1887

Chapter 14 : The Human Virome in Health and Disease

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $30.00

Preview this chapter:
Zoom in
Zoomout

The Human Virome in Health and Disease, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555819071/9781555819088.ch14-1.gif /docserver/preview/fulltext/10.1128/9781555819071/9781555819088.ch14-2.gif

Abstract:

Early studies of the human microbiome were directed at bacteria. However, just as the bacterial microbiota affects human health and disease, viruses have analogous interactions. Thus, the human microbiome should be thought of as having a viral component, which is designated the human virome (Fig. 1 and Table 1). The definition of the human virome is complicated by the complexity of viruses and their life cycles. Viruses may be associated with acute infections that may or may not produce manifestations of disease and in which the presence of the viral etiologic agent is transient. In other cases, viral infections are persistent with prolonged presence of the implicated virus and ongoing replication. Persistent infections may or may not be associated with disease. In addition, some viruses become latent following acute infection. During latency, the viral genome persists, but viral replication does not occur, although transcription of some viral genes may take place. Another component of the virome consists of sequences within the human genome that appear to have resulted from remote incorporation of viral elements into the human genome. Designated as endogenous human retroviruses, these sequences cannot generate infectious viral particles. They occupy approximately 4.8% of the human genome (1). Finally, bacteriophages are viruses that infect the bacteria that make up the human endogenous microbiota. While all of the forms of viral infection described above may legitimately be considered part of the human virome, this chapter will focus on the first three groups: namely, viruses that infect eukaryotic cells and are capable of independent replication. The reason for that focus is that these are the viruses that have been associated to date with human disease and are the targets of diagnostic testing.

Citation: Wylie K, Storch G. 2016. The Human Virome in Health and Disease, p 156-166. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch14
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of FIGURE 1
FIGURE 1

Components of the human virome.

Citation: Wylie K, Storch G. 2016. The Human Virome in Health and Disease, p 156-166. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch14
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2
FIGURE 2

Approaches for detecting viral sequences using metagenomic shotgun sequencing. Nucleic acid can be extracted directly from a population of microbes, after which viral sequences, represented by red lines, may be a minor component of the total nucleic acid, as depicted on the left side of the figure. Sequencing libraries can be constructed directly from DNA or reverse-transcribed RNA, and rare viral sequences can be detected by ultra-deep sequencing. Alternatively, viral particles can be enriched prior to nucleic acid extraction and sequencing by filtration, DNase treatment, or ultracentrifugation. Postenrichment, the majority of nucleic acid is from viruses, as is depicted on the right side of the figure. Relative strengths and weaknesses of sequencing by these approaches are represented by the circles in the bottom panel, with red representing relative strength, yellow representing a relative weakness, and shades of orange falling in between.

Citation: Wylie K, Storch G. 2016. The Human Virome in Health and Disease, p 156-166. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch14
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3
FIGURE 3

The human virome in five human body habitats. All of the viruses detected in the five body habitats are shown. Each virus is represented by a colored bar and labeled on the -axis on the right side. The relative height of the bar reflects the percentage of subjects sampled at each body site in whom the virus was detected. The bar representing roseoloviruses in the oral samples reflects the maximum bar height because 98% of the individuals who were sampled in the mouth harbored roseoloviruses. Reprinted without modification from reference under Creative Commons License 4.0 (http://creativecommons.org/licenses).

