Gut virome in HIV-exposed vs unexposed Kenyan infants
Longitudinal cohort study of 122 gut virome samples from infants in Nairobi, Kenya, comparing those HIV-exposed-uninfected (mothers on long-term ART) versus HIV-unexposed over the first 18 months of life. machine-written summary
122 samples · 122 runs · KE · Infant / toddler · 2025 · 1.91 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 488 sample values (collection date, country, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 244 sample values (location locality, location site) · PMC12927066 |
| ○ 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 |
longitudinal
33 of 53 people sampled more than once (102 samples; median 3, up to 7 per person) · follow-up median 6 mo (max 18 mo) · median interval between samples 3 mo (time from collection dates). Schedule stated by the source: “Infant stool: home visit ~4 days postpartum; clinic visits at week 6, week 10, then every 3 months from month 6 to month 24” (time origin: birth); stated follow-up 2.0 y.
Each row is one person (33 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 52 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 | 122 | 100% | ||||
| country | 122 | 100% | 122 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 122 | 100% | 122 | |||
| collection_date | 122 | 100% | 122 | |||
| detailed_location | 122 | 100% | ||||
| location_locality | 122 | 100% | 122 | |||
| location_site | 122 | 100% | 122 | |||
| timepoint_label | 122 | 100% | 122 |
- Comparison of gut virome in Kenyan infants born to women with and without HIV. 2026 PMID 41736871 PMC12927066 own_data
Archive description
This study is nested in the Linda Kizazi, a Nairobi, Kenya-based cohort of mother-infant pairs that aims to characterize how the virome is transmitted vertically when mothers are taking long-term, optimized ART regimens. Women living with HIV who had more than or equal to 6 months of ART and women without HIV were recruited prospectively 1 to 1 in the third trimester of pregnancy and followed through two years postpartum. This cohort provides a unique opportunity to compare health outcomes and the gut virome of HEU children whose mothers with HIV have received long-term ART and their HUU peers. We aim to compare longitudinally the taxonomic richness and diversity of the gut virome in Kenyan infants that are HEU versus HUU over the first 18 months of life.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by opus_adjudicated with confidence 0.50. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “gut virome”
- life stage study.title · “Kenyan infants in the first 18 month of life”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN39078794 | collection_date | 2019-09-13 | R1 | 0.85 | biosample.attribute:collection_date | 2019-09-13 |
| SAMN39078794 | country | KE | R1 | 0.90 | biosample_attr | Kenya:Nairobi |
| SAMN39078794 | location_locality | Nairobi | R3 | 0.70 | paper.body.fulltext | 219 stool samples collected between January 2019 and December 2020 from 69 infants enrolled in a cohort of mother-infant pairs in Nairobi, Kenya |
| SAMN39078794 | location_site | Mathare North Health Centre | R3 | 0.70 | paper.body.fulltext | were recruited at Mathare North Health Centre, an urban maternal and child health clinic |
| SAMN39078794 | subject_id | 0092 | R1 | 0.85 | biosample.attribute:ptnum | 0092 |
| SAMN39078794 | timepoint_label | HWD41 | R1 | 0.70 | sample.name_rule:title | 44110092B1HWD41100110001 |
Sequencing
122 runs over 122 samples · mean 2.78 Gbp per run (median 1.91 Gbp, total 338.91 Gbp; 122 runs with a base count) · layout PAIRED 122 · platform ILLUMINA 122 · models NextSeq 2000 (122) · 57% of runs with a Sandpiper profile · first public 2025-10-25
Authors (0)
No author record.
Downloads
PRJNA1051094.csv.gz (5.2 KB) · parquet (76.5 KB) — all 122 samples, every field with route and confidence · PRJNA1051094_determinations.csv.gz (7.0 KB) — 732 evidence rows