Vectors for Producing Virus-Like Particles and Uses Thereof

REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY

The content of the electronically submitted sequence listing (Name: 4471_0050002_Seqlisting_ST26; Size: 160,205 bytes; and Date of Creation: Sep. 29, 2022) is herein incorporated by reference in its entirety.

FIELD OF DISCLOSURE

The present disclosure provides vectors for producing virus-like particles (VLPs) and methods of treating subjects with the same.

BACKGROUND

Despite numerous advances in vaccine technologies, viral infections remain a prevalent health concern that are often under limited control. For example, the COVID-19 coronavirus pandemic became unlike anything the world had seen in over a century, both in terms of global spread and economic impact. It resulted in repeated shutdowns in much of the developed world, with continuously increasing death tolls and new infections.

COVID-19 causes a respiratory infection, along with acute respiratory distress syndrome in severe cases. Pre/asymptomatic airborne transmission and high viral titre early in the course of the disease significantly increase the infectiousness of COVID-19 compared to other coronaviruses such as SARS-CoV, making the development of vaccines critical for management of the pandemic.

VLPs represent potent vaccine candidates that mimic viral physicochemical properties and structure without potentiating viral growth (Cimica, V., & Galarza, J. M., Clin. Immunol. 183: 99-108 (2017)). As such, they confer strong humoral responses, but often limited cell-mediated responses against the ‘whole virus’ as they remain exogenously administered antigens. Furthermore, their production, purification, and storage are costly.

Existing vaccines have often shown limited cross-protection among different viral strains, complicated by the fact that viruses continue to mutate their genomes in response to evolutionary pressures.

There is a need for improved VLPs and methods of treating viral infections.

BRIEF SUMMARY

The present disclosure is directed to an expression vector comprising: an expression cassette that comprises a nucleic acid sequence encoding a recombinant protein comprising a conserved amino acid sequence from a virus fused to an immunogenic amino acid sequence, a target sequence for a first recombinase flanking each side of the expression cassette, and one or more additional target sequences for one or more additional recombinases integrated within non-binding regions of the target sequence for the first recombinase, wherein protein expressed intracellularly from the expression cassette is capable of forming a virus-like particle (VLP).

In some aspects, the immunogenic amino acid sequence is from the same virus as the conserved amino acid sequence. In some aspects, the conserved amino acid sequence is from a viral glycoprotein. In some aspects, the immunogenic amino acid sequence is from the same viral glycoprotein.

In some aspects, the expression cassette further comprises a nucleic acid sequence encoding a viral envelope protein and/or a nucleic acid sequence encoding a viral matrix protein. In some aspects, the viral envelope protein and/or the viral matrix protein are from the same virus as the conserved amino acid sequence.

In some aspects, the conserved amino acid sequence, the immunogenic amino acid sequence, the viral envelope protein, and/or the viral matrix protein is a consensus sequence.

In some aspects, the recombinant protein is capable of stimulating an immune response against the virus comprising neutralizing antibodies.

In some aspects, the recombinant protein is capable of stimulating a Th1 cell-mediated immune response against the virus.

In some aspects, the immune response is cross-reactive to a related virus or strain.

In some aspects, the recombinant protein excludes amino acid sequences from the virus that stimulate an immune response comprising non-neutralizing antibodies and/or that stimulate a Th2 cell-mediated immune response.

In some aspects, the virus is a coronavirus, an influenza virus, a human immunodeficiency virus, a human papillomavirus, a hepatitis virus, or an oncolytic virus.

In some aspects, the virus is a coronavirus. In some aspects, the coronavirus is COVID-19.

In some aspects, the expression cassette comprises nucleic acid sequences encoding a coronavirus Membrane (M) protein, a coronavirus Envelope (E) protein, and a recombinant protein comprising a conserved amino acid sequence and an immunogenic amino acid sequence from a coronavirus Spike (S) protein. In some aspects, the conserved amino acid sequence is from the S protein S2′ cleavage site and internal fusion peptide (IFP).

In some aspects, the conserved amino acid sequence comprises SEQ ID NO:12.

In some aspects, the immunogenic amino acid sequence is from the S protein receptor-binding domain (RBD).

In some aspects, the immunogenic amino acid sequence is at least about 90% identical to SEQ ID NO:11.

In some aspects, the recombinant protein further comprises a transmembrane (TM) domain sequence from the S protein.

In some aspects, the recombinant protein excludes amino acid sequences from the S protein that stimulate an immune response comprising non-neutralizing antibodies and/or that stimulate a Th2 cell-mediated immune response.

In some aspects, the amino acid sequence of the recombinant protein is at least about 90% identical to SEQ ID NO:55.

In some aspects, the expression cassette comprises a single open reading frame translated as an amino acid sequence at least about 90% identical to SEQ ID NO:57.

In some aspects, the recombinant protein is capable of stimulating an immune response against COVID-19.

In some aspects, the recombinant protein is capable of stimulating a Th1 cell-mediated immune response against COVID-19.

In some aspects, the immune response is cross-reactive to other coronaviruses. In some aspects, the immune response is cross-reactive to other severe acute respiratory syndrome coronaviruses and/or human betacoronaviruses.

In some aspects, the target sequence for the first recombinase and the one or more additional target sequences for the one or more additional recombinases are selected from the group consisting of the PY54 pal site, the N15 telRL site, the loxP site, φK02 telRL site, the FRT site, the phiC31 attP site, and the λ attP site. In some aspects, the expression vector comprises each of the target sequences. In some aspects, the expression vector comprises the Tel recombinase pal site and the telRL, loxP, and FRT recombinase target binding sequences integrated within the pal site.

In some aspects, the expression vector is for producing a bacterial sequence-free vector. In some aspects, the bacterial sequence-free vector has circular covalently closed ends. In some aspects, the bacterial sequence-free vector has linear covalently closed ends.

In some aspects, the expression vector further comprises at least one enhancer sequence flanking each side of the target sequence for the first recombinase. In some aspects, the at least one enhancer sequence is at least two enhancer sequences. In some aspects, the at least one enhancer sequence is a SV40 enhancer sequence.

The present disclosure is directed to a vector production system comprising recombinant cells designed to encode at least a first recombinase under the control of an inducible promoter, wherein the cells comprise any of the above expression vectors. In some aspects, the inducible promoter is thermally-regulated, chemically-regulated, IPTG regulated, glucose-regulated, arabinose inducible, T7 polymerase regulated, cold-shock inducible, pH inducible, or combinations thereof. In some aspects, the first recombinase is selected from telN and tel, and the expression vector incorporates the target sequence for at least the first recombinase. In some aspects, the recombinant cells have been further designed to encode a nuclease genome editing system, and wherein the expression vector further comprises a backbone sequence containing a cleavage site for the nuclease genome editing system. In some aspects, the nuclease genome editing system is a CRISPR nuclease system comprising a Cas nuclease and gRNA, and the expression vector comprises a target sequence for the gRNA within the backbone sequence.

The present disclosure is directed to a method of producing a bacterial sequence-free vector comprising incubating any of the above vector production systems under suitable conditions for expression of the first recombinase.

The present disclosure is directed to a method of producing a bacterial sequence-free vector comprising incubating any of the above vector production systems that comprise recombinant cells designed to encode a nuclease genome editing system under suitable conditions for expression of the first recombinase and the nuclease genome editing system.

In some aspects, any of the above methods of producing a bacterial sequence-free vector further comprise harvesting the bacterial sequence-free vector.

The present disclosure is directed to a bacterial sequence-free vector produced by any of the above methods of producing a bacterial sequence-free vector.

The present disclosure is directed to a bacterial sequence-free vector comprising an expression cassette that comprises a nucleic acid sequence encoding a recombinant protein comprising a conserved amino acid sequence from a virus fused to an immunogenic amino acid sequence, wherein protein expressed intracellularly from the expression cassette is capable of forming a VLP.

In some aspects, the conserved amino acid sequence, the immunogenic amino acid sequence, the viral envelope protein, and/or the viral matrix protein is a consensus sequence.

In some aspects, the recombinant protein is capable of stimulating an immune response against the virus comprising neutralizing antibodies.

In some aspects, the recombinant protein is capable of stimulating a Th1 cell-mediated immune response against the virus.

In some aspects, the immune response is cross-reactive to a related virus or strain.

In some aspects, the virus is a coronavirus, an influenza virus, a human immunodeficiency virus, a human papillomavirus, a hepatitis virus, or an oncolytic virus.

In some aspects, the virus is a coronavirus. In some aspects, the coronavirus is COVID-19.

