Title of Invention

"DENGUE TETRAVALENT VACCINE"

Abstract The invention relates to a dengue virus tetravalent vaccine containing a common 30 nucleotide deletion (Δ30) in the 3"-untranslated region of the genome of dengue virus serotypes 1, 2, 3, and 4, or antigenic chimeric dengue viruses of serotypes 1, 2, 3, and 4.
Full Text Dengue Tetravalent Vaccine
Field of the Invention
The invention relates to a dengue virus tetravalent vaccine containing a common 30 nucleotide deletion (A30) in the 3'-untranslated region of the genome of dengue virus serotypes 1, 2, 3, and 4, or antigenic chimeric dengue viruses of serotypes 1, 2, 3, and 4.
Background of the Invention
Dengue virus is a positive-sense RNA virus belonging to the Flavivirus genus of
the family Flaviviridae. Dengue virus is widely distributed throughout the tropical and
semitropical regions of the world and is transmitted to humans by mosquito vectors.
Dengue virus is a leading cause of hospitalization and death in children in at least eight
tropical Asian countries (WHO 1997 Dengue Haemorrhagic Fever: Diagnosis,
Treatment, Prevention, and Control 2nd Edition, Geneva). There are four serotypes of
dengue virus (DEN1, DEN2, DEN3, and DEN4) that annually cause an estimated 50-100
million cases of dengue fever and 500,000 cases of the more severe form of dengue virus
infection known as dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS)
(Gubler, D.J. and Meltzer, M. 1999 Adv Virus Res 53:35-70). This latter disease is seen
predominantly in children and adults experiencing a second dengue virus infection with a
serotype different than that of their first dengue virus infection and in primary infection of
infants who still have circulating dengue-specific maternal antibody (Burke, D.S. et al.
1988 Am J Trop Med Hyg 38:172-180; Halstead, S.B. et al. 1969 Am J Trop Med Hyg
18:997-1021; Thein, S. et al. 1997 Am J Trop Med Hyg 56:566-575). A dengue vaccine
is needed to lessen disease burden caused by dengue virus, but none is licensed. Because
of the association of more severe disease with secondary dengue virus infection, a
successful vaccine must simultaneously induce immunity to all four serotypes. Immunity
is primarily mediated by neutralizing antibody directed against the envelope (E)
glycoprotein, a virion structural protein. Infection with one serotype induces long-lived
homotypic immunity and a short-lived heterotypic immunity (Sabin, A. 1955 Am J Trop
Med Hyg 4:198-207). Therefore, the goal of immunization is to induce a long-lived
neutralizing antibody response against DEN1, DEN2, DEN3, and DEN4, which can best
be achieved economically using live attenuated virus vaccines. This is a reasonable goal
since a live attenuated vaccine has already been developed for the related yellow fever
virus, another mosquito-borne flavivirus present in tropical and semitropical regions of
the world (Monath, T.P. and Heinz, F.X. 1996 in: Fields Virology, Fields, D.M et al. eds. Philadelphia: Lippincott-Raven Publishers, pp. 961-1034).
Several live attenuated dengue vaccine candidates have been developed and evaluated in humans and non-human primates. The first live attenuated dengue vaccine candidates were host range mutants developed by serial passage of wild-type dengue viruses in the brains of mice and selection of mutants attenuated for humans (Kimura, R. and Hotta, S. 1944 Jpn J Bacteriol 1:96-99; Sabin, A.B. and Schlesinger, R.W. 1945 Science 101:640; Wisserman, C.L. et al. 1963 Am J Trop Med Hyg 12:620-623). Although these candidate vaccine viruses were immunogenic in humans, their poor growth in cell culture discouraged further development. Additional live attenuated DEN1, DEN2, DEN3, and DEN4 vaccine candidates have been developed by serial passage in non-human tissue culture (Angsubhakorn, S. et al. 1994 Southeast Asian J Trop Med Public Health 25:554-559; Bancroft, W.H. et al. 1981 Infect Immun 31:698-703; Bhamarapravati, N. et al. 1987 Bull World Health Organ 65:189-195; Eckels, K.H. et al. 1984 Am J Trop Med Hyg 33:684-698; Hoke, C.H. Jr. et al. 1990 Am J Trop Med Hyg 43:219-226; Kanesa-Thasan, N. et al. 2001 Vaccine 19:3179-3188) or by chemical mutagenesis (McKee, K.T. et al. 1987 Am J Trop Med Hyg 36:435-442). It has proven very difficult to achieve a satisfactory balance between attenuation and immunogenicity for each of the four serotypes of dengue virus using these approaches and to formulate a tetravalent vaccine that is safe and satisfactorily immunogenic against each of the four dengue viruses (Kanesa-Thasan, N. et al. 2001 Vaccine 19:3179-3188; Bhamarapravati, N. and Sutee, Y. 2000 Vaccine 18:44-47).
Two major advances using recombinant DNA technology have recently made it
possible to develop additional promising live attenuated dengue virus vaccine candidates.
First, methods have been developed to recover infectious dengue virus from cells
transfected with RNA transcripts derived from a full-length cDNA clone of the dengue
virus genome, thus making it possible to derive infectious viruses bearing attenuating
mutations that have been introduced into the cDNA clone by site-directed mutagenesis
(Lai, C.J. et al. 1991 PNAS USA 88:5139-5143). Second, it is possible to produce
antigenic chimeric viruses in which the structural protein coding region of the full-length
cDNA clone of dengue virus is replaced by that of a different dengue virus serotype or
from a more divergent flavivirus (Bray, M. and Lai, C.J. 1991 PNAS USA 88:10342-
10346; Chen, W. et al. 1995 J Virol 69:5186-5190; Huang, C.Y. et al. 2000 J Virol
74:3020-3028; Pletnev, A.G. and Men, R. 1998 PNAS USA 95:1746-1751). These
techniques have been used to construct intertypic chimeric dengue viruses that have been shown to be effective in protecting monkeys against homologous dengue virus challenge (Bray, M. et al. 1996 J Virol 70:4162-4166). A similar strategy is also being used to develop attenuated antigenic chimeric dengue virus vaccines based on the attenuation of the yellow fever vaccine virus or the attenuation of the cell-culture passaged dengue viruses (Monath, T.P. et al. 1999 Vaccine 17:1869-1882; Huang, C.Y. et al. 2000 J. Virol 74:3020-3028).
Another study examined the level of attenuation for humans of a DEN4 mutant bearing a 30-nucleotide deletion (A30) introduced into its 3'-untranslated region by site-directed mutagenesis and that was found previously to be attenuated for rhesus monkeys (Men, R. et al. 1996 J Virol 70:3930-3937). Additional studies were carried out to examine whether this Δ30 mutation present in the DEN4 vaccine candidate was the major determinant of its attenuation for monkeys. It was found that the Δ30 mutation was indeed the major determinant of attenuation for monkeys, and that it specified a satisfactory balance between attenuation and immunogenicity for humans (Durbin, A.P. etal. 2001 Am J Trop Med Hyg 65:405-13).
Statement of Invention A dengue virus tetravalent vaccine containing a common 30 nucleotide deletion in the 3' untranslated region of dengue types 1, 2, 3, and 4 comprising a nucleic acid comprising a first nucleotide sequence encoding at least one structural protein from a first dengue virus and a second nucleotide sequence encoding nonstructural proteins from a second dengue virus, wherein the second dengue virus is attenuated by a deletion of about 30 nucleotides from the 3' untranslated region of the dengue genome corresponding to the TL2 stem-loop structure.
Summary of the Invention The previously identified Δ30 attenuating mutation, created in dengue virus type 4 (DEN4) by the removal of 30 nucleotides from the 3'-UTR, is also capable of attenuating a wild-type strain of dengue virus type 1 (DEN1). Removal of 30 nucleotides from the DEN1 3'-UTR in a highly conserved region homologous to the DEN4 region encompassing the Δ30 mutation yielded a recombinant virus attenuated in rhesus monkeys to a level similar to recombinant virus DEN4Δ30. This establishes the transportability of the Δ30 mutation and its attenuation phenotype to a dengue virus type other than DEN4. The effective transferability of the Δ30 mutation, described by this work, establishes the usefulness of the Δ30 mutation to attenuate and improve the safety of commercializable dengue virus vaccines of any serotype. We envision a tetravalent dengue virus vaccine containing dengue virus types 1, 2, 3, and 4 each attenuated by the Δ30 mutation. We also envision a tetravalent dengue virus vaccine containing recombinant antigenic chimeric viruses in which the structural genes of dengue virus types 1, 2, and 3 replace those of DEN4Δ30; 1, 2, and 4 replace those of DEN3A30; 1,
3, and 4 replace those of DEN2A30; and 2, 3, and 4 replace those of DEN1A30. In some
instances, such chimeric dengue viruses are attenuated not only by the Δ30 mutation, but also by their chimeric nature. The presence of the Δ30 attenuating mutation in each virus component precludes the reversion to a wild-type virus by intertypic recombination. In addition, because of the inherent genetic stability of deletion mutations, the Δ30 mutation represents an excellent alternative for use as a common mutation shared among each component of a tetravalent vaccine.
Brief Description of the Drawings
Figure 1. The live attenuated tetravalent dengue virus vaccine contains dengue viruses representing each of the 4 serotypes, with each serotype containing its full set of unaltered wild-type structural ana non-structural proteins and a shared Δ30 attenuating mutation. The relative location of the Δ30 mutation in the 3' untranslated region (UTR) of each component is indicated by an arrow.
Figure 2. A. The Δ30 mutation removes 30 contiguous nucleotides (shaded) from the 3' UTR of DEN4. Nucleotides are numbered from the 3' terminus. B. Nucleotide sequence alignment of the TL2 region of DEN1, DEN2, DEN3, and DEN4 and their Δ30 derivatives. Also shown is the corresponding region for each of the four DEN serotypes. Upper case letters indicate sequence homology among all 4 serotypes, underlining indicates nucleotide pairing to form the stem structure. C. Predicted secondary structure of the TL2 region of each DEN serotype. Nucleotides that are removed by the Δ30 mutation are boxed (DEN1 - between nts 10562 - 10591, DEN2 Tonga/74 - between nts 10562 - - 10570, DEN3 Sleman/78 - between nts 10535 - 10565, and DEN4 - between nts 10478 - 10507).
Figure 3. Viremia levels in rhesus monkeys inoculated with rDEN4 vaccine candidates bearing 5-FU derives mutations. Groups of four or two (rDEN4 and rDEN4Δ30) monkeys were inoculated with 5.0 log10PFU virus subcutaneously. Serum was collected daily and virus titers were determined by plaque assay in Vero cells. The limit of virus detection was 0.7 log10,PFU/ml. Mean virus titers are indicated for each group.
Figure 4. Viremia levels in rhesus monkeys inoculated with rDEN4 vaccine candidates bearing pairs of charge-to-alanine mutations in NS5. Groups of four or two (rDEN4 and rDEN4Δ30) monkeys were inoculated with 5.0 logioPFU virus subcutaneously. Serum was collected daily and virus titers were determined by plaque
assay in Vero cells. The limit of virus detection was 1.0 logi0PFU/ml. Mean virus titers are indicated for each group. Viremia was not detected in any monkey after day 4.
Figure 5. The Δ30 mutation attenuates both DEN1 and DEN4 for rhesus monkeys. Groups of 4 monkeys were immunized subcutaneously with 5.0 log]0 PFU of the indicated virus. Serum was collected each day following immunization and virus titers were determined and are shown as mean logI0PFU/ml.
Figure 6. A. Diagram of the p2 (Tonga/74) full-length cDNA plasmid. Regions subcloned are indicated above the plasmid. Numbering begins at the 5' end of the viral sequence. B. The Δ30 mutation removes the indicated 30 nucleotides from the 3' UTR sequence to create p2A30.
Figure 7. Viremia levels in rhesus monkeys inoculated with DEN2 (Tonga/74), rDEN2, and rDEN2A30 vaccine candidate. Groups of four monkeys were inoculated with 5.0 log10PFU virus subcutaneously. Serum was collected daily and virus titers were determined by plaque assay in Vero cells. The limit of virus detection was 0.7 log10PFU/ml. Mean virus titers are indicated for each group. Viremia was not detected in any monkey after day 8.
Figure 8. A. Diagram of the p3 (Sleman/78) full-length cDNA plasmid. Regions subcloned are indicated above the plasmid. Numbering begins at the 5' end of the viral sequence. The sequence and insertion location of the Spel linker is shown. B. The Δ30 mutation removes the indicated 31 nucleotides from the 3' UTR sequence to create p3A30.
Figure 9. A. Recombinant chimeric dengue viruses were constructed by introducing either the CME or the ME regions of DEN2 (Tonga/74) into the DEN4 genetic background. The relative location of the Δ30 mutation in the 3' UTR is indicated by an arrow and intertypic junctions 1, 2, and 3 are indicated. B. Nucleotide and amino acid sequence of the intertypic junction regions. Restriction enzyme recognition sites used in assembly of each chimeric cDNA are indicated.
Figure 10. Growth kinetics in Vero cells of chimeric rDEN2/4Δ30 viruses encoding single or combined Vero cell adaptation mutations. Vero cells were infected with the
indicated viues at an MOI of 0.01. At the indicated time points post-infection, 1 ml samples of tissue culture medium were removed, clarified by centrifugation, and frozen at -80°C. The level of virus replication was assayed by plaque titration in C6/36
cells. Lower limit of detection was 0.7 log10PFU/ml. Replication levels on day 4 post-infection are
indicated by the dashed line.
Figure 11, A. Recombinant chimeric dengue viruses were constructed by introducing either the CME or the ME regions of DEN3 (Sleman/78) into the DEN4 genetic background. The relative location of the Δ30 mutation in the 3' UTR is indicated by an arrow and intertypic junctions 1, 2, and 3 are indicated. Restriction enzyme recognition sites used in assembly of each chimeric cDNA are indicated. B. Nucleotide and amino acid sequence of the intertypic junction regions. Restriction enzyme recognition sites used in assembly of each chimeric cDNA are indicated.
Figure 12. A. Recombinant chimeric dengue viruses were constructed by introducing either the CME or the ME regions of DEN1 (Puerto Rico/94) into the DEN4 genetic background. The relative location of the Δ30 mutation in the 3' UTR is indicated by an arrow and intertypic junctions 1, 2, and 3 are indicated. Restriction enzyme recognition sites used in assembly of each chimeric cDNA are indicated. B. Nucleotide and amino acid sequence of the intertypic junction regions. Restriction enzyme recognition sites used in assembly of each chimeric cDNA are. indicated.
Brief Description of the Sequences
(Sequence Removed)
Brief Description of the SEQ ID NOs
Detailed Description of the Preferred Embodiment Introduction
A molecular approach is herewith used to develop a genetically stable live
attenuated tetravalent dengue virus vaccine. Each component of the tetravalent vaccine,
namely, DEN1, DEN2, DEN3, and DEN4, must be attenuated, genetically stable, and immunogenic. A tetravalent vaccine is needed to ensure simultaneous protection against each of the four dengue viruses, thereby precluding the possibility of developing the more serious illnesses dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS), which occur in humans during secondary infection with a heterotypic wild-type dengue virus. Since dengue viruses can undergo genetic recombination in nature (Worobey, M. et al. 1999 PNAS USA 96:7352-7), the tetravalent vaccine should be genetically incapable of undergoing a recombination event between its four virus components that could lead to the generation of viruses lacking attenuating mutations. Previous approaches to develop a tetravalent dengue virus vaccine have been based on independently deriving each of the four virus components through separate mutagenic procedures, such as passage in tissue culture cells derived from a heterologous host. This strategy has yielded attenuated vaccine candidates (Bhamarapravati, N. and Sutee, Y. 2000 Vaccine 18:44-7). However, it is possible that gene exchanges among the four components of these independently derived tetravalent vaccines could occur in vaccinees, possibly creating a virulent recombinant virus. Virulent polioviruses derived from recombination have been generated in vaccinees following administration of a trivalent poliovirus vaccine (Guillot, S. et al. 2000 J Virol 74:8434-43).
The present invention describes: (1) improvements to the previously described rDEN4Δ30 vaccine candidate, 2) attenuated rDENlΔ30, rDEN2Δ30, and rDEN3Δ30 recombinant viruses containing a 30 nucleotide deletion (A30) in a section of the 3' untranslated region (UTR) that is homologous to that in the rDEN4Δ30 recombinant virus, (3) a method to generate a tetravalent dengue virus vaccine composed of rDENlΔ30, rDEN2Δ30, rDEN3Δ30, and rDEN4Δ30, 4) attenuated antigenic chimeric viruses, rDENl/4Δ30, rDEN2/4Δ30, and rDEN3/4Δ30, for which the CME, ME, or E gene regions of rDEN4Δ30 have been replaced with those derived from DEN1, DEN2, or DEN3; alternatively rDENl/3Δ30, rDEN2/3Δ30, and rDEN4/3A30 for which CME, ME, or E gene regions of rDEN3Δ30 have been replaced with those derived from DEN1, 2, or 4; alternatively rDENl/2Δ30, rDEN3/2Δ30, and rDEN4/2A30 for which CME, ME, or E gene regions of rDEN2A30 have been replaced with those derived from DEN1, 3, or, 4; and alternatively rDEN2/lΔ30, rDEN3/lΔ30, and rDEN4/lA30 for which CME, ME, or E gene regions of rDENlA30 have been replaced with those derived from DEN2, 3, or 4, and 5) a method to generate a tetravalent dengue virus vaccine composed of
rDENl/4Δ30, rDEN2/4Δ30, rDEN3/4Δ30, and rDEN4Δ30, alternatively rDENl/3Δ30, rDEN2/3Δ30, rDEN4/3Δ30, and rDEN3Δ30, alternatively rDENl/2Δ30, rDEN3/2Δ30, rDEN4/2Δ30, and rDEN2Δ30, and alternatively rDEN2/lΔ30, rDEN3/lΔ30, rDEN4/lΔ30, and rDENlA30. These tetravalent vaccines are unique since they contain a common shared attenuating mutation which eliminates the possibility of generating a virulent wild-type virus in a vaccinee since each component of the vaccine possesses the same Δ30 attenuating deletion mutation. In addition, the rDENlΔ30, rDEN2Δ30, rDEN3Δ30, rDEN4Δ30 tetravalent vaccine is the first to combine the stability of the Δ30 mutation with broad antigenicity. Since the Δ30 deletion mutation is in the 3' UTR of each virus, all of the proteins of the four component viruses are available to induce a protective immune response. Thus, the method provides a mechanism of attenuation that maintains each of the proteins of DEN 1, DEN2, DEN3, and DEN4 viruses in a state that preserves the full capability of each of the proteins of the four viruses to induce humoral and cellular immune responses against all of the structural and non-structural proteins present in each dengue virus serotype.
As previously described, the DEN4 recombinant virus, rDEN4Δ30 (previously referred to as 2AΔ30), was engineered to contain a 30 nucleotide deletion in the 3' UTR of the viral genome (Durbin, A.P. et al. 2001 AmJTrop Med Hyg 65:405-13; Men, R. et al. 1996 J Virol 70:3930-7). Evaluation in rhesus monkeys showed the virus to be significantly attenuated relative to wild-type parental virus, yet highly immunogenic and completely protective. Also, a phase I clinical trial with adult human volunteers showed the rDEN4Δ30 recombinant virus to be safe and satisfactorily immunogenic (Durbin, A.P. et al. 2001 Am J Trop Med Hyg 65:405-13). To develop a tetravalent vaccine bearing a shared attenuating mutation in a untranslated region, we selected the Δ30 mutation to attenuate wild-type dengue viruses of serotypes 1, 2, and 3 since it attenuated wild-type DEN4 virus for rhesus monkeys and was safe in humans (Figure 1).
The Δ30 mutation was first described and characterized in the DEN4 virus (Men, R. et al. 1996 J Virol 70:3930-7). In DEN4, the mutation consists of the removal of 30 contiguous nucleotides comprising nucleotides 10478 - 10507 of the 3' UTR (Figure 2A) which form a putative stem-loop structure referred to as TL2 (Proutski, V. et al. 1997 Nucleic Acids Res 25:1194-202). Among the flaviviruses, large portions of the UTR form highly conserved secondary structures (Hahn, C.S. et al. 1987 J Mol Biol 198:33-41; Proutski, V. et al. 1997 Nucleic Acids Res 25:1194-202). Although the individual
nucleotides are not necessarily conserved in these regions, appropriate base pairing preserves the stem-loop structure in each serotype, a fact that is not readily apparent when only considering the primary sequence (Figure 2B, C).
Immunogenic Dengue Chimeras and Methods for Their Preparation
Immunogenic dengue chimeras and methods for preparing the dengue chimeras are provided herein. The immunogenic dengue chimeras are useful, alone or in combination, in a pharmaceutically acceptable carrier as immunogenic compositions to minimize, inhibit, or immunize individuals and animals against infection by dengue virus.
Chimeras of the present invention comprise nucleotide sequences encoding the immunogenicity of a dengue virus of one serotype and further nucleotide sequences selected from the backbone of a dengue virus of a different serotype. These chimeras can be used to induce an immunogenic response against dengue virus.
In another embodiment, the preferred chimera is a nucleic acid chimera comprising a first nucleotide sequence encoding at least one structural protein from a dengue virus of a first serotype, and a second nucleotide sequence encoding nonstructural proteins from a dengue virus of a second serotype different from the first. In another embodiment the dengue virus of the second serotype is DEN4. In another embodiment, the structural protein can be the C protein of a dengue virus of the first serotype, the prM protein of a dengue virus of the first serotype, the E protein of a dengue virus of the first serotype, or any combination thereof.
The term "residue" is used herein to refer to an amino acid (D or L) or an amino acid mimetic that is incorporated into a peptide by an amide bond. As such, the amino acid may be a naturally occurring amino acid or, unless otherwise limited, may encompass known analogs of natural amino acids that function in a manner similar to the naturally occurring amino acids (i.e., amino acid mimetics). Moreover, an amide bond mimetic includes peptide backbone modifications well known to those skilled in the art.
