REFERENCES
1. Chica Cardenas LA, Leonard MM, Baldridge MT, Handley SA. Gut virome dynamics: from commensal to critical player in health and disease. Nat Rev Gastroenterol Hepatol. 2025;23:126-44.
2. Cao Z, Sugimura N, Burgermeister E, Ebert MP, Zuo T, Lan P. The gut virome: a new microbiome component in health and disease. eBioMedicine. 2022;81:104113.
3. Shamash M, Sinha A, Maurice CF. Improving gut virome comparisons using predicted phage host information. mSystems. 2025;10:e01364-24.
5. Lathakumari RH, Vajravelu LK, Gopinathan A, et al. The gut virome and human health: From diversity to personalized medicine. Eng Microbiol. 2025;5:100191.
6. Mahmud MR, Tamanna SK, Akter S, et al. Role of bacteriophages in shaping gut microbial community. Gut Microbes. 2024;16:2390720.
7. Hillary LS, Knotts TA, Adams SH, Ali MR, Olm MR, Emerson JB. DNA extraction and virome processing methods strongly influence recovered human gut viral community characteristics. bioRxiv 2025; bioRxiv:2025.11.25.690293. Available online: https://doi.org/10.1101/2025.11.25.690293. [accessed 18 June 2026].
8. Li J, Yang F, Xiao M, Li A. Advances and challenges in cataloging the human gut virome. Cell Host Microbe. 2022;30:908-16.
9. Ugalde V, Contreras F, Prado C, Chovar O, Espinoza A, Pacheco R. Dopaminergic signalling limits suppressive activity and gut homing of regulatory T cells upon intestinal inflammation. Mucosal Immunol. 2021;14:652-66.
10. Hanna BS, Wang G, Galván-Peña S, et al. The gut microbiota promotes distal tissue regeneration via RORγ+ regulatory T cell emissaries. Immunity. 2023;56:829-846.e8.
11. Miranda‐waldetario MCG, Curotto de lafaille MA. Oral tolerance to dietary antigens and Foxp3+ regulatory T cells. Immunol Rev. 2024;326:8-16.
12. Stockdale SR, Shkoporov AN, Khokhlova EV, et al. Interpersonal variability of the human gut virome confounds disease signal detection in IBD. Commun Biol. 2023;6:221.
13. Wu Y, Cheng R, Lin H, et al. Gut virome and its implications in the pathogenesis and therapeutics of inflammatory bowel disease. BMC Med. 2025;23:183.
14. Dagar S, Singh J, Saini A, et al. Gut bacteriome, mycobiome and virome alterations in rheumatoid arthritis. Front Endocrinol. 2023;13:1044673.
15. Tomofuji Y, Kishikawa T, Maeda Y, et al. Whole gut virome analysis of 476 Japanese revealed a link between phage and autoimmune disease. Ann Rheum Dis. 2022;81:278-88.
16. De Jonge PA, Wortelboer K, Scheithauer TPM, et al. Gut virome profiling identifies a widespread bacteriophage family associated with metabolic syndrome. Nat Commun. 2022;13:3594.
17. White Z, Cabrera I, Mei L, et al. Gut inflammation promotes microbiota-specific CD4 T cell-mediated neuroinflammation. Nature. 2025;643:509-18.
18. Barcutean L, Maier S, Burai-patrascu M, Farczadi L, Balasa R. The immunomodulatory potential of short-chain fatty acids in multiple sclerosis. Int J Mol Sci. 2024;25:3198.
19. Larson JH, Jin S, Loschi M, et al. Enforced gut homing of murine regulatory T cells reduces early graft-versus-host disease severity. Am J Transplant. 2023;23:1102-15.
20. Wei X, Zhang X, Cui M, Huang L, Gao D, Hua S. An exploration of the relationship between gut virome and cardiovascular disease: a comprehensive review. Rev Cardiovasc Med. 2025;26:36386.
21. Feng Z, Burgermeister E, Philips A, Zuo T, Wen W. The gut virome in association with the bacteriome in gastrointestinal diseases and beyond: roles, mechanisms, and clinical applications. Precis Clin Med. 2025;8:pbaf010.
22. Liang G, Cobián-Güemes AG, Albenberg L, Bushman F. The gut virome in inflammatory bowel diseases. Curr Opin Virol. 2021;51:190-8.
