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Analysis of new isolates reveals new genome organization and a hypervariable region in infectious myonecrosis virus (IMNV)
•Additional sequences revealed that IMNV genome has at least 8226bp and not 7561bp.•These additional sequences affect the sizes predicted for 5′ UTR, 3′ UTR and ORF1.•A polymorphism map based in the genome alignment of seven sequences reveals a hypervariable region in IMNV genome.•The hypervariable...
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| Published in: | Virus research 2015-05, Vol.203, p.66-71 |
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| container_title | Virus research |
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| creator | Dantas, Márcia Danielle A. Chavante, Suely F. Teixeira, Dárlio Inácio A. Lima, João Paulo M.S. Lanza, Daniel C.F. |
| description | •Additional sequences revealed that IMNV genome has at least 8226bp and not 7561bp.•These additional sequences affect the sizes predicted for 5′ UTR, 3′ UTR and ORF1.•A polymorphism map based in the genome alignment of seven sequences reveals a hypervariable region in IMNV genome.•The hypervariable region coincides with the region that encodes virion protrusions.
Infectious myonecrosis virus (IMNV) has been the cause of many losses in shrimp farming since 2002, when the first myonecrosis outbreak was reported at Brazilian's northeast coast. Two additional genomes of Brazilian IMNV isolates collected in 2009 and 2013 were sequenced and analyzed in the present study. The sequencing revealed extra 643bp and 22bp, at 5′ and 3′ ends of IMNV genome respectively, confirming that its actual size is at least 8226bp long. Considering these additional sequences in genome extremities, ORF1 can starts at nt 470, encoding a 1708 aa polyprotein. Computational predictions reveal two stem loops and two pseudoknots in the 5′ end and a putative stem loop and a slippery motif located at 3′ end, indicating that these regions can be involved in the start and termination of translation. Through a careful phylogenetic analysis, a higher genetic variability among Brazilian isolates could be observed, comparing with Indonesian IMNV isolates. It was also observed that the most variable region of IMNV genome is located in the first half of ORF1, coinciding with a region which probably encodes the capsid protrusions. The results presented here are a starting point to elucidate the viral's translational regulation and the mechanisms involved in virulence. |
| doi_str_mv | 10.1016/j.virusres.2015.03.015 |
| format | article |
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Infectious myonecrosis virus (IMNV) has been the cause of many losses in shrimp farming since 2002, when the first myonecrosis outbreak was reported at Brazilian's northeast coast. Two additional genomes of Brazilian IMNV isolates collected in 2009 and 2013 were sequenced and analyzed in the present study. The sequencing revealed extra 643bp and 22bp, at 5′ and 3′ ends of IMNV genome respectively, confirming that its actual size is at least 8226bp long. Considering these additional sequences in genome extremities, ORF1 can starts at nt 470, encoding a 1708 aa polyprotein. Computational predictions reveal two stem loops and two pseudoknots in the 5′ end and a putative stem loop and a slippery motif located at 3′ end, indicating that these regions can be involved in the start and termination of translation. Through a careful phylogenetic analysis, a higher genetic variability among Brazilian isolates could be observed, comparing with Indonesian IMNV isolates. It was also observed that the most variable region of IMNV genome is located in the first half of ORF1, coinciding with a region which probably encodes the capsid protrusions. The results presented here are a starting point to elucidate the viral's translational regulation and the mechanisms involved in virulence.</description><identifier>ISSN: 0168-1702</identifier><identifier>EISSN: 1872-7492</identifier><identifier>DOI: 10.1016/j.virusres.2015.03.015</identifier><identifier>PMID: 25849112</identifier><language>eng</language><publisher>Netherlands: Elsevier B.V</publisher><subject>Animals ; Base Sequence ; Brazil ; Cluster Analysis ; Decapoda ; dsRNA virus ; Gene Order ; Genome, Viral ; Hypervariable region ; IMNV Brazil ; IRES ; Molecular Sequence Data ; Nucleic Acid Conformation ; Open Reading Frames ; Penaeidae - virology ; Phylogeny ; Protein Biosynthesis ; RNA, Viral - genetics ; Sequence Analysis, DNA ; Sequence Homology ; Shrimp diseases ; Totiviridae - classification ; Totiviridae - genetics ; Totiviridae - isolation & purification</subject><ispartof>Virus research, 2015-05, Vol.203, p.66-71</ispartof><rights>2015 Elsevier B.V.</rights><rights>Copyright © 2015 Elsevier B.V. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c401t-1e5c5aee1dbd496344fa67b3958ab93f193cf92dc40296cae2bae131d4c873773</citedby><cites>FETCH-LOGICAL-c401t-1e5c5aee1dbd496344fa67b3958ab93f193cf92dc40296cae2bae131d4c873773</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>315,786,790,27957,27958</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25849112$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Dantas, Márcia Danielle A.</creatorcontrib><creatorcontrib>Chavante, Suely F.</creatorcontrib><creatorcontrib>Teixeira, Dárlio Inácio A.</creatorcontrib><creatorcontrib>Lima, João Paulo M.S.</creatorcontrib><creatorcontrib>Lanza, Daniel C.F.</creatorcontrib><title>Analysis of new isolates reveals new genome organization and a hypervariable region in infectious myonecrosis virus (IMNV)</title><title>Virus research</title><addtitle>Virus Res</addtitle><description>•Additional sequences revealed that IMNV genome has at least 8226bp and not 7561bp.•These additional sequences affect the sizes predicted for 5′ UTR, 3′ UTR and ORF1.•A polymorphism map based in the genome alignment of seven sequences reveals a hypervariable region in IMNV genome.•The hypervariable region coincides with the region that encodes virion protrusions.
