References
- Zhou P, Yang XL, Wang XG, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020 Mar; 579(7798):270–273.
- Wu F, Zhao S, Yu B, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020 Mar; 579(7798):265–269.
- Chen L, Liu W, Zhang Q, et al. RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak. Emerg microbes infect. 2020 Dec;9(1):313–319. doi: 10.1080/22221751.2020.1725399
- Huang C, Wang Y, Li X, et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet. 2020;395(10223):497–506. doi: 10.1016/S0140-6736(20)30183-5
- Chen N, Zhou M, Dong X, et al. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet. 2020;395(10223):507–513. doi: 10.1016/S0140-6736(20)30211-7
- Guan WJ, Ni ZY, Hu Y, et al. Clinical characteristics of coronavirus disease 2019 in China. N Engl J med. 2020 Feb 28 [Online ahead of print] DOI: 10.1056/NEJMoa2002032.
- Nelemans T, Kikkert M. Viral innate immune evasion and the pathogenesis of emerging RNA virus infections. Viruses. 2019 Oct 18;11(10):961. doi: 10.3390/v11100961
- Fehr AR, Channappanavar R, Perlman S. Middle East respiratory syndrome: emergence of a pathogenic human coronavirus. Annu rev med. 2017 Jan 14;68:387–399. doi: 10.1146/annurev-med-051215-031152
- Newton AH, Cardani A, Braciale TJ. The host immune response in respiratory virus infection: balancing virus clearance and immunopathology. Semin immunopathol. 2016 Jul;38(4):471–482. doi: 10.1007/s00281-016-0558-0
- Channappanavar R, Zhao J, Perlman S. T cell-mediated immune response to respiratory coronaviruses. Immunol res. 2014 Aug;59(1-3):118–128. doi: 10.1007/s12026-014-8534-z
- Kindler E, Thiel V. SARS-CoV and IFN: too little, too late. Cell host microbe. 2016 Feb 10;19(2):139–141. doi: 10.1016/j.chom.2016.01.012
- Channappanavar R, Fehr AR, Vijay R, et al. Dysregulated type I interferon and inflammatory monocyte-macrophage responses cause lethal pneumonia in SARS-CoV-infected mice. Cell host microbe. 2016 Feb 10;19(2):181–193. doi: 10.1016/j.chom.2016.01.007
- Chen Y, Liu Q, Guo D. Emerging coronaviruses: genome structure, replication, and pathogenesis. J med virol. 2020 Apr;92(4):418–423. doi: 10.1002/jmv.25681
- de Wit E, van Doremalen N, Falzarano D, et al. SARS and MERS: recent insights into emerging coronaviruses. Nat rev microbiol. 2016 Aug;14(8):523–534. doi: 10.1038/nrmicro.2016.81
- Zhou J, Chu H, Li C, et al. Active replication of Middle East respiratory syndrome coronavirus and aberrant induction of inflammatory cytokines and chemokines in human macrophages: implications for pathogenesis. J infect dis. 2014 May 1;209(9):1331–1342. doi: 10.1093/infdis/jit504
- Wang D, Hu B, Hu C, et al. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China. JAMA. 2020 Feb 7 [Online ahead of print] DOI: 10.1001/jama.2020.1585.
- Xu Z, Shi L, Wang Y, et al. Pathological findings of COVID-19 associated with acute respiratory distress syndrome. Lancet respir med. 2020 Feb 18 [Online ahead of print] DOI: 10.1016/S2213-2600(20)30076-X.
- Monaco G, Lee B, Xu W, et al. RNA-Seq signatures normalized by mRNA abundance allow absolute deconvolution of human immune cell types. Cell rep. 2019 Feb 5;26(6):1627–1640. e7. doi: 10.1016/j.celrep.2019.01.041
- Wilson JA, Prow NA, Schroder WA, et al. RNA-Seq analysis of chikungunya virus infection and identification of granzyme A as a major promoter of arthritic inflammation. PLoS pathog. 2017 Feb;13(2):e1006155. doi: 10.1371/journal.ppat.1006155
- Michalovich D, Rodriguez-Perez N, Smolinska S, et al. Obesity and disease severity magnify disturbed microbiome-immune interactions in asthma patients. Nat commun. 2019 Dec 13;10(1):5711. doi: 10.1038/s41467-019-13751-9
- Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013 Jan 1;29(1):15–21. doi: 10.1093/bioinformatics/bts635
- Institute B. Picard Toolkit. (2019). Available from: http://broadinstitute.github.io/picard/.
- Wang L, Wang S, Li W. RSeQC: quality control of RNA-seq experiments. Bioinformatics. 2012 Aug 15;28(16):2184–2185. doi: 10.1093/bioinformatics/bts356
- Lee CM, Barber GP, Casper J, et al. UCSC genome browser enters 20th year. Nucleic acids res. 2020 Jan 8;48(D1):D756–D761.
