Konno, Y. et al. SARS-CoV-2 ORF3b is a potent interferon antagonist whose activity is increased by a naturally occurring elongation variant. Cell Rep. 32, 108185 (2020).
Li, J. Y. et al. The ORF6, ORF8 and nucleocapsid proteins of SARS-CoV-2 inhibit type I interferon signaling pathway. Virus Res. 286, 198074 (2020).
Xia, H. et al. Evasion of type I interferon by SARS-CoV-2. Cell Rep. 33, 108234 (2020).
Chen, S. T. et al. A shift in lung macrophage composition is associated with COVID-19 severity and recovery. Sci. Transl. Med. 14, eabn5168 (2022).
Theobald, S. J. et al. Long-lived macrophage reprogramming drives spike protein-mediated inflammasome activation in COVID-19. EMBO Mol. Med. 13, e14150 (2021).
Harne, R., Williams, B., Abdelal, H. F. M., Baldwin, S. L. & Coler, R. N. SARS-CoV-2 infection and immune responses. AIMS Microbiol. 9, 245–276 (2023).
Wei, X. et al. Macrophage peroxisomes guide alveolar regeneration and limit SARS-CoV-2 tissue sequelae. Science 387, eadq2509 (2025).
Zheng, J. et al. Severe acute respiratory syndrome coronavirus 2-induced immune activation and death of monocyte-derived human macrophages and dendritic cells. J. Infect. Dis. 223, 785–795 (2021).
Lian, Q. et al. Differential effects of macrophage subtypes on SARS-CoV-2 infection in a human pluripotent stem cell-derived model. Nat. Commun. 13, 2028 (2022).
Dinnon, K. H. et al. A mouse-adapted model of SARS-CoV-2 to test COVID-19 countermeasures. Nature 586, 560–566 (2020).
Leist, S. R. et al. A mouse-adapted SARS-CoV-2 induces acute lung injury and mortality in standard laboratory mice. Cell 183, 1070–1085.e12 (2020).
Wahl, A. et al. A germ-free humanized mouse model shows the contribution of resident microbiota to human-specific pathogen infection. Nat. Biotechnol. https://doi.org/10.1038/s41587-023-01906-5 (2023).
De, C. et al. Human T cells efficiently control RSV infection. JCI Insight 8, e168110 (2023).
Wahl, A. et al. Precision mouse models with expanded tropism for human pathogens. Nat. Biotechnol. 37, 1163–1173 (2019).
Wahl, A. et al. SARS-CoV-2 infection is effectively treated and prevented by EIDD-2801. Nature 591, 451–457 (2021).
Guerrini, V. et al. Storage lipid studies in tuberculosis reveal that foam cell biogenesis is disease-specific. PLoS Pathog. 14, e1007223 (2018).
Thomas, A. C., Eijgelaar, W. J., Daemen, M. J. & Newby, A. C. The pro-fibrotic and anti-inflammatory foam cell macrophage paradox. Genom. Data 6, 136–138 (2015).
Guerrini, V. & Gennaro, M. L. Foam cells: one size doesn’t fit all. Trends Immunol. 40, 1163–1179 (2019).
Thomas, A. C., Eijgelaar, W. J., Daemen, M. J. & Newby, A. C. Foam cell formation in vivo converts macrophages to a pro-fibrotic phenotype. PLoS ONE 10, e0128163 (2015).
Buechler, C. et al. Adipophilin is a sensitive marker for lipid loading in human blood monocytes. Biochim. Biophys. Acta 1532, 97–104 (2001).
Persson, J., Degerman, E., Nilsson, J. & Lindholm, M. W. Perilipin and adipophilin expression in lipid loaded macrophages. Biochem. Biophys. Res. Commun. 363, 1020–1026 (2007).
Merritt, C. R. et al. Multiplex digital spatial profiling of proteins and RNA in fixed tissue. Nat. Biotechnol. 38, 586–599 (2020).
Yoon, J. J. et al. Orally efficacious broad-spectrum ribonucleoside analog inhibitor of influenza and respiratory syncytial viruses. Antimicrob. Agents Chemother. 62, e00766-18 (2018).
Kabinger, F. et al. Mechanism of molnupiravir-induced SARS-CoV-2 mutagenesis. Nat. Struct. Mol. Biol. 28, 740–746 (2021).
Kissler, S. M. et al. Viral dynamics of SARS-CoV-2 variants in vaccinated and unvaccinated persons. N. Engl. J. Med. 385, 2489–2491 (2021).
Milligan, E. C. et al. Infant rhesus macaques immunized against SARS-CoV-2 are protected against heterologous virus challenge 1 year later. Sci. Transl. Med. 15, eadd6383 (2023).
Almeida-González, F. R. et al. A step closer to elastogenesis on demand; inducing mature elastic fibre deposition in a natural biomaterial scaffold. Mater. Sci. Eng. C 120, 111788 (2021).
Mills, B., Akram, A. R., Scholefield, E., Bradley, M. & Dhaliwal, K. Optical screening of novel bacteria-specific probes on ex vivo human lung tissue by confocal laser endomicroscopy. J. Vis. Exp. https://doi.org/10.3791/56284 (2017).
