WO2014174078A1 - Bacterial artificial chromosomes - Google Patents

Abstract

The invention relates to the use of a bacterial artificial chromosome (BAC) for the preparation of a vaccine, wherein the BAC comprises: - an inducible bacterial ori sequence for amplification of the BAC to more than 10 copies per bacterial cell, and - a viral expression cassette comprising a cDNA of an attenuated RNA virus genome and comprising cis-regulatory elements for transcription of said viral cDNA in mammalian cells and for processing of the transcribed RNA into infectious viral RNA.

Description

BACTERIAL ARTIFICIAL CHROMOSOMES FIELD OF THE INVENTION

The present invention relates to a plasmid vector system suitable for manipulating, maintaining and propagating infectious cDNA of RNA virus genomes as well as to the use of such vector systems.

BACKGROUND OF THE INVENTION

Previously, copy DNA (cDNA) of several flaviviruses and other RNA viruses has been cloned in different low copy bacterial vectors to overcome their intrinsic toxicity (due to the large size and cryptic expression of the viral sequences) (Bredenbeek et al. (2003) J. Gen. Virol. 84, 1261-1268; Durbin, et a/. (2006) Hum Vaccin. 2, 255- 260; Fan and Bird (2008) J. Virol. Methods. 149, 309-315; Li et al. (2011) PLoS One 6, el8197; Pu et al. (2011) J. Virol. 85, 2927-2941; Rice et al. ( 1989) New Biol. 1, 285-296) Almazan et al. (2008) Methods Mol Biol. 454, 275-91). The cloned cDNAs have been used as templates for production of infectious recombinant viruses, either by in vitro synthesis and transfection of the RNA genomes (Bredenbeek et al. , 2003, cited above), or by incorporating the viral cDNA in an expression cassette, which comprise a promoter such as the CMV-IE (Cytomegalovirus Immediate Early) promoter allowing the transcription of the viral RNA from transfected plasmid DNAs (Enjuanes et al. (2001) J. Biotechnol. 88, 183- 204; Hall et al. (2003) Proc. Natl. Acad. Sci. USA. 100, 10460-10464). Such viral expression cassettes directing the expression of attenuated foot-and-mouth disease (Ward et a/. ( 1997) J. Virol. 71, 7442-7447) and Kunjin viruses (Hall et al. (2003) Proc Natl Acad Sci USA. 100, 10460-10464) have been used as experimental DNA vaccines. Although the low copy number vector systems comprising a viral expression cassette can be maintained in the bacterial host cell in a stable manner, they have the important disadvantage that they only allow the purification of infective viral cDNA in amounts that are merely sufficient for small scale experimental use. Therefore, their use as a routine source of infective viral cDNA is impossible, for instance in the production of a life cDNA vaccine.

The production of viral DNA vaccines requires a substantial amplification of cloning vectors to obtain sufficient DNA, but these amplification methods are subject to severe constraints. In order to avoid mutations, vectors comprising viral DNA are propagated under conditions which prevent mutagenic events (recombination, mutations, improving mismatch repair, and the like). Bacterial Artificial Chromosomes (BAC) are known for their stability and can contain inserts up to 500 kb or more. However the size of such a vector with foreign DNA is a serious burden for bacteria, and its replication requires a substantial metabolic effort. Furthermore, exhaustion of nucleotides can lead to increased mutations. Finally, unwanted expression of foreign DNA (so-called cryptic expression) may occur, which can lead to toxic recombinant proteins. The production of toxic proteins by cryptic transcripts is inherent to flavivirus DNA and can only be solved by lowering the copy number of plasmids. Indeed, the higher the copy number of a vector, the higher the concentration of toxic proteins. As a consequence, bacterial hosts may counterselect for mutants wherein these proteins are not expressed.

Pu et al. (2011) J. Virol. 85, 2927-2941, describes in detail various attempts to solve the intrinsic toxicity of flavivirus cDNA in bacteria. These include the in vivo ligation of plasmids comprising parts of the viral genome, specific hosts, mutants to avoid cryptic expression and also low copy number plasmids.

The use of BACs which occur as a single copy in a bacterium provides thus a solution for these problems.

The low copy number is not a drawback for those applications wherein BAG DNA is subsequently subcloned or amplified to increase the concentration and wherein the introduction of some mutations by these techniques is not critical for the envisaged experiments. However, such amplification methods cannot be applied in the manufacture of DNA vaccines, making BACs a non- preferred vehicle for large scale plasmid preparations for DNA vaccines. Very large scale cultures are required to obtain substantial amounts of BAC.

The use of inducible BAC vectors is known from Wild et al. (2002) Genome Res. 12, 1434-1444 whereby the copy number of the BAC increases from 1 copy per cell to up to 100 copies per cell, or even more. Although this system provides a method to increase the yield of BAC DNA, there is a legitimate concern that the strongly increased activity of the replication system upon induction will increase the mutation frequency. The manufacture of DNA vaccines thus requires a system wherein a high copy number of a vector is obtained, but wherein replication of the vectors occurs without intolerable introduction of mutations.

SUMMARY OF THE INVENTION

The present invention resolves the problem of the amplification of viral cDNA for the preparation of a vaccine in the vector systems of the prior art by providing a vector that can be stably maintained in the host cell at low copy number, but can be significantly amplified by modifying the culture conditions of its host, without unwanted mutagenesis events. It is a further object of the present invention to provide such vector that can be shuttled from and to both a yeast and bacterial host, thus providing a very versatile system amenable to manipulate the vector in both a yeast and bacterial genetic system.

The present invention demonstrates, against what was expected, that the inducible increase in copy number of a BAG vector provides DNA which has a surprisingly low mutation rate. Even more surprisingly, the few mutations that occur are mostly frameshift mutations or stop codons, leading to truncated versions upon expression. Point mutations, which are either without effect or which lead to modified amino acids, are underrepresented.

This unexpected effect leads to the advantageous effect that high amounts of vector are obtained and that the limited amount of errors that does occur leads to a non-functional viral genome, rather than to a mutated viral genome of which the virulence can be increased compared to originally cloned construct.

The present invention provides a bacterial artificial chromosome comprising an inducible bacterial ori sequence, which allows to induce the amplification of said bacterial artificial chromosome to a high copy number, for instance by modifying the culture conditions of the bacterial host. Bacterial artificial chromosomes as used herein further comprise a viral expression cassette comprising a cDNA of a RNA virus genome flanked by cis-regulatory elements, which upon introduction of said bacterial artificial chromosome in a mammalian cell promote the transcription of said viral cDNA and allow for the processing of the transcribed RNA into infectious viral RNA. Viral cDNA contained in the viral expression cassette can either correspond to that of a wild-type RNA virus genome or be a chimeric viral cDNA construct, wherein heterologous DNA sequences have been inserted and/or native viral sequences have been deleted, truncated, or mutated. Typically heterologous DNA sequences encode one or more peptides/proteins, which are heterologously expressed by the recombinant virus, following the introduction in a mammalian cell of a bacterial artificial chromosome according to the present invention that contains a viral expression cassette comprising such chimeric viral cDNA. The bacterial artificial chromosome can further comprise a yeast autonomously replicating sequence for shuttling to and maintaining said bacterial artificial chromosome in yeast. The possibility to shuttle to and maintain the bacterial artificial chromosome according to the present invention in a yeast cell provides the advantage that it is amenable for genetic manipulation in both the yeast and bacterial genetic systems. As such the present invention provides a single vector system suitable for manipulating, maintaining and propagating infectious cDNA of RNA virus genomes. In absence of a stimulus of the inducible ori, the bacterial artificial chromosomes according to the present invention can be used for archiving and stable cloning of infectious viral cDNA in a bacterial host, while in presence of such stimulus said cDNA can readily be amplified and subsequently isolated to be used. The bacterial artificial chromosomes according to the present invention are particularly useful in the development, stable maintenance and production of viral cDNA to be used as a life vaccine against RNA viral pathogens. Alternatively, said bacterial artificial chromosomes are used for the maintenance and propagation of native or recombinant viruses from cDNA, for instance for research purposes.

In the present invention, BACs with an inducible bacterial ori are used for the preparation of a vaccine of a viral expression cassette comprising cDNA of an RNA virus and cis regulatory elements for the transcription of viral cDNA in mammalian cells and processing of the transcribed RNA into infectious viral RNA.

Surprisingly, the generation of multiple copies of the BAG comprising the viral DNA did not lead to the disadvantages that are known to occur with high copy number systems.

Generally, toxic proteins are produced in bacterial systems, due to the cryptic expression of viral sequences. Indeed, the generation of flavivirus infectious clones has been traditionally hindered by the toxicity of their full-length cDNAs in bacteria. Various approaches have been employed to overcome this problem, including the use of very-low-copy-number plasmids and bacterial artificial chromosomes (discussed in Edmonds (2013) J. Virol. 87, 2367-2372). This is a phenomenon which relates to the insert which is cloned into the BAC, and hampers bacterial growth and metabolism. Bacteria with mutants wherein cryptic expression does not take place have a growth advantage and will overgrow the original population. In the prior art this is reflected by the size of bacterial colonies. Non-mutated constructs produce toxic proteins and typically small colonies are obtained. Mutated constructs produce less or no toxic proteins which results in the occurrence of larger colonies.

Based upon this prior art knowledge it was expected that the induction of plasmid replication would thus result in an increase of toxic transcripts and a concomitant increase in mutants wherein cryptic expression does not take place.

Surprisingly the inducible replication system appea rs to be insensitive to the toxicity of cryptic proteins. Indeed, compared to the prior art high copy number systems, the bacterial colonies are somewhat larger, which indicates that the bacterial host is less sensitive to eventual toxic proteins. More importantly, very large colonies, representing mutated plasmids are not encountered.

The finding that the inducible system is insensitive towards toxic proteins is unexpected. There were no indications in the prior art which indicated that this system would not be sensitive to toxic proteins (or perhaps that toxic proteins are not produced).

A further disadvantage of the inducible system is inherent to the generation of multiple copies of the BAC. Indeed the authors of the inducible system explain that the most important feature of BAC clones is their stability resulting from their very low copy number. Wild et al. (2002) cited above shows that the copy number can be lowered even further by the addition of glucose. This single copy state improves stability of maintenance of BAC libraries by reducing the opportunity for intracellular recombination between clones. This demonstrates that the inducible system as published by Wild et al. does not lower the changes of unwanted recombination events which occur as soon as multiple copies of a BAC are present in a host cell. It is understood by the skilled person that induction and the subsequent high copy number will reintroduce recombination events. Consequently, the skilled person would refrain of using such systems for DNA preparations that are intended to be used for vaccination purposes.

In the present invention BACs have been amplified in the inducible ori system and the amplified BAC has been tested for recombination events. Contrary to what would be expected, recombination events are rare.

Furthermore, apart from testing for recombination events, the amplifies BACs have been tested as well for the presence of other mutations. The mutation frequency which was encountered was very low, and moreover, the fraction of missense is surprisingly lower than theoretically expected. Mutations, if occurring are predominantly nonsense or frameshift mutations leading to non-functional viral RNA.

The present invention allows a significant upscale of DNA vaccine production. For example, the main manufacturers of the life-attenuated Yellow Fever vaccine are at present unable to meet the existing demands. With the technology of the present invention, it will be possible to produce DNA vaccines at significant lower costs and higher quantities than the current life-attenuated vaccine, thereby fulfilling a long felt need.

Also for other viral diseases such as JEV, WNV, measles, rubella and HIV vaccines there is a need for a vaccine preparation platform which can provide sufficient amounts of DNA.

A first aspect of the invention relates to uses of a bacterial artificial chromosome (BAC) for the preparation of a vaccine, wherein the BAC comprises:

- an inducible bacterial ori sequence for amplification of said BAC to more than 10 copies per bacterial cell, and

- a viral expression cassette comprising a cDNA of an attenuated RNA virus genome and comprising cis-regulatory elements for transcription of said viral cDNA in mammalian cells and for processing of the transcribed RNA into infectious RNA virus.

Embodiments of cDNAs of an attenuated RNA virus genome are a chimeric viral cDNA construct of an RNA virus genome, wherein a heterologous DNA sequence has been inserted or wherein a native viral sequence has been deleted, truncated, or mutated.

Embodiments of the viral expression cassette comprise

a cDNA of a positive-strand RNA virus genome,

- a RNA polymerase driven promoter preceding the 5' end of said cDNA for initiating the transcription of said cDNA, and

an element for RNA self-cleaving following the 3' end of said cDNA for cleaving the RNA transcript of said viral cDNA at a set position.

