Abstract
A recombinant vector vaccine uses an attenuated virus, bacterium, or parasite as the carrier to express a heterologous antigen(s). Many recombinant vaccine vectors and related vaccines have been developed and extensively investigated. To compare and better understand recombinant vectors and vaccines, we have generated Vaxvec (http://www.violinet.org/vaxvec), the first web-based database that stores various recombinant vaccine vectors and those experimentally verified vaccines that use these vectors. Vaxvec has now included 59 vaccine vectors that have been used in 196 recombinant vector vaccines against 66 pathogens and cancers. These vectors are classified to 41 viral vectors, 15 bacterial vectors, 1 parasitic vector, and 1 fungal vector. The most commonly used viral vaccine vectors are double-stranded DNA viruses, including herpesviruses, adenoviruses, and poxviruses. For example, Vaxvec includes 63 poxvirus-based recombinant vaccines for over 20 pathogens and cancers. Vaxvec collects 30 recombinant vector influenza vaccines that use 17 recombinant vectors and were experimentally tested in 7 animal models. In addition, over 60 protective antigens used in recombinant vector vaccines are annotated and analyzed. User-friendly web-interfaces are available for querying various data in Vaxvec. To support data exchange, the information of vaccine vectors, vaccines, and related information is stored in the Vaccine Ontology (VO). Vaxvec is a timely and vital source of vaccine vector database and facilitates efficient vaccine vector research and development.
Keywords: vaccine, recombinant vector vaccine, recombinant vaccine vector, database, Vaxvec, bioinformatics
1. Introduction
A recombinant vector vaccine is a vaccine that uses a live attenuated microbe, such as a bacterium, virus or parasite, as the vaccine vector to express a heterologous antigen(s). The first experimentally verified recombinant vector vaccine is a Vaccinia virus recombinant that expresses hepatitis B surface protein (HBsAg), which was shown to induce immunity sufficient to protect against the host chimpanzees against virulent hepatitis B viral infection [1, 2]. Since the report of the first successful recombinant vector vaccines, numerous recombinant vector vaccines and related vaccine vectors have been reported in the areas of veterinary and human vaccine research and development. Recombinant vector vaccines have been developed to treat various infectious diseases and cancers [3]. Currently, more than 10 viral vector veterinary vaccines have been licensed for commercial use [4, 5]. For example, viral vector vaccines using fowl poxvirus and herpesvirus of turkey as vectors and expressing infectious laryngotracheitis virus antigens are commercially available for poultry usage in the USA [5]. Three live bacterial vaccines have been available commercially in the world: Salmonella enterica serovar Typhi Ty21a, Vibrio cholerae CVD 103-HgR, and Mycobacterium bovis strain Bacillus Calmette–Guérin (BCG) [6]. The BCG strain has been used as a human vaccine against tuberculosis. However, with the possible exception of BCG, there is still no licensed recombinant vector vaccine or recombinant vaccine vector for human use [4].
Different types of recombinant vaccine vectors and their associated vaccines exist, and they may function with different mechanisms. Usually, vaccine vectors are bacterial or virus vectors. However, parasitic and fungal vaccine vectors also exist. Recombinant vector vaccines closely mimic a natural infection and therefore are able to stimulate robust and long-term immune responses in vivo. However, biased immune responses may be stimulated by different vectors. For example, the modified vaccinia virus Ankara (MVA) and the modified Copenhagen strain NYVAC are both poxvirus vectors. However, MVA triggers more CD8+ T cells while NYVAC favors preferentially specific CD4+ T cells [7]. The safety profiles of different vectors also differ. With the vast amounts of data related to recombinant vector vaccines published, a comparative and systematic study is required for better understanding the mechanisms of recombinant vaccine vectors and vaccines using these vectors.
VIOLIN (http://www.violinet.org) is the first web-based comprehensive vaccine database and analysis system that has included over 3,250 vaccines for over 200 infectious diseases and many non-infectious diseases (e.g., cancers and arthritis) [8, 9]. Each of the curated vaccines has been reported to induce significant protection against a disease in at least a laboratory animal model. Many of the vaccines in VIOLIN are verified recombinant vector vaccines. However, the general VIOLIN database does not include specific information about individual recombinant vaccine vectors and how these vectors are used in different vaccines.
To address the many needs related to the recombinant vector vaccines, we have developed Vaxvec (http://www.violinet.org/vaxvec), a web-based vaccine vector and vaccine database and analysis program. As a relatively independent program under the umbrella of the VIOLIN system, Vaxvec includes the information for a large set of vaccine vectors, vaccines using these vectors, and protective antigens used in these recombinant vector vaccines. The analysis of these data enhances our understanding on these topics.
2. Methods
2.1. Vaxvec system and database design
Developed with classical three-tier architecture, Vaxvec was built on two HP ProLiant DL380 G6 servers running the Redhat Enterprise Linux operating system. A Vaxvec query is submitted from the Vaxvec web user interface (presentation tier). The query is then processed using PHP/SQL (middle tier, application server) against a MySQL relational database (data tier, database server). Query results are displayed in an accessible web browser. The two HP servers regularly back up each other’s data.
Figure 1 illustrates the workflow of the Vaxvec/VIOLIN database design and implementation. For each recombinant vaccine vector, the database contains the following information: the vector name, Vaccine Ontology ID, preparation, vector function, advantage, disadvantage, storage, safety, stability, and reference. The information for each recombinant vector vaccine includes the general vaccine information, including name, antigen name, vaccine vector, vaccine status (i.e. licensed, clinical trial, or research), host animal model, vaccination route, protection protocol, and efficacy. The information of a gene encoding a protective antigen that was inserted into the vaccine vector was added to the database by an internal script to retrieve the information from NCBI using the NCBI Gene, Protein, or Nucleotide ID. The antigen was also labeled as a “protective antigen” and linked to a corresponding recombinant vector vaccine. For each record, comprehensive citation information is included. The citation information was automatically retrieved from PubMed [10] through an internal script using the PubMed ID (i.e., PMID). All vaccine vectors and vaccines are assigned with Vaccine Ontology (VO) IDs.
Figure 1. Vaxvec/VIOLIN workflow and system design.
Experimentally verified data of recombinant vaccine vectors, recombinant vector vaccines, protective antigens, is manually annotated from peer-reviewed PubMed publications and stored into the Vaxvec and VIOLIN databases. Vaccine Ontology (VO) IDs assigned for vaccines, vectors, and antigens were used for data sharing and data integration in Vaxvec. An internal program was generated to extract comprehensive citation information using a PubMed ID (PMID) of a referenced paper. The NCBI IDs for the genes, proteins, or nucleotides of protective antigens are identified and used by an internal script to retrieve detailed information about individual protective antigens. DNA and protein sequences were used for COG and Vaxign analyses. Customized BLAST analysis was also generated.
