Viral metagenomics: A tool for virus discovery and diversity in aquaculture

Indian Journal of Virology

Volumn 23, Issue 2, 2012, Pages 88-98

  Alavandi, S V ^a   Poornima, M ^a  

^a ICAR CENTRAL INSTITUTE OF BRACKISHWATER AQUACULTURE   (India)

Author keywords

Aquaculture; Bioinformatic tools; Diseases; Marine animals; Viral diversity; Viral metagenomics

Indexed keywords

NUCLEIC ACID; VIRUS DNA;

5' UNTRANSLATED REGION; AQUACULTURE; BIOINFORMATICS; DNA VIRUS; GENE SEQUENCE; MARINE ENVIRONMENT; MARINE SPECIES; METAGENOMICS; MICROBIAL DIVERSITY; MOLECULAR PHYLOGENY; NONHUMAN; PULSED FIELD GEL ELECTROPHORESIS; PYROSEQUENCING; RANDOM AMPLIFIED POLYMORPHIC DNA; REVIEW; RNA VIRUS; VIRAL GENETICS; VIRUS CULTURE; VIRUS GENOME; VIRUS INFECTION; VIRUS PATHOGENESIS; VIRUS PURIFICATION;

EID: 84879605153     PISSN: 09702822     EISSN: 09740120     Source Type: Journal    
DOI: 10.1007/s13337-012-0075-2     Document Type: Review

References (88)

