Patent Grant
10544398
The present invention relates to the field of medicine, veterinary medicine, molecular biology, immunology and biotechnology, specifically, to the development of vaccines and adjuvants therefor, and treatments. The field of application of this invention mainly corresponds to the fish farming industry. More specifically, this invention relates to a viral RNA expression plasmid and a method for obtaining viral particles based on said plasmids.
Infectious salmon anemia (ISA) is a disease that mainly affects Atlantic salmon (Salmo salar) causing huge losses in salmon farming worldwide (1, 14). The clinical signs of this disease are the presence of pale gills, ascites, hemorrhagic necrosis of the liver, splenomegaly, congestive gut and acute anemia (14). ISA was first reported in Norway in 1984 (28), later diagnosed in Canada (4), Scotland (27), United States (18), Faroe Islands (18) and Chile (16).
The etiological agent of this disease is a packaged pleomorphic virus between 45 and 140 nm of diameter, called Infectious Salmon Anemia Virus (ISAV), belonging to the Orthomixoviridae family (8). Its genome consists of 8 ssRNA of negative polarity (ns-RNA) that encode for 10 proteins and which have Untranslated Regions (UTRs) at both ends (26).
There is a limited knowledge about the functions of each ISAV protein performs. Bioinformatics evidence indicates that segments 1, 2 and 4 would encode for dependent RNA polymerase subunits (RpRd), analogous to PB2, PB1 and PA of Influenza A virus, respectively. Segment 3 encodes for NP protein, which has been reported to have the ability to bind ssRNA (2). As for Influenza, it has been proven that these four polypeptides relate to each one of the eight viral RNA segments to form Ribonucleoprotein complexes (RNPs) (23). These eight RNP units correspond to the minimum infectious unit required to initiate a cell infection (23). Segment 5 encodes for the Fusion protein (F), which has shown to be present on the surface of the viral membrane, allowing at the first steps of the infection, the fusion of the membrane of the viral particle with the cell endosome, allowing the release of the RNPs into cell cytoplasm (3). Segment 6 encodes for hemagglutinin-esterase protein (HE), which is also present on the viral surface and whose function is to bind a sialic acid residue located in the cell receptor (15). HE protein also has receptor-destroying activity (RDE, receptor destroying enzyme), favoring the release of new viral particles emerging from the cell membrane (21). Contrary to what is observed in hemagglutinin from Influenza A virus, whose stalk region is highly kept, it has been reported that ISAV's HE protein has a highly variable region towards the carboxy terminal end and adjacent to the transmembrane region, also known as Highly Polymorphic Region (HPR) (9). This HPR region encodes for 35 amino acids and, based on its high polymorphism 30 variants have been described in Europe, North America and Chile (30, 31, 32). One theory explains this variation as a deletion phenomenon from an ancestral strain present in the longest HPR region that is called HPRO (33). The first HPRO strain was identified in Scotland in wild salmon that did not show any clinical signs of ISA, being classified as an avirulent strain (34). In contrast, those strains presenting deletions in that zone are capable of developing virulent ISA-related clinical signs and mortality. It is suggested that segment 7 encodes for non-structural proteins analogous to NS1 and NS2 of influenza A virus (19). Finally, segment 8 encodes for a transcript containing two overlapping open reading frames (ORF, Open reading Frame). ORF1 encodes for the matrix protein (M), and ORF2 encodes for M2 protein. It has been shown that M2 protein is involved in the modulation of the type-I IFN response in conjunction with the NS1 protein (12).
As regards the Influenza Virus, detailed study of the virus has been possible as a result of the development of a reverse genetics system, which allows to manipulate the virus genome, being able to determine possible causes of virulence, as well as detailed study of each one of the functions of viral proteins (13). The most widely used reverse genetics system on Influenza virus is the plasmid-based system which allows to generate recombinant viruses from cloned cDNA. ISA Virus has 8 genomic RNAs transcribed under control of RNA polymerase I and the proteins making up the ribonucleoprotein complex under the command of RNA polymerase II are expressed (10, 24).
At the date there are no reports describing a successful reverse genetics system on ISAV. A relevant difficulty in generating a reverse genetics system is having the defined promoter for RNA polymerase I, which has not yet been described for Atlantic salmon. The difficulty lies in that promoters for RNA Polymerase I are strictly species-specific, they do not have a clear genetic structure and are in the IGS region of rDNA, which are vast (6). Identification of the sequences corresponding to the promoter for Pol I and its enhancers is hard work, considering that the IGS in the Salmo gender varies between 15-23 kb length (5). For this reason, and in view of the need of having a promoter with RNA Pol I characteristics, here we evaluate the capacity of the 571 pb ITS-1 region (Internal Transcribed Sequences) as previously described for Salmo salar (Atlantic salmon) (25). It has been recently described in nematodes, through bioinformatics analysis, that the ITS-1 region contains transcription promoter motifs and regulator motifs in which their function are not been demonstrated yet (29). It is suggested in this study that in the ITS-1 region of the rDNA, there are motifs having promoter characteristics and transcription regulators that have been conserved for millions of year of evolution, differing between species of the same gender, although they suggest the making of in vitro transcription assays to prove it.
