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Journal of Virology, November 2005, p. 13915-13923, Vol. 79, No. 22
0022-538X/05/$08.00+0 doi:10.1128/JVI.79.22.13915-13923.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
Modulation of the Immune Response to the Severe Acute Respiratory Syndrome Spike Glycoprotein by Gene-Based and Inactivated Virus Immunization
Wing-pui Kong,1
Ling Xu,1
Konrad Stadler,2
Jeffrey B. Ulmer,2
Sergio Abrignani,2
Rino Rappuoli,2 and
Gary J. Nabel1*
Vaccine Research Center, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bldg. 40, Room 4502, MSC-3005, 40 Convent Drive, Bethesda, Maryland 20892-3005,1
Vaccines Research, Chiron Corporation, Via Fiorentina 1, 53100 Siena, Italy, and 4650 Horton Street, Emeryville, California 946082
Received 14 May 2005/
Accepted 12 August 2005

ABSTRACT
Although the initial isolates of the severe acute respiratory
syndrome (SARS) coronavirus (CoV) are sensitive to neutralization
by antibodies through their spike (S) glycoprotein, variants
of S have since been identified that are resistant to such inhibition.
Optimal vaccine strategies would therefore make use of additional
determinants of immune recognition, either through cellular
or expanded, cross-reactive humoral immunity. Here, the cellular
and humoral immune responses elicited by different combinations
of gene-based and inactivated viral particles with various adjuvants
have been assessed. The T-cell response was altered by different
prime-boost immunizations, with the optimal CD8 immunity induced
by DNA priming and replication-defective adenoviral vector boosting.
The humoral immune response was enhanced most effectively through
the use of inactivated virus with adjuvants, either MF59 or
alum, and was associated with stimulation of the CD4 but not
the CD8 response. The use of inactivated SARS virus with MF59
enhanced the CD4 and antibody response even after gene-based
vaccination. Because both cellular and humoral immune responses
are generated by gene-based vaccination and inactivated viral
boosting, this strategy may prove useful in the generation of
SARS-CoV vaccines.

INTRODUCTION
The severe acute respiratory syndrome coronavirus (SARS-CoV)
has emerged as a respiratory pathogen caused by a newly recognized
human coronavirus (
30,
32,
45,
50). In contrast to previously
described coronaviruses, this disease syndrome is highly lethal
and is accompanied by significant pulmonary and systemic pathology
that has prompted a search for preventive vaccines. Several
studies have now demonstrated that it is possible to elicit
protective immune responses to viruses in animal models (
7,
8,
17,
61,
75). Protection against pulmonary viral replication
is mediated by antibodies in a murine vaccine model, which are
necessary and sufficient for protection (
75). As multiple isolates
of this virus have become available, increased molecular heterogeneity
has become apparent (
12,
19,
37,
76,
79). This sequence variability
is observed in a variety of gene products. Of relevance to the
development of SARS-CoV vaccines, there is amino acid sequence
variability in S, found in alternative human strains and in
animals, notably the palm civet (
54,
63). It has been recognized
recently that certain variants, including more recent specific
human isolates, as well as the palm civet isolates, are resistant
to neutralization by antibody (
73), raising concerns that vaccines
based on the original Urbani strain or closely related isolates
may not provide complete protection against those that may evolve
in the future.
