Genetic Characterization of Circulating African Swine Fever Viruses in Nigeria (2007–2015)
Summary Sequencing and analysis of three discrete genome regions of African swine fever viruses (ASFV) from archival samples collected in 2007–2011 and active and passive surveillance between 2012 and 2015 in Nigeria were carried out. Analysis was conducted by genotyping of three single‐copy African...
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| Veröffentlicht in: | Transboundary and emerging diseases 2017-10, Vol.64 (5), p.1598-1609 |
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| creator | Luka, P. D. Achenbach, J. E. Mwiine, F. N. Lamien, C. E. Shamaki, D. Unger, H. Erume, J. |
| description | Summary
Sequencing and analysis of three discrete genome regions of African swine fever viruses (ASFV) from archival samples collected in 2007–2011 and active and passive surveillance between 2012 and 2015 in Nigeria were carried out. Analysis was conducted by genotyping of three single‐copy African swine fever (ASF) genes. The E183L and B646L genes that encode structural proteins p54 and p72, respectively, were utilized to delineate genotypes before intragenotypic resolution by characterization of the tetrameric amino acid repeat region within the hypervariable central variable region of the B602L gene. The results showed no variation in the p72 and p54 gene regions sequenced. Phylogeny of p72 sequences revealed that all the Nigerian isolates belonged to genotype I, while that of the p54 recovered the Ia genotype. Analysis of B602L gene revealed the differences in the number of tetrameric repeats. Four new variants (Tet‐15, Tet‐17a, Tet‐17b and Tet‐48) were recovered, while a fifth variant (Tet‐20) was the most widely distributed in the country displacing Tet‐36 reported previously in 2003–2006. The viruses responsible for ASF outbreaks in Nigeria are from very closely related but mutated variants of the virus that have been circulating since 1997. A practical implication of the genetic variability of the Nigerian viral isolates in this study is the need for continuous sampling and analysis of circulating viruses, which will provide epidemiological information on the evolution of ASFV in the field versus new incursion for informed strategic control of the disease in the country. |
| doi_str_mv | 10.1111/tbed.12553 |
| format | Article |
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Sequencing and analysis of three discrete genome regions of African swine fever viruses (ASFV) from archival samples collected in 2007–2011 and active and passive surveillance between 2012 and 2015 in Nigeria were carried out. Analysis was conducted by genotyping of three single‐copy African swine fever (ASF) genes. The E183L and B646L genes that encode structural proteins p54 and p72, respectively, were utilized to delineate genotypes before intragenotypic resolution by characterization of the tetrameric amino acid repeat region within the hypervariable central variable region of the B602L gene. The results showed no variation in the p72 and p54 gene regions sequenced. Phylogeny of p72 sequences revealed that all the Nigerian isolates belonged to genotype I, while that of the p54 recovered the Ia genotype. Analysis of B602L gene revealed the differences in the number of tetrameric repeats. Four new variants (Tet‐15, Tet‐17a, Tet‐17b and Tet‐48) were recovered, while a fifth variant (Tet‐20) was the most widely distributed in the country displacing Tet‐36 reported previously in 2003–2006. The viruses responsible for ASF outbreaks in Nigeria are from very closely related but mutated variants of the virus that have been circulating since 1997. A practical implication of the genetic variability of the Nigerian viral isolates in this study is the need for continuous sampling and analysis of circulating viruses, which will provide epidemiological information on the evolution of ASFV in the field versus new incursion for informed strategic control of the disease in the country.</description><identifier>ISSN: 1865-1674</identifier><identifier>EISSN: 1865-1682</identifier><identifier>DOI: 10.1111/tbed.12553</identifier><identifier>PMID: 27480888</identifier><language>eng</language><publisher>Germany: Hindawi Limited</publisher><subject>African swine fever ; African Swine Fever - epidemiology ; African Swine Fever - virology ; African swine fever virus ; African Swine Fever Virus - genetics ; African Swine Fever Virus - isolation & purification ; Amino acid sequence ; Animals ; Base Sequence ; CVR ; Disease control ; Disease Outbreaks ; Epidemiology ; Fever ; Gene Expression Regulation, Viral ; Gene sequencing ; Genes ; Genetic variability ; Genetic Variation ; Genomes ; Genotype ; Genotypes ; Genotyping ; Livestock ; Nigeria ; Nigeria - epidemiology ; Outbreaks ; p54 ; p72 ; Phylogeny ; Proteins ; Sequence Analysis, DNA ; Structural proteins ; Swine ; Variable region ; Viral Structural Proteins - genetics ; Viral Structural Proteins - metabolism ; Viruses</subject><ispartof>Transboundary and emerging diseases, 2017-10, Vol.64 (5), p.1598-1609</ispartof><rights>2016 Blackwell Verlag GmbH</rights><rights>2016 Blackwell Verlag GmbH.