2.2. Semi-automatic annotation of vaccine information
To efficiently annotate, store, and review vaccine vectors and related vaccines, a semiautomatic Vaxvec annotation system was developed based on an in-house web-based literature mining and curation system called Limix [9, 11, 12]. This system includes two programs: vaccine and protective antigen data curation program, and a vaccine vector data curation program. Using a user-friendly web interface, a data curator can search peer-reviewed articles, type and edit text, and submit the annotated text to the backend database. Only after the annotated text is reviewed and approved by a domain expert, the annotated data can be available online for public searching and viewing. All annotation records in the Vaxvec annotation system are stored in the database and can be traced for checking. The two features mentioned in the above section, i.e., automatically retrieving gene or reference information using an NCBI Gene ID (or other NCBI IDs) or a PubMed PMID ID, are also integrated in the web-based data curation system.
2.3. Generation of the taxonomy tree of recombinant vaccine vectors
To classify different microbes used as vaccine vectors, a taxonomy tree of these microbes were generated. To generate such a tree, the taxonomy IDs of different microbe organisms acting as recombinant vectors were first extracted. The OntoFox tool [13] was used to extract the hierarchy of these organisms based on the NCBITaxon ontology [14]. The OntoFox option of “Include Computed Intermediates” was applied to include only the closest ancestors of more than one low level taxonomy terms. The Protégé OWL editor [15] was used to display the results.
2.4. Analysis of vaccine vectors and corresponding recombinant vector vaccines
All vaccine vectors and recombinant vector vaccines were analyzed using the frontend database search or backend database queries using MySQL scripts. The direct database queries using MySQL scripts were sometimes performed for prompt categorization and comparison of the data stored in the database.
2.5. Analysis of protective antigens utilized in recombinant vector vaccines
For each protective antigen used in recombinant vector vaccine development, the Vaxign software program was used for analysis of subcellular localization and adhesin probability [16, 17]. All protective antigens used in recombinant vector vaccines were analyzed using the Clusters of Orthologous Groups (COG) for antigen clustering analysis. A Vaxvec BLAST search program was developed for sequence similarity search. This program is accompanied with our customized BLAST library that contains the protective antigens used in the development of recombinant vector vaccines.
2.6. Vaxvec data query and result display online
The Vaxvec web interface includes three types of query: (1) query for vaccine vectors, (2) query for recombinant vector vaccines, and (3) query for protective antigens used in the recombinant vector vaccines. The three types of queries can communicate with each other. A vaccine vector page includes links to all vaccines that use the vector. A web page of a recombinant vector vaccine also includes the link to the vaccine vector page and the information of used protective antigen(s).
2.7. Vaxvec data exchange, transfer, and download
The Vaccine Ontology (VO) is a community-based biomedical ontology in the area of vaccines and vaccination [18–20]. In this study, VO is used for ontologically storing the itemized information of vaccine vectors, recombinant vector vaccines, and corresponding protective antigens.
3. Results
3.1. Vaxvec system design and statistics
The Vaxvec system is designed to focus on three aspects: recombinant vaccine vectors, recombinant vector vaccines, and protective antigens used in recombinant vector vaccines. The recombinant vaccine vectors annotated in Vaxvec have been used in at least one recombinant vector vaccine. Many recombinant vector vaccine candidates are not associated with positively reported vaccine efficacy. We have restricted our inclusion of recombinant vector vaccines to those that have been experimentally verified to be effective in at least one laboratory animal model [8]. Although the information about failed vaccines and vectors may be informative, such information is often difficult to interpret and analyze. Our restriction on experimentally verified vaccines and vectors allows us to focus our time on identifying enriched features useful for future vaccine development. The genes expressed in recombinant vector vaccines encode protective antigens. The annotation and analysis of these protective antigens provide a basis of possible rational vaccine design and enhance our understanding of protective vaccine immunity.
As of April 2, 2015, Vaxvec has included 59 recombinant vaccine vectors (Table 1). These vectors have been used by 196 recombinant vector vaccines (Table 2). In total 67 protective antigens have been found to be used in development of these recombinant vector vaccines. Frequently, one antigen was used in different recombinant vector vaccine, and more than one antigen might be used for a single recombinant vector vaccine. These vaccines are developed against cancer and the infections of 63 pathogens (Table 2). Below we provide more specific description and analysis on these records in Vaxvec.
Table 1.
Selected vaccine vectors and their associated vaccines in Vaxvec
| vector name | NCBI Taxonomy ID |
VO ID | Vaxvec ID | No. of Vaccines |
|---|---|---|---|---|
| Viral vaccine vectors (in total 41), selected: | ||||
| ALVAC vv | - | VO_0001128 | 77 | 17 |
| Fowlpox virus vv | - | VO_0001040 | 21 | 14 |
| NYVAC vv | 10249 | VO_0001093 | 37 | 9 |
| Baculovirus vv | 10469 | VO_0001084 | 19 | 7 |
| complex adenovirus vv | - | VO_0001086 | 36 | 7 |
| ORF virus vv | 10258 | VO_0001108 | 68 | 6 |
| herpesvirus of turkey vv | 37108 | VO_0001067 | 43 | 6 |
| Vesicular stomatitis virus vv | 11276 | VO_0001025 | 11 | 5 |
| Newcastle disease virus vv | 11176 | VO_0001060 | 44 | 4 |
| vaccinia virus Tian Tan (MVTT) vv | 10253 | VO_0001109 | 69 | 4 |
| Vaccinia vv | 10245 | VO_0000600 | 32 | 4 |
| Raccoon poxvirus vv | 10256 | VO_0001048 | 67 | 4 |
| Bacterial vaccine vectors (in total 15), selected: | ||||
| BCG vv | 33892 | VO_0001023 | 12 | 8 |
| Salmonella typhimurium SL3261 vv | - | VO_0001031 | 17 | 6 |
| Vibrio cholerae vv | 666 | VO_0001044 | 46 | 4 |
| Brucella abortus RB51 vv | 1198700 | VO_0000020 | 13 | 3 |
| Fungal vaccine vectors (in total 1): | ||||
| Saccharomyces cerevisiae vv | 4932 | VO_0001122 | 76 | 2 |
| Parasitic vaccine vectors (in total 1): | ||||
| Leishmania tarentolae vv | 5689 | VO_0001028 | 29 | 3 |
Note: *: vv represents “vaccine vector”. The complete list of recombinant vaccine vectors is available here: http://www.violinet.org/vaxvec/stat.php?order_by=num_vaccine&order=DESC.
