enfermedades Infecciosas Francisco Javier Muñiz Uspallata 2272, Buenos Aires C1282AEN, Argentina (I.Z.); (M.B.B.)
| | - María Belén Bouzas
- Sección Virología, Hospital de Enfermedades Infecciosas Francisco Javier Muñiz Uspallata 2272, Buenos Aires C1282AEN, Argentina (I.Z.); (M.B.B.)
| | - Adrian A. Vojnov
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
- Facultad de Medicina-Universidad del Salvador, Av. Córdoba 1601, Buenos Aires C1055AAG, Argentina
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Sui P, Sun Y, Shi Y, Ran W, Shi N, Sun D, Zheng J, Zhao J. Establishment and evaluation of a multiplex real-time RT-PCR for quantitative and differential detection of wild-type canine distemper virus from vaccine strains. Heliyon 2023; 9:e19344. [PMID: 37662817 PMCID: PMC10469063 DOI: 10.1016/j.heliyon.2023.e19344] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/07/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023] Open
Abstract
This study sought to establish a real-time reverse transcription (RT)-PCR method to differentially detect canine distemper virus (CDV) wild-type and vaccine strains. To this end, a pair of CDV universal primers and two specific minor groove binder (MGB) probes, harboring a T/C substitution in the hemagglutinin (H) gene, were designed. Using a recombinant plasmid expressing the H gene of the CDV wild-type or vaccine strain as standards, a sensitive and specific multiplex real-time RT-PCR was established for quantitative and differential detection of CDV wild-type and vaccine strains. The limit of detection for this multiplex assay was 22.5 copies/μL and 2.98 copies/μL of viral RNA for wild-type and vaccine strains, respectively. Importantly, the wild-type and vaccine MGB probes specifically hybridized different genotypes of wild-type CDV circulating in China as well as globally administered vaccine viruses, respectively, with no cross-reactivity observed with non-CDV viruses. Moreover, this method was successfully applied for the quantitative detection of CDV RNA in tissue samples of experimentally infected breeding foxes, raccoon dogs, and minks. Additionally, the multiplex real-time RT-PCR was able to detect the viral RNA in the whole blood samples as early as 3 days post-infection, 3 to 4 days prior to the onset of clinical signs in these CDV infection animals. Hence, the established multiplex real-time RT-PCR method is useful for differentiating wild-type CDV and vaccine strains in China, and for conducting canine distemper early diagnosis as well as dynamic mechanism of CDV replication studies in vivo.
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Affiliation(s)
- Ping Sui
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China
| | - Yiyang Sun
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China
| | - Yijun Shi
- Shandong Yantai Animal Disease Control Center, Yantai 264003, PR China
| | - Wei Ran
- Animal Husbandry and Fisheries, Guizhou Vocational College of Agriculture, Guiyang 551400, China
| | - Ning Shi
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Dongbo Sun
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China
| | - Jiasan Zheng
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China
| | - Jianjun Zhao
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China
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Politza AJ, Liu T, Guan W. Programmable magnetic robot (ProMagBot) for automated nucleic acid extraction at the point of need. LAB ON A CHIP 2023; 23:3882-3892. [PMID: 37551930 PMCID: PMC11218199 DOI: 10.1039/d3lc00545c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Upstream sample preparation remains the bottleneck for point-of-need nucleic acid testing due to its complexity and time-consuming nature. Sample preparation involves extracting, purifying, and concentrating nucleic acids from various matrices. These processes are critical for ensuring the accuracy and sensitivity of downstream nucleic acid amplification and detection. However, current sample preparation methods are often laboratory-based, requiring specialized equipment, trained personnel, and several hours of processing time. As a result, sample preparation often limits the speed, portability, and cost-effectiveness of point-of-need nucleic acid testing. A universal, field-deployable sample preparation device is highly desirable for this critical need and unmet challenge. Here we reported a handheld, battery-powered, reconfigurable, and field-deployable nucleic acid sample preparation device. A programmable electromagnetic actuator was developed to drive a magnetic robot (ProMagBot) in X/Y 2D space, such that various magnetic bead-based sample preparations can be readily translated from the laboratory to point-of-need settings. The control of the electromagnetic actuator requires only a 3-phase unipolar voltage in X and Y directions, and therefore, the motion space is highly scalable. We validated the ProMagBot device with a model application by extracting HIV viral RNAs from plasma samples using two widely used magnetic bead kits: ChargeSwitch and MagMAX beads. In both cases, the ProMagBot could successfully extract viral RNAs from 50 μL plasma samples containing as low as 102 copies of viral RNAs in 20 minutes. Our results demonstrated the ability of ProMagBot to prepare samples from complex mediums at the point of need. We believe such a device would enable rapid and robust sample preparation in various settings, including resource-limited or remote environments, and accelerate the development of next-generation point-of-need nucleic acid testing.
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Affiliation(s)
- Anthony J Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park 16802, USA.
| | - Tianyi Liu
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Weihua Guan
- Department of Biomedical Engineering, Pennsylvania State University, University Park 16802, USA.
