The recent technological advances in nucleic acid sequencing, called next-generation sequencing (NGS), have revolutionized the field of genomics and have also influenced viral research. Aquatic viruses, and especially those infecting fish, have also greatly benefited from NGS technologies, which provide a huge amount of molecular information at a low cost in a relatively short period of time. Here, we review the use of the current high-throughput sequencing platforms with a special focus on the associated challenges (regarding sample preparation and bioinformatics) in their applications to the field of aquatic virology, especially for: (i) discovering novel viruses that may be associated with fish mortalities, (ii) elucidating the mechanisms of pathogenesis, and finally (iii) studying the molecular epidemiology of these pathogens.

Keywords:
Viruses, Fish, Diagnostics, Next-generation sequencing, Aquatic virology
1.
Bergh O, Borsheim KY, Bratbak G, Heldal M: High abundance of viruses found in aquatic environments. Nature 1989;340:467-468.
2.
Hara S, Terauchi K, Koike I: Abundance of viruses in marine waters: assessment by epifluorescence and transmission electron microscopy. Appl Environ Microbiol 1991;57:2731-2734.
3.
Suttle CA: Viruses in the sea. Nature 2005;437:356-361.
4.
Prostor LM, Fuhrman JA: Viral mortality of marine bacteria and cyanobacteria. Nature 1990;343:60-62.
5.
Suttle CA: Marine viruses - major players in the global ecosystem. Nat Rev Microbiol 2007;5:801-812.
6.
Wen K, Ortmann AC, Suttle CA: Accurate estimation of viral abundance by epifluorescence microscopy. Appl Environ Microbiol 2004;70:3862-3867.
7.
Marhaver KL, Edwards RA, Rohwer F: Viral communities associated with healthy and bleaching corals. Environ Microbiol 2008;10:2277-2286.
8.
McDaniel L, Breitbart M, Mobberley J, Long A, Haynes M, Rohwer F, Paul JH: Metagenomic analysis of lysogeny in Tampa Bay: implications for prophage gene expression. PLoS One 2008;3:e3263.
9.
Yin Y, Fischer D: Identification and investigation of ORFans in the viral world. BMC Genomics 2008;9:24.
10.
Fuhrman JA: Marine viruses and their biogeochemical and ecological effects. Nature 1999;399:541-548.
11.
Wilhelm SW, Suttle CA: Viruses and nutrient cycles in the sea: viruses play critical roles in the structure and function of aquatic food webs. BioScience 1999;49:781-788.
12.
Wommack KE, Colwell RR: Virioplankton: viruses in aquatic ecosystems. Microbiol Mol Biol Rev 2000;64:69-114.
13.
Bacharach E, Mishra N, Briese T, Zody MC, Kembou Tsofack JE, Zamostiano R, Berkowitz A, Ng J, Nitido A, Corvelo A, Toussaint NC, Abel Nielsen SC, Hornig M, Del Pozo J, Bloom T, Ferguson H, Eldar A, Lipkin WI: Characterization of a novel orthomyxo-like virus causing mass die-offs of tilapia. MBio 2016;7:e00431-e00416.
14.
Bloch B, Gravningen K, Larsen JL: Encephalomyelitis among turbot associated with apicornavirus-like agent. Dis Aquat Organ 1991;10:65-70.
15.
van Hulten MC, Witteveldt J, Peters S, Kloosterboer N, Tarchini R, Fiers M, Sandbrink H, Lankhorst RK, Vlak JM: The white spot syndrome virus DNA genome sequence. Virology 2001;286:7-22.
16.
Yoganandhan K, Leartvibhas M, Sriwongpuk S, Limsuwan C: White tail disease of the giant freshwater prawn Macrobrachium rosenbergii in Thailand. Dis Aquat Organ 2006;69:255-258.
17.
Zhang S, Shi Z, Zhang J, Bonami JR: Purification and characterization of a new reovirus from the Chinese mitten crab, Eriocheir sinensis. J Fish Dis 2004;27:687-692.
18.
Mardones F, Perez A, Sanchez J, Alkhamis M, Carpenter T: Parameterization of the duration of infection stages of serotype O foot-and-mouth disease virus: an analytical review and meta-analysis with application to simulation models. Vet Res 2010;41:45.