Table 2.
Recombinant vector vaccines annotated in Vaxvec
| Pathogen or disease | No. of pathogen species or diseases |
No. of recombinant vector vaccines |
|
|---|---|---|---|
| Viruses | 40 (total) | 136 (total) | |
| Virus examples: | |||
| Influenza virus | 1 | 34 | |
| HIV | 1 | 12 | |
| Ebola virus | 1 | 10 | |
| Bacteria | 17 (total) | 33 (total) | |
| Bacteria examples: | |||
| M. tuberculosis | 1 | 4 | |
| A. pleuropneumoniae | 1 | 4 | |
| B. pertussis | 1 | 3 | |
| Parasites | 8 (total) | 18 (total) | |
| Parasite examples: | |||
| Plasmodium spp. | 1 | 7 | |
| Leishmania major | 1 | 2 | |
| Cancer | 1 | 8 | |
| Total | 66 | 196 (total) | |
3.2. Analysis of Vaxvec vaccine vectors
To classify the relations among different recombinant vaccine vectors, a taxonomy tree of these vectors were generated (Figure 2). The resulting tree shows that the reported recombinant vectors cover various types of microbe organisms including bacteria, viruses, parasites, and fungi.
Figure 2. The taxonomic tree of microbes used for generation of recombinant vaccine vectors.
(A) Overall taxonomic tree with details in Bacteria and Eukaryota. (B) Viruses taxonomic tree with details in Retroviruses and ssRNA viruses. (C) Taxonomic tree of dsDNA viruses. Three families of dsDNA viruses commonly used as vaccine vectors are herpesviruses (Herpesviridae), adenoviruses (Adenoviridae), and poxviruses (Poxviridae).
Recombinant viral vectors have been intensively studied [21]. Vaxvec includes 41 recombinant viral vectors. The most commonly used viral vectors include dsDNA vaccines, including adenoviruses, herpes viruses, and poxviruses. Adenoviruses are able to infect a broad range of hosts, grow in high titers in cell culture, and induce high levels of transgene production without risking potential integration of viral genes into the host genome [22]. Therefore, adenoviruses are safe to use and inexpensive to manufacture. Inherently adenovirus vectors can stimulate multi-faceted innate immune responses through Toll-like receptor (TLR)-dependent and TLR-independent pathways [22]. Via an adjuvant-like effect, the adenovirus vectors promote the generation of humoral and cellmediated immune responses against vaccine antigens. Herpesviruses are important mammalian pathogens that cause acute and chronic infections and can persist in the hosts for life. Example herpes virus vaccine vectors are human simplex virus-1 (HSV-1) [23] and cytomegalovirus (CMV) [24, 25].
The Vaxvec database includes 63 poxvirus vector vaccines (Table 3). Poxviruses are double-stranded DNA viruses. The poxvirus genome is very large and allows the insertion of more than 10 kb of foreign DNA without reducing viral infectivity and other essential functions [26]. Unlike other DNA viruses, poxviruses possess their own transcriptional machinery, enabling sufficient cytoplasmic self-replication. This feature is advantageous since it prevents potential gene mutation during the integration of viral genome into the host genomic DNA. Furthermore, the poxvirus vectors offer high level expression of foreign genes and thus result in robust cellular immunity to the gene products [22]. The three most commonly used poxvirus vector vaccines include the attenuated modified vaccinia virus Ankara (MVA), ALVAC [27], and NYVAC [28]. Different fowlpox virus vaccine vectors have also been well studied [28].
Table 3.
Poxvirus vector vaccines collected in Vaxvec
| # | Pathogen | Vaccine name | Antigen | Animal (efficacy) | Refs (PMID) |
|---|---|---|---|---|---|
| ALVAC vaccine vector | |||||
| 1 | African horse sickness virus | ALVAC-AHSV | VP2 and VP5 | horses (++) | 19490959 |
| 2 | Bluetongue virus | ALVAC-BTV-VP2/VP5 | VP2 and VP5 | sheep (++) | 17059856 |
| Cancer | ALVAC-P53 | p53 | mice (+) | 8643480 | |
| 3 | Canine distemper virus | ALVAC-CDV-H/F | H and F | ferrets (+) | 10864646 |
| 4 | Equine influenza virus | ALVAC-EIV | HA | horses (+) | 16621023 |
| 5 | Feline leukemia virus | ALVAC-FL-env/gag | env and gag | cats (++) | 8383248 |
| 6 | HIV | ALVAC-HIV-2 | env, gag and pol | monkey (+) | 11413371 |
| 7 | Influenza virus (H5N1) | ALVAC-AI-H5 | HA | pigs (+) | 19428840 |
| 8 | JEV | ALVAC-JEV | prM, E, and NS1 | rhesus monkeys (++) | 10466959 |
| 9 | Measles virus | ALVAC-MV-HA/F | HA and F glycoproteins | dogs (+) | 1736535 |
| 10 | Nipah virus | ALVAC-NiV-G | NiV glycoprotein | pigs (++) | 16873250 |
| 11 | Nipah virus | ALVAC-NiV-F | NiV fusion protein | pigs (+) | 16873250 |
| 12 | |||||
| 13 | West Nile virus | ALVAC-WNV-PrM/E | PrM and E | dogs & cats (+) | 15893618 |
| 14 | West Nile virus | ALVAC-WNV-prM/E | prM and E | horses (++) | 17687109 |
| 15 | Rabbit hemorrhagic disease virus | ALVAC-RHDV (vCP309) | capsid protein | rabbits (++) | 9041672 |
| 16 | Rabies virus | ALVAC-RV | glycoprotein G | cats (++) | 23059358 |
| Capripoxvirus vaccine vector | |||||
| 17 | Bluetongue virus | rCPV-BTV-Cpox | VP2, VP7, NS1& NS3 | goats (+) | 17669563 |
| 18 | Peste des petits ruminants | rCPV-PPR | glycoproteins H or F | sheep (++) | 24837763 |
| 19 | Peste des petits ruminants | rCPV-PPRVH | H and F | goats & sheep (++) | 20471441 |
| Fowlpox virus vaccine vector | |||||
| 20 | Classical swine fever virus | rFPV-CSFV-E0 | E0 | mice and piglets (+) | 18320824 |