Embodiments of positive-strand RNA virus are flaviviruses, hepaciviruses, pestiviruses, togaviruses, picornaviruses, coronaviruses, hepeviruses, and caliciviruses.

In a typical embodiment the viral expression cassette comprises a cDNA of a yellow fever virus, for example a cDNA of the life-attenuated YFV-17D yellow fever virus vaccine.

In other embodiments the viral expression cassette comprises a cDNA of a virus belonging to the group of negative-strand RNA viruses, double-strand RNA viruses or ambisense RNA viruses.

In specific embodiments the bacterial artificial chromosome further comprises a yeast autonomously replicating sequence for shuttling to and maintaining said bacterial artificial chromosome in yeast. An example of a yeast ori sequence is the 2μ plasmid origin or the ARS1 (autonomously replicating sequence 1) or functionally homologous derivatives thereof.

In certain embodiments the RNA polymerase driven promoter is an RNA polymerase II promoter, such as Cytomegalovirus Immediate Early (CMV-IE) promoter, the Simian virus 40 promoter or functionally homologous derivatives thereof.

In other embodiments the RNA polymerase driven promoter is an RNA polymerase I or III promoter.

Examples of an element for RNA self-cleaving is the cDNA of the genomic ribozyme of hepatitis delta virus or functionally homologous RNA elements.

In a particular embodiment the viral expression cassette comprises a cDNA of the life-attenuated YFV-17D vaccine, wherein one or more of the cDNA sequences coding for the virion surface proteins are either deleted, truncated, or mutated so that such functional virion surface protein of YFV-17D is not expressed and wherein a cDNA sequences coding for a heterologous protein is inserted in the YFV-17D cDNA. An example of such heterologous protein is a virion surface protein of a flavivirus.

Embodiments of a viral expression cassette comprises a cDNA of the life-attenuated YFV-17D vaccine, wherein one or more unrelated cDNA sequences are inserted to be expressed as one or more heterologous protein within the viral polyprotein.

In other embodiments the viral expression cassette comprises a viral cDNA wherein foreign cDNA sequences are inserted to be heterologously expressed by the said recombinant viruses.

A further aspect relates to methods of preparing a vaccine against RNA viruses comprising the steps of: a) providing a bacterial host transfected with a BAC as described in the first aspect and in the various embodiments thereof b) amplifying the BAC by adding a compound which activates said inducible ori c) isolating the amplified BAC,

d) formulating the BAC into a vaccine.

A further aspect relates to a BAC as described in the first aspect and in the various embodiments thereof for use as a vaccine.

Another aspect of the present invention relates toa BAC as described in the first aspect and in the various embodiments thereof for use in the prevention of a RNA virus infection.

A further aspect relates to uses of a BAC as described in the first aspect and in the various embodiments thereof as a life DNA vaccine. Another aspect relates to uses of a BAC as described in the first aspect and in the various embodiments thereof for the propagation of native or recombinant viruses from said cDNA.

A further aspect relates bacterial artificial chromosome (BAC) as a BAC as described in the first aspect and in the va rious embodiments thereof for the preparation of a vaccine.

DETAILED DESCRIPITON OF THE INVENTION

Legends to the figures

Figure 1. Generation of the pShuttleBAC series of RNA virus expression plasmids. (A) Sketch showing the construction of the pShuttleBAC/Pme as sta rting vector construct. (B) Sketch showing the construction of the pShuttleBAC/Pme derived flaviviral expression vectors by insertion of the viral cDNAs by homologous recombination between the SV40 promoter (SV40p) and HDV ribozyme (HDrz) . Figure 2. Enhanced plasmid stability of pShuttleBAC constructs in E.coli. Generic plasmid maps showing the principle layout of prior art flaviviral cDNA plasmids (A) and the new pShuttleBAC series of vectors (B, DNA-YFVax) . Upon transformation in E. coli a single colony of each (A) and (B) was grown overnight at 37 °C and plated on selective media . Generally constructs of type A grow into much smaller colony sizes as those of type B (Figure 2C and D, respectively) . Moreover, type A constructs give rise to progeny of a wide range of colony sizes (histogram for normalized colony diameters, right panel of figure 2C) indicative for selection and segregation of mutant plasmid clones that occasionally render the cDNAs less toxic to E. coli. Clonal analysis identified multiple possible underlying mutations, including transposon insertion in the viral E/NS1 region . By contrast, plasmid clones comprising type B constructs of the pShuttleBAC series do not seg regate a nd show a more homogenous colony size even after repeated passage in E. coli indicating high genetic stability.

Figure 3A. Detection of replicative intermediates of YFV-17D RNA replication after transfection of Vero-B cells with pShuttle/YF17D (wildtype, WT) and its replication deficient derivative pShuttle/YF17DAGDD (AGDD) by Northern blot. Antisense oriented antigenomes, (-)-RNA (A upper panel, 11 kb) and sense orientated viral genomes, (+)-RNA (A lower pa nel, l lkb), could be detected 5 days after transfection only in WT transfected cells. Ongoing replication in the presence of actinomycin D (ACD), an inhibitor of DNA directed RNA synthesis, confirms that after initial launching of YFV-17D genome transcription from pShuttle/YF17D, viral replication continues autonomously in a plasmid independent manner.

Figure 3B. Detection of proper YFV-17D RNA transcript processing by 5'- and 3'-RACE (rapid amplification of cDNA ends). pShuttle/YF17D launches transcription of nascent YFV-17D RNAs (bold cases in figure 3B) that start and end with proper 5' and 3' ends (upper and lower panel, respectively) as confirmed by rapid amplification of cDNA ends (RACE).

Figure 4A-C. Similar CPE induced by YFV-17D of different origin. YFV-17D viruses derived from in vitro transcribed and capped RNA using pACNR-FLYF17DII as a template (A) or harvested after plasmid DNA transfection of pShuttle/YF17D (B) produce an identical virus induced cytopathic effect (CPE) on BHK-21 cells 5 days post infection (d p.i.); C, uninfected cells for comparison.

Figure 4D-E. Similar plaque phenotype of YFV-17D of different origin. YFV- 17D viruses derived from in vitro transcribed and capped RNA using pACNR- FLYF17DII as a template (D) or harvested after plasmid DNA transfection of pShuttle/YF17D (E) produce a comparable number (5 days p.i. 3x 10^s plaque forming units (pfu) mL^"1 vs 2 x 10⁵ pfu mL^'1) and identical morphology of plaques (diameter 6,4 ± 0,7 mM vs 6, 1 ± 1, 1 mM ; n = 8, p-value = 0,6 by t-test) on BHK- 21 cells.

Figure 5. Detection of infectious recombinant DENV2 by immunofluorescence assay (IFA). Recombinant DENV2 NGC produced by BHK- 21 cells transfected with pShuttle/DV2 shows dose dependent infection of Vero-B cells, visualizes as viral foci by immunofluorescence staining for the viral E protein 5 days p.i. (A, undiluted supernatant, B, 100-fold diluted supernatant, C, uninfected cell control).

Figure 6. Survival of AG129 mice infected with Stamaril (open squares) or transfected with pShuttle/YF17D (crosses). About 10 to 12 days after i.p. challenge, interferon type I and II receptor deficient (AG129) mice start losing weight and develop a uniform set of symptoms, namely ruffling of the fur, tremor and flaccid hind limb paralysis. Control animals transfected with the replication deficient NS5AGDD plasmid variant (AGDD, open circles) show no pathogenesis. However, they stay susceptible to a second Stamaril ® challenge (filled triangle) 20 days after initial transfection and then die within a comparable timeframe and showing similar symptoms. Plasmid DNAs were transfected i.p. using calcium carbonate microflowers in 33% propylene glycol as carrier. Figure 7. Morbidity (A) and detection of YFV-17D RNA (B) from infected AG129 mice. (A) If infected either with Stamaril ® or transfected with pShuttle/YF17D (pYF17D), AG129 mice loose about 20 % of body weight before they have to be euthanized after an average of 12 to 13 days (MDD, mean day to death). By contrast, pShuttle/YF17DAGDD (AGDD) transfected mice gain weight, before they are challenged with Stamaril ® (AGDD + 2° Stamaril) and die from YFV-17D infection within about two weeks. (B) Comparable amounts of YFV-17D RNA can be detected by means of qRT-PCR in brain samples of AG129 mice from (A) collected at death.

Figure 8. Map of pShuttle/YF17D (synthetic construct #1). Legend: SV40p: Simian virus 40 promoter/origin, YFV-17D: yellow fever virus vaccine strain 17D cDNA, HDVrz: hepatitis delta virus ribozyme cDNA; 2μ : 5. cerevisiae 2-micron origin; TRP1 : TRP1 gene conferring prototrophic growth towards tryptophan; parABC: partitioning genes of F-plasmid; repE: repE gene of F-plasmid; oriS: origin of F-plasmid; oriV: origin of plasmid RK2; CmR: chloramphenicol resistance gene.

Figure 9. E. coli colony growth after tranformation with different YFV-17D cDNA vectors. (A) E. coli EPI-300T colonies after transformation with pACNR- FLYF17DII and growth for 16 h at 37° C. A colony size distribution with two subpopulations with major size differences can be observed, microcolonies (diameter smaller than 0.2 mm) and macrocolonies (diameter around 0.4 mm). Microcolonies represent the majority. (B+C) E. coli EPI-300T colonies after transformation with pShuttle/YFV17D. Plating on plates without inducer (B), or with 0.01% L-arabinose (C) for induction of of high copy replication mediated by the inducible high-copy origin. Large black circles are zirkonia beads of 2.5 mm diameter embedded into the agar to serve as calibrators. Inset figures are schematic line drawings representing the colony outlines observed in each setting. Figure 10. Size distribution of E. coli colonies after transformation with different YFV-17D cDNA vectors. (A) E. coli EPI-300T colonies after transformation with pACNR-FLYF17DII. (B+C) E. coli EPI-300T colonies after transformation with pShuttle/YFV17D. Plating on plates without inducer (B), or with 0.01% L-arabinose (C) for induction of high copy replication mediated by the inducible high-copy origin.

Figure 11a. Map of pShuttle/ChimeriVax-JE. pShuttle/ChimeriVax-JE contains following the SV40 promotor/origin nt 1-481 and 2452-10862 of YFV-17D, in which 477-2477 of neuroattenuated JEV vaccine strain JE SA14-14-2 are inserted. The second last two last amino acids of the JEV E-ORF are mutated from a histidin to a glycin codon to generate a Kasl site, the NS2A and NS4B-ORFs contain two adaptive G4055a and G7349a mutations found in Imojev® changing a methionine to valine in the YFV-17D NS2A and a lysine to glutamine in the NS4B ORFs, respectively. Additional silent mutations generate restriction markers at positions 406 (Xhol), 4009 (BstEII), and 7315 (Nhel) .

Figure l ib. Map of pShuttle/ChimeriVax-WN . pShuttle/ChimeriVax-WN contains following the SV40 promotor/origin nt 1-481 and 2452- 10862 of YFV-17D, in which 477-2477 of a neuroattenuated derivative of WNV strain NY-99 are inserted . The second last two last amino acids of the WN E-ORF are mutated from a histidin to a glycin codon to generate a Kasl site, the NS2A and NS4B-ORFs contain two adaptive G4055a and G7349a mutations found in Imojev® changing a methionine to valine in the YFV-17D NS2A and a lysine to glutamine in the NS4B ORFs, respectively. Additional silent mutations generate restriction markers at positions 406 (Xhol), 4009 (BstEII), and 7315 (Nhel) .

Figure 12. Map of pShuttle/EV71. pShuttle/EV71 contains the cDNA of EV71 strain BrCr-TR (Genbank AB204852.1) inserted between the SV40 promotor/origin at its 5' terminus, and a 30 nt long polyA repeat plus the hepatitis delta virus ribozyme at its 3' end .