Citation: Wylie K, Storch G. 2016. The Human Virome in Health and Disease, p 156-166. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch14
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555819071.ch14
1. Nelson PN, Hooley P, Roden D, Davari Ejtehadi H, Rylance P, Warren P, Martin J, Murray PG, Molecular Immunology Research Group. 2004. Human endogenous retroviruses: transposable elements with potential? Clin Exp Immunol 138:19[CrossRef].[PubMed]
2. Wylie KM, Mihindukulasuriya KA, Sodergren E, Weinstock GM, Storch GA. 2012. Sequence analysis of the human virome in febrile and afebrile children. PLoS One 7:e27735[CrossRef].[PubMed]
3. Wylie KM, Mihindukulasuriya KA, Zhou Y, Sodergren E, Storch GA, Weinstock GM. 2014. Metagenomic analysis of double-stranded DNA viruses in healthy adults. BMC Biol 12:71[CrossRef].[PubMed]
4. Greninger AL, Runckel C, Chiu CY, Haggerty T, Parsonnet J, Ganem D, DeRisi JL. 2009. The complete genome of klassevirus—a novel picornavirus in pediatric stool. Virol J 6:82[CrossRef].[PubMed]
5. Lysholm F, Wetterbom A, Lindau C, Darban H, Bjerkner A, Fahlander K, Lindberg AM, Persson B, Allander T, Andersson B. 2012. Characterization of the viral microbiome in patients with severe lower respiratory tract infections, using metagenomic sequencing. PLoS One 7:e30875[CrossRef].[PubMed]
6. Allander T, Emerson SU, Engle RE, Purcell RH, Bukh J. 2001. A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species. Proc Natl Acad Sci USA 98:1160911614[CrossRef].[PubMed]
7. Aw TG, Howe A, Rose JB. 2014. Metagenomic approaches for direct and cell culture evaluation of the virological quality of wastewater. J Virol Methods 210C:1521[CrossRef].[PubMed]
8. Breitbart M, Rohwer F. 2005. Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing. Biotechniques 39:729736[CrossRef].[PubMed]
9. Höper D, Hoffmann B, Beer M. 2011. A comprehensive deep sequencing strategy for full-length genomes of influenza A. PLoS One 6:e19075[CrossRef].[PubMed]
10. Rector A, Tachezy R, Van Ranst M. 2004. A sequence-independent strategy for detection and cloning of circular DNA virus genomes by using multiply primed rolling-circle amplification. J Virol 78:49934998[CrossRef].[PubMed]
11. Schowalter RM, Pastrana DV, Pumphrey KA, Moyer AL, Buck CB. 2010. Merkel cell polyomavirus and two previously unknown polyomaviruses are chronically shed from human skin. Cell Host Microbe 7:509515[CrossRef].[PubMed]
12. van der Meijden E, Janssens RW, Lauber C, Bouwes Bavinck JN, Gorbalenya AE, Feltkamp MC. 2010. Discovery of a new human polyomavirus associated with trichodysplasia spinulosa in an immunocompromized patient. PLoS Pathog 6:e1001024[CrossRef].[PubMed]
13. Cheval J, Sauvage V, Frangeul L, Dacheux L, Guigon G, Dumey N, Pariente K, Rousseaux C, Dorange F, Berthet N, Brisse S, Moszer I, Bourhy H, Manuguerra CJ, Lecuit M, Burguiere A, Caro V, Eloit M. 2011. Evaluation of high-throughput sequencing for identifying known and unknown viruses in biological samples. J Clin Microbiol 49:32683275[CrossRef].[PubMed]
14. van Dijk EL, Jaszczyszyn Y, Thermes C. 2014. Library preparation methods for next-generation sequencing: tone down the bias. Exp Cell Res 322:1220[CrossRef].[PubMed]
15. Head SR, Komori HK, LaMere SA, Whisenant T, Van Nieuwerburgh F, Salomon DR, Ordoukhanian P. 2014. Library construction for next-generation sequencing: overviews and challenges. Biotechniques 56:6164, 66, 68 passim.[PubMed]
16. Oyola SO, Otto TD, Gu Y, Maslen G, Manske M, Campino S, Turner DJ, Macinnis B, Kwiatkowski DP, Swerdlow HP, Quail MA. 2012. Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. BMC Genomics 13:1[CrossRef].[PubMed]
17. Aird D, Ross MG, Chen WS, Danielsson M, Fennell T, Russ C, Jaffe DB, Nusbaum C, Gnirke A. 2011. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol 12:R18[CrossRef].[PubMed]
