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Garbuglia AR, Lapa D, Pauciullo S, Raoul H, Pannetier D. Nipah Virus: An Overview of the Current Status of Diagnostics and Their Role in Preparedness in Endemic Countries. Viruses 2023; 15:2062. [PMID: 37896839 PMCID: PMC10612039 DOI: 10.3390/v15102062] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Nipah virus (NiV) is a paramyxovirus responsible for a high mortality rate zoonosis. As a result, it has been included in the list of Blueprint priority pathogens. Bats are the main reservoirs of the virus, and different clinical courses have been described in humans. The Bangladesh strain (NiV-B) is often associated with severe respiratory disease, whereas the Malaysian strain (NiV-M) is often associated with severe encephalitis. An early diagnosis of NiV infection is crucial to limit the outbreak and to provide appropriate care to the patient. Due to high specificity and sensitivity, qRT-PCR is currently considered to be the optimum method in acute NiV infection assessment. Nasal swabs, cerebrospinal fluid, urine, and blood are used for RT-PCR testing. N gene represents the main target used in molecular assays. Different sensitivities have been observed depending on the platform used: real-time PCR showed a sensitivity of about 103 equivalent copies/reaction, SYBRGREEN technology's sensitivity was about 20 equivalent copies/reaction, and in multiple pathogen card arrays, the lowest limit of detection (LOD) was estimated to be 54 equivalent copies/reaction. An international standard for NiV is yet to be established, making it difficult to compare the sensitivity of the different methods. Serological assays are for the most part used in seroprevalence studies owing to their lower sensitivity in acute infection. Due to the high epidemic and pandemic potential of this virus, the diagnosis of NiV should be included in a more global One Health approach to improve surveillance and preparedness for the benefit of public health. Some steps need to be conducted in the diagnostic field in order to become more efficient in epidemic management, such as development of point-of-care (PoC) assays for the rapid diagnosis of NiV.
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Affiliation(s)
- Anna Rosa Garbuglia
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (D.L.); (S.P.)
| | - Daniele Lapa
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (D.L.); (S.P.)
| | - Silvia Pauciullo
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (D.L.); (S.P.)
| | - Hervé Raoul
- French National Agency for Research on AIDS—Emerging Infectious Diseases (ANRS MIE), Maladies Infectieuses Émergentes, 75015 Paris, France;
| | - Delphine Pannetier
- Institut National de la Santé et de la Recherche Médicale, Jean Mérieux BSL4 Laboratory, 69002 Lyon, France;
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Pulscher LA, Peel AJ, Rose K, Welbergen JA, Baker ML, Boyd V, Low‐Choy S, Edson D, Todd C, Dorrestein A, Hall J, Todd S, Broder CC, Yan L, Xu K, Peck GR, Phalen DN. Serological evidence of a pararubulavirus and a betacoronavirus in the geographically isolated Christmas Island flying-fox (Pteropus natalis). Transbound Emerg Dis 2022; 69:e2366-e2377. [PMID: 35491954 PMCID: PMC9529767 DOI: 10.1111/tbed.14579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 03/27/2022] [Accepted: 04/25/2022] [Indexed: 12/30/2022]
Abstract
Due to their geographical isolation and small populations, insular bats may not be able to maintain acute immunizing viruses that rely on a large population for viral maintenance. Instead, endemic transmission may rely on viruses establishing persistent infections within hosts or inducing only short-lived neutralizing immunity. Therefore, studies on insular populations are valuable for developing broader understanding of viral maintenance in bats. The Christmas Island flying-fox (CIFF; Pteropus natalis) is endemic on Christmas Island, a remote Australian territory, and is an ideal model species to understand viral maintenance in small, geographically isolated bat populations. Serum or plasma (n = 190), oral swabs (n = 199), faeces (n = 31), urine (n = 32) and urine swabs (n = 25) were collected from 228 CIFFs. Samples were tested using multiplex serological and molecular assays, and attempts at virus isolation to determine the presence of paramyxoviruses, betacoronaviruses and Australian bat lyssavirus. Analysis of serological data provides evidence that the species is maintaining a pararubulavirus and a betacoronavirus. There was little serological evidence supporting the presence of active circulation of the other viruses assessed in the present study. No viral nucleic acid was detected and no viruses were isolated. Age-seropositivity results support the hypothesis that geographically isolated bat populations can maintain some paramyxoviruses and coronaviruses. Further studies are required to elucidate infection dynamics and characterize viruses in the CIFF. Lastly, apparent absence of some pathogens could have implications for the conservation of the CIFF if a novel disease were introduced into the population through human carriage or an invasive species. Adopting increased biosecurity protocols for ships porting on Christmas Island and for researchers and bat carers working with flying-foxes are recommended to decrease the risk of pathogen introduction and contribute to the health and conservation of the species.