| 21 | Hemorrhagic enteritis virus | rFPV- HEV | hexon of HEV | turkeys (++) | 10396636 |
| 22 | IBDV | FP-IBDV-VP2 | VP2 | chickens (+) | 23644721 |
| 23 | IBDV | rFPV-IBDV-VP2 | VP2 | chickens (+) | 10753704 |
| 24 | IBDV | rFPV-IBDV-VP 2.4.3 | VP 2, VP4 and VP3 | chickens (+) | 8394069 |
| 25 | Infectious laryngotracheitis virus | FPV-LT vaccine | gD and gI | chickens (+) | 22845318 |
| 26 | Infectious laryngotracheitis virus | rFPV-ILTV | gD and gI | chickens (+) | 21313847 |
| 27 | Influenza virus (H5N1) | vFP89-H5 | HA | ducks (++) | 23845804 |
| 28 | Influenza virus (H5N1) | rFPV-AI-H5A-IL6 | HA | cherry valley ducks (+) | 22902682 |
| 29 | Influenza virus (H5N8) | vFP89-HA | HA | chickens (++) | 20521642 |
| 30 | Influenza virus (H5N1) | rFPV-H5AI-L2 | HA | chickens (++) | 20077933 |
| 31 | Influenza virus (H5N1) | Trovac-AI-H5 | HA | pigs (+) | 19428840 |
| 32 | Newcastle disease virus | rFPV-NDV-H/F | HA and NA | chickens (++) | 2167557 |
| 33 | Plasmodium berghei | rFP9-Malaria-CSP | CSP | mice (+) | 17908809 |
| 34 | Canine distemper virus | rFP-RPV-H/F | H and F | ferrets (+) | 9185963 |
| Modified Vaccinia Ankara (MVA) virus vaccine vector | |||||
| 35 | African horse sickness virus | rMVA- AHS-VP2 | VP2 | mice (++) | 21298069 |
| 36 | CCHFV | rMVA-CCHF | Gn and Gc | mice (++) | 24621656 |
| MVTT vaccine vector | |||||
| 37 | Cancer | rMVTT- HPV16-E6/E7 | mutated HPV16 E6 and E7 | mice (+) | 12665900 |
| 38 | CCHFV | rMVA-CCHF | envelope glycoprotein | mice (+) | 24621656 |
| 39 | Chikungunya virus | MVA-CHIKV | C, E3, E2, 6K, and E1 | mice (++) | 24403588 |
| 40 | HIV | rMVTT-SIV-gpe | Gag, Pol, and Env | rhesus monkeys (+) | 23487457 |
| 41 | HIV | rMVA-SIV-CD40L | Env | rhesus macaques (+) | 24920805 |
| 42 | Influenza virus (H5N1) | rMVTT-HA-QH(H5N1) | HA | mice (++) | 24358269 |
| 43 | Plasmodium vivax | MVA-PvTRAP | TRAP | mice (+) | 24379295 |
| 44 | Rift Valley fever virus | rMVA-GnGc | Gn and Gc | lambs (+) | 24933081 |
| NYVAC | |||||
| 45 | Canine distemper virus | NYVAC- CDV-H/F | H and F | ferrets (+) | 10864646 |
| 46 | HIV-2 | NYVAC-HIV-2 | env and gag-pol | rhesus macaques (+) | 11101054 |
| 47 | Equine herpesvirus-1 | NYVAC-EHV-1-vP1014 | gene 64 | ponies (+) | 16269205 |
| 48 | HIV | NYVAC-SIV | gag, pol, and env | macaques (+) | 9557706 |
| 49 | JEV | NYVAC-JEV | prM, E, and NS1 | rhesus monkeys (++) | 10466959 |
| 50 | JEV | NYVAC-JEV-prM/E/NS1 | prM, E, and NS1 | pigs (+) | 1326813 |
| 51 | Plasmodium berghei | NYVAC-CSP | CSP | mice (+) | 8613376 |
| 52 | Plasmodium falciparum | NYVAC-Pf7 | 7 P. falciparum genes | humans (+) | 9607847 |
| 53 | Pseudorables virus | NYVAC-PRV-gII/ gp50 | gII and gp50 | pigs (+) | 8904669 |
| Other vaccinia virus vaccine vector | |||||
| 54 | Rinderpest virus | v2RVFH | H and F | cattle (++) | 11752138 |
| 55 | Influenza virus | dVV-HA5(H5N1) | HA | mice (++) | 19279103 |
| Raccoon poxvirus vaccine vector | |||||
| 56 | Influenza virus(H5N1) | RCN-HA (H5N1) | HA | mice (++) | 22921740 |
| 57 | Rabies | RCN-rabies-G | glycoprotein G | cats (+) | 15203914 |
| 58 | Yersinia pestis | RCN- F1-V | F1 and V | dogs (+) | 20158332 |
| 59 | Yersinia pestis | RCN-IRES-tPA-YpF1 | F1 protein | mice (+) | 12559803 |
| Swinepox virus vector | |||||
| 60 | Influenza virus (H1N1) | rSPV-HA1 | HA | pigs (++) | 22391400 |
| 61 | Influenza virus H1N1/H3N2 | rSPV/H3-2A-H1 | HA of H1N1 & H3N2 | pigs (++) | 23135159 |
| 62 | Porcine circovirus 2 | rSPV-PCV2-CAP | ORF2 | pigs (+) | 22884664 |
| 63 | Streptococcus suis | rSPV-MRP | truncated MRP | mice (+) | 22515033 |
Abbreviations: +: partial protection; ++: Complete protection. JEV: Japanese encephalitis virus. IBDV: Infectious bursal disease virus. CCHFV: Crimean-Congo Haemorrhagic Fever virus
Many other types of viruses, including retroviruses and ssRNA viruses, have also been used as recombinant vaccine vectors (Figure 2).
Vaxvec also collects 15 bacterial vaccine vectors, for example, Mycobacterium bovis vaccine strain BCG, Salmonella enterica strain SL3261 and Brucella abortus RB51 vaccine vectors (Table 1). The human tuberculosis BCG strain has been used as a vector for development of 8 vaccines against the infections of different pathogens including HIV [29], M. tuberculosis [30], Plasmodium spp. [31], Streptococcus pneumoniae [32], and Toxoplasma gondii [33]. Brucella abortus strain RB51 is a licensed live and attenuated cattle vaccine strain [34]. RB51 is able to stimulate strong CD4+ and CD8+ T-cell mediated immune responses [35]. Recombinant RB51 strains have been developed to overexpress Brucella antigens for enhancing its Brucella vaccine efficacy [36] or protective against heterogeneous Neospora caninum infections [37, 38].
The other types of vaccine vectors included in the Vaxvec database include one protozoan Leishmania tarentolae vaccine vector and one fungal Saccharomyces cerevisiae vaccine vector. The nonpathogenic lizard protozoan parasite L. tarentolae has been used as a vector for three vaccines against L. infantum infection [39], L. major infection [40], and HIV-1 infection [41]. The safe and stable S. cerevisiae yeast vaccine vector has been used to develop two oral vaccines against porcine pleuropneumonia [42, 43].
