Chimeric Zika-Japanese Encephalitis Virus
20220168412 · 2022-06-02
Inventors
- Kai DALLMEIER (Kessel-Lo, BE)
- Dieudonné Buh Kum (Aarschot, BE)
- Niraj Mishra (Uttar Pradesh, IN)
- Johan NEYTS (Kessel-Lo, BE)
Cpc classification
C12N2770/24134
CHEMISTRY; METALLURGY
A61K2039/57
HUMAN NECESSITIES
A61K48/00
HUMAN NECESSITIES
Y02A50/30
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
C12N15/86
CHEMISTRY; METALLURGY
International classification
A61K48/00
HUMAN NECESSITIES
Abstract
A polynucleotide comprising the sequence of a live, infectious, attenuated Zika-Japanese encephalitis (JEV) chimeric virus wherein the nucleotide sequence encoding the prME protein of said Zika virus is replaced by a nucleotide sequence encoding the prME protein of a Japanese encephalitis virus, so that said prME protein of said Japanese encephalitis virus is expressed.
Claims
1-29. (canceled)
30. A polynucleotide comprising a nucleotide sequence of a live, infectious, attenuated Zika-Japanese encephalitis chimeric virus, wherein the nucleotide sequence encodes an amino acid sequence of a prME protein of a Japanese encephalitis virus, so that the prME protein of the Japanese encephalitis virus is expressed.
31. The polynucleotide according to claim 30, wherein the nucleotide sequence encodes an amino acid sequence of a signal sequence of a C terminal part of a C protein of the Japanese encephalitis virus so that the signal sequence of the Japanese encephalitis virus is expressed.
32. The polynucleotide according to claim 30, wherein the nucleotide sequence differs compared to the wild type sequence of the Japanese encephalitis virus E gene region depicted in SEQ ID NO:1 by an A to G nucleotide substitution at position 1482.
33. The polynucleotide according to claim 30, wherein the encoded amino acid sequence of the prME protein of the Japanese encephalitis virus has the sequence of SEQ ID NO:5.
34. The polynucleotide according to claim 30, wherein the nucleotide sequence encodes an amino acid sequence of a signal sequence of a C terminal part of a C protein of the Japanese encephalitis virus, and wherein the encoded amino acid sequence of the signal sequence of the C terminal part of the C protein of the Japanese encephalitis virus has the sequence GGNEGSIMWLASLAVV (SEQ ID NO:4).
35. The polynucleotide according to claim 30, wherein the nucleotide sequence encodes an amino acid sequence linking the Zika C protein and the signal sequence of the C terminal part of the C protein of the Japanese encephalitis virus, the encoded amino acid sequence linking the Zika C protein and the signal sequence of the C terminal part of the C protein of the Japanese encephalitis virus comprising a sequence EKKRR GGNEG (SEQ ID NO:7).
36. The polynucleotide according to claim 35, wherein: the nucleotide sequence encodes an amino acid sequence linking the Zika C protein and the signal sequence of the C terminal part of the C protein of the Japanese encephalitis virus, the encoded amino acid sequence linking the Zika C protein and the signal sequence of the C terminal part of the C protein of the Japanese encephalitis virus comprising a sequence EKKRR GGNEG (SEQ ID NO:7); and/or the nucleotide sequence encodes an amino acid sequence linking the prME protein of the Japanese encephalitis virus and the Zika NS protein, the encoded amino acid sequence linking the prME protein of the Japanese encephalitis virus and the Zika NS protein comprising the sequence ATNVH ADVGC (SEQ ID NO:8).
37. The polynucleotide according to claim 30, wherein the Zika virus is the BeH819015 strain.
38. The polynucleotide according to claim 30, comprising the open reading frame from nucleotide 108 to 10379 depicted in SEQ ID NO:1 with stopcodon included.
