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Sieg M, Busch J, Böttcher D, Vahlenkamp TW. In Vitro Modeling of Feline Morbillivirus Infections Using Primary Feline Kidney Cells. Methods Mol Biol 2024; 2808:153-165. [PMID: 38743369 DOI: 10.1007/978-1-0716-3870-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Domestic cats are the natural host of feline morbilliviruses (FeMV). Although other species can also be infected (such as dogs and opossums), no laboratory animal infection model is established so far. In vitro models for studying the molecular pathogenesis are therefore needed. For this purpose, propagation and titration of FeMV are key techniques. Unlike other morbilliviruses, such as canine distemper virus (CDV) or measles virus (MV), FeMV is a slow growing virus in cell culture and is difficult to titrate using classical plaque techniques. Here we describe methods for the efficient isolation of FeMV from natural sources (e.g., urine), the propagation of viral stocks, and their titration. In addition, we establish the generation of a three-dimensional infection model mimicking the feline tubular epithelium.
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Affiliation(s)
- Michael Sieg
- Faculty of Veterinary Medicine, Institute of Virology, Leipzig University, Leipzig, Germany.
| | - Johannes Busch
- Faculty of Veterinary Medicine, Institute of Virology, Leipzig University, Leipzig, Germany
| | - Denny Böttcher
- Faculty of Veterinary Medicine, Institute of Veterinary Pathology, Leipzig University, Leipzig, Germany
| | - Thomas W Vahlenkamp
- Faculty of Veterinary Medicine, Institute of Virology, Leipzig University, Leipzig, Germany
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2
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Reyes-Calderón A, Mindreau-Ganoza E, Pardo-Figueroa B, Garcia-Luquillas KR, Yufra SP, Romero PE, Antonini C, Renom JM, Mota CR, Santa-Maria MC. Evaluation of low-cost SARS-CoV-2 RNA purification methods for viral quantification by RT-qPCR and next-generation sequencing analysis: Implications for wider wastewater-based epidemiology adoption. Heliyon 2023; 9:e16130. [PMID: 37228686 PMCID: PMC10188194 DOI: 10.1016/j.heliyon.2023.e16130] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/09/2023] [Accepted: 05/06/2023] [Indexed: 05/27/2023] Open
Abstract
Based Epidemiology (WBE) consists of quantifying biomarkers in sewerage systems to derive real-time information on the health and/or lifestyle of the contributing population. WBE usefulness was vastly demonstrated in the context of the COVID-19 pandemic. Many methods for SARS-CoV-2 RNA determination in wastewater were devised, which vary in cost, infrastructure requirements and sensitivity. For most developing countries, implementing WBE for viral outbreaks, such as that of SARS-CoV-2, proved challenging due to budget, reagent availability and infrastructure constraints. In this study, we assessed low-cost methods for SARS-CoV-2 RNA quantification by RT-qPCR, and performed variant identification by NGS in wastewater samples. Results showed that the effect of adjusting pH to 4 and/or adding MgCl2 (25 mM) was negligible when using the adsorption-elution method, as well as basal physicochemical parameters in the sample. In addition, results supported the standardized use of linear rather than plasmid DNA for a more accurate viral RT-qPCR estimation. The modified TRIzol-based purification method in this study yielded comparable RT-qPCR estimation to a column-based approach, but provided better NGS results, suggesting that column-based purification for viral analysis should be revised. Overall, this work provides evaluation of a robust, sensitive and cost-effective method for SARS-CoV-2 RNA analysis that could be implemented for other viruses, for a wider WEB adoption.