The present invention shows that ITS-1 region of the rDNA of Atlantic salmon shows transcription promoter activity, which has conserved for millions of years; however, to confirm this assertion in vitro transcription essays had to be made.
In Chile and all other salmon farmers, there is the urgent need of figure out virulence factors, pathogenesis mechanisms of ISA virus, and an efficient vaccine against the only member of the Isavirus gender, the implementation of a plasmidal reverse genetics system allowing to generate recombinant ISA virus (ISAVr) becomes a necessity. With this goal, the challenge of developing a reverse genetics system for ISAV based on plasmids and using innovative elements, such as the use of salmon's ITS-1 region which has never been described as a promoter element. A choice that turned out to be key for the success of the systems that will be described below.
Although this methodology has been initially developed to obtain viral particles of the ISA virus, it has been also confirmed that in other species of upper vertebrates this expression system is successful for the production of RNA molecules without any additional nucleotides on their ends, which significantly broadens the usefulness of this technique. This way, with this expression system it is possible to obtain any desired protein or RNA, in a countless different cell types. An example thereof is this system's capacity to transcribe viral RNA at 12 hpt in a human KEK 293 cell line as well as in a ST swine cell line, incubated at 37° C. (98.6° F.).
Therefore, the present invention seeks to solve the technical problem of providing a molecular genetics system allowing to obtain functional viral particles from ns-RNA. Other purpose of this invention is to provide a method for expressing autogenic or exogenic proteins to the viral particle used, as well as to express nucleic acids of the interference ARN-type.
Cell Lines Used
ASK cells (www.atcc.org, CRL 2747), derived from Atlantic salmon kidney, were cultured in Leibovitz medium (L-15, Hyclone), supplemented with 50 μg/mL gentamicin), 10% bovine serum (SFB, Corning Cellgro®, Mediatech), 6 mM L-glutamine (Corning Cellgro®, Mediatech) and 40 μM β-mercaptoethanol (Gibco®, Life Technologies). RTG-2 cells (www.phe-culturecollections.org.uk, ECACC 90102529), derived from rainbow trout gonad tissue, were cultured in a minimum essential medium (MEM, Hyclone) supplemented with 50 μg/mL gentamicin, 10% SFB (Corning Cellgro®, Mediatech), 10 mM L-glutamine (Corning Cellgro®, Mediatech), 1% non-essential amino acids (Hyclone) and 10 mM HEPES (Hyclone). CSE-119 cells, derived from Coho salmon embryo (www.phe-culturecollections, ECACC 95122019) were cultured in a minimum essential medium (MEM, Hyclone) supplemented with 50 μg/mL gentamicin, 10% SFB (Corning Cellgro®, Mediatech), 2 mM L-glutamine (Corning Cellgro®, Mediatech), 1% non-essential amino acids (Hyclone). The cell lines were raised at 60.8° F., without CO2, except for CSE-119.
HEK293 cells (ATCC CRL 1573), human embryonic kidney cells, were cultured in Eagle's Minimum Essential Medium (EMEM, Hyclone), supplemented with 50 μg/mL gentamicin, 10% FBS (Corning Cellgro®, Mediatech), 10 mM L-glutamine (Corning Cellgro®, Mediatech), 1% non-essential amino acids (Hyclone) and 10 mM HEPES (Hyclone). ST cells (www.atcc.org, CRL 1746) derived from swine testicles, were cultured in Eagle's Minimum Essential medium (EMEM, Hyclone) supplemented with 50 μg/mL gentamicin), 10% FBS (Corning Cellgro®, Mediatech), 10 mM L-glutamine (Corning Cellgro®, Mediatech), 1% non-essential amino acids (Hyclone) and 10 mM HEPES (Hyclone).
Purification of ISAV Viral Particles
Virus purification was performed from 40 mL of ASK cell supernatant infected with the ISAV901_09 strain. After 14 post infection days, the cell supernatant was taken and clarified at 1000×g for 20 minutes at 39.2° F. The supernatant was then ultracentrifuged at 133,200×g for 2 hours at 4° C. (39.2° F.) and the pellet obtained was suspended in 100 μL TNE buffer overnight, at 4° C. (39.2° F.). Then, the suspension was loaded into 4 mL of a 20% w/v sucrose mattress in TNE buffer, and was ultracentrifuged at 124,200×g for 2 hours at 4° C. (39.2° F.), and, finally, the resulting pellet was re-suspended in 50 μL of TNE buffer.
Viral RNA Extraction
Viral RNA extraction (vRNA) was performed from 50 μL of purified ISAV901_09 virus, using the commercial E.Z.N.A kit. Total RNA Kit II (Omega, Bio-Tek, Inc.), according to manufacturer's instructions. The purified RNA was then quantified by measuring absorbance at 260 nm through the Nanoquant Infinite M200 pro (TECAN, Austria) equipment, and a vRNA concentration of 2.7 μg/μL was obtained. The vRNA was stored at −80° C. (−112° F.), until its use.