3.3. Analysis of recombinant vector vaccines in Vaxvec
As of April 2, 2015, Vaxvec includes 196 recombinant vaccines (Table 2). These include 135 vaccines for 40 viruses, 18 vaccines for parasitic pathogens, 22 for 11 Gram-negative bacteria, 11 for Gram-positive bacteria, and 9 cancer vaccines.
As a demonstration, 30 different recombinant vector influenza vaccines are listed in Table 4. The major influenza virus serotypes are H5N1 and H1N1. These 30 vaccines use 17 different recombinant vectors and have been tested in 7 different animal models (Table 4). These results demonstrate the diversity and intensity of recombinant vector influenza vaccine research.
Table 4.
Recombinant vector influenza vaccines annotated in Vaxvec
| # | Strain | Vaccine names | Vector names | Animal (Efficacy) |
References (PMID ID) |
|---|---|---|---|---|---|
| 1 | H1N1 | AcHERV-sH1N1-HA | Baculovirus vv | pigs & mice (++) | 24260476 |
| 2 | H5N1/H7N2/ H9N2 | BV-H5/H7/H9 | Baculovirus vv | ferrets (+) | 23618102 |
| 3 | H1N1 | BPZE1-FHA (H1N1) | B. pertussis BPZE vv | mice (+) | 21624415 |
| 4 | H3N2 | rPIV5-H3 (H3N2) | Bovine parainfluenza virus vv | mice (+) | 17254623 |
| 5 | H3N8 | ALVAC-EIV (H3N8) | Canarypox vv | ponies (+) | 16621023 |
| 6 | H5N1 | ALVAC-AI-H5 | Canarypox vv | pigs (+) | 19428840 |
| 7 | H5N1 | rDEV-re6 (H5) | Duck enteritis virus vv | broilers (+) | 23267833 |
| 8 | H5N1 | rDEV-us78HA | Duck enteritis virus vv | ducks (++) | 21865383 |
| 9 | H5N1 | vFP89-H5 | Fowlpox virus vv | ducks (++) | 23845804 |
| 10 | H5N1 | rFPV-AI-H5A-IL6 | Fowlpox virus vv | ducks (+) | 22902682 |
| 11 | H5N8 | vFP89-HA (H5N1) | Fowlpox virus vv | chickens (++) | 20521642 |
| 12 | H5N1 | vPF221 | Fowlpox virus vv | chickens (++) | 20521642 |
| 13 | H5N1 | rFPV-H5AI-L2 | Fowlpox virus vv | chickens (++) | 20077933 |
| 14 | H5N1 | Trovac-AI-H5 | Fowlpox virus vv | pigs (+) | 19428840 |
| 15 | H5N1 | rHVT-H5 | herpesvirus of turkey vv | chickens (+) | 23402113 |
| 16 | H5N1 | rHVT-H5 (H5N1) | herpesvirus of turkey vv | chickens (+) | 23402112 |
| 17 | H5N1 | rMVTT-HA-QH | MVTT vv | mice (++) | 24358269 |
| 18 | H5N1 | MVTT-HA-QH | MVTT vv | mice (++) | 24358269 |
| 19 | H6N2 | rNDV-H6 | Newcastle disease virus vv | chickens & turkeys (+) | 21793434 |
| 20 | H5N1 | rNDV-H5 | Newcastle disease virus vv | chickens (+) | 24320551 |
| 21 | H5N1 | rNDV-H5 (H5N1) | Newcastle disease virus vv | ducks (++) | 23402116 |
| 22 | H5N1 | rORFV-D1701-V- HAh5n (H5N1) | ORF virus (parapoxvirus) vv | mice (+) | 24376753 |
| 23 | H5N1 | PAV3-HA (H5N1) | Porcine adenovirus 3 vv* | mice (+) | 21179494 |
| 24 | H1N1 | PrV-HA (H1N1) | Pseudorabies virus vv | pigs (+) | 24431235 |
| 25 | H5N1 | RCN-HA (H5N1) | Raccoon poxvirus vv | mice (++) | 22921740 |
| 26 | H7N7 | RSV-H7 | Rous sarcoma virus vv | chickens (+) | 2839718 |
| 27 | H1N1 | rSPV-HA1 (H1N1) | Swinepox virus vv | pigs (++) | 22391400 |
| 28 | H1N1/H3N2 | rSPV/H3-2A-H1 | Swinepox virus vv | pigs (+) | 23135159 |
| 29 | H1N1 | rVEE-HA (H1N1) | VEE vv | mice (++) | 8648713 |
| 30 | H5N1 | VSV*ΔG-H5 (H5N1) | Vesicular stomatitis virus vv | chickens (++) | 24874923 |
Abbreviations: *: vv represents “vaccine vector”. +: partial protection. ++: Complete protection
3.4. Analysis of protective antigens used in generation of recombinant vector vaccines
In total 67 protective antigens have been found to be used in the recombinant vector vaccines in Vaxvec (Note: more protective antigens are being annotated). A customized BLAST sequence similarity search is also available on the Vaxvec website for users to search antigens that share sequence similarity with an input DNA or protein sequence.
Based on a Vaxign data analysis [16, 17], 13 (19%) out of the 67 antigens are likely adhesins (Table 5). Adhesins are critical for pathogens to invade host cells. An antibody that neutralizes an adhesin function would block the invasion of a pathogen. Therefore, adhesins are typically considered as good vaccine antigen candidates [44]. Our analysis found that these adhesin antigens have been used in development of different recombinant vector vaccines using various vaccine vectors (Table 5). A previous study found that approximately 40% of protective antigens in Gram-negative bacteria and 54% of protective antigens in Gram-positive bacteria are adhesins or likely adhesins [45]. Therefore, the percentage of adhesins used in recombinant vector vaccines appears to be much less than that the percentage of protective antigens in bacteria. The implication of such a phenomenon deserves further investigation.
Table 5.
