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  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N7/00—Viruses; Bacteriophages; Compositions thereof; Preparation or purification thereof
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N5/00—Undifferentiated human, animal or plant cells, e.g. cell lines; Tissues; Cultivation or maintenance thereof; Culture media therefor
  • C12N5/0068—General culture methods using substrates
  • C12N5/0075—General culture methods using substrates using microcarriers
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12M—APPARATUS FOR ENZYMOLOGY OR MICROBIOLOGY; APPARATUS FOR CULTURING MICROORGANISMS FOR PRODUCING BIOMASS, FOR GROWING CELLS OR FOR OBTAINING FERMENTATION OR METABOLIC PRODUCTS, i.e. BIOREACTORS OR FERMENTERS
  • C12M25/00—Means for supporting, enclosing or fixing the microorganisms, e.g. immunocoatings
  • C12M25/16—Particles; Beads; Granular material; Encapsulation
  • C12M25/18—Fixed or packed bed
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N2710/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA dsDNA viruses
  • C12N2710/00011—Details
  • C12N2710/24011—Poxviridae
  • C12N2710/24111—Orthopoxvirus, e.g. vaccinia virus, variola
  • C12N2710/24132—Use of virus as therapeutic agent, other than vaccine, e.g. as cytolytic agent
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N2710/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA dsDNA viruses
  • C12N2710/00011—Details
  • C12N2710/24011—Poxviridae
  • C12N2710/24111—Orthopoxvirus, e.g. vaccinia virus, variola
  • C12N2710/24151—Methods of production or purification of viral material
• • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
  • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
  • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
  • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
  • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

• Viruses are used as therapeutics. Among such uses are as vaccines, gene therapy vectors and virotherapy agents.
• the manufacture of viruses for these purposes involves the replication of virus in suitable host cells, and then purification of the virus from the host cells.
• Host cells used for replication of viruses are either grown in anchorage-dependent, adherent culture conditions or in suspension culture conditions.
• An advantage of the suspension culture is that the cells can be cultured in a single bioreactor in large volume. Some viruses, however, do not replicate well in suspension-cultured cells.
• Anchorage-dependent cells in which viruses replicate well, are commonly cultured in roller bottles, which require a large number of bottles to obtain sufficient amounts. These processes, thus, are difficult and expensive to scale.
• the virus infected cells are harvested from the culture vessel or vessels, either the bioreactor or the roller bottles, and lysed to release the virus.
• the virus is purified from the total host cell-derived components using numerous and various steps including several or more of homogenization, sonication, centrifugation, filtration, affinity purification, chromatography, and density gradient ultracentrifugation.
• the culture conditions and the purification steps involved in the manufacture of viruses add complication and cost to the manufacturing processes, and can result in low yields. Hence, simpler and scalable methods for manufacturing viruses are needed.
• the methods employ virus-infected anchorage-dependent cells.
• virus is released from the host cells while the host cell components remain substantially attached to the culture surface.
• Host cell- derived components remain with cells remnants, while the virus is released into the cell culture medium, and the virus is purified by a simplified, cost-effective single step process of ultrafiltration or diafiltration or a two-step process of ultrafiltration and diafiltration.
• the purification process is high yield, and can be performed in a day or less.
• the process can be performed with cells grown in a bioreactor that is suitable for culturing anchorage-dependent cells, thereby combining the simplified purification methods with the advantages of bioreactor scale-up. Any virus, particularly enveloped viruses, which can infect and grow in cells that can be grown in an adherent format can be manufactured by these methods.
• the methods/processes are those for producing viruses from adherent cells cultured in bioreactors.
• the methods involve releasing virus from adherent host cells in a bioreactor, and purifying released virus by ultrafiltration and/or diafiltration. Described herein are various examples and aspects of such methods.
• the methods include the steps of: a) culturing host cells, comprising a virus, in a bioreactor, wherein the bioreactor comprises a matrix for growing adherent cells or cells entrapped therein, wherein the matrix is biocompatible; the cells are entrapped in and/or adhere to the matrix; and the density of the matrix is such that the cells remain attached under conditions in which cells are lysed and treated to release virus, and the flow of cell culture medium through the matrix is sufficient for cell growth; b) treating the cells to lyse them and release virus into the medium in the bioreactor; and then c) without further treatment, and in only one or in only two steps purifying the released virus from the cell culture medium.
• the one step is ultrafiltration or diafiltration; and the two steps are ultrafiltration and diafiltration. No other purification steps are employed. Thus, purification after lysing and releasing virus from the cells, is effected only by ultrafiltration and/or diafiltration. Purification is achieved in only the one or the two steps. The purification can be effected in 1 day or less.
• the bioreactor contains a matrix or surface onto which adherent cells attach, and suspension cells can be entrapped.
• the matrix (or macrocarrier or substrate or surface) can be a non-fixed attachment surface.
• the matrix or surface can be selected from among, but not limited to microcarrier beads, fibers, or woven mesh in suspension.
• the matrix or surface can be a fixed attachment surface.
• the bioreactor can be, for example, a packed bed bioreactor. Other configurations can be selected by the skilled artisan, as long as the bioreactor contains a matrix or surface for retaining the cells during growth and lysis.
• the host cells are cells that adhere to the matrix or that are entrapped in the matrix, including cells that normally grow in suspension, so that upon processing the cells and medium, the cells are not released. In general, the host cells are adherent cells.
• the cells can be primary cells, or cell lines.
• the particular cells are those suitable for growing a particular virus.
• the cell lines are known cell lines, such as CV-1 cells, KB cells, Vero cells, CHO cells and others.
• Cells include, but are not limited to, mammalian cells, including human and other primate cells; human cells include, for example, human fibroblast cells, epithelial cells and endothelial cells.
• the exemplified cells are CV-1 cells, and the virus is a vaccinia virus, such as a therapeutic vaccinia virus.
• the cell process medium Prior to purification, the cell process medium can be harvested. Optionally, the medium can be stored.
• the methods for producing the virus can include only steps a), b) and c), above, or can include additional steps prior to purification, which only includes the one or two steps of ultrafiltration and/or diafiltration.
• Releasing of the virus includes treatments, such as freeze /thaw and/or treatment with hypotonic medium and/or treatment with detergent, to lyse the cells.
• the virus is released into the medium from lysed cells by treatment with a protease and/or nuclease.
• the protease generally is a non-specific protease, such as a digestive enzyme, such as trypsin.
• the nuclease is a DNase or RNase, such as the endonuclease from Serratia marcescens, sold under the trademark Benzonase®. Treatment with nuclease is optional.
• the lysis and enzyme treatments can be performed sequentially or together. Lysis should precede or be conducted with the protease or nuclease treatment.
• the protease and nuclease treatments can be effected together or in any order.
• the virus can be any virus of interest, such as therapeutic viruses, including oncolytic viruses, and vaccines, and gene therapy vectors, and viruses for delivery of gene products.
• the viruses are enveloped viruses.
• Viruses include, but are not limited to, poxviruses, such as a vaccinia virus, myxoma virus, measles virus, reovirus, vesicular stomatitis virus (VSV), adenoviruses, adeno-associated virus, poliovirus, herpes viruses, Sindbis virus and Seneca Valley virus, and derivatives thereof modified to contain nucleic acid encoding a heterologous gene product.
• poxviruses such as a vaccinia virus, myxoma virus, measles virus, reovirus, vesicular stomatitis virus (VSV), adenoviruses, adeno-associated virus, poliovirus, herpes viruses, Sindbis virus and Seneca Valley
• the virus can be an oncolytic virus, such as vaccinia viruses (e.g., GL-ONC1, Pexa-Vec, wDD, JX-929, and WO- 12), vesicular stomatitis viruses (e.g., VSV-lFNbeta-NIS, VSV-E6/7, VSV-GFP), measles viruses (e.g., MV-N1S, MV-Edm, MV-NPL), seneca valley viruses (e.g., SW-001 and NTX-010), reovirus (e.g., Reolysin), adenoviruses (e.g., CGTG-102, Oncos-102, NG-348, NG-350, NG-347, NGaFAB, NG-aEpCAM, ONYX-015, CG7870, VCN-01, LOAd703, Ad5, Ad3/5, CRAd-CXCR4-5/3, O
• the viruses can be attenuated and/or modified.
• Oncolytic vaccinia viruses include, but are not limited to, Lister, such as L1VP strains and clonal strains thereof, Western Reserve (WR), Copenhagen (Cop), Bern, Paris, Tashkent, Tian Tan, Wyeth (DRYVAX), 1HD-J, 1HD-W, Brighton, Ankara, CVA382, Modified Vaccinia Ankara (MVA), Dairen 1, LC16m8, LC16M0, L1VP, ACAM2000, WR 65-16, Connaught, New York City Board of Health (NYCBH), EM-63 and NYVAC strain, and the modified Wyeth strain, JX-594.