In some aspects, the expression cassette comprises nucleic acid sequences encoding a coronavirus M protein, a coronavirus E protein, and a recombinant protein comprising a conserved amino acid sequence and an immunogenic amino acid sequence from a coronavirus S protein. In some aspects, the conserved amino acid sequence is from the S protein S2′ cleavage site and IFP.

In some aspects, the conserved amino acid sequence comprises SEQ ID NO:12.

In some aspects, the immunogenic amino acid sequence is from the S protein RBD.

In some aspects, the immunogenic amino acid sequence is at least about 90% identical to SEQ ID NO:11.

In some aspects, the recombinant protein further comprises a TM domain sequence from the S protein.

In some aspects, the amino acid sequence of the recombinant protein is SEQ ID NO:55.

In some aspects, the expression cassette comprises a single open reading frame translated as an amino acid sequence at least about 90% identical to SEQ ID NO:57.

In some aspects, the recombinant protein is capable of stimulating an immune response against COVID-19.

In some aspects, the recombinant protein is capable of stimulating a Th1 cell-mediated immune response against COVID-19.

In some aspects, the bacterial sequence-free vector further comprises at least one enhancer sequence flanking each side of the expression cassette. In some aspects, the at least one enhancer sequence is at least two enhancer sequences. In some aspects, the at least one enhancer sequence is a SV40 enhancer sequence.

In some aspects, the bacterial sequence-free vector comprises circular covalently closed ends.

In some aspects, the bacterial sequence-free vector comprises linear covalently closed ends.

The present disclosure is directed to a polynucleotide encoding an amino acid sequence at least about 90% identical to SEQ ID NO:57.

The present disclosure is directed to a recombinant cell comprising any of the above expression vectors or any of the above bacterial sequence-free vectors.

In some aspects, the present disclosure is directed to a method of producing a VLP, comprising culturing the recombinant cell under suitable conditions for production of the VLP from the expression vector or the bacterial sequence-free vector.

In some aspects, the method of producing a VLP further comprises isolating the VLP. In some aspects, the isolating is by affinity purification. In some aspects, the VLP is produced by any of the above expression vectors or any of the above bacterial sequence-free vectors wherein the virus is a coronavirus. In some aspects, the affinity purification comprises an angiotensin-converting enzyme 2 (ACE2) receptor peptide or an anti-S protein monoclonal antibody. In some aspects, the ACE2 receptor peptide comprises an amino acid sequence that is at least about 90% identical to the amino acid sequence of SEQ ID NO:70. In some aspects, the ACE2 receptor peptide comprises a biotin acceptor peptide (BAP) tag at the C-terminus or N-terminus of the peptide. In some aspects, the BAP tag comprises an amino acid sequence at least about 90% identical to the amino acid sequence of SEQ ID NO:71. In some aspects, the ACE2 receptor peptide or anti-S protein monoclonal antibody is biotinylated and immobilized on a streptavidin-coated bead. In some aspects, the affinity purification comprises microfluidics and/or chromatography. In some aspects, the present disclosure is directed to a VLP produced by any of the methods of producing a VLP.

The present disclosure is directed to a VLP comprising a recombinant protein comprising a conserved amino acid sequence from a virus fused to an immunogenic amino acid sequence. In some aspects, the immunogenic amino acid sequence is from the same virus as the conserved amino acid sequence. In some aspects, the conserved amino acid sequence is from a viral glycoprotein. In some aspects, the immunogenic amino acid sequence is from the same viral glycoprotein.

In some aspects, the VLP further comprises a viral envelope protein and/or a viral matrix protein. In some aspects, the viral envelope protein and/or the viral matrix protein are from the same virus as the conserved amino acid sequence.

In some aspects, the conserved amino acid sequence, the immunogenic amino acid sequence, the viral envelope protein, and/or the viral matrix protein is a consensus sequence.

In some aspects, the recombinant protein is capable of stimulating an immune response against the virus comprising neutralizing antibodies.

In some aspects, the recombinant protein is capable of stimulating a Th1 cell-mediated immune response against the virus.

In some aspects, the immune response is cross-reactive to a related virus or strain.

In some aspects, the virus is a coronavirus, an influenza virus, a human immunodeficiency virus, a human papillomavirus, a hepatitis virus, or an oncolytic virus. In some aspects, the virus is a coronavirus.

In some aspects, the coronavirus is COVID-19.

In some aspects, the VLP comprises a coronavirus Membrane (M) protein, a coronavirus Envelope (E) protein, and a recombinant protein comprising a conserved amino acid sequence and an immunogenic amino acid sequence from a coronavirus Spike (S) protein.

In some aspects, the conserved amino acid sequence is from the S protein S2′ cleavage site and internal fusion peptide (IFP).

In some aspects, the conserved amino acid sequence comprises SEQ ID NO:12.

In some aspects, the immunogenic amino acid sequence is from the S protein receptor-binding domain (RBD).

In some aspects, the immunogenic amino acid sequence is at least about 90% identical to SEQ ID NO:11.

In some aspects, the recombinant protein further comprises a transmembrane (TM) domain sequence from the S protein.

In some aspects, the amino acid sequence of the recombinant protein is at least about 90% identical to SEQ ID NO:55.

The present disclosure is directed to a VLP comprising a recombinant protein at least about 90% identical to SEQ ID NO:55, an M protein at least about 90% identical to SEQ ID NO:1, and an E protein at least about 90% identical to SEQ ID NO:3.

In some aspects, the recombinant protein is capable of stimulating an immune response against COVID-19.

In some aspects, the recombinant protein is capable of stimulating a Th1 cell-mediated immune response against COVID-19.

In some aspects, the immune response is cross-reactive to other coronaviruses.

In some aspects, the immune response is cross-reactive to other severe acute respiratory syndrome coronaviruses and/or human betacoronaviruses.

The present disclosure is directed to a composition comprising any of the above expression vectors, any of the above bacterial sequence-free vectors, or any of the above virus-like particles. In some aspects, the composition further comprises a delivery agent. In some aspects, the delivery agent is a nanoparticle. In some aspects, the delivery agent comprises a targeting ligand. In some aspects, the targeting ligand comprises a S protein peptide. In some aspects, the S protein peptide comprises an amino acid sequence at least about 90% identical to any one of SEQ ID NOs:76-99.

The present disclosure is directed to a method of treating a viral infection in a subject, comprising administering to the subject any of the above expression vectors, any of the above bacterial sequence-free vectors, any of the above VLPs, or any of the above compositions, wherein intracellular expression of the expression vector or the bacterial sequence-free vector produces a VLP.

In some aspects, the administering is by parenteral or non-parenteral administration. In some aspects, the administering is by oral, pulmonary, intranasal, intravenous, epidermal, transdermal, subcutaneous, intramuscular, or intraperitoneal administration, or by inhalation.

In some aspects, the VLP stimulates an immune response in the subject comprising neutralizing antibodies against the viral infection.

In some aspects, the VLP stimulates a Th1 cell-mediated immune response in the subject against the viral infection.

In some aspects, the immune response is cross-reactive to a related virus or strain.

In some aspects, the VLP does not stimulate an immune response comprising non-neutralizing antibodies in the subject and/or does not stimulate a Th2 cell-mediated immune response in the subject.

In some aspects, the VLP cross-competes with the infecting virus for binding to a viral receptor.

In some aspects, the VLP cross-competes with a related virus or strain for binding to the viral receptor.

In some aspects, the viral infection is a coronavirus, an influenza virus, a human immunodeficiency virus, a human papillomavirus, a hepatitis virus, or an oncolytic virus.

In some aspects, the viral infection is a coronavirus. In some aspects, the viral infection is COVID-19.

In some aspects, the VLP stimulates an immune response in the subject comprising neutralizing antibodies against COVID-19.

In some aspects, the VLP stimulates a Th1 cell-mediated immune response in the subject against COVID-19.

In some aspects, the immune response is cross-reactive to other coronaviruses.

In some aspects, the immune response is cross-reactive to other severe acute respiratory syndrome coronaviruses and/or human betacoronaviruses.

In some aspects, the VLP does not stimulate an immune response comprising non-neutralizing antibodies in the subject and/or does not stimulate a Th2 cell-mediated immune response in the subject.

In some aspects, the administering is by inhalation.

In some aspects, the VLP cross-competes with COVID-19 for binding to ACE2 receptor, neuropilin-1, or other receptors.

In some aspects, the VLP cross-competes with other coronaviruses for binding to ACE2 receptor, neuropilin-1, and/or other receptors.

