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      Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia

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          ABSTRACT

          Tilapia are an important global food source due to their omnivorous diet, tolerance for high-density aquaculture, and relative disease resistance. Since 2009, tilapia aquaculture has been threatened by mass die-offs in farmed fish in Israel and Ecuador. Here we report evidence implicating a novel orthomyxo-like virus in these outbreaks. The tilapia lake virus (TiLV) has a 10-segment, negative-sense RNA genome. The largest segment, segment 1, contains an open reading frame with weak sequence homology to the influenza C virus PB1 subunit. The other nine segments showed no homology to other viruses but have conserved, complementary sequences at their 5′ and 3′ termini, consistent with the genome organization found in other orthomyxoviruses. In situ hybridization indicates TiLV replication and transcription at sites of pathology in the liver and central nervous system of tilapia with disease.

          IMPORTANCE

          The economic impact of worldwide trade in tilapia is estimated at $7.5 billion U.S. dollars (USD) annually. The infectious agent implicated in mass tilapia die-offs in two continents poses a threat to the global tilapia industry, which not only provides inexpensive dietary protein but also is a major employer in the developing world. Here we report characterization of the causative agent as a novel orthomyxo-like virus, tilapia lake virus (TiLV). We also describe complete genomic and protein sequences that will facilitate TiLV detection and containment and enable vaccine development.

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          Most cited references23

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          NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

          The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of genomic, transcript and protein sequence records. These records are selected and curated from public sequence archives and represent a significant reduction in redundancy compared to the volume of data archived by the International Nucleotide Sequence Database Collaboration. The database includes over 16 000 organisms, 2.4 × 106 genomic records, 13 × 106 proteins and 2 × 106 RNA records spanning prokaryotes, eukaryotes and viruses (RefSeq release 49, September 2011). The RefSeq database is maintained by a combined approach of automated analyses, collaboration and manual curation to generate an up-to-date representation of the sequence, its features, names and cross-links to related sources of information. We report here on recent growth, the status of curating the human RefSeq data set, more extensive feature annotation and current policy for eukaryotic genome annotation via the NCBI annotation pipeline. More information about the resource is available online (see http://www.ncbi.nlm.nih.gov/RefSeq/).
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            The genomic substrate for adaptive radiation in African cichlid fish

            Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
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              Vaccines for fish in aquaculture.

              Vaccination plays an important role in large-scale commercial fish farming and has been a key reason for the success of salmon cultivation. In addition to salmon and trout, commercial vaccines are available for channel catfish, European seabass and seabream, Japanese amberjack and yellowtail, tilapia and Atlantic cod. In general, empirically developed vaccines based on inactivated bacterial pathogens have proven to be very efficacious in fish. Fewer commercially available viral vaccines and no parasite vaccines exist. Substantial efficacy data are available for new fish vaccines and advanced technology has been implemented. However, before such vaccines can be successfully commercialized, several hurdles have to be overcome regarding the production of cheap but effective antigens and adjuvants, while bearing in mind environmental and associated regulatory concerns (e.g., those that limit the use of live vaccines). Pharmaceutical companies have performed a considerable amount of research on fish vaccines, however, limited information is available in scientific publications. In addition, salmonids dominate both the literature and commercial focus, despite their relatively small contribution to the total volume of farmed fish in the world. This review provides an overview of the fish vaccines that are currently commercially available and some viewpoints on how the field is likely to evolve in the near future.
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                Author and article information

                Journal
                mBio
                MBio
                mbio
                mbio
                mBio
                mBio
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2150-7511
                5 April 2016
                Mar-Apr 2016
                : 7
                : 2
                : e00431-16
                Affiliations
                [a ]Department of Cell Research and Immunology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
                [b ]Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
                [c ]New York Genome Center, New York, New York, USA
                [d ]Department of Poultry and Fish Diseases, The Kimron Veterinary Institute, Bet Dagan, Israel
                [e ]Easter Bush Pathology, The Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Midlothian, Scotland
                [f ]Marine Medicine Program, Pathobiology, School of Veterinary Medicine, St. George's University, Grenada, West Indies
                Author notes
                Address correspondence to Avi Eldar, eldar@ 123456int.gov.il , or W. Ian Lipkin, wil2001@ 123456cumc.columbia.edu .
                [*]

                Present address: Sandra Cathrine Abel Nielson, Department of Pathology, School of Medicine, Stanford University, Stanford, California, USA.

                E.B. and N.M. contributed equally to this article.

                Editor Christine A. Biron, Brown University

                This article is a direct contribution from a Fellow of the American Academy of Microbiology. External solicited reviewers: Edward Holmes, University of Sydney; Charles Calisher, Colorado State University.

                Article
                mBio00431-16
                10.1128/mBio.00431-16
                4959514
                27048802
                f9e94d7c-7399-4e6f-8ca9-1781eb42a230
                Copyright © 2016 Bacharach et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                : 10 March 2016
                : 17 March 2016
                Page count
                supplementary-material: 5, Figures: 4, Tables: 2, Equations: 0, References: 35, Pages: 7, Words: 6154
                Funding
                Funded by: Manna Center Program in Food Safety and Security at Tel Aviv University
                Award Recipient : Japhette Esther Kembou Tsofack
                Funded by: HHS | National Institutes of Health (NIH) http://dx.doi.org/10.13039/100000002
                Award ID: AI109761
                Award Recipient : W. Ian Lipkin
                Funded by: United States - Israel Binational Agricultural Research and Development Fund (BARD) http://dx.doi.org/10.13039/100006031
                Award ID: IS-4583-13
                Award Recipient : Avi Eldar Award Recipient : W. Ian Lipkin
                Funded by: United States Agency for International Development (USAID) http://dx.doi.org/10.13039/100000200
                Award ID: PREDICT
                Award Recipient : W. Ian Lipkin
                Funded by: Ministry of Agriculture and Rural Development (MOARD) http://dx.doi.org/10.13039/501100004576
                Award ID: Grant 847-0389-14
                Award Recipient : Avi Eldar
                Categories
                Research Article
                Custom metadata
                March/April 2016

                Life sciences
                Life sciences

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