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Özgünlük İ, Yücetepe AG, Çetiner B, Keskin O, Özyörük F. Development of a Multiplex PCR Assay for Rapid Differentiation of Fowlpox and Pigeonpox Viruses. Avian Dis 2024; 68:33-37. [PMID: 38687105 DOI: 10.1637/aviandiseases-d-23-00042] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 12/24/2023] [Indexed: 05/02/2024]
Abstract
The aim of this study was to develop a multiplex PCR assay capable of rapidly differentiating two major Avipoxvirus (APV) species, Fowlpox virus (FWPV) and Pigeonpox virus (PGPV), which cause disease in bird species. Despite the importance of a rapid differentiation assay, no such assay exists that can differentiate the APV species without sequencing. To achieve this, species-specific target DNA fragments were selected from the fpv122 gene of FWPV and the HM89_gp120 gene of PGPV, which are unique to each genome. Nine samples collected from unvaccinated chickens, pigeons, and a turkey with typical pox lesions were genetically identified as FWPV and PGPV. The designed primers and target DNA fragments were validated using in silico analyses with the nucleotide Basic Local Alignment Search Tool. The multiplex PCR assay consisted of species-specific primers and previously described PanAPV primers (genus-specific) and was able to differentiate FWPV and PGPV, consistent with the phylogenetic outputs. This study represents the first successful differentiation of FWPV and PGPV genomes using a conventional multiplex PCR test. This assay has the potential to facilitate the rapid diagnosis and control of APV infections.
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Affiliation(s)
- İrfan Özgünlük
- Harran University, Faculty of Veterinary Medicine, 63200 Şanlıurfa, Türkiye
| | | | - Burak Çetiner
- Harran University, Faculty of Veterinary Medicine, 63200 Şanlıurfa, Türkiye
| | - Oktay Keskin
- Harran University, Faculty of Veterinary Medicine, 63200 Şanlıurfa, Türkiye
| | - Fuat Özyörük
- Harran University, Faculty of Veterinary Medicine, 63200 Şanlıurfa, Türkiye,
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Nardo AD, Ferretti L, Wadsworth J, Mioulet V, Gelman B, Karniely S, Scherbakov A, Ziay G, Özyörük F, Parlak Ü, Göktuna PT, Hassanzadeh R, Khalaj M, Dastoor SM, Abdollahi D, Khan EUH, Afzal M, Hussain M, Knowles NJ, King DP. Evolutionary and Ecological Drivers Shape the Emergence and Extinction of Foot-and-Mouth Disease Virus Lineages. Mol Biol Evol 2021; 38:4346-4361. [PMID: 34115138 PMCID: PMC8476141 DOI: 10.1093/molbev/msab172] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Livestock farming across the world is constantly threatened by evolutionary turnover of foot-and-mouth disease virus (FMDV) strains in endemic systems, the underlying dynamics of which remain to be elucidated. Here, we map the eco-evolutionary landscape of co-circulating FMDV lineages within an important endemic virus pool encompassing Western, Central and parts of Southern Asia, reconstructing the evolutionary history and spatial dynamics over the last 20 years that shapes the current epidemiological situation. We demonstrate that new FMDV variants periodically emerge from Southern Asia, precipitating waves of virus incursions that systematically travel in a westerly direction. We evidence how metapopulation dynamics drive the emergence and extinction of spatially structured virus populations, and how transmission in different host species regulates the evolutionary space of virus serotypes. Our work provides the first integrative framework that defines co-evolutionary signatures of FMDV in regional contexts to help understand the complex interplay between virus phenotypes, host characteristics, and key epidemiological determinants of transmission that drive FMDV evolution in endemic settings.