1. Adams IP, Glover RH, Monger WA, Mumford R, Jackeviciene E, Navalinskiene M, Samuitiene M, Boonham N. Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology. Mol Plant Pathol. 2009;10:537-45.
2. Al Rwahnih M, Daubert S, Golino D, Rowhani A. Deep sequencing analysis of RNAs from a grapevine showing Syrah decline symptoms reveals a multiple virus infection that includes a novel virus. Virology. 2009;387:395-401.
3. Allander T, Andreasson K, Gupta S, Bjerkner A, Bogdanovic G, Persson MA, Dalianis T, Ramqvist T, Andersson B. Identification of a third human polyomavirus. J Virol. 2007;81:4130-6.
4. Allander T, Emerson SU, Engle RE, Purcell RH, Bukh J. A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species. Proc Natl Acad Sci USA. 2001;98:11609-14.
5. Allander T, Tammi MT, Eriksson M, Bjerkner A, Tiveljung-Lindell A, Anderson B. Cloning of a human parvovirus by molecular screening of respiratory tract samples. Proc Natl Acad Sci USA. 2005;102:12891-6.
6. Ambrose HE, Clewley JP. Virus discovery by sequence independent genome amplification. Rev Med Virol. 2006;16:365-83.
7. Angly F, Rodiguez-Brito B, Bangor D, McNairnie P, Breitbart M, Salamon P, Felts B, Nulton J, Mahaffy J, Rohwer F. PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. BMC Bioinformatics. 2005;6:41.
8. Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, Carlson C, Chan AM, Haynes M, Kelley S, Liu H, Mahaffy J, Mueller JE, Nulton J, Olson R, Parsons R, Rayhawk S, Suttle CA, Rohwer F. The marine viromes of four oceanic regions. PLoS Biol. 2006;4:e368.
9. Angly FE, Willner D, Prieto-Davó A, Edwards RA, Schmieder R, Vega-Thurber R, Antonopoulos DA, Barott K, Cottrell MT, Desnues C, Dinsdale EA, Furlan M, Haynes M, Henn MR, Hu Y, Kirchman DL, McDole T, McPherson JD, Meyer F, Miller RM, Mundt E, Naviaux RK, Rodriguez-Mueller B, Stevens R, Wegley L, Zhang L, Zhu B, Rohwer F. The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput Biol. 2009;5:e1000593.
10. Blinkova O, Victoria J, Li Y, Keele BF, Sanz C, Ndjango JBN, Peeters M, Travis D, Lonsdorf EV, Wilson ML, Pusey AE, Hahn BH, Delwart EL. Novel circular DNA viruses in stool samples of wild-living chimpanzees. J Gen Virol. 2010;91:74-86.
11. Blomstrom AL, Widen F, Hammer AS, Belak S, Berg M. Detection of a novel astrovirus in brain tissue of mink suffering from shaking mink syndrome by use of viral metagenomics. J Clin Microbiol. 2010;48:4392-6.
12. Bonami RJ, Trumper B, Mari J, Brehelin M, Lightner DV. Purification and characterization of the infectious hypodermal and haematopoietic necrosis virus of penaeid shrimps. J Gen Virol. 1990;71:2657-64.
13. Bonami JR, Lightner DV, Redman RM, Poulos BT. Partial characterization of a togavirus (LOVV) associated with histopathological changes of the lymphoid organ of penaeid shrimps. Dis Aquat Organ. 1992;14:145-52.
14. Breitbart M, Felts B, Kelley S, Mahaffy JM, Nulton J, Salamon P, Rohwer F. Diversity and population structure of a near-shore marine-sediment viral community. Proc Royal Soc London B. 2004;271:565-74.
15. Breitbart M, Hewson I, Felts B, Mahaffy JM, Nulton J, Salamon P, Rohwer F. Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol. 2003;185:6220-3.
16. Breitbart M, Rohwer F. Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing. Biotechniques. 2005;39:729-36.
17. Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, Azam F, Rohwer F. Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci USA. 2002;99:14250-5.
18. Breitbart M. Marine Viruses: Truth or Dare. Annu Rev Mar Sci. 2011; doi: 10.1146/annurev-marine-120709-142805.
19. Briese T, Paweska JT, McMullan LK, Hutchison SK, Street C, Palacios G, Khristova ML, Weyer J, Swanepoel R, Egholm M, Nichol ST, Lipkin WL. Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated Arenavirus from Southern Africa. PLoS Pathog. 2009;5(5):e1000455.
20. Briggs M, Funge-Smith S, Subasinghe, RP, Phillips M. Introductions and movement of two penaeid shrimp species in Asia and the Pacific. FAO Fish Tech Paper 476, FAO Rome, 2005; ftp://ftp.fao.org/docrep/fao/008/a0086e/a0086e00.pdf.