Furthermore, one of skill in the art will recognize that individual substitutions, deletions or additions in the amino acid sequence, or in the nucleotide sequence encoding for the amino acids, which alter, add or delete a single amino acid or a small percentage of amino acids (typically less than 5%, more typically less than 1%) in an encoded sequence are conservatively modified variations, wherein the alterations result in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are well known in the art.
The following six groups each contain amino acids that are conservative substitutions for one another:
1) Alanine (A), Serine (S), Threonine (T);
2) Aspartic acid (D), Glutamic acid (E);
3) Asparagine (N), Glutamine (Q);
4) Arginine (R), Lysine (K);
5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); and
6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W).
As used herein, the terms "virus chimera," "chimeric virus," "dengue chimera" and "chimeric dengue virus" means an infectious construct of the invention comprising nucleotide sequences encoding the immunogenicity of a dengue virus of one serotype and further nucleotide sequences derived from the backbone of a dengue virus of a different serotype.
As used herein, "infectious construct" indicates a virus, a viral construct, a viral chimera, a nucleic acid derived from a virus or any portion thereof, which may be used to infect a cell.
As used herein, "nucleic acid chimera" means a construct of the invention comprising nucleic acid comprising nucleotide sequences encoding the immunogenicity of a dengue virus of one serotype and further nucleotide sequences derived from the backbone of a dengue virus of a different serotype. Correspondingly, any chimeric virus or virus chimera of the invention is to be recognized as an example of a nucleic acid chimera.
The structural and nonstructural proteins of the invention are to be understood to include any protein comprising or any gene encoding the sequence of the complete protein, an epitope of the protein, or any fragment comprising, for example, three or more amino acid residues thereof. Dengue Chimeras
Dengue virus is a mosquito-borne flavivirus pathogen. The dengue virus genome contains a 5' untranslated region (5' UTR), followed by a capsid protein (C) encoding region, followed by a premembrane/membrane protein (prM) encoding region, followed by an envelope protein (E) encoding region, followed by the region encoding the nonstructural proteins (NS1-NS2A-NS2B-NS3-NS4A-NS4B-NS5) and finally a 3' untranslated region (3' UTR). The viral structural proteins are C, prM and E, and the
nonstructural proteins are NS1-NS5. The structural and nonstructural proteins are translated as a single polyprotein and processed by cellular and viral proteases.
The dengue chimeras of the invention are constructs formed by fusing structural protein genes from a dengue virus of one serotype, e.g. DEN1, DEN2, DEN3, or DEN4, with non-structural protein genes from a dengue virus of a different serotype, e.g., DEN1, DEN2, DEN3, or DEN4.
The attenuated, immunogenic dengue chimeras provided herein contain one or more of the structural protein genes, or antigenic portions thereof, of the dengue virus of one serotype against which immunogenicity is to be conferred, and the nonstructural protein genes of a dengue virus of a different serotype.
The chimera of the invention contains a dengue virus genome of one serotype as the backbone, in which the structural protein gene(s) encoding C, prM, or E protein(s) of the dengue genome, or combinations thereof, are replaced with the corresponding structural protein gene(s) from a dengue virus of a different serotype that is to be protected against. The resulting viral chimera has the properties, by virtue of being chimerized with a dengue virus of another serotype, of attenuation and is therefore reduced in virulence, but expresses antigenic epitopes of the structural gene products and is therefore immunogenic.
The genome of any dengue virus can be used as the backbone in the attenuated
chimeras described herein. The backbone can contain mutations that contribute to the
attenuation phenotype of the dengue virus or that facilitate replication in the cell substrate
used for manufacture, e.g., Vero cells. The mutations can be in the nucleotide sequence
encoding nonstructural proteins, the 5' untranslated region or the 3' untranslated region.
The backbone can also contain further mutations to maintain the stability of the
attenuation phenotype and to reduce the possibility that the attenuated virus or chimera
might revert back to the virulent wild-type virus. For example, a first mutation in the 3'
untranslated region and a second mutation in the 5' untranslated region will provide
additional attenuation phenotype stability, if desired. In particular, a mutation that is a
deletion of 30 nts from the 3' untranslated region of the DEN4 genome between nts
10478-10507 results in attenuation of the DEN4 virus (Men et al. 1996 J. Virology
70:3930-3933; Durbin et al. 2001 Am J Trop Med 65:405-413, 2001). Therefore, the
genome of any dengue type 4 virus containing such a mutation at this locus can be used
as the backbone in the attenuated chimeras described herein. Furthermore, other dengue
virus genomes containing an analogous deletion mutation in the 3' untranslated region of
the genomes of other dengue virus serotypes may also be used as the backbone structure of this invention.
Such mutations may be achieved by site-directed mutagenesis using techniques known to those skilled in the art. It will be understood by those skilled in the art that the virulence screening assays, as described herein and as are well known in the art, can be used to distinguish between virulent and attenuated backbone structures. Construction of Dengue Chimeras
The dengue virus chimeras described herein can be produced by substituting at least one of the structural protein genes of the dengue virus of one serotype against which immunity is desired into a dengue virus genome backbone of a different serotype, using recombinant engineering techniques well known to those skilled in the art, namely, removing a designated dengue virus gene of one serotype and replacing it with the desired corresponding gene of dengue virus of a different serotype. Alternatively, using the sequences provided in GenBank, the nucleic acid molecules encoding the dengue proteins may be synthesized using known nucleic acid synthesis techniques and inserted into an appropriate vector. Attenuated, immunogenic virus is therefore produced using recombinant engineering techniques known to those skilled in the art.
As mentioned above, the gene to be inserted into the backbone encodes a dengue structural protein of one serotype. Preferably the dengue gene of a different serotype to be inserted is a gene encoding a C protein, a prM protein and/or an E protein. The sequence inserted into the dengue virus backbone can encode both the prM and E structural proteins of the other serotype. The sequence inserted into the dengue virus backbone can encode the C, prM and E structural proteins of the other serotype. The dengue virus backbone is the DEN1, DEN2, DEN3, or DEN4 virus genome, or an attenuated dengue virus genome of any of these serotypes, and includes the substituted gene(s) that encode the C, prM and/or E structural protein(s) of a dengue virus of a different serotype, or the substituted gene(s) that encode the prM and/or E structural protein(s) of a dengue virus of a different serotype.
Suitable chimeric viruses or nucleic acid chimeras containing nucleotide sequences encoding structural proteins of dengue virus of any of the serotypes can be evaluated for usefulness as vaccines by screening them for phenotypic markers of attenuation that indicate reduction in virulence with retention of immunogenicity. Antigenicity and immunogenicity can be evaluated using in vitro or in vivo reactivity with
dengue antibodies or immunoreactive serum using routine screening procedures known to those skilled in the art. Dengue Vaccines
The preferred chimeric viruses and nucleic acid chimeras provide live, attenuated viruses useful as immunogens or vaccines. In a preferred embodiment, the chimeras exhibit high immunogenicity while at the same time not producing dangerous pathogenic or lethal effects.
The chimeric viruses or nucleic acid chimeras of this invention can comprise the structural genes of a dengue virus of one serotype in a wild-type or an attenuated dengue virus backbone of a different serotype. For example, the chimera may express the structural protein genes of a dengue virus of one serotype in either of a dengue virus or an attenuated dengue virus background of a different serotype.
The strategy described herein of using a genetic background that contains nonstructural regions of a dengue virus genome of one serotype, and, by chimerization, the properties of attenuation, to express the structural protein genes of a dengue virus of a different serotype has lead to the development of live, attenuated dengue vaccine candidates that express structural protein genes of desired immunogenicity. Thus, vaccine candidates for control of dengue pathogens can be designed.
Viruses used in the chimeras described herein are typically grown using techniques known in the art. Virus plaque or focus forming unit (FFU) titrations are then performed and plaques or FFU are counted in order to assess the viability, titer and phenotypic characteristics of the virus grown in cell culture. Wild type viruses are mutagenized to derive attenuated candidate starting materials.
Chimeric infectious clones are constructed from various dengue serotypes. The cloning of virus-specific cDNA fragments can also be accomplished, if desired. The cDNA fragments containing the structural protein or nonstructural protein genes are amplified by reverse transcriptase-polymerase chain reaction (RT-PCR) from dengue RNA with various primers. Amplified fragments are cloned into the cleavage sites of other intermediate clones. Intermediate, chimeric dengue clones are then sequenced to verify the sequence of the inserted dengue-specific cDNA.
Full genome-length chimeric plasmids constructed by inserting the structural or nonstructural protein gene region of dengue viruses into vectors are obtainable using recombinant techniques well known to those skilled in the art.
Methods of Administration
The viral chimeras described herein are individually or jointly combined with a pharmaceutically acceptable carrier or vehicle for administration as an immunogen or vaccine to humans or animals. The terms "pharmaceutically acceptable carrier" or "pharmaceutically acceptable vehicle" are used herein to mean any composition or compound including, but not limited to, water or saline, a gel, salve, solvent, diluent, fluid ointment base, liposome, micelle, giant micelle, and the like, which is suitable for use in contact with living animal or human tissue without causing adverse physiological responses, and which does not interact with the other components of the composition in a deleterious manner.
The immunogenic or vaccine formulations may be conveniently presented in viral plaque forming unit (PFU) unit or focus forming unit (FFU) dosage form and prepared by using conventional pharmaceutical techniques. Such techniques include the step of bringing into association the active ingredient and the pharmaceutical carrier(s) or excipient(s). In general, the formulations are prepared by uniformly and intimately bringing into association the active ingredient with liquid carriers. Formulations suitable for parenteral administration include aqueous and non-aqueous sterile injection solutions which may contain anti-oxidants, buffers, bacteriostats and solutes which render the formulation isotonic with the blood of the intended recipient, and aqueous and nonaqueous sterile suspensions which may include suspending agents and thickening agents. The formulations may be presented in unit-dose or multi-dose containers, for example, sealed ampoules and vials, and may be stored in a freeze-dried (lyophilized) condition requiring only the addition of the sterile liquid carrier, for example, water for injections, immediately prior to use. Extemporaneous injection solutions and suspensions may be prepared from sterile powders, granules and tablets commonly used by one of ordinary skill in the art.
Preferred unit dosage formulations are those containing a dose or unit, or an appropriate fraction thereof, of the administered ingredient. It should be understood that in addition to the ingredients particularly mentioned above, the formulations of the present invention may include other agents commonly used by one of ordinary skill in the art.
The immunogenic or vaccine composition may be administered through different
routes, such as oral or parenteral, including, but not limited to, buccal and sublingual,
rectal, aerosol, nasal, intramuscular, subcutaneous, intradermal, and topical. The
composition may be administered in different forms, including, but not limited to, solutions, emulsions and suspensions, microspheres, particles, microparticles, nanoparticles and liposomes. It is expected that from about 1 to about 5 doses may be required per immunization schedule. Initial doses may range from about 100 to about 100,000 PFU or FFU, with a preferred dosage range of about 500 to about 20,000 PFU or FFU, a more preferred dosage range of from about 1000 to about 12,000 PFU or FFU and a most preferred dosage range of about 1000 to about 4000 PFU or FFU. Booster injections may range in dosage from about 100 to about 20,000 PFU or FFU, with a preferred dosage range of about 500 to about 15,000, a more preferred dosage range of about 500 to about 10,000 PFU or FFU, and a most preferred dosage range of about 1000 to about 5000 PFU or FFU. For example, the volume of administration will vary depending on the route of administration. Intramuscular injections may range in volume from about 0.1 ml to 1.0 ml.
The composition may be stored at temperatures of from about -100°C to about 4°C. The composition may also be stored in a lyophilized state at different temperatures including room temperature. The composition may be sterilized through conventional means known to one of ordinary skill in the art. Such means include, but are not limited to, filtration. The composition may also be combined with bacteriostatic agents to inhibit bacterial growth. Administration Schedule
The immunogenic or vaccine composition described herein may be administered to humans, especially individuals travelling to regions where dengue virus infection is present, and also to inhabitants of those regions. The optimal time for administration of the composition is about one to three months before the initial exposure to the dengue virus. However, the composition may also be administered after initial infection to ameliorate disease progression, or after initial infection to treat the disease. Adjuvants
A variety of adjuvants known to one of ordinary skill in the art may be
administered in conjunction with the chimeric virus in the immunogen or vaccine
composition of this invention. Such adjuvants include, but are not limited to, the
following: polymers, co-polymers such as polyoxyethylene-polyoxypropylene
copolymers, including block co-polymers, polymer p 1005, Freund's complete adjuvant
(for animals), Freund's incomplete adjuvant; sorbitan monooleate, squalene, CRL-8300
adjuvant, alum, QS 21, muramyl dipeptide, CpG oligonucleotide motifs and combinations
of CpG oligonucleotide motifs, trehalose, bacterial extracts, including mycobacterial extracts, detoxified endotoxins, membrane lipids, or combinations thereof. Nucleic Acid Sequences
Nucleic acid sequences of dengue virus of one serotype and dengue virus of a different serotype are useful for designing nucleic acid probes and primers for the detection of dengue virus chimeras in a sample or specimen with high sensitivity and specificity. Probes or primers corresponding to dengue virus can be used to detect the presence of a vaccine virus. The nucleic acid and corresponding amino acid sequences are useful as laboratory tools to study the organisms and diseases and to develop therapies and treatments for the diseases.
Nucleic acid probes and primers selectively hybridize with nucleic acid molecules encoding dengue virus or complementary sequences thereof. By "selective" or "selectively" is meant a sequence which does not hybridize with other nucleic acids to prevent adequate detection of the dengue virus sequence. Therefore, in the design of hybridizing nucleic acids, selectivity will depend upon the other components present in the sample. The hybridizing nucleic acid should have at least 70% complementarity with the segment of the nucleic acid to which it hybridizes. As used herein to describe nucleic acids, the term "selectively hybridizes" excludes the occasional randomly hybridizing nucleic acids, and thus has the same meaning as "specifically hybridizing." The selectively hybridizing nucleic acid probes and primers of this invention can have at least 70%, 80%, 85%, 90%, 95%, 97%, 98% and 99% complementarity with the segment of the sequence to which it hybridizes, preferably 85% or more.
The present invention also contemplates sequences, probes and primers that
selectively hybridize to the encoding nucleic acid or the complementary, or opposite,
strand of the nucleic acid. Specific hybridization with nucleic acid can occur with minor
modifications or substitutions in the nucleic acid, so long as functional species-species
hybridization capability is maintained. By "probe" or "primer" is meant nucleic acid
sequences that can be used as probes or primers for selective hybridization with
complementary nucleic acid sequences for their detection or amplification, which probes
or primers can vary in length from about 5 to 100 nucleotides, or preferably from about
10 to 50 nucleotides, or most preferably about 18-24 nucleotides. Isolated nucleic acids
are provided herein that selectively hybridize with the species-specific nucleic acids
under stringent conditions and should have at least five nucleotides complementary to the
sequence of interest as described in Molecular Cloning: A Laboratory Manual, 2nd ed.,
Sambrook, Fritsch and Maniatis, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 1989.
If used as primers, the composition preferably includes at least two nucleic acid molecules which hybridize to different regions of the target molecule so as to amplify a desired region. Depending on the length of the probe or primer, the target region can range between 70% complementary bases and full complementarity and still hybridize under stringent conditions. For example, for the purpose of detecting the presence of dengue virus, the degree of complementarity between the hybridizing nucleic acid (probe or primer) and the sequence to which it hybridizes is at least enough to distinguish hybridization with a nucleic acid from other organisms.
The nucleic acid sequences encoding dengue virus can be inserted into a vector, such as a plasmid, and recombinantly expressed in a living organism to produce recombinant dengue virus peptide and/or polypeptides.
The nucleic acid sequences of the invention include a diagnostic probe that serves to report the detection of a cDNA amplicon amplified from the viral genomic RNA template by using a reverse-transcription/polymerase chain reaction (RT/PCR), as well as forward and reverse amplimers that are designed to amplify the cDNA amplicon. In certain instances, one of the amplimers is designed to contain a vaccine virus-specific mutation at the 3'-terminal end of the amplimer, which effectively makes the test even more specific for the vaccine strain because extension of the primer at the target site, and consequently amplification, will occur only if the viral RNA template contains that specific mutation.
Automated PCR-based nucleic acid sequence detection systems have been recently developed. TaqMan assay (Applied Biosystems) is widely used. A more recently developed strategy for diagnostic genetic testing makes use of molecular beacons (Tyagi and Kramer, 1996 Nature Biotechnology 14:303-308). Molecular beacon assays employ quencher and reporter dyes that differ from those used in the TaqMan assay. These and other detection systems may used by one skilled in the art.
EXAMPLE 1 Improvement of Dengue Virus Vaccine Candidate rDEN4Δ30
The safety of recombinant live-attenuated dengue-4 vaccine candidate rDEN4Δ30
was evaluated in twenty human volunteers who received a dose of 5.0 logio plaque
forming units (PFU) (Durbin A.P. et al. 2001 Am J Trop Med Hyg 65:405-413). The
vaccine candidate was found to be safe, well-tolerated and immunogenic in all of the
vaccinees. However, five of the vaccinees experienced a transient elevation in alanine aminotransferase levels, three experienced neutropenia and ten vaccinees developed an asymptomatic macular rash, suggesting that it may be necessary to further attenuate this vaccine candidate.
Currently, a randomized, double-blind, placebo-controlled, dose de-escalation study is being conducted to determine the human infectious dose 50 (HID50) of rDEN4Δ30. Each dose cohort consists of approximately twenty vaccinees and four placebo recipients. To date, complete data for doses of 3.0 log)0 PFU and 2.0 logio PFU has been collected. rDEN4Δ30 infected 100% of vaccinees when 3.0 logio PFU was administered and 95% of vaccinees when 2.0 logio PFU was administered (Table 1). The vaccine candidate caused no symptomatic illness at either dose (Table 1). One vaccinee who received 3.0 logio PFU experienced a transient elevation in alanine aminotransferase levels and approximately one fourth of the vaccinees experienced neutropenia at both doses (Table 1). Neutropenia was transient and mild. More than half of the vaccinees developed a macular rash at both doses; the occurrence of rash was not correlated with vaccination dose or with viremia (Table 1 and Table 2). Neither peak titer nor onset of viremia differed between the 3.0 logio PFU and 2.0 logio PFU doses, though both measures of viremia were significantly lower for these doses than for a dose of 5.0 logio PFU (Table 3). The vaccine candidate was immunogenic in 95% of vaccinees at both doses and neutralizing antibody did not decline between days 28 and 42 post-vaccination (Table 4). Although the HID50 has not been determined yet, it is clearly less than 2.0 logio PFU. Interestingly, decreases in the dose of vaccine have had no consistent effect on immunogenicity, viremia, benign neutropenia or the occurrence of rash. Thus it will not necessarily be possible to further attenuate rDEN4Δ30 by decreasing the dose of virus administered, and other approaches must be developed.

