HIV-1 Mutation and Recombination Rates Are Different in Macrophages and T-cells
Identifieur interne : 001D86 ( Main/Exploration ); précédent : 001D85; suivant : 001D87HIV-1 Mutation and Recombination Rates Are Different in Macrophages and T-cells
Auteurs : Deborah Cromer [Australie] ; Timothy E. Schlub ; Redmond P. Smyth [France] ; Andrew J. Grimm ; Abha Chopra ; Simon Mallal ; Miles P. Davenport [Australie] ; Johnson Mak [Australie]Source :
- Viruses [ 1999-4915 ] ; 2016.
Descripteurs français
- KwdFr :
- Algorithmes, Cellules cultivées, Humains, Infections à VIH (virologie), Lignée cellulaire, Lymphocytes T (immunologie), Lymphocytes T (métabolisme), Lymphocytes T (virologie), Macrophages (immunologie), Macrophages (métabolisme), Macrophages (virologie), Modèles théoriques, Mutation, Recombinaison génétique, Récepteurs CCR5 (métabolisme), Récepteurs CXCR4 (métabolisme), Réplication virale, Taux de mutation, VIH-1 (Virus de l'Immunodéficience Humaine de type 1) (génétique), VIH-1 (Virus de l'Immunodéficience Humaine de type 1) (immunologie), Évolution moléculaire.
- MESH :
- génétique : VIH-1 (Virus de l'Immunodéficience Humaine de type 1).
- immunologie : Lymphocytes T, Macrophages, VIH-1 (Virus de l'Immunodéficience Humaine de type 1).
- métabolisme : Lymphocytes T, Macrophages, Récepteurs CCR5, Récepteurs CXCR4.
- virologie : Infections à VIH, Lymphocytes T, Macrophages.
- Algorithmes, Cellules cultivées, Humains, Lignée cellulaire, Modèles théoriques, Mutation, Recombinaison génétique, Réplication virale, Taux de mutation, Évolution moléculaire.
English descriptors
- KwdEn :
- Algorithms, Cell Line, Cells, Cultured, Evolution, Molecular, HIV Infections (virology), HIV-1 (genetics), HIV-1 (immunology), Humans, Macrophages (immunology), Macrophages (metabolism), Macrophages (virology), Models, Theoretical, Mutation, Mutation Rate, Receptors, CCR5 (metabolism), Receptors, CXCR4 (metabolism), Recombination, Genetic, T-Lymphocytes (immunology), T-Lymphocytes (metabolism), T-Lymphocytes (virology), Virus Replication.
- MESH :
- chemical , metabolism : Receptors, CCR5, Receptors, CXCR4.
- genetics : HIV-1.
- immunology : HIV-1, Macrophages, T-Lymphocytes.
- metabolism : Macrophages, T-Lymphocytes.
- virology : HIV Infections, Macrophages, T-Lymphocytes.
- Algorithms, Cell Line, Cells, Cultured, Evolution, Molecular, Humans, Models, Theoretical, Mutation, Mutation Rate, Recombination, Genetic, Virus Replication.
Abstract
High rates of mutation and recombination help human immunodeficiency virus (HIV) to evade the immune system and develop resistance to antiretroviral therapy. Macrophages and T-cells are the natural target cells of HIV-1 infection. A consensus has not been reached as to whether HIV replication results in differential recombination between primary T-cells and macrophages. Here, we used HIV with silent mutation markers along with next generation sequencing to compare the mutation and the recombination rates of HIV directly in T lymphocytes and macrophages. We observed a more than four-fold higher recombination rate of HIV in macrophages compared to T-cells (
Url:
DOI: 10.3390/v8040118
PubMed: 27110814
PubMed Central: 4848610
Affiliations:
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Le document en format XML
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Davenport</name><affiliation><nlm:aff id="af1-viruses-08-00118">Infection Analytics Program, Kirby Institute, UNSW Australia, Sydney NSW 2052, Australia;<email>d.cromer@unsw.edu.au</email> (D.C.);<email>andrew.j.grimm@gmail.com</email> (A.J.G.)</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af2-viruses-08-00118">Centre for Vascular Research, UNSW Australia, Sydney NSW 2052, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Vascular Research, UNSW Australia, Sydney NSW 2052</wicri:regionArea><wicri:noRegion>Sydney NSW 2052</wicri:noRegion></affiliation></author><author><name sortKey="Mak, Johnson" sort="Mak, Johnson" uniqKey="Mak J" first="Johnson" last="Mak">Johnson Mak</name><affiliation wicri:level="1"><nlm:aff id="af7-viruses-08-00118">Biosecurity Flagship, CSIRO (AAHL), Geelong VIC 3220, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Biosecurity Flagship, CSIRO (AAHL), Geelong VIC 3220</wicri:regionArea><wicri:noRegion>Geelong VIC 3220</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="af8-viruses-08-00118">School of Medicine, Deakin University and CSIRO (AAHL), Geelong VIC 3216, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>School of Medicine, Deakin University and CSIRO (AAHL), Geelong VIC 3216</wicri:regionArea><wicri:noRegion>Geelong VIC 