In some aspects, the VLP cross-competes with other severe acute respiratory syndrome coronaviruses and/or human betacoronaviruses for binding to ACE2 receptor, neuropilin-1, and/or other receptors.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a schematic representation of an exemplary expression cassette for producing a coronavirus VLP containing simian virus 40 enhancers (SV40E); a cytomegalovirus promoter (P_CMV); a sequence encoding a coronavirus Envelope (E) protein; a sequence encoding a coronavirus Membrane (M) protein; a sequence encoding a recombinant protein containing sequences from the receptor-binding domain (RBD), the second subunit cleavage domain and internal fusion peptide (S2′IFP), and transmembrane (TM) domain of a coronavirus S protein (referred to herein as a recombinant Spike (S) protein, RBD::S2′IFP::TM); sequences encoding 2A self-cleaving peptides from porcine teschovirus-1 (P2A) to separate the protein-encoding sequences of the expression cassette; and a polyadenylation (pA) signal.

FIG. 2 shows a vector map of an exemplary expression vector (pGL2-SS-CMV-VLP-BGH-SS) containing an expression cassette as described in FIG. 1, in which the pA signal is from bovine growth hormone.

FIG. 3A, FIG. 3B, and FIG. 3C show in vitro expression of genes and protein from the expression vector of FIG. 2. FIG. 3A shows a bar graph depicting relative expression of genes encoding the E protein, M protein, and recombinant S protein (RBD::S2′IFP::TM) as described in FIG. 1 from cells containing the expression vector of FIG. 2 (VLP) as well as control cells without the expression vector (CTL). ***=p<0.001 and ****=p<0.0001. FIG. 3B shows a representative Western blot depicting expression of the recombinant S protein using an antibody that binds to the RBD (α-Spike (RBD)). Detection of beta-actin with the a-beta-actin antibody served as a loading control. Control=protein from cells without the expression vector. VLP=protein from cells containing the expression vector of FIG. 2. FIG. 3C shows the relative mean intensity of recombinant S protein expression from Western blots (n=3) as described for FIG. 3B.

FIG. 4 shows an exemplary msDNA-VLP (msDNA VLP Cov 19-BGH poly) as described herein that is encoded by the expression vector of FIG. 2.

FIG. 5A and FIG. 5B show the concentration (ng/mL) of antibodies that bind to the S1 subunit of the COVID-19 Spike protein (Spike AB) in serum from C57 mice at days 0, 7, 14, 21, 28, 35, 42, and 49 following intramuscular injection with the expression vector of FIG. 2 at day 0 and day 14 (booster). FIG. 5A and FIG. 5B show a line graph and a bar graph of the antibody concentration, respectively.

FIG. 6A and FIG. 6B show a sequence conservation analysis of representative COVID-19 genomes. FIG. 6A shows a bar plot in which the horizontal bars indicate the genomic positions on the x-axis of each of the COVID-19 genes listed on the y-axis as per the Wuhan reference genome (NC_045512.2). FIG. 6B shows a histogram in which bar heights correspond to the percentage of 3928 representative COVID-19 genomes that differed from the Wuhan reference genome at each genomic position.

FIG. 7, FIG. 8A, FIG. 8B, FIG. 8C, and FIG. 8D show histograms in which bar heights correspond to the percentage of analyzed genomes that differed from the Wuhan reference genome at each genomic position, with the analyzed genomes being: (FIG. 7) 3928 representative COVID-19 genomes, 120 severe acute respiratory syndrome coronaviruses (SARS-CoV) genomes, and 257 Middle East respiratory syndrome coronaviruses (MERS-CoV) genomes, (FIG. 8A) 233 COVID-19 genomes of variant strain B.1.1.7, (FIG. 8B) 104 COVID-19 genomes of variant strain B.1.351, (FIG. 8C) 39 COVID-19 genomes of variant strain P.1, and (FIG. 8D) 62 COVID-19 genomes of variant strain B.1.427/429.

FIG. 9 shows an exemplary eukaryotic expression vector (pFastBac™ Dual-VLP) for VLP production in eukaryotic cells as described herein, containing the E, M, and recombinant S proteins as described in FIG. 1.

DETAILED DESCRIPTION

The present disclosure provides expression vectors and bacterial sequence-free vectors (e.g., ministring DNA (msDNA)) for producing virus-like particles (VLPs), vector production systems, and VLPs, as well as compositions and methods thereof. Some aspects of the present disclosure are directed to treating viral infections in a subject (e.g., coronavirus infections in a human subject, such as COVID-19).

All publications cited herein are hereby incorporated by reference in their entireties, including without limitation all journal articles, books, manuals, patent applications, and patents cited herein, to the same extent as if each individual publication was specifically and individually indicated to be incorporated by reference.

I. Terms

In order that the present disclosure can be more readily understood, certain terms are first defined. As used in this application, except as otherwise expressly provided herein, each of the following terms shall have the meaning set forth below. Additional definitions are set forth throughout the application.

It is to be noted that the term “a” or “an” entity refers to one or more of that entity; for example, “a nucleotide sequence,” is understood to represent one or more nucleotide sequences. As such, the terms “a” (or “an”), “one or more,” and “at least one” can be used interchangeably herein.

The term “and/or” where used herein is to be taken as specific disclosure of each of the two specified features or components with or without the other. Thus, the term “and/or” as used in a phrase such as “A and/or B” herein is intended to include “A and B,” “A or B,” “A” (alone), and “B” (alone). Likewise, the term “and/or” as used in a phrase such as “A, B, and/or C” is intended to encompass each of the following aspects: A, B, and C; A, B, or C; A or C; A or B; B or C; A and C; A and B; B and C; A (alone); B (alone); and C (alone).

It is understood that wherever aspects are described herein with the language “comprising,” otherwise analogous aspects described in terms of “consisting of” and/or “consisting essentially of” are also provided.

The terms “about” or “comprising essentially of” refer to a value or composition that is within an acceptable error range for the particular value or composition as determined by one of ordinary skill in the art, which will depend in part on how the value or composition is measured or determined, i.e., the limitations of the measurement system. For example, “about” or “comprising essentially of” can mean within 1 or more than 1 standard deviation per the practice in the art. Alternatively, “about” or “comprising essentially of” can mean a range of up to 10%. Furthermore, particularly with respect to biological systems or processes, the terms can mean up to an order of magnitude or up to 5-fold of a value. When particular values or compositions are provided in the application and claims, unless otherwise stated, the meaning of “about” or “comprising essentially of” should be assumed to be within an acceptable error range for that particular value or composition.

As described herein, any concentration range, percentage range, ratio range, or integer range is to be understood to include the value of any integer within the recited range and, when appropriate, fractions thereof (such as one tenth and one hundredth of an integer), unless otherwise indicated. Numeric ranges are inclusive of the numbers defining the range.

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure is related. For example, the Concise Dictionary of Biomedicine and Molecular Biology, Juo, Pei-Show, 2nd ed., 2002, CRC Press; The Dictionary of Cell and Molecular Biology, 5th ed., 2013, Academic Press; and the Oxford Dictionary Of Biochemistry And Molecular Biology, 2006, Oxford University Press, provide one of skill with a general dictionary of many of the terms used in this disclosure.

Units, prefixes, and symbols are denoted in their Systéme International de Unites (SI) accepted form.

Unless otherwise indicated, nucleotide sequences are written left to right in 5′ to 3′ orientation. Amino acid sequences are written left to right in amino to carboxy orientation.

The headings provided herein are not limitations of the various aspects of the disclosure, which can be had by reference to the specification as a whole. Accordingly, the terms defined immediately below are more fully defined by reference to the specification in its entirety.

“Amino acid” is a molecule having the structure wherein a central carbon atom (the alpha-carbon atom) is linked to a hydrogen atom, a carboxylic acid group (the carbon atom of which is referred to herein as a “carboxyl carbon atom”), an amino group (the nitrogen atom of which is referred to herein as an “amino nitrogen atom”), and a side chain group, R. When incorporated into a peptide, polypeptide, or protein, an amino acid loses one or more atoms of its amino acid carboxylic groups in the dehydration reaction that links one amino acid to another. As a result, when incorporated into a protein, an amino acid is referred to as an “amino acid residue.”