Table 1. rDEN4Δ30 clinical summary
(Table Removed)
Table 2. Pattern of rash in vaccinees
(Table Removed)
a logio pfu
b Means in each column with different letters are significantly different (a = 0.05)
Table 3. rDEN4Δ30 viremia summary
(Table Removed)
a logio pfu
b Means in each column with different letters are significantly different (a = 0.05)
Table 4. Immunogenicity of rDEN4Δ30
(Table Removed)
Two approaches have been taken to further attenuate rDEN4Δ30. This first is the generation and characterization of attenuating point mutations in rDEN4 using 5' fluorouracil mutagenesis (Blaney, J.E. Jr. et al. 2002 Virology 300: 125-139; Blaney, J.E. Jr. et al. 2001 J. Virol. 75: 9731-9740). This approach has identified a panel of point mutations that confer a range of temperature sensitivity (ts) and small plaque (sp) phenotypes in Vero and HuH-7 cells and attenuation (att) phenotypes in suckling mouse brain and SCID mice engrafted with HuH-7 cells (SCID-HuH-7 mice). In this example, a subset of these mutations has been introduced to rDEN4Δ30 and the phenotypes of the resulting viruses evaluated.
A second approach was to create a series of paired charge-to-alanine mutations in contiguous pairs of charged amino acid residues in the rDEN4 NS5 gene. As demonstrated previously, mutation of 32 individual contiguous pairs of charged amino acid residues in rDEN4 NS5 conferred a range of ts phenotypes in Vero and HuH-7 cells and a range of att phenotypes in suckling mouse brain (Hanley, K.H. et al. 2002 J. Virol. 76 525-531). As demonstrated below, these mutations also confer an att phenotype in SCID-HuH-7 mice. These mutations have been introduced, either as single pairs or sets of two pairs, into rDEN4Δ30 to determine whether they are compatible with the A30 mutation and whether they enhance the att phenotypes of rDEN4Δ30.
A panel of rDEN4 viruses bearing individual point mutations have been
characterized which possess temperature sensitive and/or small plaque phenotypes in
tissue culture and varying levels of attenuated replication in suckling mouse brain when
compared to wild type rDEN4 virus (Blaney, J. E. et al. 2002 Virology 300:125-139;
Blaney, J. E. et al. 2001 J Virol. 75:9731-9740). Three mutations have been selected to
combine with the A30 deletion mutation to evaluate their ability to further restrict
replication of rDEN4Δ30 in rhesus monkeys. First, the missense mutation in NS3 at
nucleotide 4995 (Ser > Pro) which confers temperature sensitivity in Vero and HuH-7 cells and restricted replication in suckling mouse brain was previously combined with the
Δ30 mutation (Blaney, J. E. et al. 2001 J Virol. 75:9731-9740). The resulting virus, rDEN4Δ30-4995, was found to be more restricted (1,000-fold) in mouse brain replication than rDEN4Δ30 virus ( Gly) which also confers temperature sensitivity in Vero and HuH-7 cells and 10,000-fold restricted replication in suckling mouse brain was combined with the Δ30 mutation here. Third, a substitution in the 3' UTR at nucleotide 10634 which confers temperature sensitivity in Vero and HuH-7 cells, small plaque size in HuH-7 cells, and approximately 1,000-fold restricted replication in suckling mouse brain and SCID mice transplanted with HuH-7 cells was combined with the Δ30 mutation here (Blaney, J. E. et al. 2002 Virology 300:125-139).
For the present investigation, subcloned fragments of p4 (Durbin, A.P. et al. 2001 AmJTrop Med Hyg 65:405-13) containing the above mutations were introduced into the p4A30 cDNA clone. For transcription and recovery of virus, cDNA was linearized with Acc65l (isoschizomer of Kpnl which cleaves leaving only a single 3' nucleotide) and used as template for transcription by SP6 RNA polymerase as previously described (Blaney, J. E. et al. 2002 Virology 300:125-139). C6/36 mosquito cells were transfected using liposome-mediated transfection and cell culture supernatants were harvested between days five and seven. Recovered virus was terminally diluted twice in Vero cells and passaged two (rDEN4Δ30-4995) or three (rDEN4Δ30-8092 and rDEN4Δ30-10634) times in Vero cells.
The complete genomic sequences of rDEN4Δ30-4995, rDEN4Δ30-8092, and
rDEN4Δ30-10634 viruses were determined as previously described (Durbin et al. 2001
Am. J. Trop. Med. Hyg. 65:405-413). As expected, each rDEN4Δ30 virus derivative
contained the Δ30 mutation. Unexpectedly, in rDEN4Δ30-4995 virus, the nucleotide
changes in the codon containing nucleotide 4995, resulted in a Ser > Leu amino acid
change rather than a Ser > Pro change since the p4A3 0-4995 cDNA was designed to
introduce the Ser > Pro change (Table 5). The p4A30-4995 cDNA clone was indeed
found to encode a Ser > Pro change at nucleotide 4995, so it is unclear how the virus
population acquired the Ser > Leu mutation. Nevertheless, this virus was evaluated to
assess the phenotype specified by this missense mutation. rDEN4Δ30-4995 virus was
also found to contain an incidental mutation at nucleotides 4725-6 which resulted in a
single amino acid change (Ser > Asp). The rDEN4Δ30-8092 and rDEN4Δ30-10634
viruses contained the appropriate nucleotide substitutions as well as additional incidental mutations in E, NS4B and NS4B, respectively (Table 5).
Table 5. Missense and UTR mutations present in rDEN4Δ30 virus derivatives bearing
introduced point mutations. (Table Removed)

a Amino acid position in DEN4 polyprotein beginning with the methionine residue of the C protein (nucleotides 102-104) as position 1.
b Mutation restricts replication in mouse models of DEN4 infection which were introduced by Kunkel mutagenesis.
Replication of the three modified rDEN4Δ30 viruses were compared to rDEN4Δ30 and wild type rDEN4 virus in the suckling mouse brain model and SCID mice transplanted with HuH-7 cells (SCID-HuH-7 mice). Experiments were conducted as previously described (Blaney, J. E. et al. 2002 Virology 300:125-139; Blaney, J. E. et al. 2001 J Virol. 75:9731-9740). Briefly, for infection of suckling mouse brain, groups of six seven-day-old mice were inoculated intracerebrally with 4.0 logio PFU of virus and the brain of each mouse was removed five days later. Clarified supernatants of 10% brain suspensions were then frozen at -70°C, and the virus titer was determined by plaque assay in Vero cells. For analysis of DEN4 virus replication in SCID-HuH-7 mice, four to six week-old SCID mice were injected intraperitoneally with 107 HuH-7 cells. Five to six weeks after transplantation, mice were infected by direct inoculation into the tumor with 4.0 logio PFU of virus, and serum for virus titration was obtained by tail-nicking on day 7. The virus titer was determined by plaque assay in Vero cells.
Wild type rDEN4 virus replicated to 6.0 logi0PFU/g in suckling mouse brain, and rDEN4Δ30 was restricted in replication by 0.7 logi0PFU/g, which is similar to previous
observations (Table 6) (Blaney, J. E. et al. 2001 J Virol. 75:9731-9740). rDEN4Δ30-4995, rDEN4Δ30-8092, and rDEN4Δ30-10634 viruses were found to have restricted replication in suckling mouse brain when compared to rDEN4 virus of 3.3, 2.8, and 2.4 logioPFU/g, respectively. These results indicate that the additional attenuating mutations serve to further restrict replication of the rDEN4Δ30 virus in mouse brain ranging from 50-fold (rDEN4Δ30-10634) to 400-fold (rDEN4Δ30-4995). In SCID-HuH-7 mice, virus titer of rDEN4Δ30 virus was 0.4 logioPFU/ml lower than rDEN4 virus, which is also similar to previous studies (Blaney, J. E. et al. 2002 Virology 300:125-139). Each modified rDEN4Δ30 virus was found to be further restricted in replication in SCID-HuH-7 mice (Table 6). rDEN4Δ30-4995, rDEN4Δ30-8092, and rDEN4Δ30-10634 viruses had restricted replication in SCID-HuH-7 mice when compared to rDEN4 virus of 2.9, 1.1, and 2.3 logi0PFU/g below the level of wild type rDEN4 virus, respectively. Two important observations were made: (1) The 4995, 8092 and 10634 mutations were compatible for viability with the Δ30 mutation, and (2) These three modified rDEN4Δ30 viruses had between a 10 and 1,000-fold reduction in replication in comparison to rDEN4 wild-type virus, which allows viruses with a wide range of attenuation in this model to be further evaluated in monkeys or humans. Table 6. Addition of point mutations in NS3, NS5, or the 3' UTR to rDEN4Δ30 virus further attenuates the virus for suckling mouse brain and SCID-HuH-7 mice. (Table Removed)


