Patent Application
20230124042
The present invention relates to attenuated African Swine Fever viruses. The attenuated viruses protect pigs against subsequent challenge with virulent virus. The present invention also relates to the use of such attenuated viruses to treat and/or prevent African Swine
Fever.
African swine fever is a devastating haemorrhagic disease of domestic pigs caused by a double-stranded DNA virus, African swine fever virus (ASFV). ASFV is the only member of the Asfarviridae family and replicates predominantly in the cytoplasm of cells. Virulent strains of ASFV can kill domestic pigs within about 5-14 days of infection with a mortality rate approaching 100%.
ASFV can infect and replicate in warthogs (Phacochoerus sp.), bushpigs (Potamocherus sp.) and soft ticks of the Ornithodoros species (which are thought to be a vector), but in these species few if any clinical signs are observed and long term persistent infections can be established. ASFV was first described after European settlers brought pigs into areas endemic with ASFV and, as such, is an example of an “emerging infection”. The disease is currently endemic in many sub-Saharan countries and in Europe in Sardinia. Following its introduction to Georgia in the Trans Caucasus region in 2007, ASFV has spread extensively through neighbouring countries including the Russian Federation. In 2012 the first outbreak was reported in Ukraine and in 2013 the first outbreaks in Belarus. In 2014 further outbreaks were reported in pigs in Ukraine and detection in wild boar in Lithuania and Poland.
There is currently no treatment for ASF. Prevention in countries outside Africa has been attempted on a national basis by restrictions on incoming pigs and pork products, compulsory boiling of waste animal products under license before feeding to pigs and the application of a slaughter policy when the disease is diagnosed. Prevention in Africa is based on measures to keep warthogs and materials contaminated by warthogs away from the herd.
There is thus a need for improved measures to control ASFV infection and prevent spread of the disease.
The complete genome sequences of ASFV isolate Benin 97/1 (a highly pathogenic virus from West Africa, Group1), isolate OURT88/3 (non-pathogenic, attenuated virus from Portugal, Group 1) and isolate BA71V (Vero cell tissue culture adapted non-pathogenic virus, Group 1) have been compared (Chapman et al. 2008 J. Gen Virol. 89: 397-408).
In the OURT88/3 genome, five MGF 360 genes (10L, 11L, 12L, 13L and 14L) and two MGF 505 genes (1R, 2R) are deleted, and the MGF 505R 3R gene is truncated. These genes are present in the genomes of all eight other pathogenic isolates of ASFV that have been sequenced. Chapman et al. (as above) does not determine any mutations which are causative of attenuation in OURT88/3. Further, although OURT88/3 has been shown to induce a protective immune response in certain animals, this effect does not appear to be universal. Immunisation with OURT88/3 appears to be ineffective in protecting some pigs from subsequent challenge. It is also associated with the induction of adverse immune responses, such as joint swelling, in some pigs.
In the attenuated tissue-culture adapted BA71V isolate, the genome contains the MGF 505 3R gene but lacks the other seven MGF genes and in addition the MGF 360 9L gene is truncated.
Previously six MGF 360 genes (9L, 10L, 11L, 12L, 13L and 14L) and two MGF 505 genes (1R and 2R) were deleted from the highly pathogenic South African isolate Pr4. This deletion markedly reduced viral growth in primary macrophage cell cultures (Zsak et al. 2001, as above) and led to attenuation of the virus (cited as unpublished results, Afonso et al. 2004 J. Virol 78:1858-1864). However no experiments were carried out to challenge the recovered pigs to determine if they were protected. In fact, at an African swine fever virus workshop at the Biosecurity Research Institute, Manhattan Kansas in May 2011 it was mentioned that the Pr4 deletion mutant was not protective and induced a chronic form of the disease.
It has also been shown that deletion of three MGF 360 genes (12L, 13L and 14L) and four MGF 505 genes (1R, 2R, 3R and 4R truncation) from the pathogenic virus MalawiΔDP71 reduces virus replication in pigs and in addition attenuated the virus (Neilan et al. (2002) J. Virol. 76:3095-3104). However again, no experiments were reported to determine if the recovered pigs were protected against challenge.
Deleting MGF505-1R, -2R and -3R, and MGF360-12L, -13L and -14L produced an attenuated virus that conferred protection against parental virus (O'Donnell et al. 2015 J. Virol. 89:6048-6056). However, deletion of MGF360-13L and -14L only did not result in viral attenuation (Borca et al. 2017 Sci Rep. 7: 46747).
A DIVA vaccine allows differentiation of animals that have been infected with a wild type pathogen from animals that have been immunised with the vaccine. DIVA vaccines lack at least one immunogenic antigen (a DIVA marker) which is present in the wild type pathogen. Animals infected with the wild type pathogen produce antibodies against the DIVA marker, whereas vaccinated animals do not. Antibodies to the DIVA marker may be detected using a serological assay. Infected animals (which have antibodies to the DIVA marker) may thus be differentiated from vaccinated animals (which do not have antibodies to the DIVA marker), despite both groups of animals having antibodies to other immunogens of the pathogen.
A DIVA marker should be immunogenic, but deletion of the gene should not affect the vaccine's protective capacity.
In one aspect, the present invention relates to an attenuated African Swine Fever virus in which expression and/or activity of particular multigene-family (MGF) genes is disrupted, whilst expression and/or activity of other particular MGF genes is not disrupted.
The invention also relates to the finding that the K145R and B125R genes of African Swine Fever virus are useful as DIVA markers.
The invention provides an attenuated African Swine Fever (ASF) virus in which the expression and/or activity of the following genes is disrupted:
and which comprises a functional version of the following genes:
The invention also provides an attenuated ASF virus which lacks a functional version of the K145R gene and/or the B125R gene.
The invention also provides a vaccine comprising an attenuated ASF virus according to the invention.
The invention further provides a vaccine of the invention for use in treating and/or preventing African Swine Fever in a subject.
The invention further provides a method for treating and/or preventing African Swine Fever in a subject which comprises the step of administering to the subject an effective amount of a vaccine according to the invention.
The invention yet further provides a method of attenuating an ASF virus which comprises the step of disrupting the activity and/or expression of the following genes:
whilst retaining the function of the following genes:
African swine fever virus (ASFV) is the causative agent of African swine fever (ASF). The genome structure of ASFV is known in the art, as detailed in Chapman et al. 2008 J. Gen. Virol. 89:397-408. ASFV is a large, icosahedral, double-stranded DNA virus with a linear genome containing at least 150 genes. The number of genes differs slightly between different isolates of the virus. ASFV has similarities to the other large DNA viruses, e.g., poxvirus, iridovirus and mimivirus. In common with other viral haemorrhagic fevers, the main target cells for replication are those of monocyte, macrophage lineage.
Based on sequence variation in the C-terminal region of the B646L gene encoding the major capsid protein p72, 22 ASFV genotypes (I-XXII) have been identified. All ASFV p72 genotypes have been circulating in eastern and southern Africa. Genotype I has been circulating in Europe, South America, the Caribbean and western Africa. Genotype VIII is confined to four East African countries.
Examples of strains from some of the genotypes are given below:
Genotype I: OURT88/3; Brazil/79; Lisbon/60; BA715; Pret; Benin 97/1; IC/1/96; IC/576; CAM/82; Madrid/62; Malta/78; ZAR85; Katange63; Togo; Dakar59; Ourt88/1; BEN/1/97; Dom_Rep; VAL/76; IC/2/96; Awoshie/99; NIG/1/99; NIG/1/98; ANG/70; BEL/85; SPEC120; Lisbon/57; ASFV-Warm; GHA/1/00; GAM/1/00; Ghana; HOL/86; NAM/1/80; NUR/90/1; CAM/4/85; ASFV-Teng; Tegani; ASFV-E75.
