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Mogotsi MT, Ogunbayo AE, Bester PA, O'Neill HG, Nyaga MM. Longitudinal analysis of the enteric virome in paediatric subjects from the Free State Province, South Africa, reveals early gut colonisation and temporal dynamics. Virus Res 2024; 346:199403. [PMID: 38776984 PMCID: PMC11169482 DOI: 10.1016/j.virusres.2024.199403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/23/2024] [Accepted: 05/19/2024] [Indexed: 05/25/2024]
Abstract
The gut of healthy neonates is devoid of viruses at birth, but rapidly becomes colonised by normal viral commensals that aid in important physiological functions like metabolism but can, in some instances, result in gastrointestinal illnesses. However, little is known about how this colonisation begins, its variability and factors shaping the gut virome composition. Thus, understanding the development, assembly, and progression of enteric viral communities over time is key. To explore early-life virome development, metagenomic sequencing was employed in faecal samples collected longitudinally from a cohort of 17 infants during their first six months of life. The gut virome analysis revealed a diverse and dynamic viral community, formed by a richness of different viruses infecting humans, non-human mammals, bacteria, and plants. Eukaryotic viruses were detected as early as one week of life, increasing in abundance and diversity over time. Most of the viruses detected are commonly associated with gastroenteritis and include members of the Caliciviridae, Picornaviridae, Astroviridae, Adenoviridae, and Sedoreoviridae families. The most common co-occurrences involved asymptomatic norovirus-parechovirus, norovirus-sapovirus, sapovirus-parechovirus, observed in at least 40 % of the samples. Majority of the plant-derived viruses detected in the infants' gut were from the Virgaviridae family. This study demonstrates the first longitudinal characterisation of the gastrointestinal virome in infants, from birth up to 6 months of age, in sub-Saharan Africa. Overall, the findings from this study delineate the composition and variability of the healthy infants' gut virome over time, which is a significant step towards understanding the dynamics and biogeography of viral communities in the infant gut.
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Affiliation(s)
- Milton Tshidiso Mogotsi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Ayodeji Emmanuel Ogunbayo
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Phillip Armand Bester
- Division of Virology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Hester Gertruida O'Neill
- Department of Microbiology and Biochemistry, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Martin Munene Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa.
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2
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Gupta G, Athreya A, Kataria A. Biomarkers in Kidney Transplantation: A Rapidly Evolving Landscape. Transplantation 2024:00007890-990000000-00820. [PMID: 39020463 DOI: 10.1097/tp.0000000000005122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Abstract
The last decade has seen an explosion in clinical research focusing on the use of noninvasive biomarkers in kidney transplantation. Much of the published literature focuses on donor-derived cell-free DNA (dd-cfDNA). Although initially studied as a noninvasive means of identifying acute rejection, it is now clear that dd-cfDNA is more appropriately described as a marker of severe injury and irrespective of the etiology, elevated dd-cfDNA ≥0.5% portends worse graft outcomes. Blood gene expression profiling is also commercially available and has mostly been studied in the context of early identification of subclinical rejection, although additional data is needed to validate these findings. Torque teno virus, a ubiquitous DNA virus, has emerged as a biomarker of immunosuppression exposure as peripheral blood Torque teno virus copy numbers might mirror the intensity of host immunosuppression. Urinary chemokine tests including C-X-C motif chemokine ligand 9 and C-X-C motif chemokine ligand 10 have recently been assessed in large clinical trials and hold promising potential for early diagnosis of both subclinical and acute rejection, as well as, for long-term prognosis. Urinary cellular messenger RNA and exosome vesicular RNA based studies require additional validation. Although current data does not lend itself to conclusion, future studies on multimodality testing may reveal the utility of serial surveillance for individualization of immunosuppression and identify windows of opportunity to intervene early and before the irreversible allograft injury sets in.
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Affiliation(s)
- Gaurav Gupta
- Hume-Lee Transplant Center, Virginia Commonwealth University, Richmond, VA
- Division of Nephrology, Virginia Commonwealth University, Richmond, VA
| | - Akshay Athreya
- Division of Nephrology, Virginia Commonwealth University, Richmond, VA
| | - Ashish Kataria
- Division of Nephrology, Medical College of Georgia, Augusta, GA
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Tian X, Li S, Wang C, Zhang Y, Feng X, Yan Q, Guo R, Wu F, Wu C, Wang Y, Huo X, Ma X. Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease. MICROBIOME 2024; 12:130. [PMID: 39026313 PMCID: PMC11256409 DOI: 10.1186/s40168-024-01832-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 05/08/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUND The gut virome has been implicated in inflammatory bowel disease (IBD), yet a full understanding of the gut virome in IBD patients, especially across diverse geographic populations, is lacking. RESULTS In this study, we conducted a comprehensive gut virome-wide association study in a Chinese cohort of 71 IBD patients (15 with Crohn's disease and 56 with ulcerative colitis) and 77 healthy controls via viral-like particle (VLP) and bulk virome sequencing of their feces. By utilizing an integrated gut virus catalog tailored to the IBD virome, we revealed fundamental alterations in the gut virome in IBD patients. These characterized 139 differentially abundant viral signatures, including elevated phages predicted to infect Escherichia, Klebsiella, Enterococcus_B, Streptococcus, and Veillonella species, as well as IBD-depleted phages targeting Prevotella, Ruminococcus_E, Bifidobacterium, and Blautia species. Remarkably, these viral signatures demonstrated high consistency across diverse populations such as those in Europe and the USA, emphasizing their significance and broad relevance in the disease context. Furthermore, fecal virome transplantation experiments verified that the colonization of these IBD-characterized viruses can modulate experimental colitis in mouse models. CONCLUSIONS Building upon these insights into the IBD gut virome, we identified potential biomarkers for prognosis and therapy in IBD patients, laying the foundation for further exploration of viromes in related conditions. Video Abstract.
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Affiliation(s)
- Xiangge Tian
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan, 430076, China
| | - Chao Wang
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Yanyan Zhang
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Xiaoying Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Qiulong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China.
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan, 430076, China
| | - Fan Wu
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Chunxue Wu
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Yan Wang
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Xiaokui Huo
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China.
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
| | - Xiaochi Ma
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China.
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
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Dal Lago S, Brani P, Ietto G, Dalla Gasperina D, Gianfagna F, Giaroni C, Bosi A, Drago Ferrante F, Genoni A, Manzoor HZ, Ambrosini A, De Cicco M, Quartarone CD, Khemara S, Carcano G, Maggi F, Baj A. Torque Teno Virus: A Promising Biomarker in Kidney Transplant Recipients. Int J Mol Sci 2024; 25:7744. [PMID: 39062987 DOI: 10.3390/ijms25147744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/08/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Torque Teno Virus (TTV) is a ubiquitous component of the human virome, not associated with any disease. As its load increases when the immune system is compromised, such as in kidney transplant (KT) recipients, TTV load monitoring has been proposed as a method to assess immunosuppression. In this prospective study, TTV load was measured in plasma and urine samples from 42 KT recipients, immediately before KT and in the first 150 days after it. Data obtained suggest that TTV could be a relevant marker for evaluating immune status and could be used as a guide to predict the onset of infectious complications in the follow-up of KT recipients. Since we observed no differences considering distance from transplantation, while we found a changing trend in days before viral infections, we suggest to consider changes over time in the same subjects, irrespective of time distance from transplantation.
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Affiliation(s)
- Sara Dal Lago
- Nephrology Department, ASST Sette Laghi, University of Insubria, 21100 Varese, Italy
| | - Paola Brani
- Department of Medicine and Technological Innovation, University of Insubria, 21100 Varese, Italy
| | - Giuseppe Ietto
- Department of Medicine and Technological Innovation, University of Insubria, 21100 Varese, Italy
| | - Daniela Dalla Gasperina
- Department of Medicine and Technological Innovation, University of Insubria, 21100 Varese, Italy
| | - Francesco Gianfagna
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy
- Mediterranea Cardiocentro, 80122 Napoli, Italy
| | - Cristina Giaroni
- Department of Medicine and Technological Innovation, University of Insubria, 21100 Varese, Italy
| | - Annalisa Bosi
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy
| | | | - Angelo Genoni
- Department of Medicine and Technological Innovation, University of Insubria, 21100 Varese, Italy
| | - Hafza Zahira Manzoor
- Department of Medicine and Technological Innovation, University of Insubria, 21100 Varese, Italy
| | - Andrea Ambrosini
- Nephrology Department, ASST Sette Laghi, University of Insubria, 21100 Varese, Italy
| | - Marco De Cicco
- Nephrology Department, ASST Sette Laghi, University of Insubria, 21100 Varese, Italy
| | | | - Sara Khemara
- Nephrology Department, ASST Sette Laghi, University of Insubria, 21100 Varese, Italy
| | - Giulio Carcano
- Department of Medicine and Technological Innovation, University of Insubria, 21100 Varese, Italy
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases L. Spallanzani-IRCCS, 00149 Rome, Italy
| | - Andreina Baj
- Department of Medicine and Technological Innovation, University of Insubria, 21100 Varese, Italy
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Gholamzad A, Khakpour N, Hashemi SMA, Goudarzi Y, Ahmadi P, Gholamzad M, Mohammadi M, Hashemi M. Exploring the virome: An integral part of human health and disease. Pathol Res Pract 2024; 260:155466. [PMID: 39053136 DOI: 10.1016/j.prp.2024.155466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/06/2024] [Accepted: 07/12/2024] [Indexed: 07/27/2024]
Abstract
The human microbiome is a complex network of microorganisms that includes viruses, bacteria, and fungi. The gut virome is an essential component of the immune system, which is responsible for regulating the growth and responses of the host's immune system. The virome maintains a crucial role in the development of numerous diseases, including inflammatory bowel disease (IBD), Crohn's disease, and neurodegenerative disorders. The human virome has emerged as a promising biomarker and therapeutic target. This comprehensive review summarizes the present understanding of the virome and its implications in matters of health and disease, with a focus on the Human Microbiome Project.
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Affiliation(s)
- Amir Gholamzad
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Niloofar Khakpour
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Mohammad Ali Hashemi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Yalda Goudarzi
- Department of Biology, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Parisa Ahmadi
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mehrdad Gholamzad
- Department of Microbiology and Immunology, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mahya Mohammadi
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology ,Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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6
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Mayer KA, Schrezenmeier E, Diebold M, Halloran PF, Schatzl M, Schranz S, Haindl S, Kasbohm S, Kainz A, Eskandary F, Doberer K, Patel UD, Dudani JS, Regele H, Kozakowski N, Kläger J, Boxhammer R, Amann K, Puchhammer-Stöckl E, Vietzen H, Beck J, Schütz E, Akifova A, Firbas C, Gilbert HN, Osmanodja B, Halleck F, Jilma B, Budde K, Böhmig GA. A Randomized Phase 2 Trial of Felzartamab in Antibody-Mediated Rejection. N Engl J Med 2024; 391:122-132. [PMID: 38804514 DOI: 10.1056/nejmoa2400763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
BACKGROUND Antibody-mediated rejection is a leading cause of kidney-transplant failure. The targeting of CD38 to inhibit graft injury caused by alloantibodies and natural killer (NK) cells may be a therapeutic option. METHODS In this phase 2, double-blind, randomized, placebo-controlled trial, we assigned patients with antibody-mediated rejection that had occurred at least 180 days after transplantation to receive nine infusions of the CD38 monoclonal antibody felzartamab (at a dose of 16 mg per kilogram of body weight) or placebo for 6 months, followed by a 6-month observation period. The primary outcome was the safety and side-effect profile of felzartamab. Key secondary outcomes were renal-biopsy results at 24 and 52 weeks, donor-specific antibody levels, peripheral NK-cell counts, and donor-derived cell-free DNA levels. RESULTS A total of 22 patients underwent randomization (11 to receive felzartamab and 11 to receive placebo). The median time from transplantation until trial inclusion was 9 years. Mild or moderate infusion reactions occurred in 8 patients in the felzartamab group. Serious adverse events occurred in 1 patient in the felzartamab group and in 4 patients in the placebo group; graft loss occurred in 1 patient in the placebo group. At week 24, resolution of morphologic antibody-mediated rejection was more frequent with felzartamab (in 9 of 11 patients [82%]) than with placebo (in 2 of 10 patients [20%]), for a difference of 62 percentage points (95% confidence interval [CI], 19 to 100) and a risk ratio of 0.23 (95% confidence interval [CI], 0.06 to 0.83). The median microvascular inflammation score was lower in the felzartamab group than in the placebo group (0 vs. 2.5), for a mean difference of -1.95 (95% CI, -2.97 to -0.92). Also lower was a molecular score reflecting the probability of antibody-mediated rejection (0.17 vs. 0.77) and the level of donor-derived cell-free DNA (0.31% vs. 0.82%). At week 52, the recurrence of antibody-mediated rejection was reported in 3 of 9 patients who had a response to felzartamab, with an increase in molecular activity and biomarker levels toward baseline levels. CONCLUSIONS Felzartamab had acceptable safety and side-effect profiles in patients with antibody-mediated rejection. (Funded by MorphoSys and Human Immunology Biosciences; ClinicalTrials.gov number, NCT05021484; and EUDRACT number, 2021-000545-40.).
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Affiliation(s)
- Katharina A Mayer
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Eva Schrezenmeier
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Matthias Diebold
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Philip F Halloran
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Martina Schatzl
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Sabine Schranz
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Susanne Haindl
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Silke Kasbohm
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Alexander Kainz
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Farsad Eskandary
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Konstantin Doberer
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Uptal D Patel
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Jaideep S Dudani
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Heinz Regele
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Nicolas Kozakowski
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Johannes Kläger
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Rainer Boxhammer
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Kerstin Amann
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Elisabeth Puchhammer-Stöckl
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Hannes Vietzen
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Julia Beck
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Ekkehard Schütz
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Aylin Akifova
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Christa Firbas
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Houston N Gilbert
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Bilgin Osmanodja
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Fabian Halleck
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Bernd Jilma
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Klemens Budde
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
| | - Georg A Böhmig
- From the Departments of Medicine III (K.A.M., M.D., M.S., S.H., A.K., F.E., K.D., G.A.B.), Clinical Pathology (H.R., N.K., J.K.), and Clinical Pharmacology (S.S., C.F., B.J.) and the Center of Virology (E.P.-S., H.V.), Medical University of Vienna, Vienna; the Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland (M.D.); the Department of Nephrology, Charité Universitätsmedizin Berlin, Berlin (E.S., S.K., A.A., B.O., F.H., K.B.), MorphoSys, Planegg (R.B.), the Department of Pathology, University of Erlangen-Nürnberg, Erlangen (K.A.), and Chronix Biomedical, Göttingen (E.S., J.B.) - all in Germany; the Alberta Transplant Applied Genomics Centre, Faculty of Medicine and Dentistry, Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada (P.F.H.); and Human Immunology Biosciences, South San Francisco, CA (U.D.P., J.S.D., H.N.G.)
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Zhang P, Liu B, Zhang S, Chang X, Zhang L, Gu D, Zheng X, Chen J, Xiao S, Wu Z, Cai X, Long M, Lu W, Zheng M, Chen R, Gao R, Zheng Y, Wu J, Feng Q, He G, Chen Y, Zheng W, Zuo W, Huang Y, Zhang X. Clinical application of targeted next-generation sequencing in severe pneumonia: a retrospective review. Crit Care 2024; 28:225. [PMID: 38978111 PMCID: PMC11232260 DOI: 10.1186/s13054-024-05009-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/27/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND The precise identification of the underlying causes of infectious diseases, such as severe pneumonia, is essential, and the development of next-generation sequencing (NGS) has enhanced the effectiveness of pathogen detection. However, there is limited information on the systematic assessment of the clinical use of targeted next-generation sequencing (tNGS) in cases of severe pneumonia. METHODS A retrospective analysis was conducted on 130 patients with severe pneumonia treated in the ICU from June 2022 to June 2023. The consistency of the results of tNGS, metagenomics next-generation sequencing (mNGS), and culture with the clinical diagnosis was evaluated. Additionally, the results for pathogens detected by tNGS were compared with those of culture, mNGS, and quantitative reverse transcription PCR (RT-qPCR). To evaluate the efficacy of monitoring severe pneumonia, five patients with complicated infections were selected for tNGS microbiological surveillance. The tNGS and culture drug sensitisation results were then compared. RESULTS The tNGS results for the analysis of the 130 patients showed a concordance rate of over 70% with clinical diagnostic results. The detection of pathogenic microorganisms using tNGS was in agreement with the results of culture, mNGS, and RT-qPCR. Furthermore, the tNGS results for pathogens in the five patients monitored for complicated infections of severe pneumonia were consistent with the culture and imaging test results during treatment. The tNGS drug resistance results were in line with the drug sensitivity results in approximately 65% of the cases. CONCLUSIONS The application of tNGS highlights its promise and significance in assessing the effectiveness of clinical interventions and providing guidance for anti-infection therapies for severe pneumonia.
