Patent Application
20160122728
The present invention relates to a live avirulent infectious pancreatic necrosis virus which has been shown to be genetically stable in biological studies. Fish exposed to said virus turn out positive for the virus without showing any signs of disease and the avirulent virus has also been shown to protect the fish against IPN for an extended period of time after administration. Thus, a vaccine comprising said virus and said virus for the prophylaxis or treatment of infectious pancreatic necrosis disease is also part of the present invention.
Infectious pancreatic necrosis (IPN) is an economically significant viral disease of salmonid fish worldwide. The disease was first described in freshwater trout in North America in the 1950's and has been reported in Europe since the early 1970's. Initially, IPN was regarded as a serious disease affecting rainbow trout fry and fingerlings. However as the salmon farming industry began to expand during the 1970's, incidence of IPN disease in salmon also increased with the result that IPN is now widespread in the salmon farming industry worldwide. The economic loss due to the disease is large and outbreaks may occur in Atlantic salmon juveniles in fresh-water and in post-smolts after transfer to sea-water.
Infectious pancreatic necrosis virus (IPNV) is the causative agent of IPN and is a member of the Genus Aquabirnavirus, family Birnaviridae. Aquatic birnaviruses have a wide host range infecting many species of fish. Apart from salmonids they have been isolated from fish belonging to over 32 different families, 11 species of mollusks and four crustacean families.
The IPNV genome consists of two segments of double-stranded RNA that are surrounded by a single-shelled icosahedral capsid of 60 nm in diameter. Genomic segment A (typically 3097 nucleotides) encodes a 106 kDa precursor polyprotein composed of pVP2-VP4-VP3, in that order, and a 15 kDa non-structural VP5 protein, found only in infected cells. Segment B (typically 2777 nucleotides) encodes a minor internal polypeptide VP1 (94 kDa), which is the virion-associated RNA-dependent RNA polymerase (RdRp).
Most aquatic birnaviruses, regardless of host or geographic location, are antigenetically related and belong to a single serogroup A. Serogroup A has been divided into nine serotypes: A1-A9. The A1 serotype contains most of the isolates from the United States; serotypes A2 to A5 are primarily European isolates and serotypes A6 to A9 occur in Canada. Serogroup B comprises one serotype isolated from mollusks.
Within the various serotypes/genogroups, there is a high degree of antigenic variability and differences in the virulence and pathogenicity among the strains. Virulence of the IPNV has been associated with segment A and in particular with the VP2 structural protein.
VP2 is a major capsid protein (
Virulent strains typically have residues threonine, alanine, threonine/alanine, and tyrosine/histidine at positions 217, 221, 247 and 500 of the VP2 sequence. Further work has shown that virulent isolates possess residues Thr217 and Ala221; moderate to low virulent strains have Pro217 and Ala221; and strains containing Thr221 are almost always avirulent, irrespective of the residue at position 217.
Active immunisation of hens using vaccines based on avirulent viruses has long been the industry's standard to protect chickens from an immunosuppressive disease caused by infectious bursal disease virus (IBDV). This virus is a birnavirus like IPNV, but an important difference between IBDV and IPNV is that almost all fish surviving an IPN infection will become long-term carriers of the virus. The IPNV carrier state has no direct negative impact on affected individuals. In persistently infected fish, virus is found associated with leucocytes in blood, head kidney and spleen, presumably in macrophages. Carrier fish shed virus in their faeces, however, titers fluctuate over time and are known to increase in periods of stress.
RNA viruses such as IPNV and IBDV are prone to change through a variety of mechanisms, so it has been assumed that there always is a risk that the virus will revert to greater virulence during multiplication in the vaccinated fish. Such a strategy would require vigilance in monitoring field viruses and the natural history of the disease. So far, unawareness about factors influencing the virulence and genetic stability of IPNV has precluded the use of avirulent strains for vaccine purposes.
An alternative to the use of vaccines based on live avirulent IPNV is inactivated virus vaccines. Killed virus vaccines are prepared by growing virus in large amounts on cell cultures. The virus is then harvested and inactivated with formalin or other similar agents under conditions that ensure the retention of the immunogenic activity of the protective antigens but no virulent virus remains in the vaccine. The current strategies for an inactivated vaccine are expensive, labor intensive and subject to the risk of presence of noninactivated virus. Vaccination with inactivated virus has been tested in rainbow trout given by the oral route, immersion and injection. Protection against challenge was only obtained by injection. However, injection of a large number of fry is not practical in a hatchery situation.
Another option is to use subunit vaccines which are composed of a part of the virus particle responsible for inducing protecting immunity. As previously disclosed, VP2 is a major IPNV capsid protein and is responsible for the production of type-specific monoclonal antibodies. This makes this particular protein a very interesting candidate for use in a subunit vaccine. In fact, vaccination of presmolt with recombinant VP2 (rVP2) included in a commercial oil/glucan-adjuvanted multivalent injectable vaccine resulted in fish protection against IPN in natural outbreaks as compared to fish vaccinated with the same vaccine without the IPN component. This recombinant vaccine against IPNV in Atlantic salmon postsmolts has been approved for commercial use in Norway. However, while older fish can be vaccinated by intraperitoneal injection, this route of administration is not an option in fry due to their small size.
Some producers have also suggested that all parr should be deliberately infected with IPNV as a form of auto-vaccination of survivors, but found that apart from the legal and welfare implications of such a strategy, this would merely transfer the losses from marine to freshwater phase. This is clearly the situation when considering auto-vaccination with a virulent strain.
As it appears from the above summary of the state of the art, there is an industrial need for improved means of controlling IPNV infection in fish, which are non-toxic to the fish and can be administered in an industrially convenient manner and which protect the fish for an extended period of time after administration. Such improvement that are provided by the invention is the treatment of fish to cure or prevent IPNV infection by administering, preferably by immersion, a live avirulent IPNV which is genetically stable in the sense that it does not revert to virulence. Such an avirulent virus has not previously been used, as it hitherto has been considered not an acceptable strategy due to the risk that the avirulent strain revert to virulence.
A first aspect of the present invention relates to a live avirulent IPNV which do not revert to a virulent virus after at least 3 passages in hosts known to be susceptible to IPNV.
One embodiment relates to a live avirulent IPNV according to the first aspect of the present invention, which when delivered by immersion at a titre of 2×105 TCID50/ml to Atlantic salmon fry held in fresh water at a temperature of 12° C. causes the fry to be virus positive measured by reisolation on RTG-2 cells.
One embodiment relates to a live avirulent IPNV according to the first aspect of the present invention, which when delivered by immersion at a titre of 2×105 TCID50/ml to Atlantic salmon fry held in fresh water at a temperature of 12° C. provides the fry with protection against IPN disease as compared to non-infected fry.
One embodiment relates to a live avirulent IPNV according to the first aspect of the present invention, which when delivered by immersion at a titre of 2×105 TCID50/ml to Atlantic salmon fry held in fresh water at a temperature of 12° C. does not cause the fry to develop any signs of IPN disease.
