Systems approaches to coronavirus pathogenesis

Current Opinion in Virology

Volumn 6, Issue 1, 2014, Pages 61-69

  Schäfer, Alexandra ^a   Baric, Ralph S ^a   Ferris, Martin T ^b  

^a IL   (United Kingdom)

^b UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HOST FACTOR;

ARTICLE; CORONAVIRUS; CORONAVIRUS INFECTION; DISEASE PREDISPOSITION; DISEASE SEVERITY; EPIDEMIC; GENE EXPRESSION; GENE INTERACTION; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENETICS; HEREDITY; HUMAN; IMMUNE RESPONSE; MIDDLE EAST; MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS; MORBIDITY; MORTALITY; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; SARS CORONAVIRUS; SINGLE NUCLEOTIDE POLYMORPHISM; SYSTEMS BIOLOGY; SYSTEMS GENETICS; VIRUS PATHOGENESIS; VIRUS STRAIN; ANIMAL; CORONAVIRUS INFECTIONS; GENETIC PROCEDURES; HOST PATHOGEN INTERACTION; PHYSIOLOGY; PROCEDURES; VIROLOGY;

ANIMALS; CORONAVIRUS; CORONAVIRUS INFECTIONS; GENETIC TECHNIQUES; GENETICS; HOST-PATHOGEN INTERACTIONS; HUMANS; SYSTEMS BIOLOGY;

EID: 84901064129     PISSN: 18796257     EISSN: 18796265     Source Type: Journal    
DOI: 10.1016/j.coviro.2014.04.007     Document Type: Review

References (61)