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
- School of Electrical Engineering and Computer Science, Pennsylvania State University, University Park 16802, USA
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Cam Duyen VT, Van Toi V, Van Hoi T, Truong PL. A novel colorimetric biosensor for rapid detection of dengue virus upon acid-induced aggregation of colloidal gold. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:3991-3999. [PMID: 37545366 DOI: 10.1039/d3ay00756a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The dengue virus, once transmitted to people through a mosquito bite, causes an infectious disease called dengue fever. Dengue fever can develop into two fatal syndromes, namely dengue shock syndrome and dengue hemorrhagic fever. The existing strategies for detecting dengue infection mainly employ serological immunoassays and a real time PCR technique. Along with the positive features of efficiency, accuracy, and reproducibility, these procedures are limited by being time-consuming, costly, requiring special equipment for analysis, and unable to be carried out at the point-of-care level. Herein, we developed a colorimetric nanosensor for detecting dengue virus in clinical samples that is rapid, accurate, sensitive, and less expensive. The sensing platform relies on the specific binding between the DNA-conjugated AuNPs and genomic RNA of dengue, which results in the DNA-RNA heteroduplex structure formation that turns the gold colloid's ruby red color to blue due to the nano-aggregation in an acidic environment, which can be detected by the naked eye or measuring the absorbance. The DNA probe was designed to bind to a genomic RNA conserved region recognized in all four dengue serotypes. Dengue virus serotype 1 was utilized as a framework for virus detection; the designed nanosensor exhibited great specificity and selectivity, with the detection limit of ∼1 pg μL-1 (∼1.66 × 106 RNA copies per reaction) and time of analysis of about 1 h including the RNA extraction step. The proposed colorimetric nanosensor offers an alternative tool for specific and highly sensitive detection of dengue that eliminates the requirement for thermal cycling and primer sets in PCR-based assays.
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Affiliation(s)
- Vo Thi Cam Duyen
- School of Biomedical Engineering, International University, Ho Chi Minh City 700000, Vietnam.
- Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Vo Van Toi
- School of Biomedical Engineering, International University, Ho Chi Minh City 700000, Vietnam.
- Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Truong Van Hoi
- Department of Biochemistry and Microbiology, Ninh Thuan Hospital, Phan Rang-Thap Cham City 59100, Vietnam
| | - Phuoc Long Truong
- School of Biomedical Engineering, International University, Ho Chi Minh City 700000, Vietnam.
- Vietnam National University, Ho Chi Minh City 700000, Vietnam
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Lazov CM, Papetti A, Belsham GJ, Bøtner A, Rasmussen TB, Boniotti MB. Multiplex Real-Time RT-PCR Assays for Detection and Differentiation of Porcine Enteric Coronaviruses. Pathogens 2023; 12:1040. [PMID: 37624000 PMCID: PMC10457881 DOI: 10.3390/pathogens12081040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023] Open
Abstract
It is important to be able to detect and differentiate between distinct porcine enteric coronaviruses that can cause similar diseases. However, the existence of naturally occurring recombinant coronaviruses such as swine enteric coronavirus (SeCoV) can give misleading results with currently used diagnostic methods. Therefore, we have developed and validated three duplex real-time quantitative RT-PCR assays for the simultaneous detection of, and differentiation between, porcine epidemic diarrhea virus (PEDV) and SeCoV. Transmissible gastroenteritis virus (TGEV) is also detected by two out of these three assays. In addition, a novel triplex assay was set up that was able to detect and differentiate between these alphacoronaviruses and the porcine deltacoronavirus (PDCoV). The validated assays have low limits of detection, close to 100% efficiency, and were able to correctly identify the presence of PEDV and SeCoV in 55 field samples, whereas 20 samples of other pathogens did not give a positive result. Implementing one or more of these multiplex assays into the routine diagnostic surveillance for PEDV will ensure that the presence of SeCoV, TGEV, and PDCoV will not go unnoticed.
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Affiliation(s)
- Christina M. Lazov
- DTU Institute of Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, IZSLER, Reparto Tecnologie Biologiche Applicate, Via Bianchi, 9, 25124 Brescia, Italy
- Department of Veterinary and Animal Sciences, University of Copenhagen, 4 Stigboejlen, 1870 Frederiksberg, Denmark
| | - Alice Papetti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, IZSLER, Reparto Tecnologie Biologiche Applicate, Via Bianchi, 9, 25124 Brescia, Italy
| | - Graham J. Belsham
- Department of Veterinary and Animal Sciences, University of Copenhagen, 4 Stigboejlen, 1870 Frederiksberg, Denmark
| | - Anette Bøtner
- Department of Veterinary and Animal Sciences, University of Copenhagen, 4 Stigboejlen, 1870 Frederiksberg, Denmark
| | - Thomas Bruun Rasmussen
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen, Denmark
| | - Maria Beatrice Boniotti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, IZSLER, Reparto Tecnologie Biologiche Applicate, Via Bianchi, 9, 25124 Brescia, Italy
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Yasuura M, Tan ZL, Horiguchi Y, Ashiba H, Fukuda T. Improvement of Sensitivity and Speed of Virus Sensing Technologies Using nm- and μm-Scale Components. SENSORS (BASEL, SWITZERLAND) 2023; 23:6830. [PMID: 37571612 PMCID: PMC10422600 DOI: 10.3390/s23156830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/20/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023]
Abstract
Various viral diseases can be widespread and cause severe disruption to global society. Highly sensitive virus detection methods are needed to take effective measures to prevent the spread of viral infection. This required the development of rapid virus detection technology to detect viruses at low concentrations, even in the biological fluid of patients in the early stages of the disease or environmental samples. This review describes an overview of various virus detection technologies and then refers to typical technologies such as beads-based assay, digital assay, and pore-based sensing, which are the three modern approaches to improve the performance of viral sensing in terms of speed and sensitivity.
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Affiliation(s)
- Masato Yasuura
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba 305-8565, Ibaraki, Japan; (Z.L.T.); (Y.H.); (H.A.); (T.F.)
