101
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Hisano O, Ito T, Miura F. Short single-stranded DNAs with putative non-canonical structures comprise a new class of plasma cell-free DNA. BMC Biol 2021; 19:225. [PMID: 34649537 PMCID: PMC8518174 DOI: 10.1186/s12915-021-01160-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 09/28/2021] [Indexed: 01/08/2023] Open
Abstract
Background Cell-free DNA (cfDNA), which is extracellular DNA present in the circulating plasma and other body fluids, is currently investigated as a minimally invasive, highly informative biomarker. While nucleosome-sized cfDNA fragments have been investigated intensively, shorter DNA fragments in the plasma have not been studied due to several technical limitations. Results We aimed to investigate the existence of shorter cfDNA fragments in the blood. Using an improved cfDNA purification protocol and a 3′-end-labeling method, we found DNA fragments of approximately 50 nucleotides in length in the human plasma, present at a molar concentration comparable to that of nucleosome-sized fragments. Unfortunately, these short fragments cannot be recovered by widely used cfDNA isolation methods. In addition, they are composed of single-stranded DNA (ssDNA), thus escaping detection in previous studies. Therefore, we established a library-preparation protocol based on our unique ssDNA ligation technique and applied it to the isolated cfDNA. Deep sequencing of these libraries revealed that the short fragments are derived from hundreds of thousands of genomic sites in open chromatin regions and enriched with transcription factor-binding sites. Remarkably, antisense strands of putative G-quadruplex motifs occupy as much as one-third of the peaks by these short fragments. Conclusions We propose a new class of plasma cfDNA composed of short single-stranded fragments that potentially form non-canonical DNA structures. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01160-8.
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Affiliation(s)
- Osamu Hisano
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan.
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan.
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102
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Sloan PE, Rodriguez C, Holtz LR. Viral prevalence by gestational age and season in a large neonatal cord blood cohort. J Matern Fetal Neonatal Med 2021; 35:8482-8487. [PMID: 34587860 PMCID: PMC8960461 DOI: 10.1080/14767058.2021.1983537] [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: 10/20/2022]
Abstract
OBJECTIVE To investigate viral prevalence in a large neonatal cohort and determine the impact on pregnancy and birth outcomes. STUDY DESIGN We prospectively collected 1044 neonatal samples from remnant neonatal cord blood RPR samples. We performed qRT-PCR/qPCR reactions for: adenovirus, anellovirus (alphatorquevirus and betatorquevirus), cytomegalovirus (CMV), Epstein-Barr virus (EBV), enterovirus, human herpesvirus 6 (HHV6), parechovirus, and parvovirus B19. RESULT Overall viral prevalence was 5.6% with 58 positive samples. Alphatorquevirus (2%) and HHV6 (1.2%) were the two most prevalent viruses detected. Viral detection was most common in samples collected in the fall (September-November) and least common in those collected in winter (December-February). There was no statistical difference detected in viral prevalence or viral load by gestational age, preterm delivery, pre-eclampsia or chorioamnionitis. CONCLUSION While there is seasonal variation in viral prevalence in neonatal cord blood samples, individual virus presence does not seem to effect pregnancy or birth outcomes.
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Affiliation(s)
- Patrick E Sloan
- Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Cynthia Rodriguez
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Lori R Holtz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
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103
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Echeverria AP, Cohn IS, Danko DC, Shanaj S, Blair L, Hollemon D, Carli AV, Sculco PK, Ho C, Meshulam-Simon G, Mironenko C, Ivashkiv LB, Goodman SM, Grizas A, Westrich GH, Padgett DE, Figgie MP, Bostrom MP, Sculco TP, Hong DK, Hepinstall MS, Bauer TW, Blauwkamp TA, Brause BD, Miller AO, Henry MW, Ahmed AA, Cross MB, Mason CE, Donlin LT. Sequencing of Circulating Microbial Cell-Free DNA Can Identify Pathogens in Periprosthetic Joint Infections. J Bone Joint Surg Am 2021; 103:1705-1712. [PMID: 34293751 DOI: 10.2106/jbjs.20.02229] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND Over 1 million Americans undergo joint replacement each year, and approximately 1 in 75 will incur a periprosthetic joint infection. Effective treatment necessitates pathogen identification, yet standard-of-care cultures fail to detect organisms in 10% to 20% of cases and require invasive sampling. We hypothesized that cell-free DNA (cfDNA) fragments from microorganisms in a periprosthetic joint infection can be found in the bloodstream and utilized to accurately identify pathogens via next-generation sequencing. METHODS In this prospective observational study performed at a musculoskeletal specialty hospital in the U.S., we enrolled 53 adults with validated hip or knee periprosthetic joint infections. Participants had peripheral blood drawn immediately prior to surgical treatment. Microbial cfDNA from plasma was sequenced and aligned to a genome database with >1,000 microbial species. Intraoperative tissue and synovial fluid cultures were performed per the standard of care. The primary outcome was accuracy in organism identification with use of blood cfDNA sequencing, as measured by agreement with tissue-culture results. RESULTS Intraoperative and preoperative joint cultures identified an organism in 46 (87%) of 53 patients. Microbial cfDNA sequencing identified the joint pathogen in 35 cases, including 4 of 7 culture-negative cases (57%). Thus, as an adjunct to cultures, cfDNA sequencing increased pathogen detection from 87% to 94%. The median time to species identification for cases with genus-only culture results was 3 days less than standard-of-care methods. Circulating cfDNA sequencing in 14 cases detected additional microorganisms not grown in cultures. At postoperative encounters, cfDNA sequencing demonstrated no detection or reduced levels of the infectious pathogen. CONCLUSIONS Microbial cfDNA from pathogens causing local periprosthetic joint infections can be detected in peripheral blood. These circulating biomarkers can be sequenced from noninvasive venipuncture, providing a novel source for joint pathogen identification. Further development as an adjunct to tissue cultures holds promise to increase the number of cases with accurate pathogen identification and improve time-to-speciation. This test may also offer a novel method to monitor infection clearance during the treatment period. LEVEL OF EVIDENCE Diagnostic Level II. See Instructions for Authors for a complete description of levels of evidence.
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Affiliation(s)
| | - Ian S Cohn
- Hospital for Special Surgery Research Institute, New York, NY
| | - David C Danko
- Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine of Cornell University, New York, NY
| | - Sara Shanaj
- Hospital for Special Surgery Research Institute, New York, NY
| | | | | | - Alberto V Carli
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Peter K Sculco
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Carine Ho
- Karius, Inc., Redwood City, California
| | | | - Christine Mironenko
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, NY
| | - Lionel B Ivashkiv
- Hospital for Special Surgery Research Institute, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Susan M Goodman
- Department of Medicine, Weill Cornell Medical College, New York, NY.,Department of Rheumatology, Hospital for Special Surgery, New York, NY
| | - Alexandra Grizas
- Department of Pathology and Laboratory Medicine, Hospital for Special Surgery, New York, NY
| | - Geoffrey H Westrich
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Douglas E Padgett
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Mark P Figgie
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Mathias P Bostrom
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Thomas P Sculco
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | | | - Matthew S Hepinstall
- Department of Orthopedic Surgery, Lenox Hill Hospital, Northwell Health, New York, NY.,Department of Orthopedic Surgery, NYU Langone Health, New York, NY
| | - Thomas W Bauer
- Department of Medicine, Weill Cornell Medical College, New York, NY.,Department of Pathology and Laboratory Medicine, Hospital for Special Surgery, New York, NY
| | | | - Barry D Brause
- Department of Medicine, Weill Cornell Medical College, New York, NY.,Infectious Diseases, Department of Medicine, Hospital for Special Surgery, New York, NY
| | - Andy O Miller
- Department of Medicine, Weill Cornell Medical College, New York, NY.,Infectious Diseases, Department of Medicine, Hospital for Special Surgery, New York, NY
| | - Michael W Henry
- Department of Medicine, Weill Cornell Medical College, New York, NY.,Infectious Diseases, Department of Medicine, Hospital for Special Surgery, New York, NY
| | | | - Michael B Cross
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Christopher E Mason
- Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine of Cornell University, New York, NY.,Department of Physiology and Biophysics and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY.,The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY.,The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY
| | - Laura T Donlin
- Hospital for Special Surgery Research Institute, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY.,Department of Physiology and Biophysics and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY
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104
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Focosi D, Macera L, Spezia PG, Ceccarelli F, Lanza M, Maggi F. Molecular validation of pathogen-reduction technologies using rolling-circle amplification coupled with real-time PCR for torquetenovirus DNA quantification. Transfus Med 2021; 31:371-376. [PMID: 34390068 DOI: 10.1111/tme.12807] [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: 06/11/2021] [Accepted: 07/30/2021] [Indexed: 12/01/2022]
Abstract
BACKGROUND Pathogen reduction technologies (PRT) based on nucleic-acid damaging chemicals and/or irradiation are increasingly being used to increase safety of blood components against emerging pathogens, such as convalescent plasma in the ongoing COVID-19 pandemic. Current methods for PRT validation are limited by the resources available to the blood component manufacturer, and quality control rely over pathogen spiking and hence invariably require sacrifice of the tested blood units: quantitative real-time PCR is the current pathogen detection method but, due to the high likelihood of detecting nonviable fragments, requires downstream pathogen culture. We propose here a new molecular validation of PRT based on the highly prevalent human symbiont torquetenovirus (TTV) and rolling circle amplification (RCA). MATERIALS AND METHODS Serial apheresis plasma donations were tested for TTV before and after inactivation with Intercept® PRT using real-time quantitative PCR (conventional validation), RCA followed by real-time PCR (our validation), and reverse PCR (for cross-validation). RESULTS While only 20% of inactivated units showed significant decrease in TTV viral load using real-time qPCR, all donations tested with RCA followed by real-time PCR showed TTV reductions. As further validation, 2 units were additionally tested with reverse PCR, which confirmed absence of entire circular genomes. DISCUSSION We have described and validated a conservative and easy-to-setup protocol for molecular validation of PRT based on RCA and real-time PCR for TTV.
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Lisa Macera
- Department of Translational Research, University of Pisa, Pisa, Italy
| | | | | | - Maria Lanza
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Fabrizio Maggi
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
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105
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Méndez-Lagares G, Chin N, Chang WW, Lee J, Rosás-Umbert M, Kieu HT, Merriam D, Lu W, Kim S, Adamson L, Brander C, Luciw PA, Barry PA, Hartigan-O’Connor DJ. Cytomegalovirus mediates expansion of IL-15-responsive innate-memory cells with SIV killing function. J Clin Invest 2021; 131:148542. [PMID: 34153005 PMCID: PMC8321572 DOI: 10.1172/jci148542] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/03/2021] [Indexed: 12/13/2022] Open
Abstract
Interindividual immune variability is driven predominantly by environmental factors, including exposure to chronic infectious agents such as cytomegalovirus (CMV). We investigated the effects of rhesus CMV (RhCMV) on composition and function of the immune system in young macaques. Within months of infection, RhCMV was associated with impressive changes in antigen presenting cells, T cells, and NK cells-and marked expansion of innate-memory CD8+ T cells. These cells express high levels of NKG2A/C and the IL-2 and IL-15 receptor beta chain, CD122. IL-15 was sufficient to drive differentiation of the cells in vitro and in vivo. Expanded NKG2A/C+CD122+CD8+ T cells in RhCMV-infected macaques, but not their NKG2-negative counterparts, were endowed with cytotoxicity against class I-deficient K562 targets and prompt IFN-γ production in response to stimulation with IL-12 and IL-18. Because RhCMV clone 68-1 forms the viral backbone of RhCMV-vectored SIV vaccines, we also investigated immune changes following administration of RhCMV 68-1-vectored SIV vaccines. These vaccines led to impressive expansion of NKG2A/C+CD8+ T cells with capacity to inhibit SIV replication ex vivo. Thus, CMV infection and CMV-vectored vaccination drive expansion of functional innate-like CD8 cells via host IL-15 production, suggesting that innate-memory expansion could be achieved by other vaccine platforms expressing IL-15.
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Affiliation(s)
- Gema Méndez-Lagares
- California National Primate Research Center
- Department of Medical Microbiology and Immunology
| | - Ning Chin
- California National Primate Research Center
- Department of Medical Microbiology and Immunology
| | - W.L. William Chang
- California National Primate Research Center
- Department of Medical Microbiology and Immunology
| | - Jaewon Lee
- Graduate Group in Immunology, and
- Center for Immunology and Infectious Diseases, University of California Davis, Davis, California, USA
| | | | - Hung T. Kieu
- California National Primate Research Center
- Department of Medical Microbiology and Immunology
| | - David Merriam
- California National Primate Research Center
- Department of Medical Microbiology and Immunology
| | - Wenze Lu
- California National Primate Research Center
- Department of Medical Microbiology and Immunology
| | - Sungjin Kim
- Department of Medical Microbiology and Immunology
- Center for Immunology and Infectious Diseases, University of California Davis, Davis, California, USA
| | - Lourdes Adamson
- Center for Immunology and Infectious Diseases, University of California Davis, Davis, California, USA
| | - Christian Brander
- IrsiCaixa - AIDS Research Institute, Badalona, Barcelona, Spain
- Universitat de Vic-Universitat Central de Catalunya (UVic-UCC), Vic, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Paul A. Luciw
- California National Primate Research Center
- Center for Immunology and Infectious Diseases, University of California Davis, Davis, California, USA
- Department of Pathology and Laboratory Medicine, University of California, Davis, California, USA
| | - Peter A. Barry
- California National Primate Research Center
- Center for Immunology and Infectious Diseases, University of California Davis, Davis, California, USA
- Department of Pathology and Laboratory Medicine, University of California, Davis, California, USA
| | - Dennis J. Hartigan-O’Connor
- California National Primate Research Center
- Department of Medical Microbiology and Immunology
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, California, USA
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106
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McGinniss JE, Whiteside SA, Simon-Soro A, Diamond JM, Christie JD, Bushman FD, Collman RG. The lung microbiome in lung transplantation. J Heart Lung Transplant 2021; 40:733-744. [PMID: 34120840 PMCID: PMC8335643 DOI: 10.1016/j.healun.2021.04.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/13/2021] [Accepted: 04/19/2021] [Indexed: 12/21/2022] Open
Abstract
Culture-independent study of the lower respiratory tract after lung transplantation has enabled an understanding of the microbiome - that is, the collection of bacteria, fungi, and viruses, and their respective gene complement - in this niche. The lung has unique features as a microbial environment, with balanced entry from the upper respiratory tract, clearance, and local replication. There are many pressures impacting the microbiome after transplantation, including donor allograft factors, recipient host factors such as underlying disease and ongoing exposure to the microbe-rich upper respiratory tract, and transplantation-related immunosuppression, antimicrobials, and postsurgical changes. To date, we understand that the lung microbiome after transplant is dysbiotic; that is, it has higher biomass and altered composition compared to a healthy lung. Emerging data suggest that specific microbiome features may be linked to host responses, both immune and non-immune, and clinical outcomes such as chronic lung allograft dysfunction (CLAD), but many questions remain. The goal of this review is to put into context our burgeoning understanding of the lung microbiome in the postlung transplant patient, the interactions between microbiome and host, the role the microbiome may play in post-transplant complications, and critical outstanding research questions.
