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  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
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  • C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
  • C07K14/08—RNA viruses
  • C07K14/18—Togaviridae; Flaviviridae
  • C07K14/1816—Flaviviridae, e.g. pestivirus, mucosal disease virus, bovine viral diarrhoea virus, classical swine fever virus (hog cholera virus), border disease virus
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  • C12N7/00—Viruses; Bacteriophages; Compositions thereof; Preparation or purification thereof
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  • C12N7/06—Inactivation or attenuation by chemical treatment
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K39/00—Medicinal preparations containing antigens or antibodies
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  • A61K2039/525—Virus
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  • A61K2039/5254—Virus avirulent or attenuated
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  • A61K39/00—Medicinal preparations containing antigens or antibodies
  • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
  • A61K2039/525—Virus
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  • A61K39/00—Medicinal preparations containing antigens or antibodies
  • A61K2039/555—Medicinal preparations containing antigens or antibodies characterised by a specific combination antigen/adjuvant
  • A61K2039/55505—Inorganic adjuvants
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  • A61K39/00—Medicinal preparations containing antigens or antibodies
  • A61K2039/555—Medicinal preparations containing antigens or antibodies characterised by a specific combination antigen/adjuvant
  • A61K2039/55511—Organic adjuvants
  • A61K2039/55516—Proteins; Peptides
• • A—HUMAN NECESSITIES
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  • A61K39/00—Medicinal preparations containing antigens or antibodies
  • A61K2039/555—Medicinal preparations containing antigens or antibodies characterised by a specific combination antigen/adjuvant
  • A61K2039/55511—Organic adjuvants
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  • C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
  • C12N2770/00011—Details
  • C12N2770/24011—Flaviviridae
  • C12N2770/24111—Flavivirus, e.g. yellow fever virus, dengue, JEV
  • C12N2770/24134—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein
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  • C12N2770/00011—Details
  • C12N2770/24011—Flaviviridae
  • C12N2770/24111—Flavivirus, e.g. yellow fever virus, dengue, JEV
  • C12N2770/24151—Methods of production or purification of viral material
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  • C12N2770/00011—Details
  • C12N2770/24011—Flaviviridae
  • C12N2770/24111—Flavivirus, e.g. yellow fever virus, dengue, JEV
  • C12N2770/24161—Methods of inactivation or attenuation
  • C12N2770/24163—Methods of inactivation or attenuation by chemical treatment
• • 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

• the disclosure relates to methods for the purification of Zika viruses for use in vaccines.
• Protamine was originally isolated from the sperm of salmon and other species of fish but is now produced primarily through recombinant biotechnology. It is a highly cationic peptide that binds to negatively charged molecules such as nucleic acids to form a stable ion pair. Its use in removing host cell nucleic acid is well document.
• aspects of the invention provide processes for the purification of infectious Zika virus particles comprising the steps of (a) providing a crude harvest (a) comprising virus particles and impurities, wherein the impurities are generated from growing said virus particles on a cell substrate; (b) reducing impurities from the crude harvest (a) by precipitation with an agent comprising a protamine salt, preferably a protamine sulphate, to obtain a virus preparation (b); and further purifying the Zika virus preparation (b) by method or methods selecting for size of the Zika virus particles, such as e.g. a sucrose density gradient centrifugation to obtain a Zika virus preparation (c) comprising the infectious Zika virus particles.
• the concentration of protamine sulphate in step (b) is about 1 to 10 mg/ml, more preferably about 1 to 5 mg/ml, more preferably about 1 to 2 mg/ml. In one embodiment, the concentration of protamine sulphate in step (b) is about 2 mg/mL. In one embodiment, the concentration of protamine sulphate is 1.2 to 1.8 mg/ml, more preferably 1.4 to 1.6 mg/ml. In a preferred embodiment, the concentration of protamine sulphate in step (b) is about 1.6 mg/ml or about 2 mg/ml.
• the residual host cell DNA of the virus preparation (e) is less than 1 ⁇ g/mL, especially less than 900, 800, 700, 600, 500, 400, 300 or 200 ng/mL, preferably less than 100 ng/mL. In a preferred embodiment, the residual host cell DNA of the virus preparation (c) is less than 10 ng/mL. In some embodiments, the residual host cell protein of the final virus preparation (c) is less than 10 ⁇ g/mL, especially less than 9, 8, 7, 6, 5, 4, 3 or 2 ⁇ g/mL, preferably less than 1 ⁇ g/mL. In a preferred embodiment, the residual host cell protein of the virus preparation (c) is less than 100 ng/mL.
