{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T00:43:30Z","timestamp":1792802610993,"version":"4.5.0"},"update-to":[{"DOI":"10.1371\/journal.ppat.1011423","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,6,14]],"date-time":"2023-06-14T00:00:00Z","timestamp":1686700800000}}],"reference-count":78,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2023,6,2]],"date-time":"2023-06-02T00:00:00Z","timestamp":1685664000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Tennessee Center for AIDS Research Developmental Core Award","award":["P30 AI110527"],"award-info":[{"award-number":["P30 AI110527"]}],"id":[{"id":"https:\/\/ror.org\/05n52x113","id-type":"ROR","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["P50 AI150481"],"award-info":[{"award-number":["P50 AI150481"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["U54 AI170791"],"award-info":[{"award-number":["U54 AI170791"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01 AI157843"],"award-info":[{"award-number":["R01 AI157843"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>\n                    The mature HIV-1 capsid is stabilized by host and viral determinants. The capsid protein CA binds to the cellular metabolites inositol hexakisphosphate (IP6) and its precursor inositol (1, 3, 4, 5, 6) pentakisphosphate (IP5) to stabilize the mature capsid. In target cells, capsid destabilization by the antiviral compounds lenacapavir and PF74 reveals a HIV-1 infectivity defect due to IP5\/IP6 (IP5\/6) depletion. To test whether intrinsic HIV-1 capsid stability and\/or host factor binding determines HIV-1 insensitivity to IP5\/6 depletion, a panel of CA mutants was assayed for infection of IP5\/6-depleted T cells and wildtype cells. Four CA mutants with unstable capsids exhibited dependence on host IP5\/6 for infection and reverse transcription (RTN). Adaptation of one such mutant, Q219A, by spread in culture resulted in Vpu truncation and a capsid three-fold interface mutation, T200I. T200I increased intrinsic capsid stability as determined by\n                    <jats:italic>in vitro<\/jats:italic>\n                    uncoating of purified cores and partially reversed the IP5\/6-dependence in target cells for each of the four CA mutants. T200I further rescued the changes to lenacapavir sensitivity associated with the parental mutation. The premature dissolution of the capsid caused by the IP5\/6-dependent mutations imparted a unique defect in integration targeting that was rescued by T200I. Collectively, these results demonstrate that T200I restored other capsid functions after RTN for the panel of mutants. Thus, the hyperstable T200I mutation stabilized the instability defects imparted by the parental IP5\/6-dependent CA mutation. The contribution of Vpu truncation to mutant adaptation was linked to BST-2 antagonization, suggesting that cell-to-cell transfer promoted replication of the mutants. We conclude that interactions at the three-fold interface are adaptable, key mediators of capsid stability in target cells and are able to antagonize even severe capsid instability to promote infection.\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1011423","type":"journal-article","created":{"date-parts":[[2023,6,2]],"date-time":"2023-06-02T14:25:22Z","timestamp":1685715922000},"page":"e1011423","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":21,"title":["HIV-1 capsid stability enables inositol phosphate-independent infection of target cells and promotes integration into genes"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9071-495X","authenticated-orcid":true,"given":"Gregory A.","family":"Sowd","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiong","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashley","family":"Fulmer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"Aiken","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2023,6,2]]},"reference":[{"key":"ppat.1011423.ref001","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12977-021-00566-0","article-title":"The HIV-1 capsid and reverse transcription","volume":"18","author":"C Aiken","year":"2021","journal-title":"Retrovirology."