The present invention relates to an attenuated coronavirus comprising a gene variant of replicase, which causes the virus to have reduced pathogenicity. The present invention also relates to the use of this coronavirus in a vaccine to prevent and / or treat a disease.
The avian infectious bronchitis virus (IBV), the etiologic agent of infectious bronchitis (IB), is a highly infectious and contagious pathogen in poultry that replicates mainly in the respiratory tract, but also in the epithelial cells of the intestine, kidney and oviduct. The IBV is a member of the Order Nidovirales, Family Coronaviridae, Subfamily Corona virinae and Genus Gammacoronavirus; genetically very similar coronaviruses cause disease in turkeys, guinea fowl and pheasants.
Clinical signs of BI include sneezing, tracheal rales, runny nose and wheezing. Meat-type birds reduce weight gain, while those that lay eggs lay fewer eggs and produce poor quality eggs. Respiratory infection predisposes chickens to secondary bacterial infections that can be fatal in chicks. The virus can also cause permanent damage to the oviduct, especially in chicks, leading to reduced egg production and quality; and kidney, sometimes leading to kidney disease that can be fatal.
It has been reported that the IBV is responsible for more economic losses for the poultry industry than any other infectious disease. Although live attenuated and inactivated vaccines are universally used to control IBV, the protection obtained by using the vaccination may be lost due to the breakage of the vaccine or the introduction of a new IBV serotype that is not related to the vaccine used, presenting a risk to the poultry industry.
In addition, there is a need in the industry to develop vaccines suitable for in ovo use in order to improve the efficiency and cost-effectiveness of vaccination programs. A major challenge associated with in ovo vaccination is that the virus must be able to replicate in the presence of antibodies of maternal origin against the virus, without being pathogenic for the embryo. Current IBV vaccines are derived after multiple passages in embryonated eggs, resulting in viruses with reduced pathogenicity for chickens, so that they can be used as live attenuated vaccines. However, these viruses almost always show increased virulence for embryos and, therefore, cannot be used for vaccination in eggs, as they cause reduced hatchability. In some cases, a 70% reduction in hatchability is observed.
Attenuation after multiple passage in embryonated eggs also suffers from other disadvantages. It is an empirical method, as the attenuation of the virus is random and varies every time the virus is transmitted; therefore, the passage of the same virus through a different series of eggs for the purpose of attenuation will lead to a different set of mutations that lead to attenuation. There are also efficiency problems associated with the process: some mutations will affect the replication of the virus and some of the mutations can make the virus much lessened. Mutations in the S gene can also occur, which can also affect immunogenicity, so that the desired immune response is affected and the potential vaccine may not protect against the necessary serotype. In addition, there are problems associated with reversing vaccine virulence and stability.
It is important that new and safer vaccines are developed to control By. Thus, there is a need for vaccines against IBV that are not associated with these problems, in particular vaccines that can be used for vaccination in eggs.
The present inventors used a reverse genetic approach to rationally mitigate IBV. This approach is much more controllable than random attenuation after several passages in embryonated eggs, because the position of each mutation is known and its effect on the virus, that is, the reason for the attenuation, can be derived.
Using their reverse genetic approach, the present inventors have identified several mutations that cause the virus to have reduced levels of pathogenicity. Pathogenicity levels can be reduced so that when the virus is administered to an embryonic egg, it is able to replicate without being pathogenic to the embryo. Such viruses may be suitable for vaccination in ova, which is a significant advantage and has an improvement over the attenuated IBV vaccines produced after multiple passage in embryonated eggs.
Thus, in a first aspect, the present invention provides a live attenuated coronavirus comprising a variant replicase gene encoding polyproteins that comprises a mutation in one or more non-structural proteins (nsp) -10, nsp-14, nsp-15 or nsp -16.
The variant replicase gene can encode a protein that comprises one or more mutations of amino acids selected from the list of:
- Pro to Leu at position 85 of SEQ ID NO: 6,
- Val to Leu at position 393 of SEQ ID NO: 7;
- Read to lie at position 183 of SEQ ID NO: 8;
- Val a Ile at position 209 of SEQ ID NO: 9.
The replicase gene can encode a protein comprising the Pro to Leu amino acid mutation at position 85 of SEQ ID NO: 6.
The replicase gene can encode a protein comprising the Val to Leu amino acid mutations at position 393 of SEQ ID NO: 7; Read Ile at position 183 of SEQ ID NO: 8; and Val to Ile at position 209 of SEQ ID NO: 9.
The replicase gene can encode a protein comprising the Pro to Leu amino acid mutations at position 85 of SEQ ID NO: 6; Val to Leu at position 393 of SEQ ID NO: 7; Read to lie at position 183 of SEQ ID NO: 8; and Val to Ile at position 209 of SEQ ID NO: 9.
The replicase gene can comprise one or more nucleotide substitutions selected from the list of:
Nucleotide position C to Tat 12137;
G to C at nucleotide position 18114;
T to A at nucleotide position 19047; and
G to A at nucleotide position 20139;
compared to the sequence shown as SEQ ID NO: 1.
Coronavirus can be an infectious bronchitis virus (IBV).
The coronavirus can be IBV M41.
The coronavirus may comprise an S protein at least part of which is of an IBV serotype other than M41.
For example, S1 1 subunit or the entire S protein can be from an IBV serotype other than M41.
The coronavirus according to the first aspect of the invention has reduced pathogenicity compared to a coronavirus that expresses a corresponding wild-type replicase, so that when the virus is administered to an embryonic egg, it is able to replicate without being pathogenic to the embryo.
In a second aspect, the present invention provides a variant replicase gene as defined in connection with the first aspect of the invention.
In a third aspect, the present invention provides a protein encoded by a coronavirus replicase variant gene according to the second aspect of the invention.
In a fourth aspect, the present invention provides a plasmid comprising a replicase gene according to the second aspect of the invention.
In a fifth aspect, the present invention provides a method for producing the coronavirus according to the first aspect of the invention, which comprises the following steps:
- (i) transfecting a plasmid according to the fourth aspect of the invention into a host cell;
- (ii) infecting the host cell with a recombinant virus comprising the genome of a coronavirus strain with a replicase gene;
- (iii) allowing homologous recombination to occur between the sequences of the replicase gene in the plasmid and the corresponding sequences in the genome of the recombinant virus to produce a modified replicase gene; and
- (iv) selection of recombinant viruses comprising the modified replicase gene.
The recombinant virus can be a vaccinia virus.
The method can also include the step:
- (v) recovering recombinant coronavirus comprising the modified DNA replicase gene of the recombinant virus from step (iv).
In a sixth aspect, the present invention provides a cell capable of producing a coronavirus according to the first aspect of the invention.
In a seventh aspect, the present invention provides a vaccine comprising a coronavirus according to the first aspect of the invention and a pharmaceutically acceptable carrier.
