Molecular Characterization and Whole Genome Analysis of Infectious Pancreatic Necrosis Virus (IPNV) Isolates Obtained From Turkey
Abstract
Since the first recognition in North America, 1941, Infectious Pancreatic Necrosis Virus (IPNV) have been detected in many countries including Turkey, as a result of international trade. Sicnificant economic loss primarily occurs in fishes less than six months age. The causative agent belongs to the genus Aquabirnavirus of the family Birnaviridae and is a non-enveloped virus with a 60 nm icosahedral structure and a bi-segmented double stranded RNA genome. Segment A which codes VP2, VP3, VP4 and VP5 while segment B encodes VP1, an RNA-dependent RNA polymerase. The objective of this study was to investigate whole genome properties of IPNV isolated from six different regions of Turkey (Duzce, Sanliurfa, Tokat, K. Maras, Trabzon and Gaziantep) between 2004 and 2013. Phylogenetic analysis of whole genomic data showed that six isolates were clustered with genogroup 5, and group 1, based on segment A and Segment B data, respectively. Moreover, several substitutions in VP2 hypervariable region associates with low virulence and point mutations in the VP5 coding sequence were detected. This research may provide valuable information on the characterization of IPNV isolates circulating different geographical area of Turkey.
Keywords
Infectious pancreatic necrosis virus sequence analysis phylogenetic analysis molecular characterization whole genome
References
- Albayrak H and Özan E. (2010) Gökkuşağı alabalıklarında (Oncorhynchus mykiss Walbaum, 1792) Infeksiyöz Pankreatik Nekrozis ve Infeksiyöz Hematopoietik Nekrozis Virus Enfeksiyonlarının Varlığının Araştırılması. Ankara Üniv Vet Fak Derg 57(2):125-129. https://doi.org/10.1501/Vetfak_0000002322.
- Bain N, Gregory A and Raynard RS (2008) Genetic Analysis of Infectious Pancreatic Necrosis Virus From Scotland J Fish Dis 31(1): 37-47. https://doi.org/10.1111/j.1365-2761.2007.00864.x.
- Barrera-Mejía M, Simón-Martínez J, Ulloa-Arvizu R, Salgado-Miranda C, Soriano-Vargas E (2010) Molecular characterization of the VP1 gene of a Mexican isolate of infectious pancreatic necrosis virus. Can J Vet Res 74(3): 218-222.
- Blake S, Ma JY, Caporale DA, Jairath S, Nicholson BL (2001) Phylogenetic relationships of aquatic birnaviruses based on deduced amino acid sequences of genome segment A cDNA. Dis Aquat Organ 45(2):89-102. https://doi.org/10.3354/dao045089.
- Büyükekiz AG, Altun S, Hansen EF, Satıcıoğlu IB, Duman M, Markussen T, Rimstad E (2018) Infectious pancreatic necrosis virus (IPNV) serotype Sp is prevalent in Turkish rainbow trout farms. J Fish Dis 41(1):95-104. https://doi.org/10.1111/jfd.12675.
- Candan, A. (2002) First report on the diagnosis of infectious pancreatic necrosis (IPN) based on reverse transcription polymerase chain reaction (RT-PCR) in Turkey. Bull Eur Ass Fish Pathol 22(1):45-48.
- Cutrín JM, Barja JL, Nicholson BL, Bandín I, Blake S, Dopazo CP (2004) Restriction fragment length polymorphisms and sequence analysis: an approach for genotyping infectious pancreatic necrosis virus reference strains and other aquabirnaviruses isolated from northwestern Spain. Appl Environ Microbiol 70(2):1059-1067 https://doi.org/10.1128/AEM.70.2.1059–1067.2004.
- Dadar M, Peyghan R, Memari HR, Shapouri MR, Hasanzadeh R, Goudarzi LM, Vakharia VN (2013) Sequence analysis of infectious pancreatic necrosis virus isolated from Iranian reared rainbow trout (Oncorhynchus mykiss) in 2012. Virus Genes 47(3):574-578. https://doi.org/10.1007/s11262-013-0981-4.
