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Viruses in transplantation - not always enemies Virome and transplantation ECCMID 2018 - Madrid Prof. Laurent Kaiser Head Division of Infectious Diseases Laboratory of Virology Geneva Center for Emerging Viral Diseases University Hospital of Geneva ESCMID eLibrary © by author Conflict of interest None ESCMID eLibrary © by author The human virome: definition? Repertoire of viruses found on the surface of/inside any body fluid/tissue • Eukaryotic DNA and RNA viruses • Prokaryotic DNA and RNA viruses (phages) 25 • The “main” viral community (up to 10 bacteriophages in humans) Haynes M. 2011, Metagenomic of the human body • Endogenous viral elements integrated into host chromosomes (8% of the human genome) • NGS is shaping the definition Rascovan N et al. Annu Rev Microbiol 2016;70:125-41 Popgeorgiev N et al. Intervirology 2013;56:395-412 Norman JM et al. Cell 2015;160:447-60 ESCMID eLibraryFoxman EF et al. Nat Rev Microbiol 2011;9:254-64 © by author Viruses routinely known to cause diseases (non exhaustive) Upper resp./oropharyngeal HSV 1 Influenza CNS Mumps virus Rhinovirus JC virus RSV Eye Herpes viruses Parainfluenza HSV Measles Coronavirus Adenovirus LCM virus Cytomegalovirus Flaviviruses Rabies HHV6 Poliovirus Heart Lower respiratory HTLV-1 Coxsackie B virus Rhinoviruses Parainfluenza virus HIV Coronaviruses Respiratory syncytial virus Parainfluenza virus Adenovirus Respiratory syncytial virus Coronaviruses Gastro-intestinal Influenza virus type A and B Human Bocavirus 1 Adenovirus Hepatitis virus type A, B, C, D, E Those that cause asymptomatic reactivations/infectionsRotavirus Yellow fever Norovirus Astrovirus Coxsackie B virus Skin /mucosa are often considered as part of the virome VZV, CMV, HHV8 Human papillomavirus Genital tract Human polyomavirus HSV 2 (Merkel) Systemic / blood Human papillomavirus Parvovirus B19 Mumps virus Rubella HHV6 HIV, HBV Rubella Adenovirus Measles HTLV-1 HSV Measles Epstein-Barr virus Enteroviruses HIV Enteroviruses Cytomegalovirus Flavivirus Yellow fever VZV, CMV, HHV8 Human polyomavirus ESCMIDParvovirus B19 Hepatitis eLibraryvirus type A, B, C, D, E © by author Virome: the definition has evolved with the technology (NGS) Vertebrates: 1’500 viral species ≈ 180 viruses known to infect or detected at least once in humans P Lemercier ViralZone ESCMID eLibrary © by author NGS & the black box: you need to trust… The sample preparation The sequencing procedure The quality of the database The bioinformatics pipeline You need a tool to communicate with the average microbiologist ESCMID eLibrary © by author NGS and the basic I learned at school A diagnostic test should have excellent: Sensitivity and specificity Positive and negative predictive values PCR-based assays: Everything is done to avoid contamination ESCMID eLibrary © by author NGS at the analytical level Sensitivity: can be high but also very low Limit of detection/quantification: copies/mL vs. number of reads Specificity: could be perfect or "catastrophic“ Viral sequences in reagents… Banana bunchy top virus Endless list of “false-positive” results ESCMID eLibrary © by author CSF negative control report (RNA and DNA protocols) Canine distemper virus (positive control) Merkel cell p. Polyomavirus HSV 1 Papillomavirus ESCMID eLibrary Known as a reagent contaminant (vector ) © by author NGS and the eukaryotic human virome Viral sequences ≠ replication competent viruses We do not see the virus or any viral antigens Serological assays: not available for many viruses Association with disease: confirmed, probable, possible, none Contamination and uncertainty are part of the game ESCMID eLibrary DL Vu et al. CMI 2017 © by author Eukaryotic viruses in blood of « asymptomatic » humans (non exhaustive) Pubmed search with algorithms of keywords and MeSH > 300 papers investigating the virome in humans