In one preferred embodiment, said live avirulent IPNV comprises a nucleic acid encoding a VP2 protein, wherein the amino acid in position 252 of the VP2 protein is not Val.
In one preferred embodiment, said live avirulent IPNV comprises a nucleic acid encoding a VP2 protein, wherein the amino acid in position 252 of the VP2 protein is selected from the group consisting of Ser, Thr, Asn, Gln, Tyr and Cys; preferably selected from the group consisting of Asn and Gln; and most preferably the amino acid residue in position 252 is Asn.
In one preferred embodiment, said live avirulent IPNV comprises a nucleic acid encoding a protein comprising an amino acid sequence having at least 80% sequence identity with the amino acid sequence represented by residues 1-442 of SEQ ID NO:1, with the proviso that the amino acid residue in position 252 is not Val.
In one preferred embodiment, said live avirulent IPNV comprises a nucleic acid encoding a protein comprising an amino acid sequence having at least 80% sequence identity with the amino acid sequence represented by residues 1-442 of SEQ ID NO:1, with the proviso that the amino acid residue in position 252 of the protein is selected from the group consisting of Ser, Thr, Asn, Gln, Tyr and Cys; preferably selected from the group consisting of Asn and Gln; and most preferably the amino acid residue in position 252 is Asn.
In one preferred embodiment the amino acid residues in position 281, 282 and 319 of the protein are not Thr, Asn and Ala respectively.
In one preferred embodiment the amino acid residues in position 281, 282 and 319 of the protein are Ser, Asp and Glu respectively.
In one preferred embodiment the amino acid residues in position 252, 281, 282 and 319 of the protein are Asn, Ser, Asp and Glu respectively.
In one preferred embodiment the amino acid residue in position 221 of the protein is Thr.
In one preferred embodiment the amino acid residue in position 217 of the protein is Pro.
In one preferred embodiment said protein causes the avirulent virus not to revert to a virulent virus after at least 3 passages in hosts known to be susceptible to IPNV.
In one particularly preferred embodiment, the live avirulent IPNV according to the first aspect of the present invention is the one designated as IPNV-G700 (deposited under ECACC-No. 11 041201), deposited Apr. 12, 2011, at European Collection of Cell Cultures, Culture Collections, Public Health England, Porton Down, Salisbury, SP4 OJG, UK), or closely related strains thereof. Said closely related strains preferably being any strain which shares similar genotypic and/or phenotypic characteristics to the deposited strain.
One preferred embodiment relates to the live avirulent IPNV according to the first aspect of the present invention, which when delivered by immersion at a titre of 2×105 TCID50/ml to Atlantic salmon fry held in fresh water at a temperature of 12° C.
A second aspect of the present invention relates to a vaccine, comprising the live avirulent IPNV according to the first aspect of the present invention.
A third aspect of the present invention relates to a live avirulent IPNV according to the first aspect of the present invention, for use as a vaccine.
A fourth aspect of the present invention relates to a live avirulent IPNV according to the first aspect of the present invention or a vaccine according to the second aspect of the present invention for use as a vaccine against IPN disease in fry.
A fifth aspect of the present invention relates to a live avirulent IPNV according to the first aspect of the present invention or a vaccine according to the second aspect of the present invention for use as a vaccine against IPN disease, wherein distribution is by immersion or oral administration.
Preferred embodiments of the present invention are set forth in the dependent claims and in the detailed description of the invention.
Preferred embodiments of the present invention will now be illustrated in more detail with reference to the accompanying figures.
Percent dead fry in each sample (cumulative mortality).
Percent dead fry in each sample (cumulative mortality).
Overall number (percent) of fry that survived after challenged/not challenged with avirulent G700 strain.
1=unchallenged control
2=challenged with avirulent G700 strain
1-3=represent data from three different experiments run in parallel
An ideal vaccine for IPNV must induce long lasting protection at an early age, prevent virulent carrier formation and be effective against a large number of IPNV serotypes. Injection cannot be used for small fish, therefore either oral delivery or immersion are most preferred routes for early vaccination.
Previously it has been assumed that these attributes of an ideal IPNV vaccine must be met either by a recombinant subunit vaccine or by an inactivated viral vaccine, as a live avirulent vaccine could potentially lead to virulent carrier formation and disease in case the avirulent virus should revert to a virulent virus.
Despite the prevailing technical prejudice within the field, the inventors of the present invention have surprisingly identified an avirulent IPNV strain which induces long lasting protection at an early age, prevents virulent carrier formation, is effective against a large number of IPNV serotypes and may be delivered by oral administration or by immersion, preferably the latter.
The surprising discovery was the result of a project where two different freshwater fish farming sites were followed throughout the production cycle. The sites chosen had either a record of recurrent IPN problems throughout the production cycle, or very few IPN problems, even if the fish were mixed with the IPN-problem group of fish at sea. The fish were followed-up all the way from the brood stock through harvest by frequent samplings and IPNV isolation.
When isolated, the IPNV was subjected to sequencing for detailed characterization at the genomic level. The results demonstrated that both categories of sites harboured IPN virus, but of different genotypes. The site with a history of recurrent IPN problems had a virulent strain while the site with few IPN problems had an avirulent strain, said avirulent strain herein being referred to as the G700 strain (deposited under ECACC-No. 11 041201). Interestingly, the fish infected with the G700 strain seemed to be protected from developing IPN when mixed with fish carrying the virulent strain. These findings revealed a potential for this field strain as a live avirulent vaccine against IPN.
In order to further characterize the virus, serial dilutions of the G700 strain was propagated in CHSE-214 cells with Agarose gel (SeaPlaque) as a solid support (example 2). Three plaques were identified, harvested, purified and cloned. Two of these were subjected to further characterization by sequencing the VP2 gene. The results obtained show that the VP2 sequence of both clones were 100% identical both at nucleotide and amino acid levels and were also identical to the original G700 strain.
The DNA and RNA sequence of the G700 VP2 gene are presented in SEQ ID NO:2 and SEQ ID NO:3 respectively; and the amino acid sequences of the G700 precursor and mature VP2 protein are represented by amino acid residues 1-508 and 1-442 of SEQ ID NO:1 respectively. As will be seen, both clones had a Pro217Thr221 in the virulence motif, consistent with avirulent isolates.
In order to verify that the G700 strain is avirulent and genetically stable in biological studies, Atlantic salmon fry known to be susceptible to IPNV were exposed to the G700 strain at a concentration of 2×105 TCID50/ml (example 2). The virus was passaged three times before sampling. After sampling, some fry were subjected to stress and then observed for 28 more days before the final sampling. Mortalities were recorded daily.
As can be seen from
The VP2 sequences of re-isolated viruses were 100% identical to the original isolate (G700) at the beginning and end of the study, indicating that this variant has a high genetic stability, even after serial passages in fry. In contrast, it has been found that avirulent Pro217Ala221Ala247 and avirulent Pro217Thr221Ala247 reverse genetics made strains revert to virulent variants over one single infection round of Atlantic salmon fry, thus making the reverse genetics made variants unsuited as candidates for a live avirulent vaccine.
