The Reverse Genetics Applied to Fish RNA Viruses Stéphane Biacchesi
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Biacchesi Veterinary Research 2011, 42:12 http://www.veterinaryresearch.org/content/42/1/12 VETERINARY RESEARCH REVIEW Open Access The reverse genetics applied to fish RNA viruses Stéphane Biacchesi Abstract Aquaculture has expanded rapidly to become a major economic and food-producing sector worldwide these last 30 years. In parallel, viral diseases have emerged and rapidly spread from farm to farm causing enormous economic losses. The most problematic viruses encountered in the field are mainly, but not exclusively, RNA viruses belonging to the Novirhabdovirus, Aquabirnavirus, Alphavirus and Betanodavirus genera. The recent establishment of reverse genetics systems to recover infectious fish RNA viruses entirely from cDNA has made possible to genetically manipulate the viral genome. These systems have provided powerful tools to study all aspects of the virus biology and virus-host interactions but also gave the opportunity to use these viruses as live vaccines or as gene vectors. This review provides an overview on the recent breakthroughs achieved by using these reverse genetics systems in terms of viral protein function, virulence and host-specificity factor, vaccine development and vector design. Table of contents 1. Introduction 1. Introduction Fish farmers are faced worldwide to viral infections 2. Reverse genetics systems: description and technical which destroy each year a significant part of the produc- tricks tion and thus induce important economic losses [1,2]. In addition to direct losses and delay in the aquaculture 2.1. Alphavirus expansion, viral diseases also cause additional impacts 2.2. Aquabirnavirus including shortage of food and jobs as well as social and 2.3. Betanodavirus environmental costs. Major viral diseases are mainly due 2.4. Novirhabdovirus to two antigenetically distinct Novirhabdoviruses which can coexist in the same fish farms: the viral hemorrhagic 3. A wide panel of applications and breakthroughs septicemia virus (VHSV) and the infectious hematopoie- tic necrosis virus (IHNV). Other viruses have also a ser- 3.1. Analysis of viral proteins of unknown function ious impact in the field such as the infectious pancreatic 3.1.1. Novirhabdovirus NV protein necrosis virus (IPNV), an Aquabirnavirus infecting for 3.1.2. Betanodavirus B1 and B2 proteins instance salmonid and viruses belonging to the Betano- 3.1.3. Aquabirnavirus VP5 protein davirus genus which cause serious diseases in several 3.2. Virus vectors marine fish species. The genome of these viruses con- 3.2.1. Antigenic chimeric viruses: example of sists of either a negative-sense single-stranded RNA Novirhabdovirus glycoprotein gene exchange molecule for the Novirhabdoviruses of about 11 kilo- 3.2.2. Insertion of a foreign gene bases (kb) [3,4], two segments of double-stranded RNA 3.3. Virulence and host specificity factors (A and B) of about 2.8 and 3.1 kilobase pairs (kbp) each for the Aquabirnavirus [5,6] or two positive-sense sin- 4. Conclusion remarks gle-stranded RNA (RNA1 and RNA2) of about 1.4 and 3.1 kb each for the Betanodaviruses [7,8]. These viral diseases are the most frequent but due to the expansion of the salmonid aquaculture and the development of new fish species production, new dis- Correspondence: [email protected] eases have emerged in the recent years [2]. One of the Unité de Virologie et Immunologie Moléculaires, INRA, CRJ, 78352 Jouy-en- most striking examples is undoubtedly the emergence of Josas, France © 2011 Biacchesi; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Biacchesi Veterinary Research 2011, 42:12 Page 2 of 15 http://www.veterinaryresearch.org/content/42/1/12 the sleeping disease in farmed rainbow trout (Oncor- Europe [9]. Sleeping disease (SD) is an infectious disease hynchus mykiss) and the pancreas disease in marine- of rainbow trout reared in fresh water while salmon pan- reared Atlantic salmon (Salmo salar). These diseases are creas disease (SPD) has been recorded in farmed Atlantic known since the 80s and have now spread in most of salmon. The aetiological agents responsible for these dis- the European countries and in North America. For eases, namely SDV and SPDV, respectively, are closely instance, the sleeping disease may affect 30 to 40% of related viruses that belong to the Alphavirus genus of the the French fish farms. Viruses responsible for these dis- Togaviridae family [10,22]. Sindbis virus (SINV), one the eases, the sleeping disease virus (SDV) and the salmon most studied virus among the Alphavirus genus, is trans- pancreas disease virus (SPDV) belong to the Alphavirus mitted by mosquitoes, and its alternate vertebrate host is genus, with a genome which consists of a positive-sense usually a bird or a mammal. Like all Alphaviruses, SDV single-stranded RNA molecule of about 12 kb [9,10]. and SPDV virions are spherical (70 nm in diameter), with