HIV-1 CRF 02 AG polymerase genes in Southern Ghana are mosaics of different 02 AG strains and the protease gene cannot infer subtypes.
Identifieur interne : 000133 ( PubMed/Curation ); précédent : 000132; suivant : 000134HIV-1 CRF 02 AG polymerase genes in Southern Ghana are mosaics of different 02 AG strains and the protease gene cannot infer subtypes.
Auteurs : Kwamena W. Sagoe [Ghana] ; Magda Dwidar ; Theophilus K. Adiku ; Max Q. ArensSource :
- Virology journal [ 1743-422X ] ; 2009.
Descripteurs français
- KwdFr :
- Analyse de séquence d'ADN, Données de séquences moléculaires, Ghana, Gènes pol (génétique), Humains, Infections à VIH (virologie), Phylogénie, Protéase du VIH (génétique), Recombinaison génétique, Transcriptase inverse du VIH (génétique), VIH-1 (Virus de l'Immunodéficience Humaine de type 1) (), VIH-1 (Virus de l'Immunodéficience Humaine de type 1) (enzymologie), VIH-1 (Virus de l'Immunodéficience Humaine de type 1) (génétique).
- MESH :
- enzymologie : VIH-1 (Virus de l'Immunodéficience Humaine de type 1).
- génétique : Gènes pol, Protéase du VIH, Transcriptase inverse du VIH, VIH-1 (Virus de l'Immunodéficience Humaine de type 1).
- virologie : Infections à VIH.
- Analyse de séquence d'ADN, Données de séquences moléculaires, Ghana, Humains, Phylogénie, Recombinaison génétique, VIH-1 (Virus de l'Immunodéficience Humaine de type 1).
- Wicri :
- geographic : Ghana.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : HIV Protease, HIV Reverse Transcriptase.
- geographic : Ghana.
- classification : HIV-1.
- enzymology : HIV-1.
- genetics : Genes, pol, HIV-1.
- virology : HIV Infections.
- Humans, Molecular Sequence Data, Phylogeny, Recombination, Genetic, Sequence Analysis, DNA.
Abstract
Little is known about the detailed phylogeny relationships of CRF 02_AG HIV-1 polymerase genes in Ghana. The use of the protease gene of HIV-1 for subtyping has shown conflicting results.
DOI: 10.1186/1743-422X-6-27
PubMed: 19245688
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Adiku</name></author><author><name sortKey="Arens, Max Q" sort="Arens, Max Q" uniqKey="Arens M" first="Max Q" last="Arens">Max Q. Arens</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2009">2009</date><idno type="RBID">pubmed:19245688</idno><idno type="pmid">19245688</idno><idno type="doi">10.1186/1743-422X-6-27</idno><idno type="wicri:Area/PubMed/Corpus">000133</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000133</idno><idno type="wicri:Area/PubMed/Curation">000133</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000133</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">HIV-1 CRF 02 AG polymerase genes in Southern Ghana are mosaics of different 02 AG strains and the protease gene cannot infer subtypes.</title><author><name sortKey="Sagoe, Kwamena W" sort="Sagoe, Kwamena W" uniqKey="Sagoe K" first="Kwamena W" last="Sagoe">Kwamena W. Sagoe</name><affiliation wicri:level="1"><nlm:affiliation>Department of Microbiology, University of Ghana Medical School, Accra, Ghana. kwcsagoe@chs.edu.gh</nlm:affiliation><country xml:lang="fr">Ghana</country><wicri:regionArea>Department of Microbiology, University of Ghana Medical School, Accra</wicri:regionArea></affiliation></author><author><name sortKey="Dwidar, Magda" sort="Dwidar, Magda" uniqKey="Dwidar M" first="Magda" last="Dwidar">Magda Dwidar</name></author><author><name sortKey="Adiku, Theophilus K" sort="Adiku, Theophilus K" uniqKey="Adiku T" first="Theophilus K" last="Adiku">Theophilus K. Adiku</name></author><author><name sortKey="Arens, Max Q" sort="Arens, Max Q" uniqKey="Arens M" first="Max Q" last="Arens">Max Q. Arens</name></author></analytic><series><title level="j">Virology journal</title><idno type="eISSN">1743-422X</idno><imprint><date when="2009" type="published">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Genes, pol (genetics)</term><term>Ghana</term><term>HIV Infections (virology)</term><term>HIV Protease (genetics)</term><term>HIV Reverse Transcriptase (genetics)</term><term>HIV-1 (classification)</term><term>HIV-1 (enzymology)</term><term>HIV-1 (genetics)</term><term>Humans</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Recombination, Genetic</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Données de séquences moléculaires</term><term>Ghana</term><term>Gènes pol (génétique)</term><term>Humains</term><term>Infections à VIH (virologie)</term><term>Phylogénie</term><term>Protéase du VIH (génétique)</term><term>Recombinaison génétique</term><term>Transcriptase inverse du VIH (génétique)</term><term>VIH-1 (Virus de l'Immunodéficience Humaine de type 1) ()</term><term>VIH-1 (Virus de l'Immunodéficience Humaine de type 1) (enzymologie)</term><term>VIH-1 (Virus de l'Immunodéficience Humaine de type 1) (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>HIV