23. Chen C, Yan Q, Yao X, et al. Alterations of the gut virome in patients with systemic lupus erythematosus. Front. Immunol. 2023;13:1050895.
24. Guo R, Li S, Zhang Y, et al. Dysbiotic oral and gut viromes in untreated and treated rheumatoid arthritis patients. Microbiol Spectr. 2022;10:e00348-22.
25. Sun Z, Zhou H, Wang Y, Li Z. Regulatory T cells in stroke inflammation: therapeutic perspectives. Neural Regener Res. 2026;21:2178-90.
26. Yan Q, Huang L, Li S, et al. The Chinese gut virus catalogue reveals gut virome diversity and disease-related viral signatures. Genome Med. 2025;17:30.
27. Nishijima S, Nagata N, Kiguchi Y, et al. Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort. Nat Commun. 2022;13:5252.
28. Zhao X, Cai Y, Hou Y, et al. Commensal viruses promote intestinal stem cell regeneration following radiation damage by inhibiting hyperactivation of RIG‐I and notch signals. Adv Sci. 2025;12:e05204.
29. Leal Rodríguez C, Shah SA, Rasmussen MA, et al. The infant gut virome is associated with preschool asthma risk independently of bacteria. Nat Med. 2023;30:138-48.
30. Zou G, He L, Rao J, et al. Improving the safety and efficacy of phage therapy from the perspective of phage-mammal interactions. FEMS Microbiol Rev. 2023;47:fuad042.
31. Lam S, Bai X, Shkoporov AN, et al. Roles of the gut virome and mycobiome in faecal microbiota transplantation. Lancet Gastroenterol Hepatol. 2022;7:472-84.
32. Dikareva E, Matharu D, Lahtinen E, et al. An extended catalog of integrated prophages in the infant and adult fecal microbiome shows high prevalence of lysogeny. Front. Microbiol. 2023;14:1254535.
33. Xu M, Chen S, Pei H, Hu L, Zhang Y. Engineering bacteriophages for gut health: precision antimicrobials and beyond. J Nanobiotechnol. 2026;24:62.
34. Bao S, Wang H, Li W, et al. Dynamic alterations of the mice gut virome after Coxsackievirus B3 infection. J Med Virol. 2022;94:4959-69.
35. Zhao X, Sun C, Jin M, et al. Enrichment culture but not metagenomic sequencing identified a highly prevalent phage infecting Lactiplantibacillus plantarum in human feces. Microbiol Spectr. 2023;11:e04340-22.
36. Strine MS, Fagerberg E, Darcy PW, et al. Intestinal tuft cell immune privilege enables norovirus persistence. Sci. Immunol. 2024;9:eadi7038.
37. Hou G, Son J, Gomez Castro MF, et al. Innate immune sensing of rotavirus by intestinal epithelial cells leads to diarrhea. Cell Host Microbe. 2025;33:408-419.e8.
38. Harris KG, Morosky SA, Drummond CG, et al. RIP3 regulates autophagy and promotes Coxsackievirus B3 infection of intestinal epithelial cells. Cell Host Microbe. 2015;18:221-32.
39. Makimaa H, Ingle H, Wang L, et al. MDA5-MAVS and interferon-lambda signaling in the intestinal epithelium limit murine astrovirus infection. Mucosal Immunol. 2026;19:1749-58.
40. Janahi EM, Mustafa S, Parkar SFD, Naser HA, Eisa ZM. Detection of enteric viruses and bacterial indicators in a sewage treatment center and shallow water bay. Int J Environ Res Public Health. 2020;17:6483.
41. Kim AH, Armah G, Dennis F, et al. Enteric virome negatively affects seroconversion following oral rotavirus vaccination in a longitudinally sampled cohort of Ghanaian infants. Cell Host Microbe. 2022;30:110-123.e5.
42. Gregory AC, Zablocki O, Zayed AA, Howell A, Bolduc B, Sullivan MB. The gut virome database reveals age-dependent patterns of virome diversity in the human gut. Cell Host Microbe. 2020;28:724-740.e8.
43. Tan SK, Granados AC, Bouquet J, et al. Metagenomic sequencing of stool samples in Bangladeshi infants: virome association with poliovirus shedding after oral poliovirus vaccination. Sci Rep. 2020;10:15392.
