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Lind K, Mölsä M, Kalin-Mänttäri L, Hemmilä H, Voutilainen L, Nikkari S. Vacuum Oven Drying: A Cost-Effective Way of Producing Field-Deployable Reagents for In-house Real-Time PCR Methods. Mol Biotechnol 2023:10.1007/s12033-023-00999-2. [PMID: 38135831 DOI: 10.1007/s12033-023-00999-2] [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: 03/16/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023]
Abstract
The polymerase chain reaction (PCR), is a widely used, sensitive and reliable method for detecting pathogens. However, technical limitations may restrict its use outside sophisticated laboratories, e.g. for detecting pathogens at the site of a disease outbreak. In this study, real-time PCR reagents specific to four bacteria (Bacillus anthracis, Yersinia pestis, Francisella tularensis, and Brucella spp.) and to the Influenza A virus were dried using a vacuum oven drying method. The performance of the dried reagents stored at different temperatures, was monitored using both a standard-size and a portable real-time PCR instrument. The vacuum oven dried real-time PCR reagents were stable and retained the sensitivity for at least 14 months when stored in a refrigerator (+ 4 °C). When stored at room temperature, DNA assays remained stable for at least 10 weeks and Influenza A RNA assay for 3 weeks. These results demonstrate the feasibility of vacuum oven dried real-time PCR reagents and a portable thermocycler for the rapid and reliable detection of pathogens. The drying protocol presented here is cost-effective and easy to use, and could be applied to real-time PCR methods specific to other pathogens as well. In addition, this in-house drying protocol reduces reliance on commercial PCR tests during a time of shortage, such as that experienced during the Corovirus disease (COVID-19) crisis.
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Affiliation(s)
- Katja Lind
- Centre for Military Medicine, Finnish Defence Forces, P.O. Box 50, 00301, Helsinki, Finland.
- Finnish Institute for Health and Welfare, P.O. Box 30, 00271, Helsinki, Finland.
| | - Markos Mölsä
- Centre for Military Medicine, Finnish Defence Forces, P.O. Box 50, 00301, Helsinki, Finland
| | | | - Heidi Hemmilä
- Centre for Military Medicine, Finnish Defence Forces, P.O. Box 50, 00301, Helsinki, Finland
| | - Liina Voutilainen
- Finnish Institute for Health and Welfare, P.O. Box 30, 00271, Helsinki, Finland
| | - Simo Nikkari
- Centre for Military Medicine, Finnish Defence Forces, P.O. Box 50, 00301, Helsinki, Finland
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Choi Y, Kim Y. Application of multiplex realtime PCR detection for hemorrhagic fever syndrome viruses. J Infect Public Health 2023; 16:1933-1941. [PMID: 37866271 DOI: 10.1016/j.jiph.2023.10.012] [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: 03/30/2023] [Revised: 09/13/2023] [Accepted: 10/05/2023] [Indexed: 10/24/2023] Open
Abstract
BACKGROUND Multiplex real-time PCR is a quick and cost effective method for detection of various gene simultaneously. HFSV (Hemorrhagic Fever Syndrome Virus) is a newly emerging infectious disease because of globalization and climate change. We tried to develop a molecular diagnostic technique for various causative viruses and evaluate its usefulness for improving public health. METHODS Molecular diagnostic test method that qualitatively detects viruses causing viral hemorrhagic fevers hired Taq-Man Real-time RT-PCR technique. The Ct value was experimentally observed three or more times at the RNA concentration before and after the detection limit. After designing a multiplex real-time RT-PCR test for target gene of selected 17 viruses, the detection limit for each target and the presence or absence of cross-reaction and interference reaction were evaluated to determine its availability. RESULTS Six kinds of viruses, including Crimean-Congo hemorrhagic fever virus, Omsk hemorrhagic fever virus, Sabia virus, Chapare virus, Yellow fever virus, and Variola virus (A4L gene, B12R gene), were able to confirm the detection limit of 0.5 copies/μl, and other Ebola virus, Marburg virus, Rift Valley fever virus, Kyasanur Forest disease virus, Junin virus, Guanarito virus, Machupo virus, Chikungunya virus, Hantavirus, Dengue virus types 1-4, and Lassa virus (L gene, GPC gene), and 11 kinds of viruses, the detection limit was confirmed at 5 copies/μl. No cross-reaction or interference between detected genes was observed. CONCLUSION The virus test method developed through this study using multiplex is expected to be used for public health and quarantine as a test method that can be used when a hemorrhagic fever virus of unknown cause is introduced.
