IP Library › Granted Patent US 12,186,363
Granted Patent B2
US 12,186,363 · App. 17/478,537 · Granted Jan 7, 2025

Compositions and methods for dengue virus chimeric constructions in vaccines

Inventors: Dan T. Stinchcomb (Enumclaw, WA); Claire Kinney (Fort Collins, CO); Richard M. Kinney (Fort Collins, CO); Jill A. Livengood (Fort Collins, CO)
Assignees: Takeda Vaccines, Inc.; The Government of the United States of America as Represented by the Secretary of the Department of Health and Human Services
A61K38/162A61K31/7048A61K31/713A61K39/12C07K14/005C07K14/1825C07K19/00C12N15/09C12N15/8613A61K2039/5254A61K2039/70A61P31/14C07K2319/00C12N2770/24122C12N2770/24134C12N2770/24141C12N2770/24143C12N2770/24162Y02A50/30
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Quick Facts
Patent No.
US 12,186,363
App. No.
17/478,537
Granted
Jan 7, 2025
Kind
B2
Abstract

Embodiments herein report compositions, uses and manufacturing of dengue virus constructs and live attenuated dengue viruses. Some embodiments concern a composition that includes, but is not limited to, a tetravalent dengue virus composition. In certain embodiments, compositions can include constructs of one or more serotypes of dengue virus, such as dengue-1 (DEN-1) virus, dengue-2 (DEN-2) virus, dengue-3 (DEN-3) or dengue-4 (DEN-4) virus constructs. In other embodiments, constructs disclosed herein can be combined in a composition to generate a vaccine against more one or more dengue virus constructs that may or may not be subsequently passaged in mammalian cells.

Claims (115)

1. An immunogenic composition comprising a modified live, attenuated dengue-2 virus strain PDK-53, the immunogenic composition being a tetravalent composition, wherein the modified live, attenuated dengue-2 virus strain PDK-53

is encoded by a polynucleotide molecule encoding a modified live, attenuated dengue-2 virus strain PDK-53 polypeptide molecule,

comprises an RNA transcribed from a cDNA comprising a polynucleotide molecule encoding the modified live, attenuated dengue-2 virus strain PDK-53 polypeptide molecule,

comprises one or more polypeptide molecules encoded by a polynucleotide molecule encoding the modified live, attenuated dengue-2 virus strain PDK-53 polypeptide molecule, or

is obtainable by a method for producing a modified live, attenuated dengue-2 virus strain PDK-53, the method comprising the following steps:

a) transcribing an RNA from a cDNA comprising a polynucleotide molecule encoding the modified live, attenuated dengue-2 virus strain PDK-53 polypeptide molecule, and

b) introducing the RNA transcribed in step a) into cells for production of the modified live, attenuated dengue-2 virus strain PDK-53,

wherein the polynucleotide molecule encoding the modified live, attenuated dengue-2 virus strain PDK-53 polypeptide molecule comprises at least one mutation, wherein one or more mutation is selected from the group consisting of:

an adenine to guanine mutation at position 592 in the numbering of SEQ ID NO: 14 encoding a glutamic acid instead of a lysine in the polypeptide molecule at amino acid position 166 in the numbering of SEQ ID NO: 6 corresponding to prM-52, and

an adenine to guanine mutation at position 8803 in the numbering of SEQ ID NO: 14 encoding a valine instead of an isoleucine in the polypeptide molecule at amino acid position 2903 in the numbering of SEQ ID NO: 6 corresponding to NS5-412, and comprising a dengue-1/dengue-2 chimera, wherein the dengue-1/dengue-2 chimera

comprises an adenine to guanine mutation at position 7311 in the numbering of SEO ID NO: 13.

2. The immunogenic composition according to claim 1 , wherein the polynucleotide molecule encoding the modified live, attenuated dengue-2 virus strain PDK-53 polypeptide molecule further comprises at least one additional mutation of:

a guanine to cytosine mutation at nucleic acid position 6481 in the numbering of SEQ ID NO: 14 encoding a proline instead of an alanine in the polypeptide molecule at amino acid position 2129 in the numbering of SEQ ID NO: 6 corresponding to NS4A-36, and

a cytosine to thymine mutation at position 7156 in the numbering of SEQ ID NO: 14 encoding a phenylalanine instead of a leucine in the polypeptide molecule at amino acid position 2354 in the numbering of SEQ ID NO: 6 corresponding to NS4B-111.

3. The immunogenic composition according to claim 1 , wherein the polynucleotide molecule encoding the modified live, attenuated dengue-2 virus strain PDK-53 polypeptide molecule is represented by SEQ ID NO: 4 or SEQ ID NO: 14.