In an eighth aspect, the present invention provides a method for treating and / or preventing a disease in a subject comprising the step of administering a vaccine according to the seventh aspect of the invention to the subject.
Other aspects of the invention provide:
- the vaccine according to the seventh aspect of the invention for use in treating and / or preventing a disease in a subject.
- use of a coronavirus according to the first aspect of the invention in the manufacture of a vaccine for treating and / or preventing a disease in a subject.
The disease can be infectious bronchitis (IB).
The method of administration of the vaccine can be selected from the group consisting of; administration of eye drops, intranasal administration, drinking water, post-hatch injection and in ovo injection.
Vaccination can be done through vaccination in ova.
The present invention also provides a method for producing a vaccine according to the seventh aspect of the invention, which comprises the step of infecting a cell according to the sixth aspect of the invention with a coronavirus according to the first aspect of the invention.
The present invention provides a coronavirus comprising a replicase variant gene which, when expressed in the coronavirus, causes the virus to have reduced pathogenicity compared to a corresponding coronavirus comprising the wild-type replicase gene.
Gammacoronavirus is a genus of animal viruses belonging to the family Coronaviridae. Coronaviruses are viruses enveloped with a single-stranded positive RNA genome and helical symmetry.
The genomic size of coronaviruses ranges from approximately 27 to 32 kilobases, which is the longest size for any known RNA virus.
Coronaviruses mainly infect the upper respiratory or gastrointestinal tract of mammals and birds. Five to six different known strains of coronavirus currently infect humans. The most common human coronavirus, SARS-CoV, which causes severe acute respiratory syndrome (SARS), has a unique pathogenesis because it causes infections in the upper and lower respiratory tract and can also cause gastroenteritis. The Middle Eastern respiratory syndrome coronavirus (MERS-CoV) also causes an infection of the lower respiratory tract in humans. Coronaviruses are believed to cause a significant percentage of all common colds in human adults.
Coronaviruses also cause a range of diseases in livestock and domestic animals, some of which can be serious and pose a threat to the agricultural industry. The economically significant coronaviruses of farm animals include the infectious bronchitis virus (IBV), which mainly causes respiratory diseases in chickens and seriously affects the poultry industry worldwide; porcine coronavirus (transmissible gastroenteritis, TGE) and bovine coronavirus, which result in diarrhea in young animals. The feline coronavirus has two forms, the feline enteric coronavirus is a pathogen of less clinical significance, but the spontaneous mutation of this virus can result in feline infectious peritonitis (PIF), a disease associated with high mortality.
There are also two types of canine coronavirus (CCoV), one that causes mild gastrointestinal disease and the other that causes respiratory disease. The mouse hepatitis virus (MHV) is a coronavirus that causes an epidemic of murine disease with high mortality, especially among colonies of laboratory mice.
Coronaviruses are divided into four groups, as shown below:
- Canine coronavirus (CCoV)
- Feline coronavirus (FeCoV)
- Human coronavirus 229E (HCoV-229E)
- Porcine epidemic diarrhea virus (PEDV)
- Transmissible gastroenteritis virus (TGEV)
- Human Coronavirus NL63 (NL or New Haven)
- Bovine coronavirus (BCoV)
- Canine respiratory coronavirus (CRCoV) – common in Southeast Asia and Micronesia
- Human Coronavirus OC43 (HCoV-OC43)
- Mouse hepatitis virus (MHV)
- Swine hemagglutinating encephalomyelitis virus (HEV)
- Mouse coronavirus (Roy). Rat coronavirus is quite prevalent in eastern Australia, where, in March / April 2008, it was found among colonies of native and wild rodents.
- (No common name yet) (HCoV-HKU1)
- Severe Acute Respiratory Syndrome (SARS-CoV) Coronavirus
- Middle East Respiratory Syndrome Coronavirus (MERS-CoV)
- Infectious bronchitis virus (IBV)
- Turkey’s Coronavirus (Bluecomb disease virus)
- Pheasant Coronavirus
- Coronavirus of Guinea birds
- Bulb coronavirus (BuCoV)
- Thrush-coronavirus (ThCoV)
- Munia Coronavirus (MuCoV)
- Swine Coronavirus (PorCov) HKU15
The coronavirus replicase variant gene of the present invention can be derived from an alpha-coronavirus such as TGEV; a betacoronavirus such as MHV; or a gammacoronavirus like IBV.
As used herein, the term “derived from” means that the replicase gene comprises substantially the same nucleotide sequence as the wild-type replicase gene of the relevant coronavirus. For example, the variant replicase gene of the present invention can have up to 80%, 85%, 90%, 95%, 98% or 99% identity to the wild type replicase sequence. The coronavirus replicase variant gene encodes a protein that comprises a mutation in one or more non-structural proteins (nsp) -10, nsp-14, nsp-15 or nsp-16 when compared to the wild type sequence of the non-structural protein .
Avian infectious bronchitis (IB) is an acute and highly contagious respiratory disease in chickens that causes significant economic losses. The disease is characterized by respiratory signs, including wheezing, coughing, sneezing, tracheal rales and nasal discharge. In young chickens, severe respiratory disorders may occur. In layers, respiratory distress, nephritis, decreased egg production and loss of internal quality of eggs and eggshells are common.
In broilers, coughing and rattling are common clinical signs, spreading rapidly to all birds in the area. Morbidity is 100% in unvaccinated flocks. Mortality varies according to age, the strain of the virus and secondary infections, but can reach 60% in unvaccinated flocks.
The first IBV serotype to be identified was Massachusetts, but several serotypes are currently circulating in the United States, including Arkansas and Delaware, in addition to the originally identified type from Massachusetts.
The IBV Beaudette strain was derived from fallow at least 150 passages in chicken embryos. IBV Beaudette is no longer pathogenic to broiler chickens, but it quickly kills embryos.
H120 is a live attenuated serotype commercial vaccine strain from IBV Massachusetts, attenuated by approximately 120 passages in embryonated chicken eggs. H52 is another
Massachusetts vaccine, and represents a virus that has passed through and is slightly more pathogenic (passage 52) during the development of H120. Vaccines based on H120 are commonly used.
IB QX is a virulent field isolate from IBV. It is sometimes known as “Chinese QX”, as it was originally isolated after disease outbreaks in China’s Qingdao region in the mid-1990s. Since then, the virus has crept into Europe. Since 2004, serious problems in egg production have been identified with a very similar virus in parts of Western Europe, predominantly in the Netherlands, but also reported in Germany, France, Belgium, Denmark and the United Kingdom.
The virus isolated from Dutch cases was identified by the Deventer Dutch Research Institute as a new strain they called D388. The Chinese connection came from other tests that showed that the virus was 99% similar to the Chinese QX virus. An attenuated QX-like IBV vaccine strain was developed.
