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PRJNA624223 SRP273658

Gut virome kinetics in COVID-19 patients, longitudinal

Gut microbiome alterations and longitudinal kinetics in COVID-19 patients

73 fecal samples from COVID-19 patients and healthy controls, analyzed for gut DNA virome and bacteriome composition using viromescan, with longitudinal collection during hospitalization; some samples involved antibiotic use. machine-written summary

73 samples · 73 runs · CN, HK · Adult · 2020 · 3.50 Gbp / sample

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Sources
✓Sequence archive 250○Abstract / description✓Full text 168✓Supplementary tables 56✓External resources 230–User contribution–Human verified

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

what each source gave
✓ Sequence archive250 sample values (age, sex, subject id, timepoint)
○ Abstract / descriptionread; no usable statement
✓ Full text168 sample values (collection date, country, location locality, subject id) · PMC7237927, PMC7961713, PMC7963026, PMC8653907, PMC8664710
✓ Supplementary tables56 sample values (collection date, health condition, health condition detail)
✓ External resources230 sample values (antibiotic exposure, country, health condition, health condition detail) · from GMrepo v3, Meta2DB (LLNL)
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Interventions

intervention — arms not resolved

Antibiotic given as the study intervention (incl. eradication therapy design observational_with_procedure · population other_infection · Empirical antibiotics received by COVID-19 patients (observed, not trial-assigned)

“COVID-19 patients who received empirical antibiotics” — abstract:34915282 (study level; per-sample arms are in the intervention column below)

Samples at a glance
2 countries
Age
adult55
elderly18
Condition
other_infection57
healthy_control15
Sex
male39
female34
Country
CN70
HK3
Body site
primary73
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)all projects, 0.03–0.1 Gbp: 17,066 samples (3 %)all projects, 0.1–0.3 Gbp: 29,179 samples (5 %)all projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 1 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 22 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 46 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 3 samplesall projects, 30–100 Gbp: 3,024 samples (1 %)this project, 30–100 Gbp: 1 samplesall projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 3.50 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinal — not resolved

13 of 36 people sampled more than once (50 samples; median 4, up to 7 per person). Schedule stated by the source: “Fecal samples collected serially 2 to 3 times per week from time of hospitalization until discharge, with some follow-up after discharge” (time origin: other:hospitalization); stated follow-up 22 d.

How longitudinal and relatedness information is derived

Community composition
Bacteroides 10.4%Phocaeicola 9.6%Parabacteroides 7.9%Enterococcus_A 5.0%Bifidobacterium 4.0%Blautia_A 3.4%Mediterraneibacter 3.0%Akkermansia 2.5%Escherichia 2.3%Enterocloster 2.3%Prevotella 2.1%Roseburia 2.0%not assigned to a genus 3.9%other genera 41.5%

Genera, mean relative abundance over 66 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category73 100%
country73 100%703
health_condition72 99%72
subject_id73 100%5221
age_at_collection_days73 100%73
collection_date73 100%271
detailed_location73 100%
health_condition_detail73 100%73
location_locality73 100%73
sex73 100%73
antibiotic_exposure69 95%69
timepoint_label52 71%52
Papers (16)
  • Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization. 2020 PMID 32442562 PMC7237927 own_data
  • Variability in digestive and respiratory tract Ace2 expression is associated with the microbiome. 2021 PMID 33725024 PMC7963026 own_data
  • Metagenomics Approaches to Investigate the Gut Microbiome of COVID-19 Patients. 2021 PMID 33786001 PMC7961713 own_data
  • Alterations in the Composition of Intestinal DNA Virome in Patients With COVID-19. 2021 PMID 34900762 PMC8653907 own_data
  • Alterations of fecal antibiotic resistome in COVID-19 patients after empirical antibiotic exposure. 2022 PMID 34915282 PMC8664710 own_data
11 more
  • Microbiota and COVID-19: Long-term and complex influencing factors. 2022 PMID 36033885 PMC9417543
  • JWES: a new pipeline for whole genome/exome sequence data processing, management, and gene-variant discovery, annotation, prediction, and genotyping. 2021 PMID 34370400 PMC8409305
  • Early indicators of microbial strain dysbiosis in the human gastrointestinal microbial community of certain healthy humans and hospitalized COVID-19 patients. 2022 PMID 35449389 PMC9022020
  • Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes. 2022 PMID 36068270 PMC9446638
  • Untangling the link between the human gut microbiota composition and the severity of the symptoms of the COVID-19 infection. 2022 PMID 36086955 PMC9538590
  • Cross-cohort single-nucleotide-variant profiling of gut microbiota suggests a novel gut-health assessment approach. 2023 PMID 37905808 PMC10734426
  • Deciphering Microbial Shifts in the Gut and Lung Microbiomes of COVID-19 Patients. 2024 PMID 38930440 PMC11205787
  • Dysrupted microbial tryptophan metabolism associates with SARS-CoV-2 acute inflammatory responses and long COVID. 2024 PMID 39551951 PMC11581176
  • <i>Akkermansia muciniphila</i> primes lung-resident antiviral immunity via the gut-lung axis during SARS-CoV-2 infection. 2026 PMID 41836373 PMC12982362
  • Dissecting the Role of the Human Microbiome in COVID-19 via Metagenome-assembled Genomes 2022
  • Two dimensions of chemical variation of the human microbiome across body sites and in COVID-19 patients 2023
Details
Archive description