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Affiliation(s)
- John E McGinniss
- Division of Pulmonary, Allergy and Critical Care Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Samantha A Whiteside
- Division of Pulmonary, Allergy and Critical Care Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Aurea Simon-Soro
- Department of Orthodontics and Divisions of Community Oral Health and Pediatric Dentistry, School of Dental Medicine at the University of Pennsylvania
| | - Joshua M Diamond
- Division of Pulmonary, Allergy and Critical Care Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jason D Christie
- Division of Pulmonary, Allergy and Critical Care Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania; Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Fredrick D Bushman
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ronald G Collman
- Division of Pulmonary, Allergy and Critical Care Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania; Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
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107
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Arze CA, Springer S, Dudas G, Patel S, Bhattacharyya A, Swaminathan H, Brugnara C, Delagrave S, Ong T, Kahvejian A, Echelard Y, Weinstein EG, Hajjar RJ, Andersen KG, Yozwiak NL. Global genome analysis reveals a vast and dynamic anellovirus landscape within the human virome. Cell Host Microbe 2021; 29:1305-1315.e6. [PMID: 34320399 DOI: 10.1016/j.chom.2021.07.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/23/2021] [Accepted: 06/11/2021] [Indexed: 12/14/2022]
Abstract
Anelloviruses are a ubiquitous component of healthy human viromes and remain highly prevalent after being acquired early in life. The full extent of "anellome" diversity and its evolutionary dynamics remain unexplored. We employed in-depth sequencing of blood-transfusion donor(s)-recipient pairs coupled with public genomic resources for a large-scale assembly of anellovirus genomes and used the data to characterize global and personal anellovirus diversity through time. The breadth of the anellome is much greater than previously appreciated, and individuals harbor unique anellomes and transmit lineages that can persist for several months within a diverse milieu of endemic host lineages. Anellovirus sequence diversity is shaped by extensive recombination at all levels of divergence, hindering traditional phylogenetic analyses. Our findings illuminate the transmission dynamics and vast diversity of anelloviruses and set the foundation for future studies to characterize their biology.
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Affiliation(s)
| | | | - Gytis Dudas
- Gothenburg Global Biodiversity Centre, Gothenburg 413 19, Sweden
| | | | | | | | - Carlo Brugnara
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Tuyen Ong
- Ring Therapeutics, Cambridge, MA 02139, USA
| | - Avak Kahvejian
- Ring Therapeutics, Cambridge, MA 02139, USA; Flagship Pioneering, Cambridge, MA 02142, USA
| | - Yann Echelard
- Ring Therapeutics, Cambridge, MA 02139, USA; Flagship Pioneering, Cambridge, MA 02142, USA
| | - Erica G Weinstein
- Ring Therapeutics, Cambridge, MA 02139, USA; Flagship Pioneering, Cambridge, MA 02142, USA
| | - Roger J Hajjar
- Ring Therapeutics, Cambridge, MA 02139, USA; Flagship Pioneering, Cambridge, MA 02142, USA
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108
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Roy M, Kim JY, Lin RC. Rapid Diagnosis of Invasive Aspergillosis and Active Hepatitis-B Virus Co-Infection in a HIV-1 Infected Patient Using Cell Free DNA Sequencing. J Int Assoc Provid AIDS Care 2021; 19:2325958220976263. [PMID: 33251919 PMCID: PMC7705773 DOI: 10.1177/2325958220976263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Multiple simultaneous opportunistic infections in Human Immunodeficiency virus-1/Acquired
immunodeficiency syndrome (HIV-1/AIDS) is a known and dreaded occurrence that often leads
to poor outcomes. We present a case of disseminated aspergillosis and active Hepatitis-B
virus (HBV) infection in such a host, where cell free DNA (cfDNA) next generation
sequencing (NGS) of plasma was used to expedite diagnosis. Bronchoscopy was avoided and
treatment was started expeditiously. In this case report we discuss the interpretation of
the cfDNA NGS, and its potential role for early diagnosis and avoidance of invasive
testing.
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Affiliation(s)
- Moni Roy
- Department of Internal Medicine, 17120University of Illinois College of Medicine, Peoria, IL, USA.,OSF Saint Francis Medical Center, Peoria, IL, USA
| | - Joseph Y Kim
- Department of Internal Medicine, 17120University of Illinois College of Medicine, Peoria, IL, USA
| | - Rone-Chun Lin
- Department of Internal Medicine, 17120University of Illinois College of Medicine, Peoria, IL, USA
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109
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Dodi G, Attanasi M, Di Filippo P, Di Pillo S, Chiarelli F. Virome in the Lungs: The Role of Anelloviruses in Childhood Respiratory Diseases. Microorganisms 2021; 9:microorganisms9071357. [PMID: 34201449 PMCID: PMC8307813 DOI: 10.3390/microorganisms9071357] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 12/24/2022] Open
Abstract
More recently, increasing attention has been directed to exploring the function of the global virome in health and disease. Currently, by new molecular techniques, such as metagenomic DNA sequencing, the virome has been better unveiled. By investigating the human lung virome, we could provide novel insights into respiratory diseases. The virome, as a part of the microbiome, is characterized by a constant change in composition related to the type of diet, environment, and our genetic code, and other incalculable factors. The virome plays a substantial role in modulating human immune defenses and contributing to the inflammatory processes. Anelloviruses (AVs) are new components of the virome. AVs are already present during early life and reproduce without apparently causing harm to the host. The role of AVs is still unknown, but several reports have shown that AVs could activate the inflammasomes, intracellular multiprotein oligomers of the innate immune system, which show a crucial role in the host defense to several pathogens. In this narrative revision, we summarize the epidemiological data related to the possible link between microbial alterations and chronic respiratory diseases in children. Briefly, we also describe the characteristics of the most frequent viral family present in the lung virome, Anelloviridae. Furthermore, we discuss how AVs could modulate the immune system in children, affecting the development of chronic respiratory diseases, particularly asthma, the most common chronic inflammatory disease in childhood.
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110
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Liu Y, Wang H, Yang J, Zeng J, Sun GM. Virome of respiratory secretion from children with unknown etiological acute respiratory disease revealed recombinant human parechovirus and other significant viruses. Virol J 2021; 18:122. [PMID: 34108000 PMCID: PMC8188738 DOI: 10.1186/s12985-021-01586-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
Using viral metagenomics, viral nucleic acid in 30 respiratory secretion samples collected from children with unknown etiological acute respiratory disease were investigated. Sequences showing similarity to human parainfluenza virus 1, anellovirus, bocavirus, coxsackievirus A4, human parechovirus (HPeV), and alphaflexivirus were recovered from these samples. Complete genomes of one anellovirus, one coxsackievirus A4, three parechoviruses were determined from these libraries. The anellovirus (MW267851) phylogenetically clustered with an unpublished anellovirus (MK212032) from respiratory sample of a Vietnamese patient, forming a separate branch neighboring to strains within the genus Betatorquevirus. The genome of coxsackievirus A4 (MW267852) shares the highest sequence identity of 96.4% to a coxsackievirus A4 (MN964079) which was identified in clinical samples from children with Hand, Foot, and Mouth Disease (HFMD). Two (MW267853 and MW267854) of the three parechoviruses belong to HPeV-1 and the other one (MW267855) belongs to HPeV-6. Recombination analysis indicated that an HPeV-1 (MW267854) identified in this study is a putative recombinant occurred between HPeV-1 and HPeV-3. Whether these viruses have association with specific respiratory disease calls for further investigation.
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Affiliation(s)
- Ying Liu
- Department of Clinical Laboratory, Xuzhou Central Hospital, 199 Jiefangnan Road, Xuzhou, 221009, Jiangsu, China
| | - Hao Wang
- Department of Clinical Laboratory, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, 223002, Jiangsu, China
| | - Jie Yang
- School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jian Zeng
- School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Guang-Ming Sun
- Department of Clinical Laboratory, Xuzhou Central Hospital, 199 Jiefangnan Road, Xuzhou, 221009, Jiangsu, China.
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111
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Bueno F, Albert E, Piñana JL, Pérez A, Úbeda C, Gómez MD, Hernández-Boluda JC, Gonzalez-Barberá EM, Montoro J, Giménez E, Guerreiro M, Balaguer-Roselló A, Hernani R, Sanz J, Solano C, Navarro D. Kinetics of Torque Teno virus DNA in stools may predict occurrence of acute intestinal graft versus host disease early after allogeneic hematopoietic stem cell transplantation. Transpl Infect Dis 2021; 23:e13507. [PMID: 33176050 DOI: 10.1111/tid.13507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/09/2020] [Accepted: 10/25/2020] [Indexed: 01/15/2023]
Abstract
Torque Teno virus (TTV) DNA load in blood may act as a marker of immune competence after allogeneic hematopoietic stem cell transplant recipients (allo-HSCT). Conflicting data have been reported as to the value of this biomarker for anticipating acute Graft versus host disease (aGvHD) occurrence. Here, we hypothesized that quantitation of TTV DNA load in stool specimens early after allo-HSCT could be used to identify patients at high risk of acute intestinal graft versus host disease (aIGvHD). In this prospective two-center study, we recruited a total of 83 nonconsecutive adult patients undergoing allo-HSCT. The study period comprised the first 120 days after allo-HSCT. TTV DNA was quantitated in paired stool samples collected at a median of 2 days prior to cell infusion and at a median of 14 days after allo-HSCT by real-time PCR. Thirty-seven patients developed aGVHD, of whom 25 had aIGVHD (diagnosed at a median of 42 days after allo-HSCT). Median TTV DNA load values in posttransplant stools specimens were comparable (P = .34) in patients with or without subsequent aIGvHD; nevertheless, a falling trajectory (decrease in TTV DNA load >0.5 log10 copies/0.1 g) in paired pretransplant and posttransplant specimens was independently associated with the occurrence of aIGvHD (OR, 5.2; 95% CI, 1.3-21.3; P = .02). Notably, displaying a rising trajectory had a negative predictive value of 87.5% for aIGvHD. In summary, in this hypothesis-generating study, we suggest that the decrease in TTV DNA load from baseline in stool specimens may identify patients at risk of aIGVHD.
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Affiliation(s)
- Felipe Bueno
- Microbiology Service, Hospital Clínico Universitario, Institute for Research INCLIVA, Valencia, Spain
| | - Eliseo Albert
- Microbiology Service, Hospital Clínico Universitario, Institute for Research INCLIVA, Valencia, Spain
| | - José Luis Piñana
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Ariadna Pérez
- Hematology Service, Hospital Clínico Universitario, Institute for Research INCLIVA Valencia, Spain
| | - Carlos Úbeda
- Centro Superior de Investigacion en Salud Publica - FISABIO, Valencia, Spain
| | - María Dolores Gómez
- Microbiology Service, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | | | | | - Juan Montoro
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Estela Giménez
- Microbiology Service, Hospital Clínico Universitario, Institute for Research INCLIVA, Valencia, Spain
| | - Manuel Guerreiro
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | | | - Rafael Hernani
- Hematology Service, Hospital Clínico Universitario, Institute for Research INCLIVA Valencia, Spain
| | - Jaime Sanz
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Carlos Solano
- Hematology Service, Hospital Clínico Universitario, Institute for Research INCLIVA Valencia, Spain
- Department of Medicine, School of Medicine, University of Valencia, Valencia, Spain
| | - David Navarro
- Microbiology Service, Hospital Clínico Universitario, Institute for Research INCLIVA, Valencia, Spain
- Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain
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112
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Pyöriä L, Valtonen M, Luoto R, Grönroos W, Waris M, Heinonen OJ, Ruuskanen O, Perdomo MF. Survey of Viral Reactivations in Elite Athletes: A Case-Control Study. Pathogens 2021; 10:666. [PMID: 34071724 PMCID: PMC8229584 DOI: 10.3390/pathogens10060666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/18/2021] [Accepted: 05/26/2021] [Indexed: 12/11/2022] Open
Abstract
Exercise-induced immune perturbations have been proposed to increase susceptibility to viral infections. We investigated the replication of persisting viruses as indicators of immune function in elite cross-country skiers after ten months of sustained high-performance exercise. The viruses evaluated, nine human herpesviruses (HHVs) and torque teno virus (TTV), are typically restrained in health but replicate actively in immunosuppressed individuals. We collected sera from 27 Finnish elite cross-country skiers at the end of the competition's season and 27 matched controls who perform moderate exercise. We quantified all the HHVs and-TTV via highly sensitive qPCRs. To verify equal past exposures between the groups, we assessed the IgG antibody prevalences toward HHV-4 (Epstein-Barr virus, EBV) and HHV-5 (human cytomegalovirus, HCMV). We found equal TTV DNA prevalences in athletes (63%) and controls (63%) and loads with respective geometric means of 1.7 × 103 and 1.2 × 103 copies/mL of serum. Overall, the copy numbers were low and consistent with those of healthy individuals. Neither of the groups presented with herpesvirus viremia despite similar past exposures to HHVs (seroprevalences of EBV 70% vs. 78% and HCMV 52% vs. 44% in athletes and controls, respectively). We found no evidence of increased replication of persistent viruses in elite athletes, arguing against impaired viral immunity due to high-performance exercise.