44. Truchado P, Garre A, Gil MI, Simón-andreu PJ, Sánchez G, Allende A. Monitoring of human enteric virus and coliphages throughout water reuse system of wastewater treatment plants to irrigation endpoint of leafy greens. Sci Total Environ. 2021;782:146837.
45. Ahmed W, Smith WJ, Tiwari A, Bivins A, Simpson SL. Unveiling indicator, enteric, and respiratory viruses in aircraft lavatory wastewater using adsorption-extraction and Nanotrap® Microbiome A Particles workflows. Sci Total Environ. 2023;896:165007.
46. Toribio-Avedillo D, Blanch AR, Muniesa M, Rodríguez-Rubio L. Bacteriophages as fecal pollution indicators. Viruses. 2021;13:1089.
47. Farkas K, Walker DI, Adriaenssens EM, et al. Viral indicators for tracking domestic wastewater contamination in the aquatic environment. Water Res. 2020;181:115926.
48. Yasui M, Iso H, Torii S, Matsui Y, Katayama H. Applicability of pepper mild mottle virus and cucumber green mottle mosaic virus as process indicators of enteric virus removal by membrane processes at a potable reuse facility. Water Res. 2021;206:117735.
49. Fan S, Xu Z, Liu P, Qin Y, Chen M. Enterovirus 71 2A protease inhibits P-body formation to promote viral RNA synthesis. J Virol. 2021;95:e00922-21.
50. Wang Y, Zou W, Niu Y, et al. Phosphorylation of enteroviral 2Apro at Ser/Thr125 benefits its proteolytic activity and viral pathogenesis. J Med Virol. 2022;95:e28400.
51. Chen L, Hou X, Chu H. The novel role of phage particles in chronic liver diseases. Microorganisms. 2023;11:1181.
52. Ma L, Hung MH, Rashidi Mehrabadi F, et al. Beneficial infections of the enterovirus genus in patients with liver cancer. Gut. 2025;74:1667-79.
53. Adiliaghdam F, Amatullah H, Digumarthi S, et al. Human enteric viruses autonomously shape inflammatory bowel disease phenotype through divergent innate immunomodulation. Sci. Immunol. 2022;7:eabn6660.
54. Zhong Y, Zhang Y, Arcondo JLL, et al. Prophage induction drives soybean rhizobacterial community differentiation and nutrient cycling benefiting root development. ISME Communications. 2025;5:ycaf203.
55. Cortés-Martín A, Denise R, Guerin E, et al. Isolation and characterization of a novel lytic Parabacteroides distasonis bacteriophage φPDS1 from the human gut. Gut Microbes. 2024;16:2298254.
56. Nicolas AM, Sieradzki ET, Pett-Ridge J, et al. A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil. Nat Commun. 2023;14:5835.
57. Blanco JCG, Sylla FYD, Granados S, Noghero A, Boukhvalova MS, Kajon AE. Enterovirus D68 infection in cotton rats results in systemic inflammation with detectable viremia associated with extracellular vesicle and neurologic disease. Sci Rep. 2025;15:6514.
58. Hügel A, Weiss C, Ishikawa H, et al. Genotype-dependent cell tropism of EV-A71 at the human blood cerebrospinal fluid and blood brain barrier. Microb Pathog. 2026;210:108129.
59. Khan Mirzaei M, Khan MAA, Ghosh P, et al. Bacteriophages isolated from stunted children can regulate gut bacterial communities in an age-specific manner. Cell Host Microbe. 2020;27:199-212.e5.
60. Xiao Y, Yue X, Zhang X, Yang Y, Zhang Y, Sun L. The role of bacteriophage in inflammatory bowel disease and its therapeutic potential. Crit Rev Microbiol. 2025;51:1231-45.
61. Rothschild-Rodriguez D, Hedges M, Kaplan M, Karav S, Nobrega FL. Phage-encoded carbohydrate-interacting proteins in the human gut. Front. Microbiol. 2023;13:1083208.
62. Lourenço M, Chaffringeon L, Lamy-Besnier Q, et al. The spatial heterogeneity of the gut limits predation and fosters coexistence of bacteria and bacteriophages. Cell Host Microbe. 2020;28:390-401.e5.