Depending on the method of vaccination, different types of immune responses can be elicited by alternative vectors or proteins with adjuvants. While immunization with proteins or inactivated viruses using adjuvants primarily induces humoral immunity, gene-based vaccination with plasmid DNA and/or replication-defective adenoviral vectors elicits stronger cellular immunity, in addition to humoral responses of various degrees, depending upon the antigen (3, 5, 9, 18, 25, 26, 28, 33, 38, 41, 46, 52, 57, 58, 60, 66, 68). The effects of combined immunization with gene-based vaccination and protein boosting are less well understood in terms of the balance of cellular and humoral immunity. Though DNA priming and protein boosting have been shown to increase antibody responses (14, 20, 29, 34, 65), the effects of protein adjuvants on different DNA and recombinant adenoviral vector (rAd) immunization regimens have not been explored fully. Whether the balance of CD4 and CD8 immunity is altered or the order of immunization affects this response is unknown. In this report, we have evaluated the immune response to these by different combinations of priming and boosting with DNA, adenovirus, and inactivated viral vaccines. The ability to boost gene-based vaccines with the adjuvanted inactivated virus shows clear enhancement of the CD4 and antibody responses. The CD8 responses are not similarly enhanced after such a boost. In contrast, DNA priming followed by rAd boosting with vectors encoding S allow induction of a strong CD8 response. The ability to combine different vaccine modalities may increase the breadth of the immune response and contribute to the development of an effective SARS-CoV vaccine.

MATERIALS AND METHODS
Generation of immunogens. (i) DNA vector.
The SARS S-expressing vector has been previously described (
74,
75). Basically, a gene encoding the SARS-CoV spike (S) protein
was synthesized using human-preferred codons and expressed in
a mammalian expression vector that contains the cytomegalovirus
enhancer/promoter and splice donor and the human T-cell leukemia
virus type 1 R region (
4).
(ii) Inactivated SARS virus.
An inactivation method was developed for SARS-CoV before initiating purification steps. SARS-CoV harvested from Vero cells was inactivated with ß-propiolactone (Ferrak, Berlin Chemie, Germany) at a final concentration of 0.05% for 16 h at 4°C, followed by hydrolysis of any residual ß-propiolactone by elevating the temperature to 37°C for 3 h. Then replication incompetence of the viruses was confirmed by an inactivation assessment. An aliquot of the inactivated harvest was passaged twice in Vero cells to exclude the presence of residual infectious virus. A confluent Vero cell culture was incubated in a T175 flask with 10 ml inactivated harvest in 90 ml cell culture medium at 37°C. After 4 days, the supernatant was transferred to a second confluent Vero cell culture and cells were incubated for 1 h at 37°C. Subsequently, the supernatant was replaced by fresh medium and the cell culture was further incubated at 37°C for 4 days. Vero cells from the first passage were further incubated with fresh cell culture medium for another 4 days at 37°C. The cell cultures were evaluated for the presence of cytopathic effect which was caused by the SARS-CoV infection.
(iii) Recombinant adenoviral vector encoding S.
Replication-defective rAd encoding S (rAd-S) was generated by a modification of a previously published method (10, 33, 42, 57, 70, 72). Briefly, the synthetic SARS S adapted from the sequence described above (terminated at amino acid 1229) was subcloned into the shuttle plasmid pAdAdaptCMVmcs. 293 cells were cotransfected with 2 µg of purified, linearized shuttle plasmid, pADAPT, with an ADV cosmid by calcium phosphate transfection. After 7 to 12 days, the supernatant containing recombinant adenovirus was collected from the cell lysate, freezing and thawing at least three times. The production of recombinant adenovirus was scaled up by infection of 293 cells with the virus-containing supernatant. The viruses were purified by cesium chloride, aliquoted (1012 particles/ml), and stored in phosphate-buffered saline (PBS) with 13% glycerol at 20°C for future use.
Adjuvants and ovalbumin.
MF59 (Chiron Vaccines) was used at a 1:1 dilution with the immunogens right before immunization. CpG oligodeoxynucleotides (CpG) 1826 or CpG 7909 (25 µg in 0.05 ml; Coley Pharmaceutical Group, Wellesley, MA) was mixed with the inactivated SARS virus (5 µg in 0.05 ml) per mouse right before immunization. Alum (Pierce, Rockford, IL) was used at a 1:1 ratio (vol/vol) with each immunogen. In the experiment using ovalbumin (Sigma-Aldrich, St. Louis, MO), 50 µg of ovalbumin in 0.05 ml was mixed with adjuvants immediately before injection (total of 0.1 ml) into each mouse.