Amplification of the Complete 8 IASV 901_09 Genomic Segments, Bioinformatics Analysis and Primer Design.
The sequences including the non-coding 5′ and 3′ UTR ends of the eight genomic segments of the publications by Fourrier et al., Kulshreshtha et al., and Merour et al., (11, 17, 20), were collected. These sequences correspond to two Scottish isolates (390/98 and 982/08), one Norwegian isolate (Glesvaer/2/90), two Canadian isolates (NBISA01 and RPC NB 98-049) and a Chilean one (ADL-PM 3205 ISAV). Multiple alignment was performed using the ClustalW2 program. Based on the analysis of the alignments, the universal primers were designed to amplify the 8 complete segments, including the 5′ and 3′ UTR regions of any ISAV strain (Table I).
RT-PCR
The viral RNA of ISAV901_09 (7) was obtained by extraction from purified virus; the cDNA of the eight genomic segments was obtained via RT-PCR. To this effect, the SuperScript™ One-Step RT-PCR System with Taq Platinum DNA Polymerase kit (Invitrogen) was used following manufacturer's instructions. In order to obtain the cDNA of each segment in the RT-PCR reaction, the primer F (forward) (10 μM) and the appropriate R primer (reverse) (Table I) and 50 ng viral RNA, were used.
Sequencing
The cDNAs of the ISAV genomic segments were cloned in the pGEMT-easy vector (Promega), following manufacturer's instructions. Three clones of each plasmid were sequenced using universal primers for promoter T7 and SP6, in addition to internal primers for each segment, as described in Cottet et al (7).
The sequencing results were analyzed using the BioEdit Sequence Alignment Editor 7.1.3 program, and to confirm the identity of the sequences, a local alignment was made using the BLAST server. In addition, a multiple alignment, using the CLUSTALW2 server between the sequences obtained from the 3′ and 5′ UTR ends of all the ISAV901_09 segments, was made. Once the complete sequences of the 8 segments of ISAV901_09 (with the 3′ and 5′ UTR ends) were obtained, they were used to synthesize the ISAV901_09 genome (Genscript Co. USA), incorporating into its ends the cleavage sites for the SapI enzyme, and, thus, avoiding errors in the subsequent cloning in the pSS-URG vector.
Design of the Universal pSS-URG Vector Plasmid
In order to have a plasmid allowing for the transcription of the ISAV vRNA, a cassette that was synthesized using advances in synthetic biology (Genscript Co.), and incorporated into the pUC57 plasmid, was designed. The new vector built was called pSS-URG (plasmid for Salmo Salar Universal Reverse Genetic).
pSS-UGR/S6-NotI-HPR and pSS-UGR/S6-EGFP-HPR Vector
A construct was designed based on the pSS-URG vector having the complete sequence (including the 3′ and 5′ UTR ends) in antisense and inverted from segment 6 of ISAV 901_09. As a marker, the vector has additions, in frame, within the HPR region of segment 6, exactly nine nucleotides containing the restriction site for the NotI enzyme nt 1015 5′-gtagca[GCGGCCGCA]acatct-3′nt 1.036 (SEQ ID NO 29,
Vectors to Express PB2, PB1, PA and NP Proteins of ISAV901_09
From the ORFs of segments 1, 2, 3, and 4 of ISA virus 901_09 encoding for PB2, PB1, PA and NP, respectively, (SEQ ID NOS 7, 8, 9, 10) and which are cloned in the pGemT-easy vector, high fidelity PCR with Pfx Platinum (Invitrogen) was performed. The primers used to amplify each one of the gens are shown in Table 2, which include cutting sites for NcoI, SmaI and XhoI enzymes (New England biolabs). Cloning ORFs of PB2 and PA was made with NcoI and XhoI restriction enzymes, cloning of the ORF from PB1 was made with SmaI and XhoI restriction enzymes, and that of the ORF encoding for NP was with MluI and XbaI restriction enzymes. For the expression of PB2, PB1 and PA, the ORFs of segments 1, 2, and 3 were cloned in the pTriex3 vector (Novagen), named here PTRIEX, a commercial expression plasmid. On the other hand, for the expression of the NP protein, the ORF of segment 3 was cloned in the pCI-neo vector (Promega).
