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(12) United States Patent (10) Patent No.: US 8,158,418 B2 Polo Et Al

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(12) United States Patent (10) Patent No.: US 8,158,418 B2 Polo Et Al USOO8158418B2 (12) United States Patent (10) Patent No.: US 8,158,418 B2 Polo et al. (45) Date of Patent: *Apr. 17, 2012 (54) CHIMERICALPHAVIRUS REPLICON Frolova et al., “Packaging Signals in Alphaviruses,” Journal of Virol PARTICLES ogy, vol. 71, No. 1, 1997, pp. 248-258. Kim et al., "Adaptive Mutations in Sindbis Virus E2 and Ross River (75) Inventors: John Polo, Encinitas, CA (US); Silvia Virus El That Allow Efficient Budding of Chimeric Viruses,” Journal of Virology, vol. 74, No. 6, 2000, pp. 2663-2670. Perri, Castro Valley, CA (US); Kent Lopez et al., “Nucleocapsid-Glycoprotein Interactions Required for Thudium, Oakland, CA (US) Assembly of Alpha Virus,” Journal of Virology, vol. 68, No. 3, 1994, pp. 1316-1323. (73) Assignee: Novartis Vaccines & Diagnostics Inc., Smerdou et al., “Alpha Virus Vectors: From Protein Production to Emeryville, CA (US) Gene Therapy.” Gene Therapy and Regulation, vol. 1, No. 1, 2000, pp. 33-63. (*) Notice: Subject to any disclaimer, the term of this Berglundet al., “Enhancing Immune Responses Using Suicidal DNA patent is extended or adjusted under 35 Vaccines.” Nat. Biotech, vol. 16, 1998, pp. 562-565. U.S.C. 154(b) by 0 days. Berglund et al., “Immunization With Recombinant Semliki Forest Virus Induces Protein Against Influenza Challenge in Mice.” Vac This patent is Subject to a terminal dis cine, vol. 17, 1999, pp. 497-507. claimer. Davis et al., “Vaccination of Macaques Against Pathogenic Simian Immunodeficiency Virus With Venezuelan Equine Encephalitis Virus (21) Appl. No.: 12/372,295 Replicon Particles,” Journal of Virology, vol. 74, 2000, 371-378. Dubensky et al., “Sindbis Virus DNA-Based Expression Vectors: (22) Filed: Feb. 17, 2009 Utility for in Virto and in Vivo Gene Transfer.” Journal of Virology, vol. 70, 1996, pp. 508-519. (65) Prior Publication Data Hariharan et al., “DNA Immunization Against Herpes Simplex Virus: US 2009/0305344 A1 Dec. 10, 2009 Enhanced Efficiancy Using Sindbis Virus-Based Vector.” Journal of Virology, vol. 72, 1998, 950-958. Related U.S. Application Data Liljestrom et al., “A New Generation of Animal Cell Expression Vectors Based on the Semliki Forest Virus Replicon.” Bio/Technol (62) Division of application No. 10/123,101, filed on Apr. ogy, vol. 9, 1991, pp. 1356-1361. 11, 2002, now Pat. No. 7,531,180. Polo et al., "Stable Alphavirus Packaging Cell Lines for Sindbis Virus and Semilki Forest Virus-Derived Vectors.” PNAS, vol. 96, (60) Provisional application No. 60/295,451, filed on May 1999, pp. 4598-4603. 31, 2001. Pushko et al., “Replicon-Helper Systems From Attenuated Venezu elan Equine Encephalitis Virus: Expression of Heterologous Genes in (51) Int. Cl. Vitro and Immunization Against Heterologous Pathogens in Vivo.” CI2N 5/10 (2006.01) Virology, vol. 239, 1997, pp. 389-401. CI2N 15/86 (2006.01) Schlesinger et al., “Alphavirus Vectors for Gene Expression and CI2N 5/64 (2006.01) Vaccines.” Curr: Opin. Biotechnol., vol. 10, 1999, pp. 434-439. (52) U.S. Cl. .................... 