Erratum: Host-Associated Metagenomics: A Guide to Generating Infectious RNA Viromes (PLoS ONE (2015) 10:10 (e0139810) DOI: 10.1371/journal.pone.0139810);Host-Associated metagenomics: A guide to generating infectious RNA Viromes

PLoS ONE

Volumn 10, Issue 10, 2015, Pages

  Temmam, Sarah ^a   Monteil Bouchard, Sonia ^a   Robert, Catherine ^a   Pascalis, Hervé ^b   Michelle, Caroline ^a   Jardot, Priscilla ^a   Charrel, Rémi ^c   Raoult, Didier ^a   Desnues, Christelle ^a  

^a AIX MARSEILLE UNIVERSITÉ   (France)

^b Centre de Recherche et de Veille sur les Maladies Émergentes dans l'Océan Indien   (France)

^c Aix Marseille University IRD 190 Inserm 1207   (France)

Author keywords

[No Author keywords available]

Indexed keywords

SUCROSE; VIRUS RNA;

ARTICLE; BACTERIOPHAGE; CYTOTOXICITY; DNA CONTAMINATION; HUMAN; HUMAN CELL; METAGENOMICS; NEXT GENERATION SEQUENCING; NONHUMAN; PARTICLE SIZE; PEDICULUS HUMANUS CORPORIS; REVERSE TRANSCRIPTION; RNA PROCESSING; RNA VIRUS; VIRUS GENOME; VIRUS ISOLATION; VIRUS LOAD; VIRUS PARTICLE; VIRUS PURIFICATION; GENETICS;

METAGENOMICS; RNA, VIRAL;

EID: 84947250213     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0279054     Document Type: Erratum

References (57)

