First detection and full genome sequence of porcine circovirus type 3 in Russia

Porcine circovirus type 3 (PCV3) was firstly detected in 2016 in USA. Later PCV3 was discovered in Asia, Europe, and South America. The present investigation demonstrates for the first time the circulation of PCV3 among pigs in Russia. The viruses were detected at two geographically distant unrelate...

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Published in:	Virus genes Vol. 54; no. 4; pp. 608 - 611
Main Authors:	Yuzhakov, Anton G., Raev, Sergei A., Alekseev, Konstantin P., Grebennikova, Tatiana V., Verkhovsky, Oleg A., Zaberezhny, Alexei D., Aliper, Taras I.
Format:	Journal Article
Language:	English
Published:	New York Springer US 01.08.2018 Springer Nature B.V
Subjects:	Animals Biomedical and Life Sciences Biomedicine blood serum Circovirus - classification Circovirus - genetics commercial farms Dermatitis DNA Farms fetal death genome Genome, Viral Genomes heart Homology kidney diseases Kidneys Medical Microbiology monophyly Nephropathy Nucleotide sequence nucleotides open reading frames Peritoneum Phylogeny Plant Sciences Pleural effusion polymerase chain reaction Porcine circovirus proteins Reproductive failure RNA, Viral sequence alignment Siberia Spleen Swine Swine Diseases - virology Virology viruses Whole Genome Sequencing Russia Siberia Porcine circovirus Complete genome PCV3 Swine Sequencing
ISSN:	0920-8569, 1572-994X, 1572-994X
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Abstract	Porcine circovirus type 3 (PCV3) was firstly detected in 2016 in USA. Later PCV3 was discovered in Asia, Europe, and South America. The present investigation demonstrates for the first time the circulation of PCV3 among pigs in Russia. The viruses were detected at two geographically distant unrelated commercial farms with records of reproductive failure (abortions, stillbirth), porcine dermatitis, and nephropathy syndrome (PDNS). The two farms were located in the region of Smolensk (western part of Russia) and the region of Tyumen (West Siberia, Russia). We investigated samples collected from pigs of different ages. We performed PCR for the PCV3 DNA detection. The DNA of PCV3 was detected in serum, kidney, heart, spleen, pleural effusion, and peritoneal cavity fluid samples. Two viral genomes were sequenced and the corresponding strains were named PCV3-RU/SM17 (the strain from Smolensk region) and PCV3-RU/TY17 (the strain from Tyumen region). The full genome sequences of both strains were 2000 nucleotides in length and contained at least two ORFs, encoding the Cap and Rep proteins. Full sequence alignment revealed a 99.3% identity between the PCV3-RU/SM17 and PCV3-RU/TY17 strains. Molecular analysis showed that the two strains from Russia are highly homologous to viruses identified in other countries, with a 98.5–99.6% homology for PCV3-RU/TY17 and 97.9–99.0 for PCV3-RU/SM17. The PCV3-RU/SM17 and PCV3-RU/TY17 strains were found to form a monophyletic group in a phylogenetic tree based on PCV3 complete genome sequences.
AbstractList	Porcine circovirus type 3 (PCV3) was firstly detected in 2016 in USA. Later PCV3 was discovered in Asia, Europe, and South America. The present investigation demonstrates for the first time the circulation of PCV3 among pigs in Russia. The viruses were detected at two geographically distant unrelated commercial farms with records of reproductive failure (abortions, stillbirth), porcine dermatitis, and nephropathy syndrome (PDNS). The two farms were located in the region of Smolensk (western part of Russia) and the region of Tyumen (West Siberia, Russia). We investigated samples collected from pigs of different ages. We performed PCR for the PCV3 DNA detection. The DNA of PCV3 was detected in serum, kidney, heart, spleen, pleural effusion, and peritoneal cavity fluid samples. Two viral genomes were sequenced and the corresponding strains were