{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T21:32:08Z","timestamp":1782423128634,"version":"3.54.5"},"reference-count":77,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2025,12,25]],"date-time":"2025-12-25T00:00:00Z","timestamp":1766620800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>The human virome represents a fundamental yet understudied component of the microbiome, influencing immune regulation and disease. Given the profound immune dysregulation and microbial imbalance associated with HIV infection, understanding virome alterations during HIV and antiretroviral therapy is essential. This narrative review seeks to integrate and discuss the latest evidence regarding the structure and behavior of the human virome in healthy individuals, in the context of HIV infection, and under antiretroviral therapy. A comprehensive literature search was performed in MEDLINE and Google Scholar for peer-reviewed English-language articles published up to November 2025. Studies describing virome composition, diversity, and interactions in people living with HIV, as well as antiretroviral-induced changes, were included. Reference lists of relevant papers were screened to identify additional sources. Data were extracted and synthesized narratively, emphasizing human studies and supported by evidence from primate models where applicable. HIV infection induces profound alterations in the human virome, notably an expansion of eukaryotic viruses such as Anelloviridae, Adenoviridae, and Parvoviridae, accompanied by reduced bacteriophage diversity. Antiretroviral therapy partially restores virome balance but fails to fully re-establish pre-infection diversity, with persistent enrichment of Anelloviridae reflecting incomplete immune reconstitution. Virome perturbations correlate with immune activation, microbial translocation, and inflammation, contributing to comorbidities despite virological suppression. Emerging evidence suggests regimen-specific effects, with integrase inhibitor-based therapies showing more favorable viromic recovery. HIV and antiretroviral therapy profoundly remodel the human virome, with lasting implications for immune homeostasis and chronic inflammation. The ongoing disruption of the virome highlights its promise as both a biomarker and a potential therapeutic target in the management of HIV. Longitudinal, multi-omic studies are needed to clarify the causal role of virome alterations and guide future interventions.<\/jats:p>","DOI":"10.3390\/microorganisms14010050","type":"journal-article","created":{"date-parts":[[2025,12,26]],"date-time":"2025-12-26T02:07:58Z","timestamp":1766714878000},"page":"50","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["The Human Virome in Health and Its Remodeling During HIV Infection and Antiretroviral Therapy: A Narrative Review"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-4327-7305","authenticated-orcid":false,"given":"Federico","family":"Cesanelli","sequence":"first","affiliation":[{"name":"Unit of Infectious and Tropical Diseases, Department of Clinical and Experimental Sciences, University of Brescia and ASST Spedali Civili di Brescia, 25123 Brescia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Irene","family":"Scarvaglieri","sequence":"additional","affiliation":[{"name":"Unit of Infectious and Tropical Diseases, Department of Clinical and Experimental Sciences, University of Brescia and ASST Spedali Civili di Brescia, 25123 Brescia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2221-6286","authenticated-orcid":false,"given":"Maria Antonia","family":"De Francesco","sequence":"additional","affiliation":[{"name":"Highly Specialized Laboratory, ASST Spedali Civili of Brescia, 25123 Brescia, Italy"},{"name":"Institute of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Alberti","sequence":"additional","affiliation":[{"name":"Unit of Infectious and Tropical Diseases, Department of Clinical and Experimental Sciences, University of Brescia and ASST Spedali Civili di Brescia, 25123 Brescia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martina","family":"Salvi","sequence":"additional","affiliation":[{"name":"Unit of Infectious and Tropical Diseases, Department of Clinical and Experimental Sciences, University of Brescia and ASST Spedali Civili di Brescia, 25123 