Improved strategy for phylogenetic analysis of classical swine fever virus based on full-length E2 encoding sequences

Abstract Molecular epidemiology has proven to be an essential tool in the control of classical swine fever (CSF) and its use has significantly increased during the past two decades. Phylogenetic analysis is a prerequisite for virus tracing and thus allows implementing more effective control measures...
Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Postel, Alexander [verfasserIn] Schmeiser, Stefanie [verfasserIn] Bernau, Jennifer [verfasserIn] Meindl-Boehmer, Alexandra [verfasserIn] Pridotkas, Gediminas [verfasserIn] Dirbakova, Zuzana [verfasserIn] Mojzis, Miroslav [verfasserIn] Becher, Paul [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2012

Schlagwörter:	Wild Boar Classical Swine Fever Virus Classical Swine Fever Isolate Level Short Sequence Length

Übergeordnetes Werk:	Enthalten in: Veterinary research - London : BioMed Central, 1993, 43(2012), 1 vom: 07. Juni
Übergeordnetes Werk:	volume:43 ; year:2012 ; number:1 ; day:07 ; month:06

Links:	Volltext

DOI / URN:	10.1186/1297-9716-43-50

Katalog-ID:	SPR03181526X

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520			\|a Abstract Molecular epidemiology has proven to be an essential tool in the control of classical swine fever (CSF) and its use has significantly increased during the past two decades. Phylogenetic analysis is a prerequisite for virus tracing and thus allows implementing more effective control measures. So far, fragments of the 5´NTR (150 nucleotides, nt) and the E2 gene (190 nt) have frequently been used for phylogenetic analyses. The short sequence lengths represent a limiting factor for differentiation of closely related isolates and also for confidence levels of proposed CSFV groups and subgroups. In this study, we used a set of 33 CSFV isolates in order to determine the nucleotide sequences of a 3508–3510 nt region within the 5´ terminal third of the viral genome. Including 22 additional sequences from GenBank database different regions of the genome, comprising the formerly used short 5´NTR and E2 fragments as well as the genomic regions encoding the individual viral proteins $ N^{pro} $, C, $ E^{rns} $, E1, and E2, were compared with respect to variability and suitability for phylogenetic analysis. Full-length E2 encoding sequences (1119 nt) proved to be most suitable for reliable and statistically significant phylogeny and analyses revealed results as good as obtained with the much longer entire 5´NTR-E2 sequences. This strategy is therefore recommended by the EU and OIE Reference Laboratory for CSF as it provides a solid and improved basis for CSFV molecular epidemiology. Finally, the power of this method is illustrated by the phylogenetic analysis of closely related CSFV isolates from a recent outbreak in Lithuania.
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allfields	10.1186/1297-9716-43-50 doi (DE-627)SPR03181526X (SPR)1297-9716-43-50-e DE-627 ger DE-627 rakwb eng 630 640 ASE 46.00 bkl Postel, Alexander verfasserin aut Improved strategy for phylogenetic analysis of classical swine fever virus based on full-length E2 encoding sequences 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Molecular epidemiology has proven to be an essential tool in the control of classical swine fever (CSF) and its use has significantly increased during the past two decades. Phylogenetic analysis is a prerequisite for virus tracing and thus allows implementing more effective control measures. So far, fragments of the 5´NTR (150 nucleotides, nt) and the E2 gene (190 nt) have frequently been used for phylogenetic analyses. The short sequence lengths represent a limiting factor for differentiation of closely related isolates and also for confidence levels of proposed CSFV groups and subgroups. In this study, we used a set of 33 CSFV isolates in order to determine the nucleotide sequences of a 3508–3510 nt region within the 5´ terminal third of the viral