Protease</term><term>HIV Reverse Transcriptase</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>Ghana</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>HIV-1</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>VIH-1 (Virus de l'Immunodéficience Humaine de type 1)</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>HIV-1</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Genes, pol</term><term>HIV-1</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Gènes pol</term><term>Protéase du VIH</term><term>Transcriptase inverse du VIH</term><term>VIH-1 (Virus de l'Immunodéficience Humaine de type 1)</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Infections à VIH</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>HIV Infections</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Humans</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Recombination, Genetic</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Données de séquences moléculaires</term><term>Ghana</term><term>Humains</term><term>Phylogénie</term><term>Recombinaison génétique</term><term>VIH-1 (Virus de l'Immunodéficience Humaine de type 1)</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>Ghana</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Little is known about the detailed phylogeny relationships of CRF 02_AG HIV-1 polymerase genes in Ghana. The use of the protease gene of HIV-1 for subtyping has shown conflicting results.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">19245688</PMID><DateCreated><Year>2009</Year><Month>03</Month><Day>16</Day></DateCreated><DateCompleted><Year>2009</Year><Month>04</Month><Day>20</Day></DateCompleted><DateRevised><Year>2014</Year><Month>12</Month><Day>10</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1743-422X</ISSN><JournalIssue CitedMedium="Internet"><Volume>6</Volume><PubDate><Year>2009</Year><Month>Feb</Month><Day>26</Day></PubDate></JournalIssue><Title>Virology journal</Title><ISOAbbreviation>Virol. J.</ISOAbbreviation></Journal><ArticleTitle>HIV-1 CRF 02 AG polymerase genes in Southern Ghana are mosaics of different 02 AG strains and the protease gene cannot infer subtypes.</ArticleTitle><Pagination><MedlinePgn>27</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1743-422X-6-27</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Little is known about the detailed phylogeny relationships of CRF 02_AG HIV-1 polymerase genes in Ghana. The use of the protease gene of HIV-1 for subtyping has shown conflicting results.</AbstractText><AbstractText Label="METHODS" NlmCategory="METHODS">The partial polymerase gene sequences of 25 HIV-1 strains obtained with Viroseq reagents were aligned with reference subtypes and alignments trimmed to a 300 bp protease, 661 bp and 1005 reverse transcriptase sequence alignments. Phylogenetic relationships of these alignments were determined with the Neighbour-Joining method using 1000 replicates and recombination patterns determined for the sequences with RIP 3.0 in the HIV sequence database.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Unlike the other alignments, the protease gene had nodes with bootstrap values < 100% for repeat control sequences. Majority of the CRF 02_AG sequences from Ghana were made up of fragments of several strains of CRF 02_AG/AG strains. The protease gene alone is not suitable for phylogenetic analysis.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">The polymerase genes of HIV-1 strains from Ghana are made up of recombinants of several CRF 02_AG strains from Ghana, Senegal and Cameroon, but the clinical implications are unknown. 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Protease</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D054303" MajorTopicYN="N">HIV Reverse Transcriptase</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015497" MajorTopicYN="N">HIV-1</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName><QualifierName UI="Q000201" MajorTopicYN="N">enzymology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011995" MajorTopicYN="Y">Recombination, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading></MeshHeadingList><OtherID Source="NLM">PMC2655287</OtherID></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2008</Year><Month>12</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2009</Year><Month>02</Month><Day>26</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2009</Year><Month>2</Month><Day>28</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2009</Year><Month>2</Month><Day>28</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2009</Year><Month>4</Month><Day>21</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">19245688</ArticleId><ArticleId 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