# Patent

## Title
Poxvirus methods and compositions

## Abstract

Methods and compositions for inducing immune responses against poxviruses are disclosed. The compositions include nucleic acids that encode modified vaccinia and variola antigens. Compositions that include recombinant vaccinia and variola polypeptides are also disclosed.

## Background
STATEMENT AS TO FEDERALLY SPONSORED RESEARCH
The work described herein was funded, in part, through a grant from the National Institutes of Health (Grant No. AI057159 awarded to Shan Lu). The United States government may, therefore, have certain rights in the invention.


TECHNICAL FIELD
This invention relates to methods and compositions for inducing immune responses, and more particularly to methods and compositions for inducing immune responses to viruses.
BACKGROUND
Poxviruses, which include variola major (VARV), vaccinia virus (VACV), monkeypox, ectromelia virus (ECTV) and others, belong to the orthopoxvirus genus. Poxviruses are large, complex viruses. A poxvirus genome encodes about 200 proteins. The complexity of poxviruses has, in part, delayed the identification of protective antigens. On the other hand, considerable cross-protection has been observed between orthopox viruses. For example, vaccination with live attenuated vaccinia virus protects from infection by variola major, the virus that causes smallpox. The original smallpox vaccine, based on live attenuated vaccinia, eradicated smallpox from the worldwide human population with the last case of natural smallpox infection occurring in Somalia in 1977 (Radetsky, 1999, Pediat. Inf. Dis. J., 18:85-93). Production of the live, attenuated vaccinia approved for use as a smallpox vaccine in the United States, DryVaxTM (Wyeth Laboratories, Inc.) was discontinued in 1982. Adverse events associated with vaccination with the live attenuated virus vaccine include progressive vaccinia, eczema, post-vaccinial encephalitis, and myocarditis (Casey et al., 2005, JAMA, 294(21):2734-43; Belongia et al., 2003, Clin. Med. Res., 1(2):87-92). Despite safety concerns, live vaccinia virus remains the main form of smallpox vaccine. A new generation of live attenuated vaccinia virus vaccines are being produced in cultured cells for stockpiling in hopes that the supply will be available to protect the general population in the event of a bioterrorist attack, as the majority of the world's population no longer has immunity to smallpox (Artenstein et al., 2005, Vaccine, 23(25):3301-9; Fang et al., 2006, Virology 345(1):231-43; Monath et al., 2004, Int. J. Infect. Dis., 8 (Suppl 2):S31-44).
SUMMARY
The compositions described herein provide novel forms of poxvirus antigens, combinations of antigens, and nucleic acid sequences encoding the antigens that provide potent protection against infection. The compositions include poxvirus antigens (e.g., vaccinia virus and variola virus antigens) and nucleic acids encoding the antigens that are modified so as to be more immunogenic. Modifications that enhance immunogenicity include truncation (e.g., to remove hydrophobic regions), addition of a heterologous signal sequence, and codon optimization. For example, it has been discovered that expression of a truncated form of vaccinia D8 lacking a transmembrane domain and cytoplasmic tail in association with a heterologous signal sequence enhances its immunogenicity relative to a wild type form of D8. Codon optimization of poxvirus sequences permits enhanced expression in mammalian as well as bacterial cells, which is beneficial for use in a DNA vaccine, and for recombinant production of the pox antigens.
In addition, it has been discovered that certain variola major virus antigens provide a significant protective immune response when administered as a DNA vaccine that encodes these antigens. Immune responses to variola antigens can be induced by administration of nucleic acids and/or by administration of the variola antigen proteins themselves. Accordingly, in one aspect, the invention features isolated nucleic acid molecules including a first nucleotide sequence encoding a signal peptide, and a second nucleotide sequence encoding a first portion of a vaccinia D8 polypeptide that lacks a transmembrane domain and cytoplasmic tail, wherein the first sequence and the second sequence are linked such that the signal peptide and the portion of the D8 polypeptide are expressed as a fusion polypeptide. In various embodiments, the portion of the D8 antigen comprises a sequence at least 80%, 85%, 90%, 95%, 97%, or 99% identical to SEQ ID NO:4.
The signal peptide can be mammalian, e.g., human. For example, the signal peptide is a human tissue plasminogen activator (tPA) signal peptide. In various embodiments, the signal peptide has the following amino acid sequence: MDAMKRGLCCVLLLCGAVFVSAS (SEQ ID NO:21), or the signal peptide has the sequence of SEQ ID NO:21 with one, two, three, four, five, six, or seven amino acid substitutions or deletions.
In various embodiments, the first nucleotide sequence and second nucleotide sequence together encode a polypeptide having an amino acid sequence at least 80%, 85%, 90%, 95%, 97%, or 99% identical to SEQ ID NO:6.
In some embodiments, the nucleotide sequence encoding the portion of the vaccinia D8 polypeptide is codon optimized for expression in a mammalian cell. In some embodiments, the sequence is also optimized for expression in a bacterial cell (e.g., the sequence includes codons that are favored in both mammalian and bacterial cells).
In another aspect, the invention features compositions including one or more nucleic acid molecules encoding a signal peptide and a portion of a vaccinia D8 polypeptide, and the composition further includes one or more second nucleic acid molecules that include a nucleotide sequence encoding a second poxvirus polypeptide (e.g., a vaccinia virus polypeptide, or a variola virus polypeptide) or antigenic portion thereof (e.g., a second vaccinia polypeptide selected from the group consisting of an A27 polypeptide, a B5 polypeptide, an A33 polypeptide, and an L1 polypeptide).
In various embodiments, the A27 polypeptide has an amino acid sequence at least 80%, 85%, 90%, 95%, 97%, or 99% identical to SEQ ID NO:8; the B5 polypeptide has an amino acid sequence at least 80%, 85%, 90%, 95%, 97%, or 99% identical to SEQ ID NO:10; the L1 polypeptide has an amino acid sequence at least 80%, 85%, 90%, 95%, 97%, or 99% identical to SEQ ID NO:12; and the A33 polypeptide has an amino acid sequence at least 80%, 85%, 90%, 95%, 97%, or 99% identical to SEQ ID NO:14.
The antigenic portion of the vaccinia polypeptide can be at least 20, 30, 40, 50, 60, 70, 80, 90, or 100 amino acids in length.
The compositions can further include a third nucleic acid molecule encoding a third vaccinia polypeptide or antigenic portion thereof. In various embodiments, the second vaccinia polypeptide can be A27 and the third vaccinia polypeptide is B5.
The composition can further include a fourth nucleic acid encoding a fourth vaccinia polypeptide or antigenic portion thereof. For example, the fourth vaccinia polypeptide can be A33 or L1.
In some embodiments, the nucleotide sequence encoding the second, third, or fourth vaccinia polypeptide is codon optimized for expression in a mammalian cell. In some embodiments, the sequence is also optimized for expression in a bacterial cell (e.g., the sequence includes codons that are favored in both mammalian and bacterial cells). The sequence encoding the second, third, or fourth vaccinia polypeptide can further include a sequence encoding a signal peptide (e.g., a mammalian signal peptide, such as a human signal peptide, e.g., a human tPA signal peptide).
The invention also features cells and expression vectors that include nucleic acid molecules encoding a signal peptide and a portion of a vaccinia D8 polypeptide that lacks a transmembrane domain and cytoplasmic tail. The nucleic acid molecules can include other features described herein.
The invention also features methods for producing a modified vaccinia polypeptide by culturing cells including a nucleic acid molecule that includes a first nucleotide sequence encoding a signal peptide, and a second nucleotide sequence encoding a first portion of a vaccinia D8 polypeptide that lacks a transmembrane domain and cytoplasmic tail, under conditions in which the first sequence and second sequence are expressed as a fusion polypeptide, and isolating the expressed fusion polypeptide.
The invention also features compositions including nucleic acid molecules encoding a signal peptide and a portion of a vaccinia D8 polypeptide that lacks a transmembrane domain and cytoplasmic tail, and a pharmaceutically acceptable carrier.
The invention also features methods of inducing an immune response to a poxvirus in a mammal by administering to a mammal a composition including a nucleic acid molecule as described herein in an amount sufficient to produce an immune response in the mammal. The nucleic acid molecule can include a first nucleotide sequence encoding a signal peptide, and a second nucleotide sequence encoding a first portion of a vaccinia D8 polypeptide that lacks a transmembrane domain and cytoplasmic tail, wherein the first sequence and the second sequence are linked such that the signal peptide and the portion of the D8 polypeptide are expressed as a fusion polypeptide
The immune response produced by the nucleic acid molecule can be a protective immune response (e.g., a response that protects against a subsequent poxvirus infection).
The mammal can be a non-human mammal or a human (e.g., a human sero-negative for vaccinia or variola, e.g., a human at risk for infection with a poxvirus.).
The composition administered to the mammal can include additional nucleic acid molecules (e.g., it can include a second nucleic acid molecule including a nucleotide sequence encoding a second vaccinia polypeptide or antigenic portion thereof, or a second nucleic acid molecule encoding a variola polypeptide or antigenic portion thereof). In some embodiments, the composition administered to the mammal further includes nucleic acid molecules comprising nucleotide sequences encoding two, three, or all four of the following: an A27 polypeptide or an antigenic portion thereof, a B5 polypeptide or an antigenic portion thereof, an A33 polypeptide or an antigenic portion thereof; and an L1 polypeptide or an antigenic portion thereof.
The methods of administering nucleic acid molecules to mammals can further include administering a composition including a poxvirus polypeptide (e.g., a vaccinia polypeptide or variola peptide, e.g., a recombinant vaccinia polypeptide or variola polypeptide, e.g., a vaccinia polypeptide or variola peptide described herein). The methods can include administering a vaccinia virus composition (e.g., an attenuated vaccinia virus vaccine). The polypeptide or virus composition can be administered simultaneous with, prior to, or after administration of the nucleic acid molecule. The nucleic acid molecule(s) and/or the polypeptide or virus compositions can be administered multiple times (e.g., two, three, four, or five times).
The invention also features novel compositions including variola sequences and modified forms thereof. For example, in one aspect, the invention features isolated nucleic acid molecules including a nucleotide sequence encoding a variola F8 polypeptide or antigenic portion thereof. In some embodiments, the nucleotide sequences are codon optimized for expression in mammalian cells. The sequences can include a nucleotide sequence at least 80%, 85%, 90%, 95%, 97%, or 99% identical to SEQ ID NO:15.
In various embodiments, the codon optimized nucleotide sequences encoding F8, or a portion thereof; are linked to a nucleotide sequence encoding a signal peptide such that the signal peptide and the F8 polypeptide or portion thereof (e.g., a portion lacking a cytoplasmic tail and transmembrane region, e.g., a portion comprising 100, 125, 150, 175, 200, 225, 250, or 275 amino acids of the N-terminal sequence of the F8 polypeptide) are expressed as a fusion polypeptide. The signal peptide can be mammalian, e.g., human. For example, the signal peptide is a human tissue plasminogen activator (tPA) signal peptide. In various embodiments, the signal peptide has the following amino acid sequence: MDAMKRGLCCVLLLCGAVFVSAS (SEQ ID NO:21). In various embodiments, the signal peptide has the sequence of SEQ ID NO:21 with one, two, three, four, live, six, or seven amino acid substitutions or deletions.
In another aspect, the invention features isolated nucleic acid molecules including a nucleotide sequence encoding a variola A30 polypeptide or antigenic portion thereof. In some embodiments, the nucleotide sequence is codon optimized for expression in a mammalian cell, e.g., the sequence includes and a nucleotide sequence at least 80%, 85%, 90%, 95%, 97%, or 99% identical to SEQ ID NO:17.
In still another aspect, the invention features isolated nucleic acid molecules including a nucleotide sequence encoding a variola B7 polypeptide or antigenic portion thereof. In some embodiments, the nucleotide sequence is codon optimized for expression in a mammalian cell, e.g., the sequence a nucleotide sequence at least 80%, 85%, 90%, 95%, 97%, or 99% identical to SEQ ID NO:19. The antigenic portion of the variola polypeptide can be at least 20, 30, 40, 50, 60, 70, 80, 90, or 100 amino acids in length.
In some embodiments, the variola sequences are optimized for expression in bacterial cells (e.g., the sequence includes codons that are favored for expression in both mammalian and bacterial cells).
The invention also features methods of inducing an immune response to a poxvirus in a mammal by administering to a mammal a composition including a nucleic acid molecule, wherein the nucleic acid molecule includes one or more nucleotide sequences, each encoding a variola F8, A30, or B7 polypeptide or antigenic portion thereof. In various embodiments, one or more of the nucleotide sequences are codon optimized for expression in a mammalian cell. The composition is administered in an amount effective to produce an immune response in the mammal, e.g., the composition is administered in an amount sufficient to induce a protective immune response against a subsequent poxvirus infection. The mammal can be a non-human mammal or a human (e.g., a human sero-negative for vaccinia or variola, e.g., a human at risk for infection with a poxvirus).
In various embodiments, at least one of the one or more nucleotide sequences has a sequence at least 80%, 85%, 90%, 95%, 97%, or 99% identical to SEQ ID NO:15, 17, or 19.
In various embodiments, the methods further include administering a nucleic acid molecule encoding a vaccinia polypeptide or antigenic portion thereof. The methods of administering a nucleic acid molecule to a mammal can further include administering a composition including a poxvirus polypeptide (e.g., a vaccinia polypeptide or variola peptide, e.g., a recombinant vaccinia polypeptide or variola polypeptide, e.g., a vaccinia polypeptide or variola peptide described herein). The methods can include administering a vaccinia virus composition (e.g., an attenuated vaccinia virus vaccine). The polypeptide or virus composition can be administered simultaneous with, prior to, or after administration of the nucleic acid molecule. The nucleic acid molecule(s) and/or the polypeptide or virus compositions can be administered multiple times (e.g., two, three, four, or five times
Calculations of “homology” or “identity” between two sequences are performed as follows. The sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes). For substantial identity, the length of a reference sequence aligned for comparison purposes is at least 80%, but can be higher, e.g., at least 85%, 90%, 85%, 96%, 97%, 98%, 99%, or 100% of the length of the reference sequence. The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.
The comparison of sequences and determination of percent homology between two sequences are accomplished using a mathematical algorithm. In particular, percent homology between two amino acid sequences is determined using the Needleman and Wunsch, 1970, J. Mol. Biol., 48:444-453, algorithm which has been incorporated into the GAP program in the GCG software package, using a Blossum 62 scoring matrix with a gap penalty of 12, a gap extend penalty of 4, and a frameshift gap penalty of 5.
It is understood that the poxvirus antigens and immunogenic fragments thereof may have additional conservative or non-essential amino acid substitutions, which do not have a substantial effect on the polypeptide functions. Whether or not a particular substitution will be tolerated, i.e., will not adversely affect desired biological properties, such as binding activity, can be determined as described in Bowie et al., 1990, Science, 247:1306-1310. A “conservative amino acid substitution” is one in which an amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., glycine, alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine).
A “non-essential” amino acid residue is a residue that can be altered from the wild-type sequence of a polypeptide, such as a binding agent, e.g., an antibody, without substantially altering a biological activity (e.g., immunogenicity), whereas an “essential” amino acid residue results in such a change.
Vaccines that employ recombinant proteins and/or DNA to elicit immune responses are safer than live attenuated virus vaccines. Live vaccines are often accompanied by undesirable side effects. However, it has been difficult to generate subunit and DNA vaccines that provide protection as potent as that afforded by live virus vaccines. The discovery of modifications that enhance the immunogenicity of poxvirus DNA and polypeptide sequences as described herein allows for safe and effective means of vaccination. DNA vaccines encoding a truncated form of vaccinia D8 are potent immunogens when administered alone and advantageously enhance the protective response when administered with a second poxvirus vaccine composition, such as a polyvalent DNA vaccine.
An “antigenic portion” of a polypeptide is a fragment sufficient to elicit an antigen-specific immune response (i.e., an antigen-specific antibody response, cellular immune response, or both) in a subject.
Unless otherwise defined, 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 invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.
Other features and advantages of the invention will be apparent from the following detailed description, and from the claims.