435/325; 435/235.1: 435/69.1; Xiong et al., “Sindbis Virus: An Efficient, Broad Host Range Vector 435/69.3; 435/456; 435/320.1 for Gene Expression in Animal Cells.” Science, vol. 243, 1989, pp. (58) Field of Classification Search ........... ... None 1188-1191. See application file for complete search history. Kuhn et al., “Chimeric Sindbis-Ross River Viruses to Study Interac tions Between Alphavirus Nonstructural and Structural Regions.” (56) References Cited Journal of Virology, vol. 70, No. 11, 1996, pp. 7900-7909. Schoepp et al., “Recombinant Chimeric Western and Eastern Equine U.S. PATENT DOCUMENTS Encephalitis Viruses as Potential Vaccine Canidates.” Virology, vol. 5,789,245 A 8/1998 Dubensky, Jr. et al. 302, 2002, 299-309. 5,842,723 A 12/1998 Hartling et al. Smyth et al., “Efficient Multiplications of a Semliki Forest Virus 5,843,723 A 12/1998 Dubensky, Jr. et al. Chimera Containing Sindbis Virus Spikes,” Journal of Virology, vol. 6,015,686 A 1/2000 Dubensky, Jr. et al. 71, No. 1, 1997, pp. 818-823. 6,015,694 A 1/2000 Dubensky, Jr. et al. 6,184,024 B1 2/2001 Lai et al. (Continued) 6,261,570 B1* 7/2001 Parker et al. ............... 424,205.1 7,572,453 B2 * 8/2009 Polo et al. .................. 424,199.1 Primary Examiner — Mary E. Mosher 20090304745 A1 12, 2009 Polo (74) Attorney, Agent, or Firm — Regina Bautista; Helen Lee FOREIGN PATENT DOCUMENTS WO WO95/07994 3, 1995 (57) ABSTRACT WO WO97,38087 10, 1997 Chimeric alphaviruses and alphavirus replicon particles are WO WO 98.37911 9, 1998 WO WO 98,53077 11, 1998 provided, including methods of making and using same. Spe WO WO99, 18226 4f1999 cifically, alphavirus particles are provided having nucleic acid molecules derived from one or more alphaviruses and OTHER PUBLICATIONS structural proteins (capsid and/or envelope) from at least two London et al (PNAS 89: 207-211, 1992).* or more alphaviruses. Methods of making, using, and thera Lopez et al (Journal of Virology 68:13.16-1323, 1994; in IDS).* peutic preparations containing the chimeric alphavirus par Frolov et al., “Sindbis Virus Replicons and Sindbis Virus: Assembly ticle, are disclosed. of Chimeras and of Particles Deficient in Virus RNA.” Journal of Virology, vol. 74, No. 4, 1997, pp. 2819-2829. 11 Claims, 13 Drawing Sheets US 8,158,418 B2 Page 2 OTHER PUBLICATIONS Davis et al., “In Vitro Synthesis of Infection Venezuelan Equine Encephalitis Virus RNA From a cDNA Clone: Anaylsis of a Viable Strauss et al., “The Alphaviruses: Gene Expression, Replication, and Deletion Mutant.” Virology, vol. 171, 1989, pp. 189-204. Evolution.” Microbiological Reviews, vol. 58, No. 3, 1994, pp. 491 Lee et al., “Identification of a Protein Binding Site on the Surface of 562. the Alphavirus Nucleocapsid and Its Implication in Virus Assembly.” White et al., “Deletion Analysis of a Defective Interfering Semliki Structure, vol. 4, 1996, pp. 431-531. Forest Virus RNA Genome Defines a Region in the nsP2 Sequence Owen et al., “Identification of a Region in the Sindbis Virus That is Required for Efficient Packaging of the Genome Into Virus Nucleocapsid Protein That Is Involved in the Specificity of RNA Particles.” Virology, vol. 72, No. 5, 1998, pp. 4320-4326. Encapsidation.” Journal of Virology, vol. 75, No. 5, 1996, pp. 2757 Fields et al., “Alphaviruses.” Virology, (Third Edition), 1996, pp. 2763. 