Genotype II: Georgia 2007/1; POL/2015/Podlaskie (Polish strain); Belgium/Etalle/wb/2018; ASFV/Kyiv/2016/131; China/2018/AnhuiXCGQ
Genotype III: BOT 1/99
Genotype IV: ASFV-War; RSA/1/99/W
Genotype VI: MOZ 94/1
Genotype VII: VICT/90/1; ASFV-Mku; RSA/1/98
Genotype VIII: NDA/1/90; KAL88/1; ZAM/2/84; JON89/13; KAV89/1; DEZda; AFSV-Mal; Malawi LIL 20/1
Genotype IX: UGA/1/95
Genotype X: BUR/1/84; BUR/2/84; BUR/90/1; UGA/3/95; TAN/Kwh12; HindeII; ASFV-Ken; Virulent Uganda 65.
The attenuated ASF virus of the present invention may be derivable from a wild-type ASF virus isolate, but includes mutations in its genome such that the expression and/or activity of the following genes is disrupted: MGF 360 genes 12L, 13L and 14L and MGF 505 gene 1R.
The attenuated ASF virus of the present invention may be derivable from a wild-type ASF virus isolate, but lacks a functional version of the K145R gene or the B125R gene.
The term “wild-type” indicates that the virus existed (at some point) in the field, and was isolated from a natural host, such as a domestic pig, tick or warthog. ASFV isolates described to date are summarised in Table 1 below, together with their Genbank Accession numbers.
The genome of the attenuated ASFV of the invention may correspond to any ASFV genotype. The genome of the attenuated ASFV of the invention may essentially correspond to any ASFV genotype.
The term “corresponds to” means that the remainder of the genome of the attenuated ASFV of the invention is the same as the wild type strain. “The remainder of the genome” refers to all genes other than those to which the invention relates: MGF 360 10L, 11L, 12L, 13L and 14L, and MGF 505 1R, 2R and 3R, and B125R and K145R. Genes to which the invention relates may also correspond to the wild type strain. In an embodiment MGF 360 10L, 11L, 12L, 13L and 14L, and MGF 505 1R, 2R and 3R, and B125R and K145R correspond to the wild type strain. Where MGF 360 12L, 13L and 14L and MGF 505 1R correspond to the wild type strain, their expression and activity may be disrupted by a mutation in an intergenic region such as a promoter. In an embodiment MGF 360 12L, 13L and 14L, and MGF 505 2R and 3R, and B125R and K145R correspond to the wild type strain. In other words, the genes of the attenuated ASFV of the invention may be the same as the genes of the wild type strain. In an embodiment the genes of the attenuated ASFV of the invention are the same as the genes of the wild type strain, except for MGF 360 12L, 13L and 14L, and MGF 505 1R. In an embodiment the genes of the attenuated ASFV of the invention are the same as the genes of the wild type strain, except for MGF 360 12L, 13L and 14L, and MGF 505 1R, and B125R and/or K145R.
The term “essentially corresponds to” means the same as “corresponds to” with the additional exception that the remainder of the genome may comprise one or more mutations. The one or more mutations may be in other genes (i.e. not in genes to which the invention relates).
The genome of the attenuated ASFV may correspond or essentially correspond to genotype I. The genome of the attenuated ASFV may correspond or essentially correspond to genotype II. The genome of the attenuated ASFV may correspond or essentially correspond to genotype III. The genome of the attenuated ASFV may correspond or essentially correspond to genotype IV. The genome of the attenuated ASFV may correspond or essentially correspond to genotype V. The genome of the attenuated ASFV may correspond or essentially correspond to genotype VI. The genome of the attenuated ASFV may correspond or essentially correspond to genotype VII. The genome of the attenuated ASFV may correspond or essentially correspond to genotype VIII. The genome of the attenuated ASFV may correspond or essentially correspond to genotype IX. The genome of the attenuated ASFV may correspond or essentially correspond to genotype X.
The genome of the attenuated ASFV of the invention may correspond or essentially correspond to that of a virulent ASFV strain. Known virulent ASF virus strains include: Georgia 2007/1, Benin 97/1, Kenyan, Malawi Lil20/1, Pretorisuskop/96/4 and Tengani 62. The genome of the attenuated ASFV may correspond or essentially correspond to that of the Georgia 2007/1 strain. The genome of the attenuated ASFV may correspond or essentially correspond to that of the Benin 97/1 strain.
The genome of the attenuated ASFV of the invention may correspond or essentially correspond to that of an ASFV strain whose virulence is currently unknown, for example: Mkuzi, Warmbaths and Warthog.
In an embodiment the genome of the attenuated ASFV of the invention does not correspond to that of OURT88/3. In an embodiment the attenuated ASFV of the invention is not OURT88/3.
ASFV contains five multi-gene families which are present in the left and right variable regions of the genome. The MGFs are named after the average number of codons present in each gene: MGF100, 110, 300, 360 and 505/530. The N-terminal regions of members of MGFs 300, 360 and 505/530 share significant similarity with each other. It has been shown the MGF 360 and 505 families encode genes essential for host range function that involves promotion of infected-cell survival and suppression of type I interferon response.
The attenuated ASFV according to the present invention has disrupted expression and/or activity of the following genes:
and comprises a functional version of the following genes:
Alternatively expressed, the attenuated ASFV according to the present invention lacks a functional version of the following genes:
and comprises a functional version of the following genes:
The location of these genes in the genomes of a variety of ASFV strains is provided below in Table 2. The sequence identity of each gene to the corresponding Benin 97/1 gene is also provided.
The gene (i.e. nucleotide) sequences of MGF genes from different strains are given below.
In an embodiment the attenuated ASFV of the invention comprises a functional version of MGF 360 10L. Suitably the functional version of MGF 360 10L comprises the sequence of SEQ ID No. 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 or 23. Suitably the functional version of MGF 360 10L comprises a sequence having at least 70%, at least 80%, at least 90% or at least 95% identity with SEQ ID No. 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 or 23. Suitably the functional version of MGF 360 10L consists of the sequence of SEQ ID No. 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 or 23.
In an embodiment the attenuated ASFV of the invention comprises a functional version of MGF 360 11L. Suitably the functional version of MGF 360 11L comprises the sequence of SEQ ID No. 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 or 36. Suitably the functional 10 version of MGF 360 11L comprises a sequence having at least 70%, at least 80%, at least 90% or at least 95% identity with SEQ ID No. 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 or 36. Suitably the functional version of MGF 360 11L consists of the sequence of SEQ ID No. 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 or 36.
In an embodiment of the attenuated ASFV of the invention, the expression and/or activity of the MGF 360 12L gene is disrupted. Suitably the MGF 360 12L gene comprises the sequence of SEQ ID No. 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47 or 48. Suitably the MGF 360 12L gene comprises a sequence having at least 70%, at least 80%, at least 90% or at least 95% identity with SEQ ID No. 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47 or 48. Suitably the MGF 360 12L gene consists of the sequence of SEQ ID No. 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47 or 48.
In an embodiment of the attenuated ASFV of the invention, the expression and/or activity of 50 the MGF 360 13L gene is disrupted. Suitably the MGF 360 13L gene comprises the sequence of SEQ ID No. 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59 or 60. Suitably the MGF 360 13L gene comprises a sequence having at least 70%, at least 80%, at least 90% or at least 95% identity with SEQ ID No. 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59 or 60. Suitably the MGF 360 13L gene consists of the sequence of SEQ ID No. 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59 or 60.