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Affiliation(s)
- Yoonhyuk Choi
- Department of Convergence Engineering, Graduate School of Venture, Hoseo University, Seoul, 06724, South Korea; MDx Center, Diagnosis Division, iNtRON Biotechnology, South Korea
| | - Younghee Kim
- Department of Convergence Engineering, Graduate School of Venture, Hoseo University, Seoul, 06724, South Korea.
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Coertse J, Mortlock M, Grobbelaar A, Moolla N, Markotter W, Weyer J. Development of a Pan- Filoviridae SYBR Green qPCR Assay for Biosurveillance Studies in Bats. Viruses 2023; 15:v15040987. [PMID: 37112966 PMCID: PMC10145118 DOI: 10.3390/v15040987] [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: 03/01/2023] [Revised: 04/13/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
Recent studies have indicated that bats are hosts to diverse filoviruses. Currently, no pan-filovirus molecular assays are available that have been evaluated for the detection of all mammalian filoviruses. In this study, a two-step pan-filovirus SYBR Green real-time PCR assay targeting the nucleoprotein gene was developed for filovirus surveillance in bats. Synthetic constructs were designed as representatives of nine filovirus species and used to evaluate the assay. This assay detected all synthetic constructs included with an analytical sensitivity of 3-31.7 copies/reaction and was evaluated against the field collected samples. The assay's performance was similar to a previously published probe based assay for detecting Ebola- and Marburgvirus. The developed pan-filovirus SYBR Green assay will allow for more affordable and sensitive detection of mammalian filoviruses in bat samples.
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Affiliation(s)
- Jessica Coertse
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2131, South Africa
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa
| | - Marinda Mortlock
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa
| | - Antoinette Grobbelaar
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Naazneen Moolla
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2131, South Africa
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa
| | - Wanda Markotter
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa
| | - Jacqueline Weyer
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2131, South Africa
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa
- Department of Microbiology and Infectious Diseases, School of Pathology, University of Witwatersrand, Johannesburg 2131, South Africa
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Sun C, Wang D, Xu H, Yang G, Yan X, Liu H. A method for measuring the experimental resolution of laboratory assays (clinical biochemical, blood count, immunological, and qPCR) to evaluate analytical performance. J Clin Lab Anal 2021; 35:e24087. [PMID: 34724262 PMCID: PMC8649380 DOI: 10.1002/jcla.24087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/02/2021] [Accepted: 10/22/2021] [Indexed: 11/11/2022] Open
Abstract
Background The measurement method for experimental resolution and related data to evaluate analytical performance is poorly explored in clinical research. We established a method to measure the experimental resolution of clinical tests, including biochemical tests, automatic hematology analyzer methods, immunoassays, chemical experiments, and qPCR, to evaluate their analytical performance. Methods Serially diluted samples in equal proportions were measured, and correlation analysis was performed between the relative concentration and the measured value. Results were accepted for p ≤ 0.01 of the correlation coefficient. The minimum concentration gradient (eg, 10%) was defined as the experimental resolution. For this method, the smaller the value, the higher the experimental resolution and the better the analytical performance. Results The experimental resolution of the most common biochemical indices reached 10%, with some even reaching 1%. The results of most counting experiments showed experimental resolution up to 10%, whereas the experimental resolution of the classical chemical assays reached 1%. Unexpectedly, the experimental resolution of more sensitive assays, such as immunoassays was only 25% when using the manual method and 10% for qPCR. Conclusion This study established a method for measuring the experimental resolution of laboratory assays and provides a new index for evaluating the reliability of methods in clinical laboratories.
