Viral sequences detection by high-throughput sequencing in cerebrospinal fluid of individuals with and without central nervous system disease

Genes

Volumn 10, Issue 8, 2019, Pages 1-12

  Schibler, Manuel ^a   Brito, Francisco ^b,c   Zanella, Marie Céline ^a   Zdobnov, Evgeny M ^b,c   Laubscher, Florian ^a   L’huillier, Arnaud G ^a   Ambrosioni, Juan ^d   Wagner, Noémie ^a   Posfay Barbe, Klara M ^a   Docquier, Mylène ^e   Schiffer, Eduardo ^a,c   Savoldelli, Georges L ^a,c   Fournier, Roxane ^a   Lenggenhager, Lauriane ^a   Cordey, Samuel ^a   Kaiser, Laurent ^a,c  

^a GENEVA UNIVERSITY HOSPITALS   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^c UNIVERSITY OF GENEVA MEDICAL SCHOOL   (Switzerland)

^d UNIVERSITY OF BARCELONA   (Spain)

^e UNIVERSITY OF GENEVA   (Switzerland)

Author keywords

Acute central nervous system inflammation; Cerebrospinal fluid; Encephalitis; High throughput sequencing; Meningitis; Myelitis; Viral sequences; Viruses

Indexed keywords

VIRUS RNA;

ADOLESCENT; ADULT; CEREBROSPINAL FLUID; CHEMISTRY; CHILD; FEMALE; GENETICS; HUMAN; MALE; MIDDLE AGED; MOLECULAR DIAGNOSIS; MYELITIS; PROCEDURES; SEQUENCE ANALYSIS; VIROLOGY; VIRUS ENCEPHALITIS; VIRUS MENINGITIS;

ADOLESCENT; ADULT; CEREBROSPINAL FLUID; CHILD; ENCEPHALITIS, VIRAL; FEMALE; HUMANS; MALE; MENINGITIS, VIRAL; MIDDLE AGED; MOLECULAR DIAGNOSTIC TECHNIQUES; MYELITIS; RNA, VIRAL; SEQUENCE ANALYSIS, RNA;

EID: 85077264013     PISSN: None     EISSN: 20734425     Source Type: Journal    
DOI: 10.3390/genes10080625     Document Type: Article

References (39)

