SEPARATION DEVICE AND METHOD OF SEPARATION

Abstract

The present invention relates to the readily automated methods for the separation of biomolecules, such as proteins or nucleic acids. More specifically, the invention relates to a separation device, which includes at least one column provided with a bottom liquid inlet/outlet and adapted to receive a separation media. At least part of an elongated frit has been arranged substantially parallel to the column side walls, segregating the separation media from the bottom liquid inlet/outlet. The elongated frit may be shaped as a tube and should have a porosity that serves to retain separation media within the column during sample processing.

Further, the invention relates to a method of separating at least one target molecule from a liquid, which method comprises providing at least one column provided with a bottom liquid inlet/outlet and optionally with a top liquid inlet. The column retains a separation media; and at least part of an elongated frit has been arranged substantially parallel to the column side walls to segregate the separation media from the bottom liquid inlet/outlet. A liquid sample is processed in said column in a method including aspiration and dispensing of fluid to and from the bottom liquid inlet/outlet; adding a liquid at the top liquid inlet; or any combination thereof.

Claims

1. A separation device, which includes at least one column, which is provided with a bottom liquid inlet/outlet and which is adapted to receive a separation media; wherein at least part of an elongated frit has been arranged substantially parallel to the column side walls and segregating separation media from the bottom liquid inlet/outlet.

2. A device according to claim 1, wherein the elongated frit is not arranged horizontally in the column when said column is arranged vertically.

3. A device according to claim 2, wherein at least part of the elongated frit is arranged at an angle within a range of about 45-90 to the horizontal plane of the column when said column is arranged vertically.

4. A device according claim 1, wherein the elongated frit is arranged for allowing liquid flow which is perpendicular as well as parallel to the column side walls.

5. A device according to claim 1, which is provided with a top liquid inlet.

6. A device according to claim 1, wherein an upper frit has been arranged in said column at a position which allows the column to receive separation media below said upper frit.

7. A device according to claim 6, wherein said upper frit has been arranged in a position in the column which results in a volume comprised of separation media as well as free space below said upper frit.

8. A device according to claim 1, wherein the elongated frit comprises a mesh.

9. A device according to claim 8, wherein the mesh is maintained in position by a hollow support which includes at least one hole.

10. A device according to claim 9, wherein the hollow support is defined by a circular, oval, triangular or other angular cross section.

11. A device according to claim 8, wherein the elongated frit is comprised of a tubular support which the mesh has been wrapped at the side facing the separation media.

12. A device according to claim 1, wherein the bottom of the column is provided with a tubular column end.

13. A device according to claim 12, wherein the length of said tubular column end constitutes about one third of the length of the column.

14. A device according to claim 12, wherein the tubular column end and the elongated frit are arranged as one integral part.

15. A device according to claim 12, wherein the column is arranged with a sloped column bottom wall.

16. A device according to claim 12, wherein the column is arranged in a liquid processing system.

17. A device according to claim 12, which includes means for passing liquid between an upper end of the column and a lower end of the column.

18. A device according to claim 17, wherein said means provides positive or negative pressure.

19. A device according to claim 17, wherein said means comprises pumping means.

20. A device according claim 17, which comprises two or more columns arranged for parallel processing.

21. A method of separating at least one target molecule from a liquid, which method comprises providing at least one column, which is provided with a bottom liquid inlet/outlet and an optional top liquid inlet, which column retains a separation media; wherein at least part of an elongated frit has been arranged substantially parallel to the column side walls and segregating the separation media from the bottom liquid inlet/outlet; and processing a liquid sample in said column in a method including aspiration and dispensing of fluid to and from the bottom liquid inlet/outlet and/or adding a liquid at the top liquid inlet; or any combination thereof.

22. A method according to claim 21, which method comprises the steps of a) providing at least one column, which is provided with a bottom liquid inlet/outlet and optionally a top liquid inlet, which column retains a separation media; wherein an elongated frit has been arranged substantially parallel to the column side walls and segregating the separation media from the bottom liquid inlet/outlet; b) providing a liquid which includes said at least one target molecule in admixture with other molecules; c) placing the bottom liquid inlet/outlet of the column into said liquid; d) in an aspirating phase, applying a negative pressure to the column to bring liquid to pass from bottom liquid inlet/outlet of the column and through the elongated frit in a direction of flow which is substantially perpendicular to the column side walls, whereby the liquid flow disperses the separation media; and optionally, allowing time for capture of target molecule(s) by the separation media.

23. A method according to claim 22, which in addition comprises the steps of e) in a dispensing phase, applying a positive pressure to the column to bring liquid to pass through the elongated frit in a direction of flow which is substantially perpendicular to the column side walls towards the bottom liquid inlet/outlet of the column; and f) collecting liquid exiting the bottom liquid inlet/outlet of the column; which steps are optionally followed by g) repeating steps d) and with an eluting liquid that releases target molecules from the separation media; and h) collecting eluting liquid comprising released target molecule(s) via the bottom liquid inlet/outlet of the column, optionally followed by a step of recovering and/or analyzing eluted target molecule(s).

24. A method according to claim 21, wherein a target molecule is a biomolecule, such as a protein or nucleic acid, or a fragment thereof.

25. A method according to claim 24, wherein a target molecule is a protein selected from the group consisting of peptides and antibodies, such as Fab fragments.

26. A method according to claim 24, wherein a target molecule is a plasmid.

27. A method according to claim 24, wherein the liquid provided in step b) originates from a cell culture; or from a method of chemical synthesis.