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Affiliation(s)
- Laura A. Pulscher
- Faculty of ScienceSydney School of Veterinary ScienceUniversity of SydneySydneyNew South WalesAustralia
| | - Alison J. Peel
- Centre for Planetary Health and Food SecurityGriffith UniversityNathanQueenslandAustralia
| | - Karrie Rose
- Australian Registry of Wildlife HealthTaronga Conservation Society AustraliaMosmanNew South WalesAustralia
| | - Justin A. Welbergen
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityRichmondNew South WalesAustralia
| | - Michelle L. Baker
- Australian Centre for Disease Preparedness, Health and Biosecurity Business UnitCommonwealth Scientific and Industrial Research OrganizationGeelongVictoriaAustralia
| | - Victoria Boyd
- Australian Centre for Disease Preparedness, Health and Biosecurity Business UnitCommonwealth Scientific and Industrial Research OrganizationGeelongVictoriaAustralia
| | - Samantha Low‐Choy
- Centre for Planetary Health and Food SecurityGriffith UniversityNathanQueenslandAustralia
- Office of the Vice ChancellorArts/Education/LawGriffith UniversityBrisbaneQueenslandAustralia
| | - Dan Edson
- Department of AgricultureWater and the EnvironmentCanberraAustralian Capital TerritoryAustralia
| | - Christopher Todd
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityRichmondNew South WalesAustralia
| | - Annabel Dorrestein
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityRichmondNew South WalesAustralia
| | - Jane Hall
- Australian Registry of Wildlife HealthTaronga Conservation Society AustraliaMosmanNew South WalesAustralia
| | - Shawn Todd
- Australian Centre for Disease Preparedness, Health and Biosecurity Business UnitCommonwealth Scientific and Industrial Research OrganizationGeelongVictoriaAustralia
| | | | - Lianying Yan
- Department of MicrobiologyUniformed Services UniversityBethesdaMarylandUSA
- Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaMarylandUSA
| | - Kai Xu
- Department of Veterinary BiosciencesCollege of Veterinary MedicineThe Ohio State UniversityColumbusOhioUSA
| | - Grantley R. Peck
- Australian Centre for Disease Preparedness, Health and Biosecurity Business UnitCommonwealth Scientific and Industrial Research OrganizationGeelongVictoriaAustralia
| | - David N. Phalen
- Faculty of ScienceSydney School of Veterinary ScienceUniversity of SydneySydneyNew South WalesAustralia
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Abstract
Viruses, which are the most abundant biological entities on the planet, have been regarded as the "dark matter" of biology in the sense that despite their ubiquity and frequent presence in large numbers, their detection and analysis are not always straightforward. The majority of them are very small (falling under the limit of 0.5 μm), and collectively, they are extraordinarily diverse. In fact, the majority of the genetic diversity on the planet is found in the so-called virosphere, or the world of viruses. Furthermore, the most frequent viral agents of disease in humans display an RNA genome, and frequently evolve very fast, due to the fact that most of their polymerases are devoid of proofreading activity. Therefore, their detection, genetic characterization, and epidemiological surveillance are rather challenging. This review (part of the Curated Collection on Advances in Molecular Epidemiology of Infectious Diseases) describes many of the methods that, throughout the last few decades, have been used for viral detection and analysis. Despite the challenge of having to deal with high genetic diversity, the majority of these methods still depend on the amplification of viral genomic sequences, using sequence-specific or sequence-independent approaches, exploring thermal profiles or a single nucleic acid amplification temperature. Furthermore, viral populations, and especially those with RNA genomes, are not usually genetically uniform but encompass swarms of genetically related, though distinct, viral genomes known as viral quasispecies. Therefore, sequence analysis of viral amplicons needs to take this fact into consideration, as it constitutes a potential analytic problem. Possible technical approaches to deal with it are also described here. *This article is part of a curated collection.