DESCRIPTION OF DRAWINGS
FIG. 1 is a schematic diagram of two D8L gene inserts. Locations of the hydrophobic transmembrane (TM) domain, tPA leader sequence, and amino acid positions 1, 275, and 305 are indicated.
FIGS. 2A-2C are graphs depicting IgG antibody titers in sera of mice administered the tPA-D8L or wtD8L DNA vaccines as measured by ELISA. Control groups of mice received either the empty DNA vector (vector) or the vaccinia virus WR strain (WR). FIG. 2A depicts titers against recombinant D8 antigen produced from 293T cells. FIG. 2B depicts titers against lysates of Vero cells infected with vaccinia virus WR strain. FIG. 2C depicts titers of neutralizing antibodies for the same groups of mouse sera. Data shown are geometric means of neutralizing antibody titers which are the highest sera dilution that inhibited 50% of virus infection in the neutralization assay.
FIGS. 3A-3C are graphs depicting body weight loss as the percentage of pre-challenge weight in mice challenged with vaccinia virus WR strain by the intraperitoneal route. Prior to challenge, mice were administered individual D8L vaccines (wtD8L, tPAD8L) (FIG. 3A), a bivalent pox DNA vaccine formulation (A27L and B5R) with or without a third component (tPA-D8L) (FIG. 3B), or a 4-valent formulation (A27L, B5R, L1R, and A33R) with or without the addition of a fifth component (tPA-D8L). Mice in the positive control group were immunized with 105 pfu of vaccinia virus WR strain 2 weeks prior to challenge (WR). Mice in the negative control group (vector) received empty DNA vector. Each curve shows the group average weight loss (10 mice per group).
FIG. 4A is a graph depicting body weight loss as the percentage of pre-challenge weight in mice challenged with vaccinia virus WR strain by the intranasal route 2 weeks after the last DNA immunization. Mice were immunized with a 4-valent pox DNA formulation (A27L, B5R, L1R, and A33R) with or without the addition of a fifth component (tPA-D8L). Each curve shows the group average weight loss of surviving mice (15 per group initially).
FIG. 4B is a graph depicting percent survival at each day post-challenge. Curves represent data from the same mice as depicted in FIG. 4A.
FIGS. 5A-5F are graphs depicting IgG antibody titers induced by individual D8L or polyvalent pox DNA vaccine formulations against either the individual pox antigens including A27 (FIG. 5A), B5 (FIG. 5B), D8 (FIG. 5C), L1 (FIG. 5D), A33 (FIG. 5E), or Vero cell lysate infected with vaccinia virus (VACV) (FIG. 5F). Data are shown as the geometric means of end titration titers as determined by ELISA for each group (5 mice per group).
FIG. 5G is a graph depicting titers of neutralizing antibody responses against intracellular mature virus (IMV), shown as the geometric means of the highest serum dilutions that inhibited 50% of virus infection in a plaque reduction assay.
FIG. 6 is a table in which partial sequences of selected protective variola major and vaccinia antigens are aligned. The amino acid sequences of proteins encoded by WR and COP strains of vaccinia virus, as well as variola India1967 and Bangladesh1975 are compared. Numbers shown above amino acids indicate amino acid positions. Amino acids that are different between the strains are shown in bold. Amino acids that are identical in all viruses are shown as dots. Contiguous sequences of four or more amino acid residues are identified as SEQ ID NOs:22-49.
FIGS. 7A-7C are graphs depicting recognition of variola major and vaccinia antigens in sera of animals administered variola DNA vaccines as measured by ELISA. Immune reactivity to A30, A27 (FIG. 7A), F8, D8 (FIG. 7B), B7, and B5 (FIG. 7C) antigens are depicted for the same mouse sera from animals immunized with the combination of three DNA vaccines expressing variola major antigens A30, B7, and F8. Each curve is the average of sera assayed from 10 mice that received three immunizations. Each chart shows one pair of ortholog antigens from both variola and vaccinia.
FIG. 8 is a graph depicting percent inhibition of vaccinia IMV in the presence of sera collected from Balb/C mice after three immunizations with DNA vaccines expressing either A30 or F8 antigens, as measured by a plaque reduction neutralization assay. Sera from mice immunized with vaccinia virus is shown as a positive control. Sera from mice immunized with DNA vector is shown as a negative control. Data shown are average titers from 10 mice per group.
FIG. 9A is graph depicting IgG titers in sera from mice immunized with monovalent DNA vaccines expressing either A30, B7, or F8, as measured by ELISA for reactivity with the autologous antigens expressed in 293T cells. Sera were collected after one, two, or three DNA immunizations. The data are shown as the geometric mean titers of five animals.
FIG. 9B is a graph depicting body weight loss shown as the percentage of pre-challenge weight in mice immunized with either monovalent vaccines or with a combination of A30L, B7R, or F8L DNA vaccines. Data for mice immunized with either the positive control vaccinia (WR) or the negative control empty DNA vaccine vector are also included. Each curve shows the group average weight loss (5 mice per group) after challenge.
FIG. 10A is a graph depicting IgG titers against A30, B7, or F8 antigens in sera from animals immunized with either a combination of recombinant A30, B7, and F8 proteins (Protein), or a combination of three DNA vaccines expressing A30, B7, and F8 antigens (DNA). Animals in control groups received one immunization with vaccinia (WR). Data are shown as the geometric means of each group (5 per group) after two immunizations.
FIG. 10B is a graph depicting percent survival in mice that received three immunizations of either the combination of three recombinant variola proteins (rA30, rB7, and rF8) or the combination of three DNA vaccines expressing A30, B7, and F8 prior to lethal intranasal challenge with VACV (WR). Animals in the positive control group received one vaccinia (WR) immunization and animals in the negative control group received three immunizations with an empty DNA vaccine vector. Each curve shows the daily percentage of survivals for each group (five mice per group) after challenge.



Like reference symbols in the various drawings indicate like elements.
DETAILED DESCRIPTION
Side effects associated with live, attenuated vaccinia virus vaccines have prompted the need for safer means of immunizing against smallpox, but it has been a great challenge to develop DNA or protein subunit vaccines for immunization that have a protective efficacy comparable to that achieved with standard, live virus vaccines. The compositions described herein provide novel forms of poxvirus antigens, including variola major and vaccinia virus antigens, combinations of antigens, and nucleic acid sequences encoding the antigens that avoid the problems of live virus vaccines, yet unexpectedly provide potent protection against infection.
One of the poxvirus antigens is D8 (SEQ ID NO:2 in Table 1, below), encoded by the D8L gene (SEQ ID NO:1 in Table 1, below). D8 is an envelope protein of the IMV form of vaccinia. D8 mediates adsorption of IMV to cells (Maa et al., 1990, J. Biol. Chem., 265(3): 1569-1577). The new methods and compositions are based, at least in part, on the finding that truncation of D8 to remove its transmembrane domain and cytoplasmic tail significantly enhances its immunogenicity. One such modified form is encoded by the tPA-D8L DNA construct described herein, which expresses a truncated form of D8 as a fusion with an N-terminal human tissue plasminogen activator (tPA) leader sequence. The tPA-D8L DNA sequence (SEQ ID NO:5) and amino acid sequence (SEQ ID NO:6) are shown in Table 1, below.
It has been discovered that immunization with DNA encoding D8, or a modified form of D8, induces neutralizing antibody responses and provides protection from subsequent lethal virus challenge (i.e., it provides a protective immune response). Furthermore, the addition of DNA encoding a modified D8 antigen to polyvalent DNA vaccines significantly improves their protective efficacy. Accordingly, D8L and modified forms (e.g., truncated forms, forms expressed with a heterologous signal sequence) of D8L can be used with DNA encoding one or more additional poxvirus antigens, such as A27L, B5R, L1R, or A33R of vaccinia, or A30L, B7R, or F8L of variola major. Polypeptide compositions that include these antigens are also useful for inducing immunity to poxviruses.
Also provided herein are methods and compositions including A30, B7, and F8 antigens of variola major and nucleic acid molecules encoding these antigens. For example, modified A30L, B7R, and F8L genes that are codon optimized for expression in mammalian (e.g., human) cells are provided. A30, B7, and F8 are highly homologous to A27, B5, and D8 proteins of vaccinia, respectively. Immunization with variola DNA or protein antigen compositions provide cross-protection against subsequent infections by the homologous vaccinia antigen, and vice versa.
Herein, the genes encoding vaccinia D8, A27, B5, L1, and A33 proteins are called D8L, A27L, B5R, L1R, and A33R, respectively. The genes encoding variola A30, B7, and F8 proteins are called A30L, B7R, and F8L, respectively. The sequences are all shown in Table 1 below.
Modified Poxvirus Antigens
The expression and/or immunogenicity of poxvirus DNA vaccines and poxvirus antigens can be enhanced by modifying native poxvirus gene sequences. One type of modification that facilitates expression is to express the antigen with a heterologous signal peptide, also referred to herein as a signal sequence. The signal sequence may be cleaved from the poxvirus antigen during or after synthesis of the polypeptide. A signal sequence is a peptide that directs a polypeptide into the secretory pathway during synthesis in the cell. Signal sequences are typically located at the extreme N-terminus of a polypeptide, and can be clipped off by enzymes within the host cell prior to the final steps of trafficking and secretion. Signal sequences typically have an N-terminal region of approximately 2-15 amino acids, which has a net positive charge, followed by a hydrophobic region of 8 amino acids or more, and a neutral, but polar, C-terminal region. Residues at positions 23 and 21, relative to the signal peptidase cleavage site, must be small and neutral for cleavage to occur correctly (von Heijne, 1983, Eur. J. Biochem., 133:17-21; von Heijne, 1985, J. Mol. Biol., 184: 99-105). Numerous signal sequences are known to those of skill in the art. The use of any of these signal sequences is contemplated and those described herein are not limiting. Certain signal sequences can be found associated with a variety of proteins native to prokaryotes and eukaryotes, such as tissue plasminogen activator (tPA) signal sequence, alpha factor leader sequence, and the like. “Leader sequence, signal sequence, and signal peptide” are used interchangeably herein.
In certain embodiments, the signal sequence is a mammalian (e.g., human) signal sequence. For example, the sequence can be a tissue plasminogen activator signal sequence or a signal sequence that has the same function as a tPA signal sequence. An exemplary tPA signal sequence has the following amino acid sequence:











