HIV reservoir quantification and phylogenetic diversity.
<p>(A) Dot plots showing frequencies of total and intact HIV DNA copies in CD4 T cells measured by the Rainbow assay [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1013702#ppat.1013702.ref032" target="_blank">32</a>] for individuals...
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| _version_ | 1849927626403086336 |
|---|---|
| author | Tine Struyve (22683295) |
| author2 | Marion Pardons (6407921) Jozefien De Clercq (17737815) Liesbet Termote (22683298) Laurens Lambrechts (10532207) Ytse Noppe (22683301) Mathias Lichterfeld (57148) Sofie Rutsaert (10667718) Linos Vandekerckhove (105574) |
| author2_role | author author author author author author author author |
| author_facet | Tine Struyve (22683295) Marion Pardons (6407921) Jozefien De Clercq (17737815) Liesbet Termote (22683298) Laurens Lambrechts (10532207) Ytse Noppe (22683301) Mathias Lichterfeld (57148) Sofie Rutsaert (10667718) Linos Vandekerckhove (105574) |
| author_role | author |
| dc.creator.none.fl_str_mv | Tine Struyve (22683295) Marion Pardons (6407921) Jozefien De Clercq (17737815) Liesbet Termote (22683298) Laurens Lambrechts (10532207) Ytse Noppe (22683301) Mathias Lichterfeld (57148) Sofie Rutsaert (10667718) Linos Vandekerckhove (105574) |
| dc.date.none.fl_str_mv | 2025-11-25T18:40:21Z |
| dc.identifier.none.fl_str_mv | 10.1371/journal.ppat.1013702.s001 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/figure/HIV_reservoir_quantification_and_phylogenetic_diversity_/30713524 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biochemistry Medicine Neuroscience Biotechnology Evolutionary Biology Ecology Cancer Infectious Diseases Plant Biology Virology Computational Biology phorbol myristate acetate integration selection mechanisms xlink "> persistence small reservoir sizes treatment initiation timing clonal expansion contributes art ), irrespective individuals treated shortly reservoir persistence early reservoir persistence clonal expansion started treatment pma ), art initiation viral reservoir treated individuals inducible reservoir individuals treated 1 reservoir suggesting post proviruses integrated progressively enriched one year major barrier longitudinal analysis heterochromatin regions five years chronic cohorts cell compartment antiretroviral therapy already detected |
| dc.title.none.fl_str_mv | HIV reservoir quantification and phylogenetic diversity. |
| dc.type.none.fl_str_mv | Image Figure info:eu-repo/semantics/publishedVersion image |
| description | <p>(A) Dot plots showing frequencies of total and intact HIV DNA copies in CD4 T cells measured by the Rainbow assay [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1013702#ppat.1013702.ref032" target="_blank">32</a>] for individuals of the Acute undetectable (UD, n = 38), Acute UD + 5 (n = 5), Chronic UD (n = 10), Chronic UD + x (n = 57) cohorts. Total HIV DNA is based on RU5 region, intact HIV DNA is based on Ψ, env, gag, pol regions. 15/38 (39%), 5/5 (100%), 4/10 (40%) and 34/57 (60%) displayed a quantifiable intactness result in the Acute UD, Acute UD + 5, Chronic UD and Chronic UD + x cohort, respectively. 4/38 (10%), 1/10 (10%) and 10/57 (17%) displayed an undetectable intactness result in the Acute UD, Chronic UD and Chronic UD + x cohort, respectively. Open symbols represent undetectable values. The other participants in each cohort yielded unreportable values. Grey bars depict median values. (B) Dot plots showing frequencies of total (p = 0.0625) and intact (p = 0.0625) HIV DNA copies in CD4 T cells for paired individuals from the acute cohort (n = 5). (C) Ratio of intact HIV DNA copies to total HIV DNA copies in CD4 T cells for each individual of the Acute UD, Acute UD + 5, Chronic UD and Chronic UD + x cohorts. Grey bars depict median values. Only quantifiable results are plotted. (D) Ratio of intact HIV DNA copies to total HIV DNA copies in CD4 T cells for paired individuals from the acute cohort (n = 5; p = 0.1250). (E) Spearman’s rank correlation between time to ART (from estimated date of infection to treatment initiation, in days) and total HIV DNA copies in CD4 T cells from Acute UD and Chronic UD cohort. (F) Average intra-individual genetic distance for HXB2 coordinates 5089–9443. n represents the number of individuals in each cohort and each dot represents one individual. (G) Average intra-individual genetic distance for HXB2 coordinates 5089–9443 for paired individuals from the acute cohort (n = 5; p = 0.1250). (H-I) Maximum-likelihood phylogenetic trees for the acute (H) and chronic (I) cohorts. The trees include sequences with HXB2 coordinates 5089–9443. Sequences with hypermutations and inversions were excluded from this analysis. HXB2 subtype B is HIV-1 reference genome. (A,C-F) Kruskal-Wallis (Dunn correction for multiple comparisons) and (B,D,G) Wilcoxon tests were performed. Only significant p-values (p < 0.05) are represented on the graphs.</p> <p>(TIF)</p> |
| eu_rights_str_mv | openAccess |
| id | Manara_c5d934a8e392083099e0e4c98e0c3a94 |
| identifier_str_mv | 10.1371/journal.ppat.1013702.s001 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/30713524 |