Groups of 6 suckling mice were inoculated i.e. with 104 PFU of virus. Brains were removed 5 days later, homogenized, and titered in Vero cells.
b Comparison of mean virus titers of mice inoculated with mutant virus and concurrent rDEN4 wt control.
c Groups of HuH-7-SCID mice were inoculated directly into the tumor with 104 PFU virus. Serum was collected on day 6 and 7 and titered in Vero cells.
Based on the findings in the two mouse models of DEN4 virus infection, each of the rDEN4Δ30-4995, rDEN4Δ30-8092, and rDEN4Δ30-10634 viruses was evaluated in the rhesus macaque model of DEN4 infection which has been previously described (Durbin et al. 2001 Am. J. Trop. Med. Hyg. 65:405-413). Briefly, groups of four (rDEN4Δ30-4995, rDEN4Δ30-8092, and rDEN4Δ30-10634) or two (rDEN4, rDEN4Δ30, mock) monkeys were inoculated with 5.0 logioPFU virus subcutaneously. Monkeys were observed daily and serum was collected on days 0 to 6, 8, 10, and 12, and virus titers were determined by plaque assay in Vero cells for measurement of viremia. On day 28, serum was drawn and the level of neutralizing antibodies was tested by plaque reduction assay in Vero cells as previously described (Durbin et al. 2001 Am. J. Trop. Med. Hyg. 65:405-413).
Viremia was detected beginning on day 1 post-infection and ended by day 4 in all monkeys (Table 7, Figure 3). Viremia was present in each monkey infected with rDEN4, rDEN4Δ30, or rDEN4Δ30-10634 virus, but only 2 out of 4 monkeys infected with rDEN4Δ30-4995 or rDEN4Δ30-8092 virus had detectable viremia. As expected, infection with rDEN4 virus resulted in the highest mean number of viremic days per monkey (3.0 days) as well as mean peak virus titer (2.2 logioPFU/ml). Monkeys infected with rDEN4Δ30 virus had both a lower mean number of viremic days per monkey (2.0 days) and mean peak virus titer (1.1 logioPFU/ml) compared to rDEN4 virus. Groups of monkeys infected with each of the modified rDEN4Δ30 viruses had a further restricted mean number of viremic days with those inoculated with rDEN4Δ30-8092 virus having the lowest value, 0.5 days, a 4-fold reduction compared to rDEN4Δ30 virus. The mean peak virus titer of monkeys infected with rDEN4Δ30-4995 (0.9 logioPFU/ml) or rDEN4Δ30-8092 (0.7 logioPFU/ml) was also lower than those infected with rDEN4Δ30 virus. However, the mean peak virus titer of monkeys infected with rDEN4Δ30-10634 (1.3 log10PFU/ml) was slightly higher than those infected with rDEN4Δ30 particularly on day 2 (Figure 3).
Table 7. Addition of point mutations to rDEN4Δ30 further attenuates the virus
for rhesus monkeys. (Table Removed)
a Groups of rhesus monkeys were inoculated subcutaneously with 105 PFU of the indicated virus in a 1 ml dose. Serum was collected on days 0 to 6, 8, 10, 12, and 28. Virus titer was determined by plaque assay in Vero cells.
b Viremia was not detected in any monkey after day 4.
Serum collected on day 0 and 28 was tested for the level of neutralizing antibodies against rDEN4. No detectable neutralizing antibodies were found against DEN4 on day 0, as expected, since the monkeys were pre-screened to be negative for neutralizing antibodies against flaviviruses (Table 7). On day 28, monkeys infected with rDEN4 had a mean serum neutralizing antibody titer (reciprocal dilution) of 398 which was approximately two-fold higher than monkeys infected with rDEN4Δ30 virus (1:181). This result and the two-fold higher level of viremia in rDEN4 virus-infected monkeys are similar to results obtained previously (Durbin et al. 2001 Am. J. Trop. Med. Hyg. 65:405-413). Monkeys infected with rDEN4Δ30-4995 (1:78), rDEN4Δ30-8092 (1:61), and rDEN4Δ30-10634 (1:107) viruses each had a reduced mean serum neutralizing antibody titer compared to monkeys infected with rDEN4Δ30 virus. The four monkeys which had no detectable viremia did have serum neutralizing antibody titers indicating that they were indeed infected. Despite the slight increase in mean peak virus titer of rDEN4Δ30-10634 virus compared with rDEN4Δ30 virus, rDEN4Δ30-10634 virus had a lower mean serum neutralizing antibody titer compared to monkeys infected with rDEN4Δ30 virus. This and the lower mean number of viremic days per monkey suggests that the 10634 mutation can attenuate the replication of rDEN4Δ30 virus in monkeys.
On day 28 after inoculation, all monkeys were challenged with 5.0 log10PFU wild type rDEN4 virus subcutaneously. Monkeys were observed daily and serum was
collected on days 28 to 34, 36, and 38, and virus titers were determined by plaque assay in Vero cells for measurement of viremia after challenge. Twenty eight days after rDEN4 virus challenge, serum was drawn and the level of neutralizing antibodies was tested by plaque reduction assay in Vero cells. Mock-inoculated monkeys had a mean peak virus titer of 2.3 logioPFU/ml after challenge with a mean number of viremic days of 3.5 (Table 8). However, monkeys inoculated with rDEN4, rDEN4Δ30, or each of the modified rDEN4Δ30 viruses had no detectable viremia, indicating that despite the decreased replication and immunogenicity of rDEN4Δ30-4995, rDEN4Δ30-8092, and rDEN4Δ30-10634 viruses, each was sufficiently immunogenic to induce protection against wild type rDEN4. Increases in mean neutralizing antibody titer were minimal ( Table 8. rDEN4Δ30 containing additional point mutations protects rhesus monkeys from
wt DEN4 virus challenge (Table Removed)

a 28 days after primary inoculation with the indicated viruses, rhesus monkeys were challenged subcutaneously with 105 PFU rDEN4 virus in a 1 ml dose. Serum was collected on days 28 to 34, 36, 38, and 56. Virus titer was determined by plaque assay in Vero cells.
Taken together, these results indicate that the three point mutations, 4995, 8092, and 10634) described above do further attenuate the rDEN4Δ30 vaccine candidate in suckling mouse brain, SCID-HuH-7 mice, and rhesus monkeys. Because of additional incidental mutations (Table 4) present in each modified rDEN4Δ30 virus, the phenotypes cannot be directly attributed to the individual 4995, 8092, and 10634 point mutations. However, the presence of similar mouse-attenuation phenotypes in other rDEN4 viruses bearing one of these three mutations supports the contention that the 4995, 8092, and
10634 point mutations are responsible for the att phenotypes of the modified rDEN4Δ30 viruses. Since rDEN4Δ30-4995, rDEN4Δ30-8092, and rDEN4Δ30-10634 virus demonstrated decreased replication in rhesus monkeys while retaining sufficient immunogenicity to confer protective immunity, these viruses are contemplated as dengue vaccines for humans.
DEN4 viruses carrying both Δ30 and charge-to-alanine mutations were next generated. A subset of seven groups of charge-to-alanine mutations described above were identified that conferred between a 10-fold and 1,000-fold decrease in replication in SCID-HuH-7 mice and whose unmutated sequence was well-conserved across the four dengue serotypes. These mutations were introduced as single pairs and as two sets of pairs to rDEN4Δ30 using conventional cloning techniques. Transcription and recovery of virus and terminal dilution of viruses were conducted as described above. Assay of the level of temperature sensitivity of the charge-cluster-to-alanine mutant viruses in Vero and HuH-7 cells, level of replication in the brain of suckling mice and level of replication in SCID-HuH-7 mice was conducted as described above.
Introduction of one pair of charge-to-alanine mutations to rDEN4 produced recoverable virus in all cases (Table 9). Introduction of two pairs of charge-to-alanine mutations produced recoverable virus in two out of three cases (rDEN4Δ30-436-437-808-809 was not recoverable).
rDEN4Δ30 is not ts in Vero or HuH-7 cells. In contrast, seven of the seven sets of charge-to-alanine mutations used in this example conferred a ts phenotype in HuH-7 cells and five also conferred a ts phenotype in Vero cells. All six viruses carrying both Δ30 and charge-to-alanine mutations showed a ts phenotype in both Vero and HuH-7 cells (Table 9). rDEN4Δ30 is not attenuated in suckling mouse brain, whereas five of the seven sets of charge-to-alanine mutations conferred an att phenotype in suckling mouse brain (Table 10). Four of the viruses carrying both Δ30 and charge-to-alanine mutations were attenuated in suckling mouse brain (Table 10). In one case (rDEN4Δ30-23-24-396-397) combination of two mutations that did not attenuate alone resulted in an attenuated virus. Generally, viruses carrying both Δ30 and charge-to-alanine mutations showed levels of replication in the suckling mouse brain more similar to their charge-to-alanine mutant parent virus than to rDEN4Δ30.
rDEN4Δ30 is attenuated in SCID-HuH-7 mice, as are six of the seven charge-to-alanine mutant viruses used in this example. Viruses carrying both Δ30 and charge-to-alanine mutations tended to show similar or slightly lower levels of replication in SCID-
HuH-7 mice compared to their charge-to-alanine mutant parent virus (Table 10). In three cases, viruses carrying both Δ30 and charge-to-alanine mutations showed at least a fivefold greater reduction in SCID-HuH-7 mice than rDEN4Δ30.
The complete genomic sequence of five viruses (rDEN4-200-201, rDEN4Δ30-200-201, rDEN4-436-437 [clone 1], rDEN4Δ30-436-437, and rDEN4-23-24-200-201) that replicated to > 105 PFU/ml in Vero cells at 35°C and that showed a hundredfold or greater reduction in replication in SCID-HuH-7 mice was determined (Table 11). Each of the five contained one or more incidental mutations. In one virus, rDEN4Δ30-436-437, the one additional mutation has been previously associated with Vero cell adaptation (Blaney, J.E. Jr. et al. 2002 Virology 300:125-139). Each of the remaining viruses contained at least one incidental mutation whose phenotypic effect is unknown. Consequently, the phenotypes described cannot be directly attributed to the charge-to-alanine mutations. However, the fact that rDEN4 and rDEN4Δ30 viruses carrying the same charge-to-alanine mutations shared similar phenotypes provides strong support for the ability of charge-to-alanine mutations to enhance the attenuation of rDEN4Δ30. Because rDEN4-436-437 [clone 1] contained 4 incidental mutations, a second clone of this virus was prepared. rDEN4-436-437 [clone2] contained only one incidental mutation (Table 11), and showed the same phenotypes as rDEN4-436-437 in cell culture and SCID-HuH-7 mice. rDEN4-436-437 [clone 2] was used in the rhesus monkey study described below.
Table 9. Addition of charge-to-alanine mutations to rDEN4Δ30 confers a ts phenotype in both Vero and HuH-7 cells.

(Table Removed)
temperature when compared to the permissive temperature (35°C). b Amino acid pair(s) changed to pair of Ala residues. c Reduction in titer (logiopfu/ml) compared to the permissive temperature (35°C).
Table 10. Addition of charge-to-alanine mutations attenuates rDEN4Δ30 in suckling mouse brain and enhances attenuation in SCID-HuH-7

(Table Removed)
aGroups of six suckling mice were inoculated i.e. with 10 PFU virus in a 30 p.1 inoculum. The brain was removed 5 days later, homogenized, and virus was quantitated by titration in Vero cells.
b Determined by comparing the mean viral titers in mice inoculated with sample virus and concurrent wt controls (n = 6). The attenuation {att) phenotype is defined as a reduction of > 1.5 logioPFU/g compared to wt virus; reductions of > 1.5 are listed in boldface.
c Groups of SCID-HuH-7 mice were inoculated directly into the tumor with 104 PFU virus.
d Determined by comparing mean viral titers in mice inoculated with sample virus and concurrent wt controls. The attenuation phenotype is defined as a reduction of >1.5 logio PFU/g compared to wt virus; reductions of >1.5 are listed in boldface.
Table 11. Missense and UTR mutations present in rDEN4 virus derivatives bearing charge-to-alanine and the Δ30 mutation.
(TABLE REMOVED)
a Asterisk indicates previously identified Vero cell adaptation mutation. Bold values indicate mutations designed to occur in the designated virus. c Amino acid position in the protein product of the designated DEN4 gene; numbering starts with the amino terminus of the protein.
Based on the attenuation in the SCID-HuH7 mouse model, four of the charge-to-alanine mutant viruses (rDEN4-200-201, rDEN4Δ30-200-201, rDEN4-436-437 [clone 2], rDEN4Δ30-436-437) were evaluated in rhesus macaques as described above. As with the study of viruses carrying attenuating point mutations, viremia was detected on day 1 postinfection and ended by day 4 in all monkeys (Figure 4, Table 12). Viremia was detected in most of the monkeys infected; only one of the four monkeys infected with rDEN4Δ30-200-201 and one of the four monkeys infected with rDEN4Δ30-436-437 showed no detectable viremia. Monkeys infected with rDEN4 showed the highest mean peak virus titer; and in each case viruses carrying the Δ30 mutation showed an approximately 0.5 log decrease in mean peak virus titer relative to their parental viruses and a 0.5 to 2 day decrease in mean number of viremic days per monkey. Monkeys infected with viruses carrying both the Δ30 and charge-to-alanine mutations showed a two-fold reduction in mean peak viremia relative to those infected with rDEN4Δ30. This suggests that addition of the charge-to-alanine mutations further attenuates rDEN4Δ30 for rhesus macaques.
As expected, none of the monkeys in this study showed detectable levels of neutralizing antibody on day 0. On day 28, every monkey infected with a virus showed a detectable levels of neutralizing antibody, indicating that all of the monkeys, even those that showed no detectable viremia, had indeed been infected. As in the study of attenuating point mutations, monkeys infected with rDEN4 had a mean serum neutralizing antibody titer (reciprocal dilution) which was approximately twice that of monkeys that had been infected with rDEN4Δ30. Monkeys infected with rDEN4-200-201 and rDEN4-436-437 [clone 2] had similar mean neutralizing antibody titers to rDEN4, and those infected with rDEN4Δ30-200-201 and rDEN4Δ30-436-437 had similar mean neutralizing antibody titers to rDEN4. In each case the addition of the Δ30 mutation to a virus resulted in a two-fold decrease in neutralizing antibody. Thus, although the addition of charge-to-alanine mutations to rDEN4Δ30 decreased mean peak viremia below that of rDEN4Δ30 alone, it did not affect levels of neutralizing antibody.
Table 12. Addition of paired charge-to-alanine mutations to rDEN4Δ30 further attenuates the virus for rhesus monkeys.
(Table Removed)
a Groups of rhesus monkeys were inoculated subcutaneously with 105 PFU of the indicated virus in a 1 ml dose. Serum was collected on days 0 to 6, 8, 10 and 28. Virus titer was determined by plaque assay in Vero cells.
b Viremia was not detected in any monkey after day 4.
After challenge with rDEN4 on day 28, mock-infected monkeys had a mean peak virus titer of 1.5 logioPFU/ml and a mean number of viremic days of 3.0 (Table 13). However, none of the monkeys previously inoculated with rDEN4, rDEN4Δ30 or the charge-to-alanine mutant viruses showed detectable viremia. Additionally, none of the monkeys showed a greater than four-fold increase in serum neutralizing antibody titer. Together these data indicate that infection with any of the viruses, including those carrying both Δ30 and the charge-to-alanine mutations, protected rhesus macaques from challenge with rDEN4.

Table 13. rDEN4Δ30 containing charge-to-alanine mutations protects rhesus monkeys from wt DEN4 virus challenge
(Table Removed)
a 28 days after primary inoculation with the indicated viruses, rhesus monkeys were challenged subcutaneously with 105 PFU rDEN4 virus in a 1 ml dose. Serum was collected on days 28 to 34, 36, 10, and 56. Virus titer was determined by plaque assay in Vero cells.
Addition of charge-to-alanine mutations to rDEN4Δ30 can confer a range of ts phenotypes in both Vero and HuH-7 cells and att phenotypes in suckling mouse brain and can either enhance or leave unchanged attenuation in SCID-HuH-7 mice. Most importantly, addition of these mutations can decrease the viremia produced by rDEN4Δ30 in rhesus macaques without decreasing neutralizing antibody titer or protective efficacy. Thus addition of such mutations to rDEN4Δ30 is contemplated as enhancing attenuation in humans. Also, mutations are contemplated as being added that do not change the overall level of attenuation, but stabilize the attenuation phenotype because they themselves are independently attenuating even in the absence of the Δ30 mutation. Charge-to-alanine mutations are particularly useful because they occur outside of the structural gene regions, and so can be used to attenuate structural gene chimeric viruses. Moreover, they involve at least three nucleotide changes, making them unlikely to revert to wild type sequence.
A series of point mutations that enhance the replication of rDEN4 in Vero cells tissue culture have been identified; these are primarily located in the NS4B gene (Blaney, J. E. et. al. 2002 Virology 300:125-139; Blaney, J. E. et al. 2001 J Virol 75:9731-9740). Vero cell adaptation mutations confer two desirable features upon a vaccine candidate.
First, they enhance virus yield in Vero cells, the intended substrate for vaccine production, and thus render vaccine production more cost-effective. Second, although each of these Vero adaptation mutations are point mutations, they are likely to be extremely stable during vaccine manufacture, because they give a selective advantage in Vero cells. At least one Vero cell adaptation mutation, at position 7129, was also shown to decrease mosquito infectivity of rDEN4; poor mosquito infectivity is another desirable characteristic of a dengue vaccine candidate. To investigate the generality of this finding, we tested the effect of the remaining Vero cell adaptation mutations on the ability of rDEN4 to infect Aedes aegypti mosquitoes fed on an infectious bloodmeal. Table 14 shows the infectivity of each virus carrying a single Vero cell adaptation mutation at high titer. Of these, only one mutation, at position 7182, was associated with a large decrease in mosquito infectivity. Thus 7182 may be a particularly valuable mutation to include in an rDEN4 vaccine candidate, as it has opposite effects on replication in Vero cells and in mosquitoes.
Table 14. Effect of Vero cell adaptation mutations on rDEN4 mosquito infectivity (Table Removed)