• the residual non-infectious virus particles of the final virus preparation (c) is less than 10 ⁇ g/mL, especially less than 9, 8, 7, 6, 5, 4, 3 or 2 ⁇ g/mL, preferably less than 1 ⁇ g/mL. In a preferred embodiment, the residual non-infectious virus particles of the virus preparation (c) is less than 100 ng/mL.
• the residual protamine is less than 1 ⁇ g/mL, especially less than 900, 800, 700, 600, 500, 400, 300 or 200 ng/mL, preferably less than 100 ng/mL, more preferably is below the detection limit of HPLC, in particular below the detection limit in the final drug substance.
• the PS content is tested by HPLC or size exclusion chromatography (SEC). For example, HPLC is validated for PS determination in JEV sucrose gradient pool samples as a routine release assay and is very sensitive (i.e., LOQ 3 ⁇ g/mL; LOD 1 ⁇ g/mL). In the current invention, PS content in in Zika virus DS samples was ⁇ LOD.
• the HPLC assessment of PS content can be performed on a Superdex Peptide 10/300GL column (GE: 17-5176-01) using 30% Acetonitrile, 0,1% Trifluoroacetic acid as solvent with a flow rate of 0,6 ml/min at 25°C and detection at 214 nm.
• MS mass spectrometry
• the residual PS levels in a Zika virus preparation are tested by MS or other such highly sensitive method, e.g., nuclear magnetic resonance (NMR).
• residual PS as well as fragments and/or break-down products of PS, can be detected at trace amounts, such as levels as low as, for example, 10 6 , 10 7 or 10 8 molecules per typical sample load.
• the PS levels are tested in the sucrose gradient pool.
• the PS levels are tested in the drug product.
• the PS levels are tested in the drug substance.
• the crude harvest (a) comprising the virus particles and impurities is subjected to one or more pre-purification step(s) prior to step (b).
• the one or more pre- purification step(s) comprises digesting host cell genomic DNA in the crude harvest (a) comprising the virus particles and impurities by enzymatic treatment.
• the one or more pre- purification step(s) comprises filtration, ultrafiltration, concentration, buffer exchange and/or diafiltration.
• the one or more pre-purification steps is filtration using a filter having a pore size equal to or less than 1 ⁇ . In some embodiments, the filter has a pore size equal to or less than 0.2 ⁇ .
• the filter has a pore size of 0.2 ⁇ .
• the concentration and/or ultra/diafiltration and/or buffer exchange is performed by tangential flow filtration (TFF).
• ultra/diafiltration of the crude harvest (a) comprising the virus particles and impurities is performed using a hollow fiber membrane having a cut-off of equal to or less than 300 kDa.
• the hollow fiber membrane has a cut-off of 100 kDa.
• the Zika virus particle is a live Zika virus, a chimeric virus, an attenuated live virus, a modified live virus, or a recombinant live virus.
• the Zika virus particles of the invention may by optionally inactivated.
• the Zika virus particle is an attenuated form of the virus particle.
• the Zika virus may have reduced infectivity, virulence, and/or replication in a host, as compared to a wild-type Zika virus.
• the Zika virus is a mutated or modified Zika virus, for example the nucleic acid of the Zika virus may contain at least one mutation relative to the wild-type Zika virus.
• the Zika virus is a recombinant live Zika virus, meaning a Zika virus that is generated recombinantly and may contain nucleic acid from different sources.
• the Zika virus particle is a live virus, an attenuated live virus, a modified live virus, or a recombinant live virus.
• the Zika virus is a Zika virus from the Asian lineage.
• the relative reduction of impurity of the final Zika virus preparation relative to the liquid medium (a) comprising the Zika virus particles and impurities is in a range from 60 to 95%. In some embodiments, the residual impurity of the final Zika virus preparation is less than 1%.
• the Zika virus is propagated in a cell line selected from the group consisting of an EB66 cell line, a Vero cell line, a Vero-aHis cell line, a HeLa cell line, a HeLa-S3 cell line, a 293 cell line, a PC12 cell line, a CHO cell line, a 3T3 cell line, a PerC6 cell line, a MDSK cell line, a chicken embryonic fibroblast cell line, a duck cell line, and a diploid avian cell line.