IBV is an enveloped virus that replicates in the cell cytoplasm and contains a positive, non-segmented, single-stranded RNA genome. IBV has an RNA genome of 27.6 kb and, like all coronaviruses, it contains the four structural proteins; peak glycoprotein (S), small membrane protein (E), integral membrane protein (M) and nucleocapsid protein (N) that interacts with genomic RNA.
The genome is organized as follows: 5’UTR – polymerase gene (replicase) – structural protein genes (S-E-M-N) – 3 ‘RTU; where RTUs are untranslated regions (each ≤500 nucleotides in the IBV).
The lipid envelope contains three membrane proteins: S, M and E. IBV S protein is a type I glycoprotein that oligomerizes in the endoplasmic reticulum and is mounted on the homotrimer inserted in the virion membrane via the transmembrane domain and is associated with non- covalent interactions with protein M. After incorporation into coronavirus particles, protein S is responsible for binding to the receptor of the target cell and fusion of viral and cellular membranes. Glycoprotein S consists of four domains: a signal sequence that is cleaved during synthesis; ectodomain, which is present outside the virion particle; the transmembrane region responsible for anchoring protein S in the lipid bilayer of the virion particle; and the cytoplasmic tail.
All coronaviruses also encode a set of accessory protein genes of unknown function that are not needed for in vitro replication, but can play a role in pathogenesis. IBV encodes two accessory genes, genes 3 and 5, which express two accessory proteins 3a, 3b and 5a, 5b, respectively.
The coronavirus variant replicase gene of the present invention can be derived from an IBV. For example, the IBV can be IBV Beaudette, H120, H52, IB QX, D388 or M41.
The IBV can be IBV M41. M41 is a prototype serotype from Massachusetts that was isolated in the USA in 1941. It is an isolate used in many laboratories around the world as a pathogenic stain in the laboratory and can be obtained from ATCC (VR-21 ™). Mitigated variants are also used by several vaccine producers as IBV vaccines against Massachusetts serotypes, causing problems in the field. The present inventors chose to use this strain because they had worked on this virus for many years and because the complete genome sequence of the virus is available. The M41 isolate, M41-CK, used by the present inventors was adapted to grow on primary chick kidney (CK) cells and, therefore, was considered recoverable as an infectious virus from a complete genome cDNA. It is representative of a pathogenic IBV and, therefore, can be analyzed for mutations that cause loss or reduction in pathogenicity.
The IBV M41-CK genome sequence is provided as SEQ ID NO: 1.
In addition to the structural and accessory genes, two-thirds of a coronavirus genome comprises the replicase gene (at the 5′ end of the genome), which is expressed as two polyproteins, pp1a and pp1ab, in which pp1ab is an extension product of pp1a as a result of a −1 ribosomal shift mechanism. The two polyproteins are cleaved by two types of virus-encoded proteinases usually resulting in 16 non-structural proteins (Nsp1-16); IBV lacks Nspl thereby encoding Nsp2-16.
Thus Gene 1 in IBV encodes 15 (16 in other coronaviruses) non-structural proteins (nsp2-16), which are associated with RNA replication and transcription.
The term ‘replicase protein’ is used herein to refer to the pp1a and pp1ab polyproteins or individual nsp subunits.
The term ‘replicase gene’ is used herein to refer to a nucleic acid sequence which encodes for replicase proteins.
A summary of the functions of coronavirus nsp proteins is provided in Table 1.
The variant replicase gene encoded by the coronavirus of the present invention comprises a mutation in one or more of the sections of sequence encoding nsp-10, nsp-14, nsp-15 or nsp-16.
Nsp10 has RNA-binding activity and appears to be involved in homo and/or heterotypic interactions within other nsps from the pp1a/pp1ab region. It adopts an α/β fold comprised of five α-helices, one 310-helix and three β-strands. Two zinc-binding sites have been identified that are formed by conserved cysteine residues and one histidine residue (Cys-74/Cys-77/His-83/Cys-90; Cys-117/Cys-120/Cys-128/Cys-130). The protein has been confirmed to bind single-stranded and double-stranded RNA and DNA without obvious specificity. Nsp-10 can be cross-linked with nsp-9, suggesting the existing of a complex network of protein-protein interactions involving nsp-7, -8, -9 and -10. In addition, nsp-10 is known to interact with nsp-14 and nsp-16.
Nsp-14 comprises a 3′-to-5′ exoribonuclease (ExoN) active domain in the amino-terminal region. SARS-CoV ExoN has been demonstrated to have metal ion-dependent 3′-to-5′ exoribonuclease activity that acts on both single-stranded and double-stranded RNA, but not on DNA. Nsp-14 has been shown to have proof-reading activity. This nsp has also been shown to have N7-methyltransferase (MT) activity in the carboxyl-terminal region.
Nsp-15 associated NendoU (nidoviral endoribonuclease, specific for U) RNase activity has been reported for a number of coronaviruses, including SARS-CoV, MHV and IBV. The activities were consistently reported to be significantly enhanced by Mn2+ions and there was little activity in the presence of Mg2+ and Ca2+. NendoU cleaves at the 3′ side of uridylate residues in both single-stranded and double-stranded RNA. The biologically relevant substrate(s) of coronavirus NendoUs remains to be identified.
Nsp-16 has been predicted to mediate ribose-2′-O-methyltransferase (2′-O-MTase) activity and reverse-genetics experiments have shown that the 2′-O-MTase domain is essential for viral RNA synthesis in HCoV-229E and SARS-CoV. The enzyme may be involved in the production of the cap 1 structures of coronavirus RNAs and it may also cooperate with NendoU and ExoN in other RNA processing pathways. 2′-O-MTase might also methylate specific RNAs to protect them from NendoU-mediated cleavage.
The genomic and protein sequences for nsp-10, -14, -15 and -16 are provided as SEQ ID NO: 2-5 and 6-9, respectively.
The live, attenuated coronavirus of the present invention comprises a variant replicase gene which causes the virus to have reduced pathogenicity compared to a coronavirus expressing the corresponding wild-type gene.
The term “attenuated” as used herein, refers to a virus that exhibits said reduced pathogenicity and may be classified as non-virulent. A live, attenuated virus is a weakened replicating virus still capable of stimulating an immune response and producing immunity but not causing the actual illness.
The term “pathogenicity” is used herein according to its normal meaning to refer to the potential of the virus to cause disease in a subject. Typically the pathogenicity of a coronavirus is determined by assaying disease associated symptoms, for example sneezing, snicking and reduction in tracheal ciliary activity.
The term “reduced pathogenicity” is used to describe that the level of pathogenicity of a coronavirus is decreased, lessened or diminished compared to a corresponding, wild-type coronavirus.