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Affiliation(s)
- Lari Pyöriä
- Department of Virology, University of Helsinki, 00290 Helsinki, Finland;
| | - Maarit Valtonen
- Research Institute for Olympics Sports, 40700 Jyväskylä, Finland;
| | - Raakel Luoto
- Department of Pediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, 20521 Turku, Finland; (R.L.); (O.R.)
| | - Wilma Grönroos
- Paavo Nurmi Centre and Unit of Health and Physical Activity, University of Turku, 20520 Turku, Finland; (W.G.); (O.J.H.)
| | - Matti Waris
- Institute of Biomedicine, University of Turku and Department of Clinical Microbiology, Turku University Hospital, 20520 Turku, Finland;
| | - Olli J. Heinonen
- Paavo Nurmi Centre and Unit of Health and Physical Activity, University of Turku, 20520 Turku, Finland; (W.G.); (O.J.H.)
| | - Olli Ruuskanen
- Department of Pediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, 20521 Turku, Finland; (R.L.); (O.R.)
| | - Maria F. Perdomo
- Department of Virology, University of Helsinki, 00290 Helsinki, Finland;
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113
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van Rijn AL, Wunderink HF, Sidorov IA, de Brouwer CS, Kroes AC, Putter H, de Vries AP, Rotmans JI, Feltkamp MC. Torque teno virus loads after kidney transplantation predict allograft rejection but not viral infection. J Clin Virol 2021; 140:104871. [PMID: 34089977 DOI: 10.1016/j.jcv.2021.104871] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/16/2021] [Accepted: 05/18/2021] [Indexed: 12/15/2022]
Abstract
The main challenge of immunosuppressive therapy after solid organ transplantation is to create a new immunological balance that prevents organ rejection and does not promote opportunistic infection. Torque teno virus (TTV), a ubiquitous and non-pathogenic single-stranded DNA virus, has been proposed as a marker of functional immunity in immunocompromised patients. Here we investigate whether TTV loads predict the risk of common viral infection and allograft rejection in kidney transplantation recipients. In a retrospective cohort of 389 kidney transplantation recipients, individual TTV loads in were measured by qPCR in consecutive plasma samples during one year follow-up. The endpoints were allograft rejection, BK polyomavirus (BKPyV) viremia and cytomegalovirus (CMV) viremia. Repeated TTV measurements and rejection and infection survival data were analysed in a joint model. During follow-up, TTV DNA detection in the transplant recipients increased from 85 to 100%. The median viral load increased to 107 genome copies/ml within three months after transplantation. Rejection, BKPyV viremia and CMV viremia occurred in 23%, 27% and 17% of the patients, respectively. With every 10-fold TTV load-increase, the risk of rejection decreased considerably (HR: 0.74, CI 95%: 0.71-0.76), while the risk of BKPyV and CMV viremia remained the same (HR: 1.03, CI 95%: 1.03-1.04 and HR: 1.01, CI 95%: 1.01-1.01). In conclusion, TTV load kinetics predict allograft rejection in kidney transplantation recipients, but not the BKPyV and CMV infection. The potential use of TTV load levels as a guide for optimal immunosuppressive drug dosage to prevent allograft rejection deserves further validation.
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Affiliation(s)
- Aline L van Rijn
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Herman F Wunderink
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Igor A Sidorov
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Caroline S de Brouwer
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Aloysius Cm Kroes
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Hein Putter
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Aiko Pj de Vries
- Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Joris I Rotmans
- Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Mariet Cw Feltkamp
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
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114
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Sudhakar P, Verstockt B, Cremer J, Verstockt S, Sabino J, Ferrante M, Vermeire S. Understanding the Molecular Drivers of Disease Heterogeneity in Crohn's Disease Using Multi-omic Data Integration and Network Analysis. Inflamm Bowel Dis 2021; 27:870-886. [PMID: 33313682 PMCID: PMC8128416 DOI: 10.1093/ibd/izaa281] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Indexed: 12/12/2022]
Abstract
Crohn's disease (CD), a form of inflammatory bowel disease (IBD), is characterized by heterogeneity along multiple clinical axes, which in turn impacts disease progression and treatment modalities. Using advanced data integration approaches and systems biology tools, we studied the contribution of CD susceptibility variants and gene expression in distinct peripheral immune cell subsets (CD14+ monocytes and CD4+ T cells) to relevant clinical traits. Our analyses revealed that most clinical traits capturing CD heterogeneity could be associated with CD14+ and CD4+ gene expression rather than disease susceptibility variants. By disentangling the sources of variation, we identified molecular features that could potentially be driving the heterogeneity of various clinical traits of CD patients. Further downstream analyses identified contextual hub proteins such as genes encoding barrier functions, antimicrobial peptides, chemokines, and their receptors, which are either targeted by drugs used in CD or other inflammatory diseases or are relevant to the biological functions implicated in disease pathology. These hubs could be used as cell type-specific targets to treat specific subtypes of CD patients in a more individualized approach based on the underlying biology driving their disease subtypes. Our study highlights the importance of data integration and systems approaches to investigate complex and heterogeneous diseases such as IBD.
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Affiliation(s)
- Padhmanand Sudhakar
- Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID)
| | - Bram Verstockt
- Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID)
- University Hospitals Leuven, Department of Gastroenterology and Hepatology
| | - Jonathan Cremer
- Department of Microbiology and Immunology, Laboratory of Clinical Immunology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Sare Verstockt
- Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID)
| | - João Sabino
- Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID)
- University Hospitals Leuven, Department of Gastroenterology and Hepatology
| | - Marc Ferrante
- Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID)
- University Hospitals Leuven, Department of Gastroenterology and Hepatology
| | - Séverine Vermeire
- Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID)
- University Hospitals Leuven, Department of Gastroenterology and Hepatology
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115
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Lapa D, Del Porto P, Minosse C, D’Offizi G, Antinori A, Capobianchi MR, Visco-Comandini U, McPhee F, Garbuglia AR, Zaccarelli M. Clinical Relevance of Torque Teno Virus (TTV) in HIV/HCV Coinfected and HCV Monoinfected Patients Treated with Direct-Acting Antiviral Therapy. J Clin Med 2021; 10:jcm10102092. [PMID: 34068071 PMCID: PMC8152458 DOI: 10.3390/jcm10102092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/02/2021] [Accepted: 05/06/2021] [Indexed: 02/07/2023] Open
Abstract
Torque Teno virus (TTV) is a ubiquitous virus that causes chronic infection in humans with unknown clinical consequences. Here, we investigated the influence of TTV infection on HCV direct-acting antiviral (DAA) efficacy in HIV/HCV coinfected and HCV monoinfected patients as controls. Of 92 study patients, 79.3% were TTV DNA positive; untreated patients exhibited a significantly higher proportion of TTV DNA-positivity vs. sustained virological response (SVR) patients (100.0% vs. 65.2%, p < 0.001), while TTV positivity was not significant in DAA failure patients vs. SVR patients despite HIV/HCV coinfection. TTV DNA viral load was higher among HCV monoinfected patients vs. HIV/HCV coinfected, although marginally significant (p = 0.074) and no significant viral load difference was detected between DAA failures and SVR patients, while untreated vs. SVR patients had a significantly higher viral load (19,884, IQR 5977–333,534, vs. 469, IQR 10–4124, p = 0.004). Alpha-genogroup 3 TTV was the most prevalent genetic group, and no specific strain or genogroup was observed in relapser patients. Among HIV/HCV patients with HCV RNA detectable at end of treatment (EOT), TTV DNA was detected in 9/17 treatment responder patients and 3/5 relapser patients, thus, TTV infection does not appear to influence the control HCV viremia after EOT. Levels of IL-6 IL-4, and CD14 were not significantly different between TTV PCR-positive and -negative patients. These results suggest no association between TTV DNA positivity or viral load and HCV DAA failure whether patients were HIV/HCV coinfected or HCV monoinfected.
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Affiliation(s)
- Daniele Lapa
- Laboratory of Virology, “Lazzaro Spallanzani” National Institute for Infectious Diseases, IRCCS, 00149 Rome, Italy; (D.L.); (C.M.); (M.R.C.)
| | - Paola Del Porto
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University, 00185 Rome, Italy;
| | - Claudia Minosse
- Laboratory of Virology, “Lazzaro Spallanzani” National Institute for Infectious Diseases, IRCCS, 00149 Rome, Italy; (D.L.); (C.M.); (M.R.C.)
| | - Gianpiero D’Offizi
- Hepatology and Infectious Diseases Unit, “Lazzaro Spallanzani” National Institute for Infectious Diseases IRCCS, 00149 Rome, Italy; (G.D.); (U.V.-C.)
| | - Andrea Antinori
- Clinical Department, “Lazzaro Spallanzani ” National Institute for Infectious Diseases, IRCCS, 00149 Rome, Italy; (A.A.); (M.Z.)
| | - Maria Rosaria Capobianchi
- Laboratory of Virology, “Lazzaro Spallanzani” National Institute for Infectious Diseases, IRCCS, 00149 Rome, Italy; (D.L.); (C.M.); (M.R.C.)
| | - Ubaldo Visco-Comandini
- Hepatology and Infectious Diseases Unit, “Lazzaro Spallanzani” National Institute for Infectious Diseases IRCCS, 00149 Rome, Italy; (G.D.); (U.V.-C.)
| | | | - Anna Rosa Garbuglia
- Laboratory of Virology, “Lazzaro Spallanzani” National Institute for Infectious Diseases, IRCCS, 00149 Rome, Italy; (D.L.); (C.M.); (M.R.C.)
- Correspondence: ; Tel.: +39-06-5517-0692; Fax: +39-06-559-455
| | - Mauro Zaccarelli
- Clinical Department, “Lazzaro Spallanzani ” National Institute for Infectious Diseases, IRCCS, 00149 Rome, Italy; (A.A.); (M.Z.)
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116
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Abstract
Altered gut virome and expanded abundance of certain viruses were found in HIV-1-infected individuals. It remains largely unknown how plasma virus composition changes during HIV-1 infection and antiretroviral therapy (ART). We performed viral metagenomic analysis on viral particles enriched from human plasma from 101 men who have sex with men (MSM) with or without HIV-1 infection and whether or not on ART and compared the differences in the plasma virome. An increased plasma viral abundance of main eukaryotic viruses was observed during HIV-1 infection in MSM, especially in AIDS patients (CD4+ T cell counts of <200). Anellovirus, pegivirus and hepatitis B virus (HBV) were the most abundant blood-borne viruses detected among MSM and HIV-1-infected individuals, and anellovirus and pegivirus were closely related to HIV-1 infection. High diversity of anelloviruses was found mostly in HIV-1-infected MSM, and their abundance was positively correlated with the HIV-1 viral load, but negatively correlated with both CD4+ T cell counts and CD4+/CD8+ ratio; in contrast, the abundance of pegivirus showed opposite correlations. ART usage could restore the plasma virome toward that of HIV-1-negative individuals. These data showed an expansion in abundance of certain viruses during HIV-1 infection, indicating the higher risk of shedding some blood-borne viruses in these individuals. These investigations indicate that both anellovirus and pegivirus may play certain roles in HIV disease progression.IMPORTANCE Though an increasing number of studies have indicated the existence of an interaction between the virome and human health or disease, the specific role of these plasma viral components remains largely unsolved. We provide evidence here that an altered plasma virome profile is associated with different immune status of HIV-1 infection. Specific resident viruses, such as anellovirus and pegivirus, may directly or indirectly participate in the disease progression of HIV-1 infection. These results can help to determine their clinical relevance and design potential therapies.
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117
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A prevalent and culturable microbiota links ecological balance to clinical stability of the human lung after transplantation. Nat Commun 2021; 12:2126. [PMID: 33837203 PMCID: PMC8035266 DOI: 10.1038/s41467-021-22344-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 03/11/2021] [Indexed: 12/12/2022] Open
Abstract
There is accumulating evidence that the lower airway microbiota impacts lung health. However, the link between microbial community composition and lung homeostasis remains elusive. We combine amplicon sequencing and bacterial culturing to characterize the viable bacterial community in 234 longitudinal bronchoalveolar lavage samples from 64 lung transplant recipients and establish links to viral loads, host gene expression, lung function, and transplant health. We find that the lung microbiota post-transplant can be categorized into four distinct compositional states, 'pneumotypes'. The predominant 'balanced' pneumotype is characterized by a diverse bacterial community with moderate viral loads, and host gene expression profiles suggesting immune tolerance. The other three pneumotypes are characterized by being either microbiota-depleted, or dominated by potential pathogens, and are linked to increased immune activity, lower respiratory function, and increased risks of infection and rejection. Collectively, our findings establish a link between the lung microbial ecosystem, human lung function, and clinical stability post-transplant.
