Cited by 471Bacteriophages and microbial interactionsCytomegalovirus and herpesvirus researchHIV Research and Treatment

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Temporal Response of the Human Virome to Immunosuppression and Antiviral Therapy

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De Vlaminck, Iwijn, Khush, Kiran K., Strehl, Calvin, Kohli, Bitika, Luikart, Helen, Neff, Norma F., Okamoto, Jennifer, Snyder, Thomas M., Cornfield, David N., Nicolls, Mark R., Weill, David, Bernstein, Daniel, Valantine, Hannah A., Quake, Stephen R.·2013·Cell

DOI 10.1016/j.cell.2013.10.034PMC PMC4098717

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Abstract

There are few substantive methods to measure the health of the immune system, and the connection between immune strength and the viral component of the microbiome is poorly understood. Organ transplant recipients are treated with posttransplant therapies that combine immunosuppressive and antiviral drugs, offering a window into the effects of immune modulation on the virome. We used sequencing of cell-free DNA in plasma to investigate drug-virome interactions in a cohort of organ transplant recipients (656 samples, 96 patients) and find that antivirals and immunosuppressants strongly affect the structure of the virome in plasma. We observe marked virome compositional dynamics at the onset of the therapy and find that the total viral load increases with immunosuppression, whereas the bacterial component of the microbiome remains largely unaffected. The data provide insight into the relationship between the human virome, the state of the immune system, and the effects of pharmacological treatment and offer a potential application of the virome state to predict immunocompetence.

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Additional file 6 of 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
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Additional file 9 of 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
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Additional file 7 of 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
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Additional file 3 of 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
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Additional file 2 of 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
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Additional file 5 of 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
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Additional file 1 of 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
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Additional file 10 of 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
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Additional file 3 of Clinical application of targeted next-generation sequencing in severe pneumonia: a retrospective review
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Additional file 2 of Clinical application of targeted next-generation sequencing in severe pneumonia: a retrospective review
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Additional file 4 of Clinical application of targeted next-generation sequencing in severe pneumonia: a retrospective review
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Additional file 4 of 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
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Additional file 2 of Metagenomic sequencing reveals time, host, and body compartment-specific viral dynamics after lung transplantation
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Additional file 8 of 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
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Sreedhara, K., & Shah, P. (2026) · Current Heart Failure Reports · doi:10.1007/s11897-026-00784-7

Authors: De Vlaminck, I., Khush, K. K., Strehl, C., Kohli, B., Luikart, H., Neff, N. F., Okamoto, J., Snyder, T. M., Cornfield, D. N., Nicolls, M. R., Weill, D., Bernstein, D., Valantine, H. A., & Quake, S. R.
Affiliations: Stanford Medicine (US)
Howard Hughes Medical Institute (US)
Corresponding author: Quake, Stephen R.
ORCID: Khush, Kiran K.
Luikart, Helen
Neff, Norma F.
Snyder, Thomas M.
Cornfield, David N.
Nicolls, Mark R.
Bernstein, Daniel
Valantine, Hannah A.
Quake, Stephen R.
Venue: Cell
Publisher: Elsevier BV
Published: 2013-11
Volume: 155
Issue: 5
Pages: 1178-1187
ISSN: 0092-8674 (ISSN-L)
DOI: 10.1016/j.cell.2013.10.034
PMC: PMC4098717
OpenAlex: W2012991226
Cited by: 471
References: 43
Citations by year: 2026: 19 · 2025: 33 · 2024: 40 · 2023: 51 · 2022: 40 · 2021: 39 · 2020: 43 · 2019: 40 · 2018: 37 · 2017: 35 · 2016: 32 · 2015: 33 · 2014: 26 · 2013: 1
FWCI: 27.01
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 385 d)
Locations: Cell (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
Funders: Howard Hughes Medical Institute
National Institutes of Health (DP1OD000251, 5p01hl108797-10)
National Heart, Lung, and Blood Institute (R01HL070628, R01HL095686, P01-HL-108797, K23HL091143)
National Institute of Allergy and Infectious Diseases (RC4AI092673)
Topics: Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
Health Sciences › Medicine › Epidemiology › Cytomegalovirus and herpesvirus research
Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
Keywords: human virome, organ transplant recipients, immunosuppression, antiviral therapy, cell-free DNA, viral load, immunocompetence, immune system health
MeSH terms: Adult, Antiviral Agents, Blood, Child, DNA, Humans, Immunosuppressive Agents, Viruses, Heart Transplantation, Lung Transplantation, Antibiotic Prophylaxis

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Temporal Response of the Human Virome to Immunosuppression and Antiviral Therapy

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