genome. Including 22 additional sequences from GenBank database different regions of the genome, comprising the formerly used short 5´NTR and E2 fragments as well as the genomic regions encoding the individual viral proteins $ N^{pro} $, C, $ E^{rns} $, E1, and E2, were compared with respect to variability and suitability for phylogenetic analysis. Full-length E2 encoding sequences (1119 nt) proved to be most suitable for reliable and statistically significant phylogeny and analyses revealed results as good as obtained with the much longer entire 5´NTR-E2 sequences. This strategy is therefore recommended by the EU and OIE Reference Laboratory for CSF as it provides a solid and improved basis for CSFV molecular epidemiology. Finally, the power of this method is illustrated by the phylogenetic analysis of closely related CSFV isolates from a recent outbreak in Lithuania. Wild Boar (dpeaa)DE-He213 Classical Swine Fever Virus (dpeaa)DE-He213 Classical Swine Fever (dpeaa)DE-He213 Isolate Level (dpeaa)DE-He213 Short Sequence Length (dpeaa)DE-He213 Schmeiser, Stefanie verfasserin aut Bernau, Jennifer verfasserin aut Meindl-Boehmer, Alexandra verfasserin aut Pridotkas, Gediminas verfasserin aut Dirbakova, Zuzana verfasserin aut Mojzis, Miroslav verfasserin aut Becher, Paul verfasserin aut Enthalten in Veterinary research London : BioMed Central, 1993 43(2012), 1 vom: 07. Juni (DE-627)312853653 (DE-600)2012391-7 1297-9716 nnns volume:43 year:2012 number:1 day:07 month:06 https://dx.doi.org/10.1186/1297-9716-43-50 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_213 GBV_ILN_230 GBV_ILN_252 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 46.00 ASE AR 43 2012 1 07 06
spelling	10.1186/1297-9716-43-50 doi (DE-627)SPR03181526X (SPR)1297-9716-43-50-e DE-627 ger DE-627 rakwb eng 630 640 ASE 46.00 bkl Postel, Alexander verfasserin aut Improved strategy for phylogenetic analysis of classical swine fever virus based on full-length E2 encoding sequences 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Molecular epidemiology has proven to be an essential tool in the control of classical swine fever (CSF) and its use has significantly increased during the past two decades. Phylogenetic analysis is a prerequisite for virus tracing and thus allows implementing more effective control measures. So far, fragments of the 5´NTR (150 nucleotides, nt) and the E2 gene (190 nt) have frequently been used for phylogenetic analyses. The short sequence lengths represent a limiting factor for differentiation of closely related isolates and also for confidence levels of proposed CSFV groups and subgroups. In this study, we used a set of 33 CSFV isolates in order to determine the nucleotide sequences of a 3508–3510 nt region within the 5´ terminal third of the viral genome. Including 22 additional sequences from GenBank database different regions of the genome, comprising the formerly used short 5´NTR and E2 fragments as well as the genomic regions encoding the individual viral proteins $ N^{pro} $, C, $ E^{rns} $, E1, and E2, were compared with respect to variability and suitability for phylogenetic analysis. Full-length E2 encoding sequences (1119 nt) proved to be most suitable for reliable and statistically significant phylogeny and analyses revealed results as good as obtained with the much longer entire 5´NTR-E2 sequences. This strategy is therefore recommended by the EU and OIE Reference Laboratory for CSF as it provides a solid and improved basis for CSFV molecular epidemiology. Finally, the power of this method is illustrated by the phylogenetic analysis of closely related CSFV isolates from a recent outbreak in Lithuania. Wild Boar (dpeaa)DE-He213 Classical Swine Fever Virus (dpeaa)DE-He213 Classical Swine Fever (dpeaa)DE-He213 Isolate Level (dpeaa)DE-He213 Short Sequence Length (dpeaa)DE-He213 Schmeiser, Stefanie verfasserin aut Bernau, Jennifer verfasserin aut Meindl-Boehmer, Alexandra verfasserin aut Pridotkas, Gediminas verfasserin aut Dirbakova, Zuzana verfasserin aut Mojzis, Miroslav verfasserin aut Becher, Paul verfasserin aut Enthalten in Veterinary research London : BioMed Central, 1993 43(2012), 1 vom: 07. Juni (DE-627)312853653 (DE-600)2012391-7 1297-9716 nnns volume:43 year:2012 number:1 day:07 month:06 https://dx.doi.org/10.1186/1297-9716-43-50 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_213 GBV_ILN_230 GBV_ILN_252 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 46.00 ASE AR 43 2012 1 07 06