• Lister such as L1VP strains and clonal strains thereof, Western Reserve (WR), Copenhagen (Cop), Bern, Paris, Tashkent, Tian Tan, Wyeth (DRYVAX), 1HD-J, 1HD-W, Brighton, Ankara, CVA382, Mod
• Exemplary of oncolytic L1VP strains of the virus is the strain designated GLV-lh68 (also referred to as GL-ONC1). Included among the viruses are modified viruses that encoded a heterologous gene product(s), including therapeutic products, and reporter genes and other detectable markers.
• Virus is purified by ultrafiltration and/or diafiltration.
• the skilled person can select the appropriate form of membrane and mode of ultrafiltration.
• ultrafiltration can employ, for example a membrane having a nominal molecular weight cut off of between 300 and 750 kilodaltons or a nominal porosity of between 0.05 and 0.2 pm. It can employ a membrane that contains polyethersulfone.
• the member can be flat, or can be a hollow fiber membrane.
• the ultrafiltration can be performed in a tangential flow mode, in a cross flow mode, or other mode selected by the skilled artisan.
• Ultrafiltration can be followed by diafiltration, or diafiltration can be performed without ultrafiltration. Recovery of processed released virus is greater than 50%, and can be as high as 90%, 95% or more.
• Figure 1 shows an exemplary bioreactor, the ATM1 iCellis® Nano Bioreactor and Control /Data Management System.
• Figure 2 shows micrographic images of the crystal violet stained carriers from the iCellis® Nano bioreactor Experiment 6, below.
• Figure 3 shows fluoromicrographic images of iCellis® Nano bioreactor carriers before and after infection with the therapeutic L1VP strain vaccinia virus designated GLV-lh68 (also designated GL-ONC1).
• FIG. 4 shows CV-1 cells (widely available well-known cell line, e.g., ATCC® CCL-70 growth profile and virus amplification of iCellis® bioreactor Experiment 1 and roller bottle controls.
• Figure 5 shows CV-1 growth profile and virus amplification of iCellis® bioreactor Experiment 2 and roller bottle controls.
• Figure 6 shows CV-1 growth profile and virus amplification of iCellis® bioreactor Experiment 3 and roller bottle controls.
• Figure 7 shows CV-1 growth profile and virus amplification of iCellis® bioreactor Experiment 4 and roller bottle controls.
• Figure 8 shows CV-1 growth profile and virus amplification of iCellis® bioreactor Experiment 5 and roller bottle controls.
• Figure 9 shows CV-1 growth profile and virus amplification of iCellis® bioreactor Experiment 6 and roller bottle controls.
• Figure 10 shows Individual growth curves of iCellis® bioreactor Nano Experiments 2 to 6.
• Figure 11 shows compiled growth data of CV-1 cells in iCellis® bioreactor Experiments 2 to 6 throughout the growth phase.
• Figure 12 shows compiled growth data of CV-1 cells in iCellis® bioreactor Experiments 2 to 6 through 150 hours of the growth phase.
• Figure 13 shows compiled cell density data of CV-1 cells in roller bottle controls of Experiments 1 to 6 through 300 hours of the growth phase.
• Figure 14 shows compiled cell density data of CV-1 cells in roller bottle controls of Experiments 1 to 6 through 150 hours of the growth phase.
• Figure 15 shows individual growth curves of iCellis® bioreactor Nano Experiments 1 and 3-6 after infection with GLV-lh68.
• Figure 16 shows virus amplification data from Nano Experiments 1 and 3-6.
• Figure 17 shows CV-1 growth profile of iCellis® bioreactor Experiments 7, 8 and 9.
• Figure 18 shows an evaluation of the virus extraction conditions from bioreactor carriers (Trial 4).
• Figure 19 shows an evaluation of the virus stability in TrypLE (Trial 8).
• Figure 20 shows the recovery of the virus during the harvest step from the bioreactor.
• the bioreactor is treated sequentially by circulation of various solutions and processing medium. Recovery of the virus is quantified by testing the collected circulating solution by viral plaque assay. The results show that the majority of the virus is released from the bioreactor after treatment with IX TrypLE and washes with 10 mM Tris-CL Washes with PBS and IM NaCl do not result in substantial additional virus recovery. Extraction of the bioreactor macrocarriers (matrix) after harvest showed no substantial virus remaining demonstrating the efficiency of the harvest procedure.
• a bioreactor refers to a cell culture device.
• the bioreactor contains a matrix for culturing adherent cells.
• the matrix is one that retains the cells, such that they are not released into the cell culture medium when lysed.
• An exemplary bioreactor are those sold under the trademark iCellis® bioreactor. This bioreactor was developed by ATM1 Life Sciences and is available from PALL Biosciences.
• carrier or alternatively “substrate” refer to any solid- state material that provides a biocompatible surface onto which adherent cells adhere in culture.
• matrix type carriers contain polyester fibers, optionally held within a cage (for example, of polypropylene) to immobilize the fibers.
• process medium refers to medium in the bioreactor in which the cells are cultured, and virus is produced; the medium used in processing the cells and producing the virus.
• large-scale manufacture is defined by the single patient dose, and the annual demand for doses. It varies for the virus and treatment; but each large-scale preparation provides about 1/6 to 1/12, such as about 1/10 of the number yearly doses.
• GLV-lh68 vaccinia virus
• large scale manufacturing provides an annual production of about 10,000 treatments at a dose of about 6 x 10 9 plaque forming units (pfu) per treatment dose or 6 x 10 13 total annual pfu. Assuming 8-12, such as 10 production batches per year, each large scale batch should produce 1,000 treatment doses or about 10 11 to 10 13 , such as about 5-6 x 10 12 pfu.
• virus titer or “viral titer” refers to the concentration of a virus and is a given number of infectious virus units per volume, such as plaque forming units (pfu) /mL.
• Virus titer can be determined by serial dilution of a sample for infection of target cells in order to quantify the number of infectious or active virus in a sample. For example, virus titer can be determined using a plaque assay.
• a “virus” or virus vector refers to any of a large group of infectious entities that cannot grow or replicate without a host cell. Viruses typically contain a protein coat surrounding an RNA or DNA core of genetic material, but no semipermeable membrane, and are capable of growth and multiplication only in living cells.
• oncolytic viruses refer to viruses that replicate selectively in tumor cells in tumorous subjects. Some oncolytic viruses can kill a tumor cell following infection of the tumor cell. For example, an oncolytic virus can cause death of the tumor cell by lysing the tumor cell or inducing cell death of the tumor cell.
• a therapeutic virus such as a therapeutic oncolytic virus
• a therapeutic virus is a virus that is used to treat disease or condition. Typically they are not pathogenic or have been rendered non-pathogenic.
• vaccinia virus or “VACV” or “W” denotes a large, complex, enveloped virus belonging to the poxvirus family. It has a linear, double-stranded DNA genome approximately 190 kb pairs in length, and which encodes approximately 200 proteins.
• Vaccinia virus strains include, but are not limited to, strains of, derived from, or modified forms of Western Reserve (WR), Copenhagen, Tashkent, Tian Tan, Lister, Wyeth, 1HD-J, and 1HD-W, Brighton, Ankara, MVA, Dairen 1, L1PV, LC16M8, LC16MO, L1VP, WR 65-16, Connaught, and New York City Board of Health vaccinia virus strains.
• L1VP Lister Strain of the Institute of Viral Preparations
• L1VP virus strain refers to a virus strain that is the attenuated Lister strain (ATCC Catalog No. VR-1549) that was produced by adaption to calf skin at the Institute of Viral Preparations, Moscow, Russia (Altshteyn et al. (1985) Dokl. Akad. Nauk USSR 285:696-699).
• the L1VP strain can be obtained, for example, from the Institute of Viral Preparations, Moscow, Russia (see. e.g., Kutinova et al.
• L1VP GLV-lh68 (also designated GL-ONC1; see, e.g., U.S. Patent No. 7,588,767, and US Patent Publication No. US-2016-0339066-A1) is an L1VP virus that contains ruc-gfp (a luciferase and green fluorescent protein fusion gene (see e.g. US Patent No. 5,976,796), beta-galactosidase (LacZ) and beta-glucuronidase (gusA) reporter genes inserted into the F14.5L, J2R (thymidine kinase) and A56R (hemagglutinin) loci, respectively.
