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Hwang S, Lee W, Lee Y. Development of a nucleic acid detection method based on the CRISPR-Cas13 for point-of-care testing of bovine viral diarrhea virus-1b. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2024; 66:781-791. [PMID: 39165749 PMCID: PMC11331364 DOI: 10.5187/jast.2024.e77] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2024]
Abstract
Bovine viral diarrhea (BVD) is a single-stranded, positive-sense ribonucleic acid (RNA) virus belonging to the genus Pestivirus of the Flaviviridae family. BVD frequently causes economic losses to farmers. Among bovine viral diarrhea virus (BVDV) strains, BVDV-1b is predominant and widespread in Hanwoo calves. Reverse-transcription polymerase chain reaction (RT-PCR) is an essential method for diagnosing BVDV-1b and has become the gold standard for diagnosis in the Republic of Korea. However, this diagnostic method is time-consuming and requires expensive equipment. Therefore, Clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) systems have been used for point-of-care (POC) testing of viruses. Developing a sensitive and specific method for POC testing of BVDV-1b would be advantageous for controlling the spread of infection. Thus, this study aimed to develop a novel nucleic acid detection method using the CRISPR-Cas13 system for POC testing of BVDV-1b. The sequence of the BVD virus was extracted from National Center for Biotechnology Information (NC_001461.1), and the 5' untranslated region, commonly used for detection, was selected. CRISPR RNA (crRNA) was designed using the Cas13 design program and optimized for the expression and purification of the LwCas13a protein. Madin Darby bovine kidney (MDBK) cells were infected with BVDV-1b, incubated, and the viral RNA was extracted. To enable POC viral detection, the compatibility of the CRISPR-Cas13 system was verified with a paper-based strip through collateral cleavage activity. Finally, a colorimetric assay was used to evaluate the detection of BVDV-1b by combining the previously obtained crRNA and Cas13a protein on a paper strip. In conclusion, the CRISPR-Cas13 system is highly sensitive, specific, and capable of nucleic acid detection, making it an optimal system for the early point-of-care testing of BVDV-1b.
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Affiliation(s)
- Sungeun Hwang
- School of Biotechnology, Hankyong National
University, Anseong 17579, Korea
| | - Wonhee Lee
- School of Biotechnology, Hankyong National
University, Anseong 17579, Korea
| | - Yoonseok Lee
- School of Biotechnology, Hankyong National
University, Anseong 17579, Korea
- Center for Genetic Information, Hankyong
National University, Anseong 17579, Korea
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Gallina L, Koch MC, Gentile A, Treglia I, Bombardi C, Mandrioli L, Bolcato M, Scagliarini A, Drögemüller C, Seuberlich T, Ciulli S. Bovine viral diarrhoea virus 1b infection associated with congenital tremor and hypomyelination in Holstein calves. Vet Microbiol 2021; 256:109047. [PMID: 33866081 DOI: 10.1016/j.vetmic.2021.109047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/19/2021] [Indexed: 02/02/2023]
Abstract
Hypomyelination is a rare consequence of in utero bovine viral diarrhoea virus (BVDV) infection. We describe a BVDV outbreak in a naïve Holstein dairy herd in northern Italy, with an unusually high prevalence of calves with neurological signs, generalised tremors and ataxia. Histological analysis showed that hypomyelination was the predominant lesion and that the most typical BVDV neuropathological findings (e.g. cerebellar hypoplasia) were absent. Virological and molecular analyses showed that non-cytopathic BVDV genotype 1b was associated with the calves' neurological signs and excluded other viruses responsible for congenital infection or neurological disorders. Whole-genome sequencing of BVDVs from the brain of a calf with neurological signs and the whole blood of a persistently infected herd-mate with no such sign showed >99.7 % sequence identity. Analysis of the quasispecies distribution revealed the greatest variation rates in regions coding for the structural proteins E1 and E2. Variation was slightly greater in the brain- than in the blood-derived sequence and occurred at different sites, suggesting the occurrence of distinct evolutionary processes in the two persistently infected calves. Molecular characterisation of BVDV genomes from five other calves with neurological signs from the same farm confirmed that the E1 and E2 regions were the most variable. Several factors, including genetic variability and host factors, appear to have contributed to the observed unique BVDV disease phenotype, characterised by hypomyelination and neurological signs.