“Protein” or “polypeptide” refers to any polymer of two or more individual amino acids (whether or not naturally occurring) linked via a peptide bond, and occurs when the carboxyl carbon atom of the carboxylic acid group bonded to the alpha-carbon of one amino acid (or amino acid residue) becomes covalently bound to the amino nitrogen atom of amino group bonded to the non alpha-carbon of an adjacent amino acid. The term “protein” is understood to include the terms “polypeptide” and “peptide” (which, at times may be used interchangeably herein) within its meaning. In addition, proteins comprising multiple polypeptide subunits will also be understood to be included within the meaning of “protein” as used herein. Similarly, fragments of proteins and polypeptides are also within the scope of the disclosure and may be referred to herein as “proteins.” In one aspect of the disclosure, a polypeptide comprises a chimera of two or more parental peptide segments. The term “polypeptide” is also intended to refer to and encompass the products of post-translation modification (“PTM”) of the polypeptide, including without limitation disulfide bond formation, glycosylation, carbamylation, lipidation, acetylation, phosphorylation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage, modification by non-naturally occurring amino acids, or any other manipulation or modification, such as conjugation with a labeling component. A polypeptide can be derived from a natural biological source or produced by recombinant technology, but is not necessarily translated from a designated nucleic acid sequence. It can be generated in any manner, including by chemical synthesis. An “isolated” polypeptide or a fragment, variant, or derivative thereof refers to a polypeptide that is not in its natural milieu. No particular level of purification is required. For example, an isolated polypeptide can simply be removed from its native or natural environment. Recombinantly produced polypeptides and proteins expressed in host cells are considered isolated for the purpose of the disclosure, as are native or recombinant polypeptides which have been separated, fractionated, or partially or substantially purified by any suitable technique.

“Domain” as used herein can be used interchangeably with the term “peptide segment” and refers to a portion or fragment of a larger polypeptide or protein. A domain need not on its own have functional activity, although in some instances, a domain can have its own biological activity.

“Fused,” “operably linked,” and “operably associated” are used interchangeably herein when referring to two or more domains to broadly refer to any chemical or physical coupling of the two or more domains in the formation of a recombinant polypeptide as disclosed herein. In one embodiment, a recombinant polypeptide as disclosed herein is a chimeric polypeptide comprising a plurality of domains from two or more different polypeptides.

Recombinant polypeptides (i.e., recombinant proteins) comprising two or more domains and/or proteins as disclosed herein can be encoded by a single coding sequence that comprises polynucleotide sequences encoding each domain and/or protein. Unless stated otherwise, the polynucleotide sequences encoding each domain and/or protein are “in frame” such that translation of a single mRNA comprising the polynucleotide sequences results in a single polypeptide comprising each domain and/or protein. Typically, the domains and/or proteins in a recombinant polypeptide as described herein will be fused directly to one another or will be separated by a peptide linker. Various polynucleotide sequences encoding peptide linkers are known in the art and include, for example, self-cleaving peptides.

“Polynucleotide” or “nucleic acid” as used herein refers to a polymeric form of nucleotides. In some instances, a polynucleotide comprises a sequence that is either not immediately contiguous with the coding sequences or is immediately contiguous (on the 5′ end or on the 3′ end) with the coding sequences in the naturally occurring genome of the organism from which it is derived. The term therefore includes, for example, a recombinant DNA that is incorporated into a vector, into an autonomously replicating plasmid or virus, or into the genomic DNA of a prokaryote or eukaryote, or which exists as a separate molecule (e.g., a cDNA) independent of other sequences. The nucleotides of the disclosure can be ribonucleotides, deoxyribonucleotides, or modified forms of either nucleotide. A polynucleotide as used herein refers to, among others, single- and double-stranded DNA, DNA that is a mixture of single- and double-stranded regions, single- and double-stranded RNA, and RNA that is mixture of single- and double-stranded regions, hybrid molecules comprising DNA and RNA that may be single-stranded or, more typically, double-stranded or a mixture of single- and double-stranded regions. The term polynucleotide encompasses genomic DNA or RNA (depending upon the organism, i.e., RNA genome of viruses), as well as mRNA encoded by the genomic DNA, and cDNA. In certain embodiments, a polynucleotide comprises a conventional phosphodiester bond or a non-conventional bond (e.g., an amide bond, such as found in peptide nucleic acids (PNA)). By “isolated” nucleic acid or polynucleotide is intended a nucleic acid molecule, e.g., DNA or RNA, which has been removed from its native environment. For example, a nucleic acid molecule comprising a polynucleotide encoding a recombinant polypeptide contained in a vector is considered “isolated” for the purposes of the present disclosure. Further examples of an isolated polynucleotide include recombinant polynucleotides maintained in heterologous host cells or purified (partially or substantially) from other polynucleotides in a solution. Isolated RNA molecules include in vivo or in vitro RNA transcripts of polynucleotides of the present disclosure. Isolated polynucleotides or nucleic acids according to the present disclosure further include polynucleotides and nucleic acids (e.g., nucleic acid molecules) produced synthetically.

As used herein, a “coding region” or “coding sequence” is a portion of a polynucleotide, which consists of codons translatable into amino acids. Although a “stop codon” (TAG, TGA, or TAA) is typically not translated into an amino acid, it may be considered to be part of a coding region, but any flanking sequences, for example promoters, ribosome binding sites, transcriptional terminators, introns, and the like, are not part of a coding region. The boundaries of a coding region are typically determined by a start codon at the 5′ terminus, encoding the amino-terminus of the resultant polypeptide, and a translation stop codon at the 3′ terminus, encoding the carboxyl-terminus of the resulting polypeptide.

As used herein, the term “expression control region” refers to a transcription control element that is operably associated with a coding region to direct or control expression of the product encoded by the coding region, including, for example, promoters, enhancers, operators, repressors, ribosome binding sites, translation leader sequences, introns, polyadenylation recognition sequences, RNA processing sites, effector binding sites, stem-loop structures, and transcription termination signals. For example, a coding region and a promoter are “operably associated” (i.e., “operably linked”) if induction of promoter function results in the transcription of mRNA comprising a coding region that encodes the product, and if the nature of the linkage between the promoter and the coding region does not interfere with the ability of the promoter to direct the expression of the product encoded by the coding region or interfere with the ability of the DNA template to be transcribed. Expression control regions include nucleotide sequences located upstream (5′ non-coding sequences), within, or downstream (3′ non-coding sequences) of a coding region, and which influence the transcription, RNA processing, stability, or translation of the associated coding region. If a coding region is intended for expression in a eukaryotic cell, a polyadenylation signal and transcription termination sequence will usually be located 3′ to the coding sequence.

As used herein, the terms “host cell” and “cell” can be used interchangeably and can refer to any type of cell or a population of cells, e.g., a primary cell, a cell in culture, or a cell from a cell line, that harbors or is capable of harboring a nucleic acid molecule (e.g., a recombinant nucleic acid molecule). Host cells can be a prokaryotic cell, or alternatively, the host cells can be eukaryotic, for example, fungal cells, such as yeast cells, and various animal cells, such as insect cells or mammalian cells.

“Culture,” “to culture” and “culturing,” as used herein, means to incubate cells under in vitro conditions that allow for cell growth or division or to maintain cells in a living state. “Cultured cells,” as used herein, means cells that are propagated in vitro.

A “subject” includes any human or nonhuman animal. The term “nonhuman animal” includes, but is not limited to, vertebrates such as mammals, avians, pets, farm animals, nonhuman primates, sheep, cows, goats, pigs, chickens, dogs, cats, and rodents such as mice, rats, and guinea pigs. In preferred aspects, the subject is a human. The terms, “subject” and “patient” are used interchangeably herein.

“Administering” refers to the physical introduction of a therapeutic agent to a subject, using any of the various methods and delivery systems known to those skilled in the art.

The terms “treat,” “treating,” “treatment,” or “therapy” of a subject as used herein, refer to any type of intervention or process performed on, or administering an active agent to, the subject with the objective of reversing, alleviating, ameliorating, inhibiting, or slowing down or preventing the progression, development, severity or recurrence of a symptom, complication, condition or biochemical indicia associated with a disease or enhancing overall survival. Treatment can be of a subject having a disease or a subject who does not have a disease (e.g., for prophylaxis, such as vaccination).

The term “effective dose” “effective dosage,” or “effective amount” is defined as an amount sufficient to achieve or at least partially achieve a desired effect. A “therapeutically effective amount” or “therapeutically effective dosage” of a drug or therapeutic agent is any amount of the drug that, when used alone or in combination with another therapeutic agent, promotes disease regression evidenced by a decrease in severity of disease symptoms, an increase in frequency and duration of disease symptom-free periods, an increase in overall survival (the length of time from either the date of diagnosis or the start of treatment for a disease that patients diagnosed with the disease are still alive), or a prevention of impairment or disability due to the disease affliction. A therapeutically effective amount or dosage of a drug includes a “prophylactically effective amount” or a “prophylactically effective dosage”, which is any amount of the drug that, when administered alone or in combination with another therapeutic agent to a subject at risk of developing a disease or of suffering a recurrence of disease, inhibits the development or recurrence of the disease. The ability of a therapeutic agent to promote disease regression or inhibit the development or recurrence of the disease can be evaluated using a variety of methods known to the skilled practitioner, such as in human subjects during clinical trials, in animal model systems predictive of efficacy in humans, or by assaying the activity of the agent in in vitro assays.

Various aspects of the disclosure are described in further detail in the following subsections.