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Affiliation(s)
- Antonello Di Nardo
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, United Kingdom
| | - Luca Ferretti
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jemma Wadsworth
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, United Kingdom
| | - Valerie Mioulet
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, United Kingdom
| | - Boris Gelman
- Division of Virology, Kimron Veterinary Institute, Beit Dagan, Israel
| | - Sharon Karniely
- Division of Virology, Kimron Veterinary Institute, Beit Dagan, Israel
| | - Alexey Scherbakov
- Federal Governmental Budgetary Institution "Federal Centre for Animal Health" (FGBI "ARRIAH"), Yur'evets, Vladimir, Russia
| | - Ghulam Ziay
- Central Veterinary Diagnostic and Research Laboratory, Kabul, Afghanistan
| | - Fuat Özyörük
- Faculty of Veterinary Medicine, Harran University, Sanliurfa, Turkey
| | - Ünal Parlak
- Foot and Mouth Disease (ŞAP) Institute, Ankara, Turkey
| | | | - Reza Hassanzadeh
- Iran Veterinary Organization, Ministry of Jihad-e-Agriculture, Tehran, Iran
| | - Mehdi Khalaj
- Iran Veterinary Organization, Ministry of Jihad-e-Agriculture, Tehran, Iran
| | | | - Darab Abdollahi
- Iran Veterinary Organization, Ministry of Jihad-e-Agriculture, Tehran, Iran
| | - Ehtisham-Ul-Haq Khan
- Livestock and Dairy Development Department, Government of Punjab, Rawalpindi, Pakistan
| | - Muhammad Afzal
- Food and Agriculture Organization of the United Nations, Pakistan Office, Islamabad, Pakistan
| | - Manzoor Hussain
- Food and Agriculture Organization of the United Nations, Pakistan Office, Islamabad, Pakistan
| | - Nick J Knowles
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, United Kingdom
| | - Donald P King
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, United Kingdom
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Dhollander S, Belsham GJ, Lange M, Willgert K, Alexandrov T, Chondrokouki E, Depner K, Khomenko S, Özyörük F, Salman M, Thulke HH, Bøtner A. Assessing the potential spread and maintenance of foot-and-mouth disease virus infection in wild ungulates: general principles and application to a specific scenario in Thrace. Transbound Emerg Dis 2014; 63:165-74. [PMID: 24903641 DOI: 10.1111/tbed.12240] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Indexed: 11/29/2022]
Abstract
Foot-and-mouth disease (FMD), due to infection with serotype O virus, occurred in wild boar and within eleven outbreaks in domestic livestock in the south-east of Bulgaria, Thrace region, in 2011. Hence, the issue of the potential for the spread and maintenance of FMD virus (FMDV) infection in a population of wild ungulates became important. This assessment focused on the spread and maintenance of FMDV infection within a hypothetical wild boar and deer population in an environment, which is characterized by a climate transitional between Mediterranean and continental and variable wildlife population densities. The assessment was based on three aspects: (i) a systematic review of the literature focusing on experimental infection studies to identify the parameters describing the duration of FMDV infection in deer and wild boar, as well as observational studies assessing the occurrence of FMDV infection in wild deer and wild boar populations, (ii) prevalence survey data of wild boar and deer in Bulgaria and Turkey and (iii) an epidemiological model, simulating the host-to-host spread of FMDV infections. It is concluded, based on all three aspects, that the wildlife population in Thrace, and so wildlife populations in similar ecological settings, are probably not able to maintain FMD in the long term in the absence of FMDV infection in the domestic host population. However, limited spread of FMDV infection in time and space in the wildlife populations can occur. If there is a continued cross-over of FMDV between domestic and wildlife populations or a higher population density, virus circulation may be prolonged.