3216</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27110814</idno><idno type="pmc">4848610</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4848610</idno><idno type="RBID">PMC:4848610</idno><idno type="doi">10.3390/v8040118</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000644</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000644</idno><idno type="wicri:Area/Pmc/Curation">000643</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000643</idno><idno type="wicri:Area/Pmc/Checkpoint">000884</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000884</idno><idno type="wicri:source">PubMed</idno><idno type="wicri:Area/PubMed/Corpus">001F72</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001F72</idno><idno type="wicri:Area/PubMed/Curation">001F47</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001F47</idno><idno type="wicri:Area/PubMed/Checkpoint">001F47</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001F47</idno><idno type="wicri:Area/Ncbi/Merge">003461</idno><idno type="wicri:Area/Ncbi/Curation">003461</idno><idno type="wicri:Area/Ncbi/Checkpoint">003461</idno><idno type="wicri:Area/Main/Merge">001D83</idno><idno type="wicri:Area/Main/Curation">001D86</idno><idno type="wicri:Area/Main/Exploration">001D86</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">HIV-1 Mutation and Recombination Rates Are Different in Macrophages and T-cells</title><author><name sortKey="Cromer, Deborah" sort="Cromer, Deborah" uniqKey="Cromer D" first="Deborah" last="Cromer">Deborah Cromer</name><affiliation><nlm:aff id="af1-viruses-08-00118">Infection Analytics Program, Kirby Institute, UNSW Australia, Sydney NSW 2052, Australia;<email>d.cromer@unsw.edu.au</email> (D.C.);<email>andrew.j.grimm@gmail.com</email> (A.J.G.)</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af2-viruses-08-00118">Centre for Vascular Research, UNSW Australia, Sydney NSW 2052, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Vascular Research, UNSW Australia, Sydney NSW 2052</wicri:regionArea><wicri:noRegion>Sydney NSW 2052</wicri:noRegion></affiliation></author><author><name sortKey="Schlub, Timothy E" sort="Schlub, Timothy E" uniqKey="Schlub T" first="Timothy E." last="Schlub">Timothy E. Schlub</name><affiliation><nlm:aff id="af3-viruses-08-00118">Sydney School of Public Health, Sydney Medical School, University of Sydney, Sydney NSW 2006, Australia;<email>tim.schlub@sydney.edu.au</email></nlm:aff></affiliation></author><author><name sortKey="Smyth, Redmond P" sort="Smyth, Redmond P" uniqKey="Smyth R" first="Redmond P." last="Smyth">Redmond P. Smyth</name><affiliation><nlm:aff id="af4-viruses-08-00118">Centre for Virology, Burnet Institute, Melbourne VIC 3004, Australia;<email>r.smyth@ibmc-cnrs.unistra.fr</email></nlm:aff></affiliation><affiliation wicri:level="4"><nlm:aff id="af5-viruses-08-00118">Architecture et Réactivité de l’ARN, IBMC, CNRS, Université de Strasbourg, 67084 Strasbourg, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Architecture et Réactivité de l’ARN, IBMC, CNRS, Université de Strasbourg, 67084 Strasbourg</wicri:regionArea><wicri:noRegion>67084 Strasbourg</wicri:noRegion><placeName><settlement type="city">Strasbourg</settlement><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Alsace (région administrative)</region><settlement type="city">Strasbourg</settlement></placeName><orgName type="university">Université de Strasbourg</orgName></affiliation></author><author><name sortKey="Grimm, Andrew J" sort="Grimm, Andrew J" uniqKey="Grimm A" first="Andrew J." last="Grimm">Andrew J. Grimm</name><affiliation><nlm:aff id="af1-viruses-08-00118">Infection Analytics Program, Kirby Institute, UNSW Australia, Sydney NSW 2052, Australia;<email>d.cromer@unsw.edu.au</email> (D.C.);<email>andrew.j.grimm@gmail.com</email> (A.J.G.)</nlm:aff></affiliation></author><author><name sortKey="Chopra, Abha" sort="Chopra, Abha" uniqKey="Chopra A" first="Abha" last="Chopra">Abha Chopra</name><affiliation><nlm:aff id="af6-viruses-08-00118">Institute for Immunology and Infectious Diseases (IIID), Murdoch University, Perth WA 6150, Australia;<email>a.chopra@iiid.com.au</email> (A.C.);<email>S.Mallal@iiid.com.au</email> (S.M.)</nlm:aff></affiliation></author><author><name sortKey="Mallal, Simon" sort="Mallal, Simon" uniqKey="Mallal S" first="Simon" last="Mallal">Simon Mallal</name><affiliation><nlm:aff id="af6-viruses-08-00118">Institute for Immunology and Infectious Diseases (IIID), Murdoch University, Perth WA 6150, Australia;<email>a.chopra@iiid.com.au</email> (A.C.);<email>S.Mallal@iiid.com.au</email> (S.M.)