Based on the findings obtained for the G700 strain, a project focused on identifying the amino acid residues responsible for the genetic stability of the avirulent strain was initiated.
By comparing amino acid residues different from the virulence motif (see
In summary, the above findings demonstrate that the G700 strain is stable and does not revert to virulence after 3 passages in susceptible hosts. The stability motif of IPN virus has also been identified and consists of residues 252, 281, 282 and 319, of which Asn252Ser281Asp282Glu319 is associated with genetic stability (example 2) while Val252Thr281Asn282Ala319 is associated with instability (example 3).
A further study was initiated in order to test the protective effect of the G700 strain in Atlantic salmon (Salmo salar L.) fry. In addition, the virulence of the field strain was examined by monitoring the mortality of vaccinated (exposed to the G700 strain) but not challenged fry at the stage of their development when they are most susceptible for IPN, to confirm that they do not cause clinical outbreaks of IPN (example 1).
Four days following start-feeding, one group of fish was immunised by immersion with a dosage of 2×105 TCID50/ml of the G700 strain. A second group was vaccinated with the same dosage four days later (8 days) following start feeding. Both vaccinated groups as well as an unvaccinated control group were challenged at day 14 into start feeding, by bath challenge at a dosage of 2×105 TCID50/ml of a virulent strain. In order to examine the mortality as a result of immunization by using the G700 strain, one tank in each group was left unchallenged.
Sampling was performed before vaccination to ensure that all fish were IPN-free at the onset of the study. The second sampling was done at 14 days into start feeding, just before challenge in order to establish whether the carrier status had developed in the vaccinated fish. The sampling was repeated at two and four weeks after challenge. Mortality was recorded on a daily basis.
Fry immunized with the G700 strain were infected and remained so over the duration of the study. The fish did not show any signs of disease before challenge by clinical and laboratory observations (using histology).
Immunization group 1 had slightly better protection against the challenge than immunization group 2, confirmed by mortality rate and histology. The difference in cumulative mortality was about 1, 5% between group 1 and 2, with corresponding relative percent survival (RPS) values of 88 and 82, respectively, confirming a high level of protection.
Histology results from the sampling at 14 days post challenge from group 1 showed 1 fish with pathological presentation out of a total of 6. In group 2, five out of 6 fish had histopathological changes. These results suggest that the earlier the immunization is done after start feeding of the fry, the better the protection will be.
The non-vaccinated groups, challenged with the virulent strain had a cumulative mortality of over 33% on average. The presence of the virus in internal organs and that fish died from IPN was confirmed by immunohistochemistry (data not shown).
In conclusion, the virus strain used as a vaccine (G700 strain) is clearly avirulent since the immunized groups that were not challenge had very low mortality (less than 1, 5% cumulative mortality) and no signs of disease by histology/immunohistochemistry.
Thus, a first aspect of the present invention relates to a live avirulent infectious pancreatic necrosis virus (IPNV) which preferably do not revert to a virulent virus after at least 3 passages in hosts known to be susceptible to IPNV.
As used herein, the term “live” as applied to viruses refers to a virus that retains the ability of infecting an appropriate host (as opposed to inactivated or subunit vaccines).
As used herein, the term “avirulent” as applied to viruses is understood to mean a virus strain which has substantially lost, preferably completely lost, its ability to cause disease in fish infected with the strain, although its ability to invade fish, i.e. to penetrate into the fish by the usual route of the virus and to reproduce in the body of the fish, remains substantially intact.
The term “infectious” as applied to viruses indicates that the virus has the ability to reproduce. The virus can be pathogenic or nonpathogenic and still be infectious.
The term “pancreatic necrosis virus (IPNV)” refers to the causative agent of IPN and is a member of the Genus Aquabirnavirus, family Birnaviridae.
The term “virulent” as applied to viruses herein indicates that the virus is pathogenic, meaning that the virus causes disease to its host.
The term “revert to a virulent virus” as applied to avirulent viruses refers to the process where an avirulent virus revert to a pathogenic virus (meaning that the virus cause disease to its host) by naturally occurring processes (usually a mutation in position 217 and/or 221 of the VP2 protein).
Preferably said virus do not revert to a virulent virus after 3, 5, 10, 15, 20, 25, 30, 35 or 50 passages in hosts known to be susceptible to IPNV. More preferably said virus do not revert to a virulent virus after at least 3, 5, 10, 15, 20, 25, 30, 35 or 50 passages in hosts known to be susceptible to IPNV. Most preferably said virus do not revert to a virulent virus.
In one embodiment according to the first aspect of the present invention, the host is Atlantic salmon (Salmo salar L.) fry preferably of the AquaGen breed.
If the live avirulent IPNV according to the first aspect of the present invention is delivered by immersion at a titre of 2×105 TCID50/ml to Atlantic salmon fry held in fresh water at a temperature of 12° C. it causes the fry to be virus positive measured by reisolation on RTG-2 cells. However, the fry turned out virus negative when measured by immunohistochemistry which suggests that the virus is present in the fry only in subclinical levels.
The term “TCID50” as used herein refers to the amount of virus required to produce a cytopathic effect in 50% of inoculated tissue culture cells. Virus infection in cells is complex and results in many changes to the host cell, known collectively as the cytopathic effect (CPE). Such changes include altered shape, detachment from substrate, lysis, membrane fusion, altered membrane permeability, inclusion bodies and apoptosis. The method used to determine the TCID50 value is well known to a man skilled in the art (Beitrag zur kollektiven Behandlung pharmakologischer Reihenversueche, Kärber G., vol. 162, 1931).
Even though the virus was present in the fry only in subclinical levels, the live avirulent IPNV according to the first aspect of the present invention has been shown to provide the fry with protection against IPN disease, in particular as compared to fry which have not been exposed to the live avirulent IPNV according to the first aspect of the present invention.
Further, if the live avirulent IPNV according to the first aspect of the present invention is delivered by immersion at a titre of 2×105 TCID50/ml to Atlantic salmon fry held in fresh water at a temperature of 12° C. it does not cause the fry to develop any signs of IPN disease, in particular no pathological lesions have been observed in internal organs including the pancreas of the fry (histologically).
As previously disclosed, IPNV has typically two structural proteins which form the IPNV capsid. Virus protein 2 (VP2) of IPNV is one out of these two structural proteins and has been shown to be responsible for the production of type-specific monoclonal antibodies. It has previously been suggested that the sequence of the VP2 protein decides whether the virus is virulent or avirulent, and in case of the latter it has now been shown that certain amino acids of the VP2 protein are important determinants as to whether the avirulent virus may revert to a virulent virus.
