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Waite DW, Liefting L, Delmiglio C, Chernyavtseva A, Ha HJ, Thompson JR. Development and Validation of a Bioinformatic Workflow for the Rapid Detection of Viruses in Biosecurity. Viruses 2022; 14:v14102163. [PMID: 36298719 PMCID: PMC9610911 DOI: 10.3390/v14102163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 07/15/2022] [Accepted: 09/25/2022] [Indexed: 11/05/2022] Open
Abstract
The field of biosecurity has greatly benefited from the widespread adoption of high-throughput sequencing technologies, for its ability to deeply query plant and animal samples for pathogens for which no tests exist. However, the bioinformatics analysis tools designed for rapid analysis of these sequencing datasets are not developed with this application in mind, limiting the ability of diagnosticians to standardise their workflows using published tool kits. We sought to assess previously published bioinformatic tools for their ability to identify plant- and animal-infecting viruses while distinguishing from the host genetic material. We discovered that many of the current generation of virus-detection pipelines are not adequate for this task, being outperformed by more generic classification tools. We created synthetic MinION and HiSeq libraries simulating plant and animal infections of economically important viruses and assessed a series of tools for their suitability for rapid and accurate detection of infection, and further tested the top performing tools against the VIROMOCK Challenge dataset to ensure that our findings were reproducible when compared with international standards. Our work demonstrated that several methods provide sensitive and specific detection of agriculturally important viruses in a timely manner and provides a key piece of ground truthing for method development in this space.
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Affiliation(s)
- David W. Waite
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
- Correspondence:
| | - Lia Liefting
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
| | - Catia Delmiglio
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
| | | | - Hye Jeong Ha
- Animal Health Laboratory, Ministry for Primary Industries, Upper Hutt 5018, New Zealand
| | - Jeremy R. Thompson
- Plant Health and Environment Laboratory, Ministry for Primary Industries, P.O. Box 2095, Auckland 1140, New Zealand
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Stanton JAL, O'Brien R, Hall RJ, Chernyavtseva A, Ha HJ, Jelley L, Mace PD, Klenov A, Treece JM, Fraser JD, Clow F, Clarke L, Su Y, Kurup HM, Filichev VV, Rolleston W, Law L, Rendle PM, Harris LD, Wood JM, Scully TW, Ussher JE, Grant J, Hore TA, Moser TV, Harfoot R, Lawley B, Quiñones-Mateu ME, Collins P, Blaikie R. Uncoupling Molecular Testing for SARS-CoV-2 From International Supply Chains. Front Public Health 2022; 9:808751. [PMID: 35141190 PMCID: PMC8818800 DOI: 10.3389/fpubh.2021.808751] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/28/2021] [Indexed: 11/19/2022] Open
Abstract
The rapid global rise of COVID-19 from late 2019 caught major manufacturers of RT-qPCR reagents by surprise and threw into sharp focus the heavy reliance of molecular diagnostic providers on a handful of reagent suppliers. In addition, lockdown and transport bans, necessarily imposed to contain disease spread, put pressure on global supply lines with freight volumes severely restricted. These issues were acutely felt in New Zealand, an island nation located at the end of most supply lines. This led New Zealand scientists to pose the hypothetical question: in a doomsday scenario where access to COVID-19 RT-qPCR reagents became unavailable, would New Zealand possess the expertise and infrastructure to make its own reagents onshore? In this work we describe a review of New Zealand's COVID-19 test requirements, bring together local experts and resources to make all reagents for the RT-qPCR process, and create a COVID-19 diagnostic assay referred to as HomeBrew (HB) RT-qPCR from onshore synthesized components. This one-step RT-qPCR assay was evaluated using clinical samples and shown to be comparable to a commercial COVID-19 assay. Through this work we show New Zealand has both the expertise and, with sufficient lead time and forward planning, infrastructure capacity to meet reagent supply challenges if they were ever to emerge.