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Affiliation(s)
- Laura Gallina
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064, Ozzano Emilia, Italy
| | - Michel C Koch
- Division of Neurological Sciences, NeuroCenter, University of Bern, Bremgartenstrasse 109a, 3012, Bern, Switzerland
| | - Arcangelo Gentile
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064, Ozzano Emilia, Italy
| | - Ida Treglia
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064, Ozzano Emilia, Italy
| | - Cristiano Bombardi
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064, Ozzano Emilia, Italy
| | - Luciana Mandrioli
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064, Ozzano Emilia, Italy
| | - Marilena Bolcato
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064, Ozzano Emilia, Italy
| | - Alessandra Scagliarini
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064, Ozzano Emilia, Italy
| | - Cord Drögemüller
- Institute of Genetics, University of Bern, Bremgartenstrasse 109, 3012, Bern, Switzerland
| | - Torsten Seuberlich
- Division of Neurological Sciences, NeuroCenter, University of Bern, Bremgartenstrasse 109a, 3012, Bern, Switzerland
| | - Sara Ciulli
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064, Ozzano Emilia, Italy.
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Russell GC, Zadoks RN, Willoughby K, Bachofen C. Bovine viral diarrhoea virus loses quasispecies diversity rapidly in culture. Microb Genom 2020; 6:e000343. [PMID: 32160141 PMCID: PMC7276709 DOI: 10.1099/mgen.0.000343] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/07/2020] [Indexed: 12/25/2022] Open
Abstract
Bovine viral diarrhoea (BVD) is an important disease of cattle, with significant impacts on animal health and welfare. The wide host range of the causative pestiviruses may lead to formation of virus reservoirs in other ruminant or wildlife species, presenting a concern for the long-term success of BVD eradication campaigns. It is likely that the quasispecies nature of these RNA viruses contributes to their interspecies transmission by providing genetic plasticity. Understanding the spectrum of sequence variants present in persistently infected (PI) animals is, therefore, essential for studies of virus transmission. To analyse quasispecies diversity without amplification bias, we extracted viral RNA from the serum of a PI cow, and from cell culture fluid after three passages of the same virus in culture, to produce cDNA without amplification. Sequencing of this material using Illumina 250 bp paired-read technology produced full-length virus consensus sequences from both sources and demonstrated the quasispecies diversity of this pestivirus A genotype 1a field strain within serum and after culture. We report the distribution and diversity of over 800 SNPs and provide evidence for a loss of diversity after only three passages in cell culture, implying that cultured viruses cannot be used to understand quasispecies diversity and may not provide reliable molecular markers for source tracing or transmission studies. Additionally, both serum and cultured viruses could be sequenced as a set of 25 overlapping PCR amplicons that demonstrated the same consensus sequences and the presence of many of the same quasispecies variants. The observation that aspects of the quasispecies structure revealed by massively parallel sequencing are also detected after PCR and Sanger sequencing suggests that this approach may be useful for small or difficult to analyse samples.
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Affiliation(s)
- George C. Russell
- Moredun Research Institute, Pentlands Science Park, Midlothian EH26 0PZ, UK
| | - Ruth N. Zadoks
- Moredun Research Institute, Pentlands Science Park, Midlothian EH26 0PZ, UK
- Present address: Sydney School of Veterinary Science, University of Sydney, Camden, NSW, Australia
| | - Kim Willoughby
- Moredun Research Institute, Pentlands Science Park, Midlothian EH26 0PZ, UK
| | - Claudia Bachofen
- Moredun Research Institute, Pentlands Science Park, Midlothian EH26 0PZ, UK
- Present address: Institute of Virology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 266a, CH-8057 Zürich, Switzerland
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