Accordingly, in one embodiment according to the first aspect of the present invention the live avirulent IPNV comprises a nucleic acid encoding a mature structural protein (e.g. mature VP2), or a precursor thereof (e.g. precursor VP2), said structural protein preferably causing the avirulent virus not to revert to a virulent virus after at least 3 passages in hosts known to be susceptible to IPNV.
The term “nucleic acid” as used herein refers to a ribonucleic acid (RNA) or a deoxyribonucleic acid (DNA), preferably RNA.
The term “structural protein” as applied to viruses refers to a viral protein that is a structural component (typically a capsid component) of the mature virus.
The term “precursor protein” as used herein refers to a protein which is post- and/or co-translationally modified into its mature form (e.g. precursor VP2 4 mature VP2).
Said mature structural protein preferably being one of the two structural proteins which form the IPNV capsid, more preferably the protein forming the outermost part of the IPNV capsid. In one preferred embodiment, said mature structural protein is the protein being responsible for the production of type-specific monoclonal antibodies in hosts which have been infected with the virus. In the most preferred embodiment, said structural protein is the VP2 protein.
Further, as previously discussed it was surprisingly found that while the instable avirulent strains all have a Val residue in position 252 of the VP2 protein, the G700 strain has an Asn residue in that position.
Accordingly, in one embodiment according to the first aspect of the present invention, said virus comprises a nucleic acid encoding a VP2 protein, wherein the amino acid in position 252 of the VP2 protein is not Val.
In another embodiment according to the first aspect of the present invention, said virus comprises a nucleic acid encoding a VP2 protein, wherein the amino acid residue in position 252 of the VP2 protein is selected from the group consisting of Ser, Thr, Asn, Gln, Tyr and Cys; preferably selected from the group consisting of Asn and Gln; and most preferably the amino acid residue in position 252 is Asn.
Further, each and all of the instable avirulent strains have a Thr residue in position 281 of the VP2 protein while the G700 strain has a Ser residue in this position.
Thus, another preferred embodiment according to the present invention relates to a live avirulent IPNV comprising a nucleic acid encoding a mature VP2 and/or precursor VP2 protein, said protein preferably causing the avirulent virus not to revert to a virulent virus after at least 3 passages in hosts known to be susceptible to IPNV; wherein the amino acid in position 281 of the mature VP2 and/or precursor VP2 protein is selected from the group consisting of Ser, Asn, Gln, Tyr and Cys; preferably selected from the group consisting of Ser and Cys; and most preferably the amino acid in position 281 is a Ser residue.
In one embodiment according to the first aspect of the present invention, said virus comprises a nucleic acid encoding a VP2 protein, wherein the amino acid in position 281 of the VP2 protein is not Thr.
It was also found that while all of the instable avirulent strains have an Asn residue in position 282 and an Ala residue in position 319 of the VP2 protein, the G700 strain has an Asp residue in position 282 and a Glu residue in position 319.
Accordingly, another preferred embodiment according to the present invention relates to a live avirulent IPNV comprising a nucleic acid encoding a mature VP2 and/or precursor VP2 protein, said protein preferably causing the avirulent virus not to revert to a virulent virus after at least 3 passages in hosts known to be susceptible to IPNV; wherein the amino acid in position 282 of the mature VP2 and/or precursor VP2 protein is selected from the group consisting of Gln, Asp and Glu; most preferably the amino acid in position 282 of the mature VP2 and/or precursor VP2 protein is Asp.
In one embodiment according to the first aspect of the present invention, said virus comprises a nucleic acid encoding a VP2 protein, wherein the amino acid in position 282 of the VP2 protein is not Asn.
Another preferred embodiment according to the present invention relates to a live avirulent IPNV comprising a nucleic acid encoding a mature VP2 and/or precursor VP2 protein, said protein preferably causing the avirulent virus not to revert to a virulent virus after at least 3 passages in hosts known to be susceptible to IPNV; wherein the amino acid in position 319 of the mature VP2 and/or precursor VP2 protein is selected from the group consisting of Glu and Asp; most preferably the amino acid in position 319 of the mature VP2 and/or precursor VP2 protein is Glu.
In one embodiment according to the first aspect of the present invention, said virus comprises a nucleic acid encoding a VP2 protein, wherein the amino acid in position 319 of the VP2 protein is not Ala.
One particularly preferred embodiment relates to a live avirulent IPNV comprising a nucleic acid encoding a mature VP2 and/or precursor VP2 protein, said protein preferably causing the avirulent virus not to revert to a virulent virus after at least 3 passages in hosts known to be susceptible to IPNV; wherein said mature VP2 and/or precursor VP2 protein has a Pro residue in position 217; a Thr residue in position 221; an Asn residue in position 252; a Ser residue in position 281; an Asp residue in position 282; and a Glu residue in position 319.
The amino acid sequences of the G700 precursor and mature VP2 proteins are represented by amino acid residues 1-508 and 1-442 of SEQ ID NO:1 respectively.
Accordingly, in one particularly preferred embodiment according to the first aspect of the present invention, the live avirulent IPNV comprises a nucleic acid encoding a VP2 protein comprising an amino acid sequence having at least 80% sequence identity with the amino acid sequence represented by residues 252-282 of SEQ ID NO:1;
The term “sequence identity” indicates a quantitative measure of the degree of homology between two amino acid sequences of equal length or between two nucleotide sequences of equal length. The two sequences to be compared must be aligned to best possible fit possible with the insertion of gaps or alternatively, truncation at the ends of the protein sequences. The sequence identity can be calculated as
wherein Ndif is the total number of non-identical residues in the two sequences when aligned and wherein Nref is the number of residues in one of the sequences. A gap is counted as non-identity of the specific residue(s). Sequence identity can alternatively be calculated by the BLAST program e.g. the BLASTP program (Pearson and Lipman 1988).
In one embodiment of the invention, alignment is performed with the sequence alignment method ClustalW with default parameters as described by Thompson J., et al 1994.