- Dobos P and Roberts TE (1983) The molecular biology of infectious pancreatic necrosis virus: a review. Canad J Microb 29(4):377-384. https://doi.org/10.1139/m83-062.
- Gadan K, Sandtrø A, Marjara IS, Santi N, Munang'andu HM, Evensen Ø (2013) Stress-Induced Reversion to Virulence of Infectious Pancreatic Necrosis Virus in Naïve Fry of Atlantic Salmon (Salmo salar L.) PLoS One 8(2): e54656. https://doi.org/10.1371/journal.pone.0054656.
- Graham SC, Sarin LP, Bahar MW, Myers RA, Stuart DI, Bamford DH, Grimes JM (2011) The N-Terminus of the RNA polymerase from infectious pancreatic necrosis virus is the determinant of genome attachment. PLoS Pathog 7(6): e1002085. https://doi.org/10.1371/journal.ppat.1002085.
- Gürçay M, Turan T, Parmaksız A (2013) Türkiye’de Kültürü Yapılan Gökkuşağı Alabalıklarında (Oncorhynchus mykiss Walbaum, 1792) İnfeksiyöz Pankreatik Nekrozis Virus Varlığının Tespiti Üzerine Bir Araştırma. Kafkas Univ Vet Fak Derg 19(1):141-146. https://doi.org/10.9775/kvfd.2012.7396.
- Hill, B. J. and Way, K. (1995) Serological classification of infectious pancreatic necrosis (IPN) virus and other aquatic birnaviruses. Annu Rev Fish Dis 5:55-77. https://doi.org/10.1016/0959-8030(95)00011-9.
- Hong JR, Gong HY, Wu JL (2002) IPNV VP5, a Novel Anti-apoptosis Gene of the Bcl-2 Family, Regulates Mcl-1 and Viral Protein Expression. Virology 295(2):217-229. https://doi.org/10.1006/viro.2001.1336.
- Ji F, Zhao JZ, Liu M, Lu TY, Liu HB, Yin J, Xu LM (2017) Complete genomic sequence of an infectious pancreatic necrosis virus isolated from rainbow trout (Oncorhynchus mykiss) in China. Virus Genes 53(2):215-225. doi: https://doi.org/10.1007/s11262-016-1408-9.
- Julin K, Mennen S, Sommer AI (2013) Study of virulence in field isolates of infectious pancreatic necrosis virus obtained from the northern part of Norway. J Fish Dis 36(2):89-102. https://doi.org/10.1111/j.1365-2761.2012.01423.x.
- Kalaycı G, İnçoğlu Ş, Özyer BÖ, Küçükali Y (2012) Türkiye’de İnfeksiyöz Pankreatik Nekrozis ve Viral Hemorajik Septisemi Hastalıklarının Durumu. Bornova Vet Bil Derg 34(48):31-38.
- Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran S, Thierer T, Ashton B, Meintjes P, Drummond A (2012) Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28(12):1647-1649. https://doi.org/10.1093/bioinformatics/bts199.
- McAllister PE and Owens WJ (1995) Assessment of the virulence of fish and molluscan isolates of infectious pancreatic necrosis virus for salmonid fish by challenge of brook trout, Salvelinus fontinalis (Mitchill). J Fish Dis 18(1973):97-103. https://doi.org/10.1111/j.1365-2761.1995.tb01272.x.
- Mutoloki S and Evensen Ø (2011) Sequence similarities of the capsid gene of Chilean and European isolates of infectious pancreatic necrosis virus point towards a common origin. J Gen Virol 92:1721-1726. https://doi.org/10.1099/vir.0.030270-0
- Nishizawa T, Kinoshita S, Yoshimizu M (2005) An approach for genogrouping of Japanese isolates of aquabirnaviruses in a new genogroup, VII, based on the VP2/NS junction region. J Gen Virol 86 (7):1973-1978. https://doi.org/10.1099/vir.0.80438-0.
