Genomic Analysis of Influenza A Viruses , including Avian Flu (H5N1) Strains
Identifieur interne : 001547 ( Main/Exploration ); précédent : 001546; suivant : 001548Genomic Analysis of Influenza A Viruses , including Avian Flu (H5N1) Strains
Auteurs : Insung Ahn [Corée du Sud] ; Byeong-Jin Jeong [Corée du Sud] ; Se-Eun Bae [Corée du Sud] ; Jin Jung [Corée du Sud] ; Hyeon S. Son [Corée du Sud]Source :
- European Journal of Epidemiology [ 0393-2990 ] ; 2006-07-01.
Descripteurs français
- KwdFr :
- Afrique, Animaux, Asie, Bases de données d'acides nucléiques, Codon (génétique), Europe, Grippe chez les oiseaux (transmission), Grippe chez les oiseaux (virologie), Grippe humaine (transmission), Grippe humaine (virologie), Génome viral, Humains, Oiseaux, Orthomyxoviridae (génétique), Orthomyxoviridae (pathogénicité), Sous-type H5N1 du virus de la grippe A (génétique), Sous-type H5N1 du virus de la grippe A (pathogénicité), Virus de la grippe A (génétique), Virus de la grippe A (pathogénicité), Zoonoses (virologie).
- MESH :
- génétique : Codon, Orthomyxoviridae, Sous-type H5N1 du virus de la grippe A, Virus de la grippe A.
- pathogénicité : Orthomyxoviridae, Sous-type H5N1 du virus de la grippe A, Virus de la grippe A.
- virologie : Grippe chez les oiseaux, Grippe humaine, Zoonoses.
- Afrique, Animaux, Asie, Bases de données d'acides nucléiques, Europe, Grippe chez les oiseaux, Grippe humaine, Génome viral, Humains, Oiseaux.
- Pascal (Inist)
- Wicri :
- topic : Santé publique.
English descriptors
- KwdEn :
- Africa, Animals, Asia, Avian flu, Avian influenza, Birds, Codon, Codon (genetics), Correspondence analysis, Databases, Nucleic Acid, Epidemiology, Europe, Genome, Viral, Genomic analysis, Genomics, Humans, Influenza A, Influenza A Virus, H5N1 Subtype (genetics), Influenza A Virus, H5N1 Subtype (pathogenicity), Influenza A virus, Influenza A virus (genetics), Influenza A virus (pathogenicity), Influenza in Birds (transmission), Influenza in Birds (virology), Influenza, Human (transmission), Influenza, Human (virology), Influenzavirus A(H5N1), Orthomyxoviridae (genetics), Orthomyxoviridae (pathogenicity), Public health, Synonymous codon usage, Zoonoses (virology).
- MESH :
- chemical , genetics : Codon.
- geographic : Africa, Asia, Europe.
- genetics : Influenza A Virus, H5N1 Subtype, Influenza A virus, Orthomyxoviridae.
- pathogenicity : Influenza A Virus, H5N1 Subtype, Influenza A virus, Orthomyxoviridae.
- transmission : Influenza in Birds, Influenza, Human.
- virology : Influenza in Birds, Influenza, Human, Zoonoses.
- Animals, Birds, Databases, Nucleic Acid, Genome, Viral, Humans.
Abstract
Abstract: This study was designed to conduct genomic analysis in two steps, such as the overall relative synonymous codon usage (RSCU) analysis of the five virus species in the orthomyxoviridae family, and more intensive pattern analysis of the four subtypes of influenza A virus (H1N1, H2N2, H3N2, and H5N1) which were isolated from human population. All the subtypes were categorized by their isolated regions, including Asia, Europe, and Africa, and most of the synonymous codon usage patterns were analyzed by correspondence analysis (CA). As a result, influenza A virus showed the lowest synonymous codon usage bias among the virus species of the orthomyxoviridae family, and influenza B and influenza C virus were followed, while suggesting that influenza A virus might have an advantage in transmitting across the species barrier due to their low codon usage bias. The ENC values of the host-specific HA and NA genes represented their different HA and NA types very well, and this reveals that each influenza A virus subtype uses different codon usage patterns as well as the amino acid compositions. In NP, PA and PB2 genes, most of the virus subtypes showed similar RSCU patterns except for H5N1 and H3N2 (A/HK/1774/1999) subtypes which were suspected to be transmitted across the species barrier, from avian and porcine species to human beings, respectively. This distinguishable synonymous codon usage patterns in non-human origin viruses might be useful in determining the origin of influenza A viruses in genomic levels as well as the serological tests. In this study, all the process, including extracting sequences from GenBank flat file and calculating codon usage values, was conducted by Java codes, and these bioinformatics-related methods may be useful in predicting the evolutionary patterns of pandemic viruses.