19.
Dunlap DS, Ng TF, Rosario K, Barbosa JG, Greco AM, Breitbart M, Hewson I: Molecular and microscopic evidence of viruses in marine copepods. Proc Natl Acad Sci USA 2013;110:1375-1380.
20.
Lightner DV: Virus diseases of farmed shrimp in the Western Hemisphere (the Americas): a review. J Invertebr Pathol 2011;106:110-130.
21.
Walker PJ, Winton JR: Emerging viral diseases of fish and shrimp. Vet Res 2010;41:51.
22.
Bodewes R, Morick D, van de Bildt MW, Osinga N, Rubio Garcia A, Sanchez Contreras GJ, Smits SL, Reperant LA, Kuiken T, Osterhaus AD: Prevalence of phocine distemper virus specific antibodies: bracing for the next seal epizootic in north-western Europe. Emerg Microbes Infect 2013;2:e3.
23.
Birkun AA Jr: Viruses of whales and dolphins (in Russian). Mikrobiol Z 1996;58:100-106.
24.
Karlsson EA, Ip HS, Hall JS, Yoon SW, Johnson J, Beck MA, Webby RJ, Schultz-Cherry S: Respiratory transmission of an avian H3N8 influenza virus isolated from a harbour seal. Nat Commun 2014;5:4791.
25.
Valleron AJ, Cori A, Valtat S, Meurisse S, Carrat F, Boelle PY: Transmissibility and geographic spread of the 1889 influenza pandemic. Proc Natl Acad Sci USA 2010;107:8778-8781.
26.
Suttle CA, Chan AM, Cottrell MT: Infection of phytoplankton by viruses and reduction of primary productivity. Nature 1990;347:467-469.
27.
Nagler FP, Rake G: The use of the electron microscope in diagnosis of variola, vaccinia, and varicella. J Bacteriol 1948;55:45-51.
28.
van Rooyen CE, Scott GD: Smallpox diagnosis with special reference to electron microscopy. Can J Public Health 1948;39:467-477.
29.
Gust ID, Kaldor J, Cross GF, Waugh M, Ferris AA: Virus-like particles associated with a faecal antigen from hepatitis patients and with Australia antigen. Aust J Exp Biol Med Sci 1971;49:1-9.
30.
Kapikian AZ, Wyatt RG, Dolin R, Thornhill TS, Kalica AR, Chanock RM: Visualization by immune electron microscopy of a 27-nm particle associated with acute infectious nonbacterial gastroenteritis. J Virol 1972;10:1075-1081.
31.
Welch AB: Purification, morphology and partial characterization of a reovirus-like agent associated with neonatal calf diarrhea. Can J Comp Med 1971;35:195-202.
32.
Villena AJ: Applications and needs of fish and shellfish cell culture for disease control in aquaculture. Rev Fish Biol Fish 2003;13:111-140.
33.
Rinkevich B: Cell cultures from marine invertebrates: new insights for capturing endless stemness. Mar Biotechnol (New York) 2011;13:345-354.
34.
Pernet F, Lupo C, Bacher C, Whittington RJ: Infectious diseases in oyster aquaculture require a new integrated approach. Philos Trans R Soc Lond B Biol Sci 2016;371.
35.
Burge CA, Friedman CS, Getchell R, House M, Lafferty KD, Mydlarz LD, Prager KC, Sutherland KP, Renault T, Kiryu I, Vega-Thurber R: Complementary approaches to diagnosing marine diseases: a union of the modern and the classic. Philos Trans R Soc Lond B Biol Sci 2016;371:20150207.
36.
Cobo F: Application of molecular diagnostic techniques for viral testing. Open Virol J 2012;6:104-114.
37.
Hayden R, Persing DH: Diagnostic molecular microbiology. Curr Clin Top Infect Dis 2001;21:323-348.
38.
van Belkum A, Niesters HG: Nucleic acid amplification and related techniques in microbiological diagnostics and epidemiology. Cell Mol Biol 1995;41:615-623.
39.
