Evidence map›Paper›PMID 40640204›Full record

ArticleScientific data2025

Molecular landscape of respiratory infection: A large-scale, multi-centre blood transcriptome dataset.

Tracy Chew, Tiana M Pelaia, Amy L Phu, Sally Teoh, Ya Wang, Nandan Deshpande, Karan Kim, Velma Herwanto, Gunawan, Thomas Karvunidis and 18 more

Abstract readDataset
In one paragraph

Article in Scientific data, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. GIDISdb: a gene expression database for exploring human immune responses in infectious diseases.Database : the journal of biological databases and curation · 2026
    Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

28 authors.

Tracy Chew *Sydney Informatics Hub, Core Research Facilities, University of Sydney, Sydney, NSW, Australia. Tracy.chew@sydney.edu.au.
Tiana M Pelaia *Department of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia.
Amy L PhuResearch and Education Network, Western Sydney Local Health District, Westmead Hospital, Westmead, NSW, Australia.
Sally TeohDepartment of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia.
Ya WangDepartment of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia.
Nandan DeshpandeSydney Informatics Hub, Core Research Facilities, University of Sydney, Sydney, NSW, Australia.
Karan KimCentre for Immunology and Allergy Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW, Australia.ORCID 0000-0003-3898-3308
Velma HerwantoDepartment of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia.
GunawanMedistra Hospital, Gatot Subroto Kav. 59, Jakarta, Indonesia.
Thomas KarvunidisMedical ICU, 1st Department of Internal Medicine, Charles University and Teaching Hospital Pilsen, 323 00, Plzeň, Czech Republic.
Yoann ZerbibDepartment of Intensive Care Medicine, Amiens University Hospital, Amiens, France.
Kirsty R ShortSchool of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
Stephen MacdonaldCentre for Clinical Research in Emergency Medicine, Harry Perkins Institute of Medical Research, Royal Perth Hospital, University of Western Australia, Perth, WA, Australia.
Irani ThevarajanVictorian Infectious Disease Service, The Royal Melbourne Hospital, Melbourne, VIC, Australia.
Darawan RinchaiTranslational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar.
Win Sen KuanEmergency Medicine Department, National University Hospital, Singapore, Singapore.
Ben KnippenbergDepartment of Infectious Diseases and Microbiology, Westmead Hospital, WSLHD, Westmead, NSW, Australia.
Jonathan IredellCentre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, NSW, Australia.
Philip N BrittonDepartment of Infectious Diseases and Microbiology, the Children's Hospital at Westmead, Westmead, NSW, Australia.
Owen HutchingsRPA Virtual Hospital, Sydney Local Health District, Camperdown, NSW, Australia.
Warwick J BrittonDepartment of Clinical Immunology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.
John-Sebastian EdenCentre for Virology Research, the Westmead Institute for Medical Research, Westmead, NSW, Australia.ORCID 0000-0003-1374-3551
Sam OrdeDepartment of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia.
Benjamin TangCentre for Immunology and Allergy Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW, Australia.ORCID 0000-0002-1469-9540
Anthony McLeanDepartment of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia.
Damien ChaussabelTranslational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar.ORCID 0000-0002-6131-7242
Klaus SchughartDepartment of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Centre, Memphis, Tennessee, USA.ORCID 0000-0002-6824-7523
Maryam ShojaeiDepartment of Intensive Care Medicine, Nepean Hospital, Penrith, NSW, Australia. maryam.shojaei@sydney.edu.au.ORCID 0000-0002-5400-4029

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Respiratory infections pose significant challenges to global health, impacting millions of individuals annually. Understanding the molecular mechanisms underlying the pathogenicity of these infections is crucial for developing effective interventions. RNA sequencing provides insights into a patient's global transcriptome changes, facilitating the identification of host gene signatures in response to infection and potential therapeutic targets. Here we present an extensive whole blood transcriptome dataset from a demographically diverse cohort of 502 patients with infections including COVID-19, seasonal coronavirus, influenza A or influenza B, sepsis, septic shock, and co-infections (Viral/Viral, Bacterial/Viral, Bacterial/Viral/Fungal, Viral/Fungal, Viral/ Viral/Fungal). The cohort size and depth of data showcase its potential to unravel respiratory infection pathogenesis for the development of better diagnostics, treatments, and preventive strategies for respiratory infections and future global health crises.

Indexed as

Respiratory Tract InfectionsTranscriptomeCoinfectionCOVID-19HumansInfluenza, Human

Identifiers

PMID40640204
PMCPMC12246199

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.