4. The immunogenic composition according to claim 1 , wherein the modified, live attenuated dengue-2 virus strain PDK-53 polypeptide molecule is represented by SEQ ID NO: 5 or SEQ ID NO: 6.

5. A pharmaceutical composition comprising the immunogenic composition according to claim 1 , and a pharmaceutically acceptable excipient.

6. A method for inducing an immune response against dengue virus in a subject, the method comprising administering to the subject a pharmaceutically acceptable amount of the composition of claim 5 .

7. The immunogenic composition according to claim 1 further comprising a pharmaceutically acceptable carrier.

8. The immunogenic composition of claim 7 , wherein the dengue-1/dengue-2 chimera

is encoded by a polynucleotide molecule encoding a dengue-1/dengue-2 polypeptide chimera,

comprises an RNA transcribed from a cDNA comprising a polynucleotide molecule encoding the dengue-1/dengue-2 polypeptide chimera,

comprises one or more polypeptide molecules encoded by a polynucleotide molecule encoding the dengue-1/dengue-2 polypeptide chimera, or

is obtainable by a method for producing a dengue-1/dengue-2 chimera, the method comprising the following steps:

a) transcribing an RNA from a cDNA comprising a polynucleotide molecule encoding the dengue-1/dengue-2 polypeptide chimera, and

b) introducing the RNA transcribed in step a) into cells for production of the dengue-1/dengue-2 chimera,

wherein the polynucleotide molecule encoding the dengue-1/dengue-2 polypeptide chimera comprises a first nucleotide sequence encoding nonstructural proteins from a modified live, attenuated dengue-2 virus strain PDK-53, a second nucleotide sequence encoding at least one structural protein from dengue-1, and at least one mutation, wherein one or more mutation is selected from the group consisting of:

an adenine to cytosine mutation at position 3823 in the numbering of SEQ ID NO: 13 encoding a leucine instead of an isoleucine in the dengue-1/dengue-2 polypeptide chimera at amino acid position 1243 in the numbering of SEQ ID NO: 3 corresponding to NS2A-116; and

an adenine to thymine mutation at position 4407 in the numbering of SEQ ID NO: 13 encoding an aspartic acid instead of a glutamic acid in the dengue-1/dengue-2 polypeptide chimera at amino acid position 1437 in the numbering of SEQ ID NO: 3 corresponding to NS2B-92.

9. The immunogenic composition according to claim 8 , wherein the polynucleotide molecule encoding the dengue-1/dengue-2 polypeptide chimera further comprises at least one additional mutation of:

a cytosine to thymine mutation at position 7148 in the numbering of SEQ ID NO: 13 encoding an isoleucine instead of a threonine in the dengue-1/dengue-2 polypeptide chimera at amino acid position 2351 in the numbering of SEQ ID NO: 3 corresponding to NS4B-108; and

a guanine to cytosine mutation at position 2384 in the numbering of SEQ ID NO: 13 encoding an alanine instead of glycine in the dengue-1/dengue-2 polypeptide chimera at amino acid position 763 in the numbering of SEQ ID NO: 3 corresponding to E-483.

10. The immunogenic composition according to claim 8 , wherein the polynucleotide molecule encoding the dengue-1/dengue-2 polypeptide chimera is represented by SEQ ID NO: 1 or SEQ ID NO: 13.

11. The immunogenic composition according to claim 8 , wherein the dengue-1/dengue-2 polypeptide chimera is represented by SEQ ID NO: 2 or SEQ ID NO: 3.

12. The immunogenic composition of claim 8 , wherein the nonstructural proteins from the modified live, attenuated dengue-2 virus strain PDK-53 are selected from the group consisting of NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5.

13. The immunogenic composition of claim 8 , wherein the at least one structural protein from dengue-1 is selected from the group consisting of capsid protein (C), premembrane/membrane protein (prM) and envelope protein (E).

14. The immunogenic composition of claim 7 , further comprising a dengue-3/dengue-2 chimera, wherein the dengue-3/dengue-2 chimera

is encoded by a polynucleotide molecule encoding a dengue-3/dengue-2 polypeptide chimera,

comprises an RNA transcribed from a cDNA comprising a polynucleotide molecule encoding the dengue-3/dengue-2 polypeptide chimera,

comprises one or more polypeptide molecules encoded by a polynucleotide molecule encoding the dengue-3/dengue-2 polypeptide chimera, or

is obtainable by a method for producing a dengue-3/dengue-2 chimera, the method comprising the following steps:

a) transcribing an RNA from a cDNA comprising a polynucleotide molecule encoding the dengue-3/dengue-2 polypeptide chimera, and