Conway, E. M. et al. Understanding COVID-19-associated coagulopathy. Nat. Rev. Immunol. 22, 639–649 (2022).
Szilveszter, M. et al. The management of COVID-19-related coagulopathy: a focus on the challenges of metabolic and vascular diseases. Int. J. Mol. Sci. 24, 12782 (2023).
Klok, F. A. et al. Incidence of thrombotic complications in critically ill ICU patients with COVID-19. Thromb. Res. 191, 145–147 (2020).
Ortega-Paz, L., Capodanno, D., Montalescot, G. & Angiolillo, D. J. Coronavirus disease 2019-associated thrombosis and coagulopathy: review of the pathophysiological characteristics and implications for antithrombotic management. J. Am. Heart Assoc. 10, e019650 (2021).
Eberhardt, N. et al. SARS-CoV-2 infection triggers pro-atherogenic inflammatory responses in human coronary vessels. Nat. Cardiovasc. Res. https://doi.org/10.1038/s44161-023-00336-5 (2023).
Ryu, J. K. et al. Fibrin drives thromboinflammation and neuropathology in COVID-19. Nature https://doi.org/10.1038/s41586-024-07873-4 (2024).
Junqueira, C. et al. FcγR-mediated SARS-CoV-2 infection of monocytes activates inflammation. Nature 606, 576–584 (2022).
Labzin, L. I. et al. Macrophage ACE2 is necessary for SARS-CoV-2 replication and subsequent cytokine responses that restrict continued virion release. Sci. Signal. 16, eabq1366 (2023).
Hönzke, K. et al. Human lungs show limited permissiveness for SARS-CoV-2 due to scarce ACE2 levels but virus-induced expansion of inflammatory macrophages. Eur. Respir. J. 60, 2102725 (2022).
Barnett, K. C. et al. An epithelial-immune circuit amplifies inflammasome and IL-6 responses to SARS-CoV-2. Cell Host Microbe 31, 243–259.e6 (2023).
Katsura, H. et al. Human lung stem cell-based alveolospheres provide insights into SARS-CoV-2-mediated interferon responses and pneumocyte dysfunction. Cell Stem Cell 27, 890–904.e8 (2020).
Kato, T. et al. Prevalence and mechanisms of mucus accumulation in COVID-19 lung disease. Am. J. Respir. Crit. Care Med. 206, 1336–1352 (2022).
Hou, Y. J. et al. SARS-CoV-2 reverse genetics reveals a variable infection gradient in the respiratory tract. Cell 182, 429–446.e14 (2020).
Menachery, V. D. et al. SARS-like WIV1-CoV poised for human emergence. Proc. Natl Acad. Sci. USA 113, 3048–3053 (2016).
Menachery, V. D. et al. A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence. Nat. Med. 21, 1508–1513 (2015).
Scobey, T. et al. Reverse genetics with a full-length infectious cDNA of the Middle East respiratory syndrome coronavirus. Proc. Natl Acad. Sci. USA 110, 16157–16162 (2013).
Yount, B. et al. Reverse genetics with a full-length infectious cDNA of severe acute respiratory syndrome coronavirus. Proc. Natl Acad. Sci. USA 100, 12995–13000 (2003).
Van Rompay, K. K. A. et al. Early post-infection treatment of SARS-CoV-2 infected macaques with human convalescent plasma with high neutralizing activity had no antiviral effects but moderately reduced lung inflammation. PLoS Pathog. 18, e1009925 (2022).
Van Rompay, K. K. A. et al. Early treatment with a combination of two potent neutralizing antibodies improves clinical outcomes and reduces virus replication and lung inflammation in SARS-CoV-2 infected macaques. PLoS Pathog. 17, e1009688 (2021).
Risso, D., Ngai, J., Speed, T. P. & Dudoit, S. Normalization of RNA-seq data using factor analysis of control genes or samples. Nat. Biotechnol. 32, 896–902 (2014).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Korotkevich, G., Sukhov, V. & Sergushichev, A. Fast gene set enrichment analysis. Preprint at bioRxiv https://doi.org/10.1101/060012 (2021).
The Gene Ontology Consortium. The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res. 49, D325–D334 (2021).
Jassal, B. et al. The reactome pathway knowledgebase. Nucleic Acids Res. 48, D498–D503 (2020).
Adams, T. S. et al. Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis. Sci. Adv. 6, eaba1983 (2020).
Wright, E. S. & Vetsigian, K. H. Quality filtering of Illumina index reads mitigates sample cross-talk. BMC Genomics 17, 876 (2016).
Zhang, Y., Parmigiani, G. & Johnson, W. E. ComBat-seq: batch effect adjustment for RNA-seq count data. NAR Genom. Bioinform. 2, lqaa078 (2020).
Benjamini, Y., Krieger, A. M. & Yekutieli, D. Adaptive linear step-up procedures that control the false discovery rate. Biometrika 93, 491–507 (2006).
UNCBARC. Garcia_BLTL_covid. GitHub https://github.com/UNCBARC/Garcia_BLTL_covid (2024).