1. J.S. Peiris, Y. Guan, and K.Y. Yuen Severe acute respiratory syndrome Nat Med 10 2004 S88 S97
2. W. Li, S.K. Wong, F. Li, J.H. Kuhn, I.C. Huang, H. Choe, and M. Farzan Animal origins of the severe acute respiratory syndrome coronavirus: insight from ACE2-S-protein interactions J Virol 80 2006 4211 4219
3. S.K. Lau, P.C. Woo, K.S. Li, Y. Huang, H.W. Tsoi, B.H. Wong, S.S. Wong, S.Y. Leung, K.H. Chan, and K.Y. Yuen Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats Proc Natl Acad Sci USA 102 2005 14040 14045 (Pubitemid 41377699)
4. Y. Guan, B.J. Zheng, Y.Q. He, X.L. Liu, Z.X. Zhuang, C.L. Cheung, S.W. Luo, P.H. Li, L.J. Zhang, and Y.J. Guan et al. Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China Science 302 2003 276 278 (Pubitemid 37248756)
5. B.L. Haagmans, S.H. Al Dhahiry, C.B. Reusken, V.S. Raj, M. Galiano, R. Myers, G.J. Godeke, M. Jonges, E. Farag, and A. Diab et al. Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation Lancet Infect Dis 14 2014 140 145
6. Z.A. Memish, N. Mishra, K.J. Olival, S.F. Fagbo, V. Kapoor, J.H. Epstein, R. Alhakeem, A. Durosinloun, M. Al Asmari, and A. Islam et al. Middle East respiratory syndrome coronavirus in bats, Saudi Arabia Emerg Infect Dis 19 2013 1819 1823
7. J.S. Peiris Severe Acute Respiratory Syndrome (SARS) J Clin Virol 28 2003 245 247 (Pubitemid 37159364)
8. Z.A. Memish, A.I. Zumla, R.F. Al-Hakeem, A.A. Al-Rabeeah, and G.M. Stephens Family cluster of Middle East respiratory syndrome coronavirus infections N Engl J Med 368 2013 2487 2494
9. A. Assiri, J.A. Al-Tawfiq, A.A. Al-Rabeeah, F.A. Al-Rabiah, S. Al-Hajjar, A. Al-Barrak, H. Flemban, W.N. Al-Nassir, H.H. Balkhy, and R.F. Al-Hakeem et al. Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study Lancet Infect Dis 13 2013 752 761
10. A. Assiri, A. McGeer, T.M. Perl, C.S. Price, A.A. Al Rabeeah, D.A. Cummings, Z.N. Alabdullatif, M. Assad, A. Almulhim, and H. Makhdoom et al. Hospital outbreak of Middle East respiratory syndrome coronavirus N Engl J Med 369 2013 407 416
11. X.Y. Ge, J.L. Li, X.L. Yang, A.A. Chmura, G. Zhu, J.H. Epstein, J.K. Mazet, B. Hu, W. Zhang, and C. Peng et al. Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor Nature 503 2013 535 538
12. J.D. Cherry The chronology of the 2002-2003 SARS mini pandemic Paediatr Respir Rev 5 2004 262 269 (Pubitemid 39462668)
13. N.S. Zhong, and G.W. Wong Epidemiology of severe acute respiratory syndrome (SARS): adults and children Paediatr Respir Rev 5 2004 270 274 (Pubitemid 39462669)
14. W.I. Lipkin The changing face of pathogen discovery and surveillance Nat Rev Microbiol 11 2013 133 141
15. A. Aderem, J.N. Adkins, C. Ansong, J. Galagan, S. Kaiser, M.J. Korth, G.L. Law, J.G. McDermott, S.C. Proll, and C. Rosenberger et al. A systems biology approach to infectious disease research: innovating the pathogen-host research paradigm MBio 2 2011 e00325 e00410
16. D.W. Threadgill, D.R. Miller, G.A. Churchill, and F.P. de Villena The collaborative cross: a recombinant inbred mouse population for the systems genetic era ILAR J 52 2011 24 31
17. G.L. Law, M.J. Korth, A.G. Benecke, and M.G. Katze Systems virology: host-directed approaches to viral pathogenesis and drug targeting Nat Rev Microbiol 11 2013 455 466
18. J.E. McDermott, H. Shankaran, A.J. Eisfeld, S.E. Belisle, G. Neuman, C. Li, S. McWeeney, C. Sabourin, Y. Kawaoka, M.G. Katze, and K.M. Waters Conserved host response to highly pathogenic avian influenza virus infection in human cell culture, mouse and macaque model systems BMC Syst Biol 5 2011 190-0509-5-190
19. D.L. Gibbs, L. Gralinski, R.S. Baric, and S.K. McWeeney Multi-omic network signatures of disease Front Genet 4 2014 309
20. L.E. Gralinski, A. Bankhead 3rd, S. Jeng, V.D. Menachery, S. Proll, S.E. Belisle, M. Matzke, B.J. Webb-Robertson, M.L. Luna, and A.K. Shukla et al. Mechanisms of severe acute respiratory syndrome coronavirus-induced acute lung injury MBio 4 2013 10.1128/mBio.00271-13
21. H.D. Mitchell, A.J. Eisfeld, A.C. Sims, J.E. McDermott, M.M. Matzke, B.J. Webb-Robertson, S.C. Tilton, N. Tchitchek, L. Josset, and C. Li et al. A network integration approach to predict conserved regulators related to pathogenicity of influenza and SARS-CoV respiratory viruses PLoS ONE 8 2013 e69374
22. A. Diercks, and A. Aderem Systems approaches to dissecting immunity Curr Top Microbiol Immunol 363 2013 1 19