In one particularly preferred embodiment according to the first aspect of the present invention, the live avirulent IPNV comprises a nucleic acid encoding a VP2 protein comprising an amino acid sequence having at least 80% sequence identity with the amino acid sequence represented by residues 252-319 of SEQ ID NO:1;
In one particularly preferred embodiment according to the first aspect of the present invention, the live avirulent IPNV comprises a nucleic acid encoding a VP2 protein comprising an amino acid sequence having at least 80% sequence identity with the amino acid sequence represented by residues 200-319 of SEQ ID NO:1;
In one particularly preferred embodiment according to the first aspect of the present invention, the live avirulent IPNV comprises a nucleic acid encoding a VP2 protein comprising an amino acid sequence having at least 80% sequence identity with the amino acid sequence represented by residues 150-319 of SEQ ID NO:1;
In one particularly preferred embodiment according to the first aspect of the present invention, the live avirulent IPNV comprises a nucleic acid encoding a VP2 protein comprising an amino acid sequence having at least 80% sequence identity with the amino acid sequence represented by residues 100-319 of SEQ ID NO:1;
In one particularly preferred embodiment according to the first aspect of the present invention, the live avirulent IPNV comprises a nucleic acid encoding a VP2 protein comprising an amino acid sequence having at least 80% sequence identity with the amino acid sequence represented by residues 100-350 of SEQ ID NO:1;
In one particularly preferred embodiment according to the first aspect of the present invention, the live avirulent IPNV comprises a nucleic acid encoding a VP2 protein comprising an amino acid sequence having at least 80% sequence identity with the amino acid sequence represented by residues 50-350 of SEQ ID NO:1;
In one particularly preferred embodiment according to the first aspect of the present invention, the live avirulent IPNV comprises a nucleic acid encoding a VP2 protein comprising an amino acid sequence having at least 80% sequence identity with the amino acid sequence represented by residues 50-400 of SEQ ID NO:1;
In one particularly preferred embodiment according to the first aspect of the present invention, the live avirulent IPNV comprises a nucleic acid encoding a protein comprising an amino acid sequence having at least 80% sequence identity with the amino acid sequence represented by residues 1-442 of SEQ ID NO:1;
In one particularly preferred embodiment according to the first aspect of the present invention, the live avirulent IPNV comprises a nucleic acid encoding a protein comprising an amino acid sequence having at least 80% sequence identity with the amino acid sequence represented by residues 1-508 of SEQ ID NO:1;
In one preferred embodiment according to the first aspect of the present invention, the live avirulent IPNV comprises a nucleic acid encoding a protein comprising or consisting of an amino acid sequence having at least 80% sequence identity with the amino acid sequence represented by residues 1-442 of SEQ ID NO:1 or the amino acid sequence represented by residues 1-508 of SEQ ID NO:1; with the proviso that:
Further, it is preferred that the amino acid in position 252 is not valine.
As previously discussed, moderate to low virulent strains have Pro217 and Ala221 in the mature VP2 protein; and strains containing Thr221 are almost always avirulent, irrespective of the residue at position 217.
Accordingly, one embodiment according to the first aspect of the present invention relates to a live avirulent infectious pancreatic necrosis virus; said virus comprising a nucleic acid encoding a precursor VP2 and/or a mature VP2 protein; said protein preferably causing the avirulent virus not to revert to a virulent virus after 3 passages in hosts known to be susceptible to IPNV; said precursor VP2 and/or mature VP2 protein preferably having a Pro residue in position 217 and/or a Thr residue in position 221, more preferably at least a Thr residue in position 221.
In one embodiment, the amino acid in position 217 of the mature VP2 and/or precursor VP2 protein is not a Thr residue and/or the amino acid in position 221 of the mature VP2 and/or precursor VP2 protein is not an Ala residue.
In one preferred embodiment according to the present invention, said mature VP2 and/or precursor VP2 protein comprises an amino acid sequence having at least 80% sequence identity with the amino acid sequence represented by residues 200-319 of SEQ ID NO:1; residues 150-319 of SEQ ID NO:1; residues 100-319 of SEQ ID NO:1; residues 100-350 of SEQ ID NO:1; residues 50-300 of SEQ ID NO:1; residues 50-350 of SEQ ID NO:1; residues 50-400 of SEQ ID NO:1; residues 1-442 of SEQ ID NO:1; or residues 1-508 of SEQ ID NO:1 preferably with the proviso that:
In one preferred embodiment, said sequence identity is selected from the group consisting of at least 85% sequence identity, at least 90% sequence identity, at least 95% sequence identity and 100% sequence identity.
In one particularly preferred embodiment, said mature VP2 and/or precursor VP2 protein comprises an amino acid sequence represented by residue 1-442 of SEQ ID NO:1.
In another particularly preferred embodiment, said mature VP2 protein consists of an amino acid sequence represented by residue 1-442 of SEQ ID NO:1 and said precursor VP2 protein consists of an amino acid sequence represented by residue 1-508 of SEQ ID NO:1.
The precursor VP2 and mature VP2 amino acid sequence of the G700 strain is represented by amino acid residues 1-508 and 1-442 of SEQ ID NO:1 respectively; and provides a convenient reference for the numbering of amino acids as used herein. It is believed that those of skill in the art will readily identify the corresponding positions in other precursor VP2 and mature VP2 proteins.
As previously discussed, genomic segment A of IPNV encodes a 106 kDa precursor polyprotein composed of pVP2-VP4-VP3 in that order. When referring to a nucleic acid molecule encoding a protein, it should be understood that a nucleic acid molecule encoding a polyprotein of which said protein is part of the polyprotein is also meant to be included.
In case the nucleic acid encodes the protein in the form of a polyprotein, it is preferred that the virus also comprises means for separating the polyprotein into separate proteins. Thus, in one embodiment according to the present invention the IPNV virus further comprises a nucleic acid encoding an NS-protease, e.g. a nucleic acid encoding the VP4 protein. Optionally, the means for separating the polyprotein into separate proteins may be present in the host.
Further, in case the nucleic acid encodes a precursor protein (e.g. pVP2) it is preferred that the virus also comprises means for transforming the precursor into its mature form (e.g. mVP2). Optionally, the means for transforming the precursor into its mature form may be present in the host.
A particularly preferred embodiment according to the first aspect of the present invention relates to the G700 strain (IPNV-G700) deposited under ECACC accession No. 11 041201, or closely related strains thereof
By “closely related strains” we mean any strain which shares similar genotypic and/or phenotypic characteristics to the deposited strain. In particular this phrase encompasses slightly modified forms of the virus which retain substantially the same functional activities. Thus, for example some amino acid or nucleotide additions, deletions or alterations have very little effect; if any, on the functional activities of the virus.
The most preferred embodiment according to the first aspect of the present invention relates to the G700 strain (IPNV-G700) deposited under ECACC accession No. 11 041201.
Another particularly preferred embodiment relates to a live avirulent IPNV according to the first aspect of the present invention, which when delivered by immersion at a titre of 2×105 TCID50/ml to Atlantic salmon fry held in fresh water at a temperature of 12° C.
Another particularly preferred embodiment relates to a live avirulent IPNV according to the first aspect of the present invention, which when delivered by immersion at a titre of 2×105 TCID50/ml to Atlantic salmon fry held in fresh water at a temperature of 12° C.
As previously discussed, fish infected with the G700 strain seemed to be protected from developing IPN disease when mixed with fish carrying a virulent strain. These findings revealed a potential for this field strain as a live avirulent vaccine against IPN.
Thus, a second aspect of the present invention relates to a vaccine, comprising the live avirulent IPNV according to the first aspect of the present invention.
A third aspect of the present invention relates to the live avirulent IPNV according to the first aspect of the present invention, for use as a vaccine.
In one preferred embodiment according to the third aspect of the present invention, the live avirulent IPNV according to the first aspect of the present invention, is for use as a vaccine against IPN disease in fry and/or smolt and/or fish; more preferably for use as a vaccine against IPN disease in fry.
In one particularly preferred embodiment according to the third aspect of the present invention, the live avirulent IPNV according to the first aspect of the present invention is for vaccination of fry against IPN disease.