In an embodiment of the attenuated ASFV of the invention, the expression and/or activity of the MGF 360 14L gene is disrupted. Suitably the MGF 360 14L gene comprises the 45 sequence of SEQ ID No. 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 or 72. Suitably the MGF 360 13L gene comprises a sequence having at least 70%, at least 80%, at least 90% or at least 95% identity with SEQ ID No. 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 or 72. Suitably the MGF 360 14L gene consists of the sequence of SEQ ID No. 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 or 72.
In an embodiment of the attenuated ASFV of the invention, the expression and/or activity of 25 the MGF 505 1R gene is disrupted. Suitably the MGF 505 1R gene comprises the sequence of SEQ ID No. 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84 or 85. Suitably the MGF 505 1R gene comprises a sequence having at least 70%, at least 80%, at least 90% or at least 95% identity with SEQ ID No. 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84 or 85. Suitably the MGF 505 1R gene consists of the sequence of SEQ ID No. 73, 74, 75, 76, 77, 78, 79, 80, 30 81, 82, 83, 84 or 85.
In an embodiment the attenuated ASFV of the invention comprises a functional version of MGF 505 2R. Suitably the functional version of MGF 505 2R comprises the sequence of SEQ ID No. 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96 or 97. Suitably the functional version of MGF 505 2R comprises a sequence having at least 70%, at least 80%, at least 90% or at least 95% identity with SEQ ID No. 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96 or 97. Suitably 40 the functional version of MGF 505 2R consists of the sequence of SEQ ID No. 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96 or 97.
In an embodiment the attenuated ASFV of the invention comprises a functional version of MGF 505 3R. Suitably the functional version of MGF 505 3R comprises the sequence of SEQ ID No. 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111 or 112. Suitably the functional version of MGF 505 3R comprises a sequence having at least 70%, at least 80%, at least 90% or at least 95% identity with SEQ ID No. 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111 or 112. Suitably the functional version of MGF 505 3R consists of the sequence of SEQ ID No. 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111 or 112. In an embodiment the invention provides an attenuated ASFV which comprises the following sequences from the Benin 97/1 strain:
In an embodiment the invention provides an attenuated ASFV which comprises the following sequences from the China/2018/AnhuiXCGQ strain:
In an embodiment the invention provides an attenuated ASFV which comprises the following sequences from the Georgia 2007/1 strain:
In an embodiment the invention provides an attenuated ASFV which comprises the following sequences from the Ken05/Tk1 strain:
In an embodiment the invention provides an attenuated ASFV which comprises the following sequences from the Ken06.Bus strain:
In an embodiment the invention provides an attenuated ASFV which comprises the following sequences from the Kenya 1950 strain:
In an embodiment the invention provides an attenuated ASFV which comprises the following sequences from the L60 strain:
In an embodiment the invention provides an attenuated ASFV which comprises the following sequences from the Malawi Lil-20/1 strain:
In an embodiment the invention provides an attenuated ASFV which comprises the following sequences from the Mkuzi 1979 strain:
In an embodiment the invention provides an attenuated ASFV which comprises the following sequences from the Pretorisuskop/96/4 strain:
In an embodiment the invention provides an attenuated ASFV which comprises the following sequences from the Tengani 62 strain:
In an embodiment the invention provides an attenuated ASFV which comprises the following sequences from the Warmbaths strain:
In an embodiment the invention provides an attenuated ASFV which comprises the following sequences from the Warthog strain:
The translation products (i.e. protein sequences) of these genes from different strains are given below:
The complete genome for the African swine fever virus Georgia 2007/1 pathogenic isolate is given in Genbank Locus: FR682468.1. The complete genome for the African swine fever virus Benin 97/1 pathogenic isolate is given in Genbank Locus: AM712239.1. The complete BA71 isolate genome encodes 151 open reading frames (ORFs), the Benin 97/1 isolate encodes 157 ORFs and the OURT88/3 isolate encodes 151 ORFs.
MGF genes MGF360-10L, 11L, 12L, 13L and 14L, MGF 505-1R, 2R, 3R, 4R and 5R, and MGF110-1L inhibit activity of the transcription factors interferon regulatory factor 3 (IRF3) and NF-κB, as demonstrated in Example 2 herein (see
IRF3 and NF-κB are transcription factors that control expression of interferon and pro-inflammatory cytokines as part of the host's innate immune system response to viral infection. The inhibition of IRF3 and NF-κB by MGF genes results in decreased amounts of type I interferon (IFN) and pro-inflammatory cytokines produced by cells infected with ASFV. Expression of MGF genes allows ASFV to circumvent the host innate immune response, favouring virus replication and disrupting the development of adaptive responses.
The ability of MGF genes to inhibit IRF3 and/or NF-κB activity may be measured using luciferase reporter assays, such as described in Example 2 herein. For example, to assess whether a given MGF gene can inhibit IRF3 or NF-κB activity, the MGF gene can be expressed in cells comprising a luciferase reporter under control of a promoter that is activated by IRF3 or NF-κB, stimulating the cells in a manner that activates IRF3 or NF-κB respectively then measuring luciferase activity. The ability of modified or mutated versions of MGF genes to inhibit IRF3 and/or NF-κB activity may be assessed using such luciferase reporter assays.
The K145R gene is a late gene.
The gene (i.e. nucleotide) sequences of K145R genes from different ASFV strains are given below.
In an embodiment the attenuated ASFV of the invention lacks a functional version of the K145R gene. Suitably the K145R gene comprises the sequence of SEQ ID No. 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169 or 170. Suitably the K145R gene comprises a sequence having at least 70%, at least 80%, at least 90% or at least 95% identity with SEQ ID No. 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169 or 170. Suitably the K145R gene consists of the sequence of SEQ ID No. 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169 or 170.
The accessions numbers of K145R proteins from different strains of ASFV are listed below in Table 3.
The amino acid sequence of K145R proteins from different ASFV strain are depicted below.
K145R inhibits the host endoplasmic reticulum (ER) stress response (Barber 2015 Stress modulators encoded by African swine fever virus; PhD thesis, St Georges, University of London, 2016). This response is caused by the accumulation of unfolded proteins and may be activated during viral infections due to the substantial amounts of viral proteins being produced. ER stress leads to the increase in expression of the transcription factor CCAAT-enhancer-binding protein homologous protein (CHOP) and its accumulation in the nucleus of the cells. CHOP activity ultimately results in cell apoptosis, thus limiting viral replication.
K145R function may be tested by methods including immunofluorescence using an antibody against CHOP and assessment of its presence in the nucleus of cells following induction of ER stress, and luciferase reporter assay, where the luciferase gene is under control of the CHOP promoter.
The gene (i.e. nucleotide) sequences of B125R genes from different ASFV strains are given below.
In an embodiment the attenuated ASFV of the invention lacks a functional version of the B125R gene. Suitably the B125R gene comprises the sequence of SEQ ID No. 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194 or 195. Suitably the B125R gene comprises a sequence having at least 70%, at least 80%, at least 90% or at least 95% identity with SEQ ID No. 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194 or 195. Suitably the B125R gene consists of the sequence of SEQ ID No. 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194 or 195.
The accessions numbers of B125R proteins from different strains of ASFV are listed below in Table 4.
The amino acid sequences of B125R proteins from different ASFV strains are depicted below.
B125R was identified as one of the most abundant viral proteins expressed in infected wild boar cells (WSL-R) (Kapler et al. 2018 Sci. Rep. 8: 1471).
As shown in
The attenuated African Swine Fever (ASF) virus of one embodiment of the present invention has disrupted expression and/or activity of the following genes:
These genes may be referred to herein as the “disrupted genes”.