• said cell line is a duck cell line.
• said cell line is a diploid avian cell line.
• said cell line is EB66 cell line.
• said cell line is a Vero cell line.
• compositions for immunization against a Zika viral infection are a vaccine.
• composition or vaccine is directed against a Zika virus of the Asian lineage.
• compositions comprising the Zika virus particles obtainable by any of the processes described herein for treating and/or preventing a Zika viral infection.
• the Zika virus infection is caused by a Zika virus of the Asian lineage.
• the Zika virus is derived from the Asian lineage.
• the Zika virus is a Zika virus as described partially or fully in Sequence section of this application, i.e. any of sequences SEQ ID Nos 2 to 69 or 72, in particular all partly or fully described Zika viruses of the Asian lineages or an immunogenic variant thereof.
• the immunogenic variants of the Zika virus or Zika virus of the Asian lineages are herein defined as having at least 80% sequence identity to the nucleotide sequence of the sequences described in any of sequences SEQ ID Nos 2 to 69 or 72, especially at least 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88% 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or at least 99%> sequence identity.
• the process of the invention results in an enrichment of infectious Zika virus particles from the crude harvest comprising infectious Zika virus particles and non-infectious Zika virus particles and other Zika virus products such that the enrichment of the infectious Zika virus particles is at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, preferably at least 80%, especially 85% relative to the total virus particle content of the crude harvest (a) comprising the Zika virus particles and impurities.
• the residual impurity of the final Zika virus preparation with respect to all impurities in the crude harvest is less than 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, preferably less than 5%> as determined by SEC-HPLC (Size Exclusion Chromatography - HPLC).
• the filtration step of the Zika virus preparation (b) after contact with the solid- phase matrix is performed using a filter having a pore size equal to or greater than 1 ⁇ .
• the filter has a pore size equal to or greater than 0.2 ⁇ .
• the filter has a pore size of about 0.2 ⁇ , such as 0.22 ⁇ .
• the Zika virus is propagated in a cell line selected from the group consisting of an EB66 cell line, a Vero cell line, a Vero-aHis cell line, a HeLa cell line, a HeLa-S3 cell line, a 293 cell line, a PC12 cell line, a CHO cell line, a 3T3 cell line, a PerC6 cell line, a MDSK cell line, a chicken embryonic fibroblast cell line, a duck cell line, and a diploid avian cell line.
• said cell line is a duck cell line.
• said cell line is a diploid avian cell line.
• said cell line is EB66 cell line.
• said cell line is a Vero cell line.
• the composition is a vaccine.
• the vaccine is administered to the subject once, twice or three or more times.
• the vaccine is administered once or twice.
• the vaccine is administered only once.
• the herein disclosed in vivo data regarding immunogenicity of the inactivated Zika virus vaccine of the current invention indicates that the virus is surprisingly potently immunogenic and also highly cross- protective (very similar immunogenicity in African and Asian strains). Data indicate that immunogenicity was unexpectedly higher than the recently reported inactivated Zika virus vaccine candidate (Larocca, et.
• Inactivated viruses are among the safest vaccines and especially preferred for delivery to populations where safety is especially concerning, such as pregnant women, children and immunocompromised individuals, which makes the herein disclosed inactivated Zika virus particularly suitable. Obtaining a high titer of inactivated virus is a challenge in the field. The herein disclosed process for purifying inactivated Zika virus results in not only a high yield, but also a very pure drug substance.
• Figure 1 Average distance tree (by % identity, nt), complete genomes.
• Figure 2 Neighbor joining tree (by % identity, nt), complete genomes.
• Figure 3 Pairwise alignment- Jalview (% identity, nt), complete genomes.
• Figure 4 Average distance tree (by % identity, aa), E-protein.
• Figure 5 Neighbor joining tree (by % identity, aa), E-protein.
• Figure 6 Pairwise alignment- Jalview (% identity, aa), E-protein.
• Figure 7 Alignment (shading: % identity, aa), E-protein.
• Figure 8 An example of virus particle maturation in the host cell. As observed in flaviviruses, full maturation of the particles requires proteolytic cleavage of the precursor membrane glycoprotein (prM) by the host protease furin. Not all prM molecules are cleaved, resulting in the release of mature, mosaic or immature-like conformations from the cells. Mosaic and immature forms are generally not infectious— only mature virions are infective and have hemagglutinin (HA) / TCID50 activity. ( Figure adapted from Plevka, et al., Maturation of flaviviruses starts from one or more icosahedrally independent nucleation centres, EMBO reports (2011) 12, 602-606).