• ruc-gfp a luciferase and green fluorescent protein fusion gene
• LacZ beta-galactosidase
• gusA beta-glucuronidase
• the genome of GLV-lh68 has a sequence of nucleotides set forth in SEQ ID NO: 3 or a sequence of nucleotides that has at least 97%, 98% or 99% sequence identity to the sequence of nucleotides set forth in SEQ ID NO: 3 of copending published application US-2016-0339066-A1.
• modified virus refers to a virus that is altered compared to a parental strain of the virus.
• modified viruses have one or more truncations, mutations, insertions or deletions in the genome of the virus.
• a modified virus can have one or more endogenous viral genes modified and/or one or more intergenic regions modified.
• exemplary modified viruses can have one or more heterologous nucleic acid sequences inserted into the genome of the virus.
• Modified viruses can contain one or more heterologous nucleic acid sequences in the form of a gene expression cassette for the expression of a heterologous gene.
• a modified L1VP virus strain refers to an L1VP virus that has a genome that is not contained in L1VP, but is a virus that is produced by modification of a genome of a strain derived from L1VP.
• the genome of the virus is modified by substitution (replacement), insertion (addition) or deletion (truncation) of nucleotides. Modifications can be made using any method known to one of skill in the art such as genetic engineering and recombinant DNA methods.
• a modified virus is a virus that is altered in its genome compared to the genome of a parental virus.
• Exemplary modified viruses have one or more heterologous nucleic acid sequences inserted into the genome of the virus.
• the heterologous nucleic acid contains an open reading frame encoding a heterologous protein.
• modified viruses herein can contain one or more heterologous nucleic acid sequences in the form of a gene expression cassette for the expression of a heterologous gene.
• an average human subject when referencing dosage, such as plaque forming units (pfu) /kg, based on mass kg of the subject, an average human subject is considered to have a mass of about 70 kg-75 kg, such as 70 kg.
• a production stage in which virus is introduced into cells in which the virus can replicate, and in which the cells are cultured under conditions in which virus is produced.
• the viruses can be any suitable virus, including enveloped viruses, including but not limited to, poxviruses, such as vaccinia virus.
• the cells are then lysed to release virus, and can be treated with an enzyme or enzymes that are nucleases and/or proteases.
• the process medium is harvested, and the virus is purified only by ultrafiltration or diafiltration or both.
• the second stage is only a one or two step process involving only ultrafiltration and/or diafiltration to produce purified virus.
• the processes thus, include the steps of growing adherent host cells, generally a cell line, in a bioreactor that contains packed biocompatible woven or fibrous matrix material, such as polyester, polyethylene terephthalate.
• the matrix is of sufficient density to retain by adherence and/or entrapment the cells and also, cellular debris when the cells are lysed.
• the host cells are cultured to an appropriate density, and then inoculated with the virus, and cultured to produce virus.
• the cells are lysed, such as by freezing and thawing or exposure to hypotonic medium or both, followed by treatment with an enzyme, such as protease, particularly one that cleaves non- specifically, such as trypsin.
• the cells optionally are treated with a nuclease before, with or after the protease.
• the lysed cells are retained by the matrix material.
• Virus is purified from the medium in only one or two steps, where one step is the ultrafiltration or diafiltration. If two steps are used, they are ultrafiltration and diafiltration. No additional purification steps, other than ultrafiltration and/or diafiltration are employed.
• scalable processes for producing (also referred to as methods) purified viruses, particularly therapeutic viruses, such as oncolytic viruses, vaccines, and gene therapy vectors. Because the methods can be practiced in a bioreactor, the methods are readily scaled up. Purification, which provides high yields of the virus, can be effected in one day or less. The resulting virus is produced in high yield, with as much as 95% or more, generally at least 50%, 60%, 70%, 80%, 90% recovery. C. Bioreactor and matrix
• a bioreactor is a vessel suitable for growing cells and contains a packed matrix substrate of woven or non-woven fibers, fabric or strips of fabric whose fibers or fibrous mesh allow cell attachment (or entrapment) and growth.
• the matrix can be in a fixed or packed bed or in a fluidized bed.
• the bioreactor contains a packed matrix of microcarrier beads, woven or non-woven fibers, fabric or strips of fabric whose fibers or fibrous mesh allow cell attachment and growth.
• the matrix is such that the cells are not detached or removed from the fabric by enzymatic digestion, such as trypsin digestion.
• the cells are not detached or removed from the fabric by enzymatic digestion such as trypsin.
• a hollow fiber bioreactor would not work because cells adherent to the inner surface of the hollow fibers would not be trapped in the matrix and the cells would be able to be detached by enzymatic digestion, such as trypsin.
• a hollow fiber bioreactor is not contemplated because cells adherent to the inner surface of the hollow fibers would not be trapped in the matrix and the cells can be detached by enzymatic digestion, such as trypsin.
• cells that are retained by the matrix such as anchoragedependent (“adherent”) host cells are grown in the bioreactor; the cells are infected with virus and grown in the bioreactor on the matrix substrate.
• bioreactors are the bioreactors sold under the trademark iCELLis® (Pall Life Sciences). U.S. Patent Nos. 8,597,939 and 8,986,979 describe such bioreactors.
• the iCellis® bioreactor is exemplary of a bioreactor platform includes a scalable line of single-use high cell density bioreactors, allowing small- scale (referred as the "nano" below) to large-scale manufacturing.
• This bioreactor contains a pre-packed, fixed bed of medical grade polyester microfibers providing a large surface area for growth in a compact bioreactor volume.
• the main bioreactor is equipped with a built-in magnetic drive impeller that circulates the medium through the fixed bed from the bottom to the top, ensuring low shear stress and high cell viability.
• the medium falls as a thin film down the outer wall where it takes up O2 to maintain dissolved oxygen level(s) in the bioreactor.
• Exemplary of matrix materials are material to which cells can adhere, adherent material, that are biocompatible so that they can be used to culture cells as described herein.
• Such materials include, but are not limited to, a polyester, a polypropylene, a polyalkylene, a polyfluorochloroethylene, a polyvinyl chloride, a polystyrene, a polysulfone, a cellulose acetate, a glass fiber, a ceramic particle, and an inert metal fiber. Fibers of these materials can be used, in woven or non-woven form.
• the matrix material is polyethylene terephthalate (PET), a polyester.
• the matrix can be coated with materials that promote cell attachment such as a Matrigel® cell culture substrate, an extra cellular matrix component (e.g., fibronectin, chondronectin, laminin, ProNectin® F), a collagen, or a poly L lactic acid in order to improve its biocompatibility, its cell adherence or its cell retention.
• a Matrigel® cell culture substrate an extra cellular matrix component (e.g., fibronectin, chondronectin, laminin, ProNectin® F), a collagen, or a poly L lactic acid in order to improve its biocompatibility, its cell adherence or its cell retention.
• the density of the matrix is sufficient so that the cells and, after lysis, cell debris remain trapped, but is not too high to impede cell medium flow through the matrix and bioreactor, which is necessary for cells to grow.
• the density of the matrix is such that the cells remain entrapped in the matrix, but the density is not too high to prevent fluid flow throughout the matrix.
• the matrix can be a mesh, such as one composed of polyester fiber.
• the diameter of the fiber is typically about 10-40 micrometers.
• the mesh can be purchased from a textile manufacturer either as bulk fiber, non-woven mesh, or as woven fabric. Some manufacturers produce the fiber specifically for medical purposes; and it is qualified for biocompatibility.
• This medical grade mesh or fabric is of particular utility for the processes and methods herein in that it is compatible with cell attachment and growth in a bioreactor that is used for biopharmaceutical production.
• the density of the packing of such materials is a factor that influences cells remaining trapped in the matrix.
• the greater packing density is more restrictive to media flow and requires more agitation force to achieve the same media flow.
• Exemplary densities are about 80-160 g/L, such as 90-150 g/L, such as 96 g/L - 144 g/L. This range retains cells; the greater packing density is more restrictive to media flow and requires more agitation force to achieve the same media flow.
• the iCELLis® bioreactor system (see, e.g., Figure 1) accommodates up to 500 m 2 of growth area.
• the projected yields of virus, such as vaccinia virus, for scale-up using 25 L of fixed-bed volume, are as follows:
• the methods involve releasing virus from adherent host cells in a bioreactor, and purifying released virus by one or two steps of ultrafiltration and/or diafiltration.
• the methods are used to manufacture viruses, including for clinical use, at reduced cost relative to conventional virus manufacturing methods.
• the purification method which requires only ultrafiltration and/or diafiltration reduces the time for purification, and provides higher yields of virus. Purification can be effected in a day or less.