allfields_unstemmed	10.1186/1297-9716-43-50 doi (DE-627)SPR03181526X (SPR)1297-9716-43-50-e DE-627 ger DE-627 rakwb eng 630 640 ASE 46.00 bkl Postel, Alexander verfasserin aut Improved strategy for phylogenetic analysis of classical swine fever virus based on full-length E2 encoding sequences 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Molecular epidemiology has proven to be an essential tool in the control of classical swine fever (CSF) and its use has significantly increased during the past two decades. Phylogenetic analysis is a prerequisite for virus tracing and thus allows implementing more effective control measures. So far, fragments of the 5´NTR (150 nucleotides, nt) and the E2 gene (190 nt) have frequently been used for phylogenetic analyses. The short sequence lengths represent a limiting factor for differentiation of closely related isolates and also for confidence levels of proposed CSFV groups and subgroups. In this study, we used a set of 33 CSFV isolates in order to determine the nucleotide sequences of a 3508–3510 nt region within the 5´ terminal third of the viral genome. Including 22 additional sequences from GenBank database different regions of the genome, comprising the formerly used short 5´NTR and E2 fragments as well as the genomic regions encoding the individual viral proteins $ N^{pro} $, C, $ E^{rns} $, E1, and E2, were compared with respect to variability and suitability for phylogenetic analysis. Full-length E2 encoding sequences (1119 nt) proved to be most suitable for reliable and statistically significant phylogeny and analyses revealed results as good as obtained with the much longer entire 5´NTR-E2 sequences. This strategy is therefore recommended by the EU and OIE Reference Laboratory for CSF as it provides a solid and improved basis for CSFV molecular epidemiology. Finally, the power of this method is illustrated by the phylogenetic analysis of closely related CSFV isolates from a recent outbreak in Lithuania. Wild Boar (dpeaa)DE-He213 Classical Swine Fever Virus (dpeaa)DE-He213 Classical Swine Fever (dpeaa)DE-He213 Isolate Level (dpeaa)DE-He213 Short Sequence Length (dpeaa)DE-He213 Schmeiser, Stefanie verfasserin aut Bernau, Jennifer verfasserin aut Meindl-Boehmer, Alexandra verfasserin aut Pridotkas, Gediminas verfasserin aut Dirbakova, Zuzana verfasserin aut Mojzis, Miroslav verfasserin aut Becher, Paul verfasserin aut Enthalten in Veterinary research London : BioMed Central, 1993 43(2012), 1 vom: 07. Juni (DE-627)312853653 (DE-600)2012391-7 1297-9716 nnns volume:43 year:2012 number:1 day:07 month:06 https://dx.doi.org/10.1186/1297-9716-43-50 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_213 GBV_ILN_230 GBV_ILN_252 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 46.00 ASE AR 43 2012 1 07 06
allfieldsGer	10.1186/1297-9716-43-50 doi (DE-627)SPR03181526X (SPR)1297-9716-43-50-e DE-627 ger DE-627 rakwb eng 630 640 ASE 46.00 bkl Postel, Alexander verfasserin aut Improved strategy for phylogenetic analysis of classical swine fever virus based on full-length E2 encoding sequences 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Molecular epidemiology has proven to be an essential tool in the control of classical swine fever (CSF) and its use has significantly increased during the past two decades. Phylogenetic analysis is a prerequisite for virus tracing and thus allows implementing more effective control measures. So far, fragments of the 5´NTR (150 nucleotides, nt) and the E2 gene (190 nt) have frequently been used for phylogenetic analyses. The short