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Kimura Y, Ikeuchi M. Development of non-electrically controlled SalivaDirect LAMP (NEC-SD-LAMP), a new nonelectrical infectious disease testing method. Sci Rep 2023; 13:11791. [PMID: 37479724 PMCID: PMC10362045 DOI: 10.1038/s41598-023-38800-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/14/2023] [Indexed: 07/23/2023] Open
Abstract
In this study, non-electrically controlled SalivaDirect loop-mediated isothermal amplification (NEC-SD-LAMP), which can detect infections by amplifying viral DNA expression in saliva without using electrical control systems, was developed. By this method, only by adding water to the device, viral DNA was extracted from saliva using SalivaDirect, the extracted DNA was amplified via loop-mediated isothermal amplification (LAMP), and the results were visually confirmed. Melting palmitic acid maintained the optimal temperature for the LAMP reaction, as the temperature of palmitic acid is maintained at 62.9 °C, its melting point. By exploiting the proximity of the melting point to the optimal temperature for LAMP, LAMP can be performed without electricity. We detected several viruses in the saliva using this method. NEC-SD-LAMP could clearly distinguish 3 types of viral DNA, indicating the high specificity of this reaction. Furthermore, the viral concentration detection limit of the device was 2 copies per µL, indicating that it is possible to detect DNA viral infections in saliva even before the onset of viral infection.
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Affiliation(s)
- Yusuke Kimura
- Department of Precision Biomedical Engineering, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo, Japan
- Department of Advanced Functional Materials Research, Takasaki Advanced Radiation Research Institute, National Institutes for Quantum Science and Technology (QST), 1233 Watanuki-machi, Takasaki, Gunma, Japan
| | - Masashi Ikeuchi
- Department of Precision Biomedical Engineering, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo, Japan.
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Wong S, Jimenez S, Slavcev RA. Construction and characterization of a novel miniaturized filamentous phagemid for targeted mammalian gene transfer. Microb Cell Fact 2023; 22:124. [PMID: 37430278 DOI: 10.1186/s12934-023-02135-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/24/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND As simplistic proteinaceous carriers of genetic material, phages offer great potential as targeted vectors for mammalian transgene delivery. The filamentous phage M13 is a single-stranded DNA phage with attractive characteristics for gene delivery, including a theoretically unlimited DNA carrying capacity, amenability to tropism modification via phage display, and a well-characterized genome that is easy to genetically modify. The bacterial backbone in gene transfer plasmids consists of elements only necessary for amplification in prokaryotes, and, as such, are superfluous in the mammalian cell. These problematic elements include antibiotic resistance genes, which can disseminate antibiotic resistance, and CpG motifs, which are inflammatory in animals and can lead to transgene silencing. RESULTS Here, we examined how M13-based phagemids could be improved for transgene delivery by removing the bacterial backbone. A transgene cassette was flanked by isolated initiation and termination elements from the phage origin of replication. Phage proteins provided in trans by a helper would replicate only the cassette, without any bacterial backbone. The rescue efficiency of "miniphagemids" from these split origins was equal to, if not greater than, isogenic "full phagemids" arising from intact origins. The type of cassette encoded by the miniphagemid as well as the choice of host strain constrained the efficiency of phagemid rescue. CONCLUSIONS The use of two separated domains of the f1 ori improves upon a single wildtype origin while still resulting in high titres of miniphagemid gene transfer vectors. Highly pure lysates of miniaturized phagemids could be rapidly obtained in a straightforward procedure without additional downstream processing.
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Affiliation(s)
- Shirley Wong
- School of Pharmacy, University of Waterloo, Waterloo, Canada.
| | - Salma Jimenez
- School of Pharmacy, University of Waterloo, Waterloo, Canada
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36
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Jhingree JR, Boisvert J, Mercier G. An isotope dilution mass spectrometry assay to track Norovirus-like particles in vaccine process intermediates by quantifying capsid protein VP1. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:2729-2735. [PMID: 37199095 DOI: 10.1039/d3ay00411b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The coronavirus disease (COVID-19) pandemic shows the rapid pace at which vaccine development can occur which highlights the need for more fast and efficient analytical methodologies to track and characterize candidate vaccines during manufacturing and purification processes. The candidate vaccine in this work comprises plant-derived Norovirus-like particles (NVLPs) which are structures that mimic the virus but lack any infectious genetic material. Presented here is a liquid chromatography-tandem mass spectrometry (LC-MS/MS) methodology for the quantification of viral protein VP1, the main component of the NVLPs in this study. It combines isotope dilution mass spectrometry (IDMS) with multiple reaction monitoring (MRM) to quantify targeted peptides in process intermediates. Multiple MRM transitions (precursor/product ion pairs) for VP1 peptides were tested with varying MS source conditions and collision energies. Final parameter selection for quantification includes three peptides with two MRM transitions each offering maximum detection sensitivity under optimized MS conditions. For quantification, a known concentration of the isotopically labeled version of the peptides to be quantified was added into working standard solutions to serve as an internal standard (IS); calibration curves were generated for concentration of native peptide vs. the peak area ratio of native-to-isotope labeled peptide. VP1 peptides in samples were quantified with labeled versions of the peptides added at the same level as that of the standards. Peptides were quantified with limit of detection (LOD) as low as 1.0 fmol μL-1 and limit of quantitation (LOQ) as low as 2.5 fmol μL-1. NVLP preparations spiked with known quantities of either native peptides or drug substance (DS) comprising assembled NVLPs produced recoveries indicative of minimal matrix effects. Overall, we report a fast, specific, selective, and sensitive LC-MS/MS strategy to track NVLPs through the purification steps of the DS of a Norovirus candidate vaccine. To the best of our knowledge, this is the first application of an IDMS method to track virus-like particles (VLPs) produced in plants as well as measurements performed with VP1, a Norovirus capsid protein.
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Affiliation(s)
- Jacquelyn R Jhingree
- Medicago Inc., 2552 Boulevard du Parc-Technologique, Québec, QC, G1P 4S6, Canada.
| | - Julie Boisvert
- Medicago Inc., 2552 Boulevard du Parc-Technologique, Québec, QC, G1P 4S6, Canada.
| | - Geneviève Mercier
- Medicago Inc., 2552 Boulevard du Parc-Technologique, Québec, QC, G1P 4S6, Canada.