• the cells which are adherent cells, or cells adapted to grow in or on a matrix support, are cultured in a bioreactor.
• the host cells can be any cells suitable for growing virus; selection of the cell can depend on the particular virus. Generally, the host cells are adherent cells.
• the cells include, but are not limited to, mammalian cells of primary origin; transformed or otherwise immortalized cells; and cell lines. Exemplary of such cells are: human fibroblast cells; human epithelial cells; and human endothelial cells.
• Cell lines include, but are not limited to: CV-1 cells; Vero cells; and CHO cells. The cells can be recombinant; and/or genetically modified.
• Cells are seeded into the reactor in an appropriate amount.
• amount can be about 3-6 x 10 3 cells/cm 2 , such as about 4-5 x 10 3 cells/cm 2 , such as 4.5x 10 3 cells/cm 2 .
• the cells are grown for sufficient time, generally 8 days to 20 days depending on growth conditions, to reach an optimal density for infection with virus, such as, for example, about 1-3 x 10 5 cells/cm 2 , such as about 1.5 x 10 5 cells/cm 2 .
• the skilled person knows or can empirically determine optimal densities for growth and infection of particular cells.
• cells are seeded into the reactor at 4.5E3 cells/cm 2 , and grown to an optimal infection density of 1.5E5 cells/cm 2 , which can take about 8 days to 20 days depending on growth conditions.
• the cells are infected at a specific MOI (0.2 to 0.002, such as 0.02 to 0.1), and virus production proceeds for about 96 hours. Because the purification is only a single step (ultrafiltration and/or diafiltration), it can be conducted in a single day compared to conventional purifications which are typically 5-7 steps conducted over a number of days.
• the bioreactor can be adapted for growth of adherent cells; the iCellis® bioreactor; include elements as disclosed in US Patents 8,597,939 and 8,986,979; contain a matrix or surface onto which adherent cells may attach; contain a non-fixed attachment surface such as microcarrier beads, fibers, or woven mesh in suspension; and/or contain a fixed attachment surface as in a packed bed bioreactor.
• adherent host cells are cultured in the bioreactor under controlled conditions; in the presence of cell culture medium and medium additives that support the nutritional requirements of the cells; at a temperature suitable for optimum growth of the cells (e.g., 37 ⁇ 3° C for mammalian cells); at a pH suitable for optimal growth of the cells ⁇ e.g., pH 7.3 ⁇ 3 for mammalian cells); with agitation or circulation of the medium or culture suitable for optimal growth of the cells; in a fixed bed reactor at a linear flow velocity of medium at about 0.5 to 5 cm/second; at a dissolved oxygen level suitable for optimal growth of the cells (e.g., 50 ⁇ 25% for mammalian cells); and/or to high cell density relative to the medium volume of the bioreactor (e.g., >2x10E6 cells/mL, or >lxlOE7 cells/mL).
• a temperature suitable for optimum growth of the cells e.g., 37 ⁇ 3° C for mammalian cells
• viruses contemplated herein include, but are not limited to, therapeutic viruses, such as oncolytic viruses, viruses for vaccines, and viruses for any purpose, including for recombinant production of an encoded product.
• the viruses generally are enveloped viruses that can be released to the cell culture medium.
• Virus is introduced into the cells, which then are cultured so that the virus replicates.
• the cells are infected at a specific multiplicity of infection (MOI), which depend on the virus.
• MOI multiplicity of infection
• the virus is a vaccinia virus, and the MOI is about 0.002.
• Virus production proceeds for a time to result in maximum amount of virus, such as, for vaccinia, such as the virus designated GL-ONC1 (GLVlh-68), about 72-120, such as 90-120, such as 96, hours.
• the host cells can be infected with virus before being introduced to the bioreactor, or the adherent host cells can be infected with virus while growing in the bioreactor.
• Bioreactor medium and/or other culture conditions can be adjusted before or after introduction of infected or uninfected host cells to optimize infection efficiency and/or replication of the virus.
• Viruses include, but are not limited to, poxviruses, herpesviruses, adenoviruses, adeno-associated viruses, lentiviruses, retroviruses, rhabdoviruses, papillomaviruses, vesicular stomatitis virus, measles virus, Newcastle disease virus, picornavirus, Sindbis virus, papillomavirus, parvovirus, reovirus, coxsackievirus, influenza virus, mumps virus, poliovirus, and semliki forest virus.
• the virus can be native; wild-type; recombinant; or genetically modified.
• the virus can selected from among a Newcastle Disease virus, parvovirus, vaccinia virus, myxoma virus, measles virus, reovirus, vesicular stomatitis virus (VSV), oncolytic adenoviruses, adeno-associated virus, poliovirus, herpes viruses, Sindbis virus and Seneca Valley virus, or a derivative thereof that is modified to contain nucleic acid encoding a heterologous gene product.
• the virus can be an oncolytic virus.
• the oncolytic virus can be a vaccinia virus, wherein the vaccinia virus is selected from among Lister, Western Reserve (WR), Copenhagen (Cop), Bern, Paris, Tashkent, Tian Tan, Wyeth (DRYVAX), 1HD-J, 1HD-W, Brighton, Ankara, CVA382, Modified Vaccinia Ankara (MVA), Dairen 1, LC16m8, LC16M0, L1VP, ACAM2000, WR 65-16, Connaught, New York City Board of Health (NYCBH), EM-63, and NYVAC strains.
• the vaccinia virus can be derived from a Lister strain virus: an LIVP virus or a clonal strain of an L1VP virus.
• the virus can be a vaccinia virus, such as a recombinant vaccinia virus.
• a vaccinia virus such as a recombinant vaccinia virus.
• therapeutic vaccinia viruses are the modified LIVP strain viruses, such as those described in U.S. Patent Nos. 7,588,767, 8,857,927, 9,005,602, 8,323,959 and 7,754,221, particularly, the virus designated GLV-lh68 (GL- ONC1), and the clonal strains described in U.S. Publication No.
• modified Wyeth strain vaccinia virus such as the virus designated JX-594 (also referred to as Pexa-Vec, Sillajen Biotherapeutics), which is a replication-competent Wyeth strain vaccinia virus that is modified so that the thymidine kinase gene is inactivated, and virus encodes and expresses the human GM-CSF and LacZ genes.
• JX-594 also referred to as Pexa-Vec, Sillajen Biotherapeutics
• the virus can be a modified form containing nucleic acid encoding a heterologous gene product, wherein the heterologous gene product is a therapeutic or reporter gene product.
• the heterologous gene product is selected from among an anticancer agent, an antimetastatic agent, an antiangiogenic agent, an immunomodulatory molecule, an antigen, a cell matrix degradative gene, genes for tissue regeneration and reprogramming human somatic cells to pluripotency, enzymes that modify a substrate to produce a detectable product or signal or are detectable by antibodies, proteins that can bind a contrasting agent, genes for optical imaging or detection, genes for PET imaging and genes for MR1 imaging.
• the heterologous gene product can be a therapeutic agent selected from among a hormone, a growth factor, cytokine, a chemokine, a costimulatory molecule, ribozymes, a transporter protein, a single chain antibody, an antisense RNA, a prodrug converting enzyme, an siRNA, a microRNA, a toxin, an antitumor oligopeptide, a mitosis inhibitor protein, an antimitotic oligopeptide, an anti-cancer polypeptide antibiotic, an angiogenesis inhibitor, a tumor suppressor, a cytotoxic protein, a cytostatic protein and a tissue factor.
• the viruses can encode and, if desired, express heterologous gene products.
• the products include therapeutic products that can be delivered by the virus.
• exemplary of such products is an anticancer agent, an antimetastatic agent, an antiangiogenic agent, an immunomodulatory molecule, and an antigen.
• Other exemplary products include, but are not limited to, a therapeutic agent selected from among a hormone, a growth factor, cytokine, a chemokine, a costimulatory molecule, ribozymes, a transporter protein, a single chain antibody, an antisense RNA, a prodrug converting enzyme, an siRNA, a microRNA, a toxin, an antitumor oligopeptide, a mitosis inhibitor protein, an antimitotic oligopeptide, an anticancer polypeptide antibiotic, an angiogenesis inhibitor, a tumor suppressor, a cytotoxic protein, a cytostatic protein and a tissue factor.
• Viruses also can deliver nucleic acids encoding genes, such a cell matrix degradative gene, genes for tissue
• the viruses can encode detectable reporter products, such as, but are not limited to, enzymes that modify a substrate to produce a detectable product or signal or are detectable by antibodies, proteins that can bind a contrasting agent, genes for optical imaging or detection, genes for PET imaging and genes for MR1 imaging.