28. A method according to claim 24, wherein in step d), a liquid volume in the range of 20 mL to 5 L is aspirated, such as a range of about 100 mL to about 200 mL; about 500 mL to about 2.5 L; or about 2.5 L to about 5 L.

29. A method according to claim 24, wherein the positive and negative pressures of steps d) and f) are provided by a displacement pump.

30. A method according to claim 24, wherein in step a), at least two columns are provided and processed in parallel in the subsequent steps.

31. A method according to claim 30, wherein said at least two columns comprises separation media having different functionalities from each other, such as affinity media and ion exchange media.

32. A method according to claim 30, wherein in step d), different liquids are aspirated into at least two separate columns.

33. A method according to claim 21, wherein step d) comprises to apply back-and-forth flow to the aspirated liquid at least once.

34. A method according to claim 21, wherein a separation device is used.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

[0027] FIG. 1 is provided to illustrate how, in a column of the separation device according to the invention, the liquid flow is directed from a bottom liquid inlet 1a and up during a phase of aspirating liquid.

[0028] FIG. 2 illustrates, in the same column as in FIG. 1, how liquid can flow in the opposite direction, i.e. from the top liquid inlet 1b towards a bottom liquid outlet 1a of the column, during dispensing of liquid.

[0029] FIG. 3 is an expanded view of an elongated frit 6, here too shaped as a tube frit, arranged in separation media 7. Frit liquid passages 11 are shown schematically as holes (size not shown in dimension). The sloped column side wall 2b appears at the lower end of the column.

[0030] FIG. 4 illustrates how an elongated frit 6 may be assembled by wrapping mesh 10 around a tubular hollow support 9. In FIG. 4a, the hollow support is shown as having holes 8 enabling fluid passage. In FIG. 4b, a tube fritan example of an elongated frit 6 according to the inventionhas been assembled from a tubular hollow support 9 over which porous mesh 10 has been wrapped.

[0031] FIG. 5 is a table outlining the general performance for plasmid purification according to the invention.

DETAILED DESCRIPTION OF THE INVENTION

[0032] The present invention will now be described with reference to the drawings. As appears from above, in a first aspect, the present invention relates to a separation device comprising at least one column provided with a bottom liquid inlet/outlet 1a and adapted to receive a separation media; wherein at least part of an elongated frit 6 has been arranged substantially parallel to the column side wall 2a and segregating separation media 7 from the bottom liquid inlet/outlet 1a.

[0033] Thus, by an appropriate selection of dimensions, in particular the porosity, the elongated frit 6 may prevent separation media 7 from leaving the column.

[0034] The bottom inlet/outlet 1a is adapted for passage of liquid in and out of the column, allowing for aspiration and dispensing of liquid. Further, the present column may comprise a top liquid inlet 1b, adapted for passage of liquid into the column i.e. top down flow.

[0035] In this context, the term column side wall 2a is understood to mean the parallel (e.g. tubular) wall of the column body rather than any sloped top or end part of a column, herein denoted the column bottom wall 2b. Differently worded, at least part of the elongated frit 6 according to the invention is substantially vertically positioned within the column. As clear to the skilled person, the column will be vertically positioned during operation.

[0036] The elongated frit 6 is according to the invention arranged to provide for a direction of liquid flow which is substantially perpendicular to the column wall 2 as liquid is passed across the column during sample processing. In other words, as liquid crosses the elongated frit 6, its direction of flow will be substantially horizontal, when viewed in a vertically positioned column. Further, the elongated frit is arranged not to collect any solid contaminants, as will appear from the more detailed disclosure below.

[0037] The liquid flow in a vertically arranged separation column according to the invention will be combination of perpendicular and axial flow, since the direction of flow will change as liquid passes the elongated frit 6, optionally in a back and forth mode. In one embodiment, the liquid flow is axial at the lower part of the column, while it is perpendicular at the upper part of the column with a transition liquid flow area between. Advantageously, there will be no, or very little, dead flow areas along the outer edges of the column where the elongated frit is operating, especially at the inlet to the chamber of the column.

[0038] The flow provided according to the invention will allow for dispersion of separation media 7 as liquid is aspirated from the bottom, in turn providing for an efficient mixing and capture of a target molecule by the separation media 7.

[0039] As liquid is dispensed from the column to the bottom inlet/outlet 1a, the separation media will settle. In this context, it is understood that the bottom inlet/outlet 1a is located at the distal end of the column, as will appear from the drawings.

[0040] As the skilled person will appreciate, separation media 7 may be positioned in the column as a more or less densely packed bed, which may advantageously be dispersed by an upward flow obtained as described above, and which may be re-packed, or return to a more sedimented form, as liquid is dispensed. Advantageous bed volumes may be from the smaller sizes of about 20, 15, 10, 5, 3, 2 and 1 mL, or even as small as 50 and 100 L; and up to larger sizes of up to about 100 mL, about 1 L and about 10 L and even large sizes up to about 50, 100, or 200 L. An advantageous separation bed is of a volume selected from the group consisting of 20, 10 and 5 mL. As discussed in more detail below in relation to the second aspect of the invention, the column according to the invention allows for back-and-forth flow.

[0041] In the present context, the term substantially parallel to the column wall should be understood as not horizontally arranged in a vertically (upright) arranged column, such as positioned at an angle that provides for the direction of flow described above. For example, at least part of the elongated frit 6 may be arranged at an angle within a broader range, such as about 45-90 to the horizontal plane, assuming that the column is arranged vertically.