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Wright BR, Jelocnik M, Casteriano A, Muir YSS, Legione AR, Vaz PK, Devlin JM, Higgins DP. Development of diagnostic and point of care assays for a gammaherpesvirus infecting koalas. PLoS One 2023; 18:e0286407. [PMID: 37262062 DOI: 10.1371/journal.pone.0286407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/14/2023] [Indexed: 06/03/2023] Open
Abstract
The recent listing of koala populations as endangered across much of their range has highlighted the need for better management interventions. Disease is a key threat to koala populations but currently there is no information across the threatened populations on the distribution or impact of a gammaherpesvirus, phascolarctid gammaherpesvirus 1 (PhaHV-1). PhaHV-1 is known to infect koalas in southern populations which are, at present, not threatened. Current testing for PhaHV-1 involves lengthy laboratory techniques that do not permit quantification of viral load. In order to better understand distribution, prevalence and impacts of PhaHV-1 infections across koala populations, diagnostic and rapid point of care tests are required. We have developed two novel assays, a qPCR assay and an isothermal assay, that will enable researchers, clinicians and wildlife managers to reliably and rapidly test for PhaHV-1 in koalas. The ability to rapidly diagnose and quantify viral load will aid quarantine practices, inform translocation management and guide research into the clinical significance and impacts of PhaHV-1 infection in koalas.
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Affiliation(s)
- Belinda R Wright
- Koala Health Hub, Sydney School of Veterinary Science, University of Sydney, Camperdown, New South Wales, Australia
| | - Martina Jelocnik
- Centre for Bioinnovation, University of The Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Andrea Casteriano
- Koala Health Hub, Sydney School of Veterinary Science, University of Sydney, Camperdown, New South Wales, Australia
| | - Yasmine S S Muir
- Koala Health Hub, Sydney School of Veterinary Science, University of Sydney, Camperdown, New South Wales, Australia
| | - Alistair R Legione
- Asia Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
| | - Paola K Vaz
- Asia Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
| | - Joanne M Devlin
- Asia Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
| | - Damien P Higgins
- Koala Health Hub, Sydney School of Veterinary Science, University of Sydney, Camperdown, New South Wales, Australia
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Nevone A, Lattarulo F, Russo M, Panno G, Milani P, Basset M, Avanzini MA, Merlini G, Palladini G, Nuvolone M. A Strategy for the Selection of RT-qPCR Reference Genes Based on Publicly Available Transcriptomic Datasets. Biomedicines 2023; 11:1079. [PMID: 37189697 PMCID: PMC10135859 DOI: 10.3390/biomedicines11041079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
In the next-generation sequencing era, RT-qPCR is still widely employed to quantify levels of nucleic acids of interest due to its popularity, versatility, and limited costs. The measurement of transcriptional levels through RT-qPCR critically depends on reference genes used for normalization. Here, we devised a strategy to select appropriate reference genes for a specific clinical/experimental setting based on publicly available transcriptomic datasets and a pipeline for RT-qPCR assay design and validation. As a proof-of-principle, we applied this strategy to identify and validate reference genes for transcriptional studies of bone-marrow plasma cells from patients with AL amyloidosis. We performed a systematic review of published literature to compile a list of 163 candidate reference genes for RT-qPCR experiments employing human samples. Next, we interrogated the Gene Expression Omnibus to assess expression levels of these genes in published transcriptomic studies on bone-marrow plasma cells from patients with different plasma cell dyscrasias and identified the most stably expressed genes as candidate normalizing genes. Experimental validation on bone-marrow plasma cells showed the superiority of candidate reference genes identified through this strategy over commonly employed "housekeeping" genes. The strategy presented here may apply to other clinical and experimental settings for which publicly available transcriptomic datasets are available.
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Affiliation(s)
- Alice Nevone
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Francesca Lattarulo
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Monica Russo
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giada Panno
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Paolo Milani
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Marco Basset
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Maria Antonietta Avanzini
- Pediatric Hematology Oncology, Cell Factory, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giampaolo Merlini
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giovanni Palladini
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Mario Nuvolone
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
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Kabiraz MP, Majumdar PR, Mahmud MC, Bhowmik S, Ali A. Conventional and advanced detection techniques of foodborne pathogens: A comprehensive review. Heliyon 2023; 9:e15482. [PMID: 37151686 PMCID: PMC10161726 DOI: 10.1016/j.heliyon.2023.e15482] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/13/2023] [Accepted: 04/11/2023] [Indexed: 05/09/2023] Open
Abstract
Foodborne pathogens are a major public health concern and have a significant economic impact globally. From harvesting to consumption stages, food is generally contaminated by viruses, parasites, and bacteria, which causes foodborne diseases such as hemorrhagic colitis, hemolytic uremic syndrome (HUS), typhoid, acute, gastroenteritis, diarrhea, and thrombotic thrombocytopenic purpura (TTP). Hence, early detection of foodborne pathogenic microbes is essential to ensure a safe food supply and to prevent foodborne diseases. The identification of foodborne pathogens is associated with conventional (e.g., culture-based, biochemical test-based, immunological-based, and nucleic acid-based methods) and advances (e.g., hybridization-based, array-based, spectroscopy-based, and biosensor-based process) techniques. For industrial food applications, detection methods could meet parameters such as accuracy level, efficiency, quickness, specificity, sensitivity, and non-labor intensive. This review provides an overview of conventional and advanced techniques used to detect foodborne pathogens over the years. Therefore, the scientific community, policymakers, and food and agriculture industries can choose an appropriate method for better results.
