Gut virome in COVID-19 patients vs healthy Japanese adults
144 fecal samples from Japan, case-control design, comparing intestinal DNA phage/virome dynamics in SARS-CoV-2-infected patients against healthy individuals over time. machine-written summary
144 samples · 144 runs · JP · Age unknown · 2024 · 3.01 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 432 sample values (collection date, country, subject id) |
| ✓ Abstract / description | 144 sample values (health condition detail) |
| ○ Full text | read; no usable statement or table · PMC11705802 |
| ○ 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 |
longitudinal — not resolved
48 of 96 people sampled more than once (96 samples; median 2, up to 2 per person). Schedule stated by the source: “Stool collected at admission, at discharge, and on follow-up visits after discharge for some patients” (time origin: diagnosis).
Genera, mean relative abundance over 122 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 | 144 | 100% | 144 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 144 | 100% | 144 | |||
| collection_date | 144 | 100% | 144 | |||
| health_condition_detail | 144 | 100% | 144 |
- Dysbiosis of gut microbiota in COVID-19 is associated with intestinal DNA phage dynamics of lysogenic and lytic infection. 2025 PMID 39656008 PMC11705802 own_data
Archive description
This research aimed to understand the virus like particles in fecal samples from Japanese patients with HIV or SARS-CoV-2 infection comparing with healthy subjects.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human feces metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD00808844 | collection_date | 2017-10-04 | R1 | 0.90 | biosample.attribute:collection_date | 2017-10-04 |
| SAMD00808844 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan |
| SAMD00808844 | health_condition_detail | mixed_case_control: healthy individuals vs SARS-CoV-2 infected patients | R4 | 0.40 | paper.abstract | 19 healthy individuals and 19 patients |
| SAMD00808844 | subject_id | B-001 | R1 | 0.70 | sample.name_rule:sample_name | B-001 |
Sequencing
144 runs over 144 samples · mean 6.09 Gbp per run (median 3.01 Gbp, total 876.68 Gbp; 144 runs with a base count) · layout PAIRED 144 · platform ILLUMINA 144 · models Illumina NovaSeq 6000 (144) · 87% of runs with a Sandpiper profile · first public 2024-08-23 – 2024-08-24
Authors (13)
Ishizaka A first · Tamura A · Koga M · Mizutani T · Yamayoshi S · Iwatsuki-Horimoto K · Yasuhara A · Yamamoto S · Nagai H · Adachi E · Suzuki Y · Kawaoka Y · Yotsuyanagi H last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJDB18646.csv.gz (4.6 KB) · parquet (75.5 KB) — all 144 samples, every field with route and confidence · PRJDB18646_determinations.csv.gz (5.0 KB) — 576 evidence rows