</rights><rights>Copyright © 2017 Blackwell Verlag GmbH</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3933-7ca5965807b3ceafcf404e142afa8bd141af605ac091510571cd7ad0e4b1b17d3</citedby><cites>FETCH-LOGICAL-c3933-7ca5965807b3ceafcf404e142afa8bd141af605ac091510571cd7ad0e4b1b17d3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Ftbed.12553$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Ftbed.12553$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1416,27923,27924,45573,45574</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27480888$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Luka, P. D.</creatorcontrib><creatorcontrib>Achenbach, J. E.</creatorcontrib><creatorcontrib>Mwiine, F. N.</creatorcontrib><creatorcontrib>Lamien, C. E.</creatorcontrib><creatorcontrib>Shamaki, D.</creatorcontrib><creatorcontrib>Unger, H.</creatorcontrib><creatorcontrib>Erume, J.</creatorcontrib><title>Genetic Characterization of Circulating African Swine Fever Viruses in Nigeria (2007–2015)</title><title>Transboundary and emerging diseases</title><addtitle>Transbound Emerg Dis</addtitle><description>Summary
Sequencing and analysis of three discrete genome regions of African swine fever viruses (ASFV) from archival samples collected in 2007–2011 and active and passive surveillance between 2012 and 2015 in Nigeria were carried out. Analysis was conducted by genotyping of three single‐copy African swine fever (ASF) genes. The E183L and B646L genes that encode structural proteins p54 and p72, respectively, were utilized to delineate genotypes before intragenotypic resolution by characterization of the tetrameric amino acid repeat region within the hypervariable central variable region of the B602L gene. The results showed no variation in the p72 and p54 gene regions sequenced. Phylogeny of p72 sequences revealed that all the Nigerian isolates belonged to genotype I, while that of the p54 recovered the Ia genotype. Analysis of B602L gene revealed the differences in the number of tetrameric repeats. Four new variants (Tet‐15, Tet‐17a, Tet‐17b and Tet‐48) were recovered, while a fifth variant (Tet‐20) was the most widely distributed in the country displacing Tet‐36 reported previously in 2003–2006. The viruses responsible for ASF outbreaks in Nigeria are from very closely related but mutated variants of the virus that have been circulating since 1997. A practical implication of the genetic variability of the Nigerian viral isolates in this study is the need for continuous sampling and analysis of circulating viruses, which will provide epidemiological information on the evolution of ASFV in the field versus new incursion for informed strategic control of the disease in the country.</description><subject>African swine fever</subject><subject>African Swine Fever - epidemiology</subject><subject>African Swine Fever - virology</subject><subject>African swine fever virus</subject><subject>African Swine Fever Virus - genetics</subject><subject>African Swine Fever Virus - isolation & purification</subject><subject>Amino acid sequence</subject><subject>Animals</subject><subject>Base Sequence</subject><subject>CVR</subject><subject>Disease control</subject><subject>Disease Outbreaks</subject><subject>Epidemiology</subject><subject>Fever</subject><subject>Gene Expression Regulation, Viral</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic variability</subject><subject>Genetic Variation</subject><subject>Genomes</subject><subject>Genotype</subject><subject>Genotypes</subject><subject>Genotyping</subject><subject>Livestock</subject><subject>Nigeria</subject><subject>Nigeria - epidemiology</subject><subject>Outbreaks</subject><subject>p54</subject><subject>p72</subject><subject>Phylogeny</subject><subject>Proteins</subject><subject>Sequence Analysis, DNA</subject><subject>Structural proteins</subject><subject>Swine</subject><subject>Variable region</subject><subject>Viral Structural Proteins - genetics</subject><subject>Viral Structural Proteins - metabolism</subject><subject>Viruses</subject><issn>1865-1674</issn><issn>1865-1682</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kMtO3TAQhq2qqFDopg9QWWIDSAdm4jh2lvRwlRAsuKwqWY4zAaOcBOykiK54B96QJ8FwgAWLzmYu-ubXr5-xnwibmGprqKjexExK8YUtoS7kBAudff2YVb7Ivsd4DVBAWchvbDFTuQat9RL7s08dDd7x6ZUN1g0U_D87-L7jfcOnPrixTWt3ybeb4J3t-Omd74jv0V8K_MKHMVLkvuPH_jK9Wr6WAainh8cMUK6vsIXGtpF-vPVldr63ezY9mByd7B9Ot48mTpRCTJSzMvnSoCrhyDauySEnzDPbWF3VmKNtCpDWQYkSQSp0tbI1UF5hhaoWy2xtrnsT-tuR4mBmPjpqW9tRP0aDOiuUKDVCQlc_odf9GLrkzmAp8hIBhUzUxpxyoY8xUGNugp_ZcG8QzEvm5iVz85p5gn-9SY7VLF3f0feQE4Bz4M63dP8fKXP2e3dnLvoMGLCKcA</recordid><startdate>201710</startdate><enddate>201710</enddate><creator>Luka, P. D.</creator><creator>Achenbach, J. E.</creator><creator>Mwiine, F. N.</creator><creator>Lamien, C. E.</creator><creator>Shamaki, D.</creator><creator>Unger, H.</creator><creator>Erume, J.