| publishDate | 2025 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | HIV reservoir quantification and phylogenetic diversity.Tine Struyve (22683295)Marion Pardons (6407921)Jozefien De Clercq (17737815)Liesbet Termote (22683298)Laurens Lambrechts (10532207)Ytse Noppe (22683301)Mathias Lichterfeld (57148)Sofie Rutsaert (10667718)Linos Vandekerckhove (105574)BiochemistryMedicineNeuroscienceBiotechnologyEvolutionary BiologyEcologyCancerInfectious DiseasesPlant BiologyVirologyComputational Biologyphorbol myristate acetateintegration selection mechanismsxlink "> persistencesmall reservoir sizestreatment initiation timingclonal expansion contributesart ), irrespectiveindividuals treated shortlyreservoir persistence earlyreservoir persistenceclonal expansionstarted treatmentpma ),art initiationviral reservoirtreated individualsinducible reservoirindividuals treated1 reservoirsuggesting postproviruses integratedprogressively enrichedone yearmajor barrierlongitudinal analysisheterochromatin regionsfive yearschronic cohortscell compartmentantiretroviral therapyalready detected<p>(A) Dot plots showing frequencies of total and intact HIV DNA copies in CD4 T cells measured by the Rainbow assay [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1013702#ppat.1013702.ref032" target="_blank">32</a>] for individuals of the Acute undetectable (UD, n = 38), Acute UD + 5 (n = 5), Chronic UD (n = 10), Chronic UD + x (n = 57) cohorts. Total HIV DNA is based on RU5 region, intact HIV DNA is based on Ψ, env, gag, pol regions. 15/38 (39%), 5/5 (100%), 4/10 (40%) and 34/57 (60%) displayed a quantifiable intactness result in the Acute UD, Acute UD + 5, Chronic UD and Chronic UD + x cohort, respectively. 4/38 (10%), 1/10 (10%) and 10/57 (17%) displayed an undetectable intactness result in the Acute UD, Chronic UD and Chronic UD + x cohort, respectively. Open symbols represent undetectable values. The other participants in each cohort yielded unreportable values. Grey bars depict median values. (B) Dot plots showing frequencies of total (p = 0.0625) and intact (p = 0.0625) HIV DNA copies in CD4 T cells for paired individuals from the acute cohort (n = 5). (C) Ratio of intact HIV DNA copies to total HIV DNA copies in CD4 T cells for each individual of the Acute UD, Acute UD + 5, Chronic UD and Chronic UD + x cohorts. Grey bars depict median values. Only quantifiable results are plotted. (D) Ratio of intact HIV DNA copies to total HIV DNA copies in CD4 T cells for paired individuals from the acute cohort (n = 5; p = 0.1250). (E) Spearman’s rank correlation between time to ART (from estimated date of infection to treatment initiation, in days) and total HIV DNA copies in CD4 T cells from Acute UD and Chronic UD cohort. (F) Average intra-individual genetic distance for HXB2 coordinates 5089–9443. n represents the number of individuals in each cohort and each dot represents one individual. (G) Average intra-individual genetic distance for HXB2 coordinates 5089–9443 for paired individuals from the acute cohort (n = 5; p = 0.1250). (H-I) Maximum-likelihood phylogenetic trees for the acute (H) and chronic (I) cohorts. The trees include sequences with HXB2 coordinates 5089–9443. Sequences with hypermutations and inversions were excluded from this analysis. HXB2 subtype B is HIV-1 reference genome. (A,C-F) Kruskal-Wallis (Dunn correction for multiple comparisons) and (B,D,G) Wilcoxon tests were performed. Only significant p-values (p < 0.05) are represented on the graphs.</p> <p>(TIF)</p>2025-11-25T18:40:21ZImageFigureinfo:eu-repo/semantics/publishedVersionimage10.1371/journal.ppat.1013702.s001https://figshare.com/articles/figure/HIV_reservoir_quantification_and_phylogenetic_diversity_/30713524CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/307135242025-11-25T18:40:21Z |
| spellingShingle | HIV reservoir quantification and phylogenetic diversity. Tine Struyve (22683295) Biochemistry Medicine Neuroscience Biotechnology Evolutionary Biology Ecology Cancer Infectious Diseases Plant Biology Virology Computational Biology phorbol myristate acetate integration selection mechanisms xlink "> persistence small reservoir sizes treatment initiation timing clonal expansion contributes art ), irrespective individuals treated shortly reservoir persistence early reservoir persistence clonal expansion started treatment pma ), art initiation viral reservoir treated individuals inducible reservoir individuals treated 1 reservoir suggesting post proviruses integrated progressively enriched one year major barrier longitudinal analysis heterochromatin regions five years chronic cohorts cell compartment antiretroviral therapy already detected |
| status_str | publishedVersion |
| title | HIV reservoir quantification and phylogenetic diversity. |
| title_full | HIV reservoir quantification and phylogenetic diversity. |
| title_fullStr | HIV reservoir quantification and phylogenetic diversity. |
| title_full_unstemmed | HIV reservoir quantification and phylogenetic diversity. |
| title_short | HIV reservoir quantification and phylogenetic diversity. |
| title_sort | HIV reservoir quantification and phylogenetic diversity. |
| topic | Biochemistry Medicine Neuroscience Biotechnology Evolutionary Biology Ecology Cancer Infectious Diseases Plant Biology Virology Computational Biology phorbol myristate acetate integration selection mechanisms xlink "> persistence small reservoir sizes treatment initiation timing clonal expansion contributes art ), irrespective individuals treated shortly reservoir persistence early reservoir persistence clonal expansion started treatment pma ), art initiation viral reservoir treated individuals inducible reservoir individuals treated 1 reservoir suggesting post proviruses integrated progressively enriched one year major barrier longitudinal analysis heterochromatin regions five years chronic cohorts cell compartment antiretroviral therapy already detected |