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Affiliation(s)
- Alonso Reyes-Calderón
- Centro de Investigación y Tecnología del Agua - CITA, Universidad de Ingenieria y Tecnologia - UTEC, Jr. Medrano Silva 165, Lima, 15063, Peru
| | - Elías Mindreau-Ganoza
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Germán Amézaga s/n, Lima, 15081, Peru
| | - Braulio Pardo-Figueroa
- Centro de Investigación y Tecnología del Agua - CITA, Universidad de Ingenieria y Tecnologia - UTEC, Jr. Medrano Silva 165, Lima, 15063, Peru
| | - Katherine R Garcia-Luquillas
- Centro de Investigación y Tecnología del Agua - CITA, Universidad de Ingenieria y Tecnologia - UTEC, Jr. Medrano Silva 165, Lima, 15063, Peru
| | - Sonia P Yufra
- Departamento de Ingeniería Metalúrgica e Ingeniería Ambiental, Universidad Nacional de San Agustín, Av. Independencia s/n, Arequipa, 04001, Peru
| | - Pedro E Romero
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Germán Amézaga s/n, Lima, 15081, Peru
| | - Claudia Antonini
- Departamento de Ingeniería Industrial, Universidad de Ingenieria y Tecnologia - UTEC, Jr. Medrano Silva 165, Lima, 15063, Peru
| | - Jose-Miguel Renom
- Departamento de Ciencias, Universidad de Ingenieria y Tecnologia - UTEC, Jr. Medrano Silva 165, Lima, 15063, Peru
| | - Cesar R Mota
- Departamento de Engenharia Sanitária e Ambiental, Escola de Engenharia, Universidade Federal de Minas Gerais (UFMG), Av. Antonio Carlos, Belo Horizonte, 6.627, 31270-901, Brazil
| | - Monica C Santa-Maria
- Centro de Investigación y Tecnología del Agua - CITA, Universidad de Ingenieria y Tecnologia - UTEC, Jr. Medrano Silva 165, Lima, 15063, Peru
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3
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Sabzchi-Dehkharghani H, Samadi Kafil H, Majnooni-Heris A, Akbarzadeh A, Naderi-Ahranjani R, Fakherifard A, Mosaferi M, Gilani N, Noury M, Eydi P, Sayyari Sis S, Toghyanian N, Yegani R. Investigation of SARS-CoV-2 RNA contamination in water supply resources of Tabriz metropolitan during a peak of COVID-19 pandemic. Sustain Water Resour Manag 2022; 9:21. [PMID: 36570697 PMCID: PMC9759279 DOI: 10.1007/s40899-022-00809-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
It is crucial to have access to clean water resources during the COVID-19 pandemic for hygiene, since virus infection through wastewater leaks in metropolitan areas can be a threat. Accurate monitoring of urban water resources during the pandemic seems to be the only way to confirm safe and infected resources. Here, in this study, the amount of Severe Acute Respiratory Syndrome Coronavirus 2's Ribonucleic Acid (SARS-CoV-2 RNA) in the Tabriz urban water network located in the northwest of Iran was investigated by an extensive sampling of the city's water sources at a severe peak of the COVID-19 pandemic. The sampling process comprised a range of water sources, including wells, qanats, water treatment facilities, dams, and reservoirs. For each sample, a combination of polyethylene glycol (PEG) and sodium chloride (NaCl) was used for concentration and a laboratory RNA-based method was conducted for quantification. Before applying the extraction and quantification procedure to real samples, the proposed concentration method was verified with synthetic serum samples for the first time. After the concentration, RNA extraction was done by the BehPrep extraction column method, and Reverse Transcription Polymerase Chain Reaction (RT-PCR) detection of the virus was done by Covitech COVID-19 RT-PCR kit. In none of the water supply resources, SARS-COV-2 RNA has been detected except in a sample grabbed from a well adjacent to an urban wastewater discharge point downstream. The results of molecular analysis for the positive sample showed that the CT value and concentration of the virus genome were equal to 32.57 and 5720 copies/L, respectively. Quantitative analysis of real samples shows that the city's water network was safe at the time of the study. However, given that the positive sample was exposed to wastewater leakage, periodic sampling from wells and qanats is suggested during the pandemic until it can be proven that the leakage to these water sources is impossible.
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Affiliation(s)
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Rana Naderi-Ahranjani
- Membrane Technology Research Center, Faculty of Chemical Engineering, Sahand University of Technology, PO. BOX 51335/1996, Tabriz, Iran
| | - Ahmad Fakherifard
- Department of Water Engineering, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Mohammad Mosaferi
- Health and Environment Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Neda Gilani
- Department of Statistics and Epidemiology, Faculty of Health, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mojtaba Noury
- Iranian Water Resources Management Company, Tehran, Iran
| | - Parisa Eydi
- Membrane Technology Research Center, Faculty of Chemical Engineering, Sahand University of Technology, PO. BOX 51335/1996, Tabriz, Iran
| | - Sajjad Sayyari Sis
- Membrane Technology Research Center, Faculty of Chemical Engineering, Sahand University of Technology, PO. BOX 51335/1996, Tabriz, Iran
| | | | - Reza Yegani
- Membrane Technology Research Center, Faculty of Chemical Engineering, Sahand University of Technology, PO. BOX 51335/1996, Tabriz, Iran
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4
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Bullen CK, Davis SL, Looney MM. Quantification of Infectious SARS-CoV-2 by the 50% Tissue Culture Infectious Dose Endpoint Dilution Assay. Methods Mol Biol 2022; 2452:131-146. [PMID: 35554905 DOI: 10.1007/978-1-0716-2111-0_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A number of viral quantification methods are used to measure the concentration of infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). While the traditional plaque-based assay allows for direct enumeration of replication competent lytic virions and remains the gold standard for the quantification of infectious virus, the 50% tissue culture infectious dose (TCID50) endpoint dilution assay allows for a more rapid, large-scale analysis of experimental samples. In this chapter, we describe a well-established TCID50 assay protocol to measure the SARS-CoV-2 infectious titer in viral stocks, in vitro cell or organoid models, and animal tissue. We also present alternative assays for scoring the cytopathic effect of SARS-CoV-2 in cell culture and comparable methods to calculate the 50% endpoint by serial dilution.