63. Eriksen RS, Larsen F, Svenningsen SL, Sneppen K, Mitarai N. The dynamics of phage predation on a microcolony. Biophys J. 2024;123:147-56.
64. Lopez JA, Mckeithen-Mead S, Shi H, Nguyen TH, Huang KC, Good BH. Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome. bioRxiv 2024; bioRxiv:2024.09.27.614587. Available online: https://doi.org/10.1101/2024.09.27.614587. [accessed 18 June 2026].
65. Lopez JA, Mckeithen-Mead S, Shi H, Nguyen TH, Huang KC, Good BH. Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome. Curr Biol. 2025;35:2282-2294.e11.
66. Avellaneda-franco L, Xie L, Nakai M, Barr JJ, Marques FZ. Dietary fiber intake impacts gut bacterial and viral populations in a hypertensive mouse model. Gut Microbes. 2024;16:2407047.
67. Wu D, Zhang C, Liu Y, et al. Beyond faecal microbiota transplantation, the non-negligible role of faecal virome or bacteriophage transplantation. J Microbiol Immunol Infect. 2023;56:893-908.
68. Liu X, Han Z, Ma W, et al. Effects of Lactiplantibacillus plantarum HNU082 intervention on fungi and bacteriophages in different intestinal segments of mice. BMC Microbiol. 2025;25:69.
69. Li Y, Li X, Duan H, Yang K, Ye J. Advances and optimization strategies in bacteriophage therapy for treating inflammatory bowel disease. Front Immunol. 2024;15:1398652.
70. Xing B, Liu C, Chen W, et al. Gut Phage Biobank: a collection of bacteriophages targeting human commensal bacteria. Nat Commun. 2025;16:11050.
71. Naderian R, Alibabaei F, Paraandavaji E, Dehghan P, Eslami M. Phage-microbiota interactions in the gut: implications for health and therapeutic strategies. Probiotics Antimicro. Prot. 2025;18:3633-47.
72. Kurilovich E, Geva-zatorsky N. Effects of bacteriophages on gut microbiome functionality. Gut Microbes. 2025;17:2481178.
73. Kirsch JM, Brzozowski RS, Faith D, Round JL, Secor PR, Duerkop BA. Bacteriophage-bacteria interactions in the gut: from invertebrates to mammals. Annu. Rev. Virol. 2021;8:95-113.
74. Penix T, Favazza J, Rosch JW, Rowe HM. Lipoteichoic acid mediates binding of Streptococcus pneumoniae and influenza A virus. mSphere. 2025;10:e00504-25.
75. Ray RR. Role of virus on oral biofilm: inducer or eradicator? Appl Biochem Biotechnol. 2023;196:1652-68.
76. Stanifer ML, Karst SM, Boulant S. Regionalization of the antiviral response in the gastrointestinal tract to provide spatially controlled host/pathogen interactions. mBio. 2023:e02791-22.
77. Amatullah H, Jeffrey KL. Epigenome-metabolome-microbiome axis in health and IBD. Curr Opin Microbiol. 2020;56:97-108.
79. Jaswal K, Todd OA, Behnsen J. Neglected gut microbiome: interactions of the non-bacterial gut microbiota with enteric pathogens. Gut Microbes. 2023;15:2226916.
80. Xu Q, Tang Y, Huang G. Innate immune responses in RNA viral infection. Front. Med. 2020;15:333-46.
81. Enya T, Ross SR. Innate sensing of viral nucleic acids and their use in antiviral vaccine development. Vaccines. 2025;13:193.
82. Beirag N, Varghese PM, Kishore U. Innate immune response to viral infection. In: Kishore U, George AJT, Editors. Innate immunity: pattern recognition and effector mechanisms. Cham: Springer Nature Switzerland; 2025. pp. 199-224.
83. Boylan BT, Hwang M, Bergmann CC. The impact of innate components on viral pathogenesis in the neurotropic coronavirus encephalomyelitis mouse model. Viruses. 2023;15:2400.
84. Scarpellini E, Fagoonee S, Rinninella E, et al. Gut microbiota and liver interaction through immune system cross-talk: a comprehensive review at the time of the SARS-CoV-2 pandemic. JCM. 2020;9:2488.
85. Li L, Luo J, Zhu Z, et al. SRA suppresses antiviral innate immune response in macrophages by limiting TBK1 K63 ubiquitination via deubiquitinase USP15. Microbiol Spectr. 2022;10:e02028-22.