named PCV3-RU/SM17 (the strain from Smolensk region) and PCV3-RU/TY17 (the strain from Tyumen region). The full genome sequences of both strains were 2000 nucleotides in length and contained at least two ORFs, encoding the Cap and Rep proteins. Full sequence alignment revealed a 99.3% identity between the PCV3-RU/SM17 and PCV3-RU/TY17 strains. Molecular analysis showed that the two strains from Russia are highly homologous to viruses identified in other countries, with a 98.5-99.6% homology for PCV3-RU/TY17 and 97.9-99.0 for PCV3-RU/SM17. The PCV3-RU/SM17 and PCV3-RU/TY17 strains were found to form a monophyletic group in a phylogenetic tree based on PCV3 complete genome sequences.Porcine circovirus type 3 (PCV3) was firstly detected in 2016 in USA. Later PCV3 was discovered in Asia, Europe, and South America. The present investigation demonstrates for the first time the circulation of PCV3 among pigs in Russia. The viruses were detected at two geographically distant unrelated commercial farms with records of reproductive failure (abortions, stillbirth), porcine dermatitis, and nephropathy syndrome (PDNS). The two farms were located in the region of Smolensk (western part of Russia) and the region of Tyumen (West Siberia, Russia). We investigated samples collected from pigs of different ages. We performed PCR for the PCV3 DNA detection. The DNA of PCV3 was detected in serum, kidney, heart, spleen, pleural effusion, and peritoneal cavity fluid samples. Two viral genomes were sequenced and the corresponding strains were named PCV3-RU/SM17 (the strain from Smolensk region) and PCV3-RU/TY17 (the strain from Tyumen region). The full genome sequences of both strains were 2000 nucleotides in length and contained at least two ORFs, encoding the Cap and Rep proteins. Full sequence alignment revealed a 99.3% identity between the PCV3-RU/SM17 and PCV3-RU/TY17 strains. Molecular analysis showed that the two strains from Russia are highly homologous to viruses identified in other countries, with a 98.5-99.6% homology for PCV3-RU/TY17 and 97.9-99.0 for PCV3-RU/SM17. The PCV3-RU/SM17 and PCV3-RU/TY17 strains were found to form a monophyletic group in a phylogenetic tree based on PCV3 complete genome sequences. Porcine circovirus type 3 (PCV3) was firstly detected in 2016 in USA. Later PCV3 was discovered in Asia, Europe, and South America. The present investigation demonstrates for the first time the circulation of PCV3 among pigs in Russia. The viruses were detected at two geographically distant unrelated commercial farms with records of reproductive failure (abortions, stillbirth), porcine dermatitis, and nephropathy syndrome (PDNS). The two farms were located in the region of Smolensk (western part of Russia) and the region of Tyumen (West Siberia, Russia). We investigated samples collected from pigs of different ages. We performed PCR for the PCV3 DNA detection. The DNA of PCV3 was detected in serum, kidney, heart, spleen, pleural effusion, and peritoneal cavity fluid samples. Two viral genomes were sequenced and the corresponding strains were named PCV3-RU/SM17 (the strain from Smolensk region) and PCV3-RU/TY17 (the strain from Tyumen region). The full genome sequences of both strains were 2000 nucleotides in length and contained at least two ORFs, encoding the Cap and Rep proteins. Full sequence alignment revealed a 99.3% identity between the PCV3-RU/SM17 and PCV3-RU/TY17 strains. Molecular analysis showed that the two strains from Russia are highly homologous to viruses identified in other countries, with a 98.5-99.6% homology for PCV3-RU/TY17 and 97.9-99.0 for PCV3-RU/SM17. The PCV3-RU/SM17 and PCV3-RU/TY17 strains were found to form a monophyletic group in a phylogenetic tree based on PCV3 complete genome sequences.
Author	Aliper, Taras I. Verkhovsky, Oleg A. Yuzhakov, Anton G. Alekseev, Konstantin P. Zaberezhny, Alexei D. Grebennikova, Tatiana V. Raev, Sergei A.