[0042] In this context, the term at least part of should be understood in a broad sense, providing for a liquid flow, which constitutes a part of the total flow, directed substantially perpendicular to the column side wall 2a as it passes across the column during sample processing.

[0043] An upper frit 5 may be arranged in the above-described column at a position which allows for the column to receive separation media 7 below. Thus, the upper frit 5 is used as conventional to retain separation media 7 and prevent it from reaching the column top during liquid sample processing.

[0044] According to the present invention, a volume herein denoted a column chamber 3 may be arranged in the column, above the upper frit 5, as shown in FIGS. 1 and 2. Thus, after having dispersed the separation media 7, the liquid flow is directed upward going through the top frit 5 and into the column chamber 3. The column chamber 3 volume may be for example about 40 mL, allowing processing of 40 mL aliquots of sample liquid. However, the column according to the invention may be configured to virtually any size and column chamber size, including virtually any volume of separation media 7. As the skilled person will appreciate, an essential factor for efficient processing is that the liquid flow into the column should be strong enough to disperse the separation media 7, at least to some extent. The skilled person will also appreciate that larger columns and lower aspiration backpressure will require faster liquid flows.

[0045] In an illustrative embodiment described here, the liquid flow rate was 100 mL/min.

[0046] Further, the positioning of said upper frit 5 in accordance with the invention may allow for separation media 7 as well as free space below said upper frit 5, as appears from FIGS. 1 and 2. In other words, when separation media 7 has been arranged in the column, such as in the form of a packed bed, a free volume will be available between the separation media 7 and the upper frit 5. During processing, the said volume will be more or less occupied with dispersed separation media, as described above.

[0047] During sample processing, the dispersion of the separation media 7 in accordance with the invention will enable an efficient mixing of a liquid sample with the separation media. During such mixing, molecules from the sample, such as biomolecules, with interact with the available surface area of the media, e.g. by ionic interactions; by hydrophobic interactions; by affinity interactions of lock-key type, depending on the kind of separation media selected. Thus, target molecules, such as biomolecules, may be bound, captured or otherwise retained according to any commonly known separation principle.

[0048] The column according to the invention may retain any separation media 7 suitable for processing of a certain sample, such as particulate chromatography media. As the skilled person will appreciate, the porosity of the upper frit 5, as well as the properties of the elongated frit 6, should be adapted to retain the separation media 7 in position during processing.

[0049] Thus, the elongated frit 6 according to the invention may comprises a mesh 10 having dimensions adapted for the intended separation.

[0050] The mesh 10 of the elongated frit 6 may be maintained in position by an appropriately positioned hollow support 9 comprising one or more holes 8 at appropriate locations and of suitable sizes to allow for liquid to pass the mesh 10.

[0051] For example, the mesh 10 may be positioned anywhere sufficiently close to the support 9 to be retained in a position that allows for the above-described advantageous flow across and substantially perpendicular to the elongated frit 6. Thus, the mesh 10 may be attached to a support 9, coated on a support 9 or wrapped around a support 9. As the skilled person will appreciate, such a support 9 may be made of any suitable material which is inert towards the conditions of the intended process, such as plastic.

[0052] Specifically, the support 9 should be hollow to allow for a liquid flow to enter at one end and exit across the length of the supported mesh 10. The support 9 may be defined by a circular, oval, triangular or other angular cross section, such as a substantially circular cross section resulting in a tubular support.

[0053] Further, to allow for a desired flow, the support 9 should include some kind of liquid passages, such as holes 8. As illustrated in the FIG. 4, the elongated frit 6 according to the invention may comprise of a tubular support 9 including evenly positioned holes 8, onto which mesh 10 has been wrapped.

[0054] Various designs of the elongated frit are encompassed by the present invention. For example, as discussed above, the elongated frit may be tubular, or at least partly tubular. The elongated frit, or part thereof, may be designed as having a variable cross section, such as a tube having a smaller diameter at its lower end than at its upper end; or a smaller diameter at its upper end than at its lower end. The diameter in such a design may be changing with a constant and resemble a cone, or an upside down cone. Alternatively, it may be designed as a bulb, or any other shape as long as it provides for a liquid flow which at least partly is passing the elongated frit as discussed above.

[0055] As appears from FIGS. 1-3, the column of the device according to the invention may be provided with a tubular column end 4. The tubular column end 4 may be relatively long as compared to conventional columns and may e.g. be of a length that constitutes a suitable part of, such as about one third of, the length of the column. The skilled person can adapt the length of the column end 4 as well as the column bottom wall 2b for a desired process. Advantageously, as discussed elsewhere in the present application, the elongated tube is arranged to be of a shorter length than the actual column length, providing for a part of the column where liquid and dispersed media above the upper end of the elongated frit, as illustrated in the drawings. Thus, in a specific embodiment, the elongated frit has an end above which separation media is provided. Further, such an elongated frit will allow liquid flow substantially vertically, whereby collection of solid contaminants within the frit is avoided.

[0056] As shown in FIGS. 1-3, the tubular column end 4 and the elongated frit 6 may be arranged as an integral part (one single part, or tube, or fused parts) allowing for liquid to flow through both, in either direction.