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Affiliation(s)
- Peng Zhang
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Baoyi Liu
- Clinical Experimental Center, Jiangmen Engineering Technology Research Center of Clinical Biobank and Translational Research, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Shuang Zhang
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Xuefei Chang
- Department of Respiratory and Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Lihe Zhang
- Department of Respiratory and Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Dejian Gu
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Xin Zheng
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Jiaqing Chen
- Clinical Experimental Center, Jiangmen Engineering Technology Research Center of Clinical Biobank and Translational Research, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Saiyin Xiao
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Zhentao Wu
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Xuemin Cai
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Mingfa Long
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Wenjie Lu
- Clinical Experimental Center, Jiangmen Engineering Technology Research Center of Clinical Biobank and Translational Research, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Mingzhu Zheng
- Clinical Experimental Center, Jiangmen Engineering Technology Research Center of Clinical Biobank and Translational Research, Jiangmen Central Hospital, Jiangmen, 529030, China
| | | | - Rui Gao
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Yan Zheng
- Department of Research and Development, Guangdong Research Institute of Genetic Diagnostic and Engineering Technologies for Thalassemia, Hybribio Limited, Guangzhou, 510000, China
| | - Jinhua Wu
- Department of Clinical Laboratory, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Qiujuan Feng
- Department of Clinical Laboratory, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Gang He
- Department of Infectious Diseases, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Yantang Chen
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Weihao Zheng
- Department of Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, 529030, China
| | - Wanli Zuo
- Clinical Experimental Center, Jiangmen Engineering Technology Research Center of Clinical Biobank and Translational Research, Jiangmen Central Hospital, Jiangmen, 529030, China.
- Department of Respiratory and Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, 529030, China.
| | - Yanming Huang
- Clinical Experimental Center, Jiangmen Engineering Technology Research Center of Clinical Biobank and Translational Research, Jiangmen Central Hospital, Jiangmen, 529030, China.
- Department of Respiratory and Critical Care Medicine, Jiangmen Central Hospital, Jiangmen, 529030, China.
| | - Xin Zhang
- Clinical Experimental Center, Jiangmen Engineering Technology Research Center of Clinical Biobank and Translational Research, Jiangmen Central Hospital, Jiangmen, 529030, China.
- Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, 523808, China.
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Sinha R, Zhu Z, Park S, Rebello C, Kinsella B, Friedewald J, Kleiboeker S. Combined Metagenomic Viral Detection and Donor-Derived Cell-Free DNA Quantification in Plasma From Kidney Transplant Recipients. Transplant Proc 2024:S0041-1345(24)00348-8. [PMID: 38972761 DOI: 10.1016/j.transproceed.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/27/2024] [Accepted: 06/07/2024] [Indexed: 07/09/2024]
Abstract
BACKGROUND Kidney transplant recipients require potent immunosuppression and are predisposed to opportunistic infections, many of which have a viral etiology. Currently, viral assays detect and quantify single pathogens using PCR or qPCR. An unbiased sequencing method with comparable accuracy would allow simultaneous monitoring of multiple viral pathogens and nonpathogenic Anelloviridae. The quantification of donor-derived cell-free DNA (dd-cfDNA) is an established method for the detection of allograft rejection, and a single workflow combining dd-cfDNA quantification and viral detection represents an opportunity to improve patient monitoring and management. METHODS Whole genome sequencing of cell-free DNA was performed using 1,980 plasma samples from 256 subjects enrolled in a multi-center study. Non-human sequences underwent reference-assisted assembly and taxonomic annotation of the viral DNA pathogens. RESULTS Of the 1,980 samples tested, 1,453 (73.4%) had ≥1 viral detection(s), either a known viral pathogen or torque teno virus (TTV), with positivity rates generally declining 12-18 months post-transplant. Concordance of metagenomic NGS (mNGS) viral detection with qPCR detection was 97.7% (94.1% sensitivity, 98.2% specificity), and a linear relationship was demonstrated between mNGS viral quantitation and qPCR results. BK virus, cytomegalovirus, and Epstein-Barr virus were detected by sequencing up to 60 days prior to independently established clinical diagnoses. CONCLUSIONS Whole-genome sequencing allows simultaneous quantification of dd-cfDNA as well as sensitive and early detection of viral infection through secondary analysis of the same sequencing results. In combination with dd-cfDNA, mNGS viral detection may provide additional pathogen surveillance results and serve as a useful biomarker for both over- and under-immunosuppression.
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Affiliation(s)
- Rohita Sinha
- Eurofins Viracor Clinical Diagnostics, Lenexa, Kansas
| | - Zixuan Zhu
- Eurofins Viracor Clinical Diagnostics, Lenexa, Kansas
| | - Sookhyeon Park
- Northwestern University, Feinberg School of Medicine, Chicago, Illinois
| | | | - Bradley Kinsella
- Northwestern University, Feinberg School of Medicine, Chicago, Illinois
| | - John Friedewald
- Northwestern University, Feinberg School of Medicine, Chicago, Illinois
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9
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Abstract
This review delves into the rapidly evolving landscape of liquid biopsy technologies based on cell-free DNA (cfDNA) and cell-free RNA (cfRNA) and their increasingly prominent role in precision medicine. With the advent of high-throughput DNA sequencing, the use of cfDNA and cfRNA has revolutionized noninvasive clinical testing. Here, we explore the physical characteristics of cfDNA and cfRNA, present an overview of the essential engineering tools used by the field, and highlight clinical applications, including noninvasive prenatal testing, cancer testing, organ transplantation surveillance, and infectious disease testing. Finally, we discuss emerging technologies and the broadening scope of liquid biopsies to new areas of diagnostic medicine.
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Affiliation(s)
- Conor Loy
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA;
| | - Lauren Ahmann
- Department of Pathology, Stanford University, Stanford, California, USA;
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA;
| | - Wei Gu
- Department of Pathology, Stanford University, Stanford, California, USA;
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10
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Chauvelot L, Barba T, Saison C, Siska E, Kulifaj D, Bakker SJL, Koenig A, Rabeyrin M, Buron F, Picard C, Dijoud F, Manière L, Lina B, Morelon E, Dubois V, Thaunat O. Longitudinal monitoring of Torque Teno virus DNAemia in kidney transplant recipients correlates with long-term complications of inadequate immunosuppression. J Med Virol 2024; 96:e29806. [PMID: 39007420 DOI: 10.1002/jmv.29806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/20/2024] [Accepted: 07/06/2024] [Indexed: 07/16/2024]
Abstract
Optimization of individual immunosuppression, which reduces the risks of both graft loss and patients' death, is considered the best approach to improve long-term outcomes of renal transplantation. Torque Teno Virus (TTV) DNAemia has emerged as a potential biomarker reflecting the depth of therapeutic immunosuppression during the initial year post-transplantation. However, its efficacy in long-term monitoring remains uncertain. In a cohort study involving 34 stable kidney transplant recipients and 124 healthy volunteers, we established lower and upper TTV DNAemia thresholds (3.75-5.1 log10 cp/mL) correlating with T-cell activatability, antibody response against flu vaccine, and risk for subsequent serious infections or cancer over 50 months. Validation in an independent cohort of 92 recipients confirmed that maintaining TTV DNAemia within this range in >50% of follow-up time points was associated with reduced risks of complications due to inadequate immunosuppression, including de novo DSA, biopsy-proven antibody-mediated rejection, graft loss, infections, or cancer. Multivariate analysis highlighted "in-target" TTV DNAemia as the sole independent variable significantly linked to decreased risk for long-term complications due to inadequate immunosuppression (odds ratio [OR]: 0.27 [0.09-0.77]; p = 0.019). Our data suggest that the longitudinal monitoring of TTV DNAemia in kidney transplant recipients could help preventing the long-term complications due to inadequate immunosuppression.
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Affiliation(s)
- Luc Chauvelot
- Department of Transplantation, Nephrology and Clinical Immunology, Hospices Civils de Lyon, Groupement Hospitalier Centre, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Thomas Barba
- Department of Transplantation, Nephrology and Clinical Immunology, Hospices Civils de Lyon, Groupement Hospitalier Centre, Lyon, France
- Lyon-Est Medical Faculty, Claude Bernard University (Lyon 1), Lyon, France
- Department of Internal Medicine, Hospices Civils de Lyon, Groupement Hospitalier Centre, Lyon, France
| | - Carole Saison
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
- French National Blood Service (EFS), HLA Laboratory, Lyon, France
| | - Evangelia Siska
- BioMérieux SA, 138, Rue Louis PASTEUR, Parc Technologique Delta Sud, Verniolle, France
| | - Dorian Kulifaj
- BioMérieux SA, 138, Rue Louis PASTEUR, Parc Technologique Delta Sud, Verniolle, France
| | - Stephan J L Bakker
- Department of Internal Medicine, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Alice Koenig
- Department of Transplantation, Nephrology and Clinical Immunology, Hospices Civils de Lyon, Groupement Hospitalier Centre, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
- Lyon-Est Medical Faculty, Claude Bernard University (Lyon 1), Lyon, France
| | - Maud Rabeyrin
- Department of Pathology, Hospices Civils de Lyon, Groupement Hospitalier Est, Bron, France
| | - Fanny Buron
- Department of Transplantation, Nephrology and Clinical Immunology, Hospices Civils de Lyon, Groupement Hospitalier Centre, Lyon, France
| | - Cécile Picard
- Department of Pathology, Hospices Civils de Lyon, Groupement Hospitalier Est, Bron, France
| | - Frédérique Dijoud
- Department of Pathology, Hospices Civils de Lyon, Groupement Hospitalier Est, Bron, France
| | - Louis Manière
- Department of Transplantation, Nephrology and Clinical Immunology, Hospices Civils de Lyon, Groupement Hospitalier Centre, Lyon, France
| | - Bruno Lina
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Emmanuel Morelon
- Department of Transplantation, Nephrology and Clinical Immunology, Hospices Civils de Lyon, Groupement Hospitalier Centre, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
- Lyon-Est Medical Faculty, Claude Bernard University (Lyon 1), Lyon, France
| | - Valerie Dubois
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
- French National Blood Service (EFS), HLA Laboratory, Lyon, France
| | - Olivier Thaunat
- Department of Transplantation, Nephrology and Clinical Immunology, Hospices Civils de Lyon, Groupement Hospitalier Centre, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
- Lyon-Est Medical Faculty, Claude Bernard University (Lyon 1), Lyon, France
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11
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Maqsood R, Wu LI, Brennan DC, Lim ES. Longitudinal alterations in the urinary virome of kidney transplant recipients are influenced by BK viremia and patient sex. Microbiol Spectr 2024:e0405523. [PMID: 38916313 DOI: 10.1128/spectrum.04055-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 05/30/2024] [Indexed: 06/26/2024] Open
Abstract
Little is known about the urinary virome and how it interacts with the host, particularly in renal transplant diseases. Using metagenomic sequencing, we characterized the urinary virome of 23 kidney transplant recipients longitudinally (11 BKV+ patients and 12 BKV- patients). We applied linear mixed effects models, PERMANOVA, k-means clustering, and MaAsLin2 algorithms to determine virome signatures associated with post-transplant time, BK viremia status, and patient sex. We found that the richness and alpha diversity of urinary virome were significantly different in renal transplant recipients with BKV+ over time in comparison to BKV- (richness P = 0.012, alpha P < 0.0001). Female BKV- patients had significantly higher virome richness than males (P = 0.0063). Virome beta diversity was significantly different between patients by BKV status (P < 0.001). Additionally, we identified underlying interactions between patient sex and BKV status, in terms of virome beta diversity (P = 0.008). BK polyomavirus infections were primarily of subtypes IA, IB1, and IB2. The non-BK dominant samples clustered into six urinary virome community states. BKV- samples had more anelloviruses than BKV+ samples though this difference was not statistically significant. Lastly, we identified specific viruses, associated with BKV+ and time in our samples. Our results indicate that dynamic alterations in the urinary virome over the post-transplant period in kidney transplant recipients can be shaped by BK viremia and patient sex. These findings advance our fundamental understanding of the urinary virome and support a new line of investigation in renal disease and transplantation. IMPORTANCE The urinary microbiome is increasingly implicated in renal health and disease. While most research focuses on bacteria communities of the microbiome, factors that influence the urinary virome are not understood. Here, we investigated the urinary virome of 23 adult kidney transplant recipients longitudinally over 14 weeks post-transplant. We show that alterations in the urinary virome are associated with kidney transplant recipients with BK polyomavirus viremia that can lead to BK nephropathy and allograft rejection. By modeling the temporal dynamics post-transplant, we delineated specific profiles of the urinary virome associated with patient sex and urinary community states. These findings reveal fundamental aspects of the urinary virome that can be leveraged to better manage kidney diseases.
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Affiliation(s)
- Rabia Maqsood
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Lily I Wu
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Daniel C Brennan
- Department of Medicine, Division of Nephrology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Efrem S Lim
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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12
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Caixeta RAV, Batista AM, Caetano MW, Palmieri M, Schwab G, Zerbinati RM, Victor ASP, Gallo CDB, Tozetto-Mendoza TR, Junges R, Ortega KL, Costa ALF, Sarmento DJDS, Pallos D, Lindoso JAL, Giannecchini S, Braz-Silva PH. Investigation of Oral Shedding of Torquetenovirus (TTV) in Moderate-to-Severe COVID-19 Hospitalised Patients. Viruses 2024; 16:831. [PMID: 38932124 PMCID: PMC11209259 DOI: 10.3390/v16060831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 05/19/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Torquetenovirus (TTV) is a small DNA virus constituting the human virome. High levels of TTV-DNA have been shown to be associated with immunosuppression and inflammatory chronic disorders. AIM To assess the possible association between the salivary viral load of TTV-DNA in patients hospitalised due to COVID-19 and disease severity. METHODS Saliva samples collected from 176 patients infected with SARS-CoV-2 were used to investigate the presence of SARS-CoV-2 and TTV-DNA by use of real-time RT-PCR. RESULTS The majority of patients were male with severe COVID-19. Presence of SARS-CoV-2 was observed in the saliva of 64.77% of patients, showing TTV-DNA in 55.68% of them. Patients with impaired clinical conditions (p < 0.001), which evolved to death (p = 0.003), showed a higher prevalence of TTV-DNA. The median viral load in patients with severe condition was 4.99 log10 copies/mL, in which those who were discharged and those evolving to death had values of 3.96 log10 copies/mL and 6.27 log10 copies/mL, respectively. A statistically significant association was found between the distribution of TTV-DNA viral load in saliva samples and severity of COVID-19 (p = 0.004) and disease outcomes (p < 0.001). CONCLUSIONS These results indicate that TTV-DNA in saliva could be a useful biomarker of COVID-19 severity and prognosis.
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Affiliation(s)
- Rafael Antônio Velôso Caixeta
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo 05508-000, Brazil; (R.A.V.C.); (M.W.C.); (M.P.); (C.d.B.G.); (K.L.O.)
| | - Alexandre Mendes Batista
- Laboratory of Virology (LIM-52-HCFMUSP), Institute of Tropical Medicine, University of São Paulo School of Medicine, São Paulo 05403-000, Brazil; (A.M.B.); (G.S.); (R.M.Z.); (A.S.P.V.); (T.R.T.-M.)
| | - Matheus Willian Caetano
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo 05508-000, Brazil; (R.A.V.C.); (M.W.C.); (M.P.); (C.d.B.G.); (K.L.O.)
