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PRJEB65987 ERP151091

Norovirus evolution in immunocompromised patients, Netherlands

Intra-host evolution of Norovirus in immunocompromised individuals

140 samples from immunocompromised individuals in the Netherlands with chronic norovirus infection, including GI infection/diarrhoea and cancer-related cases, analyzed using a case-control design. machine-written summary

140 samples · 140 runs · NL · Age unknown · 2024 · 0.26 Gbp / sample

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Sources

✓Sequence archive 1,400○Abstract / description✓Full text 210○Supplementary tables–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave

✓ Sequence archive	1,400 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude)
○ Abstract / description	read; no usable statement
✓ Full text	210 sample values (family role, location site, shared setting type) · PMC11663770
○ 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

Interventions

intervention — arms not resolved

design observational_with_procedure · Intra-duodenal immunoglobulin treatment for chronic norovirus infection, observational

Samples at a glance

1 sampling locations · 1 country

Age

unknown140

Condition

transplant_or_immunocompromised74

gi_infection_or_diarrhoea62

other_cancer4

Country

NL140

Body site

primary140

Collected 2008–2022

Sequencing depth per sample · this project all projects

Sampling design and relatedness

longitudinalhouseholdssiblings

20 of 20 people sampled more than once (140 samples; median 4, up to 28 per person) · follow-up median 14 mo (max 6.3 y) · median interval between samples 2 mo (time from collection dates). Schedule stated by the source: “Irregular stool collection over course of chronic infection; timepoint labels include d0 and later days (e.g. d69, d83, d204, d434, d874, d888, d1891)”.

Each row is one person (20 shown); dots are samples at days since that person's first sample.

20 immunocompromised norovirus patients; P19 and P20 are siblings sharing a household (paper reports P19->P20 virus transmission).

sibling · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 1 linked group from explicit relations. 20 people in the project overall.

How longitudinal and relatedness information is derived

Community composition

Faecalibacterium 39.2%Ruminococcoides 23.1%Vescimonas 13.7%Nanosynbacter 3.4%Pilosibacter 0.7%Cutibacterium 0.6%Acutalibacter 0.5%UBA11524 0.5%not assigned to a genus 18.2%

Genera, mean relative abundance over 1 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage

field	samples	coverage	R1	R3
age_category	0	0%
country	140	100%	140
health_condition	140	100%	140
subject_id	140	100%	140
collection_date	140	100%	140
detailed_location	140	100%
health_condition_detail	140	100%	140
latitude	140	100%	140
location_locality	140	100%	140
location_region	140	100%	140
location_site	140	100%		140
longitude	140	100%	140
timepoint_label	140	100%	140
family_role	35	25%		35
shared_setting_type	35	25%		35

Papers (1)

Patterns of the within-host evolution of human norovirus in immunocompromised individuals and implications for treatment. 2024 PMID 39396425 PMC11663770 own_data

Details

Archive description

Norovirus will typically cause self-limiting acute enteric infections, however, the virus can cause chronic infections in immunocompromised individuals. During the course of these chronic infections, the virus will tend to accumulate mutations in the genome. The goal of this project is to determine what are the intra-host evolutionary patterns of Norovirus during chronic infections and how antiviral treatments affect the quasispecies.

How this project entered the registry

Classified as human gut / stool mixed assays of age unknown by sonnet_x2 with confidence 0.65. Assay mixed.

host run.scientific_name · “human feces metagenome”
body site run.scientific_name · “human feces metagenome”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMEA114403040	collection_date	2009-01-07	R1	0.90	biosample.attribute:collection_date	2009-01-07
SAMEA114403040	country	NL	R1	0.90	sample.attr.geographic_location_region_and_locality	Zuid-Holland, Rotterdam
SAMEA114403145	family_role	sibling	R3	0.60	paper.body.text	Patients P19 and P20 are siblings sharing the same household.
SAMEA114403040	health_condition	transplant_or_immunocompromised	R1	0.90	biosample_attr	Kidney transplantation, Chronic norovirus infection
SAMEA114403040	health_condition_detail	Kidney transplantation, Chronic norovirus infection	R1	0.90	sample.attr.host_disease_status	Kidney transplantation, Chronic norovirus infection
SAMEA114403040	latitude	51.9197	R1	0.90	biosample.attribute:geographic_location_latitude+geographic_location_longitude	51.91966299 4.47533143
SAMEA114403040	location_locality	Rotterdam	R1	0.85	biosample.attribute:geographic_location_region_and_locality	Zuid-Holland, Rotterdam
SAMEA114403040	location_region	South Holland	R1	0.75	biosample.attribute:geographic_location_region_and_locality	Zuid-Holland, Rotterdam
SAMEA114403040	location_site	Erasmus MC	R3	0.70	paper.fulltext.methods	approved by the Erasmus MC ethical committee
SAMEA114403040	longitude	4.4753	R1	0.90	biosample.attribute:geographic_location_latitude+geographic_location_longitude	51.91966299 4.47533143
SAMEA114403145	shared_setting_type	household	R3	0.60	paper.body.text	Patients P19 and P20 are siblings sharing the same household.
SAMEA114403040	subject_id	P1	R1	0.70	sample.name_rule:sample_alias	P1-d0
SAMEA114403040	timepoint_label	d0	R1	0.70	sample.name_rule:sample_alias	P1-d0

Sequencing

140 runs over 140 samples · mean 0.43 Gbp per run (median 0.26 Gbp, total 60.62 Gbp; 140 runs with a base count) · layout PAIRED 140 · platform ILLUMINA 140 · models Illumina MiSeq (140) · 4% of runs with a Sandpiper profile · first public 2024-10-09

Authors (13)

Izquierdo-Lara RW first · Villabruna N · Hesselink DA · Schapendonk CME · Ribó Pons S · Nieuwenhuijse D · Meier JIJ · Goodfellow I · Dalm VASH · Fraaij PLA · van Kampen JJA · Koopmans MPG · de Graaf M last

Downloads

PRJEB65987.csv.gz (5.7 KB) · parquet (78.9 KB) — all 140 samples, every field with route and confidence · PRJEB65987_determinations.csv.gz (13.7 KB) — 1,610 evidence rows

Samples (140 · every field this project has values for · hover a cell for its source)

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