Figure 13 depicts sequences with SEQ ID NO 1-7

Definitions

The term "bacterial artificial chromosome (BAC)" refers to a plasmid DNA construct used to clone DNA sequences in bacterial cells, such as E. coli. Typically DNA sequences ranging from 30,000 to about 300,000 base pairs can be inserted into a BAC. The BAC, with the inserted DNA, can be taken up by bacterial cells. As the bacterial cells grow and divide, the BAC DNA is stably maintained within the bacterial cells at a very low copy number per bacterial cell, preferably not exceeding 3 copies per cell, such as at a single copy per cell . The replication of a BAC is initiated at an origin of replication (ori) sequence, typically the oriS sequence. This replication is stringently regulated by gene products, generally the repE and/or repF, encoded by the BAC. The BAC further encodes for proteins, such as parA, B and C, directing the partitioning of the BAC copies to the daughter cells during division. Typically, BAC vectors further comprise selectable markers, such as antibiotic resistance or reporter enzyme ma rkers, such as lacZ allowing for blue white selection. An exa mple of a generally used BAC is the pBeloBacl l (Shizuya et al . ( 1992) Proc. Natl . Acad . Sci . USA 89, 8794-8797. ) The sequence of this vector was reported at GenBank Accession Number U51113. pBeloBacl l is a circular plasmid that includes oriS, the repE gene that produces a protein that initiates and regulates the replication at oriS, and partition genes par A, B, and C. For selection pBeloBacl l includes a chloramphenicol-resistance-encoding gene. The vector also includes a lacZa gene that can be disrupted or eliminated from the vector when an insert is cloned in the BAC.

The term "inducible bacterial ori sequence" refers to a plasmid ori sequence that functions in a bacterial host cell and is responsive to amplification-mediating protein(s). Preferably, the replication function of the inducible ori is severely suppressed or non-existing in absence of said amplification-mediating protein(s). It is further preferred that in presence of said amplification-mediating protein(s) the inducible ori amplifies the plasmid to a high copy number, preferably to more than 20 copies per cell, more preferably to more than 100, for instance to more than 500 or 1000 copies per cell. For use in the present invention it is also preferred, although not essential, that the inducible ori responds to a single amplification- mediating protein.

The oriV is particularly useful for use as an inducible bacterial ori in the present invention because of its broad host range, its known capacity to replicate DNA fragments of 100-kb or larger, its high copy number and its requirement for only one inducing protein. Examples of bacterial artificial chromosomes comprising an inducible oriV are pBeloBAC/oriV (Wild et al. (2002) Genome Res. 12, 1434-1444) and pBAC-LacZ (Addgene plasmid 13422: pBAC-lacZ,, Adgene, Cambridge MA, USA). The pBAC-lacZ plasmid is a mini-F' that can be replicated in standard E. coli strains, but because it is maintained as a single copy episome, it gives low DNA yields. pBAC-lacZ also contains a second, higher copy number origin of replication (oriV) that is only active in the presence of a trans-acting factor encoded by the trfA gene. Transformation of this plasmid in E. coli cells expressing trfA from an inducible promoter allows increasing the copy number of the pBAC-lacZ plasmid by inducing the trfA expression. TransforMax™ EPI300™ E. coli cells (Epicentre, Madison WI, USA) contain an inducible mutant trfA gene whose gene product is required for initiation of replication from the oriV origin of replication. The expression of trfA can be induced by addition of L-arabinose to the culture medium, resulting in the activation of the oriV.

"Yeast origin of replication" refers to a sequence within a plasmid, such as a bacterial artificial chromosome, which allows the replication and maintenance of this plasmid in yeast cells. The origin of replication as present in 2 μ plasmid (Huberman et al. ( 1987) Cell 51, 473-481; Brewer and Fangman ( 1987) Cell 51, 463-471; Hartley and Donelson ( 1980) Nature 286, 860-865.) has shown to be a suitable ori for shuttling the bacterial artificial chromosomes according to the present invention to yeast. Other suitable yeast ORIs have been described (Liachko et al. (2013) Genome Res. 23, 698-704, for instance the ARS1 (autonomously replicating sequence 1) and functionally homologous derivatives thereof as used in Yeast Centromeric plasmids (YCp) or the synthetic CEN6/ARSH4 origin (Frazer and O'Keefe (2007) Yeast. 24, 777-789).

"viral expression cassette" in the context of the present invention refers to a cDNA of a RNA virus genome flanked by cis-regulatory elements, which upon introduction of said bacterial artificial chromosome in a mammalian cell promote the transcription of said viral cDNA and allow for processing of the transcribed RNA into infectious viral RNA, as described in more detail below.

"infectious viral RNA" refers to viral RNA which, upon introduction in its mammalian host, is sufficient to provide all viral functions required for viral replication and production of infectious viral progeny. This includes (i) serving as a transcriptional template for viral RNA synthesis and genome amplification, and (ii) serving as translational template for synthesis of viral proteins that are required for viral replication. Other accessory functions such as for instance decoying of host cell factors involved in innate antiviral response (Moon et al. (2012) RNA. 18, 2029-40. may have to be provided by the infectious viral RNA as well.

"Attenuation" in the context of the present invention relates to the change in the virulence of a pathogen by which the harmful nature of disease-causing organisms is weakened (or attenuated); attenuated pathogens can be used as life vaccines. Attenuated vaccines can be derived in several ways from living organisms that have been wea kened, usually from cultivation under sub-optimal conditions (also called attenuation), or from genetic modification, which has the effect of reducing their ability to cause disease.

In a first aspect the present invention provides a bacterial artificial chromosome comprising an inducible bacterial ori sequence, which in presence of a stimulus induces the amplification of said bacterial artificial chromosome within a bacterial cell to a high copy number, preferably to more than 10 copies per cell, more preferably to more than 100, for instance to more than 500 or 1000 copies per cell. Generally, the amplification of said bacterial artificial chromosome as a result of said stimulus does not exceed more than 10,000, for instance no more than 5000 copies per cell. A bacterial artificial chromosome according to the present invention further comprises a viral expression cassette comprising a cDNA of a RNA virus genome flanked by cis-regulatory elements, which upon introduction of said bacterial artificial chromosome in a mammalian cell promote the transcription of said viral cDNA and allow for processing of the transcribed RNA into infectious viral RNA. The viral cDNA comprised in the viral expression cassette of a bacterial artificial chromosome according to the present invention can either be derived from a virus belonging to the group of the positive strand viruses, the negative strand viruses, double-strand RNA viruses or the viruses using an ambisence RNA strategy for replication. Said viral cDNA contained in the viral expression cassette can either correspond to that of a wild-type RNA virus genome or be a chimeric viral cDNA construct wherein heterologous DNA sequences have been inserted and/or native viral sequences have been deleted. Preferably, said heterologous DNA sequences encode one or more proteins, which are heterologously expressed by the recombinant virus following the introduction in a mammalian cell of a bacterial artificial chromosome according to the present invention that contains a viral expression cassette comprising such chimeric viral cDNA. Optionally, the bacterial artificial chromosome according to the present invention further comprises a yeast autonomously replicating sequence for shuttling to and maintaining said bacterial artificial chromosome in yeast. The possibility to shuttle to and maintain the bacterial artificial chromosome according to the present invention in a yeast cell provides the advantage that it is amenable for genetic manipulation in both the yeast and bacterial genetic systems.

In absence of a stimulus of the inducible ori, the bacterial artificial chromosomes according to the present invention can be used for archiving and stable cloning of infectious viral cDNA in a bacterial host, while in presence of such stimulus said cDNA can be amplified and subsequently isolated to be used. The bacterial artificial chromosomes according to the present invention are particularly useful in the development, stable maintenance and production of viral cDNA to be used a life vaccine against RNA viral pathogens. Alternatively, said bacterial artificial chromosomes are used for the maintenance and propagation of native or recombinant viruses from cDNA, for instance for research purposes. The bacterial artificial chromosomes according to the present invention, particularly those comprising a yeast origin of replication, have the further advantage that they provide a versatile system for genetically engineering the viral cDNA. This versatility is particularly important in the research and development uses of said bacterial artificial chromosomes, for instance in the design of a cDNA life vaccine against a RNA viral pathogen or in research aiming at elucidating the role and function of certain viral gene products using a reverse genetic approach. In case the bacterial artificial chromosome according to the present invention comprises a viral expression cassette comprising a cDNA of a positive strand RNA virus genome, it is preferred that said viral cDNA is preceded at its 5' end by an RNA polymerase driven promoter, which upon introduction in a mammalian cell initiates the transcription of the viral cDNA, while at its 3' end it is preferably followed by an element for RNA self-cleaving for cleaving the RNA transcript of said viral cDNA at a set position. Together these cis-regulatory elements allow for the transcription and processing of said viral cDNA into infectious viral RNA when introducing the bacterial artificial chromosome in a mammalian cell. Preferably, said RNA polymerase driven promoter is a RNA polymerase II operated promoter, such as for instance the Cytomegalovirus Immediate Early (CMV-IE) promoter (Thomsen et al. ( 1984) Proc. Natl. Acad. Sci. USA 81, 659-663), the Simian virus 40 promoter (Deboist and Chambon ( 1981) Nature 290, 304-310) or functionally homologous derivatives thereof such as the CMV-IE chicken beta-actin chimeric (CAG) promoter (Niwa et al. ( 1991) Gene 108, 193-199) or inducible versions of said RNA polymerase II operated promoters such as the tetracyline-operator minimal CMV-IE promoter (Gossen et al. ( 1995) Science. 268, 1766-1769; Baron and Bujard (2000) Methods Enzymol. 327, 401-421). Alternatively, said RNA polymerase driven promoter is a RNA polymerase I (Russel and Zomerdijk (2006) Biochem. Soc. Symp. 73, 203-216) or a RNA polymerase III promoter, such as the U6 or H I promoter. It is further preferred that said element for RNA self-cleaving is the cDNA of the genomic ribozyme of hepatitis delta virus (Chadalavada et al. , (2007) RNA 13, 2189-2201) or the cDNA of the functionally homologous hepatitis delta virus-like self-cleaving ribozymes RNA elements such as described in Webb and Luptak (2011) RNA Biol. 8, 719-727. Preferably, the viral cDNA of a positive stranded RNA virus contained in said viral expression cassette is derived from a virus belonging to either one of the following viral families the Flaviviridae, including yellow fever virus and other flaviviruses, the hepaciviruses including the hepatitis C virus, the pestiviruses, including the bovine viral diarrhea virus and the classical swine fever virus, the Togaviridae, including the alphavirus, Chikungunya and the rubivirus, rubella virus, the Picornaviridae, including the enteroviruses, such as poliovirus and rhinovirus, and the aphtoviruses, the Coronaviridae, including the HCoV-229E, the SARS-CoV, MERS-CoV (initially described as Novel coronavirus 2012/London l_novel CoV 2012) and the feline coronavirus, and the hepeviruses, including the hepatitis E virus, and the Caliciviridae, including the Norwalkvirus and norovirus. Said viral cDNA contained in the viral expression cassette can either correspond to that of a wild-type RNA virus genome or be a chimeric viral cDNA construct wherein heterologous DNA sequences have been inserted and/or native viral sequences have been deleted, truncated, or mutated. Preferably, said heterologous DNA sequences encode one or more peptides/proteins, which are heterologously expressed by the recombinant virus upon introduction in a mammalian of a bacterial artificial chromosome according to the present invention that contains a viral expression cassette comprising such chimeric viral cDNA.

In a particular embodiment of the present invention the bacterial artificial chromosome according to the present invention contains a viral expression cassette comprising the cDNA of the positive stranded life-attenuated yellow fever virus (YFV)-17D vaccine (Figure 6). The bacterial artificial chromosomes according to this particular embodiment can be used for the stable cloning and propagation of YFV- 17D cDNA. In addition such bacterial artificial chromosomes can serve as a DNA vaccine for live YFV-17D as an alternative for the presently used life attenuated YFV-17D virus vaccine (Stamaril® and similar preparations such as YF-Vax® and others). With respect to the existing YFV-17D virus vaccine the YFV-17 DNA vaccine according to the present invention has the advantage that it can be produced at a lower cost without the need for eukaryotic cell cultures or embryonated chicken eggs. Furthermore, its distribution does not require a cold-chain and it can be needle free administered.