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Affiliation(s)
- Chenxi Sun
- College of Medical Laboratory, Dalian Medical University, Dalian, China
| | - Dongxia Wang
- College of Medical Laboratory, Dalian Medical University, Dalian, China
| | - Henggui Xu
- College of Medical Laboratory, Dalian Medical University, Dalian, China
| | - Guang Yang
- College of Medical Laboratory, Dalian Medical University, Dalian, China
| | - Xiaomei Yan
- College of Medical Laboratory, Dalian Medical University, Dalian, China
| | - Hui Liu
- College of Medical Laboratory, Dalian Medical University, Dalian, China
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Cassedy A, Parle-McDermott A, O’Kennedy R. Virus Detection: A Review of the Current and Emerging Molecular and Immunological Methods. Front Mol Biosci 2021; 8:637559. [PMID: 33959631 PMCID: PMC8093571 DOI: 10.3389/fmolb.2021.637559] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/01/2021] [Indexed: 12/14/2022] Open
Abstract
Viruses are ubiquitous in the environment. While many impart no deleterious effects on their hosts, several are major pathogens. This risk of pathogenicity, alongside the fact that many viruses can rapidly mutate highlights the need for suitable, rapid diagnostic measures. This review provides a critical analysis of widely used methods and examines their advantages and limitations. Currently, nucleic-acid detection and immunoassay methods are among the most popular means for quickly identifying viral infection directly from source. Nucleic acid-based detection generally offers high sensitivity, but can be time-consuming, costly, and require trained staff. The use of isothermal-based amplification systems for detection could aid in the reduction of results turnaround and equipment-associated costs, making them appealing for point-of-use applications, or when high volume/fast turnaround testing is required. Alternatively, immunoassays offer robustness and reduced costs. Furthermore, some immunoassay formats, such as those using lateral-flow technology, can generate results very rapidly. However, immunoassays typically cannot achieve comparable sensitivity to nucleic acid-based detection methods. Alongside these methods, the application of next-generation sequencing can provide highly specific results. In addition, the ability to sequence large numbers of viral genomes would provide researchers with enhanced information and assist in tracing infections.
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Affiliation(s)
- A. Cassedy
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | | | - R. O’Kennedy
- School of Biotechnology, Dublin City University, Dublin, Ireland
- Hamad Bin Khalifa University, Doha, Qatar
- Qatar Foundation, Doha, Qatar
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Lucas A, Kumakamba C, Lange CE, Obel E, Miningue G, Likofata J, Gillis A, LeBreton M, McIver DJ, Euren J, Kreuder Johnson C, Goldstein T, Muyembe-Tamfum JJ, Saylors K. Serology and Behavioral Perspectives on Ebola Virus Disease Among Bushmeat Vendors in Equateur, Democratic Republic of the Congo, After the 2018 Outbreak. Open Forum Infect Dis 2020; 7:ofaa295. [PMID: 32855984 PMCID: PMC7443109 DOI: 10.1093/ofid/ofaa295] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 07/11/2020] [Indexed: 12/01/2022] Open
Abstract
After the 2018 Ebola outbreak in Equateur Province, Democratic Republic of the Congo, we conducted behavioral interviews and collected samples from bushmeat vendors and primates in Mbandaka to test for evidence of Ebola virus exposure. Although participants indicated being aware of Ebola, they did not consider themselves at occupational risk for infection. We found antibodies against Zaire ebolavirus in one participant despite no reported history of disease or contact with infected individuals. Our data underline concerns of possible subclinical or undiagnosed Ebola virus infections and the importance and challenges of risk communication to populations who are occupationally exposed to bushmeat. Following the 2018 Ebola outbreak in Equateur Province, Democratic Republic of the Congo, bushmeat vendors interviewed in Mbandaka indicated being aware of Ebola, but did not consider themselves at occupational risk. Antibodies against Zaire ebolavirus were detected in one participant.
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Affiliation(s)
| | | | | | - Erby Obel
- Metabiota Inc, Kinshasa, Democratic Republic of the Congo
| | - Guy Miningue
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Jacques Likofata
- Mbandaka Laboratory, Ministry of Health, Mbandaka, Democratic Republic of the Congo
| | | | | | | | - Jason Euren
- Metabiota Inc, San Francisco, California, USA
| | - Christine Kreuder Johnson
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Tracey Goldstein
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Jean J Muyembe-Tamfum
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
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Jääskeläinen AJ, Sironen T, Kaloinen M, Kakkola L, Julkunen I, Hewson R, Weidmann MW, Mirazimi A, Watson R, Vapalahti O. Comparison of Zaire ebolavirus realtime RT-PCRs targeting the nucleoprotein gene. J Virol Methods 2020; 284:113941. [PMID: 32707049 DOI: 10.1016/j.jviromet.2020.113941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 10/23/2022]
Abstract
In last five years, the Africa has faced two outbreaks of Zaire ebolavirus. These outbreaks have been the largest so far, and latest outbreak is still ongoing and affecting the Democratic Republic of the Congo. We tested in parallel three different Zaire ebolavirus (EBOV) realtime RT-PCRs targeting the nucleoprotein gene (EBOV NP-RT-qPCRs) described by Trombley et al. (2010); Huang et al. (2012) and Weidmann et al. (2004). These assays are used regularly in diagnostic laboratories. The limit of detection (LOD), intra-assay repeatability using different matrixes, sensitivity and specificity were determined. In addition, the primers and probes were aligned with the sequences available in ongoing and past outbreaks in order to check the mismatches. The specificity of all three EBOV NP-RT-qPCRs were excellent (100 %), and LODs were under or 10 copies per PCR reaction. Intra-assay repeatability was good in all assays, however the Ct-values were bit higher using the EDTA-blood based matrix. All of the primers and probes in EBOV NP-RT-qPCR assays have one or more mismatches in the probes and primers when the 2267 Zaire EBOV NP sequences, including strains Ituri from DRC outbreak (year 2018), was aligned. The EBOV strain of Bikoro (year 2018) circulating in DRC was 100 % match in Trombley and Weidmann assay, but had one mismatch in Huang assay.