Infectious myonecrosis virus (IMNV) has been the cause of many losses in shrimp farming since 2002, when the first myonecrosis outbreak was reported at Brazilian's northeast coast. Two additional genomes of Brazilian IMNV isolates collected in 2009 and 2013 were sequenced and analyzed in the present study. The sequencing revealed extra 643bp and 22bp, at 5′ and 3′ ends of IMNV genome respectively, confirming that its actual size is at least 8226bp long. Considering these additional sequences in genome extremities, ORF1 can starts at nt 470, encoding a 1708 aa polyprotein. Computational predictions reveal two stem loops and two pseudoknots in the 5′ end and a putative stem loop and a slippery motif located at 3′ end, indicating that these regions can be involved in the start and termination of translation. Through a careful phylogenetic analysis, a higher genetic variability among Brazilian isolates could be observed, comparing with Indonesian IMNV isolates. It was also observed that the most variable region of IMNV genome is located in the first half of ORF1, coinciding with a region which probably encodes the capsid protrusions. The results presented here are a starting point to elucidate the viral's translational regulation and the mechanisms involved in virulence.</description><subject>Animals</subject><subject>Base Sequence</subject><subject>Brazil</subject><subject>Cluster Analysis</subject><subject>Decapoda</subject><subject>dsRNA virus</subject><subject>Gene Order</subject><subject>Genome, Viral</subject><subject>Hypervariable region</subject><subject>IMNV Brazil</subject><subject>IRES</subject><subject>Molecular Sequence Data</subject><subject>Nucleic Acid Conformation</subject><subject>Open Reading Frames</subject><subject>Penaeidae - virology</subject><subject>Phylogeny</subject><subject>Protein Biosynthesis</subject><subject>RNA, Viral - genetics</subject><subject>Sequence Analysis, DNA</subject><subject>Sequence Homology</subject><subject>Shrimp diseases</subject><subject>Totiviridae - classification</subject><subject>Totiviridae - genetics</subject><subject>Totiviridae - isolation & purification</subject><issn>0168-1702</issn><issn>1872-7492</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><recordid>eNqFkUFv3CAQhVHVKtls8xcijunBLgO2MbdGUdpESttL0ivCeLxlZcMWdrfa_PribNJrJKQnMd_whnmEXAArgUHzeV3uXdyliKnkDOqSiTLLO7KAVvJCVoq_J4sMtgVIxk_JWUprxlgjZHNCTnndVgqAL8jTlTfjIblEw0A9_qUuhdFsMdGIezRjer5coQ8T0hBXxrsns3XBU-N7aujvwwbj3kRnuhFzz2ouufkMaDO3S3Q6BI82htnkeWh6eff9x69PH8mHIRvg-YsuyePXm4fr2-L-57e766v7wlYMtgVgbWuDCH3XV6oRVTWYRnZC1a3plBhACTso3meaq8Ya5J1BENBXtpVCSrEkl8d3NzH82WHa6skli-NoPOb5NEhRKxA1wNto0zYVMJXHWJLmiM4_yzkMehPdZOJBA9NzRHqtXyPSc0SaCZ0lN168eOy6Cfv_ba-ZZODLEcC8lL3DqJN16C32Luad6j64tzz-AdqTqDM</recordid><startdate>20150504</startdate><enddate>20150504</enddate><creator>Dantas, Márcia Danielle A.</creator><creator>Chavante, Suely F.</creator><creator>Teixeira, Dárlio Inácio A.</creator><creator>Lima, João Paulo M.S.</creator><creator>Lanza, Daniel C.F.</creator><general>Elsevier B.V</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>7X8</scope><scope>7U9</scope><scope>8FD</scope><scope>FR3</scope><scope>H94</scope><scope>P64</scope><scope>RC3</scope></search><sort><creationdate>20150504</creationdate><title>Analysis of new isolates reveals new genome organization and a hypervariable region in infectious myonecrosis virus (IMNV)</title><author>Dantas, Márcia Danielle A. ; Chavante, Suely F. ; Teixeira, Dárlio Inácio A. ; Lima, João Paulo M.S. ; Lanza, Daniel C.F.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c401t-1e5c5aee1dbd496344fa67b3958ab93f193cf92dc40296cae2bae131d4c873773</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Animals</topic><topic>Base Sequence</topic><topic>Brazil</topic><topic>Cluster Analysis</topic><topic>Decapoda</topic><topic>dsRNA virus</topic><topic>Gene Order</topic><topic>Genome, Viral</topic><topic>Hypervariable region</topic><topic>IMNV Brazil</topic><topic>IRES</topic><topic>Molecular Sequence Data</topic><topic>Nucleic Acid Conformation</topic><topic>Open Reading Frames</topic><topic>Penaeidae - virology</topic><topic>Phylogeny</topic><topic>Protein Biosynthesis</topic><topic>RNA, Viral - genetics</topic><topic>Sequence Analysis, DNA</topic><topic>Sequence Homology</topic><topic>Shrimp diseases</topic><topic>Totiviridae - classification</topic><topic>Totiviridae - genetics</topic><topic>Totiviridae - isolation & purification</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Dantas, Márcia Danielle A.