843-848. Weiss et al., “Interactions Between Sindbis Virus RNAS and a 68 London et al., “Infectious Enveloped RNA Virus Antigenic Chime Amino Acid Derivative of the Viral Capsid Protein Further Defines ras.” Proc. Natl. Acad. Sci., vol. 89, 1992, pp. 207-211. the Capsid Binding Site.” Nucleic Acids Research, vol. 22, No. 5, Duggan et al., “Isolation of Single-Chain Antibody Fragments 1994, pp. 780-786. Against Venezuelan Equine Encephalomyelitis Virus From Two Dif Gardner et al., “Infection of Human Dendrtitic Cells by a Sindbis ferent Immune Sources.” Viral Immunology, vol. 14, No. 3, 2001, pp. Virus Replicon Vector Is Determined by a Single Amino Acid Sub 263-273. stitution in the E2 Glycoprotein.” Journal of Virology, vol. 74, No. 24. Geigenmuller-Gnirke et al., “Deletion Analysis of the Capsid Protein 2000, pp. 11849-11857. of Sindbis Virus: Indentification of the RNA Binding Region.” Jour Biosafety in Microbiological and Biomedical Laboratories, 5th Ed. nal of Virology, vol. 67, No. 3, 1993, pp. 263-273. U.S. DHHS, Public Health Service, Centers for Disease Control and Guirakhoo et al., “Construction Safety, and Immmunogencity in Prevention, National Institutes of Health. HHS Pub. No. (CDC) Nonhuman Primates of a Chimeric Yellow Fever-Dengue Virus 21/11 12, Revised Dec. 2009, 233-267. Tetravalent Vaccine.” Journal of Virology, vol. 75, No. 16, 2001, pp. Vihinen et al., “Elimination of phosphorylation sites of Semliki For T290-7304. est virus replicase protein nsP3.” J Biol Chem. Feb. 2001. Monath et al., “Chimeric Yellow Fever Virus 17D-Japanese 23:276(8):5745-5752. Encephalitis Virus Vaccine: Dose-Response Effectiveness and Zhou et al., “Self-replicating Semliki Forest virus RNA as recombi Extended Safety Testing in Rhesus Monkeys,” Journal of Virology, nant vaccine.” Vaccine. Dec. 1994; 12(16): 1510-4. vol. 74, No. 4, 2000, pp. 1742-1751. Cheng et al., "Nucleocapsid and glycoprotein organization in an Powers et al., “The Use of Chimeric Venezuelan Equine Encephalitis enveloped virus.” Cell. Feb. 24, 1995:80(4):621-630. Viruses as an Approach for the Molecular Identification of Natural Barth et al., “Alphavirus assembly and entry: role of the cytoplasmic Virulence Determinants.” Journal of Virology, vol. 74, No. 9, 2000, tail of the E1 spike subunit.” JVirol. Dec. 1992;66(12):7560-4. pp. 4258-4263. Oberste et al., "Complete sequence of Venezuelan equine encephali Yao et al., “Interactions Between PE2, E1, and 6K Required for tis virus Subtype IE reveals conserved and hypervariable domains Assembly of Alphaviruses Studied With Chimeric Viruses,” Journal within the C terminus of nsP3, Virology. May 1, 1996:219(1):314 of Virology, vol. 70, No. 11, 1996, pp. 7910-7920. 20. Van Der Most et al., “Chimeric Yellow Fever/Dengue Virus. As a Driver et al., “Plasmid DNA-based alphavirus expression vectors for Candidate Dengue Vaccine: Quanitation of the Dengue Virus-Spe nucleic acid immunization.”IDrugs. Oct. 1998;1(6):678-85. cific CD8 T-Cell Response.” Journal of Virology, vol. 74, No. 17. 2000, pp. 8094-8101. * cited by examiner U.S. Patent Apr. 17, 2012 Sheet 1 of 13 US 8,158,418 B2 (6719)|uueW G: U.S. Patent Apr. 17, 2012 Sheet 2 of 13 US 8,158,418 B2 VEE FRAGMENT #2 (HpaI659-BciVI 1344; ANSP1) 656 CTAGAGTTA ACGGCTCGTA ACATAGGCCT ATGCAGCTCT GACGTTATGG TCAA TGCCGAGCAT TGTATCCGGA TACGTCGAGA CTGCAATACC WEE 2 - 26 EE 2 as 25 AGCGGTCAC TAGAGGGATG CCACA GAAAGAAGTA GAAACCA TCGCCAGGC ATCTCCCTAC AGGTAAGAA CTCCAAAACGG 756 TCCAACAATG TTCTAITC C TGGGCCG ACCACACC ACGAGAAGAG.
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