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References	PalinskiRPineyroPShangPYuanFGuoRFangYByersEHauseBMA novel porcine circovirus distantly related to known circoviruses is associated with porcine dermatitis and nephropathy syndrome and reproductive failureJ Virol201791e01879-1610.1128/JVI.01879-1627795441 ZhengSWuXZhangLThe occurrence of porcine circovirus 3 without clinical infection signs in Shandong ProvinceTransbound Emerg Dis201710.1111/tbed.1266729285888 FuxRSöcklerCLinkFull genome characterization of porcine circovirus type 3 isolates reveals the existence of two distinct groups of virus strainsVirol J2018152510.1186/s12985-018-0929-3293785975789634 KwonTYooSJParkCKLyooYSPrevalence of novel porcine circovirus 3 in Korean pig populationsVet Microbiol201710.1016/j.vetmic.2017.06.01328757021 FacciniSBarbieriIGilioliADetection and genetic characterization of Porcine circovirus type 3 in ItalyTransbound Emerg Dis20172892187010.1111/tbed.12714 FranzoGLegnardiMHjulsagerCKFull-genome sequencing of porcine circovirus 3 field strains from Denmark, Italy and Spain demonstrates a high within-Europe genetic heterogeneityTransbound Emerg Dis201810.1111/tbed.1283630126059 International Committee on Taxonomy of Viruses, A.M.Q. King (2012) Virus taxonomy: classification and nomenclature of viruses. In: Ninth report of the International Committee on Taxonomy of Viruses. Academic Press, London KuXChenFLiPIdentification and genetic characterization of porcine circovirus type 3 in ChinaTransbound Emerg Dis20172831732610.1111/tbed.12638 YeXBergMFossumCDetection and genetic characterisation of porcine circovirus 3 from pigs in SwedenVirus Genes2018595186810.1007/s11262-018-1553-429564688 MadsonDMPattersonARRamamoorthySPalNMengXJOpriessnigTReproductive failure experimentally induced in sows via artificial insemination with semen spiked with porcine circovirus type 2Vet Pathol200946470771610.1354/vp.08-VP-0234-O-FL192760451:STN:280:DC%2BD1Mvks1GisA%3D%3D KumarSStecherGTamuraKMEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasetsMol Biol Evol2016331870187410.1093/molbev/msw054270049041:CAS:528:DC%2BC28XhsF2ltrzN FanSKuXChenFWangYYuXHeQComplete genome sequence of a novel porcine circovirus type 3 strain, PCV3/CN/Hubei-618/2016, isolated from ChinaGenome Announc2017515210.1128/genomeA.00100-17 KedkovidRWoonwongYArunoratJSirisereewanCSangpratumNLumyaiMKesdangsakonwutSTeankumKJittimaneeSThanawongnuwechRPorcine circovirus type 3 (PCV3) infection in grower pigs from a Thai farm suffering from porcine respiratory disease complex (PRDC)Vet Microbiol2018215717610.1016/j.vetmic.2018.01.00429426409 PhanTGGiannittiFRossowSMarthalerDKnutsonTLiLDengXResendeTVannucciFDelwartEDetection of a novel circovirus PCV3 in pigs with cardiac and multi-systemic inflammationVirol J20161318410.1186/s12985-016-0642-z278359425105309 StadejekTWozniakAMiłekDBiernackaKFirst detection of porcine circovirus type 3 on commercial pig farms in PolandTransbound Emerg Dis201710.1111/tbed.1267228649803 CollinsPJMcKillenJAllanGPorcine circovirus type 3 in the UKVet Rec201718159910.1136/vr.j5505291920471:STN:280:DC%2BC1M3ms1egtA%3D%3D TochettoCLimaDAVarelaAPMFull-genome sequence of porcine circovirus type 3 recovered from serum of sows with stillbirths in BrazilTransbound Emerg Dis20172902737210.1111/tbed.12735 ShenHLiuXZhangPGenome characterization of a porcine circovirus type 3 in South ChinaTransbound Emerg Dis201710.1111/tbed.1263928296271 S Kumar (1582_CR18) 2016; 33 1582_CR1 TG Phan (1582_CR3) 2016; 13 X Ye (1582_CR14) 2018 R Kedkovid (1582_CR9) 2018; 215 X Ku (1582_CR5) 2017 G Franzo (1582_CR12) 2018 S Faccini (1582_CR11) 2017 S Zheng (1582_CR7) 2017 T Kwon (1582_CR8) 2017 C Tochetto (1582_CR15) 2017 DM Madson (1582_CR2) 2009; 46 PJ Collins (1582_CR13) 2017; 181 R Palinski (1582_CR16) 2017; 91 S Fan (1582_CR4) 2017; 5 T Stadejek (1582_CR10) 2017 R Fux (1582_CR17) 2018; 15 H Shen (1582_CR6) 2017 28653486 - Transbound Emerg Dis. 2017 Oct;64(5):1337-1341 29378597 - Virol J. 2018 Jan 29;15(1):25 29192047 - Vet Rec. 2017 Dec;181(22):599 27795441 - J Virol. 