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118
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Okumura T, Horiba K, Kamei H, Takeuchi S, Suzuki T, Torii Y, Kawada JI, Takahashi Y, Ogura Y, Ogi T, Ito Y. Temporal dynamics of the plasma microbiome in recipients at early post-liver transplantation: a retrospective study. BMC Microbiol 2021; 21:104. [PMID: 33823791 PMCID: PMC8025517 DOI: 10.1186/s12866-021-02154-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 03/16/2021] [Indexed: 01/07/2023] Open
Abstract
Background Immunosuppression during liver transplantation (LT) enables the prevention and treatment of organ rejection but poses a risk for severe infectious diseases. Immune modulation and antimicrobials affect the plasma microbiome. Thus, determining the impact of immunosuppression on the microbiome may be important to understand immunocompetence, elucidate the source of infection, and predict the risk of infection in LT recipients. We characterized the plasma microbiome of LT recipients at early post-LT and assessed the association between the microbiome and clinical events. Results In this study, 51 patients who received LT at Nagoya University Hospital from 2016 to 2018 were enrolled. Plasma samples were retrospectively collected at the following time points: 1) within a week after LT; 2) 4 ± 1 weeks after LT; 3) 8 ± 1 weeks after LT; and 4) within 2 days after a positive blood culture. A total of 111 plasma samples were analyzed using shotgun next-generation sequencing (NGS) with the PATHDET pipeline. Relative abundance of Anelloviridae, Nocardiaceae, Microbacteriaceae, and Enterobacteriaceae significantly changed during the postoperative period. Microbiome diversity was higher within a week after LT than that at 8 weeks after LT. Antimicrobials were significantly associated with the microbiome of LT recipients. In addition, the proportion of Enterobacteriaceae was significantly increased and the plasma microbiome diversity was significantly lower in patients with acute cellular rejection (ACR) than non-ACR patients. Sequencing reads of bacteria isolated from blood cultures were predominantly identified by NGS in 8 of 16 samples, and human herpesvirus 6 was detected as a causative pathogen in one recipient with severe clinical condition. Conclusions The metagenomic NGS technique has great potential in revealing the plasma microbiome and is useful as a comprehensive diagnostic procedure in clinical settings. Temporal dynamics of specific microorganisms may be used as indirect markers for the determination of immunocompetence and ACR in LT recipients. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02154-w.
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Affiliation(s)
- Toshihiko Okumura
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Kazuhiro Horiba
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.,Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan.,Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hideya Kamei
- Department of Transplantation Surgery, Nagoya University Hospital, Nagoya, Japan
| | - Suguru Takeuchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yasuhiro Ogura
- Department of Transplantation Surgery, Nagoya University Hospital, Nagoya, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan.,Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
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119
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Erdem G, Kaptsan I, Sharma H, Kumar A, Aylward SC, Kapoor A, Shimamura M. Cerebrospinal Fluid Analysis for Viruses by Metagenomic Next-Generation Sequencing in Pediatric Encephalitis: Not Yet Ready for Prime Time? J Child Neurol 2021; 36:350-356. [PMID: 33206020 DOI: 10.1177/0883073820972232] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Metagenomic next-generation sequencing offers an unbiased approach to identifying viral pathogens in cerebrospinal fluid of patients with meningoencephalitis of unknown etiology. METHODS In an 11-month case series, we investigated the use of cerebrospinal fluid metagenomic next-generation sequencing to diagnose viral infections among pediatric hospitalized patients presenting with encephalitis or meningoencephalitis of unknown etiology. Cerebrospinal fluid from patients with known enterovirus meningitis were included as positive controls. Cerebrospinal fluid from patients with primary intracranial hypertension were included to serve as controls without known infections. RESULTS Cerebrospinal fluid metagenomic next-generation sequencing was performed for 37 patients. Among 27 patients with encephalitis or meningoencephalitis, 4 were later diagnosed with viral encephalitis, 6 had non-central nervous system infections with central nervous system manifestations, 6 had no positive diagnostic tests, and 11 were found to have a noninfectious diagnosis. Metagenomic next-generation sequencing identified West Nile virus (WNV) in the cerebrospinal fluid of 1 immunocompromised patient. Among the 4 patients with known enterovirus meningitis, metagenomic next-generation sequencing correctly identified enteroviruses and characterized the viral genotype. No viral sequences were detected in the cerebrospinal fluid of patients with primary intracranial hypertension. Metagenomic next-generation sequencing also identified sequences of nonpathogenic torque Teno virus in cerebrospinal fluid specimens from 13 patients. CONCLUSIONS Our results showed viral detection by cerebrospinal fluid metagenomic next-generation sequencing only in 1 immunocompromised patient and did not offer a diagnostic advantage over conventional testing. Viral phylogenetic characterization by metagenomic next-generation sequencing could be used in epidemiologic investigations of some viral pathogens, such as enteroviruses. The finding of torque Teno viruses in cerebrospinal fluid by metagenomic next-generation sequencing is of unknown significance but may merit further exploration for a possible association with noninfectious central nervous system disorders.
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Affiliation(s)
- Guliz Erdem
- Division of Infectious Diseases, Department of Pediatrics, 2650Nationwide Children's Hospital and The Ohio State University, Columbus, OH, USA
| | - Irina Kaptsan
- Center for Vaccines and Immunity, the Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Himanshu Sharma
- Center for Vaccines and Immunity, the Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Arvind Kumar
- Center for Vaccines and Immunity, the Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Shawn C Aylward
- Division of Neurology, Department of Pediatrics, 2650Nationwide Children's Hospital and The Ohio State University, Columbus, OH, USA
| | - Amit Kapoor
- Center for Vaccines and Immunity, the Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Masako Shimamura
- Division of Infectious Diseases, Department of Pediatrics, 2650Nationwide Children's Hospital and The Ohio State University, Columbus, OH, USA.,Center for Vaccines and Immunity, the Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
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120
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Deng MC. The evolution of patient-specific precision biomarkers to guide personalized heart-transplant care. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2021; 6:51-63. [PMID: 33768160 DOI: 10.1080/23808993.2021.1840273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Introduction In parallel to the clinical maturation of heart transplantation over the last 50 years, rejection testing has been revolutionized within the systems biology paradigm triggered by the Human Genome Project. Areas Covered We have co-developed the first FDA-cleared diagnostic and prognostic leukocyte gene expression profiling biomarker test in transplantation medicine that gained international evidence-based medicine guideline acceptance to rule out moderate/severe acute cellular cardiac allograft rejection without invasive endomyocardial biopsies. This work prompted molecular re-classification of intragraft biology, culminating in the identification of a pattern of intragraft myocyte injury, in addition to acute cellular rejection and antibody-mediated rejection. This insight stimulated research into non-invasive detection of myocardial allograft injury. The addition of a donor-organ specific myocardial injury marker based on donor-derived cell-free DNA further strengthens the non-invasive monitoring concept, combining the clinical use of two complementary non-invasive blood-based measures, host immune activity-related risk of acute rejection as well as cardiac allograft injury. Expert Opinion This novel complementary non-invasive heart transplant monitoring strategy based on leukocyte gene expression profiling and donor-derived cell-free DNA that incorporates longitudinal variability measures provides an exciting novel algorithm of heart transplant allograft monitoring. This algorithm's clinical utility will need to be tested in an appropriately designed randomized clinical trial which is in preparation.
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Affiliation(s)
- Mario C Deng
- Advanced Heart Failure/Mechanical Support/Heart Transplant, David Geffen School of Medicine at UCLA, Ronald Reagan UCLA Medical Center, 100 Medical Plaza Drive, Suite 630, Los Angeles, CA 90095
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121
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Deep viral blood metagenomics reveals extensive anellovirus diversity in healthy humans. Sci Rep 2021; 11:6921. [PMID: 33767340 PMCID: PMC7994813 DOI: 10.1038/s41598-021-86427-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/15/2021] [Indexed: 02/08/2023] Open
Abstract
Human blood metagenomics has revealed the presence of different types of viruses in apparently healthy subjects. By far, anelloviruses constitute the viral family that is more frequently found in human blood, although amplification biases and contaminations pose a major challenge in this field. To investigate this further, we subjected pooled plasma samples from 120 healthy donors in Spain to high-speed centrifugation, RNA and DNA extraction, random amplification, and massive parallel sequencing. Our results confirm the extensive presence of anelloviruses in such samples, which represented nearly 97% of the total viral sequence reads obtained. We assembled 114 different viral genomes belonging to this family, revealing remarkable diversity. Phylogenetic analysis of ORF1 suggested 28 potentially novel anellovirus species, 24 of which were validated by Sanger sequencing to discard artifacts. These findings underscore the importance of implementing more efficient purification procedures that enrich the viral fraction as an essential step in virome studies and question the suggested pathological role of anelloviruses.
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122
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Mwesigwa S, Williams L, Retshabile G, Katagirya E, Mboowa G, Mlotshwa B, Kyobe S, Kateete DP, Wampande EM, Wayengera M, Mpoloka SW, Mirembe AN, Kasvosve I, Morapedi K, Kisitu GP, Kekitiinwa AR, Anabwani G, Joloba ML, Matovu E, Mulindwa J, Noyes H, Botha G, Brown CW, Mardon G, Matshaba M, Hanchard NA. Unmapped exome reads implicate a role for Anelloviridae in childhood HIV-1 long-term non-progression. NPJ Genom Med 2021; 6:24. [PMID: 33741997 PMCID: PMC7979878 DOI: 10.1038/s41525-021-00185-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/25/2021] [Indexed: 01/31/2023] Open
Abstract
Human immunodeficiency virus (HIV) infection remains a significant public health burden globally. The role of viral co-infection in the rate of progression of HIV infection has been suggested but not empirically tested, particularly among children. We extracted and classified 42 viral species from whole-exome sequencing (WES) data of 813 HIV-infected children in Botswana and Uganda categorised as either long-term non-progressors (LTNPs) or rapid progressors (RPs). The Ugandan participants had a higher viral community diversity index compared to Batswana (p = 4.6 × 10-13), and viral sequences were more frequently detected among LTNPs than RPs (24% vs 16%; p = 0.008; OR, 1.9; 95% CI, 1.6-2.3), with Anelloviridae showing strong association with LTNP status (p = 3 × 10-4; q = 0.004, OR, 3.99; 95% CI, 1.74-10.25). This trend was still evident when stratified by country, sex, and sequencing platform, and after a logistic regression analysis adjusting for age, sex, country, and the sequencing platform (p = 0.02; q = 0.03; OR, 7.3; 95% CI, 1.6-40.5). Torque teno virus (TTV), which made up 95% of the Anelloviridae reads, has been associated with reduced immune activation. We identify an association between viral co-infection and prolonged AIDs-free survival status that may have utility as a biomarker of LTNP and could provide mechanistic insights to HIV progression in children, demonstrating the added value of interrogating off-target WES reads in cohort studies.
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Affiliation(s)
| | | | | | - Eric Katagirya
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gerald Mboowa
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Samuel Kyobe
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - David P Kateete
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Misaki Wayengera
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Angella N Mirembe
- Baylor College of Medicine Children's Foundation Uganda (Baylor Uganda), Kampala, Uganda
| | | | | | - Grace P Kisitu
- Baylor College of Medicine Children's Foundation Uganda (Baylor Uganda), Kampala, Uganda
| | - Adeodata R Kekitiinwa
- Baylor College of Medicine Children's Foundation Uganda (Baylor Uganda), Kampala, Uganda
| | - Gabriel Anabwani
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
| | - Moses L Joloba
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - Enock Matovu
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Julius Mulindwa
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Harry Noyes
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Gerrit Botha
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Chester W Brown
- University of Tennessee Health Science Center, Le Bonheur Children's Hospital, Memphis, TN, USA
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Mogomotsi Matshaba
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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BK Polyomavirus Nephropathy in Kidney Transplantation: Balancing Rejection and Infection. Viruses 2021; 13:v13030487. [PMID: 33809472 PMCID: PMC7998398 DOI: 10.3390/v13030487] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/12/2021] [Accepted: 03/14/2021] [Indexed: 12/16/2022] Open
Abstract
BK polyomavirus nephropathy (BKVN) and allograft rejection are two closely-associated diseases on opposite ends of the immune scale in kidney transplant recipients. The principle of balancing the immune system remains the mainstay of therapeutic strategy. While patient outcomes can be improved through screening, risk factors identification, and rapid reduction of immunosuppressants, a lack of standard curative therapy is the primary concern during clinical practice. Additionally, difficulty in pathological differential diagnosis and clinicopathology’s dissociation pose problems for a definite diagnosis. This article discusses the delicate evaluation needed to optimize immunosuppression and reviews recent advances in molecular diagnosis and immunological therapy for BKVN patients. New biomarkers for BKVN diagnosis are under development. For example, measurement of virus-specific T cell level may play a role in steering immunosuppressants. The development of cellular therapy may provide prevention, even a cure, for BKVN, a complex post-transplant complication.
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Cai HZ, Zhang H, Yang J, Zeng J, Wang H. Preliminary assessment of viral metagenome from cancer tissue and blood from patients with lung adenocarcinoma. J Med Virol 2021; 93:5126-5133. [PMID: 33595122 DOI: 10.1002/jmv.26887] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/30/2021] [Accepted: 02/15/2021] [Indexed: 12/18/2022]
Abstract
In this study, using a viral metagenomic method, we investigated the composition of virome in blood and cancer tissue samples that were collected from 25 patients with lung adenocarcinoma. Results indicated that virus sequences showing similarity to human pegivirus (HPgV), anellovirus, human endogenous retrovirus (HERV), and polyomavirus were recovered from this cohort. Three different complete genomes of HPgV were acquired from the blood samples and one complete genome of polyomavirus was determined from the cancer tissue sample. Phylogenetic analysis indicated that the three HPgV strains belonged to genotype 3 and the polyomavirus showed the highest sequence identity (99.73%) to trichodysplasia spinulosa-associated polyomavirus. PCR screening results indicated that the three HPgVs were present in 5 out of the 25 blood samples and the polyomavirus only existed in a cancer tissue sample pool. Whether infections with viruses have an association with lung cancer needs further study with a larger size of sampling.