86. Li Q, Qin Y, Wang W, Jia M, Zhao W, Zhao C. KAP1-mediated epigenetic suppression in anti-RNA viral responses by direct targeting RIG-I and MDA5. J Immunol. 2021;207:1903-10.
87. Rivera-Calzada A, Arribas-Bosacoma R, Ruiz-Ramos A, et al. Structural basis for the inactivation of cytosolic DNA sensing by the vaccinia virus. Nat Commun. 2022;13:7062.
88. Chabot E, Durantel D, Lucifora J. TRIM proteins: A ‘swiss army knife’ of antiviral immunity. PLoS Pathog. 2025;21:e1013147.
89. Kalugotla G, Marmerstein V, Baldridge MT. Regulation of host/pathogen interactions in the gastrointestinal tract by type I and III interferons. Curr Opin Immunol. 2024;87:102425.
90. Wan SW, Lee YR, Ho TS, Chang CP. Regulation of innate immune signaling pathways by autophagy in dengue virus infection. IUBMB Life. 2021;74:170-9.
91. Zhou X, Xie F, Wang L, et al. The function and clinical application of extracellular vesicles in innate immune regulation. Cell Mol Immunol. 2020;17:323-34.
92. Raychoudhuri A, Naru AK, Kanubothula SR, Uddala R. Development of an experimental inactivated vaccine from Vero cell adapted Enterovirus D68. Virus Res. 2021;304:198528.
93. Jin W, Lu J, Zhang X, et al. Efficacy of Coxsackievirus A5 vaccine candidates in an actively immunized mouse model. J Virol. 2021;95:e01743-20.
94. Zhang H, Song Z, Zou J, et al. An infectious clone of enterovirus 71(EV71) that is capable of infecting neonatal immune competent mice without adaptive mutations. Emerg Microbes Infect. 2020;9:427-38.
95. Massimino L, Palmieri O, Facoetti A, et al. Gut virome-colonising Orthohepadnavirus genus is associated with ulcerative colitis pathogenesis and induces intestinal inflammation in vivo. Gut. 2023;72:1838-47.
96. Hamade H, Tsuda M, Oshima N, et al. Toll-like receptor 7 protects against intestinal inflammation and restricts the development of colonic tissue-resident memory CD8+ T cells. Front. Immunol. 2024;15:1465175.
97. Wang H, Wang Y, Wu S, et al. STING restricts EV-A71 infection by regulating T Cell development and enhancing immune cell effector function. Int J Mol Sci. 2025;26:11441.
98. Ruohtula T, Kondrashova A, Lehtonen J, et al. ; the DIABIMMUNE Study Group. Immunomodulatory effects of rhinovirus and enterovirus infections during the first year of life. Front. Immunol. 2021;11:567046.
99. Yang X, Shui X, Dai X, et al. PLAC8 promotes EV71 infected inflammatory lesion by disturbing Th-cell-related cytokines release in neonatal mouse. Virology. 2021;564:39-45.
100. Schulte BM, Kramer M, Ansems M, et al. Phagocytosis of enterovirus-infected pancreatic β-cells triggers innate immune responses in human dendritic cells. Diabetes. 2010;59:1182-91.
101. Li L, Huang R, Liu X, et al. Modulation of plasmacytoid dendritic cell and CD4+ T cell differentiation accompanied by upregulation of the cholinergic anti-inflammatory pathway induced by enterovirus 71. Arch Virol. 2024;169:73.
102. Zhao M, Wang L, Lian G, et al. Characterization of lymphocyte subsets in peripheral blood cells of children with EV71 infection. J Microbiol Immunol Infect. 2020;53:705-14.
103. Aida K, Nishida Y, Tanaka S, et al. RIG-I- and MDA5-initiated innate immunity linked with adaptive immunity accelerates β-cell death in fulminant type 1 diabetes. Diabetes. 2011;60:884-9.
104. Moise L, Gutierrez AH, Bailey-Kellogg C, et al. The two-faced T cell epitope: Examining the host-microbe interface with JanusMatrix. Hum Vacc Immunother. 2013;9:1577-86.
105. Liu W, Moussawi M, Roberts B, Boyson JE, Huber SA. Cross-regulation of T regulatory - cell response after Coxsackievirus B3 infection by NKT and γδ T cells in the mouse. Am J Pathol. 2013;183:441-9.