b) introducing the RNA transcribed in step a) into cells for production of the dengue-3/dengue-2 chimera,

wherein the polynucleotide molecule encoding the dengue-3/dengue-2 polypeptide chimera comprises a first nucleotide sequence encoding nonstructural proteins from a modified live, attenuated dengue-2 virus strain PDK-53, a second nucleotide sequence encoding at least one structural protein from dengue-3, and at least one mutation, wherein one or more mutation is selected from the group consisting of:

an adenine to thymine mutation at position 1603 in the numbering of SEQ ID NO: 15 encoding a serine instead of a threonine in the dengue-3/dengue-2 polypeptide chimera at amino acid position 503 in the numbering of SEQ ID NO: 9 corresponding to E-223; and

an adenine to guanine mutation at position 7620 in the numbering of SEQ ID NO: 15.

15. The immunogenic composition of claim 14 , wherein the polynucleotide molecule encoding the dengue-3/dengue-2 polypeptide chimera further comprises a guanine to adenine mutation at position 6436 in the numbering of SEQ ID NO: 15 encoding an asparagine instead of an aspartic acid in the dengue-3/dengue-2 polypeptide chimera at amino acid position 2114 in the numbering of SEQ ID NO: 19 corresponding to NS4A-23.

16. The immunogenic composition of claim 14 , wherein the polynucleotide molecule encoding the dengue-3/dengue-2 polypeptide chimera is represented by SEQ ID NO: 7 or SEQ ID NO: 15.

17. The immunogenic composition of claim 14 , wherein the dengue-3/dengue-2 polypeptide chimera is represented by SEQ ID NO: 8 or SEQ ID NO: 9.

18. The immunogenic composition of claim 14 , wherein the nonstructural proteins from the modified live, attenuated dengue-2 virus strain PDK-53 are selected from the group consisting of NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5.

19. The immunogenic composition of claim 14 , wherein the at least one structural protein from dengue-3 is selected from the group consisting of capsid protein (C), premembrane/membrane protein (prM) and envelope protein (E).

20. The immunogenic composition of claim 7 , further comprising a dengue-4/dengue-2 chimera, wherein the dengue-4/dengue-2 chimera

is encoded by a polynucleotide molecule encoding a dengue-4/dengue-2 polypeptide chimera,

comprises an RNA transcribed from a cDNA comprising a polynucleotide molecule encoding the dengue-4/dengue-2 polypeptide chimera,

comprises one or more polypeptide molecules encoded by a polynucleotide molecule encoding the dengue-4/dengue-2 polypeptide chimera, or

is obtainable by a method for producing a dengue-4/dengue-2 chimera, the method comprising the following steps:

a) transcribing an RNA from a cDNA comprising a polynucleotide molecule encoding the dengue-4/dengue-2 polypeptide chimera, and

b) introducing the RNA transcribed in step a) into cells for production of the dengue-4/dengue-2 chimera,

wherein the polynucleotide molecule encoding the dengue-4/dengue-2 polypeptide chimera comprises a first nucleotide sequence encoding nonstructural proteins from a modified live, attenuated dengue-2 virus strain PDK-53, a second nucleotide sequence encoding at least one structural protein from dengue-4, and at least one mutation, wherein one or more mutation is selected from the group consisting of:

an adenine to thymine mutation at position 225 in the numbering of SEQ ID NO: 16;

an adenine to guanine mutation at position 3674 in the numbering of SEQ ID NO: 16 encoding a glycine instead of an aspartic acid in the dengue-4/dengue-2 polypeptide chimera at amino acid position 1193 in the numbering of SEQ ID NO: 12 corresponding to NS2A-66;

a cytosine to thymine mutation at position 5391 in the numbering of SEQ ID NO: 16;

a cytosine to thymine mutation at position 6437 in the numbering of SEQ ID NO: 16 encoding a valine instead of an alanine in the dengue-4/dengue-2 polypeptide chimera at amino acid position 2114 in the numbering of SEQ ID NO: 12 corresponding to NS4A-21, and

an adenine to cytosine mutation at position 9750 in the numbering of SEQ ID NO: 16.

21. The immunogenic composition of claim 20 , wherein the polynucleotide molecule encoding the dengue-4/dengue-2 polypeptide chimera further comprises a thymine to cytosine mutation at position 7026 in the numbering of SEQ ID NO: 16.

22. The immunogenic composition of claim 20 , wherein the polynucleotide molecule encoding the dengue-4/dengue-2 polypeptide chimera further comprises an adenine to guanine mutation at position 3773 in the numbering of SEQ ID NO: 16 encoding an arginine instead of a lysine in the dengue-4/dengue-2 polypeptide chimera at amino acid position 1226 in the numbering of SEQ ID NO: 12 corresponding to NS2A-99.