Ex Vivo Transcription Trial, ASK Cell Transfection Kinetics with pSS-URG/Seg6-NotI Vector
To test the functionality of the pSS-URG base vector, ASK cells were seeded at a density of 2.5×104 cell/cm2 per well in a 24-well plate (SPL) in Leibovitz Medium (L-15, Hyclone), supplemented with gentamicin (50 μg/mL) and 10% fetal bovine serum (SFB, Hyclone) being cultured at 18° C. (64.4° F.), until reaching 80% confluence. The cells were transfected with the pSS-URG/S6-NotI-HPR vector using Fugene 6 (Promega) at a 1:6 ratio, following manufacturer's specifications. The cells were incubated at 16° C. (60.8° F.) for 3 hours, the mixture being then removed and the cells washed 2 twice with PBS, starting with transfection kinetics that is at 0, 3, 6, 9, 12 and 15 hours. From each well, at each point of the kinetics, total RNA was extracted from the cells using E.Z.N.A. Total RNA Kit II (Omega, Bio-Tek), DNA was eliminated by using RQ-DNase treatment (promega). The RNA obtained was subjected to RT-PCR using primers for the NotI restriction site and the 5′UTR end of viral segment 6 (Table 3).
cDNA was obtained through reverse transcription (RT) using the M-MuLV Reverse Transcriptase enzyme (Moloney Murine Leukemia Virus Reverse Transcriptase, 200 U/μL New England BioLabs). The reverse transcription mixture was made at a final 25 μL volume, in accordance with manufacturer's specifications. cDNA was then used to carry out a PCR reaction with DNA polymerase Paq5000 (Agilent Technologies). PCR products were visualized by electrophoresis at 90 volts for 1 hour on a 2% ethidium bromide-stained (10 mg/mL) agarose gel (
Generation of Recombinant ISAV (ISAVr) Through Plasmid-Based Reverse Genetics System
ASK cells were seeded at a density of 2.5×104 cell/cm2 on Nunc™ Lab-Tek™ II Chamber Slide™ System plates, and then incubated for 72 hours at 18° C. (64.4° F.). The cells were transfected with Fugene 6 (Promega) 1:6, in accordance with manufacturer's specifications. As for the generation of ISAVr901_09, a total of 250 ng of a mixture of vectors PTRIEX3-PB2, PTRIEX3-PB1, PTRIEX3-PA and pCI-neo-NP and 1 μg of the total eight pSS-URG (pSS-URG/1-8) vectors. Recovery of the rISAVS6-NotI-HPR and rISAVS6-EGFP-HPR viruses was performed by replacing pSS-URG/6 with pSS-UGR/S6-NotI-HPR and pSS-URG/S6-EGFP-HPR, respectively. The cells were then incubated with 1 mL of L-15 medium, for 7 days at 16° C. (60.8° F.) (
Infection of ASK Cells with ISAVrS6-EGFP-HPR
ASK cells were seeded at a density of 2.5×10 4 cell/cm2 per well, in 8-well Nunc™ Lab-Tek™ II Chamber Slide™ System plates, and were cultured at 16° C. (60.8° F.), until reaching 90% confluency. Then, the cells were washed with PBS twice, and blind passages were made with 100 μL of a 1:10 dilution of the supernatant either from passage 0 (P0) at 7 days post-transfection or from the different passages at 7 days post infection of ISAVrS6-EGFP-HPR in L-15 medium without SFB with gentamicin (50 μg/mL). The cells were incubated for 4 hours at 16° C. (60.8° F.), then washed twice with PBS and 500 μL of L-15 medium was added with 10% SFB and gentamicin (50 μg/mL), being then incubated for 7 days at 16° C. (60.8° F.). Each viral passage was obtained with this procedure every 7 days up to the fourth ISAVrS6-EGFP-HPR passage, in addition to P0. The supernatant of each passage was stored at −20° C., until further analysis thereof (
ISAVrS6-EGFP-HPR Detection
RNA Extraction, RT-PCR and qRT-PCR in Real Time:
To detect ISAVrS6-EGFP-HPR, a total RNA of 350 μL was extracted from the ASK cells' supernatant as transfected with the 12 plasmids at 7 post-transfection days (ISAVrS6-EGFP-HPR) or supernatants from the 1st to 4th blind passages, with RNAv extracted from RNAv of segment 6, EGFP and Segment 6-EGFP being detected through RT-PCR.
Prior to the RT-PCR reaction, the RNA was treated with RNase-free DNase (Promega). For the reverse transcription reaction (RT), F-UTR-S6 primers (Table 1), F-S6 primers (Table 3), or EGFP primers (Table 4) were used, using the M-MLV RT enzyme (200 U/μL Promega), in accordance with manufacturer's specifications.
For PCR, the GoTaq® Green Master Mix kit (Promega) and Forward (S6 or EGFP) and Reverse (S6 or EGFP) primers were used. The thermal program used was: 95° C. for 2 minutes, 35 95° C. cycles for 30 seconds, 59.1° C. for EGFP, or 54° C. for S6 or S6-EGFP, 30 seconds, 72° C. for 30 seconds, and a final extension of 72° C. for 5 minutes. In all of the cases, re-amplification of the PCR products was carried out, using the same primers. The products of the PCR re-amplification were visualized via electrophoresis on 1% (w/v) agarose gel, run at 90 V for 45 minutes, and stained with ethidium bromide (10 mg/mL).