Vaccine antigens in Vaxvec with predicted adhesin or adhesin characteristics
| # | Antigen | Pathogen | Vaxge n ID |
RefSeq / GenBank |
Location | Vaccine name |
Vector |
|---|---|---|---|---|---|---|---|
| 1 | S1 | Infectious bronchitis virus | 1673 | AAV52771.1 | Extracel. | Ac-CMV-S1 | baculovirus vv |
| 2 | gp70 | Feline leukemia virus FeLV | 1411 | AAB30310.1 | Unknown | ALVAC-FL-env/gag | ALVAC vv |
| 3 | E | Japanese encephalitis virus | 554 | AAK31640.1 | Unknown | NYVAC-JEV-prM/E/ NS1 | NYVAC vv |
| 4 | VP60 | Rabbit hemorrhagic disease virus | 1669 | CAA80883.1 | Extracel. | rORFV-RHDV-VP60 | ORF virus vv |
| 5 | E | West Nile virus | 590 | ABH06950.1 | Unknown | ALVAC-WNV-PrM/E | ALVAC vv |
| 6 | PspA | Streptococcus pneumoniae | 620 | YP_815641.1 | OM | pspA-rBCG | BCG vv |
| 7 | Ag85B | M. tuberculosis | 118 | NP_216402.1 | Periplasm | LT-BCG-Ag85B /Rv3425 | Lentivirus vv |
| 8 | GP | Zaire ebolavirus | 452 | NP_066246.1 | Extracel. | AdC7-ZGP | chimpanzee adenovirus vv |
| 9 | Ag85A | M. tuberculosis | 154 | NP_218321.1 | Periplasm | rBCG-Ag85A/ Ag85B | BCG vv |
| 10 | VP7 | Murine rotavirus | 676 | AAA50493.1 | Unknown | HSVT[VP7/6/2] | HSV-1 vv |
| 11 | VP2 | Infectious bursal disease virus | 1636 | AAP84370.1 | Unknown | rFPV-IBDV-VP2 | fowlpox vv |
| 12 | P97 | Mycoplasma hyopneumoniae | 1062 | YP_115696.1 | OM | rAd-P97c | porcine adenovirus 3 vv |
| 13 | VP60 | Rabbit hemorrhagic disease virus | 1669 | CAA80883.1 | Periplasm | RB51-SRS2 | RB51 vv |
Note: All antigens have a predicted adhesin probability > 0.51. Extracel.: Extracellular.
3.5. Vaxvec data query and display
The Vaxvec provides user-friendly web interfaces for users to query and analyze the data stored in the Vaxvec database. Specifically, Vaxvec include three query programs that query three different types of data: recombinant vectors, recombinant vector vaccines, and protective antigens used in recombinant vector vaccines. The results of these three Vaxvec query programs are interlinked as shown in the query example Figure 3. This query example starts with a query of the keyword term “BCG” (Figure 3A). The BCG vaccine vector has been used in nine vaccines (Figure 3B), including a malaria vaccine rBCGMSP1-15 [31] (Figure 3C). This malaria vaccine uses a Plasmodium yoelii protein merozoite surface protein 1 precursor (MSP1). The detailed information about the protein is available in another web page (Figure 3D). Therefore, this example demonstrates how the three key query features are interlinked. A user can also start by querying a specific recombinant vector vaccine or a protective antigen directly.
Figure 3. Example of Vaxvec queries for vaccine vector, vaccine, and protective antigen information.
(A) The vaccine vector name “BCG” is queried in Vaxvec. (B) Resulting vaccines in Vaxvec. (C) Detailed information for one recombinant vector vaccine rBCGMSP1-15. (D) The information for the gene (MSP1) used in the vaccine generation.
3.6. Vaxvec data sharing
The Vaccine Ontology (VO) is a community-based ontology that logically represents the terms of vaccines, vaccine components (including recombinant vaccine vectors), vaccination, vaccine-induced immune responses, and the relations among these terms [19, 20]. All the recombinant vectors, recombinant vector vaccines, and protective antigens used in these recombinant vector vaccines, and the relations among these terms, have been ontologically represented in VO. Figure 4 provides a demonstration of how VO represents a recombinant vaccine vector ‘canarypox vaccine vector’ (VO_0001043). Developed using the human- and computer-interpretable Web Ontology Language (OWL) format [46], these VO represented data can be retrieved and processed easily using software programs and applied for different usages.
Figure 4. VO representation of ‘canarypox vaccine vector’.
This is an example demonstration of how VO represents a recombinant vaccine vector. The figure was generated as a screenshot from the Ontobee [49] website (http://purl.obolibrary.org/obo/VO_0001043).
4. Discussion
To the best of our knowledge, Vaxvec is the first web-based, publically available database and analysis system that targets the curation and analysis of recombinant vaccine vectors, recombinant vector vaccines that use these vectors, and related protective antigens. The data contained in the Vaxvec database are all manually curated. Analysis of Vaxvec data uncovers important statistics and many enriched patterns from these experimentally verified recombinant vaccine vectors, recombinant vector vaccines, and protective antigens.
While we have tried our efforts to annotate as many recombinant vectors and associated vaccines as possible, it is most likely that we have missed many vectors and vaccines reported in the literature. However, our studies have already provided valuable insights about the important topic of recombinant vectors and recombinant vector vaccines. We intend to frequently update our database in the future. In addition to the manual curation method, we will also investigate how computational methods, such as ontology-based literature mining and meta-analysis [19, 47, 48], would improve the database annotations and updates.
The Vaxvec resource may be used for different applications. For example, the records of recombinant vectors and experimentally verified vaccines that use these vectors provide us a basis for designing our future recombinant vector vaccines. The enriched patterns of protective antigens used in these recombinant vector vaccines may also facilitate rational design of protective antigens to be used in recombinant vector vaccine development. In addition, the records stored in Vaxvec may be used to further our systematic understanding of the fundamental mechanisms of recombinant vaccine vectors and recombinant vector vaccines. Current Vaxvec research includes the information of host immune responses and vaccine efficacy against virulent pathogen challenge. However, we have not focused in this paper on the analysis of differential host immune responses for different vectors and vaccines, such as vaccine-induced antibody titers. We will later focus our efforts on the host-side responses to vectors and vaccine administrations. In the era of booming vaccine research, Vaxvec provides a timely repository and platform for advanced research and development of recombinant vaccine vectors and recombinant vector vaccines.
Acknowledgements
This research and the publication charge were supported by USA NIH National Institute of Allergy and Infectious Diseases (NIAID) grant R01AI081062. CM and RP are supported by the Undergraduate Research Opportunity Program (UROP) at the University of Michigan.
Footnotes
Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Conflict of Interest
The authors declare no conflict of interest.
