METHOD OF RAPIDLY PRODUCING IMPROVED VACCINES FOR ANIMALS

1 . A method of producing a vaccine to protect an animal from a biotype of a microorganism, the method comprising,

a) obtaining a biological sample from at least one animal where said animal has been exposed to a microorganism;

b) obtaining from said sample a nucleic acid molecule of interest or fragment thereof (NOI) of said microorganism;

c) producing a protective molecule from said NOI, said protective molecule, selected from the group consisting of:

(i) a nucleic acid molecule comprising the sequence of said NOI or a fragment thereof;

(ii) a polypeptide or fragment thereof expressed by said NOI;

(iii) at least one RNA molecule comprising a sequence that corresponds to all or a portion of said NOI and forms a dsRNA;

(iv) at least one RNA molecule that is antisense to all or a portion of said NOI;

(v) a replicon particle comprising or producing any one of (i)-(v); and

d) producing a vaccine comprising said protective molecule wherein said protective molecule, when administered protects said animal from said biotype of said microorganism.

2 . The method of claim 1 , wherein said vaccine is produced in one month or less from the time of obtaining said sample.

3 . The method of claim 1 , further comprising introducing a alphavirus replicon vector comprising said NOI into a host cell, expressing a polypeptide or fragment thereof from said NOI, and extracting said polypeptide or fragment from said host, wherein said extracted polypeptide or fragment thereof comprises said protective molecule.

4 . The method of claim 3 , wherein said vector comprises a Viral Equine Encephalitis (VEE) vector, said host comprises Vero cells and said polypeptide or fragment thereof is extracted by lysing said Vero cells.

5 . The method of claim 1 , wherein said protective molecule comprises an alphavirus replicon particle, and said alphavirus replicon particle comprises said NOI or a fragment thereof.

6 . The method of claim 1 , wherein said protective molecule comprises an alphavirus replicon particle, and said alphavirus replicon particle produces a dsRNA molecule.

7 . The method of claim 1 , wherein said animal is selected from the group consisting of swine, cattle, canines, felines and aquatic invertebrates.

8 . The method of claim 1 , wherein said NOI is obtained by a process selected from the group consisting of polymerase chain reaction of said nucleic acid molecule or fragment thereof in said sample, and synthesis of said nucleic acid molecule or fragment thereof.

10 . The method of claim 1 , further comprising producing said vaccine such that the amount of protective molecule is sufficient to protect an animal from said biotype of said microorganism and said vaccine is cost effective to produce.

11 . The method of claim 1 , further comprising,

a) obtaining from an animal a biological sample which sample comprises a component of said microorganism which distinguishes the biotype of the microorganism;

b) testing the component to determine the biotype of the microorganism; and

c) producing said vaccine if said test determines the microorganism is a biotype different from those for which vaccines exist.

12 . The method of claim 1 , wherein it is not necessary to isolate said microorganism.

13 . A vaccine to protect an animal from a biotype of a microorganism, said vaccine comprising, a protective molecule selected from the group consisting of:

(i) a nucleic acid molecule comprising the sequence of a nucleic acid molecule of interest or a fragment thereof (NOI) which NOI is obtained from a sample from an animal which has been exposed to said microorganism;

(ii) a polypeptide or fragment thereof expressed by said NOI;

(iii) at least one RNA molecule comprising a sequence that corresponds to all or a portion of said NOI and forms a dsRNA;

(iv) at least one RNA molecule that is antisense to all or a portion of said NOI;

(v) a nucleic acid molecule producing (iii) or (iv); and

(vi) a replicon particle comprising or producing any one of (i)-(v); and

e) wherein said NOI is obtained from a biotype of the microorganism for which available vaccines provide no or a reduced protective response when administered to an animal, compared to the protective response obtained when administering said vaccine, and wherein said vaccine, when administered protects said animal from said biotype of said microorganism.

14 . The vaccine of claim 13 further comprising an adjuvant comprising a non-mutated E. coli heat labile enterotoxin.

15 . The vaccine of claim 13 wherein said vaccine comprises an alphavirus replicon particle.

16 . The vaccine of claim 15 , wherein said alphavirus replicon particle comprises said NOI or fragment thereof.

17 . The vaccine of claim 15 , wherein said alphavirus replicon particle produces a dsRNA molecule.

18 . A method of protecting an animal from a biotype of a microorganism, the method comprising,

a) obtaining a biological sample from at least one animal where said animal has been exposed to a microorganism;

b) obtaining from said sample a nucleic acid molecule of interest or fragment thereof (NOI) of said microorganism;

c) producing a protective molecule from said NOI, said protective molecule, selected from the group consisting of:

(i) a nucleic acid molecule comprising the sequence of said NOI or a fragment thereof;

(ii) a polypeptide or fragment thereof expressed by said NOI;

(iii) at least one RNA molecule comprising a sequence that corresponds to all or a portion of said NOI and forms a dsRNA;

(iv) at least one RNA molecule that is antisense to all or a portion of said NOI;

(v) a nucleic acid molecule producing (iii) or (iv); and

(vi) a replicon particle comprising or producing any one of (i)-(v);

d) producing a vaccine comprising said protective molecule wherein said protective molecule, when administered protects said animal from said biotype of said microorganism;

e) administering said protective molecule to said animal or to an animal exposed to said microorganism or at risk of exposure to said microorganism; and

f) producing a protective response to said biotype of said microorganism in said animal.

19 . The method of claim 18 , wherein said vaccine is administered to a plurality of animals in a geographic area which have been or are at risk of being exposed to said microorganism.

20 . A method of determining if an animal has been vaccinated with a vaccine for a biotype of a microorganism, the method comprising,

a) obtaining a biological sample from said animal;

b) detecting the present of a nucleic acid molecule comprising the sequence of a nucleic acid molecule of said biotype of a pathogenic microorganism; and

c) detecting the presence or absence of additional nucleic acid molecules of said microorganism, wherein the absence of additional nucleic acid molecule of said microorganism indicates the animal has been vaccinated with said vaccine.