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Affiliation(s)
- C Korin Bullen
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Stephanie L Davis
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Monika M Looney
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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5
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Terada T, Morozumi T, Wada E, Sukegawa S. Two immune-based methods using immortalized porcine kidney macrophages for quantifying neutralizing activity against porcine reproductive and respiratory syndrome virus-2. J Virol Methods 2022; 303:114494. [PMID: 35181347 DOI: 10.1016/j.jviromet.2022.114494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/10/2022] [Accepted: 02/13/2022] [Indexed: 11/17/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) causes a serious infectious disease in pigs in farms worldwide. Neutralizing antibody titer is an effective index for evaluating immunity to PRRSV; however, PRRSV has different neutralizing cross-reactivity between strains. Therefore, quantitative measurement of neutralizing antibody titers against field PRRSV strains would be required to evaluate whether neutralizing antibodies in pigs could possess neutralizing activity against individual or multiple strains. Immune-based methods, such as image cytometry (ICM) and cell-based enzyme-linked immune sorbent assay (ELISA), are quantitative and can be used to evaluate many samples. Using immortalized porcine kidney macrophages (IPKMs), which are highly susceptible to infection from field PRRSV-2 strains compared with other cell lines, immune-based methods could enable the evaluation of the neutralizing activity of porcine serum against field strains of PRRSV-2 that are difficult to isolate in conventional cells. In summary, we adapted two methods, namely ICM and cell-based ELISA, to IPKMs for quantitative neutralizing antibody titer measurements. Two immune-based methods using IPKMs are adequate for quantifying neutralizing activity of porcine serum against PRRSV-2, including field strains.
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Affiliation(s)
- Takumi Terada
- Research & Development Center, NH Foods Ltd., 3-3 Midorigahara, Tsukuba, Ibaraki, 300-2646, Japan
| | - Takeya Morozumi
- Research & Development Center, NH Foods Ltd., 3-3 Midorigahara, Tsukuba, Ibaraki, 300-2646, Japan.
| | - Emi Wada
- Research & Development Center, NH Foods Ltd., 3-3 Midorigahara, Tsukuba, Ibaraki, 300-2646, Japan
| | - Shin Sukegawa
- Research & Development Center, NH Foods Ltd., 3-3 Midorigahara, Tsukuba, Ibaraki, 300-2646, Japan
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6
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Whale AS, von der Heide EK, Kohlenberg M, Brinckmann A, Baedker S, Karalay O, Fernandez-Gonzalez A, Busby EJ, Bustin SA, Hauser H, Missel A, O'Sullivan DM, Huggett JF, Pfaffl MW, Nolan T. Digital PCR can augment the interpretation of RT-qPCR Cq values for SARS-CoV-2 diagnostics. Methods 2021; 201:5-14. [PMID: 34454016 PMCID: PMC8387146 DOI: 10.1016/j.ymeth.2021.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 12/19/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is an infectious, acute respiratory disease caused mainly by person-to-person transmission of the coronavirus SARS-CoV-2. Its emergence has caused a world-wide acute health crisis, intensified by the challenge of reliably identifying individuals likely to transmit the disease. Diagnosis is hampered by the many unknowns surrounding this disease, including those relating to infectious viral burden. This uncertainty is exacerbated by disagreement surrounding the clinical relevance of molecular testing using reverse transcription quantitative PCR (RT-qPCR) for the presence of viral RNA, most often based on the reporting of quantification cycles (Cq), which is also termed the cycle threshold (Ct) or crossing point (Cp). Despite it being common knowledge that Cqs are relative values varying according to a wide range of different parameters, there have been efforts to use them as though they were absolute units, with Cqs below an arbitrarily determined value, deemed to signify a positive result and those above, a negative one. Our results investigated the effects of a range of common variables on Cq values. These data include a detailed analysis of the effect of different carrier molecules on RNA extraction. The impact of sample matrix of buccal swabs and saliva on RNA extraction efficiency was demonstrated in RT-qPCR and the impact of potentially inhibiting compounds in urine along with bile salts were investigated in RT-digital PCR (RT-dPCR). The latter studies were performed such that the impact on the RT step could be separated from the PCR step. In this way, the RT was shown to be more susceptible to inhibitors than the PCR. Together, these studies demonstrate that the consequent variability of test results makes subjective Cq cut-off values unsuitable for the identification of infectious individuals. We also discuss the importance of using reliable control materials for accurate quantification and highlight the substantial role played by dPCR as a method for their development.