Since many years, goals of different laboratories a lipid envelop containing heterodimeric glycoprotein around the world have been mainly but not exclusively spikes composed of two virus glycoproteins (E1 and E2). devoted to the development of new vaccine approaches Some alphaviruses may contain a third envelop protein based in part on live attenuated viruses to prevent viral (E3). The envelope is tightly organized around an icosahe- diseases in aquaculture [11,12] and the determination of dral nucleocapsid which contains the genomic RNA. The potential genetic factors that could explain the differ- viral genome consists of a positive-sense single-stranded ences of virulence existing between virus strains and RNA molecule of about 12 kb in length, which is capped their host range restriction. For that, a way allowing the at the 5’-terminus and polyadenylated at the 3’-terminus, manipulation of the viral genome is required. A major and contains two open reading frames (ORF). The 5’ two- step in engineering a viral RNA genome is the ability to thirds of the genome encode four non-structural proteins recoverlivevirusfromaDNAcopyoftheRNAgen- (nsP1 to nsP4) that are translated directly from the geno- ome: this is called “reverse genetics”. First success in mic RNA as a polyprotein precursor, which undergoes reverse genetics for a positive-stranded RNA virus, the subsequent proteolytic cleavage. The four non-structural poliovirus (Picornaviridae family), was in 1981 [13]. proteins are involved in genome replication and the synth- Thirteen years later, a reverse genetics system was estab- esis of a subgenomic RNA from the negative-strand copy lished for the recovery of a nonsegmented negative- of the genome that corresponds to the 3’ third of the viral stranded RNA virus, the rabies virus (RV) [14]. The abil- genome and encodes the second ORF. This second ORF is ity to manipulate a cDNA intermediate, exact copy of translated as a polyprotein, which is processed to produce the viral RNA genome, opens the possibility of deleting the viral structural proteins: the capsid, the glycoproteins genes for studying their function, introducing targeted E3, E2, E1 and the 6K protein. In contrast to the other mutations to determine potential genetic factors of viru- Alphaviruses, an arthropod-independent transmission has lence or inserting heterologous genes of interest and been demonstrated for salmonid Alphaviruses by cohabi- using these recombinant viruses as gene vectors. tation experiments [9]. Reverse genetics systems have been now established Based on the observation that genomic RNA from most for several fish RNA viruses such as the Novirhabdo- of the positive-stranded RNA viruses could serve as mes- viruses IHNV and VHSV [15-18], the Alphavirus SDV senger RNA (mRNA) and initiate infection upon transfec- [19], the Aquabirnavirus IPNV [20] and also for several tion in a permissive cell line, the recovery of infectious Betanodavirus species such as for the striped jack ner- virus from complementary DNA (cDNA) was first vous necrosis virus (SJNNV) [21]. A large number of described for poliovirus by Racaniello and Baltimore, various recombinant viruses have been generated by dif- almost 30 years ago [13]. The first infectious cDNA for a ferent groups. Some of them are currently being evalu- member of the Alphavirus genus was established for SINV ated as live vaccines in field trials and some others are few years later by Rice et al. [23]. The recovery of recombi- being used as gene vectors in fish. Some examples of nant alphavirus from cDNA was typically based on the such recombinant viruses will be described and the transfection into cells of synthetic capped RNA transcripts advances in terms of vaccine development, virulence generated by in vitro transcription from SP6- or T7-driven and host-specificity factor mapping and vector design full-length viral cDNA constructs. Although less efficient will be discussed. than transfection of in vitro-synthesized RNA, transfection of viral genome cDNA copy under the control of a RNA 2. Reverse genetics systems: description and polymerase II promoter (the cytomegalovirus (CMV) technical tricks immediate early promoter) was also described (for review 2.1 Alphavirus [24]). Similar approaches for SDV failed to produce infec- Salmonid Alphaviruses are recognized as serious patho- tious recombinant virus [19,25]. The key to recover SDV gens of farmed Atlantic salmon and rainbow trout in was found by fusing a self-cleaving hammerhead ribozyme Biacchesi Veterinary Research 2011, 42:12 Page 3 of 15 http://www.veterinaryresearch.org/content/42/1/12 sequence at the 5’-end of the cDNA copy of SDV full- of the temperature requirement of each virus (37°C and length genome [19]. Indeed, a precise 5’-end of SDV RNA 10°C for vTF7-3 and SDV, respectively), cells were first genome appears to be crucial to initiate an infectious incubated at least 7 h at 37°C to allow their infection by cycle.