23. A.C. Sims, S.C. Tilton, V.D. Menachery, L.E. Gralinski, A. Schafer, M.M. Matzke, B.J. Webb-Robertson, J. Chang, M.L. Luna, and C.E. Long et al. Release of severe acute respiratory syndrome coronavirus nuclear import block enhances host transcription in human lung cells J Virol 87 2013 3885 3902
24. M.L. DeDiego, J.L. Nieto-Torres, J.M. Jimenez-Guardeno, J.A. Regla-Nava, E. Alvarez, J.C. Oliveros, J. Zhao, C. Fett, S. Perlman, and L. Enjuanes Severe acute respiratory syndrome coronavirus envelope protein regulates cell stress response and apoptosis PLoS Pathog 7 2011 1002315
25. A. Danesh, C.M. Cameron, A.J. Leon, L. Ran, L. Xu, Y. Fang, A.A. Kelvin, T. Rowe, H. Chen, and Y. Guan et al. Early gene expression events in ferrets in response to SARS coronavirus infection versus direct interferon-alpha2b stimulation Virology 409 2011 102 112
26. M.J. Cameron, L. Ran, L. Xu, A. Danesh, J.F. Bermejo-Martin, C.M. Cameron, M.P. Muller, W.L. Gold, S.E. Richardson, and S.M. Poutanen et al. Interferon-mediated immunopathological events are associated with atypical innate and adaptive immune responses in patients with severe acute respiratory syndrome J Virol 81 2007 8692 8706 (Pubitemid 47242843)
27. J. Zhao, J. Zhao, K. Legge, and S. Perlman Age-related increases in PGD(2) expression impair respiratory DC migration, resulting in diminished T cell responses upon respiratory virus infection in mice J Clin Invest 121 2011 4921 4930
28. K. Zhao, H. Wang, and C. Wu The immune responses of HLA-A*0201 restricted SARS-CoV S peptide-specific CD8(+) T cells are augmented in varying degrees by CpG ODN, PolyI:C and R848 Vaccine 29 2011 6670 6678
29. S.F. Wang, K.H. Chen, M. Chen, W.Y. Li, Y.J. Chen, C.H. Tsao, M.Y. Yen, J.C. Huang, and Y.M. Chen Human-leukocyte antigen class I Cw 1502 and class II DR 0301 genotypes are associated with resistance to severe acute respiratory syndrome (SARS) infection Viral Immunol 24 2011 421 426
30. K.Y. Chan, J.C. Ching, M.S. Xu, A.N. Cheung, S.P. Yip, L.Y. Yam, S.T. Lai, C.M. Chu, A.T. Wong, and Y.Q. Song et al. Association of ICAM3 genetic variant with severe acute respiratory syndrome J Infect Dis 196 2007 271 280 (Pubitemid 47047467)
31. K.Y. Chan, M.S. Xu, J.C. Ching, V.S. Chan, Y.C. Ip, L. Yam, C.M. Chu, S.T. Lai, K.M. So, and T.Y. Wong et al. Association of a single nucleotide polymorphism in the CD209 (DC-SIGN) promoter with SARS severity Hong Kong Med J 16 2010 37 42
32. M.T. Ferris, and M.T. Heise Quantitative genetics in the study of virus-induced disease Adv Virus Res 88 2014 193 225
33. Y. Huang, W.A. Paxton, S.M. Wolinsky, A.U. Neumann, L. Zhang, T. He, S. Kang, D. Ceradini, Z. Jin, and K. Yazdanbakhsh et al. The role of a mutant CCR5 allele in HIV-1 transmission and disease progression Nat Med 2 1996 1240 1243 (Pubitemid 26375409)
34. B.M. Imbert-Marcille, L. Barbe, M. Dupe, B. Le Moullac-Vaidye, B. Besse, C. Peltier, N. Ruvoen-Clouet, and J. Le Pendu A FUT2 gene common polymorphism determines resistance to rotavirus A of the P[8] genotype J Infect Dis 209 2014 1227 1230
35. L. Lindesmith, C. Moe, S. Marionneau, N. Ruvoen, X. Jiang, L. Lindblad, P. Stewart, J. LePendu, and R. Baric Human susceptibility and resistance to Norwalk virus infection Nat Med 9 2003 548 553 (Pubitemid 36597100)
36. Y. Nozawa, T. Umemura, S. Joshita, Y. Katsuyama, S. Shibata, T. Kimura, S. Morita, M. Komatsu, A. Matsumoto, E. Tanaka, and M. Ota KIR, HLA, and IL28B variant predict response to antiviral therapy in genotype 1 chronic hepatitis C patients in Japan PLoS ONE 8 2013 e83381
37. L. Hou, and H. Zhao A review of post-GWAS prioritization approaches Front Genet 4 2013 280
38. D.W. Threadgill, and G.A. Churchill Ten years of the collaborative cross. G3 (Bethesda) 2 2012 153 156
39. R.H. Blair, D.J. Kliebenstein, and G.A. Churchill What can causal networks tell us about metabolic pathways? PLoS Comput Biol 8 2012 e1002458
40. A. Roberts, D. Deming, C.D. Paddock, A. Cheng, B. Yount, L. Vogel, B.D. Herman, T. Sheahan, M. Heise, and G.L. Genrich et al. A mouse-adapted SARS-coronavirus causes disease and mortality in BALB/c mice PLoS Pathog 3 2007 e5
41. A. Roberts, E.W. Lamirande, L. Vogel, J.P. Jackson, C.D. Paddock, J. Guarner, S.R. Zaki, T. Sheahan, R. Baric, and K. Subbarao Animal models and vaccines for SARS-CoV infection Virus Res 133 2008 20 32 (Pubitemid 351374756)
42. Collaborative Cross Consortium The genome architecture of the Collaborative Cross mouse genetic reference, population Genetics 190 2012 389 401
43. K.L. Svenson, D.M. Gatti, W. Valdar, C.E. Welsh, R. Cheng, E.J. Chesler, A.A. Palmer, L. McMillan, and G.A. Churchill High-resolution genetic mapping using the mouse diversity outbred population Genetics 190 2012 437 447