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Affiliation(s)
- Alexandra S Whale
- National Measurement Laboratory, LGC, Queens Road, Teddington, Middlesex TW11 0LY, UK.
| | - Eva K von der Heide
- LGC Genomics GmbH, Research and Development, TGS Haus 8, Ostendstraße 25, 12459 Berlin, Germany.
| | - Max Kohlenberg
- LGC Genomics GmbH, Research and Development, TGS Haus 8, Ostendstraße 25, 12459 Berlin, Germany.
| | - Anja Brinckmann
- LGC Genomics GmbH, Research and Development, TGS Haus 8, Ostendstraße 25, 12459 Berlin, Germany.
| | - Silke Baedker
- QIAGEN GmbH, Research and Development, QIAGEN Strasse 1, 40724 Hilden, Germany.
| | - Oezlem Karalay
- QIAGEN GmbH, Research and Development, QIAGEN Strasse 1, 40724 Hilden, Germany.
| | | | - Eloise J Busby
- National Measurement Laboratory, LGC, Queens Road, Teddington, Middlesex TW11 0LY, UK.
| | - Stephen A Bustin
- Molecular Diagnostics Unit, Medical Technology Research Centre, Anglia Ruskin University, UK.
| | - Heiko Hauser
- LGC Genomics GmbH, Research and Development, TGS Haus 8, Ostendstraße 25, 12459 Berlin, Germany.
| | - Andreas Missel
- QIAGEN GmbH, Research and Development, QIAGEN Strasse 1, 40724 Hilden, Germany.
| | - Denise M O'Sullivan
- National Measurement Laboratory, LGC, Queens Road, Teddington, Middlesex TW11 0LY, UK.
| | - Jim F Huggett
- National Measurement Laboratory, LGC, Queens Road, Teddington, Middlesex TW11 0LY, UK; School of Biosciences & Medicine, Faculty of Health & Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK.
| | - Michael W Pfaffl
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.
| | - Tania Nolan
- LGC Genomics GmbH, Research and Development, TGS Haus 8, Ostendstraße 25, 12459 Berlin, Germany; Molecular Diagnostics Unit, Medical Technology Research Centre, Anglia Ruskin University, UK.
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7
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Jabanathan SG, Xuan LZ, Ramanathan B. High-Throughput Screening Assays for Dengue Antiviral Drug Development. Methods Mol Biol 2021; 2296:279-302. [PMID: 33977455 DOI: 10.1007/978-1-0716-1358-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Dengue is an arthropod-borne viral disease that has become endemic and a global threat in over 100 countries. The increase in prevalence would require a long-term measure to control outbreaks. Sanofi Pasteur has licensed the tetravalent dengue vaccine (Dengvaxia) in certain dengue endemic countries. However, the efficacy of the vaccine is limited against certain dengue serotypes and can only be used for individuals from the age from 9 to 45 years old. Over the years, there has been intense research conducted on the development of antivirals against dengue virus (DENV) through either inhibiting the virus replication or targeting the host cell mechanism to block the virus entry. However, no approved antiviral drug against dengue is yet available. In this chapter, we describe the dengue antiviral development workflow including (i) prophylactic, (ii) virucidal, and (iii) postinfection assays that are employed in the antiviral drug screening process against DENV. Further, we demonstrate different methods that can be used to enumerate the reduction in virus foci number including foci-forming unit reduction assay (FFURA), estimation of viral RNA copy number through quantitative real-time PCR, and a high-throughput enzyme linked immunosorbent assay (ELISA)-based quantification of virus particles.
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Bajaber NAOA, Ramanathan B. Methods in Screening Antiviral Drugs Against Enterovirus 71. Methods Mol Biol 2021; 2296:167-84. [PMID: 33977447 DOI: 10.1007/978-1-0716-1358-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Enteroviruses 71 (EV71) is a single-stranded, neurotrophic RNA virus responsible for the numerous outbreaks of hand, foot, and mouth disease (HFMD) in the Asia-Pacific regions. HFMD primarily affects children to cause range of infection, from mild symptoms to acute flaccid paralysis, and hemorrhage. Despite increased incidence of EV71 epidemics globally and research against EV71 becoming prioritized, no antiviral agent against EV71 has yet been licensed and approved worldwide. In this chapter, detailed EV71 antiviral screening techniques are described, including plaque assay which determines viral titers through the use of a semisolid overlay, carboxymethyl cellulose to allow even viral spread and infection across the host cellular monolayers as well as a crystal violet, a distinct counterstain to visualize circular regions of infectious zones-plaques. qRT-PCR is used to quantify the viral genomic RNA in the infected samples and MTS cell viability assay to quantify the cell viability after infection or toxicity of the compound on the cells. Furthermore, various antiviral inhibition assays including prophylactic, post infection, and virucidal assays are demonstrated for estimation of the antiviral activity of potential antiviral drugs against EV71. These methods can be effectively utilized in virology laboratories for effective high-throughput screening of antiviral molecules against EV71 that can assist in the future development of antiviral drugs.