a Virus titer ingested, assuming a 2 jul bloodmeal.
b Percentage of mosquitoes with IFA detectable antigen in midgut or head tissue prepared 21 days after oral infection.
EXAMPLE 2 Generation and Characterization of a Recombinant DEN1 Virus Containing
the Δ30 Mutation
We first sought to determine if the Δ30 mutation was able to satisfactorily attenuate a wild-type DEN virus other than the DEN4 serotype. To do this, the Δ30
mutation was introduced into the cDNA for DENl (Western Pacific). The pRS424DENl WP cDNA clone (Puri, B. et al. 2000 Virus Genes 20:57-63) was digested with BamHl and used as template in a PCR using Pfu polymerase with forward primer 30 (DENl nt 10515-10561 and 10592-10607) and the M13 reverse sequencing primer (101 nt beyond the 3' end of DENl genome sequence). The resulting PCR product was 292 bp and contained the Δ30 mutation. The pRS424DENlWP cDNA was partially digested with Apa I, then digested to completion with Sac II and the vector was gel isolated, mixed with PCR product, and used to transform yeast strain YPH857 to yield growth on plates lacking tryptophan (Polo, S. et al. 1997 J Virol 71:5366-74). Positive yeast colonies were confirmed by PCR and restriction enzyme analysis. DNA isolated from two independent yeast colonies was used to transform E. coli strain STBL2. Plasmid DNA suitable for generating RNA transcripts was prepared and the presence of the Δ30 mutation was verified by sequence analysis.
For transcription and generation of virus, cDNA (designated pRS424DENlA30) that was linearized with Sac II was used as template in a transcription reaction using SP6 RNA polymerase as described (Polo, S. et al. 1997 J Virol 71:5366-74). Transcription reactions were electroporated into LLC-MK2 cells and infection was confirmed by observation of CPE and immunofluorescence and harvested on day 14. Virus stocks were amplified on C6/36 mosquito cells and titered on LLC-MK2 cells. The genome of the resulting virus, rDENlΔ30, was sequenced to confirm the presence of the Δ30 mutation. The Δ30 mutation removes nucleotides 10562-10591 of DENl (Figure 2B, C), which corresponds to the TL2 of DENl. The virus replicates efficiently in Vero cell culture to titers of 6.5 logio PFU/ml, indicating that the Δ30 mutation is compatible with efficient growth of DENl in cell culture, a property essential for manufacture of the vaccine. Using similar techniques, parent virus rDENl was generated. Incidental mutations arising from virus passage in tissue culture were identified in both rDENl and rDENl Δ30 using sequence analysis and are listed in Table 15. An additional rDENlA30 virus was derived by transfection and amplification in Vero cells. Although this virus was not evaluated in the studies described below, its sequence analysis is included in Table 15. The properties of rDENl Δ30 as a vaccine in vivo were next examined.
Table 15. Missense mutations present among the recombinant DEN1 viruses and
correlation of NS4B region mutations with those found in DEN4

(Table Removed)
+Homology among all four serotypes Nucleotides are underlined in even multiples of 10.
Evaluation of the replication, immunogenicity, and protective efficacy of
rDENlA30 and wild-type parental rDENl virus (derived from the pRS424DENlWP
cDNA) in juvenile rhesus monkeys was performed as follows. Dengue virus-
seronegative monkeys were injected subcutaneously with 5.0 logio PFU of virus in a 1 ml
dose divided between two injections in each side of the upper shoulder area. Monkeys
were observed daily and blood was collected on days 0-10 and 28 and serum was stored
at -70°C. Titer of virus in serum samples was determined by plaque assay in Vero cells
as described previously (Durbin, A.P. et al. 2001 Am J Trop Med Hyg 65:405-13). Plaque reduction neutralization titers were determined for the day 28 serum samples as previously described (Durbin, A.P. et al. 2001 Am J Trop Med Hyg 65:405-13). All monkeys were challenged on day 28 with a single dose of 5.0 logio PFU of wild-type rDENl and blood was collected for 10 days. Virus titer in post-challenge sera was determined by plaque assay in Vero cells. Monkeys inoculated with full-length wild-type rDENl were viremic for 2 - 3 days with a mean peak titer of 2.1 logio PFU/ml (Table 16), and monkeys inoculated with rDENlA30 were viremic for less than 1 day with a mean peak titer of 0.8 logio PFU/ml, indicating that the A30 mutation is capable of attenuating DEN1. As expected for an attenuated virus, the immune response, as measured by neutralizing antibody titer, was lower following inoculation with rDENl A30 compared to inoculation with wild-type rDENl (Table 16), yet sufficiently high to protect the animals against wild-type DEN1 virus challenge. Wild-type rDENl virus was not detected in any serum sample collected following virus challenge, indicating that monkeys were completely protected following immunization with either full-length wild-type rDENl or recombinant virus rDENlA30. The level of attenuation specified by the A30 mutation was comparable in both the DEN1 and DEN4 genetic backgrounds (Figure 5).
Table 16. The A30 mutation attenuates rDENl for rhesus monkeys
(Table Removed)
* Rhesus monkeys were inoculated subcuateously with 5.0 logio PFU of virus. Serum samples were collected daily for 10 days. Serum for neutralization assay was collected on day 28. All monkeys were challenged on day 28 with 5.0 logio PFU of rDENl.
As previously reported, rDEN4 virus replicated to greater than 6.0 logioPFU/ml serum in SCID-HuH-7 mice, while the replication of rDEN4 virus bearing the A30 mutation was reduced by about 10-fold (Blaney, J.E. Jr. et al. 2002 Virology 300:125-139). The replication of rDENlA30 was compared to that of wt rDENl in SCID-HuH-7 mice (Table 17). rDENlA30 replicated to a level approximately 100-fold less than its wt rDENl parent. This result further validates the use of the SCID-HuH-7 mouse model for
the evaluation of attenuated strains of DEN virus, with results correlating closely with those observed in rhesus monkeys.
Table 17. The Δ30 mutation attenuates rDENl for HuH-7-SCID mice
(Table Removed)
5 Groups of HuH-7-SCID mice were inoculated directly into the tumor with 4.0
logiopfu virus. Serum was collected on day 6 and 7, and virus titer was determined by
plaque assay in Vero cells.
6 Significant difference was found between rDENl and rDENlA30 viruses,
Tukey-Kramer test (P Finally, the infectivity of rDENl and rDENlA30 for mosquitoes was assessed, using the methods described in detail in Example 5. Previously, the Δ30 mutation was shown to decrease the ability of rDEN4 to cross the mosquito midgut barrier and establish a salivary gland infection (Troyer, J.M. et al. 2001 Am J Trop Med Hyg 65:414-419). However neither rDENl nor rDENl Δ30 was able to infect the midgut of Aedes aegypti mosquitoes efficiently via an artificial bloodmeal (Table 18), so it was not possible to determine whether Δ30 might further block salivary gland infection. A previous study also showed that the Δ30 had no effect on the infectivity of rDEN4 for Toxorhynchites splendens mosquitoes infected via intrathoracic inoculation (Troyer, J.M. et al. 2001 Am J Trop Med Hyg 65:414-419), and a similar pattern was seen for rDENl and rDENlA30 (Table 18). The genetic basis for the inability of rDENl to infect the mosquito midgut has not been defined at this time. However, this important property of restricted infectivity for the mosquito midgut is highly desirable in a vaccine candidate since it would serve to greatly restrict transmission of the vaccine virus from a vaccinee to a mosquito vector.
Table 18. DEN1 and DEN1A30 viruses are both highly infectious for
Toxorhynchites splendens, but do not infect Aedes aegypti efficiently.

(Table Removed)
a Amount of virus present in 0.22 ^1 inoculum.
b Percentage of mosquitoes with IFA detectable antigen in head tissue prepared 14 days after inoculation.
c Virus titer ingested, assuming a 2 ul bloodmeal.
Percentage of mosquitoes with IFA detectable antigen in midgut or head tissue prepared 21 days after oral infection. When virus infection was detected, but did not exceed a frequency of 50% at the highest dose of virus ingested, the MID50 was estimated by assuming that a 10-fold more concentrated virus dose would infect 100% of the mosquitoes.
Thus, the Δ30 mutation, first described in DEN4, was successfully transferred to rDENl. The resulting virus, rDENlΔ30, was shown to be attenuated in monkeys and SCID-HuH-7 mice to levels similar to recombinant virus rDEN4Δ30, thereby establishing the conservation of the attenuation phenotype specified by the Δ30 mutation in a different DEN virus background. Based on the favorable results of rDEN4Δ30 in recent clinical trials (Durbin, A.P. et al. 2001 Am J Trop Med Hyg 65:405-13), it is predicted that rDENlA30 will be suitably attenuated in humans. To complete the tetravalent vaccine, attenuated rDEN2 and rDEN3 recombinant viruses bearing the Δ30 mutation are contemplated as being prepared (See Examples 3 and 4 below). The demonstration that the Δ30 mutation specifies a phenotype that is transportable to another DEN serotype has important implications for development of the tetravalent vaccine. This indicates that the Δ30 mutation is expected to have a corresponding effect on DEN2 and DEN3 wild-type viruses.
EXAMPLE 3 Generation and Characterization of a Recombinant DEN2 Virus Containing the Δ30
Mutation
Evaluation of rDENlA30 showed that it was satisfactorily attenuated. Based on this result, we sought to extend our technology to the creation of a DEN2 vaccine candidate. To do this, the Δ30 mutation was introduced into the cDNA of DEN2. A DEN2 virus isolate from a 1974 dengue epidemic in the Kingdom of Tonga (Tonga/74) (Gubler, D. J. et al 1978 Am J Trop Med Hyg 27:581-589) was chosen to represent wt DEN2. The genome of DEN2 (Tonga/74) was sequenced in its entirety and served as consensus sequence for the construction of a full-length cDNA clone (Appendix 1). cDNA fragments of DEN2 (Tonga/74) were generated by reverse-transcription of the genome as indicated in Figure 6A. Each fragment was subcloned into a plasmid vector and sequenced to verify that it matched the consensus sequence as determined for the virus. This yielded seven cloned cDNA fragments spanning the genome. Cloned fragments were modified as follows: Fragment X, representing the 5' end of the genome was abutted to the SP6 promoter; Fragment L was modified to contain a translationally-silent Spel restriction site at genomic nucleotide 2353; Fragment R was modified to contain a translationally-silent Spel restriction site also at genomic nucleotide 2353, and to stabilize the eventual full-length clone, two additional translationally-silent mutations at nucleotides 2362 - 2364 and 2397 were created to ensure that translation stop codons were present in all reading frames other than that used to synthesize the virus polyprotein; Fragment A was modified at nucleotide 3582 to ablate a naturally occurring Spel restriction site and at nucleotide 4497 to ablate a naturally occurring Kpnl restriction site; Fragment C was modified at nucleotide 9374 to ablate a naturally occurring Kpnl restriction site; and Fragment Y, representing the 3' end of the genome was abutted to a Kpnl restriction site. Each fragment was added incrementally between the Ascl and Kpnl restriction sites of DEN4 cDNA clone p4 (Durbin, A.P. et al. 2001 Am J Trop Med Hyg 65:405-13) to generate a full-length DEN2 cDNA clone (p2) with the same vector background successfully used to generate rDEN4 and rDEN4Δ30. cDNA clone p2 was sequenced to confirm that the virus genome region matched the DEN2 (Tonga/74) consensus sequence, with the exception of the translationally-silent modifications noted above. The Δ30 mutation was introduced into Fragment Y to generate Fragment YA30.
To create p2A30, the Fragment Y region of p2 was replaced with Fragment YA30 (Figure 6A, B).
For transcription and generation of infectious virus, cDNA (p2 and p2A30) was linearized with Acc65l (isoschizomer of Kpnl which cleaves leaving only a single 3' nucleotide) and used as template in a transcription reaction using SP6 RNA polymerase as previously described (Blaney, J. E. et. al. 2002 Virology 300:125-139). Transcripts were introduced into Vero cells or C6/36 mosquito cells using liposome-mediated transfection and cell culture supernatants were harvested on day 7.
rDEN2 virus was recovered from the p2 cDNA in both Vero and C6/36 cells, while rDEN2A30 was recovered from the p2A30 cDNA clone in only C6/36 cells (Table 19). The level of infectious virus recovered in C6/36 cells was comparable for the p2 and p2A30 cDNA clones when assayed by plaque titration and immunostaining in Vero or C6/36 cells. As previously observed, the efficiency of transfection in C6/36 cells was higher than that in Vero cells. Two rDEN2A30 viruses were recovered from independent cDNA clones, #2 and #10.
Table 19. rDEN2 virus is recovered in Vero and C6/36 cells, but rDEN2A30 virus is
recovered only in C6/36 cells.
(Table Removed)
To produce working stocks of rDEN2 and rDEN2A30 viruses, transfection harvests were passaged and terminally diluted in Vero cells, and genomic sequences of the viruses were determined. The Vero cell transfection harvest of rDEN2 virus was terminally diluted once in Vero cells, and individual virus clones were passaged once in Vero cells. To assess whether any homologous Vero cell adaptation mutations identified in the rDEN4 NS4B 7100-7200 region were present in these virus clones, seven independent terminally diluted clones were sequenced over this region. Each of the seven
rDEN2 viruses contained a single nucleotide substitution in this region at nucleotide 7169 (U > C) resulting in a Val > Ala amino acid change. This nucleotide corresponds to the 7162 mutation identified in rDEN4 (Blaney, J. E. et. al. 2002 Virology 300:125-139), which has a known Vero cell adaptation phenotype suggesting that this mutation may confer a replication enhancement phenotype in rDEN2 virus. One rDEN2 virus clone was completely sequenced and in addition to the 7169 mutation, a missense mutation (Glu > Ala) was found in NS5 at residue 3051 (Table 20).
Table 20. Missense mutations which accumulate in rDEN2 and rDEN2A30 viruses after
transfection or passage in Vero cells.
(Table Removed)
a Amino acid position in DEN2 polyprotein beginning with the methionine residue of the C protein (nucleotides 97-99) as position 1.
b Virus was recovered in Vero cells and terminally-diluted once in Vero cells. Virus stock was prepared in Vero cells.
c Same nucleotide position as 7162 in rDEN4.
d Virus was recovered in C6/36 cells and passaged three times in Vero cells. Virus was then terminally diluted and a stock was prepared in Vero cells.
Because both rDEN2 and rDEN2A30 viruses grown in Vero cells acquired the same mutation at nucleotide 7169, which corresponds to the Vero cell adaptation mutation previously identified in rDEN4 at nucleotide 7162, it was reasoned that this mutation is associated with growth adaptation of rDEN2 and rDEN2A30 in Vero cells. In anticipation that the 7169 mutation may allow rDEN2A30 to be recovered directly in Vero cells, the mutation was introduced into the rDEN2A30 cDNA plasmid to create p2A30-7169. Transcripts synthesized from p2A30-7169, as well as p2 and p2A30 were introduced into Vero cells or C6/36 mosquito cells using liposome-mediated transfection as described above. Virus rDEN2A30-7169 was recovered from the p2A30-7169 cDNA in both Vero and C6/36 cells, while rDEN2A30 was recovered from the p2A30 cDNA clone in only C6/36 cells (Table 21). The 7169 mutation is both necessary and sufficient for the recovery of rDEN2A30 in Vero cells.
Table 21. rDEN2A30-7169 virus containing the 7169 Vero cell adaptation mutation is recovered in both Vero and C6/36 cells
(Table Removed)
a Nucleotide 7169 in rDEN2 corresponds to nucleotide 7162 in rDEN4 which has been shown to be associated with growth adaptation in Vero cells.
To initially assess the ability of the A30 mutation to attenuate rDEN2 virus in an animal model, the replication of DEN2 (Tonga/74), rDEN2, and rDEN2A30 viruses was evaluated in SCID-HuH-7 mice. Previously, attenuation of vaccine candidates in SCID-HuH-7 mice has been demonstrated to be predictive of attenuation in the rhesus monkey model of infection (Examples 1 and 2). The recombinant viruses tested in this experiment were recovered in C6/36 cells. The DEN2 Tonga/74 virus isolate, rDEN2, and two independent rDEN2A30 viruses, (clones 20A and 21 A) which were derived from two independent p2A30 cDNA clones, were terminally diluted twice in C6/36 cells prior to production of a working stock in C6/36 cells. These viruses should not contain any Vero cell adaptation mutations. DEN2 Tonga/74 virus replicated to a mean virus titer of 6.2 logioPFU/ml in the serum of SCID-HuH-7 mice, and rDEN2 virus replicated to a similar level, 5.6 logi0PFU/ml (Table 22). Both rDEN2A30 viruses were greater than 100-fold restricted in replication compared to rDEN2 virus. These results indicate that the A30 mutation has an attenuating effect on replication of rDEN2 virus similar to that observed for rDEN4 and rDENl viruses.
Table 22. The A30 mutation restricts rDEN2 virus replication in SCID-HuH-7 mice

(Table Removed)
a Groups of SCID-HuH-7 mice were inoculated directly into the tumor with 10 PFU virus grown in C6/36 cells. Serum was collected on day 7 and titered in C6/36 cells.
b Comparison of mean virus titers of mice inoculated with mutant virus and concurrent rDEN2 control.
DEN2 virus replication in SCID-HuH-7 mice was also determined using DEN2 (Tonga/74), rDEN2, and rDEN2A30 which were passaged in Vero cells (see Table 20, footnotes b and d). Both rDEN2 and rDEN2A30 had acquired a mutation in NS4B, nucleotide 7169, corresponding to the 7162 mutation identified in rDEN4 as Vero cell adaptation mutation. In the presence of the 7169 mutation, the Δ30 mutation reduced replication of rDEN2A30 by 1.0 logioPFU/ml (Table 23). Previously, using virus grown in C6/36 cells and lacking the 7169 mutation, the Δ30 mutation reduced replication of rDEN2A30 by about 2.5 logioPFU/ml (Table 22). These results indicate that Vero cell growth adaptation in DEN2 may also confer a slight growth advantage in HuH-7 liver cells. Nevertheless, the attenuation conferred by the Δ30 mutation is still discernible in these Vero cell growth adapted viruses.
Table 23. The Δ30 mutation restricts Vero cell adapted rDEN2 virus replication in
SCID-HuH-7 mice.