1. Suttle CA. Viruses in the sea (2005) Nature 437: 356-361.
2. Chiu CY. Viral pathogen discovery (2013) Curr Opin Microbiol 16: 468-478. doi: 10.1016/j.mib.2013. 05.001
3. Capobianchi MR, Giombini E, Rozera G (2013) Next-generation sequencing technology in clinical virology (2013) Clin Microbiol Infect 19: 15-22. doi: 10.1111/1469-0691.12056
4. Barzon L, Lavezzo E, Militello V, Toppo S, Palu G. Applications of next-generation sequencing technologies to diagnostic virology (2011) Int J Mol Sci 12: 7861-7884. doi: 10.3390/ijms12117861
5. Belák S, Karlsson OE, Blomström AL, Berg M, Granberg F. New viruses in veterinary medicine, detected by metagenomic approaches (2013) Vet Microbiol 165: 95-101. doi: 10.1016/j.vetmic.2013.01.022
6. Blomström AL. Viral metagenomics as an emerging and powerful tool in veterinary medicine (2011) Vet Q. doi: 10.1080/01652176.2011.604971
7. Temmam S, Davoust B, Berenger JM, Raoult D, Desnues C. Viral metagenomics on animals as a tool for the detection of zoonoses prior to human infection? (2014) Int J Mol Sci 15: 10377-10397. doi: 10.3390/ijms150610377
8. Roossinck MJ. Plant virus metagenomics: biodiversity and ecology (2012) Annu Rev Genet 46: 359-369. doi: 10.1146/annurev-genet-110711-155600
9. Ng TF, Duffy S, Polston JE, Bixby E, Vallad GE, Breitbart M. Exploring the diversity of plant DNA viruses and their satellites using vector-enabled metagenomics on whiteflies (2011) PLos One. doi: 10.1371/journal.pone.0019050
10. Cox-Foster DL, Conlan S, Holmes EC, Palacios G, Evans JD, Moran NA, et al. A metagenomic survey of microbes in honey bee colony collapse disorder (2007) Science. 318: 283-287.
11. Granberg F, Vicente-Rubiano M, Rubio-Guerri C, Karlsson OE, Kukielka D, Belák S, et al. Metagenomic detection of viral pathogens in Spanish honeybees: co-infection by Aphid Lethal Paralysis, Israel Acute Paralysis and Lake Sinai Viruses (2013) PLos One. doi: 10.1371/journal.pone.0057459
12. Popgeorgiev N, Temmam S, Raoult D, Desnues C. Describing the silent human virome with an emphasis on giant viruses (2013) Intervirology 56: 395-412. doi: 10.1159/000354561
13. Rosario K, Breitbart M. Exploring the viral world through metagenomics (2011) Curr Opin Virol 1: 289-297. doi: 10.1016/j.coviro.2011.06.004
14. Fancello L, Trape S, Robert C, Boyer M, Popgeorgiev N, Raoult D, et al. Viruses in the desert: A metagenomic survey of viral communities in four perennial ponds of the Mauritanian Sahara (2013) ISME J 7: 359-369. doi: 10.1038/ismej.2012.101
15. Whon TW, Kim MS, Roh SW, Shin NR, Lee HW, Bae JW. Metagenomic characterization of airborne viral DNA diversity in the near-surface atmosphere (2012) J Virol 86: 8221-8231. doi: 10.1128/JVI. 00293-12
16. Djikeng A, Kuzmickas R, Anderson NG, Spiro DJ. Metagenomic analysis of RNA viruses in a fresh water lake (2009). PLos One. doi: 10.1371/journal.pone.0007264
17. Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, Carlson C, et al. The marine viromes of four oceanic regions (2006) PLos Biol. 4: e368.
18. Thurber RV (2011) Methods in Viral Metagenomics. In: de Bruijn FJ, editor. Handbook of Molecular Microbial Ecology, Volume II: Metagenomics in Different Habitats. Wiley-Blackwell. pp 15-24.
19. Thurber RV, Haynes M, Breitbart M, Wegley L, Rohwer F. Laboratory procedures to generate viral metagenomes (2009) Nat Protoc 4: 470-483. doi: 10.1038/nprot.2009.10
20. Hall RJ, Wang J, Todd AK, Bissielo AB, Yen S, Strydom H, et al. Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery (2014) J Virol Methods 195: 194-204. doi: 10.1016/j.jviromet.2013.08.035
21. Stang A, Korn K, Wildner O, Uberla K. Characterization of virus isolates by particle-Associated nucleic acid PCR (2005) J Clin Microbiol 43: 716-720.
22. Weynberg KD, Wood-Charlson EM, Suttle CA, van Oppen MJ. Generating viral metagenomes from the coral holobiont (2014) Front Microbiol. doi: 10.3389/fmicb.2014.00206
23. Drosten C, Göttig S, Schilling S, Asper M, Panning M, Schmitz H, et al. Rapid detection and quantification of RNA of Ebola and Marburg viruses, Lassa virus, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus, dengue virus, and yellow fever virus by real-Time reverse transcription-PCR (2002) J Clin Microbiol 40: 2323-2330.
24. Watkins-Riedel T, Woegerbauer M, Hollemann D, Hufnagl P. Rapid diagnosis of enterovirus infections by real-Time PCR on the LightCycler using the TaqMan format (2002) Diagn Microbiol Infect Dis 42: 99-105.
25. van Elden LJ, Nijhuis M, Schipper P, Schuurman R, van Loon AM. Simultaneous detection of influenza viruses A and B using real-Time quantitative PCR (2001) J Clin Microbiol 39: 196-200.
26. Ninove L, Nougairede A, Gazin C, Thirion L, Delogu I, Zandotti C, et al. RNA and DNA bacteriophages as molecular diagnosis controls in clinical virology: A comprehensive study of more than 45,000 routine PCR tests (2011) PLos One. doi: 10.1371/journal.pone.0016142
27. Breitbart M, Rohwer F. Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing (2005) Biotechniques 39: 729-736.
28. Sangaré AK, Boutellis A, Drali R, Audoly G, Weber P, Rolain JM, et al. Doxycycline kills human lice through its activity on their bacterial symbiont (2015) Int J Antimicrob Agents 45: 675-676. doi: 10.1016/j.ijantimicag.2015.02.008
29. Froussard P. A random-PCR method (rPCR) to construct whole cDNA library from low amounts of RNA (1992) Nucleic Acids Res 20: 2900.
30. Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, Ganem D, et al. Microarray-based detection and genotyping of viral pathogens (2002) Proc Natl Acad Sci U S A 99: 15687-15692.
31. Victoria JG, Kapoor A, Dupuis K, Schnurr DP, Delwart EL. Rapid identification of known and new RNA viruses from animal tissues (2008) PLoS Pathog. doi: 10.1371/journal.ppat.1000163
32. Trudel M, Payment P (1989) Purification et analyse de virus par ultracentrifugation. In: Manuel de Techniques Virologiques, Presses de l'Université du Québec.
33. King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (2011) Virus Taxonomy: ninth report of the International Committee on Taxonomy of Viruses. Elsevier Academic Press.
34. Lawrence JE, Steward GF (2010) Purification of viruses by centrifugation. In: Wilhelm SW, Weinbauer MG and Suttle CA, editors. Manual of Aquatic Viral Ecology. ASLO. Pp 166-181.
35. Tidona CA, Darai G (2001). The Springer Index of Viruses. Springer.
36. Kleiner M, Hooper LV, Duerkop BA. Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes (2015) BMC Genomics. doi: 10.1186/s12864-014-1207-4
37. Cheval J, Sauvage V, Frageul L, Dacheux L, Guignon G, Dumey N, et al. Evaluation of high-Throughput sequencing for identifying known and unknown viruses in biological samples (2011) J Clin Microbiol. 49: 3268-3275. doi: 10.1128/JCM.00850-11
38. Frey KG, Herrera-Galeano JE, Redden CL, Luu TV, Servetas SL, Mateczun AJ, et al. Comparison of three next-generation sequencing platforms for metagenomic sequencing and identification of pathogens in blood (2014) BMC Genomics. doi: 10.1186/1471-2164-15-96
39. Phan TG, Vo NP, Bonkoungou IJ, Kapoor A, Barro N, O'Ryan M, et al. Acute diarrhea in West African children: diverse enteric viruses and a novel parvovirus genus (2012) J Virol 86: 11024-11030.
40. Ng TF, Marine R, Wang C, Simmonds P, Kapusinszky B, Bodhidatta L, et al. High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage (2012) J Virol 86: 12161-12175. doi: 10.1128/JVI.00869-12
41. Colson P, de Lamballerie X, Fournous G, Raoult D. Reclassification of giant viruses composing a fourth domain of life in the new order Megavirales (2012) 55: 321-332.
42. Daly GM, Bexfield N, Heaney J, Stubbs S, Mayer AP, Palser A, et al. A viral discovery methodology for clinical biopsy samples utilising massively parallel next generation sequencing (2011) PLos One. doi: 10.1371/journal.pone.0028879
43. Yang Y, Griffiths MW. Enzyme treatment reverse transcription-PCR to differentiate infectious and inactivated F-specific RNA phages (2014) Appl Environ Microbiol. 80: 3334-3340. doi: 10.1128/AEM. 03964-13
44. Hurwitz BL, Deng L, Poulos BT, Sullivan MB. Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics (2013) Environ Microbiol 15: 1428-1440. doi: 10.1111/j.1462-2920.2012.02836.x
45. Sachsenröder J, Twardziok S, Hammerl JA, Janczyk P, Wrede P, Hertwig S, et al. Simultaneous identification of DNA and RNA viruses present in pig faeces using process-controlled deep sequencing (2012) PLos One. doi: 10.1371/journal.pone.0034631
46. Marston DA, McElhinney LM, Ellis RJ, Horton DL, Wise EL, Leech SL, et al. Next generation sequencing of viral RNA genomes (2013) BMC Genomics. doi: 10.1186/1471-2164-14-444
47. Maillard P, Walic M, Meuleman P, Roohvand F, Huby T, Le Goff W, et al. Lipoprotein lipase inhibits hepatitis C virus (HCV) infection by blocking virus cell entry (2011) PLoS One. doi: 10.1371/journal.pone. 0026637
48. Kohl C, Brinkmann A, Dabrowski PW, Radonić A, Nitsche A, Kurth A. Protocol for metagenomic virus detection in clinical specimens (2015) Emerg Infect Dis. 21: 48-57. doi: 10.3201/eid2101.140766
49. Mathieson W, Thomas GA. Simultaneously extracting DNA, RNA, and protein using kits: is sample quantity or quality prejudiced? (2013) Anal Biochem 433: 10-18. doi: 10.1016/j.ab.2012.10.006
50. Kim KH, Bae JW. Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses (2011) Appl Environ Microbiol 77: 7663-7668. doi: 10.1128/AEM. 00289-11
51. Marine R, McCarren C, Vorrasane V, Nasko D, Crowgey E, Polson SW, et al. Caught in the middle with multiple displacement amplification: The myth of pooling for avoiding multiple displacement amplification bias in a metagenome (2014) Microbiome. doi: 10.1186/2049-2618-2-3
52. Berthet N, Reinhardt AK, Leclercq I, van Ooyen S, Batéjat C, Dickinson P, et al. Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR (2008) BMC Mol Biol. doi: 10.1186/1471-2199-9-77
53. Delwart EL. Viral metagenomics (2007) Rev Med Virol 17:115-131.
54. Karlsson OE, Belák S, Granberg F. The effect of preprocessing by sequence-independent, singleprimer amplification (SISPA) on metagenomic detection of viruses (2013) Biosecur Bioterror 11 Suppl 1: 227-234.
55. Rosseel T, Van Borm S, Vandenbussche F, Hoffmann B, van den Berg T, Beer M, et al. The origin of biased sequence depth in sequence-independent nucleic acid amplification and optimization for efficient massive parallel sequencing (2013) PLos One. doi: 10.1371/journal.pone.0076144
56. Koch R. Investigations into bacteria: V. The etiology of anthrax, based on the ontogenesis of Bacillus anthracis (1876) Cohns Beitrage zur Biologie der Pflanzen 2: 277-310.
57. Rivers TM. Viruses and Koch's Postulates. (1937) J Bacteriol 33: 1-12.