</creatorcontrib><creatorcontrib>Chavante, Suely F.</creatorcontrib><creatorcontrib>Teixeira, Dárlio Inácio A.</creatorcontrib><creatorcontrib>Lima, João Paulo M.S.</creatorcontrib><creatorcontrib>Lanza, Daniel C.F.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><jtitle>Virus research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Dantas, Márcia Danielle A.</au><au>Chavante, Suely F.</au><au>Teixeira, Dárlio Inácio A.</au><au>Lima, João Paulo M.S.</au><au>Lanza, Daniel C.F.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Analysis of new isolates reveals new genome organization and a hypervariable region in infectious myonecrosis virus (IMNV)</atitle><jtitle>Virus research</jtitle><addtitle>Virus Res</addtitle><date>2015-05-04</date><risdate>2015</risdate><volume>203</volume><spage>66</spage><epage>71</epage><pages>66-71</pages><issn>0168-1702</issn><eissn>1872-7492</eissn><notes>ObjectType-Article-1</notes><notes>SourceType-Scholarly Journals-1</notes><notes>ObjectType-Feature-2</notes><notes>content type line 23</notes><abstract>•Additional sequences revealed that IMNV genome has at least 8226bp and not 7561bp.•These additional sequences affect the sizes predicted for 5′ UTR, 3′ UTR and ORF1.•A polymorphism map based in the genome alignment of seven sequences reveals a hypervariable region in IMNV genome.•The hypervariable region coincides with the region that encodes virion protrusions.
Infectious myonecrosis virus (IMNV) has been the cause of many losses in shrimp farming since 2002, when the first myonecrosis outbreak was reported at Brazilian's northeast coast. Two additional genomes of Brazilian IMNV isolates collected in 2009 and 2013 were sequenced and analyzed in the present study. The sequencing revealed extra 643bp and 22bp, at 5′ and 3′ ends of IMNV genome respectively, confirming that its actual size is at least 8226bp long. Considering these additional sequences in genome extremities, ORF1 can starts at nt 470, encoding a 1708 aa polyprotein. Computational predictions reveal two stem loops and two pseudoknots in the 5′ end and a putative stem loop and a slippery motif located at 3′ end, indicating that these regions can be involved in the start and termination of translation. Through a careful phylogenetic analysis, a higher genetic variability among Brazilian isolates could be observed, comparing with Indonesian IMNV isolates. It was also observed that the most variable region of IMNV genome is located in the first half of ORF1, coinciding with a region which probably encodes the capsid protrusions. The results presented here are a starting point to elucidate the viral's translational regulation and the mechanisms involved in virulence.</abstract><cop>Netherlands</cop><pub>Elsevier B.V</pub><pmid>25849112</pmid><doi>10.1016/j.virusres.2015.03.015</doi><tpages>6</tpages></addata></record> |
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| source | ScienceDirect Freedom Collection 2022-2024 |
| subjects | Animals Base Sequence Brazil Cluster Analysis Decapoda dsRNA virus Gene Order Genome, Viral Hypervariable region IMNV Brazil IRES Molecular Sequence Data Nucleic Acid Conformation Open Reading Frames Penaeidae - virology Phylogeny Protein Biosynthesis RNA, Viral - genetics Sequence Analysis, DNA Sequence Homology Shrimp diseases Totiviridae - classification Totiviridae - genetics Totiviridae - isolation & purification |
| title | Analysis of new isolates reveals new genome organization and a hypervariable region in infectious myonecrosis virus (IMNV) |
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