(Table Removed)
a Groups of SCID-HuH-7 mice were inoculated directly into the tumor with 104 PFU virus. Serum was collected on day 7 and titered in C6/36 cells.
b Comparison of mean virus titers of mice inoculated with rDEN2A30 and rDEN2 control.
Evaluation of the replication, immunogenicity, and protective efficacy of rDEN2A30 and wild-type parental rDEN2 virus in juvenile rhesus monkeys was performed as follows. Dengue virus-seronegative monkeys were injected subcutaneously with 5.0 logio PFU of virus in a 1 ml dose divided between two injections in each side of the upper shoulder area. Monkeys were observed daily and blood was collected on days 0 - 10 and 28 and serum was stored at -70°C. Viruses used in this experiment were passaged in Vero cells, and recombinant viruses contained the mutations shown in Table 20 (See footnotes b and d). Titer of virus in serum samples was determined by plaque assay in Vero cells as described previously (Durbin, A.P. et al. 2001 Am J Trop Med Hyg 65:405-13). Plaque reduction neutralization titers were determined for the day 28 serum samples as previously described (Durbin, A.P. et al. 2001 Am J Trop Med Hyg 65:405-13). All monkeys were challenged on day 28 with a single dose of 5.0 logio PFU of wt DEN2 (Tonga/74) and blood was collected for 10 days. Virus titer in post-challenge sera was determined by plaque assay in Vero cells. Monkeys inoculated with wt DEN2 (Tonga/74) or rDEN2 were viremic for 4 - 5 days with a mean peak titer of 2.1 or 1.9 logio PFU/ml, respectively.
Monkeys inoculated with rDEN2A30 were viremic for 2 - 3 days with a mean peak titer of 1.7 logio PFU/ml (Table 24, Figure 7), indicating that the Δ30 mutation is capable of attenuating DEN2, although not to the same low level observed in rDENlA30 (Table 16). As expected for an attenuated virus, the immune response, as measured by neutralizing antibody titer, was lower following inoculation with rDEN2A30 compared to inoculation with wt DEN2 (Tonga/74) or rDEN2 (Table 24), yet sufficiently high to protect the animals against wt DEN2 virus challenge (Table 25). Thus, the decreased number of days of viremia for rDEN2Δ30, the decreased mean peak titer, and the decreased serum antibody response indicate that the 30 mutation attenuates rDEN2 for rhesus monkeys.
Table 24. rDEN2A30 is slightly more attenuated for rhesus monkeys than rDEN2

(Table Removed)
a Groups of rhesus monkeys were inoculated subcutaneously with 105 PFU of the indicated virus in a 1 ml dose. Serum was collected on days 0 to 6, 8, 10, 12, and 28. Virus titer was determined by plaque assay in Vero cells.
b Viremia was not detected in any monkey after day 8.
Table 25. rDEN2A30 protects rhesus monkeys from wt DEN2 virus challenge

(Table Removed)
8 28 days after inoculation with the indicated viruses, monkeys were challenged subcutaneously with 105 PFU DEN2 (Tonga/74) in a 1 ml dose. Serum was collected on days 28 to 34, 36, 38, and 56. Virus titer was determined by plaque assay in Vero cells.
The infectivity of DEN2 (Tonga/74), rDEN2 and rDEN2A30 for Aedes aegypti mosquitoes via an artificial bloodmeal was evaluated using the methods described in detail in Example 5. However at doses of 3.3 to 3.5 logio pfu ingested, none of these three viruses infected any mosquitoes, indicating that DEN2 (Tonga/74) is poorly infectious for Aedes aegypti. As with rDENl, the genetic basis for this lack of infectivity remains to be defined. The important property of restricted infectivity for the mosquito midgut is highly desirable in a vaccine candidate because it would serve to greatly restrict transmission of the virus from a vaccinee to a mosquito vector.
Several missense mutation identified in rDEN4 have been demonstrated to confer attenuated replication in suckling mouse brain and/or SCID-HuH-7 mice (Blaney, J. E. et al. 2002 Virology 300:125-139; Blaney, J. E. et al. 2001 J Virol 75:9731-9740). In addition, missense mutations that enhance replication of rDEN4 virus in Vero cells have been characterized. The significant sequence conservation among the DEN virus serotypes provides a strategy by which the mutations identified in rDEN4 viruses are contemplated as being used to confer similar phenotypes upon rDEN2 virus. Six mutations identified in rDEN4 virus that are at a site conserved in rDEN2 virus are being introduced into the p2 and p2A30 cDNA clones (Table 26). Specifically, two rDEN4 mutations, NS3 4891 and 4995, which confer Vero cell adaptation phenotypes and decreased replication in mouse brain, one mutation, NS4B 7182, which confers a Vero cell adaptation phenotype, and three mutations, NS1 2650, NS3 5097, and 3' UTR 10634 which confer decreased replication in mouse brain and SCID-HuH-7 mice are being evaluated. These mutations have been introduced into sub-cloned fragments of the p2 and p2A30 cDNA clones, and have been used to generate mutant full-length cDNA clones (Table 26), from which virus has been recovered in C6/36 cells (Table 27). The evaluation of these mutant rDEN2 viruses is contemplated as determining that such point mutations can be transported into a different DEN virus serotype and confer a similar useful phenotype, as has been demonstrated for the 30 deletion mutation.
Table 26. Introduction of conserved point mutations characterized in rDEN4 viruses into rDEN2 Tonga/74 virus.
(Table Removed)
a Presence of the indicated mutation increases plaque size in Vero cells two-fold or greater than rDEN4 virus.
b Presence of the indicated mutation restricts replication in 7-day-old mouse brain greater than 100-fold compared to rDEN4 virus.
c Presence of the indicated mutation restricts replication in SCID-HuH-7 mice greater than 100-fold compared to rDEN4 virus.
d Amino acid position in DEN4 or DEN2 polyprotein beginning with the methionine residue of the C protein (nucleotides 102-104 or 97-99, respectively) as position 1.
e Primers were engineered which introduced (underline) translationally-silent restriction enzyme (RE) sites. Lowercase letters indicate nt changes and bold letters indicate the site of the 5-FU mutation, which in some oligonucleotides differs from the original nucleotide substitution change in order to create a unique RE site. The change preserves the codon for the amino acid substitution.
f Nucleotide substitution in the 3' UTR is U > C in DEN4 and DEN2 virus.
Table 27. rDEN2 viruses containing conserved 5-FU mutations are recovered in C6/36 cells.
(Table Removed)
EXAMPLE 4 Generation and Characterization of a Recombinant DEN3 Virus Containing the Δ30
Mutation
Because rDENlA30 was satisfactorily attenuated, we sought to extend our technology to the creation of a DEN3 vaccine candidate. To do this, the Δ30 mutation was introduced into the cDNA of DEN3, similar to the method used to create rDEN2A30. A DEN3 virus isolate from a 1978 dengue epidemic in rural Sleman, Central Indonesia (Sleman/78) (Gubler, D. J. et al. 1981 Am J Trop Med Hyg 30:1094-1099) was chosen to represent wt DEN3. The genome of DEN3 (Sleman/78) was sequenced in its entirety and served as consensus sequence for the construction of a full-length cDNA clone (Appendix 2). cDNA fragments of DEN3 (Sleman/78) were generated by reverse-transcription of the genome as indicated in Figure 8A. Each fragment was subcloned into a plasmid vector and sequenced to verify that it matched the consensus sequence as determined for the virus. This yielded six cloned cDNA fragments spanning the genome. Cloned fragments were modified as follows: Fragment 5, representing the 5' end of the genome was abutted to the SP6 promoter preceded by an Ascl restriction site; Fragment 1L was modified to contain a translationally-silent Spel restriction site at genomic nucleotide 2345; Fragment 1R was modified to contain a translationally-silent Spel restriction site also at genomic nucleotide 2345, and to stabilize the eventual full-length clone, three additional translationally-silent mutations at nucleotides 2354 - 2356, 2360 - 2362, and 2399 were created to ensure that translation stop codons were present in all reading frames other than that used to synthesize the virus polyprotein; Fragment 3 was modified at nucleotide 9007 to ablate a naturally occurring Kpnl restriction site; and Fragment 4,
representing the 3' end of the genome was abutted to a Kpnl restriction site. Each fragment was added incrementally between the Ascl and Kpnl restriction sites of DEN4 cDNA clone p4 (Durbin, A.P. et ah 2001 Am J Trop Med Hyg 65:405-13) to generate a full-length DEN3 cDNA clone with the same vector background successfully used to generate rDEN4 and rDEN2. However, a stable, full-length clone could not be recovered in E. coli when fragments 1L and 1R were combined into the same cDNA molecule. To overcome this instability, a synthetic DNA linker (Figure 8A) containing redundant termination codons in each of the forward and reverse open reading frames was introduced into the Spel restriction site at the same time that fragment 1L was added to complete the full-length cDNA construct. The resulting p3 clone containing the linker sequence was stable in E. coli, indicating that the linker sequence was sufficient to interrupt whatever deleterious element exists in this region. cDNA clone p3 was sequenced and the virus genome was found to match the DEN3 (Sleman/78) consensus sequence, with the exception of the linker sequence and translationally-silent modifications noted above (Appendix 2 - shown with the linker sequence removed). The Δ30 mutation was introduced into Fragment 4 to generate Fragment 4A30. To create p3Δ30, the Fragment 4 region of p3 was replaced with Fragment 4A30 (Figure 8A, B).
For transcription and generation of infectious virus, cDNA plasmids p3 and p3 Δ30 were digested with Spel and re-ligated to remove the linker sequence, linearized with Acc65l (isoschizomer of Kpnl which cleaves leaving only a single 3' nucleotide), and used as templates in a transcription reaction using SP6 RNA polymerase as previously described (Blaney, J. E. et. al. 2002 Virology 300:125-139). Transcripts were introduced into Vero cells or C6/36 mosquito cells using liposome-mediated transfection and cell culture supernatants were harvested on day 14.
rDEN3 virus was recovered from the p3 cDNA in both Vero and C6/36 cells, while rDEN330 was recovered from the p330 cDNA clone in only C6/36 cells (Table 28). The level of infectious virus recovered in C6/36 cells was comparable for the p3 and p3A30 cDNA clones when assayed by plaque titration in Vero or C6/36 cells. As previously observed, the efficiency of transfection in C6/36 cells was higher than that in Vero cells. Two rDEN3Δ30 viruses were recovered from independent cDNA clones, #22 and #41.
Table 28. rDEN3 virus is recovered in Vero and C6/36 cells, but rDEN3Δ30 virus is
recovered only in C6/36 cells.
(Table Removed)
To produce working stocks of viruses, transfection harvests will be passaged and terminally diluted in Vero cells, and genomic sequences of the viruses will be determined. To improve virus yield in Vero cells, the Vero cell adaptation mutation previously identified in rDEN4 at nucleotide 7162 was introduced into the homologous NS4B region of p3 and p3A30 to create p3-7164 and p3A30-7164. This mutation creates a Val to Ala substitution at amino acid position 2357. As demonstrated for rDEN2Δ30, this mutation allowed for the direct recovery of virus in Vero cells (Table 27) and is anticipated to have the same effect for rDEN3Δ30.
To initially assess the ability of the Δ30 mutation to attenuate rDEN3 virus in an animal model, the replication of DEN3 (Sleman/78), rDEN3, and rDEN3Δ30 viruses will be evaluated in SCID-HuH-7 mice and rhesus monkeys. Previously, attenuation of vaccine candidates in SCID-HuH-7 mice has been demonstrated to be predictive of attenuation in the rhesus monkey model of infection (Examples 1 and 2). The evaluation of these mutant rDEN3 viruses is contemplated as determining that the Δ30 deletion mutations can be transported into the DEN3 virus serotype and confer a similar useful phenotype, as has been demonstrated for DEN1, DEN2, and DEN4.
In summary, the strategy of introducing the Δ30 mutation into wild-type DEN viruses of each serotype to generate a suitably attenuated tetravalent vaccine formulation is a unique and attractive approach for several reasons. First, the mutation responsible for attenuation is a 30-nucleotide deletion in the 3' UTR, thus assuring that all of the structural and non-structural proteins expressed by each of the four components of the tetravalent vaccine are authentic wild-type proteins. Such wild-type proteins should elicit
an antibody response that is broad based, rather than based solely on the M and E proteins that are present in chimeric dengue virus vaccine candidates (Guirakhoo, F. et al. 2001 J Virol 75:7290-304; Huang, C.Y. et al. 2000 J Virol 74:3020-8). The uniqueness of this approach derives from the fact that other live attenuated dengue virus vaccines have mutations in their structural or non-structural proteins (Butrapet, S. et al. 2000 J Virol 74:3011-9; Puri, B. et al. 1997 J Gen Virol 78:2287-91), therefore the immune response induced by these viruses will be to a mutant protein, rather than a wild-type protein. Second, deletion mutations are genetically more stable than point mutations, and reversion of the attenuation phenotype is unlikely. In humans, DEN4Δ30 present in serum of vaccinees retained its Δ30 mutation, confirming its genetic stability in vivo (Durbin, A.P. et al. 2001 Am J Trop Med Hyg 65:405-13). The attenuating mutations in other existing dengue live attenuated vaccine candidates are based on less stable point mutations (Butrapet, S. et al. 2000 J Virol 74:3011-9: Puri, B. et al. 1997 J Gen Virol 78:2287-91). Third, since the Δ30 mutation is common to each of the four viruses of the tetravalent vaccine, recombination between any of the four vaccine serotypes would not lead to loss of the attenuating mutation or reversion to a wild-type phenotype. Recombination between components of the trivalent polio vaccine has been observed (Guillot, S. et al. 2000 J Virol 74:8434-43), and naturally occurring recombinant dengue viruses have been described (Worobey, M. et al. 1999 PNAS USA 96:7352-7) indicating the ability of this flavivirus to exchange genetic elements between two different viruses. Clearly, gene exchange is readily achieved between different DEN virus serotypes using recombinant cDNA techniques (Bray, M. and Lai, CJ. 1991 PNAS USA 88:10342-6). Fourth, viruses with wild-type structural proteins appear more infectious than viruses with altered structural proteins (Huang, C.Y. et al. 2000 J Virol 74:3020-80). This permits the use of a low quantity of each of the four virus components in the final vaccine, contributing to the low cost of manufacture. Low-cost manufacture is an essential element in defining the ultimate utility of a dengue virus vaccine.
EXAMPLE 5 Generation and Characterization of Intertypic Chimeric DEN2 Viruses Containing
the Δ30 Mutation
The four serotypes of dengue virus are defined by antibody responses induced by the structural proteins of the virus, primarily by a neutralizing antibody response to the envelope (E) protein. These structural proteins include the E glycoprotein, a membrane
protein (M), and a capsid (C) protein. The mature virus particle consists of a well-organized outer protein shell surrounding a lipid bilayer membrane and a less-well-defined inner nucleocapsid core (Kuhn, R.J. et al. 2002 Cell 108:717-25). The E glycoprotein is the major protective antigen and readily induces virus neutralizing antibodies that confer protection against dengue virus infection. An effective dengue vaccine must therefore minimally contain the E protein of all four serotypes, namely DEN1, DEN2, DEN3, and DEN4, thereby inducing broad immunity and precluding the possibility of developing the more serious illnesses DHF/DSS, which occur in humans during secondary infection with a heterotypic wild-type dengue virus. Based on a previously reported strategy (Bray, M. and Lai, C.J. 1991 PNAS USA 88:10342-6), a recombinant cDNA technology is being used to develop a live attenuated tetravalent dengue virus vaccine composed of a set of intertypic chimeric dengue viruses bearing the structural proteins of each serotype.
Following the identification of a suitably attenuated and immunogenic DEN4 recombinant virus, namely DEN4Δ30 (Durbin, A.P et al. 2001 Am J Trop Med Hyg 65:405-13), chimeric viruses based on the DEN4 cDNA have been generated in which the C-M-E (CME) or M-E (ME) genes have been replaced with the corresponding genes derived from the prototypic DEN2 New Guinea C (NGC) strain (Figure 9A). To create the CME chimeric viruses, the Bglll I Xhol region of the cDNA for either rDEN4 or rDEN4Δ30 was replaced with a similar region derived from DEN2. Likewise, to create the ME chimeric viruses, the Pstl I Xhol region of the cDNA for either rDEN4 or rDEN4Δ30 was replaced with a homologous region derived from DEN2. The nucleotide and amino acid sequences of the resulting junctions are shown in Figure 9B. The GenBank accession number for the nucleotide sequence of rDEN4Δ30 is AF326837. The GenBank accession number for DEN2 NGC is M29095, which represents the mouse neurovirulent strain of DEN2 NGC and differs from the prototypic strain used here as previously documented (Bray, M. et al. 1998 J Virol 72:1647-51).
For transcription and generation of virus, chimeric cDNA clones were linearized and used as template in a transcription reaction using SP6 RNA polymerase as described (Durbin, A.P et al. 2001 Am J Trop Med Hyg 65:405-13). Transcripts were introduced into Vero cells using liposome-mediated transfection and recombinant dengue virus was harvested on day 7. The genomes of the resulting viruses were confirmed by sequence analysis of viral RNA isolated from recovered virus as previously described (Durbin, A.P
et al. 2001 Am J Trop Med Hyg 65:405-13). Incidental mutations arising from virus passage in tissue culture were identified in all viruses and are listed in Table 29. Notably, each virus contained a missense mutation in NS4B corresponding to a previously identified mutation from rDEN4 and associated with adaptation to replication in Vero cells (See Table 30 for correlation of nucleotide positions between rDEN4 and chimeric viruses). All viruses replicated in Vero cells to titers in excess of 6.0 log10 PFU/ml, indicating that the chimeric viruses, even those containing the Δ30 mutation, replicate efficiently in cell culture, a property essential for manufacture of the vaccine. Table 29. Missense mutations observed among the Vero cell-grown chimeric DEN2/4
(Table Removed)
aSame nucleotide position as 7163 in rDEN4. bSame nucleotide position as 7546 in rDEN4.
Table 30. Nucleotide (nt) length differences for DEN chimeric viruses compared
to rDEN4.