References
- 1.Moss B, Smith GL, Gerin JL, Purcell RH. Live recombinant vaccinia virus protects chimpanzees against hepatitis B. Nature. 1984;311:67–69. doi: 10.1038/311067a0. [DOI] [PubMed] [Google Scholar]
- 2.Smith GL, Mackett M, Moss B. Infectious vaccinia virus recombinants that express hepatitis B virus surface antigen. Nature. 1983;302:490–495. doi: 10.1038/302490a0. [DOI] [PubMed] [Google Scholar]
- 3.Larocca C, Schlom J. Viral vector-based therapeutic cancer vaccines. Cancer J. 2011;17:359–371. doi: 10.1097/PPO.0b013e3182325e63. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Draper SJ, Heeney JL. Viruses as vaccine vectors for infectious diseases and cancer. Nat Rev Microbiol. 2010;8:62–73. doi: 10.1038/nrmicro2240. [DOI] [PubMed] [Google Scholar]
- 5.Vagnozzi A, Zavala G, Riblet SM, Mundt A, Garcia M. Protection induced by commercially available live-attenuated and recombinant viral vector vaccines against infectious laryngotracheitis virus in broiler chickens. Avian Pathol. 2012;41:21–31. doi: 10.1080/03079457.2011.631983. [DOI] [PubMed] [Google Scholar]
- 6.Kotton CN, Hohmann EL. Enteric pathogens as vaccine vectors for foreign antigen delivery. Infect Immun. 2004;72:5535–5547. doi: 10.1128/IAI.72.10.5535-5547.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Esteban M. Attenuated poxvirus vectors MVA and NYVAC as promising vaccine candidates against HIV/AIDS. Hum Vaccin. 2009;5:867–871. doi: 10.4161/hv.9693. [DOI] [PubMed] [Google Scholar]
- 8.He Y, Racz R, Sayers S, Lin Y, Todd T, Hur J, et al. Updates on the web-based VIOLIN vaccine database and analysis system. Nucleic acids research. 2014;42:D1124–D1132. doi: 10.1093/nar/gkt1133. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Xiang Z, Todd T, Ku KP, Kovacic BL, Larson CB, Chen F, et al. VIOLIN: vaccine investigation and online information network. Nucleic acids research. 2008;36:D923–D928. doi: 10.1093/nar/gkm1039. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.The US National Library of Medicine. [accessed on September 5, 2013];The PubMed database. http://www.ncbi.nlm.nih.gov/pubmed/
- 11.Xiang Z, Zheng W, He Y. BBP: Brucella genome annotation with literature mining and curation. BMC bioinformatics. 2006;7:347. doi: 10.1186/1471-2105-7-347. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Yang B, Sayers S, Xiang Z, He Y. Protegen: a web-based protective antigen database and analysis system. Nucleic acids research. 2011;39:D1073–D1078. doi: 10.1093/nar/gkq944. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Xiang Z, Courtot M, Brinkman RR, Ruttenberg A, He Y. OntoFox: web-based support for ontology reuse. BMC Res Notes. 2010;3(175):1–12. doi: 10.1186/1756-0500-3-175. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.OBO Foundry wiki. Introduction of the NCBITaxon ontology [Google Scholar]
- 15.The protege ontology editor: http://protege.stanford.edu/ [Google Scholar]
- 16.Xiang Z, He Y. Genome-wide prediction of vaccine targets for human herpes simplex viruses using Vaxign reverse vaccinology. BMC Bioinformatics. 2013;14(Suppl 4):S2. doi: 10.1186/1471-2105-14-S4-S2. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 17.He Y, Xiang Z, Mobley HL. Vaxign: the first web-based vaccine design program for reverse vaccinology and applications for vaccine development. J Biomed Biotechnol. 2010;2010:297505. doi: 10.1155/2010/297505. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 18.He Y, Cowell L, Diehl AD, Mobley HL, Peters B, Ruttenberg A, et al. VO: Vaccine Ontology. Nature Precedings; The 1st International Conference on Biomedical Ontology (ICBO-2009); Buffalo, NY, USA. 2009. http://precedings.nature.com/documents/3552/version/1. [Google Scholar]
- 19.Ozgur A, Xiang Z, Radev DR, He Y. Mining of vaccine-associated IFN-gamma gene interaction networks using the Vaccine Ontology. Journal of biomedical semantics. 2011;2(Suppl 2):S8. doi: 10.1186/2041-1480-2-S2-S8. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 20.Lin Y, He Y. Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses. Journal of biomedical semantics. 2012;3:17. doi: 10.1186/2041-1480-3-17. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 21.Small JC, Ertl HC. Viruses - from pathogens to vaccine carriers. Current opinion in virology. 2011;1:241–245. doi: 10.1016/j.coviro.2011.07.009. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 22.Choi Y, Chang J. Viral vectors for vaccine applications. Clin Exp Vaccine Res. 2013;2:97–105. doi: 10.7774/cevr.2013.2.2.97. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 23.Laimbacher AS, Esteban LE, Castello AA, Abdusetir Cerfoglio JC, Arguelles MH, Glikmann G, et al. HSV-1 amplicon vectors launch the production of heterologous rotavirus-like particles and induce rotavirus-specific immune responses in mice. Molecular therapy : the journal of the American Society of Gene Therapy. 2012;20:1810–1820. doi: 10.1038/mt.2012.108. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 24.Tsuda Y, Caposio P, Parkins CJ, Botto S, Messaoudi I, Cicin-Sain L, et al. A replicating cytomegalovirus-based vaccine encoding a single Ebola virus nucleoprotein CTL epitope confers protection against Ebola virus. PLoS Negl Trop Dis. 2011;5:e1275. doi: 10.1371/journal.pntd.0001275. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 25.Xu G, Smith T, Grey F, Hill AB. Cytomegalovirus-based cancer vaccines expressing TRP2 induce rejection of melanoma in mice. Biochemical and biophysical research communications. 2013;437:287–291. doi: 10.1016/j.bbrc.2013.06.068. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 26.Kim JW, Gulley JL. Poxviral vectors for cancer immunotherapy. Expert Opin Biol Ther. 2012;12:463–478. doi: 10.1517/14712598.2012.668516. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 27.Poulet H, Minke J, Pardo MC, Juillard V, Nordgren B, Audonnet JC. Development and registration of recombinant veterinary vaccines. The example of the canarypox vector platform. Vaccine. 2007;25:5606–5612. doi: 10.1016/j.vaccine.2006.11.066. [DOI] [PubMed] [Google Scholar]