- Laboratory of Virology (LIM-52-HCFMUSP), Institute of Tropical Medicine, University of São Paulo School of Medicine, São Paulo 05403-000, Brazil; (A.M.B.); (G.S.); (R.M.Z.); (A.S.P.V.); (T.R.T.-M.)
| | - Michelle Palmieri
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo 05508-000, Brazil; (R.A.V.C.); (M.W.C.); (M.P.); (C.d.B.G.); (K.L.O.)
| | - Gabriela Schwab
- Laboratory of Virology (LIM-52-HCFMUSP), Institute of Tropical Medicine, University of São Paulo School of Medicine, São Paulo 05403-000, Brazil; (A.M.B.); (G.S.); (R.M.Z.); (A.S.P.V.); (T.R.T.-M.)
| | - Rodrigo Melim Zerbinati
- Laboratory of Virology (LIM-52-HCFMUSP), Institute of Tropical Medicine, University of São Paulo School of Medicine, São Paulo 05403-000, Brazil; (A.M.B.); (G.S.); (R.M.Z.); (A.S.P.V.); (T.R.T.-M.)
| | - Andressa Silva Pereira Victor
- Laboratory of Virology (LIM-52-HCFMUSP), Institute of Tropical Medicine, University of São Paulo School of Medicine, São Paulo 05403-000, Brazil; (A.M.B.); (G.S.); (R.M.Z.); (A.S.P.V.); (T.R.T.-M.)
| | - Camila de Barros Gallo
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo 05508-000, Brazil; (R.A.V.C.); (M.W.C.); (M.P.); (C.d.B.G.); (K.L.O.)
| | - Tânia Regina Tozetto-Mendoza
- Laboratory of Virology (LIM-52-HCFMUSP), Institute of Tropical Medicine, University of São Paulo School of Medicine, São Paulo 05403-000, Brazil; (A.M.B.); (G.S.); (R.M.Z.); (A.S.P.V.); (T.R.T.-M.)
| | - Roger Junges
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, 0313 Oslo, Norway;
| | - Karem L. Ortega
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo 05508-000, Brazil; (R.A.V.C.); (M.W.C.); (M.P.); (C.d.B.G.); (K.L.O.)
- Oral Medicine, Oral Surgery and Implantology Unit (MedOralRes), Faculty of Medicine and Dentistry, University of Santiago de Compostela, 15705 Santiago de Compostela, Spain
| | | | | | - Débora Pallos
- School of Dentistry, University of Santo Amaro, São Paulo 04743-030, Brazil;
| | - José Angelo Lauletta Lindoso
- Emílio Ribas Institute of Infectious Diseases, São Paulo 01246-900, Brazil;
- Laboratory of Protozoology (LIM-49-HC-FMUSP), Institute of Tropical Medicine, University of São Paulo School of Medicine, São Paulo 01246-903, Brazil
- Department of Infectious Diseases, University of São Paulo School of Medicine, São Paulo 01246-903, Brazil
| | - Simone Giannecchini
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
| | - Paulo Henrique Braz-Silva
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo 05508-000, Brazil; (R.A.V.C.); (M.W.C.); (M.P.); (C.d.B.G.); (K.L.O.)
- Laboratory of Virology (LIM-52-HCFMUSP), Institute of Tropical Medicine, University of São Paulo School of Medicine, São Paulo 05403-000, Brazil; (A.M.B.); (G.S.); (R.M.Z.); (A.S.P.V.); (T.R.T.-M.)
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13
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Bhagchandani T, Haque MMU, Sharma S, Malik MZ, Ray AK, Kaur US, Rai A, Verma A, Sawlani KK, Chaturvedi R, Dandu H, Kumar A, Tandon R. Plasma Virome of HIV-infected Subjects on Suppressive Antiretroviral Therapy Reveals Association of Differentially Abundant Viruses with Distinct T-cell Phenotypes and Inflammation. Curr Genomics 2024; 25:105-119. [PMID: 38751600 PMCID: PMC11092910 DOI: 10.2174/0113892029279786240111052824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/16/2023] [Accepted: 12/29/2023] [Indexed: 05/18/2024] Open
Abstract
Background The plasma virome represents the overall composition of viral sequences present in it. Alteration in plasma virome has been reported in treatment naïve and immunocompromised (CD4 count < 200) people with HIV (PWH). However, the effect of ART on virome composition in PWH on ART with preserved CD4 counts is poorly understood. Objectives We aimed to assess the alterations in plasma virome in PWH on ART in comparison to HIV-negative uninfected controls and to further investigate possible associations of plasma viruses with inflammation and immune dysfunction, namely, immunosenescence and immune exhaustion. Methods Plasma viral DNA from PWH on ART and controls was used for sequencing on the Illumina Nextseq500 platform, followed by the identification of viral sequences using an automated pipeline, VIROMATCH. Multiplex cytokine assay was performed to measure the concentrations of various cytokines in plasma. Immunophenotyping was performed on PBMCs to identify T cell markers of immunosenescence and immune exhaustion. Results In our observational, cross-sectional pilot study, chronically infected PWH on ART had significantly different viral species compositions compared to controls. The plasma virome of PWH showed a significantly high relative abundance of species Human gammaherpesvirus 4, also known as Epstein-Barr virus (EBV). Moreover, EBV emerged as a significant viral taxon differentially enriched in PWH on ART, which further correlated positively with the exhaustion phenotype of T cells and significantly increased TNF-α in PWH on ART. Additionally, a significantly increased proportion of senescent T cells and IL-8 cytokine was detected in PWH on ART. Conclusion Altered plasma virome influenced the inflammatory response and T-cell phenotype in PWH on ART.
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Affiliation(s)
- Tannu Bhagchandani
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Mohammad M. Ul Haque
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Shilpa Sharma
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Md Zubbair Malik
- Host-Pathogen Interaction Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ashwini K. Ray
- Laboratory of Metabolic Disorder and Environmental Biotechnology, Department of Environmental Studies, Faculty of Science, University of Delhi, New Delhi, India
| | - Urvinder S. Kaur
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ankita Rai
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Anjali Verma
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Kamal K. Sawlani
- Department of Medicine, King George’s Medical University, Lucknow, India
| | - Rupesh Chaturvedi
- Host-Pathogen Interaction Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
- Special Centre for System Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Himanshu Dandu
- Department of Medicine, King George’s Medical University, Lucknow, India
| | - Abhishek Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore; India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Ravi Tandon
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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14
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Albert E, Giménez E, Hernani R, Piñana JL, Solano C, Navarro D. Torque Teno Virus DNA Load in Blood as an Immune Status Biomarker in Adult Hematological Patients: The State of the Art and Future Prospects. Viruses 2024; 16:459. [PMID: 38543824 PMCID: PMC10974055 DOI: 10.3390/v16030459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/11/2024] [Accepted: 03/15/2024] [Indexed: 05/23/2024] Open
Abstract
A solid body of scientific evidence supports the assumption that Torque teno virus (TTV) DNA load in the blood compartment may behave as a biomarker of immunosuppression in solid organ transplant recipients; in this clinical setting, high or increasing TTV DNA levels precede the occurrence of infectious complications, whereas the opposite anticipates the development of acute rejection. The potential clinical value of the TTV DNA load in blood to infer the risk of opportunistic viral infection or immune-related (i.e., graft vs. host disease) clinical events in the hematological patient, if any, remains to be determined. In fact, contradictory data have been published on this matter in the allo-SCT setting. Studies addressing this topic, which we review and discuss herein, are highly heterogeneous as regards design, patient characteristics, time points selected for TTV DNA load monitoring, and PCR assays used for TTV DNA quantification. Moreover, clinical outcomes are often poorly defined. Prospective, ideally multicenter, and sufficiently powered studies with well-defined clinical outcomes are warranted to elucidate whether TTV DNA load monitoring in blood may be of any clinical value in the management of hematological patients.
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Affiliation(s)
- Eliseo Albert
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, 46010 Valencia, Spain; (E.A.); (E.G.)
| | - Estela Giménez
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, 46010 Valencia, Spain; (E.A.); (E.G.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, 28029 Madrid, Spain
| | - Rafael Hernani
- Hematology Service, Hospital Clínico Universitario, INCLIVA Health Research Institute, 46010 Valencia, Spain; (R.H.); (J.L.P.); (C.S.)
| | - José Luis Piñana
- Hematology Service, Hospital Clínico Universitario, INCLIVA Health Research Institute, 46010 Valencia, Spain; (R.H.); (J.L.P.); (C.S.)
| | - Carlos Solano
- Hematology Service, Hospital Clínico Universitario, INCLIVA Health Research Institute, 46010 Valencia, Spain; (R.H.); (J.L.P.); (C.S.)
- Department of Medicine, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - David Navarro
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, 46010 Valencia, Spain; (E.A.); (E.G.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, 28029 Madrid, Spain
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain
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15
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Loy CJ, Servellita V, Sotomayor-Gonzalez A, Bliss A, Lenz J, Belcher E, Suslovic W, Nguyen J, Williams ME, Oseguera M, Gardiner MA, Choi JH, Hsiao HM, Wang H, Kim J, Shimizu C, Tremoulet A, Delaney M, DeBiasi RL, Rostad CA, Burns JC, Chiu CY, Vlaminck ID. Plasma Cell-free RNA Signatures of Inflammatory Syndromes in Children. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.06.24303645. [PMID: 38496479 PMCID: PMC10942512 DOI: 10.1101/2024.03.06.24303645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Inflammatory syndromes, including those caused by infection, are a major cause of hospital admissions among children and are often misdiagnosed because of a lack of advanced molecular diagnostic tools. In this study, we explored the utility of circulating cell-free RNA (cfRNA) in plasma as an analyte for the differential diagnosis and characterization of pediatric inflammatory syndromes. We profiled cfRNA in 370 plasma samples from pediatric patients with a range of inflammatory conditions, including Kawasaki disease (KD), Multisystem Inflammatory Syndrome in Children (MIS-C), viral infections and bacterial infections. We developed machine learning models based on these cfRNA profiles, which effectively differentiated KD from MIS-C - two conditions presenting with overlapping symptoms - with high performance (Test Area Under the Curve (AUC) = 0.97). We further extended this methodology into a multiclass machine learning framework that achieved 81% accuracy in distinguishing among KD, MIS-C, viral, and bacterial infections. We further demonstrated that cfRNA profiles can be used to quantify injury to specific tissues and organs, including the liver, heart, endothelium, nervous system, and the upper respiratory tract. Overall, this study identified cfRNA as a versatile analyte for the differential diagnosis and characterization of a wide range of pediatric inflammatory syndromes.
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16
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Yuan L, Zhu Q, Chen Q, Lai LM, Liu P, Liu Y. The microbiological diagnostic performance of metagenomic next-generation sequencing in patients with infectious diseases. Lab Med 2024; 55:132-139. [PMID: 37289931 DOI: 10.1093/labmed/lmad046] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023] Open
Abstract
OBJECTIVE Metagenomic next-generation sequencing (mNGS) can be used to detect pathogens in clinical infectious diseases through the sequencing analysis of microbial and host nucleic acids in clinical samples. This study aimed to assess the diagnostic performance of mNGS in patients with infections. METHODS In this study, 641 patients with infectious diseases were enrolled. These patients simultaneously underwent pathogen detection by both mNGS and microbial culture. Through statistical analysis, we judged the diagnostic performance of mNGS and microbial culture on different pathogens. RESULTS Among 641 patients, 276 cases of bacteria and 95 cases of fungi were detected by mNGS, whereas 108 cases of bacteria and 41 cases of fungi were detected by traditional cultures. Among all mixed infections, combined bacterial and viral infections were the highest (51%, 87/169), followed by combined bacterial with fungal infections (16.57%, 28/169) and mixed bacterial, fungal, and viral infections (13.61%, 23/169). Among all sample types, bronchoalveolar lavage fluid (BALF) samples had the highest positive rate (87.8%, 144/164), followed by sputum (85.4%, 76/89) and blood samples (61.2%, 158/258). For the culture method, sputum samples had the highest positive rate (47.2%, 42/89), followed by BALF (37.2%, 61/164). The positive rate of mNGS was 69.89% (448/641), which was significantly higher than that of traditional cultures (22.31% [143/641]) (P < .05). CONCLUSIONS Our results show that mNGS is an effective tool for the rapid diagnosis of infectious diseases. Compared with traditional detection methods, mNGS also showed obvious advantages in mixed infections and infections with uncommon pathogens.
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Affiliation(s)
- Lei Yuan
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Qing Zhu
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Qiang Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Lan Min Lai
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Peng Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Yang Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
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17
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Sabbaghian M, Gheitasi H, Shekarchi AA, Tavakoli A, Poortahmasebi V. The mysterious anelloviruses: investigating its role in human diseases. BMC Microbiol 2024; 24:40. [PMID: 38281930 PMCID: PMC10823751 DOI: 10.1186/s12866-024-03187-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/08/2024] [Indexed: 01/30/2024] Open
Abstract
Anelloviruses (AVs) that infect the human population are members of the Anelloviridae family. They are widely distributed in human populations worldwide. Torque teno virus (TTV) was the first virus of this family to be identified and is estimated to be found in the serum of 80-90% of the human population. Sometime after the identification of TTV, Torque teno mini virus (TTMV) and Torque teno midi virus (TTMDV) were also identified and classified in this family. Since identifying these viruses, have been detected in various types of biological fluids of the human body, including blood and urine, as well as vital organs such as the liver and kidney. They can be transmitted from person to person through blood transfusions, fecal-oral contact, and possibly sexual intercourse. Recent studies on these newly introduced viruses show that although they are not directly related to human disease, they may be indirectly involved in initiating or exacerbating some human population-related diseases and viral infections. Among these diseases, we can mention various types of cancers, immune system diseases, viral infections, hepatitis, and AIDS. Also, they likely use the microRNAs (miRNAs) they encode to fulfill this cooperative role. Also, in recent years, the role of proliferation and their viral load, especially TTV, has been highlighted to indicate the immune system status of immunocompromised people or people who undergo organ transplants. Here, we review the possible role of these viruses in diseases that target humans and highlight them as important viruses that require further study. This review can provide new insights to researchers.
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Affiliation(s)
- Mohammad Sabbaghian
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamidreza Gheitasi
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Akbar Shekarchi
- Department of Pathology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ahmad Tavakoli
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Vahdat Poortahmasebi
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran.
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18
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Reineke M, Morath C, Speer C, Rudek M, Bundschuh C, Klein JA, Mahler CF, Kälble F, Nusshag C, Beimler J, Zeier M, Bartenschlager R, Schnitzler P, Benning L. Dynamics of torque teno virus load in kidney transplant recipients with indication biopsy and therapeutic modifications of immunosuppression. Front Med (Lausanne) 2024; 11:1337367. [PMID: 38327708 PMCID: PMC10847215 DOI: 10.3389/fmed.2024.1337367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 01/04/2024] [Indexed: 02/09/2024] Open
Abstract
Following kidney transplantation, lifelong immunosuppressive therapy is essential to prevent graft rejection. On the downside, immunosuppression increases the risk of severe infections, a major cause of death among kidney transplant recipients (KTRs). To improve post-transplant outcomes, adequate immunosuppressive therapy is therefore a challenging but vital aspect of clinical practice. Torque teno virus load (TTVL) was shown to reflect immune competence in KTRs, with low TTVL linked to an elevated risk for rejections and high TTVL associated with infections in the first year post-transplantation. Yet, little is known about the dynamics of TTVL after the first year following transplantation and how TTVL changes with respect to short-term modifications in immunosuppressive therapy. Therefore, we quantified TTVL in 106 KTRs with 108 clinically indicated biopsies, including 65 biopsies performed >12 months post-transplantation, and correlated TTVL to histopathology. In addition, TTVL was quantified at 7, 30, and 90 days post-biopsy to evaluate how TTVL was affected by changes in immunosuppression resulting from interventions based on histopathological reporting. TTVL was highest in patients biopsied between 1 and 12 months post-transplantation (N = 23, median 2.98 × 107 c/mL) compared with those biopsied within 30 days (N = 20, median 7.35 × 103 c/mL) and > 1 year post-transplantation (N = 65, median 1.41 × 104 c/mL; p < 0.001 for both). Patients with BK virus-associated nephropathy (BKVAN) had significantly higher TTVL than patients with rejection (p < 0.01) or other pathologies (p < 0.001). When converted from mycophenolic acid to a mTOR inhibitor following the diagnosis of BKVAN, TTVL decreased significantly between biopsy and 30 and 90 days post-biopsy (p < 0.01 for both). In KTR with high-dose corticosteroid pulse therapy for rejection, TTVL increased significantly between biopsy and 30 and 90 days post-biopsy (p < 0.05 and p < 0.01, respectively). Of note, no significant changes were seen in TTVL within 7 days of changes in immunosuppressive therapy. Additionally, TTVL varied considerably with time since transplantation and among individuals, with a significant influence of age and BMI on TTVL (p < 0.05 for all). In conclusion, our findings indicate that TTVL reflects changes in immunosuppressive therapy, even in the later stages of post-transplantation. To guide immunosuppressive therapy based on TTVL, one should consider inter- and intraindividual variations, as well as potential confounding factors.