1. Dalmau, J.; Graus, F. Antibody-Mediated Encephalitis. N. Engl. J. Med. 2018, 378, 840–851. [CrossRef] [PubMed]
2. Granerod, J.; Ambrose, H.E.; Davies, N.W.; Clewley, J.P.; Walsh, A.L.; Morgan, D.; Cunningham, R.; Zuckerman, M.; Mutton, K.J.; Solomon, T.; et al. Causes of encephalitis and differences in their clinical presentations in England: A multicentre, population-based prospective study. Lancet Infect. Dis. 2010, 10, 835–844. [CrossRef]
3. Mailles, A.; Stahl, J.P.; Steering, C.; Investigators, G. Infectious encephalitis in france in 2007: A national prospective study. Clin. Infect. Dis. 2009, 49, 1838–1847. [CrossRef]
4. Swanson, P.A., II; McGavern, D.B. Viral diseases of the central nervous system. Curr. Opin. Virol. 2015, 11, 44–54. [CrossRef] [PubMed]
5. Boucher, A.; Herrmann, J.L.; Morand, P.; Buzele, R.; Crabol, Y.; Stahl, J.P.; Mailles, A. Epidemiology of infectious encephalitis causes in 2016. Med. Mal. Infect. 2017, 47, 221–235. [CrossRef] [PubMed]
6. Mailles, A.; Stahl, J.P.; Bloch, K.C. Update and new insights in encephalitis. Clin. Microbiol. Infect. 2017, 23, 607–613. [CrossRef]
7. Wilson, M.R.; Sample, H.A.; Zorn, K.C.; Arevalo, S.; Yu, G.; Neuhaus, J.; Federman, S.; Stryke, D.; Briggs, B.; Langelier, C.; et al. Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis. N. Engl. J. Med. 2019, 380, 2327–2340. [CrossRef] [PubMed]
8. Zanella, M.C.; Lenggenhager, L.; Schrenzel, J.; Cordey, S.; Kaiser, L. High-throughput sequencing for the aetiologic identification of viral encephalitis, meningoencephalitis, and meningitis. A narrative review and clinical appraisal. Clin. Microbiol. Infect. 2019, 25, 422–430. [CrossRef]
9. Chen, C.Y.; Chang, Y.C.; Huang, C.C.; Lui, C.C.; Lee, K.W.; Huang, S.C. Acute flaccid paralysis in infants and young children with enterovirus 71 infection: MR imaging findings and clinical correlates. Am. J. Neuroradiol. 2001, 22, 200–205. [PubMed]
10. Kraushaar, G.; Patel, R.; Stoneham, G.W. West Nile Virus: A case report with flaccid paralysis and cervical spinal cord: MR imaging findings. Am. J. Neuroradiol. 2005, 26, 26–29. [PubMed]
11. Venkatesan, A.; Tunkel, A.R.; Bloch, K.C.; Lauring, A.S.; Sejvar, J.; Bitnun, A.; Stahl, J.P.; Mailles, A.; Drebot, M.; Rupprecht, C.E.; et al. Case definitions, diagnostic algorithms, and priorities in encephalitis: Consensus statement of the international encephalitis consortium. Clin. Infect. Dis. 2013, 57, 1114–1128. [CrossRef] [PubMed]
12. Leber, A.L.; Everhart, K.; Balada-Llasat, J.M.; Cullison, J.; Daly, J.; Holt, S.; Lephart, P.; Salimnia, H.; Schreckenberger, P.C.; DesJarlais, S.; et al. Multicenter Evaluation of BioFire FilmArray Meningitis/Encephalitis Panel for Detection of Bacteria, Viruses, and Yeast in Cerebrospinal Fluid Specimens. J. Clin. Microbiol. 2016, 54, 2251–2261. [CrossRef] [PubMed]
13. Petty, T.J.; Cordey, S.; Padioleau, I.; Docquier, M.; Turin, L.; Preynat-Seauve, O.; Zdobnov, E.M.; Kaiser, L. Comprehensive human virus screening using high-throughput sequencing with a user-friendly representation of bioinformatics analysis: A pilot study. J. Clin. Microbiol. 2014, 52, 3351–3361. [CrossRef]
14. Wright, E.S.; Vetsigian, K.H. Quality filtering of Illumina index reads mitigates sample cross-talk. BMC Genom. 2016, 17, 876. [CrossRef] [PubMed]
