Scalable purification method for AAV9

1. A method for separating recombinant adeno-associated virus serotype 9 (AAV9) (rAAV9) viral particles having packaged genomic sequences from genome-deficient AAV9 capsid intermediates, said method comprising:

(a) performing filtration through a series of depth filters to afford a clarified rAAV9 production culture harvest;

(b) treating the clarified rAAV9 production culture harvest with a nuclease or a combination of nucleases to digest contaminating high molecular weight nucleic acid and to afford a mixture comprising rAAV9 viral particles and genome-deficient AAV9 capsid intermediates;

(c) concentrating the nuclease-treated mixture of (b) via tangential flow filtration (TFF) to afford a concentrated rAAV9 feedstream;

(d) contacting the concentrated rAAV9 feedstream of (c) comprising the rAAV9 viral particles and genome-deficient AAV9 capsid intermediates with a high-performance AAV9-capsid binding affinity resin to afford purified mixture;

(e) performing anion exchange chromatography with an anion exchange resin on the affinity purified mixture of (d) containing the rAAV9 viral particles at a pH of 10.0 to 10.4;

(f) monitoring an eluate of (e) for ultraviolet absorbance at 260 nm (A260) and at 280 nm (A280); and

(g) collecting rAAV9 viral particles from fractions eluted when the ratio of A260 to A280 (A260/A280) reaches an inflection point.

2. The method according to claim 1 , wherein prior to the step of (a), the rAAV production culture harvest is from a production cell culture system, wherein cells were lysed to release the rAAV9 viral particles and the genome-deficient AAV9 capsid intermediates.

3. The method according claim 1 , wherein the method comprises performing anion exchange chromatography of (e) having a sample loading flow rate less than or equal to the elution flow rate.

4. The method according to claim 1 , wherein the anion exchange resin is a quaternary amine strong anion exchange resin.

5. The method according to claim 1 , wherein the anion exchange resin is in a column.

6. The method according to claim 1 , wherein the method further comprises one or more of the following: heat inactivation of helper virus, rAAV9 capture by hydrophobic interaction chromatography, buffer exchange by size exclusion chromatography (SEC), and nanofiltration.

7. A method for separating recombinant adeno-associated virus (AAV) serotype 9 (rAAV9) viral particles from genome-deficient AAV9 capsid intermediates, said method comprising:

(a) performing filtration through a series of depth filters to afford a clarified rAAV9 production culture harvest;

(b) treating the clarified rAAV9 production culture harvest with a nuclease or a combination of nucleases to digest contaminating high molecular weight nucleic acid and to afford a mixture comprising rAAV9 viral particles and genome-deficient AAV9 capsid intermediates;

(c) contacting the mixture of (b) comprising the rAAV9 viral particles and genome-deficient AAV9 capsid intermediates with a high-performance AAV9-capsid binding affinity resin to afford a purified mixture;

(d) mixing a suspension of the affinity purified mixture of (c) comprising rAAV9 viral particles and genome-deficient AAV9 capsid intermediates and a first buffer at a neutral pH;

(e) loading the suspension of (d) onto a strong anion exchange resin column;

(f) washing the loaded anion exchange resin with a second buffer having a pH of about 10.2 and further comprising a salt in an amount equivalent to 10 mM to 40 mM NaCl or salt equivalent and Bis-Tris Propane (BTP);

(g) applying an increasing salt concentration gradient to the loaded and washed anion exchange resin, wherein the salt gradient is sufficient to elute the rAAV9 viral particles;

and

(h) collecting rAAV9 viral particles which are at least about 90% purified from genome-deficient AAV9 capsid intermediates.

8. The method according to claim 7 , wherein the rAAV9 viral particles and genome-deficient AAV9 capsid intermediates of step (d) have been affinity purified at a high salt concentration.

9. The method according to claim 7 , wherein the anion exchange resin is a quaternary amine ion exchange resin.

10. The method according to claim 7 , wherein the anion exchange resin column comprises trimethylamine and a support matrix comprising poly(glycidyl methacrylate-co-ethylene dimethacrylate).

11. The method according to claim 7 , wherein when the anion exchange resin column is a monolith column and where column loading, washing and elution occur in about 60 column volumes.

12. The method according to claim 1 , wherein the affinity capture is performed using high performance affinity resin.

13. The method according to claim 1 , wherein the anion exchange chromatography of (e) is performed with a salt gradient which has an ionic strength equivalent to at least 10 mM to 190 mM NaCl, or a salt gradient having an ionic strength equivalent thereto, and wherein the ionic strength is calculatable using a formula l=

1

2

⁢

∑

i

=

1

n

c

i

⁢

z

i

2

,

where c i is the molar concentration of ion i (M, mol/L), z i is the charge number of that ion, and I is taken over all ions in the solution.

14. The method according to claim 1 , wherein genome-deficient AAV9 capsid intermediates are eluted from the anion exchange resin when a salt gradient reaches an ionic strength equivalent to about 50 mM NaCl or greater, or a salt gradient having an ionic strength equivalent thereto, and wherein the ionic strength is calculatable using a formula

I

=

1

2

⁢

∑

i

=

1

n

c

i

⁢

z

i

2

,

where c i is the molar concentration of ion i (M, mol/L), z i is the charge number of that ion, and I is taken over all ions in the solution.

15. The method according to claim 1 , wherein genome deficient AAV9 capsid intermediates are eluted from the anion exchange resin when a salt gradient reaches an ionic strength equivalent to about 50 mM KCl or greater, or a salt gradient having an ionic strength equivalent thereto, and wherein the ionic strength is calculatable using a formula

I

=

1

2

⁢

∑

i

=

1

n

c

i

⁢

z

i

2

,

where c i is the molar concentration of ion i (M, mol/L), z i is the charge number of that ion, and I is taken over all ions in the solution.

16. The method according to claim 1 , wherein the rAAV9 viral particles and the genome-deficient AAV9 capsid intermediates of step (d) have been affinity purified at a high salt concentration.

17. The method according to claim 16 , wherein the salt concentration is 400 mM to 650 mM NaCl or a salt equivalent.

18. The method according to claim 1 , wherein the series of depth filters of (a) comprise filters of 0.2 μm or greater pore size.

19. The method according to claim 1 , wherein the series of depth filters of (a) comprise filters in the range of about 0.045 μm to about 0.2 μm pore size.

20. The method according to claim 1 , wherein the anion exchange chromatography of (e) is performed at a pH of about 10.2.

21. The method according to claim 7 , wherein the series of depth filters of (a) comprise filters of 0.2 μm or greater pore size.

22. The method according to claim 7 , wherein the series of depth filters of (a) comprise filters in the range of about 0.045 μm to about 0.2 μm pore size.

23. The method according to claim 7 , wherein the washing buffer of (f) comprising BTP comprises 20 mM to 50 mM BTP.

24. The method according to claim 8 , wherein the salt concentration is 400 mM to 650 mM NaCl or a salt equivalent.