</creator><general>Hindawi Limited</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7T7</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>M7N</scope><scope>P64</scope><scope>7X8</scope></search><sort><creationdate>201710</creationdate><title>Genetic Characterization of Circulating African Swine Fever Viruses in Nigeria (2007–2015)</title><author>Luka, P. D. ; Achenbach, J. E. ; Mwiine, F. N. ; Lamien, C. E. ; Shamaki, D. ; Unger, H. ; Erume, J.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3933-7ca5965807b3ceafcf404e142afa8bd141af605ac091510571cd7ad0e4b1b17d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>African swine fever</topic><topic>African Swine Fever - epidemiology</topic><topic>African Swine Fever - virology</topic><topic>African swine fever virus</topic><topic>African Swine Fever Virus - genetics</topic><topic>African Swine Fever Virus - isolation & purification</topic><topic>Amino acid sequence</topic><topic>Animals</topic><topic>Base Sequence</topic><topic>CVR</topic><topic>Disease control</topic><topic>Disease Outbreaks</topic><topic>Epidemiology</topic><topic>Fever</topic><topic>Gene Expression Regulation, Viral</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genetic variability</topic><topic>Genetic Variation</topic><topic>Genomes</topic><topic>Genotype</topic><topic>Genotypes</topic><topic>Genotyping</topic><topic>Livestock</topic><topic>Nigeria</topic><topic>Nigeria - epidemiology</topic><topic>Outbreaks</topic><topic>p54</topic><topic>p72</topic><topic>Phylogeny</topic><topic>Proteins</topic><topic>Sequence Analysis, DNA</topic><topic>Structural proteins</topic><topic>Swine</topic><topic>Variable region</topic><topic>Viral Structural Proteins - genetics</topic><topic>Viral Structural Proteins - metabolism</topic><topic>Viruses</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Luka, P. D.</creatorcontrib><creatorcontrib>Achenbach, J. E.</creatorcontrib><creatorcontrib>Mwiine, F. N.</creatorcontrib><creatorcontrib>Lamien, C. 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D.</au><au>Achenbach, J. E.</au><au>Mwiine, F. N.</au><au>Lamien, C. E.</au><au>Shamaki, D.</au><au>Unger, H.</au><au>Erume, J.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genetic Characterization of Circulating African Swine Fever Viruses in Nigeria (2007–2015)</atitle><jtitle>Transboundary and emerging diseases</jtitle><addtitle>Transbound Emerg Dis</addtitle><date>2017-10</date><risdate>2017</risdate><volume>64</volume><issue>5</issue><spage>1598</spage><epage>1609</epage><pages>1598-1609</pages><issn>1865-1674</issn><eissn>1865-1682</eissn><abstract>Summary
Sequencing and analysis of three discrete genome regions of African swine fever viruses (ASFV) from archival samples collected in 2007–2011 and active and passive surveillance between 2012 and 2015 in Nigeria were carried out. Analysis was conducted by genotyping of three single‐copy African swine fever (ASF) genes. The E183L and B646L genes that encode structural proteins p54 and p72, respectively, were utilized to delineate genotypes before intragenotypic resolution by characterization of the tetrameric amino acid repeat region within the hypervariable central variable region of the B602L gene. The results showed no variation in the p72 and p54 gene regions sequenced. Phylogeny of p72 sequences revealed that all the Nigerian isolates belonged to genotype I, while that of the p54 recovered the Ia genotype. Analysis of B602L gene revealed the differences in the number of tetrameric repeats. Four new variants (Tet‐15, Tet‐17a, Tet‐17b and Tet‐48) were recovered, while a fifth variant (Tet‐20) was the most widely distributed in the country displacing Tet‐36 reported previously in 2003–2006. The viruses responsible for ASF outbreaks in Nigeria are from very closely related but mutated variants of the virus that have been circulating since 1997. A practical implication of the genetic variability of the Nigerian viral isolates in this study is the need for continuous sampling and analysis of circulating viruses, which will provide epidemiological information on the evolution of ASFV in the field versus new incursion for informed strategic control of the disease in the country.</abstract><cop>Germany</cop><pub>Hindawi Limited</pub><pmid>27480888</pmid><doi>10.1111/tbed.12553</doi><tpages>12</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | African swine fever African Swine Fever - epidemiology African Swine Fever - virology African swine fever virus African Swine Fever Virus - genetics African Swine Fever Virus - isolation & purification Amino acid sequence Animals Base Sequence CVR Disease control Disease Outbreaks Epidemiology Fever Gene Expression Regulation, Viral Gene sequencing Genes Genetic variability Genetic Variation Genomes Genotype Genotypes Genotyping Livestock Nigeria Nigeria - epidemiology Outbreaks p54 p72 Phylogeny Proteins Sequence Analysis, DNA Structural proteins Swine Variable region Viral Structural Proteins - genetics Viral Structural Proteins - metabolism Viruses |
| title | Genetic Characterization of Circulating African Swine Fever Viruses in Nigeria (2007–2015) |
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