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Affiliation(s)
- Marvin Reineke
- Department of Nephrology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christian Morath
- Department of Nephrology, Heidelberg University Hospital, Heidelberg, Germany
- German Center for Infection Research, DZIF, Heidelberg Partner Site, Heidelberg, Germany
| | - Claudius Speer
- Department of Nephrology, Heidelberg University Hospital, Heidelberg, Germany
- Department of Molecular Medicine Partnership Unit Heidelberg, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Markus Rudek
- Department of Nephrology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christian Bundschuh
- Medical Faculty Heidelberg, Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
| | - Julian A.F. Klein
- Medical Faculty Heidelberg, Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
| | - Christoph F. Mahler
- Department of Nephrology, Heidelberg University Hospital, Heidelberg, Germany
| | - Florian Kälble
- Department of Nephrology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christian Nusshag
- Department of Nephrology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jörg Beimler
- Department of Nephrology, Heidelberg University Hospital, Heidelberg, Germany
| | - Martin Zeier
- Department of Nephrology, Heidelberg University Hospital, Heidelberg, Germany
| | - Ralf Bartenschlager
- German Center for Infection Research, DZIF, Heidelberg Partner Site, Heidelberg, Germany
- Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg University, Heidelberg, Germany
- Division Virus-Associated Carcinogenesis, German Cancer Research Center, Heidelberg, Germany
| | - Paul Schnitzler
- German Center for Infection Research, DZIF, Heidelberg Partner Site, Heidelberg, Germany
- Medical Faculty Heidelberg, Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
| | - Louise Benning
- Department of Nephrology, Heidelberg University Hospital, Heidelberg, Germany
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Jonker J, Doorenbos CSE, Kremer D, Gore EJ, Niesters HGM, van Leer-Buter C, Bourgeois P, Connelly MA, Dullaart RPF, Berger SP, Sanders JSF, Bakker SJL. High-Density Lipoprotein Particles and Torque Teno Virus in Stable Outpatient Kidney Transplant Recipients. Viruses 2024; 16:143. [PMID: 38257843 PMCID: PMC10818741 DOI: 10.3390/v16010143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/11/2024] [Accepted: 01/17/2024] [Indexed: 01/24/2024] Open
Abstract
Torque teno virus (TTV) is emerging as a potential marker for monitoring immune status. In transplant recipients who are immunosuppressed, higher TTV DNA loads are observed than in healthy individuals. TTV load measurement may aid in optimizing immunosuppressive medication dosing in solid organ transplant recipients. Additionally, there is a growing interest in the role of HDL particles in immune function; therefore, assessment of both HDL concentrations and TTV load may be of interest in transplant recipients. The objective of this study was to analyze TTV loads and HDL parameters in serum samples collected at least one year post-transplantation from 656 stable outpatient kidney transplant recipients (KTRs), enrolled in the TransplantLines Food and Nutrition Cohort (Groningen, the Netherlands). Plasma HDL particles and subfractions were measured using nuclear magnetic resonance spectroscopy. Serum TTV load was measured using a quantitative real-time polymerase chain reaction. Associations between HDL parameters and TTV load were examined using univariable and multivariable linear regression. The median age was 54.6 [IQR: 44.6 to 63.1] years, 43.3% were female, the mean eGFR was 52.5 (±20.6) mL/min/1.73 m2 and the median allograft vintage was 5.4 [IQR: 2.0 to 12.0] years. A total of 539 participants (82.2%) had a detectable TTV load with a mean TTV load of 3.04 (±1.53) log10 copies/mL, the mean total HDL particle concentration was 19.7 (±3.4) μmol/L, and the mean HDL size was 9.1 (±0.5) nm. The univariable linear regression revealed a negative association between total HDL particle concentration and TTV load (st.β = -0.17, 95% CI st.β: -0.26 to -0.09, p < 0.001). An effect modification of smoking behavior influencing the association between HDL particle concentration and TTV load was observed (Pinteraction = 0.024). After adjustment for age, sex, alcohol intake, hemoglobin, eGFR, donor age, allograft vintage and the use of calcineurin inhibitors, the negative association between HDL particle concentration and TTV load remained statistically significant in the non-smoking population (st.β = -0.14, 95% CI st.β: -0.23 to -0.04, p = 0.006). Furthermore, an association between small HDL particle concentration and TTV load was found (st.β = -0.12, 95% CI st.β: -0.22 to -0.02, p = 0.017). Higher HDL particle concentrations were associated with a lower TTV load in kidney transplant recipients, potentially indicative of a higher immune function. Interventional studies are needed to provide causal evidence on the effects of HDL on the immune system.
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Affiliation(s)
- Jip Jonker
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Caecilia S. E. Doorenbos
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Daan Kremer
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Edmund J. Gore
- Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Hubert G. M. Niesters
- Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Coretta van Leer-Buter
- Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | | | | | - Robin P. F. Dullaart
- Department of Internal Medicine, Division of Endocrinology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Stefan P. Berger
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Jan-Stephan F. Sanders
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Stephan J. L. Bakker
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
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20
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Pourkarim MR. Navigating Evolving Challenges in Blood Safety. Viruses 2024; 16:123. [PMID: 38257823 PMCID: PMC10821029 DOI: 10.3390/v16010123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/11/2024] [Accepted: 01/14/2024] [Indexed: 01/24/2024] Open
Abstract
Blood safety remains a paramount public health concern, and health authorities maintain a high level of vigilance to prevent transfusion-transmitted infections (TTIs) [...].
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Affiliation(s)
- Mahmoud Reza Pourkarim
- Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, Herestraat 49, 3000 Leuven, Belgium;
- Health Policy Research Centre, Institute of Health, Shiraz University of Medical Sciences, Shiraz 71348-14336, Iran
- Blood Transfusion Research Centre, High Institute for Research and Education in Transfusion, Tehran 14665-1157, Iran
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21
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van der Bie S, Haaksma ME, Vermin B, van Assema H, van Gorp ECM, Langerak T, Endeman H, Snijders D, van den Akker JPC, van Houten MA, van Lelyveld SFL, Goeijenbier M. A Systematic Review of the Pulmonary Microbiome in Patients with Acute Exacerbation COPD Requiring ICU Admission. J Clin Med 2024; 13:472. [PMID: 38256606 PMCID: PMC10816170 DOI: 10.3390/jcm13020472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/03/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024] Open
Abstract
Background: Chronic obstructive pulmonary disease (COPD) is a major health concern. Acute exacerbations (AECOPD) may require intensive care unit (ICU) admission and mechanical ventilation. Acute infections and chronic colonization of the respiratory system are known to precipitate AECOPD. Detailed knowledge of the respiratory microbiome could lead to effective treatment and prevention of exacerbations. Objective: The aim of this review is to summarize the available evidence on the respiratory microbiome of patients with a severe AECOPD requiring mechanical ventilation and intensive care admission. Methods: A systematic literature search was conducted to identify the published papers until January 2023. The collected data were then subjected to qualitative analysis. After the first analysis, a secondary focused review of the most recent publications studying the relationship between microbiome and mortality in AECOPD was performed. Results: Out of 120 screened articles six articles were included in this review. Potentially pathogenic microorganisms (PPMs) were identified in 30% to 72% of the patients with community-acquired bacteria, gram-negative enteric bacilli, Stenotrophomonas and Pseudomonas being the most frequently isolated. During hospitalization, 21% of patients experienced colonization by PPMs. Adequate antimicrobial therapy resulted in the eradication of 77% of the identified PPMs. However, 24% of the bacteria displayed multi-drug resistance leading to prolonged or failure of eradication. Conclusion: PPMs are prevalent in a significant proportion of patients experiencing an AECOPD. The most identified PPMs include community-acquired pathogens and gram-negative enteric bacilli. Notably, no differences in mortality or duration of ventilation were observed between patients with and without isolated PPMs. However, the included studies did not investigate the virome of the patients, which may influence the microbiome and the outcome of infection. Therefore, further research is essential to comprehensively investigate the complete microbial and viral composition of the lower respiratory system in COPD patients admitted to the ICU.
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Affiliation(s)
- Sjoerd van der Bie
- Department of Intensive Care Medicine, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands; (S.v.d.B.); (M.E.H.); (B.V.); (H.v.A.)
| | - Mark E. Haaksma
- Department of Intensive Care Medicine, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands; (S.v.d.B.); (M.E.H.); (B.V.); (H.v.A.)
| | - Ben Vermin
- Department of Intensive Care Medicine, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands; (S.v.d.B.); (M.E.H.); (B.V.); (H.v.A.)
| | - Hidde van Assema
- Department of Intensive Care Medicine, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands; (S.v.d.B.); (M.E.H.); (B.V.); (H.v.A.)
| | - Eric C. M. van Gorp
- Department of Viroscience, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.C.M.v.G.); (T.L.)
| | - Thomas Langerak
- Department of Viroscience, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.C.M.v.G.); (T.L.)
| | - Henrik Endeman
- Department of Intensive Care Medicine, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (H.E.); (J.P.C.v.d.A.)
| | - Dominic Snijders
- Department of Pulmonology, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands;
| | | | - Marlies A. van Houten
- Department of Pediatric Medicine, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands;
| | | | - Marco Goeijenbier
- Department of Intensive Care Medicine, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands; (S.v.d.B.); (M.E.H.); (B.V.); (H.v.A.)
- Department of Viroscience, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.C.M.v.G.); (T.L.)
- Department of Intensive Care Medicine, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (H.E.); (J.P.C.v.d.A.)
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22
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Timmerman AL, Commandeur L, Deijs M, Burggraaff MGJM, Lavell AHA, van der Straten K, Tejjani K, van Rijswijk J, van Gils MJ, Sikkens JJ, Bomers MK, van der Hoek L. The Impact of First-Time SARS-CoV-2 Infection on Human Anelloviruses. Viruses 2024; 16:99. [PMID: 38257799 PMCID: PMC10818381 DOI: 10.3390/v16010099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Members of the Anelloviridae family dominate the blood virome, emerging early in life. The anellome, representing the variety of anelloviruses within an individual, stabilizes by adulthood. Despite their supposedly commensal nature, elevated anellovirus concentrations under immunosuppressive treatment indicate an equilibrium controlled by immunity. Here, we investigated whether anelloviruses are sensitive to the immune activation that accompanies a secondary infection. As a model, we investigated 19 health care workers (HCWs) with initial SARS-CoV-2 infection, with blood sampling performed pre and post infection every 4 weeks in a 3-month-follow-up during the early 2020 COVID-19 pandemic. A concurrently followed control group (n = 27) remained SARS-CoV-2-negative. Serum anellovirus loads were measured using qPCR. A significant decrease in anellovirus load was found in the first weeks after SARS-CoV-2 infection, whereas anellovirus concentrations remained stable in the uninfected control group. A restored anellovirus load was seen approximately 10 weeks after SARS-CoV-2 infection. For five subjects, an in-time anellome analysis via Illumina sequencing could be performed. In three of the five HCWs, the anellome visibly changed during SARS-CoV-2 infection and returned to baseline in two of these cases. In conclusion, anellovirus loads in blood can temporarily decrease upon an acute secondary infection.
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Affiliation(s)
- Anne L. Timmerman
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
| | - Lisanne Commandeur
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
| | - Maarten G. J. M. Burggraaff
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
| | - A. H. Ayesha Lavell
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
- Department of Internal Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Karlijn van der Straten
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
- Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Khadija Tejjani
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
| | - Jacqueline van Rijswijk
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
| | - Marit J. van Gils
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
| | - Jonne J. Sikkens
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
- Department of Internal Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Marije K. Bomers
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
- Department of Internal Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
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Doorenbos CSE, Jonker J, Hao J, Gore EJ, Kremer D, Knobbe TJ, de Joode AAE, Sanders JSF, Thaunat O, Niesters HGM, Van Leer-Buter CC, Bakker SJL. Smoking, Alcohol Intake and Torque Teno Virus in Stable Kidney Transplant Recipients. Viruses 2023; 15:2387. [PMID: 38140628 PMCID: PMC10748022 DOI: 10.3390/v15122387] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Torque Teno Virus (TTV) is a non-pathogenic virus that is highly prevalent among kidney transplant recipients (KTRs). Its circulating load is associated with an immunological status in KTR and is considered a promising tool for guiding immunosuppression. To allow for optimal guidance, it is important to identify other determinants of TTV load. We aimed to investigate the potential association of smoking and alcohol intake with TTV load. For this cross-sectional study, serum TTV load was measured using PCR in stable kidney transplant recipients at ≥1 year after transplantation, and smoking status and alcohol intake were assessed through questionnaires and measurements of urinary cotinine and ethyl glucuronide. A total of 666 KTRs were included (57% male). A total of 549 KTR (82%) had a detectable TTV load (3.1 ± 1.5 log10 copies/mL). In KTR with a detectable TTV load, cyclosporin and tacrolimus use were positively associated with TTV load (St. β = 0.46, p < 0.001 and St. β = 0.66, p < 0.001, respectively), independently of adjustment for potential confounders. Current smoking and alcohol intake of >20 g/day were negatively associated with TTV load (St. β = -0.40, p = 0.004 and St. β = -0.33, p = 0.009, respectively), independently of each other and of adjustment for age, sex, kidney function, time since transplantation and calcineurin inhibitor use. This strong association of smoking and alcohol intake with TTV suggests a need to account for the smoking status and alcohol intake when applying TTV guided immunosuppression in KTR.
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Affiliation(s)
- Caecilia S. E. Doorenbos
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (J.J.)
| | - Jip Jonker
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (J.J.)
| | - Jiasi Hao
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Edmund J. Gore
- Department of Medical Microbiology, Division of Clinical Virology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Daan Kremer
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (J.J.)
| | - Tim J. Knobbe
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (J.J.)
| | - Anoek A. E. de Joode
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (J.J.)
| | - Jan Stephan F. Sanders
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (J.J.)
| | - Olivier Thaunat
- Department of Transplantation Nephrology and Clinical Immunology Hospices Civils de Lyon, Claude Bernard Lyon I University, INSERM Unit 1111, 69003 Lyon, France
| | - Hubert G. M. Niesters
- Department of Medical Microbiology, Division of Clinical Virology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Coretta C. Van Leer-Buter
- Department of Medical Microbiology, Division of Clinical Virology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Stephan J. L. Bakker
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (J.J.)
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Spiertz A, Tsakmaklis A, Farowski F, Knops E, Heger E, Wirtz M, Kaiser R, Holtick U, Vehreschild MJGT, Di Cristanziano V. Torque teno virus-DNA load as individual cytomegalovirus risk assessment parameter upon allogeneic hematopoietic stem cell transplantation. Eur J Haematol 2023; 111:963-969. [PMID: 37772680 DOI: 10.1111/ejh.14111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 09/30/2023]
Abstract
BACKGROUND Immune recovery following allogeneic hematopoietic stem cell transplantation (allo-HSCT) decisively influences the occurrence of opportunistic infections, one of the leading causes of death among this group of patients. Yet, today, there are no laboratory parameters mirroring immune function sufficiently. Torque teno virus (TTV) has already proven itself as a functional immune marker in other settings. AIMS In this analysis, we investigated whether monitoring of TTV-DNA load in whole blood is able to provide additional information on the capacity of the immune system to control cytomegalovirus (CMV) replication in allo-HSCT recipients. METHODS Whole blood samples from 59 patients were collected upon allo-HSCT (between Day -7 and +10), on Day +14, +21, +28, +56, +90, and +365 post-transplant. TTV-DNA loads and other relevant clinical information were correlated with the risk of CMV infections or reactivations, defined by evidence of viral replication in blood. RESULTS CMV serostatus of the recipient and a TTV load below 1000 copies/mL upon allo-HSCT were significantly associated with an increased incidence of CMV infection or reactivation. CONCLUSIONS Quantification of TTV load in the early phase of allo-HSCT procedure could provide additional information in order to identify patients at risk for CMV infection or reactivation.