- Ogut H and Altuntas C (2012) Occurrence and prevalence of infectious pancreatic necrosis virus in rainbow trout (Oncorhynchus mykiss) cultured in cages in the Black Sea. Aquacult Res 43(10):1550-1556. c10.1111/j.1365-2109.2011.02959.x.
- OIE (2009) Infectious Pancreatic Necrosis in: Manual Of Diagnostic Test for Aquatic Animals. Office International des Épizooties.
- Panzarin V, Holmes EC, Abbadi M, Zamperin G, Quartesan R, Milani A, Schivo A, Bille L, Pozza MD, Monne I, Toffan A (2018) Low evolutionary rate of infectious pancreatic necrosis virus (IPNV) in Italy is associated with reduced virulence in trout. Virus Evol 4(2):1-11. https://doi.org/10.1093/ve/vey019.
- Romero-Brey I, Bandín I, Cutrín JM, Vakharia VN, Dopazo CP (2009) Genetic analysis of aquabirnaviruses isolated from wild fish reveals occurrence of natural reassortment of infectious pancreatic necrosis virus. J Fish Dis 32(7):585-595. doi: 10.1111/j.1365-2761.2009.01020.x.
- Ruane NM, McCarthy LJ, Swords D, Henshilwood K (2009) Molecular differentiation of infectious pancreatic necrosis virus isolates from farmed and wild salmonids in Ireland. J Fish Dis 32(7):585-95.https://doi.org/10.1111/j.1365-2761.2009.01020.x.
- Santi N, Song H, Vakharia VN Evensen O (2005a) Infectious Pancreatic Necrosis Virus VP5 Is Dispensable for Virulence and Persistence. J Virol 79(14):9206-9216. https://doi.org/10.1128/JVI.79.14.9206-9216.2005.
- Santi N, Song H, Vakharia VN and Evensen Ø (2005b) Molecular Determinants of Infectious Pancreatic Necrosis Virus Virulence and Cell Culture Adaptation. J Virol 79(14):9206-9216 https://doi.org/10.1128/JVI.79.16.10289.
- Santi N, Vakharia VN, Evensen Ø (2004) Identification of putative motifs involved in the virulence of infectious pancreatic necrosis virus. Virology 322(1):31-40. https://doi.org/10.1016/j.virol.2003.12.016.
- Shivappa RB, Song H, Yao K, Aas-Eng A, Evensen O, Vakharia VN (2004) Molecular characterization of Sp serotype strains of infectious pancreatic necrosis virus exhibiting differences in virulence. Dis Aquat Organ 61(1-2):23-32. https://doi.org/10.3354/dao061023.
- Toplu N, Albayrak H, Aydogan A, Epikmen ET, Nursal M (2010) Gökkuşağı Alabalıklarında (Oncorhynchus mykiss Walbaum, 1792) Enfeksiyöz Pankreatik Nekrozun Patogenezisinde Apoptozisin Rolü. Ankara Üniv Vet Fak Derg 57(3):191-196. https://doi.org/10.1501/Vetfak_0000002374.
- Williams K, Sweeney A, Nicholson BL (1999) Multiplex Reverse Transcriptase PCR Assay for Simultaneous Detection of Three Fish Viruses. J Clin Microbiol 37(12):4139-4141.
- Wolf K (1988) Fish Viruses and Fish Viral Diseases. Cornell University Press, New York.
