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Type: Journal article
Title: Profiling of lung SARS-CoV-2 and influenza virus infection dissects virus-specific host responses and gene signatures
Author: Kulasinghe, A.
Tan, C.W.
Ribeiro Dos Santos Miggiolaro, A.F.
Monkman, J.
SadeghiRad, H.
Bhuva, D.D.
Motta Junior, J.D.S.
Busatta Vaz de Paula, C.
Nagashima, S.
Baena, C.P.
Souza-Fonseca-Guimaraes, P.
de Noronha, L.
McCulloch, T.
Rossi, G.R.
Cooper, C.
Tang, B.
Short, K.R.
Davis, M.J.
Souza-Fonseca-Guimaraes, F.
Belz, G.T.
et al.
Citation: European Respiratory Journal, 2022; 59(6):2101881-2101881
Publisher: European Respiratory Society (ERS)
Issue Date: 2022
ISSN: 0903-1936
Statement of
Arutha Kulasinghe, Chin Wee Tan, Anna Flavia Ribeiro dos Santos Miggiolaro, James Monkman, Habib SadeghiRad, Dharmesh D. Bhuva, Jarbas da Silva Motta Junior, Caroline Busatta Vaz de Paula, Seigo Nagashima, Cristina Pellegrino Baena, Paulo Souza-Fonseca-Guimaraes, Lucia de Noronha, Timothy McCulloch, Gustavo Rodrigues Rossi, Caroline Cooper, Benjamin Tang, Kirsty R. Short, Melissa J. Davis, Fernando Souza-Fonseca-Guimaraes, Gabrielle T. Belz, and Ken O, Byrne
Abstract: BACKGROUND: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which emerged in late 2019 has spread globally, causing a pandemic of respiratory illness designated coronavirus disease 2019 (COVID-19). A better definition of the pulmonary host response to SARS-CoV-2 infection is required to understand viral pathogenesis and to validate putative COVID-19 biomarkers that have been proposed in clinical studies. METHODS: Here, we use targeted transcriptomics of formalin-fixed paraffin-embedded tissue using the NanoString GeoMX platform to generate an in-depth picture of the pulmonary transcriptional landscape of COVID-19, pandemic H1N1 influenza and uninfected control patients. RESULTS: Host transcriptomics showed a significant upregulation of genes associated with inflammation, type I interferon production, coagulation and angiogenesis in the lungs of COVID-19 patients compared to non-infected controls. SARS-CoV-2 was non-uniformly distributed in lungs (emphasising the advantages of spatial transcriptomics) with the areas of high viral load associated with an increased type I interferon response. Once the dominant cell type present in the sample, within patient correlations and patient-patient variation, had been controlled for, only a very limited number of genes were differentially expressed between the lungs of fatal influenza and COVID-19 patients. Strikingly, the interferon-associated gene IFI27, previously identified as a useful blood biomarker to differentiate bacterial and viral lung infections, was significantly upregulated in the lungs of COVID-19 patients compared to patients with influenza. CONCLUSION: Collectively, these data demonstrate that spatial transcriptomics is a powerful tool to identify novel gene signatures within tissues, offering new insights into the pathogenesis of SARS-COV-2 to aid in patient triage and treatment.
Keywords: COVID-19
Influenza A Virus, H1N1 Subtype
Influenza, Human
Interferon Type I
Rights: ©The authors 2022. This version is distributed under the terms of the Creative Commons Attribution Non-Commercial Licence 4.0. For commercial reproduction rights and permissions contact
DOI: 10.1183/13993003.01881-2021
Grant ID:
Appears in Collections:Medical Sciences publications

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