106. Shi Y, Fukuoka M, Li G, et al. Regulatory T cells protect mice against Coxsackievirus-induced myocarditis through the transforming growth factor β - Coxsackie-Adenovirus receptor pathway. Circulation. 2010;121:2624-34.
107. Andronik A, Lewandowski D, Sulik A, Toczylowski K. The host immune response to enterovirus A71 (EV-A71): from viral immune evasion to immunopathology and prognostic biomarkers of severe disease - a narrative review. Viruses. 2025;17:1540.
108. Li Q, Wang Y, Xue W, et al. Immunomodulatory effects of platelets on the severity of hand, foot, and mouth disease infected with enterovirus 71. Pediatr Res. 2020;89:814-22.
109. Jansen D, Matthijnssens J. The emerging role of the gut virome in health and inflammatory bowel disease: challenges, covariates and a viral imbalance. Viruses. 2023;15:173.
110. Cao Z, Fan D, Sun Y, et al. The gut ileal mucosal virome is disturbed in patients with Crohn’s disease and exacerbates intestinal inflammation in mice. Nat Commun. 2024;15:1638.
111. Tian X, Li S, Wang C, et al. Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease. Microbiome. 2024;12:130.
112. Vásquez J, Doncel P, Camacho J, Ruiz E, Recio V, Tarragó D. Targeted virome deep sequencing reveals frequent herpesvirus detection in intestinal biopsies of inflammatory bowel disease patients. PLoS ONE. 2025;20:e0337322.
113. Yan A, Butcher J, Schramm L, Mack DR, Stintzi A. Multiomic spatial analysis reveals a distinct mucosa-associated virome. Gut Microbes. 2023;15:2177488.
114. Yan A, Butcher J, Mack DR, Stintzi A. The colonic mucosal virome in inflammatory bowel disease reveals Crassvirales depletion and disease-specific virome features. Gut Microbes. 2025;17:2539450.
115. Yang F, Xiong L, Li M, et al. A signature-protein-based approach for accurate and efficient profiling of the human gut virome. Cell Rep Methods. 2026;6:101250.
116. Sinha A, Li Y, Mirzaei MK, et al. Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates the severity of DSS colitis. Microbiome. 2022;10:105.
117. Coffey MJ, Low I, Stelzer-Braid S, et al. The intestinal virome in children with cystic fibrosis differs from healthy controls. PLoS ONE. 2020;15:e0233557.
118. Singh G, Ansari S, Yadav S, Aran KR. Gut microbiota’s role in NAFLD- and HBV/HCV-related hepatocellular carcinoma: Mechanisms and therapeutic implications. Microb Pathog. 2026;211:108273.
119. Liu L, Liang L, Liang H, et al. Microbiome-metabolome generated bile acids gatekeep infliximab efficacy in Crohn’s disease by licensing M1 suppression and Treg dominance. J Adv Res. 2026;83:789-806.
120. Rashed R, Valcheva R, Dieleman LA. Manipulation of gut microbiota as a key target for Crohn’s disease. Front. Med. 2022;9:887044.
121. Jin J, Yao G, Zhang X, et al. Gut virome dysbiosis contributes to premature ovarian insufficiency by modulating gut bacteriome. Gut Microbes. 2026;18:2611645.
122. Zhang J, Zhang Y, Xia Y, Sun J. Imbalance of the intestinal virome and altered viral-bacterial interactions caused by a conditional deletion of the vitamin D receptor. Gut Microbes. 2021;13:1957408.
123. Poma AM, Hammerstad SS, Genoni A, Basolo A, Dahl-Jorgensen K, Toniolo A. Immune transcriptome of cells infected with enterovirus strains obtained from cases of autoimmune thyroid disease. Microorganisms. 2021;9:876.
124. Sioofy-khojine A, Richardson SJ, Locke JM, et al. Detection of enterovirus RNA in peripheral blood mononuclear cells correlates with the presence of the predisposing allele of the type 1 diabetes risk gene IFIH1 and with disease stage. Diabetologia. 2022;65:1701-9.