},{"key":"ppat.1011423.ref002","doi-asserted-by":"crossref","first-page":"e1002439","DOI":"10.1371\/journal.ppat.1002439","article-title":"HIV-1 Capsid-Cyclophilin Interactions Determine Nuclear Import Pathway, Integration Targeting and Replication Efficiency","volume":"7","author":"T Schaller","year":"2011","journal-title":"PLoS Pathog"},{"key":"ppat.1011423.ref003","doi-asserted-by":"crossref","first-page":"e1003693","DOI":"10.1371\/journal.ppat.1003693","article-title":"Nucleoporin NUP153 Phenylalanine-Glycine Motifs Engage a Common Binding Pocket within the HIV-1 Capsid Protein to Mediate Lentiviral Infectivity.","volume":"9","author":"KA Matreyek","year":"2013","journal-title":"PLoS Pathog"},{"key":"ppat.1011423.ref004","first-page":"8","article-title":"CPSF6 Defines a Conserved Capsid Interface that Modulates HIV-1 Replication.","author":"AJ Price","year":"2012","journal-title":"PLoS Pathog"},{"key":"ppat.1011423.ref005","first-page":"10","article-title":"Host Cofactors and Pharmacologic Ligands Share an Essential Interface in HIV-1 Capsid That Is Lost upon Disassembly.","author":"AJ Price","year":"2014","journal-title":"PLoS Pathog"},{"key":"ppat.1011423.ref006","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1128\/JVI.01148-12","article-title":"Differential Effects of Human Immunodeficiency Virus Type 1 Capsid and Cellular Factors Nucleoporin 153 and LEDGF\/p75 on the Efficiency and Specificity of Viral DNA Integration","volume":"87","author":"Y Koh","year":"2013","journal-title":"J Virol"},{"key":"ppat.1011423.ref007","first-page":"7","article-title":"HIV integration targeting: A pathway involving transportin-3 and the nuclear pore protein RanBP2.","author":"KE Ocwieja","year":"2011","journal-title":"PLoS Pathog."},{"key":"ppat.1011423.ref008","first-page":"E1054","article-title":"A critical role for alternative polyadenylation factor CPSF6 in targeting HIV-1 integration to transcriptionally active chromatin","volume":"113","author":"GA Sowd","year":"2016","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ppat.1011423.ref009","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1016\/j.chom.2018.08.002","article-title":"Capsid-CPSF6 Interaction Licenses Nuclear HIV-1 Trafficking to Sites of Viral DNA Integration.","volume":"24","author":"V Achuthan","year":"2018","journal-title":"Cell Host Microbe"},{"key":"ppat.1011423.ref010","first-page":"1","article-title":"HIV-1 replication complexes accumulate in nuclear speckles and integrate into speckle-associated genomic domains.","volume":"11","author":"AC Francis","year":"2020","journal-title":"Nat Commun 2020 111"},{"key":"ppat.1011423.ref011","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1016\/j.ebiom.2016.04.039","article-title":"LEDGIN-mediated Inhibition of Integrase-LEDGF\/p75 Interaction Reduces Reactivation of Residual Latent HIV.","volume":"8","author":"LS Vranckx","year":"2016","journal-title":"EBioMedicine."},{"key":"ppat.1011423.ref012","doi-asserted-by":"crossref","first-page":"7801","DOI":"10.1093\/nar\/gkaa536","article-title":"The chromatin landscape at the HIV-1 provirus integration site determines viral expression","volume":"48","author":"G Vansant","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"ppat.1011423.ref013","doi-asserted-by":"crossref","first-page":"1","DOI":"10.7554\/eLife.34655","article-title":"Distinct chromatin functional states correlate with HIV latency reactivation in infected primary CD4+ T cells.","volume":"7","author":"E Battivelli","year":"2018","journal-title":"Elife."},{"key":"ppat.1011423.ref014","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1038\/nsmb.3328","article-title":"Position effects influence HIV latency reversal","volume":"24","author":"HC Chen","year":"2017","journal-title":"Nat Struct Mol Biol"},{"key":"ppat.1011423.ref015","doi-asserted-by":"crossref","first-page":"5667","DOI":"10.1128\/JVI.76.11.5667-5677.2002","article-title":"Formation of a Human Immunodeficiency Virus Type 1 Core of Optimal Stability Is Crucial for Viral Replication","volume":"76","author":"BM Forshey","year":"2002","journal-title":"J Virol"},{"key":"ppat.1011423.ref016","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1016\/j.virol.2006.03.013","article-title":"Saturation of TRIM5 alpha-mediated restriction of HIV-1 infection depends on the stability of the incoming viral capsid","volume":"350","author":"J Shi","year":"2006","journal-title":"Virology"},{"key":"ppat.1011423.ref017","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1742-4690-9-30","article-title":"Second-site suppressors of HIV-1 capsid mutations: Restoration of intracellular activities without correction of intrinsic capsid stability defects.","volume":"9","author":"R Yang","year":"2012","journal-title":"Retrovirology."