[0057] The present column is advantageously dimensioned to fit a liquid processing system. Such systems are conventionally used in the area of chromatography and other separation, such as biomolecule processing, and may include a computer that controls all of, or parts of the process using the appropriate software.

[0058] Thus, the device according to the invention may include means for passing liquid between the upper and the lower end of the column, which means are capable of providing positive and negative pressure.

[0059] As the skilled person will appreciate, said means may be a pump, such as a displacement pump.

[0060] Alternatively, or additionally, specific means are provided to support for top down flow, i.e. for adding liquid to a top liquid inlet 1b of the column and allowing the liquid to descend either by gravity, or by pumping. As the skilled person will appreciate, a device according to the invention may be used in top down and/or aspiration/dispensing, or in any mix or combination thereof. The invention may for example provide for a process wherein sample and elution liquid are both aspirated and dispensed at the bottom liquid inlet/outlet 1a, while wash liquid may be added at the top liquid inlet 1b, and for example allowed to pass the column by gravity. In such a wash step, the column may be taken out of the liquid processing step to allow for convenient wash using the top liquid inlet 1b, and reinserted after the completed wash to proceed e.g. with a step of eluting target molecules.

[0061] As discussed above, the separation media 7 present in the column may be dispersed during liquid aspiration, i.e. in the upward stroke of the pump. This dispersion enhances the contact of the sample with the column media and capture of target molecules is made fast and more complete than many prior art methods.

[0062] In the downward stroke of the pump, the column bed repacks and fluid flows through the bed. The liquid flow diverts, moving perpendicular to the separation media back through the elongated frit and out the end of the column. This process can be repeated as many times as necessary. Thus, the device of the invention may advantageously be used in back-and-forth flow, also known as dual flow chromatography (DFC).

[0063] The present invention has been shown to lower the backpressure in automatic processing of liquid samples, allowing for fast flows into the column and hence efficient sample processing.

[0064] Finally, the column volume of the separation device according to the invention is increased by the present design, so that up to 40 mL of sample can be processed in one stroke.

[0065] The device according to the invention may comprise two or more columns arranged for parallel processing, such as in automated processing.

[0066] The device according to the invention has been developed to capture, clean and recover biomolecules. In other words, the device may be used for one or more steps of a sample processing protocol preceding analysis of target molecule(s). Alternatively, the invention may be used in the separation of target molecules from complex liquid contents, where the device of the invention may be used in one or more steps of purification, optionally combined with conventional steps of purification of biomolecules such as centrifugation, chromatography, filtration, etc.

[0067] Thus, in a second aspect, the present invention relates to a method of separating at least one target molecule from a liquid, which method comprises providing at least one column, which is provided with a bottom liquid inlet/outlet 1a and optionally with a top liquid inlet 1b, which column retains a separation media 7; wherein at least part of an elongated frit 6 has been arranged substantially parallel to the column wall 2 and segregating the separation media 7 from the bottom liquid inlet/outlet 1a; and processing a liquid sample in said column in a method including aspiration and dispensing of fluid to and from the bottom liquid inlet/outlet 1a; adding a liquid at the top liquid inlet 1b; or any combination of using the bottom liquid inlet/outlet 1a and the top liquid inlet 1b.

[0068] More specifically, the method of the invention may comprise the steps of [0069] a) providing at least one column, which is provided with a bottom liquid inlet/outlet 1a and which retains a separation media 7; wherein at least part of an elongated frit 6 has been arranged substantially parallel to the column wall 2 and segregating the separation media 7 from the bottom liquid inlet/outlet 1a; [0070] b) providing a liquid which includes said at least one target molecule in admixture with other molecules; [0071] c) placing the bottom liquid inlet/outlet 1a of the column into said liquid; [0072] d) in an aspirating phase, applying a negative pressure to the column to bring liquid to pass from bottom liquid inlet/outlet 1a of the column and through the elongated frit 6 in a direction of flow which is substantially perpendicular to the column wall 2, whereby the liquid flow disperses the separation media 7; and, optionally, allowing time for capture of target molecule(s) by the separation media 7.

[0073] The method may comprise the further steps of [0074] e) in a dispensing phase, applying a positive pressure to the column to bring liquid to pass through the elongated frit 6 in a direction of flow which is substantially perpendicular to the column wall 2 towards the bottom liquid inlet/outlet 1a of the column; and [0075] f) collecting liquid exiting the bottom liquid inlet/outlet 1a of the column.

[0076] Optionally, the steps above are followed by the steps of [0077] g) repeating steps d) and f) with an eluting liquid that releases target molecules from the separation media 7; and [0078] h) collecting eluting liquid comprising released target molecule(s) via the bottom liquid inlet/outlet 1a of the column, optionally followed by a step of recovering and/or analyzing eluted target molecule(s).

[0079] The analysis of target molecule(s) may include any conventional or advantageous method, such as mass spectrometry (MS), optionally combined with chromatography, such as HPLC.

[0080] Further, the method may use back and forth flow of sample, wash and/or eluting liquid. Back and forth flow, also known as dual chromatography, is by now well known to the skilled person in this field, see e.g. U.S. Pat. No. 7,482,169 wherein processing with back and forth flow is described in detail.

[0081] As discussed above, since liquid may also be added to the top liquid inlet 1b of the column, the skilled person may vary the direction of liquid flow in a flexible way adapted to she specific circumstances.

[0082] As the skilled person will appreciate, one or more wash steps may be included after the aspiration of sample. Such wash step may be performed in the same manner as the aspiration step. One or more types of buffers may be used in the wash, and these washes may be performed in serial steps.