125. Richardson SJ, Rodriguez-Calvo T, Laiho JE, et al. ; for the nPOD-Virus Group. Joint analysis of the nPOD-Virus Group data: the association of enterovirus with type 1 diabetes is supported by multiple markers of infection in pancreas tissue. Diabetologia. 2025;68:1226-41.
126. Mønsted MØ, Pedersen K, Jensen MH, et al. Genetic and transcriptional dysregulation of innate antiviral immune pathways in type 1 diabetes. Immunol Lett. 2025;276:107060.
127. Tekin B, Boire N, Shah K, Hanson J, Bridges AG. Viral panniculitis in a patient with disseminated opportunistic Enterovirus infection. J Cutan Pathol. 2020;48:434-8.
128. Jayaraman S, Tiniakou E, Morgenlander WR, Na M, Christopher‐Stine L, Larman HB. Comprehensive enteroviral serology links infection and anti-melanoma differentiation-associated protein 5 dermatomyositis. ACR Open Rheumatol. 2024;7:e11752.
129. Real-Fernández F, Gallo A, Nuti F, et al. ELISA based on peptide antigens reproducing cross-reactive viral epitopes to detect antibodies in latent autoimmune diabetes in adults vs. type 1 diabetes. MethodsX. 2021;8:101452.
130. Garg I, Meyer BI, Gallo RA, Wester ST, Pelaez D. A novel association between human papillomavirus and thyroid eye disease. medRxiv 2024; medRxiv:2024.04.27.24306443. Available online: https://doi.org/10.1101/2024.04.27.24306443. [accessed 18 June 2026].
131. Morse ZJ, Simister RL, Crowe SA, Horwitz MS, Osborne LC. Virus induced dysbiosis promotes type 1 diabetes onset. Front Immunol. 2023;14:1096323.
132. Veronese-Paniagua DA, Millman JR. The perfect storm: unraveling the interplay of genetic predisposition and viral triggers in type 1 diabetes pathogenesis. Front Endocrinol. 2025;16:1734431.
133. Yang C, Sun F, Wang F, et al. The interferon regulatory factors, a double-edged sword, in the pathogenesis of type 1 diabetes. Cell Immunol. 2022;379:104590.
134. Butrym M, Byvald F, Blanter M, et al. Vemurafenib inhibits the replication of diabetogenic enteroviruses in intestinal epithelial and pancreatic beta cells. Antiviral Res. 2024;231:106021.
135. Stögbauer J, Schegerer V, Berger FK, et al. Severe coxsackie virus B5 encephalitis mimics autoimmune limbic encephalitis in a young woman under long-term B-cell depletion with ocrelizumab: a case report. Mult Scler. 2025;31:1258-61.
136. You S, Wang L, Tsai H, Teresa Teng Y, Chen S, Wang S. Therapeutic determinants of melatonin in hepatitis caused by Coxsackievirus B3 infection. Antiviral Res. 2025;239:106191.
137. Kimura T, Flynn CT, Whitton JL. Hepatocytes trap and silence coxsackieviruses, protecting against systemic disease in mice. Commun Biol. 2020;3:580.
138. Park J, Shin H, Rhyu H, Kim S, Jeon E, Lim B. Vascular endothelial integrity affects the severity of enterovirus-mediated cardiomyopathy. Int J Mol Sci. 2021;22:3053.
139. Hsueh T, Lin W, Dalley JW, Tsai T. The pharmacological effects and pharmacokinetics of active compounds of artemisia capillaris. Biomedicines. 2021;9:1412.
140. Bharathwajchetty B, Kumar A, Deevi P, et al. Gut microbiota and their influence in brain cancer milieu. J Neuroinflammation. 2025;22:129.
141. Guerin E, Hill C. Shining light on human gut bacteriophages. Front Cell Infect Microbiol. 2020;10:481.
142. Da Silva AF, Wallau GL. Bioinformatic identification of viral genomes from high-throughput metagenomic sequencing data. In: Muley VY, Editors. Computational virology. New York, NY: Springer US; 2025. pp. 1-22.
143. Casey E, Mcdonnell B, White K, et al. Needle in a Whey-Stack: PhRACS as a discovery tool for unknown phage-host combinations. mBio. 2022;13:e03334-21.
144. Schmitz D, Zwagemaker F, Nooij S, et al. Accessible viral metagenomics for public health and clinical domains with Jovian. Sci Rep. 2024;14:26018.