MDAMKRGLCCVLLLCGAVFVSAS.
(SEQ ID NO: 21)







Another type of modification involves deletion of a region of the native poxvirus gene sequence. In various embodiments, regions of a poxvirus gene sequence are deleted to construct a modified antigen. For example, D8L constructs are generated in which a hydrophobic (e.g., transmembrane) region is deleted. The transmembrane region of D8 is located at amino acids 275-294 of SEQ ID NO:2 (see Table 1, below). In some embodiments, the cytosolic tail of D8 is deleted. The cytosolic tail of D8 is located at amino acids 295-304 of SEQ ID NO:2. Sequences modified in this manner can be more efficiently expressed in cells. In some cases, truncated antigens are differentially glycosylated as well. It was discovered that the truncated D8 polypeptide encoded by the tPA-D8L construct is glycosylated, whereas D8 expressed by vaccinia virus is primarily non-glycosylated.
Another type of modification of poxvirus antigens is codon optimization. Viral proteins and proteins that are naturally expressed at low levels can provide challenges for efficient expression by recombinant means. Viral proteins often display a codon usage that is inefficiently translated in a host cell. Alteration of the native viral codons can facilitate more robust expression of these proteins. Codon preferences for abundantly-expressed proteins have been determined in a number of species, and can provide guidelines for codon substitution. Examples of human proteins for which codon preferences have been determined include rhodopsin. Substitution of viral codons can be done by known methods, such as site-directed mutagenesis, or construction of oligonucleotides corresponding to the optimized sequence and synthesis of sequences by PCR. See, e.g., the construction method described in Mirzabekov T. et al., 1999, J. Biol. Chem., 274(40):28745-50. The optimization should also include consideration of other factors that can affect synthesis of oligos and/or expression. For example, long runs of G and/or C residues can interfere with synthesis, and should be avoided in the resulting optimized sequence.
We have surprisingly found that certain codon optimized sequences can be successfully expressed in both mammalian and bacterial cells. Codon optimization for both mammalian and bacterial (e.g., E. coli) expression is performed as follows. Some codons that are most preferred for mammalian expression (i.e., most efficiently translated in mammalian cells) are also most preferred for bacterial expression. Substitution of viral codons for these most preferred codons allows optimization for expression in both systems. However, some codons that are most preferred for mammalian expression are not most preferred for bacterial expression. For these codons, both mammalian and E. coli preferred codons and codons expressed with intermediate efficiency in both types of cells may be used to substitute for the viral codon. In addition, during the sequence optimization, following cis-acting sequence motifs are avoided: internal TATA-boxes, chi-sites and ribosomal entry sites; AT-rich or GC-rich sequence stretches; ARE, INS, CRS sequence elements; cryptic splice donor and acceptor sites; and branch points. Codon optimized sequences can retain some of the original codons. For example, a codon optimized sequence retains less than 70%, 60%, 50%, 40%, 30%, 20%, or 10% of the original viral codons.
Exemplary codon optimized variola sequences are shown in Table 1 (below).








TABLE 1







Poxvirus Antigen Sequences










Gene/protein




name
Sequence





D8L
atgccgcaacaactatctcctattaatatagaaactaaaaaagcaatttctaacg




cgcgattgaagccgttagacatacattataatgagtcgaaaccaaccactatcca



gaacactggaaaactagtaaggattaattttaaaggaggatatataagtggaggg



tttctccccaatgaatatgtgttatcatcactacatatatattggggaaaggaag



acgattatggatccaatcacttgatagatgtgtacaaatactctggagagattaa



tcttgttcattggaataagaaaaaatatagttcttatgaagaggcaaaaaaacac



gatgatggacttatcattatttctatattcttacaagtattggatcataaaaatg



tatattttcaaaagatagttaatcaattggattccattagatccgccaatacgtc



tgcaccgtttgattcagtattttatctagacaatttgctgcctagtaagttggat



tattttacatatctaggaacaactatcaaccactctgcagacgctgtatggataa



tttttccaacgccaataaacattcattctgatcaactatctaaattcagaacact



attgtcgtcgtctaatcatgatggaaaaccgcattatataacagagaactataga



aatccgtataaattgaacgacgacacgcaagtatattattctggggagattatac



gagcagcaactacctctccagcgcgcgagaactattttatgagatggttgtccga



tttgagagagacatgtttttcatattatcaaaaatatatcgaagagaataaaaca



ttcgcaattattgccatagtattcgtgtttatacttaccgctattctctttttta



tgagtcgacgatattcgcgagaaaaacaaaactag



(SEQ ID NO: 1)


 


D8
MPQQLSPINIETKKAISNARLKPLDIHYNESKPTTIQNTGKLVRINFKGGYISGG



FLPNEYVLSSLHIYWGKEDDYGSNHLIDVYKYSGEINLVHWNKKKYSSYEEAKKH



DDGLIIISIFLQVLDHKNVYFQKIVNQLDSIRSANTSAPFDSVFYLDNLLPSKLD



YFTYLGTTINHSADAVWIIFPTPINIHSDQLSKFRTLLSSSNHDGKPHYITENYR



NPYKLNDDTQVYYSGEIIRAATTSPARENYFMRWLSDLRETCFSYYQKYIEENKT



FAIIAIVFVFILTAILFFMSRRYSREKQN



(SEQ ID NO: 2)


 


D8L(1-275)
atgccgcaacaactatctcctattaatatagaaactaaaaaagcaatttctaacg



cgcgattgaagccgttagacatacattataatgagtcgaaaccaaccactatcca



gaacactggaaaactagtaaggattaattttaaaggaggatatataagtggaggg



tttctccccaatgaatatgtgttatcatcactacatatatattggggaaaggaag



acgattatggatccaatcacttgatagatgtgtacaaatactctggagagattaa



tcttgttcattggaataagaaaaaatatagttcttatgaagaggcaaaaaaacac



gatgatggacttatcattatttctatattcttacaagtattggatcataaaaatg



tatattttcaaaagatagttaatcaattggattccattagatccgccaatacgtc



tgcaccgtttgattcagtattttatctagacaatttgctgcctagtaagttggat



tattttacatatctaggaacaactatcaaccactctgcagacgctgtatggataa



tttttccaacgccaataaacattcattctgatcaactatctaaattcagaacact



attgtcgtcgtctaatcatgatggaaaaccgcattatataacagagaactataga



aatccgtataaattgaacgacgacacgcaagtatattattctggggagattatac



gagcagcaactacctctccagcgcgcgagaactattttatgagatggttgtccga



tttgagagagacatgtttttcatattatcaaaaatatatcgaagagaataaaaca



(SEQ ID NO: 3)


 


D8(1-275)
MPQQLSPINIETKKAISNARLKPLDIHYNESKPTTIQNTGKLVRINFKGGYISGG



FLPNEYVLSSLHIYWGKEDDYGSNHLIDVYKYSGEINLVHWNKKKYSSYEEAKKH



DDGLIIISIFLQVLDHKNVYFQKIVNQLDSIRSANTSAPFDSVFYLDNLLPSKLD



YFTYLGTTINHSADAVWIIFPTPINIHSDQLSKFRTLLSSSNHDGKPHYITENYR



NPYKLNDDTQVYYSGEIIRAATTSPARENYFMRWLSDLRETCFSYYQKYIEENKT



(SEQ ID NO: 4)


 


tPA-D8L
ATGGATGCAATGAAGAGAGGGCTCTGCTGTGTGCTGCTGCTGTGTGGAGCAGTCT



TCGTTTCGGCTAGCCCGCAACAACTATCTCCTATTAATATAGAAACTAAAAAAGC



AATTTCTAACGCGCGATTGAAGCCGTTAGACATACATTATAATGAGTCGAAACCA



ACCACTATCCAGAACACTGGAAAACTAGTAAGGATTAATTTTAAAGGAGGATATA



TAAGTGGAGGGTTTCTCCCCAATGAATATGTGTTATCATCACTACATATATATTG



GGGAAAGGAAGACGATTATGGATCCAATCACTTGATAGATGTGTACAAATACTCT



GGAGAGATTAATCTTGTTCATTGGAATAAGAAAAAATATAGTTCTTATGAAGAGG



CAAAAAAACACGATGATGGACTTATCATTATTTCTATATTCTTACAAGTATTGGA



TCATAAAAATGTATATTTTCAAAAGATAGTTAATCAATTGGATTCCATTAGATCC



GCCAATACGTCTGCACCGTTTGATTCAGTATTTTATCTAGACAATTTGCTGCCTA



GTAAGTTGGATTATTTTACATATCTAGGAACAACTATCAACCACTCTGCAGACGC



TGTATGGATAATTTTTCCAACGCCAATAAACATTCATTCTGATCAACTATCTAAA



TTCAGAACACTATTGTCGTCGTCTAATCATGATGGAAAACCGCATTATATAACAG



AGAACTATAGAAATCCGTATAAATTGAACGACGACACGCAAGTATATTATTCTGG



GGAGATTATACGAGCAGCAACTACCTCTCCAGCGCGCGAGAACTATTTTATGAGA



TGGTTGTCCGATTTGAGAGAGACATGTTTTTCATATTATCAAAAATATATCGAAG



AGAATAAAACATTCGCATAG



(SEQ ID NO: 5)


 


tPA-D8
MDAMKRGLCCVLLLCGAVFVSASPQQLSPINIETKKAISNARLKPLDIHYNESKP



TTIQNTGKLVRINFKGGYISGGFLPNEYVLSSLHIYWGKEDDYGSNHLIDVYKYS



GEINLVHWNKKKYSSYEEAKKHDDGLIIISIFLQVLDHKNVYFQKIVNQLDSIRS



ANTSAPFDSVFYLDNLLPSKLDYFTYLGTTINHSADAVWIIFPTPINIHSDQLSK



FRTLLSSSNHDGKPHYITENYRNPYKLNDDTQVYYSGEIIRAATTSPARENYFMR



WLSDLRETCFSYYQKYIEENKTFA



(SEQ ID NO: 6)


 


A27L
atggacggaactcttttccccggagatgacgatcttgcaattccagcaactgaat



ttttttctacaaaggctgctaaaaagccagaggctaaacgcgaagcaattgttaa



agccgatgaagacgacaatgaggaaactctcaaacaacggctaactaatttggaa



aaaaagattactaatgtaacaacaaagtttgaacaaatagaaaagtgttgtaaac



gcaacgatgaagttctatttaggttggaaaatcacgctgaaactctaagagcggc



tatgatatctctggctaaaaagattgatgttcagactggacggcgcccatatgag



taa



(SEQ ID NO: 7)