- Liao Y, Smyth GK, Shi W. Featurecounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014 Apr 1;30(7):923–930. doi: 10.1093/bioinformatics/btt656
- Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome biol. 2014;15(12):550. doi: 10.1186/s13059-014-0550-8
- Yu G, Wang LG, Han Y, et al. Clusterprofiler: an R package for comparing biological themes among gene clusters. Omics: J integr biol. 2012 May;16(5):284–287. doi: 10.1089/omi.2011.0118
- Carbon S, Ireland A, Mungall CJ, et al. AmiGO: online access to ontology and annotation data. Bioinformatics. 2009 Jan 15;25(2):288–289. doi: 10.1093/bioinformatics/btn615
- Kanehisa M, Sato Y, Furumichi M, et al. New approach for understanding genome variations in KEGG. Nucleic acids res. 2019 Jan 8;47(D1):D590–D595. doi: 10.1093/nar/gky962
- Wang Y, Song F, Zhu J, et al. GSA: genome sequence archive < sup/>. Genom proteom bioinform. 2017 Feb;15(1):14–18. doi: 10.1016/j.gpb.2017.01.001
- National Genomics Data Center M, Partners. Database resources of the National Genomics Data Center in 2020. Nucleic acids res. 2020 Jan 8;48(D1):D24–D33.
- Jiang Y, Xu J, Zhou C, et al. Characterization of cytokine/chemokine profiles of severe acute respiratory syndrome. Am J respir crit care med. 2005 Apr 15;171(8):850–857. doi: 10.1164/rccm.200407-857OC
- Thaker SK, Ch'ng J, Christofk HR. Viral hijacking of cellular metabolism. BMC biol. 2019 Jul 18;17(1):59. doi: 10.1186/s12915-019-0678-9
- Huang KJ, Su IJ, Theron M, et al. An interferon-gamma-related cytokine storm in SARS patients. J med virol. 2005 Feb;75(2):185–194. doi: 10.1002/jmv.20255
- Teijaro JR, Walsh KB, Rice S, et al. Mapping the innate signaling cascade essential for cytokine storm during influenza virus infection. Proc. natl. acad. sci. U.S.A.. 2014 Mar 11;111(10):3799–3804. doi: 10.1073/pnas.1400593111
- Okabayashi T, Kariwa H, Yokota S, et al. Cytokine regulation in SARS coronavirus infection compared to other respiratory virus infections. J med virol. 2006 Apr;78(4):417–424. doi: 10.1002/jmv.20556
- Griffith JW, Sokol CL, Luster AD. Chemokines and chemokine receptors: positioning cells for host defense and immunity. Annu rev immunol. 2014;32:659–702. doi: 10.1146/annurev-immunol-032713-120145
- Sheahan T, Morrison TE, Funkhouser W, et al. Myd88 is required for protection from lethal infection with a mouse-adapted SARS-CoV. PLoS pathog. 2008 Dec;4(12):e1000240. doi: 10.1371/journal.ppat.1000240
- Ng PC, Lam CW, Li AM, et al. Inflammatory cytokine profile in children with severe acute respiratory syndrome. Pediatrics. 2004 Jan;113(1 Pt 1):e7–14. doi: 10.1542/peds.113.1.e7
- Zhang Y, Li J, Zhan Y, et al. Analysis of serum cytokines in patients with severe acute respiratory syndrome. Infect immun. 2004 Aug;72(8):4410–4415. doi: 10.1128/IAI.72.8.4410-4415.2004
- Bordon J, Aliberti S, Fernandez-Botran R, et al. Understanding the roles of cytokines and neutrophil activity and neutrophil apoptosis in the protective versus deleterious inflammatory response in pneumonia. Int J infect dis. 2013 Feb;17(2):e76–e83. doi: 10.1016/j.ijid.2012.06.006
- Saxena V, Lienesch DW, Zhou M, et al. Dual roles of immunoregulatory cytokine TGF-beta in the pathogenesis of autoimmunity-mediated organ damage. J immunol. 2008 Feb 1;180(3):1903–1912. doi: 10.4049/jimmunol.180.3.1903
- Yu X, Buttgereit A, Lelios I, et al. The cytokine TGF-beta promotes the development and homeostasis of alveolar macrophages. Immunity. 2017 Nov 21;47(5):903–912 e4. doi: 10.1016/j.immuni.2017.10.007
- Panesar NS. What caused lymphopenia in SARS and how reliable is the lymphokine status in glucocorticoid-treated patients? Med hypotheses. 2008 Aug;71(2):298–301. doi: 10.1016/j.mehy.2008.03.019
- O'Donnell R, Tasker RC, Roe MF. SARS: understanding the coronavirus: apoptosis may explain lymphopenia of SARS. Br med J. 2003 Sep 13;327(7415):620. doi: 10.1136/bmj.327.7415.620-b
- Panesar NS. Lymphopenia in SARS. Lancet. 2003 Jun 7;361(9373):1985. doi: 10.1016/S0140-6736(03)13557-X
- Cui W, Fan Y, Wu W, et al. Expression of lymphocytes and lymphocyte subsets in patients with severe acute respiratory syndrome. Clin infect dis. 2003 Sep 15;37(6):857–859. doi: 10.1086/378587
- Gu J, Gong E, Zhang B, et al. Multiple organ infection and the pathogenesis of SARS. J exp med. 2005 Aug 1;202(3):415–424. doi: 10.1084/jem.20050828
- Stockman LJ, Bellamy R, Garner P. SARS: systematic review of treatment effects. PLoS med. 2006 Sep;3(9):e343. doi: 10.1371/journal.pmed.0030343
- Panesar NS. Glucocorticoid treatment of patients with SARS: implications for mechanisms of immunopathology. Nat rev immunol. 2006 2006/04/01;6(4):334–334. doi: 10.1038/nri1835-c1
- Russell CD, Millar JE, Baillie JK. Clinical evidence does not support corticosteroid treatment for 2019-nCoV lung injury. Lancet. 2020 Feb 15;395(10223):473–475. doi: 10.1016/S0140-6736(20)30317-2