- 28.Paoletti E. Applications of pox virus vectors to vaccination: an update. Proceedings of the National Academy of Sciences of the United States of America. 1996;93:11349–11353. doi: 10.1073/pnas.93.21.11349. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 29.Ami Y, Izumi Y, Matsuo K, Someya K, Kanekiyo M, Horibata S, et al. Priming-boosting vaccination with recombinant Mycobacterium bovis bacillus Calmette-Guerin and a nonreplicating vaccinia virus recombinant leads to long-lasting and effective immunity. J Virol. 2005;79:12871–12879. doi: 10.1128/JVI.79.20.12871-12879.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 30.Wang C, Fu R, Chen Z, Tan K, Chen L, Teng X, et al. Immunogenicity and protective efficacy of a novel recombinant BCG strain overexpressing antigens Ag85A and Ag85B. Clin Dev Immunol. 2012;2012:563838. doi: 10.1155/2012/563838. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 31.Matsumoto S, Yukitake H, Kanbara H, Yamada T. Recombinant Mycobacterium bovis bacillus Calmette-Guerin secreting merozoite surface protein 1 (MSP1) induces protection against rodent malaria parasite infection depending on MSP1-stimulated interferon gamma and parasite-specific antibodies. J Exp Med. 1998;188:845–854. doi: 10.1084/jem.188.5.845. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 32.Langermann S, Palaszynski SR, Burlein JE, Koenig S, Hanson MS, Briles DE, et al. Protective humoral response against pneumococcal infection in mice elicited by recombinant bacille Calmette-Guerin vaccines expressing pneumococcal surface protein A. J Exp Med. 1994;180:2277–2286. doi: 10.1084/jem.180.6.2277. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 33.Yu Q, Huang X, Gong P, Zhang Q, Li J, Zhang G, et al. Protective immunity induced by a recombinant BCG vaccine encoding the cyclophilin gene of Toxoplasma gondii. Vaccine. 2013;31:6065–6071. doi: 10.1016/j.vaccine.2013.10.015. [DOI] [PubMed] [Google Scholar]
- 34.Schurig GG, Roop RMd, Bagchi T, Boyle S, Buhrman D, Sriranganathan N. Biological properties of RB51; a stable rough strain of Brucella abortus. Vet Microbiol. 1991;28:171–188. doi: 10.1016/0378-1135(91)90091-s. [DOI] [PubMed] [Google Scholar]
- 35.He Y, Vemulapalli R, Zeytun A, Schurig GG. Induction of specific cytotoxic lymphocytes in mice vaccinated with Brucella abortus RB51. Infect Immun. 2001;69:5502–5508. doi: 10.1128/IAI.69.9.5502-5508.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 36.Vemulapalli R, He Y, Cravero S, Sriranganathan N, Boyle SM, Schurig GG. Overexpression of protective antigen as a novel approach to enhance vaccine efficacy of Brucella abortus strain RB51. Infect Immun. 2000;68:3286–3289. doi: 10.1128/iai.68.6.3286-3289.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 37.Ramamoorthy S, Sanakkayala N, Vemulapalli R, Jain N, Lindsay DS, Schurig GS, et al. Prevention of vertical transmission of Neospora caninum in C57BL/6 mice vaccinated with Brucella abortus strain RB51 expressing N. caninum protective antigens. International journal for parasitology. 2007;37:1531–1538. doi: 10.1016/j.ijpara.2007.04.021. [DOI] [PubMed] [Google Scholar]
- 38.Vemulapalli R, Sanakkayala N, Gulani J, Schurig GG, Boyle SM, Lindsay DS, et al. Reduced cerebral infection of Neospora caninum in BALB/c mice vaccinated with recombinant Brucella abortus RB51 strains expressing N. caninum SRS2 and GRA7 proteins. Veterinary parasitology. 2007;148:219–230. doi: 10.1016/j.vetpar.2007.06.029. [DOI] [PubMed] [Google Scholar]
- 39.Saljoughian N, Taheri T, Zahedifard F, Taslimi Y, Doustdari F, Bolhassani A, et al. Development of novel prime-boost strategies based on a tri-gene fusion recombinant L. tarentolae vaccine against experimental murine visceral leishmaniasis. PLoS Negl Trop Dis. 2013;7:e2174. doi: 10.1371/journal.pntd.0002174. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 40.Zahedifard F, Gholami E, Taheri T, Taslimi Y, Doustdari F, Seyed N, et al. Enhanced protective efficacy of nonpathogenic recombinant leishmania tarentolae expressing cysteine proteinases combined with a sand fly salivary antigen. PLoS Negl Trop Dis. 2014;8:e2751. doi: 10.1371/journal.pntd.0002751. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 41.Breton M, Zhao C, Ouellette M, Tremblay MJ, Papadopoulou B. A recombinant non-pathogenic Leishmania vaccine expressing human immunodeficiency virus 1 (HIV-1) Gag elicits cell-mediated immunity in mice and decreases HIV-1 replication in human tonsillar tissue following exposure to HIV-1 infection. J Gen Virol. 2007;88:217–225. doi: 10.1099/vir.0.81995-0. [DOI] [PubMed] [Google Scholar]
- 42.Shin MK, Kang ML, Jung MH, Cha SB, Lee WJ, Kim JM, et al. Induction of protective immune responses against challenge of Actinobacillus pleuropneumoniae by oral administration with Saccharomyces cerevisiae expressing Apx toxins in pigs. Vet Immunol Immunopathol. 2013;151:132–139. doi: 10.1016/j.vetimm.2012.11.003. [DOI] [PubMed] [Google Scholar]
- 43.Kim JM, Jung DI, Eom YJ, Park SM, Yoo HS, Jang YS, et al. Surface-displayed expression of a neutralizing epitope of ApxIIA exotoxin in Saccharomyces cerevisiae and oral administration of it for protective immune responses against challenge by Actinobacillus pleuropneumoniae. Biosci Biotechnol Biochem. 2010;74:1362–1367. doi: 10.1271/bbb.90941. [DOI] [PubMed] [Google Scholar]
- 44.He Y, Rappuoli R, De Groot AS, Chen RT. Emerging vaccine informatics. J Biomed Biotechnol. 2010;2010:218590. doi: 10.1155/2010/218590. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 45.He Y, Xiang Z. Bioinformatics analysis of bacterial protective antigens in manually curated Protegen database. Procedia in Vaccinology. 2012;6:3–9. [Google Scholar]
- 46.W3C. OWL 2 Web Ontology Language Quick Reference Guide (Second Edition) [Accessed on August 10, 2013];W3C Recommendation. 2012 Dec 11; 2012: http://www.w3.org/TR/owl2-quick-reference/. [Google Scholar]
- 47.Hur J, Xiang Z, Feldman EL, He Y. Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network. BMC Immunol. 2011;12:49. doi: 10.1186/1471-2172-12-49. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 48.He Y. Ontology-supported research on vaccine efficacy, safety and integrative biological networks. Expert Rev Vaccines. 2014;13:825–841. doi: 10.1586/14760584.2014.923762. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 49.Xiang Z, Mungall C, Ruttenberg A, He Y. Ontobee: A linked data server and browser for ontology terms. CEUR Workshop Proceedings; The 2nd International Conference on Biomedical Ontologies (ICBO); Buffalo, NY, USA. 2011. pp. 279–281. [ http://ceur-ws.org/Vol-833/paper48.pdf]. [Google Scholar]