 


A27
MDGTLFPGDDDLAIPATEFFSTKAAKKPEAKREAIVKADEDDNEETLKQRLTNLE



KKITNVTTKFEQIEKCCKRNDEVLFRLENHAETLRAAMISLAKKIDVQTGRRPYE



(SEQ ID NO: 8)


 


B5R
atgaaaacgatttccgttgttacgttgttatgcgtactacctgctgttgtttatt



caacatgtactgtacccactatgaataacgctaaattaacgtctaccgaaacatc



gtttaatgataaacagaaagttacgtttacatgtgatcagggatatcattcttcg



gatccaaatgctgtctgcgaaacagataaatggaaatacgaaaatccatgcaaaa



aaatgtgcacagtttctgattacatctctgaattatataataaaccgctatacga



agtgaattccaccatgacactaagttgcaacggcgaaacaaaatattttcgttgc



gaagaaaaaaatggaaatacttcttggaatgatactgttacgtgtcctaatgcgg



aatgtcaacctcttcaattagaacacggatcgtgtcaaccagttaaagaaaaata



ctcatttggggaatatatgactatcaactgtgatgttggatatgaggttattggt



gcttcgtacataagttgtacagctaattcttggaatgttattccatcatgtcaac



aaaaatgtgatatgccgtctctatctaatggattaatttccggatctacattttc



tatcggtggcgttatacatcttagttgtaaaagtggttttacactaacggggtct



ccatcatccacatgtatcgacggtaaatggaatcccgtactcccaatatgtgtac



gaactaacgaagaatttgatccagtggatgatggtcccgacgatgagacagattt



gagcaaactctcgaaagacgttgtacaatatgaacaagaaatagaatcgttagaa



gcaacttatcatataatcatagtggcgttaacaattatgggcgtcatatttttaa



tctccgttatagtattagtttgttcctgtgacaaaaataatgaccaatataagtt



ccataaattgctaccgtaa



(SEQ ID NO: 9)


 


B5
MKTISVVTLLCVLPAVVYSTCTVPTMNNAKLTSTETSFNDKQKVTFTCDQGYHSS



DPNAVCETDKWKYENPCKKMCTVSDYISELYNKPLYEVNSTMTLSCNGETKYFRC



EEKNGNTSWNDTVTCPNAECQPLQLEHGSCQPVKEKYSFGEYMTINCDVGYEVIG



ASYISCTANSWNVIPSCQQKCDMPSLSNGLISGSTFSIGGVIHLSCKSGFTLTGS



PSSTCIDGKWNPVLPICVRTNEEFDPVDDGPDDETDLSKLSKDVVQYEQEIESLE



ATYHIIIVALTIMGVIFLISVIVLVCSCDKNNDQYKFHKLLP



(SEQ ID NO: 10)


 


L1R
atgggtgccgcggcaagcatacagacgacggtgaatacactcagcgaacgtatct



cgtctaaattagaacaagaagcgaatgctagtgctcaaacaaaatgtgatataga



aatcggaaatttttatatccgacaaaaccatggatgtaacctcactgttaaaaat



atgtgctctgcggacgcggatgctcagttggatgctgtgttatcagccgctacag



aaacatatagtggattaacaccggaacaaaaagcatacgtgccagctatgtttac



tgctgcgttaaacattcagacgagtgtaaacactgttgttagagattttgaaaat



tatgtgaaacagacttgtaattctagcgcggtcgtcgataacaaattaaagatac



aaaacgtaatcatagatgaatgttacggagccccaggatctccaacaaatttgga



atttattaatacaggatctagcaaaggaaattgtgccattaaggcgttgatgcaa



ttgacgactaaggccactactcaaatagcacctaaacaagttgctggtacaggag



ttcagttttatatgattgttatcggtgttataatattggcagcgttgtttatgta



ctatgccaagcgtatgttgttcacatccaccaatgataaaatcaaacttatttta



gccaataaggaaaacgtccattggactacttacatggacacattctttagaactt



ctccgatggttattgctaccacggatatgcaaaactga



(SEQ ID NO: 11)


 


L1
MGAAASIQTTVNTLSERISSKLEQEANASAQTKCDIEIGNFYIRQNHGCNLTVKN



MCSADADAQLDAVLSAATETYSGLTPEQKAYVPAMFTAALNIQTSVNTVVRDFEN



YVKQTCNSSAVVDNKLKIQNVIIDECYGAPGSPTNLEFINTGSSKGNCAIKALMQ



LTTKATTQIAPKQVAGTGVQFYMIVIGVIILAALFMYYAKRMLFTSTNDKIKLIL



ANKENVHWTTYMDTFFRTSPMVIATTDMQN



(SEQ ID NO: 12)


 


A33R
atgatgacaccagaaaacgacgaagagcagacatctgtgttctccgctactgttt



acggagacaaaattcaaggaaagaataaacgcaaacgcgtgattggtctatgtat



tagaatatctatggttatttcactactatctatgattaccatgtccgcgtttctc



atagtgcgcctaaatcaatgcatgtctgctaacgaggctgctattactgacgccg



ctgttgccgttgctgctgcatcatctactcatagaaaggttgcgtctagcactac



acaatatgatcacaaagaaagctgtaatggtttatattaccagggttcttgttat



atattacattcagactaccagttattctcggatgctaaagcaaattgcactgcgg



aatcatcaacactacccaataaatccgatgtcttgattacctggctcattgatta



tgttgaggatacatggggatctgatggtaatccaattacaaaaactacatccgat



tatcaagattctgatgtatcacaagaagttagaaagtatttttgtgttaaaacaa



tgaactaa



(SEQ ID NO: 13)


 


A33
MMTPENDEEQTSVFSATVYGDKIQGKNKRKRVIGLCIRISMVISLLSMITMSAFL



IVRLNQCMSANEAAITDAAVAVAAASSTHRKVASSTTQYDHKESCNGLYYQGSCY



ILHSDYQLFSDAKANCTAESSTLPNKSDVLITWLIDYVEDTWGSDGNPITKTTSD



YQDSDVSQEVRKYFCVKTMN



(SEQ ID NO: 14)


 


codon
CTGCAGGCTAGCATGAGCCAGCAACTGAGCCCCATCAACATCGAGACCAAGAAGG


optimized
CCATCAGCAACGCACGCCTGAAGCCCCTGAACATCCACTACAACGAGAGCAAGCC


F8L
CACCACCATCCAGAACACCGGCAAGCTGGTGCGCATCAACTTCAAGGGAGGCTAC



CTGAGCGGAGGCTTCCTTCCCAACGAGTACGTGCTGAGCAGCCTGCACATCTACT



GGGGCAAGGAGGATGACTACGGCAGCAACCACCTGATCGACGTGTACAAGTACAG



CGGCGAGATCAACCTGGTGCACTGGAACAAGAAGAAGTACAGCAGCTACGAGGAA



GCCAAGAAGCACGACGATGGCCTGATCATCATCAGCATCTTCCTTCAGGTGAGCG



ACCACAAGAACGTGTACTTCCAGAAGATCGTGAACCAACTGGACAGCATCCGCAC



TGCCAACACCAGCGCTCCCTTCGACAGCGTGTTCTACCTGGACAACCTGCTGCCC



AGCAAGCTGGACTACTTCAAGTACCTAGGCACCACCATCAACCACAGTGCCGACG



CCGTGTGGATCATCTTTCCCACCCCTATCAACATCCACAGCGACCAACTGAGCAA



GTTCCGCACCCTGCTGAGCCTGAGCAACCATGAGGGCAAGCCCCACTACATCACC



GAGAACTACCGCAATCCCTACAAGCTGAACGACGATACCGAGGTGTACTACAGTG



GCGAGATCATCCGAGCCGCCACCACCAGCCCTGCTCGCGAGAACTACTTCATGCG



CTGGCTGAGCGACCTGCGCGAGACCTGCTTCAGCTACTACCAGAAGTACATCGAG



GGCAACAAGACCTTCGCCATCATCGCCATCGTGTTCGTGTACATCCTGACCGCCA



TCCTGTTCCTGATGAGCCGCCGATACAGCCGCGAGAAGCAGAACTAAGGATCC



(SEQ ID NO: 15)


 


F8
MSQQLSPINIETKKAISNARLKPLNIHYNESKPTTIQNTGKLVRINFKGGYLSGGFLPNEY



VLSSLHIYWGKEDDYGSNHLIDVYKYSGEINLVHWNKKKYSSYEEAKKHDDGLIIISIFLQ



VSDHKNVYFQKIVNQLDSIRTANTSAPFDSVFYLDNLLPSKLDYFKYLGTTINHSADAVWI



IFPTPINIHSDQLSKFRTLLSLSNHEGKPHYITENYRNPYKLNDDTEVYYSGEIIRAATTS



PARENYFMRWLSDLRETCFSYYQKYIEGNKTFAIIAIVFVYILTAILFLMSRRYSREKQN



(SEQ ID NO: 16)


 


codon
CTGCAGGCTAGCATGGACGGCACCCTGTTCCCTGGCGACGACGACCTGGCCATCC


optimized
CCGCCACCGAGTTCTTCAGCACCAAGGCTGCCAAGAAGCCTGAGGCCAAGCGCGA


A30L
GGCCATCGTGAAGGCTGACGGCGACAACAACGAGGAGACCCTGAAGCAGCGCCTG



ACCAACCTGGAGAAGAAGATCACCAACGTGACCACCAAGTTCGAGCAGATCGAGA



AGTGCTGCAAGCGCAACGACGACGTGCTGTTCCGCCTGGAGAACCACGCCGAGAC



CCTGCGCGCTGCCATGATCAGCCTGGCCAAGAAGATCGACGTGCAGACTGGCAGA



CGCCCCTACGAGTAAGGATCC



(SEQ ID NO: 17)


 


A30
MDGTLFPGDDDLAIPATEFFSTKAAKKPEAKREAIVKADGDNNEETLKQRLTNLE



KKITNVTTKFEQIEKCCKRNDDVLFRLENHAETLRAAMISLAKKIDVQTGRRPYE



(SEQ ID NO: 18)


 


codon
CTGCAGATGAAGACCATCAGCGTGGTGACCCTGCTGTGCGTGCTTCCTGCCGTGG


optimized
TGTACAGCACCTGCACCGTGCCCACCATGAACAACGCCAAGCTGACCAGCACCGA


B7R
GACCAGCTTCAACGACAAGCAGAAAGTGACCTTCACCTGCGACAGCGGCTACTAC



AGCCTGGACCCCAACGCTGTGTGCGAGACCGACAAGTGGAAGTACGAGAATCCCT



GCAAGAAGATGTGCACCGTGAGCGACTACGTGAGCGAGCTGTACAACAAACCCCT



GTACGAGGTGAACGCTATCATCACCCTGATCTGCAAGGACGAGACCAAGTACTTC



CGCTGCGAGGAGAAGAATGGCAACACCAGCTGGAACGACACCGTGACCTGCCCCA



ACGCTGAGTGCCAGAGCCTCCAGCTGGACCACGGCAGCTGCCAGCCCGTGAAGGA



GAAGTACAGCTTCGGCGAGCACATCACCATCAACTGCGACGTGGGCTACGAGGTG



ATCGGTGCCAGCTACATCACCTGCACCGCTAACAGCTGGAACGTGATCCCCAGCT



GCCAGCAGAAGTGCGACATTCCCAGCCTGAGCAACGGCCTGATCAGTGGCAGCAC



CTTCAGCATCGGTGGCGTGATCCACCTGAGCTGCAAGAGCGGCTTCATCCTGACT



GGCAGTCCCAGCAGCACCTGCATCGACGGCAAGTGGAACCCTGTGCTTCCCATCT



GCATCCGCAGCAACGAGGAGTTCGACCCCGTGGAGGACGGTCCCGACGACGAGAC



CGACCTGAGCAAGCTGAGCAAAGACGTGGTGCAGTACGAGCAGGAGATCGAGAGC



CTTGAGGCTACCTACCACATCATTATCGTGGCTCTGACCATCATGGGCGTGATCT



TCCTGATCAGCGTGATCGTGCTGGTGTGCAGCTGCAACAAGAACAACGACCAGTA



CAAGTTCCACAAGCTGCTTCTGTAAGGATCC



(SEQ ID NO: 19)