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Affiliation(s)
- Arlene Spiertz
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Anastasia Tsakmaklis
- Department of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Fedja Farowski
- Department of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, University of Cologne, Cologne, Germany
- Department of Internal Medicine, Infectious Diseases, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Elena Knops
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Eva Heger
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Maike Wirtz
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Rolf Kaiser
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Udo Holtick
- Department of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Maria J G T Vehreschild
- Department of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, University of Cologne, Cologne, Germany
- Department of Internal Medicine, Infectious Diseases, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Veronica Di Cristanziano
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
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Thijssen M, Devos T, Meyfroidt G, Van Ranst M, Pourkarim MR. Exploring the relationship between anellovirus load and clinical variables in hospitalized COVID-19 patients: Implications for immune activation and inflammation. IJID REGIONS 2023; 9:49-54. [PMID: 37868342 PMCID: PMC10587511 DOI: 10.1016/j.ijregi.2023.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/24/2023]
Abstract
Objectives Anelloviruses have been linked with host-immunocompetence and inflammation. Here, we studied the anellovirus load in hospitalized COVID-19 patients. Methods We collected samples of patients recruited in the DAWN-Plasma trial that received convalescent plasma (CP) therapy (four plasma units) combined with standard of care (SOC) or SOC of alone. Plasma samples were collected on day 0 and 6 of hospitalization and we quantified anellovirus load. With multivariate models, clinical variables were associated with changes in anellovirus load. Results Samples were collected on day 0 and 6 of 150 patients (103 CP + SOC and 47 SOC). Anellovirus load was higher on day 0 compared to day 6 and we found a significant drop in SOC patients. Patients receiving immunosuppressive drug had a lower anellovirus load (coefficient: 1.021, 95% confidence interval [CI] 0.270-1.772, P = 0.008), while patients admitted to the emergency room displayed a higher abundance on day 0 (1.308, 95% CI 0.443-2.173, P = 0.003). Unspecific markers of inflammation and organ damage, D-dimer (0.001, 95% CI <0.001-0.001, P = 0.001) and lactate dehydrogenase (0.002, 95% CI 0.001-0.004, P = 0.044), were positively associated with anellovirus load. Finally, anellovirus load on day 0 (-39.9, 95% CI -75.72 to -4.27, P = 0.029) was negatively associated with SARS-CoV-2 antibody response on day. Conclusion The results showed associations between clinical variables and anellovirus load in COVID-19 patients. Many variables share properties related to host immunocompetence or inflammation. Therefore, we expect that anellovirus abundance displays the net state of immune activation.
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Affiliation(s)
- Marijn Thijssen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium
| | - Timothy Devos
- University Hospitals Leuven, Department of Haematology, Department of Microbiology and Immunology, Laboratory of Molecular Immunology (Rega Institute), KU Leuven, Leuven, Belgium
| | - Geert Meyfroidt
- University Hospitals Leuven, Department of Intensive Care Medicine, Department of Cellular and Molecular Medicine, Laboratory of Intensive Care Medicine, KU Leuven, Leuven, Belgium
| | - Marc Van Ranst
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium
| | - Mahmoud Reza Pourkarim
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium
- Shiraz University of Medical Sciences, Health Policy Research Centre, Institute of Health, Shiraz, Iran
- Blood Transfusion Research Centre, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
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26
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Benning L, Reineke M, Bundschuh C, Klein JAF, Kühn T, Zeier M, Bartenschlager R, Schnitzler P, Morath C, Speer C. Quantification of Torque Teno Virus Load to Monitor Short-term Changes in Immunosuppressive Therapy in Kidney Transplant Recipients. Transplantation 2023; 107:e363-e369. [PMID: 37798825 DOI: 10.1097/tp.0000000000004816] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
BACKGROUND Quantification of torque teno virus (TTV) has been proposed as a surrogate parameter to monitor immunocompetence in kidney transplant recipients (KTRs) early after transplantation. However, its use in monitoring short-term changes of immunosuppression in KTRs late after transplantation requires further investigation. METHODS In this post hoc analysis, we quantified TTV load in sera of 76 KTRs, with 43 pausing mycophenolic acid (MPA) 1 wk before to 4 wk after COVID-19 vaccination to increase vaccine response. TTV load was quantified before, 4 wk, and 3 mo postvaccination. Results were compared to 33 KTRs with continued standard immunosuppressive therapy and with 18 hemodialysis as well as 18 healthy control subjects. RESULTS TTV load before vaccination was with a median (interquartile range) of 1.39 × 10 4 copies/milliliter (c/mL) (9.17 × 10 1 -2.66 × 10 5 c/mL) highest in KTRs compared to 1.73 × 10 3 c/mL (1.07 × 10 3 -1.31 × 10 4 c/mL) in hemodialysis patients and 1.53 × 10 2 c/mL (6.38-1.29 × 10 3 c/mL) in healthy controls. In KTRs with MPA withdrawal, TTV load decreased significantly from a median (interquartile range) of 1.11 × 10 4 c/mL (4.75 × 10 2 -1.92 × 10 5 c/mL) to 5.24 × 10 3 c/mL (6.92 × 10 2 -6.91 × 10 4 c/mL) 4-5 wk after initiation of MPA withdrawal ( P = 0.003). In patients with MPA withdrawal, TTV load was significantly inversely correlated with COVID-19 or SARS-CoV-2-specific antibodies 4 wk and 3 mo postvaccination ( P = 0.009 and P = 0.004). CONCLUSIONS TTV load reflects changes in immunosuppressive therapy even late after transplantation, supporting its use to monitor immunocompetence in KTRs.
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Affiliation(s)
- Louise Benning
- Department of Nephrology, Heidelberg University, Heidelberg, Germany
| | - Marvin Reineke
- Department of Nephrology, Heidelberg University, Heidelberg, Germany
| | - Christian Bundschuh
- Department of Infectious Diseases, Virology, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Julian A F Klein
- Department of Infectious Diseases, Virology, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Tessa Kühn
- Department of Nephrology, Heidelberg University, Heidelberg, Germany
| | - Martin Zeier
- Department of Nephrology, Heidelberg University, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Nephrology, Heidelberg University, Heidelberg, Germany
- Department of Infectious Diseases, Virology, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
- Division Virus-Associated Carcinogenesis, German Cancer Research Center, Heidelberg, Germany
- German Center for Infection Research, DZIF, Heidelberg Partner Site, Heidelberg, Germany
- Department of Molecular Medicine Partnership Unit Heidelberg, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Paul Schnitzler
- Department of Infectious Diseases, Virology, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
- German Center for Infection Research, DZIF, Heidelberg Partner Site, Heidelberg, Germany
| | - Christian Morath
- Department of Nephrology, Heidelberg University, Heidelberg, Germany
- German Center for Infection Research, DZIF, Heidelberg Partner Site, Heidelberg, Germany
| | - Claudius Speer
- Department of Nephrology, Heidelberg University, Heidelberg, Germany
- Department of Molecular Medicine Partnership Unit Heidelberg, European Molecular Biology Laboratory, Heidelberg, Germany
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27
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Starrett GJ, Foster H, Sigel K, Liu Y, Engels EA. Brief Report: The Virome of Bladder Tumors Arising in People Living With HIV. J Acquir Immune Defic Syndr 2023; 94:337-340. [PMID: 37884054 PMCID: PMC10662940 DOI: 10.1097/qai.0000000000003283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 08/01/2023] [Indexed: 10/28/2023]
Abstract
BACKGROUND People living with HIV (PLWH) have elevated risk for developing virus-related cancers. Bladder cancer risk is not increased in PLWH but is elevated among immunosuppressed solid organ transplant recipients (SOTRs). BK polyomavirus and, to a lesser extent, other viruses have been detected in bladder cancers from SOTRs. OBJECTIVE To characterize the virome of bladder tumors in PLWH. DESIGN Retrospective case series. METHODS We sequenced DNA and RNA from archived formalin-fixed bladder tumors from PLWH. Nonhuman reads were assembled and matched to a database of known viruses. RESULTS Fifteen bladder tumors from PLWH (13 carcinomas, 2 benign tumors) were evaluated. Fourteen tumors were in men, and the median age at diagnosis was 59 years (median CD4 count 460 cells/mm3). All but 1 tumor yielded both sufficient DNA and RNA. One bladder cancer, arising in a 52-year-old man with a CD4 count of 271 cells/mm3, manifested diverse Alphatorquevirus DNA and RNA sequences. A second cancer arising in a 58-year-old male former smoker (CD4 count of 227 cells/mm3) also showed Alphatorquevirus and Gammatorquevirus DNA sequences. Neither tumor exhibited viral integration. CONCLUSIONS Alphatorqueviruses and Gammatorqueviruses are anelloviruses, which have also been detected in bladder cancers from SOTRs, but anelloviruses are common infections, and detection may simply reflect increased abundance in the setting of immunosuppression. The lack of detection of BK polyomavirus among bladder tumors from PLWH parallels the lower level of bladder cancer risk seen in PLWH compared with SOTRs, indirectly supporting a role for BK polyomavirus in causing the excess risk in SOTRs.
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Affiliation(s)
- Gabriel J. Starrett
- Center for Cancer Research and Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Haidn Foster
- Center for Cancer Research and Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Keith Sigel
- Departments of Medicine and Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yuxin Liu
- Departments of Medicine and Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric A. Engels
- Center for Cancer Research and Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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28
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Mageiros L, Megremis S, Papadopoulos NG. The virome in allergy and asthma: A nascent, ineffable player. J Allergy Clin Immunol 2023; 152:1347-1351. [PMID: 37778473 DOI: 10.1016/j.jaci.2023.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/28/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023]
Abstract
Allergic diseases can be affected by virus-host interactions and are increasingly linked with the tissue-specific microbiome. High-throughput metagenomic sequencing has offered the opportunity to study the presence of viruses as an ecologic system, namely, the virome. Even though virome studies are technically challenging conceptually and analytically, they are already producing novel data expanding our understanding of the pathophysiologic mechanisms related to chronic inflammation and allergy. The importance of interspecies and intraspecies interactions is becoming apparent, as they can significantly, directly or indirectly, affect the host's response and antigenic state. Here, we emphasize the challenges and potential insights related to study of the virome in the context of allergy and asthma. We review the limited number of studies that have investigated the virome in these conditions, underlining the need for prospective, repeated sampling designs to unravel the virome's impact on disease development and its interplay with microbiota and immunity. The potential therapeutic use of bacteriophages, which are highly complex components of the virome, is discussed. There is clearly a need for further in-depth investigation of the virome as a system in allergic diseases.
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Affiliation(s)
- Leonardos Mageiros
- Allergy Department, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Nikolaos G Papadopoulos
- Allergy Department, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece; University of Manchester, Manchester, United Kingdom.
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29
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Berg R, Clemmensen TS, Petersen MS, Mogensen LJH, Christiansen M, Rolid K, Nytrøen K, Møller BK, Gullestad L, Eiskjær H, Koefoed-Nielsen P. Kinetics of Torque Teno virus in heart transplant patients. Hum Immunol 2023; 84:110720. [PMID: 37867096 DOI: 10.1016/j.humimm.2023.110720] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/13/2023] [Accepted: 10/13/2023] [Indexed: 10/24/2023]
Abstract
End-stage heart failure often requires heart transplantation as a life-prolonging treatment. Immunosuppressive therapy is necessary to avoid rejection, but is associated with serious adverse effects. New approaches are needed to monitor immune function in heart transplant patients. We here report the kinetics of Torque Teno Virus (TTV) after transplantation in a large cohort of heart transplant patients and examine its possible role in predicting rejection. We included 106 patients from Aarhus University Hospital and Oslo University Hospital. Patients were followed for 3 years with clinical assessments, biopsies, TTV measurements, and flowcytometric phenotyping. We observed TTV levels reaching a maximum 3 months after transplantation for all 106 patients, after which levels gradually declined. 38 patients (38 %) had biopsy-proven rejection within the first year. We did not find evidence of an association between TTV and serum trough levels, events of rejection, nor flow cytometric immunophenotype. We report data on a large cohort of heart transplant patients and contribute to the understanding of how TTV behaves in transplant patients. Despite not finding an association with rejection, our results provide important insights into the kinetics of TTV levels after transplantation, which may be useful in future studies of immune function in heart transplant patients.
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Affiliation(s)
- Randi Berg
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark.
| | - Tor S Clemmensen
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark
| | - Mikkel S Petersen
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Lone J H Mogensen
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark
| | - Mette Christiansen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Katrine Rolid
- Department of Cardiology, Oslo University Hospital, Oslo, Norway
| | - Kari Nytrøen
- Department of Cardiology, Oslo University Hospital, Oslo, Norway
| | - Bjarne K Møller
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Gullestad
- Department of Cardiology, Oslo University Hospital, Oslo, Norway; KG Jebsen Center for Cardiac Research, University of Oslo, Oslo, Norway
| | - Hans Eiskjær
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark
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30
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Bhagchandani T, Nikita, Verma A, Tandon R. Exploring the Human Virome: Composition, Dynamics, and Implications for Health and Disease. Curr Microbiol 2023; 81:16. [PMID: 38006423 DOI: 10.1007/s00284-023-03537-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/24/2023] [Indexed: 11/27/2023]
Abstract
Humans are colonized by large number of microorganisms-bacteria, fungi, and viruses. The overall genome of entire viruses that either lives on or inside the human body makes up the human virome and is indeed an essential fraction of the human metagenome. Humans are constantly exposed to viruses as they are ubiquitously present on earth. The human virobiota encompasses eukaryotic viruses, bacteriophages, retroviruses, and even giant viruses. With the advent of Next-generation sequencing (NGS) and ongoing development of numerous bioinformatic softwares, identification and taxonomic characterization of viruses have become easier. The viruses are abundantly present in humans; these can be pathogenic or commensal. The viral communities occupy various niches in the human body. The viruses start colonizing the infant gut soon after birth in a stepwise fashion and the viral composition diversify according to their feeding habits. Various factors such as diet, age, medications, etc. influence and shape the human virome. The viruses interact with the host immune system and these interactions have beneficial or detrimental effects on their host. The virome composition and abundance change during the course of disease and these alterations impact the immune system. Hence, the virome population in healthy and disease conditions influences the human host in numerous ways. This review presents an overview of assembly and composition of the human virome in healthy asymptomatic individuals, changes in the virome profiles, and host-virome interactions in various disease states.
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Affiliation(s)
- Tannu Bhagchandani
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Nikita
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Anjali Verma
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ravi Tandon
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
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31
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Wang H, Xu S, Li S, Su B, Sherrill-Mix S, Liang G. Virome in immunodeficiency: what we know currently. Chin Med J (Engl) 2023; 136:2647-2657. [PMID: 37914672 PMCID: PMC10684123 DOI: 10.1097/cm9.0000000000002899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Indexed: 11/03/2023] Open
Abstract
ABSTRACT Over the past few years, the human virome and its complex interactions with microbial communities and the immune system have gained recognition as a crucial factor in human health. Individuals with compromised immune function encounter distinctive challenges due to their heightened vulnerability to a diverse range of infectious diseases. This review aims to comprehensively explore and analyze the growing evidence regarding the role of the virome in immunocompromised disease status. By surveying the latest literature, we present a detailed overview of virome alterations observed in various immunodeficiency conditions. We then delve into the influence and mechanisms of these virome changes on the pathogenesis of specific diseases in immunocompromised individuals. Furthermore, this review explores the clinical relevance of virome studies in the context of immunodeficiency, highlighting the potential diagnostic and therapeutic gains from a better understanding of virome contributions to disease manifestations.
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Affiliation(s)
- Hu Wang
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Siqi Xu
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Shuang Li
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Bin Su
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Scott Sherrill-Mix
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Guanxiang Liang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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32
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Yadav D, Patil-Takbhate B, Khandagale A, Bhawalkar J, Tripathy S, Khopkar-Kale P. Next-Generation sequencing transforming clinical practice and precision medicine. Clin Chim Acta 2023; 551:117568. [PMID: 37839516 DOI: 10.1016/j.cca.2023.117568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/17/2023]
Abstract
Next-generation sequencing (NGS) has revolutionized the field of genomics and is rapidly transforming clinical diagnosis and precision medicine. This advanced sequencing technology enables the rapid and cost-effective analysis of large-scale genomic data, allowing comprehensive exploration of the genetic landscape of diseases. In clinical diagnosis, NGS has proven to be a powerful tool for identifying disease-causing variants, enabling accurate and early detection of genetic disorders. Additionally, NGS facilitates the identification of novel disease-associated genes and variants, aiding in the development of targeted therapies and personalized treatment strategies. NGS greatly benefits precision medicine by enhancing our understanding of disease mechanisms and enabling the identification of specific molecular markers for disease subtypes, thus enabling tailored medical interventions based on individual characteristics. Furthermore, NGS contributes to the development of non-invasive diagnostic approaches, such as liquid biopsies, which can monitor disease progression and treatment response. The potential of NGS in clinical diagnosis and precision medicine is vast, yet challenges persist in data analysis, interpretation, and protocol standardization. This review highlights NGS applications in disease diagnosis, prognosis, and personalized treatment strategies, while also addressing challenges and future prospects in fully harnessing genomic potential within clinical practice.