In one preferred embodiment according to the third aspect of the present invention, the vaccine is distributed by immersion or oral administration; more preferably distributed to fry by immersion or oral administration.
In another preferred embodiment according to the third aspect of the present invention, said fry are kept in an environment which is free of virulent IPNV for at least 10 days post vaccination with said avirulent IPNV.
In another preferred embodiment according to the third aspect of the present invention, said virus or vaccine is distributed no later than at day 4 after start feeding the fry.
In another preferred embodiment according to the third aspect of the present invention, distribution is by immersion using a virus dosage in the range 1×104 TCID50/ml to 1×106 TCID50/ml; more preferably 5×104 TCID50/ml to 5×105 TCID50/ml; even more preferably 1×105 TCID50/ml to 5×105 TCID50/ml; and most preferably about 2×105 TCID50/ml.
The present invention also relates to a live avirulent IPNV according to the first aspect of the present invention; or a vaccine according to the second aspect of the present invention; for the prophylaxis or treatment of IPN disease.
The present invention also relates to a live avirulent IPNV according to the first aspect of the present invention; or vaccine according to the second aspect of the present invention; for the prophylaxis or treatment of IPN, wherein distribution is by injection, immersion or as a food additive, preferably immersion or as a food additive, most preferably by immersion.
The present invention also relates to a live avirulent IPNV according to the first aspect of the present invention; or a vaccine according to the second aspect of the present invention, for the prophylaxis or treatment of IPN disease in fish and/or fry; preferably fry.
The present invention also relates to a live avirulent IPNV according to the first aspect of the present invention; or a vaccine according to the second aspect of the present invention; for the prophylaxis or treatment of IPN disease in fry, wherein said fry are kept in an environment which is free of virulent IPNV for at least 10 days post vaccination with said avirulent IPNV.
The present invention also relates to a live avirulent IPNV according to the first aspect of the present invention; or a vaccine according to the second aspect of the present invention, for the prophylaxis or treatment of IPN disease in fry, wherein said virus or vaccine is administered no later than at day 4 after start feeding the fry.
The present invention also relates to a live avirulent IPNV according to the first aspect of the present invention; or a vaccine according to the second aspect of the present invention, for the prophylaxis or treatment of IPN disease, wherein distribution is by immersion using a virus dosage in the range 1×104 TCID50/ml to 1×106 TCID50/ml; more preferably 5×104 TCID50/ml to 5×105 TCID50/ml; even more preferably 1×105 TCID50 ml to 5×105 TCID50/ml; and most preferably about 2×105 TCID50/ml.
Having now fully described the present invention in some detail by way of illustration and example for purpose of clarity of understanding, it will be obvious to one of ordinary skill in the art that same can be performed by modifying or changing the invention by with a wide and equivalent range of conditions, formulations and other parameters thereof, and that such modifications or changes are intended to be encompassed within the scope of the appended claims.
The following examples are meant to illustrate how to make and use the invention. They are not intended to limit the scope of the invention in any manner or to any degree.
The vaccine strain, herein referred to as the G700 strain, was a field isolate of IPNV collected from one year old fish in sea. The fish from which the virus was isolated was clinically healthy and not suffering from IPN. The vaccine strain was propagated in RTG-2 cells and titrated in CHSE-214 cells. (Titer: 2.0×108 TCID50/ml, dose per tank: 2.0 ml, diluted to 10 ml using L-15 medium.
The challenge strain of IPNV was the virulent V-1244 strain. This strain was propagated in RTG-2 cells and titrated in CHSE cells. (Titer: 9.8×106 TCID50/ml, dose per tank: 20 ml.)
The fish used were wild salmon fry, approximately 1560 in total, originating from the river Rauma. The eggs came from brood fish kept at the living gene bank Haukvik, S-Trøndelag for more than 10 years. The eggs were hatched at VESO Vikan's hatchery, and transferred to the research station when ready for start-feeding. The fish were fed according to S-2002.
Water quality: Fresh water
Temperature: 12±1° C.
Oxygen level: Minimum 8 mg/L at outlet
Flow: Flow should be kept at a level to ensure sufficient pO2 (0.1 L per tank per minute)
Immunization groups 1A-D and 2A-D as well as non-immunized groups (3A-E) were sampled before challenge at experimental day 14. The immunized groups turned out positive for IPNV after reisolation on RTG-2 cells. This was confirmed with positive RT PCR results. The non-immunized groups were negative on both cell culture and RT PCR (table 1).
The sampling was repeated after challenge at experimental day 28. The results show that all groups that has been either immunized and/or challenged (groups 1A-D, 2A-D and 3A-C) were positive for the virus. The non-immunized and non-challenged groups (3D-E) were negative by cell culture. However, 2 out of 12 samples turned out positive by PCR (table 1).
The last sampling at experimental day 42 shows positive results in immunization group 1 and 2 (1A-C and 2A-C), but 7 of the samples in group 2 were found positive by PCR. Similarly, 4 out of 18 samples in the non-immunized/challenged groups (3A-C) were also found positive by PCR, although not by virus re-isolation. The negative controls (3D-E) were all negative on cell culture and RT PCR (table 1).
Virus re-isolation results of fry sampled at different time points. Homogenates were tested by cell-culture (RTG-2) inoculation and observation for CPE followed by verification by RT-PCR. Numbers in brackets represent positive results only by RT-PCR (PCR have higher sensitivity than cell culture).
Mortality was recorded daily and dead fish (if any) were removed from the tanks daily. Results are presented in
Plaques of IPNV were obtained by propagating serial dilutions of the G700 strain in CHSE-214 cells, with Agarose gel (SeaPlaque) as a solid support. Three plaques were identified, harvested, purified and cloned. Two of these were subjected to further characterization by sequencing the VP2 gene.
The results obtained show that the VP2 sequences of both clones were 100% identical both at nucleotide and amino acid levels and were identical to the original G700 strain. The clones had Pro217Thr221 in the virulence motif, consistent with low virulent isolates. However, only one the two clones were used in subsequent challenge experiments.
The nucleotide sequence of the G700 VP2 gene is presented in SEQ ID NO:2 and the amino acid sequence of the G700 mature VP2 protein is represented by amino acid residue 1-442 of SEQ ID NO:1.
Challenge of fry was done at Veso-Vikan, an accredited experimental facility meeting the requirements of existing regulations (based on General European Pharmacopoeia monographs for documentation of live virus vaccines). Atlantic salmon fry of the AquaGen breed known to be susceptible to IPNV were used. The fry were exposed to the virus solution (challenged) at the point of start-feeding. Although the initial objective was to passage the virus 6 times in fry, it was only possible to undertake 3 passages owing to the seasonality in the availability of fry. The study ran as discontinuous experimental blocks, one after another, with laboratory work (virus re-isolation and propagation for use in the next experiment) in-between. Each experiment comprised three parallels, 100 fry in each bucket. A fourth bucket containing 100 fry was also included as control against background mortality. The dosage of virus was about 2×105 TCID50/ml and was administered by bath at approximately 6 days after start-feeding. The first sampling was done at day 21 following virus exposure. After sampling, the fry were subjected to stress (lowering the water content in the buckets combined with movement of a netpen around in the buckets for a period of 10 min; this procedure repeated daily for 1 week) in the 1st and 3rd experimental blocks. These fry were then observed for 28 more days before the final sampling. Mortalities were recorded daily.