(Table Removed)
Results of a safety, immunogenicity, and efficacy study in monkeys are presented in Table 31. Monkeys inoculated with wild-type DEN2 were viremic for approximately 5
days with a mean peak titer of 2.1 logio PFU/ml, while monkeys inoculated with any of the chimeric DEN2 viruses were viremic for 1.2 days or less and had a mean peak titer of less than 1.0 logio PFU/ml. This reduction in the magnitude and duration of viremia clearly indicates that the chimeric viruses containing either the CME or ME proteins of DEN2 were more attenuated than the parental DEN2 NGC virus. Neither the animals receiving the wild-type DEN2 nor the DEN2/4 chimeric viruses were ill. The decreased replication of the attenuated viruses in monkeys is accompanied by a reduction in the immune response of inoculated monkeys. This is indicated in Table 31 by approximately a 5-fold reduction in the level of neutralizing antibody following inoculation with the chimeric viruses in comparison to titers achieved in animals inoculated with wild-type virus. Addition of the Δ30 mutation to the CME chimeric virus further attenuated the virus, such that rDEN2/4Δ30(CME) did not replicate in monkeys to a detectable level and did not induce a detectable immune response. This virus appeared over-attenuated, and if similar results were seen in humans, this virus would not be suitable for use as a vaccine. However, addition of the Δ30 mutation to the ME chimeric virus did not further attenuate this chimeric virus and the resulting rDEN2/4Δ30(ME) virus appears satisfactorily attenuated and immunogenic for use as a vaccine.
Table 31. Chimerization between dengue virus types 2 and 4 results in recombinant viruses which are attenuated for rhesus monkeys.
(Table Removed)
* Rhesus monkeys were inoculated subcutaneously with 5.0 logio PFU of virus. Serum samples were collected daily for 10 days. Serum for neutralization assay was collected on day 28. Serum samples obtained before virus inoculation had a neutralizing antibody titer of As described in the previous examples, SCID mice transplanted with the HuH-7
cells are a sensitive model for the evaluation of dengue virus attenuation. Each chimeric
DEN2/4 virus was inoculated into groups of SCID-HuH-7 mice and levels of virus in the
serum were determined (Table 32). Chimeric viruses replicated to levels between 20- and
150-fold lower than either of the parental viruses (rDEN4 and DEN2-NGC). CME chimeric viruses were slightly more attenuated than the comparable ME chimeric viruses, with the Δ30 mutation providing a 0.5 logio reduction in replication. This level of attenuation exerted by the Δ30 mutation was similar to that observed previously for rDEN4Δ30.
Table 32. Chimerization between dengue virus types 2 and 4 results in recombinant viruses which are attenuated for HuH-7-SCID mice.
(Table Removed)
aGroups of HuH-7-SCID mice were inoculated into the tumor with 4.0 logio PFU of the indicated virus. Serum was collected on day 7 and virus titer was determined in Vero cells.
bMean peak titers were assigned to statistical groups using the Tukey post-hoc test (P To evaluate the replication levels of each DEN2/4 chimeric virus in mosquitoes, two different genera of mosquitoes were experimentally infected. Aedes aegypti were infected by ingesting a virus-containing blood meal. By evaluating the presence of virus antigen in both the midgut and head tissue, infectivity could be determined for the local tissues (midgut), and the ability of virus to disseminate and replicate in tissues beyond the midgut barrier (head) could also be measured. The presence of virus in the head is limited by the ability of the ingested virus to replicate in the midgut and then disseminate to the salivary glands in the head, as well as the innate ability of the virus to replicate in the salivary glands. Intrathoracic inoculation of virus into Toxorhynchites splendens bypasses the mosquito midgut barrier. Parental viruses rDEN4 and DEN2-NGC readily infect Ae. aegypti and T. splendens (Table 33), with DEN2-NGC appearing to be much more infectious in T. splendens. Each of the rDEN2/4 chimeric viruses was also tested in both mosquito types. In many cases it was not possible to inoculate Ae. aegypti with an undiluted virus stock of sufficient titer to achieve a detectable infection due to the very
low infectivity of several of the viruses. Nevertheless, it is clear that the rDEN2/4 chimeric viruses are less infectious for the midgut and head. Parental viruses rDEN4 and DEN2-NGC, administered at a maximum dose of approximately 4.0 logioPFU, were detectable in 74% and 94% of midgut preparations, and 32% and 71% of head preparations, respectively. Among the chimeric viruses, the highest level of infectivity, as observed for rDEN2/4Δ30(CME), resulted in only 26% infected midgut samples and 6% head samples. In the more permissive T. splendens, the rDEN2/4 chimeric viruses were generally less infectious than either parental virus, with CME chimeric viruses being less infectious than ME viruses. It has previously been reported for DEN4 that the Δ30 mutation does not have a discernable effect on virus infectivity in T. splendens similar to that observed here for the rDEN2/4 chimeric viruses (Troyer, J.M. et al. 2001 Am J Trop med hyg 65:414-419).
Table 33. Dengue 2/4 chimeric viruses are less infectious compared to either parental
virus strain in mosquitoes
(Table Removed)
a Amount of virus present in 0.22 u.1 inoculum.
b Percentage of mosquitoes with IFA detectable antigen in head tissue prepared 14 days after inoculation.
c Virus titer ingested, assuming a 2 p.1 bloodmeal.
Percentage of mosquitoes with IFA detectable antigen in midgut or head tissue prepared 21 days after oral infection. When virus infection was detected, but did not exceed a frequency of 50% at the highest dose of virus ingested, the MID50 was estimated by assuming that a 10-fold more concentrated virus dose would infect 100% of the mosquitoes.
enc = not calculated, since virus antigen was not detected.
Chimerization of the DEN2 structural genes with rDEN4Δ30 virus resulted in a virus, rDEN2/4Δ30(CME), that had decreased replication in Vero cells compared to either parent virus. To evaluate Vero cell adaptation mutations (Blaney, J. E. et al. 2002 Virology 300:125-139) as a means of increasing the virus yield of a DEN vaccine candidate in Vero cells, selected mutations were introduced into this chimeric virus. Accordingly, rDEN2/4Δ30(CME) viruses bearing adaptation mutations were recovered,
terminally diluted, and propagated in C6/36 cells to determine if the virus yield in Vero cells could be increased.
rDEN2/4Δ30(CME) viruses bearing Vero cell adaptation mutations were generated as follows. DNA fragments were excised from rDEN4 cDNA constructs encompassing single or double DEN4 Vero cell adaptation mutations and introduced into the cDNA clone of rDEN2/4Δ30(CME). The presence of the Vero cell adaptation mutation was confirmed by sequence analysis, and RNA transcripts derived from the mutant cDNA clones were transfected, terminally diluted, and propagated in C6/36 cells.
For evaluation of growth kinetics, Vero cells were infected with the indicated viruses at a multiplicity of infection (MOI) of 0.01. Confluent cell monolayers in duplicate 25-cm2 tissue culture flasks were washed and overlaid with a 1 ml inoculum containing the indicated virus. After a two hour incubation at 37°C, cells were washed three times in MEM and 5 ml of MEM supplemented with 2% FBS was added. A 1 ml aliquot of tissue culture medium was removed, replaced with fresh medium, and designated the day 0 time-point. At the indicated time points post-infection, 1 ml samples of tissue culture medium were removed, clarified by centrifugation, and frozen at -80°C. The level of virus replication was assayed by plaque titration in C6/36 cells and visualized by immunoperoxidase staining. The limit of detection was The growth properties of rDEN2/4Δ30(CME) viruses bearing single Vero cell adaptation mutations at NS4B -7153, -7162, -7163, -7182, NS5 -7630 or three combinations of mutations were compared in Vero cells with rDEN2/4Δ30(CME) virus (Figure 10). Without an introduced Vero cell adaptation mutation, rDEN2/4Δ30(CME) virus yield peaked at 4.4 logi0PFU/ml. Each individual adaptation mutation and the combined mutations conferred a substantial increase in replication. Specifically, rDEN2/4Δ30(CME)-7182 grew to the highest titer of 7.1 logioPFU/ml, which was a 500-fold increase in yield. rDEN2/4Δ30(CME)-7162 had the lowest yield but still was increased 125-fold over the level of replication by rDEN2/4Δ30(CME) virus. Introduction of two adaptation mutations into rDEN2/4Δ30(CME) virus did not significantly increase virus yield over that of viruses bearing single Vero cell adaptation mutations. The observed increase of up to 500-fold in virus yield by the introduction of a Vero cell adaptation mutation into this chimeric vaccine candidate demonstrates the value of identifying and characterizing specific replication-promoting sequences in DEN viruses.
These results have particular significance for the development of a live attenuated dengue virus vaccine. First, it is clear that chimerization leads to attenuation of the resulting virus, as indicated by studies in rhesus monkeys, HuH7-SCID mice and mosquitoes. Although this conclusion was not made in the previous study with DEN2/DEN4 or DEN1/DEN4 chimeric viruses (Bray, M. et al. 1996 J Virol 70:4162-6), careful examination of the data would suggest that the chimeric viruses are more attenuated in monkeys compared to the wild-type parent viruses. Second, the Δ30 mutation can further augment this attenuation in a chimeric-dependent manner. Specifically, in this example, chimeric viruses bearing the CME region of DEN2 were over-attenuated by the addition of Δ30, whereas the attenuation phenotype of chimeric viruses bearing just the ME region of DEN2 was unaltered by the addition of the Δ30 mutation. This unexpected finding indicates that in a tetravalent vaccine comprised of individual component viruses bearing a shared attenuating mutation, such as the Δ30 mutation, only ME chimeric viruses can be utilized since CME chimeric viruses bearing the Δ30 mutation can be over-attenuated in rhesus monkeys and might provide only limited immunogenicity in humans.
EXAMPLE 6 Generation and Characterization of Intertypic Chimeric DEN3 Viruses Containing
the Δ30 Mutation
Chimeric viruses based on the DEN4 cDNA have been generated in which the CME or ME genes have been replaced with the corresponding genes derived from DEN3 (Sleman/78), a virus isolate from the 1978 dengue outbreak in the Sleman region of Indonesia (Gubler, D.J. et al. 1981 Am J Trop MedHyg 30:1094-1099) (Appendix 2). As described in Example 5 for the DEN2 chimeric viruses, CME chimeric viruses for DEN3 were generated by replacing the BgHl I Xhol region of the cDNA for either rDEN4 or rDEN4Δ30 with a similar region derived from DEN3 (Sleman/78) (Figure 11A). Likewise, to create the ME chimeric viruses, the Pstl I Xhol region of the cDNA for either rDEN4 or rDEN4Δ30 was replaced with a similar region derived from DEN3 (Sleman/78). The nucleotide and amino acid sequences of the resulting junctions are shown in Figure 1 IB. The genomes of the resulting viruses were confirmed by sequence analysis of viral RNA isolated from recovered virus as previously described (Durbin, A.P et al. 2001 Am J Trop Med Hyg 65:405-13). Incidental mutations arising from virus passage in tissue culture were identified in all viruses and are listed in Table 34. Notably,
each virus contained a missense mutation in NS4B corresponding to a previously identified mutation from rDEN4 and associated with adaptation to growth in Vero cells (See Table 30 for correlation of nucleotide positions between rDEN4 and chimeric viruses). All viruses replicated in Vero cells to titers in excess of 5.7 log10 PFU/ml, indicating that the chimeric viruses, even those containing the Δ30 mutation, replicate efficiently in cell culture, a property essential for manufacture of the vaccine.
Table 34. Missense mutations observed among Vero cell-grown chimeric DEN3/4
Viruses
(Table Removed)
aSame nucleotide position as 7162 in rDEN4. bSame nucleotide position as 7183 in rDEN4.
As described in the previous examples, SCID mice transplanted with HuH-7 cells are a sensitive model for the evaluation of dengue virus attenuation. Each chimeric DEN3/4 virus was inoculated into groups of SCID-HuH-7 mice and levels of virus in the serum were determined (Table 35). While chimeric virus rDEN3/4 (CME) was not attenuated, the remaining chimeric viruses replicated to levels between 40- and 400-fold lower than either of the parental viruses (rDEN4 and DEN3-Sleman/78). In the CME chimeric virus, the Δ30 mutation providing a remarkable 2.7 logio reduction in replication. This level of attenuation conferred by the Δ30 mutation in the CME chimeric virus was much greater than that observed previously for rDEN4Δ30. The rDEN3/4 (ME) virus was 100-fold reduced in replication compared to either parent virus indicating that the ME chimerization was attenuating per se. Addition of the Δ30 mutation to rDEN3/4 (ME) did not result in additional attenuation.
Table 35. Chimerization between dengue virus types 3 and 4 results in recombinant viruses which are attenuated for HuH-7-SCID mice.