Türkiye'den Elde Edilen İnfeksiyöz Pankreatik Nekrozis Virusu İzolatlarının Moleküler Karakterizasyonu ve Tam Genom Analizi
Abstract
İnfeksiyöz Pankreatik Nekrozis Virusu (IPNV), Kuzey Amerika’da 1941 yılındaki ilk tespitinden bu yana uluslararası ticaretin bir sonucu olarak Türkiye de dahil olmak üzere birçok ülkede saptanmıştır. Kayda değer ekonomik kayıplar özellikle altı aylık yaştan küçük balıkların enfekte olmasıyla ortaya çıkmaktadır. Enfeksiyonu oluşturan ajan Birnaviridae ailesi içerisinde yer alan Aquabirnavirus genusuna yer almakta olup 60 nm çapında, ikozahedral simetrili, zarfsız kapside ve iki segmentli ve iki iplikli RNA genoma sahiptir. Segment A VP2, VP3, VP4 ve VP5 proteinlerini, segment B ise bir RNA-bağımlı RNA polimeraz enzimi olan VP1’i kodlamaktadır. Bu çalışmada altı farklı ilden 2004-2013 yılları arasında Türkiye’de toplam altı ilden (Düzce, Şanlıurfa, Tokat, K. Maraş, Trabzon ve Gaziantep) elde edilen IPNV izolatlarının tam genom dizililiminin saptanarak moleküler karakterizasyonunun yapılması amaçlanmıştır. Tam genomik verilerin filogenetik analizi seçilen altı izolatın segment A’ya göre genogrup 5’e, segment B’ye göre grup 1’e dâhil olduğunu ortaya çıkarmıştır. Ayrıca VP2 geninin çok değişken bölgesi üzerinde düşük virülense işaret eden mutasyonlar ve VP5 geni üzerinde nonsense nokta mutasyonlar saptanmıştır. Bu çalışmanın Türkiye’de farklı coğrafik alanlarında sirküle olan IPNV izolatlarının nitelendirilmesine yönelik önemli katkı sağlayabileceği düşünülmektedir.
Keywords
infeksiyöz pankreatik nekrozis virusu sekans analizi filogenetik analiz moleküler karakterizasyon tam genom
References
- Albayrak H and Özan E. (2010) Gökkuşağı alabalıklarında (Oncorhynchus mykiss Walbaum, 1792) Infeksiyöz Pankreatik Nekrozis ve Infeksiyöz Hematopoietik Nekrozis Virus Enfeksiyonlarının Varlığının Araştırılması. Ankara Üniv Vet Fak Derg 57(2):125-129. https://doi.org/10.1501/Vetfak_0000002322.
- Bain N, Gregory A and Raynard RS (2008) Genetic Analysis of Infectious Pancreatic Necrosis Virus From Scotland J Fish Dis 31(1): 37-47. https://doi.org/10.1111/j.1365-2761.2007.00864.x.
- Barrera-Mejía M, Simón-Martínez J, Ulloa-Arvizu R, Salgado-Miranda C, Soriano-Vargas E (2010) Molecular characterization of the VP1 gene of a Mexican isolate of infectious pancreatic necrosis virus. Can J Vet Res 74(3): 218-222.
- Blake S, Ma JY, Caporale DA, Jairath S, Nicholson BL (2001) Phylogenetic relationships of aquatic birnaviruses based on deduced amino acid sequences of genome segment A cDNA. Dis Aquat Organ 45(2):89-102. https://doi.org/10.3354/dao045089.
- Büyükekiz AG, Altun S, Hansen EF, Satıcıoğlu IB, Duman M, Markussen T, Rimstad E (2018) Infectious pancreatic necrosis virus (IPNV) serotype Sp is prevalent in Turkish rainbow trout farms. J Fish Dis 41(1):95-104. https://doi.org/10.1111/jfd.12675.
- Candan, A. (2002) First report on the diagnosis of infectious pancreatic necrosis (IPN) based on reverse transcription polymerase chain reaction (RT-PCR) in Turkey. Bull Eur Ass Fish Pathol 22(1):45-48.
- Cutrín JM, Barja JL, Nicholson BL, Bandín I, Blake S, Dopazo CP (2004) Restriction fragment length polymorphisms and sequence analysis: an approach for genotyping infectious pancreatic necrosis virus reference strains and other aquabirnaviruses isolated from northwestern Spain. Appl Environ Microbiol 70(2):1059-1067 https://doi.org/10.1128/AEM.70.2.1059–1067.2004.