Histologically, no pathological lesions were observed in internal organs including the pancreas of the fry before or after stress. Furthermore, no IPN virus was detected by immunohistochemistry in any of the immunized fry although the virus was re-isolated from them. This suggests that the virus was present in the fry only in subclinical levels.
The VP2 sequences of re-isolated viruses were 100% identical to the original isolate (G700) at the beginning and end of the study. In the 2nd and 3rd passage prior to stress however, a mutation from leucine to phenylalanine at position 336 was observed. This is a conserved mutation and has no influence on the virulence of the virus since it falls outside the critical motifs. This is supported by the low mortalities associated with the isolates. It is also noteworthy that the mutation reverted following stress of the fry in the 3rd experiment.
Chinock salmon embryo (cells (CHSE-214; ATCC CCL-1681) were maintained at 20° C. in L-15 medium (Sigma-Aldrich) supplemented with 5% fetal bovine serum (FBS, Medprobe), 2 mM L-glutamine (Sigma-Aldrich) and 50 μg ml−1 gentamicin (Sigma-Aldrich). Rainbow trout gonad cells (RTG-2; ATCC CCL-55) were grown at 20° C. in L-15 medium supplemented with 10% fetal bovine serum, 2 mM L-glutamine and 50 μg ml−1 gentamicin.
The virus isolates were propagated in RTG-2 cells by inoculation of 100 μl virus stock solution (stored at −20° C. in 30% glycerol, titer ˜107 TCID50/ml) onto 70% confluent T-162 cm2 cell culture flasks. The supernatants were harvested when widespread cytopathic effect was visible, 5-7 days post infection. The cell culture supernatants were obtained after a centrifugation at 2500×g for 10 minutes, and sterile filtration (0.22 μl). The infectious titer was determined by end point dilution on CHSE-214 cells, and the TCID50 was estimated by the method of Kärber (1931. Beitrage zur kollektiven Behandlung pharmakologischer Reihenversuche. Arch.Exp.Pathol.Pharmakol 162:480-483.).
Construction of Full-Length cDNA Clones
Generation of full-length cDNA clones of the entire coding and non-coding regions of NVI-015 RNA segment A and B was performed according to procedures described by Yao and Vakharia (1998. Generation of infectious pancreatic necrosis virus from cloned cDNA. J Virol. 72:8913-8920). The recombinant IPNV Sp isolate rNVI-15PA (also named rNVI15VP2) was generated as described previously by Song and co-workers (2005. Molecular determinants of infectious pancreatic necrosis virus virulence and cell culture adaptation. Journal of Virology 79:10289-10299). This recombinant isolate originates from rNVI-15TA (also named rNV115) and the 5′ end of Sp103. This resulted in the recovery of the viral progeny with a virulence motif similar to the parent isolate Sp103 Pro217Ala221Ala247 (2005. Molecular determinants of infectious pancreatic necrosis virus virulence and cell culture adaptation. Journal of Virology 79:10289-10299). Sp103 is an IPNV isolate obtained from a field outbreak of IPN, and causes moderate to low rates of mortality (2005. Infectious pancreatic necrosis virus induces apoptosis in vitro and in vivo independent of VP5 expression. Virology 342:13-25; 2004. Identification of putative motifs involved in the virulence of infectious pancreatic necrosis virus. Virology 322:31-40). The recombinant rNVI-15PA virus was subjected to two rounds of plaque purification on CHSE-214 cells before propagation in RTG-2 cells to obtain a stock. The nucleic acid of the virus was sequenced completely to ensure that no advert mutation occurred due to cell adaptation.
The genetically engineered virus strains were propagated on RTG-2 monolayers. The supernatants were harvested following centrifugation at 2500×g for 10 minutes and sterile filtration (0.22 μl). RNA extraction using the QIAamp viral mini kit (Qiagen) was carried out according to the manufacturer's recommendation. To ensure that the generated clones had the correct residues, the genomes of segment A and B were sequenced as described by Yao and Vakharia (1998. Generation of infectious pancreatic necrosis virus from cloned cDNA. J Virol. 72:8913-8920) and the chromatograms were analyzed.
To generate the final mutant virus in residue 221 of VP2 we passaged the obtained ProAlaAla recombinant virus 10 times (passages) in CHSE-214 cells (2005. Molecular determinants of infectious pancreatic necrosis virus virulence and cell culture adaptation. Journal of Virology 79:10289-10299). Then the isolate was plaque purified by inoculating RTG-2 monolayers on six well plates with 10-fold dilution (10−3 to 10−8) of cell culture supernatants. After 1 hr adsorption at room temperature the inoculum was removed and the cells were overlaid with 0.8% SeaPlaque Agarose (BioWhittaker) in 2×L-15 medium (Sigma) containing 5 FBS and 1% L-glutamine. The cells were incubated at 15° C. for 4 days and plaques formed by cytopathic effect (CPE) were picked by insertion of a 3 mm punch biopsy (Miltex) through the agar to the plate. The plaques were subsequently inoculated on RTG-2 monolayers and incubated at 15° C. until full CPE was observed. Then the supernatant was harvested following a centrifugation at 2500×g for 10 minutes and sterile filtration (0.22 μl). RNA was extracted using the QIAamp Viral RNA mini kit according to the manufacturer's recommendations. Complete nucleotide sequences of segment A and B of each virus was determined as described before. The chromatographs were checked to ensure a “clean” ATT codon encoding Thr221 was used in the study. No other mutations were found in the entire genome of the virus compared to rNVI-15PA. Prior to challenge the isolates were propagated by one passage in RTG-2 cells.
The challenge was conducted at VESO Vikan's research facility, Namsos, Norway. This was part of a larger study including in total 1020 Atlantic salmon (Salmo salar L.) fry of the AquaGen strain hatched at the VESO Vikan hatchery were included in the experiment. The fry had recently started to feed (Micro 015, Ewos) and had an average weight of 0.2 grams (n=20). The fish were divided into 4 buckets, each of 250 fry. After an acclimatization period of one week, the fry were starved one day prior to challenge.
Fish were challenged by immersion with rNVI-15PT at a dose of 5×104 TCID50/ml in a total volume of 4 liters (Tank 1). One control tank was mock-infected by adding cell culture medium (Tank 2). The water was aerated during the challenge. After a period of 3 hours the water volume was reduced to 2 liters and normal flow was resumed. Mortality was recorded and dead fish were collected and frozen at −70° C. on daily basis. Sampling of ten fish from each tank was performed at ten days post challenge, and after this first sampling, ten fish were sampled from each tank once a month, up until six months post challenge.
