References
- Wiersinga WJ, Rhodes A, Cheng AC, et al. Pathophysiology, transmission, diagnosis, and treatment of coronavirus disease 2019 (COVID-19): a review. JAMA. 2020;324(8):782–793. DOI:10.1001/jama.2020.12839
- https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports.
- Vkovski P, Kratzel A, Steiner S, et al. Coronavirus biology and replication: implications for SARS-CoV-2. Nat Rev Microbiol. 2021;19(3):155–170. DOI:10.1038/s41579-020-00468-6
- Gheblawi M, Wang K, Viveiros A, et al. Angiotensin-Converting enzyme 2: SARS-CoV-2 receptor and regulator of the Renin-Angiotensin system: celebrating the 20th Anniversary of the discovery of ACE2. Circ Res. 2020;126(10):1456–1474. DOI:10.1161/CIRCRESAHA.120.317015
- Gupta S, Wang W, Hayek SS, et al. Association between early treatment with Tocilizumab and mortality among critically ill patients with COVID-19. JAMA Intern Med. 2021;181:41–51.
- Stawicki SP, Jeanmonod R, Miller AC, et al. The 2019-2020 Novel coronavirus (severe acute respiratory syndrome coronavirus 2) pandemic: a joint American college of academic international medicine-world academic council of emergency medicine multidisciplinary COVID-19 working group consensus paper. Glob Infect Dis. 2020;12(2):47–93. DOI:10.4103/jgid.jgid_86_20
- Reilly MP, Bornfeldt KE. Integrative Multiomics approaches for discovery of new drug targets for cardiovascular disease. Circulation. 2021;143(25):2471–2474.
- Pucher BM, Zeleznik OA, Thallinger GG. Comparison and evaluation of integrative methods for the analysis of multilevel omics data: a study based on simulated and experimental cancer data. Brief Bioinform. 2019;20(2):671–681.
- Asselah T, Durantel D, Pasmant E, et al. COVID-19: Discovery, diagnostics and drug development. J Hepatol. 2021;74(1):168–184. DOI:10.1016/j.jhep.2020.09.031
- Smyrlaki I, Ekman M, Lentini A, et al. Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-PCR. Nat Commun. 2020;11(1):4812. DOI:10.1038/s41467-020-18611-5
- Wee SK, Sivalingam SP, Yap EP. Rapid direct nucleic acid amplification test without RNA extraction for SARS-CoV-2 using a portable PCR thermocycler. Genes (Basel). 2020;11(6):664.
- West R, Kobokovich A, Connell N, et al. COVID-19 antibody tests: a valuable public health tool with limited relevance to individuals. Trends Microbiol. 2021;29(3):214–223. DOI:10.1016/j.tim.2020.11.002
- Taleghani N, Taghipour F. Diagnosis of COVID-19 for controlling the pandemic: a review of the state-of-the-art. Biosens Bioelectron. 2021;174:112830.
- Zoldos V, Horvat T, Lauc G. Glycomics meets genomics, epigenomics and other high throughput omics for system biology studies. Curr Opin Chem Biol. 2013;17(1):34–40.
- Chiu CY, Miller SA. Clinical metagenomics. Nat Rev Genet. 2019;20(6):341–355.
- Wilson MR, Naccache SN, Samayoa E, et al. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med. 2014;370(25):2408–2417. DOI:10.1056/NEJMoa1401268
- Zhou P, Yang XL, Wang XG, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020;579(7798):270–273. DOI:10.1038/s41586-020-2012-7
- Lu R, Zhao X, Li J, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet. 2020;395(10224):565–574. DOI:10.1016/S0140-6736(20)30251-8
- Korber B, Fischer WM, Gnanakaran S, et al. Tracking changes in Sars-cov-2 spike: evidence that D614g increases infectivity of the Covid-19 virus. Cell. 2020;182(4):812–827. DOI:10.1016/j.cell.2020.06.043
- Xiao M, Liu X, Ji J, et al. Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples. Genome Med. 2020;12(1):57. DOI:10.1186/s13073-020-00751-4
- Golebiewski M, Tretyn A. Generating amplicon reads for microbial community assessment with next-generation sequencing. J Appl Microbiol. 2020;128(2):330–354.