- Dadar M, Peyghan R, Memari HR, Shapouri MR, Hasanzadeh R, Goudarzi LM, Vakharia VN (2013) Sequence analysis of infectious pancreatic necrosis virus isolated from Iranian reared rainbow trout (Oncorhynchus mykiss) in 2012. Virus Genes 47(3):574-578. https://doi.org/10.1007/s11262-013-0981-4.
- Dobos P and Roberts TE (1983) The molecular biology of infectious pancreatic necrosis virus: a review. Canad J Microb 29(4):377-384. https://doi.org/10.1139/m83-062.
- Gadan K, Sandtrø A, Marjara IS, Santi N, Munang'andu HM, Evensen Ø (2013) Stress-Induced Reversion to Virulence of Infectious Pancreatic Necrosis Virus in Naïve Fry of Atlantic Salmon (Salmo salar L.) PLoS One 8(2): e54656. https://doi.org/10.1371/journal.pone.0054656.
- Graham SC, Sarin LP, Bahar MW, Myers RA, Stuart DI, Bamford DH, Grimes JM (2011) The N-Terminus of the RNA polymerase from infectious pancreatic necrosis virus is the determinant of genome attachment. PLoS Pathog 7(6): e1002085. https://doi.org/10.1371/journal.ppat.1002085.
- Gürçay M, Turan T, Parmaksız A (2013) Türkiye’de Kültürü Yapılan Gökkuşağı Alabalıklarında (Oncorhynchus mykiss Walbaum, 1792) İnfeksiyöz Pankreatik Nekrozis Virus Varlığının Tespiti Üzerine Bir Araştırma. Kafkas Univ Vet Fak Derg 19(1):141-146. https://doi.org/10.9775/kvfd.2012.7396.
- Hill, B. J. and Way, K. (1995) Serological classification of infectious pancreatic necrosis (IPN) virus and other aquatic birnaviruses. Annu Rev Fish Dis 5:55-77. https://doi.org/10.1016/0959-8030(95)00011-9.
- Hong JR, Gong HY, Wu JL (2002) IPNV VP5, a Novel Anti-apoptosis Gene of the Bcl-2 Family, Regulates Mcl-1 and Viral Protein Expression. Virology 295(2):217-229. https://doi.org/10.1006/viro.2001.1336.
- Ji F, Zhao JZ, Liu M, Lu TY, Liu HB, Yin J, Xu LM (2017) Complete genomic sequence of an infectious pancreatic necrosis virus isolated from rainbow trout (Oncorhynchus mykiss) in China. Virus Genes 53(2):215-225. doi: https://doi.org/10.1007/s11262-016-1408-9.
- Julin K, Mennen S, Sommer AI (2013) Study of virulence in field isolates of infectious pancreatic necrosis virus obtained from the northern part of Norway. J Fish Dis 36(2):89-102. https://doi.org/10.1111/j.1365-2761.2012.01423.x.
- Kalaycı G, İnçoğlu Ş, Özyer BÖ, Küçükali Y (2012) Türkiye’de İnfeksiyöz Pankreatik Nekrozis ve Viral Hemorajik Septisemi Hastalıklarının Durumu. Bornova Vet Bil Derg 34(48):31-38.
- Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran S, Thierer T, Ashton B, Meintjes P, Drummond A (2012) Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28(12):1647-1649. https://doi.org/10.1093/bioinformatics/bts199.
- McAllister PE and Owens WJ (1995) Assessment of the virulence of fish and molluscan isolates of infectious pancreatic necrosis virus for salmonid fish by challenge of brook trout, Salvelinus fontinalis (Mitchill). J Fish Dis 18(1973):97-103. https://doi.org/10.1111/j.1365-2761.1995.tb01272.x.