In an embodiment the invention provides an attenuated African Swine Fever (ASF) virus in which the expression of the following genes is disrupted:
The term “expression” with respect to a gene refers to the ability of the ASF virus to produce the product of the gene, such as RNA and/or protein. Disruption of expression of a gene means that production of the gene product is decreased. Expression of the gene may be decreased by at least 50%, at least 60%, at least 70%, at least 80%, at least 90% and/or at least 95%. Expression of the gene may be decreased to the extent that production of the gene product, such as RNA and/or protein, is entirely abolished (i.e. the gene product is not produced at all). Disruption of gene expression decreases expression of the gene relative to the expression of the gene when it is not disrupted. For example, a mutated gene may have decreased expression in comparison to a wild type version of the gene.
A gene the expression of which is disrupted may not be fully transcribed and translated. Transcription of the gene may be decreased by at least 50%, at least 60%, at least 70%, at least 80%, at least 90% and/or at least 95%. Transcription of the gene may be abolished (i.e. the gene may not be transcribed). Translation of the gene may be decreased by at least 50%, at least 60%, at least 70%, at least 80%, at least 90% and/or at least 95%. Translation of the gene may be abolished. The gene may be transcribed but not translated. The gene may be transcribed and translated but the protein too rapidly degraded to carry out its function. The gene may be transcribed and translated but the protein may be non-functional.
Gene expression may be measured by techniques known in the art. For example, the amount of mRNA transcribed from a gene may be quantified, such as by using quantitative polymerase chain reaction (qPCR). Alternatively or additionally, the amount of protein may be quantified, such as by using Western blotting or mass spectrometry.
In an embodiment the invention provides an attenuated African Swine Fever (ASF) virus in which the activity of the following genes is disrupted:
The term “activity” with respect to a gene refers to the ability of the gene to carry out its functions. Different genes have different activities i.e. different functions they fulfil. A given gene may have multiple activities; disruption of gene activity means disruption of one or more of those activities. One or more activity of the gene may be disrupted whilst one or more other activities are not disrupted. Disruption of gene activity decreases the activity of the gene relative to the activity of the gene when it is not disrupted. For example, a mutated gene may have decreased activity in comparison to a wild type version of the gene. Gene activity may be decreased to the extent that gene activity is entirely abolished.
The attenuated ASFV according to the present invention may comprise a non-functional version of the disrupted genes.
Disruption of expression of a gene may also disrupt activity of that gene as the decreased amount of gene product means the gene cannot as effectively carry out one or more of its activities.
In an embodiment, the activity of the gene that is disrupted is the ability of the gene to inhibit IRF3 and/or NFκB activity. In an embodiment, the invention provides an attenuated African Swine Fever (ASF) virus in which the ability of the following genes to inhibit IRF3 and/or NFκB activity is disrupted:
In an embodiment, the invention provides an attenuated ASF virus in which the ability of the MGF 360 12L, 13L and 14L, and MGF 505 1R genes to inhibit IRF3 activity is disrupted. In an embodiment, the invention provides an attenuated ASF virus in which the ability of the MGF 360 12L, 13L and 14L, and MGF 505 1R genes to inhibit NFκB activity is disrupted. The ability of MGF 360 12L, 13L and 14L, and/or MGF 505 1R to inhibit IRF3 and/or NFκB activity may be measured using a luciferase reporter assay as described herein.
Disruption of the ability to inhibit IRF3 and/or NFκB activity means that the ability to inhibit IRF3 and/or NFκB activity is decreased. In other words, the version of the MGF gene in the attenuated ASF virus of the invention inhibits IRF3 and/or NFκB activity less than would a wild type version of the same MGF gene. The ability to inhibit IRF3 and/or NFκB activity may be decreased by at least 50%, at least 60%, at least 70%, at least 80%, or at least 90%. In an embodiment the ability of the MGF gene to inhibit IRF3 and/or NFκB activity may be abolished i.e. the MGF gene does not inhibit IRF3 and/or NFκB activity. In that case, the activity of IRF3 and/or NFκB would be as high as if no MGF gene were present. A decrease in inhibition means IRF3 and/or NFκB activity is higher than it would be with the wild type version of the MGF gene. IRF3 and/or NFκB activity may be twice as high as it would be with the wild type version of the MGF gene, such as three times as high, four times as high, five times as high or six times as high.
IRF3 and NFκB are transcription factors that activate transcription of various genes, controlling expression of interferon and pro-inflammatory cytokines as part of the host's innate immune system response to viral infection. Inhibition of IRF3 and/or NFκB activity means decreasing activation of expression of their target genes. The degree of activation of IRF3 and/or NFκB target gene expression may be measured using a luciferase reporter assay in which an IRF3-activatable or NFκB-activatable promoter is linked to a luciferase reporter.
Suitably the ability of MGF 360 12L to inhibit IRF3 activity is disrupted. Suitably the ability of MGF 360 13L to inhibit IRF3 activity is disrupted. Suitably the ability of MGF 360 14L to inhibit IRF3 activity is disrupted. Suitably the ability of MGF 505 1R to inhibit IRF3 activity is disrupted. Suitably the ability of MGF 360 12L to inhibit NFκB activity is disrupted. Suitably the ability of MGF 360 13L to inhibit NFκB activity is disrupted. Suitably the ability of MGF 360 14L to inhibit NFκB activity is disrupted. Suitably the ability of MGF 505 1R to inhibit NFκB activity is disrupted.
IRF3 and NFκB function by binding to target DNA and activating transcription. An MGF gene may inhibit IRF3 and/or NFκB activity by inhibiting the ability of IRF3 and/or NFκB to activate transcription. In an embodiment the ability of MGF 360 12L to inhibit transcriptional activation by IRF3 and/or NFκB is disrupted. Suitably the ability of MGF 360 12L to inhibit transcriptional activation by IRF3 is disrupted. Suitably the ability of MGF 360 12L to inhibit transcriptional activation by NFκB is disrupted.
Mutation Disrupting Expression and/or Activity
Gene expression and/or activity are disrupted by mutating the ASFV genome i.e. by mutating the ASFV genome. A “mutation” means a change in the nucleotide sequence of the ASFV genome relative to a known ASFV genotype. Mutations include changing one or more nucleotides to different nucleotides (i.e. substitution), adding nucleotides, deleting nucleotides and/or a combination of these.
In an embodiment the attenuated ASF virus of the invention comprises mutations that disrupt the expression and/or activity of the following genes:
Gene expression and/or activity may be disrupted by disrupting transcription of the gene into mRNA i.e. by decreasing gene transcription, such as completely abolishing gene transcription. Gene expression and/or activity may be disrupted by disrupting translation of mRNA into protein. In an embodiment the attenuated ASF virus comprises mutations that decrease transcription and/or translation of the genes. In an embodiment the attenuated ASF virus comprises mutations that cause the genes to not be transcribed and/or translated (i.e. complete abolition of transcription and/or translation).
Gene expression and/or activity may be disrupted by mutating a non-coding sequence associated with the gene, such as a promoter. In an embodiment the attenuated ASF virus comprises mutations in promoters of one or more of the disrupted genes.
Gene expression and/or activity may be disrupted by mutating a coding sequence of one or more of the disrupted genes.
The attenuated ASFV of the invention comprises a functional version of the following genes:
Suitably the attenuated ASFV of the invention comprises functional versions of MGF 360 10L and 11L. Suitably the attenuated ASFV of the invention comprises functional versions of MGF 505 2R and 3R. Suitably the attenuated ASFV of the invention comprises functional versions of MGF 360 10L and MGF 505 2R. Suitably the attenuated ASFV of the invention comprises functional versions of MGF 360 10L and MGF 505 3R. Suitably the attenuated ASFV of the invention comprises functional versions of MGF 360 11L and MGF 505 2R. Suitably the attenuated ASFV of the invention comprises functional versions of MGF 360 11L and MGF 505 3R. Suitably the attenuated ASFV of the invention comprises functional versions of MGF 360 10L and MGF 505 2R and 3R. Suitably the attenuated ASFV of the invention comprises functional versions of MGF 360 11L and MGF 505 2R and 3R. Suitably the attenuated ASFV of the invention comprises functional versions of MGF 360 10L and 11L and MGF 505 2R. Suitably the attenuated ASFV of the invention comprises functional versions of MGF 360 10L and 11L and MGF 505 3R. Suitably the attenuated ASFV of the invention comprises functional versions of MGF 360 10L and 11L and MGF 505 2R and 3R.