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Affiliation(s)
- Meera Probha Kabiraz
- Department of Biotechnology, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Priyanka Rani Majumdar
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, 2052, Australia
- Department of Fisheries and Marine Science, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - M.M. Chayan Mahmud
- CASS Food Research Centre, School of Exercise and Nutrition Sciences, Deakin University, 221 Burwood Highway, VIC, 3125, Australia
| | - Shuva Bhowmik
- Department of Fisheries and Marine Science, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
- Centre for Bioengineering and Nanomedicine, Faculty of Dentistry, Division of Health Sciences, University of Otago, Dunedin, 9054, New Zealand
- Department of Food Science, University of Otago, Dunedin, 9054, New Zealand
- Corresponding author. Centre for Bioengineering and Nanomedicine, Faculty of Dentistry, Division of Health Sciences, University of Otago, Dunedin, 9054, New Zealand.
| | - Azam Ali
- Centre for Bioengineering and Nanomedicine, Faculty of Dentistry, Division of Health Sciences, University of Otago, Dunedin, 9054, New Zealand
- Corresponding author.
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Jang YO, Kim NH, Roh Y, Koo B, Lee HJ, Kim JY, Kim SH, Shin Y. Self-directed molecular diagnostics (SdMDx) system for COVID-19 via one-pot processing. SENSORS AND ACTUATORS. B, CHEMICAL 2023; 378:133193. [PMID: 36570722 PMCID: PMC9759472 DOI: 10.1016/j.snb.2022.133193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/03/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Rapid, sensitive, and specific detection of the severe acute respiratory syndrome coronavirus (SARS-CoV)- 2 during early infection is pivotal in controlling the spread and pathological progression of Coronavirus Disease 2019 (COVID-19). Thus, highly accurate, affordable, and scalable point-of-care (POC) diagnostic technologies are necessary. Herein, we developed a rapid and efficient self-directed molecular diagnostic (SdMDx) system for SARS-CoV-2. This system combines the sample preparation step, including virus enrichment and extraction processes, which involve dimethyl suberimidate dihydrochloride and diatomaceous earth functionalized with 3-aminopropyl(diethoxy)methylsilane, and the detection step using loop-mediated isothermal amplification-lateral flow assay (LAMP-LFA). Using the SdMDx system, SARS-CoV-2 could be detected within 47 min by hand without the need for any larger instruments. The SdMDx system enabled detection as low as 0.05 PFU in the culture fluid of SARS-CoV-2-infected VeroE6 cells. We validated the accuracy of the SdMDx system on 38 clinical nasopharyngeal specimens. The clinical utility of the SdMDx system for targeting the S gene of SARS-CoV-2 showed 94.4% sensitivity and 100% specificity. This system is more sensitive than antigen and antibody assays, and it minimizes the use of complicated processes and reduces contamination risks. Accordingly, we demonstrated that the SdMDx system enables a rapid, accurate, simple, efficient, and inexpensive detection of SARS-CoV-2 at home, in emergency facilities, and in low-resource sites as a pre-screening platform and POC testing through self-operation and self-diagnosis.
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Affiliation(s)
- Yoon Ok Jang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Nam Hun Kim
- INFUSIONTECH, 38 Heungan-daero, 427 beon-gil, Dongan-gu, Anyang-si 14059, Republic of Korea
| | - Yeonjeong Roh
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Bonhan Koo
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Hyo Joo Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Ji Yeun Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Republic of Korea
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Republic of Korea
| | - Yong Shin
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
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41
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Yang H, Tu K, Zhao Y, Sun L, Zhao J, Zhang G. Development of SYBR green RT-qPCR assay for titrating bivalent live infectious bronchitis vaccines. J Virol Methods 2023; 313:114675. [PMID: 36592741 DOI: 10.1016/j.jviromet.2022.114675] [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: 11/08/2022] [Revised: 12/20/2022] [Accepted: 12/30/2022] [Indexed: 01/01/2023]
Abstract
Infectious bronchitis (IB) is a highly contagious viral disease of chickens caused by IB virus (IBV) that can cause substantial economic losses in the poultry industry. IBV variant infections have been continuously reported since the initial description in the 1930s. QX-like IBVs are the predominant circulating genotype globally. A homologous QX vaccine has superior protection efficacy compared with that of other available vaccines, and the combination of Massachusetts (Mass)-like and QX-like strains is being used to combat QX-like IBV infections. Inoculation of embryonated chicken eggs is the standard method for the titration of IBV, and the titer is expressed as 50% egg infectious dose (EID50). However, this method cannot effectively distinguish or quantify different genotypic strains in a mixture of different viruses, especially in the absence of neutralizing monoclonal antibodies. In this study, quantitative real-time PCR (RT-qPCR) was applied using specific primers for the QX- and Mass-like strains to quantitate IBV infection and for comparison with the conventional virus titration quantitative method. A strong positive correlation was observed between RT-qPCR cycle threshold values and the different EID50 concentrations. This method was further used to titrate bivalent IB vaccines, and the amount of individual genotype virus was determined based on specific primers. Thus, this RT-qPCR assay may be used as a highly specific, sensitive, and rapid alternative to the EID50 assay for titering IBVs.