21. Cox-Foster DL, Conlan S, Holmes EC, Palacios G, Evans JD, Moran NA, Quan P, Briese T, Hornig M, Geiser DM, Martinson V, van Engelsdorp D, Kalkstein AL, Drysdale A, Hui J, Zhai J, Cui L, Hutchison SK, Simons JF, Egholm M, Pettis JS, Lipkin WI. A metagenomic survey of microbes in honey bee colony collapse disorder. Science. 2007;318:283-7.
22. Culley AI, Lang AS, Suttle CA. High diversity of unknown picorna-like viruses in the sea. Nature. 2003;424:1054-7.
23. Culley AI, Lang AS, Suttle CA. Metagenomic analysis of coastal RNA virus communities. Science. 2006;312:1795-8.
24. Dean FB, Nelson JR, Giesler TL, Lasken RS. Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res. 2001;1:1095-9.
25. Delwart EL. Viral metagenomics. Rev Med Virol. 2007;17:115-31.
26. Desnues C, Rodriguez-Brito B, Rayhawk S, Kellev S, Trati T, Havnes M, Liu H, Furlan M, Weglev L, Chau B, Ruan Y, Hall D, Anglv FE, Edwards RA, Li L, Thurber RV, Reid RP, Siefert J, Souza V, Valentine DL, Swan BK, Bieitbart M, Rohwer F. Biodiversity and biogeography of phages in modern stromatolites and thromatolites. Nature. 2008;452:340-3.
27. Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, Brulc JM, Furlan M, Desnues C, Haynes M, Li L, McDaniel L, Moran MA, Nelson KE, Nilsson C, Olson R, Paul J, Brito BR, Ruan Y, Swan BK, Stevens R, Valentine DL, Thurber RV, Wegley L, White BA, Rohwer F. Functional metagenomic profiling of nine biomes. Nature. 2008;452:629-32.
28. Edwards RA, Rohwer F. Viral metagenomics. Nat Rev Microbiol. 2005;3:504-10.
29. Essbauer S, Ahne W. Viruses of lower vertebrates. J Vet Med (B) Infect Dis Vet Public Health. 2001;48:403-75.
30. Fauquet CM, Mayo MA, Maniloj J, Desselberger U, Ball LA. Virus Taxonomy, VIII Report of the ICTV. London: Elsevier/Academic Press, 2005.
31. Flegel TW. Special topic review: major viral diseases of the black tiger prawn (Penaeus monodon) in Thailand. World J Microbiol Biotechnol. 1997;13:433-42.
32. Fraser CA, Owens L. Spawner-isolated mortality virus from Australian Penaeus monodon. Dis Aquat Organ. 1996;27:141-8.
33. Greenblatt RJ, Sutton CA, Casey RN, Casey JW, Work TM, Balazs GH. The Ozobranchus leech is a candidate mechanical vector for the fibropapilloma- associated turtle herpesvirus found latently infecting skin tumors on Hawaiian green turtles (Chelonia mydas). Virology. 2004;321:101-10.
34. Greninger AL, Runckel C, Chiu CY, Haggerty T, Parsonnet J, Ganem D, DeRis JL. The complete genome of klassevirus - a novel picornavirus in pediatric stool. Virol J. 2009;6:82.
35. Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol. 1998;5:245-9.
36. Harrington ED, Singh AH, Doerks T, Letunic I, von Mering C, Jensen U, Raes J, Bork P. Quantitative assessment of protein function prediction from metagenomics shotgun sequences. Proc Natl Acad Sci USA. 2007;104:13913-8.
37. Hasson KW, Lightner DV, Poulos BT, Redman RM, White BL, Brock JA, Bonami JR. Taura syndrome in Penaeus vannamei: demonstration of a viral etiology. Dis Aquat Organ. 1995;23:115-26.
38. Helton RR, Wommack KE. Seasonal dynamics and metagenomic characterization of estuarine viriobenthos assemblages by randomly amplified polymorphic DNA PCR. Appl Environ Microbiol. 2009;75:2259-65.
39. Honkavuori KS, Shivaprasad HL, Williams BL, Quan PL, Hornig M, Street C, Palacios G, Hutchison SK, Franca M, Egholm M, Briese T, Lipkin WI. Novel borna virus in psittacine birds with proventricular dilatation disease. Emerg Infect Dis. 2008;14:1883-6.
40. Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res. 2007;17:377-86.
41. Johne R, Muller H, Rector A, van Ranst M, Stevens H. Rolling-circle amplification of viral DNA genomes using phi29 polymerase. Trends Microbiol. 2009;17:205-11.
42. Jones MS, Kapoor A, Lukashov VV, Simmonds P, Hecht F, Delwart E. New DNA viruses identified in patients with acute viral infection syndrome. J Virol. 2005;79:8230-6.
43. Kapoor A, Victoria J, Simmonds P, Wang C, Shafer RW, Nims R, Nielsen O, Delwart E. A highly divergent picornavirus in a marine mammal. J Virol. 2008;82:311-20.