In an embodiment, the attenuated ASFV of the invention comprises a DIVA mutation that is lack of a functional version of the K145R gene and/or lack of a functional version of the B125R gene.
In another aspect the invention provides an attenuated ASFV which lacks a functional version of the K145R gene and/or the B125R gene.
The expression “functional version” of a gene refers to a gene the expression and activity of which have not been disrupted. In other words, a functional version of a gene is not mutated in a manner that disrupts gene expression or gene activity. A functional version of a gene may not comprise any mutations. The coding sequence of a functional version of a gene may be complete and uninterrupted. A functional version of a gene may be fully transcribed and translated.
The function of an MGF gene may refer its ability to inhibit IRF3 and/or NFκB activity. A functional version of an MGF gene may inhibit IRF3 and/or NFκB activity. In an embodiment the attenuated ASFV of the invention comprises a version of the following genes that inhibits IRF3 and/or NFκB activity:
The ability of MGF 360 10L and/or 11L, and MGF 505 2R and/or 3R to inhibit IRF3 and/or NFκB activity may be measured using a luciferase reporter assay as described herein.
A functional version of a gene may correspond to the gene in a wild-type ASFV isolate. A functional version of a gene may correspond to the gene in a virulent ASFV strain. The sequence of a functional version of a gene may be identical to the sequence of the gene in a wild-type ASFV isolate or virulent ASFV strain. The sequence of a functional version of a gene may be identical to the sequence of the gene in the wild-type ASFV isolate from which the attenuated ASFV of the invention is derived. A functional version of a gene may be a natural variant of the gene in a wild-type ASFV isolate.
A functional version of a gene may comprise mutations. However, the mutations should not disrupt the expression or activity of the gene. In other words, the mutations should not affect the function of the gene. A functional version of a gene may comprise one or more synonymous mutations (i.e. mutations which do not alter the amino acid sequence of the protein the gene encodes). A functional version of a gene may comprise one or more silent mutations, which may be synonymous or non-synonymous. A functional version of a gene may comprise deletions that do not disrupt the expression or activity of the gene. A functional version of a gene may comprise one or more single nucleotide polymorphisms (SNPs) that do not disrupt the expression or activity of the gene.
An attenuated ASFV that lacks a functional version of a gene may not express the gene i.e. the gene may not be correctly transcribed and translated. The gene may not be transcribed. The gene may be transcribed but not translated. The gene may be transcribed and translated but the protein too rapidly degraded to carry out its function. The gene may be transcribed and translated but the protein may be non-functional.
Gene expression may be measured by techniques known in the art. For example, the amount of mRNA transcribed from a gene may be quantified, such as by using quantitative polymerase chain reaction (qPCR). Alternatively or additionally, the amount of protein may be quantified, such as by using Western blotting or mass spectrometry.
An attenuated ASFV that lacks a functional version of a gene may comprise a mutation that causes the ASFV to not express the gene. The mutation may be a deletion as described herein. The mutation may be an interruption as described herein.
Lack of a functional version of the K145R gene may mean that the ability of the K145R gene to inhibit the host endoplasmic reticulum (ER) stress response is decreased. K145R function may be tested by methods including immunofluorescence using an antibody against CHOP and assessment of its presence in the nucleus of cells following induction of ER stress, and luciferase reporter assay, where the luciferase gene is under control of the CHOP promoter.
In an embodiment the attenuated ASFV of the invention comprises a Differentiating Infected from Vaccinated Animals (DIVA) mutation. Suitably the DIVA mutation is lack of a functional version of the K145R gene and/or lack of a functional version of the B125R gene.
In an embodiment, the invention provides an attenuated ASFV in which the expression and/or activity of the following genes is disrupted:
which comprises a functional version of the following genes:
and which comprises a DIVA mutation.
In an embodiment, the invention provides an attenuated ASFV in which the expression and/or activity of the following genes is disrupted:
which comprises a functional version of the following genes:
and which lacks a functional version of the K145R gene and/or the B125R gene.
In another aspect the invention provides an attenuated ASFV which lacks a functional version of the K145R gene and/or the B125R gene. Suitably the attenuated ASFV of the invention lacks a functional version of the K145R gene. Suitably the attenuated ASFV of the invention lacks a functional version of the B125R gene.
In another aspect the invention provides an attenuated ASFV that lacks a functional version of the DP148R gene and comprises a DIVA mutation. In an embodiment the attenuated ASFV of the invention lacks a functional version of the following genes:
In an embodiment the attenuated ASFV of the invention may lack a functional version of the DP148R gene and the K145R gene. In an embodiment the attenuated ASFV of the invention may lack a functional version of the DP148R gene and the B125R gene. Suitably the DP148R gene is partially or completely deleted. Suitably the K145R gene is partially or completely deleted. Suitably the B125R gene is partially or completely deleted. In an embodiment of the attenuated ASFV the following genes are completely deleted: DP148R and K145R. In an embodiment of the attenuated ASFV the following genes are completely deleted: DP148R and B125R.
In the attenuated ASFV of the invention, expression and/or activity of genes may be disrupted by deletion. In other words, expression and/or activity of a gene may be disrupted by a mutation that is a deletion.
An attenuated ASFV of the invention may be made to lack a functional version of a gene by deletion. In other words, the mutation that causes the ASFV to lack a functional version of a gene may be a deletion.
“Deletion” means removal of part of the ASFV genome nucleotide sequence. The deletion may be continuous, or may comprise deletion of a plurality of sections of sequence. Deletion may disrupt gene expression and/or activity in any of the ways described herein. Deletion may cause the ASFV to lack a functional version of the gene in any of the ways described herein.
Deletion may disrupt transcription of the gene into mRNA. For example, deleting a promoter of a gene would disrupt transcription. Deletion may disrupt translation of mRNA into protein. For example, deleting a start codon would disrupt translation. Gene expression and/or activity may be disrupted by deleting non-coding sequence associated with the gene, such as a promoter.
Gene expression and/or activity may be disrupted by deleting coding sequence of the gene. The ASFV may be made to lack a functional version of the gene by deleting coding sequence of the gene. Deletion of coding sequence may be partial (i.e. part of the coding sequence is deleted). The deletion may, for example, remove at least 50, 60, 70, 80 or 90% of the coding sequence of the gene. The deletion may be complete, in which case 100% of the coding sequence of the gene is absent when compared to the corresponding genome of the wild-type isolate.
Deletion of coding sequence may be continuous, or may comprise deletion of a plurality of sections of coding sequence. The deletion should remove a sufficient amount of coding sequence such that deletion disrupts the expression and/or activity of the gene i.e. a functional gene product, such as a protein, is no longer produced from the gene. The expression “deletion of a gene” (such as “partially deleted”) refers to deletion of a sufficient amount of coding sequence such that expression and/or activity of the gene is disrupted. The amount of coding sequence required to be deleted to disrupt gene expression and/or activity may be very small. For example, deletion of just the start codon (ATG) may be sufficient to disrupt expression and/or activity of the gene to attenuate the virus.