We aim to provide proof evidence of fecal microbiome alterations in COVID-19 and investigated microbiome and SARS-CoV-2 kinetics in 15 diagnosed COVID-19 cases

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of adult and elderly by deterministic_prior with confidence 0.90. Assay shotgun_dna.

  • host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
  • body site study.title · “Gut microbiome alterations and”
  • body site study.description · “proof evidence of fecal microbiome alterations in”
  • life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
  • life stage sample.attr.age · “71 (n=20/73)”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN15064737age_at_collection_days14610.0R10.85sample.attr.age40
SAMN15064737antibiotic_exposurenoR20.70external.meta2db sourceantibiotics: FALSE
SAMN15064788collection_date2020-02-27R20.75paper.supp.Table_1.xlsx[Sheet1!Stool collection]CoV9 | Stool collection: 2020-02-27
SAMN15064737collection_date2020-02-05/2020-03-17R30.70paper.fulltext.methodsrecruited between February 5 and March 17, 2020
SAMN15064737countryCNR20.75external.gmrepo sourcecountry: China
SAMN15064753countryCNR20.70external.meta2db sourcegeo_loc_name: China:Hong Kong
SAMN15064752countryHKR30.70paper.fulltext.methodsPrince of Wales Hospital or the United Christian Hospital, Hong Kong
SAMN15064737health_conditionhealthy_controlR20.80paper.supp.Table_1.xlsx[Sheet1!Group]Healthy control
SAMN15064753health_conditionother_infectionR20.70external.meta2db sourcepneumonia
SAMN15064758health_conditionother_infectionR20.75external.gmrepo sourcephenotype: COVID-19
SAMN15064737health_condition_detailHealthy controlR20.85paper.supp.Table_1.xlsx[Sheet1!Group]Healthy control
SAMN15064759health_condition_detailCOVID-19R20.75external.gmrepo sourcephenotype: COVID-19
SAMN15064767health_condition_detailSARS-CoV-2R20.70external.meta2db sourceSARS-CoV-2
SAMN15064737location_localityHong KongR30.70paper.fulltext.abstractHong Kong, from February 5 through March 17, 2020
SAMN15064737sexmaleR10.90sample.attr.host_sexmale
SAMN15064758subject_idCoV1R10.70sample.name_rule:isolateCoV1D0
SAMN15064737subject_idSAMN15064737R30.65design.one_sample_per_subject:fulltext6 patients hospitalized with community-acquired pneumonia (pneumonia controls), and 15 healthy individuals (healthy controls)
SAMN15064758timepoint_label0R10.70sample.name_rule:isolateCoV1D0
Sequencing

73 runs over 73 samples · mean 4.80 Gbp per run (median 3.50 Gbp, total 350.44 Gbp; 73 runs with a base count) · layout PAIRED 73 · platform ILLUMINA 73 · models NextSeq 550 (73) · 90% of runs with a Sandpiper profile · first public 2020-07-28

Authors (29)

Ke S first · Weiss ST · Liu YY last · Mancabelli L first · Milani C · Fontana F · Lugli GA · Tarracchini C · Viappiani A · Ciociola T · Ticinesi A · Nouvenne A · Meschi T · Turroni F · Ventura M last · Alessandri G · De Biase R · Bocchio F · De Conto F · Bussolati O · Cecchi R · Pusadkar V first · Mazumder A · Azad A · Patil D · Azad RK last · van Sinderen D · Dick JM first last · Liu Y last

Downloads

PRJNA624223.csv.gz (3.2 KB) · parquet (74.2 KB) — all 73 samples, every field with route and confidence · PRJNA624223_determinations.csv.gz (7.7 KB) — 704 evidence rows

Samples (73 · every field this project has values for · hover a cell for its source)
Loading the sample table…