Immunization.
In this study, experiments were performed with different primary immunizations, either one rAd, three DNA, or three DNA with one rAd injection. After the primary injections, animals were boosted with inactivated SARS viruses with or without adjuvants. Each test group contained 10 BALB/c mice, and control groups contained 5 mice. Immunizations were performed at 3-week intervals, and intracellular cytokine staining was performed 10 days after the last injection. For the experiment with DNA immunizations, each animal was injected with 50 µg of the plasmid DNA in 100 µl of PBS in the quadriceps muscle for a total of three injections. For experiments with rAd immunization, the replication-defective adenoviral vector encoding the SARS spike was injected (109 particles) intramuscularly in 100 µl of PBS. In each experiment, the inactivated SARS virus boost-immunization was performed 3 weeks after the last prime immunization. Five micrograms of inactivated SARS virus was mixed immediately with or without different adjuvants in a final volume of 100 µl in PBS before intramuscular injection into each animal. Negative control groups were immunized with empty vector plasmid or control rAd following the same schedule as the test groups in each experiment. Animal experiments were carried out in compliance with all relevant federal and National Institutes of Health policies. Because of the large number of animals and because the immunization regimens vary depending on the combination of immunogens, it was not technically possible to perform all comparisons within the same experiment; however, because the animals were inbred and the vaccines were stable, some comparisons between groups could be made.
Assessment of cellular immune responses by intracellular cytokine staining.
CD4+ and CD8+ T-cell responses were evaluated using intracellular cytokine staining (ICS) by flow cytometry for gamma interferon (IFN-
) and tumor necrosis factor alpha (TNF-
) as previously described (28, 67, 75) with peptide pools (17- to 19-mers overlapping by 10 amino acids; 2.5 µg/ml each) covering the SARS-CoV spike protein. Cells were then fixed, permeabilized, and stained using rat monoclonal anti-mouse CD3, CD4, CD8, IFN-
, and TNF-
antibodies (BD-Pharmingen). The IFN-
- and TNF-
-positive cells in the CD4+ and CD8+ cell populations were analyzed with the program FlowJo (Tree Star, Inc.).
Analysis of the humoral immune response.
Mouse anti-SARS-S immunoglobulin G (IgG) enzyme-linked immunosorbent assay (ELISA) titer was measured using a modified lectin capture method described previously (28, 67, 75), except the Myc-tagged, transmembrane domain-truncated SARS-CoV spike protein (SARS-S
TM-Myc) was used for capture. Serial dilutions of the mouse serum were tested to ensure reliability of the results. For simplicity, only the 1:1,000 dilution data are shown in the figures, with error bars indicating the standard deviations.
Statistical analysis.
Each individual animal immune response was counted as an individual value for statistical analysis. The significance of the cellular and humoral immune responses was calculated by Student's t test (tails = 2, type = 2) as indicated by the P value.

RESULTS
To analyze the immune response elicited by alternative vectors
encoding S and inactivated virus, mice were immunized with DNA
or with inactivated SARS virus alone or mixed with MF59 adjuvant,
an oil squalene-in-water emulsion (
47), compared to an adenoviral
vector encoding S alone (Fig.
1). CD4, CD8, and antibody responses
were assessed 10 days after the final boost by each vaccine.
Intracellular cytokine staining on unstimulated cells was used
to standardize for background staining in the assay, and there
was little variation in unimmunized mice. DNA vaccination induced
a low level of CD4 immunity and was similar to inactivated SARS
or adenoviral vector alone, in contrast to the inactivated SARS
virus with MF59, which induced an increase in CD4 immunity (Fig.
1, left panel). In contrast, adenoviral immunization induced
a substantial CD8 response while inactivated SARS virus with
MF59 induced a negligible CD8 response. The immunoglobulin response
paralleled that of the CD4 response, with the highest levels
in the inactivated SARS plus MF59 group. A similar CD4 and IgG
response was observed with the inactivated SARS virus without
adjuvant, though of lower magnitude. Interestingly, the adenoviral
immunization alone also elicited a significant increase in the
IgG titers.