Partial and full deletions of a gene can be made using known techniques in the art, such as conditional targeting via Cre-LoxP and Flp-FRT systems, or by inducing a double strand break (DSB) and repair using engineered nucleases such as meganucleases, zinc finger nucleases (ZFNs), transcription-activator like effector nucleases (TALENs) and Cas in CRISPR-Cas systems. The DSB repair can be exploited to introduce a desired mutation by providing a vector comprising the desired mutated nucleotide sequence within a sequence that is homologous to the sequences flanking either side of the DSB. This results in the desired mutation being inserted at the site of the DSB. Nucleases such as those above can be engineered to induce DSB at a specific site within the genome. For example, chimeric meganucleases can be readily generated by combining known protein units to recognise a target recognition sequence within a gene or genomic region of interest. ZFNs can also be designed to target specific sequences, for example combining zinc-finger units with known specificities to bind specific regions of DNA. TALENs are artificial restriction enzymes designed by fusing a nuclease domain to DNA-binding TALE (transcription activator-like effector) domains. TALE domains are tandem arrays of amino acid repeats that recognise a single nucleotide and can be designed to target a specific region of DNA. CRISPR-Cas systems consist of a Cas (CRISPR-associated protein) nuclease and a CRISPR (clustered regularly interspaced short palindromic repeat) RNA sequence that guides the Cas protein to recognise and cleave a specific strand of DNA complementary to the CRISPR sequence. Single-stranded guide RNA (sgRNA) can therefore be designed to bind to a specific region of DNA and guide the Cas to introduce a DSB. Accordingly, provided the nucleotide (e.g. DNA or cDNA) sequence of a gene is known, a known nuclease system can be utilised to introduce a partial or full deletion to the gene.
In an embodiment of the attenuated ASF virus of the present invention the following genes may be at least partially deleted:
One or more (such as two or more, three or more or all four) of the disrupted genes may be at least partially deleted. The coding sequences of one or more (such as two or more, three or more or all four) of the disrupted genes may be at least partially deleted.
In an embodiment of the attenuated ASF virus of the present invention the following genes may be completely deleted:
One or more (such as two or more, three or more or all four) of the disrupted genes may be completely deleted. The coding sequences of one or more (such as two or more, three or more or all four) of the disrupted genes may be completely deleted.
In an embodiment, an attenuated ASFV of the invention lacks a functional version of the K145R gene and/or the B125R gene. The gene may be wholly or partially deleted. The coding sequence of the gene may be wholly or partially deleted. Suitably the K145R gene coding sequence is wholly or partially deleted. Suitably the B125R gene coding sequence is wholly or partially deleted.
In an embodiment, an attenuated ASFV of the invention lacks a functional version of the K145R gene and/or the B125R gene. The K145R gene and/or the B125R gene may be wholly or partially deleted. The coding sequence of the gene may be partially or completely deleted. Suitably the K145R gene coding sequence is partially or completely deleted. Suitably the B125R gene coding sequence is partially or completely deleted.
In an embodiment of the attenuated ASFV of the present invention the following genes may be at least partially deleted:
One or more (such as two or more, three or more, four or more, five or more or all six) of the genes may be at least partially deleted. The coding sequences of one or more (such as two or more, three or more, four or more, five or more or all six) of the genes may be at least partially deleted.
In an embodiment of the attenuated ASFV of the present invention the following genes may be completely deleted:
One or more (such as two or more, three or more, four or more, five or more or all six) of the genes may be completely deleted. The coding sequences of one or more (such as two or more, three or more, four or more, five or more or all six) of the genes may be completely deleted.
The expression and/or activity of the genes may be disrupted by interruption of the gene. In other words, the mutation that disrupts expression and/or activity of a gene may be one that interrupts the gene.
An attenuated ASFV of the invention may be made to lack a functional version of a gene by interruption of the gene. In other words, the mutation that causes the ASFV to lack a functional version of a gene may be one that interrupts the gene.
In an embodiment of the attenuated ASFV of the present invention the following genes may be interrupted:
One or more (such as two or more, three or more or all four) of the genes may be interrupted.
In another embodiment of the attenuated ASF virus of the invention the K145R gene and/or the B125R gene may be interrupted. Suitably the K145R gene may be interrupted. Suitably the B125R gene may be interrupted.
In an embodiment of the attenuated ASFV of the present invention the following genes may be interrupted:
One or more (such as two or more, three or more, four or more, five or more or all six) of the genes may be interrupted.
“Interruption” means the mutation alters the coding sequence of the gene such that a functional gene product, such as a protein, is no longer produced. The term “interruption” may be used herein to refer to a mutation that interrupts a gene. The mutation(s) should interrupt the coding sequence in a manner such that expression and/or activity of the gene is disrupted i.e. a functional gene product, such as a protein, is no longer produced from the gene.
The interruption may entirely abolish gene product production. For example, where the gene product is a protein, the interruption may render the mRNA nonsensical, causing the mRNA to be degraded and the protein to not be translated, thereby abolishing protein production.
The interruption may alter the gene product that is produced. The interruption may cause the gene to not be transcribed and/or translated.
The interruption may be a point mutation (i.e. substitution, insertion or deletion of a single nucleotide). An interruption may be a deletion. A gene may comprise multiple mutations that lead to interruption of the gene.
The interruption may be a frame shift mutation. A frame shift causes the codons downstream of the frame shift to be read as different amino acids. The protein produced may be non-functional.
The interruption may be mutation of a start codon. A start codon is typically ATG. Mutation of a start codon (e.g. point mutation of one, two or three of the nucleotides) means that translation will not start at that codon. Translation may begin at a subsequent start codon further downstream. If the subsequent start codon is in frame a version of the protein is produced that is N-terminally truncated and so may be non-functional. If the subsequent start codon is not in frame an entirely different or nonsense protein is produced, which would be non-functional. If there is no subsequent start codon, translation is entirely abolished and no protein is produced.
The interruption may be mutation of a stop codon (TAG, TAA or TGA). Mutation of a stop codon (also referred to as a nonstop mutation) causes continued translation of mRNA into a sequence that should not be translated. The resulting protein may be non-functional due to its excessive length.
The mutations that disrupt gene expression and/or activity described herein may be combined in an attenuated ASFV of the invention. In other words, each of the disrupted genes (MGF 360 genes 12L, 13L and 14L, MGF 505 gene 1R) in an attenuated ASFV of the invention may be disrupted by the same type of mutation as any of the other genes or by a different type of mutation as any of the other genes.
In an embodiment of the attenuated ASFV of the invention, one or more of the disrupted genes may be disrupted by mutation of a promoter sequence, whilst one or more other disrupted genes may be disrupted by partial deletion of coding sequence, whilst one or more other genes may be disrupted by complete deletion of coding sequence, whilst one or more other genes may be disrupted by interruption of the gene.
The present invention also provides a vaccine comprising an attenuated ASF virus of the invention.
The term “vaccine” as used herein refers to a preparation which, when administered to a subject, induces or stimulates a protective immune response. A vaccine can render an organism immune to a particular disease, in the present case ASF. The vaccine of the present invention thus induces an immune response in a subject which is protective against subsequent ASF virus challenge. A vaccine comprising an attenuated ASFV of the invention may be capable of inducing a cross-protective immune response against a plurality of ASF virus genotypes. In an embodiment a vaccine comprising an attenuated ASFV of the invention of a single genotype may be capable of inducing a cross-protective immune response against a plurality of ASF virus genotypes.
The vaccine may comprise a plurality of attenuated ASF viruses. The plurality of attenuated ASF viruses may correspond to a plurality of different isolates, for example, different isolates of high or unknown virulence. Such a vaccine may be capable of inducing a cross-protective immune response against a plurality of ASF virus genotypes.
The vaccine may be useful in preventing African Swine Fever. Accordingly the invention provides a vaccine of the invention for use in treating and/or preventing African Swine Fever in a subject.