(Table Removed)
aGroups of HuH-7-SCID mice were inoculated into the tumor with 4.0 logio PFU of the indicated virus. Serum was collected on day 7 and virus titer was determined in Vero cells.
bMean peak titers were assigned to statistical groups using the Tukey post-hoc test (P Evaluation of the replication and immunogenicity of the DEN3 chimeric recombinant viruses and wild-type DEN3 virus in monkeys was performed as described in Example 5. Results of this safety and immunogenicity study in monkeys are presented in Table 36. Monkeys inoculated with rDEN3/4(CME) and wild-type DEN (Sleman/78) were viremic for approximately 2 days with a mean peak titer of between 1.6 and 1.8 logio PFU/ml, respectively, indicating that chimerization of the CME structural genes of DEN3 did not lead to attenuation of virus replication, a different pattern than that observed for DEN2 chimerization (Table 31). However, chimerization of the ME structural genes resulted in attenuated viruses with undetectable viremia in monkeys, although all monkeys seroconverted with a greater than 10-fold increase in serum antibody levels. As expected for an attenuated virus, the immune response, as measured by neutralizing antibody titer, was lower following inoculation with any of the chimeric viruses compared to inoculation with wt DEN3 (Sleman/78), yet sufficiently high to protect the animals against wt DEN3 virus challenge (Table 37). It is clear that addition of the Δ30 mutation to rDEN3/4(CME) was capable of further attenuating the resulting virus rDEN3/4A30(CME).
Table 36. The Δ30 mutation further attenuates rDEN3/4(CME) for rhesus monkeys

(Table Removed)
a Groups of rhesus monkeys were inoculated subcutaneously with 105 PFU of the indicated virus in a 1 ml dose. Serum was collected on days 0 to 6, 8, 10, 12, and 28. Virus titer was determined by plaque assay in Vero cells.
b Viremia was not detected in any monkey after day 4.
Table 37. rDEN3/4 chimeric viruses protect rhesus monkeys from wt DEN3 virus
challenge

(Table Removed)
a 28 days after primary inoculation with the indicated viruses, rhesus monkeys were challenged subcutaneously with 105 PFU DEN3 (Sleman/78) virus in a 1 ml dose. Serum was collected on days 28 to 34, 36, 38, and 56. Virus titer was determined by plaque assay in Vero cells.
To evaluate the replication levels of each DEN3/4 chimeric virus in mosquitoes, Aedes aegypti were infected by ingesting a virus-containing blood meal (Table 38). Parental viruses rDEN4 and DEN3 (Sleman/78) readily infect Ae. aegypti. Each of the rDEN3/4 chimeric viruses was also tested. In many cases it was not possible to infect Ae. aegypti with an undiluted virus stock of sufficient titer to achieve a detectable infection due to the very low infectivity of several of the viruses. At a dose of approximately 2.8 -
2.9 log10PFU, rDEN4, DEN3 (Sleman/78), and rDEN3/4(CME) were equally infectious and disseminated to the head with equal efficiency. For the remaining chimeric viruses, infection was not detectable even at a dose of 3.4 logioPFU, indicating that replication of rDEN3/4(ME) and rDEN3/4A30(CME) is restricted in Ae. aegypti. By comparing infectivity of rDEN3/4(CME) and rDEN3/4A30(CME), it is clear that the Δ30 mutation is capable of further attenuating the chimeric virus for mosquitoes. Table 38. Ability of DEN3/4 chimeric viruses to infect Aedes aegypti fed an infectious
bloodmeal.
(Table Removed)
a Amount of virus ingested, assuming a 2|n bloodmeal.
b Number (percentage) of mosquitoes with detectable dengue virus in midgut tissue; mosquitoes were assayed 21 days post feed, and dengue virus antigen was identified by I FA.
c When infection was detected, but did not exceed a frequency of 50% at the highest dose of virus ingested, the MID50 was estimated by assuming that a 10-fold more concentrated virus dose would infect 100% of the mosquitoes.
d When no infection was detected, the MID50 was assumed to be greater than a 10-fold higher dose of virus than the one used.
e Number (percentage) of mosquitoes with detectable dengue virus antigen in both midgut and head tissue.
EXAMPLE 7 Generation and Characterization of Intertypic Chimeric DENl Viruses Containing
the Δ30 Mutation

Chimeric viruses based on the DEN4 cDNA have been generated in which the CME or ME genes have been replaced with the corresponding genes derived from DENl (Puerto Rico/94), a virus isolate from a 1994 dengue outbreak in Puerto Rico (Appendices 3 and 4). As described in Example 4 for the DEN2 chimeric viruses, CME chimeric viruses for DENl were generated by replacing the BgUl I Xhol region of the cDNA for either rDEN4 or rDEN4Δ30 with a similar region derived from DENl (Puerto Rico/94) (Figure 12A). Likewise, to create the ME chimeric viruses, the Pstl I Xhol region of the cDNA for either rDEN4 or rDEN4Δ30 was replaced with a similar region derived from DENl (Puerto Rico/94). The nucleotide and amino acid sequences of the resulting junctions are shown in Figure 12B.
For transcription and generation of virus, chimeric cDNA clones were linearized and used as template in a transcription reaction using SP6 RNA polymerase as described. Transcripts were introduced into C6/36 mosquito cells using liposome-mediated transfection and recombinant dengue virus was harvested between day 7 and 14. Viruses were subsequently grown in Vero cells and biologically cloned by terminal dilution in Vero cells. All viruses replicated in Vero cells to titers in excess of 6.0 logio PFU/ml, indicating that the chimeric viruses, even those containing the Δ30 mutation, replicate efficiently in cell culture. Genomic sequence analysis is currently underway to identify incidental mutations arising from virus passage in tissue culture.
To evaluate the replication levels of DEN1/4(CME) and rDENl/4A30(CME) chimeric virus in mosquitoes, Aedes aegypti were infected by ingesting a virus-containing blood meal (Table 39). Parental virus rDEN4 infects Ae. aegypti with an MID50 of 4.0 logioPFU. However, parental virus DENl(Puerto Rico/94), is unable to infect Ae. aegypti at a dose of up to 3.4 log10PFU. Thus CME chimeric viruses DEN 1/4 and rDENl/4A30 share this inability to infect Ae. aegypti. Therefore, it is unnecessary in Ae. aegypti to evaluate the effect of the Δ30 mutation on the infectivity of the DEN1/4 chimeric viruses, in a manner similar to that used for the DEN2/4 and DEN3/4 chimeric viruses.
Table 39. Inability of DEN 1/4 chimeric viruses to infect Aedes aegypti fed an infectious
bloodmeal.
(Table Removed)
aAmount of virus ingested, assuming a 2µl bloodmeal.
'Number (percentage) of mosquitoes with detectable dengue virus in midgut tissue; mosquitoes were assayed 21 days post feed, and dengue virus antigen was identified by IFA.
cWhen infection was detected, but did not exceed a frequency of 50% at the highest dose of virus ingested, the MID50 was estimated by assuming that a 10-fold more concentrated virus dose would infect 100% of the mosquitoes.
d When no infection was detected, the MID50 was assumed to be greater than a 10-fold higher dose of virus than the one used.
Number (percentage) of mosquitoes with detectable dengue virus antigen in both midgut and head tissue.
As described in the previous examples, SCID mice transplanted with the HuH-7 cells are a sensitive model for the evaluation of dengue virus attenuation. Each chimeric DENl/4 virus was inoculated into groups of SCID-HuH-7 mice and levels of virus in the serum were determined (Table 40). Chimeric viruses replicated to levels between 15- and 250-fold lower than either of the parental viruses, rDEN4 and DEN1 (Puerto Rico/94). CME chimeric viruses were more attenuated than the comparable ME chimeric viruses, with the Δ30 mutation providing a 0.8 logio reduction in replication. This level of attenuation exerted by the Δ30 mutation in the CME chimeric viruses was similar to that observed previously for rDEN4Δ30. However, the attenuating effect of the Δ30 mutation in the ME chimeric viruses is indiscernible.
Table 40. Chimerization between dengue virus types 1 and 4 results in recombinant viruses which are attenuated for HuH-7-SCID mice.
(Table Removed)
"Groups of HuH-7-SCID mice were inoculated into the tumor with 4.0 logio PFU of the indicated virus. Serum was collected on day 7 and virus titer was determined in Vero cells.
bMean peak titers were assigned to statistical groups using the Tukey post-hoc test (P APPENDIX 1 Nucleotide and amino acid sequence of DEN2 (Tonga/74) cDNA plasmid p2
(Sequence Removed)
APPENDIX 2 Nucleotide and amino acid sequence of DEN3 (Sleman/78) cDNA plasmid p3
(Sequence Removed)
APPENDIX 3
Nucleotide and amino acid sequence of DEN1 (Puerto Rico/94) CME chimeric region
(Sequence Removed)
APPENDIX 4 Nucleotide and amino acid sequence of DEN 1 (Puerto Rico/94) ME chimeric region
(Sequence Removed)
While the present invention has been described in some detail for purposes of clarity and understanding, one skilled in the art will appreciate that various changes in form and detail can be made without departing from the true scope of the invention. All figures, tables, appendices, patents, patent applications and publications, referred to above, are hereby incorporated by reference.





WE CLAIM:
1. A dengue tetravalent vaccine containing a common 30 nucleotide deletion in the 3' untranslated region of dengue types 1, 2, 3, and 4 comprising a nucleic acid comprising a first nucleotide sequence encoding at least one structural protein from a first dengue virus and a second nucleotide sequence encoding nonstructural proteins from a second dengue virus, wherein the second dengue virus is attenuated by a deletion of about 30 nucleotides from the 3' untranslated region of the dengue genome corresponding to the TL2 stem-loop structure, optionally comprising a mutation as described herein.
2. A dengue tetravalent vaccine as claimed in Claim 1, wherein the nucleic acid further comprises a mutation generating a mutant having a phenotype wherein the phenotype is temperature sensitive in Vero cells or the human liver cell line HuH-7, host-cell restriction in mosquito cells or the human liver cell line HuH-7, host-cell adaptation for improved replication in Vero cells, or attenuation in mice or monkeys.
3. A dengue tetravalent vaccine as claimed in Claim 1 or 2, wherein the serotype of the first dengue virus is the same as the serotype of the second dengue virus.
4. A dengue tetravalent vaccine as claimed in Claim 3, wherein the serotype is type 1.
5. A dengue tetravalent vaccine as claimed in Claim 4, wherein the deletion is a deletion of about 30 nucleotides from the 3' untranslated region of the dengue type 1 genome corresponding to the TL2 stem-loop structure between about nucleotides 10562-10591.
6. A dengue tetravalent vaccine as claimed in Claim 3, wherein the serotype is type 2.
7. A dengue tetravalent vaccine as claimed in Claim 6, wherein the deletion is a deletion of about 30 nucleotides from the 3' untranslated region of the dengue type 2 genome corresponding to the TL2 stem-loop structure between about nucleotides 10541-10570.
8. A dengue tetravalent vaccine as claimed in Claim 3, wherein the serotype is type 3.
9. A dengue tetravalent vaccine as claimed in Claim 8, wherein the deletion is by a deletion of about 30 nucleotides from the 3' untranslated region of the dengue type 3 genome corresponding to the TL2 stem-loop structure between about nucleotides 10535-10565.
10. A dengue tetravalent vaccine as claimed in Claim 3, wherein the serotype is type 4.
11. A dengue tetravalent vaccine as claimed in Claim 10, wherein the deletion is a deletion of about 30 nucleotides from the 3' untranslated region of the dengue type 4 genome corresponding to the TL2 stem-loop structure between about nucleotides 10478-10507.
12. A dengue tetravalent vaccine as claimed in Claim 1 or 2, wherein the serotype of the first dengue virus is different from the serotype of the second dengue virus and wherein nucleic acid is a nucleic acid chimera.
13. A dengue tetravalent vaccine as claimed in Claim 12, wherein the serotype of the second dengue virus having the deletion is type 1.
14. A dengue tetravalent vaccine as claimed in Claim 13, wherein the serotype of the first dengue virus is type 2.
15. A dengue tetravalent vaccine as claimed in Claim 13, wherein the serotype of the first dengue virus is type 3.
16. A dengue tetravalent vaccine as claimed in Claim 13, wherein the serotype of the first dengue virus is type 4.
17. A dengue tetravalent vaccine as claimed in any of Claims 13-16, wherein the first nucleotide sequence encodes at least two structural proteins of the first dengue virus.
18. A dengue tetravalent vaccine as claimed in Claim 17, wherein the structural proteins are prM and E proteins.
19. A dengue tetravalent vaccine as claimed in any of Claims 13-18, wherein the deletion is a deletion of about 30 nucleotides from the 3' untranslated region of the dengue type 1 genome corresponding to the TL2 stem-loop structure between about nucleotides 10562 and 10591.
20. A dengue tetravalent vaccine as claimed in Claim 12, wherein the serotype of the second dengue virus having the deletion is type 2.
21. A dengue tetravalent vaccine as claimed in Claim 20, wherein the serotype of the first dengue virus is type 1.
22. A dengue tetravalent vaccine as claimed in Claim 20, wherein the serotype of the first dengue virus is type 3.
23. A dengue tetravalent vaccine as claimed in Claim 20, wherein the serotype of the first dengue virus is type 4.
24. A dengue tetravalent vaccine as claimed in any of Claims 20-23, wherein the first nucleotide sequence encodes at least two structural proteins of the first dengue virus.
25. A dengue tetravalent vaccine as claimed in Claim 24, wherein the structural proteins are prM and E proteins.
26. A dengue tetravalent vaccine as claimed in any of Claims 20-25, wherein the deletion is a deletion of about 30 nucleotides from the 3' untranslated region of the dengue type 2 genome corresponding to the TL2 stem-loop structure between about nucleotides 10541 and 10570.
27. A dengue tetravalent vaccine as claimed in Claim 12, wherein the serotype of the second dengue virus having the deletion is type 3.
28. A dengue tetravalent vaccine as claimed in Claim 27, wherein the serotype of the first dengue virus is type 1.
29. A dengue tetravalent vaccine as claimed in Claim 27, wherein the serotype of the first dengue virus is type 2.
30. A dengue tetravalent vaccine as claimed in Claim 27, wherein the serotype of the first dengue virus is type 4.
31. A dengue tetravalent vaccine as claimed in any of Claims 27-30, wherein the first nucleotide sequence encodes at least two structural proteins of the first dengue virus.
32. A dengue tetravalent vaccine as claimed in Claim 31, wherein the structural proteins are prM and E proteins.
33. A dengue tetravalent vaccine as claimed in any of Claims 27-32, wherein the deletion is a deletion of about 30 nucleotides from the 3' untranslated region of the dengue type 3 genome corresponding to the TL2 stem-loop structure between about nucleotides 10535 and 10565.
34. A dengue tetravalent vaccine as claimed in Claim 12, wherein the serotype of the second dengue virus having the deletion is type 4.
35. A dengue tetravalent vaccine as claimed in Claim 34, wherein the serotype of the first dengue virus is type 1.
36. A dengue tetravalent vaccine as claimed in Claim 34, wherein the serotype of the first dengue virus is type 2.
37. A dengue tetravalent vaccine as claimed in Claim 34, wherein the serotype of the first dengue virus is type 3.
38. A dengue tetravalent vaccine as claimed in any of Claims 34-37, wherein the first nucleotide sequence encodes at least two structural proteins of the first dengue virus.
39. A dengue tetravalent vaccine as claimed in Claim 38, wherein the structural proteins are prM and E proteins.
40. A dengue tetravalent vaccine as claimed in any of Claims 34-39, wherein the deletion is a deletion of about 30 nucleotides from the 3' untranslated region
of the dengue type 4 genome corresponding to the TL2 stem-loop structure between about nucleotides 10478 and 10507.
41. A dengue tetravalent vaccine as claimed in any of Claims 1-40 wherein the one or more nucleic acid or nucleic acid chimera comprises a virus or virus chimera.
42. A dengue tetravalent vaccine as claimed herein above, optionally comprising a mutation selected from the group consisting of temperature sensitivity in Vero cells or the human liver cell line HuH-7, host-cell restriction in mosquito cells or the human liver cell line HuH-7, host-cell adaptation for improved replication in Vero cells, or attenuation in mice or monkeys, the composition comprising a member selected from the group consisting of:
(Sequence Removed)
wherein the ratio of the constituents of the composition is an amount that is safe and immunogenic for each particular serotype and is about 25% of each of the four constituents
43. A dengue tetravalent vaccine as substantially herein before described.

Documents:

3450-delnp-2004-abstract.pdf

3450-delnp-2004-assignment.pdf

3450-delnp-2004-claims.pdf

3450-delnp-2004-complete specification (as files).pdf

3450-delnp-2004-complete specification (granted).pdf

3450-DELNP-2004-Correspondence Others-(10-10-2011).pdf

3450-delnp-2004-correspondence-others.pdf

3450-delnp-2004-correspondence-po.pdf

3450-delnp-2004-drawings.pdf

3450-delnp-2004-form-1.pdf

3450-delnp-2004-form-13.pdf

3450-delnp-2004-form-19.pdf

3450-delnp-2004-form-2.pdf

3450-delnp-2004-form-26.pdf

3450-delnp-2004-form-3.pdf

3450-delnp-2004-form-5.pdf

3450-delnp-2004-pct-101.pdf

3450-delnp-2004-pct-210.pdf

3450-delnp-2004-pct-220.pdf

3450-delnp-2004-pct-304.pdf

3450-delnp-2004-pct-306.pdf

3450-delnp-2004-petition-137.pdf


Patent Number 242661
Indian Patent Application Number 3450/DELNP/2004
PG Journal Number 37/2010
Publication Date 10-Sep-2010
Grant Date 03-Sep-2010
Date of Filing 05-Nov-2004
Name of Patentee THE GOVERNMENT OF THE UNITED STATES OF AMERICA
Applicant Address NATIONAL INSTITUTE OF HEALTH, OFFICE OF TECHNOLOGY TRANSFER, 6011 EXECUTIVE BLVD., SUITE 325, ROCKVILLE, MD 20852-3804, U.S.A
Inventors:
# Inventor's Name Inventor's Address
1 WHITEHEAD, STEPHEN, S 7 PRAIRIE ROSE LANE GAITHERSBURG, MD 20878 (US)
2 MARKOFF, LEWIS 6908 NEVIS ROAD BETHESDA, MD 20817 (US)
3 HANLEY, KATHRYN 8003 NEWDALE ROAD BETHESDA, MD 20814 (US)
4 MURPHY, BRIAN, R 5410 TUSCAWARUS ROAD BETHESDA, MD 20816 (US)
5 FLAGOUT, BARRY 4929 WATERFOWL WAY ROCKVILLE, MD 20853 (US)
6 BLANEY, JOSEPH 8206 BLUE HERON DRIVE, UNIT 1D FREDERICK, MD 21701 (US)
PCT International Classification Number A61K
PCT International Application Number PCT/US2003/13279
PCT International Filing date 2003-04-25
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 60/377,860 2002-05-03 U.S.A.
2 60/436,500 2002-12-23 U.S.A.