},{"key":"ppat.1011423.ref018","first-page":"7","article-title":"IP6 is an HIV pocket factor that prevents capsid collapse and promotes DNA synthesis","author":"DL Mallery","year":"2018","journal-title":"Elife"},{"key":"ppat.1011423.ref019","first-page":"17","article-title":"A lysine ring in HIV capsid pores coordinates IP6 to drive mature capsid assembly.","author":"N Renner","year":"2021","journal-title":"PLoS Pathog."},{"key":"ppat.1011423.ref020","first-page":"509","article-title":"Inositol phosphates are assembly co-factors for HIV-1","author":"RA Dick","year":"2018","journal-title":"Nature. Nature Publishing Group"},{"key":"ppat.1011423.ref021","first-page":"370","article-title":"Reconstitution and visualization of HIV-1 capsid-dependent replication and integration in vitro","author":"DE Christensen","year":"2020","journal-title":"Science"},{"key":"ppat.1011423.ref022","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/mBio.02820-20","article-title":"The host cell metabolite inositol hexakisphosphate promotes efficient endogenous hiv-1 reverse transcription by stabilizing the viral capsid.","volume":"11","author":"J Jennings","year":"2020","journal-title":"MBio"},{"key":"ppat.1011423.ref023","first-page":"315","article-title":"The expanding significance of inositol polyphosphate multikinase as a signaling hub","author":"E Kim","year":"2017","journal-title":"Molecules and Cells. Korean Society for Molecular and Cellular Biology"},{"key":"ppat.1011423.ref024","doi-asserted-by":"crossref","first-page":"e1009190","DOI":"10.1371\/journal.ppat.1009190","article-title":"Inositol phosphates promote HIV-1 assembly and maturation to facilitate viral spread in human CD4+ T cells.","volume":"17","author":"GA Sowd","year":"2021","journal-title":"PLOS Pathog"},{"key":"ppat.1011423.ref025","doi-asserted-by":"crossref","first-page":"3983","DOI":"10.1016\/j.celrep.2019.11.050","article-title":"Cellular IP6 Levels Limit HIV Production while Viruses that Cannot Efficiently Package IP6 Are Attenuated for Infection and Replication","volume":"29","author":"DL Mallery","year":"2019","journal-title":"Cell Rep"},{"key":"ppat.1011423.ref026","first-page":"16","article-title":"Primate lentiviruses require Inositol hexakisphosphate (IP6) or inositol pentakisphosphate (IP5) for the production of viral particles.","author":"CL Ricana","year":"2020","journal-title":"PLoS Pathog."},{"key":"ppat.1011423.ref027","first-page":"1","article-title":"HIV-1 is dependent on its immature lattice to recruit IP6 for mature capsid assembly","author":"N Renner","year":"2023","journal-title":"Nat Struct Mol Biol 2023"},{"key":"ppat.1011423.ref028","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1126\/science.abb4808","article-title":"Structural and mechanistic bases for a potent HIV-1 capsid inhibitor","volume":"370","author":"SM Bester","year":"2020","journal-title":"Science (80-)."},{"key":"ppat.1011423.ref029","first-page":"95","article-title":"HIV-1 CA Inhibitors Are Antagonized by Inositol Phosphate Stabilization of the Viral Capsid in Cells","author":"GA Sowd","year":"2021","journal-title":"J Virol"},{"key":"ppat.1011423.ref030","doi-asserted-by":"crossref","first-page":"542","DOI":"10.1128\/JVI.01406-10","article-title":"Small-Molecule Inhibition of Human Immunodeficiency Virus Type 1 Infection by Virus Capsid Destabilization","volume":"85","author":"J Shi","year":"2011","journal-title":"J Virol"},{"key":"ppat.1011423.ref031","doi-asserted-by":"crossref","first-page":"e1001220","DOI":"10.1371\/journal.ppat.1001220","article-title":"HIV Capsid is a Tractable Target for Small Molecule Therapeutic Intervention.","volume":"6","author":"WS Blair","year":"2010","journal-title":"PLoS Pathog"},{"key":"ppat.1011423.ref032","doi-asserted-by":"crossref","first-page":"5808","DOI":"10.1128\/JVI.03116-15","article-title":"Roles of Capsid-Interacting Host Factors in Multimodal Inhibition of HIV-1 by PF74","volume":"90","author":"A Saito","year":"2016","journal-title":"J