1. Ustaçelebi Ş, Us D. Genel Viroloji. Ankara: Pelikan Tıp ve Kitapçılık; 2008.
2. Ustaçelebi Ş. Virüslerin genel özellikleri ve sınıflandırılmaları, s1-9. Kitap: Us D, Ergünay K, editörler. Moleküler, Klinik ve Tanısal Viroloji. Ankara: Bilimsel Tıp; 2012.
3. Burrell CJ, HowardCR, Murphy FA. Fenner and White’s Medical Virology. 5th edition. Londra: Academic Press, Elsevier Inc; 2017.
4. Choo QL, Kuo G, Weiner AJ, Overby LR, Bradley DW, Houghton M. Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome. Science 1989; 244:359-62.
5. Us D. Virusların moleküler, kimyasal ve morfolojik yapıları, s11-31. Kitap: Us D, Ergünay K, editörler. Moleküler, Klinik ve Tanısal Viroloji. Ankara: Bilimsel Tıp; 2012.
6. Ryu WS. Virus Life Cycle. Kitap: Molecular Virology of Human Pathogenic Viruses. Londra: Academic Press, Elsevier Inc.; 2017, p31–45.
7. Koonin EV, Krupovic M, Agol VI. The Baltimore classification of viruses 50 years later: how does it stand in the light of virus evolution? Microbiol Mol Biol Rev 2021; 85(3):e00053- 21.
8. Murray PR, Rosenthal KS, Pfaller MA Medical Microbiology, 9th edition. Edinburgh: Elsevier. 2021, p361-387.
9. Murray PR, Rosenthal KS, Kobayashi GS, Pfaller MA, Medical Microbiology, 4 th edition, St Louis: Mosby Inc., 2002, 65.
10. Cheng S, Brooks CL III. Viral Capsid Proteins Are Segregated in Structural Fold Space. PLoS Comput Biol 2013, 9(2): e1002905
11. Das A, Rivera-Serrano EE, Yin X, Walker CM, Feng Z, Lemon SM. Cell entry and release of quasi-enveloped human hepatitis viruses. Nat Rev Microbiol. 2023;21(9):573-589.
12. Grove J, Marsh M. The cell biology of receptor-mediated virus entry. J Cell Biol. 2011;195(7): 1071–1082.
13. Maginnis MS. Virus-Receptor Interactions: The Key to Cellular Invasion. J Mol Biol 2018; 430(17):2590-2611.
14. Graham M, Zhang P. Cryo-electron tomography to study viral infection. Biochem Soc Trans. 2023; 51(4):1701-1711.
15. Jones JE, Le Sage V, Lakdawala SS. Viral and host heterogeneity and their effects on the viral life cycle. Nat Rev Microbiol 2021;19(4):272-282.
16. Abacıoğlu H. Virüs-hücre etkileşimi: Ölmek ya da ölmemek, s:911-924. Kitap: Badur S, Abacıoğlu H, Öngen B, editörler. Enfeksiyon Patogenezi ve Bağışıklık. İstanbul: Akademi Yayınevi;
2015.
17. S. Moller-Tank, W. Maury, Phosphatidylserine receptors: enhancers of enveloped virus entry and infection. Virology 2014; 468-470. 565–580.
18. T. Stehle, Z.M. Khan, Rules and exceptions: sialic acid variants and their role in determining viral tropism. J Virol 2014; 88:7696–7699.
19. Stencel-Baerenwald JE, Reiss K, Reiter D.M, Stehle T, Dermody TS. The sweet spot: defining virus–sialic acid interactions. Nat Rev Microbiol 2014; 12:739–749.
20. D. Bhella. The role of cellular adhesion molecules in virus attachment and entry. Philos Trans R Soc. Lond. Ser. B Biol Sci 370 (2015) 20140035.
21. Erensoy S. HIV enfeksiyonlarında patogenez. s:1149-62. Kitap: Badur S, Abacıoğlu H, Öngen B, editörler. Enfeksiyon Patogenezi ve Bağışıklık. İstanbul: Akademi Yayınevi; 2015.