sequence lengths represent a limiting factor for differentiation of closely related isolates and also for confidence levels of proposed CSFV groups and subgroups. In this study, we used a set of 33 CSFV isolates in order to determine the nucleotide sequences of a 3508–3510 nt region within the 5´ terminal third of the viral genome. Including 22 additional sequences from GenBank database different regions of the genome, comprising the formerly used short 5´NTR and E2 fragments as well as the genomic regions encoding the individual viral proteins $ N^{pro} $, C, $ E^{rns} $, E1, and E2, were compared with respect to variability and suitability for phylogenetic analysis. Full-length E2 encoding sequences (1119 nt) proved to be most suitable for reliable and statistically significant phylogeny and analyses revealed results as good as obtained with the much longer entire 5´NTR-E2 sequences. This strategy is therefore recommended by the EU and OIE Reference Laboratory for CSF as it provides a solid and improved basis for CSFV molecular epidemiology. Finally, the power of this method is illustrated by the phylogenetic analysis of closely related CSFV isolates from a recent outbreak in Lithuania. Wild Boar (dpeaa)DE-He213 Classical Swine Fever Virus (dpeaa)DE-He213 Classical Swine Fever (dpeaa)DE-He213 Isolate Level (dpeaa)DE-He213 Short Sequence Length (dpeaa)DE-He213 Schmeiser, Stefanie verfasserin aut Bernau, Jennifer verfasserin aut Meindl-Boehmer, Alexandra verfasserin aut Pridotkas, Gediminas verfasserin aut Dirbakova, Zuzana verfasserin aut Mojzis, Miroslav verfasserin aut Becher, Paul verfasserin aut Enthalten in Veterinary research London : BioMed Central, 1993 43(2012), 1 vom: 07. Juni (DE-627)312853653 (DE-600)2012391-7 1297-9716 nnns volume:43 year:2012 number:1 day:07 month:06 https://dx.doi.org/10.1186/1297-9716-43-50 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_213 GBV_ILN_230 GBV_ILN_252 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 46.00 ASE AR 43 2012 1 07 06
allfieldsSound	10.1186/1297-9716-43-50 doi (DE-627)SPR03181526X (SPR)1297-9716-43-50-e DE-627 ger DE-627 rakwb eng 630 640 ASE 46.00 bkl Postel, Alexander verfasserin aut Improved strategy for phylogenetic analysis of classical swine fever virus based on full-length E2 encoding sequences 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Molecular epidemiology has proven to be an essential tool in the control of classical swine fever (CSF) and its use has significantly increased during the past two decades. Phylogenetic analysis is a prerequisite for virus tracing and thus allows implementing more effective control measures. So far, fragments of the 5´NTR (150 nucleotides, nt) and the E2 gene (190 nt) have frequently been used for phylogenetic analyses. The short sequence lengths represent a limiting factor for differentiation of closely related isolates and also for confidence levels of proposed CSFV groups and subgroups. In this study, we used a set of 33 CSFV isolates in order to determine the nucleotide sequences of a 3508–3510 nt region within the 5´ terminal third of the viral genome. Including 22 additional sequences from GenBank database different regions of the genome, comprising the formerly used short 5´NTR and E2 fragments as well as the genomic regions encoding the individual viral proteins $ N^{pro} $, C, $ E^{rns} $, E1, and E2, were compared with respect to variability and suitability for phylogenetic analysis. Full-length E2 encoding sequences (1119 nt) proved to be most suitable for reliable and statistically significant phylogeny and analyses revealed results as good as obtained with the much longer entire 5´NTR-E2 sequences. This strategy is therefore recommended by the EU and OIE Reference Laboratory for CSF as it provides a solid and improved basis for CSFV molecular epidemiology. Finally, the power of this method is illustrated by the phylogenetic analysis of closely related CSFV isolates from a recent outbreak in Lithuania. Wild Boar (dpeaa)DE-He213 