44. M.T. Ferris, D.L. Aylor, D. Bottomly, A.C. Whitmore, L.D. Aicher, T.A. Bell, B. Bradel-Tretheway, J.T. Bryan, R.J. Buus, and L.E. Gralinski et al. Modeling host genetic regulation of influenza pathogenesis in the collaborative cross PLoS Pathog 9 2013 e196 e1003
45. A.C. Boon, J. deBeauchamp, A. Hollmann, J. Luke, M. Kotb, S. Rowe, D. Finkelstein, G. Neale, L. Lu, R.W. Williams, and R.J. Webby Host genetic variation affects resistance to infection with a highly pathogenic H5N1 influenza A virus in mice J Virol 83 2009 10417 10426
46. D. Bottomly, M.T. Ferris, L.D. Aicher, E. Rosenzweig, A. Whitmore, D.L. Aylor, B.L. Haagmans, L.E. Gralinski, B.G. Bradel-Tretheway, and J.T. Bryan et al. Expression quantitative trait loci for extreme host response to Influenza A in pre-collaborative cross mice Genes Genomes Genet 2 2012 213 221
47. T. Nedelko, H. Kollmus, F. Klawonn, S. Spijker, L. Lu, M. Hessmann, R. Alberts, R.W. Williams, and K. Schughart Distinct gene loci control the host response to influenza H1N1 virus infection in a time-dependent manner BMC Genomics 13 2012 411
48. K. Podshivalova, and D.R. Salomon MicroRNA regulation of T-lymphocyte immunity: modulation of molecular networks responsible for T-cell activation, differentiation, and development Crit Rev Immunol 33 2013 435 476
49. Z. Li, T.C. Chao, K.Y. Chang, N. Lin, V.S. Patil, C. Shimizu, S.R. Head, J.C. Burns, and T.M. Rana The long noncoding RNA THRIL regulates TNFalpha expression through its interaction with hnRNPL Proc Natl Acad Sci USA 111 2014 1002 1007
50. G. Swaminathan, S. Navas-Martin, and J. Martin-Garcia MicroRNAs and HIV-1 Infection: antiviral activities and beyond J Mol Biol 426 2014 1178 1197
51. X. Peng, L. Gralinski, C.D. Armour, M.T. Ferris, M.J. Thomas, S. Proll, B.G. Bradel-Tretheway, M.J. Korth, J.C. Castle, and M.C. Biery et al. Unique signatures of long noncoding RNA expression in response to virus infection and altered innate immune signaling MBio 1 2010 6 10 10.1128/mBio.00206-10
52. X. Peng, L. Gralinski, M.T. Ferris, M.B. Frieman, M.J. Thomas, S. Proll, M.J. Korth, J.R. Tisoncik, M. Heise, and S. Luo et al. Integrative deep sequencing of the mouse lung transcriptome reveals differential expression of diverse classes of small RNAs in response to respiratory virus infection MBio 2 2011 10 10.1128/mBio.00198-11
53. A. Zhou, S. Li, J. Wu, F.A. Khan, and S. Zhang Interplay between microRNAs and host pathogen recognition receptors (PRRs) signaling pathways in response to viral infection Virus Res 184C 2014 1 6
54. J.Y. Cheong, H.D. Shin, Y.J. Kim, and S.W. Cho Association of polymorphism in MicroRNA 219-1 with clearance of hepatitis B virus infection J Med Virol 85 2013 808 814
55. L. Josset, V.D. Menachery, L.E. Gralinski, S. Agnihothram, P. Sova, V.S. Carter, B.L. Yount, R.L. Graham, R.S. Baric, and M.G. Katze Cell host response to infection with novel human coronavirus EMC predicts potential antivirals and important differences with SARS coronavirus MBio 4 2013 e00165-13
56. L. Josset, H. Zeng, S.M. Kelly, T.M. Tumpey, and M.G. Katze Transcriptomic characterization of the novel avian-origin Influenza A (H7N9) virus: specific host response and responses intermediate between Avian (H5N1 and H7N7) and human (H3N2) viruses and implications for treatment options MBio 5 2014 10.1128/mBio.01102-13
57. H.I. Nakaya, J. Wrammert, E.K. Lee, L. Racioppi, S. Marie-Kunze, W.N. Haining, A.R. Means, S.P. Kasturi, N. Khan, and G.M. Li et al. Systems biology of vaccination for seasonal influenza in humans Nat Immunol 12 2011 786 795
58. A.R. Everitt, S. Clare, T. Pertel, S.P. John, R.S. Wash, S.E. Smith, C.R. Chin, E.M. Feeley, J.S. Sims, and D.J. Adams et al. IFITM3 restricts the morbidity and mortality associated with influenza Nature 484 2012 519 523
59. J. Seok, H.S. Warren, A.G. Cuenca, M.N. Mindrinos, H.V. Baker, W. Xu, D.R. Richards, G.P. McDonald-Smith, H. Gao, and L. Hennessy et al. Genomic responses in mouse models poorly mimic human inflammatory diseases Proc Natl Acad Sci USA 110 2013 3507 3512
60. O.M. Siggs Dissecting mammalian immunity through mutation Immunol Cell Biol 2014 Feb 11
61. A.K. Zaas, M. Chen, J. Varkey, T. Veldman, A.O. Hero 3rd, J. Lucas, Y. Huang, R. Turner, A. Gilbert, and R. Lambkin-Williams et al. Gene expression signatures diagnose influenza and other symptomatic respiratory viral infections in humans Cell Host Microbe 6 2009 207 217