15. Peng, Y.; Leung, H.C.; Yiu, S.M.; Chin, F.Y. IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 2012, 28, 1420–1428. [CrossRef] [PubMed]
16. Arvia, R.; Sollai, M.; Pierucci, F.; Urso, C.; Massi, D.; Zakrzewska, K. Droplet digital PCR (ddPCR) vs quantitative real-time PCR (qPCR) approach for detection and quantification of Merkel cell polyomavirus (MCPyV) DNA in formalin fixed paraffin embedded (FFPE) cutaneous biopsies. J. Virol. Methods 2017, 246, 15–20. [CrossRef] [PubMed]
17. Chivero, E.T.; Bhattarai, N.; Rydze, R.T.; Winters, M.A.; Holodniy, M.; Stapleton, J.T. Human pegivirus RNA is found in multiple blood mononuclear cells in vivo and serum-derived viral RNA-containing particles are infectious in vitro. J. Gen. Virol. 2014, 95, 1307–1319. [CrossRef] [PubMed]
18. Kimura, H.; Morita, M.; Yabuta, Y.; Kuzushima, K.; Kato, K.; Kojima, S.; Matsuyama, T.; Morishima, T. Quantitative analysis of Epstein-Barr virus load by using a real-time PCR assay. J. Clin. Microbiol. 1999, 37, 132–136. [PubMed]
19. Masouridi-Levrat, S.; Pradier, A.; Simonetta, F.; Kaiser, L.; Chalandon, Y.; Roosnek, E. Torque teno virus in patients undergoing allogeneic hematopoietic stem cell transplantation for hematological malignancies. Bone Marrow Transplant. 2016, 51, 440–442. [CrossRef]
20. Verheyen, J.; Timmen-Wego, M.; Laudien, R.; Boussaad, I.; Sen, S.; Koc, A.; Uesbeck, A.; Mazou, F.; Pfister, H. Detection of adenoviruses and rotaviruses in drinking water sources used in rural areas of Benin, West Africa. Appl. Environ. Microbiol. 2009, 75, 2798–2801. [CrossRef]
21. Cordey, S.; Vu, D.L.; Schibler, M.; L’Huillier, A.G.; Brito, F.; Docquier, M.; Posfay-Barbe, K.M.; Petty, T.J.; Turin, L.; Zdobnov, E.M.; et al. Astrovirus MLB2, a New Gastroenteric Virus Associated with Meningitis and Disseminated Infection. Emerg. Infect. Dis. 2016, 22, 846–853. [CrossRef] [PubMed]
22. Kriesel, J.D.; Hobbs, M.R.; Jones, B.B.; Milash, B.; Nagra, R.M.; Fischer, K.F. Deep sequencing for the detection of virus-like sequences in the brains of patients with multiple sclerosis: Detection of GBV-C in human brain. PLoS ONE 2012, 7, e31886. [CrossRef] [PubMed]
23. Liu, Z.; Zhang, Y.; Wei, F.; Xu, M.; Mou, D.; Zhang, T.; Li, W.; Chen, D.; Wu, H. Detection of GB virus C genomic sequence in the cerebrospinal fluid of a HIV-infected patient in China: A case report and literature review. Epidemiol. Infect. 2016, 144, 106–112. [CrossRef] [PubMed]
24. Hardie, D.; Smuts, H. Human pegivirus-1 in the CSF of patients with HIV-associated neurocognitive disorder (HAND) may be derived from blood in highly viraemic patients. J. Clin. Virol. 2017, 91, 58–61. [CrossRef] [PubMed]
25. Maggi, F.; Fornai, C.; Vatteroni, M.L.; Siciliano, G.; Menichetti, F.; Tascini, C.; Specter, S.; Pistello, M.; Bendinelli, M. Low prevalence of TT virus in the cerebrospinal fluid of viremic patients with central nervous system disorders. J. Med. Virol. 2001, 65, 418–422. [CrossRef] [PubMed]
26. Pollicino, T.; Raffa, G.; Squadrito, G.; Costantino, L.; Cacciola, I.; Brancatelli, S.; Alafaci, C.; Florio, M.G.; Raimondo, G. TT virus has a ubiquitous diffusion in human body tissues: Analyses of paired serum and tissue samples. J. Viral Hepat. 2003, 10, 95–102. [CrossRef] [PubMed]
27. Zhou, C.; Zhang, S.; Gong, Q.; Hao, A. A novel gemycircularvirus in an unexplained case of child encephalitis. Virol. J. 2015, 12, 197. [CrossRef]