- McNamara RP, Caro-Vegas C, Landis JT, et al. High-Density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States. Cell Rep. 2020;33(5):108352. DOI:10.1016/j.celrep.2020.108352
- Marotz C, Belda-Ferre P, Ali F, et al. SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment. Microbiome. 2021;9(1):132. DOI:10.1186/s40168-021-01083-0
- Brihn A, Chang J, Oyong K, et al. Diagnostic performance of an antigen test with RT-PCR for the detection of SARS-CoV-2 in a hospital setting - Los Angeles County, California,June-August 2020. MMWR Morb Mortal Wkly Rep. 2021;70(19):702–706. DOI:10.15585/mmwr.mm7019a3
- Harvey MG, Smith BT, Glenn TC, et al. Sequence capture versus restriction site associated DNA sequencing for shallow systematics. Syst Biol. 2016;65(5):910–924. DOI:10.1093/sysbio/syw036
- Kim KW, Deveson IW, Pang C, et al. Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing. Sci Rep. 2021;11(1):3934. DOI:10.1038/s41598-021-83642-x
- Maurano MT, Ramaswami S, Zappile P, et al. Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City region. Genome Res. 2020;30(12):1781–1788. DOI:10.1101/gr.266676.120
- Harvey WT, Carabelli AM, Jackson B, et al. SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol. 2021;19(7):409–424. DOI:10.1038/s41579-021-00573-0
- Schulthei C, Paschold L, Simnica D, et al. Next-Generation sequencing of T and B cell receptor repertoires from COVID-19 patients showed signatures associated with severity of disease. Immunity. 2020;53(2):442–455. DOI:10.1016/j.immuni.2020.06.024
- Saviano A, Henderson NC, Baumert TF. Single-Cell genomics and spatial transcriptomics: Discovery of novel cell states and cellular interactions in liver physiology and disease biology. J Hepatol. 2020;73(5):1219–1230.
- Kim D, Lee JY, Yang JS, et al. The architecture of SARS-CoV-2 transcriptome. Cell. 2020;181(4):914–921. DOI:10.1016/j.cell.2020.04.011
- Ren X, Wen W, Fan X, et al. COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas. Cell. 2021;184(7):1895–1913. DOI:10.1016/j.cell.2021.01.053
- Tang H, Gao Y, Li Z, et al. The noncoding and coding transcriptional landscape of the peripheral immune response in patients with COVID-19. Clin Transl Med. 2020;10(6):e200. DOI:10.1002/ctm2.200
- Su Y, Chen D, Yuan D, et al. Multi-Omics resolves a sharp disease-state shift between mild and moderate COVID-19. Cell. 2020;183(6):1479–1495. DOI:10.1016/j.cell.2020.10.037
- Altelaar AFM, Munoz J, Heck AJR. Next-Generation proteomics: towards an integrative view of proteome dynamics. Nat Rev Genet. 2013;14(1):35–48.
- Nie X, Qian L, Sun R, et al. Multi-Organ proteomic landscape of COVID-19 autopsies. Cell. 2021;184(3):775–791. DOI:10.1016/j.cell.2021.01.004
- Shu T, Ning W, Wu D, et al. Plasma proteomics identify biomarkers and pathogenesis of COVID-19. Immunity. 2020;53(5):1108–1122. DOI:10.1016/j.immuni.2020.10.008
- Demichev V, Tober-Lau P, Lemke O, et al. A time-resolved proteomic and prognostic map of COVID-19. Cell Syst. 2021;12(8):780–794.e7. DOI:10.1016/j.cels.2021.05.005
- Messner CB, Demichev V, Wendisch D, et al. Ultra-High-Throughput clinical proteomics reveals classifiers of COVID-19 Infection. Cell Syst. 2020;11(4):11–24. DOI:10.1016/j.cels.2020.05.012
- Zhang X, Liu H, Gao J, et al. Metabolic disorder in the progression of heart failure. Sci China Life Sci. 2019;62(9):1153–1167. DOI:10.1007/s11427-019-9548-9
- Tokarz J, Haid M, Cecil A, et al. Endocrinology Meets Metabolomics: achievements, pitfalls, and challenges. Trends Endocrinol Metab. 2017;28(10):705–721. DOI:10.1016/j.tem.2017.07.001
- Wu D, Shu T, Yang X, et al. Special Section: SARS-CoV-2 Plasma metabolomic and lipidomic alterations associated with COVID-19. Natl Sci Rev. 2020;7(7):1157–1168. DOI:10.1093/nsr/nwaa086
- Song JW, Lam SM, Fan X, et al. Omics-Driven systems interrogation of metabolic dysregulation in covid-19 pathogenesis. Cell Metab. 2020;32(2):188–202. DOI:10.1016/j.cmet.2020.06.016
- Chahar HS, Bao X, Casola A. Exosomes and their role in the life cycle and pathogenesis of RNA viruses. Viruses. 2015;7(6):3204–3225.
- Stencel-Baerenwald JE, Reiss K, Reiter DM, et al. The sweet spot: defining virus-sialic acid interactions. Nat Rev Microbiol. 2014;12(11):739–749. DOI:10.1038/nrmicro3346
- Shi S, Qin M, Shen B, et al. Association of cardiac injury with mortality in hospitalized patients with COVID-19 in Wuhan, China. JAMA Cardiol. 2020;5(7):802–810. DOI:10.1001/jamacardio.2020.0950
- Li S, Ma F, and Yokota T, et al. Metabolic reprogramming and epigenetic changes of vital organs in SARS-CoV-2 induced systemic toxicity. JCI Insight. 2021;6(2):e145027. doi:10.1172/jci.insight.145027.
