Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes

PLoS ONE

Volumn 6, Issue 6, 2011, Pages

  Ng, Terry Fei Fan ^a,f   Willner, Dana L ^b   Lim, Yan Wei ^b,d   Schmieder, Robert ^c   Chau, Betty ^b   Nilsson, Christina ^d   Anthony, Simon ^e   Ruan, Yijun ^d   Rohwer, Forest ^b   Breitbart, Mya ^a  

^a UNIVERSITY OF SOUTH FLORIDA   (United States)

^b SAN DIEGO STATE UNIVERSITY   (United States)

^c SAN DIEGO STATE UNIVERSITY   (United States)

^d GENOME INSTITUTE OF SINGAPORE   (Singapore)

^e INSTITUTE FOR CONSERVATION RESEARCH   (United States)

^f UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS DNA;

ANELLOVIRUS; ANIMAL VIRUS; ARTICLE; BACTERIOPHAGE; CIRCOVIRUS; CONTROLLED STUDY; CULEX; CULEX ERYTHROTHORAX; DENSOVIRUS; DNA VIRUS; GENETIC VARIABILITY; HERPES VIRUS; INSECT VIRUS; METAGENOMICS; MOSQUITO; NONHUMAN; NUCLEOTIDE SEQUENCE; PAPILLOMA VIRUS; PLANT INSECT INTERACTION; PLANT VIRUS; POXVIRUS; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; UNITED STATES; VIRUS CELL INTERACTION; VIRUS IDENTIFICATION; ANIMAL; BIODIVERSITY; CLASSIFICATION; DISEASE CARRIER; DNA SEQUENCE; GENETICS; HUMAN; METHODOLOGY; MOLECULAR GENETICS; VIROLOGY; VIRUS GENOME;

ANIMALIA; BACTERIA (MICROORGANISMS); CULEX ERYTHROTHORAX; DENSOVIRUS; DNA VIRUSES; HEXAPODA; PAPILLOMAVIRIDAE; VERTEBRATA;

ANIMALS; BACTERIOPHAGES; BIODIVERSITY; CULICIDAE; DNA VIRUSES; DNA, VIRAL; GENOME, VIRAL; HUMANS; INSECT VECTORS; METAGENOMICS; MOLECULAR SEQUENCE DATA; PLANT VIRUSES; SEQUENCE ANALYSIS, DNA;

EID: 79958145122     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0020579     Document Type: Article

References (65)