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Aoki K, Tanaka H, Kawahara T. Multiplexed Microsphere Suspension-Array Assay for Urine Mitochondrial DNA Typing by C-Stretch Length in Hypervariable Regions. J Clin Med Res 2018; 10:552-561. [PMID: 29904439 PMCID: PMC5997413 DOI: 10.14740/jocmr3302w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 04/10/2018] [Indexed: 11/11/2022] Open
Abstract
Background The standard method for personal identification and verification of urine samples in doping control is short tandem repeat (STR) analysis using nuclear DNA (nDNA). The DNA concentration of urine is very low and decreases under most conditions used for sample storage; therefore, the amount of DNA from cryopreserved urine samples may be insufficient for STR analysis. We aimed to establish a multiplexed assay for urine mitochondrial DNA typing containing only trace amounts of DNA, particularly for Japanese populations. Methods A multiplexed suspension-array assay using oligo-tagged microspheres (Luminex MagPlex-TAG) was developed to measure C-stretch length in hypervariable region 1 (HV1) and 2 (HV2), five single nucleotide polymorphisms (SNPs), and one polymorphic indel. Based on these SNPs and the indel, the Japanese population can be classified into five major haplogroups (D4, B, M7a, A, D5). The assay was applied to DNA samples from urine cryopreserved for 1 - 1.5 years (n = 63) and fresh blood (n = 150). Results The assay with blood DNA enabled Japanese subjects to be categorized into 62 types, exhibiting a discriminatory power of 0.960. The detection limit for cryopreserved urine was 0.005 ng of nDNA. Profiling of blood and urine pairs revealed that 5 of 63 pairs showed different C-stretch patterns in HV1 or HV2. Conclusions The assay described here yields valuable information in terms of the verification of urine sample sources employing only trace amounts of recovered DNA. However, blood cannot be used as a reference sample.
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Affiliation(s)
- Kimiko Aoki
- Anti-doping Research Laboratory, Japan Chemical Analysis Center, 6-39-4, Minami Senju, Arakawa-ku, Tokyo, 116-0003, Japan.,Nihon Pharmaceutical University, 10281, Komuro, Inamachi, Kitaadachi-gun, Saitama 362-0806, Japan
| | - Hiroyuki Tanaka
- Anti-doping Research Laboratory, Japan Chemical Analysis Center, 6-39-4, Minami Senju, Arakawa-ku, Tokyo, 116-0003, Japan
| | - Takashi Kawahara
- Anti-doping Research Laboratory, Japan Chemical Analysis Center, 6-39-4, Minami Senju, Arakawa-ku, Tokyo, 116-0003, Japan
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van Brunschot SL, Bergervoet JHW, Pagendam DE, de Weerdt M, Geering ADW, Drenth A, van der Vlugt RAA. Development of a multiplexed bead-based suspension array for the detection and discrimination of pospiviroid plant pathogens. PLoS One 2014; 9:e84743. [PMID: 24404188 PMCID: PMC3880322 DOI: 10.1371/journal.pone.0084743] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 11/19/2013] [Indexed: 12/25/2022] Open
Abstract
Efficient and reliable diagnostic tools for the routine indexing and certification of clean propagating material are essential for the management of pospiviroid diseases in horticultural crops. This study describes the development of a true multiplexed diagnostic method for the detection and identification of all nine currently recognized pospiviroid species in one assay using Luminex bead-based suspension array technology. In addition, a new data-driven, statistical method is presented for establishing thresholds for positivity for individual assays within multiplexed arrays. When applied to the multiplexed array data generated in this study, the new method was shown to have better control of false positives and false negative results than two other commonly used approaches for setting thresholds. The 11-plex Luminex MagPlex-TAG pospiviroid array described here has a unique hierarchical assay design, incorporating a near-universal assay in addition to nine species-specific assays, and a co-amplified plant internal control assay for quality assurance purposes. All assays of the multiplexed array were shown to be 100% specific, sensitive and reproducible. The multiplexed array described herein is robust, easy to use, displays unambiguous results and has strong potential for use in routine pospiviroid indexing to improve disease management strategies.