In one embodiment, the coronavirus of the present invention has a reduced pathogenicity compared to the parental M41-CK virus from which it was derived or a control coronavirus. The control coronavirus may be a coronavirus with a known pathogenicity, for example a coronavirus expressing the wild-type replicase protein.
The pathogenicity of a coronavirus may be assessed utilising methods well-known in the art. Typically, pathogenicity is assessed by assaying clinical symptoms in a subject challenged with the virus, for example a chicken.
As an illustration, the chicken may be challenged at 8-24 days old by nasal or ocular inoculation. Clinical symptoms, associated with IBV infection, may be assessed 3-10 days post-infection. Clinical symptoms commonly assessed to determine the pathogenicity of a coronavirus, for example an IBV, include gasping, coughing, sneezing, snicking, depression, ruffled feathers and loss of tracheal ciliary activity.
The variant replicase of the present invention, when expressed in a coronavirus, may cause a reduced level of clinical symptoms compared to a coronavirus expressing a wild-type replicase.
For example a coronavirus expressing the variant replicase may cause a number of snicks per bird per minute which is less than 90%, less than 80%, less than 70%, less than 60%, less than 50%, less than 40%, less than 30%, less than 20% or less than 10% of the number of snicks caused by a virus expressing the wild type replicase.
A coronavirus expressing a variant replicase according to the present invention may cause wheezing in less than 70%, less than 60%, less than 50%, less than 40%, less than 30%, less than 20% or less than 10% of the number of birds in a flock infected with the a virus expressing the wild type replicase.
A coronavirus expressing a variant replicase according to the present invention may result in tracheal ciliary activity which is at least 60%, at least 70%, at least 80%, at least 90% or at least 95% of the level of tracheal ciliary activity in uninfected birds.
A coronavirus expressing a variant replicase according to the present invention may cause clinical symptoms, as defined in Table 2, at a lower level than a coronavirus expressing the wild type replicase.
The variant replicase of the present invention, when expressed in a coronavirus, may cause the virus to replicate at non-pathogenic levels in ovo.
While developing vaccines to be administered in ovo to chicken embryos, attention must be paid to two points: the effect of maternal antibodies on the vaccines and the effect of the vaccines on the embryo. Maternal antibodies are known to interfere with active immunization. For example, vaccines with mild strains do not induce protective antibody levels when administered to broiler chickens with maternal antibodies as these strains are neutralized by the maternal antibody pool.
Thus a viral particle must be sufficiently efficient at replicating and propagating to ensure that it is not neutralized by the maternally-derived antibodies against the virus. Maternally-derived antibodies are a finite pool of effective antibodies, which decrease as the chicken ages, and neutralization of the virus in this manner does not equate to the establishment of long-term immunity for the embryo/chick. In order to develop long-term immunity against the virus, the embryo and hatched chicken must develop an appropriate protective immune response which is distinct to the effect of the maternally-derived antibodies.
To be useful for in ovo vaccination, the virus must also not replicate and propagate at a level which causes it to be pathogenic to the embryo.
Reduced pathogenicity in terms of the embryo may mean that the coronavirus causes less reduction in hatchability compared to a corresponding, wild-type control coronavirus. Thus the term “without being pathogenic to the embryo” in the context of the present invention may mean “without causing reduced hatchability” when compared to a control coronavirus.
A suitable variant replicase may be identified using methods which are known in the art. For example comparative challenge experiments following in ovo vaccination of embryos with or without maternally-derived antibodies may be performed (i.e. wherein the layer has or has not been vaccinated against IBV).
If the variant replicase enables the virus to propagate at a level which is too high, the embryo will not hatch or will not be viable following hatching (i.e. the virus is pathogenic to the embryo). A virus which is pathogenic to the embryo may kill the embryo.
If the variant replicase causes a reduction in viral replication and propagation which is too great, the virus will be neutralised by the maternally-derived antibodies. Subsequent challenge of the chick with IBV will therefore result in the development of clinical symptoms (for example wheezing, snicking, loss of ciliary activity) and the onset of disease in the challenged chick; as it will have failed to develop effective immunity against the virus.
As used herein, the term ‘variant’ is synonymous with ‘mutant’ and refers to a nucleic acid or amino acid sequence which differs in comparison to the corresponding wild-type sequence.
A variant/mutant sequence may arise naturally, or may be created artificially (for example by site-directed mutagenesis). The mutant may have at least 70, 80, 90, 95, 98 or 99% sequence identity with the corresponding portion of the wild type sequence. The mutant may have less than 20, 10, 5, 4, 3, 2 or 1 mutation(s) over the corresponding portion of the wild-type sequence.
The term “wild type” is used to mean a gene or protein having a nucleotide or amino acid sequence which is identical with the native gene or protein respectively (i.e. the viral gene or protein).
Identity comparisons can be conducted by eye, or more usually, with the aid of readily available sequence comparison programs. These commercially available computer programs can calculate % identity between two or more sequences. A suitable computer program for carrying out such an alignment is the GCG Wisconsin Bestfit package (University of Wisconsin, U.S.A.; Devereux et al., 1984, Nucleic Acids Research 12:387). Examples of other software that can perform sequence comparisons include, but are not limited to, the BLAST package (see Ausubel et al., 1999 ibid—Chapter 18), FASTA (Atschul et al., 1990, J. Mol. Biol., 403-410) and the GENEWORKS suite of comparison tools, ClustalX (see Larkin et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics, 23:2947-2948). Both BLAST and FASTA are available for offline and online searching (see Ausubel et al., 1999 ibid, pages 7-58 to 7-60). However, for some applications, it is preferred to use the GCG Bestf it program. A new tool, called BLAST 2 Sequences is also available for comparing protein and nucleotide sequence (see FEMS Microbiol Lett 1999 174(2): 247-50; FEMS Microbiol Lett 1999 177(1): 187-8 and email@example.com).
The sequence may have one or more deletions, insertions or substitutions of amino acid residues which produce a silent change and result in a functionally equivalent molecule. Deliberate amino acid substitutions may be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues as long as the activity is retained. For example, negatively charged amino acids include aspartic acid and glutamic acid; positively charged amino acids include lysine and arginine; and amino acids with uncharged polar head groups having similar hydrophilicity values include leucine, isoleucine, valine, glycine, alanine, asparagine, glutamine, serine, threonine, phenylalanine, and tyrosine.
Conservative substitutions may be made, for example according to the Table below. Amino acids in the same block in the second column and preferably in the same line in the third column may be substituted for each other:
The coronavirus of the present invention may comprise a variant replicase gene which encodes a protein which comprises a mutation compared to any one of SEQ ID NO: 6, 7, 8 or 9 which, when expressed in a coronavirus, causes the virus to have reduced pathogenicity compared to a coronavirus expressing the corresponding wild-type replicase.