II. Vectors for Producing VLPs

Bacterial sequence-free vectors and their production are described in U.S. Pat. Nos. 9,290,778 and 9,862,954; Nafissi and Slavcev, Microbial Cell Factories 11:154 (2012); and Nafissi et al., Nucleic Acids 3(6):e165 (2014), incorporated by reference herein in their entireties. These bacterial sequence-free vectors are produced from an expression vector (e.g., a plasmid) that contains specialized “Super Sequence” (“SS”) sites comprising target sequences for recombinases. The SS sites flank an expression cassette containing a nucleic acid(s) of interest. When the expression vector is present in a recombinant cell that expresses an appropriate recombinase, bacterial sequence-free vector containing the expression cassette is separated from the backbone DNA of the expression vector. To produce a circular covalently closed (CCC) bacterial sequence-free vector, a production system is used in which the recombinant cell expresses a Cre or Flp recombinase, for example, and the expression vector contains corresponding target sequences for the recombinases. To produce a linear covalently closed (LCC) bacterial sequence-free vector, also referred to herein as a ministring DNA (msDNA), a production system is used in which the recombinant cell expresses a TelN or Tel recombinase, for example, and the expression vector contains corresponding target sequences for the recombinases The bacterial sequence-free vector can then be purified from the cells and used directly as a delivery vector. See U.S. Pat. Nos. 9,290,778 and 9,862,954, Nafissi and Slavcev, and Nafissi et al.

msDNA vectors with LCC ends are torsion-free and not subject to gyrase-directed negative supercoiling during their production in E. coli. Exemplary msDNA vectors carry an expression cassette with a eukaryotic promoter, gene of interest (GOI), intron, and polyA sequence, and nuclear translocation enhancing sequences (Nafissi and Slavcev, and Nafissi et al.). Furthermore, due to its double stranded LCC topology, integration of msDNA into a cell's chromosome causes a chromosomal break, thereby eliminating the cell from the population. Thus, msDNA eliminates any risk of insertional mutagenesis, protecting patients who are administered the msDNA from potential genotoxicity and cancer (Nafissi et al.).

In some aspects, bacterial sequence-free vectors for producing VLPs as disclosed herein include CCC or LCC vectors produced according to any other method known in the art.

A. Expression Vectors, Expression Cassettes, and Vector Production Systems for Producing Bacterial Sequence-Free Vectors and VLPs

Provided herein is an expression vector comprising: an expression cassette that comprises a nucleic acid sequence encoding a recombinant protein comprising a conserved amino acid sequence from a virus fused to an immunogenic amino acid sequence, a target sequence for a first recombinase flanking each side of the expression cassette, and one or more additional target sequences for one or more additional recombinases integrated within non-binding regions of the target sequence for the first recombinase, wherein protein expressed intracellularly from the expression cassette is capable of forming a VLP.

Conserved and immunogenic amino acid sequences include those known in the art as well as those determined through known techniques. For example, genome-based reverse vaccinology can be applied towards comparative genomics analysis, a field of biological research that can be used to compare genomic sequences between different pathogenic strains (see, e.g., Sieb et al., Clin. Microbiol. Infect. 18(Suppl. 5):109-116 (2012)). Other sequencing, structural, and computational approaches can also be used (see, e.g., Liljeroos et al., J. Immunol. Res. 2015: 156241; Sette and Rappuoli, Immunity 33(4):530-541 (2010)).

In some aspects, the conserved amino acid sequence, the immunogenic amino acid sequence, the viral envelope protein, and/or the viral matrix protein is a consensus sequence.

In some aspects, the recombinant protein is capable of stimulating an immune response against the virus comprising neutralizing antibodies. Conserved sites, for example, are often recognized by broadly neutralizing antibodies and are susceptible to antibody inactivation (see, e.g., Nabel, N. Engl. J. Med. 368(6): 551-560 (2013)).

In some aspects, the recombinant protein is capable of stimulating a Th1 cell-mediated immune response against the virus. Cell-mediated immunity is the process by which cytotoxic T cells recognize antigen infected cells, to induce cell lysis.

In some aspects, the immune response is cross-reactive to a related virus or strain. For example, conserved sequences among different viral serotypes/strains can be utilized to provide protection against multiple serotypes/strains, including as a universal vaccine.

In some aspects, the expression cassette comprises a single open reading frame comprising a nucleic acid sequence encoding a self-cleaving peptide between each nucleic acid sequence encoding a protein such that the translation product of the expression cassette is cleaved intracellularly into two or more proteins. In some aspects, the self-cleaving peptide is a 2A self-cleaving peptide. In some aspects, the 2A self-cleaving peptide is P2A from porcine teschovirus-1. In some aspects, the 2A self-cleaving peptide is T2A from those a asigna virus 2A.

In some aspects, the expression cassette comprises a nucleic acid sequence encoding a self-cleaving peptide between nucleic acid sequences encoding a viral matrix protein and a viral envelope protein, between nucleic acid sequences encoding a viral matrix protein and the recombinant protein, and/or between nucleic acid sequences encoding a viral envelope protein and the recombinant protein. In some aspects, the expression cassette comprises nucleic acid sequences from 5′ to 3′ encoding a viral matrix protein, a self-cleaving peptide, a viral envelope protein, a self-cleaving peptide, and the recombinant protein. In some aspects, the expression cassette comprises nucleic acid sequences from 5′ to 3′ encoding a viral envelope protein, a self-cleaving peptide, a viral matrix protein, a self-cleaving peptide, and the recombinant protein.

In some aspects, the expression cassette further comprises a nucleic acid sequence encoding a marker for gene expression. In some aspects, the marker for gene expression is a fluorescent reporter gene, such as green fluorescent protein (GFP), red fluorescent protein (RFP), yellow fluorescent protein (YFP), or near-infrared fluorescent protein (iRFP); a bioluminescent reporter genes such as luciferase; a selectable antibiotic marker; or LacZ. In some aspects, the expression cassette comprises a nucleic acid sequence encoding a self-cleaving peptide between the nucleic acid sequence encoding a marker for gene expression and any other nucleic acid sequence encoding a protein.

The expression cassette can contain any expression control region known to those of skill in the art operably linked to the protein-encoding nucleic acid sequence(s). In some aspects, the expression control region is a promoter, enhancer, operator, repressor, ribosome binding site, translation leader sequence, intron, polyadenylation recognition sequence, RNA processing site, effector binding site, stem-loop structure, transcription termination signal, or combination thereof.

The source of the conserved amino acid sequence, the immunogenic amino acid sequence, and/or a viral protein as disclosed herein can be any virus associated with human or animal infection.

In some aspects, the virus is a coronavirus, an influenza virus, a human immunodeficiency virus, a human papillomavirus, a hepatitis virus, or an oncolytic virus.

In some aspects, the influenza virus is an influenza A virus. In some aspects, the influenza A virus is H1N1, H5N1, or H3N2.

In some aspects, the influenza virus is an influenza B virus.

In some aspects, the coronavirus is a human coronavirus such as, but not limited to, HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1, SARS-CoV-1, SARS-CoV-2 (i.e., COVID-19)), and/or MERS-CoV.

In some aspects, the coronavirus is COVID-19 (i.e., Wuhan-Hu-1 or a variant thereof such as, but not limited to, U.K. variant B.1.1.7, South African variant B.1.351, Brazilian variant P.1, or Californian variant B.1.427/429).

Provided herein is a vector production system comprising recombinant cells designed to encode at least a first recombinase under the control of an inducible promoter, wherein the cells comprise an expression vector as disclosed herein comprising a target for the at least first recombinase. In some aspects, the inducible promoter is thermally-regulated, chemically-regulated, IPTG regulated, glucose-regulated, arabinose inducible, T7 polymerase regulated, cold-shock inducible, pH inducible, or combinations thereof. In some aspects, the at least first recombinase is selected from telN and tel, and the expression vector incorporates the target sequence for the at least first recombinase. In some aspects, the at least first recombinase is selected from Cre or Flp, and the expression vector incorporates the target sequence for the at least first recombinase. In some aspects, the recombinant cells have been further designed to encode a nuclease genome editing system, and the expression vector further comprises a backbone sequence containing a cleavage site for the nuclease genome editing system. In some aspects, the nuclease genome editing system is a CRISPR nuclease system comprising a Cas nuclease and gRNA, and the expression vector comprises a target sequence for the gRNA within the backbone sequence.

Provided herein is a method of producing a bacterial sequence-free vector comprising incubating a vector production system as described herein under suitable conditions for expression of the at least first recombinase or the first recombinase and the nuclease genome editing system. In some aspects, the method further comprises harvesting the bacterial sequence-free vector. The present disclosure is also directed to a bacterial sequence-free vector produced by the method.