Engelsma MY, Way K, Dodge MJ, Voorbergen-Laarman M, Panzarin V, Abbadi M, El-Matbouli M, Frank Skall H, Kahns S, Stone DM: Detection of novel strains of cyprinid herpesvirus closely related to koi herpesvirus. Dis Aquat Organ 2013;107:113-120.
40.
Maxam AM, Gilbert W: A new method for sequencing DNA. Proc Natl Acad Sci USA 1977;74:560-564.
41.
Sanger F, Nicklen S, Coulson AR: DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 1977;74:5463-5467.
42.
Mardis ER: Next-generation sequencing platforms. Annu Rev Anal Chem 2013;6:287-303.
43.
Ansorge W, Sproat BS, Stegemann J, Schwager C: A non-radioactive automated method for DNA sequence determination. J Biochem Biophys Methods 1986;13:315-323.
44.
Ansorge W, Sproat B, Stegemann J, Schwager C, Zenke M: Automated DNA sequencing: ultrasensitive detection of fluorescent bands during electrophoresis. Nucleic Acids Res 1987;15:4593-4602.
45.
Lander ES, Linton LM, Birren B, et al; International Human Genome Sequencing Consortium: Initial sequencing and analysis of the human genome. Nature 2001;409:860-921.
46.
Venter JC, Adams MD, Myers EW, et al: The sequence of the human genome. Science (New York) 2001;291:1304-1351.
47.
Naidoo N, Pawitan Y, Soong R, Cooper DN, Ku CS: Human genetics and genomics a decade after the release of the draft sequence of the human genome. Hum Genomics 2011;5:577-622.
48.
Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M: Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012;2012:251364.
49.
Bleidorn C: Third generation sequencing: technology and its potential impact on evolutionary biodiversity research. Syst Biodivers 2016;14:1-8.
50.
Rothberg JM, Leamon JH: The development and impact of 454 sequencing. Nat Biotechnol 2008;26:1117-1124.
51.
Chi KR: The year of sequencing. Nat Methods 2008;5:11-14.
52.
Mardis ER: Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 2008;9:387-402.
53.
Mardis ER: The impact of next-generation sequencing technology on genetics. Trends Genet 2008;24:133-141.
54.
Illumina: Sequencing power for every scale. 2016. http://www.illumina.com/systems/sequencing.html.
55.
Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y: A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 2012;13:341.
56.
Eid J, Fehr A, Gray J, et al: Real-time DNA sequencing from single polymerase molecules. Science (New York) 2009;323:133-138.
57.
Lee H, Gurtowski J, Yoo S, Marcus S, McCombie WR, Schatz M: Error correction and assembly complexity of single molecule sequencing reads. bioRxiv 2014.
https://doi.org/10.1101/006395
.
58.
Rhoads A, Au KF: PacBio sequencing and its applications. Genomics Proteomics Bioinformatics 2015;13:278-289.
59.
Feng Y, Zhang Y, Ying C, Wang D, Du C: Nanopore-based fourth-generation DNA sequencing technology. Genomics Proteomics Bioinformatics 2015;13:4-16.
60.
Wang J, Moore NE, Deng YM, Eccles DA, Hall RJ: MinION nanopore sequencing of an influenza genome. Front Microbiol 2015;6:766.
61.
Kilianski A, Haas JL, Corriveau EJ, Liem AT, Willis KL, Kadavy DR, Rosenzweig CN, Minot SS: Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer. Gigascience 2015;4:1-8.
62.
Goodwin S, McPherson JD, McCombie WR: Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 2016;17:333-351.
63.
Datta S, Budhauliya R, Das B, Chatterjee S, Vanlalhmuaka, Veer V: Next-generation sequencing in clinical virology: discovery of new viruses. World J Virol 2015;4:265-276.
64.
Tringe SG, Rubin EM: Metagenomics: DNA sequencing of environmental samples. Nat Rev Genet 2005;6:805-814.
65.
Daly GM, Bexfield N, Heaney J, Stubbs S, Mayer AP, Palser A, Kellam P, Drou N, Caccamo M, Tiley L, Alexander GJ, Bernal W, Heeney JL: A viral discovery methodology for clinical biopsy samples utilising massively parallel next generation sequencing. PLoS One 2011;6:e28879.
66.