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Affiliation(s)
- Hua-Zhong Cai
- Department of Emergency, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Heteng Zhang
- Department of Clinical Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jie Yang
- Department of Clinical Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jian Zeng
- Department of Clinical Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Hao Wang
- Department of Clinical Laboratory, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu, China
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125
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Kaczorowska J, van der Hoek L. Human anelloviruses: diverse, omnipresent and commensal members of the virome. FEMS Microbiol Rev 2021; 44:305-313. [PMID: 32188999 PMCID: PMC7326371 DOI: 10.1093/femsre/fuaa007] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/02/2020] [Indexed: 12/12/2022] Open
Abstract
Anelloviruses are small, single stranded circular DNA viruses. They are extremely diverse and have not been associated with any disease so far. Strikingly, these small entities infect most probably the complete human population, and there are no convincing examples demonstrating viral clearance from infected individuals. The main transmission could be via fecal-oral or airway route, as infections occur at an early age. However, due to the lack of an appropriate culture system, the virus–host interactions remain enigmatic. Anelloviruses are obviously mysterious viruses, and their impact on human life is not yet known, but, with no evidence of a disease association, a potential beneficial effect on human health should also be investigated.
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Affiliation(s)
- Joanna Kaczorowska
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Location AMC, University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Location AMC, University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
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126
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Torque Teno Virus plasma level as novel biomarker of retained immunocompetence in HIV-infected patients. Infection 2021; 49:501-509. [PMID: 33537915 PMCID: PMC8159784 DOI: 10.1007/s15010-020-01573-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 12/30/2020] [Indexed: 02/06/2023]
Abstract
PURPOSE To predict the course of immune recovery (IR) in HIV-1-infected patients after initiation of combined antiretroviral therapy (cART) by determination of the plasma concentration of Torque Teno Virus (TTV). TTV has been identified as marker for risk assessment in immunosuppressed patients after transplantation procedures. Here, TTV was analyzed in HIV-1-infected therapy-naïve patients to evaluate its use as predictor of the course of IR for guidance of individualized treatment. METHODS TTV DNA was quantified in plasma samples of 301 therapy-naïve HIV-1-infected patients and correlated to CD4+ cell count, HIV viral load, presence of the herpes viruses CMV, EBV and HHV-8, age and sex. Patients were classified according to their initial CD4+ cell count and to the extent of CD4+ T-cell increase within the first year of cART. RESULTS TTV DNA was detectable in 96% of the patients' plasma samples with a median TTV plasma concentration of 5.37 log10 cop/ml. The baseline CD4+ cell count was negatively correlated with TTV plasma concentration (p = 0.003). In patients with a CD4+ cell recovery < 50 cells/µl, the median TTV plasma concentration was significantly higher compared to patients with a CD4+ cell recovery of > 200 CD4+ cells/µl (5.68 log10 cop/ml versus 4.99 log10 cop/ml; p = 0.011). TTV plasma concentration in combination with baseline CD4+ cell count were significantly correlated to CD4+ cell recovery (p = 0.004). For all other parameters considered, no significant correlation for CD4+ cell recovery was found. CONCLUSION Within the cohort, the significantly elevated TTV plasma concentration in patients with diminished CD4+ cell recovery indicates a more profound immune defect. Baseline TTV plasma concentrations and CD4+ cell count are predictive for the course of immune recovery in HIV-1-infected patients with severe immunodeficiency.
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Viral load-guided immunosuppression after lung transplantation (VIGILung)-study protocol for a randomized controlled trial. Trials 2021; 22:48. [PMID: 33430927 PMCID: PMC7798016 DOI: 10.1186/s13063-020-04985-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 12/18/2020] [Indexed: 12/31/2022] Open
Abstract
Background Immunosuppression including high-dose calcineurin inhibitors (CNI) is essential after lung transplantation. Dosing is usually guided by therapeutic drug monitoring adjusted to target trough levels of CNIs to keep the balance between over-dose causing severe toxicity and increased risk of infections or under-dose with a risk of graft injury. Adaptation of CNI-based immunosuppression by monitoring of torque teno virus (TTV), a latent nonpathogenic DNA virus, measured in the whole blood in addition to conventional therapeutic drug monitoring may reduce the toxicity of immunosuppression with similar efficacy. Methods/design An open-label, randomized, controlled, parallel-group, multicenter trial in lung transplant recipients will be conducted to investigate the safety and efficacy of immunosuppression guided by TTV monitoring as an add-on to conventional therapeutic drug monitoring. Adult lung transplant recipients 21 to 42 days after transplantation are eligible to participate. Patients (N = 144) will be randomized 1:1 to the experimental intervention (arm 1: immunosuppression guided by TTV monitoring in addition to conventional therapeutic drug monitoring of tacrolimus trough levels) and control intervention (arm 2: conventional therapeutic drug monitoring). Outcomes will be assessed 12 months after randomization with the change in glomerular filtration rate as the primary endpoint. Secondary endpoints will be additional measurements of renal function, allograft function, incidence of acute rejections, incidence of chronic lung allograft dysfunction, graft loss, and infections. Discussion The results of this randomized controlled trial may reduce the toxicity of immunosuppression after lung transplantation while maintaining the efficacy of immunosuppression. Study results are transferable to all other solid organ transplantations. Trial registration ClinicalTrials.gov NCT04198506. Registered on 12 December 2019
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128
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Zhang HT, Wang H, Wu HS, Zeng J, Yang Y. Comparison of viromes in vaginal secretion from pregnant women with and without vaginitis. Virol J 2021; 18:11. [PMID: 33407663 PMCID: PMC7789296 DOI: 10.1186/s12985-020-01482-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/23/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Although some studies have investigated the bacterial community in vaginal tract of pregnant women, there are few reports about the viral community (virome) in this type of microenvironment. METHODS To investigate the composition of virome in vaginal secretion samples, 40 vaginal secretion samples from pregnant women with vaginitis and 20 vaginal secretion samples from pregnant women without vaginitis, pooled into 4 and 2 sample pools, respectively, were subjected to viral metagenomic analysis. RESULTS Results indicated virus sequences showing similarity to human papillomavirus (HPV), anellovirus, and norovirus were recovered from this cohort of pregnant women. Further analysis indicated that 15 different defined types and one unclassified type of HPV were detected from pregnant women with vaginitis while only 3 defined types of HPV were detected in pregnant women without vaginitis. Five different groups of viruses from the family Anelloviridae were present in pregnant women with but none of them were detected in pregnant women without vaginitis. Norovirus was detected in 3 out of the 4 sample pools from pregnant women with vaginitis but none in the pregnant women without vaginitis. Twelve complete genomes belonging to 10 different types of HPV, and 5 novel anllovirus genomes belonging 2 different genera in Anelloviridae were acquired from these libraries, based on which phylogenetical analysis and pairwise sequence comparison were performed. Phageome in these samples was also briefly characterized and compared between two groups. CONCLUSION Our data suggested that virome might play an important role in the progression of vaginitis in pregnant women.
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Affiliation(s)
- He-Teng Zhang
- Department of Obstetrics and Gynecology, The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, 212001, Jiangsu, China
- School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Hao Wang
- Department of Clinical Laboratory, Huai'an Hospital, Xuzhou Medical University, Huai'an, 223002, Jiangsu, China
| | - Hai-Sheng Wu
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, 810021, Qinghai, China
| | - Jian Zeng
- School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yan Yang
- Department of Obstetrics and Gynecology, The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, 212001, Jiangsu, China.
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Li N, Cai Q, Miao Q, Song Z, Fang Y, Hu B. High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings. SMALL METHODS 2021; 5:2000792. [PMID: 33614906 PMCID: PMC7883231 DOI: 10.1002/smtd.202000792] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/24/2020] [Indexed: 05/25/2023]
Abstract
The application of sequencing technology is shifting from research to clinical laboratories owing to rapid technological developments and substantially reduced costs. However, although thousands of microorganisms are known to infect humans, identification of the etiological agents for many diseases remains challenging as only a small proportion of pathogens are identifiable by the current diagnostic methods. These challenges are compounded by the emergence of new pathogens. Hence, metagenomic next-generation sequencing (mNGS), an agnostic, unbiased, and comprehensive method for detection, and taxonomic characterization of microorganisms, has become an attractive strategy. Although many studies, and cases reports, have confirmed the success of mNGS in improving the diagnosis, treatment, and tracking of infectious diseases, several hurdles must still be overcome. It is, therefore, imperative that practitioners and clinicians understand both the benefits and limitations of mNGS when applying it to clinical practice. Interestingly, the emerging third-generation sequencing technologies may partially offset the disadvantages of mNGS. In this review, mainly: a) the history of sequencing technology; b) various NGS technologies, common platforms, and workflows for clinical applications; c) the application of NGS in pathogen identification; d) the global expert consensus on NGS-related methods in clinical applications; and e) challenges associated with diagnostic metagenomics are described.
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Affiliation(s)
- Na Li
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Qingqing Cai
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Qing Miao
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Zeshi Song
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Yuan Fang
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Bijie Hu
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
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Uhl P, Heilos A, Bond G, Meyer E, Böhm M, Puchhammer-Stöckl E, Arbeiter K, Müller-Sacherer T, Csaicsich D, Aufricht C, Rusai K. Torque teno viral load reflects immunosuppression in paediatric kidney-transplanted patients-a pilot study. Pediatr Nephrol 2021; 36:153-162. [PMID: 32524259 PMCID: PMC7701084 DOI: 10.1007/s00467-020-04606-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/01/2020] [Accepted: 05/08/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Chronic deterioration of kidney graft function is related to inadequate immunosuppression (IS). A novel tool to assess the individual net state of IS in transplanted patients might be the monitoring of Torque teno virus (TTV) viral load. TTV is a non-pathogen virus detectable in almost all individuals. TTV level in the peripheral blood has been linked to the immune-competence of its host and should thus reflect IS after solid organ transplantation. METHODS TTV plasma load was quantified monthly by RT-PCR for a period of 1 year in 45 kidney-transplanted children. Post-transplant time was at least 3 months. The relation of the virus DNA levels to IS and transplant-specific clinical and laboratory parameters was analysed longitudinally. RESULTS TTV DNA was detectable in 94.5% of the plasma samples. There was a significant association with the post-transplant follow-up time as well as with the type of IS regimen, with lower virus loads in patients after longer post-transplant time and mTOR inhibitor-based IS. Furthermore, a significant positive correlation with the dose of prednisolone and mycophenolate mofetil was found. CONCLUSIONS TTV levels show an association/correlation with the strength of IS. Further studies are needed in order to evaluate TTV measurement as a tool for IS monitoring for hard clinical outcomes such as presence of donor-specific antibodies, rejections or infections-common consequences of insufficient or too intense IS.
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Affiliation(s)
- Phoebe Uhl
- Department of Paediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Division of Paediatric Nephrology and Gastroenterology, Medical University of Vienna, Vienna, Austria
| | - Andreas Heilos
- Department of Paediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Division of Paediatric Nephrology and Gastroenterology, Medical University of Vienna, Vienna, Austria
| | - Gregor Bond
- Department of Medicine III, Division of Nephrology and Dialysis, Medical University of Vienna, Vienna, Austria
| | - Elias Meyer
- Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Michael Böhm
- Department of Paediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Division of Paediatric Nephrology and Gastroenterology, Medical University of Vienna, Vienna, Austria
| | | | - Klaus Arbeiter
- Department of Paediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Division of Paediatric Nephrology and Gastroenterology, Medical University of Vienna, Vienna, Austria
| | - Thomas Müller-Sacherer
- Department of Paediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Division of Paediatric Nephrology and Gastroenterology, Medical University of Vienna, Vienna, Austria
| | - Dagmar Csaicsich
- Department of Paediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Division of Paediatric Nephrology and Gastroenterology, Medical University of Vienna, Vienna, Austria
| | - Christoph Aufricht
- Department of Paediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Division of Paediatric Nephrology and Gastroenterology, Medical University of Vienna, Vienna, Austria
| | - Krisztina Rusai
- Department of Paediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Division of Paediatric Nephrology and Gastroenterology, Medical University of Vienna, Vienna, Austria.
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Zhong Y, Xu F, Wu J, Schubert J, Li MM. Application of Next Generation Sequencing in Laboratory Medicine. Ann Lab Med 2021; 41:25-43. [PMID: 32829577 PMCID: PMC7443516 DOI: 10.3343/alm.2021.41.1.25] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/24/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
The rapid development of next-generation sequencing (NGS) technology, including advances in sequencing chemistry, sequencing technologies, bioinformatics, and data interpretation, has facilitated its wide clinical application in precision medicine. This review describes current sequencing technologies, including short- and long-read sequencing technologies, and highlights the clinical application of NGS in inherited diseases, oncology, and infectious diseases. We review NGS approaches and clinical diagnosis for constitutional disorders; summarize the application of U.S. Food and Drug Administration-approved NGS panels, cancer biomarkers, minimal residual disease, and liquid biopsy in clinical oncology; and consider epidemiological surveillance, identification of pathogens, and the importance of host microbiome in infectious diseases. Finally, we discuss the challenges and future perspectives of clinical NGS tests.