28. Maggi, F.; Fornai, C.; Zaccaro, L.; Morrica, A.; Vatteroni, M.L.; Isola, P.; Marchi, S.; Ricchiuti, A.; Pistello, M.; Bendinelli, M. TT virus (TTV) loads associated with different peripheral blood cell types and evidence for TTV replication in activated mononuclear cells. J. Med. Virol. 2001, 64, 190–194. [CrossRef]
29. Desai, M.; Pal, R.; Deshmukh, R.; Banker, D. Replication of TT virus in hepatocyte and leucocyte cell lines. J. Med. Virol. 2005, 77, 136–143. [CrossRef]
30. Maggi, F.; Bendinelli, M. Human anelloviruses and the central nervous system. Rev. Med. Virol. 2010, 20, 392–407. [CrossRef]
31. Phan, T.G.; Mori, D.; Deng, X.; Rajindrajith, S.; Ranawaka, U.; Fan Ng, T.F.; Bucardo-Rivera, F.; Orlandi, P.; Ahmed, K.; Delwart, E. Small circular single stranded DNA viral genomes in unexplained cases of human encephalitis, diarrhea, and in untreated sewage. Virology 2015, 482, 98–104. [CrossRef] [PubMed]
32. Lamberto, I.; Gunst, K.; Muller, H.; Zur Hausen, H.; de Villiers, E.M. Mycovirus-like DNA virus sequences from cattle serum and human brain and serum samples from multiple sclerosis patients. Genome Announc. 2014, 2. [CrossRef] [PubMed]
33. Asplund, M.; Kjartansdottir, K.R.; Mollerup, S.; Vinner, L.; Fridholm, H.; Herrera, J.A.R.; Friis-Nielsen, J.; Hansen, T.A.; Jensen, R.H.; Nielsen, I.B.; et al. Contaminating viral sequences in high-throughput sequencing viromics: A linkage study of 700 sequencing libraries. Clin. Microbiol. Infect. 2019. [CrossRef]
34. Sadeghi, F.; Salehi-Vaziri, M.; Alizadeh, A.; Ghodsi, S.M.; Bokharaei-Salim, F.; Fateh, A.; Monavari, S.H.; Keyvani, H. Detection of Merkel cell polyomavirus large T-antigen sequences in human central nervous system tumors. J. Med. Virol. 2015, 87, 1241–1247. [CrossRef] [PubMed]
35. Lam, W.Y.; Leung, B.W.; Chu, I.M.; Chan, A.C.; Ng, H.K.; Chan, P.K. Survey for the presence of BK, JC, KI, WU and Merkel cell polyomaviruses in human brain tissues. J. Clin. Virol. 2010, 48, 11–14. [CrossRef] [PubMed]
36. Giraud, G.; Ramqvist, T.; Pastrana, D.V.; Pavot, V.; Lindau, C.; Kogner, P.; Orrego, A.; Buck, C.B.; Allander, T.; Holm, S.; et al. DNA from KI, WU and Merkel cell polyomaviruses is not detected in childhood central nervous system tumours or neuroblastomas. PLoS ONE 2009, 4, e8239. [CrossRef] [PubMed]
37. Cordey, S.; Bel, M.; Petty, T.J.; Docquier, M.; Sacco, L.; Turin, L.; Cherpillod, P.; Emonet, S.; Louis-Simonet, M.; Zdobnov, E.M.; et al. Toscana virus meningitis case in Switzerland: An example of the ezVIR bioinformatics pipeline utility for the identification of emerging viruses. Clin. Microbiol. Infect. 2015, 21, 387.e1–387.e4. [CrossRef] [PubMed]
38. Cordey, S.; Hartley, M.A.; Keitel, K.; Laubscher, F.; Brito, F.; Junier, T.; Kagoro, F.; Samaka, J.; Masimba, J.; Said, Z.; et al. Detection of novel astroviruses MLB1 and MLB2 in the sera of febrile Tanzanian children. Emerg. Microbes Infect. 2018, 7, 1–3. [CrossRef] [PubMed]
39. Williams, S.H.; Cordey, S.; Bhuva, N.; Laubscher, F.; Hartley, M.A.; Boillat-Blanco, N.; Mbarack, Z.; Samaka, J.; Mlaganile, T.; Jain, K.; et al. Investigation of the Plasma Virome from Cases of Unexplained Febrile Illness in Tanzania from 2013 to 2014: A Comparative Analysis between Unbiased and VirCapSeq-VERT High-Throughput Sequencing Approaches. mSphere 2018, 3. [CrossRef]