ESCMIDDiem Lan Vu Cantero Samuel CordeyeLibraryMarie-Céline Zanella © by author Blood Virome Association with diseases (confirmed, probable, possible or none) Herpesviridae HSV1-2, VZV, EBV, CMV, HHV6, HHV8 HHV7 Polyomaviridae BK virus, JC virus Merkel, TdS PyV HPyV 6-7-9 Adenoviridae adenovirus A-F Parvoviridae parvovirus B19 bocavirus, parvo 4 Papillomaviridae Different serotypes Anelloviridae TTV, TTMV, TTMDV Cycloviridae cyclovirus Vietnam Circoviridae human circovirus Picornaviridae enterovirus cardiovirus, salivirus Flaviviridae human pegivirus 1-2 Picobirnaviruses ESCMID eLibrary © by author Blood DNA virome 8’000 individuals Healthy or with comorbidities/chronic diseases “by-product” of a large human genome study Viral sequences mapped 94 viruses Prevalence: age dependent ESCMID eLibraryMoustafa A et al. 2017 PLoS Pathog © by author HHV7 Primary infection during childhood : roseola Seroprevalence > 90% in adults Tropism : CD4 T lymphocytes Lusso P PNAS 1994 SOT: primary infection or reactivation in up to 46% of patients HSCT: primary infection or reactivation in 44% (adults) ESCMID eLibraryAgut H et al. Human Herpesviruses 6A, 6B, and 7. Microbiol Spectr . 2016 Jun;4(3) © by author HHV7: possible associations with diseases Fever and acute myelitis Fever, rash, hepatitis, pneumonitis in IC hosts Bronchiolitis obliterans syndrome after lung transplantation Allograft rejection and dysfunction in case of co-infection with HHV-6 Association with CMV infection and disease ESCMID eLibraryAgut H et al. Human Herpesviruses 6A, 6B, and 7. Microbiol Spectr . 2016 Jun;4(3) © by author NGS/virome in transplant recipients ESCMID eLibrary © by author DNA virome in Heart & Lung transplant recipients Cell free DNA in plasma (656 samples) Anelloviridae 68% Heart recipients: pediatric (24) and Herpesvirales 13% adults (41) Caudovirales 5% Lung recipients: adults (31) Polyomaviridae 5% Adenoviridae 2% Poxviridae 1% Retroviridae 1% Other 5% ESCMID eLibraryI De Vlaminck. Cell. 2013 Nov 21;155(5):1178 -87. © by author Response to immunosuppression & antiviral therapy (valaciclovir / tacrolimus) Temporal association ? Effect on adenoviruses? ESCMID eLibraryI De Vlaminck. Cell. 2013 Nov 21;155(5):1178 -87. © by author Polyomaviridae Bialasiewicz Am J Transplant 2016, Bialasiewicz J Clin Virol 2009, Moens Patholog Res Int 2011, Rockette PlosOne 2013, Dialanis Virology 2013 Seroprevalence DNA detection in clinical samples Children Adult blood urine GI skin resp CNS HPyV1 BK polyomavirus 73% 82-87.6% ? ? HPyV2 JC polyomavirus 21% 35-58% ? HPyV3 Karolinska Insitute polyomavirus 56% 55-91.3 ? ? ? ? HPyV4 Washington University polyomavirus 54% 69-97.4% HPyV5 Merkel cell polyomavirus 23-34% 25-70.4% HPyV6 unkown 69-73.7% HPyV7 unkown 35% Trichodysplasia spinulosa associated HPyV8 polyomavirus unkown 80.9% HPyV9 20% 17.6-47% HPyV10 Malawi polyomavirus unkown 99.1% HPyV11 Saint Louis polyomavirus 34-61% 90-93.3% HPyV12 34-80% 90-97.3% ESCMIDHPyV13 New Jersey polyomavirus 7.5 -33%eLibrary 31.4-57.5% © by author Post-transplant Merkel cell carcinoma Neuroendocrine skin cancer Very rare but 66 to 182 fold increased risk in transplant recipients V Koljonen Acta Dermato Venerologica 2016 ESCMID eLibraryFeng Science 2008 © by author Trichodysplasia Spinulosa Polyomavirus Rare skin disease (> 35 cases reported) Acute primary infection (not reactivation/chronic infection) with high viral load (skin, blood and CSF) may be the cause of complications ESCMID eLibraryE van der Meijden J Infect Dis. 2016 © by author New Jersey polyomavirus Pancreas transplantation Acute myopathy, retinal blindness and skin lesions High viral load in skin lesions and blood Histopathology suggest endothelial tropism ESCMID eLibraryN Mishra J Infect Dis. 2014 © by author Disease association: confirmed, probable, possible, none Seroprevalence DNA detection in clinical samples Children Adult