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Affiliation(s)
- Anne J Jääskeläinen
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Finland.
| | - Tarja Sironen
- University of Helsinki, Department of Virology, Helsinki, Finland; Faculty of Veterinary Medicine, Department of Veterinary Biosciences, University of Helsinki, Finland
| | - Minttu Kaloinen
- University of Helsinki, Department of Virology, Helsinki, Finland
| | - Laura Kakkola
- University of Turku, Institute of Biomedicine, Turku, Finland
| | - Ilkka Julkunen
- University of Turku, Institute of Biomedicine, Turku, Finland
| | - Roger Hewson
- National Infection Service, Public Health England, Porton Down, Salisbury, United Kingdom
| | - Manfred W Weidmann
- University of Stirling, Institute of Aquaculture, Stirling, United Kingdom
| | - Ali Mirazimi
- Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden; Karolinska University Hospital and Karolinska Institute, Department of Laboratory Medicine (LABMED), Stockholm, Sweden; National Veterinary Institute, Uppsala, Sweden
| | - Robert Watson
- National Infection Service, Public Health England, Porton Down, Salisbury, United Kingdom
| | - Olli Vapalahti
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Finland; Faculty of Veterinary Medicine, Department of Veterinary Biosciences, University of Helsinki, Finland
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Bonney LC, Watson RJ, Slack GS, Bosworth A, Wand NIV, Hewson R. A flexible format LAMP assay for rapid detection of Ebola virus. PLoS Negl Trop Dis 2020; 14:e0008496. [PMID: 32735587 PMCID: PMC7423149 DOI: 10.1371/journal.pntd.0008496] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/12/2020] [Accepted: 06/16/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The unprecedented 2013/16 outbreak of Zaire ebolavirus (Ebola virus) in West Africa has highighted the need for rapid, high-throughput and POC diagnostic assays to enable timely detection and appropriate triaging of Ebola Virus Disease (EVD) patients. Ebola virus is highly infectious and prompt diagnosis and triage is crucial in preventing further spread within community and healthcare settings. Moreover, due to the ecology of Ebola virus it is important that newly developed diagnostic assays are suitable for use in both the healthcare environment and low resource rural locations. METHODOLOGY/PRINCIPLE FINDINGS A LAMP assay was successfully developed with three detection formats; a real-time intercalating dye-based assay, a real-time probe-based assay to enable multiplexing and an end-point colourimetric assay to simplify interpretation for the field. All assay formats were sensitive and specific, detecting a range of Ebola virus strains isolated in 1976-2014; with Probit analysis predicting limits of detection of 243, 290 and 75 copies/reaction respectively and no cross-detection of related strains or other viral haemorrhagic fevers (VHF's). The assays are rapid, (as fast as 5-7.25 mins for real-time formats) and robust, detecting Ebola virus RNA in presence of minimally diluted bodily fluids. Moreover, when tested on patient samples from the 2013/16 outbreak, there were no false positives and 93-96% of all new case positives were detected, with only a failure to detect very low copy number samples. CONCLUSION/SIGNIFICANCE These are a set of robust and adaptable diagnostic solutions, which are fast, easy-to-perform-and-interpret and are suitable for use on a range of platforms including portable low-power devices. They can be readily transferred to field-laboratory settings, with no specific equipment needs and are therefore ideally placed for use in locations with limited resources.
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Affiliation(s)
- Laura C. Bonney
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Robert J. Watson
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Gillian S. Slack
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Andrew Bosworth
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Nadina I. Vasileva Wand
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Roger Hewson
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, United Kingdom
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