The present invention also provides a pharmaceutical composition which comprises one or more attenuated ASF virus(es) of the invention. The pharmaceutical composition may be used for treating African Swine Fever.
The vaccine or pharmaceutical composition may comprise one or more attenuated ASF virus(es) of the invention and optionally one or more adjuvants, excipients, carriers and diluents. The choice of pharmaceutical excipient, carrier 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. The pharmaceutical compositions typically should be sterile and stable under the conditions of manufacture and storage. Formulations for parenteral administration include, but are not limited to, suspensions, solutions, emulsions in oily or aqueous vehicles, pastes, and implantable sustained-release or biodegradable formulations. Sterile injectable formulations may be prepared using a nontoxic parenterally acceptable diluent or solvent. A pharmaceutical composition of the present invention may include pharmaceutically acceptable dispersing agents, wetting agents, suspending agents, isotonic agents, coatings, antibacterial and antifungal agents, carriers, excipients, salts, or stabilizers which are nontoxic to the subjects at the dosages and concentrations employed. Preferably, such a composition can further comprise a pharmaceutically acceptable carrier or excipient for use in the treatment of disease that that is compatible with a given method and/or site of administration, for instance for parenteral (e.g. sub-cutaneous, intradermal, or intravenous injection) or intrathecal administration.
The vaccine or pharmaceutical composition may comprise one or more attenuated ASF virus(es) of the invention in an effective amount.
In an embodiment the invention provides an attenuated ASF virus of the invention which when administered to a subject induces an immune response which is protective against subsequent challenge with virulent ASF virus. In an embodiment the invention provides an attenuated ASF virus of the invention which when administered to a subject induces an immune response which is protective against subsequent challenge with virulent ASF virus of a different genotype to the attenuated ASF virus of the vaccine.
The present invention also provides a method of preventing and/or treating ASF in a subject by administration to the subject of an effective amount of an attenuated virus, vaccine, or pharmaceutical composition of the invention.
The term “preventing” is intended to refer to averting, delaying, impeding or hindering the contraction of ASF. The vaccine may, for example, prevent or reduce the likelihood of an infectious ASFV entering a cell.
The term “treating” is intended to refer to reducing or alleviating at least one symptom of an existing ASF infection.
The subject may be any animal which is susceptible to ASF infection. ASF susceptible animals include domestic pigs, warthogs, bush pigs and ticks.
The subject vaccinated according to the present invention may be a domestic pig.
The vaccine of the invention may be administered by any convenient route, such as by intramuscular injection. Other suitable routes of administration include intranasal, oral, subcutaneous, transdermal and vaginal (e.g. during artificial insemination). In one embodiment, oral administration comprises adding the vaccine to animal feed or drinking water. In another embodiment, the vaccine may be added to bait for a wild animal, for example bait suitable for wild boar, wild pigs, bushpigs or warthogs.
The dose for pig immunisation may be less than 104 HAD50 or TCID50 per pig. For example the dose may be between 102-103 HAD50 or TCI D50. The dose may be about 102 HAD50 or TCID50 per pig. The dose may be determined by a veterinary practitioner within the scope of sound veterinary judgment.
The vaccine may be administered following a prime-boost regime. For example, after the first inoculation, the subjects may receive a second boosting administration some time (such as about 7, 14, 21 or 28 days) later. Typically the boosting administration is at a higher dose than the priming administration. The boosting dose may be about 102, 103 or 104 HAD50 or TCID50 of the recombinant attenuated virus per pig.
The present invention also provides a method of attenuating an ASF virus, which comprises the step of disrupting the expression and/or activity of the following genes:
whilst retaining the function of the following genes:
Disruption of gene expression and/or activity may be achieved by mutating the ASFV genome in any of the ways described herein.
The following genes may be partially or completely deleted:
One or more (such as two or more, three or more or all four) of the disrupted genes may be at least partially or completely deleted. The coding sequences of one or more (such as two or more, three or more or all four) of the disrupted genes may be at least partially or completely deleted.
The following genes may be interrupted:
One or more (such as two or more, three or more or all four) of the genes may be interrupted.
Methods for mutation of viral genes are known in the art. In particular, methods for deletion of viral genes are known in the art. For example, homologous recombination may be used, in which a transfer vector is created in which the relevant gene(s) are missing and used to transfect virus-infected cells. Recombinant viruses expressing the new portion of sequence may then be selected. Similar procedures may be used in order to interrupt gene expression, for example by deletion of the ATG start codon.
“Retaining the function” of a gene means that expression and activity of the gene is not affected during the attenuation process. The resultant attenuated virus should express a functional version of the gene. Suitably, the genes the function of which is to be retained are unaltered by the method of attenuation. Suitably, the sequences of the genes the function of which is to be retained are unaltered by the method of attenuation.
In some embodiments of the present invention, the method of attenuating an ASF virus may comprise retaining the function of MGF 360 10L and MGF 505 2R. In some embodiments, the method may comprise retaining the function of MGF 360 11L and MGF 505 2R. In some embodiments, the method may comprise retaining the function of MGF 360 10L and MGF 505 3R. In some embodiments, the method may comprise retaining the function of MGF 360 11L and MGF 505 3R. In some embodiments, the method may comprise retaining the function of MGF 360 10L and 11L and MGF 505 2R. In some embodiments, the method may comprise retaining the function of MGF 360 10L and 11L and MGF 505 3R. In some embodiments, the method may comprise retaining the function of MGF 360 10L and MGF 505 2R and 3R. In some embodiments, the method may comprise retaining the function of MGF 360 11L and MGF 505 2R and 3R. In some embodiments, the method may comprise retaining the function of MGF 360 10L and 11L and MGF 505 2R and 3R.
This disclosure is not limited by the exemplary methods and materials disclosed herein, and any methods and materials similar or equivalent to those described herein can be used in the practice or testing of embodiments of this disclosure. Numeric ranges are inclusive of the numbers defining the range. Unless otherwise indicated, any nucleic acid sequences are written left to right in 5′ to 3′ orientation; amino acid sequences are written left to right in amino to carboxy orientation, respectively.
It must be noted that as used herein and in the appended claims, the singular forms “a”, “an”, and “the” include plural referents unless the context clearly dictates otherwise.
The terms “comprising”, “comprises” and “comprised of” as used herein are synonymous with “including”, “includes” or “containing”, “contains”, and are inclusive or open-ended and do not exclude additional, non-recited members, elements or method steps. The terms “comprising”, “comprises” and “comprised of” also include the term “consisting of”.
The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that such publications constitute prior art to the claims appended hereto.
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.
The effect of MGF genes on activity of interferon regulatory factor 3 (IRF3) and NF-κB was tested using a luciferase reporter assay. IRF-3 and NF-κB are transcription factors that control expression of interferon and pro-inflammatory cytokines as part of the host's innate immune system response to viral infection.
HEK293T cells were transfected with a luciferase reporter under control of a promoter specifically activated by IRF3. The cells were also transfected with a plasmid expressing an MGF gene (MGF360-10L, 11L, 12L, 13L or 14L, MGF 505-1R, 2R, 3R, 4R or 5R, or MGF110-1L), an empty vector (as negative control) or a plasmid expressing CSFV Npro (a known IRF3 inhibitor protein, as positive control). The cells were then stimulated with Sendai Virus (SeV) to activate IRF3. The levels of luciferase following stimulation provide a measure of the ability of MGFs to modulate the signalling cascades controlled by IRF-3 and NF-kB. As shown in
An equivalent experiment was performed to test the effect of MGF genes on NF-κB expression. For this experiment, the cells were instead transfected with a luciferase reporter under control of a promoter specifically activated by NF-κB, a poxvirus MC160 protein that inhibits NF-κB was used for the positive control and NF-κB was activated by transfection of the cells with NF-κB sub-unit p65. The results, shown in
A further experiment was performed to further investigate how MGF genes inhibit IRF3 and NF-κB activity.