Brescia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7366-871X","authenticated-orcid":false,"given":"Giorgio","family":"Tiecco","sequence":"additional","affiliation":[{"name":"Unit of Infectious and Tropical Diseases, Department of Clinical and Experimental Sciences, University of Brescia and ASST Spedali Civili di Brescia, 25123 Brescia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9161-7804","authenticated-orcid":false,"given":"Francesco","family":"Castelli","sequence":"additional","affiliation":[{"name":"Unit of Infectious and Tropical Diseases, Department of Clinical and Experimental Sciences, University of Brescia and ASST Spedali Civili di Brescia, 25123 Brescia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1452-9100","authenticated-orcid":false,"given":"Eugenia","family":"Quiros-Roldan","sequence":"additional","affiliation":[{"name":"Unit of Infectious and Tropical Diseases, Department of Clinical and Experimental Sciences, University of Brescia and ASST Spedali Civili di Brescia, 25123 Brescia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,12,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.coviro.2019.05.007","article-title":"Virome and bacteriome: Two sides of the same coin","volume":"37","author":"Stern","year":"2019","journal-title":"Curr. Opin. Virol."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Xie, Y., Sun, J., Wei, L., Jiang, H., Hu, C., Yang, J., Huang, Y., Ruan, B., and Zhu, B. (2021). Altered gut microbiota correlate with different immune responses to HAART in HIV-infected individuals. BMC Microbiol., 21.","DOI":"10.1186\/s12866-020-02074-1"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Shrivastav, K., Nasser, H., Ikeda, T., and Nema, V. (2025). Possible Crosstalk and Alterations in Gut Bacteriome and Virome in HIV-1 Infection and the Associated Comorbidities Related to Metabolic Disorder. Viruses, 17.","DOI":"10.20944\/preprints202505.1447.v1"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1038\/nrmicro2848","article-title":"Microbial translocation in HIV infection: Causes, consequences and treatment opportunities","volume":"10","author":"Sandler","year":"2012","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1111\/imr.12065","article-title":"Immune activation and HIV persistence: Implications for curative approaches to HIV infection","volume":"254","author":"Klatt","year":"2013","journal-title":"Immunol. Rev."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1146\/annurev-immunol-020711-075001","article-title":"Microbial translocation across the GI tract","volume":"30","author":"Brenchley","year":"2012","journal-title":"Annu. Rev. Immunol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2737","DOI":"10.1097\/QAD.0000000000001289","article-title":"The gut microbiome and HIV-1 pathogenesis: A two-way street","volume":"30","author":"Dillon","year":"2016","journal-title":"AIDS"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Nazli, A., Chan, O., Dobson-Belaire, W.N., Ouellet, M., Tremblay, M.J., Gray-Owen, S.D., Arsenault, A.L., and Kaushic, C. (2010). Exposure to HIV-1 directly impairs mucosal epithelial barrier integrity allowing microbial translocation. PLoS Pathog., 6.","DOI":"10.1371\/journal.ppat.1000852"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1016\/j.immuni.2015.09.003","article-title":"Interleukin-23-Independent IL-17 Production Regulates Intestinal Epithelial Permeability","volume":"43","author":"Lee","year":"2015","journal-title":"Immunity"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"(2017). Antiretroviral Therapy Cohort Collaboration. Survival of HIV-positive patients starting antiretroviral therapy between 1996 and 2013: A collaborative analysis of cohort studies. Lancet HIV, 4, e349\u2013e356.","DOI":"10.1016\/S2352-3018(17)30066-8"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1097\/QAD.0000000000003772","article-title":"Life expectancy of people with HIV on antiretroviral therapy in Spain","volume":"38","author":"Rava","year":"2024","journal-title":"AIDS"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"S44","DOI":"10.1093\/infdis\/jiw275","article-title":"Immunologic Biomarkers, Morbidity, and Mortality in Treated HIV Infection","volume":"214","author":"Hunt","year":"2016","journal-title":"J. Infect. Dis."