Virol"},{"key":"ppat.1011423.ref033","doi-asserted-by":"crossref","first-page":"5439","DOI":"10.1128\/JVI.77.9.5439-5450.2003","article-title":"Functional Surfaces of the Human Immunodeficiency Virus Type 1 Capsid Protein.","volume":"77","author":"UK von Schwedler","year":"2003","journal-title":"J Virol"},{"key":"ppat.1011423.ref034","doi-asserted-by":"crossref","first-page":"780","DOI":"10.1006\/jmbi.1997.1051","article-title":"Molecular recognition in the HIV-1 Capsid\/Cyclophilin A complex","volume":"269","author":"S Yoo","year":"1997","journal-title":"J Mol Biol"},{"key":"ppat.1011423.ref035","doi-asserted-by":"crossref","first-page":"3712","DOI":"10.1128\/JVI.80.8.3712-3720.2006","article-title":"Evidence for a Functional Link between Uncoating of the Human Immunodeficiency Virus Type 1 Core and Nuclear Import of the Viral Preintegration Complex","volume":"80","author":"DJ Dismuke","year":"2006","journal-title":"J Virol"},{"key":"ppat.1011423.ref036","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1742-4690-10-29","article-title":"The NTD-CTD intersubunit interface plays a critical role in assembly and stabilization of the HIV-1 capsid.","volume":"10","author":"EL Yufenyuy","year":"2013","journal-title":"Retrovirology."},{"key":"ppat.1011423.ref037","doi-asserted-by":"crossref","first-page":"1772","DOI":"10.1128\/JVI.77.3.1772-1783.2003","article-title":"A Structurally Disordered Region at the C Terminus of Capsid Plays Essential Roles in Multimerization and Membrane Binding of the Gag Protein of Human Immunodeficiency Virus Type 1","volume":"77","author":"C Liang","year":"2003","journal-title":"J Virol"},{"key":"ppat.1011423.ref038","doi-asserted-by":"crossref","first-page":"9675","DOI":"10.1128\/JVI.78.18.9675-9688.2004","article-title":"The conserved carboxy terminus of the capsid domain of human immunodeficiency virus type 1 gag protein is important for virion assembly and release","volume":"78","author":"D Melamed","year":"2004","journal-title":"J Virol"},{"key":"ppat.1011423.ref039","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1016\/j.chom.2010.02.007","article-title":"Flexible Use of Nuclear Import Pathways by HIV-1","volume":"7","author":"KE Lee","year":"2010","journal-title":"Cell Host Microbe"},{"key":"ppat.1011423.ref040","doi-asserted-by":"crossref","first-page":"780","DOI":"10.1016\/j.cell.2009.10.010","article-title":"Structural Convergence between Cryo-EM and NMR Reveals Intersubunit Interactions Critical for HIV-1 Capsid Function","volume":"139","author":"IJL Byeon","year":"2009","journal-title":"Cell"},{"key":"ppat.1011423.ref041","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1016\/j.virol.2011.09.012","article-title":"The Interdomain Linker Region of HIV-1 Capsid Protein is a Critical Determinant of Proper Core Assembly and Stability","volume":"421","author":"J Jiang","year":"2011","journal-title":"Virology"},{"key":"ppat.1011423.ref042","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1038\/nature12162","article-title":"Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics","volume":"497","author":"G Zhao","year":"2013","journal-title":"Nature"},{"key":"ppat.1011423.ref043","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1126\/science.aaa5936","article-title":"STRUCTURAL VIROLOGY. X-ray crystal structures of native HIV-1 capsid protein reveal conformational variability","volume":"349","author":"AT Gres","year":"2015","journal-title":"Science"},{"key":"ppat.1011423.ref044","article-title":"In vitro Uncoating of HIV-1 Cores","author":"VB Shah","year":"2021","journal-title":"J Vis Exp. 2011"},{"key":"ppat.1011423.ref045","article-title":"Chemical Stabilization of the HIV-1 Capsid Results in Efficient HIV-1 Reverse Transcription in vitro.","author":"J Jennings","year":"2020","journal-title":"bioRxiv"},{"key":"ppat.1011423.ref046","doi-asserted-by":"crossref","first-page":"e156","DOI":"10.1371\/journal.ppat.0030156","article-title":"Evidence for Direct Involvement of the Capsid Protein in HIV Infection of Nondividing Cells.","volume":"3","author":"M Yamashita","year":"2007","journal-title":"PLoS Pathog"},{"key":"ppat.1011423.ref047","doi-asserted-by":"crossref","first-page":"e1006570","DOI":"10.1371\/journal.ppat.1006570","article-title":"Dynamics and regulation of nuclear import and nuclear movements of HIV-1 complexes.","volume":"13","author":"RC Burdick","year":"2017","journal-title":"PLOS Pathog."