18. Rosseel T, Van Borm S, Vandenbussche F, Hoffmann B, van den Berg T, Beer M, Höper D. 2013. The origin of biased sequence depth in sequence-independent nucleic acid amplification and optimization for efficient massive parallel sequencing. PLoS One 8:e76144[CrossRef].[PubMed]
19. Hoeijmakers WA, Bártfai R, Françoijs KJ, Stunnenberg HG. 2011. Linear amplification for deep sequencing. Nat Protoc 6:10261036[CrossRef].[PubMed]
20. Dean FB, Hosono S, Fang L, Wu X, Faruqi AF, Bray-Ward P, Sun Z, Zong Q, Du Y, Du J, Driscoll M, Song W, Kingsmore SF, Egholm M, Lasken RS. 2002. Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci USA 99:52615266[CrossRef].[PubMed]
21. Yilmaz S, Allgaier M, Hugenholtz P. 2010. Multiple displacement amplification compromises quantitative analysis of metagenomes. Nat Methods 7:943944[CrossRef].[PubMed]
22. Skewes-Cox P, Sharpton TJ, Pollard KS, DeRisi JL. 2014. Profile hidden Markov models for the detection of viruses within metagenomic sequence data. PLoS One 9:e105067[CrossRef].[PubMed]
23. Brister JR, Ako-Adjei D, Bao Y, Blinkova O. 2015. NCBI viral genomes resource. Nucleic Acids Res 43(D1):D571D577[CrossRef].[PubMed]
24. Bibby K, Viau E, Peccia J. 2011. Viral metagenome analysis to guide human pathogen monitoring in environmental samples. Lett Appl Microbiol 52:386392[CrossRef].[PubMed]
25. Breitbart M, Haynes M, Kelley S, Angly F, Edwards RA, Felts B, Mahaffy JM, Mueller J, Nulton J, Rayhawk S, Rodriguez-Brito B, Salamon P, Rohwer F. 2008. Viral diversity and dynamics in an infant gut. Res Microbiol 159:367373[CrossRef].[PubMed]
26. Minot S, Sinha R, Chen J, Li H, Keilbaugh SA, Wu GD, Lewis JD, Bushman FD. 2011. The human gut virome: inter-individual variation and dynamic response to diet. Genome Res 21:16161625[CrossRef].[PubMed]
27. Finkbeiner SR, Holtz LR, Jiang Y, Rajendran P, Franz CJ, Zhao G, Kang G, Wang D. 2009. Human stool contains a previously unrecognized diversity of novel astroviruses. Virol J 6:161[CrossRef].[PubMed]
28. Victoria JG, Kapoor A, Li L, Blinkova O, Slikas B, Wang C, Naeem A, Zaidi S, Delwart E. 2009. Metagenomic analyses of viruses in stool samples from children with acute flaccid paralysis. J Virol 83:46424651[CrossRef].[PubMed]
29. Smits SL, Schapendonk CM, van Beek J, Vennema H, Schürch AC, Schipper D, Bodewes R, Haagmans BL, Osterhaus AD, Koopmans MP. 2014. New viruses in idiopathic human diarrhea cases, the Netherlands. Emerg Infect Dis 20:12181222[CrossRef].[PubMed]
30. Holtz LR, Cao S, Zhao G, Bauer IK, Denno DM, Klein EJ, Antonio M, Stine OC, Snelling TL, Kirkwood CD, Wang D. 2014. Geographic variation in the eukaryotic virome of human diarrhea. Virology 468–470C:556564.
31. Willner D, Furlan M, Haynes M, Schmieder R, Angly FE, Silva J, Tammadoni S, Nosrat B, Conrad D, Rohwer F. 2009. Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. PLoS One 4:e7370[CrossRef].[PubMed]
32. Colvin JM, Muenzer JT, Jaffe DM, Smason A, Deych E, Shannon WD, Arens MQ, Buller RS, Lee WM, Weinstock EJ, Weinstock GM, Storch GA. 2012. Detection of viruses in young children with fever without an apparent source. Pediatrics 130:e1455e1462[CrossRef].[PubMed]
33. McElvania TeKippe E, Wylie KM, Deych E, Sodergren E, Weinstock G, Storch GA. 2012. Increased prevalence of anellovirus in pediatric patients with fever. PLoS One 7:e50937[CrossRef].[PubMed]
34. Young JC, Chehoud C, Bittinger K, Bailey A, Diamond JM, Cantu E, Haas AR, Abbas A, Frye L, Christie JD, Bushman FD, Collman RG. 2015. Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipients. Am J Transplant 15:200209[CrossRef].[PubMed]
35. Jones MS, Kapoor A, Lukashov VV, Simmonds P, Hecht F, Delwart E. 2005. New DNA viruses identified in patients with acute viral infection syndrome. J Virol 79:82308236[CrossRef].[PubMed]
36. De Vlaminck I, Khush KK, Strehl C, Kohli B, Luikart H, Neff NF, Okamoto J, Snyder TM, Cornfield DN, Nicolls MR, Weill D, Bernstein D, Valantine HA, Quake SR. 2013. Temporal response of the human virome to immunosuppression and antiviral therapy. Cell 155:11781187[CrossRef].[PubMed]