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2467168","DOI":"10.1080\/21505594.2025.2467168","article-title":"Short-term antiretroviral therapy may not correct the dysregulations of plasma virome and cytokines induced by HIV-1 infection","volume":"16","author":"Ma","year":"2025","journal-title":"Virulence"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"100191","DOI":"10.1016\/j.engmic.2025.100191","article-title":"The gut virome and human health: From diversity to personalized medicine","volume":"5","author":"Lathakumari","year":"2025","journal-title":"Eng. Microbiol."},{"key":"ref_15","unstructured":"Ullah, K., Kanwar, R., Ali, S., Uddin, S., Izza, I., Ahmad, I., Alzahrani, K.J., Qadeer, A., Chu, C.T., and Chen, C.C. (2025). Gut Virome and Aging: Phage-Driven Microbial Stability and Immune Modulation. Aging Dis."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"800","DOI":"10.1111\/apt.14280","article-title":"Review article: The human intestinal virome in health and disease","volume":"46","author":"Carding","year":"2017","journal-title":"Aliment. Pharmacol. Ther."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1038\/s41579-021-00536-5","article-title":"The human virome: Assembly, composition and host interactions","volume":"19","author":"Liang","year":"2021","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1016\/j.tim.2013.07.001","article-title":"The human virome: New tools and concepts","volume":"21","author":"Lecuit","year":"2013","journal-title":"Trends Microbiol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1007\/s007050050689","article-title":"Identification of a new human DNA virus (TTV-like mini virus, TLMV) intermediately related to TT virus and chicken anemia virus","volume":"145","author":"Takahashi","year":"2000","journal-title":"Arch. Virol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"893","DOI":"10.1007\/s00705-015-2363-9","article-title":"Human anelloviruses: An update of molecular, epidemiological and clinical aspects","volume":"160","author":"Spandole","year":"2015","journal-title":"Arch. Virol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1600","DOI":"10.1093\/ecco-jcc\/jjaa094","article-title":"Dynamics of the Stool Virome in Very Early-Onset Inflammatory Bowel Disease","volume":"14","author":"Liang","year":"2020","journal-title":"J. Crohns Colitis"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1111\/ajt.13031","article-title":"Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipients","volume":"15","author":"Young","year":"2015","journal-title":"Am. J. Transplant."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"104586","DOI":"10.1016\/j.jcv.2020.104586","article-title":"Redondovirus DNA in human respiratory samples","volume":"131","author":"Spezia","year":"2020","journal-title":"J. Clin. Virol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1016\/j.cell.2015.01.002","article-title":"Disease-specific alterations in the enteric virome in inflammatory bowel disease","volume":"160","author":"Norman","year":"2015","journal-title":"Cell"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Chio, C.C., Chien, J.C., Chan, H.W., and Huang, H.I. (2024). Overview of the Trending Enteric Viruses and Their Pathogenesis in Intestinal Epithelial Cell Infection. Biomedicines, 12.","DOI":"10.3390\/biomedicines12122773"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"654","DOI":"10.1038\/ni.2614","article-title":"Resident viruses and their interactions with the immune system","volume":"14","author":"Duerkop","year":"2013","journal-title":"Nat. Immunol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1186\/s40168-016-0177-y","article-title":"Research on the human virome: Where are we and what is next","volume":"4","author":"Zou","year":"2016","journal-title":"Microbiome"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1016\/j.chom.2019.09.009","article-title":"The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific","volume":"26","author":"Shkoporov","year":"2019","journal-title":"Cell Host Microbe"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1146\/annurev-micro-102215-095431","article-title":"Metagenomics and the Human Virome in Asymptomatic Individuals","volume":"70","author":"Rascovan","year":"2016","journal-title":"Annu. Rev. Microbiol."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Cebri\u00e1-Mendoza, M., Bracho, M.A., Arbona, C., Larrea, L., D\u00edaz, W., Sanju\u00e1n, R., and Cuevas, J.M. (2021). Exploring the Diversity of the Human Blood Virome. Viruses, 13.","DOI":"10.21203\/rs.3.rs-741472\/v1"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"199004","DOI":"10.1016\/j.virusres.2022.199004","article-title":"An atlas of the blood virome in healthy individuals","volume":"323","author":"Feng","year":"2023","journal-title":"Virus Res."