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Affiliation(s)
- Huiming Yang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Kaihang Tu
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Ye Zhao
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Lu Sun
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Jing Zhao
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
| | - Guozhong Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
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42
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Angles R, Adkesson MJ, Cárdenas-Alayza S, Adamovicz L, Allender MC. DETECTION AND PREVALENCE OF SPHENISCID ALPHA-HERPESVIRUS-1 (SpAHV-1) IN A SAMPLE OF HUMBOLDT PENGUINS ( SPHENISCUS HUMBOLDTI) AT PUNTA SAN JUAN, PERU. J Zoo Wildl Med 2023; 54:159-163. [PMID: 36971641 DOI: 10.1638/2022-0105] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2022] [Indexed: 03/29/2023] Open
Abstract
Infections with herpesvirus have contributed to respiratory, enteric, and neurological disease reports in avian species worldwide. Herpesviruses have been detected in penguin species before but have not been studied extensively. To better understand the impact of these viruses in free-living populations, an initial retrospective survey was performed on a wild population of Humboldt penguins (Spheniscus humboldti) in the Punta San Juan Marine Protected Area, Peru (15°22'S, 75°12'W) using tracheal swabs collected from 28 penguins in 2016 and 34 penguins in 2018. DNA extracted from these swabs was analyzed using a consensus herpesviral PCR assay targeting the DNA polymerase gene, and positive samples were sequenced. A single sample from 2016 was positive for spheniscid alpha-herpesvirus-1 (SpAHV-1), establishing an overall sample prevalence of 1.6% (95% CI: 0-8.6%). The positive animal was an adult male that did not show any clinical signs of herpesviral infection and was otherwise healthy based on physical exam and laboratory findings. This is the first detection of a herpesvirus in penguins at Punta San Juan, Peru, and the first step toward characterizing the implications of SpAHV-1 for Humboldt penguins. This investigation highlights the importance of continual disease surveillance in wild populations over time to monitor for changes that may impact long-term population viability.
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Affiliation(s)
- Rachel Angles
- Wildlife Epidemiology Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802, USA,
| | | | | | - Laura Adamovicz
- Wildlife Epidemiology Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802, USA
| | - Matthew C Allender
- Wildlife Epidemiology Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802, USA
- Chicago Zoological Society, Brookfield Zoo, Brookfield, IL 60513, USA
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43
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Yang S, Zhang Z, Xian Q, Song Q, Liu Y, Gao Y, Wen W. An Aluminum-Based Microfluidic Chip for Polymerase Chain Reaction Diagnosis. Molecules 2023; 28:molecules28031085. [PMID: 36770751 PMCID: PMC9921548 DOI: 10.3390/molecules28031085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
Real-time polymerase chain reaction (real-time PCR) tests were successfully conducted in an aluminum-based microfluidic chip developed in this work. The reaction chamber was coated with silicone-modified epoxy resin to isolate the reaction system from metal surfaces, preventing the metal ions from interfering with the reaction process. The patterned aluminum substrate was bonded with a hydroxylated glass mask using silicone sealant at room temperature. The effect of thermal expansion was counteracted by the elasticity of cured silicone. With the heating process closely monitored, real-time PCR testing in reaction chambers proceeded smoothly, and the results show similar quantification cycle values to those of traditional test sets. Scanning electron microscope (SEM) and atomic force microscopy (AFM) images showed that the surface of the reaction chamber was smoothly coated, illustrating the promising coating and isolating properties. Energy-dispersive X-ray spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS), and inductively coupled plasma-optical emission spectrometer (ICP-OES) showed that no metal ions escaped from the metal to the chip surface. Fourier-transform infrared spectroscopy (FTIR) was used to check the surface chemical state before and after tests, and the unchanged infrared absorption peaks indicated the unreacted, antifouling surface. The limit of detection (LOD) of at least two copies can be obtained in this chip.
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Affiliation(s)
- Siyu Yang
- Division of Emerging Interdisciplinary Areas, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China
| | - Ziyi Zhang
- Division of Emerging Interdisciplinary Areas, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China
| | - Qingyue Xian
- Division of Emerging Interdisciplinary Areas, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China
| | - Qi Song
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China
| | - Yiteng Liu
- Division of Emerging Interdisciplinary Areas, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China
| | - Yibo Gao
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China
| | - Weijia Wen
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China
- Thrust of Advanced Materials, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou 511400, China
- HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen 518000, China
- Correspondence: ; Tel.: +852-2358-5781
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44
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Rubio-Monterde A, Quesada-González D, Merkoçi A. Toward Integrated Molecular Lateral Flow Diagnostic Tests Using Advanced Micro- and Nanotechnology. Anal Chem 2023; 95:468-489. [PMID: 36413136 DOI: 10.1021/acs.analchem.2c04529] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Ana Rubio-Monterde
- Paperdrop Diagnostics S.L., MRB, Campus UAB, 08193 Bellaterra, Spain.,Nanobioelectronics and Biosensors Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, 08193 Barcelona, Spain
| | | | - Arben Merkoçi
- Paperdrop Diagnostics S.L., MRB, Campus UAB, 08193 Bellaterra, Spain.,Nanobioelectronics and Biosensors Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, 08193 Barcelona, Spain.,The Barcelona Institute of Science and Technology (BIST), Campus UAB, 08036 Bellaterra, Barcelona Spain.,ICREA, Institució Catalana de Recerca i Estudis Avançats, Pg. Lluis Companys 23, 08010 Barcelona, Spain
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45
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Kumar A, Sharma A, Tirpude NV, Thakur S, Kumar S. Combating the Progression of Novel Coronavirus SARS-CoV-2 Infectious Disease: Current State and Future Prospects in Molecular Diagnostics and Drug Discovery. Curr Mol Med 2023; 23:127-146. [PMID: 34344288 DOI: 10.2174/1566524021666210803154250] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 04/07/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022]
Abstract
A highly infectious and life-threatening virus was first reported in Wuhan, China, in late 2019, and it rapidly spread all over the world. This novel virus belongs to the coronavirus family and is associated with severe acute respiratory syndrome (SARS), causing respiratory disease known as COVID-19. In March 2020, WHO has declared the COVID-19 outbreak a global pandemic. Its morbidity and mortality rates are swiftly rising day by day, with the situation becoming more severe and fatal for the comorbid population. Many COVID-19 patients are asymptomatic, but they silently spread the infection. There is a need for proper screening of infected patients to prevent the epidemic transmission of disease and for early curative interventions to reduce the risk of developing severe complications from COVID-19. To date, the diagnostic assays are of two categories, molecular detection of viral genetic material by real-time RTpolymerase chain reaction and serological test, which relies on detecting antiviral antibodies. Unfortunately, there are no effective prophylactics and therapeutics available against COVID-19. However, a few drugs have shown promising antiviral activity against it, and these presently are being referred for clinical trials, albeit FDA has issued an Emergency Use Authorization (EUA) for the emergency use of a few drugs for SARSCoV- 2 infection. This review provides an insight into current progress, challenges and future prospects of laboratory detection methods of COVID-19, and highlights the clinical stage of the major evidence-based drugs/vaccines recommended against the novel SARS-CoV-2 pandemic virus.