Transcription factors (TF) generally possess two major domains: a transcriptional activation domain (TAD) and a DNA binding domain (DBD). These domains are interchangeable and therefore chimeric proteins containing TAD and DBD from different TFs can be used to further explore cell signalling pathways.
Chimeras containing the NF-κB p65 or the IRF3 TADs fused to the GAL4 DBD were used to evaluate the ability of the MGFs to directly inhibit NF-κB p65 or IRF3 transcriptional activity. In this case, the reporter plasmid contained the luciferase gene under the control of a responsive element that is recognised by the GAL4 DBD. Therefore, the luciferase activity was not dependent on the ability of IRF3 or NF-κB to bind their promoters but rather solely on their activation status.
Taken together, these results indicate that all the MGF genes tested are able to inhibit IRF-3 and NF-kB function by binding to DNA and/or recruitment of co-activators. MGF360-12 L also inhibits the activity of these transcription factors directly, therefore providing a possible explanation for the stronger inhibition of IRF3 and NF-kB observed with MGF 360-12L compared to the other MGF genes. The NF-kB promoter binding element is present in promoters for additional genes to type I interferon and inhibition of this pathway is likely to affect a broader range of genes including those involved in activating a proinflammatory response.
Two sets of genes of the multigene families 360 and 505 were deleted in ASFV Georgia 2007/1 strain.
In MGFA the complete coding regions of genes MGF360-12L, MGF360-13L, MGF360-14L and MGF505-1R were deleted.
In MGFB the complete coding regions of genes MGF360-13L, MGF360-14L, MGF505-2R and MGF505-3R were deleted.
The MGFA and MGFB deletions are shown schematically in
The MGFA deletion was made in combination with deletion of the K145R gene (GeorgiaΔK145RΔMGFA) or the B125R gene (GeorgiaΔB125RΔMGFA).
The MGFB deletion was made in combination with deletion of the K145R gene (GeorgiaΔK145RΔMGFB).
Groups of 6 large white landrace pigs were immunised intramuscularly with 104 TCID50/m1 GeorgiaΔK145RΔMGFA (Group C), GeorgiaΔK145RΔMGFB (Group D) or GeorgiaΔB125RΔMGFA (Group BA) viruses.
Pigs from group D were culled at the humane endpoint after immunisation.
Pigs in Groups C and BA were boosted and then challenged with parental virulent Georgia strain.
The experimental protocol is depicted in
Pigs from Group D (GeorgiaΔK152RΔMGFB) were all culled between day 5 and 9 post-immunisation at moderate severity endpoint (
Pigs from Group C (GeorgiaΔK145RΔMGFA) and Group BA (GeorgiaΔB125RΔMGFA) survived immunisation and boost.
After challenge, 2 pigs from Group C were culled at days 7 or 11 (
Pigs in Groups C and BA showed no rise in temperature (
At days 5 or 6 post-challenge all pigs (except one pig from Group C) developed temperatures above 40.5° C. and other signs which lasted between 1 and 3 days (except for pigs which were culled at the moderate severity end-point). Remaining pigs showed no further signs until the experiment was terminated.
The levels of virus genome in whole blood were measured by quantitative PCR throughout the experiment. One pig immunised in Group C had very low genome level at day 6 post-immunisation but no other pigs in Group C or Group AB had detectable virus genome following immunisation or boost (
After challenge virus genome was detected in blood from all pigs. In Group C a peak varying between 10e4 and 10e6 genome copies per ml was detected at day 7 post-challenge in all pigs that survived decreasing slowly after this. As expected in the two pigs that didn't survive higher levels of virus genome were detected. In Group BA, virus genome was detected at similar levels in pigs that survived and at higher levels in those that didn't survive.
The levels of infectious virus in whole blood was measured after challenge (
Peripheral blood mononuclear cells (PBMCs) were collected pre-immunisation, pre-boost and pre-challenge and stimulated with live ASFV (either the homologous virulent Georgia 2007/1 strain or heterologous genotype I virulent strain Benin 97/1). Numbers of interferon gamma producing cells were measured by Elispot assays (
As expected no responses were detected pre-immunisation. In Group C low responses to Georgia virus stimulation were detected pre-boost but these increased several fold before challenge (
The antibody response to the major ASFV capsid protein p72/B646L was measured post-immunisation using a commercial competitive ELISA (Ingenasa). Antibody responses above the cut-off were detected by day 30 post-immunisation (after the boost) in pigs from Group C, increasing thereafter but not reaching 100% until after challenge (
To screen for genes that could serve as Differentiating Infected from Vaccinated Animals (DIVA) markers in ASFV, 71 plasmids coding for individual ASFV genes (excluding known essential genes) fused to an HA or V5 epitope tag were transfected into Vero cells. The cells were fixed and permeabilised and stained with antisera from different immunised pigs followed by a fluorescently labelled secondary antibody. Confocal microscopy was used to assess whether the expressed gene could be detected.
In parallel the cells were stained with an antibody against the HA or V5 tag fused to the ASFV gene and a different fluorescently labelled secondary antibody to confirm expression of the protein.
The pig sera used for staining the cells were from immunisation studies using the following viruses: BeninΔDP148R (5 pigs), BeninΔMGF (6 pigs), OURT88/3 (5 pigs) and GeorgiaΔMGF (4 pigs). For each pig, a pre-immunisation serum sample (as a control) and a post-immunisation, pre-challenge serum sample were used.
An initial screen of the genes was conducted using sera from BeninΔDP148R immunised pigs (pre-immunisation sera from day 0, post-immunisation sera from day 38 post-immunisation). ASFV genes CP204L, B646L and E183L were used as positive controls and were detected using post-immunisation sera. Pre-immunisation sera did not detect any genes.
Six ASFV genes were detected using BeninΔDP148R post-immunisation sera, as shown below in Table 5 (++ indicates strong detection, + indicates weak detection, − indicates no detection).
The six ASFV genes detected in the initial screen were then tested with pig serum from other immunisation studies.
Table 6 below shows detection of ASFV genes using post-immunisation sera from 6 pigs immunised with BeninΔMGF virus (boosted on day 15, post-immunisation serum taken on day 38 post-immunisation; pre-immunisation sera were negative).
Table 7 below shows detection of ASFV genes using post-immunisation sera from 5 pigs immunised with OURT88/3 virus (post-immunisation serum taken on day 20 post-immunisation; pre-immunisation sera were negative except for pig 2).
Table 8 below shows detection of ASFV genes using post-immunisation sera from 4 pigs immunised with GeorgiaΔMGF virus (post-immunisation serum taken on day 34 post-immunisation; pre-immunisation sera taken on day −3 were negative). 2 pigs (A) were immunised with 103 GeorgiaΔMGF; 2 pigs (B) were immunised with 104 GeorgiaΔMGF.
Vero cells were transfected with a plasmid expressing the B125R gene fused to an HA-epitope tag. Cells were fixed and permeabilised then stained with an anti-HA antibody followed by appropriate secondary antibody.
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 virology, molecular biology or related fields are intended to be within the scope of the following claims.
| Number | Date | Country | Kind |
|---|---|---|---|
| 2003289.2 | Mar 2020 | GB | national |
| 2003292.6 | Mar 2020 | GB | national |
| 2005878.0 | Apr 2020 | GB | national |
| 2005880.6 | Apr 2020 | GB | national |
| 2013541.4 | Aug 2020 | GB | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/GB2021/050561 | 3/5/2021 | WO |