39. The polynucleotide according to claim 30, comprising the nucleotide sequence depicted in SEQ ID NO:1.
40. The polynucleotide according to claim 30, wherein the nucleotide sequence encodes the polypeptide sequence depicted in SEQ ID NO:2.
41. The polynucleotide according to claim 30, which is a Bacterial Artificial Chromosome.
42. The polynucleotide according to claim 41, wherein the Bacterial Artificial Chromosome comprises: an inducible bacterial ori sequence for amplification of the Bacterial Artificial Chromosome to more than 10 copies per bacterial cell; and a viral expression cassette comprising a cDNA of the Zika-Japanese encephalitis chimeric virus and comprising cis-regulatory elements for transcription of the viral cDNA in mammalian cells and for processing of the transcribed RNA into infectious RNA virus.
43. A live, infectious, attenuated Zika-Japanese encephalitis chimeric virus, wherein a prME protein of the chimeric virus is the prME protein of a Japanese encephalitis virus.
44. The Zika-Japanese encephalitis chimeric virus according to claim 43, wherein a signal sequence of the C terminal part of the C protein of the chimeric virus is the signal sequence of the C terminal part of the C protein of a Japanese encephalitis virus.
45. The Zika-Japanese encephalitis chimeric virus according to claim 43, comprising in a prME polypeptide the sequence QAAEFTV (SEQ ID NO:9).
46. The Zika-Japanese encephalitis chimeric virus according to claim 43, wherein the signal sequence and the prME protein of the Japanese encephalitis virus has the amino acid sequence depicted in SEQ ID NO:4 and SEQ ID NO:5.
47. The Zika-Japanese encephalitis chimeric virus according to claim 43, wherein the Japanese encephalitis virus is SA14-14-2.
48. The Zika-Japanese encephalitis chimeric virus according to claim 43, wherein the Zika virus is the BeH819015 strain.
49. The Zika-Japanese encephalitis chimeric virus according to claim 43, comprising an amino acid sequence GGNEGSIMWLASLAVV (SEQ ID NO:4), and comprising at a junction of the C protein of the Zika virus and a signal peptide of the Japanese encephalitis virus an amino acid sequence EKKRR GGNEG (SEQ ID NO:7).
50. A pharmaceutical composition comprising: a polynucleotide sequence encoding a Zika-Japanese encephalitis chimeric virus according to claim 30; and a pharmaceutical acceptable carrier.
51. A pharmaceutical composition comprising: a Zika-Japanese encephalitis chimeric virus according to claim 43; and a pharmaceutical acceptable carrier.
52. A method of preparing a vaccine against a Zika and/or Japanese encephalitis infection, the method comprising: (a) providing a Bacterial Artificial Chromosome, the Bacterial Artificial Chromosome comprising: an inducible bacterial ori sequence for amplification of the Bacterial Artificial Chromosome to more than 10 copies per bacterial cell; and a viral expression cassette comprising: a cDNA of a Zika-Japanese encephalitis chimeric virus according to claim 30; and cis-regulatory elements for transcription of the viral cDNA in mammalian cells and for processing of the transcribed RNA into infectious RNA virus; (b) transfecting mammalian cells with the Bacterial Artificial Chromosome of (a) and passaging infected cells; (c) validating replicated virus of the transfected cells of (b) for virulence and the capacity of generating antibodies and inducing protection against Zika virus infection; (d) cloning the virus validated in (c) into a vector; and (e) formulating the vector into a vaccine formulation.
53. The method according to claim 52, wherein the vector is a Bacterial Artificial Chromosome which comprises an inducible bacterial ori sequence for amplification of the Bacterial Artificial Chromosome to more than 10 copies per bacterial cell.
54. A method of inducing a neutralizing and/or protective antibody response against Japanese encephalitis virus and/or Zika virus in a subject, thereby preventing an infection by Japanese encephalitis virus and/or Zika, the method comprising: administering to the subject the Zika-Japanese encephalitis chimeric virus of claim 43.