</nlm:aff></affiliation></author><author><name sortKey="Davenport, Miles P" sort="Davenport, Miles P" uniqKey="Davenport M" first="Miles P." last="Davenport">Miles P. Davenport</name><affiliation><nlm:aff id="af1-viruses-08-00118">Infection Analytics Program, Kirby Institute, UNSW Australia, Sydney NSW 2052, Australia;<email>d.cromer@unsw.edu.au</email> (D.C.);<email>andrew.j.grimm@gmail.com</email> (A.J.G.)</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af2-viruses-08-00118">Centre for Vascular Research, UNSW Australia, Sydney NSW 2052, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Vascular Research, UNSW Australia, Sydney NSW 2052</wicri:regionArea><wicri:noRegion>Sydney NSW 2052</wicri:noRegion></affiliation></author><author><name sortKey="Mak, Johnson" sort="Mak, Johnson" uniqKey="Mak J" first="Johnson" last="Mak">Johnson Mak</name><affiliation wicri:level="1"><nlm:aff id="af7-viruses-08-00118">Biosecurity Flagship, CSIRO (AAHL), Geelong VIC 3220, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Biosecurity Flagship, CSIRO (AAHL), Geelong VIC 3220</wicri:regionArea><wicri:noRegion>Geelong VIC 3220</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="af8-viruses-08-00118">School of Medicine, Deakin University and CSIRO (AAHL), Geelong VIC 3216, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>School of Medicine, Deakin University and CSIRO (AAHL), Geelong VIC 3216</wicri:regionArea><wicri:noRegion>Geelong VIC 3216</wicri:noRegion></affiliation></author></analytic><series><title level="j">Viruses</title><idno type="eISSN">1999-4915</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Cell Line</term><term>Cells, Cultured</term><term>Evolution, Molecular</term><term>HIV Infections (virology)</term><term>HIV-1 (genetics)</term><term>HIV-1 (immunology)</term><term>Humans</term><term>Macrophages (immunology)</term><term>Macrophages (metabolism)</term><term>Macrophages (virology)</term><term>Models, Theoretical</term><term>Mutation</term><term>Mutation Rate</term><term>Receptors, CCR5 (metabolism)</term><term>Receptors, CXCR4 (metabolism)</term><term>Recombination, Genetic</term><term>T-Lymphocytes (immunology)</term><term>T-Lymphocytes (metabolism)</term><term>T-Lymphocytes (virology)</term><term>Virus Replication</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Cellules cultivées</term><term>Humains</term><term>Infections à VIH (virologie)</term><term>Lignée cellulaire</term><term>Lymphocytes T (immunologie)</term><term>Lymphocytes T (métabolisme)</term><term>Lymphocytes T (virologie)</term><term>Macrophages (immunologie)</term><term>Macrophages (métabolisme)</term><term>Macrophages (virologie)</term><term>Modèles théoriques</term><term>Mutation</term><term>Recombinaison génétique</term><term>Récepteurs CCR5 (métabolisme)</term><term>Récepteurs CXCR4 (métabolisme)</term><term>Réplication virale</term><term>Taux de mutation</term><term>VIH-1 (Virus de l'Immunodéficience Humaine de type 1) (génétique)</term><term>VIH-1 (Virus de l'Immunodéficience Humaine de type 1) (immunologie)</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Receptors, CCR5</term><term>Receptors, CXCR4</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>HIV-1</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>VIH-1 (Virus de l'Immunodéficience Humaine de type 1)</term></keywords><keywords scheme="MESH" qualifier="immunologie" xml:lang="fr"><term>Lymphocytes T</term><term>Macrophages</term><term>VIH-1 (Virus de l'Immunodéficience Humaine de type 1)</term></keywords><keywords scheme="MESH" qualifier="immunology" xml:lang="en"><term>HIV-1</term><term>Macrophages</term><term>T-Lymphocytes</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Macrophages</term><term>T-Lymphocytes</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Lymphocytes T</term><term>Macrophages</term><term>Récepteurs CCR5</term><term>Récepteurs CXCR4</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Infections à VIH</term><term>Lymphocytes T</term><term>Macrophages</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>HIV Infections</term><term>Macrophages</term><term>T-Lymphocytes</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Cell Line</term><term>Cells, Cultured</term><term>Evolution, Molecular</term><term>Humans</term><term>Models, Theoretical</term><term>Mutation</term><term>Mutation Rate</term><term>Recombination, Genetic</term><term>Virus Replication</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Cellules cultivées</term><term>Humains</term><term>Lignée cellulaire</term><term>Modèles théoriques</term><term>Mutation</term><term>Recombinaison génétique</term><term>Réplication virale</term><term>Taux de