 


B7
MKTISVVTLLCVLPAVVYSTCTVPTMNNAKLTSTETSFNDKQKVTFTCDSGYYSL



DPNAVCETDKWKYENPCKKMCTVSDYVSELYNKPLYEVNAIITLICKDETKYFRC



EEKNGNTSWNDTVTCPNAECQSLQLDHGSCQPVKEKYSFGEHITINCDVGYEVIG



ASYITCTANSWNVIPSCQQKCDIPSLSNGLISGSTFSIGGVIHLSCKSGFILTGS



PSSTCIDGKWNPVLPICIRSNEEFDPVEDGPDDETDLSKLSKDVVQYEQEIESLE



ATYHIIIVALTIMGVIFLISVIVLVCSCNKNNDQYKFHKLLL



(SEQ ID NO: 20)









Nucleic Acid Compositions

The new compositions described herein include nucleic acid compositions that encode poxvirus antigens (e.g., vaccinia antigens and variola antigens). There are many ways of presenting nucleic acid encoding antigen to a host. For example, DNA vaccines can include a naked DNA plasmid that encodes one or more virus antigens. Bacterial vectors (e.g., Listeria vectors, Bacille Calmette-Guérin (BCG) vectors), replicon vectors, live attenuated bacteria, DNA vaccine co-delivery with live attenuated vectors, and viral vectors for expression of heterologous genes also can be used. In the case of naked DNA replicon vectors, a mammalian expression plasmid serves as a vehicle for the initial transcription of the replicon. The replicon is amplified within the cytoplasm, resulting in more abundant mRNA encoding the heterologous gene such that initial transfection efficiency may be less important for immunogenicity. In some embodiments, a poxvirus antigen is expressed using a live attenuated viral vector (e.g., recombinant vaccinia (e.g., modified vaccinia Ankara (MVA), IDT Germany), recombinant adenovirus, avian poxvirus (e.g., canarypox (e.g., ALVAC®, Aventis Pasteur) or fowlpox), poliovirus, and alphavirus virion vectors). The avian poxviruses are defective in mammalian hosts, but can express inserted heterologous genes under early promoters. Recombinant adenovirus and poliovirus vectors can thrive in the gut and stimulate efficient mucosal immune responses.
Nucleic acid uptake can be improved in various ways. For example, DNA uptake via intramuscular (IM) delivery of the vaccine can be improved by the addition of sodium phosphate to the formulation. Increased DNA uptake via IM delivery can also be accomplished by electrotransfer (e.g., applying a series of electrical impulses to muscle immediately after DNA immunization). Adjuvants that can also be added to the vaccine (e.g., to improve DNA stability and uptake and/or immune induction) include water emulsions (e.g., complete and incomplete Freund's adjuvant), oil, Corynebacterium parvum, BCG, QS-21, iron oxide, sodium alginate, aluminum hydroxide, aluminum and calcium salts (i.e., alum), unmethylated CpG motifs, glucan, and dextran sulfate. Synthetic polymers (e.g., polyamino acids, co-polymers of amino acids, saponin, paraffin oil, muramyl dipeptide, RegressinTM (Vetrepharm, Athens Ga.), and Avridine), and liposomal formulations. These adjuvants can be added to vaccine formulations to improve DNA stability and DNA uptake by the host cells, and may decrease the dosage required to induce an effective immune response. Coinjection of cytokines, ubiquitin, or costimulatory molecules can also help improve immune induction, The antigens described herein can also be fused with cytokine genes, helper epitopes, ubiquitin, or signal sequences to enhance an immune response. Fusions can also be used to aid in targeting to certain cell types.
The medium in which the DNA vector is introduced should be physiologically acceptable for safety reasons. Suitable pharmaceutical carriers include sterile water, Tris-EDTA (TE) buffer, saline, dextrose, glucose, phosphate buffered saline (PBS), or other buffered solutions. Included in the medium can be physiologically acceptable preservatives, stabilizers, diluents, emulsifying agents, pH buffering agents, viscosity enhancing agents, colors, etc.
Once the DNA vaccine is delivered, the nucleic acid molecules (e.g., DNA plasmids; are taken up into host cells, which then express the plasmid DNA as protein. Once expressed, the protein is processed and presented in the context of self-major histocompatibility (MHC) class I and class II molecules. The host then develops an immune response against the DNA-encoded immunogen. To improve the effectiveness of the vaccine, multiple injections can be used for therapy or prophylaxis over extended periods of time. To improve immune induction, a prime-boost strategy can he employed. Priming vaccination with DNA and a different modality for boosting (e.g., live viral vector or protein antigen) has been successful in inducing cell-mediated immunity. The timing between priming and boosting varies and is adjusted for each vaccine.
Nucleic acid vaccines can be administered by many modes and routes. For example, they can be administered intradermally (ID), intramuscularly (IM), and by either route, they can be administered by needle injection, gene gun (e.g., Helios® Gene Gun, Bio-Rad), or needle-less jet injection (e.g., BiojectorTM (Bioject Inc., Portland, Oreg.). Other modes of administration include oral, intravenous, intraperitoneal, intrapulmonary, intravitreal, and subcutaneous inoculation. Topical inoculation is also possible, and can be referred to as mucosal vaccination. These include intranasal, ocular, oral, vaginal, or rectal topical routes. Delivery by these topical routes can be by nose drops, eye drops, inhalants, suppositories, or microspheres.
Suitable doses of nucleic acid compositions for humans can range from 1 μg/kg to 1 mg/kg of total nucleic acid, e.g., from 5 μg/kg-500 mg/kg of total DNA, 10 μg/kg-250 μg/kg of total DNA, or 10 μg/kg -170 μg/kg of total DNA. In one embodiment, a human subject (18-50 years of age, 45-75 kg) is administered 1.2 mg-7.2 mg of DNA. “Total DNA” and “total nucleic acid” refers to a pool of nucleic acids encoding distinct antigens. For example, a dose of 5 mg of total DNA encoding 5 different poxvirus antigens can have 1 mg of each antigen. DNA vaccines can be administered multiple times, e.g., between two-six times, e.g., three times. In an exemplary method, 100 μg of a DNA composition is administered to a human subject at 0, 4, and 12 weeks (100 μg per administration).
Protein Compositions
Proteins, e.g., recombinant proteins, which are antigens of poxviruses, can be administered as vaccines or as vaccine “boosts” following vaccination with nucleic acid compositions. Recombinant proteins can also be administered in conjunction with other immunogenic compositions (e.g., live attenuated vaccinia vaccine preparations). Recombinant proteins (e.g., proteins produced by cloning DNA encoding antigens of poxvirus isolates using standard molecular biological techniques) can be one source of isolated proteins for boosting. Proteins used for boosting an individual can include the same sequences as encoded by the DNA vaccines previously administered to the individual, e.g., vaccinia D8L, A27, B5, L1R, or A33R, or portions thereof.
For large-scale production of recombinant viral proteins, transfectant cell lines are generated (e.g., Chinese Hamster Ovary cell transfectants), and cell lines that stably express the proteins are generated from the transfectants. Lines that overexpress the protein are selected for production. Master and working cell banks of selected cells are maintained. Proteins are expressed by growing cells in large-scale cultures in protein-free medium. Supernatants of the cells are harvested. Protein is then purified (e.g., using affinity chromatography, ion exchange chromatography, and/or gel filtration chromatography), and tested for purity. Proteins are purified and concentrated using techniques such as gel filtration and ion exchange chromatography. Next, proteins are evaluated for identity, potency, purity, quantity, sterility, the presence of endotoxin, and general safety according to Good Manufacturing Practice (GMP) guidelines. Identity can also be determined with ELISA with antibodies specific for the clade of the protein. Potency can also be evaluated with ELISA (e.g., reactivity of rabbit sera with the purified protein). Purity can be evaluated With SDS-PAGE and silver stain analyses of the protein, and size-exclusion high-performance liquid chromatography. Quantities can be determined by Coomassie-based assays, spectrophotometric assays, and volume measurements. The quality of protein preparations can be determined by visual inspection and pH measurements. Sterility can be determined by methods described in 21 C.F.R. 610.12. Endotoxin can be determined by Limulus Amebocyte assays. General safety can be determined by methods described in 21 C.F.R. 610.11.
Protein compositions containing an immunogenically effective amount of a recombinant poxvirus protein, or fragments thereof, can be administered by various routes and methods of administration. Suitable compositions can include, for example, lipopeptides (e.g., Vitiello et al., 1995, J. Clin. Invest., 95:341), peptide compositions encapsulated in poly(DL-lactide-co-glycolide) (“PLG”) microspheres (see, e.g., Eldridge et al., 1991, Molec. Immunol., 28:287-94; Alonso et al., 1994, Vaccine, 12:299-306; Jones et al., 1995, Vaccine, 13:675-81), and peptide compositions contained in immune stimulating complexes (ISCOMS) (see, e.g., Takahashi et al., 1990, Nature, 344:873-75; Hu et at, 1998, Clin. Exp, Immunol., 113:235-43).
Useful carriers that can be used with the immunogenic compositions and vaccines described herein are well known, and include, for example, thyroglobulin, albumins such as human serum albumin, tetanus toxoid, polyamino acids such as poly L-lysine and poly L-glutamic acid, influenza, hepatitis B virus core protein, and the like. The compositions and vaccines can contain a physiologically tolerable (i.e., acceptable) diluent such as water, or saline, typically phosphate buffered saline. The compositions and vaccines also typically include an adjuvant. Adjuvants such as QS-21, incomplete Freund's adjuvant, aluminum phosphate, aluminum hydroxide, or alum, are examples of materials well known in the art. Additionally, CTL responses can be primed by conjugating S proteins (or fragments, derivative or analogs thereof) to lipids, such as tripalmitoyl-S-glcerylcysteinyl-seryl-serine (P3CSS).
Immunization with a composition containing a poxvirus protein composition, e.g., via injection, aerosol, oral, transdermal, transmucosal, intrapleural, intrathecal, or other suitable routes, induces the immune system of the host to respond to the composition.
An exemplary range for an immunogenic amount of protein composition is 5 μg/kg-500 μg/kg, e.g., 10-100 μg/kg of total protein, with adjuvant. In one embodiment, a dose of 325 μg of a protein composition is administered to a human (18-55 years of age, 45-75 kg). An exemplary program of administration of the protein composition includes a first intramuscular boost 8 weeks after the final nucleic acid immunization, followed by a second intramuscular boost with the protein composition 8 weeks after the first boost.
The immunogenic DNA and protein compositions described herein can be administered to subjects at risk for exposure to variola, and to laboratory workers who are exposed to vaccinia, cowpox, monkey pox, variola, or other members of the Orthopoxvirus genus.
Kits
Kits comprising the nucleic acid and protein compositions are provided. The kits can include one or more other elements including: instructions for use; other reagents, e.g., a diluent, devices or other materials for preparing the composition for administration; pharmaceutically acceptable carriers; and devices or other materials for administration to a subject. Instructions for use can include instructions for therapeutic application (e.g., DNA vaccination and protein boosting) including suggested dosages and/or modes of administration, e.g., in a human subject, as described herein.
The kit can further contain at least one additional reagent, such as a diagnostic or therapeutic agent, e.g., a diagnostic agent to monitor a response to immune response to the compositions in the subject, or an additional therapeutic agent as described herein.
In one embodiment, the kit includes a vial (or other suitable container) containing nucleic acids encoding two, three, four, five, or six distinct poxvirus antigens. The kit also includes a second vial containing recombinant poxvirus polypeptides (e.g., polypeptides that are the same as those encoded by the nucleic acids in the kit). The kit can include QS-21 adjuvant (50 μg/dose/subject) and cyclodextrin as an excipient (30 mg/subject). The adjuvant and the excipient are formulated with the protein, and can be included in the formulation or packaged separately within the kit.
Evaluating Immune Responses to Vaccinations
ELISA assays and Western blots can be used to assess humoral immune Responses. In particular, ELISA and Western blots can be used to assess antibody binding, antibody neutralizing capability, antibody-mediated fusion inhibition, and antibody-dependent cytotoxicity.
Techniques for evaluating cellular immune responses include intracellular staining (e.g., flow cytometry) and ELISPOT (an enzyme-linked immunosorbent assay format), which allow detection and quantitation of cells producing cytokines (e.g., TNFα and IFN-γ) in response to antigens. For example, isolation of splenocytes or peripheral blood monocyte cells (PBMCs) from animals or human patients followed by in vitro challenge with a poxvirus antigen such as D8, and finally testing by ELISPOT and/or intracellular cytokine staining (ICS), can determine the potential for a cell-mediated immune response in vaccine recipients. A standard chromium release assay can be used to assess cytotoxicity. To assess a cell-mediated immune response to a DNA vaccine, the traditional approaches of measuring T cell proliferation in response to antigen and CTL-mediated killing of autologous cells expressing poxvirus epitopes can also be used.