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Affiliation(s)
- Jo-Ann L. Stanton
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- *Correspondence: Jo-Ann L. Stanton
| | - Rory O'Brien
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- MicroGEM NZ Ltd., Dunedin, New Zealand
| | - Richard J. Hall
- Animal Health Laboratory, Ministry for Primary Industries—Manatu Ahu Matua, Upper Hutt, New Zealand
| | - Anastasia Chernyavtseva
- Animal Health Laboratory, Ministry for Primary Industries—Manatu Ahu Matua, Upper Hutt, New Zealand
| | - Hye Jeong Ha
- Animal Health Laboratory, Ministry for Primary Industries—Manatu Ahu Matua, Upper Hutt, New Zealand
| | - Lauren Jelley
- Clinical Virology, Institute of Environmental Science and Research Limited (ESR), Upper Hutt, New Zealand
| | - Peter D. Mace
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Alexander Klenov
- Hudak Lab, Department of Biology, York University, Toronto, ON, Canada
| | - Jackson M. Treece
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - John D. Fraser
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Fiona Clow
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Lewis Clarke
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Yongdong Su
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | | | | | | | - Lee Law
- South Pacific Sera, Timaru, New Zealand
| | - Phillip M. Rendle
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Lawrence D. Harris
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - James M. Wood
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Thomas W. Scully
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - James E. Ussher
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- Molecular Pathology, Southern Community Laboratories, Dunedin, New Zealand
| | - Jenny Grant
- Molecular Pathology, Southern Community Laboratories, Dunedin, New Zealand
| | - Timothy A. Hore
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Tim V. Moser
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Rhodri Harfoot
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Blair Lawley
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Miguel E. Quiñones-Mateu
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | | | - Richard Blaikie
- Research and Enterprise, University of Otago, Dunedin, New Zealand
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Dittmer KE, Chernyavtseva A, Marshall JC, Cabrera D, Wolber FM, Kruger M. Expression of Renal Vitamin D and Phosphatonin-Related Genes in a Sheep Model of Osteoporosis. Animals (Basel) 2021; 12:ani12010067. [PMID: 35011173 PMCID: PMC8749731 DOI: 10.3390/ani12010067] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/23/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Osteoporosis is a significant public health issue around the world, with post-menopausal osteoporosis due to estrogen deficiency resulting in approximately ¾ of cases. Treatment with glucocorticoids is another common cause of osteoporosis in humans. Sheep are a well-established model for osteoporosis in humans. In this study, aged sheep had their ovaries removed (ovariectomy) to simulate estrogen deficiency, and some sheep were also treated with glucocorticoids. The results showed that expression of the gene klotho in the kidney had the most marked difference in ovariectomized sheep treated with glucocorticoids for 2 months followed by a recovery period of 3 months. Klotho is known as the “anti-aging” hormone and is an important regulator of calcium and phosphorus metabolism. It may therefore be involved in the recovery of bone mineral density seen in ovariectomized sheep treated with glucocorticoids for 2 months followed by euthanasia at 5 months. As such, it could be an important treatment target for osteoporosis in humans. Abstract Osteoporosis is a significant public health issue around the world, with post-menopausal osteoporosis due to estrogen deficiency resulting in approximately ¾ of cases. In this study, 18 aged Merino ewes were ovariectomized, and 10 were controls. Three of the ovariectomized ewes were treated weekly with 400 mg of methylprednisolone for 5 months and three were treated weekly for 2 months, followed by a 3-month recovery period. At 2 months, five control animals and six ovariectomized animals were euthanized. At 5 months, all the remaining ewes were euthanized. Kidney samples were collected postmortem for qPCR analysis of NPT1, PTH1R, NPT2a, NPT2c, Klotho, FGFR1IIIc, VDR, CYP24A1, CYP27B1, TRPV5, TRPV6, CalD9k, CalD28k, PMCA and NCX1. Ovariectomized sheep had significantly greater VDR expression compared with other groups. Ovariectomized sheep treated with glucocorticoids for 2 months followed by euthanasia at 5 months showed significant differences in TRPV5, CYP24A1 and klotho gene expression compared to other groups. Differences in klotho expression were most marked after adjustment for repeated measures (p = 0.1). Klotho is known as the “anti-aging” hormone and is involved in calcium and phosphorus metabolism. Klotho may be involved in the recovery of bone mineral density in ovariectomized sheep treated with glucocorticoids for 2 months followed by euthanasia at 5 months. Further research on the role of klotho is recommended.
