1.Lederer DJ, Martinez FJ: Idiopathic Pulmonary Fibrosis. N Engl J Med 2018, 378:1811–1823.
2.Tang YW, Johnson JE, Browning PJ, Cruz-Gervis RA, Davis A, Graham BS, Brigham KL, Oates JA, Loyd JE, Stecenko AA: Herpesvirus DNA is consistently detected in lungs of patients with idiopathic pulmonary fibrosis. Journal of Clinical Microbiology 2003, 41:2633–2640.
3.Cheng G, Feng Z, He B: Herpes simplex virus 1 infection activates the endoplasmic reticulum resident kinase PERK and mediates eIF–2alpha dephosphorylation by the gamma(1)34.5 protein. J Virol 2005, 79:1379–1388.
4.Ueda T, Ohta K, Suzuki N, Yamaguchi M, Hirai K, Horiuchi T, Watanabe J, Miyamoto T, Ito K: Idiopathic pulmonary fibrosis and high prevalence of serum antibodies to hepatitis C virus. Am Rev Respir Dis 1992, 146:266–268.
5.Arase Y, Suzuki F, Suzuki Y, Akuta N, Kobayashi M, Kawamura Y, Yatsuji H, Sezaki H, Hosaka T, Hirakawa M, et al: Hepatitis C virus enhances incidence of idiopathic pulmonary fibrosis. World J Gastroenterol 2008, 14:5880–5886.
6.Kuwano K, Nomoto Y, Kunitake R, Hagimoto N, Matsuba T, Nakanishi Y, Hara N: Detection of adenovirus E1A DNA in pulmonary fibrosis using nested polymerase chain reaction. European Respiratory Journal 1997, 10:1445–1449.
7.Calabrese F, Kipar A, Lunardi F, Balestro E, Perissinotto E, Rossi E, Nannini N, Marulli G, Stewart JP, Rea F: Herpes Virus Infection Is Associated with Vascular Remodeling and Pulmonary Hypertension in Idiopathic Pulmonary Fibrosis. Plos One 2013, 8.
8.Tsukamoto K, Hayakawa H, Sato A, Chida K, Nakamura H, Miura K: Involvement of Epstein-Barr virus latent membrane protein 1 in disease progression in patients with idiopathic pulmonary fibrosis. Thorax 2000, 55:958–961.
9.Hayakawa H, Shirai M, Uchiyama H, Imokawa S, Suda T, Chida K, Muro H: Lack of evidence for a role of Epstein-Barr virus in the increase of lung cancer in idiopathic pulmonary fibrosis. Respir Med 2003, 97:281–284.
10.Irving WL, Day S, Johnston ID: Idiopathic pulmonary fibrosis and hepatitis C virus infection. Am Rev Respir Dis 1993, 148:1683–1684.
11.Wootton SC, Kim DS, Kondoh Y, Chen E, Lee JS, Song JW, Huh JW, Taniguchi H, Chiu C, Boushey H, et al: Viral infection in acute exacerbation of idiopathic pulmonary fibrosis. Am J Respir Crit Care Med 2011, 183:1698–1702.
12.Matsui R, Goldstein RH, Mihal K, Brody JS, Steele MP, Fine A: Type I collagen formation in rat type II alveolar cells immortalised by viral gene products. Thorax 1994, 49:201–206.
13.Isler JA, Skalet AH, Alwine JC: Human cytomegalovirus infection activates and regulates the unfolded protein response. J Virol 2005, 79:6890–6899.
14.Lawson WE, Crossno PF, Polosukhin VV, Roldan J, Cheng DS, Lane KB, Blackwell TR, Xu C, Markin C, Ware LB, et al: Endoplasmic reticulum stress in alveolar epithelial cells is prominent in IPF: association with altered surfactant protein processing and herpesvirus infection. American Journal of Physiology-Lung Cellular and Molecular Physiology 2008, 294:L1119-L1126.
15.Naik PN, Horowitz JC, Moore TA, Wilke CA, Toews GB, Moore BB: Pulmonary Fibrosis Induced by gamma-Herpesvirus in Aged Mice Is Associated With Increased Fibroblast Responsiveness to Transforming Growth Factor-beta. Journals of Gerontology Series a-Biological Sciences and Medical Sciences 2012, 67:714–725.
16.Keating DT, Sadlier DM, Patricelli A, Smith SM, Walls D, Egan JJ, Doran PP: Microarray identifies ADAM family members as key responders to TGF-beta1 in alveolar epithelial cells. Respir Res 2006, 7:114.
17.Cayrol C, Flemington EK: Identification of cellular target genes of the Epstein-Barr virus transactivator Zta: activation of transforming growth factor beta igh3 (TGF-beta igh3) and TGF-beta 1. J Virol 1995, 69:4206–4212.
18.Park GB, Kim D, Kim YS, Kim S, Lee HK, Yang JW, Hur DY: The Epstein-Barr Virus Causes Epithelial-Mesenchymal Transition in Human Corneal Epithelial Cells Via Syk/Src and Akt/Erk Signaling Pathways. Investigative Ophthalmology & Visual Science 2014, 55:1770–1779.
19.Sides MD, Klingsberg RC, Shan B, Gordon KA, Nguyen HT, Lin Z, Takahashi T, Flemington EK, Lasky JA: The Epstein-Barr virus latent membrane protein 1 and transforming growth factor—beta1 synergistically induce epithelial—mesenchymal transition in lung epithelial cells. Am J Respir Cell Mol Biol 2011, 44:852–862.
20.Ozsolak F, Milos PM: RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 2011, 12:87–98.
