A Roadmap to the Human Virome

1. EdwardsRA, RohwerF (2005) Viral metagenomics. Nat Rev Microbiol 3: 504–510.

2. WeinstockGM (2012) Genomic approaches to studying the human microbiota. Nature 489: 250–256.

3. DelwartEL (2007) Viral metagenomics. Rev Med Virol 17: 115–131.

4. WylieKM, WeinstockGM, StorchGA (2012) Emerging view of the human virome. Transl Res 160: 283–290.

5. AllanderT, EmersonSU, EngleRE, PurcellRH, BukhJ (2001) A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species. Proc Natl Acad Sci U S A 98: 11609–11614.

6. WangD, CoscoyL, ZylberbergM, AvilaPC, BousheyHA, et al. (2002) Microarray-based detection and genotyping of viral pathogens. Proc Natl Acad Sci U S A 99: 15687–15692.

7. WoolhouseM, ScottF, HudsonZ, HoweyR, Chase-ToppingM (2012) Human viruses: discovery and emergence. Philos Trans R Soc Lond B Biol Sci 367: 2864–2871.

8. WolfeND, DunavanCP, DiamondJ (2007) Origins of major human infectious diseases. Nature 447: 279–283.

9. LiL, DelwartE (2011) From orphan virus to pathogen: the path to the clinical lab. Curr Opin Virol 1: 282–288.

10. FredricksDN, RelmanDA (1998) Infectious agents and the etiology of chronic idiopathic diseases. Curr Clin Top Infect Dis 18: 180–200.

11. FelgnerPL, KayalaMA, VigilA, BurkC, Nakajima-SasakiR, et al. (2009) A Burkholderia pseudomallei protein microarray reveals serodiagnostic and cross-reactive antigens. Proc Natl Acad Sci U S A 106: 13499–13504.

12. VirginHW, WherryEJ, AhmedR (2009) Redefining chronic viral infection. Cell 138: 30–50.

13. Sancho-ShimizuV, de DiegoRP, JouanguyE, ZhangSY, CasanovaJL (2011) Inborn errors of anti-viral interferon immunity in humans. Curr Opin Virol 1: 487–496.

14. KingMQ, AdamsMJ, CarstensEB, LefkowitzEJ (2012) Virus taxonomy: ninth report of the International Committee on Taxonomy of Viruses. Elsevier Academic Press

15. MokiliJL, RohwerF, DutilhBE (2012) Metagenomics and future perspectives in virus discovery. Curr Opin Virol 2: 63–77.

16. RosarioK, BreitbartM (2011) Exploring the viral world through metagenomics. Curr Opin Virol 1: 289–297.

17. KooninEV, SenkevichTG, DoljaVV (2006) The ancient virus world and evolution of cells. Biol Direct 1: 29.

18. BolducB, ShaughnessyDP, WolfYI, KooninEV, RobertoFF, YoungM (2012) Identification of novel positive-strand RNA viruses by metagenomic analysis of archaea-dominated Yellowstone hot springs. J Virol 86: 5562–5573.

19. ZhangT, BreitbartM, LeeWH, RunJQ, WeiCL, et al. (2005) RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol 4: e3 doi:10.1371/journal.pbio.0040003.

20. ShanT, LiL, SimmondsP, WangC, MoeserA, DelwartE (2011) The fecal virome of pigs on a high-density farm. J Virol 85: 11697–11708.

21. KapoorA, SimmondsP, LipkinWI, ZaidiS, DelwartE (2010) Use of nucleotide composition analysis to infer hosts for three novel picorna-like viruses. J Virol 84: 10322–10328.

22. LysholmF, WetterbomA, LindauC, DarbanH, BjerknerA, et al. (2012) Characterization of the viral microbiome in patients with severe lower respiratory tract infections, using metagenomic sequencing. PLoS ONE 7: e30875 doi:10.1371/journal.pone.0030875.

23. AlterHJ, MikovitsJA, SwitzerWM, RuscettiFW, LoSC, et al. (2012) A multicenter blinded analysis indicates no association between chronic fatigue syndrome/myalgic encephalomyelitis and either xenotropic murine leukemia virus-related virus or polytropic murine leukemia virus. MBio 3 (5) e00266–12.

24. ScallanE, GriffinPM, AnguloFJ, TauxeRV, HoekstraRM (2011) Foodborne illness acquired in the United States—unspecified agents. Emerg Infect Dis 17: 16–22.

25. GlaserCA, GilliamS, SchnurrD, ForghaniB, HonarmandS, et al. (2003) In search of encephalitis etiologies: diagnostic challenges in the California Encephalitis Project, 1998–2000. Clin Infect Dis 36: 731–742.

26. ur HausenH (2009) The search for infectious causes of human cancers: where and why. Virology 392: 1–10.

27. KapusinszkyB, MinorP, DelwartE (2012) Nearly constant shedding of diverse enteric viruses by two healthy infants. J Clin Microbiol 50: 3427–3434.

28. KatzourakisA, GiffordRJ (2010) Endogenous viral elements in animal genomes. PLoS Genet 6: e1001191 doi:10.1371/journal.pgen.1001191.

29. FengH, ShudaM, ChangY, MoorePS (2008) Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science 319: 1096–1100.

30. LipkinWI (2009) Microbe hunting in the 21st century. Proc Natl Acad Sci U S A 106: 6–7.