- Overmyer KA, Shishkova E, Miller IJ, et al. Large-Scale multi-omic analysis of covid-19 severity. Cell Syst. 2021;12(1):23–40. DOI:10.1016/j.cels.2020.10.003
- Sanders JM, Monogue ML, Jodlowski TZ, et al. Pharmacologic treatments for coronavirus disease 2019 (COVID-19): a review. Jama. 2020;323(18):1824–1836. DOI:10.1001/jama.2020.6019
- Bojkova D, Klann K, Koch B, et al. Proteomics of SARS-CoV-2-infected host cells reveals therapy targets. Nature. 2020;583(7816):469–472. DOI:10.1038/s41586-020-2332-7
- Nogales A, Martínez-Sobrido L. Reverse genetics approaches for the development of influenza vaccines. Int J Mol Sci. 2017;18(1):20.
- Thi NTT, Labroussaa F, Ebert N, et al. Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform. Nature. 2020;582(7813):561–565. DOI:10.1038/s41586-020-2294-9
- Gordon DE, Jang GM, Bouhaddou M, et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020;583(7816):459–468. DOI:10.1038/s41586-020-2286-9
- Gil C, Ginex T, Maestro I, et al. COVID-19: Drug targets and potential treatments. Med Chem. 2020;63(21):12359–12386. DOI:10.1021/acs.jmedchem.0c00606
- Diaz JH. Hypothesis: angiotensin-converting enzyme inhibitors and angiotensin receptor blockers may increase the risk of severe COVID-19. J Travel Med. 2020 May 18;27(3):taaa041. 10.1093/jtm/taaa041. PMID: 32186711; PMCID: PMC7184445
- Zhang Z, Lin L, Li M, et al. The SARS-CoV-2 host cell receptor ACE2 correlates positively with immunotherapy response and is a potential protective factor for cancer progression. Comput Struct Biotechnol J. 2020;18:2438–2444.
- Wrapp D, Wang N, Corbett KS, et al. Cryo-EM Structure of the 2019-nCov Spike in the prefusion conformation. Science. 2020;367:1260–1263.
- Vir Biotechnology and GSK announce VIR-7831 reduces hospitalisation and risk of death in early treatment of adults with COVID-19 [cited 2021 Mar 11]. Available from: https://www.gsk.com/en-gb/media/press-releases/vir-biotechnology-and-gsk-announce-vir-7831-reduces-hospitalisaton-and-risk-of-death-in-early-treatment-of-adults-with-covid-19/.
- Hoffmann M, Kleine-Weber H, Schroeder S, et al. SARS-CoV-2 Cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell. 2020;181(2):271–280.e8. DOI:10.1016/j.cell.2020.02.052
- Shen LW, Mao HJ, Wu YL, et al. TMPRSS2: a potential target for treatment of influenza virus and coronavirus infections. Biochimie. 2017;142:1–10.
- Gao Y, Yan L, Huang Y, et al. Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science. 2020;368(6492):779–782. DOI:10.1126/science.abb7498
- https://www.gilead.com/news-and-press/press-room/press-releases/2021/6/gileads-veklury-remdesivir-associated-with-a-reduction-in-mortality-rate-in-hospitalized-patients-with-covid19-across-three-analyses-of-large-ret.
- Grein J, Ohmagari N, Shin D, et al. Compassionate use of Remdesivir for patients with severe Covid-19. N Engl J Med. 2020;382(24):2327–2336. DOI:10.1056/NEJMoa2007016
- Wang Y, Zhang D, Du G, et al. Remdesivir in adults with severe COVID-19: a randomised, double-blind, placebo-controlled, multicentre trial. Lancet. 2020;395(10236):1569–1578. DOI:10.1016/S0140-6736(20)31022-9
- Zhang L, Lin D, Sun X, et al. Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science. 2020;368(6489):409–412. DOI:10.1126/science.abb3405
- Jin Z, Du X, Xu Y, et al. Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature. 2020;582(7811):289–293. DOI:10.1038/s41586-020-2223-y
- Cao B, Wang Y, Wen D, et al. A trial of Lopinavir–Ritonavir in adults hospitalized with severe Covid-19. N Engl J Med. 2020;382(19):1787–1799. DOI:10.1056/NEJMoa2001282
- Shin D, Mukherjee R, Grewe D, et al. Papain-Like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature. 2020;587(7835):657–662. DOI:10.1038/s41586-020-2601-5
- Gao X, Qin B, Chen P, et al. Crystal structure of SARS-CoV-2 papain-like protease. Acta Pharm Sin B. 2021;11(1):237–245. DOI:10.1016/j.apsb.2020.08.014