44. Kibenge FS, Munir K, Kibenge MJ, Joseph T, Moneke E. Infectious salmon anemia virus: causative agent, pathogenesis and immunity. Anim Health Res Rev. 2004;5:65-78.
45. Kim K, Chang H, Nam Y, Rob SW, Kim M, Sting Y, Jeon CO, Oh H, Bae J. Amplification of uncultured single-stranded DNA viruses from rice paddy soil. Appl Environ Microbiol. 2008;74:5975-85.
46. Kirkland PD, Frost MJ, Finlaison DS, King KR, Ridpath JF, Gu X. Identification of a novel virus in pigs-Bungowannah virus: a possible new species of pestivirus. Virus Res. 2007;129:26-34.
47. Kostic AD, Ojesina AI, Pedamallu CS, Jung J, Verhaak RG, Getz G, Meyerson M. PathSeq: software to identify or discover microbes by deep sequencing of human tissue. Nat Biotechnol. 2011;29:393-6.
48. Krause L, Diaz NN, Goesmann A, Kelley S, Nattkemper TW, Rohwer F, Edwards PA, Stoye J. Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res. 2008;36:2230-9.
49. Kumagai A, Takahashi K, Fukuda H. Infection source of herpesvirus disease in coho salmon culture and its control. Fish Pathol. 1997;32:103-8.
50. Lauck M, Hyeroba D, Tumukunde A, Weny G, Lank SM, Chapman CA, O'Connor DH, Friedrich TC, Goldberg TL. Novel, divergent simian hemorrhagic fever viruses in a wild ugandan red colobus monkey discovered using direct pyrosequencing. PLoS ONE. 2011;6:e19056. doi: 10.1371/journal.pone.0019056.
51. Li L, Victoria JG, Wang C, Jones M, Fellers GM, Kunz TH, Delwart E. Bat Guano virome: predominance of dietary viruses from insects and plants plus novel mammalian viruses. J Virol. 2010;84:6955-65.
52. Lightner DV. A handbook of pathology and diagnostic procedures for diseases of penaeid shrimp. Baton Rouge: World Aquaculture Society; 1996.
53. Lightner DV, Redman RM. A putative iridovirus from the penaeid shrimp Protrachypene precipua Burkenroad (Crustacea: Decapoda). J Invertebr Pathol. 1993;62:107-9.
54. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen Y, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzvk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim J, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005;437:376-80.
55. Marhaver KL, Edwards RA, Rohwer F. Viral communities associated with healthy and bleaching corals. Environ Microbiol. 2008;10:2277-86.
56. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet. 2010;11:31-46.
57. Munday BL, Kwang J, Moody N. Betanodavirus infections of teleost fish: a review. J Fish Dis. 2002;25:127-42.
58. Munn CB. Viruses as pathogens of marine organisms-from bacteria to whales. J Mar Biological Assn UK. 2006;86:453-67.
59. Nadala ECB Jr, Lu Y, Loh PC, Brock JA. Infection of Penaeus stylirostris (Boone) with a rhabdovirus isolated from Penaeus spp. Fish Pathol. 1992;27:143-7.
60. Nakamura S, Yang C-S, Sakon N, Ueda M, Tougan T, Yamashita A, Goto N, Takahashi K, Yasunaga T, Ikuta K, Mizutani T, Okamoto Y, Tagami M, Morita R, Maeda N, Kawai J, Hayashizaki Y, Nagai Y, Horii T, Iida T, Nakaya T. Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach. PLoS ONE. 2009;4(1):e4219.
61. Ng TF, Alavandi SV, Breitbart M. Metagenomic studies reveal novel viruses in shrimp. Sixth International symposium on 'Aquatic animal health, Global strategies for a changing Environment' Sep 5-9, 2010 Tampa.
62. Ng TF, Manire C, Borrowman K, Langer T, Ehrhart L, Breitbart M. Discovery of a novel single-stranded DNA virus from a sea turtle fibropapilloma using viral metagenomics. J Virol. 2009;83:2500-9.
63. Ng TF, Suedmeyer WK, Wheeler E, Gulland F, Breitbart M. Novel anellovirus discovered from a mortality event of captive California sea lions. J Gen Virol. 2009;90:1256-61.
64. Ng TF, Wheeler E, Greig D, Waltzek TB, Gulland F, Breitbart M. Metagenomic identification of a novel anellovirus in Pacific harbor seal (Phoca vitulina richardsii) lung samples and its detection in samples from multiple years. J Gen Virol. 2011;92:1318-23.
65. Owens L, De Beer S, Smith J. Lymphoidal parvovirus-like particles in Australian penaeid prawns. Dis Aquat Organ. 1991;11:129-34.
66. Pareek CS, Smoczynski R, Tretyn A. Sequencing technologies and genome sequencing. J Appl Genet. 2011;52:413-35.