Classical Swine Fever Virus (dpeaa)DE-He213 Classical Swine Fever (dpeaa)DE-He213 Isolate Level (dpeaa)DE-He213 Short Sequence Length (dpeaa)DE-He213 Schmeiser, Stefanie verfasserin aut Bernau, Jennifer verfasserin aut Meindl-Boehmer, Alexandra verfasserin aut Pridotkas, Gediminas verfasserin aut Dirbakova, Zuzana verfasserin aut Mojzis, Miroslav verfasserin aut Becher, Paul verfasserin aut Enthalten in Veterinary research London : BioMed Central, 1993 43(2012), 1 vom: 07. Juni (DE-627)312853653 (DE-600)2012391-7 1297-9716 nnns volume:43 year:2012 number:1 day:07 month:06 https://dx.doi.org/10.1186/1297-9716-43-50 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_213 GBV_ILN_230 GBV_ILN_252 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 46.00 ASE AR 43 2012 1 07 06
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source	Enthalten in Veterinary research 43(2012), 1 vom: 07. Juni volume:43 year:2012 number:1 day:07 month:06
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author	Postel, Alexander
spellingShingle	Postel, Alexander ddc 630 bkl 46.00 misc Wild Boar misc Classical Swine Fever Virus misc Classical Swine Fever misc Isolate Level misc Short Sequence Length Improved strategy for phylogenetic analysis of classical swine fever virus based on full-length E2 encoding sequences
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topic_title	630 640 ASE 46.00 bkl Improved strategy for phylogenetic analysis of classical swine fever virus based on full-length E2 encoding sequences Wild Boar (dpeaa)DE-He213 Classical Swine Fever Virus (dpeaa)DE-He213 Classical Swine Fever (dpeaa)DE-He213 Isolate Level (dpeaa)DE-He213 Short Sequence Length (dpeaa)DE-He213
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title	Improved strategy for phylogenetic analysis of classical swine fever virus based on full-length E2 encoding sequences
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title_full	Improved strategy for phylogenetic analysis of classical swine fever virus based on full-length E2 encoding sequences
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title_sort	improved strategy for phylogenetic analysis of classical swine fever virus based on full-length e2 encoding sequences
title_auth	Improved strategy for phylogenetic analysis of classical swine fever virus based on full-length E2 encoding sequences
abstract	Abstract Molecular epidemiology has proven to be an essential tool in the control of classical swine fever (CSF) and its use has significantly increased during the past two decades. Phylogenetic analysis is a prerequisite for virus tracing and thus allows implementing more effective control measures. So far, fragments of the 5´NTR (150 nucleotides, nt) and the E2 gene (190 nt) have frequently been used for phylogenetic analyses. The short sequence lengths represent a limiting factor for differentiation of closely related isolates and also for confidence levels of proposed CSFV groups and subgroups. In this study, we used a set of 33 CSFV isolates in order to determine the nucleotide sequences of a 3508–3510 nt region within the 5´ terminal third of the viral genome. Including 22 additional sequences from GenBank database different regions of the genome, comprising the formerly used short 5´NTR and E2 fragments as well as the genomic regions encoding the individual viral proteins $ N^{pro} $, C, $ E^{rns} $, E1, and E2, were compared with respect to variability and suitability for phylogenetic analysis. Full-length E2 encoding sequences (1119 nt) proved to be most suitable for reliable and statistically significant phylogeny and analyses revealed results as good as obtained with the much longer entire 5´NTR-E2 sequences. This strategy is therefore recommended by the EU and OIE Reference Laboratory for CSF as it provides a solid and improved basis for CSFV molecular epidemiology. Finally, the power of this method is illustrated by the phylogenetic analysis of closely related CSFV isolates from a recent outbreak in Lithuania.