2016 Dec 16;91(1) 28649803 - Transbound Emerg Dis. 2017 Oct;64(5):1350-1353 28408664 - Genome Announc. 2017 Apr 13;5(15) 28921870 - Transbound Emerg Dis. 2017 Dec;64(6):1661-1664 28317326 - Transbound Emerg Dis. 2017 Jun;64(3):703-708 29426409 - Vet Microbiol. 2018 Feb;215:71-76 19276045 - Vet Pathol. 2009 Jul;46(4):707-16 28296271 - Transbound Emerg Dis. 2018 Feb;65(1):264-266 29027372 - Transbound Emerg Dis. 2018 Feb;65(1):5-9 27835942 - Virol J. 2016 Nov 11;13(1):184 29564688 - Virus Genes. 2018 Jun;54(3):466-469 27004904 - Mol Biol Evol. 2016 Jul;33(7):1870-4 28757021 - Vet Microbiol. 2017 Aug;207:178-180 29453822 - Transbound Emerg Dis. 2018 Jun;65(3):602-606
References_xml	– reference: FranzoGLegnardiMHjulsagerCKFull-genome sequencing of porcine circovirus 3 field strains from Denmark, Italy and Spain demonstrates a high within-Europe genetic heterogeneityTransbound Emerg Dis201810.1111/tbed.1283630126059 – reference: ShenHLiuXZhangPGenome characterization of a porcine circovirus type 3 in South ChinaTransbound Emerg Dis201710.1111/tbed.1263928296271 – reference: YeXBergMFossumCDetection and genetic characterisation of porcine circovirus 3 from pigs in SwedenVirus Genes2018595186810.1007/s11262-018-1553-429564688 – reference: MadsonDMPattersonARRamamoorthySPalNMengXJOpriessnigTReproductive failure experimentally induced in sows via artificial insemination with semen spiked with porcine circovirus type 2Vet Pathol200946470771610.1354/vp.08-VP-0234-O-FL192760451:STN:280:DC%2BD1Mvks1GisA%3D%3D – reference: KedkovidRWoonwongYArunoratJSirisereewanCSangpratumNLumyaiMKesdangsakonwutSTeankumKJittimaneeSThanawongnuwechRPorcine circovirus type 3 (PCV3) infection in grower pigs from a Thai farm suffering from porcine respiratory disease complex (PRDC)Vet Microbiol2018215717610.1016/j.vetmic.2018.01.00429426409 – reference: TochettoCLimaDAVarelaAPMFull-genome sequence of porcine circovirus type 3 recovered from serum of sows with stillbirths in BrazilTransbound Emerg Dis20172902737210.1111/tbed.12735 – reference: FanSKuXChenFWangYYuXHeQComplete genome sequence of a novel porcine circovirus type 3 strain, PCV3/CN/Hubei-618/2016, isolated from ChinaGenome Announc2017515210.1128/genomeA.00100-17 – reference: ZhengSWuXZhangLThe occurrence of porcine circovirus 3 without clinical infection signs in Shandong ProvinceTransbound Emerg Dis201710.1111/tbed.1266729285888 – reference: CollinsPJMcKillenJAllanGPorcine circovirus type 3 in the UKVet Rec201718159910.1136/vr.j5505291920471:STN:280:DC%2BC1M3ms1egtA%3D%3D – reference: International Committee on Taxonomy of Viruses, A.M.Q. King (2012) Virus taxonomy: classification and nomenclature of viruses. In: Ninth report of the International Committee on Taxonomy of Viruses. Academic Press, London – reference: PalinskiRPineyroPShangPYuanFGuoRFangYByersEHauseBMA novel porcine circovirus distantly related to known circoviruses is associated with porcine dermatitis and nephropathy syndrome and reproductive failureJ Virol201791e01879-1610.1128/JVI.01879-1627795441 – reference: StadejekTWozniakAMiłekDBiernackaKFirst detection of porcine circovirus type 3 on commercial pig farms in PolandTransbound Emerg Dis201710.1111/tbed.1267228649803 – reference: KuXChenFLiPIdentification and genetic characterization of porcine circovirus type 3 in ChinaTransbound Emerg Dis20172831732610.1111/tbed.12638 – reference: PhanTGGiannittiFRossowSMarthalerDKnutsonTLiLDengXResendeTVannucciFDelwartEDetection of a novel circovirus PCV3 in pigs with cardiac and multi-systemic inflammationVirol J20161318410.1186/s12985-016-0642-z278359425105309 – reference: FuxRSöcklerCLinkFull genome characterization of porcine circovirus type 3 isolates reveals the existence of two distinct groups of virus strainsVirol J2018152510.1186/s12985-018-0929-3293785975789634 – reference: KumarSStecherGTamuraKMEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasetsMol Biol Evol2016331870187410.1093/molbev/msw054270049041:CAS:528:DC%2BC28XhsF2ltrzN – reference: KwonTYooSJParkCKLyooYSPrevalence of novel porcine circovirus 3 in Korean pig populationsVet