Hall RJ, Wang J, Todd AK, Bissielo AB, Yen S, Strydom H, Moore NE, Ren X, Huang QS, Carter PE, Peacey M: Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery. J Virol Methods 2014;195:194-204.
67.
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;98:11609-11614.
68.
He S, Wurtzel O, Singh K, Froula JL, Yilmaz S, Tringe SG, Wang Z, Chen F, Lindquist EA, Sorek R, Hugenholtz P: Validation of two ribosomal RNA removal methods for microbial metatranscriptomics. Nat Methods 2010;7:807-812.
69.
Li SK, Zhou JW, Yim AK, Leung AK, Tsui SK, Chan TF, Lau TC: Organism-specific rRNA capture system for application in next-generation sequencing. PLoS One 2013;8:e74286.
70.
Dupinay T, Nguyen A, Croze C, Barbet F, Rey C, Mavingui P, Pépin M, Lachuer J, Legras-Lachuer C: Next-generation sequencing of ultra-low copy samples: from clinical FFPE samples to single cell sequencing. Curr Top Virol 2012;10:63-83.
71.
Lefterova MI, Suarez CJ, Banaei N, Pinsky BA: Next-generation sequencing for infectious disease diagnosis and management: a report of the association for molecular pathology. J Mol Diagn 2015;17:623-634.
72.
Mertes F, Elsharawy A, Sauer S, van Helvoort JM, van der Zaag PJ, Franke A, Nilsson M, Lehrach H, Brookes AJ: Targeted enrichment of genomic DNA regions for next-generation sequencing. Brief Funct Genomics 2011;10:374-386.
73.
Jones MR, Good JM: Targeted capture in evolutionary and ecological genomics. Mol Ecol 2016;25:185-202.
74.
Briese T, Kapoor A, Mishra N, Jain K, Kumar A, Jabado OJ, Lipkin WI: Virome capture sequencing enables sensitive viral diagnosis and comprehensive virome analysis. mBio 2015;6:e01491-e01415.
75.
Wylie TN, Wylie KM, Herter BN, Storch GA: Enhanced virome sequencing using targeted sequence capture. Genome Res 2015;25:1910-1920.
76.
Hammoumi S, Vallaeys T, Santika A, Leleux P, Borzym E, Klopp C, Avarre JC: Targeted genomic enrichment and sequencing of CyHV-3 from carp tissues confirms low nucleotide diversity and mixed genotype infections. PeerJ 2016;4:e2516.
77.
Chaudhary N, Sharma AK, Agarwal P, Gupta A, Sharma VK: 16S classifier: a tool for fast and accurate taxonomic classification of 16S rRNA hypervariable regions in metagenomic datasets. PLoS One 2015;10:e0116106.
78.
Mizrahi-Man O, Davenport ER, Gilad Y: Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs. PLoS One 2013;8:e53608.
79.
Sakowski EG, Munsell EV, Hyatt M, Kress W, Williamson SJ, Nasko DJ, Polson SW, Wommack KE: Ribonucleotide reductases reveal novel viral diversity and predict biological and ecological features of unknown marine viruses. Proc Natl Acad Sci USA 2014;111:15786-15791.
80.
Bidle KD: Elucidating marine virus ecology through a unified heartbeat. Proc Natl Acad Sci USA 2014;111:15606-15607.
81.
Freitas TA, Li PE, Scholz MB, Chain PS: Accurate read-based metagenome characterization using a hierarchical suite of unique signatures. Nucleic Acids Res 2015;43:e69.
82.
Ounit R, Wanamaker S, Close TJ, Lonardi S: CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers. BMC Genomics 2015;16:236.
83.
Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009;10:R25.
84.
Caboche S, Audebert C, Lemoine Y, Hot D: Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data. BMC Genomics 2014;15:264.
85.
Lunter G, Goodson M: Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res 2011;21:936-939.
86.
Sedlazeck FJ, Rescheneder P, von Haeseler A: NextGenMap: fast and accurate read mapping in highly polymorphic genomes. Bioinformatics (Oxford) 2013;29:2790-2791.
87.
Turki T, Roshan U: MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence. BMC Genomics 2014;15:969.
88.