In a more particular embodiment the bacterial artificial chromosome according to the present invention contains a viral expression cassette comprising the cDNA of the life-attenuated YFV-17D vaccine wherein heterologous DNA sequences have been inserted and/or native viral sequences have been deleted. For instance, with reference to US6962708, the nucleotide sequence encoding the prM-E protein in the cDNA of YFV-17D can either be deleted, truncated, or mutated so that the functional prM-E protein of YFV-17D is not expressed, while, a nucleotide sequence encoding the viral envelope protein of a second, different virus, so that the viral envelope protein of the second virus is expressed from the altered genome of the YFV-17D vaccine. Preferably, said second virus is also a flavivirus, such as Japanese Encephalitis (JE, e.g., JE SA14-14-2), Dengue (DEN, e.g., any of Dengue types 1-4; for example, Dengue-2 strain PUO-218) (Gruenberg et at. ( 1988) J. Gen. Virol. 67, 1391-1398.), Murray Valley Encephalitis (MVE), St. Louis Encephalitis (SLE), West Nile (WN), Tick-borne Encephalitis (TBE) (i.e., Central European Encephalitis (CEE) and Russian Spring-Summer Encephalitis (RSSE) viruses), and Hepatitis C (HCV) viruses. Additional flaviviruses for use as the second flavivirus include Kunjin virus, Powassan virus, Kyasanur Forest Disease virus, Zika virus, Usutu virus and Omsk Hemorrhagic Fever virus. Introduction of such bacterial artificial chromosome comprising a chimeric YFV-17D cDNA in a mammalian cell results in the production of a chimeric virus composed of the genes and gene products responsible for intracellular replication belonging to YFV-17D and the genes and gene products of the envelope of the second virus. Since the viral envelope contains antigenic determinants responsible for inducing neutralizing antibodies, the result of infection with the chimeric virus is that such antibodies are generated against the second virus. Alternatively, the nucleotide sequence encoding the prM-E and/or the NS1 protein in the cDNA of YFV-17D can either be deleted, truncated, or mutated so that the functional prM-E and/or NS1 protein of the YFV-17D is not expressed as such, while, a nucleotide sequence encoding for a peptide/protein containing a specific epitope/antigen so that said protein is expressed from the altered genome of the YFV-17D vaccine. Alternatively, cDNAs encoding for heterologous proteins can be inserted at other positions in the cDNA YFV-17D within the bacterial artificial chromosome according to the present invention such as insertions between E and NS1 genes (Bonaldo et a/. (2007) Virol. J. 4, 115.), insertion in the C gene (Jones et al. (2005) Virology 331, 247-259; Schoggings et a/. (2012) Proc. Natl. Acad. Sci. USA 109, 14610-14615) or the untranslated regions of the YFV-17D cDNA (Jones et a/. (2005) cited above). Preferably, said epitope/antigen-containing protein is a tumor antigen, or an antigen of a viral, bacterial of parasitic pathogen. Introduction of such bacterial artificial chromosome comprising a chimeric YFV-17D cDNA in a mammalian cell results in the production of a chimeric virus composed of the genes and gene products responsible for intracellular replication belonging to YFV-17D and a gene and gene product of said epitope/antigen-containing protein. Since the viral envelope contains antigenic determinants responsible for inducing neutralizing antibodies, the result of infection with the chimeric virus is that such antibodies are generated against said epitope/antigen-containing protein.

In case the bacterial artificial chromosome according to the present invention comprises a viral expression cassette comprising cDNA of a negative strand RNA virus genome, the construct as previously described for positive strand RNA viruses has to be modified in a way that the viral genomic cDNA is present in its sense (antigenomic) orientation with respect to the cis elements driving its expression (Radecke et al. ( 1995) EMBO J. 14, 5773-5784), and that it further comprises in sense orientation the cDNA's encoding the viral gene products in sense orientation that together with the viral RNA make part of the viral replicase complex needed for the rescue of viral RNA replication. These cDNA's are flanked by the regulatory cis elements required for expressing these viral gene products that build the viral replicase complex from the plasmid. In the case of the unsegmented negative strand RNA viruses (Conzelmann (1998) Annu. Rev. Genet. 32, 123-162) these viral gene products are the N (NP), P and L proteins. Expression of the antigenomic cDNA of the negative strand RNA genome can be driven by either RNA polymerase I or II promoters (Martin et a/., (2006) J Virol. 80, 5708-5715; while the expression cassette for the viral proteins that build the viral replicase complex may be either polycistronic as encountered naturally in the viruses themselves or monocistronic employing a set of different RNA polymerase promoters (Morita et al. (2012) Biotechniques O, 1-5) for balanced expression of each replicase component. The rescue of negative strand RNA viruses with segmented RNA genomes from an artificial bacterial chromosomes according to the present inventions requires modification with respect to the system as described for negative strand RNA viruses with non-segmented RNA genomes; more particularly an expression cassettes for each genome segment (Neumann and Kawaoka (2004) Curr. Top. Microbiol. Immunol. 283, 43-60) driven by appropriate RNA polymerase I and II promoters (Fodor et al. ( 1999) J. Virol. 73, 9679-9682) needs to be incorporated. Due to the limited vector capacity of the plasmid vector systems used for this purpose according to the prior art all the functions required for the rescue of such viruses have to be provided in the prior art by co-transfection of several plasmids, for instance for the rescue of influenza viruses using up to 8 or 12 plasmids was previously described in Hoffmann et al. (2002) Proc. Natl. Acad. Sci. USA 99, 11411-11416 and Fodor et al. 1999 (cited above) respectively. The high vector capacity of bacterial artificial chromosomes according to the present invention to contain large inserts, allows expressing negative strand RNA virus genomes or genome segments plus additional viral protein coding sequences from a single bacterial artificial chromosomes in a similar way as for positive strand RNA virus genomes.

Preferably, said viral cDNA of a negative stranded RNA virus contained in said viral expression cassette and the additional expression cassettes needed for rescue of viral replication is derived from a virus belonging to either one of the following viral families the Orthomyxoviridae , including the influenza A, B and C virus, and the paramoxyviruses, including measles virus, mumps virus and respiratory syncytial virus. Said viral cDNA contained in the viral expression cassette can either correspond to that of a wild-type RNA virus genome or be a chimeric viral cDNA construct wherein heterologous DNA sequences have been inserted and/or native viral sequences have been deleted, truncated, or mutated. Preferably, said heterologous DNA sequences encode one or more peptides/proteins, which are heterologously expressed by the recombinant virus upon introduction in a mammalian of a bacterial artificial chromosome according to the present invention that contains a viral expression cassette comprising such chimeric viral cDNA.

In case the bacterial artificial chromosome according to the present invention comprises a viral expression cassette comprising the cDNAs of a double strand RNA virus genome the construct has to be modified such that all viral RNA genome segments needed for the rescue of viral RNA replication as described in Boyce et al. (2008) J. Virol. 82, 8339-8348), i.e. 10 RNAs in the case of the bluetongue virus, can be expressed from RNA polymerase II promoters, which allow proper processing, mainly capping, of the nascent transcripts. Alternatively RNA polymerase I and III promoters can be used for this purpose. Preferably, said viral cDNA of a double stranded RNA virus contained in said viral expression cassettes is derived from a virus belonging to either one of the following viral families the of the Reoviridae, including reovirus, rotavirus and bluetongue virus. Said viral cDNAs contained in the viral expression cassette can either correspond to that of a wild- type RNA virus genome or be a chimeric viral cDNA construct wherein heterologous DNA sequences have been inserted and/or native viral sequences have been deleted, truncated, or mutated. Preferably, said heterologous DNA sequences encode one or more peptides/proteins, which are heterologously expressed by the recombinant virus upon introduction in a mammalian of a bacterial artificial chromosome according to the present invention that contains a viral expression cassette comprising such chimeric viral cDNA.

In case the bacterial artificial chromosome according to the present invention comprises a viral expression cassette comprising a cDNA of a virus using an ambisence RNA strategy for replication the construct has to be modified in a way that all viral RNA genome segments needed for the rescue of viral RNA replication as described (Lowen et al. (2004) Virology 330, 493-500), are expressed from RNA polymerase I or II promoters. Preferably, said viral cDNA of a virus using an ambisence RNA strategy for replication contained in said viral expression cassette is derived from a virus belonging to either one of the following viral families the Bunyaviridae, including Rift Valley fever virus, Hantaan virus and Schmallenberg virus, and the Arenavirdae, including the Lassa virus. Said viral cDNA contained in the viral expression cassette can either correspond to that of a wild-type RNA virus genome or be a chimeric viral cDNA construct wherein heterologous DNA sequences have been inserted and/or native viral sequences have been deleted, truncated, or mutated. Preferably, said heterologous DNA sequences encode one or more peptides/proteins, which are heterologously expressed by the recombinant virus upon introduction in a mammalian of a bacterial artificial chromosome according to the present invention that contains viral expression cassettes comprising such chimeric viral cDNA. As described above and illustrated by the examples, the present invention allows to generate high amounts of viral cDNA of a sufficiently high quality to be used in DNA vaccines.

The formulation of DNA into a vaccine preparation is known in the art and is described in detail in for example chapter 6 to 10 of "DNA Vaccines" Methods in Molecular Medicine Vol 127, (2006) Springer Saltzman, Shen and Brandsma (Eds.) Humana Press. Totoma, NJ . and in chapter 61 Alternative vaccine delivery methods, Pages 1200-1231, of Vaccines (6^th Edition) (2013) (Plotkin et al. Eds.). Details on acceptable carrier, diluents, excipient and adjuvant suitable in the preparation of DNA vaccines can also be found in WO2005042014, as indicated below.

"Acceptable carrier, diluent or excipient" refers to an additional substance that is acceptable for use in human and/or veterinary medicine, with particular regard to immunotherapy.

By way of example, an acceptable carrier, diluent or excipient may be a solid or liquid filler, diluent or encapsulating substance that may be safely used in systemic or topic administration. Depending upon the particular route of administration, a variety of carriers, well known in the art may be used. These carriers may be selected from a group including sugars, starches, cellulose and its derivatives, malt, gelatine, talc, calcium sulfate, vegetable oils, synthetic oils, polyols, alginic acid, phosphate buffered solutions, emulsifiers, isotonic saline and salts such as mineral acid salts including hydrochlorides, bromides and sulfates, organic acids such as acetates, propionates and malonates and pyrogen-free water.

A useful reference describing pharmaceutically acceptable carriers, diluents and excipients is Remington's Pharmaceutical Sciences (Mack Publishing Co. N . J. USA, 1991) which is incorporated herein by reference.

Any safe route of administration may be employed for providing a patient with the DNA vaccine. For example, oral, rectal, parenteral, sublingual, buccal, intravenous, intra-articular, intra-muscular, intra-dermal, subcutaneous, inhalational, intraocular, intraperitoneal, intracerebroventricular, transdermal and the like may be employed. Intra-muscular and subcutaneous injection may be appropriate, for example, for administration of immunotherapeutic compositions, proteinaceous vaccines and nucleic acid vaccines. It is also contemplated that microparticle bombardment or electroporation may be particularly useful for delivery of nucleic acid vaccines.

Dosage forms include tablets, dispersions, suspensions, injections, solutions, syrups, troches, capsules, suppositories, aerosols, transdermal patches and the like. These dosage forms may also include injecting or implanting controlled releasing devices designed specifically for this purpose or other forms of implants modified to act additionally in this fashion. Controlled release of the therapeutic agent may be effected by coating the same, for example, with hydrophobic polymers including acrylic resins, waxes, higher aliphatic alcohols, polylactic and polyglycolic acids and certain cellulose derivatives such as hydroxy propyl methyl cellulose. In addition, the controlled release may be effected by using other polymer matrices, liposomes and/or microspheres.

DNA vaccines suitable for oral or parenteral administration may be presented as discrete units such as capsules, sachets or tablets each containing a pre- determined amount of plasmid DNA, as a powder or granules or as a solution or a suspension in an aqueous liquid, a non-aqueous liquid, an oil-in-water emulsion or a water-in-oil liquid emulsion. Such compositions may be prepared by any of the methods of pharmacy but all methods include the step of bringing into association one or more agents as described above with the carrier which constitutes one or more necessary ingredients. In general, the compositions are prepared by uniformly and intimately admixing the DNA plasmids with liquid carriers or finely divided solid carriers or both, and then, if necessary, shaping the product into the desired presentation.

The above compositions may be administered in a manner compatible with the dosage formulation, and in such amount as is effective. The dose administered to a patient, should be sufficient to effect a beneficial response in a patient over an appropriate period of time. The quantity of agent (s) to be administered may depend on the subject to be treated inclusive of the age, sex, weight and general health condition thereof, factors that will depend on the judgement of the practitioner.