Microbiol201710.1016/j.vetmic.2017.06.01328757021 – reference: FacciniSBarbieriIGilioliADetection and genetic characterization of Porcine circovirus type 3 in ItalyTransbound Emerg Dis20172892187010.1111/tbed.12714 – year: 2017 ident: 1582_CR7 publication-title: Transbound Emerg Dis doi: 10.1111/tbed.12667 – year: 2017 ident: 1582_CR8 publication-title: Vet Microbiol doi: 10.1016/j.vetmic.2017.06.013 – year: 2017 ident: 1582_CR10 publication-title: Transbound Emerg Dis doi: 10.1111/tbed.12672 – year: 2018 ident: 1582_CR14 publication-title: Virus Genes doi: 10.1007/s11262-018-1553-4 – volume: 5 start-page: 2 issue: 15 year: 2017 ident: 1582_CR4 publication-title: Genome Announc doi: 10.1128/genomeA.00100-17 – year: 2018 ident: 1582_CR12 publication-title: Transbound Emerg Dis doi: 10.1111/tbed.12836 – year: 2017 ident: 1582_CR5 publication-title: Transbound Emerg Dis doi: 10.1111/tbed.12638 – volume: 33 start-page: 1870 year: 2016 ident: 1582_CR18 publication-title: Mol Biol Evol doi: 10.1093/molbev/msw054 – year: 2017 ident: 1582_CR11 publication-title: Transbound Emerg Dis doi: 10.1111/tbed.12714 – volume: 215 start-page: 71 year: 2018 ident: 1582_CR9 publication-title: Vet Microbiol doi: 10.1016/j.vetmic.2018.01.004 – volume: 91 start-page: e01879-16 year: 2017 ident: 1582_CR16 publication-title: J Virol doi: 10.1128/JVI.01879-16 – volume: 46 start-page: 707 issue: 4 year: 2009 ident: 1582_CR2 publication-title: Vet Pathol doi: 10.1354/vp.08-VP-0234-O-FL – year: 2017 ident: 1582_CR6 publication-title: Transbound Emerg Dis doi: 10.1111/tbed.12639 – volume: 181 start-page: 599 year: 2017 ident: 1582_CR13 publication-title: Vet Rec doi: 10.1136/vr.j5505 – volume: 13 start-page: 184 year: 2016 ident: 1582_CR3 publication-title: Virol J doi: 10.1186/s12985-016-0642-z – year: 2017 ident: 1582_CR15 publication-title: Transbound Emerg Dis doi: 10.1111/tbed.12735 – ident: 1582_CR1 – volume: 15 start-page: 25 year: 2018 ident: 1582_CR17 publication-title: Virol J doi: 10.1186/s12985-018-0929-3 – reference: 28408664 - Genome Announc. 2017 Apr 13;5(15): – reference: 27795441 - J Virol. 2016 Dec 16;91(1): – reference: 28653486 - Transbound Emerg Dis. 2017 Oct;64(5):1337-1341 – reference: 29426409 - Vet Microbiol. 2018 Feb;215:71-76 – reference: 19276045 - Vet Pathol. 2009 Jul;46(4):707-16 – reference: 27835942 - Virol J. 2016 Nov 11;13(1):184 – reference: 29192047 - Vet Rec. 2017 Dec;181(22):599 – reference: 28921870 - Transbound Emerg Dis. 2017 Dec;64(6):1661-1664 – reference: 29453822 - Transbound Emerg Dis. 2018 Jun;65(3):602-606 – reference: 28757021 - Vet Microbiol. 2017 Aug;207:178-180 – reference: 29378597 - Virol J. 2018 Jan 29;15(1):25 – reference: 28649803 - Transbound Emerg Dis. 2017 Oct;64(5):1350-1353 – reference: 29027372 - Transbound Emerg Dis. 2018 Feb;65(1):5-9 – reference: 28296271 - Transbound Emerg Dis. 2018 Feb;65(1):264-266 – reference: 29564688 - Virus Genes. 2018 Jun;54(3):466-469 – reference: 27004904 - Mol Biol Evol. 2016 Jul;33(7):1870-4 – reference: 28317326 - Transbound Emerg Dis. 2017 Jun;64(3):703-708
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Snippet	Porcine circovirus type 3 (PCV3) was firstly detected in 2016 in USA. Later PCV3 was discovered in Asia, Europe, and South America. The present investigation...
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SubjectTerms	Animals Biomedical and Life Sciences Biomedicine blood serum Circovirus - classification Circovirus - genetics commercial farms Dermatitis DNA Farms fetal death genome Genome, Viral Genomes heart Homology kidney diseases Kidneys Medical Microbiology monophyly Nephropathy Nucleotide sequence nucleotides open reading frames Peritoneum Phylogeny Plant Sciences Pleural effusion polymerase chain reaction Porcine circovirus proteins Reproductive failure RNA, Viral sequence alignment Siberia Spleen Swine Swine Diseases - virology Virology viruses Whole Genome Sequencing
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Title	First detection and full genome sequence of porcine circovirus type 3 in Russia
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