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Affiliation(s)
- Deepali Yadav
- Central Research Facility, Dr. D.Y Patil Medical College, Hospital & Research Centre, Dr. D. Y. Patil Vidyapeeth, Pimpri Pune 411018, India; Department of Biotechnology, Dr. D. Y. Patil Arts Science and Commerce College, Pimpri Pune 411018, India
| | - Bhagyashri Patil-Takbhate
- Central Research Facility, Dr. D.Y Patil Medical College, Hospital & Research Centre, Dr. D. Y. Patil Vidyapeeth, Pimpri Pune 411018, India
| | - Anil Khandagale
- Department of Biotechnology, Dr. D. Y. Patil Arts Science and Commerce College, Pimpri Pune 411018, India
| | - Jitendra Bhawalkar
- Department of Community Medicine, Dr. D.Y Patil Medical College, Hospital & Research Centre, Dr. D. Y. Patil Vidyapeeth, Pimpri Pune 411018, India
| | - Srikanth Tripathy
- Central Research Facility, Dr. D.Y Patil Medical College, Hospital & Research Centre, Dr. D. Y. Patil Vidyapeeth, Pimpri Pune 411018, India.
| | - Priyanka Khopkar-Kale
- Central Research Facility, Dr. D.Y Patil Medical College, Hospital & Research Centre, Dr. D. Y. Patil Vidyapeeth, Pimpri Pune 411018, India.
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Imhof C, Messchendorp L, van Baarle D, Gansevoort RT, Van Leer-Buter C, Sanders JSF. The Time-Dependent Association of Torque Teno Virus Load with the Level of SARS-CoV-2 S1 IgG Antibodies Following COVID-19 Vaccination in Kidney Transplant Recipients. Viruses 2023; 15:2189. [PMID: 38005867 PMCID: PMC10674182 DOI: 10.3390/v15112189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/26/2023] [Accepted: 10/28/2023] [Indexed: 11/26/2023] Open
Abstract
Kidney transplant recipients (KTR) show an impaired humoral immune response to COVID-19 vaccination due to their immunocompromised status. Torque teno virus (TTV) is a possible marker of immune function. This marker may be helpful in predicting the immune response after COVID-19 vaccination in order to decide which vaccination strategy should be applied. We therefore investigated whether TTV load is associated with the humoral response after COVID-19 vaccination. Of the KTR who participated in two prospective vaccination studies and received two to four doses of the mRNA-1273 COVID-19 vaccine, 122 were included. TTV load was measured prior to vaccination, and S1 IgG antibody levels were measured 28 days after vaccination. TTV load was independently inversely associated with S1 IgG antibodies after COVID-19 vaccination (B: -2.19 (95% CI: -3.6--0.8), p = 0.002). Interestingly, we found a significant interaction between TTV load and time after transplantation (p = 0.005). When patients were longer after transplantation, TTV load was less predictive for S1 IgG antibody response after vaccination compared to patients that were shorter after transplantation. Our data suggest that TTV load is a good marker in predicting COVID-19 vaccination antibody response and may be helpful in selecting a strategy shortly after transplantation. However, this marker should be handled with caution longer after transplantation.
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Affiliation(s)
- Céline Imhof
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Lianne Messchendorp
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Debbie van Baarle
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Ron T. Gansevoort
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Coretta Van Leer-Buter
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Jan-Stephan F. Sanders
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
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Minosse C, Matusali G, Meschi S, Grassi G, Francalancia M, D’Offizi G, Spezia PG, Garbuglia AR, Montalbano M, Focosi D, Girardi E, Vaia F, Ettorre GM, Maggi F. Torquetenovirus Loads in Peripheral Blood Predict Both the Humoral and Cell-Mediated Responses to SARS-CoV-2 Elicited by the mRNA Vaccine in Liver Transplant Recipients. Vaccines (Basel) 2023; 11:1656. [PMID: 38005988 PMCID: PMC10674741 DOI: 10.3390/vaccines11111656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
Three years into the COVID-19 pandemic, mass vaccination campaigns have largely controlled the disease burden but have not prevented virus circulation. Unfortunately, many immunocompromised patients have failed to mount protective immune responses after repeated vaccinations, and liver transplant recipients are no exception. Across different solid organ transplant populations, the plasma levels of Torquetenovirus (TTV), an orphan and ubiquitous human virus under control of the immune system, have been shown to predict the antibody response after COVID-19 vaccinations. We show here a single-institution experience with TTV viremia in 134 liver transplant recipients at their first or third dose. We found that TTV viremia before the first and third vaccine doses predicts serum anti-SARS-CoV-2 Spike receptor-binding domain (RBD) IgG levels measured 2-4 weeks after the second or third dose. Pre-vaccine TTV loads were also associated with peripheral blood anti-SARS-CoV-2 cell-mediated immunity but not with serum SARS-CoV-2 neutralizing antibody titers.
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Affiliation(s)
- Claudia Minosse
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy; (C.M.); (G.M.); (M.F.); (P.G.S.); (A.R.G.); (F.M.)
| | - Giulia Matusali
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy; (C.M.); (G.M.); (M.F.); (P.G.S.); (A.R.G.); (F.M.)
| | - Silvia Meschi
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy; (C.M.); (G.M.); (M.F.); (P.G.S.); (A.R.G.); (F.M.)
| | - Germana Grassi
- Laboratory of Cellular Immunology and Pharmacology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy;
| | - Massimo Francalancia
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy; (C.M.); (G.M.); (M.F.); (P.G.S.); (A.R.G.); (F.M.)
| | - Gianpiero D’Offizi
- Department of Liver Transplantation POIT, Clinical and Research Department of Infectious Diseases, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy; (G.D.); (M.M.); (G.M.E.)
| | - Pietro Giorgio Spezia
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy; (C.M.); (G.M.); (M.F.); (P.G.S.); (A.R.G.); (F.M.)
| | - Anna Rosa Garbuglia
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy; (C.M.); (G.M.); (M.F.); (P.G.S.); (A.R.G.); (F.M.)
| | - Marzia Montalbano
- Department of Liver Transplantation POIT, Clinical and Research Department of Infectious Diseases, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy; (G.D.); (M.M.); (G.M.E.)
| | - Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, 56124 Pisa, Italy;
| | - Enrico Girardi
- Scientific Direction, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy;
| | - Francesco Vaia
- General Direction, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy;
| | - Giuseppe Maria Ettorre
- Department of Liver Transplantation POIT, Clinical and Research Department of Infectious Diseases, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy; (G.D.); (M.M.); (G.M.E.)
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy; (C.M.); (G.M.); (M.F.); (P.G.S.); (A.R.G.); (F.M.)
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Sajiki AF, Koyanagi Y, Ushida H, Kawano K, Fujita K, Okuda D, Kawabe M, Yamada K, Suzumura A, Kachi S, Kaneko H, Komatsu H, Usui Y, Goto H, Nishiguchi KM. Association Between Torque Teno Virus and Systemic Immunodeficiency in Patients With Uveitis With a Suspected Infectious Etiology. Am J Ophthalmol 2023; 254:80-86. [PMID: 37356647 DOI: 10.1016/j.ajo.2023.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/27/2023] [Accepted: 06/03/2023] [Indexed: 06/27/2023]
Abstract
PURPOSE To determine the correlation between the presence of torque teno virus (TTV) in the aqueous humor of patients with uveitis and clinical information, including immunodeficiency history. DESIGN Multicenter, retrospective, cross-sectional study. METHODS Fifty-eight patients with uveitis with a suspected infectious etiology and 24 controls with cataract or age-related macular degeneration were included. We used quantitative polymerase chain reaction to test all subjects for TTV and multiplex polymerase chain reaction to test uveitis subjects for common ocular pathogens. When possible, both serum and aqueous humor samples were tested. Ocular TTV positivity was compared with age, sex, and a history of systemic immunodeficiency with logistic analysis. RESULTS Ocular TTV positivity was found in 23%, 11%, and 0% of patients with herpetic uveitis, nonherpetic uveitis, and controls, respectively. Among patients with herpes infection, positivity for ocular TTV was found in 43%, 8%, 14%, and 50% of patients with cytomegalovirus retinitis, iridocyclitis, acute retinal necrosis, and Epstein-Barr virus-positive uveitis, respectively. Patients with cytomegalovirus retinitis showed a significantly higher rate of ocular TTV infection than controls (P = .008). Serum analysis revealed TTV positivity in 90% of patients with uveitis and in 100% of controls. Age- and gender-adjusted logistic analysis revealed a correlation between ocular TTV positivity and systemic immunodeficiency (P = .01), but no correlations between ocular TTV and age, gender, or viral pathogenic type. CONCLUSIONS These findings suggest that positivity for ocular TTV was correlated with a clinical history of systemic immunodeficiency.
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Affiliation(s)
- Ai Fujita Sajiki
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.).
| | - Yoshito Koyanagi
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.)
| | - Hiroaki Ushida
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.).
| | - Kenichi Kawano
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.); Department of Ophthalmology, Yokkaichi Municipal Hospital, Yokkaichi, Japan (K.K.)
| | - Kosuke Fujita
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.)
| | - Daishi Okuda
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.)
| | - Mitsuki Kawabe
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.)
| | - Kazuhisa Yamada
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.)
| | - Ayana Suzumura
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.)
| | - Shu Kachi
- Shohzankai Medical Foundation, Miyake Eye Hospital, Nagoya, Japan (S.K.)
| | - Hiroki Kaneko
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.)
| | - Hiroyuki Komatsu
- Department of Ophthalmology, Tokyo Medical University, Tokyo, Japan (H.K., Y.U., H.G.)
| | - Yoshihiko Usui
- Department of Ophthalmology, Tokyo Medical University, Tokyo, Japan (H.K., Y.U., H.G.)
| | - Hiroshi Goto
- Department of Ophthalmology, Tokyo Medical University, Tokyo, Japan (H.K., Y.U., H.G.)
| | - Koji M Nishiguchi
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.)
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Marcozzi S, Bigossi G, Giuliani ME, Lai G, Giacconi R, Piacenza F, Malavolta M. Spreading Senescent Cells' Burden and Emerging Therapeutic Targets for Frailty. Cells 2023; 12:2287. [PMID: 37759509 PMCID: PMC10528263 DOI: 10.3390/cells12182287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
The spreading of senescent cells' burden holds profound implications for frailty, prompting the exploration of novel therapeutic targets. In this perspective review, we delve into the intricate mechanisms underlying senescent cell spreading, its implications for frailty, and its therapeutic development. We have focused our attention on the emerging age-related biological factors, such as microbiome and virome alterations, elucidating their significant contribution to the loss of control over the accumulation rate of senescent cells, particularly affecting key frailty domains, the musculoskeletal system and cerebral functions. We believe that gaining an understanding of these mechanisms could not only aid in elucidating the involvement of cellular senescence in frailty but also offer diverse therapeutic possibilities, potentially advancing the future development of tailored interventions for these highly diverse patients.
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Affiliation(s)
- Serena Marcozzi
- Advanced Technology Center for Aging Research and Geriatric Mouse Clinic, IRCCS INRCA, 60121 Ancona, Italy; (S.M.); (G.B.); (M.E.G.); (R.G.); (F.P.)
- Scientific Direction, IRCCS INRCA, 60124 Ancona, Italy
| | - Giorgia Bigossi
- Advanced Technology Center for Aging Research and Geriatric Mouse Clinic, IRCCS INRCA, 60121 Ancona, Italy; (S.M.); (G.B.); (M.E.G.); (R.G.); (F.P.)
| | - Maria Elisa Giuliani
- Advanced Technology Center for Aging Research and Geriatric Mouse Clinic, IRCCS INRCA, 60121 Ancona, Italy; (S.M.); (G.B.); (M.E.G.); (R.G.); (F.P.)
| | - Giovanni Lai
- Advanced Technology Center for Aging Research and Geriatric Mouse Clinic, IRCCS INRCA, 60121 Ancona, Italy; (S.M.); (G.B.); (M.E.G.); (R.G.); (F.P.)
| | - Robertina Giacconi
- Advanced Technology Center for Aging Research and Geriatric Mouse Clinic, IRCCS INRCA, 60121 Ancona, Italy; (S.M.); (G.B.); (M.E.G.); (R.G.); (F.P.)
| | - Francesco Piacenza
- Advanced Technology Center for Aging Research and Geriatric Mouse Clinic, IRCCS INRCA, 60121 Ancona, Italy; (S.M.); (G.B.); (M.E.G.); (R.G.); (F.P.)
| | - Marco Malavolta
- Advanced Technology Center for Aging Research and Geriatric Mouse Clinic, IRCCS INRCA, 60121 Ancona, Italy; (S.M.); (G.B.); (M.E.G.); (R.G.); (F.P.)
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Forqué L, Albert E, Piñana JL, Pérez A, Hernani R, Solano C, Navarro D, Giménez E. Monitoring of plasma Torque teno virus, total Anelloviridae and Human Pegivirus 1 viral load for the prediction of infectious events and acute graft versus host disease in the allogeneic hematopoietic stem cell transplantation setting. J Med Virol 2023; 95:e29107. [PMID: 37721473 DOI: 10.1002/jmv.29107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 09/19/2023]
Abstract
Anelloviridae and Human Pegivirus 1 (HPgV-1) blood burden have been postulated to behave as surrogate markers for immunosuppression in transplant recipients. Here, we assessed the potential utility plasma Torque teno virus (TTV), total Anelloviridae (TAV), and HPgV-1 load monitoring for the identification of allogeneic hematopoietic stem cell transplantation recipients (allo-HSCT) at increased risk of infectious events or acute graft versus host disease (aGvHD). In this single-center, observational study, plasma TTV DNA, TAV DNA, and HPgV-1 RNA loads were monitored in 75 nonconsecutive allo-HSCT recipients (median age, 54 years). Monitoring was conducted before at baseline or by days +30, +60, +90, +120, and +180 after transplantation. Pneumonia due to different viruses or Pneumocystis jirovecii, BK polyomavirus-associated haemorrhagic cystitis (BKPyV-HC), and Cytomegalovirus DNAemia were the infectious events considered in the current study. Kinetics of plasma TTV, TAV DNA, and HPgV-1 RNA load was comparable, with though and peak levels measured by days +30 and day +90 (+120 for HPgV-1). Forty patients (53%) developed one or more infectious events during the first 180 days after allo-HSCT, whereas 29 patients (39%) had aGvHD (grade II-IV in 18). Neither, TTV, TAV, nor HPgV-1 loads were predictive of overall infection or CMV DNAemia. A TTV DNA load cut-off ≥4.40 log10 (pretransplant) and ≥4.58 log10 (baseline) copies/mL predicted the occurrence of BKPyV-HC (sensitivity ≥89%, negative predictive value, ≥96%). TTV DNA loads ≥3.38 log10 by day +30 anticipated the occurrence of aGvHD (sensitivity, 90%; negative predictive value, 97%). Pretransplant HPgV-1 loads were significantly lower (p = 0.03) in patients who had aGvHD than in those who did not. Monitoring of TTV DNA or HPgV-1 RNA plasma levels either before or early after transplantation may be ancillary to identify allo-HSCT recipients at increased risk of BKPyV-HC or aGvHD.
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Affiliation(s)
- Lorena Forqué
- Microbiology Service, Clinic University Hospital, INCLIVA Biomedical Research Institute, Valencia, Spain
| | - Eliseo Albert
- Microbiology Service, Clinic University Hospital, INCLIVA Biomedical Research Institute, Valencia, Spain
| | - José L Piñana
- Hematology Service, Clinic University Hospital, INCLIVA Biomedical Research Institute, Valencia, Spain
| | - Ariadna Pérez
- Hematology Service, Clinic University Hospital, INCLIVA Biomedical Research Institute, Valencia, Spain
| | - Rafael Hernani
- Hematology Service, Clinic University Hospital, INCLIVA Biomedical Research Institute, Valencia, Spain
| | - Carlos Solano
- Hematology Service, Clinic University Hospital, INCLIVA Biomedical Research Institute, Valencia, Spain
- Department of Medicine, School of Medicine, University of Valencia, Valencia, Spain
| | - David Navarro
- Microbiology Service, Clinic University Hospital, INCLIVA Biomedical Research Institute, Valencia, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain
| | - Estela Giménez
- Microbiology Service, Clinic University Hospital, INCLIVA Biomedical Research Institute, Valencia, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
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Goldberg JF, Truby LK, Agbor-Enoh S, Jackson AM, deFilippi CR, Khush KK, Shah P. Selection and Interpretation of Molecular Diagnostics in Heart Transplantation. Circulation 2023; 148:679-694. [PMID: 37603604 PMCID: PMC10449361 DOI: 10.1161/circulationaha.123.062847] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
The number of heart transplants performed annually in the United States and worldwide continues to increase, but there has been little change in graft longevity and patient survival over the past 2 decades. The reference standard for diagnosis of acute cellular and antibody-mediated rejection includes histologic and immunofluorescence evaluation of endomyocardial biopsy samples, despite invasiveness and high interrater variability for grading histologic rejection. Circulating biomarkers and molecular diagnostics have shown substantial predictive value in rejection monitoring, and emerging data support their use in diagnosing other posttransplant complications. The use of genomic (cell-free DNA), transcriptomic (mRNA and microRNA profiling), and proteomic (protein expression quantitation) methodologies in diagnosis of these posttransplant outcomes has been evaluated with varying levels of evidence. In parallel, growing knowledge about the genetically mediated immune response leading to rejection (immunogenetics) has enhanced understanding of antibody-mediated rejection, associated graft dysfunction, and death. Antibodies to donor human leukocyte antigens and the technology available to evaluate these antibodies continues to evolve. This review aims to provide an overview of biomarker and immunologic tests used to diagnose posttransplant complications. This includes a discussion of pediatric heart transplantation and the disparate rates of rejection and death experienced by Black patients receiving a heart transplant. This review describes diagnostic modalities that are available and used after transplant and the landscape of future investigations needed to enhance patient outcomes after heart transplantation.