- Mutoloki S and Evensen Ø (2011) Sequence similarities of the capsid gene of Chilean and European isolates of infectious pancreatic necrosis virus point towards a common origin. J Gen Virol 92:1721-1726. https://doi.org/10.1099/vir.0.030270-0
- Nishizawa T, Kinoshita S, Yoshimizu M (2005) An approach for genogrouping of Japanese isolates of aquabirnaviruses in a new genogroup, VII, based on the VP2/NS junction region. J Gen Virol 86 (7):1973-1978. https://doi.org/10.1099/vir.0.80438-0.
- Ogut H and Altuntas C (2012) Occurrence and prevalence of infectious pancreatic necrosis virus in rainbow trout (Oncorhynchus mykiss) cultured in cages in the Black Sea. Aquacult Res 43(10):1550-1556. c10.1111/j.1365-2109.2011.02959.x.
- OIE (2009) Infectious Pancreatic Necrosis in: Manual Of Diagnostic Test for Aquatic Animals. Office International des Épizooties.
- Panzarin V, Holmes EC, Abbadi M, Zamperin G, Quartesan R, Milani A, Schivo A, Bille L, Pozza MD, Monne I, Toffan A (2018) Low evolutionary rate of infectious pancreatic necrosis virus (IPNV) in Italy is associated with reduced virulence in trout. Virus Evol 4(2):1-11. https://doi.org/10.1093/ve/vey019.
- Romero-Brey I, Bandín I, Cutrín JM, Vakharia VN, Dopazo CP (2009) Genetic analysis of aquabirnaviruses isolated from wild fish reveals occurrence of natural reassortment of infectious pancreatic necrosis virus. J Fish Dis 32(7):585-595. doi: 10.1111/j.1365-2761.2009.01020.x.
- Ruane NM, McCarthy LJ, Swords D, Henshilwood K (2009) Molecular differentiation of infectious pancreatic necrosis virus isolates from farmed and wild salmonids in Ireland. J Fish Dis 32(7):585-95.https://doi.org/10.1111/j.1365-2761.2009.01020.x.
- Santi N, Song H, Vakharia VN Evensen O (2005a) Infectious Pancreatic Necrosis Virus VP5 Is Dispensable for Virulence and Persistence. J Virol 79(14):9206-9216. https://doi.org/10.1128/JVI.79.14.9206-9216.2005.
- Santi N, Song H, Vakharia VN and Evensen Ø (2005b) Molecular Determinants of Infectious Pancreatic Necrosis Virus Virulence and Cell Culture Adaptation. J Virol 79(14):9206-9216 https://doi.org/10.1128/JVI.79.16.10289.
- Santi N, Vakharia VN, Evensen Ø (2004) Identification of putative motifs involved in the virulence of infectious pancreatic necrosis virus. Virology 322(1):31-40. https://doi.org/10.1016/j.virol.2003.12.016.
- Shivappa RB, Song H, Yao K, Aas-Eng A, Evensen O, Vakharia VN (2004) Molecular characterization of Sp serotype strains of infectious pancreatic necrosis virus exhibiting differences in virulence. Dis Aquat Organ 61(1-2):23-32. https://doi.org/10.3354/dao061023.
- Toplu N, Albayrak H, Aydogan A, Epikmen ET, Nursal M (2010) Gökkuşağı Alabalıklarında (Oncorhynchus mykiss Walbaum, 1792) Enfeksiyöz Pankreatik Nekrozun Patogenezisinde Apoptozisin Rolü. Ankara Üniv Vet Fak Derg 57(3):191-196. https://doi.org/10.1501/Vetfak_0000002374.
- Williams K, Sweeney A, Nicholson BL (1999) Multiplex Reverse Transcriptase PCR Assay for Simultaneous Detection of Three Fish Viruses. J Clin Microbiol 37(12):4139-4141.
- Wolf K (1988) Fish Viruses and Fish Viral Diseases. Cornell University Press, New York.
Details
| Primary Language | English |
|---|---|
| Subjects | Veterinary Surgery |
| Journal Section | Research Article |
| Authors | |
| Publication Date | April 19, 2019 |
| Published in Issue | Year 2019Volume: 1 Issue: 1 |
