Open Access
Research (Published online: 19-08-2023)
14. Evaluation of a novel real-time polymerase chain reaction assay for identifying H3 equine influenza virus in Kazakhstan
Nurlan Sandybayev, Vitaliy Strochkov, Vyacheslav Beloussov, Shynggys Orkara, Aidyn Kydyrmanov, Yelizaveta Khan, Zhanat Batanova, and Markhabat Kassenov
Veterinary World, 16(8): 1682-1689

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.
Vyacheslav Beloussov: TreeGene Molecular Genetics Laboratory, Almaty 050009, 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.

doi: 10.14202/vetworld.2023.1682-1689

Article history: Received: 26-04-2023, Accepted: 18-07-2023, Published online: 19-08-2023

Corresponding author: Nurlan Sandybayev

E-mail: nurlan.s@kaznaru.edu.kz

Citation: Sandybayev N, Strochkov V, Beloussov V, Orkara S, Kydyrmanov A, Khan Y, Batanova Z, and Kassenov M (2023) Evaluation of a novel real-time polymerase chain reaction assay for identifying H3 equine influenza virus in Kazakhstan, Veterinary World, 16(8): 1682-1689.
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.

Keywords: equine influenza, hemagglutinin, horses, primers, probe, real-time polymerase chain reaction assay, virus.