Typically the DNA vaccines are used for prophylactic or therapeutic immunisation of humans, but can for certain viruses also be applied on vertebrate animals (typically mammals, birds and fish) including domestic animals such as livestock and companion animals. The vaccination is envisaged of animals which are a live reservoir of viruses (zoonosis) such as monkeys, mice, rats, birds and bats. In certain embodiments vaccines may include an adjuvant, i.e. one or more substances that enhances the immunogenicity and/or efficacy of a vaccine composition However, life vaccines may eventually be harmed by adjuvants that may stimulate innate immune response independent of viral replication. Non- limiting examples of suitable adjuvants include squalane and squalene (or other oils of animal origin); block copolymers; detergents such as Tween-80; Quill A, mineral oils such as Drakeol or Marcol, vegetable oils such as peanut oil; Corynebacterium- derived adjuvants such as Corynebacterium parvum; Propionibacterium-der^'wed adjuvants such as Propionibacterium acne; Mycobacterium bovis (Bacille Calmette and Guerin or BCG); interleukins such as interleukin 2 and interleukin 12; monokines such as interleukin 1; tumour necrosis factor; interferons such as gamma interferon; combinations such as saponin-aluminium hydroxide or Quil-A aluminium hydroxide; liposomes; ISCOMt) and ISCOMATRIX (B) adjuvant; mycobacterial cell wall extract; synthetic glycopeptides such as muramyl dipeptides or other derivatives; Avridine; Lipid A derivatives; dextran sulfate; DEAE-Dextran or with aluminium phosphate; carboxypolymethylene such as Carbopol'EMA; acrylic copolymer emulsions such as Neocryl A640; vaccinia or animal poxvirus proteins; sub-viral particle adjuvants such as cholera toxin, or mixtures thereof. The present invention is further illustrated by way of the following examples:

Examples

Example 1: Animals, viruses, cells, bacteria and yeasts used in the experimental work presented in Examples 2 and 3

Animals.

129/Sv mice with knockout of both interferon type I and II receptors (AG129 mice; B&K Universal Ltd/UK) were bred in house.

Viruses and cells.

Vero-B (African green Monkey kidney; American Type Culture Collection (ATCC) CCL-81) and BHK-21 (Baby hamster kidney cells; ATCC CCL-10) cells were obtained from ATCC. All cells were cultured essentially as described (De Burghgraeve et al. (2012) PLoS ONE 7, e37244). Yellow fever virus vaccine strain 17D (Stamaril ®) was purchased from Sanofi Pasteur MSD, Brussels, Belgium. Bacteria and yeast.

Bacterial strains used for routine cloning and propagation of pShuttle-BAC propagation were E. coli Top 10 (Invitrogen) and Epi300-T (Epicenter), respectively. Bacteria transformed with full length flavivirus cDNA plasmids pACNR- FL17DII, pACNR-DENV2, and p4 (see below) were routinely grown at 28 °C and plasmid DNA yields increased by chloramphenicol amplification. Shuttle plasmid containing Epi-300T cells were grown at 37 °C and amplified as described below. Yeast strain Saccharomyces cerevisiae YPH500 (genotype: MATa ura3-52 Iys2- 801_amber ade2-101_ochre trpl -A63 his3-A200 Ieu2-Al ) was grown on selective media from Difco-BD Biosciences and Sigma-Aldrich. Transformation of competent yeast cells was carried out using the lithium acetate method, and yeasts were grown at 28 °C.

Primers which are used in the experimental section are shown below

Table 1: primer list

GCGAGGAGGCTGGGACCATGCCGGCCa

457 YF17D(- GAGGCTGGGACCATGCCGGCCaGTGGTT 28

) 10862_HDrz TTGTG 1 1 1 GTCATCC

458 DV2(-) 10724_HDrz GAGGCTGGGACCATGCCGGCCaGAACCT 29

GTTGATTCAACAGCACC

474 SV40(-)__HDrz/Pme CGAGGAGGCTGGGACCATGCCGGCCaGG 30

TC ACCg ttta aacGGCCgaggcgg cctcg g cc

475 HDrz(+)_Sfi/Pme/Bs ttta tgcagaggccgaggccgcctcGGCCgtttaaa 31

tE cGGTGACCtGGCCGGCATGGTCCC

552 SV40(-)-l Gaggcggcctcggcctctgca 32

553 HDrz( + )5' tGGCCGGCATGGTCCCAGCCT 33

856 SV40/DV4(+) 1 gactaa tttttttta ttta tgcagagg ccg aggccgcct 34

cAGTTGTTAGTCTGTGTGGAC

857 DV4(-) 10649_HDrz GAGGCTGGGACCATGCCGGCCaGAACCT 35

GTTGGATCAACAACACC

946 HA-tag_H l(-) ttaTGCATAGTCAGGCACGTCATATGGATA 36

ggatcc

947 YF17D(+)7637_T7p TCGACTAATACGACTCACTATAG GGggagc 37

gcgaatggaaaaac

948 YF17D(-)8136_Sp6p CGCGCA 1 ALGA 1 1 1 AGG 1 GACAC 1 A 1 AGg 38

ta tea a g a a ctctca egg

208 AGTAAATCCTGTGTGCTAATT 39

94 GGCAATCACGACTCGTTGCG 40

953 AGA I G I A I C I I CA I A I 1 1 AGAG 41

954 ACA 1 1 I GC I 1 I GG I CC I G I C I 42

453 SV40(+)-76 ctccgcccagttccgccca ttctccg ccccat 43

ggctgactaa tttttttta ttta tgcag

988 SV40/hRV14(+) l gactaa tttttttta ttta tgcagaggccgaggccgcct 44

cTTAAAACAGCGGATGGGT

989 hRV14pA(-) GAGGCTGGGACCATGCCGGCCtttttttttttt 45

ttttttttttttttttttATAAACTCC

7214_30xA_HDrz

991 SV40/EV71(+) 1 gactaa tttttttta ttta tgcagaggccgaggccgcct 46

cTTAAAACAGCCTGTGGGT

992 EV71pA(-) GAGGCTGGGACCATGCCGGCCtttttttttttt 47

ttttttttttttttttttGCTATTCTG

7408_30xA_HDrz

990 HDrz(-)5'#2 CCCTCGGAATGTTGCCCAGCCGGCGCCA 48

GCGAGGAGGCTGGGACCATGCCGGCC

Example 2: Production of bacterial artificial chromosomes according to the present invention containing viral cDNA of YFV-17D, Dengue fever type 2 (DENV2) and Dengue fever type 4 (Denv4), respectively Bacterial artificial chromosomes containing viral cDNA of YFV-17D, Dengue fever type 2 (DENV2) and Dengue fever type 4 (Denv4), respectively were prepared as described below.

Material and methods

Plasmid constructs (bacterial artificial chromosomes).

All plasmid constructs were generated by standard techniques and confirmed by Sanger sequencing. The inducible shuttle vector pShuttleBAC/Pme was generated in several steps as follows (FIG 1). First, the lacZ gene present in pBAC/LacZ (Addgene plasmid # 13422), a derivative of the arabinose-inducible pBeloBAC/oriV (Wild et a/. (2002) Genome Res. 12, 1434-1444), was replaced by a synthetic DNA cassette containing (i) the Simian virus 40 (SV40) promoter/origin (SEQ ID 1) driving the hph gene conferring resistance to hygromycin B, (ii) the synthetic cDNA of the genomic ribozyme of hepatitis delta virus (HDrz) (Chadalavada et al. (2007) RNA 13, 2189-2201) (SEQ ID NO 2), and (iii) the Saccharomyces cerevisiae episomal 2μ plasmid origin and (iv) TRP1 gene confering prototrophic growth for tryptophan. Building block (i) was PCR amplified from pBABE-hygro (Morgenstern et al. ( 1990) Nucleic Acids Res. 18, 3587-3996; Addgene plasmid # 1765) using primers #334 and #425. Building block (ii-iv) was PCR amplified from pJet(- )/Trpl_2micron-YF3'_HDrz_BstE using primers #426 and #231. Plasmid pJet(- )/Trpl_2micron-YF3'_HDrz_BstE is a derivative of pJetl.2/blunt (CloneJET PCR cloning kit, Fermentas) that contains a fusion of the 3'-terminus of the YFV-17D cDNA (comprising viral nt 9466 through 10862) to (ii) the HDrz (assembled from DNA nucleotides # 109, 110 and 111), and the (iii+iv) 2p-TRPl sequences that were originally derived from pRE637 (Esteban & Fujimura, (2003) Proc. Natl. Acad. Sci. USA 100, 2568-2573) using PCR primers # 194 and # 195. Building block (i) was fused to (ii-iv) by overlap extension PCR prior to cloning into the Sail sites of pBAC/LacZ to give rise to the pShuttleBAC/SV40_Hygro_HDrz intermediate construct. Subsequently, the hph gene stuffer element was replaced from pShuttleBAC/SV40_Hygro_HDrz for a multiple cloning site (Sfil-Pmel-BstEll) in the final pShuttleBAC/Pme shuttle vector (Figure 1A) by a inverted PCR spanning the full plasmid using primers #474 and #475 and recirularization by T4 DNA ligase prior to transformation and cloning in E.coli.

The virus expression constructs pShuttle/YF17D, pShuttle/DV2 and pShuttle/DV4 were generated by pasting the cDNAs of YFV-17D (SEQ ID NO 3), DENV2 strain New Guinea-C (NGC) and DENV4 strain Dominica, respectively, into pShuttleBAC/Pme by homologous recombination in S. cerevisiae (Figure IB). To that end, the viral cDNAs were amplified by three rounds of PCR introducing terminal extensions containing the -76 bp of the SV40 promoter/origin (Ghosh et al. (1981) Proc. Natl. Acad. Sci. USA 78, 100- 104) at their 5' and the 86 nt HDrz sequence (Chadalavada et al., (2007) RNA 13, 2189-2201) at their 3' ends. The first PCR (10 cycles) used virus specific primer combinations #454 plus #457, #455 plus #458 and #856 plus #857, respectively, followed by 10 cycles each using the SV40 and HDrz specific #453 plus #456, and finally #453 plus # 111 primers. The respective viral cDNA templates were pACNR-FLYFlDII (Bredenbeek et al. , (2003) cited above), pACNR-DENV2 and p4 (Durbin et al. (2001) Am J Trop Med Hyg. 65, 405-413). Plasmid pACNR-DENV2 is a derivative of pACNR-FLYF17D in which the YFV-17D sequence was replaced for the DENV2 NGC cDNA derived pDVWS601 (Gualano et al. (1998) Gen. Virol. 79, 437-446), yet containing additional, translationally silent Agel and SsfEII sites at nt positions 7537 and 10232 of the viral genome, respectively. The linearized vector part needed for recombination was made by an inverted PCR on pShuttleBAC/Pme that was prelinearized with Pmel using primers #552 plus #553. Vector amplicons were treated with Dpnl prior to gel purification and transformation into yeast YPH500 to reduce background form carry-over of possibly uncut plasmid template. Yeast clones were grown in the absence of tryptophan to select for recombinant shuttle plasmids. Plasmid DNAs recovered from yeast minipreps were transferred into E. coli Epi300-T cells (Epicenter) and amplified as described (Wild et al. (2000) cited above) by addition of 0.1% (w/v) of L-arabinose to overnight cultures diluted 6-fold into fresh LB medium (supplemented with 20 mM magnesium chloride) and growth for 6 hrs at 37 °C with vigorous shaking.

A YFV-17D va riant containing a non-converting lethal mutation in its NS5 ORF (RdRp AGDD) was generated by homologous recombination of a 3,6 kb long Bglll- Pstl restriction fragment derived from the yeast episomal plasmid (YEp) p404Gal l/HA-NS5AGDD_ura3 comprising a appropriately mutated YFV-17D cDNA downstream of nt 9294 into pShuttle/YF17D linearized by Clal (downstream of YFV- 17D nt 9656) and Kasl (upstream of the HDrz nt position +27) to yield pShuttle/YF17DAGDD.

Results

A series of synthetic DNA constructs (pShuttleBAC series) has been assembled from several DNA building blocks to serve as RNA virus expression plasmids (Figure 1). The co mMon vector construct pShuttleBAC/Pme is a bacterial artificial chromosome that contains a second origin (oriV) for conditional amplification in E. coli, and a yeast 2 μ origin and TRP1 auxotropic marker for episomal replication in Saccharomyces cerevisiae (Figure 1A). The cDNA of the YFV-17D vaccine has been inserted to yield pShuttle/YF17D by homologous between the SV40 promoter and HDV ribozyme present in pShuttleBAC/Pme (Figure IB). The map of pShuttle/YF17D is shown in Figure 8 (SEQ ID NO 4). The cDNAs of other flaviviruses have been inserted as well. In contrast to prior art flaviviral cDNA clones, such as pACNR-FLYF17DII, pShuttle/YF17D shows an superior genetic stability in E. coli (Figure 2) yet can be induced to produce high plasmid DNA yields.