• detectable reporter products such as, but are not limited to, enzymes that modify a substrate to produce a detectable product or signal or are detectable by antibodies, proteins that can bind a contrasting agent, genes for optical imaging or detection, genes for PET imaging and genes for MR1 imaging.
• virus In the production stage of the process, the cells in the bioreactor, are lysed, and treated to release virus. In accord with the methods herein, virus can be released from host cells without substantial mechanical homogenization.
• the lysis method should be such that the cells remain adhered to or are entrapped in the matrix.
• the cells are lysed by freezing and thawing.
• release and recovery of the virus can be enhanced by hypotonic shock. This can be effected, for example, by, addition of aqueous solutions with total ionic strength less than approximately 0.05 M, such as 0.01 M or less, or such as 0.001 M to the freeze /thawed bioreactor.
• the cells and lysed cell debris remains attached/entrapped in the matrix and is not released, or is substantially not released, into the cell culture medium with the virus.
• Release of the virus from the entrapped/adhered cells is effected by suitable methods to effect lysis, such as freeze/thaw of the bioreactor and/or exposure to hypotonic medium, and, then, enzymatic digestion with enzymes, such as proteases and, optionally, nucleases.
• proteases include trypsin, and other such proteases normally used to detach cells, but that by virtue of the matrix do not detach the cells.
• proteases are trypsin (porcine pancreatic source), TrypLE (recombinant bacterially-produced enzyme with trypsin-like enzymatic activity), Accutase® solution (Sigma Aldrich; a mixture of proteolytic and collagenolytic enzyme activities), proteinase-K, papain and subtilisin, other such protease with nonspecific cleavage sites to digest proteins, bromelain, ficain, and others.
• trypsin porcine pancreatic source
• TrypLE recombinant bacterially-produced enzyme with trypsin-like enzymatic activity
• Accutase® solution Sigma Aldrich; a mixture of proteolytic and collagenolytic enzyme activities
• proteinase-K proteinase-K
• papain and subtilisin other such protease with nonspecific cleavage sites to digest proteins, bromelain, ficain, and others.
• virus can be released from host cells by a process involving freeze/thaw.
• virus can be released from cells in a fixed bed reactor in a process where the culture medium is removed and the bioreactor is frozen at about ⁇ 10°C for >60 minutes, or at ⁇ -60 °C for >15 minutes, or at ⁇ -120 °C for
• the bioreactor can be frozen, for example, by placing it into a freezer, by jacketed refrigeration, by immersion in dry ice, by immersion in liquid nitrogen, by infusion of liquid nitrogen vapor, or other such methods.
• the bioreactor can be thawed by suitable methods, such as exposure to room temperature air, by addition of liquid medium, such as phosphate buffered saline (PBS), or by other such methods known to those of skill in the art.
• liquid medium can be added to the bioreactor at temperature selected to maximize cell lysis while optimizing the stability of the virus (e.g., ⁇ 50 °C or 37 ⁇ 3 °C).
• hypotonic shock can be effected, for example, by the addition of aqueous solutions so that the total ionic strength is less than approximately 0.05 M, such as 0.01 M or less, or 0.001 M to the freeze/thawed bioreactor.
• the virus can be released from host cells by exposure to hypotonic medium.
• the hypotonic medium can be water or aqueous buffer with ionic strength ⁇ 50 mM.
• Hypotonic condition can be accomplished by dilution of the bioreactor medium with hypotonic solution such as water to achieve a final ionic strength ⁇ 50 mM.
• the medium can be removed and replaced with hypotonic medium of ionic strength ⁇ 50 mM.
• the hypotonic medium can be agitated or circulated.
• release and recovery of the virus can be enhanced by treatment with an enzyme with DNase and/or RNase activity either during or after the freeze/thaw and/or hypotonic shock or after in a suitable buffer.
• a nuclease is the an endonuclease sold under the trademark Benzonase® endonuclease or other enzyme with DNase and/or RNase activity.
• Benzonase® nuclease sold by Millipore; see, e.g., Franke et al, (1998) FEBS Letters 425 ⁇ 517-522), which digests native or heat-denatured DNA and RNA, is a genetically engineered endonuclease from Serratia marcescens.
• Serratia nuclease it is a protein dimer of 30 kDa subunits with two essential disulfide bonds.
• Conditions for releasing virus from host cells can be selected to maximize cell lysis while optimizing the stability of the virus.
• the temperature can be ⁇ 50°C; the pH can be >4 and ⁇ 10; and/or the linear flow velocity through a packed bed bioreactor can be >2 cm/sec.
• Virus can be released from host cells by exposure to medium containing detergent.
• the detergent can be ionic, cationic or anionic.
• the concentration of detergent can be, for example, ⁇ 1%.
• Virus can be released from host cells by digestion with one or more enzymes.
• the cells are exposed to a digestion medium, which has an ionic strength and pH optimal for the selected digestive enzyme(s).
• Exemplary digestion medium can be buffered at pH ⁇ 8, such as neutral pH between 7 and 8, such as pH 7.4, such as can be PBS.
• Digestion medium contains a sodium salt; and/or contains a magnesium salt.
• the digestive enzyme can be a protease, as discussed above, such as trypsin, or recombinant trypsin (TrypLE).
• the protease treatment can be effective combined with or replaced with a nuclease such as the endonuclease from Serratia marcescens sold as Benzonase®.
• Digestion can employ the nuclease and the protease sequentially or in combination.
• Digestion temperature can be set to optimize enzymatic digestion and optimize stability of the virus (e.g., 31 °C).
• the digestion time can be set to optimize enzymatic digestion and optimize stability of the virus ⁇ e.g., >1 hour).
• Virus can be harvested by removing the digestion medium, and purifying the virus therefrom.
• the rinsing medium can be water; can be a buffer of low ionic strength; can be a buffer of high ionic strength; has a pH >9; and/or can be 10 mM Tris-Cl, pH 9.0.
• the purification process following release of the virus from the cells and enzyme digestion is a single (or dual) step of ultrafiltration or diafiltration or both. No other purification steps are employed or needed. Purification can be conducted in a single day. Conventional prior art purifications typically employ 5-7 steps conducted over a number of days. Not only is there a reduction in time and a cost savings and higher yield by virtue of the purification method provided herein, the fewer steps and shorter time reduces degradation and inactivation of virus that occurs over time during processing.
• Released virus in the culture medium is purified by ultrafiltration or diafiltration, or both. No other purification steps are employed. Released virus can be purified by ultrafiltration.
• the skilled person can select appropriate filtration membranes and protocols.
• filtration medium can be chosen to optimize removal of impurities and optimize stability of the virus; can be water; can be an aqueous buffer; can be high ionic strength; can be low ionic strength; can be physiological ionic strength; and/or can be suitable for administration to animals or humans.
• the recovery of processed released virus can be greater than 50%; greater than 70%; greater than 80%; greater than 90%; or greater than 95%.
• Virus can be purified using large porosity ultrafiltration membranes typically used to remove contaminating viruses from biopharmaceutical preparations. Such membranes typically have porosities of greater than or equal to 300,000 daltons molecular weight cut off such that protein products pass through the membrane while viruses are retained. Using these “virus clearance” membranes in the opposite mode (tangential flow or cross flow filtration mode rather than a single pass-through mode) viruses can be retained and purified while proteins, nucleic acids, and other impurities are removed.
• the ultrafiltration membrane can be chosen to minimize virus binding and maximize virus retention.
• the ultrafiltration membrane can be one that has a porosity with a permeability cut off to prevent virus passage through the pores.
• the ultrafiltration membrane has a nominal molecular weight cut off of between 300 and 750 kilo-daltons or a nominal porosity between 0.05 and 0.2 pm;
• the ultrafiltration membrane includes polyethersulfone (PES);
• the ultrafiltration membrane can be, for example, a flat membrane or a hollow fiber membrane; ultrafiltration can be performed in a tangential flow or cross flow mode; ultrafiltration can be performed under conditions to optimize virus retention and optimize virus stability and/or ultrafiltration can be performed at ⁇ 10 °C.
• Membranes composed of materials that have low binding of virus are suitable for high virus recovery.
• Examples of such membranes include, but are not limited to Centramate T-series cassette flat membranes (300 kd mwco, PALL Life Sciences, Inc.) and MidiKros hollow fiber membrane cartridges (500 or 750 kd mwco, Spectrum Laboratories, Inc.), all composed of polyethersulfone (PES).
• Centramate T-series cassette flat membranes 300 kd mwco, PALL Life Sciences, Inc.