In order to detect the number of copies of the vRNA, a qRT-PCR was carried out in real time using the absolute method as described by Munir and Kibenge (22), a standard curve being made from the pSS-URG/S8 plasmid. The RT-PCR analysis in real time was carried out on the Eco Real-Time PCR System equipment (Illumina), using the SensiMix™ SYBR® Hi-ROX Kit (Bioline), following manufacturer's instructions, using the F-S8 and R-S8 primers (Table 4). The thermal profile used to amplify the region of segment 8 was 1 initial denaturation cycle of 10 minutes a 95° C., followed by 40 amplification cycles (15 seconds at 95° C., 15 seconds at 60° C., and 15 seconds at 72° C.). Following the amplification cycles, a dissociation cycle (30 seconds at 95° C., 30 seconds at 55° C., and 30 seconds at 95° C., was carried out. This procedure was performed for passage 4 of the recombinant virus. The results obtained were analyzed on EcoStudy software.
Confocal Microscopy
On the 7th post-infection day, ASK cells infested with rISAVS6-EGFP-HPR in each passage of the recombinant virus were analyzed via confocal microscopy, using the procedure as described by Rivas-Aravena et al. (45). The fixed cells were observed using a LSM 510 confocal microscope (Zeiss), utilizing the LSM image Browser software to detect rISAVS6-EGFP-HPR by visualizing EGFP fluorescence. In addition, rISAV was detected using anti-HE monoclonal antibody (BiosChile), as was already described (45).
Tagging by Lysis Plate Trial
ASK cells were seeded at a density of 2.5×10 4 cell/cm2 per well of a 12-well plate (SPL) and were incubated at 16° C. until reaching 100% confluency. The ISAVrS6-EGFP-HPR variant of Passage 4 was tagged. The procedure was performed as described by Castillo-Cerda et al (35).
ISAVrS6-EGFP-HPR Fluorescence Quantification Trial
ASK cells were seeded at a density of 2.5×10 4 cell/cm2 per well, in a 48-well plate (SPL), and were incubated at 16° C. until reaching 100% confluency. Passage 4 of ISAVrS6-EGFP-HPR was tagged. To this effect, serial dilutions of each viral inoculum were performed using a 10-dilution factor, from 10−1 to 10−6 in L-15 medium, without FBS. The culture medium was then removed and 400 μL of viral inoculum was added to each well, and it was incubated at 16° C. for 4 hours to allow virus absorption. Subsequently, the inoculum was removed from each well, the cells were washed twice with PBS and, then, the L-15 medium was added, being supplemented with 10% SFB, 6 mM L-glutamine (Corning Cellgro®, Mediatech), 40 μM β-mercaptoethanol (Gibco®, Life Technologies), 50 μg/ml gentamicin. The plates were incubated for 7 days at 16° C. At the end of the infection, the supernatants from each well were analyzed, fluorescence being quantified using the Nanoquant Infinite M200 pro equipment (TECAN, Austria), exciting at 485 nm, and capturing the emission at 535 nm. These supernatants were also used for extracting total RNA and subsequent qRT-PCR, in real-time, to quantify the RNAv in ISAV segment 8, and for determining, this way, the number of copies of the cell culture from segment 8, as described above.
Infection Kinetics of ISAV901_09, ISAVr901_09, ISAVrS6/EGFP-HPR
Infections of ASK cells were carried out with the fourth passage of ISAVrS6/EGFP-HPR, using the fourth passage of ISAVr901_09 as control, in addition to wild ISAV901_09. For each virus isolate, an infection was carried out with a MOI of 0.01. The infection kinetics was carried out by collecting samples at 0, 2, 4 and 7 days after the infection, then a RNA extraction, DNase treatment, and then a real-time qRT-PCR were carried out, to quantify RNAv of ISAV segment 8 of each cell culture supernatant (22).
Visualization of Particles
The ASK cells were seeded as indicated above and cultured at 16° C. until reaching 90% confluence. Cells were then infected with 400 μL of a 1:10 dilution of ISAVrS6/EGFP-HPR virus in its 4th passage, or the 4th passage of rISAV901_09 or wild ISAV901_09 as control. Four days after infection, the cells were fixed with 2.5% glutaraldehyde in cacodylate buffer 0.1 M at pH 7.2 for 6 hours at room temperature, and then washed with sodium cacodylate buffer 0.1 M at pH 7.2 for 18 hours at 4° C. The samples were then fixed with 1% aqueous osmium tetroxide for 90 minutes, and then washed with distilled water and stained with an aqueous solution of 1% uranyl acetate for 60 minutes. Samples were then dehydrated with washes of 20 minutes each time with a series of buffers containing acetone 50, 70, 2×95 and 3×100%. Samples were finally embedded in epon resin/acetone at 1:1 ratio overnight, and then embedded in pure epon resin which was polymerized at 60° C. for 24 hours. Thin sections (60-70 nm) were obtained in ultramicrotome Sorvall MT-5000, and then mounted on copper grids, and then stained with 4% uranyl acetate in methanol for 2 min, and then citrate for 5 min. The samples were observed with a 12 to 80 kV electron microscope Philips Tecnai (
ISAV 901_09 Strain Genome Adapted to Cell Culture
The complete genome of a virus isolate adapted to cell culture, such as ISAV 901_09 (HPR 1c), was sequenced.
