Molecular Epidemiology of a novel re-assorted epidemic strain of equine influenza virus in Pakistan in 2015-16.
Abstract: A widespread epidemic of equine influenza (EI) occurred in nonvaccinated equine population across multiple districts in Khyber Pakhtunkhwa Province of Pakistan during 2015-2016. An epidemiological surveillance study was conducted from Oct 2015 to April 2016 to investigate the outbreak. EI virus strains were isolated in embryonated eggs from suspected equines swab samples and were subjected to genome sequencing using M13 tagged segment specific primers. Phylogenetic analyses of the nucleotide sequences were concluded using Geneious. Haemagglutinin (HA), Neuraminidase (NA), Matrix (M) and nucleoprotein (NP) genes nucleotide and amino acid sequences of the isolated viruses were aligned with those of OIE recommended, FC-1, FC-2, and contemporary isolates of influenza A viruses from other species. HA and NA genes amino acid sequences were very similar to Tennessee/14 and Malaysia/15 of FC-1 and clustered with the contemporary isolates recently reported in the USA. Phylogenetic analysis showed that these viruses were mostly identical (with 99.6% and 97.4% nucleotide homology) to, and were reassortants containing chicken/Pakistan/14 (H7N3) and Canine/Beijing/10 (H3N2) like M and NP genes. Genetic analysis indicated that A/equine/Pakistan/16 viruses were most probably the result of several re-assortments between the co-circulating avian and equine viruses, and were genetically unlike the other equine viruses due to the presence of H7N3 or H3N2 like M and NP genes. Epidemiological data analysis indicated the potential chance of mixed, and management such as mixed farming system by keeping equine, canine and backyard poultry together in confined premises as the greater risk factors responsible for the re-assortments. Other factors might have contributed to the spread of the epidemic, including low awareness level, poor control of equine movements, and absence of border control disease strategies.
Copyright © 2017 Elsevier B.V. All rights reserved.
Publication Date: 2017-07-27 PubMed ID: 28757141DOI: 10.1016/j.virusres.2017.07.022Google Scholar: Lookup
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Summary
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The study explores a widespread outbreak of equine influenza in Pakistan during 2015-2016, identifies new virus strains and establishes possible reasons behind such re-assortments and their rapid spread.
Investigation of the Outbreak
- An outbreak of equine influenza (EI) took place in Khyber Pakhtunkhwa Province of Pakistan and was majorly reported in unvaccinated equine populations across various districts.
- The scientists conducted an epidemiological surveillance study from October 2015 to April 2016 to investigate this outbreak.
- Equine influenza virus strains were isolated from suspected equines swab samples and genome sequencing was conducted using M13 tagged segment specific primers.
Analysis of Virus Strains
- The virus strains were analyzed by aligning nucleotide and amino acid sequences of Haemagglutinin (HA), Neuraminidase (NA), Matrix (M) and Nucleoprotein (NP) genes with those of OIE recommended, FC-1, FC-2, and contemporary isolates of influenza A viruses from other species.
- Amino acid sequences of HA and NA genes appeared similar to Tennessee/14 and Malaysia/15 of FC-1 and clustered with recently reported isolates in the USA.
Findings of Phylogenetic Analysis
- In phylogenetic analysis, the viruses were found to be almost identical (with 99.6% and 97.4% nucleotide homology) to, and were reassortants containing, the Chicken/Pakistan/14 (H7N3) and Canine/Beijing/10 (H3N2) like M and NP genes.
- The viruses were distinguished from other equine viruses due to the presence of H7N3 or H3N2 like M and NP genes.
Epidemiological Data Analysis
- Epidemiological data analysis suggested the A/equine/Pakistan/16 viruses were most likely the result of several re-assortments between avian and equine viruses.
- Animal management systems such as mixed farming by keeping equines, canines, and backyard poultry together in confined premises emerged as major risk factors for such re-assortments.
- Other factors that could have contributed to the epidemic’s spread include low awareness levels, inadequate border control disease strategies, and poor control of equine movements.
Cite This Article
APA
Khan A, Mushtaq MH, Ahmad MUD, Nazir J, Farooqi SH, Khan A.
(2017).
Molecular Epidemiology of a novel re-assorted epidemic strain of equine influenza virus in Pakistan in 2015-16.
Virus Res, 240, 56-63.
https://doi.org/10.1016/j.virusres.2017.07.022 Publication
Researcher Affiliations
- Department of Epidemiology and Public Health, The University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan. Electronic address: dramjadkhan77@gmail.com.
- Department of Epidemiology and Public Health, The University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan. Electronic address: hassan.mushtaq@uvas.edu.pk.
- Department of Epidemiology and Public Health, The University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan. Electronic address: mansuruddin@uvas.edu.pk.
- Department of Veterinary Microbiology, The University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan. Electronic address: rehan.rolfe1989@gmail.com.
- Department of Clinical Medicine and Surgery, The University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan. Electronic address: shahid.farooqivet@gmail.com.
- Department of Clinical Medicine, Arid Agricultural University, Rawalpindi, 44000, Pakistan. Electronic address: drasghar07@gmail.com.
MeSH Terms
- Animals
- Horse Diseases / epidemiology
- Horse Diseases / virology
- Horses
- Influenza A virus / classification
- Influenza A virus / genetics
- Influenza A virus / isolation & purification
- Molecular Epidemiology
- Orthomyxoviridae Infections / epidemiology
- Orthomyxoviridae Infections / veterinary
- Orthomyxoviridae Infections / virology
- Pakistan
- Phylogeny
- Reassortant Viruses / classification
- Reassortant Viruses / genetics
- Reassortant Viruses / isolation & purification
- Recombination, Genetic
Citations
This article has been cited 4 times.- Pellegrini F, Buonavoglia A, Omar AH, Diakoudi G, Lucente MS, Odigie AE, Sposato A, Augelli R, Camero M, Decaro N, Elia G, Bányai K, Martella V, Lanave G. A Cold Case of Equine Influenza Disentangled with Nanopore Sequencing. Animals (Basel) 2023 Mar 24;13(7).
- Gahan J, Garvey M, Asmah Abd Samad R, Cullinane A. Whole Genome Sequencing of the First H3N8 Equine Influenza Virus Identified in Malaysia. Pathogens 2019 May 10;8(2).
- Singh RK, Dhama K, Karthik K, Khandia R, Munjal A, Khurana SK, Chakraborty S, Malik YS, Virmani N, Singh R, Tripathi BN, Munir M, van der Kolk JH. A Comprehensive Review on Equine Influenza Virus: Etiology, Epidemiology, Pathobiology, Advances in Developing Diagnostics, Vaccines, and Control Strategies. Front Microbiol 2018;9:1941.
- Gonzalez-Obando J, Zuluaga-Cabrera A, Moreno I, Úsuga J, Ciuderis K, Forero JE, Diaz A, Rojas-Arbeláez C, Hernández-Ortiz JP, Ruiz-Saenz J. First Molecular Detection and Epidemiological Analysis of Equine Influenza Virus in Two Regions of Colombia, 2020-2023. Viruses 2024 May 24;16(6).
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