• MidiKros hollow fiber membrane cartridges 500 or 750 kd mwco, Spectrum Laboratories, Inc.
• Ultrafiltration can be followed by diafiltration with high ionic strength, neutral pH and/or low ionic strength, high pH filtration solutions. As disclosed herein, such methods are capable of recovering greater than 90% of the virus from the lysed cells at high purity.
• released virus can be purified by diafiltration.
• diafiltration can be performed with a membrane chosen to minimize virus binding and maximize virus retention; the diafiltration membrane can be the same one used for ultrafiltration; diafiltration can be performed by addition of filtration medium to the ultrafiltration retentate; and/or diafiltration can be conducted by addition of >5 filtration volumes, each equivalent to the retentate volume.
• the resulting virus is any virus of interest, particularly vaccinia virus.
• the virus can be biologically active, can be used to infect cells, can be used to express homologous or heterologous genes or proteins, and/or can be used to elicit an immunological response.
• CV-1 cell cultivation All CV-1 cells used in these experiments were derived from CV-1 Working Cell Bank (WuXi Apptec Acc# 09-002346, Lot# 090170885, 6.0x106 cells/vial in 1.0 mL, Freeze date 09DEC2009, Passage 45). These cells were further expanded and cryopreserved at passage 55. Aliquots of these cells were used in the iCellis® bioreactor Nano experiments. CV-1 cells were cultivated in DMEM supplemented with 10% FBS in T-flasks and roller bottles in 37°C, 5% CO2 incubators.
• iCellis® bioreactor Nano experiment cultures were infected with GLV-lh68, a recombinant vaccinia virus derived from the L1VP strain.
• GLV-lh68 P3 2-28-14 was used for infection of Nano Experiments 1- 6 and GLV-lh68 P3 8-28-14 for Nano Experiments 7-11.
• the amount of seed virus used was calculated based on the cell number at time of infection, the titer of the seed virus, and the specified MOI.
• iCellis® bioreactor Nano Bioreactor procedures were calculated based on the cell number at time of infection, the titer of the seed virus, and the specified MOI.
• the iCellis® bioreactor Nano Bioreactor was set-up and operated according to the manufacturer’s recommended procedures (“Integrity iCellis® bioreactor Nano Bioreactor with Control System User Guide”-Document reference USG_nano_mycontrol_01, version 01, February 2014.)
• Viral Plaque Assay was conducted on bioreactor and purification samples infected with GLV-lh68. Samples of reactor medium were removed and frozen at -20°C. Samples of macrocarrier (the matrix) in the bioreactor containing 1 or 2 carriers were removed from the bioreactor and placed in a microcentrifuge tube containing 1 mL of fresh DMEM-10% FBS medium and frozen at -20°C. Prior to testing, medium and carrier samples were thawed at room temperature or 37°C, diluted in DMEM-2% FBS and plated on CV-1 cells for plaque formation.
• VP A Viral Plaque Assay
• Trypsinization of carriers was conducted by placing one carrier into 0.5 mL of 0.05% Trypsin/0.53 mM EDTA or lx TrypLE in PBS and incubating at 37°C for up to 60 minutes with intermittent vortex mixing. Samples were diluted by addition of 1.0 mL of DMEM-10% FBS. Purification samples were stored on ice and tested without prior freezing. VPA was conducted using CV-1 cells according in 24-well multi-well plates. Viral plaques were visualized by crystal violet staining.
• E-Glucuronidase Assay (GUS-A) was conducted on samples of reactor medium and macrocarriers, diluted in DMEM-2% FBS and tested.
• the Anorogenic substrate Cl-MUGlcU (stock solution: 36.5mM in DMSO) was used in assay buffer consisting of phosphate buffered saline solution containing 2% FBS.
• Assays were carried out in 96-well multi-well plates and read in the SpectraMax® M5 plate reader using SoftMaxPro v5.4.4 software.
• Protein and DNA content were measured using Quant-iT Protein Assay Kit (Invitrogen) and Quant-iT dsDNA Assay Kit (high sensitivity, Invitrogen), respectively. Assays were carried out in 96-well multi-well plates and read in the SpectraMax® M5 plate reader using SoftMaxPro v5.4.4 software.
• the seeding density for all experiments was 4.5xl0 4 cells /cm 2 , matching the seeding density of CV-1 cells in roller bottles.
• the target cell density for infection was 1.0 to 2.0xl0 5 cells/cm 2 .
• FIG. 3 shows carriers at preinfection, 24 hours post-infection, and post-harvest. Clearly evident was the intense green GFP fluorescence associated uniformly with the fibers 24 hours post-infection. At higher magnification, individual fluorescing centers were observed on the fibers corresponding to the location of the cells. The fluorescence was considerably reduced.
• Virus amount was either expressed as PFU/cm 2 of surface area, PFU/cell (cell number determined at time of infection), or as total PFU in the reactor (either carrier- associated or in the medium).
• the reactor was seeded with CV-1 cells of passage 71 at 4.5xl0 4 cells /cm 2 and at 24 hours, 3.4xl0 4 cells/cm 2 were attached to the bioreactor (76%).
• the agitation rate of the culture was set to create a linear flow velocity of 1.6 cm/sec during cell seeding and raised to 2.5 cm/sec through Day 10.
• the flow velocity was reduced to 1.6 cm/sec on Day 10, 1.0 cm/sec on Day 14, and 0.5 cm/sec on Day 16.
• the volume culture medium was increased from 600 mL to 762 mL after seeding and to 2286 mL on Day 3.
• the medium was exchanged on Days 3, 6, 10, 14, and 16.
• Nano Experiment 2 was performed by reducing the flow velocity immediately after cell seeding.
• the reactor was seeded with CV-1 cells of passage 76 at 4.5xl0 4 cells/cm 2 in 600 mL of medium at a linear flow velocity of 1.6 cm/sec. After 1 hour the volume of culture medium was increased to 1342 mL, and the linear velocity was increased to 2.5 cm/sec. After 24 hours the attached cell density was 3.5xl0 4 cells/cm 2 (78%). On Day 1, the volume the culture medium was increased to 2286 mL, and the flow velocity was reduced and maintained at 0.5 cm/sec. The culture medium was changed on Day 5.
• Nano Experiment 3 was a repeat of Experiment 2 except that the linear flow velocity after Day 1 was further reduced to 0.44 cm/sec.
• the reactor was seeded with CV-1 cells of passage 78 at 4.5xl0 4 cells/cm 2 and after 24 hours, 3.9xl0 4 cells/cm 2 were attached (87% seeding efficiency).
• the cell density had achieved 1.7xl0 5 cells/cm 2 .
• the culture was infected with GLV-lh68 at an MOI of 0.1 (1.74xl0 8 pfu). The flow velocity was increased and maintained at 0.5 cm/sec. Virus increased immediately on the carriers, whereas the virus in the culture medium remained low. Virus amplification was intentionally extended to Day 8 post-infection to examine the full amplification profile. Virus increased through Day 2 postinfection, then remained relatively stable through Day 6, before decreasing significantly at Days 7 and 8. The decrease did not correspond with an increase in virus in the culture medium.
• the reactor was seeded with CV-1 cells of passage 81 at 4.5xl0 4 cells/cm 2 and at 24 hours, the cell density was 4.5xl0 4 cells/cm 2 (100% seeding efficiency).
• the flow velocity was set at 0.44 cm/sec and the media volume was increased to 2286 mL. There was a single media change on Day 7. On Day 10, the flow velocity was increased and maintained at 1.5 cm/sec.
• Nano Experiment 5 was seeded at 4.5xl0 4 cells /cm 2 and at 24 hours, 4.7xl0 4 cells/cm 2 were attached (104% seeding efficiency).
• the volume of the culture medium was increased to 2286 mL, and the linear flow velocity was set at 0.44 cm/sec. A single change of culture medium occurred on Day 4, and on Day 9 the flow velocity was increased to 0.9 cm/sec.
• Nano Experiment 6 was conducted with CV-1 cells of passage 62, continued passage of the cells used in Experiment 5. The procedure repeated that of Experiment 5, except that no change in the flow velocity occurred during the growth phase after its reduction to 0.44 cm/sec at 24 hours post-seeding and the single change of culture medium did not occur until Day 6.
• the reactor was seeded with 4.5xl0 4 cells/cm 2 and at 24 hours, 5.3xl0 4 cells/cm 2 were attached to the reactor (118% seeding efficiency).
• Virus production in the iCellis® bioreactor was assessed by sampling carriers and the medium from the reactor every 24 hours after infection.
• the viral titer of the medium was assayed directly by viral plaque assay (VPA), whereas the carriers were subjected to freeze/thaw in fresh medium and then titered.