EXAMPLES
The invention is further described in the following examples, which do not limit the scope of the invention described in the claims.
Example 1
Construction and Expression of DNA Vaccines Expressing Vaccinia D8 Antigens
The gene encoding the D8 protein was cloned into a DNA vaccine vector pSW3891, which uses a CMV IE promoter, and an Intron A sequence downstream of the CMV promoter, to drive the expression of coded antigen insert (Wang et al., 2005,J. Virol., 79(3):1906-1910). To produce more immunogenic D8L DNA vaccines, two versions of D8L gene inserts were produced (FIG. 1). The first one, wtD8L, has a full length coding sequence of the wild type D8L gene. The second one, tPAD8L, encodes a D8protein with an N-terminal human tissue plasminogen activator (tPA) leader sequence and a deletion of the transmembrane (TM) region and cytoplasmic tail. The wild type D8L gene does not encode a natural leader sequence.
To construct the wtD8L DNA vaccine, the D8L gene was PCR amplified from WR strain of vaccinia virus (VACV) using pfu DNA polymerase (Stratagene, Calif.). DNA inserts were then subcloned into pSW3891 after the CMV immediately early (IE) promoter (Wang et al., 2005,J. Virol., 79(3):1906-1910). For the tPA-D8L construct, the PCR amplified genes were subcloned into the same vector downstream of the tPA leader sequence (Lu et al., 1998, Meth. Molec. Med., 29:355-374; Wang et al., 2004, Vaccine 22(25-26):3348-3357; Wang et al., 2006, Vaccine, 24(21):4531-4540). Each DNA vaccine plasmid transformed in E. coli (HB101 strain) was checked by restriction digestion and DNA sequencing before large amounts of DNA plasmids were prepared with a Mega purification kit (Qiagen, Valencia, Calif.).
Additional vaccinia genes (A27L, B5R, L1R, and A33R) were PCR amplified from WR strain of VACV using pfu DNA polymerase subcloned into pSW3891 after the CMV immediately early (IE) promoter (Wang et al., 2005, J. Virol., 79(3):1906-1910). Studies with these constructs are described below.
Expression of D8 from the DNA vaccines was examined by Western blot using culture supernatants and cell lysates from 293T cells transiently transfected with each of these two D8L DNA vaccine plasmids. Cells were transiently transfected by a calcium phosphate co-precipitation method using 10 μg of plasmid DNA for 2×106 cells in a 60-mm dish. Cells were harvested 72 hours later. Both supernatants and cell lysates were collected for ELISA or Western blot analysis.
To produce the D8-specific rabbit sera used for the Western blot analysis of D8 antigen expression described above, New Zealand White (NZW) rabbits of 2-3 kg body weight were purchased from Millbrook Farm (Amherst, Mass.). Each rabbit received 3 bi-weekly immunizations of 36 μg D8L DNA vaccines at each immunization by a gene gun at the shaved abdominal skin. Sera were collected 2 weeks after the last immunization. D8-specific rabbit serum R274 was used for Western blot analysis.
To perform Western blots, 10 ng of protein/sample was resolved by SDS-PAGE and transferred onto PVDF membranes (Bio-Rad, Hercules, Calif.). Membranes were blocked overnight at 4° C. in blocking buffer (0.2% IQblock, 0.1% Tween®-20 in 1X PBS). Membranes were incubated with a 1:300 dilution of antisera from a rabbit immunized with D8L. After washing, blots were incubated with alkaline phosphatase-conjugated goat anti-rabbit IgG (Tropix, Bedford, Mass.) at 1:5000 dilution for 1 hour at room temperature, and signals were detected using a chemiluminescence Western-Light Kit (Tropix, Bedford, Mass.).
The tPA D8L DNA vaccine was expressed at a higher level than the wtD8L construct. The tPA-D8L was particularly effective at increasing the secretion of D8 antigen to supernatants. When analyzed by SDS-PAGE, the apparent molecular weight of tPA-D8L protein was higher than wtD8L in supernatant, suggesting additional post-translational processing steps for this modified D8L gene design. One possibility was the glycosylation of D8 protein since tPA-D8L has three putative N-glycan sites (N29, N94 and N144). To examine this, transiently expressed tPAD8L proteins were treated with peptide N-glycosidase F (PNGaseF). PNGaseF (New England Bio Lab, Beverly, Mass.) was added to denatured samples prepared from the supernatants of transiently transfected 293T cells according to manufacturer's instructions. After incubating overnight at 37° C., samples were resolved by SDS-PAGE and analyzed by Western blot as described above.
PNGaseF reduced the molecular weight of D8 both in lysate and supernatant to that of the precursor form of D8, indicating that newly expressed tPA-D8L in 293T cells was glycosylated. Interestingly, D8 expressed by vaccinia virus was primarily non-glycosylated, based on its apparent molecular weight and resistance to PNGaseF treatment. The identity of newly expressed D8 antigen was further confirmed by the strong reactivity between mouse sera immunized with vaccinia virus and the tPA-D8L protein expressed in 293T cells.
Example 2
Immunogenicity of the D8L DNA Vaccines
The immunogenicity of both forms of D8L DNA vaccines was tested in BALB/c mice. Control groups of mice received either empty vector DNA (negative control) or were administered vaccinia virus WR strain (positive control).
Six to eight week old female BALB/c mice were purchased from Taconic Farms (Germantown, N.Y.). The animals were immunized with a Helios® gene gun (Bio-Rad Laboratories, Hercules, Calif.) at the shaved abdominal skin as previously reported (Wang et al. 2004, Methods Mol. Biol., 245:185-196).
Each mouse received 4 bi-weekly immunizations with six DNA shots of 2 μg each per immunization. Mice immunized with VACV received 105 pfu of VACV in 10 μl PBS by intradermal inoculation into the ear pinnae 1 month before challenge (Tscharke et al., 2002,J. Gen. Virol., 83:1977-1986; Tscharke and Smith., 1999, J. Gen. Virol., 80:2751-2755). At least 5 mice were included in each group for immunogenicity studies. Blood samples were collected peri-orbitally prior to the first immunization and 2 weeks after each immunization.
To measure antibody responses by ELISA, individual mouse sera from each animal group were collected. ELISA plates were coated with 100 μl of antigen at 1 μg/ml harvested from 293T cells transiently transfected with the DNA vaccine plasmids and incubated overnight at 4° C. In addition to measuring reactivity to recombinant D8L antigen produced in transfected 293T cells, antisera were tested for reactivity to lysates of Vero cells infected with vaccinia virus WR strain. For the latter assays, ELISA plates were coated with 105 pfu of vaccinia virus (VACV) per well and fixed with 2% paraformaldehyde (Wyatt et al., 2004, Proc. Natl. Acad. Sci. U.S.A. 101(13):4590-4595). The WR strain of VACV used in these studies was propagated in Vero cells. Clarified cell lysates were used for Western blot analysis and ELISA. VACV stock for challenge was prepared in L929 cells (Selin et al., 1994, J. Exp. Med., 179(6):1933-1943) and purified from serum contaminants by centrifugation on sucrose gradients (Chen et al., 2001, Nat, Immunol., 2(11):1067-1076). Viral titer assays were performed on Vero cells (Selin et al., 1994, J. Exp. Med., 179(6):1933-1943; Selin et al., 1998, J. Exp. Med., 188(9):1705-1715).
Serially diluted mouse sera (100 μl) were added to each well and assayed in duplicate after blocking. The plates were incubated with biotinylated anti-mouse IgC (Vector Laboratories, Burlingame, Calif.) diluted at 1:1000 (100 μl per well), followed by horseradish peroxidase-conjugated streptavidin (Vector Laboratories) diluted at 1:2000 and finally developed with 3,3-,5,5-tetramethybenzidine (Sigma-Aldrich, St. Louis, Mo.) solution (100 μl per well). The reactions were stopped by adding 25 μl of 2M H2SO4, and the plates were read at OD450 nm. The endpoint titer was calculated as the serum dilution resulting in absorbance greater than 2 standard deviations above the absorbance in wells incubated with negative control mouse serum.
Serum anti-D8 IgG responses increased with each immunization as measured by ELISA (data not shown) and they reached the peak level at 2 weeks after the fourth DNA immunization (FIGS. 2A-2C). Both wtD8L and tPA-D8L DNA vaccines elicited positive anti-D8 IgG responses. The geometric mean titer of the tPA-D8L, DNA vaccine group was higher than the wtD8L DNA vaccine group, as measured against both the recombinant D8 antigen produced from 293T cells (FIG. 2A) or the lysates of Vero cells infected with the vaccinia virus (FIG. 2B).
As expected, the positive control mouse sera, from animals immunized with the vaccinia virus WR strain, had higher titers against the cell lysates infected with the vaccinia virus than the recombinant D8 antigen due to the presence of multiple poxvirus antigens in the infected cell lysates. Likewise, the levels of D8-specific antibodies elicited by both D8L DNA vaccines were higher than that elicited by the vaccinia virus WR strain, presumably due to the fact that anti-D8 antibody is only part of the broad antibody responses against a wide range of antigens in sera immunized with vaccinia viruses.
To measure neutralizing antibody responses elicited by the DNA vaccines, plaque neutralizing assays were performed. Fifty percent plaque reduction titer was determined by standard techniques (Frey et at., 2002, N. Engl. J. Med., 346(17):1275-1280). Briefly, sera from immunized animals were heat inactivated for 30 minutes at 56° C. and serial dilutions of antibodies were incubated with 50 pfu of VACV for 1 hour at 37° C.
Confluent Vero cells monolayers were infected with antibody-virus mixtures for 1 hour, washed with PBS and incubated under liquid overlay for 2 days. Monolayers were then stained with 0.5% of crystal violet for 5 minutes and plaques were counted. The neutralization was calculated as the percentage of the number of plaque counts reduced at the testing serum in an assay compared to the mean of the plaque counts for the three virus controls (without sera) in the same assay.
The mouse sera elicited by D8L DNA vaccines were able to neutralize vaccinia virus as measured in a plaque reduction assay (FIG. 2C). The tPA-D8L DNA vaccine induced higher neutralizing antibodies than the wtD8L DNA vaccine. It was unexpected. that the neutralizing titer of anti-tPA-D8L sera was almost the same as that of the mouse sera immunized with the vaccinia virus (FIG. 2C). It appears that either high titers of antibodies against one major poxvirus antigen (such as D8) or relatively lower titers of immune sera against multiple poxvirus antigens could achieve the same neutralizing effect as measured by this in vitro neutralization assay against the IMV form of poxvirus.
Example 3
Protective Efficacy of D8L DNA Vaccines in Mice Against Lethal Vaccinia Challenges
The protective potential of D8 antigen, either alone or in combination with other reported protective poxvirus antigens, was evaluated in BALB/c mice against lethal vaccinia challenge. In this series of challenge studies, each mouse received four bi-weekly gene gun-mediated DNA vaccinations with a fixed total dose of 12 μg DNA plasmids at each vaccination.
First, protection studies against a lethal dose of vaccinia virus (5×107pfu per animal) delivered by intraperitoneal (i.p.) route were conducted. Age matched female BALB/c mice (10 per group) were used in all experiments. Two weeks after the last immunization, BALB/c mice were anesthetized intramuscularly with ketamine-xylasine and then injected with 5×107 pfu WR strain of VACV in 100 μl of PBS by intraperitoneal route. Alternatively, BALB/c mice at 2 weeks after the last immunization received 5×106 pfu WR strain of VACV in 25 μl of PBS by intranasal inoculation. Mice were weighed and observed daily as previously described (Selin et al., 1994, J. Exp. Med. 179(6):1933-1943).
As a result of the high dose virus challenge, control mice inoculated with empty DNA vector lost weight progressively until death as early as 3-4 days after challenge (FIG. 3A; Table 2, below). Both forms of D8L DNA vaccines, when delivered alone, were able to protect mice from continuous weight loss and ultimate death as compared to the control group mice that received the empty DNA vector (FIG. 3A). None of the D8L DNA vaccinated mice died. The tPA-D8L DNA vaccine appears slightly more effective in controlling the weight loss than the wtD8L DNA vaccine, but neither of them were quite as effective as the positive control immunization with vaccinia virus WR strain in controlling weight loss (FIG. 3A). This result is consistent with the previous reports that a single poxvirus antigen vaccine could not achieve the same level of protection provided by the live attenuated poxvirus vaccines (Fogg et al., 2004, J. Virol. 78(19):10230-10237; Hooper et al., 2000, Virology 266(2):329-339; Pulford et al., 2004, Vaccine 22(25-26):3358-3366). However, these data are the first report that D8 antigen alone was able to achieve a 100% protection from death by a lethal vaccinia challenge.







