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The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease


Much attention has been focused on the role of the bacterial microbiome in human health, but the virome is understudied. Although previously investigated in individuals with inflammatory bowel diseases or solid-organ transplants1,2, virome dynamics in allogeneic hematopoietic stem cell transplantation (HSCT) and enteric graft-versus-host disease (GVHD) remain unexplored. Here we characterize the longitudinal gut virome in 44 recipients of HSCT using metagenomics. A viral 'bloom' was identified, and significant increases were demonstrated in the overall proportion of vertebrate viral sequences following transplantation (P = 0.02). Increases in both the rates of detection (P < 0.0001) and number of sequences (P = 0.047) of persistent DNA viruses (anelloviruses, herpesviruses, papillomaviruses and polyomaviruses) over time were observed in individuals with enteric GVHD relative to those without, a finding accompanied by a reduced phage richness (P = 0.01). Picobirnaviruses were detected in 18 individuals (40.9%), more frequently before or within a week after transplant than at later time points (P = 0.008). In a time-dependent Cox proportional-hazards model, picobirnaviruses were predictive of the occurrence of severe enteric GVHD (hazard ratio, 2.66; 95% confidence interval (CI) = 1.46–4.86; P = 0.001), and correlated with higher fecal levels of two GVHD severity markers, calprotectin and α1-antitrypsin. These results reveal a progressive expansion of vertebrate viral infections over time following HSCT, and they suggest an unexpected association of picobirnaviruses with early post-transplant GVHD.

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Figure 1: Collection of stool samples for virome analysis according to stage of enteric GVHD.
Figure 2: Microbiome and phage virome dynamics.
Figure 3: Evolution of the enteric virome following transplantation.
Figure 4: Frequency and diversity of PBVs in individuals with or without enteric GVHD.


  1. De Vlaminck, I. et al. Temporal response of the human virome to immunosuppression and antiviral therapy. Cell 155, 1178–1187 (2013).

    CAS  Article  Google Scholar 

  2. Norman, J.M. et al. Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell 160, 447–460 (2015).

    CAS  Article  Google Scholar 

  3. Feghoul, L. et al. Adenovirus infection and disease in paediatric haematopoietic stem cell transplant patients: clues for antiviral pre-emptive treatment. Clin. Microbiol. Infect. 21, 701–709 (2015).

    CAS  Article  Google Scholar 

  4. Pichereau, C. et al. The complex relationship between human herpesvirus 6 and acute graft-versus-host disease. Biol. Blood Marrow Transplant. 18, 141–144 (2012).

    Article  Google Scholar 

  5. Zerr, D.M. et al. HHV-6 reactivation and associated sequelae after hematopoietic cell transplantation. Biol. Blood Marrow Transplant. 18, 1700–1708 (2012).

    Article  Google Scholar 

  6. Jenq, R.R. et al. Regulation of intestinal inflammation by microbiota following allogeneic bone marrow transplantation. J. Exp. Med. 209, 903–911 (2012).

    CAS  Article  Google Scholar 

  7. Minot, S. et al. The human gut virome: inter-individual variation and dynamic response to diet. Genome Res. 21, 1616–1625 (2011).

    CAS  Article  Google Scholar 

  8. Schwartz, S. et al. Norovirus gastroenteritis causes severe and lethal complications after chemotherapy and hematopoietic stem cell transplantation. Blood 117, 5850–5856 (2011).

    CAS  Article  Google Scholar 

  9. Yang, J.Y. et al. Enteric viruses ameliorate gut inflammation via Toll-like receptor 3 and Toll-like receptor 7-mediated interferon-β production. Immunity 44, 889–900 (2016).

    CAS  Article  Google Scholar 

  10. Finkbeiner, S.R. et al. Metagenomic analysis of human diarrhea: viral detection and discovery. PLoS Pathog. 4, e1000011 (2008).

    Article  Google Scholar 

  11. Phan, T.G. et al. Acute diarrhea in West African children: diverse enteric viruses and a novel parvovirus genus. J. Virol. 86, 11024–11030 (2012).

    CAS  Article  Google Scholar 

  12. Victoria, J.G. et al. Metagenomic analyses of viruses in stool samples from children with acute flaccid paralysis. J. Virol. 83, 4642–4651 (2009).

    CAS  Article  Google Scholar 

  13. Naccache, S.N. et al. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res. 24, 1180–1192 (2014).

    CAS  Article  Google Scholar 

  14. Rodriguez-Otero, P. et al. Fecal calprotectin and alpha-1 antitrypsin predict severity and response to corticosteroids in gastrointestinal graft-versus-host disease. Blood 119, 5909–5917 (2012).

    CAS  Article  Google Scholar 

  15. Alhabbab, R. et al. Diversity of gut microflora is required for the generation of B cell with regulatory properties in a skin graft model. Sci. Rep. 5, 11554 (2015).

    CAS  Article  Google Scholar 

  16. Mathewson, N.D. et al. Gut microbiome-derived metabolites modulate intestinal epithelial cell damage and mitigate graft-versus-host disease. Nat. Immunol. 17, 505–513 (2016).

    CAS  Article  Google Scholar 

  17. Kim, K.S. et al. Dietary antigens limit mucosal immunity by inducing regulatory T cells in the small intestine. Science 351, 858–863 (2016).

    CAS  Article  Google Scholar 

  18. Ganesh, B. et al. Picobirnavirus infections: viral persistence and zoonotic potential. Rev. Med. Virol. 22, 245–256 (2012).