Alignments between the noncoding regions (UTR) of the 5′ and 3′ ends of complete sequences of the six ISAV isolates, two Scots (390/98 and 982/08), one Norwegian (Glesvær/2/90), two Canadian (NBISA01 and RPC NB 98-049), and one Chilean (ADL-PM 3205 ISAV) have high conservation at the ends of each viral genome segment, allowing to design universal primers described in Table I. The primers were used to amplify the genome of the Chilean ISAV 901_09 strain. The result of sequencing the eight viral genome segments is shown in Table IV. The sizes of the eight viral segments range from 2267 bp to 906 bp for segments 1 and 8, respectively.
The sequence of the 3′UTR regions ranged from 7 nucleotides in segment 6 to 48 nucleotides in segment 3, and there were no differences in the size of each 3′UTR end previously described for the 6 genomes analyzed, except for the addition of a nucleotide at the 3′UTR end of segment 7. The sequences of the 5′UTR ends of ISAV 901_09 range from 67 nucleotides in segment 4 to 147 nucleotides in segment 3. The alignment of the UTR regions also indicates that ISAV 901_09 has a high similarity with the ISAV Glesær/2/90 strain (between 97% and 98% identity).
Universal Vector Design for ISAV Reverse Genetics
In order to achieve a vector which expresses segments of full-length viral RNA without additional nucleotides, taking advantage of advances in synthetic biology, an innovative design was made integrating elements previously used in reverse genetics of RNA viruses, such as Hammerhead ribozymes and delta (δ) hepatitis virus, together with genome elements of the Salmo salar species. The designed vector was called pSS-URG (plasmid for Salmo salar Universal Reverse Genetic). The correctly connected components contained by the vector and ordered from left to right are: As a promoter ITS-1 region of Salmo salar, a sequence of Hammerhead ribozyme, the ribozyme of delta (δ) hepatitis virus, and the sequences of the two ribozymes incorporate two cutting sites for Sap I enzyme (New England Biolabs), and finally incorporated as transcription terminator is rabbit beta globin terminator (
Once the pSS-URG plasmid is synthesized, subcloning of the eight genome segments of ISAV was achieved from synthetic genomes using distant cut enzyme Sap I (Data not shown). In addition to cloning the eight viral segments, as a genetic marker and in order to prove that generated viruses are recombinant agents and do not correspond to a contamination of the procedure, two genetic elements were inserted in the HPR area of the universal vector containing segment 6. The first genetic variant corresponds to the insertion in the HPR area of a sequence of nine nucleotides with the cutting site for the NotI enzyme, calling this new vector pSS-URG/S6-NotI-HPR. A second genetic variant corresponds to the product of cloning the sequence which codes for EGFP using previously created NotI site, thus the new vector called pSS-URG/S6-EGFP-HPR is obtained.
Analysis of Functionality for pSS-URG Vector by Ex Vivo Transcription Trial
To determine whether all the elements included in the vector allow the expression of viral RNA in salmon cells, and due to the uncertainty of functionality of the promoter suggested in ITS-1 region of Salmo salar, ASK cells were transfected with pSS-URG/S6-NotI-HPR plasmid in an ex vivo transcription trial. To determine the existence of a transcription process, the functionality analysis was made by detecting the RNAV at times 0, 3, 6, 9, 12 and 15 after transfection (hpt) through RT-PCR. The reverse transcription reaction was made using a single first complementary to the Not I restriction site. Surprisingly, the analysis result can display a PCR product from three hpt, which increases in intensity until 15 hpt (
These results suggest the use of the ITS-1 region and the inclusion in pSS-URG vector to express any type of RNA inside the cells. For example, RNA can be expressed as interfering RNA, silencing RNA or also micro RNAs.
Obtaining Recombinant ISA Virus (ISAVr)
As it has been reported for Influenza virus, the functional minimum unit of the virus corresponds to the ribonucleoprotein (RNP) complex, which consists of viral RNA that is bound by multiple copies of NP and by the viral polymerase including PB1, PB2 and PA subunits. In order to form the RNP complexes in salmon cells, ORFs of segments 1 to 4 of ISAV901_09 were cloned into expression vectors commanded by the Cytomegalovirus promoter. Thus, using the pTriEx-3 vector (Novagen), ORFs of segments 1, 2 and 4 were cloned, obtaining PTRIEX3-PB2, PTRIEX PB1, PTRIEX3-PA vectors. Besides, using the pCI-neo vector (Promega), segment 3 was cloned generating pCI-neo-NP vector (Data not shown). Transfection of these vectors into salmon cells allows expression of recombinant proteins PB2, PB1, PA and NP, respectively.