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.ccm.2016.11.001","article-title":"The Virome of the Human Respiratory Tract","volume":"38","author":"Wylie","year":"2017","journal-title":"Clin. Chest Med."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Porto, B.N. (2022). Insights Into the Role of the Lung Virome During Respiratory Viral Infections. Front. Immunol., 13.","DOI":"10.3389\/fimmu.2022.885341"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1186\/s12985-025-02742-6","article-title":"Identification and characterization of novel CRESS-DNA viruses in the human respiratory tract","volume":"22","author":"Zhang","year":"2025","journal-title":"Virol. J."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Pannaraj, P.S., Ly, M., Cerini, C., Saavedra, M., Aldrovandi, G.M., Saboory, A.A., Johnson, K.M., and Pride, D.T. (2018). Shared and Distinct Features of Human Milk and Infant Stool Viromes. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.01162"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1016\/S2352-4642(19)30024-0","article-title":"Transmission of CMV, HTLV-1, and HIV through breastmilk","volume":"3","author":"Prendergast","year":"2019","journal-title":"Lancet Child. Adolesc. Health"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1186\/s40168-017-0282-6","article-title":"Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission","volume":"5","author":"Duranti","year":"2017","journal-title":"Microbiome"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1017\/S2040174415001233","article-title":"Early microbial contact, the breast milk microbiome and child health","volume":"7","author":"Rautava","year":"2016","journal-title":"J. Dev. Orig. Health Dis."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1159\/000354561","article-title":"Describing the silent human virome with an emphasis on giant viruses","volume":"56","author":"Popgeorgiev","year":"2013","journal-title":"Intervirology"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Trunfio, M., Scutari, R., Fox, V., Vuaran, E., Dastgheyb, R.M., Fini, V., Granaglia, A., Balbo, F., Tortarolo, D., and Bonora, S. (2025). The cerebrospinal fluid virome in people with HIV: Links to neuroinflammation and cognition. Front. Microbiol., 16.","DOI":"10.3389\/fmicb.2025.1704392"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1016\/j.chom.2022.02.013","article-title":"The gut-brain axis goes viral","volume":"30","author":"Sampson","year":"2022","journal-title":"Cell Host Microbe"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1016\/j.chom.2022.01.013","article-title":"Caudovirales bacteriophages are associated with improved executive function and memory in flies, mice, and humans","volume":"30","author":"Puig","year":"2022","journal-title":"Cell Host Microbe"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1126","DOI":"10.1111\/j.1469-0691.2011.03690.x","article-title":"Detection and identification of plasma bacterial and viral elements in HIV\/AIDS patients in comparison to healthy adults","volume":"18","author":"Li","year":"2012","journal-title":"Clin. Microbiol. Infect"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1128\/CMR.13.4.559","article-title":"Multiplex PCR: Optimization and application in diagnostic virology","volume":"13","author":"Elnifro","year":"2000","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Chou, C.C., Lee, T.T., Chen, C.H., Hsiao, H.Y., Lin, Y.L., Ho, M.S., Yang, P.C., and Peck, K. (2006). Design of microarray probes for virus identification and detection of emerging viruses at the genus level. BMC Bioinform., 7.","DOI":"10.1186\/1471-2105-7-232"},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Pargin, E., Roach, M.J., Skye, A., Papudeshi, B., Inglis, L.K., Mallawaarachchi, V., Grigson, S.R., Harker, C., Edwards, R.A., and Giles, S.K. (2023). The human gut virome: Composition, colonization, interactions, and impacts on human health. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.963173"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Bai, G.H., Lin, S.C., Hsu, Y.H., and Chen, S.Y. (2022). The Human Virome: Viral Metagenomics, Relations with Human Diseases, and Therapeutic Applications. Viruses, 14.","DOI":"10.3390\/v14020278"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1186\/s40168-020-00990-y","article-title":"VirSorter2: A multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses","volume":"9","author":"Guo","year":"2021","journal-title":"Microbiome"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1016\/j.chom.2016.02.011","article-title":"Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome","volume":"19","author":"Monaco","year":"2016","journal-title":"Cell Host Microbe"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1186\/s12977-018-0402-9","article-title":"Assessment of the gorilla gut virome in association with natural simian immunodeficiency virus infection","volume":"15","author":"Furtado","year":"2018","journal-title":"Retrovirology"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1016\/j.cell.2012.09.024","article-title":"Pathogenic simian immunodeficiency virus infection is associated with expansion of the enteric virome","volume":"151","author":"Handley","year":"2012","journal-title":"Cell"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1016\/j.chom.2016.02.010","article-title":"SIV Infection-Mediated Changes in Gastrointestinal Bacterial Microbiome and Virome Are Associated with Immunodeficiency and Prevented by Vaccination","volume":"19","author":"Handley","year":"2016","journal-title":"Cell Host Microbe"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"eadq1152","DOI":"10.1126\/sciadv.adq1152","article-title":"Large expansion of plasma commensal viruses is associated with SIV pathogenesis in Macaca leonina","volume":"10","author":"Li","year":"2024","journal-title":"Sci. Adv."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Zhang, Y., Sharma, S., Tom, L., Liao, Y.T., and Wu, V.C.H. (2023). Gut Phageome-An Insight into the Role and Impact of Gut Microbiome and Their Correlation with Mammal Health and Diseases. Microorganisms, 11.","DOI":"10.3390\/microorganisms11102454"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"21658","DOI":"10.1038\/s41598-022-25979-5","article-title":"Impact of HIV infection and integrase strand transfer inhibitors-based treatment on the gut virome","volume":"12","author":"Jansen","year":"2022","journal-title":"Sci. Rep."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"3223","DOI":"10.1093\/nar\/gkad199","article-title":"Unmasking the tissue-resident eukaryotic DNA virome in humans","volume":"51","author":"Pratas","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"e0144722","DOI":"10.1128\/spectrum.01447-22","article-title":"Plasma Virome Reveals Blooms and Transmission of Anellovirus in Intravenous Drug Users with HIV-1, HCV, and\/or HBV Infections","volume":"10","author":"Li","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Ramos Pe\u00f1a, D.E., Pillet, S., Grupioni Louren\u00e7o, A., Pozzetto, B., Bourlet, T., and Motta, A.C.F. (2024). Human immunodeficiency virus and oral microbiota: Mutual influence on the establishment of a viral gingival reservoir in individuals under antiretroviral therapy. Front. Cell Infect. Microbiol., 14.","DOI":"10.3389\/fcimb.2024.1364002"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"7904","DOI":"10.1038\/s41467-025-63158-y","article-title":"Longitudinal cervicovaginal bacteriome and virome alterations associate with discordant shedding and ART duration in women living with HIV in Peru","volume":"16","author":"Kaelin","year":"2025","journal-title":"Nat. Commun."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/j.trsl.2016.07.008","article-title":"Lung microbiome in human immunodeficiency virus infection","volume":"179","author":"Twigg","year":"2017","journal-title":"Transl. Res."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"635","DOI":"10.3748\/wjg.v28.i6.635","article-title":"Effects of viremia and CD4 recovery on gut \u201cmicrobiome-immunity\u201d axis in treatment-na\u00efve HIV-1-infected patients undergoing antiretroviral therapy","volume":"28","author":"Russo","year":"2022","journal-title":"World J. Gastroenterol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"6387","DOI":"10.1038\/s41598-020-63196-0","article-title":"Microbial Dysbiosis During Simian Immunodeficiency Virus Infection is Partially Reverted with Combination Anti-retroviral Therapy","volume":"10","author":"Blum","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1186\/s40168-024-01925-7","article-title":"Alterations