[0083] As the skilled person will appreciate, the wash may be performed in a top down flow of fluid where the fluid is introduced at the top liquid inlet 1b of the column. The fluid may flow through the column by gravity flow or a pump may be engaged to force fluid flow through the column

[0084] The elution may also be performed in in back-and-forth fluid flow or in top down fluid flow.

[0085] The target molecule may be a biomolecule, such as a protein or nucleic acid, or a fragment thereof.

[0086] For example, the target molecule may be a protein selected from the group consisting of peptides and antibodies, such as Fab fragments.

[0087] Alternatively, the target molecule(s) may be a DNA or an RNA molecule, such as a plasmid, e.g. a conjugative or non-conjugative plasmid.

[0088] The liquid provided in step b) may originate from a cell culture or a chemical synthesis. In step d), a liquid volume may be in the range of about 20 mL to about 1 L is aspirated. For example, a liquid sample of 40 mL may be aspirated, or any larger volume, depending on the application.

[0089] The positive and negative pressures of steps d) and f) may be provided by a suitable pump, such as a displacement pump.

[0090] In step a), at least two columns may be provided and processed in parallel in subsequent steps.

[0091] The columns may comprise different separation media; and/or different liquids may be aspirated into the separate columns. Back-and-forth flow, also known as dual flow chromatography (DFC), may be utilized in sample aspiration and/or elution, to increase the contact time between liquid and separation media.

[0092] The separation device according to the invention may be used in the present method. Thus, all details provided herein in relation to the device of the first aspect may be applicable to the method, and vice versa.

[0093] In one aspect of the invention, the above-discussed biomolecule may be a carrier of genetic material such as DNA or RNA. The carrier may be a modified or non-modified virus.

[0094] In this context, the term a non-modified virus is understood as a virus which carries at least one gene incapsulated by a protein coating and/or a lipid envelope, which virus is capable of reproduction inside the cells of a living host.

[0095] The term a modified virus is understood herein as any virus which has been modified as compared to its native state, for example a functional modification resulting in an attenuated virus; or a structural modification. The term a modified virus also include mutated virus forms.

[0096] Specifically, the target molecule separated according to the present invention may be an adenoassociated virus (AAV), which are replication-defective, non-enveloped viruses and have linear single-stranded DNA (ssDNA) genomes.

[0097] Since they are not capable of replication, AAV is commonly used as a vector to transport genetic material, for example in the context of gene therapy or vaccination.

[0098] Thus, in a specific aspect the present invention relates to a method of separating carriers of genetic information, preferably in the form of DNA or RNA, using a separation device as described in this application. Advantageously said carriers are viruses, such as adenoassociated virus (AAV).

[0099] The invention includes the separation of separating virus which includes genetic information. In an alternative, the invention includes the separation of virus envelopes, i.e. virus which do not comprise any genetic information. The latter kind of empty viruses are useful as vectors in vaccine or gene therapy applications, and enables its user to insert any relevant genetic material to obtain the desired result.

[0100] Since the present separation device is easily adaptable to automatic processing, this aspect of the invention may constitute one step in an automated process for the manufacture of vaccines or gene therapy preparations.

[0101] Thus, in this aspect, the invention relates to a method of separating viruses which, using a at least one column provided with a bottom liquid inlet/outlet and including separation media; wherein at least part of an elongated frit has been arranged substantially parallel to the column walls and segregating the separation media from the bottom liquid inlet/outlet.

[0102] The column may part of a separation device as described in the present application. Illustrative volumes of such columns may be in the range e.g. of 1 or 2 liters chamber sizes, wherein the bed size may be 10 or 20 mL at the low end and up to 200 or 400 mL volumes of separation media. However, larger columns are equally useful, such as chamber volumes of 3 or 4 liters or above. This aspect of the invention may also be applied to the larger bio manufacturing size, such as 1 meter diameter columns as commonly used in the field.

[0103] The above-discussed carriers may be virus, e.g. adenoassociated virus (AAV) or parts or fragments thereof. Such AAV may include genetic information; or may be virus without genetic information capable of having inserted DNA or RNA, as desired, using technology well known to the skilled person.

[0104] Ion exchange carriers may be applied to any virus. Other affinity carriers may be applied to viruses. This involves developing affinity groups that select for proteins on the surface of the virus and attaching these group to separation media.

[0105] The separation media used in this aspect may comprise native polymers, such as agarose or cellulose. Such separation media are well known to the skilled person, and may be obtained e.g. for the capture step of the herein discussed carriers using affinity chromatography wherein a sample originating from a mammalian cell culture is applied to the column. Such sample may have been pre-treated to remove cells, which is preferred in the case of mammalian cells that secrete the carriers produced therein into the cell culture.

[0106] Thus, the invention includes an affinity chromatography method wherein the separation media comprises ligands which have been specifically designed to capture virus.

[0107] An advantage of this aspect of the invention is that the pressures will be low so plastic and column liners can be used, which is an advantage when separating fragile biomolecules, such as viral vectors, in comparison to the currently used stainless steel. Also, providing the herein described columns with separation media is very easy, since there will be no requirement pack uniformly nor under pressure.