The variant replicase gene may encode a protein which comprises at least one or more amino acid mutations in any combination of nsp-10, nsp-14, nsp-15 and nsp-16.
The variant replicase gene of the coronavirus of the present invention may encode a protein comprising a mutation as defined in the M41 mod sequences presented in
The variant replicase gene of the coronavirus of the present invention may encode a protein which comprises one or more amino acid mutations selected from the list of:
- Pro to Leu at position 85 of SEQ ID NO: 6,
- Val to Leu at position 393 of SEQ ID NO: 7;
- Leu to Ile at position 183 of SEQ ID NO: 8;
- Val to Ile at position 209 of SEQ ID NO: 9.
The variant replicase gene of the coronavirus of the present invention may encode a protein which does not comprise a mutation in nsp-2, nsp-3, nsp-6 or nsp-13.
The variant replicase gene of the coronavirus of the present invention may encode a protein which does not comprise a mutation in nsp10 which corresponds to the threonine to isoleucine mutation caused by a mutation at nucleotide position 12,008 in the gene reported by Ammayappan el al. (Arch Virol (2009) 154:495-499).
Ammayappan et al (as above) reports the identification of sequence changes responsible for the attenuation of IBV strain Arkansas DPI. The study identified 17 amino acid changes in a variety of IBV proteins following multiple passages, approx. 100, of the virus in embryonated eggs. It was not investigated whether the attenuated virus (Ark DPI 101) is capable of replicating in the presence of maternally-derived antibodies against the virus in ovo, without being pathogenic to the embryo. Given that this virus was produced by multiple passage in SPF embryonated eggs, similar methodology for classical IBV vaccines, it is likely that this virus is pathogenic for embryos. The virus may also be sensitive to maternally-derived antibodies if the hens were vaccinated with a similar serotype.
The variant replicase gene of the coronavirus of the present invention may encode a protein which comprises any combination of one or more amino acid mutations provided in the list above.
The variant replicase gene may encode a protein which comprises the amino acid mutation Pro to Leu at position 85 of SEQ ID NO: 6.
The variant replicase gene may encode a protein which comprises the amino acid mutation Val to Leu at position 393 of SEQ ID NO: 7.
The variant replicase gene may encode a protein which comprises the amino acid mutation Leu to Ile at position 183 of SEQ ID NO: 8.
The variant replicase gene may encode a protein which comprises the amino acid mutation Val to Ile at position 209 of SEQ ID NO: 9.
The variant replicase gene may encode a protein which comprises the amino acid mutations Pro to Leu at position 85 of SEQ ID NO: 6, and Val to Leu at position 393 of SEQ ID NO: 7.
The variant replicase gene may encode a protein which comprises the amino acid mutations Pro to Leu at position 85 of SEQ ID NO: 6 Leu to Ile at position 183 of SEQ ID NO: 8.
The variant replicase gene may encode a protein which comprises the amino acid mutations Pro to Leu at position 85 of SEQ ID NO: 6 and Val to Ile at position 209 of SEQ ID NO: 9.
The variant replicase gene may encode a protein which comprises the amino acid mutations Val to Leu at position 393 of SEQ ID NO: 7 and Leu to Ile at position 183 of SEQ ID NO: 8.
The variant replicase gene may encode a protein which comprises the amino acid mutations Val to Leu at position 393 of SEQ ID NO: 7 and Val to Ile at position 209 of SEQ ID NO: 9.
The variant replicase gene may encode a protein which comprises the amino acid mutations Leu to Ile at position 183 of SEQ ID NO: 8 and Val to Ile at position 209 of SEQ ID NO: 9.
The variant replicase gene may encode a protein which comprises the amino acid mutations Pro to Leu at position 85 of SEQ ID NO: 6, Val to Leu at position 393 of SEQ ID NO: 7 and Leu to Ile at position 183 of SEQ ID NO: 8.
The variant replicase gene may encode a protein which comprises the amino acid mutations Pro to Leu at position 85 of SEQ ID NO: 6 Leu to Ile at position 183 of SEQ ID NO: 8 and Val to Ile at position 209 of SEQ ID NO: 9.
The variant replicase gene may encode a protein which comprises the amino acid mutations Pro to Leu at position 85 of SEQ ID NO: 6, Val to Leu at position 393 of SEQ ID NO: 7 and Val to Ile at position 209 of SEQ ID NO: 9.
The variant replicase gene may encode a protein which comprises the amino acid mutations Val to Leu at position 393 of SEQ ID NO: 7, Leu to Ile at position 183 of SEQ ID NO: 8 and Val to Ile at position 209 of SEQ ID NO: 9.
The variant replicase gene may encode a protein which comprises the amino acid mutations Pro to Leu at position 85 of SEQ ID NO: 6, Val to Leu at position 393 of SEQ ID NO: 7, Leu to Ile at position 183 of SEQ ID NO: 8 and Val to Ile at position 209 of SEQ ID NO: 9.
The variant replicase gene may also be defined at the nucleotide level.
For example the nucleotide sequence of the variant replicase gene of the coronavirus of the present invention may comprise one or more nucleotide substitutions within the regions selected from the list of: 11884-12318, 16938-18500, 18501-19514 and 19515-20423 of SEQ ID NO:1.
For example the nucleotide sequence of the variant replicase gene of the coronavirus of the present invention may comprise one or more nucleotide substitutions selected from the list of:
- C to Tat nucleotide position 12137;
- G to C at nucleotide position 18114;
- I to A at nucleotide position 19047; and
- G to A at nucleotide position 20139;
compared to the sequence shown as SEQ ID NO: 1.
As used herein, the term “substitution” is synonymous with the term mutation and means that the nucleotide at the identified position differs to that of the wild-type nucleotide sequence.
The nucleotide sequence may comprise any combination of the nucleotide substitutions selected from the list of:
- C to Tat nucleotide position 12137;
- G to Cat nucleotide position 18114;
- T to A at nucleotide position 19047; and
- G to A at nucleotide position 20139;
compared to the sequence shown as SEQ ID NO: 1.
The nucleotide sequence may comprise the substitution C12137T.
The nucleotide sequence may comprise substitution G18114C.
The nucleotide sequence may comprise the substitution T19047A.
The nucleotide sequence may comprise the substitution G20139A.
The nucleotide sequence may comprise the substitutions C12137T and G18114C.
The nucleotide sequence may comprise the substitutions C12137T and T19047A.
The nucleotide sequence may comprise the substitutions C12137T and G20139A.
The nucleotide sequence may comprise the substitutions G18114C and T19047A.
The nucleotide sequence may comprise the substitutions G18114C and G20139A.
The nucleotide sequence may comprise the substitutions T19047A and G20139A.
The nucleotide sequence may comprise the substitutions C12137T, G18114C and T19047A.