A.1 Expression Cassettes comprising Coronavirus Sequences

Coronaviruses include any virus of the family Coronaviridae, including the subfamily Coronovirinae, and including the genuses Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus. See, e.g., Fung and Liu (2019). Coronaviruses include human coronaviruses (HCoVs), such as HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1, severe acute respiratory syndrome coronaviruses (SARS-CoV, e.g., SARS-CoV-1 and SARS-CoV-2 (i.e., COVID-19)), Middle East respiratory syndrome coronaviruses (MERS-CoV), zoonotic coronaviruses (e.g., SARS-CoVs and MERS-CoVs), bat coronaviruses (BtCoVs), Avian coronavirus, Murine coronavirus, and bulbol coronavirus (BuCoV).

Coronavirus genomes are positive-sense, nonsegmented, single-stranded RNA ranging from about 27 to 32 kilobases (see, e.g., Fung and Liu, Annu. Rev. Microbiol. 73:529-557 (2019)). For example, the complete genome of COVID-19 (also termed Wuhan-Hu-1 coronavirus (WHCV), SARS-CoV-2, and 2019-nCoV) has a size of 29.9 kb, compared to SARS-CoV and MERS-CoV with genomes of 27.9 kb and 30.1 kb, respectively (Zhou et al., Nature 579: 270-273 (2020)). The COVID-19 genome has been found to be 96.2% identical to the Bat CoV RaTG13 genome, which is a type of SARS-CoV-2 found in bats and is likely the source of the virus transmitted to humans via unknown intermediate hosts.

Coronaviruses have a membrane (M) protein, which is the most abundant structural protein that supports the viral envelope and embeds in the envelope with three transmembrane domains. The M protein is essential for virus assembly and budding.

Envelope (E) protein is a small transmembrane protein in coronaviruses that is also present in the envelope at a lower amount than M protein. E protein is also engaged in virus assembly and egress.

The nucleocapsid (N) protein in coronaviruses binds to the RNA genome like beads-on-a-string, forming the helically symmetric nucleocapsid.

The virion surface of coronaviruses is decorated with the trimeric Spike (S) protein. Some betacoronaviruses also have dimeric hemagglutinin-esterase (HE) protein that make up shorter projections on the virion surface. S and HE protein each are type I transmembrane proteins with a large ectodomain and a short endodomain.

The S protein contains two subunits, S1 and S2, and is anchored in the viral envelope at its C-terminus. The S1 subunit of COVID-19, for example, contains the N-terminal domain (NTD) and receptor-binding domain (RBD), while the S2 subunit contains the fusion peptide (FP), internal fusion peptide (IFP), heptad repeat 1/2 (HR1/2), and the transmembrane domain (TM). The S protein's large ectodomain trimerizes and forms the characteristic coronavirus spikes at the virion's surface. The S protein is responsible for receptor binding and virion entry to host cells (Fehr and Perlman, Coronaviruses: An Overview of Their Replication and Pathogenesis. In: Maier H., Bickerton E., Britton P. (eds) Coronaviruses. Methods in Molecular Biology, vol 1282. Humana Press, New York, N.Y.; Wall et al., Cell 180: 1-12 (2020)).

Fusion proteins from many viruses require a proteolytic event near a fusion peptide to enable the pathogen's entry into the target cell. For example, the S protein from COVID-19 possesses two cleavage sites, the first of which sits at the S1/S2 boundary but is not closely linked to the fusion peptide. A second cleavage site (S2′) exposes the internal fusion peptide (IFP), a motif just downstream of S2′ that is highly conserved across all sequenced coronaviruses. The sequence of IFP is SFIEDLLFNKVTLADAGF (SEQ ID NO:7), within which the bolded LLF residues are critical for membrane fusion and infectivity (Madu et al., J. Virol. 83(15): 7411-7421 (2009)). COVID-19 demonstrates the presence of a canonical furin-like cleavage motif at the S1/S2 site not found in other coronaviruses in the same clade, but similarly found in particularly virulent forms of influenza (H5N1). Cleavage via other proteases such as furin at the S1/S2 interface likely widens the tropism of the virus, making animal to human transmission more likely (Coutard et al., Antiviral Res. 176:104742 (2020)).

In some aspects, the expression cassette comprises nucleic acid sequences encoding a coronavirus Membrane (M) protein, a coronavirus Envelope (E) protein, and a recombinant protein comprising a conserved amino acid sequence and an immunogenic amino acid sequence from a coronavirus Spike (S) protein. The M, E, and S proteins can be interchangeably referred to herein as M, E, and S glycoproteins.

In some aspects, the M protein comprises an amino acid sequence at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:1. In some aspects, the M protein comprises SEQ ID NO:1. In some aspects, the M protein is SEQ ID NO:1.

In some aspects, the nucleic acid sequence encoding the M protein is at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:2. In some aspects, the nucleic acid sequence encoding the M protein comprises SEQ ID NO:2. In some aspects, the nucleic acid sequence encoding the M protein is SEQ ID NO:2.

In some aspects, the E protein comprises an amino acid sequence at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:3. In some aspects, the E protein comprises SEQ ID NO:3. In some aspects, the E protein is SEQ ID NO:3. In some aspects, the E protein comprises a replacement of the proline located at amino acid number 71 in SEQ ID NO:3 (i.e., at P71 in SEQ ID NO:3) with another amino acid. In some aspects, the replacement at P71 in SEQ ID NO:3 is a change from proline to leucine (i.e., P71L).

In some aspects, the nucleic acid sequence encoding the E protein is at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:4. In some aspects, the nucleic acid sequence encoding the E protein comprises SEQ ID NO:4. In some aspects, the nucleic acid sequence encoding the E protein is SEQ ID NO:4. In some aspects, the nucleic acid sequence encoding the E protein comprises a replacement of the codon for proline at nucleotide numbers 211-213 in SEQ ID NO:4 with a codon for another amino acid. In some aspects, the codon for proline at nucleotide numbers 211-213 in SEQ ID NO:4 is replaced with a codon for leucine.

In some aspects, the conserved amino acid sequence is from the S1 subunit or the S2 subunit of the S protein, the RBD of the S protein, the S protein S2′ cleavage site and internal fusion peptide (IFP) of the S protein (referred to herein as STIFP), the M protein, or the E protein.

In some aspects, the conserved amino acid sequence is at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to any one of SEQ ID NOs:12-54. In some aspects, the conserved amino acid sequence comprises any one of SEQ ID NOs:12-54. In some aspects, the conserved amino acid sequence is any one of SEQ ID NOs:12-54.

In some aspects, the conserved amino acid sequence is at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:7. In some aspects, the conserved amino acid sequence comprises SEQ ID NO:7. In some aspects, the conserved amino acid sequence is SEQ ID NO:7.

In some aspects, the nucleic acid sequence encoding the conserved amino acid sequence of the recombinant protein is at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:8. In some aspects, the nucleic acid sequence encoding the conserved amino acid sequence of the recombinant protein comprises SEQ ID NO:8. In some aspects, the nucleic acid sequence encoding the conserved amino acid sequence of the recombinant protein is SEQ ID NO:8.

In some aspects, the immunogenic amino acid sequence is from the S protein receptor-binding domain (RBD).

In some aspects, the immunogenic amino acid sequence is at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:11. In some aspects, the immunogenic amino acid sequence comprises SEQ ID NO:11. In some aspects, the immunogenic amino acid sequence is SEQ ID NO:11. In some aspects, the immunogenic protein comprises a replacement of one or more of: lysine located at amino acid number 88 (i.e., K88), leucine located at amino acid number 123 (i.e., L123), glutamate located at amino acid number 155 (i.e., E155), or asparagine located at amino acid number 172 (i.e., N172) in SEQ ID NO:11 (corresponding to K417, L452, E484, and N501 in SEQ ID NO:5, respectively) with another amino acid. In some aspects, the replacement at K88 is K88N (i.e., a change from lysine to asparagine). In some aspects, the replacement at K88 is K88T (i.e., a change from lysine to threonine). In some aspects, the replacement at L123 is L123R (i.e., a change from leucine to arginine). In some aspects, the replacement at E155 is E155K (i.e., a change from glutamate to lysine). In some aspects, the replacement at N172 is N172Y (i.e., a change from asparagine to tyrosine).