145. Farfán J, Gonzalez JM, Vives M. The immunomodulatory potential of phage therapy to treat acne: a review on bacterial lysis and immunomodulation. PeerJ. 2022;10:e13553.
146. Suda T, Hanawa T, Tanaka M, et al. Modification of the immune response by bacteriophages alters methicillin-resistant Staphylococcus aureus infection. Sci Rep. 2022;12:15656.
147. Su J, Wu Y, Wang Z, et al. Probiotic biofilm modified scaffolds for facilitating osteomyelitis treatment through sustained release of bacteriophage and regulated macrophage polarization. Materials Today Bio. 2025;30:101444.
148. Islam MS, Wei P, Zhang K, Nime I, Pan F. Phage therapy modulates the gut microbiome and immune responses in non-typhoidal Salmonella-induced colitis. Food Res Int. 2025;219:117003.
149. Cheng F, Soleimani Samarkhazan H, Khazaei Y. CRISPR-engineered microbiome: living therapeutics revolutionize blood cancer immunotherapy. npj Biofilms Microbiomes. 2025;12:17.
150. Getz LJ, Patel PH, Maxwell KL. A solution to the postantibiotic era: phages as precision medicine. Curr Opin Microbiol. 2025;86:102613.
151. Liu J, Lu X, Zhou W. Elevated circulating miR-494 in plasma of children with enterovirus 71 induced hand, foot, and mouth disease and its potential diagnostic value. Acta Virol. 2020;64:338-43.
152. Morichi S, Suzuki S, Nishimata S, Yamanaka G, Kashiwagi Y, Kawashima H. Increased platelet-derived growth factor and cytokine levels in the cerebrospinal fluid of patients of sudden unexpected death with or without viral infection. Indian J Pediatr. 2021;88:879-84.
153. Lei L, Li Q, Xu S, et al. Transplantation of enterovirus 71 virion protein particle vaccine protects against enterovirus 71 infection in a neonatal mouse model. Ann Transplant. 2021;26:924461.
154. Chin CL, Lin YL, Cheng PY, Lee P, Chiang BL. Effective mucosal adjuvantation of the intranasal enterovirus A71 vaccine with zymosan. Immunology. 2025;174:349-62.
155. Swain SK, Panda S, Sahu BP, Sarangi R. Activation of host cellular signaling and mechanism of enterovirus 71 viral proteins associated with hand, foot and mouth disease. Viruses. 2022;14:2190.
156. Shimizu H. Inactivated enterovirus A71 vaccines and moving forward. Lancet Reg Health West Pac. 2021;16:100292.
157. Ye L, Chen J, Fang T, et al. Vaccination coverage estimates and utilization patterns of inactivated enterovirus 71 vaccine post vaccine introduction in Ningbo, China. BMC Public Health. 2021;21:1118.
158. Jiang H, Zhang Z, Rao Q, et al. The epidemiological characteristics of enterovirus infection before and after the use of enterovirus 71 inactivated vaccine in Kunming, China. Emerg Microbes Infect. 2021;10:619-28.
159. Duan X, Zhang L, Ding L, et al. Effectiveness of enterovirus A71 vaccine against pediatric HFMD and disease profile of post-vaccination infection. Vaccine. 2024;42:2317-25.
160. Zhang P, Zou W, Xiong R, Wu Y, Fan C, Peng Y. Enterovirus A71 2A‐S125A acts as an attenuated vaccine candidate, indicating a universal approach in developing enterovirus vaccines. J Med Virol. 2024;96:e29838.
161. Zimina A, Kouiavskaia D, Viktorova EG, et al. Viral vector-driven trans-encapsidation of replicon RNAs as a rapid approach for the development of safe and economically attractive anti-enterovirus vaccines. bioRxiv 2025; bioRxiv:2025.12.01.691592. Available online: https://doi.org/10.1101/2025.12.01.691592. [accessed 18 June 2026].
162. Cinti L, Spezia PG, Roberto P, et al. Assessment of Torquetenominivirus (TTMV) and Torquetenomidivirus (TTMDV) as Complementary Biomarkers to Torquetenovirus (TTV). Int J Mol Sci. 2025;26:1022.
163. Camargo AP, Nayfach S, Chen IA, et al. IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata. Nucleic Acids Res. 2023;51:D733-43.