• prM membrane glycoprotein
• FIG. 9 An exemplary downstream Zika virus purification process from the crude harvest to formulation of the drug substance (vaccine), a preferred embodiment of the process of the invention (A).
• a flow-chart of an exemplary Zika virus inactivation process is shown in (B).
• FIG. 10 PS treatment results in selective removal of Zika virus aggregates and Vero HCP and LMW impurities (SEC-HPLC of 30x concentrated Zika Virus harvest day 5).
• FIG. 11 SEC-HPLC of individual 30x concentrated Zika harvest prior to PS treatment at different time points.
• FIG. 12 SEC-HPLC of individual 3 Ox concentrated Zika harvest post PS treatment at different time points.
• the smaller graph indicates the observed cytopathic effect (CPE) over time.
• FIG. 13 Preparation of the sucrose gradient for Zika virus purification.
• Figure 14 Representative SDS-PAGE from the sucrose gradient harvest of a Zika virus purification is shown.
• Figure 15 Comparison of JEV and ZikaV harvest schedules/yields.
• FIG. 16 SEC-HPLC elution profile of ZikaV neutralized inactivated virus (NIV). Data were processed on Dionex Ultimate 3000 / Superose 6 Increase column. Both panels are from the same chromatogram. The upper graph is the complete elution profile; the lower graph is an enlargement of the ZikaV elution peak.
• NMV ZikaV neutralized inactivated virus
• Figure 17 SEC-MALLS analysis of inactivated ZikaV.
• Figure 18 Cumulative particle size distribution of Zika NIV.
• Figure 19 Graphical representation of the neutralization of the Zika virus H/PF/2013 with pooled mouse sera. The number of plaques without serum was set to 100%. The EC50 was calculated using the 3- parameter method.
• Figure 20 Graphical representation of the neutralization of the Zika virus MR766 with pooled mouse sera. The number of plaques without serum was set to 100%. The EC50 was calculated using the 3- parameter method.
• Figure 21 Correlation between JEV antigen content in neutralized inactivated virus (NIV) analysed by ELISA and SEC-HPLC (Dionex Ultimate 3000, Superose 6 column).
• the processes disclosed are characterized by the removal of undesired byproducts of Zika virus production on host cells, such as non-infectious Zika virus particles and aggregated and immature Zika virus by-products.
• the processes provided herein allow the production of highly- purified Zika virus preparations comprising mostly infectious Zika virus particles.
• protamine sulphate (PS) added to remove contaminating DNA during Zika virus purification, resulted not only in removal of contaminating DNA, but also in the loss of a high percentage of total Zika virus particles present in the preparation.
• Protamines are small arginine-rich nuclear proteins, present in high amounts in the sperm of fish, which have an important role in DNA packaging during spermatogenesis.
• Protamine sulfate (or "protamine” or “PS") can form a stable ion pair with heparin and is thus commonly used during certain surgeries when the anti -coagulation effect of heparin is no longer needed.
• protamine sulfate administered alone can also have a weak anticoagulant effect (“Protamine sulfate”.
• Protamine Sulphate is additionally routinely used in biotechnology applications such as DNA precipitation (e.g., removal of host cell DNA from cell culture processes), purification of DNA binding proteins and retroviral-mediated gene transfer.
• Protamine is obtained from salmon sperm or produced recombinantly and is used as a sulphate salt.
• the four major peptides which constitute almost the entire nitrogen-containing material in salmon protamine, have been fully characterized and found to be polypeptides of 30-32 amino acids in length, of which 21— 22 residues are arginine.
• the average molecular mass is in the range of 4250 Da for the following sequence: PRRRRSSSRP VRRRRRPRVS RRRRGGRR RR (SEQ ID NO: 1).
• protamine is also referred to as protamine salt, or preferably protamine sulphate.
• the present invention relates to the use of protamine sulphate (PS) in a process of purification of a live Zika virus, wherein the protamine sulphate facilitates the removal of impurities from a crude virus harvest, including non-infectious virus particles and aggregates.
• PS protamine sulphate
• the present invention also relates to the enrichment of infectious virus particles from a crude harvest containing a mixture of virus particles and other viral products in various stages of maturation.