22. Yu A, Skorupka KA, Pak AJ, Ganser-Pornillos BK, Voth GA. TRIM5α self-assembly and compartmentalization of the HIV-1 viral capsid. Nat Commun 2020; 11:1307.
23. Connolly SA, Jackson JO, Jardetzky TS, Longnecker R. Fusing structure and function: a structural view of the herpesvirus entry machinery. Nat Rev Microbiol 2011; 9(5):369381.
24. Mercer J, Schelhaas M, Helenius A. Virus entry by endocytosis. Annu Rev Biochem 2010; 79:803833.
25. Sattentau, Q. Avoiding the void: cell-to-cell spread of human viruses. Nat Rev Microbiol 2008; 6(11):815826.
26. Vigant F, Santos NC, Lee B. Broad-spectrum antivirals against viral fusion. Nat Rev Microbiol 2015; 13(7):426437.
27. Yamauchi Y, Helenius A. Virus entry at a glance. J Cell Sci 2013; 126:12891295.
28. Tati S, Alisaraie L. Recruitment of dynein and kinesin to viral particles. FASEB J. 2022; 36:e22311.
29. Çolak D, Dağlar D. Latent virüs enfeksiyonlarında patogenez. s:1175-86. Kitap: Badur S, Abacıoğlu H, Öngen B, editörler. Enfeksiyon Patogenezi ve Bağışıklık. İstanbul: Akademi Yayınevi; 2015.
30. Guo L, Liu J-J, Long S, et al. TIM22 and TIM29 inhibit HBV replication by up-regulating SRSF1 expression. J Med Virol 2024; 96:e29439.
31. Newman LE, Novak SW, Rojas GR, et al. Mitochondrial DNA replication stress triggers a pro-inflammatory endosomal pathway of nucleoid disposal. Nature Cell Biology 2024; 26:194-206.
32. Carter J, Saunders V, Saunders VA. Virology: Principles and Applications. Hoboken, New Jersey: John Wiley & Sons p9-26; 2007.
33. Karimzadeh S, Bhopal R, Nguyen Tien H. Review of infective dose, routes of transmission and outcome of COVID-19 caused by the SARS-COV-2: comparison with other respiratory viruses.
Epidemiology and Infection 2021; 149:e96, 1–8.
34. Atkinson J, Chartier Y, Pessoa-Silva CL, Jensen P, Li Y, Seto W-H. Respiratory droplets. Annex C: Natural Ventilation for Infection Control in Health-Care Settings. Geneva: World Health
Organization 2009.
35. Basu, S. Computational characterization of inhaled droplet transport to the nasopharynx. Nature Portfolio, Sci Rep. 2021; 11:6652.
36. Jagirdhar GSK, Pulakurthi YS, Chigurupati HD, Surani S. Gastrointestinal tract and viral pathogens. World J Virol 2023; 12(3):136-150.
37. Vollmuth N, Sin J, Kim BJ. Host-microbe interactions at the blood-brain barrier through the lens of induced pluripotent stem cell-derived brain-like endothelial cells. mBio 2024;
15(2):e0286223.
38. Megli, CJ, Coyne, CB. Infections at the maternal–fetal interface: an overview of pathogenesis and defence. Nat Rev Microbiol 2022; 20:67–82.
39. Kim J, Koo B-K, Knoblich JA. Human organoids: model systems for human biology and medicine. Nature Reviews Molecular Cell Biology 2020; 21(10):571-584.
40. Emily Speranza. Understanding virus–host interactions in tissues. Nature Microbiology 2023; 8:1397–1407.
41. Ho JSY, Angel, Ma Y, et al. Hybrid gene origination creates human-virus chimeric proteins during Infection. Cell 2020; 181:1502–1517.
42. Heldman MR, Job C, Maalouf J, et al. Association of inherited chromosomally integrated human herpesvirus 6 with neurologic symptoms and management after allogeneic hematopoietic cell
transplantation. Transplantation and Cellular Therapy 2021; 27(9):795.e1-795.e8.
43. Wang, L.-F. & Anderson, D. E. Viruses in bats and potential spillover to animals and humans. Curr Opin Virol 2019; 34:79–89.