1. Molaei G, Andreadis TA, Armstrong PM, Anderson JF, Vossbrinck CR, (2006) Host feeding patterns of Culex mosquitoes and West Nile virus transmission, northeastern United States. Emerging Infectious Diseases 12: 468-474.
2. Ng TFF, Bixby E, Vallad G, Duffy S, Polston JE, et al. (2011) Exploring the Diversity of Plant DNA Viruses and Their Satellites Using Vector-Enabled Metagenomics on Whiteflies. PLoS ONE (in Press).
3. Huang C, Slater B, Campbell W, Howard J, White D, (2001) Detection of arboviral RNA directly from mosquito homogenates by reverse-transcription-polymerase chain reaction. Journal of Virological Methods 94: 121-128.
4. Kuno G, (1998) Universal diagnostic RT-PCR protocol for arboviruses. Journal of Virological Methods 72: 27-41.
5. Delwart EL, (2007) Viral metagenomics. Reviews in Medical Virology 17: 115-131.
6. Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, et al. (2002) Microarray-based detection and genotyping of viral pathogens. Proceedings of the National Academy of Sciences of the United States of America 99: 15687-15692.
7. Edwards RA, Rohwer F, (2005) Viral metagenomics. Nature Reviews Microbiology 3: 504-510.
8. Allander T, Tammi MT, Eriksson M, Bjerkner A, Tiveljung-Lindell A, et al. (2005) Cloning of a human parvovirus by molecular screening of respiratory tract samples. Proceedings of the National Academy of Sciences of the United States of America 102: 12891-12896.
9. Breitbart M, Hewson I, Felts B, Mahaffy JM, Nulton J, et al. (2003) Metagenomic analyses of an uncultured viral community from human feces. Journal of Bacteriology 185: 6220-6223.
10. Victoria JG, Kapoor A, Li LL, Blinkova O, Slikas B, et al. (2009) Metagenomic analyses of viruses in stool samples from children with acute flaccid paralysis. Journal of Virology 83: 4642-4651.
11. Jones MS, Kapoor A, Lukashov VV, Simmonds P, Hecht F, et al. (2005) New DNA viruses identified in patients with acute viral infection syndrome. Journal of Virology 79: 8230-8236.
12. Breitbart M, Rohwer F, (2005) Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing. Biotechniques 39: 729-736.
13. Ng TFF, Suedmeyer WK, Gulland F, Wheeler E, Breitbart M, (2009) Novel anellovirus discovered from a mortality event of captive California sea lions. Journal of General Virology 90: 1256-1261.
14. Willner D, Furlan M, Haynes M, Schmieder R, Angly FE, et al. (2009) Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. Plos One 4.
15. Ng TFF, Manire C, Borrowman K, Langer T, Ehrhart L, et al. (2009) Discovery of a novel single-stranded DNA virus from a sea turtle fibropapilloma by using viral metagenomics. Journal of Virology 83: 2500-2509.
16. Rosario K, Nilsson C, Lim YW, Ruan YJ, Breitbart M, (2009) Metagenomic analysis of viruses in reclaimed water. Environmental Microbiology 11: 2806-2820.
17. Ekström J, Forslund O, Dillner J, (2010) Three novel papillomaviruses (HPV109, HPV112 and HPV114) and their presence in cutaneous and mucosal samples. Virology 397: 331-336.
18. Tietze NS, Stephenson MF, Sidhom NT, Binding PL, (2003) Mark-recapture of Culex erythrothorax in Santa Cruz County, California. Journal of the American Mosquito Control Association 19: 134-138.
19. Walton WE, Workman PD, Tempelis CH, (1999) Dispersal, survivorship, and host selection of Culex erythrothorax (Diptera: Culicidae) associated with a constructed wetland in southern California. Journal of Medical Entomology 36: 30-40.
20. Antonsson A, Forslund O, Ekberg H, Sterner G, Hansson BG, (2000) The ubiquity and impressive genomic diversity of human skin papillomaviruses suggest a commensalic nature of these viruses. Journal of Virology 74: 11636-11641.
21. Dalmat HT, (1958) Arthropod transmission of rabbit papillomatosis. Journal of Experimental Medicine 108: 9-&.
22. Biagini P, Pierre G, Cantaloube JF, Attoui H, de Micco P, et al. (2006) Distribution and genetic analysis of TTV and TTMV major phylogenetic groups in French blood donors. Journal of Medical Virology 78: 298-304.
23. Shibata I, Okuda Y, Yazawa S, Ono M, Sasaki T, et al. (2003) PCR detection of Porcine circovirus type 2 DNA in whole blood, serum, oropharyngeal swab, nasal swab, and feces from experimentally infected pigs and field cases. Journal of Veterinary Medical Science 65: 405-408.
24. Todd D, (2000) Circoviruses: immunosuppressive threats to avian species: a review. Avian Pathology 29: 373-394.
25. Lopez-Bueno A, Tamames J, Velazquez D, Moya A, Quesada A, et al. (2009) High diversity of the viral community from an Antarctic lake. Science 326: 858-861.
26. Rosario K, Duffy S, Breitbart M, (2009) Diverse circovirus-like genome architectures revealed by environmental metagenomics. Journal of General Virology 90: 2418-2424.
27. Li L, Victoria JG, Wang C, Jones M, Fellers GM, et al. (2010) Bat guano virome: predominance of dietary viruses from insects and plants plus novel mammalian viruses. Journal of Virology 84: 6955-6965.
28. Li L, Kapoor A, Slikas B, Oderinde BS, Wang C, et al. (2010) Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces. Journal of virology 91: 74-86.
29. Blinkova O, Rosario K, Li L, Kapoor A, Slikas B, et al. (2009) Frequent detection of highly diverse variants of cardiovirus, cosavirus, bocavirus, and circovirus in sewage samples collected in the United States. Journal of Clinical Microbiology 47: 3507-3513.
30. Blinkova O, Victoria J, Li Y, Keele BF, Sanz C, et al. (2010) Novel circular DNA viruses in stool samples of wild-living chimpanzees. J Gen Virol 91: 74-86.
31. Weaver SC, Barrett ADT, (2004) Transmission cycles, host range, evolution and emergence of arboviral disease. Nature Reviews Microbiology 2: 789-801.