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Affiliation(s)
- Yiming Zhong
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA,
USA
| | - Feng Xu
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Jinhua Wu
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Jeffrey Schubert
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Marilyn M. Li
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA,
USA
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
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Bezdan D, Grigorev K, Meydan C, Pelissier Vatter FA, Cioffi M, Rao V, MacKay M, Nakahira K, Burnham P, Afshinnekoo E, Westover C, Butler D, Mozsary C, Donahoe T, Foox J, Mishra T, Lucotti S, Rana BK, Melnick AM, Zhang H, Matei I, Kelsen D, Yu K, Lyden DC, Taylor L, Bailey SM, Snyder MP, Garrett-Bakelman FE, Ossowski S, De Vlaminck I, Mason CE. Cell-free DNA (cfDNA) and Exosome Profiling from a Year-Long Human Spaceflight Reveals Circulating Biomarkers. iScience 2020; 23:101844. [PMID: 33376973 PMCID: PMC7756145 DOI: 10.1016/j.isci.2020.101844] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/12/2020] [Accepted: 11/18/2020] [Indexed: 12/11/2022] Open
Abstract
Liquid biopsies based on cell-free DNA (cfDNA) or exosomes provide a noninvasive approach to monitor human health and disease but have not been utilized for astronauts. Here, we profile cfDNA characteristics, including fragment size, cellular deconvolution, and nucleosome positioning, in an astronaut during a year-long mission on the International Space Station, compared to his identical twin on Earth and healthy donors. We observed a significant increase in the proportion of cell-free mitochondrial DNA (cf-mtDNA) inflight, and analysis of post-flight exosomes in plasma revealed a 30-fold increase in circulating exosomes and patient-specific protein cargo (including brain-derived peptides) after the year-long mission. This longitudinal analysis of astronaut cfDNA during spaceflight and the exosome profiles highlights their utility for astronaut health monitoring, as well as cf-mtDNA levels as a potential biomarker for physiological stress or immune system responses related to microgravity, radiation exposure, and the other unique environmental conditions of spaceflight.
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Affiliation(s)
- Daniela Bezdan
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1305 York Avenue, Y13-05, New York, NY 10021, USA
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital, Tubingen, Germany
| | - Kirill Grigorev
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1305 York Avenue, Y13-05, New York, NY 10021, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1305 York Avenue, Y13-05, New York, NY 10021, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Fanny A. Pelissier Vatter
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | - Michele Cioffi
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | - Varsha Rao
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew MacKay
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1305 York Avenue, Y13-05, New York, NY 10021, USA
| | | | - Philip Burnham
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1305 York Avenue, Y13-05, New York, NY 10021, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Craig Westover
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1305 York Avenue, Y13-05, New York, NY 10021, USA
| | - Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1305 York Avenue, Y13-05, New York, NY 10021, USA
| | - Chris Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1305 York Avenue, Y13-05, New York, NY 10021, USA
| | - Timothy Donahoe
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1305 York Avenue, Y13-05, New York, NY 10021, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1305 York Avenue, Y13-05, New York, NY 10021, USA
| | - Tejaswini Mishra
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Serena Lucotti
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | - Brinda K. Rana
- Department of Psychiatry University of California, San Diego, La Jolla, CA, USA
| | - Ari M. Melnick
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Haiying Zhang
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irina Matei
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | - David Kelsen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kenneth Yu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David C. Lyden
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | - Lynn Taylor
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Susan M. Bailey
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Michael P. Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Francine E. Garrett-Bakelman
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
- University of Virginia Cancer Center, Charlottesville, VA, USA
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Iwijn De Vlaminck
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1305 York Avenue, Y13-05, New York, NY 10021, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
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Alex CE, Fahsbender E, Altan E, Bildfell R, Wolff P, Jin L, Black W, Jackson K, Woods L, Munk B, Tse T, Delwart E, Pesavento PA. Viruses in unexplained encephalitis cases in American black bears (Ursus americanus). PLoS One 2020; 15:e0244056. [PMID: 33332429 PMCID: PMC7745964 DOI: 10.1371/journal.pone.0244056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 12/02/2020] [Indexed: 11/29/2022] Open
Abstract
Viral infections were investigated in American black bears (Ursus americanus) from Nevada and northern California with and without idiopathic encephalitis. Metagenomics analyses of tissue pools revealed novel viruses in the genera Circoviridae, Parvoviridae, Anelloviridae, Polyomaviridae, and Papillomaviridae. The circovirus and parvovirus were of particular interest due to their potential importance as pathogens. We characterized the genomes of these viruses and subsequently screened bears by PCR to determine their prevalence. The circovirus (Ursus americanus circovirus, UaCV) was detected at a high prevalence (10/16, 67%), and the chaphamaparvovirus (Ursus americanus parvovirus, UaPV) was found in a single bear. We showed that UaCV is present in liver, spleen/lymph node, and brain tissue of selected cases by in situ hybridization (ISH) and PCR. Infections were detected in cases of idiopathic encephalitis and in cases without inflammatory brain lesions. Infection status was not clearly correlated with disease, and the significance of these infections remains unclear. Given the known pathogenicity of a closely related mammalian circovirus, and the complex manifestations of circovirus-associated diseases, we suggest that UaCV warrants further study as a possible cause or contributor to disease in American black bears.
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Affiliation(s)
- Charles E. Alex
- Department of Pathology, Microbiology, and Immunology, University of California—Davis School of Veterinary Medicine, Davis, California, United States of America
| | - Elizabeth Fahsbender
- Vitalant Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California—San Francisco, San Francisco, California, United States of America
| | - Eda Altan
- Vitalant Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California—San Francisco, San Francisco, California, United States of America
| | - Robert Bildfell
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
- Oregon Veterinary Diagnostic Laboratory, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
| | - Peregrine Wolff
- Nevada Department of Wildlife, Reno, Nevada, United States of America
| | - Ling Jin
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
- Oregon Veterinary Diagnostic Laboratory, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
| | - Wendy Black
- Oregon Veterinary Diagnostic Laboratory, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
| | - Kenneth Jackson
- Department of Pathology, Microbiology, and Immunology, University of California—Davis School of Veterinary Medicine, Davis, California, United States of America
| | - Leslie Woods
- California Animal Health and Food Safety Laboratory, Davis, California, United States of America
| | - Brandon Munk
- California Department of Fish and Wildlife, Rancho Cordova, California, United States of America
| | - Tiffany Tse
- Department of Pathology, Microbiology, and Immunology, University of California—Davis School of Veterinary Medicine, Davis, California, United States of America
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California—San Francisco, San Francisco, California, United States of America
| | - Patricia A. Pesavento
- Department of Pathology, Microbiology, and Immunology, University of California—Davis School of Veterinary Medicine, Davis, California, United States of America
- * E-mail:
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134
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Kulifaj D, Tilloy V, Scaon E, Guerin E, Essig M, Pichon N, Hantz S, De Bernardi A, Joannes M, Barranger C, Alain S. Viral metagenomics analysis of kidney donors and recipients: Torque teno virus genotyping and prevalence. J Med Virol 2020; 92:3301-3311. [PMID: 32658305 DOI: 10.1002/jmv.26298] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/07/2020] [Indexed: 12/11/2022]
Abstract
The viral load of the ubiquitous and nonpathogenic torque teno virus (TTV) is associated with the grade of immunosuppression of its host. The development of next-generation sequencing (NGS) allowed to describe the human virome of the blood compartment in transplanted patients, and showed that TTV is the most important part of the virome. This study is a descriptive retrospective pilot study of sequencing plasma samples from 15 matched donors and recipients. After sample processing, nucleic acids were amplified by rolling circle amplification and submitted to NGS by ion proton sequencing technology. Results were analyzed after mapping of reads on the 29 TTV reference genomes and de novo assembling of the reads with MIRA software. The number of TTV species present in donors and recipients was, on average, 12 in donors and 33 in recipients. TTV species predominantly present in donors were TTV-13 and TTV-18; and in recipients were TTV-P15-2, TTV-27, TTV-HD14a, and TTV-22. We highlighted a significant variability in abundance and composition in sequential samples from recipients. Temporal evolution of TTV populations was clearly observed in recipients, but no preferential transmission of a species from donor to recipient was evidenced. Diversity and population expansion were observed in kidney recipients. Further study of TTV species could help assess the potential impact of each species of this virus.
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Affiliation(s)
- Dorian Kulifaj
- INSERM UMR 1092, Université Limoges, Limoges, France
- R&D Molecular Diagnostics, bioMérieux, Verniolle, France
| | - Valentin Tilloy
- INSERM UMR 1092, Université Limoges, Limoges, France
- Herpesviruses National Reference Center, CHU Limoges, Limoges, France
- UF9481 Bioinformatics, CHU Limoges, Limoges, France
| | - Erwan Scaon
- Bioinformatics, UMS BISCEM, GEIST, Université Limoges, Limoges, France
| | - Emilie Guerin
- INSERM UMR 1092, Université Limoges, Limoges, France
- UF8843 Medical Genomics Department, CHU Limoges, Limoges, France
| | - Marie Essig
- Nephrology Department, CHU Limoges, Limoges, France
| | - Nicolas Pichon
- Intensive Care Unit Department, CHU Limoges, Limoges, France
| | - Sébastien Hantz
- INSERM UMR 1092, Université Limoges, Limoges, France
- Herpesviruses National Reference Center, CHU Limoges, Limoges, France
| | | | | | - Côme Barranger
- R&D Molecular Diagnostics, bioMérieux, Verniolle, France
| | - Sophie Alain
- INSERM UMR 1092, Université Limoges, Limoges, France
- Herpesviruses National Reference Center, CHU Limoges, Limoges, France
- UF8843 Medical Genomics Department, CHU Limoges, Limoges, France
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135
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Mrzljak A, Vilibic-Cavlek T. Torque teno virus in liver diseases and after liver transplantation. World J Transplant 2020; 10:291-296. [PMID: 33312890 PMCID: PMC7708878 DOI: 10.5500/wjt.v10.i11.291] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 09/22/2020] [Accepted: 10/09/2020] [Indexed: 02/06/2023] Open
Abstract
Torque teno virus (TTV) has been proposed as a surrogate biomarker for immune monitoring in different patient cohorts. Historically, TTV has been associated with different liver diseases such as post-transfusion hepatitis, hepatitis B, and hepatitis C, but the virus's pathogenicity is controversial. TTV is a ubiquitous DNA virus, highly prevalent and mostly indolent in the general population. Thus, TTV viral load is more relevant than prevalence to understand TTV infection. In the context of liver transplantation, TTV viral load is modulated by the immune, viral, and inflammatory status. After liver transplantation, the TTV viral load positively correlates with the intensity of immunosuppression (IS), and low TTV viral burden is a predictor of acute rejection episodes, making it an attractive marker for the efficacy of IS. However, the TTV role as a single or a panel biomarker needs to be evaluated in further independent prospective trails.
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Affiliation(s)
- Anna Mrzljak
- Department of Medicine, Merkur University Hospital, School of Medicine, University of Zagreb, Zagreb 10000, Croatia
| | - Tatjana Vilibic-Cavlek
- Department of Virology, Croatian Institute of Public Health; School of Medicine, University of Zagreb, Zagreb 10000, Croatia
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136
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Giménez E, Monzó C, Albert E, Fuentes-Trillo A, Seda E, Piñana JL, Hernández Boluda JC, Solano C, Chaves J, Navarro D. Diversity and dynamic changes of anelloviruses in plasma following allogeneic hematopoietic stem cell transplantation. J Med Virol 2020; 93:5167-5172. [PMID: 33174620 DOI: 10.1002/jmv.26661] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 01/20/2023]
Abstract
Monitoring of alphatorquevirus (torque teno virus [TTV]) DNA in plasma may prove to be useful to assess the net state of immune competence following allogeneic hematopoietic stem cell transplantation (allo-HSCT). There are scarce data published on the prevalence of beta (torque teno mini virus [TTMV]) and gammatorqueviruses (torque teno midi virus [TTMDV]) and, in particular, on the dynamics of anelloviruses in allo-HSCT patients. Twenty-five allo-HSCT recipients with available plasma specimens obtained before conditioning and after engraftment were included. Degenerated primers targeting a highly conserved genomic sequence across all anelloviruses were designed for genomic amplification and high-throughput sequencing. Co-detection of TTV, TTMV, and TTMDV both in pre-transplant and post-engraftment plasma specimens was documented in more than two-thirds of patients. The use of quantitative real-time polymerase chain reaction (PCR) assays targeting TTMV and TTMDV in addition to TTV may add value to TTV-specific PCR assays in the inference of the net state of immunosuppresion or immune competence in this clinical setting.
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Affiliation(s)
- Estela Giménez
- Microbiology Service, Hospital Clínico Universitario, INCLIVA Research Institute, Valencia, Spain
| | - Carolina Monzó
- Genomics and Genetic Diagnosis Unit, INCLIVA Research Institute, Valencia, Spain
| | - Eliseo Albert
- Microbiology Service, Hospital Clínico Universitario, INCLIVA Research Institute, Valencia, Spain
| | | | - Enrique Seda
- Genomics and Genetic Diagnosis Unit, INCLIVA Research Institute, Valencia, Spain
| | - José Luis Piñana
- Hematology Service, Hospital Clínico Universitario, INCLIVA Research Institute, Valencia, Spain
| | | | - Carlos Solano
- Hematology Service, Hospital Clínico Universitario, INCLIVA Research Institute, Valencia, Spain.,Department of Medicine, School of Medicine, University of Valencia, Valencia, Spain
| | - Javier Chaves
- Genomics and Genetic Diagnosis Unit, INCLIVA Research Institute, Valencia, Spain
| | - David Navarro
- Microbiology Service, Hospital Clínico Universitario, INCLIVA Research Institute, Valencia, Spain.,Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain
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137
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Neri L, Spezia PG, Suraci S, Macera L, Scribano S, Giusti B, Focosi D, Maggi F, Giannecchini S. Torque teno virus microRNA detection in cerebrospinal fluids of patients with neurological pathologies. J Clin Virol 2020; 133:104687. [PMID: 33176237 DOI: 10.1016/j.jcv.2020.104687] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/26/2020] [Accepted: 11/01/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Torque teno virus (TTV) is a widespread anellovirus that establishes persistent infections in humans and represents the most abundant component of the human virome. TTV encodes microRNAs (miRNA) which are found both in viremic and not viremic subjects being potentially ideal tools for the virus to evade the immune system response and to maintain chronic infection in the host. OBJECTIVE To investigate TTV-DNA loads and TTV-miRNAs expression in cerebrospinal fluids (CSF) from subjects under analysis for the assessment of neurological diseases. STUDY DESIGN Detection of TTV-DNA and TTV-miRNAs (e. g. miRNA t1a, t3b, and tth8) were carried out from CSF samples of 93 subjects with neurological diseases by using universal real-time PCR, real-time RT-PCR, and next-generation sequencing (NGS) analyses. RESULTS TTV-DNA was detected in 11 of 93 (12 %) CSFs with a mean TTV load of 155 copies/mL. Conversely, 29 CSF samples (31 %) were positive for at least one TTV-miRNA, while 15 (16 %) CSFs contained all the TTV-miRNAs examined. Overall, TTV-miRNA tth8 was detected in 62 % of samples, followed by TTV miRNA t3b (56 %), and t1a (29 %). Interestingly, TTV-miRNAs were found in CSF samples that were negative for the presence of TTV-DNA. Next-generation sequencing analysis carried out from 4 TTV-DNA negative CSF samples detected reads mapped in TTV-miRNA sequences region. CONCLUSIONS These results shed novel light on the relationship between TTV and the central nervous system and make compelling furthered studies for investigating the potential role of TTV-miRNAs in neurological disorders.