Virus Re-Isolation from Persistently Infected Fish
Fry samples stored at −70° C. without conservatives were added phosphate buffered saline (PBS) (1:5, weight/volume) and homogenized using a stomacher. 100 μl of this homogenate was transferred to 600 μl RLT buffer containing 2-mercaptoethanol (RNeasy Mini kit, Qiagen) and stored at −70° C. The rest of the homogenate was diluted 1:2 in L-15 medium supplemented with 2 mM L-glutamine and 50 μg ml−1 gentamicin. After a brief centrifugation at 2500×g for 10 minutes the supernatant were inoculated onto RTG-2 cells grown in 24 well plates in final dilutions of 1% and 0.1%, and incubated for one week at 15° C. The cell culture medium from the first passage was used to infect new monolayers. The samples were considered negative when no CPE was observed after 1-week incubation of the second passage. RNA was isolated from the fish homogenate for all negative samples on cell culture using the RNeasy Mini kit (Qiagen) in accordance with the supplier's protocol, and RT-PCR was performed to amplify a 224-bp IPNV-specific DNA fragment, as described by Santi et al. (2004. Identification of putative motifs involved in the virulence of infectious pancreatic necrosis virus. Virology 322:31-40) with minor modifications. The PCR products were separated by agarose gel electrophoresis and visualized by staining with SYBR® Safe DNA gel stain (Invitrogen).
RNA was isolated from homogenate stored on RLT buffer containing 2-mercaptoethanol (RNeasy Mini kit, Qiagen) stored at −70° C. after homogenisation. RT-PCR was performed to amplify a 400-bp IPNV-specific DNA fragment using Qiagen's OneStep RT-PCR kit according to the manufacturer's instructions, with 0.5 μg RNA and 15 pmol each of primer A-Sp500F and A-Sp1689R (2004. Identification of putative motifs involved in the virulence of infectious pancreatic necrosis virus. Virology 322:31-40) in a total reaction volume of 25 μl. The cycling conditions were 50° C. for 30 min., 95° C. for 15 min., followed by 40 cycles at 94° C. for 45 s, 57° C. for 45 s, 72° C. for 2 min 15 s, and finally 72° C. for 10 min. The PCR products were separated by agarose gel electrophoresis and analyzed by staining with SYBR® Safe DNA gel stain.
To purify the DNA fragments from agarose gel, the Quantum Prep Freeze N′ Squeeze DNA Gel Extraction Spin Column (BIO-RAD) was used according to the manufacturer's instructions. The recovered DNA was sequenced by a commercial sequencing service (Eurofins MWG operon) using primer A-Sp500F (2004. Identification of putative motifs involved in the virulence of infectious pancreatic necrosis virus. Virology 322:31-40). The sequence data were analyzed using VectorNTI software (Invitrogen).
Four samples with different mixtures of bases in position 217 and 221 were picked for cloning and sequencing. Taq polymerase-amplified PCR products from the sequencing step were cloned into a TOPO® Vector by using TOPO TA Cloning® according to the manufacturers' instructions (Invitrogen). The One Shot® Chemically Competent E. coli cells were transformed according to the protocol and 50 μl were spread on prewarmed agar plates containing 50 μg/ml ampicillin and pre-incubated for 30 min at 37° C. with 40 μl 40 mg/ml X-gal (Invitrogen) in dimethylformamide for white blue selection. 80-96 white colonies were picked from each Petri dish and placed one in each well on a 96 well agar plate with 150 mg ampicillin (GATC Biotech). Plasmid were isolated and sequenced by a commercial sequencing company, GATC Biotech. The sequence data were analyzed using VectorNTl software.
The isolate used for challenge had the following amino acid combinations in position 217, 221, and 247; ProThrAla. Amino acids in position 252, 281, 282 and 319 were ValThrAsnAla.
In detail, constructs including combinations of original constructs pUC19NVI15VP2 and pUC19NVI15B resulted in the recovery of NVI-15PA (2005.
Molecular determinants of infectious pancreatic necrosis virus virulence and cell culture adaptation. Journal of Virology 79:10289-10299) which was subsequently passaged 10 times resulting in a mutation in position 221 in VP2 (Ala221Thr), and after plaque purification the rNVI-15PT isolate was recovered with the ProThrAla amino acid combination.
The genomic RNAs of the recovered viruses were analyzed after RT-PCR amplification, and the sequence analysis of the RT-PCR products confirmed the expected mutations in the VP2 and VP1 regions. Furthermore, complete nucleotide sequences of segment A of both viruses were determined, which did not exhibit any other unwanted nucleotide substitutions.
The challenge dose used in this study was lower than what is used in standard challenge studies (2004. Identification of putative motifs involved in the virulence of infectious pancreatic necrosis virus. Virology 322:31-40), due to establish a persistent infection in fry and to retain a high number of surviving fish (>95%). Of all the sampled fish during the experiment 94% were persistently infected.
Reisolation and Characterization of IPNV from Infected Fry
In order to document that the fish were infected and remained persistently infected we collected fry once every 30 days from month 1-6 post infection. At each time point 10 fish were examined using cell culture and RT-PCR. Overall IPNV were reisolated by culture or detected by RT-PCR in 94% of the three groups. All fish were positive by 6 months post challenge, either by virus reisolation or RT-PCR.
Progression from acute infection to persistence has been associated with increase in genome complexity of hypervariable regions of viruses, particularly documented for HCV (2000. The outcome of acute hepatitis C predicted by the evolution of the viral quasispecies. Science 288:339-344. doi:8445 [pii]) and result in development of quasispecies. With the purpose to determine complexity of the virus genomes of the hypervariable region of the VP2 protein (amino acid positions 180-360) and any mutations in individual fish over the persistence period, RNA isolated from each of 5 fish from each group at all sampling points was amplified by RT-PCR and PCR-products were purified by gel electrophoresis and sent for sequencing. This showed that the ProThrAla strain had mutations in the genome yielding a combination of a ProThrAla (the challenge isolate) and a new ThrAlaThr variant, representing a high virulent, reverted strain of IPNV (
The material in the ASCII text file, named “UDL-53506-SequenceListing.txt”, created Dec. 11, 2015, file size of 24,576 bytes, is hereby incorporated by reference.
| Number | Date | Country | Kind |
|---|---|---|---|
| 20110402 | Mar 2011 | NO | national |
| 20110650 | May 2011 | NO | national |
This application is a continuation of application Ser. No. 14/005,333, Nov. 25, 2013, which is a national stage application of International Application PCT/NO2012/050040, filed Mar. 14, 2012, and which claims priority of Norway patent application no. 20110402, filed Mar. 16, 2011, and Norway patent application no. 20110650, filed May 2, 2011, all of which are hereby incorporated by reference.
| Number | Date | Country | |
|---|---|---|---|
| Parent | 14005333 | Nov 2013 | US |
| Child | 14980182 | US |