},{"key":"ppat.1011423.ref048","doi-asserted-by":"crossref","first-page":"E4780","DOI":"10.1073\/pnas.1315996110","article-title":"Nuclear import of APOBEC3F-labeled HIV-1 preintegration complexes","volume":"110","author":"RC Burdick","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ppat.1011423.ref049","doi-asserted-by":"crossref","first-page":"4730","DOI":"10.1128\/JVI.00099-11","article-title":"Second-Site Compensatory Mutations of HIV-1 Capsid Mutations.","volume":"85","author":"CM Noviello","year":"2011","journal-title":"J Virol"},{"key":"ppat.1011423.ref050","first-page":"425","article-title":"Tetherin inhibits retrovirus release and is antagonized by HIV-1 Vpu.","volume":"451","author":"SJD Neil","year":"2008","journal-title":"Nat 2008 4517177"},{"key":"ppat.1011423.ref051","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.ppat.1000869","article-title":"Multilayered mechanism of CD4 downregulation by HIV-1 Vpu involving distinct ER retention and ERAD targeting steps.","volume":"6","author":"JG Magad\u00e1n","year":"2010","journal-title":"PLoS Pathog"},{"key":"ppat.1011423.ref052","first-page":"8","article-title":"HIV-1 Vpu is a potent transcriptional suppressor of NF-\u03baB-elicited antiviral immune responses.","author":"S Langer","year":"2019","journal-title":"Elife"},{"key":"ppat.1011423.ref053","doi-asserted-by":"crossref","first-page":"12958","DOI":"10.1128\/JVI.01699-10","article-title":"Determinants of tetherin antagonism in the transmembrane domain of the human immunodeficiency virus type 1 Vpu protein","volume":"84","author":"R Vigan","year":"2010","journal-title":"J Virol"},{"key":"ppat.1011423.ref054","first-page":"8","article-title":"A cytoplasmic tail determinant in HIV-1 Vpu mediates targeting of tetherin for endosomal degradation and counteracts interferon-induced restriction.","author":"T Kueck","year":"2012","journal-title":"PLoS Pathog."},{"key":"ppat.1011423.ref055","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/mBio.00934-16","article-title":"Vpu-mediated counteraction of tetherin is a major determinant of HIV-1 interferon resistance.","volume":"7","author":"D Kmiec","year":"2016","journal-title":"MBio."},{"key":"ppat.1011423.ref056","first-page":"7","article-title":"A stable immature lattice packages IP6 for HIV capsid maturation.","author":"DL Mallery","year":"2021","journal-title":"Sci Adv."},{"key":"ppat.1011423.ref057","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1038\/s41564-021-00868-1","article-title":"Sec24C is an HIV-1 host dependency factor crucial for virus replication.","volume":"6","author":"V. Rebensburg S","year":"2021","journal-title":"Nat Microbiol."},{"key":"ppat.1011423.ref058","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1128\/JVI.07177-11","article-title":"The Host Proteins Transportin SR2\/TNPO3 and Cyclophilin A Exert Opposing Effects on HIV-1 Uncoating","volume":"87","author":"VB Shah","year":"2013","journal-title":"J Virol"},{"key":"ppat.1011423.ref059","first-page":"7","article-title":"Kinetics of HIV-1 capsid uncoating revealed by single-molecule analysis.","author":"CL M\u00e1rquez","year":"2018","journal-title":"Elife."},{"key":"ppat.1011423.ref060","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1016\/j.mam.2010.08.002","article-title":"HIV-1 Vpu targets cell surface markers CD4 and BST-2 through distinct mechanisms.","volume":"31","author":"A Andrew","year":"2010","journal-title":"Mol Aspects Med."},{"key":"ppat.1011423.ref061","doi-asserted-by":"crossref","first-page":"9040","DOI":"10.1073\/pnas.1820333116","article-title":"Mutations in the HIV-1 envelope glycoprotein can broadly rescue blocks at multiple steps in the virus replication cycle","volume":"116","author":"R Van Duyne","year":"2019","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ppat.1011423.ref062","doi-asserted-by":"crossref","first-page":"7169","DOI":"10.1128\/JVI.00231-11","article-title":"Multiploid inheritance of HIV-1 during cell-to-cell infection","volume":"85","author":"A Del Portillo","year":"2011","journal-title":"J Virol"},{"key":"ppat.1011423.ref063","first-page":"95","article-title":"Cell-to-cell spread of HIV permits ongoing replication despite antiretroviral therapy.","volume":"477","author":"A Sigal","year":"2011","journal-title":"Nat 2011 