Systematic analysis of protein identity between Zika virus and other arthropod-borne viruses
Identifieur interne : 001A96 ( Ncbi/Curation ); précédent : 001A95; suivant : 001A97Systematic analysis of protein identity between Zika virus and other arthropod-borne viruses
Auteurs : Hsiao-Han Chang ; Roland G. Huber [Singapour] ; Peter J. Bond [Singapour] ; Yonatan H. Grad [États-Unis] ; David Camerini [États-Unis] ; Sebastian Maurer-Stroh [Singapour] ; Marc LipsitchSource :
- Bulletin of the World Health Organization [ 0042-9686 ] ; 2016.
Descripteurs français
- KwdFr :
- Animaux, Bases de données de protéines, Flavivirus (ultrastructure), Humains, Polymorphisme génétique, Vecteurs insectes, Virus Zika (ultrastructure), Virus de l'encéphalite japonaise (espèce) (ultrastructure), Virus de la dengue (ultrastructure), Virus de la fièvre jaune (ultrastructure), Virus du Nil occidental (ultrastructure), Virus du chikungunya (ultrastructure).
- MESH :
English descriptors
- KwdEn :
- Animals, Chikungunya virus (ultrastructure), Databases, Protein, Dengue Virus (ultrastructure), Encephalitis Virus, Japanese (ultrastructure), Flavivirus (ultrastructure), Humans, Insect Vectors, Polymorphism, Genetic, West Nile virus (ultrastructure), Yellow fever virus (ultrastructure), Zika Virus (ultrastructure).
- MESH :
Abstract
To analyse the proportions of protein identity between Zika virus and dengue, Japanese encephalitis, yellow fever, West Nile and chikungunya viruses as well as polymorphism between different Zika virus strains.
We used published protein sequences for the Zika virus and obtained protein sequences for the other viruses from the National Center for Biotechnology Information (NCBI) protein database or the NCBI virus variation resource. We used BLASTP to find regions of identity between viruses. We quantified the identity between the Zika virus and each of the other viruses, as well as within-Zika virus polymorphism for all amino acid
In total, we identified 294 Zika virus protein fragments with both low proportion of identity with other viruses and low levels of polymorphisms among Zika virus strains. The list includes protein fragments from all Zika virus proteins, except NS3. NS4A has the highest number (190
We provide a candidate list of protein fragments that could be used when developing a sensitive and specific serological test to detect previous Zika virus infections.
Url:
DOI: 10.2471/BLT.16.182105
PubMed: 28670016
PubMed Central: 5487971
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Hsiao-Han Chang<affiliation><nlm:aff id="aff1">Department of Epidemiology, Center for Communicable Disease Dynamics, Harvard TH Chan School of Public Health, 677 Huntington Ave, Boston, Massachusetts, 02115, United States of America (USA).</nlm:aff><wicri:noCountry code="subfield">United States of America (USA).</wicri:noCountry></affiliation><affiliation><nlm:aff id="aff1">Department of Epidemiology, Center for Communicable Disease Dynamics, Harvard TH Chan School of Public Health, 677 Huntington Ave, Boston, Massachusetts, 02115, United States of America (USA).</nlm:aff><wicri:noCountry code="subfield">United States of America (USA).</wicri:noCountry></affiliation>Le document en format XML
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Huber</name><affiliation wicri:level="1"><nlm:aff id="aff2">Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR),<country>Singapore</country>.</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Bond, Peter J" sort="Bond, Peter J" uniqKey="Bond P" first="Peter J" last="Bond">Peter J. Bond</name><affiliation wicri:level="1"><nlm:aff id="aff2">Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR),<country>Singapore</country>.</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Grad, Yonatan H" sort="Grad, Yonatan H" uniqKey="Grad Y" first="Yonatan H" last="Grad">Yonatan H. Grad</name><affiliation wicri:level="1"><nlm:aff id="aff3">Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston,<country>USA</country>.</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Camerini, David" sort="Camerini, David" uniqKey="Camerini D" first="David" last="Camerini">David Camerini</name><affiliation wicri:level="1"><nlm:aff id="aff4">Antigen Discovery Inc., Irvine,<country>USA</country>.