• protamine sulphate can follow crude cell lysis or any further step after cell lysis (e.g. including after a pre-purification with filtration, chromatography etc) wherein the Zika virus particles are further enriched or concentrated and/or other impurities are removed and/or buffer components are exchanged.
• the further steps may comprise filtration or concentration of the crude cell lysate.
• the protamine sulphate may comprise the sequence PRRRRSSSRP VRRRRRPRVS RRRRRRGGRR RR (SEQ ID NO: 1) or a variant thereof wherein the amino acid sequence comprises from 28-35 amino acids, preferably 29-34, more preferably 30-33 amino acids, most preferably 31 or 32 amino acids.
• the protamine sulphate preferably comprises at least 19 arginine residues, more preferably at least 20 arginine residues, more preferably at least 21 arginine residues, even more preferably at least 22 residues, most preferably 20 or 21 arginine residues.
• protamine salt herein shall serve to encompass natural variations on SEQ ID NO: 1, preferably, but not limited to, the protamine sulphate forms.
• the process comprising the use of protamine sulphate of the invention can be applied to purification of Zika virus for use in pharmaceutical compositions, for example, for a pharmaceutical composition such as a vaccine where it is important that the Zika virus is in its infectious form.
• the Zika virus to be purified may be a live virus, a live attenuated virus or a live chimeric virus, preferably a live wild type Zika virus, such as a Zika virus of the Asian lineage.
• the Zika virus particle is also be later inactivated.
• the Zika virus is inactivated with formaldehyde.
• the process according to the current invention may also comprise the use of a sucrose gradient, preferably an optimized sucrose gradient.
• the sucrose gradient is preferably optimized for the removal of protamine sulfate, also for the removal of immature viral particles or other viral particles which are noninfectious or host cell proteins or nucleic acids (DNA, RNA, mRNA, etc) or other host cell debris.
• the optimized sucrose gradient comprises at least two, at least three, at least four layers of sucrose solutions with different densities.
• the virus preparation to be purified is provided in a sucrose solution which has a density of about 8%, about 9%, about 10%, about 11%, about 12% sucrose (w/w), preferably about 10%>.
• one sucrose solution in the gradient has a density of about 45%, about 46%, about 47%, about 48%, about 49%, about 50%, about 51%, about 52%, about 53%, about 54%, about 55%> sucrose (w/w), preferably about 50%.
• one sucrose solution in the gradient has a density of about 30%, about 31%, about 32%, about 33%>, about 34%, about 35%, about 36%, about 37%>, about 38%>, about 39%>, about 40% sucrose (w/w), preferably about 35%>.
• one sucrose solution in the gradient has a density of about 10%, about 11%, about 12%, about 13%, about 14%, about 15%, about 16%, about 17%, about 18%, about 19%, about 20% sucrose (w/w), preferably about 15% sucrose.
• the sucrose gradient comprises three layers of sucrose solutions of about 50%, about 35%> and about 15% (w/w) sucrose and the virus composition to be purified is contained in about 10% (w/w) sucrose. Because the invention provided for means to not only test for host cell DNA but also immature viral particles, the skilled person in the art is able to more precisely optimize the sucrose gradient for most efficient purification and include additional tools such as PRNT assay to monitor purification success.
• the produced Zika virus is derived from the Asian lineage (which includes the strains found in South America and all strains derived from any Asian lineage).
• the produced Zika virus is a Zika virus as described in the Sequence section of this application (SEQ ID NO: 2 to 69).
• the Zika virus comprises the RNA corresponding to the DNA sequence provided by SEQ ID NO: 72 or variants thereof.
• the Zika virus encodes the entire polyprotein as provided by SEQ ID NO: 73.
• Degrees Brix is the sugar content of an aqueous solution.
• One degree Brix is 1 gram of sucrose in 100 grams of solution and represents the strength of the solution as percentage by mass.
• °Bx corresponds to the sucrose content in % (w/w), eg. 45 °Bx equals 45 % (w/w) sucrose.
• Oligoname gene- Pair restriction sites (lower case) primer
• size [bp] specific
• Oligoname gene- Pair restriction sites (lower case) primer) size [bp] specific
• Oligoname gene- Pair restriction sites (lower case) primer
• size [bp] specific
• nucleic acid sequences of the genomes of Zika viruses that may be used in the methods, compositions, and/or vaccines described herein.

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