DETAILED DESCRIPTION OF THE DRAWINGS

[0108] FIG. 1 is provided to illustrate how, in a column 1 of the separation device according to the invention, in use the liquid flow is directed from a bottom liquid inlet 1a and up during a phase of aspirating liquid. It appears clearly how liquid is aspirated and passed inside the column end 4 and on into the elongated frit 6, here shown as a hollow tube which has been integrated into one piece with the column end 4, were the aspirated liquid flows at an angle substantially perpendicular to an upper frit 5; or to the surface of the separation media 7.

[0109] A pump (not shown) may be fitted to the column top applying negative and positive pressures. In the dispersion mode, negative pressure is applied to the column top and liquid flows into the column at the distal end. The liquid flows into the column through the elongated frit 6 and disperses the separation media 7. The flow continues to travel into the column chamber 3. Dispersed separation media 7 is contained in the column by the upper frit 5. A typical column has an overall length of 206 mm with an end tube length of 67 mm and a column body diameter of 35 mm.

[0110] The liquid flow into the column disperses the separation media 7, allowing a quicker capture of target molecules, such as plasmids.

[0111] FIG. 2 illustrates, in the same column as in FIG. 1, how liquid can flow in the opposite direction, i.e. from the top towards a bottom liquid outlet of the column, during dispensing of liquid. It appears clearly how the liquid passes through the elongated frit 6 at an angle substantially perpendicular to the upper frit 5, in order to leave the column via the elongated frit 6 and the column end 4.

[0112] The liquid flow out of the column will repack the separation media similar to its original state, such as a more or less packed bed.

[0113] FIG. 3 is an expanded view of an elongated frit 6, here too shaped as a tube frit, arranged in separation media 7. Frit liquid passages 11 are shown schematically as holes 8 (size not shown in dimension). In the embodiment shown here the bottom holes 8 are larger allowing better drainage of the column in reverse flow mode (dispensing liquid). The number, size and density of the holes will vary depending on the particular column embodiment and the strength of the pump to disperse the separation media. As the skilled person will appreciate, as the holes' sizes are decreased, the velocity of the liquid flow increases, which in turn increases the dispersing ability of the elongated frit. FIG. 3 also illustrates an advantageous feature of the column of the device of the invention in that the parallel column walls 2 ends, and the lower wall has a slope of about to the vertical. Said slope of the lower wall may be varied, but is advantageously not to the vertical.

[0114] FIG. 4 illustrates how an elongated frit 6 may be assembled by wrapping mesh 10 around a tubular hollow support 9.

[0115] In FIG. 4a, the hollow support 9 is shown as having holes 8 enabling fluid passage. In FIG. 4b, a tube fritan example of an elongated frit 6 according to the inventionhas been assembled from a tubular hollow support 9 over which porous mesh 10 has been wrapped. Specifically, each hole 8 covered with mesh 10 will constitute a frit liquid passage 11. Thus, due to the mesh 10, the holes 8 of the hollow support 9 will not allow separation media 7 to leave the column.

[0116] FIG. 5 is a table outlining the general performance for plasmid purification according to the invention, specifically envisaged for three sizes having an elongated frit designed as a tube frit.

EXPERIMENTAL PART

[0117] The present examples are provided for illustrative purposes only and should not be construed as limiting the invention as defined by the appended claims. All references provided below and elsewhere in the present application are hereby included herein via reference.

Example 1. Maxi Prep Purification Process Using a 5 mL Bed Volume Column in an Automated Instrument for Plasmid Purification

[0118]

TABLE-US-00001 TABLE 1 Buffers for maxi prep purification Maxi Prep Storage Volume Temperature Buffers (mL) Container for best yield Resuspension Buffer 29 60 mL bottle 4 C. overnight (RB) Lysis Buffer (LB) 34 60 mL bottle Room temperature Precipitation Buffer 41 60 mL bottle 4 C. overnight (PB) Endotoxin Removal 20 50 mL conical tube 4 C. overnight Buffer (ERB) Equilibration Buffer 30 30 mL conical tube Room (EQB) temperature Wash Buffer (WB) 120 Wash Buffer container Room temperature Elution Buffer 60 30 mL conical tube Room (2) temperature

[0119] The buffers consist of: [0120] Resuspension Buffer: 50 mM Tris-HCl, pH8.0; 10 mM EDTA [0121] Lysis Buffer: 0.2 M NaOH; 2.5% SDS [0122] Precipitation Buffer: 2.04 M KOAc, pH 4.5 [0123] Endotoxin Removal Buffer: Surfactant [0124] Equilibration Buffer: 50 mM Tris HCl, pH 7.0 [0125] Wash Buffer: 50 mM Tris HCl, pH 7.0; 300 mM NaCl [0126] Elution Buffer: 50 mM Tris HCl, pH 8.5; 500 mM NaCl

[0127] Buffer Aliquot (Manual) [0128] Aliquot the buffers according to the table below, the volumes are enough for one sample. [0129] Add 29 L of 0.1 mM thymolphthalein into the resuspension buffer. [0130] Store the buffers at recommended temperature overnight before usage.