55. A method of inducing a protective immune response against Japanese encephalitis virus and/or Zika virus in a subject, thereby preventing an infection by Japanese encephalitis virus and/or Zika, the method comprising: administering to the subject the Zika-Japanese encephalitis chimeric virus of claim 43.
Description
BRIEF DESCRIPTION OF THE DRAWINGS
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DETAILED DESCRIPTION
[0081] Flaviviruses belong to the viral family of Flaviviridae and comprise many medically important viruses, including Dengue virus (DENV), Japanese encephalitis virus (JEV), West Nile virus (WNV), Tick-borne encephalitis virus (TBEV), Yellow fever virus (YFV) and Zika virus (ZIKV), Japanese Encephalitis virus (JEV), Murray Valley Encephalitis virus (MVE), St. Louis Encephalitis virus (SLE), Tick-borne Encephalitis (TBE) virus, Russian Spring-Summer Encephalitis virus (RSSE), Kunjin virus, Powassan virus, Kyasanur Forest Disease virus, Usutu virus, Wesselsbron and Omsk Hemorrhagic Fever virus. Flaviviruses are enveloped with a ˜10-11 kb long (+)ssRNA genome encoding for 3 structural proteins (core, C; premembrane, prM; and envelope, E), which are incorporated in the virions, and 7 nonstructural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5).
[0082] The signal peptide at the C terminus of the C protein (C-signal peptide; also called C-anchor domain (“canch”) regulates flavivirus packaging through coordination of sequential cleavages at the N terminus (by viral NS2B/NS3 protease in the cytoplasm) and C terminus (by host signalase in the endoplasmic reticulum [ER] lumen) of the signal peptide sequence.
[0083] Generally, a c-LAV (Chimeric Life Attenuated Vaccine) of the prior art is defined as an infectious live-attenuated vaccine virus in which the nucleotide sequences of the structural prM and E proteins are replaced with those of another Flavivirus (e.g. JEV, DENY, ZIKV etc.). The generic structure of such c-LAV can be described as A-B-A with (i) building blocks A comprise parts of a particular virus A originally used as vector backbone [typically the encoding the C protein and the Ns proteins](vector) and (ii) building blocks B representing the genetic material of another virus B and encoding for the antigenic surface proteins of B (vaccine target) that has originally been introduced into A for the purpose of inducing protection from said virus B infection following vaccination.
[0084] Following the same A-B-A blueprint, other DENY c-LAVs are currently in development, yet using attenuated DENY strains (Torresi et al. (2017) Hum Vaccin Immunother. 13, 1059-1072) or ZIKV (Xie et al (2017) MBio. 8, e02134-16) as vector backbone. Similar c-LAV candidates has been developed for a variety of Flaviviruses each time targeting for neutraling antibody (nAb) responses by the envelope and membrane protein (Lai et al. (2003) Adv Virus Res. 61, 469-509) including DENV4/TBEV (Langatvirus) chimeras to protect from TBEV by nAb neutralizing TBEV (Pletnev & Men (1998) Proc Natl Acad Sci USA. 95, 1746-1751).
[0085] Prior vaccine strategies focused on the induction of nAb responses that protect from Flavivirus infections and are mostly directed against the respective envelope protein [Li et al. (2014) Hum Vaccin Immunother. 10, 3579-3593]. However, in addition to this widely accepted correlate of vaccine-mediated protection by nAb, historical as well as recently published evidence suggested that, in addition, nonstructural proteins and, due to its antigenic and secreted nature, in particular NS1 may contribute to some extent to vaccine efficacy via protective cellular and humoral immune responses [Pierson et al. (2008) Cell Host Microbe. 4, 229-238; Putnak et al. (1990) J Gen Virol. 71(Pt 8), 1697-1702; Schlesinger et al. (1993) Virology 92(1), 132-141; Amorim et al. (2016) Virology 487, 41-49; Rastogi et al. (2016) Virol J. 13, 131; Watterson et al. (2016) Antiviral Res. 130, 7-18]. We here show that, unexpectedly, a c-LAV Flavivirus vaccine approved to protect against JEV has the potential to fully protect from massively lethal vaccine challenge fully without induction of any relevant nAb and may therefore be developed as dual vaccines, also protecting against a second Flavivirus, namely against Zika virus which provided the backbone of non-structural proteins for replication of the c-LAV. In other words, c-LAVs of the generic structure A-B-A protect against infection with two viruses B and A because these chimeric vaccines contain the structural proteins of one virus B (JE) and the nonstructural proteins of a second virus A (Zika).