23. The immunogenic composition of claim 20 , wherein the polynucleotide molecule encoding the dengue-4/dengue-2 polypeptide chimera further comprises a cytosine to thymine mutation at position 7538 in the numbering of SEQ ID NO: 16 encoding a phenylalanine instead of a serine in the dengue-4/dengue-2 polypeptide chimera at amino acid position 2481 in the numbering of SEQ ID NO: 12 corresponding to NS4B-238.

24. The immunogenic composition of claim 20 , wherein the polynucleotide molecule encoding the dengue-4/dengue-2 polypeptide chimera is represented by SEQ ID NO: 10 or SEQ ID NO: 16.

25. The immunogenic composition of claim 20 , wherein the dengue-4/dengue-2 polypeptide chimera is represented by SEQ ID NO: 11 or SEQ ID NO: 12.

26. The immunogenic composition of claim 20 , wherein the nonstructural proteins from the modified live, attenuated dengue-2 virus strain PDK-53 are selected from the group consisting of NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5.

27. The immunogenic composition of claim 20 , wherein the at least one structural protein from dengue-4 is selected from the group consisting of capsid protein (C), premembrane/membrane protein (prM) and envelope protein (E).

28. The immunogenic composition of claim 1 ,

wherein the dengue-1/dengue-2 chimera

is encoded by a polynucleotide molecule encoding a dengue-1/dengue-2 polypeptide chimera,

comprises an RNA transcribed from a cDNA comprising a polynucleotide molecule encoding the dengue-1/dengue-2 polypeptide chimera,

comprises one or more polypeptide molecules encoded by a polynucleotide molecule encoding the dengue-1/dengue-2 polypeptide chimera,

or

is obtainable by a method for producing a dengue-1/dengue-2 chimera, the method comprising the following steps:

 a) transcribing an RNA from a cDNA comprising a polynucleotide molecule encoding the dengue-1/dengue-2 polypeptide chimera, and

 b) introducing the RNA transcribed in step a) into cells for production of the dengue-1/dengue-2 chimera,

wherein the polynucleotide molecule encoding the dengue-1/dengue-2 polypeptide chimera comprises a first nucleotide sequence encoding nonstructural proteins from a modified live, attenuated dengue-2 virus strain PDK-53, a second nucleotide sequence encoding at least one structural protein from dengue-1, and at least one mutation, wherein one or more mutation is selected from the group consisting of:

an adenine to cytosine mutation at position 3823 in the numbering of SEQ ID NO: 13 encoding a leucine instead of an isoleucine in the dengue-1/dengue-2 polypeptide chimera at amino acid position 1243 in the numbering of SEQ ID NO: 3 corresponding to NS2A-116;

an adenine to thymine mutation at position 4407 in the numbering of SEQ ID NO: 13 encoding an aspartic acid instead of a glutamic acid in the dengue-1/dengue-2 polypeptide chimera at amino acid position 1437 in the numbering of SEQ ID NO: 3 corresponding to NS2B-92; and

an adenine to guanine mutation at position 7311;

and further comprising one or more of:

ii) a dengue-3/dengue-2 chimera, wherein the dengue-3/dengue-2 chimera

is encoded by a polynucleotide molecule encoding a dengue-3/dengue-2 polypeptide chimera,

comprises an RNA transcribed from a cDNA comprising a polynucleotide molecule encoding the dengue-3/dengue-2 polypeptide chimera,

comprises one or more polypeptide molecules encoded by a polynucleotide molecule encoding the dengue-3/dengue-2 polypeptide chimera,

or

is obtainable by a method for producing a dengue-3/dengue-2 chimera, the method comprising the following steps:

 a) transcribing an RNA from a cDNA comprising a polynucleotide molecule encoding the dengue-3/dengue-2 polypeptide chimera, and

 b) introducing the RNA transcribed in step a) into cells for production of the dengue-3/dengue-2 chimera,

wherein the polynucleotide molecule encoding the dengue-3/dengue-2 polypeptide chimera comprises a first nucleotide sequence encoding nonstructural proteins from a modified live, attenuated dengue-2 virus strain PDK-53, a second nucleotide sequence encoding at least one structural protein from dengue-3, and at least one mutation, wherein one or more mutation is selected from the group consisting of:

an adenine to thymine mutation at position 1603 in the numbering of SEQ ID NO: 15 encoding a serine instead of a threonine in the dengue-3/dengue-2 polypeptide chimera at amino acid position 503 in the numbering of SEQ ID NO: 9 corresponding to E-223; and

