Gut virome in HIV infection, cross-sectional, Mexico
201 stool samples from adults in Mexico, from HIV-negative individuals and people living with HIV, examining gut virome composition (including Anelloviridae, Adenoviridae, Papillomaviridae, and plant viruses) in relation to CD4 T cell status and ART; cross-sectional design. machine-written summary
201 samples · 201 runs · MX · Adult · 2024 · 1.69 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,005 sample values (collection date, country, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11483978 |
| ○ 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 155 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 | 201 | 100% | ||||
| country | 201 | 100% | 201 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 201 | 100% | 201 | |||
| detailed_location | 201 | 100% | ||||
| latitude | 201 | 100% | 201 | |||
| location_region | 201 | 100% | 201 | |||
| longitude | 201 | 100% | 201 |
- Alterations of the gut microbiome in HIV infection highlight human anelloviruses as potential predictors of immune recovery. 2024 PMID 39420423 PMC11483978 own_data
Archive description
The gastrointestinal tract is a major site of HIV replication, resulting in a massive depletion of mucosal CD4 T cells in the small and large intestine during both acute and chronic phases of HIV infection. Here we characterized the gut virome at different stages of HIV infection and after antiretroviral therapy (ART) initiation. We used metagenomic viral sequencing to describe the RNA and DNA virome in stool samples from 145 individuals in Mexico, including 53 HIV-negative subjects and 92 people living with HIV (PLWH). Low CD4 T cell counts were associated with an expansion of human virus sequences belonging to the families Anelloviridae, Adenoviridae and Papillomaviridae as well as a depletion of the plant viruses PMMoV and TSAMV. These alterations of the gut virome in PLWH with severe immunodeficiency were progressivley reduced after ART initiation. Notably, both low baseline CD4 T cell counts and detection of human Anelloviridae sequences in stool samples before cART initiation independently predicted poor immune recovery. Thus, the expansion of some human viruses such as anelloviruses in stool samples from PLWH may be a marker of the immune status and a predictor of immune recovery after ART initiation.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Gut virome in HIV”
- body site study.description · “The gastrointestinal tract is a”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN39597609 | collection_date | 2016 | R1 | 0.90 | biosample.attribute:collection_date | 2016 |
| SAMN39597609 | country | MX | R1 | 0.90 | sample.attr.geo_loc_name | Mexico |
| SAMN39597609 | latitude | 19.4300 | R1 | 0.90 | biosample.attribute:lat_lon | 19.43 N 99.13 W |
| SAMN39597609 | location_region | Mexico City | R1 | 0.60 | biosample.attribute:lat_lon | 19.43 N 99.13 W |
| SAMN39597609 | longitude | -99.1300 | R1 | 0.90 | biosample.attribute:lat_lon | 19.43 N 99.13 W |
Sequencing
201 runs over 201 samples · mean 1.68 Gbp per run (median 1.69 Gbp, total 338.45 Gbp; 201 runs with a base count) · layout PAIRED 201 · platform ILLUMINA 201 · models NextSeq 500 (201) · 87% of runs with a Sandpiper profile · first public 2024-07-26 – 2024-08-25
Authors (9)
Boukadida C first · Peralta-Prado A · Chávez-Torres M · Romero-Mora K · Rincon-Rubio A · Ávila-Ríos S · Garrido-Rodríguez D · Reyes-Terán G · Pinto-Cardoso S last
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJNA1068646.csv.gz (5.4 KB) · parquet (76.9 KB) — all 201 samples, every field with route and confidence · PRJNA1068646_determinations.csv.gz (5.6 KB) — 1,005 evidence rows