Generation of ISAVrS6-NotI-HPR
For the generation of ISAVr S6-NotI-HPR, ASK cells were cotransfected with twelve plasmids, four of which correspond to expression vectors PTRIEX3-PB2, PTRIEX PB1, PTRIEX3 PA and pCI-neo-NP, and the remaining eight correspond to plasmids for pSS-URG reverse genetics with each of the eight genome segments of ISAV901_09 as DNA, replacing native segment 6 by Seg6-NotI-HPR. In order to amplify and determine the presence of recombinant virus, after transfection of cells, two blind passages were made in ASK cells infecting with the supernatants obtained from the previous transfections. On the one hand, the presence of RNAV of segment 6 (NotI/HPR) was detected, through RT-PCR, obtaining a product of an expected 306 bp size, both in the RNA extracted from the transfection supernatant and from the two subsequent passages, which suggests the presence of infectious viruses. The second passage supernatant was used to infect a greater amount of ASK cells. From the infected cells, which showed an obvious cytopathic effect (data not shown), the recombinant virus was visualized by transmission electron microscopy.
Generation of ISAVrS6-EGFP-HPR
In order to generate recombinant ISA virus containing a reporter gene, such as EGFP, in order to facilitate ex vivo monitoring and discard that results are artifactual results or contamination, ASK cells were co-transfected with twelve plasmids simultaneously: four of them correspond to expression vectors PTRIEX3-PB2, PTRIEX-PB1, PTRIEX3 PA and pCI-neo-NP; the remaining eight plasmids correspond to vectors pSS-URG/1, pSS-URG/2, pSS-URG/3, pSS-URG/4, pSS-URG/5, pSS-URG/7 and pSS-URG/8; also incorporating segment 6 with vector pSS-URG/S6-EGFP-HPR; the virus which contains EGFP in the HPR area of the protein is called ISAVrS6-EGFP-HPR.
To determine whether recombinant viral particles were generated after transfection, the culture supernatant (passage 0, P0) was analyzed 7 days after transfection (dpt). For this purpose, it was initially detected by RT-PCR RNAv of Segment 6, as well as the EGFP coding sequence in a second PCR product, and finally an area containing both part of Segment 6 and the EGFP. The results showed that RT-PCR products for Segment 6 have a different migration distance of the PCR products for the native virus (˜300 bp) and the recombinant virus having EGFP in the HE protein (1,000 bp). The RT-PCR of the EGFP coding sequence has a ˜500 bp product, which is not observed in the native virus analyzed. For RT-PCR of S6-EGFP, an amplification product of ˜800 bp was obtained for the recombinant virus as expected.
Infectivity of ISAVrS6-EGFP-HPR in ASK Cells
To determine whether the supernatant of ASK cells transfected with twelve plasmids indeed contains the viral variant ISAVrS6-EGFP-HPR with the characteristics of an infectious agent, EGFP fluorescence was used as a reporter. The ASK cells infected with the supernatant that would contain the first progeny ISAVrS6-EGFP-HPR were analyzed under confocal microscope 7 days after infection. The results show that it is possible to visualize cells emitting green fluorescence attributable to EGFP, corresponding to the first passage of the ISAVrS6-EGFP-HPR virus. Distribution of the EGFP mark is found mainly in the cytoplasm and towards the plasma membrane, fluorescence being not observed in the cell nucleus. To confirm that the supernatant of transfected cells (passage 0) contains the ISAVrS6-EGFP-HPR virus with lytic capacity, a lysis plaque trial was carried out on ASK cells. The result of the lysis plaque trial showed that the recombinant virus has the ability to generate lysis plaques like the wild virus, obtaining a virus titre in the order of 1×104 PFU/m L.
Stability of ISAVrS6-EGFP-HPR
Subsequently, the ability of this recombinant virus to maintain infectiousness and fluorescence was assessed in cell culture. Four blind passages of infection in ASK cells were carried out with 7-day gaps. Then, in each supernatant of the recombinant virus passages, a RT-PCR was carried out to detect RNAv both of Segment 6 and of the coding sequence for EGFP, and a region of the EGFP-S6 hybrid sequence. The result made possible to visualize a PCR product of 500 bp EGFP and EGFP-S6 hybrid sequences of 800 bp, indicating the presence of segment 6 containing the EGFP gene in all supernatants analyzed. The PCR product of segment 6 shows a 300 bp product in the supernatant of infected ASK cells with ISAV901_09 wild virus, as expected, in contrast to the 1,000 bp of the PCR product obtained in each of the four passages of ISAVrS6-EGFP-HPR virus, whose larger size is the result of having incorporated the EGFP gene in segment 6.