44. Bjarnsholt T, Whiteley M, Rumbaugh KP, Stewart PS, Jensen PØ, Frimodt-Møller N. The importance of understanding the infectious microenvironment. Lancet Infect Dis 2022;22(3):
e88-e92.
45. Puschhof J, Pleguezuelos-Manzano C, Clevers H. Organoids and organs-on-chips: Insights into human gut-microbe interactions. Cell Host Microbe. 2021;29(6):867-878.
46. Maisch B. Cardio-immunology of myocarditis: Focus on immune mechanisms and treatment options. Front Cardiovasc Med 2019; 6:48.
47. Soy M, Keser G, Atagündüz P, Tabak F, Atagündüz I, Kayhan S. Cytokine storm in COVID-19: pathogenesis and overview of anti-inflammatory agents used in treatment. Clin Rheumatol
2020; 39(7):2085–2094.
48. Darmarajan T, Paudel KR, Candasamy M, et al. Autoantibodies and autoimmune disorders in SARS-CoV-2 infection: pathogenicity and immune regulation. Environ Sci Pollut Res Int.
2022;29(36):54072-54087.
49. Sherwani S, Ahmed Khan M, Suliman Almogbel M. Autoantibodies in Viral Infections. In (Ed. Khan WA) Autoantibodies and Cytokines. IntechOpen, 2019. Erişim: http://dx.doi.org/10.5772/
intechopen.80471
50. Nagata K, Kumata K, Nakayama Y, et al. Epstein-Barr virus lytic reactivation activates B cells polyclonally and induces activation-induced cytidine deaminase expression: A mechanism un-
derlying autoimmunity and its contribution to Graves’ Disease. Viral Immunol 2017; 30(3):240-249.
51. Barzilai O, Ram M, Shoenfeld Y. Viral infection can induce the production of autoantibodies. Current Opinion in Rheumatology 2007; 19:636-643.
52. Plotz PH. Autoantibodies are anti-idiotype antibodies to antiviral antibodies. Lancet. 1983; 322(8354):824-6.
53. Kanduc D, Shoenfeld Y. On the molecular determinants of the SARS-CoV-2 attack. Clin Immunol. 2020; 215:108426.
54. Lucchese G, Flöel A. Molecular mimicry between SARS-CoV-2 and respiratory pacemaker neurons. Autoimmun Rev. 2020; 19(7):102556.
55. Häggström, M. Medical gallery of Mikael Häggström. WikiJournal of Medicine 2014; 1(2):25.
56. International Committee on Taxonomy of Viruses Executive Committee. The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks. Nat Microbiol. 2020;
5(5):668-674.
57. Caetano-Anollés G, Claverie J-M and Nasir A. A critical analysis of the current state of virus taxonomy. Front Microbiol 2023; 14:1240993.
58. Simmonds P, Adriaenssens EM, Zerbini FM, et al. Four principles to establish a universal virus taxonomy. PLoS Biol 2023; 21(2): e3001922.
59. Krupovic M, Dolja VV, Koonin EV. Origin of viruses: Primordial replicators recruiting capsids from hosts. Nat Rev Microbiol. 2019; 17:449–458.
60. Koonin EV, Dolja VV, Krupovic M, et al. global organization and proposed megataxonomy of the virus world. Microbiol Mol Biol Rev. 2020; 84(2):e00061-19.
61. Koonin EV, Dolja VV, Krupovic M. The healthy human virome: From virus–host symbiosis to disease. Current Opinion in Virology 2021; 47:86-94.
62. Ergünay K. New viruses on the rise: a One health and ecosystem-based perspective on emerging viruses. Future Virol. 2021;10.2217/fvl-2021-0215.
63. Zhang YZ, Chen YM, Wang W, Qin XC, Holmes EC. Expanding the RNA virosphere by unbiased metagenomics. Annu Rev Virol 2019; 6(1):119–139.
64. Kay A, Zoulim F. Hepatitis B virus genetic variability and evolution. Virus Research 2007; 127(2):164-176.
65. Coppola N, Onorato L, Minichini C, Di Caprio G, Starace M, Sagnelli C, Sagnelli E. Clinical significance of hepatitis B surface antigen mutants. World J Hepatol. 2015;7(27):2729-39.