Effect of priming and boosting of gene-based and inactivated SARS virus vaccine.
The effect of priming and boosting was next analyzed using different
combinations. In all cases, stimulation of the T-cell responses
was markedly increased compared to immunization with single
agents alone. In particular, DNA priming followed by adenoviral
boosting induced a substantial CD4 response that was lower in
magnitude than DNA priming and inactivated virus, either with
or without adjuvant, and the MF59 adjuvant gave the optimal
CD4 ICS response (Fig.
2, left panel). In contrast, the DNA
prime/rAd boost induced predominantly a CD8 response, with more
than 4% positive cells by intracellular cytokine staining (Fig.
2, middle panel), while the DNA priming followed by protein
boosting with or without adjuvant stimulated minimal CD8 responses.
In all cases, a substantial immunoglobulin response was induced,
and there were no significant differences between these groups
(Fig.
2, right panel). These findings suggest that the prime
and boost combinations are highly effective at inducing cellular
and humoral immunity, although the cellular response appears
to be biased toward CD8 cells for adenoviral boosting and toward
CD4 for inactivated virus boosting.
CpG oligonucleotides do not cross-prime the CD8 response following inactivated virus boosting.
Since CpG oligodeoxynucleotides have been shown to facilitate
cross-priming that enhances cellular immunity in the absence
of protein adjuvants (
1,
51,
78), the ability of these oligonucleotides
to enhance the CD8 responses was evaluated after DNA priming
and inactivated SARS virus boosting. Specifically, we asked
whether CpGs improved cellular immunity in the presence of MF59
following a DNA/inactivated virus prime-boost vaccination. All
combinations of priming and protein boosting yielded substantial
CD4 responses, as in the previous experiment, compared to no
adjuvant, but this response was not increased by the inclusion
of either of two previously identified oligodeoxynucleotides,
CpG1826 or CpG7909 (Fig.
3, left panel). In addition, these
CpGs did not increase the CD8 response; a minor diminution was
noted with both CpGs that was statistically significant for
CpG1826 (Fig.
3, middle panel). However, the IgG responses were
substantial and the CpG7909 oligodeoxynucleotide group was slightly
higher than either the MF59-alone group or the CpG1826 oligodeoxynucleotide
group (
P = 0.043 and 0.044, respectively) (Fig.
3, right panel).
The ability of MF59 and CpG to influence immune responses after
DNA priming and rAd boosting was next assessed to evaluate whether
the CD8 response could be reelicited once a potent gene-based
vaccine had been administered. Secondary boosting with the different
combinations of inactivated SARS virus and adjuvant with and
without CpG revealed a similar effect, with no substantial modulation
of the CD4 response (Fig.
4, left panel), and a slight decrease
in the CD8 response was observed in the presence of CpG (Fig.
4, middle panel). No significant difference was observed in
the CD8 response between inactivated SARS virus with or without
MF59 in these studies. Again, a strong IgG response was observed
and did not appear influenced by the inclusion of MF59 or CpG
adjuvant (Fig.
4, right panel). This response was not unexpected,
given that the CD4 responses were substantially increased in
all groups compared to the control (Fig.
4, left panel, column
1 versus 2 to 5).
The boosting effect of inactivated SARS virus was next evaluated
after rAd priming alone, and no significant effect was observed
for the CD4 response (Fig.
5, left panel). A small increase
in the CD8 response was observed by inclusion of the MF59 adjuvant
with inactivated SARS compared to the inactivated virus alone.
This increase was affected by the CpGs (Fig.
5, middle panel).
The IgG responses were similarly not significantly different
among these groups (Fig.
5, right panel).
Boosting of gene-based vaccine responses by inactivated virus and adjuvant is antigen specific.