Url:
DOI: 10.1007/s10654-006-9031-z
Affiliations:
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Le document en format XML
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(virology)</term><term>Influenza, Human (transmission)</term><term>Influenza, Human (virology)</term><term>Influenzavirus A(H5N1)</term><term>Orthomyxoviridae (genetics)</term><term>Orthomyxoviridae (pathogenicity)</term><term>Public health</term><term>Synonymous codon usage</term><term>Zoonoses (virology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Afrique</term><term>Animaux</term><term>Asie</term><term>Bases de données d'acides nucléiques</term><term>Codon (génétique)</term><term>Europe</term><term>Grippe chez les oiseaux (transmission)</term><term>Grippe chez les oiseaux (virologie)</term><term>Grippe humaine (transmission)</term><term>Grippe humaine (virologie)</term><term>Génome viral</term><term>Humains</term><term>Oiseaux</term><term>Orthomyxoviridae (génétique)</term><term>Orthomyxoviridae (pathogénicité)</term><term>Sous-type H5N1 du virus de la grippe A (génétique)</term><term>Sous-type H5N1 du virus de la grippe A (pathogénicité)</term><term>Virus de la grippe A (génétique)</term><term>Virus de la grippe A (pathogénicité)</term><term>Zoonoses (virologie)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Codon</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>Africa</term><term>Asia</term><term>Europe</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Influenza A Virus, H5N1 Subtype</term><term>Influenza A virus</term><term>Orthomyxoviridae</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Codon</term><term>Orthomyxoviridae</term><term>Sous-type H5N1 du virus de la grippe A</term><term>Virus de la grippe A</term></keywords><keywords scheme="MESH" qualifier="pathogenicity" xml:lang="en"><term>Influenza A Virus, H5N1 Subtype</term><term>Influenza A virus</term><term>Orthomyxoviridae</term></keywords><keywords scheme="MESH" qualifier="pathogénicité" xml:lang="fr"><term>Orthomyxoviridae</term><term>Sous-type H5N1 du virus de la grippe A</term><term>Virus de la grippe A</term></keywords><keywords scheme="MESH" qualifier="transmission" xml:lang="en"><term>Influenza in Birds</term><term>Influenza, Human</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Grippe chez les oiseaux</term><term>Grippe humaine</term><term>Zoonoses</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Influenza in Birds</term><term>Influenza, Human</term><term>Zoonoses</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Birds</term><term>Databases, Nucleic Acid</term><term>Genome, Viral</term><term>Humans</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Afrique</term><term>Animaux</term><term>Asie</term><term>Bases de données d'acides nucléiques</term><term>Europe</term><term>Grippe chez les oiseaux</term><term>Grippe humaine</term><term>Génome viral</term><term>Humains</term><term>Oiseaux</term></keywords><keywords scheme="Pascal" xml:lang="fr"><term>Analyse correspondance</term><term>Codon</term><term>Epidémiologie</term><term>Grippe A</term><term>Grippe aviaire</term><term>Génomique</term><term>Influenzavirus A(H5N1)</term><term>Santé publique</term><term>Souche H5N1</term><term>Virus grippal A</term></keywords><keywords scheme="Wicri" type="topic" xml:lang="fr"><term>Santé publique</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Abstract: This study was designed to conduct genomic analysis in two steps, such as the overall relative synonymous codon usage (RSCU) analysis of the five virus species in the orthomyxoviridae family, and more intensive pattern analysis of the four subtypes of influenza A virus (H1N1, H2N2, H3N2, and H5N1) which were isolated from human population. All the subtypes were categorized by their isolated regions, including Asia, Europe, and Africa, and most of the synonymous codon usage patterns were analyzed by correspondence analysis (CA). As a result, influenza A virus showed the lowest synonymous codon usage bias among the virus species of the orthomyxoviridae family, and influenza B and influenza C virus were followed, while suggesting that influenza A virus might have an advantage in transmitting across the species barrier due to their low codon usage bias. The ENC values of the host-specific HA and NA genes represented their different HA and NA types very well, and this reveals that each influenza A virus subtype uses different codon usage patterns as well as the amino acid compositions. In NP, PA and PB2 genes, most of the virus subtypes showed similar RSCU patterns except for H5N1 and H3N2 (A/HK/1774/1999) subtypes which were suspected to be transmitted across the species barrier, from avian and porcine species to human beings, respectively. This distinguishable synonymous codon usage patterns in non-human origin viruses might be useful in determining the origin of influenza A viruses in genomic levels as well as the serological tests. In this study, all the process, including extracting sequences from GenBank flat file and calculating codon usage values, was conducted by Java codes, and these bioinformatics-related methods may be useful in predicting the evolutionary patterns of pandemic viruses.</div></front></TEI><affiliations><list><country><li>Corée du Sud</li></country><region><li>Région capitale de Séoul</li></region><settlement><li>Séoul</li></settlement><orgName><li>Université nationale de Séoul</li></orgName></list><tree><country name="Corée du Sud"><noRegion><name sortKey="Ahn, Insung" sort="Ahn, Insung" uniqKey="Ahn I" first="Insung" last="Ahn">Insung Ahn</name></noRegion><name sortKey="Ahn, Insung" sort="Ahn, Insung" uniqKey="Ahn I" first="Insung" last="Ahn">Insung Ahn</name><name sortKey="Bae, Se Eun" sort="Bae, Se Eun" uniqKey="Bae S" first="Se-Eun" last="Bae">Se-Eun Bae</name><name sortKey="Jeong, Byeong Jin" sort="Jeong, Byeong Jin" uniqKey="Jeong B" first="Byeong-Jin" last="Jeong">Byeong-Jin Jeong</name><name sortKey="Jeong, Byeong Jin" sort="Jeong, Byeong Jin" uniqKey="Jeong B" first="Byeong-Jin" last="Jeong">Byeong-Jin Jeong</name><name sortKey="Jung, Jin" sort="Jung, Jin" uniqKey="Jung J" first="Jin" last="Jung">Jin Jung</name><name sortKey="Son, Hyeon S" sort="Son, Hyeon S" uniqKey="Son H" first="Hyeon S." last="Son">Hyeon S. Son</name><name sortKey="Son, Hyeon S" sort="Son, Hyeon S" uniqKey="Son H" first="Hyeon S." last="Son">Hyeon S. Son</name><name sortKey="Son, Hyeon S" sort="Son, Hyeon S" uniqKey="Son H" first="Hyeon S." last="Son">Hyeon S. Son</name><name sortKey="Son, Hyeon S" sort="Son, Hyeon S" uniqKey="Son H" first="Hyeon S." last="Son">Hyeon S. Son</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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