Alavandi SV, Poornima M: Viral metagenomics: a tool for virus discovery and diversity in aquaculture. Indian J Virol 2012;23:88-98.
89.
Dolled-Filhart MP, Lee M Jr, Ou-Yang CW, Haraksingh RR, Lin JC: Computational and bioinformatics frameworks for next-generation whole exome and genome sequencing. Sci World J 2013;2013:730210.
90.
Meiring TL, Salimo AT, Coetzee B, Maree HJ, Moodley J, Hitzeroth, II, Freeborough MJ, Rybicki EP, Williamson AL: Next-generation sequencing of cervical DNA detects human papillomavirus types not detected by commercial kits. Virol J 2012;9:164.
91.
Thomas T, Gilbert J, Meyer F: Metagenomics - a guide from sampling to data analysis. Microb Inform Exp 2012;2:3.
92.
Rampelli S, Soverini M, Turroni S, Quercia S, Biagi E, Brigidi P, Candela M: ViromeScan: a new tool for metagenomic viral community profiling. BMC Genomics 2016;17:165.
93.
Roux S, Tournayre J, Mahul A, Debroas D, Enault F: Metavir 2: new tools for viral metagenome comparison and assembled virome analysis. BMC Bioinformatics 2014;15:76.
94.
Vinithkumar NV: Marine bioinformatics. Advanced Biotech. 2006. https://www.researchgate.net/publication/265564431_Marine_Bioinformatics.
95.
Hurwitz BL, Sullivan MB: The Pacific Ocean virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS One 2013;8:e57355.
96.
Ignacio-Espinoza JC, Solonenko SA, Sullivan MB: The global virome: not as big as we thought? Curr Opin Virol 2013;3:566-571.
97.
Hurwitz BL, Brum JR, Sullivan MB: Depth-stratified functional and taxonomic niche specialization in the “core” and “flexible” Pacific Ocean virome. ISME J 2015;9:472-484.
98.
Seguritan V, Alves N Jr, Arnoult M, Raymond A, Lorimer D, Burgin AB Jr, Salamon P, Segall AM: Artificial neural networks trained to detect viral and phage structural proteins. PLoS Comput Biol 2012;8:e1002657.
99.
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS: MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 2009;37:W202-W208.
100.
Mann NH, Cook A, Millard A, Bailey S, Clokie M: Marine ecosystems: bacterial photosynthesis genes in a virus. Nature 2003;424:741.
101.
Tzahor S, Man-Aharonovich D, Kirkup BC, Yogev T, Berman-Frank I, Polz MF, Beja O, Mandel-Gutfreund Y: A supervised learning approach for taxonomic classification of core-photosystem-II genes and transcripts in the marine environment. BMC Genomics 2009;10:229.
102.
Miller JR, Koren S, Sutton G: Assembly algorithms for next-generation sequencing data. Genomics 2010;95:315-327.
103.
Archer J, Whiteley G, Casewell NR, Harrison RA, Wagstaff SC: VTBuilder: a tool for the assembly of multi isoform transcriptomes. BMC Bioinformatics 2014;15:389.
104.
Toseland A, Moxon S, Mock T, Moulton V: Metatranscriptomes from diverse microbial communities: assessment of data reduction techniques for rigorous annotation. BMC Genomics 2014;15:901.
105.
Yang X, Charlebois P, Gnerre S, Coole MG, Lennon NJ, Levin JZ, Qu J, Ryan EM, Zody MC, Henn MR: De novo assembly of highly diverse viral populations. BMC Genomics 2012;13:475.
106.
Chen YC, Liu T, Yu CH, Chiang TY, Hwang CC: Effects of GC bias in next-generation-sequencing data on de novo genome assembly. PLoS One 2013;8:e62856.
107.
Gawad C, Koh W, Quake SR: Single-cell genome sequencing: current state of the science. Nat Rev Genet 2016;17:175-188.
108.
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA: SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012;19:455-477.
109.
Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo MJ, Dupont CL, Badger JH, Novotny M, Rusch DB, Fraser LJ, Gormley NA, Schulz-Trieglaff O, Smith GP, Evers DJ, Pevzner PA, Lasken RS: Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat Biotechnol 2011;29:915-921.