[0131] Cell Lysate Preparation (Manual) [0132] Weight out 3 g of wet, fully thaw E. coli cell pellet [0133] Add RNase (20 mg) into Resuspension Buffer and mix well [0134] Add Resuspension Buffer with added RNase into the cell pellet and shake vigorously to break up the pellet [0135] Add Lysis Buffer into the cell mixture and gently capsizing the mixture until the solution turn completely blue (around 20-30 times) [0136] Add Precipitation Buffer into the cell mixture and gently capsizing the mixture until the solution turn completely white and no more blue color observed (around 20 times) [0137] Keep the cell bottle upside down until the separation between the cell lysate and cell debris is observed [0138] Gently pour the cell lysate sample into the filter in Instrument Sample Box to separate the cell lysate from cell debris [0139] Final collected cell lysate sample will be around 60-80 mL

[0140] Automated instrument: A fully automated instrument for plasmid purification was obtained from Phynexus (http/phynexus.com), adapted for the herein used sample volumes and provided with an elongated frit designed as a tube frit at its bottom end. Specifically, the tube frit used herein was designed in accordance with the drawings.

[0141] Refiltration: [0142] Sample volume after filtration: 60-80 mL [0143] Aspirating 20 mL from sample box and expel 20 mL at rate=30 mL/min on top of the filter [0144] Do this for 10 additions

[0145] Incubation: [0146] Transfer 15 mL of ERB endotoxin removal buffer to the sample box [0147] Delay for 30 min

[0148] Equilibrate column: [0149] Engage the tube frit column [0150] Aspirate and expel 30 mL of EQB (4 times)

[0151] Capture: [0152] Aspirate 30 mL of semi-clarified lysate and expel into first position, A1B1. [0153] Aspirate and expel 25 mL 7 times [0154] Input pauses after each cycle (to collect sample for agarose gel)

[0155] Wash: [0156] Aspirate and expel 30 mL of wash buffer [0157] Aspirate 30 mL of wash buffer from the wash buffer reservoir [0158] Expel 30 mL of wash buffer into the WASTE position [0159] Do into of 60 mL of wash buffer. [0160] Input pause to collect wash sample for agarose gel

[0161] Elution: Maxi Prep [0162] Aspirate 30 mL from elution buffer [0163] Expel 30 mL of elution buffer into another conical tube. [0164] Collect 20 mL, Concentration is 150 g/mL

Example 2. Buffer Volumes and Pellet Weights for Purifying Giga Prep and Mega Prep Scale Plasmid Purifications

[0165] The instrument described in Example 1 was used in this example 2.

TABLE-US-00002 TABLE 2a Buffer volumes and pellet weight for purifying giga prep scale plasmid purification Giga Prep (Cell Pellet Weight = 15 g) Volume Buffer (mL) Resuspension Buffer 87 Lysis Buffer 103 Precipitation Buffer 123 Endotoxin Removal Buffer 30 Equilibration Buffer 30 Wash Buffer 500 Elution Buffer 60 two aliquots Column Resin Volume 20

Refiltration

[0166] Transfer 40 mL of semi clarified lysate out of the sample reservoir and into the first position (A1B1) [0167] Aspirate 20 mL of semi clarified lysate and expel 20 mL (30 mL/min) on top of the filter. [0168] This is repeated 10 times

Incubation

[0169] 25 mL of Endotoxin Removal Buffer (ERB) is added to the sample reservoir. [0170] Incubate for 28 minutes

Equilibration

[0171] Column aspirates and expels 30 mL of equilibration buffer for 4 cycles

Capture

[0172] 30 mL of lysate is transferred from sample box to positions A1B1-A4B4. [0173] Each cycle aspirates 25 mL (500 mL/min) and expels 25 mL (70 mL/min) [0174] The column will perform the 8, 4, 2 and 2 cycles in A1B1, A2B2, A3B3, and A4B4, respectively.

Elution: Giga Prep

[0175] Aspirate 30 mL from elution buffer [0176] Expel 30 mL of elution buffer into another conical tube. [0177] Repeat Process on next sample aliquot

TABLE-US-00003 TABLE 2b Sample volumes giga prep scale Nucleic Sample Acid A260/ A260/ Vol Yield Name (ng/L) A280 A230 A260 A280 (mL) (mg) 15 g giga 188.97 1.87 2.22 3.78 2.02 29.44 5.56 elution 1 15 g giga 227.56 1.87 2.24 4.36 2.33 28.88 6.57 elution 2 12.14 mg total volume

Example 3. Buffer Volumes and Pellet Weight for Mega Prep Scale Plasmid Purification

[0178] The instrument described in Example 1 was used in this example 3.

TABLE-US-00004 TABLE 3 Buffer volumes and pellet weight for mega prep scale plasmid purification Mega Prep (Cell Pellet Weight = 7.5 g) Volume Buffer (mL) Resuspension Buffer 44 Lysis Buffer 52 Precipitation Buffer 62 Endotoxin Removal Buffer 20 Equilibration Buffer 30 Wash Buffer 300 Elution Buffer 60 Column Resin Volume 10

Example 4. Purification of wtAd5 AAV Virus

[0179] Any solid phase separation media having a functional group or a solid surface that can bind or partially bind virus particles may be used in the column of the invention.

[0180] In this example, serotype-specific Capture Select resins AAV8 and AAV9 are used for the purification of wtAd5 AAV virus. AAV vectors are produced by transient transfection. HEK293 cells are transfected using polyethyleneimine, polyethylene imine (PEI), and a 1:1:1 ratio of the three plasmids (inverted terminal repeat [ITR] vector, AAV rep/cap, and Ad helper plasmid). Transfected cells are grown in the presence of puromycin and are screened for AAV productivity following infection with wtAd5 virus. Cell pellets are harvested by centrifugation. The cell pellet is resuspended in 20 mM Tris [pH 7.5], 150 mM NaCl, 10 mM MgCl.sub.2. Benzonase and 0.1% Triton X-100 are added to suspended cells and the mixture is incubated at 37 degrees C. for 15 min to lyse the cells. The lysed mixture is centrifuged, and the supernatant is removed. The supernatant is filtered to produce clarified cell lysate containing AAV vector.