Example 3: In vitro and in vivo characterization of the bacterial artificial chromosome according to the present invention comprising the cDNA of the YFV-17D vaccine

It was found that the characteristics of YFV-17D expressed from a bacterial artificial chromosome according to the present invention are identical to that of the original vaccine virus (such as efficiency of replication, virus yield and plaque phenotype). Moreover, when this naked YFV-71D plasmid DNA was injected i.p. in AG129 mice, it resulted in the same pathology, morbidity and mortality as the parent virus. This convenient, robust and reproducible system provides a DNA vaccine for YFV at low costs without the need for eukaryotic cell cultures or embryonated chicken eggs. It will no longer require a cold-chain and can be needle free administered.

Material and methods

In vitro transcription, in vitro capping and electroporation.

Plasmid pACNR-FLYF17DII (Bredenbeek et a/. (2003) J. Gen. Virol. 84, 1261-1268) containing the full-length YFV-17D cDNA was linearized with Aflll and purified by proteinase K digestion, phenol-chloroform extraction, and ethanol precipitation. Alternatively, full-length cDNA templates for in vitro transcription (IVT) were made by PGR of pACNR-FLYF17DII using primers # 173 and #55 and KAPA High Fidelity DNA polymerase to overcome limited plasmid yields. Run-off RNA transcripts were produced in vitro by using Sp6 RNA polymerase (Ribomax Large Scale RNA production kit, Promega). Transcripts were capped using purified vaccinia virus 7- methyl guanosin transferase (Scriptcap 7mG capping system, Epicenter) and used for electroporation of BHK-21 cells using an excess of total RNA extracted from BHK-21 cells as carrier RNA. Cell culture medium was harvested at the time the transfected cells displayed nearly complete cytopathogenicity. Medium was cleared from cell debris by centrifugation and subsequently used to prepare virus stocks on BHK-21 cells.

Plasmid transfection

Vero-B cells were seeded in medium containing 10% foetal calf serum into 6-well plates to 70% confluency and transfected the day after with 2.5 pg of plasmid DNA using Transit-LTl reagent (Mirus) in a DNA-to-vehicle ratio of 1 : 3. Plasmid pmRFPl was co-transfected in a ration of 1 : 10 to serve as a visual control to assure equal transfection efficacies. For long-term maintenance and production of virus stocks medium was changed after incubation overnight to contain only 2% serum.

Mapping of viral RNA ends.

Proper processing of from the pShuttleBAC vector derived viral RNA was analysed by rapid amplification of cDNA ends (RACE). 5' RACE following a novel reverse ligation/ amplification protocol has been published in great detail (Dallmeier & Neyts (2013) Anal. Biochem. 434, 1-3). 3' RACE of the non-polyadenylated YFV- 17D genomic RNA was performed essentially as described before. In brief, 5μΙ_ of DNase I treated total RNA of pShuttle/YF17D transfected Vero cells (approximately 1 μg of RNA) was ligated to the 5'-adenylated and 3'-dideoxycytosine (ddC) modified linker #393 (miRNA Cloning Linker 1, IDT DNA Technologies) by the activity of the K227Q mutant of T4 RNA ligase 2 (New England Biolabs) in the presence of 15% polyethylene glycol (PEG)-8000 in a total reaction volume of 10 μΙ_ ove might at 16 °C. Ligation products were amplified by One-Step RT-PCR (Qiagen) using the YFV-17D and linker specific primers #391 and #394, respectively. Amplicons of 265bp were gel purified and cloned into pJetl.2/blunt (CloneJet PCR cloning kit, Fermentas) after polishing the 3' adenine overhangs generated by the Taq DNA polymerase and analysed by Sanger sequencing.

Detection of intracellular viral replicative RNA forms.

Northern blotting and detection of viral replicative intermediates after denaturing agarose gel electrophoresis was performed essentially as described (Dallmeier et a/. (2008) PLoS Pathog. 4, el000230) with slight modifications regarding the gel system and probe design employed. Briefly, 3 of total RNA were heat denatured and separated through a 1% agarose gel in 20 mM 3-(N-morpholino) propane sulfonic acid (MOPS), pH 7.0, 5 mM sodium acetate and 2 mM ethylenediaminetetraacetic acid (EDTA) containing 1% formamide and 0.01 μς ethidium bromide mL^{" 1} followed by capillary transfer on positively charged nylon membranes (Roche Diagnostics) in 20x SSC (3M sodium chloride, 300 mM sodium citrate, pH 7.0). Strand-specific DIG labelled single-stranded DNA probes complementary to the 5' end of the NS5 region of YFV-17D (nt 7637-8136) were generated according to Knuchel et al. (2000) J. Histochem. Cytochem. 48, 285- 294, using primers #947 and #948. Hybridizations and immunodetection was according to the DIG application manual for filter hybridization (Roche Diagnostics). Virus quantification by plaque assay and RT-qPCR.

Infectious virus released from transfected cells was quantified by virus plaque assay 7 days p.i. of confluent monolayers of BHK-21 cells using a 1% microcristalline cellulose (Avicell) overlay in 0.5x maintenance medium as described before (Kaptein et al. (2010) Antimicrob Agents Chemother. 54, 5269-8520). For quantification of viral RNA loads in infected mouse tissues, snap frozen necropsies where disrupted in a Precellys bead mill in RLT buffer (RNeasy, Qiagen), and subsequently total RNA was extracted according to the manufatcurer's instruction. Quantitative reverse transcriptase PGR (RT-qPCR) for the YFV-17D RNA was performed exactly as described (Kaptein et al. (2010) cited above) using primers and probes targeting an about 150 nt stretch of the NS3 gene and serial dilutions of same cloned YFV-17D cDNA fragment as standards.

Immunofluorescence assay.

Cleared supernatants of pShuttle/DV2 transfected BHK-21 cells 7d p.t. were used to inoculate subconfluent Vero-B cultures that were fixed after 5 days in 4% paraformaldehyde and immunostained essentially as described previously (De Burghgraeve et al. (2012) PLoS ONE 7, e37244). Intracellular E protein expression was detected either by the DENV2 serotype specific monoclonal-antibody (mAb) 3H5.1 (Millipore), and a secondary Alexa Fluor-488 labelled Ab (Millipore). Following DAPI staining, cells were visualized using a FLoid Cell Imaging station (Life Technologies).

In vivo transfection of mice.

10 to 20 pg plasmid DNA was mixed with 20 pg calcium carbonate microflowers as carrier (Fumoto et al. (2012) Mol. Pharm. 9, 1962-1970) in 33% propylene glycol and injected intra peritoneally into adult (about 20 g) AG129 mice. Alternatively, half a dose of life-attenuated YFV-17D vaccine (Stamaril®, Sanofi Pasteur MSD, Brussels) was injected intraperitoneal^. Weight and behaviour was monitored on a daily basis.

Results

If transfected into mammalian cells, the transcription of properly processed YFV- 17D RNA is launched from pShuttle/YF17D (Figure 3B) that initiates intracellular self-sustained virus replication (Figure 3A). Cells transfected with pShuttle/YF17D finally secrete infectious virions that phenotypically cannot be distinguished from the parental YFV-17D virus regarding their ability to induce a cytopathic effect in tissue culture (Figure 4A-C), the virus yield and the plaque phenotype (Figure 4D+E). The recombinant viruses thus generated can hence be considered to be biologically identical (quantitatively and qualitatively). Likewise, cells transfected with pShutte/DV2 produce recombinant infectious DENV2 New Guinea strain C (Figure 5).

Intraperitoneal transfection of pShuttle/YF17D in AG129 mice, an established lethal in vivo mouse model of YFV-17D infection (Meier et al. (2009) PLoS Pathog. 5, el000614; Thibodeaux et al. (2012) Vaccine 30, 3180-3187), causes similar virus induced mortality (Figure 6) and morbidity (Figure 7) as the genuine YFV vaccine Stamaril®. In conclusion, his convenient, robust and reproducible system may allow developing a DNA vaccine for YFV at low costs without the need for eukaryotic cell cultures or embryonated chicken eggs. It will no longer require a cold-chain and might be needle free administered.

Example 4: Morbidity and mortality induced by pShuttle/YF17D (DNA- YFVax) in AG129 mice infected by the subcutaneous route, and by a needle-free jet injection of naked plasmid DNA.

To assess the feasibility of other routes for the application of pShuttle/YF17D (DNA- YFVax) than the intraperitoneal route, groups (n = 3) of 9 weeks old male AG 129 mice (male, weight 22 to 25 g) were injected with 25 pg of DNA-YFVax in 100 μΙ_ phosphate buffered saline (PBS) either (i) subcutaneously (s.c.) using a syringe and a G27 needle, or (ii) transdermally (t.d.) by a needle-free jet injector (Injex-30, Injex Pharma GmbH, Berlin Germany) approved for human clinical use for t.d. application of, for instance, insulin or anaesthetics. AG129 injected i.p. with 25 pg DNA-YFVax formulated with calcium carbonate microcristals in 200 μΙ_ of 33% propylene glycol as before served as control group. Morbidity and mortality was scored as before, the experiment was terminated after 30 days (see table 2).

Table 2: Mortality in male AG129 mice injected with DNA-YFVax via different routes.

MDD - mean day to death; n.a. - not applicable

At least some of the AG 129 mice injected with DNA-YFVax by the s.c. and t.d. route developed signs of YFV-17D induced disease (weight loss, ruffling of the fur, hunched back, hind limb paralysis) and had to be euthanized. Most importantly, all mice injected by needle-free jet injection died consistently from YFV-17D induced encephalitis within 17 ± 2 days while all i.p. injected control mice survived the time course of the experiment (30 days). The lack of mortality in the control group during course of inspection (compared a MDD of 13 ± 2 presented in example 3) can readily be explained by the higher weight and the male sex of the animals used.

Of note, using calcium carbonate as carrier for DNA-YFVax is not necessa rily optimal for vaccine delivery; namely there was occasionally even some inhibitory effect observed in hamsters (see example 5) depending on both, the route of injection and the variability between different batches of calcium carbonate microflowers. In conclusion, DNA-YFVax can be delivered successfully in different formulations and by different routes of injection, including by needle-free jet injection.

Example 5: Seroconversion of Syrian golden hamsters following immunization with pShuttle/YF17D (DNA-YFVax)

To assess the induction of protective immunity to YFV by the DNA-YFVax, the preclinical Syrian golden hamsters (Mesocricetus auratus) model was used (Tesh et al. (2001) J Infect Dis. 183, 1431-1436). To that end groups of female hamsters (8 to 10 weeks old, 90 - 100 g) were immunized by intraperitoneal (i.p.) injection of either 1/5 dose of Stamaril® ( 100 μΙ_), or 20 pg pShuttle/YF17D (DNA-YFVax) formulated with calcium carbonate microcristals in 200 μΙ_ of 33% propylene glycol as before. In a repeat 10 pg DNA-YFVax was applied instead. Blood was drawn weekly by cardiac puncture under full surgical anaesthesia, sera were harvested by centrifugation and stored frozen at -80 °C. Two untreated hamsters served as donors for normal sera. To score for relevant immune correlates of protection, sera were analysed (i) by indirect immunofluorescence assay (UFA), and (ii) by plaque- reduction neutralization test (PRNT).

Indirect immunofluorescence assay (UFA). YFV-17D (Stamaril® and DNA- YFVax) specific IgG antibodies in immunized hamster serum were determined using a commercial YFV UFA kit (EUROIMMUN Medizinische Labordiagnostika AG, L ibeck, Germany, catalogue no. FI-2665-1005G and FI-2665-1010G) validated for human clinical use (Niedrig et al. (2008) Clin Vaccine Immunol. 15, 177-81) according to the manufacturer's instructions with some modifications. Hamster serum was diluted 20-, 66-, 200-, 660- and 2000-folds in sample buffer and 30 μΙ_ of serum- dilution was applied on the YFV-IIFA slides. Slides were incubated for 30 min at room temperature and then washed in PBS containing 0.2% Tween-20 for 5 min. For detection of antibodies induced in Mesocricetus, FITC-labeled anti-hamster IgG secondary antibody (Jackson Immuno Research Laboratories Inc., catalogue number 307-095-003) was diluted 1 : 50 in PBS containing 2% BSA and used instead of the anti-human secondary antibody provided in the kit. Slides were counterstained with DAPI, and end point titres determined by fluorescence microscopy.

