Gut virome in Cameroonian GI-infection patients near bats
63 samples from Cameroon (Kumba and Lysoka) from patients with GI infection/diarrhoea, studied to identify viral gastroenteritis agents linked to interspecies transmission from bats; cross-sectional design. machine-written summary
63 samples · 63 runs · CM · Age unknown · 2018 · 1.15 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 378 sample values (collection date, country, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC6344602, PMC8143477, PMC8201803 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 126 sample values (health condition, health condition detail) · from African Human Microbiome Portal (H3ABioNet) |
| – 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 54 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 | 63 | 100% | 63 | |||
| health_condition | 63 | 100% | 63 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 63 | 100% | 63 | |||
| detailed_location | 63 | 100% | ||||
| health_condition_detail | 63 | 100% | 63 | |||
| latitude | 63 | 100% | 63 | |||
| location_locality | 63 | 100% | 63 | |||
| location_region | 63 | 100% | 63 | |||
| longitude | 63 | 100% | 63 |
- A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases. 2021 PMID 34083435 PMC8201803 own_data
- Gut Virome Analysis of Cameroonians Reveals High Diversity of Enteric Viruses, Including Potential Interspecies Transmitted Viruses. 2019 PMID 30674646 PMC6344602 own_data
- Novel Siphoviridae Bacteriophages Infecting Bacteroides uniformis Contain Diversity Generating Retroelement. 2021 PMID 33919474 PMC8143477 unsure
Archive description
To identify viral gastroenteritis aetiological agents in Cameroonian patients arising as a result of interspecies transmission from bats.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.80. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “Gut virome of Cameroonians”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN10080877 | collection_date | 2014 | R1 | 0.90 | biosample.attribute:collection_date | 2014 |
| SAMN10080877 | country | CM | R1 | 0.90 | sample.attr.geo_loc_name | Cameroon: Kumba |
| SAMN10080877 | health_condition | gi_infection_or_diarrhoea | R2 | 0.70 | external.ahmp source | DISEASE: Diarrhea |
| SAMN10080877 | health_condition_detail | Diarrhea | R2 | 0.70 | external.ahmp source | DISEASE: Diarrhea |
| SAMN10080877 | latitude | 4.6333 | R1 | 0.90 | biosample.attribute:lat_lon | 4.6333 N 9.445 E |
| SAMN10080877 | location_locality | Kumba | R1 | 0.85 | biosample.attribute:geo_loc_name | Cameroon: Kumba |
| SAMN10080877 | location_region | South-West Province | R1 | 0.60 | biosample.attribute:lat_lon | 4.6333 N 9.445 E |
| SAMN10080877 | longitude | 9.4450 | R1 | 0.90 | biosample.attribute:lat_lon | 4.6333 N 9.445 E |
Sequencing
63 runs over 63 samples · mean 1.37 Gbp per run (median 1.15 Gbp, total 86.16 Gbp; 63 runs with a base count) · layout PAIRED 63 · platform ILLUMINA 63 · models NextSeq 500 (63) · 89% of runs with a Sandpiper profile · first public 2018-09-24
Authors (27)
Yinda CK first · Vanhulle E · Conceição-Neto N · Beller L · Deboutte W · Shi C · Ghogomu SM · Maes P · Van Ranst M · Matthijnssens J last · Hedžet S first · Rupnik M · Accetto T last · Tisza MJ first · Buck CB last · Zeng S first · Almeida A · Li S · Ying J · Wang H · Qu Y · Paul Ross R · Stanton C · Zhou Z · Niu X · Mu D · Wang S last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata
Downloads
PRJNA491626.csv.gz (2.4 KB) · parquet (72.0 KB) — all 63 samples, every field with route and confidence · PRJNA491626_determinations.csv.gz (4.2 KB) — 504 evidence rows