[0181] Two 50 mL chamber volume tube frit columns are packed with 10 mL each of AAV8 and AAV9 capture media. The columns are operated in back and forth flow at 100 mL/min. The columns were equilibrated with phosphate buffered saline (PBS) pH 7-7.5.

[0182] In other examples the column may be equilibrated with 10-50 mM sodium phosphate or Tris pH 6-8. 0.1-0.2 M NaCl or KCl may added to the conditioning buffer to prevent nonspecific adsorption due to protein/protein interactions.

[0183] 40 mL of the clarified cell lysate containing the rAAV vector is loaded onto the columns. The column is fully loaded. Addition aliquots of the sample virus are added as needed to fully load the column. After loading of the virus, unbound non-virus material is washed from the column.

[0184] Generally, two 40 mL washes are used. Samples with high impurity levels may require more wash steps with fresh wasting solution. Washing with a secondary or intermediate wash can increase impurity removal and make impurity clearance more predictable especially when there is interaction with the protein of interest and the impurity.

[0185] Secondary wash options include high-salt washes of up to 1 M NaCl. A Tris buffer may be added testing the effect of pH. Other additives include surfactants such as up to 0.05% (v/v) Tween 20. Chaotropic salts such as up to 0.2 M MgCl.sub.2 may be added. However, buffers containing phosphates must be avoided to prevent precipitation with Mg cation. Up to 20% ethanol may be added provided the lipid and capsid structure of the virus is not damaged.

[0186] Target virus particles differ in their binding and elution behavior and optimum elution conditions are determined experimentally. A starting point may be 50-100 mM citric acid pH 3.0. This can be lowered to pH 2. Other elution buffer components that can be used include phosphate, hydrochloric acid, glycine, acetate, or other components that buffer well at low pH. Other additives may be up to 2 M pH 7 MgCl.sub.2 and/or up to 50% propylene glycol. Combinations of these components can be used to optimize elution conditions.

[0187] A step gradient elution is used remove impurities and obtain a concentrated elution fraction. A fully loaded column is used. Otherwise, there may not be efficient release of the virus due to re-binding events during elution. The recovered virus is immediately neutralized to prevent denaturation of some molecules at low pH. The eluted virus solution was neutralized by adding 1 M pH 8.7 Tris-HCl.

Example 5. Purification of Influenza and Dengue Viruses

[0188] A single-step purification of influenza and dengue viruses using CHT XT Media (BioRad). A tube frit column having a 50 mL chamber was packed with 20 mL of the media. The two samples are ssRNA Influenza virus 80-120 nm diameter and ssRNA Dengue virus 50 nm diameter.

[0189] Production of the Influenza virus, Strain A/California/07/2009, is cultured on MOCK cells in minimal essential medium (MEM; Gibco) containing 10% fetal bovine serum (FBS) and L-glutamine in 225 mL flasks. When the cells are almost confluent, influenza virus is inoculated onto the cell monolayer at a 1:3,000 dilution in 75 ml of D-MEM/F-12 with trypsin, penicillin, and streptomycin (flu culture medium). The supernatant is harvested on days 3, 4, and 11 and clarified through 0.45 m filters.

[0190] Production of the Dengue virus: Type 2 strain ThNH7/93 is cultured on C6/36 cells. Cells are grown in 225 mL flasks that are precoated with poly-L-lysine at 100 lag/ml in phosphate buffered saline (PBS). Cells are cultured in modified EMEM Minimum Essential culture medium (MP Biomedicals) containing 10% FBS at 28 C. for 1 week. After the cells reach confluence, dengue virus type 2 is inoculated at a 1:1000 dilution onto the cell monolayer in 75 mL of modified EMEM containing 0.5% FBS and MEM Vitamin Solution (Invitrogen Corporation) and then cultured at 28 C. The medium is changed at day 3 and culture fluid (about 75 mL) was collected at day 7. The culture fluid was filtered through a 0.45 m filter to remove cells and large cell debris.

[0191] The columns are operated in back and forth flow at 100 mL/min. The viral purifications are performed as shown in Table 4 for influenza virus and Table 5 for dengue virus.

TABLE-US-00005 TABLE 4 Influenza purification protocol Step Buffer solvent pH Volume, mL Pre-wash 1M NaOH 40 Wash 600 mM sodium phosphate 7.2 40 Equilibration 10 mM sodium phosphate 7.2 40 Sample loading 144 mM sodium phosphate 7.2 40 (repeated until fully loaded) Wash 144 mM sodium phosphate 7.2 40 Elution Step gradient elution from 7.2 40 144-600 mM sodium phosphate

TABLE-US-00006 TABLE 5 Dengue purification protocol Step Buffer solvent pH Volume, mL Pre-wash 1M NaOH 40 Wash 600 mM sodium phosphate 7.2 40 Equilibration 10 mM sodium phosphate 7.2 40 Sample loading 144 mM sodium phosphate 7.2 40 (repeated until fully loaded) Wash 10 mM sodium phosphate 7.2 40 Elution Step gradient elution from 7.2 40 144-600 mM sodium phosphate

[0192] Wash and loading conditions may be varied to optimize the yield and purity of the virus.