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Sandybayev N, Strochkov V, Beloussov V, Orkara S, Kydyrmanov A, Khan Y, Batanova Z, Kassenov M. Evaluation of a novel real-time polymerase chain reaction assay for identifying H3 equine influenza virus in Kazakhstan. Vet World 2023; 16:1682-1689. [PMID: 37766711 PMCID: PMC10521171 DOI: 10.14202/vetworld.2023.1682-1689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/18/2023] [Indexed: 09/29/2023] Open
Abstract
Background and Aim Equine influenza (EI) is a highly contagious disease that causes fever and upper respiratory tract inflammation. It is caused by influenza virus A, belonging to the Orthomyxoviridae family, with subtypes H3N8 and H7N7. This study presents data on the development of a real-time polymerase chain reaction (RT-PCR) assay using TaqMan probes to detect the H3 subtype of EI virus (EIV). Materials and Methods The evaluation of the developed RT-PCR assay involved five strains of EIV as positive controls and ten nasopharyngeal swab samples collected from horses. RNA was isolated using the GeneJet Viral DNA and RNA Purification Kit, and primers and probes were designed using the Integrated DNA Technology PrimerQuest Tool. The assay was optimized by investigating the annealing temperature, primer and probes concentrations, sensitivity, and specificity. Sequencing was performed using the Thermo Fisher 3130 Genetic Analyzer, and the evolutionary history was inferred using the Neighbor-Joining method. Results The designed primers and probes, targeting the H3 gene, were found to be specific to the EIV. The RT-PCR assay was capable of detecting as low as 50 femtogram (f) or 3 × 103 copies of genomic RNA. No cross-reactions were observed with other respiratory viral and bacterial pathogens, indicating the high specificity of the assay. To evaluate its effectiveness, ten nasopharyngeal swab samples collected from farms in North Kazakhstan regions during disease monitoring were analyzed. The accuracy of the analysis was confirmed by comparing the results with those obtained from a commercial RT-PCR assay for EI identification. The developed RT-PCR assay exhibited high sensitivity and specificity for detecting the EIV. Conclusion The results demonstrate that the developed RT-PCR assay is suitable for diagnosing EI. This simple, highly sensitive, and specific assay for detecting H3 EIV can be a reliable tool for diagnosing and surveilling EI. Implementing this RT-PCR assay in veterinary practice will enhance and expedite the timely response to potential outbreaks of EI, thus positively impacting the overall epizootic well-being of EI in Kazakhstan.
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Affiliation(s)
- Nurlan Sandybayev
- Kazakhstan-Japan Innovation Centre, Kazakh National Agrarian Research University, 050010 Almaty, Kazakhstan
| | - Vitaliy Strochkov
- Kazakhstan-Japan Innovation Centre, Kazakh National Agrarian Research University, 050010 Almaty, Kazakhstan
| | | | - Shynggys Orkara
- Kazakhstan-Japan Innovation Centre, Kazakh National Agrarian Research University, 050010 Almaty, Kazakhstan
| | - Aidyn Kydyrmanov
- Research and Production Center for Microbiology and Virology, Almaty 050060, Kazakhstan
| | - Yelizaveta Khan
- Research and Production Center for Microbiology and Virology, Almaty 050060, Kazakhstan
| | - Zhanat Batanova
- Faculty of Veterinary, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
| | - Markhabat Kassenov
- Laboratory of Virology, Kazakh Scientific Research Veterinary Institute, Almaty 050016, Kazakhstan
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Altan E, Hui A, Li Y, Pesavento P, Asín J, Crossley B, Deng X, Uzal FA, Delwart E. New Parvoviruses and Picornavirus in Tissues and Feces of Foals with Interstitial Pneumonia. Viruses 2021; 13:v13081612. [PMID: 34452477 PMCID: PMC8402702 DOI: 10.3390/v13081612] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/20/2021] [Accepted: 07/27/2021] [Indexed: 12/12/2022] Open
Abstract
Six foals with interstitial pneumonia of undetermined etiology from Southern California were analyzed by viral metagenomics. Spleen, lung, and colon content samples obtained during necropsy from each animal were pooled, and nucleic acids from virus-like particles enriched for deep sequencing. The recently described equine copiparvovirus named eqcopivirus, as well as three previously uncharacterized viruses, were identified. The complete ORFs genomes of two closely related protoparvoviruses, and of a bocaparvovirus, plus the partial genome of a picornavirus were assembled. The parvoviruses were classified as members of new ungulate protoparvovirus and bocaparvovirus species in the Parvoviridae family. The picornavirus was classified as a new species in the Salivirus genus of the Picornaviridae family. Spleen, lung, and colon content samples from each foal were then tested for these viral genomes by nested PCR and RT-PCR. When present, parvoviruses were detected in both feces and spleen. The picornavirus, protoparvovirus, and eqcopivirus genomes were detected in the lungs of one animal each. Three foals were co-infected with the picornavirus and either a protoparvovirus, bocaparvovirus, or eqcopivirus. Two other foals were infected with a protoparvovirus only. No viral infection was detected in one animal. The complete ORFs of the first equine protoparvoviruses and bocaparvovirus, the partial ORF of the third equine picornavirus, and their detection in tissues of foals with interstitial pneumonia are described here. Testing the involvement of these viruses in fatal interstitial pneumonia or other equine diseases will require larger epidemiological and/or inoculation studies.
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Affiliation(s)
- Eda Altan
- Vitalant Research Institute, San Francisco, CA 94118, USA; (E.A.); (A.H.); (Y.L.); (X.D.)
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA
| | - Alvin Hui
- Vitalant Research Institute, San Francisco, CA 94118, USA; (E.A.); (A.H.); (Y.L.); (X.D.)
| | - Yanpeng Li
- Vitalant Research Institute, San Francisco, CA 94118, USA; (E.A.); (A.H.); (Y.L.); (X.D.)
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA
| | - Patricia Pesavento
- Department of Pathology Microbiology and Immunology, UC Davis, Davis, CA 95616, USA; (P.P.); (J.A.); (F.A.U.)
| | - Javier Asín
- Department of Pathology Microbiology and Immunology, UC Davis, Davis, CA 95616, USA; (P.P.); (J.A.); (F.A.U.)
- California Animal Health and Food Safety Laboratory System, UC Davis, Davis, CA 95616, USA;
| | - Beate Crossley
- California Animal Health and Food Safety Laboratory System, UC Davis, Davis, CA 95616, USA;
- Department of Medicine and Epidemiology, UC Davis, Davis, CA 95616, USA
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA 94118, USA; (E.A.); (A.H.); (Y.L.); (X.D.)
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA
| | - Francisco A. Uzal
- Department of Pathology Microbiology and Immunology, UC Davis, Davis, CA 95616, USA; (P.P.); (J.A.); (F.A.U.)
- California Animal Health and Food Safety Laboratory System, UC Davis, Davis, CA 95616, USA;
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA 94118, USA; (E.A.); (A.H.); (Y.L.); (X.D.)
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA
- Correspondence:
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