110.
Peng Y, Leung HC, Yiu SM, Chin FY: IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics (Oxford) 2012;28:1420-1428.
111.
Lopez-Barragan MJ, Quinones M, Cui K, Lemieux J, Zhao K, Su XZ: Effect of PCR extension temperature on high-throughput sequencing. Mol Biochem Parasitol 2011;176:64-67.
112.
Van Nieuwerburgh F, Soetaert S, Podshivalova K, Ay-Lin Wang E, Schaffer L, Deforce D, Salomon DR, Head SR, Ordoukhanian P: Quantitative bias in Illumina TruSeq and a novel post amplification barcoding strategy for multiplexed DNA and small RNA deep sequencing. PLoS One 2011;6:e26969.
113.
Johnson SS, Zaikova E, Goerlitz DS, Bai Y, Tighe SW: Real-time DNA sequencing in the Antarctic dry valleys using the Oxford Nanopore Sequencer. J Biomol Tech 2017;28:2-7.
114.
Quick J, Loman NJ, Duraffour S, et al: Real-time, portable genome sequencing for Ebola surveillance. Nature 2016;530:228-232.
115.
Palacios G, Lovoll M, Tengs T, Hornig M, Hutchison S, Hui J, Kongtorp RT, Savji N, Bussetti AV, Solovyov A, Kristoffersen AB, Celone C, Street C, Trifonov V, Hirschberg DL, Rabadan R, Egholm M, Rimstad E, Lipkin WI: Heart and skeletal muscle inflammation of farmed salmon is associated with infection with a novel reovirus. PLoS One 2010;5:e11487.
116.
Haugland O, Mikalsen AB, Nilsen P, Lindmo K, Thu BJ, Eliassen TM, Roos N, Rode M, Evensen O: Cardiomyopathy syndrome of atlantic salmon (Salmo salar L.) is caused by a double-stranded RNA virus of the Totiviridae family. J Virol 2011;85:5275-5286.
117.
Lovoll M, Wiik-Nielsen J, Grove S, Wiik-Nielsen CR, Kristoffersen AB, Faller R, Poppe T, Jung J, Pedamallu CS, Nederbragt AJ, Meyerson M, Rimstad E, Tengs T: A novel totivirus and piscine reovirus (PRV) in Atlantic salmon (Salmo salar) with cardiomyopathy syndrome (CMS). Virol J 2010;7:309.
118.
Lopez-Bueno A, Mavian C, Labella AM, Castro D, Borrego JJ, Alcami A, Alejo A: Concurrence of iridovirus, polyomavirus and a unique member of a new group of fish papillomaviruses in lymphocystis disease affected gilthead seabream. J Virol 2016;90:8768-8779.
119.
Mavian C, Lopez-Bueno A, Fernandez Somalo MP, Alcami A, Alejo A: Complete genome sequence of the European sheatfish virus. J Virol 2012;86:6365-6366.
120.
Davison AJ, Kurobe T, Gatherer D, Cunningham C, Korf I, Fukuda H, Hedrick RP, Waltzek TB: Comparative genomics of carp herpesviruses. J Virol 2013;87:2908-2922.
121.
Li W, Lee X, Weng S, He J, Dong C: Whole-genome sequence of a novel Chinese cyprinid herpesvirus 3 isolate reveals the existence of a distinct European genotype in East Asia. Vet Microbiol 2015;175:185-194.
122.
Falk K, Aspehaug V, Vlasak R, Endresen C: Identification and characterization of viral structural proteins of infectious salmon anemia virus. J Virol 2004;78:3063-3071.
123.
Fourrier M, Lester K, Markussen T, Falk K, Secombes CJ, McBeath A, Collet B: Dual mutation events in the haemagglutinin-esterase and fusion protein from an infectious salmon anaemia virus HPR0 genotype promote viral fusion and activation by an ubiquitous host protease. PLoS One 2015;10:e0142020.
124.
Markussen T, Sindre H, Jonassen CM, Tengs T, Kristoffersen AB, Ramsell J, Numanovic S, Hjortaas MJ, Christiansen DH, Dale OB, Falk K: Ultra-deep pyrosequencing of partial surface protein genes from infectious salmon anaemia virus (ISAV) suggest novel mechanisms involved in transition to virulence. PLoS One 2013;8:e81571.