blood urine GI skin resp CNS HPyV1 BK polyomavirus 73% 82-87.6% ? ? HPyV2 JC polyomavirus 21% 35-58% ? HPyV3 Karolinska Insitute polyomavirus 56% 55-91.3 ? ? ? ? HPyV4 Washington University polyomavirus 54% 69-97.4% HPyV5 Merkel cell polyomavirus 23-34% 25-70.4% HPyV6 unkown 69-73.7% HPyV7 unkown 35% Trichodysplasia spinulosa associated HPyV8 polyomavirus unkown 80.9% HPyV9 20% 17.6-47% HPyV10 Malawi polyomavirus unkown 99.1% HPyV11 Saint Louis polyomavirus 34-61% 90-93.3% HPyV12 34-80% 90-97.3% ESCMIDHPyV13 New Jersey polyomavirus 7.5 -33%eLibrary 31.4-57.5% © by author Disease association: confirmed, probable, possible, none Seroprevalence DNA detection in clinical samples Children Adult blood urine GI skin resp CNS HPyV1 BK polyomavirus 73% 82-87.6% ? ? HPyV2 JC polyomavirus 21% 35-58% ? HPyV3 Karolinska Insitute polyomavirus 56% 55-91.3 ? ? ? ? HPyV4 Washington University polyomavirus 54% 69-97.4% HPyV5 Merkel cell polyomavirus 23-34% 25-70.4% HPyV6 unkown 69-73.7% HPyV7 unkown 35% Trichodysplasia spinulosa associated HPyV8 polyomavirus unkown 80.9% HPyV9 20% 17.6-47% HPyV10 Malawi polyomavirus unkown 99.1% HPyV11 Saint Louis polyomavirus 34-61% 90-93.3% HPyV12 34-80% 90-97.3% ESCMIDHPyV13 New Jersey polyomavirus 7.5 -33%eLibrary 31.4-57.5% © by author 55 year old man. Allogeneic HSCT for T cell lymphoma in October . CMV D+/R+, EBV D+/R+ December: acute grade 3 intestinal GVHD -> high dose steroids BK virus: urine 3.59 copies/mL, 2.84 in plasma CMV: 2.42 copies/mL in plasma, 2.72 copies/mL in BAL EBV in plasma: 4.24 copies/mL Adenovirus : 6.52 copies/mL in plasma (and prolonged stool carriage) Norovirus: prolonged stool carriage ESCMID eLibrary © by author dsDNA viruses in the plasma of HSCT recipients Weekly samples during 100
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  • The LUCA and Its Complex Virome in Another Recent Synthesis, We Examined the Origins of the Replication and Structural Mart Krupovic , Valerian V

    The LUCA and Its Complex Virome in Another Recent Synthesis, We Examined the Origins of the Replication and Structural Mart Krupovic , Valerian V

    PERSPECTIVES archaea that form several distinct, seemingly unrelated groups16–18. The LUCA and its complex virome In another recent synthesis, we examined the origins of the replication and structural Mart Krupovic , Valerian V. Dolja and Eugene V. Koonin modules of viruses and posited a ‘chimeric’ scenario of virus evolution19. Under this Abstract | The last universal cellular ancestor (LUCA) is the most recent population model, the replication machineries of each of of organisms from which all cellular life on Earth descends. The reconstruction of the four realms derive from the primordial the genome and phenotype of the LUCA is a major challenge in evolutionary pool of genetic elements, whereas the major biology. Given that all life forms are associated with viruses and/or other mobile virion structural proteins were acquired genetic elements, there is no doubt that the LUCA was a host to viruses. Here, by from cellular hosts at different stages of evolution giving rise to bona fide viruses. projecting back in time using the extant distribution of viruses across the two In this Perspective article, we combine primary domains of life, bacteria and archaea, and tracing the evolutionary this recent work with observations on the histories of some key virus genes, we attempt a reconstruction of the LUCA virome. host ranges of viruses in each of the four Even a conservative version of this reconstruction suggests a remarkably complex realms, along with deeper reconstructions virome that already included the main groups of extant viruses of bacteria and of virus evolution, to tentatively infer archaea. We further present evidence of extensive virus evolution antedating the the composition of the virome of the last universal cellular ancestor (LUCA; also LUCA.