Plaque reduction neutralization test (PRNT). Neutralizing antibody-titres in yellow fever vaccinated hamster sera were determined using PRNT. In brief, 0.5 x 10^s BHK cells/well were plated in 12 well plates overnight in growth medium (MEM medium supplemented with 10% FCS, 1% sodium bicarbonate and 1% glutamine). All sera were assayed in triplet in serial dilutions 1 : 20, 1 : 66, 1 : 200, 1 : 660, 1 : 2000 and 1 : 6600. 30 μΙ_ serum dilution was mixed with in 30 μΙ_ assay medium (identical to growth medium but containing only 2% FCS) containing 40 plaques forming of YFV-17D virus (Stamaril®, lot G5400P1, passaged once on Vero-B cells). After this pre-adsorption for 1 h at 37 °C, 440 μΙ_ assay medium was added, and 500 μΙ_ of each mixture added to BHK cells. After 1 h incubation at room temperature, cells were washed and overlayed with assay medium supplemented with LMP agarose (Invitrogen) at a final concentration of 0.5%. Subsequently, cells were cultured for 5 days at 37 °C, fixed with 8% formaldehyde for 2 hr and stained with Giemsa stain. Plaques were counted and the 50% neutralization titres were calculated according to Reed and Munch (Reed & Muench ( 1938) Am. J. Hyg. 27, 493-497).

Overall, detection of cross-reacting antibodies by UFA (table 3), and of neutralizing antibodies by PRNT was consistent (table 4). With regards to vaccine efficacy, DNA- YFVax showed no inferiority to Stamaril®; in both trial groups 2 out of 3 individuals ( 1/5 Stamaril® vs. 20 μg DNA-YFVax), and 4 out of 5 versus 2 out of 4 individuals ( 1/5 Stamaril® vs. 10μg DNA-YFVax) seroconverted to high titers of YFV cross- reactive and neutralizing antibodies (see table 3 and 4). These values can be considered representing full protective immunity (immune correlates of protection), with PRNT titres of >40 are protective in a lethal YFV challenge hamster model (Julander et al. (2011) Vaccine 29, 6008-6016). Most importantly, the WHO states a log neutralization index (LNI) of already >0.7 correlates with immunological protection following vaccination in primates, and this applies for humans (WHO position paper (2013) Wkly. Epidemiol. Rec. 88, 269-283.). This benchmark of PRNT Log 10 titers > 0.7 is exceeded by DNA-YFVax in hamsters by several orders of magnitude, by more than 150-fold (see Table 4). Moreover, immune response was more homogenous in DNA-YFVax vaccinated individuals if compared to Stamaril®, with seroconversion to high PRNT titers detected consistently within 3 weeks, rather than only after 4 weeks, i.e. 3 weeks later than the other seroconverter from the Stamaril® group.

Table 3: YFV cross-reacting antibody responses in Stamaril® and DNA- YFVax immunized Syrian golden hamsters

ND - no detection; * (x/x) = no. individuals seroconverted of no. of individuals tested

Table 4. Neutralizing antibody responses in Stamaril® and DNA-YFVax immunized Syrian golden hamsters

ND - no detection

Example 6: Assessing genetic instability of cloned YFV-17D cDNAs. (a) Starting material: Large scale plasmid preparations of pACNR-FLYF17DII (Bredenbeek et al. (2003) above and pShuttle/YFV-17D were made using standard techniques. To that end, pACNR-FLYF17DII was transformed in a standard E. coli K12 derivative strain, plated on LB-agar containing 100 μg/mL ampicillin and grown overnight at 28 °C (instead of 37 °C) to favour plasmid stability. A small colony was scaled up and grown in LB containing 100 μg/mL at 28°C under vigorous shaking in two consecutive overnight cultures, to finally reach a 1 L batch culture. This batch was grown overnight at 28 °C, and finally amplified by addition of chloramphenicol to a final concentration of 20 pg/mL for another 8 h at 28° C. Similarly, pShuttle/YFV-17D was transformed in E. coli strain EPI300-T cells (Epicentre), plated on LB-agar containing 20 pg/mL chloramphenicol, yet grown overnight at 37 °C. Latter plasmid was scaled up accordingly, yet all growth was in presence of 20 μg/mL chloramphenicol and at 37 °C. The final overnight batch culture was diluted one in six into fresh LB medium containing 20 pg/mL chloramphenicol and 0.01% L-arabinose, and grown for not more than 6 h. Plasmids were purified using standard column affinity purification (Qiagen), dissolved in TE ( 10 mM Tris-HCI, 1 mM EDTA) to a final concentration of 1 pg/mL, and stored frozen at -20 °C.

(b) Colony growth and size. Both plasmids were transformed into E. coli EPI300- T and streaked on MacConkey agar (2% peptone, 0.5% NaCI, 1% lactose, 0.15% bile salts, 0.003% neutral red, 0.0001% crista I violet, 1.35% agar) containing appropriate antibiotic as a selective medium. Sterile zirkonia beads (diameter 2.5 mm) were embedded into the agar to serve as calibrators for absolute size measurements. For one aliquot of bacteria transformed with pShuttle/YFV-17D, the agar contained additional 0.01% L-arabinose. After incubation for 16 h at 37°C, pictures were taken using a regular digital camera (Canon Powershot SX10IS) and stored as JPEG files (see Figure 9). Images were submitted to OpenCFU version 3.8.11 for image analysis regarding colony count and size Geissman (2013) PLoS One. 8, e54072..

E. coli clones harbouring pShuttle/YFV-17D grew to much larger sizes and to much more homogenous populations (Figure 9 B) than pACNR-FLYF17DII containing clones (Figure 9 A). Unexpectedly this seemingly lower toxicity of pShuttle/YFV-17D remains even in the arabinose-induced state (Figure 9 C). Larger colonies present in the pACNR-FLYF17DII transformant population (Figure 9 A) most likely contain plasmids with mutations ablating cryptic expression of toxic viral proteins (see Example 6). Image analysis revealed a significantly higher homogeneity in pShuttle/YFV- 17D versus pACNR-FLYF17DII containing clones (Ta ble 5) . In fact, the pACNR-FLYF17D transformants can obviously be divided into at least two subpopulations of different size means, resulting in (i) a large standard deviation from the mean (Table 5), a non-Gaussian size distribution (Figure 10 A), and (iii) a large difference, for instance, between calculated arithmetic means and median colony sizes (Table 5) . By contrast, transformants harbouring pShuttle/YFV- 17D show a more homogenous colony size (Table 5) and bell-shaped Gaussian size distribution (Figure 10 B) . Unexpectedly, the latter fully applies to the arabinose-induced state of pShuttle/YFV- 17D as well (Table 5 Figure 10 C) .

Table 5. Descriptive statistics scoring transformant colony sizes (in mm)

Example 7 Mutational pattern and frequency during propagation of cloned YFV-17D cDNAs in E. coli.

In order to add ress the clona l genetic stability of the YFV- 17D cDNA containing plasmids, both plasmids as described in Example 6 were transformed into E. coli EPI300-T and streaked on MacConkey agar containing appropriate a ntibiotic as a selective medium as before (see Example 6b) . The pACNR-FLYF17DII clones were incubated at 28 °C for 24 h while the pShuttle/YF17D clones were incubated at 37 °C for 16 h . From each plasmid two series of each 24 to 48 colonies were picked for plasmid growth into 200 μΙ_ liquid medium (LB containing appropriate antibiotic supplemented with 20 mM MgCI2). One pACNR-FLYF17DII series was chosen to start from small colonies (pAS series), and one from large colonies (pAL series), respectively. For pShuttle/Y17D where no major size differences could be observed (see Example 6b) colonies with reasonable size differences were chosen as two series of cultures starting from smaller (pSS series) and larger colonies (pSL series), respectively.

Bacteria containing the pACNR plasmid were incubated for 24 h at 28 °C while the pShuttle colonies were incubated overnight at 37 °C and subsequently for 6 h in 600 μΙ_ LB containing chloramphenicol and 0.01% arabinose. Part of these cultures [considered as plasmids of passage 0 (P0)] where subjected directly to PGR for amplification (GoTaq Green Mastermix, Promega) using primers #208 and #94 (corresponding YFV-17D nt 1 - 940, and #953 and #954 (corresponding YFV-17D nt 2500 - 3600, respectively.

Amplicons were affinity purified (Qiagen) and sequenced directly (Bigdye, Applied Biosystems) using primers #208 and #953, respectively. The cDNA regions analysed were expected to contain cDNA with previously known determinants of toxicity, namely cryptic promoters for illegitimate transcription and translation in E. coli in the viral 5' untranslated region (Li et a/. (2011) cited above; Pu et a/. (2011) cited above) and an especially hydrophobic protein stretch within the viral E-NS1 regions (Yamshchikov et a/. (2001) Virology 281, 272-280), respectively.

Another part of each cultured clone was diluted 1/100 in fresh medium and grown as before to give rise to a next passage (PI). The latter was repeated up to 10 passages (P10). Plasmids from PI, P3 and P3 where analysed by PGR and sequencing as before. For P10, plasmid was grown in a larger volume of 5 mL of medium and plasmids isolated by a standard alkaline plasmid miniprep procedure. These plasmid minipreps were subjected to (i) PGR analysis (targeting both nt 1 - 940 and 2500 - 3600 regions) followed by agarose gel electrophoretic inspection, (ii) direct sequencing (if PCR amplicons could be detected), and (iii) by restriction analysis using Pstl. The sequencing result of P0, PI, P3 and P10 are summarized in Table 6 and 7. The results of the PCR and restriction analyses of P10 are summarized in Table 8. Mutations found at early passages.

Direct sequencing of plasmids from ea rly passages (low passage numbers P0 to P3) of the pAS and pAL series (Table 6) revealed a rather high mutation frequency of up to 13% in an originally clonal plasmid preparation (see Example 6a). Almost all mutations found were nonsense or frameshift mutations (FS) due to introduction of premature stop codons (PMSt) and single nucleotide deletions/insertions, respectively. These mutations obviously completely ablate expression of the full- length YFV-17D open reading frame (ORF). In the pSL series similar mutations were found in PI, though less frequently. In the pSS series at P0, missense mutations were found that will not abolish expression of the viral ORF.

In conclusion, large scale preparations of originally clonal plasmids (see Example 6a) carrying the cDNA of YFV-17D contain readily detectable amounts of mutant plasmid variants. In the case of pACNR-FLYF17DII, the majority of the mutations ablate expression of the full-lenghth viral polyprotein obviously rendering the viral RNA generated from the respective mutant cDNAs replication incompetent. This is the case for more than 10% of all plasmid clones. In the case of pShuttle/YFV-17D, the mutation frequency is lower (less than 10%), and most importantly, a smaller fraction of mutants will hence constitute a priori replication incompetent viruses.

Mutations found at passage plO.

When plasmids from pAL and pAS series were analysed at passage P10, the majority of plasmids contained large structural rearrangements that led in 10 out of 48 (21%) and 44 out of 48 (92%) plasmid clones, respectively, to complete failure to amplify the nt 2500-3600 region (Table 8). This was accompanied by an aberrant restriction pattern of the latter mutant plasmids with up to several kilobases of DNA missing from the plasmids. Of note, all mutant clones tested still contained the nt 1-940 region (Table 6) and where thus most likely offspring of the original pACNR-FLYF17DII (Table 8) rather than irrelevant contaminants. Deletion of such toxic cDNA fragments is expected and reported for prior art (Yamshchikov et al. (2001) cited above).

By contrast, similar rearrangements and deletions where never found in the pShuttle-YFV17D series. Here only 2 out of 48 (4%) showed missense mutation that obviously change a possible in frame ATG initiation codon (nt 2957-2959) in the E-NS1 coding region. This will not abolish expression of the viral ORF.

In conclusion, repeated passaging of originally clonal pACNR-FLYF17DII (see example 6a) leads large deletions in the viral cDNA and hence loss of functional cDNA in up to 90% and more of all plasmid clones most obviously rendering the viral RNA generated from the respective mutant cDNAs fully unfunctional. In the case of pShuttle/YFV-17D, the mutation frequency is much lower (less than 5%), and most importantly, no mutants can be observed that constitute a priori replication incompetent viruses that would unable their use as, for instance, life- attenuated DNA vaccine.

Table 6: Mutations occurring in cloned YFV-17D cDNA during passag

E. coli (early passages)

n.a. - not applicable; PMSt - premature STOP codon generated (nonsense mutation); FS - frameshift due to single nucleotide insertion ore deletion; MS - missense mutation changing codon; S - silent synonymous codon exchange

* one FS observed in non-coding region immediately upstream of start codon

** mixed population of all three alternate codons, but not the synonymous wildtype codon

Table 7: Mutations occurring in cloned YFV-17D cDNA during passag

E. coli (late passage PIO) clone series passage region mutant type of

frequency mutation mutant clones introduced out of all

clones

analysed (%)

pAL P10 1-940 0/48 (0) n.a.