The nucleotide sequence may comprise the substitutions C12137T, T19047A and G20139A.
The nucleotide sequence may comprise the substitutions C12137T, G18114C and G20139A.
The nucleotide sequence may comprise the substitutions G18114C, T19047A and G20139A.
The nucleotide sequence may comprise the substitutions C12137T, G18114C, T19047A and G20139A.
The nucleotide sequence may not comprise a substitution which corresponds to the C12008T substitution reported by Ammayappan et al. (as above).
The nucleotide sequence may be natural, synthetic or recombinant. It may be double or single stranded, it may be DNA or RNA or combinations thereof. It may, for example, be cDNA, PCR product, genomic sequence or mRNA.
The nucleotide sequence may be codon optimised for production in the host/host cell of choice.
It may be isolated, or as part of a plasmid, virus or host cell.
A plasmid is an extra-chromosomal DNA molecule separate from the chromosomal DNA which is capable of replicating independently of the chromosomal DNA. They are usually circular and double-stranded.
Plasmids, or vectors (as they are sometimes known), may be used to express a protein in a host cell. For example a bacterial host cell may be transfected with a plasmid capable of encoding a particular protein, in order to express that protein. The term also includes yeast artificial chromosomes and bacterial artificial chromosomes which are capable of accommodating longer portions of DNA.
The plasmid of the present invention comprises a nucleotide sequence capable of encoding a defined region of the replicase protein. It may also comprise one or more additional coronavirus nucleotide sequence(s), or nucleotide sequence(s) capable of encoding one or more other coronavirus proteins such as the S gene and/or gene 3.
The plasmid may also comprise a resistance marker, such as the guanine xanthine phosphoribosyltransferase gene (gpt) from Escherichia coil, which confers resistance to mycophenolic acid (MPA) in the presence of xanthine and hypoxanthine and is controlled by the vaccinia virus P7.5 early/late promoter.
Recombinant Vaccinia Virus
The present invention also relates to a recombinant vaccinia virus (rVV) comprising a variant replicase gene as defined herein.
The recombinant vaccinia virus (rVV) may be made using a vaccinia-virus based reverse genetics system.
In this respect, the present invention also provides a method for making a viral particle by:
- (i) transfecting a plasmid as described in the previous section into a host cell;
- (ii) infecting the host cell with a recombining virus comprising the genome of a coronavirus strain with a replicase gene;
- (iii) allowing homologous recombination to occur between the replicase gene sequences in the plasmid and the corresponding sequences in the recombining virus genome to produce a modified replicase gene;
- (iv) selecting for recombining virus comprising the modified replicase gene.
The term ‘modified replicase gene’ refers to a replicase gene which comprises a variant replicase gene as described in connection with the first aspect of the present invention. Specifically, the term refers to a gene which is derived from a wild-type replicase gene but comprises a nucleotide sequence which causes it to encode a variant replicase protein as defined herein.
The recombination may involve all or part of the replicase gene. For example the recombination may involve a nucleotide sequence encoding for any combination of nsp-10, nsp-14, nsp-15 and/or nsp-16. The recombination may involve a nucleotide sequence which encodes for an amino acid mutation or comprises a nucleotide substitution as defined above.
The genome of the coronavirus strain may lack the part of the replicase protein corresponding to the part provided by the plasmid, so that a modified protein is formed through insertion of the nucleotide sequence provided by the plasmid.
The recombining virus is one suitable to allow homologous recombination between its genome and the plasmid. The vaccinia virus is particularly suitable as homologous recombination is routinely used to insert and delete sequences for the vaccinia virus genome.
The above method optionally includes the step:
- (v) recovery of recombinant coronavirus comprising the modified replicase gene from the DNA from the recombining virus from step (iv).
Methods for recovering recombinant coronavirus, such as recombinant IBV, are known in the art (See Britton et al (2005) see page 24; and PCT/GB2010/001293).
For example, the DNA from the recombining virus from step (iv) may be inserted into a plasmid and used to transfect cells which express cytoplasmic T7 RNA polymerase. The cells may, for example be pre-infected with a fowlpox virus expressing T7 RNA polymerase. Recombinant coronavirus may then be isolated, for example, from the growth medium.
When the plasmid is inserted into the vaccinia virus genome, an unstable intermediate is formed. Recombinants comprising the plasmid may be selected for e.g. using a resistance marker on the plasmid.
Positive recombinants may then be verified to contain the modified replicase gene by, for example, PCR and sequencing.
Large stocks of the recombining virus including the modified replicase gene (e.g. recombinant vaccinia virus, (rVV) may be grown up and the DNA extracted in order to carry out step (v)).
Suitable reverse genetics systems are known in the art (Casais et al (2001) J. Virol 75:12359-12369; Casais et al (2003) J. Virol. 77:9084-9089; Britton et al (2005) J. Virological Methods 123:203-211; Armesto et al (2008) Methods in Molecular Biology 454:255-273).
The coronavirus may be used to infect a cell.
Coronavirus particles may be harvested, for example from the supernatant, by methods known in the art, and optionally purified.
The cell may be used to produce the coronavirus particle.
Thus the present invention also provides a method for producing a coronavirus which comprises the following steps:
(i) infection of a cell with a coronavirus according to the invention;
(ii) allowing the virus to replicate in the cell; and
(iii) harvesting the progeny virus.
The present invention also provides a cell capable of producing a coronavirus according to the invention using a reverse genetics system. For example, the cell may comprise a recombining virus genome comprising a nucleotide sequence capable of encoding the replicase gene of the present invention.
The cell may be able to produce recombinant recombining virus (e.g. vaccinia virus) containing the replicase gene.
Alternatively the cell may be capable of producing recombinant coronavirus by a reverse genetics system. The cell may express or be induced to express T7 polymerase in order to rescue the recombinant viral particle.
The coronavirus may be used to produce a vaccine. The vaccine may by a live attenuated form of the coronavirus of the present invention and may further comprise a pharmaceutically acceptable carrier. As defined herein, “pharmaceutically acceptable carriers” suitable for use in the invention are well known to those of skill in the art. Such carriers include, without limitation, water, saline, buffered saline, phosphate buffer, alcohol/aqueous solutions, emulsions or suspensions. Other conventionally employed diluents and excipients may be added in accordance with conventional techniques. Such carriers can include ethanol, polyols, and suitable mixtures thereof, vegetable oils, and injectable organic esters. Buffers and pH adjusting agents may also be employed. Buffers include, without limitation, salts prepared from an organic acid or base. Representative buffers include, without limitation, organic acid salts, such as salts of citric acid, e.g., citrates, ascorbic acid, gluconic acid, histidine-Hel, carbonic acid, tartaric acid, succinic acid, acetic acid, or phthalic acid, Iris, trimethanmine hydrochloride, or phosphate buffers. Parenteral carriers can include sodium chloride solution, Ringer’s dextrose, dextrose, trehalose, sucrose, and sodium chloride, lactated Ringer’s or fixed oils. Intravenous carriers can include fluid and nutrient replenishers, electrolyte replenishers, such as those based on Ringer’s dextrose and the like. Preservatives and other additives such as, for example, antimicrobials, antioxidants, chelating agents (e.g., EDTA), inert gases and the like may also be provided in the pharmaceutical carriers. The present invention is not limited by the selection of the carrier. The preparation of these pharmaceutically acceptable compositions, from the above-described components, having appropriate pH isotonicity, stability and other conventional characteristics is within the skill of the art. See, e.g., texts such as Remington: The Science and Practice of Pharmacy, 20th ed, Lippincott Williams & Wilkins, pub!., 2000; and The Handbook of Pharmaceutical Excipients, 4.sup.th edit., eds. R. C. Rowe et al, APhA Publications, 2003.