• Experiments 7, 8 and 9 Three consecutive bioreactor runs were conducted (Nano Experiments 7, 8 and 9).
• Experiments 7 and 8 were derived from CV-1 cells continuously expanded from the same working cell bank (WCB) stock vial, but of subsequent linear passages.
• Experiment 9 was expanded from a different vial, but of the same WCB stock.
• Experiments 7, 8 and 9 also varied slightly in linear flow velocity during the growth phase (0.44, 0.56 and 0.67 cm/sec, respectively).
• Cell growth of Experiments 7, 8 and 9 proceeded to slightly different endpoints prior to infection (1.6xl0 5 , 1.8xl0 5 , 1.5xl0 5 cells/cm 2 , respectively).
• Experiments 7, 8 and 9 varied from the previous Nano Experiments 1-6 in that GLV-lh68 infection was conducted at MOI 0.2 (3.1xl0 8 , 3.7xl0 8 and 3.1xl0 8 pfu for Nano Experiment 7, 8 and 9, respectively) and was amplified for 72 hours postinfection. Finally, minimum sampling of the carriers was done to minimize disturbance of the culture and reduce the depletion of carriers from the bioreactor.
• the growth characteristics of the CV-1 cells in bioreactor Experiments 7, 8 and 9 are shown in Figure 28.
• the reactors were each seeded with 4.5xl0 4 cells/cm 2 .
• the cells for Experiments 7, 8 and 9 were of passage 65, 77 and 59, respectively.
• Experiment 7 had 4.6 xlO 4 cells/cm 2 (102% seeding efficiency)
• Experiment 8 had 5.8xl0 4 cells/cm 2 (127% seeding efficiency)
• Experiment 9 had 4.4 xlO 4 cells/cm 2 (98% seeding efficiency).
• the growth rate for Experiment 8 was greater than Experiments 7 and 9.
• Experiment 8 achieved infection density of 1.8xl0 5 cells/cm 2 on Day 8, prior to its scheduled change in culture medium and therefore had the culture medium was not changed The culture medium Experiments 7 and 9 was changed on Days 10 and 12, respectively. Experiments 7 and 9 achieved infection densities of 1.6 xlO 5 cells/cm 2 on Day 13 and 1.5 xlO 5 cells/cm 2 on Day 15, respectively. The calculated population doubling time (PDT) for Experiment 8 was 87 hours.
• Trypsin treatment was investigated for extraction of the virus from bioreactor carriers that had undergone lysis by hypo osmotic shock (post-lysis carriers).
• Trial 1 compared the effects of the extraction medium, either PBS, Trypsin/EDTA (porcine trypsin), TrypLE (recombinant trypsin) or water. Additionally, the effects of freeze /thaw and sonication were evaluated. The results showed that each extraction method was successful, with the most effective extraction being obtained with TrypLE with added benefit from freeze/thaw alone or freeze /thaw and sonication.
• the virus extracted was 7.2 PFU/celL With freeze/thaw and sonication, 3.3 PFU/cell were extracted in the PBS.
• Trial 2 repeated the comparison of TrypLE with and without freeze/thaw and sonication. The TrypLE with freeze/thaw and sonication extracted 7.0 PFU/cell.
• Trial 3 compared Trypsin/EDTA, TrypLE, and 1mm Tris pH 9.0 with and without freeze/thaw and sonication for extraction of bioreactor carriers without prior lysis (pre-lysis carriers). TrypLE with freeze/thaw and sonication extracted 9.1 PFU/cell.
• TrypLE yielded 40.4 PFU/cell.
• the carriers used in Trial 4 were extracted a second time using the same conditions. In this case, TrypLE, TrypLE with freeze /thaw, and TrypLE with freeze /thaw and sonication each extracted less than 1.3 PFU/cell.
• Extraction of the carriers sampled at 48 hpi yielded less virus than the 72 hpi carriers. TrypLE alone, TrypLE with freeze /thaw, and TrypLE with freeze/thaw and sonication extracted 12.2, 25.1 and 22.1 PFU/cell, respectively. The carriers sampled at 24 hours extracted 13.7, 18.3 and 19.8 PFU/cell under the three methods, respectively.
• Virus aliquots of known titer were incubated in TrypLE at either 21°C or 37°C for 5, 10, 15, 30, 45 or 60 minutes. There was no substantial reduction in viral titer at either temperature. If anything, the viral titer increased with incubation with TrypLE.
• Experiments 7, 8 and 9 were infected with GLV-lh68 in 600 mL of infection medium at MOI of 0.2 in order to achieve rapid and efficient infection of the cells.
• the amplification period was set at 72 hours for all three experiments. The result was achieved as evident by the rapid decline in cell density immediately after infection ( Figure 27).
• the reactors were harvested by draining the medium and rinsing with PBS.
• the Experiment 7 bioreactor was harvested immediately.
• the bioreactors of Experiments 8 and 9 were frozen and processed later. TrypLE solution was added to the reactor in PBS and circulated by agitation. The harvest volume was collected and the reactor was rinsed with additional volumes. The harvest and rinse volumes were sampled and analyzed for virus content by VP A.
• Experiment 7 was harvested with 300 mL of lx TrypLE at 21°C for 45 minutes, followed by 9 consecutive rinses with 300 or 500 mL of 10 mM Tris- HCL pH 9.0.
• the reactor was not frozen prior to harvest. Analysis of the virus content of the harvest and rinse fractions indicated that virus was harvested from the bioreactor continuously throughout the process. The 3rd rinse fraction, with the maximum virus content, was only 16% of the total virus harvested. In fact, the last rinse fraction still had 4% of the total virus harvested. 1.3xl0 10 pfu of GLV-lh68 was recovered.
• Experiment 8 was harvested after freeze/thaw of the bioreactor. TrypLE (prepared by dilution of lOx TrypLE to 300 mL in PBS) at 21°C for 45 minutes, followed by 10 consecutive rinses with 300 mL each of 10 mM Tris-HCL pH 9.0. The first 5 rinses were carried out with continuous maximum agitation and the final rinses used multiple intermittent burst agitations. Compared to Experiment 7, the 2nd rinse fraction had the maximum virus content, with 20% of the total virus harvested. Successive rinse fractions had appreciable virus and the last rinse fraction still had 5% of the total virus harvested. The total virus harvested was 1.7xl0 10 pfu of GLV-11168. Table 2: Virus Harvest of Nano Experiment 8
• Carriers were sampled from the bioreactor after harvest, extracted and tested by VP A.
• the carriers contained 4.9xl0 6 PFU/carrier, which for the entire bioreactor at time of harvest containing 914 carriers indicated a residual postharvestvirus content of 4.5xl0 9 PFU or 6% of the total virus harvested. Therefore, the recovery of virus during the harvest procedure was estimated to be at least 94%.
• the virus harvest of Nano Experiment 7 (3,500 mL in total) was frozen at -20° C in aliquots. For each experiment, an aliquot of the virus harvest was thawed at 4° C and/or at room temperature just prior to use. For other experiments, the virus harvest was purified directly by UF /DF without prior freezing.
• Virus was harvested from the Nano Experiment 8 bioreactor in 3.5 L. Ultrafiltration was performed using a Centramate LV 300 kdco filter at an initial flow rate of 9.1 L/min/M 2 until the retentate volume was reduced to 900 mL. The retentate was stored at -20° C overnight. UF was resumed until the retentate volume was reduced to 500 mL. Diafiltration was conducted by adding seven successive diavolumes of PBS. The final retentate and filter washes were combined for a total volume of 300 mL. The viral titer of samples was determined by VPA and the protein and DNA contents were determined by protein and DNA assays.
• the protein content of the UF retentate was 21.3 mg/10 9 pfu and the DNA content was 455 pg/10 9 pfu.
• the protein content of the DF retentate was reduced to 9.0 mg/10 9 pfu (2.4 fold reduction) and the DNA content was reduced to 17 pg/10 9 pfu (26 fold).
• Virus recovery after initial concentration of the virus harvest from 1000 ml to 200 mL was 67%. After diafiltration against PBS, the virus recovery was 16%. After subsequent diafiltration against 10 mM Tris-CL, pH 9.0, the virus recovery returned to 81%.
• Virus was harvested from the Nano Experiment 9 bioreactor in 3.5 L.
• Ultrafiltration was performed using a Centramate LV 300 kdco filter at an initial flow rate of 4.4 L/min/M 2 until the retentate volume was reduced to 200 mL. Diafiltration was conducted by adding five successive diavolumes of PBS (200 mL each) followed by adding five successive diavolumes of 10 mM Tris-CL, pH 9.0 (200 mL each). Samples of the UF and DF retentate and permeate fractions were tested for viral titer by VPA and protein and DNA contents by protein and DNA assays.