21.Vukmirovic M, Herazo-Maya JD, Blackmon J, Skodric-Trifunovic V, Jovanovic D, Pavlovic S, Stojsic J, Zeljkovic V, Yan X, Homer R, et al: Identification and validation of differentially expressed transcripts by RNA-sequencing of formalin-fixed, paraffin-embedded (FFPE) lung tissue from patients with Idiopathic Pulmonary Fibrosis. BMC Pulm Med 2017, 17:15.
22.Xu G, Strong MJ, Lacey MR, Baribault C, Flemington EK, Taylor CM: RNA CoMPASS: a dual approach for pathogen and host transcriptome analysis of RNA-seq datasets. PLoS One 2014, 9:e89445.
23.Yin Q, Wang X, Fewell C, Cameron J, Zhu H, Baddoo M, Lin Z, Flemington EK: MicroRNA miR–155 inhibits bone morphogenetic protein (BMP) signaling and BMP-mediated Epstein-Barr virus reactivation. J Virol 2010, 84:6318–6327.
24.Lin L, Fevery J, Hiem Yap S: A novel strand-specific RT-PCR for detection of hepatitis C virus negative-strand RNA (replicative intermediate): evidence of absence or very low level of HCV replication in peripheral blood mononuclear cells. J Virol Methods 2002, 100:97–105.
25.Caserta MT, Hall CB, Schnabel K, Lofthus G, McDermott MP: Human herpesvirus (HHV)–6 and HHV–7 infections in pregnant women. J Infect Dis 2007, 196:1296–1303.
26.Folcik VA, Garofalo M, Coleman J, Donegan JJ, Rabbani E, Suster S, Nuovo A, Magro CM, Di Leva G, Nuovo GJ: Idiopathic pulmonary fibrosis is strongly associated with productive infection by herpesvirus saimiri. Modern Pathology 2014, 27:851–862.
27.Agoni L, Guha C, Lenz J: Detection of Human Endogenous Retrovirus K (HERV-K) Transcripts in Human Prostate Cancer Cell Lines. Front Oncol 2013, 3:180.
28.Strong MJ, Xu G, Coco J, Baribault C, Vinay DS, Lacey MR, Strong AL, Lehman TA, Seddon MB, Lin Z, et al: Differences in gastric carcinoma microenvironment stratify according to EBV infection intensity: implications for possible immune adjuvant therapy. PLoS Pathog 2013, 9:e1003341.
29.Meliconi R, Andreone P, Fasano L, Galli S, Pacilli A, Miniero R, Fabbri M, Solforosi L, Bernardi M: Incidence of hepatitis C virus infection in Italian patients with idiopathic pulmonary fibrosis. Thorax 1996, 51:315–317.
30.Garson JA, Ring C, Tuke P, Tedder RS: Enhanced detection by PCR of hepatitis C virus RNA. Lancet 1990, 336:878–879.
31.Ablashi DV, Dahlberg JE, Cannon GB, Fischetti G, Loeb W, Hinds W, Schatte C, Levine PH: Detection of antibodies to Herpesvirus saimiri late antigens in human sera. Intervirology 1988, 29:217–226.
32.Kowalczyk MJ, Danczak-Pazdrowska A, Szramka-Pawlak B, Zaba R, Silny W, Osmola-Mankowska A: Expression of selected human endogenous retroviral sequences in skin and peripheral blood mononuclear cells in morphea. Arch Med Sci 2012, 8:819–825.
33.Bergallo M, Pinon M, Galliano I, Montanari P, Dapra V, Gambarino S, Calvo PL: EBV induces HERV-K and HERV-W expression in pediatrics liver transplant recipients? Minerva Pediatr 2015.
34.Fok V, Mitton-Fry RM, Grech A, Steitz JA: Multiple domains of EBER 1, an Epstein-Barr virus noncoding RNA, recruit human ribosomal protein L22. RNA 2006, 12:872–882.
35.Gross H, Barth S, Pfuhl T, Willnecker V, Spurk A, Gurtsevitch V, Sauter M, Hu B, Noessner E, Mueller-Lantzsch N, et al: The NP9 protein encoded by the human endogenous retrovirus HERV-K(HML–2) negatively regulates gene activation of the Epstein-Barr virus nuclear antigen 2 (EBNA2). Int J Cancer 2011, 129:1105–1115.
36.Sutkowski N, Conrad B, Thorley-Lawson DA, Huber BT: Epstein-Barr virus transactivates the human endogenous retrovirus HERV-K18 that encodes a superantigen. Immunity 2001, 15:579–589.
37.Hsiao FC, Lin M, Tai A, Chen G, Huber BT: Cutting edge: Epstein-Barr virus transactivates the HERV-K18 superantigen by docking to the human complement receptor 2 (CD21) on primary B cells. J Immunol 2006, 177:2056–2060.
38.Cobbs CS, Harkins L, Samanta M, Gillespie GY, Bharara S, King PH, Nabors LB, Cobbs CG, Britt WJ: Human cytomegalovirus infection and expression in human malignant glioma. Cancer Res 2002, 62:3347–3350.
39.Stragliotto G, Rahbar A, Solberg NW, Lilja A, Taher C, Orrego A, Bjurman B, Tammik C, Skarman P, Peredo I, Soderberg-Naucler C: Effects of valganciclovir as an add-on therapy in patients with cytomegalovirus-positive glioblastoma: a randomized, double-blind, hypothesis-generating study. Int J Cancer 2013, 133:1204–1213.
40.Strong MJ, Blanchard Et, Lin Z, Morris CA, Baddoo M, Taylor CM, Ware ML, Flemington EK: A comprehensive next generation sequencing-based virome assessment in brain tissue suggests no major virus - tumor association. Acta Neuropathol Commun 2016, 4:71.