[0086] A BAC as referred to in the present application comprises: [0087] an inducible bacterial ori sequence for amplification of said BAC to more than 10 copies per bacterial cell, and [0088] a viral expression cassette comprising a cDNA of an the RNA virus genome and comprising cis-regulatory elements for transcription of said viral cDNA in mammalian cells and for processing of the transcribed RNA into infectious RNA virus.
[0089] As is the case in the present invention the RNA virus genome is a chimeric viral cDNA construct of two RNA virus genomes.
[0090] In these BACS, the viral expression cassette comprises a cDNA of a positive-strand RNA virus genome, an typically [0091] a RNA polymerase driven promoter preceding the 5′ end of said cDNA for initiating the transcription of said cDNA, and [0092] an element for RNA self-cleaving following the 3′ end of said cDNA for cleaving the RNA transcript of said viral cDNA at a set position.
[0093] The BAC may further comprise a yeast autonomously replicating sequence for shuttling to and maintaining said bacterial artificial chromosome in yeast. An example of a yeast ori sequence is the 2μ plasmid origin or the ARS1 (autonomously replicating sequence 1) or functionally homologous derivatives thereof.
[0094] The RNA polymerase driven promoter of this first aspect of the invention can be an RNA polymerase II promoter, such as Cytomegalovirus Immediate Early (CMV-IE) promoter, or the Simian virus 40 promoter or functionally homologous derivatives thereof.
[0095] The RNA polymerase driven promoter can equally be an RNA polymerase I or III promoter.
[0096] The BAC may also comprise an element for RNA self-cleaving such as the cDNA of the genomic ribozyme of hepatitis delta virus or functionally homologous RNA elements.
[0097] The formulation of DNA into a vaccine preparation is known in the art and is described in detail in for example chapter 6 to 10 of “DNA Vaccines” Methods in Molecular Medicine Vol 127, (2006) Springer Saltzman, Shen and Brandsma (Eds.) Humana Press. Totoma, N.J. and in chapter 61 Alternative vaccine delivery methods, Pages 1200-1231, of Vaccines (6th Edition) (2013) (Plotkin et al. Eds.). Details on acceptable carrier, diluents, excipient and adjuvant suitable in the preparation of DNA vaccines can also be found in WO2005042014, as indicated below.
[0098] “Acceptable carrier, diluent or excipient” refers to an additional substance that is acceptable for use in human and/or veterinary medicine, with particular regard to immunotherapy.
[0099] By way of example, an acceptable carrier, diluent or excipient may be a solid or liquid filler, diluent or encapsulating substance that may be safely used in systemic or topic administration. Depending upon the particular route of administration, a variety of carriers, well known in the art may be used. These carriers may be selected from a group including sugars, starches, cellulose and its derivatives, malt, gelatine, talc, calcium sulphate and carbonates, vegetable oils, synthetic oils, polyols, alginic acid, phosphate buffered solutions, emulsifiers, isotonic saline and salts such as mineral acid salts including hydrochlorides, bromides and sulphates, organic acids such as acetates, propionates and malonates and pyrogen-free water.
[0100] A useful reference describing pharmaceutically acceptable carriers, diluents and excipients is Remington's Pharmaceutical Sciences (Mack Publishing Co. N. J. USA, 1991) which is incorporated herein by reference.
