Norovirus-positive stool metagenomics, Netherlands, 2015-2019
Shotgun metagenomic sequencing of 71 norovirus RT-qPCR-positive fecal samples from Dutch gastroenteritis surveillance (2015-2019), spanning age groups from neonates to elderly, in a cross-sectional design to recover norovirus and off-target enteric virus genomes. machine-written summary
71 samples · 71 runs · NL · Age unknown · 2023 · 0.36 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 353 sample values (age, collection date, country, sex, subject id) |
| ✓ Abstract / description | 142 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC10434279, PMC11522440 |
| ○ 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 |
Genera, mean relative abundance over 9 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 | 70 | 99% | ||||
| country | 71 | 100% | 71 | |||
| health_condition | 71 | 100% | 71 | |||
| subject_id | 71 | 100% | 71 | |||
| collection_date | 71 | 100% | 71 | |||
| health_condition_detail | 71 | 100% | 71 | |||
| age_at_collection_days | 70 | 99% | 70 | |||
| sex | 70 | 99% | 70 |
- Metagenomic Surveillance of Viral Gastroenteritis in a Public Health Setting. 2023 PMID 37432120 PMC10434279 own_data
- Accessible viral metagenomics for public health and clinical domains with Jovian. 2024 PMID 39472593 PMC11522440 own_data
Archive description
To investigate Norovirus (NoV) epidemiology there is a need for whole genome sequences. We performed Illumina shotgun metagenomic sequencing on 71 RT-qPCR NoV positive feces (Ct below 30) from the Netherlands NoV surveillance program between 2015-109. Sixty complete and 10 partial NoV genomes were generated, as well as off-target Adenovirus, Aichivirus, Coxsackievirus, Bocaparvovirus, human Parechovirus, Rotavirus A and Sapovirus. We hope these genomes help contextualize outbreak investigation and genetic epidemiology.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of elderly and adult by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host run.scientific_name · “human feces metagenome”
- body site study.description · “RT-qPCR NoV positive feces”
- body site run.scientific_name · “human feces metagenome”
- life stage sample.attr.host_age · “88 (n=33/71)”
- life stage sample.attr.host_age · “1 (n=21/71)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA110434721 | age_at_collection_days | 32481.0 | R1 | 0.85 | sample.attr.host_age | 89 |
| SAMEA110434721 | collection_date | 2016-01-25 | R1 | 0.90 | biosample.attribute:collection_date | 2016-01-25 |
| SAMEA110434721 | country | NL | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Netherlands |
| SAMEA110434721 | health_condition | gi_infection_or_diarrhoea | R4 | 0.50 | study.description | RT-qPCR NoV positive feces |
| SAMEA110434721 | health_condition_detail | Norovirus positive samples from surveillance program | R4 | 0.50 | study.description | RT-qPCR NoV positive feces |
| SAMEA110434721 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMEA110434721 | subject_id | R01-01 | R1 | 0.85 | sample.attr.host_subject_id | R01-01 |
Sequencing
71 runs over 71 samples · mean 0.56 Gbp per run (median 0.36 Gbp, total 39.55 Gbp; 71 runs with a base count) · layout PAIRED 71 · platform ILLUMINA 71 · models NextSeq 550 (63), Illumina MiSeq (8) · 13% of runs with a Sandpiper profile · first public 2023-07-06
Authors (12)
Schmitz D first · Zwagemaker F · van der Veer B · Vennema H · Laros JFJ · Koopmans MPG · De Graaf M · Kroneman A last · Nooij S · Janssens TKS · Cremer J · Verhagen R
Downloads
PRJEB54724.csv.gz (3.3 KB) · parquet (74.1 KB) — all 71 samples, every field with route and confidence · PRJEB54724_determinations.csv.gz (4.2 KB) — 495 evidence rows