4777362"},{"key":"ppat.1011423.ref064","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1016\/j.virol.2013.05.005","article-title":"Multiple proviral integration events after virological synapse-mediated HIV-1 spread","volume":"443","author":"RA Russell","year":"2013","journal-title":"Virology"},{"key":"ppat.1011423.ref065","doi-asserted-by":"crossref","first-page":"e53138","DOI":"10.1371\/journal.pone.0053138","article-title":"Cell-to-Cell Transmission Can Overcome Multiple Donor and Target Cell Barriers Imposed on Cell-Free HIV.","volume":"8","author":"P Zhong","year":"2013","journal-title":"PLoS One"},{"key":"ppat.1011423.ref066","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1038\/385645a0","article-title":"CCR3 and CCR5 are co-receptors for HIV-1 infection of microglia","volume":"385","author":"J He","year":"1997","journal-title":"Nature"},{"key":"ppat.1011423.ref067","first-page":"10","article-title":"flowCore: a Bioconductor package for high throughput flow cytometry","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"ppat.1011423.ref068","article-title":"flowDensity: Sequential Flow Cytometry Data Gating","author":"M. Taghiya","year":"2022","journal-title":"R Packag version 1320."},{"key":"ppat.1011423.ref069","doi-asserted-by":"crossref","first-page":"1632","DOI":"10.1002\/dvdy.24183","article-title":"Poly peak parser: Method and software for identification of unknown indels using sanger sequencing of polymerase chain reaction products","volume":"243","author":"JT Hill","year":"2014","journal-title":"Dev Dyn"},{"key":"ppat.1011423.ref070","doi-asserted-by":"crossref","first-page":"W276","DOI":"10.1093\/nar\/gkac240","article-title":"Search and sequence analysis tools services from EMBL-EBI in 2022","volume":"50","author":"F Madeira","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"ppat.1011423.ref071","doi-asserted-by":"crossref","first-page":"e0185056","DOI":"10.1371\/journal.pone.0185056","article-title":"BBMerge\u2013Accurate paired shotgun read merging via overlap.","volume":"12","author":"B Bushnell","year":"2017","journal-title":"PLoS One"},{"key":"ppat.1011423.ref072","first-page":"907","article-title":"Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype.","volume":"37","author":"D Kim","year":"2019","journal-title":"Nat Biotechnol 2019 378."},{"key":"ppat.1011423.ref073","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"AR Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"ppat.1011423.ref074","first-page":"2016","article-title":"Amplification, next-generation sequencing, and genomic DNA mapping of retroviral integration sites","author":"E Serrao","year":"2016","journal-title":"J Vis Exp"},{"key":"ppat.1011423.ref075","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera\u2014a visualization system for exploratory research and analysis","volume":"25","author":"EF Pettersen","year":"2004","journal-title":"J Comput Chem"},{"key":"ppat.1011423.ref076","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1038\/s41594-020-0489-2","article-title":"Atomic-resolution structure of HIV-1 capsid tubes by magic-angle spinning NMR","volume":"27","author":"M Lu","year":"2020","journal-title":"Nat Struct Mol Biol"},{"key":"ppat.1011423.ref077","doi-asserted-by":"crossref","first-page":"1434","DOI":"10.1126\/science.aah4972","article-title":"The structure and flexibility of conical HIV-1 capsids determined within intact virions","volume":"354","author":"S Mattei","year":"2016","journal-title":"Science (80-)."},{"key":"ppat.1011423.ref078","author":"GA Sowd","year":"2023","journal-title":"Research data. Dryad"}],"updated-by":[{"DOI":"10.1371\/journal.ppat.1011423","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,6,14]],"date-time":"2023-06-14T00:00:00Z","timestamp":1686700800000}}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1011423","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,14]],"date-time":"2023-06-14T13:46:37Z","timestamp":1686750397000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1011423"}},"subtitle":[],"editor":[{"given":"Owen","family":"Pornillos","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,6,2]]},"references-count":78,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2023,6,2]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1011423","relation":{},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,6,2]]}}}