[0101] Any safe route of administration may be employed for providing a patient with the DNA vaccine. For example, oral, rectal, parenteral, sublingual, buccal, intravenous, intra-articular, intra-muscular, intra-dermal, subcutaneous, inhalational, intraocular, intraperitoneal, intracerebroventricular, transdermal and the like may be employed. Intra-muscular and subcutaneous injection may be appropriate, for example, for administration of immunotherapeutic compositions, proteinaceous vaccines and nucleic acid vaccines. It is also contemplated that microparticle bombardment or electroporation may be particularly useful for delivery of nucleic acid vaccines.
[0102] Dosage forms include tablets, dispersions, suspensions, injections, solutions, syrups, troches, capsules, suppositories, aerosols, transdermal patches and the like. These dosage forms may also include injecting or implanting controlled releasing devices designed specifically for this purpose or other forms of implants modified to act additionally in this fashion. Controlled release of the therapeutic agent may be effected by coating the same, for example, with hydrophobic polymers including acrylic resins, waxes, higher aliphatic alcohols, polylactic and polyglycolic acids and certain cellulose derivatives such as hydroxypropylmethyl cellulose. In addition, the controlled release may be effected by using other polymer matrices, liposomes and/or microspheres.
[0103] DNA vaccines suitable for oral or parenteral administration may be presented as discrete units such as capsules, sachets or tablets each containing a pre-determined amount of plasmid DNA, as a powder or granules or as a solution or a suspension in an aqueous liquid, a non-aqueous liquid, an oil-in-water emulsion or a water-in-oil liquid emulsion. Such compositions may be prepared by any of the methods of pharmacy but all methods include the step of bringing into association one or more agents as described above with the carrier which constitutes one or more necessary ingredients. In general, the compositions are prepared by uniformly and intimately admixing the DNA plasmids with liquid carriers or finely divided solid carriers or both, and then, if necessary, shaping the product into the desired presentation.
[0104] The above compositions may be administered in a manner compatible with the dosage formulation, and in such amount as is effective. The dose administered to a patient, should be sufficient to effect a beneficial response in a patient over an appropriate period of time. The quantity of agent (s) to be administered may depend on the subject to be treated inclusive of the age, sex, weight and general health condition thereof, factors that will depend on the judgement of the practitioner.
[0105] Furthermore DNA vaccine may be delivered by bacterial transduction as using live-attenuated strain of Salmonella transformed with said DNA plasmids as exemplified by Darji et al. (2000) FEMS Immunol Med Microbiol 27, 341-349 and Cicin-Sain et al. (2003) J. Virol. 77, 8249-8255 given as reference.
[0106] Typically the DNA vaccines are used for prophylactic or therapeutic immunisation of humans, but can for certain viruses also be applied on vertebrate animals (typically mammals, birds and fish) including domestic animals such as livestock and companion animals. The vaccination is envisaged of animals which are a live reservoir of viruses (zoonosis) such as monkeys, mice, rats, birds and bats.
[0107] In certain embodiments vaccines may include an adjuvant, i.e. one or more substances that enhances the immunogenicity and/or efficacy of a vaccine composition However, life vaccines may eventually be harmed by adjuvants that may stimulate innate immune response independent of viral replication. Non-limiting examples of suitable adjuvants include squalane and squalene (or other oils of animal origin); block copolymers; detergents such as Tween-80; Quill A, mineral oils such as Drakeol or Marcol, vegetable oils such as peanut oil; Corynebacterium-derived adjuvants such as Corynebacterium parvum; Propionibacterium-derived adjuvants such as Propionibacterium acne; Mycobacterium bovis (Bacille Calmette and Guerin or BCG); interleukins such as interleukin 2 and interleukin 12; monokines such as interleukin 1; tumour necrosis factor; interferons such as gamma interferon; combinations such as saponin-aluminium hydroxide or Quil-A aluminium hydroxide; liposomes; ISCOMt) and ISCOMATRIX (B) adjuvant; mycobacterial cell wall extract; synthetic glycopeptides such as muramyl dipeptides or other derivatives; Avridine; Lipid A derivatives; dextran sulfate; DEAE-Dextran or with aluminium phosphate; carboxypolymethylene such as Carbopol'EMA; acrylic copolymer emulsions such as Neocryl A640; vaccinia or animal poxvirus proteins; sub-viral particle adjuvants such as cholera toxin, or mixtures thereof.