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Affiliation(s)
- Jason F Goldberg
- Department of Heart Failure and Transplantation, Inova Heart and Vascular Institute, Falls Church, VA (J.F.G., C.R.d., P.S.)
- Department of Pediatrics, Inova L.J. Murphy Children's Hospital, Falls Church, VA (J.F.G.)
| | - Lauren K Truby
- Department of Medicine, University of Texas Southwestern, Dallas (L.K.T.)
| | - Sean Agbor-Enoh
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD (S.A.-E.)
- Applied Precision Genomics, National Heart, Lung and Blood Institute, Bethesda, MD (S.A.-E.)
| | - Annette M Jackson
- Department of Surgery, Duke University School of Medicine, Durham, NC (A.M.J.)
| | - Christopher R deFilippi
- Department of Heart Failure and Transplantation, Inova Heart and Vascular Institute, Falls Church, VA (J.F.G., C.R.d., P.S.)
| | - Kiran K Khush
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, CA (K.K.K.)
| | - Palak Shah
- Department of Heart Failure and Transplantation, Inova Heart and Vascular Institute, Falls Church, VA (J.F.G., C.R.d., P.S.)
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Moufarrej MN, Bianchi DW, Shaw GM, Stevenson DK, Quake SR. Noninvasive Prenatal Testing Using Circulating DNA and RNA: Advances, Challenges, and Possibilities. Annu Rev Biomed Data Sci 2023; 6:397-418. [PMID: 37196360 PMCID: PMC10528197 DOI: 10.1146/annurev-biodatasci-020722-094144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Prenatal screening using sequencing of circulating cell-free DNA has transformed obstetric care over the past decade and significantly reduced the number of invasive diagnostic procedures like amniocentesis for genetic disorders. Nonetheless, emergency care remains the only option for complications like preeclampsia and preterm birth, two of the most prevalent obstetrical syndromes. Advances in noninvasive prenatal testing expand the scope of precision medicine in obstetric care. In this review, we discuss advances, challenges, and possibilities toward the goal of providing proactive, personalized prenatal care. The highlighted advances focus mainly on cell-free nucleic acids; however, we also review research that uses signals from metabolomics, proteomics, intact cells, and the microbiome. We discuss ethical challenges in providing care. Finally, we look to future possibilities, including redefining disease taxonomy and moving from biomarker correlation to biological causation.
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Affiliation(s)
| | - Diana W Bianchi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development and Section on Prenatal Genomics and Fetal Therapy, Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gary M Shaw
- Department of Pediatrics and March of Dimes Prematurity Research Center at Stanford University, Stanford University School of Medicine, Stanford, California, USA
| | - David K Stevenson
- Department of Pediatrics and March of Dimes Prematurity Research Center at Stanford University, Stanford University School of Medicine, Stanford, California, USA
| | - Stephen R Quake
- Department of Bioengineering and Department of Applied Physics, Stanford University, Stanford, California, USA
- Chan Zuckerberg Initiative, Redwood City, California, USA
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Laubscher F, Kaiser L, Cordey S. SCANellome: Analysis of the Genomic Diversity of Human and Non-Human Primate Anelloviruses from Metagenomics Data. Viruses 2023; 15:1575. [PMID: 37515261 PMCID: PMC10384568 DOI: 10.3390/v15071575] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/04/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Anelloviruses are extremely prevalent in the human population and are considered to be commensal parts of the human virome. The best-known member in humans is the Torque teno virus. Recent metagenomic next-generation sequencing investigations have helped reveal the considerable number of species and genotypes from the same genus that can be co-detected within a single individual and that this diversity increases as a function of age during the first months/years of life. As a result, to date, the bioinformatics analysis of this genetic diversity remains complex and constraining for researchers. Here, we present SCANellome, a user-friendly tool to investigate the anellome composition at the genus, species, and genotype levels of samples from metagenomics data generated by the Illumina and Nanopore platforms. SCANellome is based on an in-house up-to-date database that includes all human and non-human primate anellovirus reference sequences available on GenBank and meets the latest classification criteria established by the International Committee on Taxonomy of Viruses.
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Affiliation(s)
- Florian Laubscher
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
| | - Laurent Kaiser
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Samuel Cordey
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
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Mafi S, Essig M, Rerolle JP, Lagathu G, Crochette R, Brodard V, Schvartz B, Gouarin S, Bouvier N, Engelmann I, Garstka A, Bressollette-Bodin C, Cantarovitch D, Germi R, Janbon B, Archimbaut C, Heng AE, Garnier F, Gomes-Mayeras M, Labrunie A, Hantz S, Alain S. Torque teno virus viremia and QuantiFERON ®-CMV assay in prediction of cytomegalovirus reactivation in R+ kidney transplant recipients. Front Med (Lausanne) 2023; 10:1180769. [PMID: 37425298 PMCID: PMC10323437 DOI: 10.3389/fmed.2023.1180769] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/12/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction Cytomegalovirus (CMV) is the most frequent infectious complication following solid organ transplantation. Torque teno viruses (TTV) viremia has been proposed as a biomarker of functional immunity in the management of kidney transplant recipients (KTR). The QuantiFERON®-CMV (QF-CMV) is a commercially available assay that allows the assessment of CD8+ T-cell responses in routine diagnostic laboratories. Methods In a prospective national multicenter cohort of 64 CMV-seropositive (R+) KTR, we analyzed the value of TTV load and the two markers of the QF-CMV assay [QF-Ag (CMV-specific T-cell responses) and QF-Mg (overall T-cell responses)], alone and in combination, in prediction of CMV reactivation (≥3 log10 IU/ ml) in the first post-transplant year. We compared previously published cut-offs and specific cut-offs optimized from ROC curves for our population. Results Using the conventional cut-off (3.45 log10 copies/ml), TTV load at D0 [inclusion visit on the day of transplantation before induction (D0)], or at M1 (1-month post-transplant visit) perform better in predicting CMV viremia control than CMV reactivation. Survival analyses suggest a better performance of our optimized TTV cut-offs (3.78 log10 copies/ml at D0 and 4.23 log10 copies/ml at M1) for risk stratification of CMV reactivation in our R+ KTR cohort. The QF-CMV (QF-Ag = 0.2 IU/ml, and QF-Mg = 0.5 IU/ml) also appears to better predict CMV viremia control than CMV reactivation. Moreover, survival analyses suggest that the QF-Mg would perform better than the QF-Ag in stratifying the risk of CMV reactivation. The use of our optimized QF-Mg cut-off (1.27 IU/ml) at M1 further improved risk stratification of CMV reactivation. Using conventional cut-offs, the combination of TTV load and QF-Ag or TTV load and QF-Mg did not improve prediction of CMV viremia control compared to separate analysis of each marker but resulted in an increase of positive predictive values. The use of our cut-offs slightly improved risk prediction of CMV reactivation. Conclusion The combination of TTV load and QF-Ag or TTV load and QF-Mg could be useful in stratifying the risk of CMV reactivation in R+ KTR during the first post-transplant year and thereby have an impact on the duration of prophylaxis in these patients. Clinical trial registration ClinicalTrials.gov registry, identifier NCT02064699.
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Affiliation(s)
- Sarah Mafi
- French National Reference Center for Herpesviruses, Bacteriology, Virology, Hygiene Department, Centre Hospitalier Universitaire de Limoges, Limoges, France
- Inserm, RESINFIT, U1092, Université de Limoges, Limoges, France
| | - Marie Essig
- Nephrology and Transplantation Department, Centre Hospitalier Universitaire de Limoges, Limoges, France
| | - Jean-Philippe Rerolle
- Nephrology and Transplantation Department, Centre Hospitalier Universitaire de Limoges, Limoges, France
| | - Gisèle Lagathu
- Virology Department, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Romain Crochette
- Nephrology and Transplantation Department, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Véronique Brodard
- Virology Department, Centre Hospitalier Universitaire de Reims, Reims, France
| | - Betoul Schvartz
- Nephrology and Transplantation Department, Centre Hospitalier Universitaire de Reims, Reims, France
| | - Stephanie Gouarin
- Virology Department, Centre Hospitalier Universitaire de Caen, Caen, France
| | - Nicolas Bouvier
- Nephrology and Transplantation Department, Centre Hospitalier Universitaire de Caen, Caen, France
| | - Ilka Engelmann
- Virology Department, Centre Hospitalier Universitaire de Lille, Lille, France
| | - Antoine Garstka
- Nephrology and Transplantation Department, Centre Hospitalier Universitaire de Lille, Lille, France
| | | | - Diego Cantarovitch
- Nephrology and Transplantation Department, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Raphaële Germi
- Virology Department, Centre Hospitalier Universitaire de Grenoble, Grenoble, France
| | - Benedicte Janbon
- Nephrology and Transplantation Department, Centre Hospitalier Universitaire de Grenoble, Grenoble, France
| | - Christine Archimbaut
- Virology Department, Centre Hospitalier Universitaire de Clermont-Ferrand, Clermont-Ferrand, France
| | - Anne-Elizabeth Heng
- Nephrology and Transplantation Department, Centre Hospitalier Universitaire de Clermont-Ferrand, Clermont-Ferrand, France
| | - Françoise Garnier
- French National Reference Center for Herpesviruses, Bacteriology, Virology, Hygiene Department, Centre Hospitalier Universitaire de Limoges, Limoges, France
- Inserm, RESINFIT, U1092, Université de Limoges, Limoges, France
| | - Melissa Gomes-Mayeras
- French National Reference Center for Herpesviruses, Bacteriology, Virology, Hygiene Department, Centre Hospitalier Universitaire de Limoges, Limoges, France
- Inserm, RESINFIT, U1092, Université de Limoges, Limoges, France
| | - Anaïs Labrunie
- Biostatistics Department, Centre Hospitalier Universitaire de Limoges, Limoges, France
| | - Sébastien Hantz
- French National Reference Center for Herpesviruses, Bacteriology, Virology, Hygiene Department, Centre Hospitalier Universitaire de Limoges, Limoges, France
- Inserm, RESINFIT, U1092, Université de Limoges, Limoges, France
| | - Sophie Alain
- French National Reference Center for Herpesviruses, Bacteriology, Virology, Hygiene Department, Centre Hospitalier Universitaire de Limoges, Limoges, France
- Inserm, RESINFIT, U1092, Université de Limoges, Limoges, France
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Valantine HA. Applying Genomics to Unravel Health Disparities in Organ Transplantation: Paul I. Terasaki State-of-the-art Lecture; American Transplant Congress 2021. Transplantation 2023; 107:1258-1264. [PMID: 36584376 DOI: 10.1097/tp.0000000000004456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
An extensive body of research about team science provides empirical evidence that diverse teams outperform homogenous teams in creating more innovative solutions to complex problems. At the core of diverse and inclusive teams is a rich diversity of perspectives, experiences, and backgrounds that invite new questions and broaden the scope of research. Diverse perspectives are especially relevant for biomedicine, which seeks to find solutions for challenging problems affecting the human condition. It is essential that diversity and inclusion in biomedicine is prioritized as a key driver of innovation, both through the people who conduct the research and the science itself. Key questions have been articulated as important drivers for funding research: (1) Who is doing the science and who is building the tools? (2) What science and technology is being done and how? and (3) Who has access to the knowledge and benefits of scientific innovation? I will briefly review the empirical evidence supporting diversity as a powerful enhancer of the quality and outputs of research and clinical care. I offer my own research as a case study of incorporating a framework of diversity, equity, and inclusion into research that uses new emerging genomic tools for earlier and more precise diagnosis of organ transplant rejection. I will demonstrate how these same tools hold great promise for accelerating the discovery of hitherto unexplored mechanisms that drive the poor outcomes for African ancestry organ transplant recipients, which in turn will identify new diagnostics and therapeutic targets that benefit transplant recipients across all ancestries.
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Starrett GJ, Yu K, Golubeva Y, Lenz P, Piaskowski ML, Petersen D, Dean M, Israni A, Hernandez BY, Tucker TC, Cheng I, Gonsalves L, Morris CR, Hussain SK, Lynch CF, Harris RS, Prokunina-Olsson L, Meltzer PS, Buck CB, Engels EA. Evidence for virus-mediated oncogenesis in bladder cancers arising in solid organ transplant recipients. eLife 2023; 12:e82690. [PMID: 36961501 PMCID: PMC10446826 DOI: 10.7554/elife.82690] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 03/22/2023] [Indexed: 03/25/2023] Open
Abstract
A small percentage of bladder cancers in the general population have been found to harbor DNA viruses. In contrast, up to 25% of tumors of solid organ transplant recipients, who are at an increased risk of developing bladder cancer and have an overall poorer outcomes, harbor BK polyomavirus (BKPyV). To better understand the biology of the tumors and the mechanisms of carcinogenesis from potential oncoviruses, we performed whole genome and transcriptome sequencing on bladder cancer specimens from 43 transplant patients. Nearly half of the tumors from this patient population contained viral sequences. The most common were from BKPyV (N=9, 21%), JC polyomavirus (N=7, 16%), carcinogenic human papillomaviruses (N=3, 7%), and torque teno viruses (N=5, 12%). Immunohistochemistry revealed variable Large T antigen expression in BKPyV-positive tumors ranging from 100% positive staining of tumor tissue to less than 1%. In most cases of BKPyV-positive tumors, the viral genome appeared to be clonally integrated into the host chromosome consistent with microhomology-mediated end joining and coincided with focal amplifications of the tumor genome similar to other virus-mediated cancers. Significant changes in host gene expression consistent with the functions of BKPyV Large T antigen were also observed in these tumors. Lastly, we identified four mutation signatures in our cases, with those attributable to APOBEC3 and SBS5 being the most abundant. Mutation signatures associated with an antiviral drug, ganciclovir, and aristolochic acid, a nephrotoxic compound found in some herbal medicines, were also observed. The results suggest multiple pathways to carcinogenesis in solid organ transplant recipients with a large fraction being virus-associated.
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Affiliation(s)
| | - Kelly Yu
- DCEG, NCI, NIHRockvilleUnited States
| | | | - Petra Lenz
- Leidos Biomedical Research IncFrederickUnited States
| | | | | | | | - Ajay Israni
- Department of Medicine, Nephrology Division, Hennepin Healthcare System, University of MinnesotaMinneapolisUnited States
| | | | - Thomas C Tucker
- The Kentucky Cancer Registry, University of KentuckyLexingtonUnited States
| | - Iona Cheng
- Department of Epidemiology and Biostatistics,and Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoFremontUnited States
| | - Lou Gonsalves
- Connecticut Tumor Registry, Connecticut Department of Public HealthHartfordUnited States
| | - Cyllene R Morris
- California Cancer Reporting and Epidemiologic Surveillance Program, University of California, DavisDavisUnited States
| | - Shehnaz K Hussain
- Cedars-Sinai Cancer and Department of Medicine, Cedars-Sinai Medical CenterLos AngelesUnited States
| | - Charles F Lynch
- The Iowa Cancer Registry, University of IowaIowa CityUnited States
| | - Reuben S Harris
- Howard Hughes Medical Institute, University of MinnesotaMinneapolisUnited States
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Haupenthal F, Rahn J, Maggi F, Gelas F, Bourgeois P, Hugo C, Jilma B, Böhmig GA, Herkner H, Wolzt M, Doberer K, Vossen M, Focosi D, Neuwirt H, Banas M, Banas B, Budde K, Viklicky O, Malvezzi P, Rostaing L, Rotmans JI, Bakker SJL, Eller K, Cejka D, Pérez AM, Rodriguez-Arias D, König F, Bond G. A multicentre, patient- and assessor-blinded, non-inferiority, randomised and controlled phase II trial to compare standard and torque teno virus-guided immunosuppression in kidney transplant recipients in the first year after transplantation: TTVguideIT. Trials 2023; 24:213. [PMID: 36949445 PMCID: PMC10032258 DOI: 10.1186/s13063-023-07216-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/02/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND Immunosuppression after kidney transplantation is mainly guided via plasma tacrolimus trough level, which cannot sufficiently predict allograft rejection and infection. The plasma load of the non-pathogenic and highly prevalent torque teno virus (TTV) is associated with the immunosuppression of its host. Non-interventional studies suggest the use of TTV load to predict allograft rejection and infection. The primary objective of the current trial is to demonstrate the safety, tolerability and preliminary efficacy of TTV-guided immunosuppression. METHODS For this purpose, a randomised, controlled, interventional, two-arm, non-inferiority, patient- and assessor-blinded, investigator-driven phase II trial was designed. A total of 260 stable, low-immunological-risk adult recipients of a kidney graft with tacrolimus-based immunosuppression and TTV infection after month 3 post-transplantation will be recruited in 13 academic centres in six European countries. Subjects will be randomised in a 1:1 ratio (allocation concealment) to receive tacrolimus either guided by TTV load or according to the local centre standard for 9 months. The primary composite endpoint includes the occurrence of infections, biopsy-proven allograft rejection, graft loss, or death. The main secondary endpoints include estimated glomerular filtration rate, graft rejection detected by protocol biopsy at month 12 post-transplantation (including molecular microscopy), development of de novo donor-specific antibodies, health-related quality of life, and drug adherence. In parallel, a comprehensive biobank will be established including plasma, serum, urine and whole blood. The date of the first enrolment was August 2022 and the planned end is April 2025. DISCUSSION The assessment of individual kidney transplant recipient immune function might enable clinicians to personalise immunosuppression, thereby reducing infection and rejection. Moreover, the trial might act as a proof of principle for TTV-guided immunosuppression and thus pave the way for broader clinical applications, including as guidance for immune modulators or disease-modifying agents. TRIAL REGISTRATION EU CT-Number: 2022-500024-30-00.