32. Biagini P, Uch R, Belhouchet M, Attoui H, Cantaloube JF, et al. (2007) Circular genomes related to anelloviruses identified in human and animal samples by using a combined rolling-circle amplification/sequence-independent single primer amplification approach. Journal of General Virology 88: 2696-2701.
33. Hino S, Miyata H, (2007) Torque teno virus (TTV): current status. Reviews in Medical Virology 17: 45-57.
34. Leary TP, Erker JC, Chalmers ML, Desai SM, Mushahwar IK, (1999) Improved detection systems for TT virus reveal high prevalence in humans, non-human primates and farm animals. Journal of General Virology 80: 2115-2120.
35. Davidson I, Shulman LM, (2008) Unraveling the puzzle of human anellovirus infections by comparison with avian infections with the chicken anemia virus. Virus Research 137: 1-15.
36. Jones DR, (2003) Plant viruses transmitted by whiteflies. European Journal of Plant Pathology 109: 195-219.
37. Oneill SL, Kittayapong P, Braig HR, Andreadis TG, Gonzalez JP, et al. (1995) Insect densoviruses may be widespread in mosquito cell-lines. Journal of General Virology 76: 2067-2074.
38. Ren XX, Hoiczyk E, Rasgon JL, (2008) Viral paratransgenesis in the malaria vector Anopheles gambiae. Plos Pathogens 4.
39. Barreau C, Jousset FX, Bergoin M, (1997) Venereal and vertical transmission of the Aedes albopictus parvovirus in Aedes aegypti mosquitoes. American Journal of Tropical Medicine and Hygiene 57: 126-131.
40. Carlson J, Suchman E, Buchatsky L, (2006) Densoviruses for control and genetic manipulation of mosquitoes. Insect Viruses: Biotechnological Applications 68: 361-392.
41. Rwegoshora RT, Kittayapong P, (2004) Pathogenicity and infectivity of the Thai-strain densovirus (AThDNV) in Anopheles minimus s.l. Southeast Asian Journal of Tropical Medicine and Public Health 35: 630-634.
42. Cheng LP, Chen SX, Zhou ZH, Zhang JQ, (2007) Structure comparisons of Aedes albopictus densovirus with other parvoviruses. Science in China Series C-Life Sciences 50: 70-74.
43. Lood R, Morgelin M, Holmberg A, Rasmussen M, Collin M, (2008) Inducible Siphoviruses in superficial and deep tissue isolates of Propionibacterium acnes. Bmc Microbiology 8.
44. Van der Wilk F, Dullemans AM, Verbeek M, van den Heuvel J, (1999) Isolation and characterization of APSE-1, a bacteriophage infecting the secondary endosymbiont of Acyrthosiphon pisum. Virology 262: 104-113.
45. Oliver KM, Degnan PH, Hunter MS, Moran NA, (2009) Bacteriophages encode factors required for protection in a symbiotic mutualism. Science 325: 992-994.
46. Moran NA, Degnan PH, Santos SR, Dunbar HE, Ochman H, (2005) The players in a mutualistic symbiosis: Insects, bacteria, viruses, and virulence genes. Proceedings of the National Academy of Sciences of the United States of America 102: 16919-16926.
47. Degnan PH, Moran NA, (2008) Diverse phage-encoded toxins in a protective insect endosymbiont. Applied and Environmental Microbiology 74: 6782-6791.
48. Yen JH, Barr AR, (1971) New hypothesis of the cause of cytoplasmic incompatibility in Culex pipiens L. Nature 232: 657-658.
49. Pidiyar VJ, Jangid K, Patole MS, Shouche YS, (2004) Studies on cultured and uncultured microbiota of wild Culex quinquefasciatus mosquito midgut based on 16s ribosomal RNA gene analysis. American Journal of Tropical Medicine and Hygiene 70: 597-603.
50. Yu X, Li B, Fu Y, Jiang D, Ghabrial SA, et al. (2010) A geminivirus-related DNA mycovirus that confers hypovirulence to a plant pathogenic fungus. Proceedings of the National Academy of Sciences of the United States of America 107: 8387-8392.
51. Hall-Mendelin S, Ritchie SA, Johansen CA, Zborowski P, Cortis G, et al. (2010) Exploiting mosquito sugar feeding to detect mosquito-borne pathogens. Proceedings of the National Academy of Sciences of the United States of America 107: 11255-11259.
52. Zhang T, Breitbart M, Lee WH, Run JQ, Wei CL, et al. (2006) RNA viral community in human feces: prevalence of plant pathogenic viruses. Plos Biology 4: 108-118.
53. Pinard R, de Winter A, Sarkis GJ, Gerstein MB, Tartaro KR, et al. (2006) Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing. Bmc Genomics 7: 21.
54. Kim K-H, Chang H-W, Nam Y-D, Roh SW, Kim M-S, et al. (2008) Amplification of uncultured single-stranded DNA viruses from rice paddy soil. Appl Environ Microbiol 74: 5975-5985.
55. Haible D, Kober S, Jeske H, (2006) Rolling circle amplification revolutionizes diagnosis and genomics of geminiviruses. Journal of Virological Methods 135: 9-16.
56. Thurber RV, Haynes M, Breitbart M, Wegley L, Rohwer F, (2009) Laboratory procedures to generate viral metagenomes. Nature Protocols 4: 470-483.
57. Patel A, Noble RT, Steele JA, Schwalbach MS, Hewson I, et al. (2007) Virus and prokaryote enumeration from planktonic aquatic environments by epifluorescence microscopy with SYBR Green I. Nature Protocols 2: 269-276.
58. Sambrook J, Russell DW, (2001) Molecular cloning: A laboratory manual. New York Cold Spring Harbor Laboratory Press.
59. Schmieder R, Edwards R, (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics.
60. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
61. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25: 3389-3402.
62. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, et al. (2000) Artemis: sequence visualization and annotation. Bioinformatics 16: 944-945.
63. Hall TA, (1999) BioEdit:a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41: 95-98.
64. Tamura K, Dudley J, Nei M, Kumar S, (2007) MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599.
65. Zhai YG, Lv XJ, Sun XH, Fu SH, Gong ZD, et al. (2008) Isolation and characterization of the full coding sequence of a novel densovirus from the mosquito Culex pipiens pallens. Journal of General Virology 89: 195-199.