Gut microbiome in HIV-1 trial with vaccine and ART pause
73 fecal metagenome samples from HIV-1-infected participants in the BCN02 trial, combining MVA.HIVconsv vaccination with romidepsin latency-reversal and an ART pause; longitudinal design examining gut microbiome links to viral control. machine-written summary
73 samples · 73 runs · ES · Age unknown · 2022 · 2.96 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 219 sample values (health condition, health condition detail, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 219 sample values (collection date, country, location locality) · PMC9004083 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Non-antibiotic pharmaceutical given as the study intervention (metformin Vaccination as the study intervention design single_arm_before_after · MVA.HIVconsv therapeutic vaccine plus romidepsin latency-reversing agent
“combining MVA.HIVconsv vaccination with romidepsin” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
13 of 13 people sampled more than once (73 samples; median 6, up to 8 per person). Schedule stated by the source: “pre-Vax, 1wk post-MVA1, 1wk post-RMD, 4wk post-MVA2, during MAP (4-34wk post-ART pause), 24wk post-ART resumption” (time origin: intervention_start).
Genera, mean relative abundance over 69 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 73 | 100% | 73 | |||
| health_condition | 73 | 100% | 73 | |||
| subject_id | 73 | 100% | 73 | |||
| collection_date | 73 | 100% | 73 | |||
| detailed_location | 73 | 100% | ||||
| health_condition_detail | 73 | 100% | 73 | |||
| location_locality | 73 | 100% | 73 |
- Gut microbiome signatures linked to HIV-1 reservoir size and viremia control. 2022 PMID 35410461 PMC9004083 own_data
Archive description
Factors associated to post-treatment viral control in response to therapeutic T cell vaccination have not been fully deciphered. In the pilot BCN02 kick and kill trial, combining MVA.HIVconsv vaccination with romidepsin given as latency-reversing agent in early-treated HIV-1 infected individuals1, 3/13 participants showed sustained viral suppression during a monitored ART pause (MAP) for 32 weeks. In this sub-study, we longitudinally characterized the gut microbiome of BCN02 participants using fecal shotgun metagenomics to deepen our understanding on its potential role in the binary MAP outcome (MAP-Controllers vs MAP-Non-controllers).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.75. Assay shotgun_dna.
- host study.description · “early-treated HIV-1 infected individuals”
- body site study.description · “fecal shotgun metagenomics”
- body site run.scientific_name · “feces metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA7984826 | collection_date | 2016-02/2017-10 | R3 | 0.70 | paper.fulltext.methods | conducted between February 2016 and October 2017 |
| SAMEA7984826 | country | ES | R3 | 0.70 | paper.fulltext.methods | two HIV-1 units from university hospitals in Barcelona |
| SAMEA7984826 | health_condition | other_infection | R1 | 0.70 | sample.name_rule:alias | ROMI_A04_0_MVA1_w0_1 |
| SAMEA7984826 | health_condition_detail | ROMI_A04_0_MVA1_w0_1 | R1 | 0.70 | sample.name_rule:alias | ROMI_A04_0_MVA1_w0_1 |
| SAMEA7984826 | location_locality | Barcelona | R3 | 0.70 | paper.fulltext.methods | university hospitals in Barcelona |
| SAMEA7984826 | subject_id | A04 | R1 | 0.70 | sample.name_rule:alias | ROMI_A04_0_MVA1_w0_1 |
Sequencing
73 runs over 73 samples · mean 3.04 Gbp per run (median 2.96 Gbp, total 221.93 Gbp; 73 runs with a base count) · layout PAIRED 73 · platform ILLUMINA 73 · models Illumina HiSeq 2500 (73) · 95% of runs with a Sandpiper profile · first public 2022-05-20
Authors (24)
Borgognone A first · Noguera-Julian M · Oriol B · Noël-Romas L · Ruiz-Riol M · Guillén Y · Parera M · Casadellà M · Duran C · Puertas MC · Català-Moll F · De Leon M · Knodel S · Birse K · Manzardo C · Miró JM · Clotet B · Martinez-Picado J · Moltó J · Mothe B · Burgener A · Brander C · Paredes R · BCN02 Study Group last
Downloads
PRJEB42384.csv.gz (2.8 KB) · parquet (72.9 KB) — all 73 samples, every field with route and confidence · PRJEB42384_determinations.csv.gz (4.4 KB) — 438 evidence rows