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Affiliation(s)
- Arbind Kumar
- COVID-19 Testing Facility, CSIR-Institute of Himalayan Bioresource& Technology (IHBT), Palampur, India
| | - Aashish Sharma
- COVID-19 Testing Facility, CSIR-Institute of Himalayan Bioresource& Technology (IHBT), Palampur, India
| | - Narendra Vijay Tirpude
- COVID-19 Testing Facility, CSIR-Institute of Himalayan Bioresource& Technology (IHBT), Palampur, India
| | - Sharad Thakur
- COVID-19 Testing Facility, CSIR-Institute of Himalayan Bioresource& Technology (IHBT), Palampur, India
| | - Sanjay Kumar
- COVID-19 Testing Facility, CSIR-Institute of Himalayan Bioresource& Technology (IHBT), Palampur, India
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46
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Ji G, Kim HS, Cha SH, Lee HT, Kim HJ, Lee SW, Ahn KJ, Kim KH, Ahn YH, Park HR. Terahertz virus-sized gold nanogap sensor. NANOPHOTONICS (BERLIN, GERMANY) 2023; 12:147-154. [PMID: 39633635 PMCID: PMC11501242 DOI: 10.1515/nanoph-2022-0706] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/07/2024]
Abstract
We demonstrated an ultra-sensitive terahertz virus detection method combined with virus-sized gold nanogaps filled with Al2O3. Large-area high-density 20 nm-gap rectangular loop structures, containing a resonant frequency in the terahertz range, were fabricated on a 4-inch wafer using atomic layer lithography. When target viruses with a 60 nm diameter were located on the nanogaps, we observed a significant redshift of the resonant peak already with an average number of about 100 viruses per unit loop due to the strong field confinement and enhancement near the gap. Furthermore, when the virus was tightly attached to an etched gap like a bridge connecting metals, its sensitivity is doubled compared to the unetched gap, which resulted in 400% more resonance frequency shift per single virus particle than our previous work. Full-wave simulations and theoretical calculations based on modal expansions were in good agreement with the experiments, revealing that the resonant transmission spectrum was mostly determined by the change in refractive index in a two-dimensional-like optical hotspot near the nanogap. A further step could be taken to increase sensitivity by tuning nanogap-loops to the absorption frequencies associated with the intermolecular vibrational modes of the viruses and fingerprinting them as well.
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Affiliation(s)
- Gangseon Ji
- Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan449419, Republic of Korea
| | - Hwan Sik Kim
- Department of Physics, Department of Energy Systems Research, Ajou University, Suwon16499, Republic of Korea
| | - Seong Ho Cha
- Department of Physics, Department of Energy Systems Research, Ajou University, Suwon16499, Republic of Korea
| | - Hyoung-Taek Lee
- Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan449419, Republic of Korea
| | - Hye Ju Kim
- Department of Physics, Department of Energy Systems Research, Ajou University, Suwon16499, Republic of Korea
| | - Sang Woon Lee
- Department of Physics, Department of Energy Systems Research, Ajou University, Suwon16499, Republic of Korea
| | - Kwang Jun Ahn
- Department of Physics, Department of Energy Systems Research, Ajou University, Suwon16499, Republic of Korea
| | - Kyoung-Ho Kim
- Department of Physics, Research Institute for Nanoscale Science and Technology, Chungbuk National University, Cheongju28644, Republic of Korea
| | - Yeong Hwan Ahn
- Department of Physics, Department of Energy Systems Research, Ajou University, Suwon16499, Republic of Korea
| | - Hyeong-Ryeol Park
- Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan449419, Republic of Korea
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Chen S, Xin Y, Tang K, Wu Y, Guo Y. Nardosinone and aurantio-obtusin, two medicine food homology natural compounds, are anti-influenza agents as indicated by transcriptome signature reversion. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 108:154515. [PMID: 36347176 DOI: 10.1016/j.phymed.2022.154515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 10/06/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Medicine food homology (MFH) refers to food that can be used as medicine, and compounds isolated from MFH materials are valuable in novel drug discovery due to their good safety. Transcriptome signature reversion (TSR) is an attractive method for discovering drugs through transcriptional reverse matching; namely, the changes in transcriptional signatures induced by compounds are matched to a certain disease. This strategy can be used to discover anti-influenza agents among MFH natural compounds. PURPOSE MFH natural compounds with anti-influenza activities were identified through analyses of the reversal in the expression of multiple informative genes followed by in vitro evaluation of the cytopathic effect (CPE) caused by influenza infection and relative quantification of the nucleoprotein (NP) gene in viral RNA (vRNA). The combined effect of active compounds was determined through network-based separation score prediction followed by quantification of the viral hemagglutinin (HA) level. METHODS The transcriptome profiles of 4 lung or airway cell lines infected with 7 influenza virus strains were analyzed by robust rank aggregation (RRA) to identify informative genes in the signature of influenza virus infection. The identified informative genes were then matched to a transcriptomic profile library of MFH natural compounds. The anti-influenza activities of MFH natural compounds with negative enrichment scores (ESs) were evaluated in vitro using a CPE assay and relative quantification of the NP gene in the vRNA in the supernatant and cytoplasm to identify anti-influenza agents. The effects of combinations of active compounds were analyzed using network-based calculations followed by confirmation through bioassays for quantifying the viral HA levels. RESULTS Among the 159 MFH natural compounds, 54 compounds had negative ESs, as determined through TSR, and the anti-influenza activities of nardosinone and aurantio-obtusin were confirmed by bioassays. The half-maximal effective concentrations (EC50) of nardosinone and aurantio-obtusin were 4.3-84.4 μM and 31.9-113.6 μM, respectively. The separation score between the informative genes with expression that was negatively regulated by nardosinone and aurantio-obtusin in the human protein-protein interaction (PPI) network was calculated to be 0.10, which indicated that the two compounds potentially exert a synergistic effect, and this effect was confirmed by the finding that the combination indexes (CIs) were calculated to equal 0.86 at inhibition level of 50% and 0.44 at inhibition level of 90%. CONCLUSION The TSR analysis and in vitro evaluation identified nardosinone and aurantio-obtusin as anti-influenza agents. Their antiviral activities were exerted by reversing the expression of multiple informative genes of the host cells. The separation analysis between the informative genes that were reversely regulated by nardosinone and aurantio-obtusin indicated that their combination may exert a synergistic effect, which was confirmed in vitro.