mutation</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>High rates of mutation and recombination help human immunodeficiency virus (HIV) to evade the immune system and develop resistance to antiretroviral therapy. Macrophages and T-cells are the natural target cells of HIV-1 infection. A consensus has not been reached as to whether HIV replication results in differential recombination between primary T-cells and macrophages. Here, we used HIV with silent mutation markers along with next generation sequencing to compare the mutation and the recombination rates of HIV directly in T lymphocytes and macrophages. We observed a more than four-fold higher recombination rate of HIV in macrophages compared to T-cells (<italic>p</italic> < 0.001) and demonstrated that this difference is not due to different reliance on C-X-C chemokine receptor type 4 (CXCR4) and C-C chemokine receptor type 5 (CCR5) co-receptors between T-cells and macrophages. We also found that the pattern of recombination across the HIV genome (hot and cold spots) remains constant between T-cells and macrophages despite a three-fold increase in the overall recombination rate. This indicates that the difference in rates is a general feature of HIV DNA synthesis during macrophage infection. In contrast to HIV recombination, we found that T-cells have a 30% higher mutation rate than macrophages (<italic>p</italic> < 0.001) and that the mutational profile is similar between these cell types. Unexpectedly, we found no association between mutation and recombination in macrophages, in contrast to T-cells. Our data highlights some of the fundamental difference of HIV recombination and mutation amongst these two major target cells of infection. Understanding these differences will provide invaluable insights toward HIV evolution and how the virus evades immune surveillance and anti-retroviral therapeutics.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Ho, D" uniqKey="Ho D">D. Ho</name></author><author><name sortKey="Neumann, A" uniqKey="Neumann A">A. Neumann</name></author><author><name sortKey="Perelson, A" uniqKey="Perelson A">A. Perelson</name></author><author><name sortKey="Chen, W" uniqKey="Chen W">W. Chen</name></author><author><name sortKey="Leonard, J" uniqKey="Leonard J">J. Leonard</name></author><author><name sortKey="Markowitz, M" uniqKey="Markowitz M">M. Markowitz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Smyth, R P" uniqKey="Smyth R">R.P. Smyth</name></author><author><name sortKey="Davenport, M P" uniqKey="Davenport M">M.P. Davenport</name></author><author><name sortKey="Mak, J" uniqKey="Mak J">J. Mak</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rambaut, A" uniqKey="Rambaut A">A. Rambaut</name></author><author><name sortKey="Posada, D" uniqKey="Posada D">D. Posada</name></author><author><name sortKey="Crandall, K A" uniqKey="Crandall K">K.A. Crandall</name></author><author><name sortKey="Holmes, E C" uniqKey="Holmes E">E.C. 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Kim</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Australie</li><li>France</li></country><region><li>Alsace (région administrative)</li><li>Grand Est</li></region><settlement><li>Strasbourg</li></settlement><orgName><li>Université de Strasbourg</li></orgName></list><tree><noCountry><name sortKey="Chopra, Abha" sort="Chopra, Abha" uniqKey="Chopra A" first="Abha" last="Chopra">Abha Chopra</name><name sortKey="Grimm, Andrew J" sort="Grimm, Andrew J" uniqKey="Grimm A" first="Andrew J." last="Grimm">Andrew J. Grimm</name><name sortKey="Mallal, Simon" sort="Mallal, Simon" uniqKey="Mallal S" first="Simon" last="Mallal">Simon Mallal</name><name sortKey="Schlub, Timothy E" sort="Schlub, Timothy E" uniqKey="Schlub T" first="Timothy E." last="Schlub">Timothy E. Schlub</name></noCountry><country name="Australie"><noRegion><name sortKey="Cromer, Deborah" sort="Cromer, Deborah" uniqKey="Cromer D" first="Deborah" last="Cromer">Deborah Cromer</name></noRegion><name sortKey="Davenport, Miles P" sort="Davenport, Miles P" uniqKey="Davenport M" first="Miles P." last="Davenport">Miles P. Davenport</name><name sortKey="Mak, Johnson" sort="Mak, Johnson" uniqKey="Mak J" first="Johnson" last="Mak">Johnson Mak</name><name sortKey="Mak, Johnson" sort="Mak, Johnson" uniqKey="Mak J" first="Johnson" last="Mak">Johnson Mak</name></country><country name="France"><region name="Grand Est"><name sortKey="Smyth, Redmond P" sort="Smyth, Redmond P" uniqKey="Smyth R" first="Redmond P." last="Smyth">Redmond P. Smyth</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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