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Affiliation(s)
- Lorenzo Neri
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | | | - Samuele Suraci
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Lisa Macera
- Department of Translational Research, University of Pisa, Italy
| | - Stefano Scribano
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Betti Giusti
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Fabrizio Maggi
- Department of Medicine and Surgery, University of Insubria, and Laboratory of Clinical Microbiology, ASST dei Sette Laghi, Varese, Italy
| | - Simone Giannecchini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.
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138
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Torque Teno Virus Viral Load as a Marker of Immune Function in Allogeneic Haematopoietic Stem Cell Transplantation Recipients. Viruses 2020; 12:v12111292. [PMID: 33187285 PMCID: PMC7696489 DOI: 10.3390/v12111292] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 01/04/2023] Open
Abstract
Torque teno virus (TTV) has been proposed as a surrogate biomarker of T-cell function in allogeneic–haematopoietic–stem-cell transplantation (allo-HSCT). Conflicting data exists regarding the value of TTV to assess the degree of immunosuppression. The aim of the present study was to investigate the correlation between TTV viral load and immune function. Using samples from a prospective cohort composed of healthy-volunteers (HV) and allo-HSCT recipients at 6 months post-transplantation, we assessed the correlation between TTV viraemia and immune cell counts or T-cell proliferation capacity post-phytohaemagglutinin stimulation. TTV viraemia was detected in 68% of HV (n = 80) and 100% of allo-HSCT recipients (n = 41; p < 0.001); it was significantly higher in allo-HSCT recipients (3.9 vs. 2.1 Log copies/mL, p < 0.001). There was no correlation between T-cell function and CD3+T-cell count (rho: 0.002) suggesting that T-cell count can normalise without full functional recovery. Furthermore, no significant correlation was observed between TTV viraemia and absolute total/subset lymphocyte counts (rho: <0.13). The highest correlation was observed between TTV viral load and T-cell proliferation capacity (rho: −0.39). We therefore report an inverse correlation between T-cell function and TTV viraemia that is independent of T-cell count. Monitoring of TTV viraemia could be a fast suitable option to objectively assess the competence of immune function in at-risk populations.
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139
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Gu W, Deng X, Lee M, Sucu YD, Arevalo S, Stryke D, Federman S, Gopez A, Reyes K, Zorn K, Sample H, Yu G, Ishpuniani G, Briggs B, Chow ED, Berger A, Wilson MR, Wang C, Hsu E, Miller S, DeRisi JL, Chiu CY. Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids. Nat Med 2020; 27:115-124. [PMID: 33169017 DOI: 10.1038/s41591-020-1105-z] [Citation(s) in RCA: 316] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 09/17/2020] [Indexed: 12/20/2022]
Abstract
We developed a metagenomic next-generation sequencing (mNGS) test using cell-free DNA from body fluids to identify pathogens. The performance of mNGS testing of 182 body fluids from 160 patients with acute illness was evaluated using two sequencing platforms in comparison to microbiological testing using culture, 16S bacterial PCR and/or 28S-internal transcribed ribosomal gene spacer (28S-ITS) fungal PCR. Test sensitivity and specificity of detection were 79 and 91% for bacteria and 91 and 89% for fungi, respectively, by Illumina sequencing; and 75 and 81% for bacteria and 91 and 100% for fungi, respectively, by nanopore sequencing. In a case series of 12 patients with culture/PCR-negative body fluids but for whom an infectious diagnosis was ultimately established, seven (58%) were mNGS positive. Real-time computational analysis enabled pathogen identification by nanopore sequencing in a median 50-min sequencing and 6-h sample-to-answer time. Rapid mNGS testing is a promising tool for diagnosis of unknown infections from body fluids.
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Affiliation(s)
- Wei Gu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Xianding Deng
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Marco Lee
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Yasemin D Sucu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Shaun Arevalo
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Doug Stryke
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Allan Gopez
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Kevin Reyes
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Kelsey Zorn
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Hannah Sample
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Guixia Yu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Gurpreet Ishpuniani
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Benjamin Briggs
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Amy Berger
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Michael R Wilson
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Candace Wang
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Elaine Hsu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. .,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA. .,Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA.
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140
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Liang G, Conrad MA, Kelsen JR, Kessler LR, Breton J, Albenberg LG, Marakos S, Galgano A, Devas N, Erlichman J, Zhang H, Mattei L, Bittinger K, Baldassano RN, Bushman FD. Dynamics of the Stool Virome in Very Early-Onset Inflammatory Bowel Disease. J Crohns Colitis 2020; 14:1600-1610. [PMID: 32406906 PMCID: PMC7648169 DOI: 10.1093/ecco-jcc/jjaa094] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS Dysbiosis of the gut microbiota is a well-known correlate of the pathogenesis of inflammatory bowel disease [IBD]. However, few studies have examined the microbiome in very early-onset [VEO] IBD, which is defined as onset of IBD before 6 years of age. Here we focus on the viral portion of the microbiome-the virome-to assess possible viral associations with disease processes, reasoning that any viruses potentially associated with IBD might grow more robustly in younger subjects, and so be more detectable. METHODS Virus-like particles [VLPs] were purified from stool samples collected from patients with VEO-IBD [n = 54] and healthy controls [n = 23], and characterized by DNA and RNA sequencing and VLP particle counts. RESULTS The total number of VLPs was not significantly different between VEO-IBD and healthy controls. For bacterial viruses, the VEO-IBD subjects were found to have a higher ratio of Caudovirales vs to Microviridae compared to healthy controls. An increase in Caudovirales was also associated with immunosuppressive therapy. For viruses infecting human cells, Anelloviridae showed higher prevalence in VEO-IBD compared to healthy controls. Within the VEO-IBD group, higher levels of Anelloviridae DNA were also positively associated with immunosuppressive treatment. To search for new viruses, short sequences enriched in VEO-IBD samples were identified, and some could be validated in an independent cohort, although none was clearly viral; this provides sequence tags to interrogate in future studies. CONCLUSIONS These data thus document perturbations to normal viral populations associated with VEO-IBD, and provide a biomarker-Anelloviridae DNA levels-potentially useful for reporting the effectiveness of immunosuppression.
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Affiliation(s)
- Guanxiang Liang
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Maire A Conrad
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Judith R Kelsen
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lyanna R Kessler
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jessica Breton
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lindsey G Albenberg
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sarah Marakos
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alissa Galgano
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nina Devas
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jessi Erlichman
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Huanjia Zhang
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lisa Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Robert N Baldassano
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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141
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Torii Y, Horiba K, Hayano S, Kato T, Suzuki T, Kawada JI, Takahashi Y, Kojima S, Okuno Y, Ogi T, Ito Y. Comprehensive pathogen detection in sera of Kawasaki disease patients by high-throughput sequencing: a retrospective exploratory study. BMC Pediatr 2020; 20:482. [PMID: 33059644 PMCID: PMC7557310 DOI: 10.1186/s12887-020-02380-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022] Open
Abstract
Background Kawasaki disease (KD) is an idiopathic systemic vasculitis that predominantly damages coronary arteries in children. Various pathogens have been investigated as triggers for KD, but no definitive causative pathogen has been determined. As KD is diagnosed by symptoms, several days are needed for diagnosis. Therefore, at the time of diagnosis of KD, the pathogen of the trigger may already be diminished. The aim of this study was to explore comprehensive pathogens in the sera at the acute stage of KD using high-throughput sequencing (HTS). Methods Sera of 12 patients at an extremely early stage of KD and 12 controls were investigated. DNA and RNA sequences were read separately using HTS. Sequence data were imported into the home-brew meta-genomic analysis pipeline, PATHDET, to identify the pathogen sequences. Results No RNA virus reads were detected in any KD case except for that of equine infectious anemia, which is known as a contaminant of commercial reverse transcriptase. Concerning DNA viruses, human herpesvirus 6B (HHV-6B, two cases) and Anelloviridae (eight cases) were detected among KD cases as well as controls. Multiple bacterial reads were obtained from KD and controls. Bacteria of the genera Acinetobacter, Pseudomonas, Delfita, Roseomonas, and Rhodocyclaceae appeared to be more common in KD sera than in the controls. Conclusion No single pathogen was identified in serum samples of patients at the acute phase of KD. With multiple bacteria detected in the serum samples, it is difficult to exclude the possibility of contamination; however, it is possible that these bacteria might stimulate the immune system and induce KD.
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Affiliation(s)
- Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Kazuhiro Horiba
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.,Department of Genetics, Research Institute of Environmental Medicine Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.,Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Satoshi Hayano
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Taichi Kato
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yusuke Okuno
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.,Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.,Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
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142
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Thijssen M, Tacke F, Beller L, Deboutte W, Yinda KC, Nevens F, Laleman W, Van Ranst M, Pourkarim MR. Clinical relevance of plasma virome dynamics in liver transplant recipients. EBioMedicine 2020; 60:103009. [PMID: 32979836 PMCID: PMC7519289 DOI: 10.1016/j.ebiom.2020.103009] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/25/2020] [Accepted: 09/02/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The role of the microbiome in liver transplantation (LT) outcome has received a growing interest in the past decades. In contrast to bacteria, the role of endogenous viral communities, known as the virome, is poorly described. Here, we applied a viral metagenomic approach to study the dynamic evolution of circulating viruses in the plasma of LT recipients and its effect on the clinical course of patients. METHODS Patients chronically infected with hepatitis B virus (HBV) that received a LT due to endstage liver disease were included in this study. Longitudinal plasma samples were collected pre- and post-LT. Intact viral particles were isolated and sequenced on an Illumina HiSeq 2500 platform. Short read libraries were analysed with an in-house bioinformatics pipeline. Key endpoints were the dynamics of viral families and post-LT complications. FINDINGS The initiation of immunosuppression induced a bloom of the Anelloviridae that dominated the post-LT plasma virome. A variety of post-LT complication were observed. Nephrotoxicity was reported in 38% of the patients and was associated with a high abundance of anelloviruses. Besides nephrotoxicity, 16 (67%) patients experienced flares of viral or bacterial infections in post-transplant follow-up. These flares were recognized by an increased burden of anelloviruses (p < 0.05). Interestingly, no mortality was observed in patients infected with human pegivirus. INTERPRETATION These findings suggest a diagnostic potential for the Anelloviridae family in post-LT complications. Furthermore, the impact of human pegivirus infection on post-transplant survival should be further investigated. FUNDING This trial was supported by Gilead Sciences grant number BE-2017-000133.
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Affiliation(s)
- Marijn Thijssen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Post box 1040, BE-3000 Leuven, Belgium
| | - Frank Tacke
- Department of Hepatology and Gastroenterology, Charité - Universitätsmedizin Berlin, Campus Charité Mitte and Campus Virchow-Klinikum, Berlin, Germany
| | - Leen Beller
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Post box 1040, BE-3000 Leuven, Belgium
| | - Ward Deboutte
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Post box 1040, BE-3000 Leuven, Belgium
| | - Kwe Claude Yinda
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Post box 1040, BE-3000 Leuven, Belgium
| | - Frederik Nevens
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Wim Laleman
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Marc Van Ranst
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Post box 1040, BE-3000 Leuven, Belgium
| | - Mahmoud Reza Pourkarim
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Post box 1040, BE-3000 Leuven, Belgium; Health Policy Research Centre, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran; Blood Transfusion Research Centre, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran.
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143
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Tozetto-Mendoza TR, Bongiovanni AM, Minis E, Linhares IM, Boester A, Freire WS, Lima SH, de Oliveira NPG, Mendes-Correa MC, Forney LJ, Witkin SS. Torquetenovirus Titer in Vaginal Secretions from Pregnant and Postpartum Women: Association with Absence of Lactobacillus crispatus and Levels of Lactic Acid and Matrix Metalloproteinase-8. Reprod Sci 2020; 27:2075-2081. [PMID: 32944879 DOI: 10.1007/s43032-020-00227-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/28/2020] [Indexed: 12/13/2022]
Abstract
Vaginal samples from women with term deliveries were tested for torquetenovirus (TTV) by gene amplification, matrix metalloproteinase (MMP)-8 and D- and L-lactic acid by ELISA, and microbiome composition by analysis of the bacterial 16S ribosomal RNA gene. TTV was detected in 43.2%, 31.5%, and 41.4% of first trimester, third trimester, and postpartum samples, respectively. The viral titer was higher in postpartum than in the first (p = 0.0018) or third (p = 0.0013) trimester. The mean gestational age at delivery was lower in women positive for TTV in their first trimester (p = 0.0358). In the first and third trimester, the MMP-8 level was higher if TTV was also present (p < 0.0091). The D-lactic acid level was lower in first trimester samples if TTV was present (p = 0.0334). Lactobacillus crispatus dominance in first and third trimester samples was higher when TTV was absent (p < 0.0033). We conclude that TTV is present in the vagina in many women with normal pregnancy outcomes and that its occurrence is associated with a lack of L. crispatus dominance, an increase in vaginal MMP-8 and a decrease in D-lactic acid.