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Duda NCB, Ortiz LC, Valle SF, da Costa FVA, Varela APM, Nunes NJS, Okano FY, Franco AC, Roehe PM, González FHD. Laboratory and clinical findings and their association with viral and proviral loads in cats naturally infected with feline leukemia virus. Comp Immunol Microbiol Infect Dis 2020; 71:101491. [PMID: 32450457 DOI: 10.1016/j.cimid.2020.101491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 04/10/2020] [Accepted: 04/20/2020] [Indexed: 11/29/2022]
Abstract
This study was conducted to correlate clinical, laboratory, and bone marrow (BM) changes in cats naturally infected with feline leukemia virus and their association with viral loads in blood and BM and proviral loads in BM. Cats were classified into five groups based on antigenemia, clinical and/or laboratory findings and viral/proviral loads, according to a prospective study: symptomatic progressive (GI); asymptomatic progressive (GII); regressive (GIII); unclassified (GIV); or healthy (GV). |Correlations between these five groups and viral/proviral loads were evaluated. High viral and proviral loads were detected in GI and GII and viral loads were significantly associated with laboratory signs. Proviral loads detected in BM were significantly lower in GIII and GIV. GI cats were more likely to develop hematopoietic disorders than those from the other groups. Hematological and clinical disorders and disease severity are related to higher viral blood and proviral BM loads.
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Affiliation(s)
- Naila C B Duda
- Department of Veterinary Clinical Pathology, School of Veterinary Medicine at the Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Lucía Cano Ortiz
- Department of Microbiology, Immunology, and Parasitology, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Stella Faria Valle
- Department of Veterinary Clinical Pathology, School of Veterinary Medicine at the Federal University of Rio Grande do Sul, Porto Alegre, Brazil.
| | - Fernanda V A da Costa
- Department of Animal Medicine, School of Veterinary Medicine, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Ana Paula Muterle Varela
- Department of Microbiology, Immunology, and Parasitology, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Felipe Yuji Okano
- Department of Veterinary Clinical Pathology, School of Veterinary Medicine at the Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Ana Cláudia Franco
- Department of Microbiology, Immunology, and Parasitology, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Paulo Michel Roehe
- Department of Microbiology, Immunology, and Parasitology, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Félix H D González
- Department of Veterinary Clinical Pathology, School of Veterinary Medicine at the Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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10
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Ramesh SV, Shivakumar M, Ramteke R, Bhatia VS, Chouhan BS, Goyal S, Singh A, Praveen S, Gill BS, Chand S. Quantification of a legume begomovirus to evaluate soybean genotypes for resistance to yellow mosaic disease. J Virol Methods 2019; 268:24-31. [PMID: 30890330 DOI: 10.1016/j.jviromet.2019.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 02/28/2019] [Accepted: 03/05/2019] [Indexed: 11/19/2022]
Abstract
Mungbean yellow mosaic India virus (MYMIV) infecting soybean and other legumes causes yellow mosaic disease (YMD). Evaluation of soybean genotypes for YMD resistance involves field screening at disease hot spots or in a protected environment using infectious clones or viruliferous whiteflies as sources of virus inocula. Development of efficient virus inoculation and quantification protocols to screen soybean genetic stocks against YMD is imperative for breeding resistant varieties. Binary plasmids harbouring complete, tandem dimeric genomic components DNA A and DNA B of MYMIV-soybean isolate were engineered. The infectivity of the clones was demonstrated in soybean genotypes JS335 and UPSM534 that display contrasting YMD resistance. As a follow-up, soybean germplasm lines, breeding lines, and representative cultivars that were initially screened at an YMD hot-spot were then subjected to Agrobacterium-based infection with MYMIV. Quantitative real time polymerase chain reaction (qRT-PCR) based copy number analysis of MYMIV genomic components allowed soybean genotypes to be classified into three discrete categories; resistant, moderately resistant and susceptible to the viral infection. Thus, a soybean germplasm disease screening system based on agro-infection and qRT-PCR based quantification of MYMIV was developed to facilitate breeding YMD resistant soybean. The implications of this study for obtaining YMD resistant soybean cultivars are discussed.
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Affiliation(s)
- Shunmugiah V Ramesh
- ICAR-Indian Institute of Soybean Research, Khandwa Road, Indore, Madhya Pradesh, India.