125.
Campbell S, Collet B, Einer-Jensen K, Secombes CJ, Snow M: Identifying potential virulence determinants in viral haemorrhagic septicaemia virus (VHSV) for rainbow trout. Dis Aquat Organ 2009;86:205-212.
126.
Kim SH, Thu BJ, Skall HF, Vendramin N, Evensen O: A single amino acid mutation (I1012F) of the RNA polymerase of marine viral hemorrhagic septicemia virus changes in vitro virulence to rainbow trout gill epithelial cells. J Virol 2014;88:7189-7198.
127.
Schonherz AA, Lorenzen N, Guldbrandtsen B, Buitenhuis B, Einer-Jensen K: Ultra-deep sequencing of VHSV isolates contributes to understanding the role of viral quasispecies. Vet Res 2016;47:10.
128.
Depledge DP, Kundu S, Jensen NJ, Gray ER, Jones M, Steinberg S, Gershon A, Kinchington PR, Schmid DS, Balloux F, Nichols RA, Breuer J: Deep sequencing of viral genomes provides insight into the evolution and pathogenesis of varicella zoster virus and its vaccine in humans. Mol Biol Evol 2014;31:397-409.
129.
Depledge DP, Palser AL, Watson SJ, Lai IY, Gray ER, Grant P, Kanda RK, Leproust E, Kellam P, Breuer J: Specific capture and whole-genome sequencing of viruses from clinical samples. PLoS One 2011;6:e27805.
130.
Lui VW, Yau DM, Cheung CS, Wong SC, Chan AK, Zhou Q, Wong EY, Lau CP, Lam EK, Hui EP, Hong B, Hui CW, Chan AS, Ng PK, Ng YK, Lo KW, Tsang CM, Tsui SK, Tsao SW, Chan AT: FGF8b oncogene mediates proliferation and invasion of Epstein-Barr virus-associated nasopharyngeal carcinoma cells: implication for viral-mediated FGF8b upregulation. Oncogene 2011;30:1518-1530.
131.
Donohoe OH, Henshilwood K, Way K, Hakimjavadi R, Stone DM, Walls D: Identification and characterization of cyprinid herpesvirus-3 (CyHV-3) encoded microRNAs. PLoS One 2015;10:e0125434.
132.
Kim Y, Aw TG, Teal TK, Rose JB: Metagenomic investigation of viral communities in ballast water. Environ Sci Technol 2015;49:8396-8407.
133.
Byrd AL, Segre JA: Infectious disease: adapting Koch's postulates. Science (New York) 2016;351:224-226.
134.
Rivers TM: Viruses and Koch's postulates. J Bacteriol 1937;33:1-12.
135.
Fredricks DN, Relman DA: Sequence-based identification of microbial pathogens: a reconsideration of Koch's postulates. Clin Microbiol Rev 1996;9:18-33.
136.
Lipkin WI: The changing face of pathogen discovery and surveillance. Nat Rev Microbiol 2013;11:133-141.
137.
Berthet N, Dickinson P, Filliol I, Reinhardt AK, Batejat C, Vallaeys T, Kong KA, Davies C, Lee W, Zhang S, Turpaz Y, Heym B, Coralie G, Dacheux L, Burguière AM, Bourhy H, Old IG, Manuguerra JC, Cole ST, Kennedy GC: Massively parallel pathogen identification using high-density microarrays. Microb Biotechnol 2008;1:79-86.
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2017
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Copyright: All rights reserved. No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, microcopying, or by any information storage and retrieval system, without permission in writing from the publisher.
Drug Dosage: The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in government regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any changes in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug.
Disclaimer: The statements, opinions and data contained in this publication are solely those of the individual authors and contributors and not of the publishers and the editor(s). The appearance of advertisements or/and product references in the publication is not a warranty, endorsement, or approval of the products or services advertised or of their effectiveness, quality or safety. The publisher and the editor(s) disclaim responsibility for any injury to persons or property resulting from any ideas, methods, instructions or products referred to in the content or advertisements.
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