In some aspects, the nucleic acid sequence encoding the immunogenic amino acid sequence of the recombinant protein is at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:101. In some aspects, the nucleic acid sequence encoding the immunogenic amino acid sequence of the recombinant protein comprises SEQ ID NO:101. In some aspects, the nucleic acid sequence encoding the immunogenic amino acid sequence of the recombinant protein is SEQ ID NO:101. In some aspects, the nucleic acid sequence encoding the immunogenic protein comprises a replacement of one or more of: the codon for lysine at nucleotide numbers 262-264 of SEQ ID NO:101 with a codon for another amino acid, the codon for leucine at nucleotide numbers 367-369 of SEQ ID NO:101 with a codon for another amino acid, the codon for glutamate at nucleotide numbers 463-465 of SEQ ID NO:101 with a codon for another amino acid, or the codon for asparagine at nucleotide numbers 514-516 of SEQ ID NO:101 with a codon for another amino acid. In some aspects, the codon for lysine at nucleotide numbers 262-264 is replaced with a codon for asparagine or threonine. In some aspects, the codon for leucine at nucleotide numbers 367-369 is replaced with a codon for arginine. In some aspects, the codon for glutamate at nucleotide numbers 463-465 is replaced with a codon for lysine. In some aspects, the codon for asparagine at nucleotide numbers 514-516 is replaced with a codon for tyrosine.

In some aspects, the recombinant protein further comprises a transmembrane (TM) domain sequence from the S protein.

In some aspects, the TM domain sequence comprises an amino acid sequence at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:102. In some aspects, the TM domain sequence comprises SEQ ID NO:102. In some aspects, the TM domain sequence is SEQ ID NO:102.

In some aspects, the nucleic acid sequence encoding the TM domain sequence of the recombinant protein is at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:103. In some aspects, the nucleic acid sequence encoding the TM domain sequence of the recombinant protein comprises SEQ ID NO:103. In some aspects, the nucleic acid sequence encoding the TM domain sequence of the recombinant protein is SEQ ID NO:103.

In some aspects, the recombinant protein comprises a conserved amino acid sequence from S2′IFP, an immunogenic amino acid sequence from the RBD, and a TM domain sequence of the S protein.

In some aspects, the amino acid sequence of the recombinant protein is at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:55. In some aspects, the amino acid sequence of the recombinant protein comprises SEQ ID NO:55. In some aspects, the amino acid sequence of the recombinant protein is SEQ ID NO:55. In some aspects, the recombinant protein comprises a replacement of one or more of K88, L123, E155, or N172 in SEQ ID NO:55 with another amino acid. In some aspects, the replacement at K88 is K88N. In some aspects, the replacement at K88 is K88T. In some aspects, the replacement at L123 is L123R. In some aspects, the replacement at E155 is E155K. In some aspects, the replacement at N172 is N172Y.

In some aspects, the nucleic acid sequence encoding the recombinant protein is at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:56. In some aspects, the nucleic acid sequence encoding the recombinant protein comprises SEQ ID NO:56. In some aspects, the nucleic acid sequence encoding the recombinant protein is SEQ ID NO:56. In some aspects, the nucleic acid sequence encoding the recombinant protein comprises a replacement of one or more of: the codon for lysine at nucleotide numbers 262-264 of SEQ ID NO:56 with a codon for another amino acid, the codon for leucine at nucleotide numbers 367-369 of SEQ ID NO:56 with a codon for another amino acid, the codon for glutamate at nucleotide numbers 463-465 of SEQ ID NO:56 with a codon for another amino acid, or the codon for asparagine at nucleotide numbers 514-516 of SEQ ID NO:56 with a codon for another amino acid. In some aspects, the codon for lysine at nucleotide numbers 262-264 is replaced with a codon for asparagine or threonine. In some aspects, the codon for leucine at nucleotide numbers 367-369 is replaced with a codon for arginine. In some aspects, the codon for glutamate at nucleotide numbers 463-465 is replaced with a codon for lysine. In some aspects, the codon for asparagine at nucleotide numbers 514-516 is replaced with a codon for tyrosine.

In some aspects, the expression cassette comprises a single open reading frame translated as an amino acid sequence at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:57. In some aspects, the expression cassette comprises a single open reading frame translated as an amino acid sequence comprising SEQ ID NO:57. In some aspects, the expression cassette comprises a single open reading frame translated as an amino acid sequence that is SEQ ID NO:57. In some aspects, the expression cassette comprises a single open reading frame translated as an amino acid sequence that comprises a replacement of one or more of P71, K423, L458, E490, or N507 in SEQ ID NO:57 with another amino acid. In some aspects, the replacement at P71 is P71L. In some aspects, the replacement at K423 is K423N. In some aspects, the replacement at K423 is K423T. In some aspects, the replacement at L458 is L458R. In some aspects, the replacement at E490 is E490K. In some aspects, the replacement at N507 is N507Y.

In some aspects, the expression cassette comprises a single open reading frame that is at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:58. In some aspects, the expression cassette comprises a single open reading frame that comprises SEQ ID NO:58. In some aspects, the expression cassette comprises a single open reading frame that is SEQ ID NO:58. In some aspects, the expression cassette comprises a single open reading frame that comprises a replacement of one or more of: the codon for proline at nucleotide numbers 211-213 in SEQ ID NO:58 with a codon for another amino acid, the codon for lysine at nucleotide numbers 1267-1269 of SEQ ID NO:58 with a codon for another amino acid, the codon for leucine at nucleotide numbers 1372-1374 of SEQ ID NO:58 with a codon for another amino acid, the codon for glutamate at nucleotide numbers 1468-1470 of SEQ ID NO:58 with a codon for another amino acid, or the codon for asparagine at nucleotide numbers 1519-1521 of SEQ ID NO:58 with a codon for another amino acid. In some aspects, the codon for proline at nucleotide numbers 211-213 in SEQ ID NO:58 is replaced with a codon for leucine. In some aspects, the codon for lysine at nucleotide numbers 1267-1269 is replaced with a codon for asparagine or threonine. In some aspects, the codon for leucine at nucleotide numbers 1372-1374 is replaced with a codon for arginine. In some aspects, the codon for glutamate at nucleotide numbers 1468-1470 is replaced with a codon for lysine. In some aspects, the codon for asparagine at nucleotide numbers 1519-1521 is replaced with a codon for tyrosine.

In some aspects, the expression cassette is at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to the nucleic acid sequence of any one of SEQ ID NOs:59-62. In some aspects, the expression cassette comprises the nucleic acid sequence of any one of SEQ ID NOs:59-62. In some aspects, the expression cassette is the nucleic acid sequence of any one of SEQ ID NOs:59-62.

In some aspects, the recombinant protein is capable of stimulating an immune response against COVID-19.

In some aspects, the recombinant protein is capable of stimulating a Th1 cell-mediated immune response against COVID-19.

In some aspects, the immune response against COVID-19 is against Wuhan-Hu-1 and/or one or more variants such as, but not limited to, the U.K. variant B.1.1.7, the South African variant B.1.351, the Brazilian variant P.1, or the Californian variant B.1.427/429.

Provided herein is a polynucleotide encoding an amino acid sequence at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:57. In some aspects, the polynucleotide encodes an amino acid sequence comprising SEQ ID NO:57. In some aspects, the polynucleotide encodes an amino acid sequence that is SEQ ID NO:57. In some aspects, the polynucleotide encodes an amino acid sequence that comprises a replacement of one or more of P71, K423, L458, E490, or N507 in SEQ ID NO:57 with another amino acid. In some aspects, the replacement at P71 is P71L. In some aspects, the replacement at K423 is K423N. In some aspects, the replacement at K423 is K423T. In some aspects, the replacement at L458 is L458R. In some aspects, the replacement at E490 is E490K. In some aspects, the replacement at N507 is N507Y.

Provided herein is a polynucleotide comprising a nucleic acid sequence at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:58. In some aspects, the polynucleotide comprises SEQ ID NO:58. In some aspects, the polynucleotide is SEQ ID NO:58. In some aspects, the polynucleotide comprising a nucleic acid sequence that comprises a replacement of one or more of: the codon for proline at nucleotide numbers 211-213 in SEQ ID NO:58 with a codon for another amino acid, the codon for lysine at nucleotide numbers 1267-1269 of SEQ ID NO:58 with a codon for another amino acid, the codon for leucine at nucleotide numbers 1372-1374 of SEQ ID NO:58 with a codon for another amino acid, the codon for glutamate at nucleotide numbers 1468-1470 of SEQ ID NO:58 with a codon for another amino acid, or the codon for asparagine at nucleotide numbers 1519-1521 of SEQ ID NO:58 with a codon for another amino acid. In some aspects, the codon for proline at nucleotide numbers 211-213 in SEQ ID NO:58 is replaced with a codon for leucine. In some aspects, the codon for lysine at nucleotide numbers 1267-1269 is replaced with a codon for asparagine or threonine. In some aspects, the codon for leucine at nucleotide numbers 1372-1374 is replaced with a codon for arginine. In some aspects, the codon for glutamate at nucleotide numbers 1468-1470 is replaced with a codon for lysine. In some aspects, the codon for asparagine at nucleotide numbers 1519-1521 is replaced with a codon for tyrosine.