an adenine to guanine mutation at position 7620 in the numbering of SEQ ID NO: 15; and

iii) a dengue-4/dengue-2 chimera, wherein the dengue-4/dengue-2 chimera

is encoded by a polynucleotide molecule encoding a dengue-4/dengue-2 polypeptide chimera,

comprises an RNA transcribed from a cDNA comprising a polynucleotide molecule encoding the dengue-4/dengue-2 polypeptide chimera,

comprises one or more polypeptide molecules encoded by a polynucleotide molecule encoding the dengue-4/dengue-2 polypeptide chimera,

or

is obtainable by a method for producing a dengue-4/dengue-2 chimera, the method comprising the following steps:

 a) transcribing an RNA from a cDNA comprising a polynucleotide molecule encoding the dengue-4/dengue-2 polypeptide chimera, and

 b) introducing the RNA transcribed in step a) into cells for production of the dengue-4/dengue-2 chimera,

wherein the polynucleotide molecule encoding the dengue-4/dengue-2 polypeptide chimera comprises a first nucleotide sequence encoding nonstructural proteins from a modified live, attenuated dengue-2 virus strain PDK-53, a second nucleotide sequence encoding at least one structural protein from dengue-4, and at least one mutation, wherein one or more mutation is selected from the group consisting of:

an adenine to thymine mutation at position 225 in the numbering of SEQ ID NO: 16;

an adenine to guanine mutation at position 3674 in the numbering of SEQ ID NO: 16 encoding a glycine instead of an aspartic acid in the dengue-4/dengue-2 polypeptide chimera at amino acid position 1193 in the numbering of SEQ ID NO: 12 corresponding to NS2A-66;

a cytosine to thymine mutation at position 5391 in the numbering of SEQ ID NO: 16;

a cytosine to thymine mutation at position 6437 in the numbering of SEQ ID NO: 16 encoding a valine instead of an alanine in the dengue-4/dengue-2 polypeptide chimera at amino acid position 2114 in the numbering of SEQ ID NO: 12 corresponding to NS4A-21, and

an adenine to cytosine mutation at position 9750 in the numbering of SEQ ID NO: 16.

29. The immunogenic composition of claim 1 , in combination with an immunogenic composition for a flavivirus selected from the group consisting of yellow fever virus, tick-borne encephalitis virus, Japanese encephalitis virus, West Nile virus, hepatitis C virus, and a combination of two or more thereof.

30. A kit comprising

at least one immunogenic composition according to claim 1 ; or

at least one composition comprising an immunogenic composition according to claim 1 and a pharmaceutically acceptable excipient;

and a container.

Assignments (5)
CORRECTIVE ASSIGNMENT TO CORRECT THE NATURE OF CONVEYANCE FROM ASSIGNMENT TO MERGER AND CHANGE OF NAME PREVIOUSLY RECORDED ON REEL 065144 FRAME 0910. ASSIGNOR(S) HEREBY CONFIRMS THE MERGER AND CHANGE OF NAME. Recorded Nov 1, 2023
From: INVIRAGEN, INC.; TAKEDA VACCINES (MONTANA), INC.; TAKEDA VACCINES, INC.
To: TAKEDA VACCINES, INC.
Reel/Frame 065417/0075 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Oct 6, 2023
From: STINCHCOMB, DAN T.; LIVENGOOD, JILL A.
To: INVIRAGEN, INC.
Reel/Frame 065144/0527 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Oct 6, 2023
From: HUANG, CLAIRE Y.; KINNEY, RICHARD M.
To: THE GOVERNMENT OF THE UNITED STATES OF AMERICA AS REPRESENTED BY THE SECRETARY OF THE DEPARTMENT OF HEALTH AND HUMAN SERVICES
Reel/Frame 065144/0658 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Oct 6, 2023
From: INVIRAGEN, INC.; TAKEDA VACCINES (MONTANA), INC.; TAKEDA VACCINES, INC.
To: TAKEDA VACCINES, INC.
Reel/Frame 065144/0910 →
MERGER AND CHANGE OF NAME Recorded Oct 6, 2023
From: INVIRAGEN, INC.; TAKEDA VACCINES (MONTANA), INC.
To: TAKEDA VACCINES, INC.
Reel/Frame 065145/0140 →
Continuity (5)
Continuation 16561755 · Sep 5, 2019
Continuation 15492981 · Apr 20, 2017
Division 14209808 · Mar 13, 2014
Provisional Application 61800204 · Mar 15, 2013
Related Publication 20220062375A1 · Mar 3, 2022
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