To determine that each of the four passages not only had a virus with infectivity, but also was capable of fluorescing, indicating the correct folding of HE with EGFP in the HPR area, an analysis was carried out by confocal microscopy in infected ASK cells. Confocal microscopy showed cells that emit green fluorescence in all passages analyzed, increasing in each passage the abundance of fluorescent cells. These results suggest that the region of the HE protein elected to incorporate EGFP is not affected by the incorporation of this ORF, thus allowing the generation of a chimeric recombinant ISA virus capable of replicating, infecting and spreading in multiple passages without losing the ability to fluoresce. Titration of the fourth blind passage made to ISAVrS6-EGFP-HPR virus by qRT-PCR in real time resulted in a titre of 3.63×106 copies Seg 8/mL and a value of 6.5×105 PFU/mL obtained by lysis plaque trial, showing a lysis plaque size similar to that observed after conducting plaque trial on ISAV901_09 wild virus.
Infectivity of ISAVrS6-EGFP-HPR in Salmonid Cell Lines
In order to determine whether by incorporating a sequence in the HPR area of the ISAVrS6-EGFP-HPR virus, this acquires the ability to infect other salmonid species or lose infectivity in permissive cells (ASK cells), an infection kinetics was carried out in RTG-2, CSE-119 and ASK cells. The ex vivo trial was conducted for 7 days using the fourth passage of the fluorescent recombinant virus and compared to the ISAV901_09 wild virus, and the fourth passage of a wild recombinant virus generated for this trial rISAV901_9 (MOI of 0.01). The analysis at 0, 2, 4 and 7 dpi by qRT-PCR quantifying the number of copies of segment 8 in each supernatant showed that none of the three viruses analyzed had the ability to replicate in RTG-2 cells or in CSE-119 cells.
In contrast, the infection kinetics carried out on ASK cells showed that initially the ISAV 901_09 virus has a larger number of copies than recombinant viruses, rISAV901 and rISAVS6-EGFP-HPR. On the second day after infection, however, an increase occurs in the number of copies of the recombinant viruses, reaching titres near 1,000 segment 8/mL, with values similar to the wild virus. These results suggest that the incorporation of EGFP in the HPR area of HE protein does not alter the replicative behavior of the fluorescent recombinant virus in ASK cells, and does not extend the host range at least in the ex vivo trials in RTG-2 cells or in CSE-119 cells.
These results can lead to the conclusion that it is possible to incorporate into the pSS-URG plasmid a sequence encoding both for a viral protein and for an exogenous or chimeric protein, thus achieving the generation of a modified or chimeric recombinant ISA virus; these modifications would not alter or affect its infectious or propagation characteristics.
Functionality of pSS-URG Plasmid in Salmon, Swine and Human Cell Lines
To determine the ability of the pSS-URG/S6-NotI-HPR vector for transcribing segment 6 as RNAv, it was transfected into ASK cells using Fugene 6 (Promega) at a 1:6 ratio and according to manufacturers' specifications. 0 hpt is considered as the time when adding the transfection mix to the cells. The initial incubation takes place for 3 hours at 16° C. F. Once the incubation time had elapsed, the transfection mix was removed and the cells were washed twice with PBS, this being a 3-hpt time. At each point of the transfection kinetics, which occurs at 0, 3, 6, 9, 12 and 15 hpt, the cells are removed for extraction of total RNA, possible contaminating DNA was removed with DNase I. With the RNA obtained, RNAv of segment 6 NotI was detected by RT-PCR using specific primers for segment 6 NotI. The analysis allows to observe a PCR product of expected 306 bps size from 3 hpt, which increases in intensity until 15 hpt (
Surprisingly, the ability to transcribe the viral RNA is not restricted to salmon cells cultured at 16° C. Using the same procedure (with incubations at 37° C.), but conducted only at 12 hpt, functionality was observed in human cell line HEK 293 and swine cell line ST, incubated at 37° C. (
ISAVrS6-EGFP-HPR: Correlation Between the Number of Viral Copies and Measured Fluorescence
Since the ISAVrS6-EGFP-HPR virus has similar characteristics to the wild virus when infecting ASK cells, and also has the advantage of monitoring the infection by incorporating EGFP as reporter, the goal is to determine whether there is correlation between the viral load and fluorescence in the supernatant of infection caused by this recombinant virus. The analysis carried out on serial dilutions of fluorescent recombinant virus through qRT-PCR and fluorescence quantitation established that there is a direct relationship showing an increased fluorescence detected when the viral titer of the solution increases, showing a fluorescence intensity of 500 units/mL for a titer of 2×106 copies/mL.
| Number | Date | Country | Kind |
|---|---|---|---|
| 3146-2014 | Nov 2014 | CL | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/CL2016/050002 | 1/6/2016 | WO | 00 |
| Publishing Document | Publishing Date | Country | Kind |
|---|---|---|---|
| WO2016/077938 | 5/26/2016 | WO | A |
| Number | Date | Country |
|---|---|---|
| 0104333 | Jan 2001 | WO |
| 2007144773 | Dec 2007 | WO |
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| GenBank: AF201312.1 Salmo salar internal transcribed spacer 1, complete sequence. |
| Number | Date | Country | |
|---|---|---|---|
| 20180030416 A1 | Feb 2018 | US |