37. Li SK, Leung RK, Guo HX, Wei JF, Wang JH, Kwong KT, Lee SS, Zhang C, Tsui SK. 2012. Detection and identification of plasma bacterial and viral elements in HIV/AIDS patients in comparison to healthy adults. Clin Microbiol Infect 18:11261133[CrossRef].[PubMed]
38. Antonsson A, Erfurt C, Hazard K, Holmgren V, Simon M, Kataoka A, Hossain S, Håkangård C, Hansson BG. 2003. Prevalence and type spectrum of human papillomaviruses in healthy skin samples collected in three continents. J Gen Virol 84:18811886[CrossRef].[PubMed]
39. Antonsson A, Karanfilovska S, Lindqvist PG, Hansson BG. 2003. General acquisition of human papillomavirus infections of skin occurs in early infancy. J Clin Microbiol 41:25092514[CrossRef].[PubMed]
40. Feng H, Shuda M, Chang Y, Moore PS. 2008. Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science 319:10961100[CrossRef].[PubMed]
41. Rinaldo CH, Hirsch HH. 2013. The human polyomaviruses: from orphans and mutants to patchwork family. APMIS 121:681684[CrossRef].[PubMed]
42. Mishra N, Pereira M, Rhodes RH, An P, Pipas JM, Jain K, Kapoor A, Briese T, Faust PL, Lipkin WI. 2014. Identification of a novel polyomavirus in a pancreatic transplant recipient with retinal blindness and vasculitic myopathy. J Infect Dis 210:15951599[CrossRef].[PubMed]
43. Foulongne V, Sauvage V, Hebert C, Dereure O, Cheval J, Gouilh MA, Pariente K, Segondy M, Burguière A, Manuguerra JC, Caro V, Eloit M. 2012. Human skin microbiota: high diversity of DNA viruses identified on the human skin by high throughput sequencing. PLoS One 7:e38499[CrossRef].[PubMed]
44. Oh J, Byrd AL, Deming C, Conlan S, Kong HH, Segre JA, NISC Comparative Sequencing Program. 2014. Biogeography and individuality shape function in the human skin metagenome. Nature 514:5964[CrossRef].[PubMed]
45. Blinkova O, Rosario K, Li L, Kapoor A, Slikas B, Bernardin F, Breitbart M, Delwart E. 2009. Frequent detection of highly diverse variants of cardiovirus, cosavirus, bocavirus, and circovirus in sewage samples collected in the United States. J Clin Microbiol 47:35073513[CrossRef].[PubMed]
46. Symonds EM, Griffin DW, Breitbart M. 2009. Eukaryotic viruses in wastewater samples from the United States. Appl Environ Microbiol 75:14021409[CrossRef].[PubMed]
47. Cantalupo PG, Calgua B, Zhao G, Hundesa A, Wier AD, Katz JP, Grabe M, Hendrix RW, Girones R, Wang D, Pipas JM. 2011. Raw sewage harbors diverse viral populations. MBio 2:e00180e11[CrossRef].[PubMed]
48. Tang K-W, Alaei-Mahabadi B, Samuelsson T, Lindh M, Larsson E. 2013. The landscape of viral expression and host gene fusion and adaptation in human cancer. Nat Commun 4:2513[CrossRef].[PubMed]
49. Cancer Genome Atlas Research Network. 2014. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature 507:315322[CrossRef].[PubMed]
50. Bass AJ, , et al, Cancer Genome Atlas Research Network. 2014. Comprehensive molecular characterization of gastric adenocarcinoma. Nature 513:202209[CrossRef].[PubMed]

Tables

Generic image for table
TABLE 1

Components of the human virome with clinical significance

Citation: Wylie K, Storch G. 2016. The Human Virome in Health and Disease, p 156-166. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch14
Generic image for table
TABLE 2

Common high-throughput sequencing platforms

Citation: Wylie K, Storch G. 2016. The Human Virome in Health and Disease, p 156-166. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch14
Generic image for table
TABLE 3

Viruses detected by sequencing in nasopharyngeal secretions from febrile and afebrile children 2 to 36 months of age

Citation: Wylie K, Storch G. 2016. The Human Virome in Health and Disease, p 156-166. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch14

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error