| | - Maranna Shivakumar
- ICAR-Indian Institute of Soybean Research, Khandwa Road, Indore, Madhya Pradesh, India
| | - Rajkumar Ramteke
- ICAR-Indian Institute of Soybean Research, Khandwa Road, Indore, Madhya Pradesh, India
| | - Virender S Bhatia
- ICAR-Indian Institute of Soybean Research, Khandwa Road, Indore, Madhya Pradesh, India
| | - Bhagat S Chouhan
- School of Life Sciences, Devi Ahilya Vishwavidhyalaya, Indore, Madhya Pradesh, India
| | - Shwetha Goyal
- ICAR-Indian Institute of Soybean Research, Khandwa Road, Indore, Madhya Pradesh, India
| | - Ajeet Singh
- ICAR-Indian Agricultural Research Institute, (ICAR-IARI), New Delhi, India
| | - Shelly Praveen
- ICAR-Indian Agricultural Research Institute, (ICAR-IARI), New Delhi, India
| | | | - Suresh Chand
- School of Life Sciences, Devi Ahilya Vishwavidhyalaya, Indore, Madhya Pradesh, India
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11
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van Tricht E, Geurink L, Galindo Garre F, Schenning M, Backus H, Germano M, Somsen GW, Sänger-van de Griend CE. Implementation of at-line capillary zone electrophoresis for fast and reliable determination of adenovirus concentrations in vaccine manufacturing. Electrophoresis 2019; 40:2277-2284. [PMID: 30951206 DOI: 10.1002/elps.201900068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/01/2019] [Accepted: 03/12/2019] [Indexed: 11/09/2022]
Abstract
A CZE method was validated and implemented for fast and accurate in-process determination of adenovirus concentrations of downstream process samples obtained during manufacturing of adenovirus vector-based vaccines. An analytical-quality-by-design approach was embraced for method development, method implementation, and method maintenance. CZE provided separation of adenovirus particles from sample matrix components, such as cell debris, residual DNA and proteins. The intermediate precision of the virus particle concentration was 6.9% RSD and the relative bias was 2.3%. In comparison, the CZE method is intended to replace a quantitative polymerase chain reaction method which requires three replicates in three analytical runs to achieve an intermediate precision of 8.1% RSD. Given that, in addition, the time from sampling till reporting results of the CZE method was less than 2 h, whereas quantitative polymerase chain reaction requires 3 days, it follows that the CZE method enables faster processing times in downstream processing.
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Affiliation(s)
- Ewoud van Tricht
- Pharmaceutical and Analytical Development, Janssen Vaccines and Prevention, Leiden, The Netherlands
| | - Lars Geurink
- Pharmaceutical and Analytical Development, Janssen Vaccines and Prevention, Leiden, The Netherlands.,Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Analytical Pharmaceutical Chemistry, Uppsala University, Uppsala, Sweden
| | - Francisca Galindo Garre
- Pharmaceutical and Analytical Development, Janssen Vaccines and Prevention, Leiden, The Netherlands
| | - Martijn Schenning
- Pharmaceutical and Analytical Development, Janssen Vaccines and Prevention, Leiden, The Netherlands
| | - Harold Backus
- Pharmaceutical and Analytical Development, Janssen Vaccines and Prevention, Leiden, The Netherlands
| | - Marta Germano
- Pharmaceutical and Analytical Development, Janssen Vaccines and Prevention, Leiden, The Netherlands
| | - Govert W Somsen
- Vrije Universiteit Amsterdam, Division of BioMolecular Analysis, Amsterdam Institute of Molecules, Medicines and Systems, Amsterdam, The Netherlands
| | - Cari E Sänger-van de Griend
- Kantisto BV, Baarn, The Netherlands.,Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Analytical Pharmaceutical Chemistry, Uppsala University, Uppsala, Sweden
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12
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Farkas K, Marshall M, Cooper D, McDonald JE, Malham SK, Peters DE, Maloney JD, Jones DL. Seasonal and diurnal surveillance of treated and untreated wastewater for human enteric viruses. Environ Sci Pollut Res Int 2018; 25:33391-33401. [PMID: 30259243 PMCID: PMC6245017 DOI: 10.1007/s11356-018-3261-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 09/14/2018] [Indexed: 04/16/2023]
Abstract
Understanding the abundance and fate of human viral pathogens in wastewater is essential when assessing the public health risks associated with wastewater discharge to the environment. Typically, however, the microbiological monitoring of wastewater is undertaken on an infrequent basis and peak discharge events may be missed leading to the misrepresentation of risk levels. To evaluate diurnal patterns in wastewater viral loading, we undertook 3-day sampling campaigns with bi-hourly sample collection over three seasons at three wastewater treatment plants. Untreated influent was collected at Ganol and secondary-treated effluent was sampled at Llanrwst and Betws-y-Coed (North Wales, UK). Our results confirmed the presence of human adenovirus (AdV), norovirus genotypes I and II (NoVGI and NoVGII) in both influent and effluent samples while sapovirus GI (SaVGI) was only detected in influent water. The AdV titre was high and relatively constant in all samples, whereas the NoVGI, NoVGII and SaVGI showed high concentrations during autumn and winter and low counts during the summer. Diurnal patterns were detected in pH and turbidity for some sampling periods; however, no such changes in viral titres were observed apart from slight fluctuations in the influent samples. Our findings suggest that viral particle number in wastewater is not affected by daily chemical fluctuations. Hence, a grab sample taken at any point during the day may be sufficient to enumerate the viral load of wastewater effluent within an order of magnitude while four samples a day are recommended for testing wastewater influent samples.