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Affiliation(s)
- Frederik Haupenthal
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Jette Rahn
- Coordination Center for Clinical Trials, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases L. Spallanzani, Rome, Italy
| | - Fanny Gelas
- bioMérieux SA, Centre Christophe Merieux, Grenoble, France
| | | | - Christian Hugo
- Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden, Dresden, Germany
| | - Bernd Jilma
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Georg A Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Harald Herkner
- Department of Emergency Medicine, Medical University of Vienna, Vienna, Austria
| | - Michael Wolzt
- Clinical Trials Coordination Centre, Medical University of Vienna, Vienna, Austria
| | - Konstantin Doberer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Matthias Vossen
- Division of Infectious diseases and Tropical Medicine, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | | | - Hannes Neuwirt
- Department of Internal Medicine IV, Nephrology and Hypertension, Medical University Innsbruck, Innsbruck, Austria
| | - Miriam Banas
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Bernhard Banas
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Klemens Budde
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ondrej Viklicky
- Transplant Center, Department of Nephrology, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Paolo Malvezzi
- Department of Nephrology, Hemodialysis, Apheresis and Kidney Transplantation, CHU-Grenoble-Alpes, Grenoble, France
| | - Lionel Rostaing
- Department of Nephrology, Hemodialysis, Apheresis and Kidney Transplantation, CHU-Grenoble-Alpes, Grenoble, France
| | - Joris I Rotmans
- Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Stephan J L Bakker
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Kathrin Eller
- Division of Nephrology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Daniel Cejka
- Ordensklinikum Linz GmbH Elisabethinen, Linz, Austria
| | - Alberto Molina Pérez
- Institute for Advanced Social Studies, Spanish National Research Council, Madrid, Spain
| | | | - Franz König
- Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Gregor Bond
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria.
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Patterson CM, Jolly EC, Burrows F, Ronan NJ, Lyster H. Conventional and Novel Approaches to Immunosuppression in Lung Transplantation. Clin Chest Med 2023; 44:121-136. [PMID: 36774159 DOI: 10.1016/j.ccm.2022.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Most therapeutic advances in immunosuppression have occurred over the past few decades. Although modern strategies have been effective in reducing acute cellular rejection, excess immunosuppression comes at the price of toxicity, opportunistic infection, and malignancy. As our understanding of the immune system and allograft rejection becomes more nuanced, there is an opportunity to evolve immunosuppression protocols to optimize longer term outcomes while mitigating the deleterious effects of traditional protocols.
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Affiliation(s)
- Caroline M Patterson
- Transplant Continuing Care Unit, Royal Papworth Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Elaine C Jolly
- Division of Renal Medicine, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Fay Burrows
- Department of Pharmacy, St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Nicola J Ronan
- Transplant Continuing Care Unit, Royal Papworth Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Haifa Lyster
- Cardiothoracic Transplant Unit, Royal Brompton and Harefield Hospitals, Part of Guy's & St Thomas' NHS Foundation Trust, London, United Kingdom; Kings College, London, United Kingdom; Pharmacy Department, Royal Brompton and Harefield Hospitals, Part of Guy's & St Thomas' NHS Foundation Trust, London, United Kingdom.
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Stout MJ, Brar AK, Herter BN, Rankin A, Wylie KM. The plasma virome in longitudinal samples from pregnant patients. Front Cell Infect Microbiol 2023; 13:1061230. [PMID: 36844406 PMCID: PMC9949529 DOI: 10.3389/fcimb.2023.1061230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction Nucleic acid from viruses is common in peripheral blood, even in asymptomatic individuals. How physiologic changes of pregnancy impact host-virus dynamics for acute, chronic, and latent viral infections is not well described. Previously we found higher viral diversity in the vagina during pregnancy associated with preterm birth (PTB) and Black race. We hypothesized that higher diversity and viral copy numbers in the plasma would show similar trends. Methods To test this hypothesis, we evaluated longitudinally collected plasma samples from 23 pregnant patients (11 term and 12 preterm) using metagenomic sequencing with ViroCap enrichment to enhance virus detection. Sequence data were analyzed with the ViroMatch pipeline. Results We detected nucleic acid from at least 1 virus in at least 1 sample from 87% (20/23) of the maternal subjects. The viruses represented 5 families: Herpesviridae, Poxviridae, Papillomaviridae, Anelloviridae, and Flaviviridae. We analyzed cord plasma from 18 of the babies from those patients and found nucleic acid from viruses in 33% of the samples (6/18) from 3 families: Herpesviridae, Papillomaviridae, and Anelloviridae. Some viral genomes were found in both maternal plasma and cord plasma from maternal-fetal pairs (e.g. cytomegalovirus, anellovirus). We found that Black race associated with higher viral richness (number of different viruses detected) in the maternal blood samples (P=0.003), consistent with our previous observations in vaginal samples. We did not detect associations between viral richness and PTB or the trimester of sampling. We then examined anelloviruses, a group of viruses that is ubiquitous and whose viral copy numbers fluctuate with immunological state. We tested anellovirus copy numbers in plasma from 63 pregnant patients sampled longitudinally using qPCR. Black race associated with higher anellovirus positivity (P<0.001) but not copy numbers (P=0.1). Anellovirus positivity and copy numbers were higher in the PTB group compared to the term group (P<0.01, P=0.003, respectively). Interestingly, these features did not occur at the time of delivery but appeared earlier in pregnancy, suggesting that although anelloviruses were biomarkers for PTB they were not triggering parturition. Discussion These results emphasize the importance of longitudinal sampling and diverse cohorts in studies of virome dynamics during pregnancy.
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Affiliation(s)
- Molly J. Stout
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Anoop K. Brar
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
| | - Brandi N. Herter
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
| | - Ananda Rankin
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
| | - Kristine M. Wylie
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States,The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, United States,*Correspondence: Kristine M. Wylie,
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Roberto P, Cinti L, Napoli A, Paesani D, Riveros Cabral RJ, Maggi F, Garofalo M, Pretagostini R, Centofanti A, Carillo C, Venuta F, Gaeta A, Antonelli G. Torque teno virus (TTV): A gentle spy virus of immune status, predictive marker of seroconversion to COVID-19 vaccine in kidney and lung transplant recipients. J Med Virol 2023; 95:e28512. [PMID: 36661060 PMCID: PMC10108096 DOI: 10.1002/jmv.28512] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023]
Abstract
To date, no comprehensive marker to monitor the immune status of patients is available. Given that Torque teno virus (TTV), a known human virome component, has previously been identified as a marker of immunocompetence, it was retrospectively investigated whether TTV viral load may also represent a marker of ability to develop antibody in response to COVID-19-BNT162B2 vaccine in solid organ transplant recipients (SOT). Specifically, 273 samples from 146 kidney and 26 lung transplant recipients after successive doses of vaccine were analyzed. An inverse correlation was observed within the TTV copy number and anti-Spike IgG antibody titer with a progressive decrease in viremia the further away from the transplant date. Analyzing the data obtained after the second dose, a significant difference in TTV copy number between responsive and nonresponsive patients was observed, considering a 5 log10 TTV copies/mL threshold to discriminate between the two groups. Moreover, for 86 patients followed in their response to the second and third vaccination doses a 6 log10 TTV copies/mL threshold was used to predict responsivity to the booster dose. Although further investigation is necessary, possibly extending the analysis to other patient categories, this study suggests that TTV can be used as a good marker of vaccine response in transplant patients.
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Affiliation(s)
- Piergiorgio Roberto
- Department of Molecular Medicine, Laboratory of Microbiology and Virology, Sapienza University of Rome, Rome, Italy
| | - Lilia Cinti
- Department of Molecular Medicine, Laboratory of Microbiology and Virology, Sapienza University of Rome, Rome, Italy
| | - Anna Napoli
- Department of Molecular Medicine, Laboratory of Microbiology and Virology, Sapienza University of Rome, Rome, Italy
| | | | - Rodolfo J Riveros Cabral
- Department of Molecular Medicine, Laboratory of Microbiology and Virology, Sapienza University of Rome, Rome, Italy
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Manuela Garofalo
- General Surgery and Organ Transplantation Unit, Sapienza University of Rome, Rome, Italy
| | - Renzo Pretagostini
- General Surgery and Organ Transplantation Unit, Sapienza University of Rome, Rome, Italy
| | - Anastasia Centofanti
- Department of General and Specialistic Surgery "Paride Stefanini", Sapienza University of Rome, Rome, Italy
| | - Carolina Carillo
- Department of General and Specialistic Surgery "Paride Stefanini", Sapienza University of Rome, Rome, Italy
| | - Federico Venuta
- Department of General and Specialistic Surgery "Paride Stefanini", Sapienza University of Rome, Rome, Italy
| | - Aurelia Gaeta
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Guido Antonelli
- Department of Molecular Medicine, Laboratory of Microbiology and Virology, Sapienza University of Rome, Rome, Italy.,Microbiology and Virology Unit, Sapienza University Hospital Policlinico Umberto I, Rome, Italy
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Dynamics of Human Anelloviruses in Plasma and Clinical Outcomes Following Kidney Transplantation. Transplantation 2023; 107:511-520. [PMID: 36042550 DOI: 10.1097/tp.0000000000004292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND Torque teno virus, the major member of the genus Alphatorquevirus , is an emerging biomarker of the net state of immunosuppression after kidney transplantation. Genetic diversity constitutes a main feature of the Anelloviridae family, although its posttransplant dynamics and clinical correlates are largely unknown. METHODS The relative abundance of Alphatorquevirus , Betatorquevirus , and Gammatorquevirus genera was investigated by high-throughput sequencing in plasma specimens obtained at various points during the first posttransplant year (n = 91 recipients). Total loads of all members of the Anelloviridae family were also quantified by an "in-house" polymerase chain reaction assay targeting conserved DNA sequences (n = 195 recipients). In addition to viral kinetics, clinical study outcomes included serious infection, immunosuppression-related adverse event (opportunistic infection and cancer)' and acute rejection. RESULTS Alphatorquevirus DNA was detected in all patients at every point, with an increase from pretransplantation to month 1. A variable proportion of recipients had detectable Betatorquevirus and Gammatorquevirus at lower frequencies. At least 1 change in the predominant genus (mainly as early transition to Alphatorquevirus predominance) was shown in 35.6% of evaluable patients. Total anelloviruses DNA levels increased from baseline to month 1, to peak by month 3 and decrease thereafter, and were higher in patients treated with T-cell depleting agents. There was a significant albeit weak-to-moderate correlation between total anelloviruses and TTV DNA levels. No associations were found between the predominant Anelloviridae genus or total anelloviruses DNA levels and clinical outcomes. CONCLUSIONS Our study provides novel insight into the evolution of the anellome after kidney transplantation.
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Kong C, Liu G, Kalady MF, Jin T, Ma Y. Dysbiosis of the stool DNA and RNA virome in Crohn's disease. J Med Virol 2023; 95:e28573. [PMID: 36772850 DOI: 10.1002/jmv.28573] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/20/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023]
Abstract
Pathogenesis of Crohn's disease (CD) relates to gut microbiome dysbiosis. However, less is known about the viral microbiome, consisting of bacteriophages and eukaryotic viruses, in CD. Here, we profiled the stool virome, viral functions, and viral-bacterial correlations that involved in CD pathogenesis. Metagenomics and metaviromics with novel viral identification and data analysis workflow were performed on stool of non-CD household controls, CD flare and remission patients. Both bacteriome and DNA/RNA virome alterations were characterized and correlated with disease status. There was a decreased diversity and extreme heterogeneity in both DNA and RNA virome in CD. We observed CD-specific dysbiosis in virome, particularly the prominent DNA eukaryotic Torque teno virus (TTV), disease-associated Faecalibacterium phage and Escherichia phage, and RNA tomato diet-related virus in CD, while some diverse prokaryotic viruses were more abundant in healthy subjects. Compared with the remission, inflammation-associated eukaryotic TTV and prokaryotic Staphylococcus phages were predominated in the flare, and displayed a link with complications and multiple therapeutic approaches. Multiple viral functions, particularly functions of viral DNA replication, integration and modification as well as the eukaryotic TTV-related capsid protein, were markedly enriched in CD. Furthermore, the virus-bacteria interactions became more specialized in CD, and the combination of bacteriome and virome composition provided better classification between CD and health. Our study presents a global view of the comprehensive viral component change in the CD patients' gut microbiome, and highlights the great potential of virome biomarkers in pathogenesis and accurate diagnostics of CD risk and disease status.
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Affiliation(s)
- Cheng Kong
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Gastrointestinal Surgery, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Guang Liu
- Guangdong Magigene Biotechnology Co, Ltd, Guangdong, China
| | - Matthew F Kalady
- Division of Colon and Rectal Surgery, The Ohio State University Wexner Medical Center, James Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Tao Jin
- Guangdong Magigene Biotechnology Co, Ltd, Guangdong, China
| | - Yanlei Ma
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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Feng B, Liu B, Cheng M, Dong J, Hu Y, Jin Q, Yang F. An atlas of the blood virome in healthy individuals. Virus Res 2023; 323:199004. [PMID: 36402209 PMCID: PMC10194198 DOI: 10.1016/j.virusres.2022.199004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/14/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
Abstract
Emerging evidence indicates that gut virome plays a role in human health and disease, however, much less is known about the viral communities in blood. Here we conducted a direct metatranscriptomic sequencing of virus-like-particles in blood from 1200 healthy individuals, without prior amplification to avoid potential amplification bias and with a strictly bioinformatic and manual check for candidate viral reads to reduce false-positive matches. We identified 55 different viruses from 36 viral families, including 24 human DNA, RNA and retroviruses in 70% of the studied pools. The study showed that anelloviruses are widely distributed and dominate the blood virome in healthy individuals. Human herpesviruses and pegivirus-1 are commonly prevalent in asymptomatic humans. We identified the prevalence of RNA viruses often causing acute infection, like HEV, HPIV, RSV and HCoV-HKU1, revealing of a transmissible risk of asymptomatic infection. Several viruses possible related to transfusion safety were identified, including human Merkel cell polyomavirus, papillomavirus, parvovirus B19 and herpesvirus 8 in addition to HBV. In addition, phages in Caudovirales and Microviridae, were commonly found in pools of samples with a very low abundance; a few sequences for invertebrate, plant and giant viruses were found in some of individuals; however, the remaining 31 viruses mostly reflect extensive contamination from commercial reagents and the work environments. In conclusion, this study is the first comprehensive investigation of blood virome in healthy individuals by metatranscriptomic sequencing of VLP in China. Further investigation of potential false positives representing a major challenge for the identification of novel viruses in mNGS, will offer a systemic idea and means to reveal true viral infections of human.
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Affiliation(s)
- Bo Feng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing 100730, PR China
| | - Bo Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing 100730, PR China
| | - Min Cheng
- China Institute of Veterinary Drug Control, Beijing 100081, PR China
| | - Jie Dong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing 100730, PR China
| | - Yongfeng Hu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing 100730, PR China.
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing 100730, PR China.
| | - Fan Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing 100730, PR China.
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