TABLE 2







Average weight loss after VACV challenge













P value



A27L/B5R
D8L/A27L/B5R
(paired













% of initial
Standard
% of initial
Standard
Student's


Day
weight
deviation
Weight
deviation
t test)















0
100
0
100
0
N/A


1
90.6
2.5
93.6
1.5
p > 0.05


2
89.5
3.5
95.2
1.8
p < 0.05


3
90.8
3.8
97.7
1.7
p < 0.05


4
93.4
5.8
99.7
0.8
p > 0.05


5
94.6
8.9
99.2
0.9
p > 0.05









Next, we evaluated the D8L DNA vaccine in combination with other subunit-based polyvalent poxvirus vaccines to determine whether the addition or D8L improved the efficacy of the polyvalent vaccines. A DNA vaccine construct with the tPA-D8L insert was used in this study, because measurements on both antibody response and weight loss indicated that the tPA-D8L DNA vaccine was more effective than the wtD8L DNA vaccine. DNA vaccines were subcloned into the pSW3981 vector.
DNA vaccines were administered i.p., and animals were challenged with VACV, as described above. The efficacy of a bivalent formulation with two poxvirus antigens, A27 and B5, was significantly improved with the addition of tPA-D8L DNA vaccine as the third component (FIG. 3B). Mice immunized with bivalent formulation had lost 9.2% of weight on day 3 after challenge, whereas mice immunized with the 3-valent formulation including A27, B5, and D8 had lost only 2.3% (p<0.05). Protection provided by this 3-valent formulation was similar to that provided with the vaccinia virus vaccination. Addition of a D8 antigen also improved the protective efficacy of a 4-valent formulation (A27, B5, L1, and A33) by minimizing the weight loss during the first 1-3 days after challenge (FIG. 3C) when studied in the same i.p. challenge model. Mice immunized with the 5-valent formulation that included D8 antigen regained initial body weight at 2.5 days after challenge, as compared to 4.2 days in the 4-valent formulation group that did not include D8 (p<0.05).
The above finding was further confirmed in an airway infection model in which mice were challenged with 5×106 pfu of vaccinia virus delivered by the intranasal (i.n.) route as previously reported (Galmiche et al., 1999, Virology, 254(1):71-80). In this study, mice that received the 5-valent formulation including D8 not only had stopped losing weight earlier than those that received the 4-valent formulation (FIG. 4A), but also achieved 66% protection (10 out of 15 mice) as compared to the 26% protection (4 out of 15) by the 4-valent formulation against lethal challenge (FIG. 4). The difference in survival between two formulations was statistically significant (p<0.05), but the difference in body weight loss was not.
Statistical analyses described herein were performed using Epi InfoTM software for windows available from the CDC web site. Survival curves were analyzed using Kaplan-Meier test. Comparisons between the mean percentage body-weight changes for different groups at each day after challenge were performed using an unpaired, two-tailed Student's t test (Microsoft Excel software, version 2003) in consultation with a biostatistician. Significance levels were set at a P value less than 0.05.
Example 4
Antibody Responses Induced by Polyvalent Vaccine Formulations in Mice
To further characterize the specific antibody responses against individual pox antigens included in the polyvalent vaccine formulation and vaccinia vaccine, more detailed analyses were conducted with mice sera immunized with different polyvalent vaccine formulations included in the above animal studies.
A27, D8, and L1 are highly immunogenic antigens. Anti-A27 antibody had the highest titers especially when Mice received the bivalent (A27 and B5) formulation (FIG. 5A). Anti-D8 antibody titers remained high in mice immunized with either 3-valent or 5-valent formulations (FIG. 5C). Similarly, anti-L1 antibody titers were high in mice immunized with either 4-valent or 5-valent formulations (FIG. 5D). B5 was less immunogenic with lower antibody titers against the autologous antigen (FIG. 5B) A33 was the least immunogenic among antigens included in the 4-valent and 5-valent formulations (FIG. 5E). It should be noted that since ELISA assays were carried out with crude lysates of cells transiently transfected with the DNA vaccines, low titers of anti-A33 antibodies may be attributed to either a low level of specific IgG or to a low level of A33 expression in 293T cells. However, induction of anti-vaccinia antibodies by A33 DNA immunization was indeed confirmed by Western blot against vaccinia virus (data not shown).
In our study, the total DNA vaccine dose was fixed no matter how many antigen components were included in various polyvalent formulations. There was a decrease of less than 10-fold in anti-A27 titers when D8 was added to the bivalent formulation containing A27 and B5. Otherwise, the levels of antigen specific antibody responses showed only a small decrease when more poxvirus antigens were added, suggesting that the effect of antigen dilution due to the addition of new antigens was present, but not significant. Mouse sera immunized with the vaccinia vaccine had positive antibodies against each of the five poxvirus antigens, confirming that these proteins were effective antigens during vaccinia immunization. However, the levels of such antibodies varied. Anti-D8 IgG titer was the highest and anti-A33 IgG titer was the lowest. Both vector control sera and sent lacking a particular antigen did not show specific reactivity against that antigen.
Sera from mice immunized with polyvalent DNA vaccines had high titers of IgG responses against VACV antigens, and such titers increased when more antigens were added to the polyvalent DNA vaccine formulations (FIG. 5F). On the other hand, the anti-VACV titer for vaccinia virus immunized mouse sera was lower than most of the polyvalent formulations. This finding suggested that while the vaccinia virus could induce antibody responses against a very broad array of poxvirus antigens, subunit-based polyvalent formulations could develop higher total antibody responses even with fewer antigens. More importantly, titer of anti-VACV antibody response (FIG. 5F) did not correlate with protection (FIGS. 3A-5G).
Levels of neutralizing antibody responses were also analyzed. In our assay, the neutralizing antibodies mainly targeted the IMV form of the poxvirus. Each of the polyvalent formulations included elicited positive neutralizing antibody responses at levels similar to or even better than that induced by the vaccinia vaccine (FIG. 5G). The 3-valent formulation including D8L elicited the strongest neutralizing antibody responses, presumably due to the combination of two strong IMV antigens, A27 and D8. The 5-valent formulation was somewhat less effective in generating neutralizing antibodies, most likely due to the diluting effect when the numbers of antigen components were increased. Interestingly, protection was not correlated with the levels of IMV-mediated neutralizing antibody responses. Rather, better protection was achieved with more antigens included in the vaccine formulations.
Example 5
Sequence Homology Between Variola Major and Vaccinia Protective Antigens
Although poxviruses are highly conserved in the regions that encode protective antigens, it is possible that antibodies induced by variola antigens may confer a higher level of protection against smallpox challenge as compared to those responses induced by vaccinia antigens. A protein subunit-based vaccine or DNA plasmid vaccine does not incorporate live viruses into its design and therefore eliminates the safety concerns over using a live smallpox virus vaccine as a means to induce responses to variola antigens.
As a first step in the production of variola sequence-based vaccines, amino acid sequences of three well-characterized protective antigens (A27, B5, and D8) from VACV were compared with orthologous proteins from the variola major (VARV) virus (FIG. 6). Sequences of orthopoxviruses were derived from the NCBI genome database and aligned using MacVector 7.0. For VACV sequences, two frequently used strains, Western Reserve (WR) and Copenhagen (COP), were included for the analysis. For VARV, the India 1967 (VARV-IND) and Bangladesh 1975 (VARV-BSH) strain sequences were used. The orthologous VARV protein for the VACV A27 antigen is A30 for VARV-IND and A31 for VARV-BSH; for the B5 antigen the orthologous protein is B7 for VARV-IND and B6 for VARV-BSH, and for the D8 antigen the orthologous protein for both VARV-IND and VARV-BSH is F8 (Shchelkunov, 1995, Virus Genes, 10(1):53-71; Shchelkunov et al., 1995, Virus Res., 36(1):107-18).
Sequences of these three proteins are highly homologous, but not completely identical to the VACV antigen sequences: three amino acid differences exist between A27 and A30/A31, 23 amino acid differences between B5 and B6/B7, and 12 amino acid differences between D8 and F8 proteins (FIG. 6, which shows the portions of sequences that include amino acid differences, in bold font). Some of these differences occurred in only one of the two VARV strains. Employing variola sequences can minimize the chance of reduced protection due to these sequence differences that exist between the variola and vaccinia antigens, particularly when antigen-specific immune responses, such as neutralizing antibody determinants and/or dominant T-cell epitopes, are involved.
Example 6
Construction of Codon Optimized VARV DNA Vaccines and Production of Recombinant A30, F8, and B7 in an E. coil Expression System
Codon modified A30L, B7R, and F8L genes of Variola Major India1967 (VARV-IND) sequences were chemically synthesized. Variola sequences were altered to include codons used by mammalian cells and E. coil cells without changing the amino acids encoded by the sequences. To achieve this effect, codons that are most preferred for expression (i.e., most efficiently translated) in both human cells and in E. coil cells were substituted for certain viral codons. However, some codons that are most preferred for mammalian expression are not most preferred for bacterial expression. For these codons, both mammalian and E. coli preferred codons and codon with intermediate efficiency in both types of cells may be used to substitute the viral codon. For example, the mammalian cell most preferred codon is “GCC” for the amino acid Alanine “Ala” while the most preferred codon is “GCT” in E. coli, therefore, “GCT” or “GCC”, or an intermediate codon, “GCA”, may be used in the codon optimized sequence. In addition, during the sequence optimization, the following cis-acting sequence motifs are avoided: internal TATA-boxes, chi-sites and ribosomal entry sites; AT-rich or GC-rich sequence stretches; ARE, INS, CRS sequence elements; cryptic splice donor and acceptor sites; and branch points.
Codon optimization of DNA vaccines improves antigen expression and immunogenicity in mammals and permits high levels of expression in bacteria. The codon optimized synthetic genes encoding VARV A30, F8, or B7 proteins were individually cloned into the DNA vaccine vector pSW3891 immediately after the CMV immediate early (IE) promoter (Wang et al., 2005, J. Viral., 79(3):1906-10). Tables 3-5 provide a comparison of codon usage in the wild type A30L, B7R, and F8L gene sequences and the codon optimized gene sequences that were produced.