of the gut microbiome in HIV infection highlight human anelloviruses as potential predictors of immune recovery","volume":"12","author":"Boukadida","year":"2024","journal-title":"Microbiome"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"115094","DOI":"10.1016\/j.diagmicrobio.2020.115094","article-title":"Clinical, molecular, and epidemiological characterization of the SARS-CoV-2 virus and the Coronavirus Disease 2019 (COVID-19), a comprehensive literature review","volume":"98","author":"Guaman","year":"2020","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"960","DOI":"10.1038\/s41598-020-80247-8","article-title":"Impact of long-term antiretroviral therapy on gut and oral microbiotas in HIV-1-infected patients","volume":"11","author":"Imahashi","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"e0220524","DOI":"10.1128\/spectrum.02205-24","article-title":"The human gut microbiome and its metabolic pathway dynamics before and during HIV antiretroviral therapy","volume":"13","author":"Dolo","year":"2025","journal-title":"Microbiol. Spectr."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1016\/j.virol.2009.08.036","article-title":"Torquetenovirus DNA drives proinflammatory cytokines production and secretion by immune cells via toll-like receptor 9","volume":"394","author":"Rocchi","year":"2009","journal-title":"Virology"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"e00081-21","DOI":"10.1128\/mSphere.00081-21","article-title":"HIV-1 Infection Alters the Viral Composition of Plasma in Men Who Have Sex with Men","volume":"6","author":"Liu","year":"2021","journal-title":"mSphere"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"24691","DOI":"10.1038\/s41598-024-73870-2","article-title":"Torque teno virus: A potential marker of immune reconstitution in youths with vertically acquired HIV","volume":"14","author":"Carrasco","year":"2024","journal-title":"Sci. Rep."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"e437","DOI":"10.1093\/infdis\/jiae014","article-title":"Torque Teno Virus Load Is Associated with Centers for Disease Control and Prevention Stage and CD4+ Cell Count in People Living with Human Immunodeficiency Virus but Seems Unrelated to AIDS-Defining Events and Human Pegivirus Load","volume":"230","author":"Esser","year":"2024","journal-title":"J. Infect. Dis."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/jmv.20756","article-title":"Progression towards AIDS leads to increased Torque teno virus and Torque teno minivirus titers in tissues of HIV infected individuals","volume":"79","author":"Thom","year":"2007","journal-title":"J. Med. Virol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1007\/s15010-020-01573-7","article-title":"Torque Teno Virus plasma level as novel biomarker of retained immunocompetence in HIV-infected patients","volume":"49","author":"Schmidt","year":"2021","journal-title":"Infection"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1097\/00002030-200103300-00004","article-title":"Inverse relationship between the titre of TT virus DNA and the CD4 cell count in patients infected with HIV","volume":"15","author":"Shibayama","year":"2001","journal-title":"AIDS"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1056\/NEJMoa003364","article-title":"Effect of coinfection with GB virus C on survival among patients with HIV infection","volume":"345","author":"Xiang","year":"2001","journal-title":"N. Engl. J. Med."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1056\/NEJMoa030107","article-title":"Persistent GB virus C infection and survival in HIV-infected men","volume":"350","author":"Williams","year":"2004","journal-title":"N. Engl. J. Med."},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"Deme, P., Rubin, L.H., Yu, D., Xu, Y., Nakigozi, G., Nakasujja, N., Anok, A., Kisakye, A., Quinn, T.C., and Reynolds, S.J. (2022). Immunometabolic Reprogramming in Response to HIV Infection Is Not Fully Normalized by Suppressive Antiretroviral Therapy. Viruses, 14.","DOI":"10.3390\/v14061313"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1097\/QCO.0000000000000341","article-title":"HIV-associated changes in the enteric microbial community: Potential role in loss of homeostasis and development of systemic inflammation","volume":"30","author":"Gootenberg","year":"2017","journal-title":"Curr. Opin. Infect. 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