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Affiliation(s)
| | - G J Belsham
- National Veterinary Institute, Technical University of Denmark, Kalvehave, Denmark
| | - M Lange
- UFZ, Helmholtz Centre for Environmental Research Leipzig/Halle, Leipzig, Germany
| | - K Willgert
- European Food Safety Authority, Parma, Italy
| | - T Alexandrov
- Food and Agriculture Organization of the United Nations, Rome, Italy
| | | | - K Depner
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - S Khomenko
- Food and Agriculture Organization of the United Nations, Rome, Italy
| | - F Özyörük
- Foot and Mouth Disease Institute, Ankara, Turkey
| | - M Salman
- Colorado State University, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, CO, USA
| | - H H Thulke
- UFZ, Helmholtz Centre for Environmental Research Leipzig/Halle, Leipzig, Germany
| | - A Bøtner
- National Veterinary Institute, Technical University of Denmark, Kalvehave, Denmark
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Çokçalışkan C, Özyörük F, Gürsoy RN, Alkan M, Günbeyaz M, Arca HÇ, Uzunlu E, Şenel S. Chitosan-based systems for intranasal immunization against foot-and-mouth disease. Pharm Dev Technol 2013; 19:181-8. [DOI: 10.3109/10837450.2013.763263] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Valdazo-González B, Polihronova L, Alexandrov T, Normann P, Knowles NJ, Hammond JM, Georgiev GK, Özyörük F, Sumption KJ, Belsham GJ, King DP. Reconstruction of the transmission history of RNA virus outbreaks using full genome sequences: foot-and-mouth disease virus in Bulgaria in 2011. PLoS One 2012; 7:e49650. [PMID: 23226216 PMCID: PMC3511503 DOI: 10.1371/journal.pone.0049650] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [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: 08/13/2012] [Accepted: 10/11/2012] [Indexed: 11/19/2022] Open
Abstract
Improvements to sequencing protocols and the development of computational phylogenetics have opened up opportunities to study the rapid evolution of RNA viruses in real time. In practical terms, these results can be combined with field data in order to reconstruct spatiotemporal scenarios that describe the origin and transmission pathways of viruses during an epidemic. In the case of notifiable diseases, such as foot-and-mouth disease (FMD), these analyses provide important insights into the epidemiology of field outbreaks that can support disease control programmes. This study reconstructs the origin and transmission history of the FMD outbreaks which occurred during 2011 in Burgas Province, Bulgaria, a country that had been previously FMD-free-without-vaccination since 1996. Nineteen full genome sequences (FGS) of FMD virus (FMDV) were generated and analysed, including eight representative viruses from all of the virus-positive outbreaks of the disease in the country and 11 closely-related contemporary viruses from countries in the region where FMD is endemic (Turkey and Israel). All Bulgarian sequences shared a single putative common ancestor which was closely related to the index case identified in wild boar. The closest relative from outside of Bulgaria was a FMDV collected during 2010 in Bursa (Anatolia, Turkey). Within Bulgaria, two discrete genetic clusters were detected that corresponded to two episodes of outbreaks that occurred during January and March-April 2011. The number of nucleotide substitutions that were present between, and within, these separate clusters provided evidence that undetected FMDV infection had occurred. These conclusions are supported by laboratory data that subsequently identified three additional FMDV-infected livestock premises by serosurveillance, as well as a number of antibody positive wild boar on both sides of the border with Turkish Thrace. This study highlights how FGS analysis can be used as an effective on-the-spot tool to support and help direct epidemiological investigations of field outbreaks.
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Affiliation(s)
- Begoña Valdazo-González
- Division of Livestock Viral Diseases, The Pirbright Institute, Pirbright, Surrey, United Kingdom.