B. Bacterial Sequence-Free Vectors

A bacterial sequence-free vector of the present disclosure can include any expression cassette of the present disclosure.

Provided herein is a bacterial sequence-free vector comprising an expression cassette that comprises a nucleic acid sequence encoding a recombinant protein comprising a conserved amino acid sequence from a virus fused to an immunogenic amino acid sequence, wherein protein expressed intracellularly from the expression cassette is capable of forming a VLP.

In some aspects, the conserved amino acid sequence, the immunogenic amino acid sequence, the viral envelope protein, and/or the viral matrix protein is a consensus sequence.

In some aspects, the recombinant protein is capable of stimulating an immune response against the virus comprising neutralizing antibodies.

In some aspects, the recombinant protein is capable of stimulating a Th1 cell-mediated immune response against the virus.

In some aspects, the immune response is cross-reactive to a related virus or strain.

In some aspects, the expression cassette comprises a single open reading frame comprising a nucleic acid sequence encoding a self-cleaving peptide between each nucleic acid sequence encoding a protein. Expression cassettes and self-cleaving peptides include those discussed above with respect to expression vectors.

In some aspects, the virus is a coronavirus, an influenza virus, a human immunodeficiency virus, a human papillomavirus, a hepatitis virus, or an oncolytic virus.

In some aspects, the influenza virus is an influenza A virus. In some aspects, the influenza A virus is H1N1, H5N1, or H3N2.

In some aspects, the influenza virus is an influenza B virus.

In some aspects, the coronavirus is a human coronavirus such as, but not limited to, HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1, SARS-CoV-1, SARS-CoV-2 (i.e., COVID-19)), and/or MERS-CoV.

In some aspects, the E protein comprises an amino acid sequence at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:3. In some aspects, the E protein comprises SEQ ID NO:3. In some aspects, the E protein is SEQ ID NO:3. In some aspects, the E protein comprises a replacement of P71 in SEQ ID NO:3 with another amino acid. In some aspects, the replacement at P71 in SEQ ID NO:3 is P71L.

In some aspects, the conserved amino acid sequence is at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:7. In some aspects, the conserved amino acid sequence comprises SEQ ID NO:7. In some aspects, the conserved amino acid sequence is SEQ ID NO:7.

In some aspects, the immunogenic amino acid sequence is from the S protein receptor-binding domain (RBD).

In some aspects, the nucleic acid sequence encoding the immunogenic amino acid sequence of the recombinant protein is at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:101. In some aspects, the nucleic acid sequence encoding the immunogenic amino acid sequence of the recombinant protein comprises SEQ ID NO:101. In some aspects, the nucleic acid sequence encoding the immunogenic amino acid sequence of the recombinant protein is SEQ ID NO:101. In some aspects, the nucleic acid sequence encoding the immunogenic amino acid sequence comprises a replacement of one or more of: the codon for lysine at nucleotide numbers 262-264 of SEQ ID NO:101 with a codon for another amino acid, the codon for leucine at nucleotide numbers 367-369 of SEQ ID NO:101 with a codon for another amino acid, the codon for glutamate at nucleotide numbers 463-465 of SEQ ID NO:101 with a codon for another amino acid, or the codon for asparagine at nucleotide numbers 514-516 of SEQ ID NO:101 with a codon for another amino acid. In some aspects, the codon for lysine at nucleotide numbers 262-264 is replaced with a codon for asparagine or threonine. In some aspects, the codon for leucine at nucleotide numbers 367-369 is replaced with a codon for arginine. In some aspects, the codon for glutamate at nucleotide numbers 463-465 is replaced with a codon for lysine. In some aspects, the codon for asparagine at nucleotide numbers 514-516 is replaced with a codon for tyrosine.

In some aspects, the recombinant protein further comprises a transmembrane (TM) domain sequence from the S protein.

In some aspects, the recombinant protein comprises a conserved amino acid sequence from S2′IFP, an immunogenic amino acid sequence from the RBD, and a TM domain sequence of the S protein.

In some aspects, the amino acid sequence of the recombinant protein is at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:55. In some aspects, the amino acid sequence of the recombinant protein comprises SEQ ID NO:55. In some aspects, the amino acid sequence of the recombinant protein is SEQ ID NO:55. In some aspects, the amino acid sequence of the recombinant protein comprises a replacement of one or more of K88, L123, E155, or N172 in SEQ ID NO:55 with another amino acid. In some aspects, the replacement at K88 is K88N. In some aspects, the replacement at K88 is K88T. In some aspects, the replacement at L123 is L123R. In some aspects, the replacement at E155 is E155K. In some aspects, the replacement at N172 is N172Y.

In some aspects, the expression cassette is at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to any one of SEQ ID NOs:59-62. In some aspects, the expression cassette comprises any one of SEQ ID NOs:59-62. In some aspects, the expression cassette is any one of SEQ ID NOs:59-62.

In some aspects, the recombinant protein is capable of stimulating an immune response against COVID-19.

In some aspects, the recombinant protein is capable of stimulating a Th1 cell-mediated immune response against COVID-19.

In some aspects, the bacterial sequence-free vector comprises circular covalently closed ends.

In some aspects, the bacterial sequence-free vector comprises linear covalently closed ends. In some aspects, the bacterial sequence-free vector is a msDNA as disclosed herein. A vector map for an exemplary msDNA is shown in FIG. 4.

In some aspects, the bacterial sequence-free vector is at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:104. In some aspects, the bacterial sequence-free vector comprises SEQ ID NO:104. In some aspects, the bacterial sequence-free vector is SEQ ID NO:104.

III. VLPs

In some aspects, a VLP as disclosed herein is produced from the expression cassette of an expression vector and/or the expression cassette of a bacterial sequence-free vector as described herein.

Provided herein is a recombinant cell comprising an expression vector or a bacterial sequence-free vector as described herein.

In some aspects, the recombinant cell is a yeast, bacteria, archaebacteria, fungi, insect, or animal cell, including a mammalian cell. In some aspects, recombinant cells include Drosophila melanogaster cells, Saccharomyces cerevisiae or other yeasts, E. coli, Bacillus subtilis, Sf9 cells, C129 cells, HEK293 cells, Neurospora, BHK, CHO, COS, HeLa cells, Hep G2 cells, and human cells and cell lines.

In some aspects, the expression vector is for expression in a human cell or cell line such as the exemplary vector shown in FIG. 2.

In some aspects, the expression vector is a baculovirus vector such as the exemplary vector shown in FIG. 9 and the cell type is an insect cell (e.g., Sf9 cells).

In some aspects, the present disclosure is directed to a method of producing a VLP, comprising culturing the recombinant cell comprising the expression vector or the bacterial sequence-free vector under suitable conditions for production of the VLP from the expression vector or the bacterial sequence-free vector.

In some aspects, the method of producing a VLP further comprises isolating the VLP. In some aspects, the VLP produced by any of the above expression vectors or any of the above bacterial sequence-free vectors wherein the virus is a coronavirus.

In some aspects, the VLP is isolated from a cell lysate.

In some aspects, the isolating is by affinity purification. In some aspects, the affinity purification comprises microfluidics and/or chromatography.

In some aspects, the affinity purification comprises an angiotensin-converting enzyme 2 (ACE2) receptor peptide or an anti-S protein monoclonal antibody.

In some aspects, the ACE2 receptor peptide comprises an amino acid sequence that is at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:70. In some aspects, the ACE2 receptor peptide comprises SEQ ID NO:70. In some aspects, the ACE2 receptor peptide is SEQ ID NO:70.

In some aspects, the ACE2 receptor peptide comprises a biotin acceptor peptide (BAP) tag at the C-terminus or N-terminus of the peptide. In some aspects, the BAP tag comprises an amino acid sequence at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:71. In some aspects, the BAP tag comprises SEQ ID NO:71. In some aspects, the BAP tag is SEQ ID NO:71.

In some aspects, the ACE2 receptor peptide or anti-S protein monoclonal antibody is biotinylated and immobilized on a streptavidin-coated bead. In some aspects, the affinity purification comprises microfluidics and/or chromatography.

In some aspects, the present disclosure is directed to a VLP produced by the method.

Provided herein is a VLP comprising a recombinant protein comprising a conserved amino acid sequence from a virus fused to an immunogenic amino acid sequence.

In some aspects, the immunogenic amino acid sequence is from the same virus as the conserved amino acid sequence.

In some aspects, the conserved amino acid sequence is from a viral glycoprotein. In some aspects, the immunogenic amino acid sequence is from the same viral glycoprotein.