67. Poulos BT, Tang KFJ, Pantoja CR, Bonami JR, Lightner DV. Purification and characterization of infectious myonecrosis virus of penaeid shrimp. J Gen Virol. 2006;87:987-96.
68. Reyes GR, Kim JP. Sequence-independent, single primer amplification (SISPA) of complex DNA populations. Mol Cell Probes. 1991;5:473-81.
69. Rohwer F, Seguritan V, Choi DH, Segall AM, Azam F. Production of shotgun libraries using random amplification. Biotechniques 2001;31:108-12, 114-16, 118.
70. Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M. CAMERA: a community resource for metagenomics. PLoS Biol. 2007;5:e75.
71. Skall HF, Olesen NJ, Mellergaard S. Viral haemorrhagic septicaemia virus in marine fish and its implications for fish farming-a review. J Fish Dis. 2005;28:509-29.
72. Sritunyalucksana K, Apisawetakan S, Boon-nat A, Withyachumnarnkul B, Flegel TW. A new RNA virus found in black tiger shrimp Penaeus monodon from Thailand. Virus Res. 2006;118:31-8.
73. Svraka S, Rosario K, Duizer E, van der Avoort H, Breitbart M, Koopmans M. Metagenomic sequencing for virus identification in a public-health setting. J Gen Virol. 2010;91:2846-56.
74. Thurber RV, Haynes M, Breitbart M, Wegley L, Rohwer F. Laboratory procedures to generate viral metagenomes. Nat Protocols. 2009;4:470-83.
75. Tomlins SA, Mehia R, Rhodes DR, Shah RB, Rubin MA, Bruening E, Makarov V, Chinnaiyan AM. Whole transcriptome amplification for gene expression profiling and development of molecular archives. Neoplasia. 2006;8:153-62.
76. Van Bressem MF, Van Waerebeek K, Raga JA. A review of virus infections of cetaceans and the potential impact of morbilliviruses, poxviruses and papillomaviruses on host population dynamics. Dis Aquat Organ. 1999;38:53-65.
77. Van Etten JL, Lane LC, Dunigan DD. DNA viruses: the really big ones (giruses). Annu Rev Microbiol. 2010;64:83-99.
78. Vázquez A, Sánchez-Seco MP, Palacios G, Molero F, Reyes N, Ruiz S, Aranda C, Marqués E, Escosa R, Moreno J, Figuerola J, Tenorio A. Novel Flaviviruses detected in different species of mosquitoes in spain. Vector Borne Zoonotic Dis. 2011; doi: 10.1089/vbz.2011.0687.
79. Victoria JG, Kapoor A, Li L, Blinkova O, Slikas B, Wang C, Naeem A, Zaidi S, Delwart E. Metagenomic analyses of viruses in stool samples from children with acute flaccid paralysis. J Virol. 2009;83:4642-51.
80. Victoria JG, Kapoor A, Dupuis K, Schnurr DP, Delwart EL. Rapid identification of known and new RNA viruses from animal tissues. PLoS Pathog. 2008;4:el000163.
81. Walker PJ, Mohan CV. Viral disease emergence in shrimp aquaculture: origins, impact and the effectiveness of health management strategies. Rev Aquacult. 2009;1:125-54.
82. Williamson SJ. Viral Metagenomics. In: de Bruijn, editor, Handbook of molecular microbial ecology II: metagenomics in different habitats. Wiley-Blackwell. 2011. p. 4-12.
83. Willner DL. Viral metagenomics in host-associated systems. San Diego: San Diego state University; 2010.
84. Winget DM, Wommack KE. Randomly amplified polymorphic DNA PCR as a tool for assessment of marine viral richness. Appl Environ Microbiol. 2008;74:2612-8.
85. Wommack KE, Ravel J, Hill RT, Chun J, Colwell RR. Population dynamics of Chesapeake Bay virioplankton: total-community analysis by pulsed-field gel electrophoresis. Appl Environ Microbiol. 1999;65:231-40.
86. Wongteerasupaya C, Sriurairatana S, Vickers JE, Anutara A, Boonsaeng V, Panyim S, Tassanakajon A, Withyachumnarnkul B, Flegel TW. Yellow-head virus of Penaeus monodon is an RNA virus. Dis Aquat Organ. 1995;22:45-50.
87. Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, Joachimiak MP, van Belle C, Chandonia J, Soergel DA, Zhai Y, Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A, Eisenberg D, Dixon JE, Taylor SS, Strausberg RL, Frazier M, Venter JC. The Sorcerer II Global Ocean sampling expedition: expanding the universe of protein families. PLoS Biol. 2007;5:e16.
88. Zsak L, Strother KO, Kisary J. Partial genome sequence analysis of parvoviruses associated with enteric disease in poultry. Avian Pathol. 2008;37:435-41.