abstractGer	Abstract Molecular epidemiology has proven to be an essential tool in the control of classical swine fever (CSF) and its use has significantly increased during the past two decades. Phylogenetic analysis is a prerequisite for virus tracing and thus allows implementing more effective control measures. So far, fragments of the 5´NTR (150 nucleotides, nt) and the E2 gene (190 nt) have frequently been used for phylogenetic analyses. The short sequence lengths represent a limiting factor for differentiation of closely related isolates and also for confidence levels of proposed CSFV groups and subgroups. In this study, we used a set of 33 CSFV isolates in order to determine the nucleotide sequences of a 3508–3510 nt region within the 5´ terminal third of the viral genome. Including 22 additional sequences from GenBank database different regions of the genome, comprising the formerly used short 5´NTR and E2 fragments as well as the genomic regions encoding the individual viral proteins $ N^{pro} $, C, $ E^{rns} $, E1, and E2, were compared with respect to variability and suitability for phylogenetic analysis. Full-length E2 encoding sequences (1119 nt) proved to be most suitable for reliable and statistically significant phylogeny and analyses revealed results as good as obtained with the much longer entire 5´NTR-E2 sequences. This strategy is therefore recommended by the EU and OIE Reference Laboratory for CSF as it provides a solid and improved basis for CSFV molecular epidemiology. Finally, the power of this method is illustrated by the phylogenetic analysis of closely related CSFV isolates from a recent outbreak in Lithuania.
abstract_unstemmed	Abstract Molecular epidemiology has proven to be an essential tool in the control of classical swine fever (CSF) and its use has significantly increased during the past two decades. Phylogenetic analysis is a prerequisite for virus tracing and thus allows implementing more effective control measures. So far, fragments of the 5´NTR (150 nucleotides, nt) and the E2 gene (190 nt) have frequently been used for phylogenetic analyses. The short sequence lengths represent a limiting factor for differentiation of closely related isolates and also for confidence levels of proposed CSFV groups and subgroups. In this study, we used a set of 33 CSFV isolates in order to determine the nucleotide sequences of a 3508–3510 nt region within the 5´ terminal third of the viral genome. Including 22 additional sequences from GenBank database different regions of the genome, comprising the formerly used short 5´NTR and E2 fragments as well as the genomic regions encoding the individual viral proteins $ N^{pro} $, C, $ E^{rns} $, E1, and E2, were compared with respect to variability and suitability for phylogenetic analysis. Full-length E2 encoding sequences (1119 nt) proved to be most suitable for reliable and statistically significant phylogeny and analyses revealed results as good as obtained with the much longer entire 5´NTR-E2 sequences. This strategy is therefore recommended by the EU and OIE Reference Laboratory for CSF as it provides a solid and improved basis for CSFV molecular epidemiology. Finally, the power of this method is illustrated by the phylogenetic analysis of closely related CSFV isolates from a recent outbreak in Lithuania.
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title_short	Improved strategy for phylogenetic analysis of classical swine fever virus based on full-length E2 encoding sequences
url	https://dx.doi.org/10.1186/1297-9716-43-50
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author2	Schmeiser, Stefanie Bernau, Jennifer Meindl-Boehmer, Alexandra Pridotkas, Gediminas Dirbakova, Zuzana Mojzis, Miroslav Becher, Paul
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Phylogenetic analysis is a prerequisite for virus tracing and thus allows implementing more effective control measures. So far, fragments of the 5´NTR (150 nucleotides, nt) and the E2 gene (190 nt) have frequently been used for phylogenetic analyses. The short sequence lengths represent a limiting factor for differentiation of closely related isolates and also for confidence levels of proposed CSFV groups and subgroups. In this study, we used a set of 33 CSFV isolates in order to determine the nucleotide sequences of a 3508–3510 nt region within the 5´ terminal third of the viral genome. Including 22 additional sequences from GenBank database different regions of the genome, comprising the formerly used short 5´NTR and E2 fragments as well as the genomic regions encoding the individual viral proteins $ N^{pro} $, C, $ E^{rns} $, E1, and E2, were compared with respect to variability and suitability for phylogenetic analysis. Full-length E2 encoding sequences (1119 nt) proved to be most suitable for reliable and statistically significant phylogeny and analyses revealed results as good as obtained with the much longer entire 5´NTR-E2 sequences. This strategy is therefore recommended by the EU and OIE Reference Laboratory for CSF as it provides a solid and improved basis for CSFV molecular epidemiology. 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Improved strategy for phylogenetic analysis of classical swine fever virus based on full-length E2 encoding sequences

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