The vaccine of the invention will be administered in a “therapeutically effective amount”, which refers to an amount of an active ingredient, e.g., an agent according to the invention, sufficient to effect beneficial or desired results when administered to a subject or patient. An effective amount can be administered in one or more administrations, applications or dosages. A therapeutically effective amount of a composition according to the invention may be readily determined by one of ordinary skill in the art. In the context of this invention, a “therapeutically effective amount” is one that produces an objectively measured change in one or more parameters associated Infectious Bronchitis condition sufficient to effect beneficial or desired results .An effective amount can be administered in one or more administrations. For purposes of this invention, an effective amount of drug, compound, or pharmaceutical composition is an amount sufficient to reduce the incidence of Infectious Bronchitis. As used herein, the term “therapeutic” encompasses the full spectrum of treatments for a disease, condition or disorder. A “therapeutic” agent of the invention may act in a manner that is prophylactic or preventive, including those that incorporate procedures designed to target animals that can be identified as being at risk (pharmacogenetics); or in a manner that is ameliorative or curative in nature; or may act to slow the rate or extent of the progression of at least one symptom of a disease or disorder being treated.
The present invention also relates to a method for producing such a vaccine which comprises the step of infecting cells, for example Vero cells, with a viral particle comprising a replicase protein as defined in connection with the first aspect of the invention.
The coronavirus of the present invention may be used to treat and/or prevent a disease.
To “treat” means to administer the vaccine to a subject having an existing disease in order to lessen, reduce or improve at least one symptom associated with the disease and/or to slow down, reduce or block the progression of the disease.
To “prevent” means to administer the vaccine to a subject who has not yet contracted the disease and/or who is not showing any symptoms of the disease to prevent or impair the cause of the disease (e.g. infection) or to reduce or prevent development of at least one symptom associated with the disease.
The disease may be any disease caused by a coronavirus, such as a respiratory disease and and/or gastroenteritis in humans and hepatitis, gastroenteritis, encephalitis, or a respiratory disease in other animals.
The disease may be infectious bronchitis (IB); Porcine epidemic diarrhoea; Transmissible gastroenteritis; Mouse hepatitis virus; Porcine haemagglutinating encephalomyelitis; Severe acute respiratory syndrome (SARS); or Bluecomb disease.
The disease may be infectious bronchitis.
The vaccine may be administered to hatched chicks or chickens, for example by eye drop or intranasal administration. Although accurate, these methods can be expensive e.g. for large broiler flocks. Alternatives include spray inoculation of administration to drinking water but it can be difficult to ensure uniform vaccine application using such methods.
The vaccine may be provided in a form suitable for its administration, such as an eye-dropper for intra-ocular use.
The vaccine may be administered by in ovo inoculation, for example by injection of embryonated eggs. In ovo vaccination has the advantage that it provides an early stage resistance to the disease. It also facilitates the administration of a uniform dose per subject, unlike spray inoculation and administration via drinking water.
The vaccine may be administered to any suitable compartment of the egg, including allantoic fluid, yolk sac, amnion, air cell or embryo. It may be administered below the shell (aircell) membrane and chorioallantoic membrane.
Usually the vaccine is injected into embryonated eggs during late stages of embryonic development, generally during the final quarter of the incubation period, such as 3-4 days prior to hatch. In chickens, the vaccine may be administered between day 15-19 of the 21 -day incubation period, for example at day 17 or 18.
The process can be automated using a robotic injection process, such as those described in WO 2004/078203.
The vaccine may be administered together with one or more other vaccines, for example, vaccines for other diseases, such as Newcastle disease virus (NDV). The present invention also provides a vaccine composition comprising a vaccine according to the invention together with one or more other vaccine(s). The present invention also provides a kit comprising a vaccine according to the invention together with one or more other vaccine(s) for separate, sequential or simultaneous administration.
The vaccine or vaccine composition of the invention may be used to treat a human, animal or avian subject. For example, the subject may be a chick, chicken or mouse (such as a laboratory mouse, e.g. transgenic mouse).
Typically, a physician or veterinarian will determine the actual dosage which will be most suitable for an individual subject or group of subjects and it will vary with the age, weight and response of the particular subject(s).
The composition may optionally comprise a pharmaceutically acceptable carrier, diluent, excipient or adjuvant. The choice of pharmaceutical carrier, excipient or diluent can be selected with regard to the intended route of administration and standard pharmaceutical practice. The pharmaceutical compositions may comprise as (or in addition to) the carrier, excipient or diluent, any suitable binder(s), lubricant(s), suspending agent(s), coating agent(s), solubilising agent(s), and other carrier agents that may aid or increase the delivery or immunogenicity of the virus.
The invention will now be further described by way of Examples, which are meant to serve to assist one of ordinary skill in the art in carrying out the invention and are not intended in any way to limit the scope of the invention.
A M41-CK full-length cDNA was produced by replacement of the Beaudette cDNA in the Vaccinia virus reverse genetics system previously described in PCT/GB2010/001293 (herein incorporated by reference) with synthetic cDNA derived from the M41 consensus sequence.