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Affiliation(s)
- Sharon L. van Brunschot
- Plant Biosecurity Cooperative Research Centre, Bruce, Australian Capital Territory, Australia
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Jan H. W. Bergervoet
- Plant Research International, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Daniel E. Pagendam
- Commonwealth Scientific and Industrial Research Organisation Mathematics, Informatics and Statistics, Dutton Park, Queensland, Australia
| | - Marjanne de Weerdt
- Plant Research International, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Andrew D. W. Geering
- Plant Biosecurity Cooperative Research Centre, Bruce, Australian Capital Territory, Australia
- Centre for Plant Science, The University of Queensland, St Lucia, Queensland, Australia
| | - André Drenth
- Centre for Plant Science, The University of Queensland, St Lucia, Queensland, Australia
| | - René A. A. van der Vlugt
- Plant Research International, Wageningen University and Research Centre, Wageningen, The Netherlands
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Christopher-Hennings J, Araujo KPC, Souza CJH, Fang Y, Lawson S, Nelson EA, Clement T, Dunn M, Lunney JK. Opportunities for bead-based multiplex assays in veterinary diagnostic laboratories. J Vet Diagn Invest 2013; 25:671-91. [DOI: 10.1177/1040638713507256] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bead-based multiplex assays (BBMAs) are applicable for high throughput, simultaneous detection of multiple analytes in solution (from several to 50–500 analytes within a single, small sample volume). Currently, few assays are commercially available for veterinary applications, but they are available to identify and measure various cytokines, growth factors and their receptors, inflammatory proteins, kinases and inhibitors, neurobiology proteins, and pathogens and antibodies in human beings, nonhuman primates, and rodent species. In veterinary medicine, various nucleic acid and protein-coupled beads can be used in, or for the development of, antigen and antibody BBMAs, with the advantage that more data can be collected using approximately the same amount of labor as used for other antigen and antibody assays. Veterinary-related BBMAs could be used for detection of pathogens, genotyping, measurement of hormone levels, and in disease surveillance and vaccine assessment. It will be important to evaluate whether BBMAs are “fit for purpose,” how costs and efficiencies compare between assays, which assays are published or commercially available for specific veterinary applications, and what procedures are involved in the development of the assays. It is expected that many veterinary-related BBMAs will be published and/or become commercially available in the next few years. The current review summarizes the BBMA technology and some of the currently available BBMAs developed for veterinary settings. Some of the human diagnostic BBMAs are also described, providing an example of possible templates for future development of new veterinary-related BBMAs.
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Affiliation(s)
- Jane Christopher-Hennings
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Karla P. C. Araujo
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Carlos J. H. Souza
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Ying Fang
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Steven Lawson
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Eric A. Nelson
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Travis Clement
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Michael Dunn
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Joan K. Lunney
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
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