Methods and compositions for alphavirus replicons

1. A recombinant replicon nucleic acid comprising:

a) a nucleic acid sequence encoding a first alphavirus 5′ untranslated region (5′ UTR) and a 51 nucleotide conserved sequence element (51 -nt CSE);

b) a nucleic acid sequence encoding alphavirus nonstructural proteins nsP1, nsP2, nsP3 and nsP4;

c) a nucleic acid sequence encoding an alphavirus subgenornic promoter;

d) a nucleic acid sequence encoding a second alphavirus 5′ untranslated region (5′ UTR) and 51 nucleotide conserved sequence element (51 -nt CSE);

e) a nucleic acid sequence encoding a protease;

f) a nucleic acid sequence encoding a heterologous protein; and

g) a nucleic acid sequence encoding an alphavirus 3′ untranslated region (3′ UTR).

2. The recombinant replicon nucleic acid of claim 1 , wherein the nucleic acid sequence of (d) is modified to move all AUGs in the nucleic acid sequence into the same open reading frame as the initiating AUG.

3. The recombinant replicon nucleic acid of claim 1 , wherein the protease is selected from the group consisting of a 2A protease from foot and mouth disease virus (FMDV), ubiquitin, a ubiquitin-like protein, Npro of pestiviruses and alphavirus capsid-encoded protease.

4. The recombinant replicon nucleic acid of claim 1 , further comprising a nucleic acid sequence encoding an alphavirus capsid and the first 2 or more amino acids of E3 protein upstream of the nucleic acid sequence of (f).

5. A recombinant replicon nucleic acid comprising:

a) a nucleic acid sequence encoding a first aiphavirus 5 untranslated region (5′ UTR) and a 51 nucleotide conserved sequence element (51 -nt CSE);

b) a nucleic acid sequence encoding alphavirus nonstructural proteins nsP1, nsP 2 ; ns P3 and nsP4;

c) a nucleic acid sequence encoding a first alphavirus subgenomic promoter;

d) a nucleic acid sequence encoding a second alphavirus 5′ untranslated region (5′ UTR) and a 51 nucleotide conserved sequence element (51 -nt CSE);

e) a nucleic acid sequence encoding a second alphavirus subgenomic promoter;

f) a nucleic acid sequence encoding a heterologous protein; and

g) a nucleic, acid sequence encoding an alphavirus 3′ untranslated region (3′ UTR).

6. A recombinant replicon nucleic acid comprising:

a) a nucleic acid sequence encoding a first alphavirus 5′ untranslated region (5′ UTR) and a first 51 nucleotide conserved sequence element (51 -nt CSE);

b) a nucleic acid sequence encoding alphavirus nonstructural proteins nsP1, nsP2, nsP3 and nsP4;

c) a nucleic acid sequence encoding a first alphavirus subgenomic promoter;

d) a nucleic acid sequence encoding a second alphavirus 5′ untranslated region (5′ UTR) or a modified 5′ UTR comprising a cellular Asp tRNA sequence, and a second 51 nucleotide conserved sequence element (51 -nt CSE);

e) a nucleic acid sequence encoding a second alphavirus subgenomic promoter;

f) a nucleic acid sequence encoding a translational enhancer derived from an Old World alphavirus;

g) a nucleic acid sequence encoding a protease;

h) a nucleic acid sequence encoding a heterologous protein; and

i) a nucleic acid sequence encoding an alphavirus 3′ untranslated region (3′ UTR).

7. The recombinant replicon nucleic acid of claim 6 , wherein the protease is selected from the group consisting of a 2A protease from FMDV, ubiquitin, a ubiquitin-like protein, alphavirus capsid protein and Npro of pestiviruses.

8. The recombinant replicon nucleic acid of claim 1 , wherein the nucleic acid is RNA.

9. The recombinant replicon nucleic acid of claim 1 , wherein the nucleic acid is DNA cloned under control of SP6, T7 or DNA-dependent RNA polymerase I or II.

10. An alphavirus particle comprising the recombinant replicon nucleic acid of claim 1 .

11. A population of alphavirus particles, comprising the alphavirus particle of claim 10 .

12. A composition comprising the population of claim 11 in a pharmaceutically acceptable carrier.

13. A composition comprising the recombinant replicon nucleic acid of claim 1 , in a pharmaceutically acceptable carrier,

14. An isolated cell comprising the recombinant replicon nucleic acid of claim 1 .

15. A method of producing a heterologous protein in a cell, comprising introducing the recombinant replicon nucleic acid of claim 1 into the cell under conditions whereby the nucleic acid sequence of (f) is expressed, wherein the cell is in a cell culture thereby producing the heterologous protein in the cell.

16. The method of claim 15 , further comprising the step of harvesting the heterologons protein from the cell culture.

17. A method eliciting an immune response to a heterologous protein in a subject, comprising administering to the subject an immunogenic amount of the recombinant replicon nucleic acid of claim 1 , thereby eliciting an immune response to the heterologous protein encoded by the nucleic acid sequence of (f).

18. A method of delivering a therapeutic heterologous protein to a subject, comprising administering to the subject a therapeutic amount of the recombinant replicon nucleic acid of claim 1 , wherein the nucleic acid sequence of (f) encodes a therapeutic heterologous protein, thereby delivering a therapeutic heterologous protein to the subject.

19. A method of making infectious, defective alphavirus particles, comprising:

a) introducing into a cell the following:

(i) the recombinant replicon nucleic acid of claim 1 ; and

(ii) one or more helper nucleic acids encoding alphavirus structural proteins,

wherein the one or more helper nucleic acids produce all of the alphavirus structural proteins, and

b) producing said alphavirus particles in the cell.