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Affiliation(s)
- Keren E. Dittmer
- School of Veterinary Science, Massey University, Palmerston North 4442, New Zealand;
- Correspondence:
| | | | - Jonathan C. Marshall
- School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand;
| | - Diana Cabrera
- School of Food and Advanced Technology, Massey University, Palmerston North 4442, New Zealand; (D.C.); (F.M.W.)
| | - Frances M. Wolber
- School of Food and Advanced Technology, Massey University, Palmerston North 4442, New Zealand; (D.C.); (F.M.W.)
| | - Marlena Kruger
- School of Health Sciences, Massey University, Palmerston North 4442, New Zealand;
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Chernyavtseva A, Cave NJ, Munday JS, Dunowska M. Differential recognition of peptides within feline coronavirus polyprotein 1 ab by sera from healthy cats and cats with feline infectious peritonitis. Virology 2019; 532:88-96. [PMID: 31048107 PMCID: PMC7112048 DOI: 10.1016/j.virol.2019.04.003] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/08/2019] [Accepted: 04/10/2019] [Indexed: 11/17/2022]
Abstract
The aim of the study was to identify peptides within the polyprotein (Pp) 1 ab that are differentially recognised by cats with either enteric or systemic disease following infection with feline coronavirus. Overlapping 12-mer peptides (n = 28,426) across the entire Pp1ab were arrayed on peptide chips and reacted with pooled sera from coronavirus seropositive cats and from one seronegative cat. Eleven peptides were further tested in ELISA with individual serum samples, and three were selected for further screening. Two peptides (16433 and 4934) in the nsp3 region encoding the papain 1 and 2 proteases were identified for final testing. Peptide 4934 reacted equally with positive sera from healthy cats and cats with feline infectious peritonitis (FIP), while peptide 16433 was recognized predominantly by FIP-affected cats. The value of antibody tests based on these peptides in differentiating between the enteric and FIP forms of feline coronavirus infection remains to be determined. Cats develop antibodies to polyprotein 1 ab (Pp1ab) of feline coronavirus. This is most evident for cats with feline infectious peritonitis (FIP). Differences exist in responses to selected peptides between FIP and non-FIP cats. Such differences may be utilised for development of a serological test for FIP.
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Affiliation(s)
| | - Nick J Cave
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - John S Munday
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Magdalena Dunowska
- School of Veterinary Science, Massey University, Palmerston North, New Zealand.
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Jolly RD, Dittmer KE, Garrick DJ, Chernyavtseva A, Hemsley KM, King B, Fietz M, Shackleton NM, Fairley R, Wylie K. β-Mannosidosis in German Shepherd Dogs. Vet Pathol 2019; 56:743-748. [PMID: 30983534 DOI: 10.1177/0300985819839239] [Citation(s) in RCA: 5] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A neurological disease was investigated in 3 German Shepherd pups from the same litter that failed to grow normally, appeared stiff, were reluctant to move, and were deaf. They developed intermittent seizures and ataxia and had proprioceptive defects. Histopathology showed severe vacuolation of neurons, astrocytes in nervous tissue, renal tubular epithelial cells, and macrophages in nervous tissue, spleen, and liver. Vacuoles appeared empty with no storage material stained by periodic acid-Schiff (PAS) or Sudan black stains, leading to a diagnosis of a lysosomal storage disease and in particular an oligosaccharidosis. Biochemical and genomic studies showed that this was β-mannosidosis, not previously diagnosed in dogs. A c.560T>A transition in exon 4 of the MANBA gene was found, which segregated in these and other family members in a manner consistent with it being the causative mutation of an autosomal recessive disease. This mutation led to substitution of isoleucine to asparagine at position 187 of the 885 amino acid enzyme, a change expected to have functional significance.
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Affiliation(s)
- Robert D Jolly
- 1 School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Keren E Dittmer
- 1 School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Dorian J Garrick
- 1 School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | | | - Kim M Hemsley
- 2 Childhood Dementia Research Group, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Barbara King
- 2 Childhood Dementia Research Group, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Michael Fietz
- 3 SA Pathology, North Adelaide, South Australia, Australia
| | | | - Robert Fairley
- 5 Gribbles Veterinary Pathology Ltd., Christchurch, New Zealand
| | - Kirsten Wylie
- 6 Total Veterinary Services, Christchurch, New Zealand
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