P10 2500-3600 10/48 (21) DEL

pAS P10 1-940 0/47 (0) n.a.

P10 2500-3600 44/48 (92) DEL

pSL* P10 2500-3600 2/48 (4) 2x MSi n .a . - not applicable; DEL - large (kilobase range) deletions, for more details see Table 8; MSi - missense mutation changing possible in frame ATG initiation codon * When overnight cultures derived from passage P0 were plated, pSS a nd pSL clones grew to the same size of colonies, and were therefore not considered sepa rately anymore at P10.

Table 8: Large structural changes in plasmids carrying cloned YFV-17D cDNA during passaging in E. coli (passage P10)

n.d. - not determined

* When overnight cultures derived from passage P0 were plated, pSS and pSL clones grew to the same size of colonies, and were therefore not considered separately anymore at P10. Example 8: Construction of pShuttle/YFV-JE, pShuttle/YFV-WN, and pShuttle/YFV-USU as expression vectors for chimeric flavivirus vaccines.

Recombinant chimeric derivatives of YFV- 17D are developed and used as vaccines in which the YFV- 17D serves as a vector for heterologous antigens (Guy et al. (2010) Vaccine 28, 632-49; US patent application 20100278773), for instance for the surface glycoproteins of other pathogenic flavivirus antigens such as the prM and E proteins of the Japanese encephalitis virus (JEV) and the West Nile virus (WNV), developed as ChimeriVax-JE (Imojev® Sanofi Pasteur-MSD) a nd ChimeriVax-WN20, respectively. The pShuttle/YFV- 17D (DNA-YFVax) according to this invention can be modified as such that is can lauch these foramentioned ChimeriVax vaccine viruses directly from transfected plasmid DNA and can thus fully substitute for said life-attenuated ChimeriVax-JE (Imojev®) and ChimeriVax- WN20 vaccines containing life viruses. The BAC expressing ChimeriVax-JE, pShuttle/ChimeriVax-JE (Figure 11a), is generated by substituting nt 482-2451 of YFV-17D in pShuttle/YFV17D for nt 477- 2477 of neuroattenuated JEV vaccine strain JE SA14-14-2 (Chambers (1999) J. Virol. 73(4), 3095-3101; Arroyo et al. (2001) J. Virol. 75, 934-942.) plus two adaptive mutation in the NS2A and NS4B genes of the YFV-17D backbone (Pugachev et al. (2004) J. Virol. 78, 1032-1038). This is achieved by homologous recombination and joining of three plasmid fragments; two PCR amplicons of pShuttle/YFV17D (nt 7228-481, and nt 3966-7342) and a chimeric YFV-JEV cDNA fragment made by custom DNA synthesis (IDT Integrated DNA Technologies, Haasrode, Belgium). The later comprises nt 359 - 4105 of ChimeriVax-JE (Figure 11a). The final construct has a sequence as specified in SEQ ID NO: 5.

The BAC expressing ChimeriVax-WN02, pShuttle/ChimeriVax-WN02 (Figure l ib), is generated by substituting the prM-E gene region of pShuttle/ChimeriVax-JE for that of region WNV (NY99 strain) that contains three neuroattenuating mutations in the E proteins according to Monath et al. (2006) (Proc Natl Acad Sci USA. 103, 6694- 6699), namely L107F, A316V, and K440R. To that end a chimeric YFV-WNV cDNA fragment is made by custom DNA synthesis (IDT Integrated DNA Technologies, Haasrode, Belgium) and recombined into the Xhol (nt 406) and Kasl (nt 2477) sites of pShuttle/ChimeriVax-JE. The final construct has a sequence as specified in SEQ ID NO: 6.

Example 9: Construction of pShuttle/EV71 as expression vectors for different picornaviruses

Enteroviruses are (+)-RNA viruses that belong to the family of picornaviruses of small non-enveloped viruses with a RNA genome in sense-orientation. Typically the genome of picornaviruses is not capped yet carry a 5' terminal covalently attached VPg protein instead. In lack of a cap structure, an internal ribosomal entry site (IRES) recruits the cellular translation machinery to the viral RNA for viral protein expression. In principal, picornaviral replication and production of infectious virus progeny can be launched intracellular following heterologous transcription of the viral genome. In the prior art, the viral genome is expressed from a cDNA that is under control of a phage promoter and transcribed only if the cognate phage RNA polymerase is co-transfected and expressed in a producer cell (two-plasmid system). Likewise the said phage polymerase can be expressed intracellular^ upon transduction of the respective cDNAs using a helpervirus such as an recombinant baculovirus (Yap ef al. ( 1997) Virology. 231, 192-200). Instead of the more complicated approach of the prior art, the picornaviral cDNA can be expressed intracellularly from a derivative of pShuttle-BAC (one-plasmid system) for direct launching of viral replication, as exemplified in the following for the human enterovirus 71 (EV71). To that end, the EV71 genome is cloned as an expression cassette into pShuttle-BAC with a 5' SV40 promoter and a 3' terminal polyA tail followed by a hepatitis delta virus ribozyme. This is accomplished by amplifying the cDNA of EV71 by PCR using primers #991 and #992, and reamplification with primers #453 and #990 to generate a respective expression cassette. Different nucleic acid sources can be used as template for this PCR to appropriately amplify the about 7.4kb long EV71 cDNA; (i) an already cloned cDNA of EV71 such as that described by Chua et a\. (2008) J. Gen. Virol. 89, 1622-1632) and Zhang et al. (2013) Virus Genes. 47, 235-243), or (ii) the product of reverse transcription of any tissue culture, or human or animal tissue derived full-length genomic RNA of EV71. Alternatively, (iii) the EV71 cDNA can be made by custom gene synthesis. Irrespectively of the source of cDNA, the expression cassette thus generated will be inserted into pShuttle/BAC-Pme that has been linearized by restriction endonuclease digest using Pmel, preferably by recombination in yeast. Such a construct has a sequence as specified in SEQ ID NO: 7 for the EV71 strain BrCr-TR (Arita et a/. (2005) J. Gen. Virol. 86, 1391-401).

A similar strategy can be followed for the cloning of other enteroviruses such as for instance the human rhinovirus 14 (hRV14), changing only the first set of primers for initial amplification of the viral cDNA. Suitable primers for hRV14 are #988 and #989.

Infectious EV71 and hRV14 viruses will be generated by transfection of the pShuttle/EV71 and pShuttle/hRV14 plasmids, respectively, in cultured mammalian cells such as human cervix carcinoma (HeLa) cells or by transfection in vivo. Attenuated variants thereof can be generated in a similar way and used as life- attenuated vaccines.

Claims

ims

Use of a bacterial artificial chromosome (BAC) for the preparation of a vaccine, wherein the BAC comprises:

- an inducible bacterial ori sequence for amplification of said BAC to more than 10 copies per bacterial cell, and

- a viral expression cassette comprising a cDNA of an attenuated RNA virus genome and comprising cis-regulatory elements for transcription of said viral cDNA in mammalian cells and for processing of the transcribed RNA into infectious RNA virus.

The use according to claim 1, wherein said cDNA of an attenuated RNA virus genome is a chimeric viral cDNA construct of an RNA virus genome, wherein a heterologous DNA sequence has been inserted or wherein a native viral sequence has been deleted, truncated, or mutated.

The use according to claim 1, wherein said viral expression cassette comprises

a cDNA of a positive-strand RNA virus genome,

a RNA polymerase driven promoter preceding the 5' end of said cDNA for initiating the transcription of said cDNA, and

an element for RNA self-cleaving following the 3' end of said cDNA for cleaving the RNA transcript of said viral cDNA at a set position.

The use according to claim 3, wherein said positive-strand RNA virus is selected from the group consisting of flaviviruses, hepaciviruses, pestiviruses, togaviruses, picornaviruses, coronaviruses, hepeviruses,and caliciviruses.

The use according to any one of claims 1 to 4, wherein said viral expression cassette comprises a cDNA of a yellow fever virus.

The use according to any one of claims 1 to 4, wherein said viral expression cassette comprises a cDNA of the life-attenuated YFV-17D yellow fever virus vaccine. The use according to claim 1, wherein said viral expression cassette comprises a cDNA of a virus belonging to the group of negative-strand RNA viruses, double-strand RNA viruses or ambisense RNA viruses.

The use according to any one of claims 1 to 7, wherein said bacterial artificial chromosome further comprises a yeast autonomously replicating sequence for shuttling to and maintaining said bacterial artificial chromosome in yeast.

The use according to claim 8, wherein said yeast ori sequence is the 2μ plasmid origin or the ARS1 (autonomously replicating sequence 1) or functionally homologous derivatives thereof.

The use according to claim 3, wherein said RNA polymerase driven promoter is an RNA polymerase II promoter.

The use according to claim 10, wherein said RNA polymerase II promoter is the Cytomegalovirus Immediate Early (CMV-IE) promoter, the Simian virus 40 promoter or functionally homologous derivatives thereof.

The use according to claim 3, wherein said RNA polymerase driven promoter is an RNA polymerase I or III promoter.

The use according to any one of claims 3 to 11, wherein said element for RNA self-cleaving is the cDNA of the genomic ribozyme of hepatitis delta virus or functionally homologous RNA elements.

The use according to claim 6, wherein said viral expression cassette comprises a cDNA of the life-attenuated YFV-17D vaccine, wherein one or more of the cDNA sequences coding for the virion surface proteins are either deleted, truncated, or mutated so that such functional virion surface protein of YFV-17D is not expressed and wherein a cDNA sequences coding for a heterologous protein is inserted in the YFV-17D cDNA.

The use according to claim 14, wherein said heterologous protein is a virion surface protein of a flavivirus.

16. The use according to claims 14 or 15, wherein said viral expression cassette comprises a cDNA of the life-attenuated YFV-17D vaccine, wherein one or more unrelated cDNA sequences are inserted to be expressed as one or more heterologous protein within the viral polyprotein.

The use according to any one of claims 1 to 16, wherein said viral expression cassette comprises a viral cDNA wherein foreign cDNA sequences are inserted to be heterologously expressed by the said recombinant viruses.

A method of preparing a vaccine against RNA viruses comprising the steps of: a) providing a bacterial host transfected with a BAC which comprises:

- an inducible bacterial ori sequence for amplification of said BAC to more than 10 copies per bacterial cell, and

- a viral expression cassette comprising a cDNA of an attenuated RNA virus genome and comprising cis-regulatory elements for transcription of said viral cDNA in mammalian cells and for processing of the transcribed RNA into infectious viral RNA,

b) amplifying the BAC by adding a compound which activates said inducible ori

c) isolating the amplified BAC,

d) formulating the BAC into a vaccine.

A BAC comprising :

- an inducible bacterial ori sequence for amplification of said BAC to more than 10 copies per bacterial cell, and

- a viral expression cassette comprising a cDNA of an attenuated RNA virus genome and comprising cis-regulatory elements for transcription of said viral cDNA in mammalian cells and for processing of the transcribed RNA into infectious viral RNA,

for use as a vaccine. 20. A BAC comprising :

- an inducible bacterial ori sequence for amplification of said BAC to more than 10 copies per bacterial cell, and

- a viral expression cassette comprising a cDNA of an attenuated RNA virus genome, or

- a viral expression cassette comprising a cDNA of an attenuated RNA virus genome and comprising cis-regulatory elements for transcription of said viral cDNA in mammalian cells and for processing of the transcribed RNA into infectious viral RNA,

for use in the prevention of a RNA virus infection.

The use of the bacterial artificial chromosome according to any one of the claims 1 to 18 as a life DNA vaccine.

The use of the bacterial artificial chromosome according to any one of the claims 1 to 18 for the maintenance of cDNA of a native or recombinant RNA virus genome and for the propagation of native or recombinant viruses from said cDNA.

A bacterial artificial chromosome (BAC) for the preparation of a vaccine, wherein the BAC comprises:

- an inducible bacterial ori sequence for amplification of said BAC to more than 10 copies per bacterial cell, and

- a viral expression cassette comprising a cDNA of an attenuated RNA virus genome and comprising cis-regulatory elements for transcription of said viral cDNA in mammalian cells and for processing of the transcribed RNA into infectious viral RNA.