</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Maurer Stroh, Sebastian" sort="Maurer Stroh, Sebastian" uniqKey="Maurer Stroh S" first="Sebastian" last="Maurer-Stroh">Sebastian Maurer-Stroh</name><affiliation wicri:level="1"><nlm:aff id="aff2">Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR),<country>Singapore</country>.</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Lipsitch, Marc" sort="Lipsitch, Marc" uniqKey="Lipsitch M" first="Marc" last="Lipsitch">Marc Lipsitch</name><affiliation><nlm:aff id="aff1">Department of Epidemiology, Center for Communicable Disease Dynamics, Harvard TH Chan School of Public Health, 677 Huntington Ave, Boston, Massachusetts, 02115, United States of America (USA).</nlm:aff><wicri:noCountry code="subfield">United States of America (USA).</wicri:noCountry></affiliation></author></analytic><series><title level="j">Bulletin of the World Health Organization</title><idno type="ISSN">0042-9686</idno><idno type="eISSN">1564-0604</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Chikungunya virus (ultrastructure)</term><term>Databases, Protein</term><term>Dengue Virus (ultrastructure)</term><term>Encephalitis Virus, Japanese (ultrastructure)</term><term>Flavivirus (ultrastructure)</term><term>Humans</term><term>Insect Vectors</term><term>Polymorphism, Genetic</term><term>West Nile virus (ultrastructure)</term><term>Yellow fever virus (ultrastructure)</term><term>Zika Virus (ultrastructure)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Animaux</term><term>Bases de données de protéines</term><term>Flavivirus (ultrastructure)</term><term>Humains</term><term>Polymorphisme génétique</term><term>Vecteurs insectes</term><term>Virus Zika (ultrastructure)</term><term>Virus de l'encéphalite japonaise (espèce) (ultrastructure)</term><term>Virus de la dengue (ultrastructure)</term><term>Virus de la fièvre jaune (ultrastructure)</term><term>Virus du Nil occidental (ultrastructure)</term><term>Virus du chikungunya (ultrastructure)</term></keywords><keywords scheme="MESH" qualifier="ultrastructure" xml:lang="en"><term>Chikungunya virus</term><term>Dengue Virus</term><term>Encephalitis Virus, Japanese</term><term>Flavivirus</term><term>West Nile virus</term><term>Yellow fever virus</term><term>Zika Virus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Databases, Protein</term><term>Humans</term><term>Insect Vectors</term><term>Polymorphism, Genetic</term></keywords><keywords scheme="MESH" qualifier="ultrastructure" xml:lang="fr"><term>Animaux</term><term>Bases de données de protéines</term><term>Flavivirus</term><term>Humains</term><term>Polymorphisme génétique</term><term>Vecteurs insectes</term><term>Virus Zika</term><term>Virus de l'encéphalite japonaise (espèce)</term><term>Virus de la dengue</term><term>Virus de la fièvre jaune</term><term>Virus du Nil occidental</term><term>Virus du chikungunya</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Abstract</title><sec><title>Objective</title><p>To analyse the proportions of protein identity between Zika virus and dengue, Japanese encephalitis, yellow fever, West Nile and chikungunya viruses as well as polymorphism between different Zika virus strains.</p></sec><sec><title>Methods</title><p>We used published protein sequences for the Zika virus and obtained protein sequences for the other viruses from the National Center for Biotechnology Information (NCBI) protein database or the NCBI virus variation resource. We used BLASTP to find regions of identity between viruses. We quantified the identity between the Zika virus and each of the other viruses, as well as within-Zika virus polymorphism for all amino acid <italic>k</italic>-mers across the proteome, with <italic>k</italic> ranging from 6 to 100. We assessed accessibility of protein fragments by calculating the solvent accessible surface area for the envelope and nonstructural-1 (NS1) proteins. </p></sec><sec><title>Findings</title><p>In total, we identified 294 Zika virus protein fragments with both low proportion of identity with other viruses and low levels of polymorphisms among Zika virus strains. The list includes protein fragments from all Zika virus proteins, except NS3. NS4A has the highest number (190 <italic>k</italic>-mers) of protein fragments on the list. </p></sec><sec><title>Conclusion</title><p>We provide a candidate list of protein fragments that could be used when developing a sensitive and specific serological test to detect previous Zika virus infections.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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