    CAS  Article  Google Scholar 

  19. Bányai, K. et al. Sequence heterogeneity among human picobirnaviruses detected in a gastroenteritis outbreak. Arch. Virol. 148, 2281–2291 (2003).

    Article  Google Scholar 

  20. Bhattacharya, R. et al. Molecular epidemiology of human picobirnaviruses among children of a slum community in Kolkata, India. Infect. Genet. Evol. 6, 453–458 (2006).

    CAS  Article  Google Scholar 

  21. van Leeuwen, M. et al. Human picobirnaviruses identified by molecular screening of diarrhea samples. J. Clin. Microbiol. 48, 1787–1794 (2010).

    CAS  Article  Google Scholar 

  22. Grohmann, G.S. et al. Enteric viruses and diarrhea in HIV-infected patients. N. Engl. J. Med. 329, 14–20 (1993).

    CAS  Article  Google Scholar 

  23. Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30, 2725–2729 (2013).

    CAS  Article  Google Scholar 

  24. Bhattacharya, R. et al. Detection of Genogroup I and II human picobirnaviruses showing small genomic RNA profile causing acute watery diarrhoea among children in Kolkata, India. Infect. Genet. Evol. 7, 229–238 (2007).

    CAS  Article  Google Scholar 

  25. Masachessi, G. et al. Maintenance of picobirnavirus (PBV) infection in an adult orangutan (Pongo pygmaeus) and genetic diversity of excreted viral strains during a three-year period. Infect. Genet. Evol. 29, 196–202 (2015).

    Article  Google Scholar 

  26. Smits, S.L. et al. New viruses in idiopathic human diarrhea cases, the Netherlands. Emerg. Infect. Dis. 20, 1218–1222 (2014).

    Article  Google Scholar 

  27. Glucksberg, H. et al. Clinical manifestations of graft-versus-host disease in human recipients of marrow from HL-A-matched sibling donors. Transplantation 18, 295–304 (1974).

    CAS  Article  Google Scholar 

  28. Przepiorka, D. et al. 1994 Consensus Conference on Acute GVHD Grading. Bone Marrow Transplant. 15, 825–828 (1995).

    CAS  PubMed  Google Scholar 

  29. Abraham, J. et al. Clinical severity scores in gastrointestinal graft-versus-host disease. Transplantation 97, 965–971 (2014).

    CAS  PubMed  Google Scholar 

  30. O'Meara, A. et al. Fecal calprotectin and α1-antitrypsin dynamics in gastrointestinal GvHD. Bone Marrow Transplant. 50, 1105–1109 (2015).

    CAS  Article  Google Scholar 

  31. Kleiner, M., Hooper, L.V. & Duerkop, B.A. Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes. BMC Genomics 16, 7 (2015).

    Article  Google Scholar 

  32. Li, L. et al. Comparing viral metagenomics methods using a highly multiplexed human viral pathogens reagent. J. Virol. Methods 213, 139–146 (2015).

    CAS  Article  Google Scholar 

  33. Chen, E.C., Miller, S.A., DeRisi, J.L. & Chiu, C.Y. Using a pan-viral microarray assay (Virochip) to screen clinical samples for viral pathogens. J. Vis. Exp. 50, 2536 (2011).

    Google Scholar 

  34. Zaharia, M. et al. Faster and more accurate sequence alignment with SNAP. Preprint at arXiv (2011).

  35. Zhao, Y., Tang, H. & Ye, Y. RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics 28, 125–126 (2012).

    CAS  Article  Google Scholar 

  36. Lan, Y., Wang, Q., Cole, J.R. & Rosen, G.L. Using the RDP classifier to predict taxonomic novelty and reduce the search space for finding novel organisms. PLoS One 7, e32491 (2012).

    CAS  Article  Google Scholar 

  37. You, F.M. et al. BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 9, 253 (2008).

    Article  Google Scholar 

  38. Langmead, B. & Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

    CAS  Article  Google Scholar 

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This study was supported by a research grant from Abbott Laboratories to C.Y.C. We would also like to acknowledge funding from the US–France Fulbright Commission, Foundation Monahan and Foundation Phillippe for funding J.L. for a research sabbatical year to perform this research.

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Authors and Affiliations



J.L. conceived of the study, performed the experiments, analyzed the data, designed the figures and wrote the manuscript. M.R.-R. performed the statistical analyses and designed the figures. J.B. ran PCR confirmation for picobirnaviruses and analyzed the data. M.R. collected clinical data. S.M.-D., prepared patient samples for virome analysis and microbiome analysis. S.N.N., S.F. and E.S. contributed to the analysis of patient, microbiome and virome data. C.R. and N.K. contributed to the analysis of microbiome and stool biomarkers. P.P. contributed to statistical analysis. F.S. provided funding and resources and contributed to the discussion. G.S. conceived of the study, analyzed the data and wrote the manuscript. C.Y.C. conceived of the study, analyzed the data, designed the figures and wrote the manuscript. All authors provided feedback on the manuscript. F.S., G.S., J.L. and C.Y.C. supervised the project. J.L. and C.Y.C. secured funding for the study.

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Correspondence to Charles Y Chiu.

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Competing interests

C.Y.C. is the director of the UCSF–Abbott Viral Diagnostics and Discovery Center and receives research support from Abbott Laboratories.

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Supplementary Results, Supplementary Tables 1–11 and Supplementary Figures 1–4 (PDF 1303 kb)

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Legoff, J., Resche-Rigon, M., Bouquet, J. et al. The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease. Nat Med 23, 1080–1085 (2017).

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