• the protein content of the UF retentate was 1.3 mg/10 9 pfu and the DNA content was 20 p.g/10 9 pfu. After diafiltration, the protein content of the DF retentate was reduced to 0.6 mg/10 9 pfu (1.4 fold reduction) and the DNA content was reduced to 16 pg/10 9 pfu (0.8 fold).
• Table 8 Protein and DNA analysis of Nano Experiment 9 virus harvest UF/DF purified using Centramate LV 300 kdco filter
• Virus harvest purification by UF/DF using MidiKros hollow-fiber filter cartridges The Centramate LV uses flat membrane filters.
• the MidiKros filters are cartridges assembled from hollow fibers with porosities of 500 kdco and 750 kdco.
• UF/DF purification of the virus harvest was evaluated with these filter cartridges to determine the effect of filter geometry and increased porosity. Aliquots of the virus harvest from Nano Experiment 7 stored at -20 C were thawed and used in UF/DF purification.
• the MidiKros 500 kdco hollow-fiber filter was used to concentrate 500 mL of the virus harvest to a volume of 100 mL, followed by diafiltration against 10 diavolumes of 10 mM Tris-Cl, pH 9.0 (CFF 12). Samples of the starting material, UF and DF permeate and retentate fractions were tested for titer by VPA and protein and DNA content. The results showed a virus recovery of 79% after UF and 68% after DF. No virus was detected in the permeate fractions either during UF or DF. Similarly, 500 mL of the virus harvest was purified by UF/DF using the MidiKros 750 kdco hollowfiber filter (CFF 13).
• the virus recovery was 66% after UF and 43% after DF.
• the protein and DNA content of the starting material was 5.1 mg/10 9 pfu and 400 pg/10 9 pfu, respectively.
• the protein and DNA content of the retentate of the MidiKros 500 kdco filter was 1.3 mg/10 9 pfu and 90 pg/10 9 pfu, respectively (4.0 and 4.5 fold reductions, respectively).
• the protein and DNA content of the retentate of the MidiKros 750 kdco filter was 1.9 mg/10 9 pfu and 63 pg/10 9 pfu, respectively (2.7 and 6.4 fold reductions, respectively).
• Table 10 Nano Experiment 7 virus harvest UF/DF purification using MidiKros 750 kdco hollow-fiber filter x None detected.
• Table 11 Protein and DNA analysis of Nano Experiment 7 virus harvest UF/DF purification using MidiKros 500 kdco and 750 kdco hollow-fiber filter
• Nano Experiment 10 virus harvest purified by UF/DF using MidiKros 750 kdco hollow-fiber filter
• the virus harvest from Nano Experiment 10 was purified by UF /DF using a MidiKros 750 kdco hollow-fiber filter cartridge.
• 3.5 L of the virus harvest was concentrated by ultrafiltration to 200 mL followed by diafiltration against 10 diavolumes of 10 mM Tris-Cl, pH 9.0 (200 mL each). Samples of the permeate and retentate fractions were tested for virus titer by VPA and protein and DNA content. Virus recovery after UF concentration was 112% and after diafiltration was 97%.
• the protein content of the UF starting material was 4.0 mg/10 9 pfu and the DNA content was 166 pg/10 9 pfu. After diafiltration, the retentate was 1.0 mg/10 9 pfu (4 fold reduction over the starting material) and the DNA content was 15 pg/10 9 pfu (11.1 fold reduction over the starting material).
• Table 12 Nano Experiment 10 virus harvest purified by UF/DF using MidiKros
• the virus harvest from Nano Experiment 11 was purified by UF /DF using a MidiKros 500 kdco hollow-fiber filter cartridge. 2.5 L of the virus harvest was concentrated by ultrafiltration to 200 mL followed by diafiltration against 10 diavolumes of 10 mM Tris-Cl, pH 9.0 (200 mL each). Samples of the permeate and retentate fractions were tested for virus titer by VPA and protein and DNA content. Virus recovery after UF concentration was 147% and after diafiltration was 105%. The protein content of the UF starting material was 5.1 mg/10 9 pfu and the DNA content was 166 pg/10 9 pfu.
• the retentate was 1.1 mg/10 9 pfu (4.9 fold reduction over the starting material) and the DNA content was 22 pg/10 9 pfu (7.4 fold reduction over the starting material).
• the retentate was 1.4 mg/10 9 pfu (3.8 fold reduction over the starting material) and the DNA content was 25 pg/10 9 pfu (6.5 fold reduction over the starting material).
• Table 14 Nano Experiment 11 virus harvest purified by UF/DF using MidiKros x None detected.
• Table 15 Protein and DNA analysis of Nano Experiment 11 virus harvest purified by UF /DF using MidiKros 500 kdco hollow-fiber filter
• Nano Experiment 12 virus harvest purified by UF/DF using MidiKros 500 kdco hollow-fiber filter
• the virus was harvested from Nano Experiment 12 by thawing the frozen bioreactor by addition of 500 mL 10 mM Tris-HCl, 2 mM MgC12, pH 9.0.
• Benzonase® Recombinant Benzonase®, Speed BioSystems, Inc.
• the Benzonase® nuclease digestion medium was removed and replaced with 500 mL of PBS containing lx TrypLE and further incubated with agitation at 37 Q C for 60 minutes.
• the TrypLE harvest medium was removed and the bioreactor was flushed twice with 500 mL of 10 mM Tris-HCl, pH 9.0 with agitation at 37 Q C for 10 minutes each.
• the TrypLE harvest and both flush volumes were combined as the virus harvest (1.5L).
• Viral titer analysis by VPA indicated that the TrypLE virus harvest fraction contained 80.1% of the virus, the first 10 mM Tris-HCl flush contained 16.3%, and the second flush contained 2.4%. Therefore, 98.8% of the virus was released from the bioreactor and collected in the virus harvest.
• the Benzonase® nuclease digestion fraction contained 0.4% of the virus and the macrocarriers after harvest contained less than 0.1%.
• the virus harvest was purified by UF /DF using a MidiKros 500 kdco hollow-fiber filter cartridge. 1.5 L of the virus harvest was concentrated by ultrafiltration to 200 mL followed by diafiltration against 10 diavolumes of 10 mM Tris-Cl, pH 9.0 (200 mL each). Samples of the permeate and retentate fractions were tested for virus titer by VPA and protein and DNA content. Virus recovery after UF concentration was 45% and after diafiltration was 123%. The protein content of the UF starting material was 4.3 mg/10 9 pfu and the DNA content was 38 pg/10 9 pfu.
• the retentate was 4.0 mg/10 9 pfu (1.1 fold reduction over the starting material) and the DNA content was 5 pg/10 9 pfu (8.7 fold reduction over the starting material).
• the retentate was 1.6 mg/10 9 pfu (2.7 fold reduction over the starting material) and the DNA content was 1 pg/10 9 pfu (42 fold reduction over the starting material).
• Table 16 Nano Experiment 12 virus harvest purified by UF/DF using MidiKros 500 kdco hollow-fiber filter iNone detected.
• Table 17 Protein and DNA analysis of Nano Experiment 12 virus harvest purified by UF /DF using MidiKros 500 kdco hollow-fiber filter
• Virus was produced by several processes employed in the art, and the results compared.
• One process referred to as the “CEF” process is the production of virus from primary cells obtained from chicken eggs, grown in suspension culture, and infected with virus. The cells are harvested by centrifugation, lysed by homogenization, purified by filtration, followed by two sucrose gradient centrifugations, followed by formulation and fill/finish.
• Process A is the production of virus in a continuous cell line, CV-1, grown in roller bottles (adherent culture), infected with the virus, the cells dissociated from the substrate with trypsin and collected by centrifugation. The cells lysed by freeze thaw and the virus purified from the total cell lysate by affinity chromatography, followed by concentration by centrifugation, resuspension in formulation buffer and fill/finish.
• Process B is a process as described herein. CV-1 cells are grown in a fixed-bed bioreactor (adherent culture), infected with the virus, the reactor drained of medium and frozen.
• the lysed adherent cells in the bioreactor are treated with Benzonase® nuclease followed by trypsin to release the virus, leaving the cell debris adhered to the matrix in the bioreactor.
• the virus is purified and formulated ultrafiltration and diafiltration, and filled/finished.
• EXAMPLE 7 Exemplary large-scale process for producing vaccinia virus in a bioreactor, such as the 333 m 2 iCellis® 500 Bioreactor by the methods herein.

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