TABLE 3







Comparison of codon usage between wild type and codon optimized


A30L gene sequences










% Codon usage
















Codon




Amino
Wild type
optimized



Codon
Acid
gene
gene
















GCG
Ala
9
0



GCA

27
0



GCT

55
27



GCC

9
73



AGG
Arg
14
0



AGA

14
14



CGG

29
0



CGA

0
0



CGT

0
0



CGC

43
86



AAT
Asn
100
0



AAC

0
100



GAT
Asp
67
0



GAC

33
100



TGT
Cys
100
0



TGC

0
100



TGA
End
0
0



TAG

0
0



TAA

100
100



CAG
Gln
33
100



CAA

67
0



GAG
Glu
27
100



GAA

73
0



GGG
Gly
0
0



GGA

75
0



GGT

25
0



GGC

0
100



CAT
His
0
0



CAC

100
100



ATA
Ile
33
0



ATT

67
0



ATC

0
100



TTG
Leu
22
0



TTA

0
0



CTG

11
100



CTA

33
0



CTT

22
0



CTC

11
0



AAG
Lys
38
100



AAA

62
0



ATG
Met
100
100



TTT
Phe
60
0



TTC

40
100



CCG
Pro
0
0



CCA

75
0



CCT

25
50



CCC

0
50



AGT
Ser
0
0



AGC

0
100



TCG

0
0



TCA

0
0



TCT

100
0



TCC

0
0



ACG
Thr
0
0



ACA

30
0



ACT

70
10



ACC

0
90



TGG
Trp
0
0



TAT
Tyr
100
0



TAC

0
100



GTG
Val
0
100



GTA

25
0



GTT

75
0



GTC

0
0

















TABLE 4







Comparison of codon usage between wild type and codon optimized


B7R gene sequences










% Codon usage
















Codon




Amino
Wild type
optimized



Codon
Acid
gene
gene
















GCG
Ala
33
0



GCA

11
0



GCT

44
67



GCC

11
33



AGG
Arg
0
0



AGA

0
0



CGG

0
0



CGA

50
0



CGT

50
0



CGC

0
100



AAT
Asn
80
10



AAC

20
90



GAT
Asp
78
0



GAC

22
100



TGT
Cys
95
0



TGC

5
100



TGA
End
100
0



TAG

0
0



TAA

0
100



CAG
Gln
0
100



CAA

100
0



GAG
Glu
15
100



GAA

85
0



GGG
Gly
7
0



GGA

47
0



GGT

33
20



GGC

13
80



CAT
His
80
0



CAC

20
100



ATA
Ile
52
0



ATT

24
8



ATC

24
92



TTG
Leu
21
0



TTA

29
0



CTG

8
79



CTA

25
0



CTT

8
17



CTC

8
4



AAG
Lys
5
86



AAA

95
14



ATG
Met
100
100



TTT
Phe
89
0



TTC

11
100



CCG
Pro
14
0



CCA

50
0



CCT

14
14



CCC

21
86



AGT
Ser
6
6



AGC

3
94



TCG

16
0



TCA

16
0



TCT

42
0



TCC

16
0



ACG
Thr
19
0



ACA

50
0



ACT

27
4



ACC

4
96



TGG
Trp
100
100



TAT
Tyr
71
0



TAC

29
100



GTG
Val
4
100



GTA

27
0



GTT

58
0



GTC

12
0

















TABLE 5







Comparison of codon usage between wild type and codon optimized


F8L gene sequences










% Codon usage
















Codon




Amino
Wild type
optimized



Codon
Acid
gene
gene
















GCG
Ala
8
0



GCA

62
8



GCT

15
15



GCC

15
77



AGG
Arg
8
0



AGA

42
0



CGG

0
0



CGA

42
17



CGT

0
0



CGC

8
83



AAT
Asn
65
4



AAC

35
96



GAT
Asp
73
20



GAC

27
80



TGT
Cys
100
0



TGC

0
100



TGA
End
0
0



TAG

100
0



TAA

0
100



CAG
Gln
11
67



CAA

89
33



GAG
Glu
53
93



GAA

47
7



GGG
Gly
23
0



GGA

69
15



GGT

0
0



GGC

8
85



CAT
His
70
10



CAC

30
90



ATA
Ile
41
0



ATT

45
0



ATC

14
100



TTG
Leu
32
0



TTA

18
0



CTG

4
89



CTA

25
4



CTT

18
7



CTC

4
0



AAG
Lys
22
100



AAA

78
0



ATG
Met
100
100



TTT
Phe
71
7



TTC

29
93



CCG
Pro
36
0



CCA

36
0



CCT

18
18



CCC

9
82



AGT
Ser
14
7



AGC

0
93



TCG

14
0



TCA

18
0



TCT

46
0



TCC

7
0



ACG
Thr
12
0



ACA

35
0



ACT

29
6



ACC

24
94



TGG
Trp
100
100



TAT
Tyr
92
0



TAC

8
100



GTG
Val
17
100



GTA

67
0



GTT

8
0



GTC

8
0










Each DNA vaccine plasmid transformed in E. coil (HB101 strain) was checked by restriction digestion and DNA sequencing before large amounts of DNA plasmids were prepared with a Mega purification kit (Qiagen, Valencia, Calif.).
Expression of these codon-optimized VARV antigen DNA vaccines was verified in culture supernatants and cell lysates from 293T cells transiently transfected with each of the three VARV antigen DNA plasmids and examined by Western blot using a polyclonal anti-vaccinia virus serum. All three of these antigens were present in both the cell lysates and culture supernatant and their molecular weights matched that from the VACV-WR strain grown in Vero cells. Non-transfected 293T cells and uninfected Vero cells did not express pox-specific antigens. Recombinant A30, B7, and F8proteins (rA30, rF8, and rB7) were successfully produced and purified from an E. coil expression system using the same synthetic A30, B7, and F8 genes. These results also show that the B7 protein forms dimers in its non-denatured condition. According to sequence analysis, the B7 protein has potential sites for N-glycosylation, which was confirmed by its sensitivity to PNGase treatment (data not shown).
Example 7
Immunogenicity of the A30, F8, and B7 DNA Vaccines
Six to eight week old female BALB/c mice (Taconic Farms, Germantown, N.Y.) were immunized with a Helios® gene gun (Bio-Rad) at the shaved abdominal skin as previously reported (Wang et al,. 2004, Vaccine, 22(25-26);3348-57). Each mouse received 3-4 monthly immunizations with six DNA shots of 2 μg each per immunization. Ten mice per group were immunized. Blood samples were collected peri-orhitally prior to the first immunization and 2 weeks after each immunization.
Immunization with VARV DNA vaccines elicited overall high levels of antigen-specific IgG antibody responses in mice. FIGS. 7A, 7B, and 7C depict responses to A30 and A27; F8 and D8; and B7 and B5, respectively, as measured by ELISA. A30 was the most immunogenic, followed by F8and B7 DNA vaccines. As shown in the figures, antibodies induced by immunization with codon optimized variola DNA vaccines recognized both vaccinia and variola antigens expressed in the supernatant of transiently transected 293T cells. Given the polyclonal nature of the immune sera, it was not surprising that we detected no significant difference in recognition of variola or vaccinia antigens by ELISA.
Immunization with DNA vaccines, expressing the two VARV IMV antigens F8 and A30, produced antibodies that neutralized VACV in a plaque reduction assay that measures IMV antibodies (FIG. 8) as observed with DNA vaccines made with their VACV counterparts, D8 and A27, as described in Example 4, above. Similar to the results observed with VACV IMV antigens, the subunit VARV IMV antigens were more effective than an intact vaccinia infection in eliciting IMV neutralizing antibodies.
Example 8
Protective Efficacy of VARV DNA Vaccines Expressing A30, F8,and B7 Antigens Against Lethal VACV Challenges in Mice
Protection by mono- and polyvalent DNA vaccines expressing VARV antigens was tested in a lethal VACV challenge model. Age matched female BALB/c mice (5 per group) were used in all experiments. Mice received three DNA immunizations every 2 weeks, rested 1 month, and received another boost 2 weeks prior to challenge. Mice were then inoculated intraperitoneally (i.p.) with a lethal dose (5×107 pfu) of VACV (WR). Ten days after the last immunization, one group of mice was anesthetized, intramuscularly with ketamine-xylazine (100/10 mg/kg), and then injected, intraperitoneally, with 5×107 pfu of VACV-WR in 100 μl of PBS. Mice were weighed and observed daily, as previously described (Selin et al, 1994, J. Exp. Med., 179(6):1933-43). VARV antigen-specific antibodies after 1, 2, or 3 monovalent DNA vaccine inoculations were measured by ELISA (FIG. 9A).
FIG. 9A is a graph depicting anti-IgG ELISA titers against A30, F8, and B7 antigens in sera of immunized animals. DNA vaccines expressing each of the three VARV antigens induced high titers of antibodies to each of the A30, F8, and B7 antigens after the 2nd immunization (FIG. 9A). A third DNA vaccination was not needed to further boost the levels of antibody responses (FIG. 9A). As an indicator of protection against lethal challenge with VACV, average weight loss of the surviving mice in each group was measured. FIG. 9B is a graph depicting the percent of initial body weight following challenge. All negative control mice inoculated with the vector progressively lost weight and died by day 5. Mice that received either the mono- or polyvalent VARV DNA vaccines survived the challenge and regained body weight. Mice that received the polyvalent VARV DNA vaccine recovered their initial body weight sooner than mice that received any of the monovalent DNA vaccines (FIG. 9B).
Although intraperitoneal VACV challenge leads to lethal poxvirus infection, it does not represent the natural aerosol spread of the virus. The intranasal method of infection requires significantly less virus to produce a lethal infection and causes death at a later time point suggesting a different virus-host interaction. In addition, the intranasal mode of infection represents a more stringent challenge model. Therefore, we investigated the relative efficacy of different types of subunit-based VARV vaccines in providing protection in an intranasal challenge model.
Groups of mice (five per group) were administered 5×106 pfu VACV-WR in 25 μl of PBS by intranasal inoculation. In this intranasal challenge study, groups of mice received 2 immunizations of either a polyvalent rA30, rB7, and rF8 protein vaccine or a polyvalent DNA vaccine expressing the A30, B7, and F8 antigens. Mice immunized with the vaccinia vaccine served as a positive control, and the negative control group received only vector DNA (FIGS. 10A-10B). Pox-specific antibodies induced by either the DNA or protein formulations and immunizations with vaccinia vaccine were analyzed by ELISA (FIG. 10A). Immunization with the polyvalent recombinant VARV protein vaccines was significantly more immunogenic than immunization with live vaccinia vaccine (p=0.0039)(FIG. 10A). In contrast, immunization with the polyvalent DNA-based VARV vaccines induced only marginally higher antibody responses when compared to immunization with VACV, except for the B7-specific antibody, which probably occurred as a result of such a low anti-B7 antibody responses in VACV immunized mice.
Mice were challenged with a lethal intranasal dose of VACV (WR) (5×106 pfu) two weeks after the second immunization. While all mice in the control group died by day 11 (FIG. 10B), mice that received either the polyvalent recombinant VARV protein vaccination or the vaccinia vaccine immunization were fully protected, as indicated by a 100% survival rate following the intranasal challenge (FIG. 10B). Two immunizations with the polyvalent DNA vaccine induced partial protection with 4 out of 5 mice surviving by day 14 (80% survival, FIG. 10B). Both protein and DNA subunit vaccine formulations induced statistically significant greater levels of protection when compared to the vector control group (p=0.0017 and p=0.0211, respectively), as determined, by the Kaplan Meier survival test.
In summary, these data show that a vaccine based on antigens from the VARV virus can confer protective immunity against both intranasal and intraperitoneal challenge with the vaccinia virus and induce neutralizing antibodies against vaccinia. These studies demonstrate that a variola antigen-based vaccine is feasible and can confer increased immune responses and/or greater protection following exposure to variola.
OTHER EMBODIMENTS
It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.

## Claims

1. A method of inducing an immune response to a poxvirus in a mammal, the method comprising administering to a mammal a composition comprising at least one nucleic acid molecule comprising, a nucleotide sequence encoding a variola F8 polypeptide, wherein the nucleotide sequence is codon optimized for expression in both a mammalian cell and a bacterial cell, and has a nucleotide sequence at least 99% identical to SEQ ID NO:15, and wherein the composition is administered in an amount effective to produce an immune response in the mammal against a subsequent poxvirus infection.

2. The method of claim 1, wherein the composition further comprises a nucleotide sequence encoding one or more of variola A30 and B7 polypeptides.

3. The method of claim 1, wherein the composition comprises nucleotide sequences encoding all three of variola F8, A30, and B7 polypeptides.

4. The method of claim 2, wherein the nucleotide sequence encoding one or more of variola A30 and B7 polypeptides is codon optimized for expression in both a mammalian cell and a bacterial cell.

5. The method of claim 4, wherein the nucleotide sequence encoding the variola A30 polypeptide comprises the nucleotide sequence of SEQ ID NO:17.

6. The method of claim 4, wherein the nucleotide sequence encoding the variola B7 polypeptide comprises the nucleotide sequence of SEQ ID NO:19.

7. The method of claim 3, wherein the nucleotide sequences encoding the variola A30 and B7 polypeptides are codon optimized for expression in both a mammalian cell and a bacterial cell.

8. The method of claim 7, wherein the nucleotide sequence encoding the variola A30 polypeptide comprises the nucleotide sequence of SEQ ID NO:17.

9. The method of claim 7, wherein the nucleotide sequence encoding the variola B7 polypeptide comprises the nucleotide sequence of SEQ ID NO:19.