The IBV cDNA within recombinant Vaccinia virus (rVV) rVV-BeauR-Rep-M41 structure described in Armesto, Cavanagh and Britton (2009). PLoS ONE 4(10): e7384. doi:10.1371/journal.pone.0007384, which consisted of the replicase derived from IBV
Beaudette strain and the structural and accessory genes and 3′ UTR from IBV M41-CK, was further modified by replacement of the Beaudette 5′ UTR-Nsp2-Nsp3 sequence with the corresponding sequence from IBV M41-CK. The resulting IBV cDNA consisted of 5′ UTR-Nsp2-Nsp3 from M41, Nsp4-Nsp16 from Beaudette and the structural and accessory genes and 3′ UTR from M41. This cDNA was further modified by the deletion of the Beaudette Nsp4-Nsp16 sequence. The resulting cDNA, lacking Nsp4-16, was modified in four further steps in which the deleted Nsps were sequentially replaced with the corresponding sequences from M41-CK, the replacement cDNAs represented M41-CK Nsp4-8, Nsp9-12, Nsp12-14 and finally Nsp15-16. Each replacement cDNA contained approx. 500 nucleotides at the 5′ end corresponding to the 3′ most M41 sequence previously inserted and approx. 500 nucleotides at the 3′ end corresponding to the M41 S gene sequence. This allowed insertion of the M41 cDNA sequence by homologous recombination and sequential addition of contiguous M41 replicase gene sequence. The synthetic cDNAs containing the M41-derived Nsp sequences were added by homologous recombination utilising the inventor’s previous described transient dominant selection (IDS) system (see PCT/GB2010/001293). The M41-derived cDNAs containing sequence corresponding to the M41 Nsps-10, -14, -15 and -16 contained the modified amino acids at positions 85, 393, 183 and 209, respectively, as indicated in
A full-length cDNA representing the genome of M41-CK was generated in Vaccinia virus representing the synthetic sequences. Two rIBVs, M41-R-6 and M41-R-12, were rescued and shown to grow in a similar manner as M41-CK (
The viruses rescued in Example 1 were used to infect 8-day-old specific pathogen free (SPF) chicks by ocular and nasal inoculation to test them for pathogenicity, as observed by clinical signs on a daily basis 3-7 days post-infection and for ciliary activity days 4 and 6 post-infection. Loss of ciliary activity is a well-established method for determining the pathogenicity of IBV. The two M41-R viruses were found to be apathogenic when compared to M41 -CK though they did show some clinical signs in comparison to uninfected control chicks (
Thus, the M41-R molecular clones of M41-CK were not pathogenic when compared to the parental virus M41-CK.
The inventors identified several nucleotide differences in the M41-R compared to the M41-CK sequences. The majority of these were synonymous mutations, as the nucleotide change did not affect the amino acid sequence of the protein associated with the sequence. However, four non-synonymous mutations were identified in the IBV replicase gene specific to Nsp-10, Nsp-14, Nsp-15 and Nsp-16 components of the replicase gene, these mutations resulted in amino acid changes (Table 3).
Repair of M41-R rIBVs
In order to determine whether the identified mutations were responsible for the loss of pathogenicity associated with M41-R, the Nsp10 mutation was repaired and the mutations in Nsp-14, -15 & -16 were repaired and shown to grow in a similar manner as M41-CK (
The rIBVs were assessed for pathogenicity in chicks as described previously. Both rIBVs showed increased pathogenicity when compared to M41-R but not to the level observed with M41-CK (
To determine the roles of the Nsps in pathogenicity the full-length cDNA corresponding to M41 R-nspl Orep was used to repair the mutations in Nsps14, 15 & 16 using a synthetic cDNA containing the correct nucleotides utilising the TDS system.
The following rlBVs were produced:
M41R-nsp10, 15rep—M41-R with the mutations in Nsp-10 and Nsp-15 repaired
M41R-nsp10, 14, 15rep—M41-R with mutations in Nsp-10, -14 and -15 repaired
M41R-nsp10, 14, 16rep—M41-R with mutations in Nsp-10, -14 and -16 repaired
M41 R-nsp10, 15, 16rep—M41-R with mutations in Nsp-10, -15 and -16 repaired
M41-K—All four mutations, Nsp-10,-14,-15 & -16 repaired in M41-R
The rIBVs were shown to grow in a similar manner as M41-CK (
The inventors also generated rIBV M41R-nsp 10, 14 rep (nsp 10 and 14 are repaired, nsp 15 and 16 contain mutations) and rIBV M41R-nsp 10, 16 rep (nsp 10 and 16 are repaired, nsp 14 and 15 contain mutations) and assessed the pathogenicity of these viruses.
rIBV M41 R-nsp 10, 14 rep less pathogenic than M41-K but caused around 50% ciliostasis on days 4-6 post-infection. rIBV M41R-nsp 10, 16 rep was almost apathogenic and caused no ciliostasis (see
Thus the genome associated with M41-R is a potentialbackbone genome for a rationally attenuated IBV.
Vaccination/Challenge Study with M41-R
Candidate vaccine viruses were tested in studies in which fertilized chicken eggs were vaccinated in ovo at 18 days embryonation and in which the hatchability of the inoculated eggs was determined. The clinical health of the chickens was investigated and the chickens were challenged at 21 days of age with a virulent IB M41 challenge virus at 103.65 EID50. per dose.
Clinical signs were investigated after challenge protection by the vaccine and a ciliostasis test was performed at 5 days after challenge to investigate the effect of the challenge viruses on movement of the cilia and protection by the vaccine against ciliostasis (inhibition of cilia movement).
In Ovo Vaccination in Commercial Broiler Eggs
The design of the experiment is given in Table 4 and the clinical results are given in Table 5. Hatchability of the eggs inoculated with IB M41-R was good and chickens were healthy. IB M41-R protected against clinical signs after challenge in the broilers (placebo: 19/19 affected, 1B M41-R: 3/18 affected and 1 dead). The results of the ciliostasis test are given in Table 6. IB M41-R generated protection against ciliostasis.
In Ovo Vaccination in Specific Pathogen-Free (SPF) Eggs
The design of the study in SPF eggs is given in Table 7 and is similar with the design of the studies with commercial broilers, but the vaccination dose for 1B M41-R was higher, (105 EID50. per dose).
The results (Table 8) show that the hatch percentage for IB M41-R hatch was low, and 19 of 40 hatched and the chicks were weak. Eight chicks died. The remaining 11 chickens were challenged and 11 of the chicks hatched from the eggs which had been inoculated with saline were challenged.
In the ciliostasis test after challenge it appeared that all chickens vaccinated in ovo with IB M41-R were protected, whereas none of the controls was protected, see Table 9.
In conclusion, IB M41-R was safe in commercial eggs, generated protection against clinical signs and to an extent against ciliostasis.
In SPF eggs vaccinated with IB M41 R a relatively low number of chickens hatched. This may be due to the 105 EID50. per egg of 1B M41-R used. This was 10-fold higher than the dose used in earlier studies in which there was a higher level of hatchability. The lower hatch percentages may also be caused by a particularly high susceptibility of the batch of SPF eggs for viruses, as in other studies the level of embryo mortality was also higher that had previously been observed.
After challenge all surviving chickens after hatch were completely protected against ciliostasis. It is concluded that IB M41-R has great potential as vaccine to be administered in ovo.
All publications mentioned in the above specification are herein incorporated by reference. Various modifications and variations of the described methods and system of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention which are obvious to those skilled in molecular biology, virology or related fields are intended to be within the scope of the following claims.