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Affiliation(s)
- Kata Farkas
- School of Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK.
| | - Miles Marshall
- School of Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK
- Centre for Ecology and Hydrology, Environment Centre Wales, Deiniol Road, Bangor, LL57 2UW, UK
| | - David Cooper
- Centre for Ecology and Hydrology, Environment Centre Wales, Deiniol Road, Bangor, LL57 2UW, UK
| | - James E McDonald
- School of Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK
| | - Shelagh K Malham
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, LL59 5AB, UK
| | - Dafydd E Peters
- School of Medical Sciences, Bangor University, Brigantia Building, Penrallt Road, Bangor, Gwynedd, LL57 2AS, UK
| | - John D Maloney
- School of Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK
| | - Davey L Jones
- School of Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK
- UWA School of Agriculture and Environment, University of Western Australia, Crawley, WA, 6009, Australia
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13
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Miranda JA, Steward GF. Variables influencing the efficiency and interpretation of reverse transcription quantitative PCR (RT-qPCR): An empirical study using Bacteriophage MS2. J Virol Methods 2016; 241:1-10. [PMID: 27940257 DOI: 10.1016/j.jviromet.2016.12.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 09/16/2016] [Accepted: 12/02/2016] [Indexed: 11/28/2022]
Abstract
Reverse transcription, quantitative PCR (RT-qPCR) is a sensitive method for quantification of specific RNA targets, but the first step of the assay, reverse transcription, is notoriously variable and sensitive to reaction conditions. In this study, we used purified Bacteriophage MS2 genomic RNA as a model virus target to test two different RT enzymes (SuperScript II and SuperScript III), two RT-priming strategies (gene-specific primers and random hexamers), and varying background RNA concentrations (0-50ngμl-1) to determine how these variables influence the efficiency of reverse transcription over a range of target concentrations (101-107 copies μl-1). The efficiency of the RT reaction was greatly improved by increasing both background RNA and primer concentrations, but the benefit provided by background RNA was source dependent. At a given target concentration, similar RT efficiencies were achieved with gene-specific primers and random hexamers, but the latter required much higher concentrations. With random hexamers, we observed a systematic variation in RT reaction efficiency as a function of target concentration. Using an RNA standard curve that was also subject to RT effectively normalized for this systematic variability, but the assay accuracy depended critically on the length of the standard RNA extending to the 3' end of the qPCR target site. Our results shed some light on previous contradictory conclusions in the literature, and provide insights that may aid in the design of RT-qPCR assays and the design of synthetic RNA standards when full-length material is not available.
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Affiliation(s)
- Jaclyn A Miranda
- Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawai'i at Mānoa, 1950 East-West Road, Honolulu, Hawai'i 96822, United States
| | - Grieg F Steward
- Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawai'i at Mānoa, 1950 East-West Road, Honolulu, Hawai'i 96822, United States.
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14
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Oma VS, Tråvén M, Alenius S, Myrmel M, Stokstad M. Bovine coronavirus in naturally and experimentally exposed calves; viral shedding and the potential for transmission. Virol J 2016; 13:100. [PMID: 27296861 PMCID: PMC4906604 DOI: 10.1186/s12985-016-0555-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/03/2016] [Indexed: 12/15/2022] Open
Abstract
Background Bovine coronavirus (BCoV) is a widely distributed pathogen, causing disease and economic losses in the cattle industry worldwide. Prevention of virus spread is impeded by a lack of basic knowledge concerning viral shedding and transmission potential in individual animals. The aims of the study were to investigate the duration and quantity of BCoV shedding in feces and nasal secretions related to clinical signs, the presence of virus in blood and tissues and to test the hypothesis that seropositive calves are not infectious to naïve in-contact calves three weeks after BCoV infection. Methods A live animal experiment was conducted, with direct contact between animal groups for 24 h as challenge procedure. Four naïve calves were commingled with a group of six naturally infected calves and sequentially euthanized. Two naïve sentinel calves were commingled with the experimentally exposed group three weeks after exposure. Nasal swabs, feces, blood and tissue samples were analyzed for viral RNA by RT-qPCR, and virus isolation was performed on nasal swabs. Serum was analyzed for BCoV antibodies. Results The calves showed mild general signs, and the most prominent signs were from the respiratory system. The overall clinical score corresponded well with the shedding of viral RNA the first three weeks after challenge. General depression and cough were the signs that correlated best with shedding of BCoV RNA, while peak respiratory rate and peak rectal temperature appeared more than a week later than the peak shedding. Nasal shedding preceded fecal shedding, and the calves had detectable amounts of viral RNA intermittently in feces through day 35 and in nasal secretions through day 28, however virus isolation was unsuccessful from day six and day 18 from the two calves investigated. Viral RNA was not detected in blood, but was found in lymphatic tissue through day 42 after challenge. Although the calves were shedding BCoV RNA 21 days after infection the sentinel animals were not infected. Conclusions Prolonged shedding of BCoV RNA can occur, but detection of viral RNA does not necessarily indicate a transmission potential. The study provides valuable information with regard to producing scientifically based biosecurity advices. Electronic supplementary material The online version of this article (doi:10.1186/s12985-016-0555-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Veslemøy Sunniva Oma
- Department of Production Animal Clinical Sciences, Norwegian University of Life Sciences, Ullevålsvegen 72, 0454, Oslo, Norway.