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Affiliation(s)
- Shubing Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; Department of Pharmacology, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Yijing Xin
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; Department of Pharmacology, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Ke Tang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; Department of Pharmacology, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - You Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; Department of Pharmacology, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Ying Guo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; Department of Pharmacology, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
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Jeon H, Bae J, Kim H, Kim MS. VPrimer: A Method of Designing and Updating Primer and Probe With High Variant Coverage for RNA Virus Detection. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:775-784. [PMID: 34951850 DOI: 10.1109/tcbb.2021.3138145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Fatal infectious diseases caused by RNA viruses, such as COVID-19, have emerged around the world. RT-PCR is widely employed for virus detection, and its accuracy depends on the primers and probes since RT-PCR can detect a virus only when the primers and probes bind to the target gene of the virus. Most of primer design methods are for a single host and so require a great deal of effort to design for RNA virus detection, including homology tests among the host and all the viruses for the host using BLAST-like tools. Furthermore, they do not consider variant sequences, which are very common in viruses. In this study, we describe VPrimer, a method of designing high-quality primer-probe sets for RNA viruses. VPrimer can find primer-probe sets that cover more than 95% of the variants of a target virus but do not cover any sequences of other viruses or the host. With VPrimer, we found 381,698,582 primer-probe sets for 3,104 RNA viruses. Multiplex PCR assays using the top 2 primer-probe sets suggested by VPrimer usually cover 100% of variants. To address the rapid changes in viral genomes, VPrimer finds the best and up-to-date primer-probe sets incrementally against the most recently reported variants.
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Viral Quantification in Bee Samples Using Synthetic DNA Sequences with Real-Time PCR (qPCR). Methods Mol Biol 2022; 2610:57-66. [PMID: 36534281 DOI: 10.1007/978-1-0716-2895-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Pathogen spillover between honey bees and wild pollinators is a relatively new and exciting field of study. It is known that some viral diseases are a major threat to honey bee health and, thus, the diagnosis and quantification of honey bee viruses in wild pollinators have gained attention. Pathogen spillover from honey bees to wild bees and the consequences of viral replication to their health still need to be investigated. However, finding positive samples to produce standard curves and include positive controls in real-time PCR (qPCR) assays is challenging. Here we describe the use of synthetic DNA sequences of two variants of deformed wing virus (DWV-A and DWV-B), black queen cell virus (BQCV), sacbrood virus (SBV), chronic bee paralysis virus (CBPV), Kashmir bee virus (KBV), acute bee paralysis virus (ABPV), and Israeli acute paralysis virus (IAPV), to construct standard curves for viral quantification, and for their use as positive controls in qPCR assays.
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Artika IM, Dewi YP, Nainggolan IM, Siregar JE, Antonjaya U. Real-Time Polymerase Chain Reaction: Current Techniques, Applications, and Role in COVID-19 Diagnosis. Genes (Basel) 2022; 13:genes13122387. [PMID: 36553654 PMCID: PMC9778061 DOI: 10.3390/genes13122387] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Successful detection of the first SARS-CoV-2 cases using the real-time polymerase chain reaction (real-time PCR) method reflects the power and usefulness of this technique. Real-time PCR is a variation of the PCR assay to allow monitoring of the PCR progress in actual time. PCR itself is a molecular process used to enzymatically synthesize copies in multiple amounts of a selected DNA region for various purposes. Real-time PCR is currently one of the most powerful molecular approaches and is widely used in biological sciences and medicine because it is quantitative, accurate, sensitive, and rapid. Current applications of real-time PCR include gene expression analysis, mutation detection, detection and quantification of pathogens, detection of genetically modified organisms, detection of allergens, monitoring of microbial degradation, species identification, and determination of parasite fitness. The technique has been used as a gold standard for COVID-19 diagnosis. Modifications of the standard real-time PCR methods have also been developed for particular applications. This review aims to provide an overview of the current applications of the real-time PCR technique, including its role in detecting emerging viruses such as SARS-CoV-2.
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Affiliation(s)
- I Made Artika
- Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Bogor 16680, Indonesia
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Bogor 16911, Indonesia
- Correspondence:
| | - Yora Permata Dewi
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia
| | - Ita Margaretha Nainggolan
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Bogor 16911, Indonesia
| | - Josephine Elizabeth Siregar
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Bogor 16911, Indonesia
| | - Ungke Antonjaya
- Eijkman Oxford Clinical Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia
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