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Valdazo-González B, Knowles NJ, Wadsworth J, King DP, Hammond JM, Özyörük F, Fırat-Saraç M, Parlak Ü, Polyhronova L, Georgiev GK. Foot-and-mouth disease in Bulgaria. Vet Rec 2011; 168:247. [DOI: 10.1136/vr.d1352] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
| | - Nick J. Knowles
- EU Community Reference Laboratory for FMD; IAH; Ash Road, Pirbright Surrey GU24 0NF
| | - Jemma Wadsworth
- EU Community Reference Laboratory for FMD; IAH; Ash Road, Pirbright Surrey GU24 0NF
| | - Donald P. King
- EU Community Reference Laboratory for FMD; IAH; Ash Road, Pirbright Surrey GU24 0NF
| | - Jef M. Hammond
- EU Community Reference Laboratory for FMD; IAH; Ash Road, Pirbright Surrey GU24 0NF
| | - Fuat Özyörük
- Foot-and-Mouth Disease Institute; PO Box 714, 06044, Ulus Ankara Turkey
| | - Müge Fırat-Saraç
- Foot-and-Mouth Disease Institute; PO Box 714, 06044, Ulus Ankara Turkey
| | - Ünal Parlak
- Foot-and-Mouth Disease Institute; PO Box 714, 06044, Ulus Ankara Turkey
| | - Lilyana Polyhronova
- National Diagnostic and Research Veterinary Medical Institute; 1606 Sofia Bulgaria
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Knowles NJ, Nazem Shirazi MH, Wadsworth J, Swabey KG, Stirling JM, Statham RJ, Li Y, Hutchings GH, Ferris NP, Parlak Ü, Özyörük F, Sumption KJ, King DP, Paton DJ. Recent Spread of a New Strain (A-Iran-05) of Foot-and-Mouth Disease Virus Type A in the Middle East. Transbound Emerg Dis 2009; 56:157-69. [DOI: 10.1111/j.1865-1682.2009.01074.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Klein J, Parlak Ü, Özyörük F, Christensen LS. The molecular epidemiology of foot-and-mouth disease virus serotypes A and O from 1998 to 2004 in Turkey. BMC Vet Res 2006; 2:35. [PMID: 17144917 PMCID: PMC1698480 DOI: 10.1186/1746-6148-2-35] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2006] [Accepted: 12/04/2006] [Indexed: 12/04/2022] Open
Abstract
Background Foot-and-Mouth Disease (FMD) causes significant economic losses in Turkish livestock. We have analysed the genetic diversity of the 1D sequences, encoding the hypervariable surface protein VP1, of Turkish isolates of serotype A and O collected from 1998 to 2004 in order to obtain epidemiological and immunological information. Results The 1D coding region of 33 serotype O and 20 serotype A isolates, obtained from outbreaks of FMD between 1998 and 2004, was sequenced. For serotype A, we confirmed the occurrence of the two subtypes IRN99 and IRN96. These subtypes are most divergent within the region encoding the immuno-dominant GH-loop. Also a close relationship to Foot-and-Mouth Disease virus (FMDV) serotype A isolates obtained from outbreaks in Iraq and Iran were detected and a clustering of isolates collected during the same period of time were found. The analysis of the deduced amino-acid sequences of these subtypes revealed evidence of positive selection in one site and one deletion, both within the GH-loop region. By inferring the ancestral history of the positively selected codon, two potential precursors were found. Furthermore, the structural alignment of IRN99 and IRN96 revealed differences between the tertiary structures of these subtypes. The similarity plot of the serotype O isolates suggested a more homogeneous group than the serotype A isolates. However, phylogenetic analysis revealed two major groups, each further divided in subgroups, of which some only consisted of Turkish isolates. Positively selected sites and structural differences of the Turkish isolates analysed, were not found. Conclusion The sequence and structural analysis of the IRN99 strains is indicative of positive selection suggesting an immunological advantage compared to IRN96. However, results of antigenic comparison reported elsewhere do not substantiate such a conclusion. There is evidence that IRN99 was introduced to Turkey, in all probability from Iran. Since, a member of the IRN96 lineage was included as a component of the FMDV vaccine produced since 2000, the outbreaks caused by IRN96 strains in 2004 could be due to incomplete vaccine coverage. The Turkish type O strains, all with a VP1 structure similar to the O1/Manisa/69 vaccine, appear in several sublineages. Whether these sublineages reflect multiple samplings from a limited number of outbreaks, or if they reflect cross-boundary introductions is not clear.
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Affiliation(s)
- Joern Klein
- Danish Institute for Food and Veterinary Research, Department of Virology, Lindholm, 4771 Kalvehave, Denmark
| | - Ünal Parlak
- Foot-and-Mouth Disease Institute, Ankara, Turkey
| | - Fuat Özyörük
- Foot-and-Mouth Disease Institute, Ankara, Turkey
| | - Laurids S Christensen
- Danish Institute for Food and Veterinary Research, Department of Virology, Lindholm, 4771 Kalvehave, Denmark
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