| | - Madeleine Tråvén
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Stefan Alenius
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Mette Myrmel
- Department of Food Safety and Infection Biology, Norwegian University of Life Sciences, Ullevålsvegen 72, 0454, Oslo, Norway
| | - Maria Stokstad
- Department of Production Animal Clinical Sciences, Norwegian University of Life Sciences, Ullevålsvegen 72, 0454, Oslo, Norway
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15
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Montero R, Mundy D, Albright A, Grose C, Trought MC, Cohen D, Chooi KM, MacDiarmid R, Flexas J, Bota J. Effects of Grapevine Leafroll associated Virus 3 (GLRaV-3) and duration of infection on fruit composition and wine chemical profile of Vitis vinifera L. cv. Sauvignon blanc. Food Chem 2016; 197 Pt B:1177-83. [PMID: 26675855 DOI: 10.1016/j.foodchem.2015.11.086] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 10/22/2015] [Accepted: 11/16/2015] [Indexed: 12/19/2022]
Abstract
In order to determine the effects of Grapevine Leafroll associated Virus 3 (GLRaV-3) on fruit composition and chemical profile of juice and wine from Vitis vinifera L. cv. Sauvignon blanc grown in New Zealand, composition variables were measured on fruit from vines either infected with GLRaV-3 (established or recent infections) or uninfected vines. Physiological ripeness (20.4°Brix) was the criterion established to determine the harvest date for each of the three treatments. Date of grape ripeness was strongly affected by virus infection. In juice and wine, GLRaV-3 infection prior to 2008 reduced titratable acidity compared with the uninfected control. Differences observed in amino acids from the three infection status groups did not modify basic wine chemical properties. In conclusion, GLRaV-3 infection slowed grape ripening, but at equivalent ripeness to result in minimal effects on the juice and wine chemistry. Time of infection produced differences in specific plant physiological variables.
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16
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Fujioka H, Yamasaki K, Furusawa K, Tamura K, Oguro K, Kurihara S, Seki S, Oshima SI, Imajoh M. Prevalence and characteristics of Cyprinid herpesvirus 3 (CyHV-3) infection in common carp (Cyprinus carpio L.) inhabiting three rivers in Kochi Prefecture, Japan. Vet Microbiol 2014; 175:362-8. [PMID: 25554244 DOI: 10.1016/j.vetmic.2014.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 11/28/2014] [Accepted: 12/02/2014] [Indexed: 12/11/2022]
Abstract
Cyprinid herpesvirus 3 (CyHV-3) causes lethal disease in common and koi carp. Mortality by CyHV-3 disease has not been reported since 2011 in Kochi Prefecture, Japan. Here, we detected and quantified CyHV-3 in common carp inhabiting three rivers in the prefecture to examine if the carp are carriers of CyHV-3 as a source of infection. CyHV-3 DNA was detected in 16.7% (12/72) of brain samples in Kagami River, 3.9% (3/76) of brain and 3.9% (3/76) of gill samples in Monobe River, and 5.1% (4/79) of brain and 1.3% (1/79) of gill samples in Wajiki River. CyHV-3 genotypes identified in the 23 samples were classified as the J genotype A1 that has been found in Japan. The CyHV-3 DNA load did not differ statistically between sampling months, indicating that CyHV-3 has been silent in common carp, unlike Lake Biwa where the annual reactivation occurs in spring. Taken together, our results represented definitive evidence that seasonal changes in water temperature do not affect CyHV-3 activity in carp. Considering that infectious virus was not isolated from CyHV-3 DNA-positive samples, it was suggested that CyHV-3 establishes a latent infection in carp populations inhabiting Kagami River, Monobe River and Wajiki River. Further, the presence of circular or concatameric CyHV-3 DNA was detected in five of 23 CyHV-3 DNA-positive samples. Common carp inhabiting Lake Biwa were reported previously to harbor linear but not circular CyHV-3 DNA. This difference suggested that the CyHV-3 genome may be circularized for long-term maintenance without active viral replication.
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Affiliation(s)
- Hiroya Fujioka
- Graduate School of Kuroshio Science, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Kenichi Yamasaki
- Fish Disease Laboratory, Department of Aquaculture, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Keiki Furusawa
- Fish Disease Laboratory, Department of Aquaculture, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Kazuki Tamura
- Fish Disease Laboratory, Department of Aquaculture, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Kazuki Oguro
- Fish Disease Laboratory, Department of Aquaculture, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Sumire Kurihara
- Fish Disease Laboratory, Department of Aquaculture, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Shingo Seki
- Fish Ecology Laboratory, Department of Aquaculture, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Syun-ichirou Oshima
- Graduate School of Kuroshio Science, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Masayuki Imajoh
- Fish Disease Laboratory, Department of Aquaculture, Kochi University, Nankoku, Kochi 783-8502, Japan.
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