To determine whether the effects of rAd priming and inactivated
SARS boosting were antigen specific or adjuvant dependent, we
evaluated the response to inactivated SARS virus or to an unrelated
protein, ovalbumin, comparing MF59 or alum adjuvants. The enhanced
CD4 response was observed only in the presence of inactivated
SARS virus with both the MF59 and alum adjuvants (Fig.
6, left
panel, columns 1 and 3). In both cases, this effect was antigen
specific, as ovalbumin did not elicit a similar response (Fig.
6, left panel, columns 2 and 4). No significant differences
were observed in the CD8 responses using either adjuvant comparing
the inactivated virus to the ovalbumin protein control (Fig.
6, middle panel). The IgG responses were similar to those observed
with CD4 and were seen in the presence of the inactivated SARS
virus but not ovalbumin with either adjuvant (Fig.
6, right
panel). Therefore, the protein boost effect was antigen specific
and elicited by two independent adjuvants.

DISCUSSION
The effects of gene-based vaccination on immune responses are
becoming increasingly understood. For example, DNA priming followed
by adenoviral boosting for several different antigens can elicit
strong CD4 and CD8 cellular immune responses (
9,
25,
26,
28,
46,
52,
57,
66,
68). In contrast, protein vaccines typically
utilize adjuvants that elicit strong CD4 responses and minimal
CD8 responses (
21,
31,
40,
55,
71,
77). More recently, Toll
receptor agonists, particularly CpGs, have been shown to improve
the cellular immune responses elicited by proteins, particularly
in murine models and in some nonhuman primate systems (
11,
15,
27,
44,
53). Because we have found previously that the increase
in SARS S antibody titers generated by DNA/rAd or rAd immunization
do not broaden protection against civet and recent SARS-CoV
isolates (
73), we have focused on gene-based vaccination and
protein adjuvant combinations that increase the antibody response
at the same time they maintain or enhance balanced T-cell immunity.
Genetic vaccination in combination with inactivated virus boosting showed that boosting with adjuvanted proteins induces a qualitatively different immune response, with increased CD4 responses relative to CD8 and strong antibody responses; gene-based responses, particularly those using rAd vector boosting, elicit strong CD8 responses and less marked CD4 responses, although the immunoglobulin response is substantial. These disparate effects are likely due to the nature of the interaction of the various vaccines with dendritic cells. rAd is thought to infect immature dendritic cells, which upon maturation can present synthesized antigens within class I major histocompatibility complex proteins to stimulate CD8 immunity, while alum and other protein adjuvants typically boost CD4 and humoral responses through class II major histocompatibility complex pathways. When inactivated virus with adjuvant was used to boost animals primed with rAd vectors, an antigen-specific increase in the CD4 response was observed (Fig. 6). In contrast, the CD8 response was not affected either by the antigen or by the adjuvant and was also similar in magnitude to the stimulation seen without boosting (Fig. 1, middle panel, lane 5). We interpret this finding to indicate that the adjuvant effect after rAd priming, which induces a CD8 response, is CD4 specific. This finding is consistent with its ability to boost the T-dependent antibody response.
These results suggest that the final boost of a gene-based vaccine with adjuvanted protein can lead to a CD4-enhanced response and diminish the CD8 response, although the antibody responses in many instances can be comparable. In contrast, DNA priming followed by rAd boosting causes stronger antigen-specific CD8 expansion. Though the mechanism of this selective activation is not completely understood, this effect is most likely due to the ability of rAd to synthesize the gene product within dendritic cells that promote better class I antigen presentation. In the case of the inactivated virus, such a response would require uptake of preformed protein antigens. Cross-presentation would therefore be required to induce a CD8 response, which is less efficient. These responses are typically Th1 responses, based on the isotypes of the antibodies and the pattern of cytokine secretion, and we have not observed changes in isotype ratios that indicate a shift to a Th2 response with any of the alternative immunizations.