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Affiliation(s)
- Tania R Tozetto-Mendoza
- Virology laboratory (LIM 52), Tropical Medicine Institute, Medicine School, São Paulo University, Rua Dr. Enéas de Carvalho Aguiar, 470, Cerqueira Cesar, São Paulo, Brazil.
| | | | - Evelyn Minis
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, USA
| | - Iara M Linhares
- Department of Gynecology and Obstetrics, University of Sao Paulo Medical School, Sao Paulo, Brazil
| | - Allison Boester
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, USA
| | - Wilton S Freire
- Virology laboratory (LIM 52), Tropical Medicine Institute, Medicine School, São Paulo University, Rua Dr. Enéas de Carvalho Aguiar, 470, Cerqueira Cesar, São Paulo, Brazil
| | - Silvia H Lima
- Virology laboratory (LIM 52), Tropical Medicine Institute, Medicine School, São Paulo University, Rua Dr. Enéas de Carvalho Aguiar, 470, Cerqueira Cesar, São Paulo, Brazil
| | - Natan P G de Oliveira
- Virology laboratory (LIM 52), Tropical Medicine Institute, Medicine School, São Paulo University, Rua Dr. Enéas de Carvalho Aguiar, 470, Cerqueira Cesar, São Paulo, Brazil
| | - Maria C Mendes-Correa
- Virology laboratory (LIM 52), Tropical Medicine Institute, Medicine School, São Paulo University, Rua Dr. Enéas de Carvalho Aguiar, 470, Cerqueira Cesar, São Paulo, Brazil
| | - Larry J Forney
- Department of Biological Sciences and the Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA
| | - Steven S Witkin
- Virology laboratory (LIM 52), Tropical Medicine Institute, Medicine School, São Paulo University, Rua Dr. Enéas de Carvalho Aguiar, 470, Cerqueira Cesar, São Paulo, Brazil.,Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, USA
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144
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Wang XC, Wang H, Tan SD, Yang SX, Shi XF, Zhang W. Viral metagenomics reveals diverse anelloviruses in bone marrow specimens from hematologic patients. J Clin Virol 2020; 132:104643. [PMID: 32961430 DOI: 10.1016/j.jcv.2020.104643] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/11/2020] [Accepted: 09/13/2020] [Indexed: 01/01/2023]
Abstract
BACKGROUND An infectious etiology has been proposed for many human cancers, but rarely have specific agents been identified. Viral metagenomic technique is useful for identification of viral pathogens potentially existing in bone marrow specimens from hematologic patients. METHODS A total of 24 patients were included in this study, including 14 female (58.3 %) and 10 male patients (41.7 %) with a mean age of 55.20 ± 18.02 years (16-89 years).Twenty-four bone marrow specimens were collected from 24 hematologic patients (diagnosed with hypoferric anemia, diffuse large B cell lymphoma, myelodysplastic syndrome, acute myelo-monocytic leukemia, acute myelocytic leukemia with maturation, multiple myeloma, lymphoma angioimmunoblastic T cell, acute myeloid leukemia-M1, polycythemia vera/hypoferric anemia, leukocythemia, or megaloblastic anemia). Viral nucleic acid from marrow samples of hematologic patients were subjected to viral metagenomic analysis. PCR method was used to investigate the prevalence of these new viruses in this cohort of hematologic patients. Phylogenetic tree was established to elucidate the relationship of anelloviruses found here and the previously define ones. RESULTS Anelloviridae family are the main group of viruses detected in all the 4 libraries. Forty-six different species of Anelloviruses belonging to genera Alphatorquevirus, Betatorquevirus and Gammatorquevirus and unclassified anellovirus were recovered. Fifteen novel strains with complete ORF1 coding sequence were acquired and phylogenetically analyzed, indicating 8 of the 15 strains are proposed novel species belonging to genus Gammatorquevirus. Nested-PCR were then performed for these15 novel anellovirus strains in the 24 individual bone marrow samples, which showed 13 of them were present in more than one bone marrow samples. CONCLUSIONS Diverse types of anellovirus were present in bone marrow samples of hematologic patients. Whether these novel anelloviruses have association with certain hematonosis needs further investigation.
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Affiliation(s)
- Xiao-Chun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Hao Wang
- Department of Clinical Laboratory, Huai'an Hospital, Xuzhou Medical University, Huai'an 223002, China.
| | - Shi-Dong Tan
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Shi-Xing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Xiao-Feng Shi
- Department of Hematology, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212001, China
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China.
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145
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Maev IV, Karlovich TI, Burmistrov AI, Chekmazov IA, Andreev DN, Reshetnyak VI. Current Views of Torque Teno Virus (TTV) in Liver Diseases. RUSSIAN JOURNAL OF GASTROENTEROLOGY, HEPATOLOGY, COLOPROCTOLOGY 2020; 30:7-22. [DOI: 10.22416/1382-4376-2020-30-4-7-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Affiliation(s)
- I. V. Maev
- Moscow State University of Medicine and Dentistry
| | - T. I. Karlovich
- Central Clinical Hospital with Outpatient Care of the Russian President Administration
| | | | - I. A. Chekmazov
- Central Clinical Hospital with Outpatient Care of the Russian President Administration
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146
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Early life microbial exposures and allergy risks: opportunities for prevention. Nat Rev Immunol 2020; 21:177-191. [PMID: 32918062 DOI: 10.1038/s41577-020-00420-y] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2020] [Indexed: 02/07/2023]
Abstract
Allergies, including asthma, food allergy and atopic dermatitis, are increasing in prevalence, particularly in westernized countries. Although a detailed mechanistic explanation for this increase is lacking, recent evidence indicates that, in addition to genetic predisposition, lifestyle changes owing to modernization have an important role. Such changes include increased rates of birth by caesarean delivery, increased early use of antibiotics, a westernized diet and the associated development of obesity, and changes in indoor and outdoor lifestyle and activity patterns. Most of these factors directly and indirectly impact the formation of a diverse microbiota, which includes bacterial, viral and fungal components; the microbiota has a leading role in shaping (early) immune responses. This default programme is markedly disturbed under the influence of environmental and lifestyle risk factors. Here, we review the most important allergy risk factors associated with changes in our exposure to the microbial world and the application of this knowledge to allergy prevention strategies.
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147
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Beyond Cytomegalovirus and Epstein-Barr Virus: a Review of Viruses Composing the Blood Virome of Solid Organ Transplant and Hematopoietic Stem Cell Transplant Recipients. Clin Microbiol Rev 2020; 33:33/4/e00027-20. [PMID: 32847820 DOI: 10.1128/cmr.00027-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Viral primary infections and reactivations are common complications in patients after solid organ transplantation (SOT) and hematopoietic stem cell transplantation (HSCT) and are associated with high morbidity and mortality. Among these patients, viral infections are frequently associated with viremia. Beyond the usual well-known viruses that are part of the routine clinical management of transplant recipients, numerous other viral signatures or genomes can be identified in the blood of these patients. The identification of novel viral species and variants by metagenomic next-generation sequencing has opened up a new field of investigation and new paradigms. Thus, there is a need to thoroughly describe the state of knowledge in this field with a review of all viral infections that should be scrutinized in high-risk populations. Here, we review the eukaryotic DNA and RNA viruses identified in blood, plasma, or serum samples of pediatric and adult SOT/HSCT recipients and the prevalence of their detection, with a particular focus on recently identified viruses and those for which their potential association with disease remains to be investigated, such as members of the Polyomaviridae, Anelloviridae, Flaviviridae, and Astroviridae families. Current knowledge of the clinical significance of these viral infections with associated viremia among transplant recipients is also discussed. To ensure a comprehensive description in these two populations, individuals described as healthy (mostly blood donors) are considered for comparative purposes. The list of viruses that should be on the clinicians' radar is certainly incomplete and will expand, but the challenge is to identify those of possible clinical significance.
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148
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Doberer K, Schiemann M, Strassl R, Haupenthal F, Dermuth F, Görzer I, Eskandary F, Reindl‐Schwaighofer R, Kikić Ž, Puchhammer‐Stöckl E, Böhmig GA, Bond G. Torque teno virus for risk stratification of graft rejection and infection in kidney transplant recipients-A prospective observational trial. Am J Transplant 2020; 20:2081-2090. [PMID: 32034850 PMCID: PMC7496119 DOI: 10.1111/ajt.15810] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 01/28/2020] [Accepted: 01/31/2020] [Indexed: 01/25/2023]
Abstract
The nonpathogenic and ubiquitous torque teno virus (TTV) is associated with immunosuppression in solid organ transplant recipients. Studies in kidney transplant patients proposed TTV quantification for risk stratification of graft rejection and infection. In this prospective trial (DRKS00012335) 386 consecutive kidney transplant recipients were subjected to longitudinal per-protocol monitoring of plasma TTV load by polymerase chain reaction for 12 months posttransplant. TTV load peaked at the end of month 3 posttransplant and reached steady state thereafter. TTV load after the end of month 3 was analyzed in the context of subsequent rejection diagnosed by indication biopsy and infection within the first year posttransplant, respectively. Each log increase in TTV load decreased the odds for rejection by 22% (odds ratio [OR] 0.78, 95% confidence interval [CI] 0.62-0.97; P = .027) and increased the odds for infection by 11% (OR 1.11, 95% CI 1.06-1.15; P < .001). TTV was quantified at a median of 14 days before rejection was diagnosed and 27 days before onset of infection, respectively. We defined a TTV load between 1 × 106 and 1 × 108 copies/mL as optimal range to minimize the risk for rejection and infection. These data support the initiation of an interventional trial assessing the efficacy of TTV-guided immunosuppression to reduce infection and graft rejection in kidney transplant recipients.
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Affiliation(s)
- Konstantin Doberer
- Division of Nephrology and DialysisDepartment of Medicine IIIMedical University ViennaViennaAustria
| | - Martin Schiemann
- Division of Nephrology and DialysisDepartment of Medicine IIIMedical University ViennaViennaAustria
| | - Robert Strassl
- Division of VirologyDepartment of Laboratory MedicineMedical University ViennaViennaAustria
| | - Frederik Haupenthal
- Division of Nephrology and DialysisDepartment of Medicine IIIMedical University ViennaViennaAustria
| | - Florentina Dermuth
- Division of Nephrology and DialysisDepartment of Medicine IIIMedical University ViennaViennaAustria
| | - Irene Görzer
- Center for VirologyMedical University ViennaViennaAustria
| | - Farsad Eskandary
- Division of Nephrology and DialysisDepartment of Medicine IIIMedical University ViennaViennaAustria
| | | | - Željko Kikić
- Division of Nephrology and DialysisDepartment of Medicine IIIMedical University ViennaViennaAustria
| | | | - Georg A. Böhmig
- Division of Nephrology and DialysisDepartment of Medicine IIIMedical University ViennaViennaAustria
| | - Gregor Bond
- Division of Nephrology and DialysisDepartment of Medicine IIIMedical University ViennaViennaAustria
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149
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Legoff J, Michonneau D, Socie G. The virome in hematology-Stem cell transplantation and beyond. Semin Hematol 2020; 57:19-25. [PMID: 32690140 DOI: 10.1053/j.seminhematol.2020.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 05/06/2020] [Indexed: 12/23/2022]
Abstract
The virome has been recently studied in hematology and mostly in the setting of allogeneic hematopoietic stem cell transplantation. However, in hematology (as in the setting of nonhematological disorders) the study of the microbiome (that indeed includes the virome) is a growing field. The overall field is moving beyond species catalogue to the understanding of the complex ecological relationship that microbes have with each other and with their host. Here we review the existing literature on the virome in transplant recipients and in other settings, and discuss potential applications of the virome study in hematology.
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Affiliation(s)
- Jérôme Legoff
- Université de Paris, INSERM U976, Paris, France; Microbiology department, Virology laboratory, Saint Louis Hospital, Paris, France
| | - David Michonneau
- Université de Paris, INSERM U976, Paris, France; Hematology-Transplantation, Saint Louis Hospital, Paris, France
| | - Gérard Socie
- Université de Paris, INSERM U976, Paris, France; Hematology-Transplantation, Saint Louis Hospital, Paris, France.
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150
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Biomarkers for PTLD diagnosis and therapies. Pediatr Nephrol 2020; 35:1173-1181. [PMID: 31240394 DOI: 10.1007/s00467-019-04284-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/14/2019] [Accepted: 05/31/2019] [Indexed: 02/08/2023]
Abstract
Post-transplant lymphoproliferative disorder (PTLD) represents a spectrum of lymphoproliferative disorders and is a serious complication of pediatric transplantation. The majority of PTLD are associated with Epstein Barr virus (EBV) and the characteristic EBV+ B cell lymphomas are the leading post-transplant malignancy in children. EBV+ PTLD remains a formidable issue in pediatric transplantation and is thought to result from impaired immunity to EBV as a result of immunosuppression. However, the key viral and immune factors that determine whether EBV+ PTLD develops remain unknown. Recently, there has been much interest in developing biomarkers in order to improve and achieve more personalized approaches, in the clinical diagnosis, management, and treatment of EBV+ PTLD. Here, we review the status of immune-, viral-, and B cell lymphoma-derived candidates for biomarkers of EBV+ PTLD.
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