EXAMPLES
Example 1
Construction of ZIK-JEprM/E
[0108] The ZIKV strain BeH819015 cDNA was cloned into pShuttleBAC according to WO2014174078A1 to yield pShuttle-ZIKV. A chimeric replication competent flavivirus vaccine was generated by exchanging the prM/E coding sequence of the ZIKV in pShuttle-ZIKV for the respective JEV sequence (vaccine strain SA14-14-2) using standard recombinant DNA techniques and recombination in yeast. Two variants pShuttle-ZIK-JEprM/E_JECanch and pShuttle-ZIK-JEprM/E_ZIKCanch were generated containing either the ZIKV or JEV derived Canch domains (
[0109] Transfection of both constructs in Vero E6 cells and unbiased monitoring of replication of the recombinant virus progeny by immune fluorescence microscopy revealed that unexpectedly the ZIKCanch variant failed to produce infectious progeny, by contrast to prior evidence from the construction of similar yellow fever virus ZIKV chimeras (Kum et al. (2018) NPJ Vaccines. 3, 56). Likewise, only the JECanch variant was fully replication competent (
TABLE-US-00001 TABLE 1 Correspondence between nucleotide and amino acid substitution Nucleotide position in ZIK-JEprM/E JECanch: A1482G ZIK-JEprM/E JECanch K459E polyprotein JEV SA14-14-2 prM/E protein K333E JEV SA14-14-2 E protein K166E
[0110] The resulting ZIK-JEprM/E chimeric virus was attenuated as compared to the parental ZIKV, demonstrated by reduced replication kinetics on Vero E6 cells (
Example 2
Attenuation, Immunogenicity and Vaccine Efficacy of ZIK-JEprM/E
[0111] The ZIK-JEprM/E vaccine virus was well tolerated when inoculated intraperitoneally (i.p.) into interferon alpha/beta (IFN-α/β)-deficient (AG129) mice at a dose of 10.sup.4 PFU (plaque forming units) of ZIK-JEprM/E; mice inoculated with a similar or even much lower dose (<10.sup.2 PFU) of wild-type ZIKV uniformly die from infection again proving the favorable attenuation of the ZIK-JEprM/E vaccine virus.
[0112] Virus-specific neutralizing antibodies (nAb) are regularly elicited against the respective E protein present in or expressed by a particular flavivirus vaccine. High titres of nAb against a specific flavivirus are generally accepted to confer protection from infection with that specific virus. In lack of ZIKV E sequences ZIK-JEprM/E can therefore not induce other than JEV specific nAb. In line, AG129 vaccinated with ZIK-JEprM/E developed high titers of anti-JEV neutralizing antibodies (nAb), yet no nAb against ZIKV.
[0113] However, antibodies that are not neutralising, yet bind other proteins of ZIKV (non-nAb most likely directed against the ZIKV NS1 protein) were readily detectable in ZIK-JEprM/E AG129 mice by an indirect immune fluorescence assay. AG129 vaccinated with ZIK-JEprM/E also showed the strong induction of cell mediated immunity against the ZIKV, as demonstrated by a high number of ZIKV-specific IFN-γ secreting splenocytes as detected by ELISPOT ten weeks post vaccination with ZIK-JEprM/E (
[0114] ZIK-JEprM/E vaccinated AG129 mice survived a lethal challenge with JEV (
[0115] In contrast to the licensed JEV vaccine Chimerivax-JE, ZIK-JEprM/E also protected against a subsequent lethal ZIKV infection (