The ability to stimulate the CD4 responses may be desirable if the immune response is largely dependent on neutralizing antibodies; however, in the case of SARS, several S glycoproteins have been identified that are resistant to neutralization. In some instances, it appears that these S glycoproteins either emerged more recently or have been derived from palm civet viruses. The S glycoprotein recognizes a cellular receptor, the human ACE-2 protein (35). The region sensitive to neutralization maps to the receptor binding domain (36, 56, 73). Recent data suggest that the antibody-resistant strains preferentially recognize the civet ACE-2 and may not have adapted as effectively as the isolates that were identified during the outbreaks in late 2003 and 2004 (36). The ability to induce a strong humoral response would be desirable if it is possible to generate antibodies to these new strains; however, it is not possible to elicit such antibodies using homologous immunization in animals with this same strain. Therefore, it would appear desirable presently to elicit cellular immunity by vaccination. Whether there are alternative means to combine the protein with different Toll receptor agonists, including novel CpGs or small molecule Toll receptor agonists such as imiquimod or resiquimod (6, 22, 43, 49, 62), is yet unknown but would be highly desirable. Though the coupling of CpGs directly to inactivated virus or proteins might enhance cellular immunity similar to gene-based vaccination, the present data suggest that the simple addition of the CpG to the adjuvant does not provide the type of cross-priming in a murine model that would be desirable for improvement of CD8 responses. In this study, inactivated virus rather than purified S protein was used as an immunogen. Though inactivated virus contains additional virus proteins and contains more epitopes than purified S protein, the inactivated virus was studied here for two reasons. First, the inactivated viral particles contain native SARS S protein, the most relevant antigenic structure with respect to neutralizing antibodies. Previous studies have shown that this antigen is capable of inducing such neutralizing antibody responses (13, 23, 48, 59, 69, 75), and the structure found on the virion presents the relevant native conformation. Second, similar vaccines are being tested or are under development for human clinical studies (2, 39). Therefore, the ability to perform a prime-boost immunization with clinically relevant products and to analyze their immunogenicity affords an opportunity to examine synergy between these different vaccine candidates that have clinical implications. The neutralization of the prototypic human SARS coronavirus is encouraging, and the neutralization titer has also correlated with ELISA titers for the Urbani strain (73, 75). It may be tempting to pursue a vaccine strategy based on antibody neutralization, but it is important to recognize that vaccines for animal coronaviruses which rely on humoral immunity have not proven efficacious (16, 24, 64). Current animal models of SARS infection that faithfully replicate human disease do not exist. Moreover, it is not possible to propagate viruses which preferentially utilize the palm civet ACE-2 receptor that are insensitive to antibody neutralization (36, 73). It is presently not possible to evaluate relative vaccine efficacy; however, a variety of novel approaches, including adaptation of virus to different species, the development of transgenic animals expressing the human ACE-2 receptor, and the use of aged animals in challenge models, may assist in this effort in the future. Further analysis of vaccine candidates with alternative immunologic profiles in relevant animal models will assist in the selection of vaccines that will be most appropriate for development in humans.

ACKNOWLEDGMENTS
We thank Cheng Cheng and James Lee for assistance in the laboratory,
Ati Tislerics for assistance with manuscript preparation, Toni
Garrison and Brenda Hartman for figure preparation, and members
of the Nabel lab for helpful discussions and advice.
This research was supported in part by the Intramural Research Program of the U.S. National Institutes of Health, Vaccine Research Center, NIAID, and by the Chiron Corporation with support from the 6th Framework Program of the European Commission (FP6-511065).

FOOTNOTES
* Corresponding author. Mailing address: Vaccine Research Center, NIAID, NIH, Bldg. 40, Room 4502, MSC-3005, 40 Convent Drive, Bethesda, MD 20892-3005. Phone: (301) 496-1852. Fax: (301) 480-0274. E-mail:
gnabel{at}nih.gov.


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Journal of Virology, November 2005, p. 13915-13923, Vol. 79, No. 22
0022-538X/05/$08.00+0 doi:10.1128/JVI.79.22.13915-13923.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
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