Patent Application
20230304041
A computer readable form of the Sequence Listing is filed with this application by electronic submission and is incorporated into this application by reference in its entirety. The Sequence Listing is contained in the ST.26 XML file created on Mar. 21, 2023, having the file name “20-1939-US_Sequence-Listing.xml” and is 41,216 bytes in size.
Coronavirus disease in 2019 (COVID-19) is a highly transmissible respiratory disease and caused by SARS-CoV-2 (SARS2) [1-4]. More than 450 million people have been infected and more than 6 million have died from this infection worldwide since late 2019 [5]. Infected people develop headache, fever, coughing, diarrhea, and pneumonia with a higher mortality in the elderly and those with compromised immune system, diabetes, and other chronic respiratory and heart diseases [6, 7]. Thus, COVID-19 has been a profound global health threat. The method of choice for detection and diagnosis of SARS2 infection is real-time RT-PCR, which is very sensitive and accurate and has successfully been adapted for various human specimens including nasal swabs and sputum [8, 9]. Vaccines against SARS2 have been proven to be effective in preventing viral transmission and improving clinical outcomes [10-13]. Antiviral drugs Remdesivir and Molnupiravir can be used to treat and prevent COVID-19, but with a very modest efficacy [14-19]. In addition, over 30% of the population who were infected with SARS2 and recovered from COVID-19 have experienced the long-COVID symptoms [20-25]. The continued emergence of SARS2 variants, lack of effective and direct SARS2 targeting drugs, and a large population with long-COVID symptoms make it imperative to develop more effective and SARS2-specific antiviral drugs to treat and prevent the disease.
SARS2 belongs to a member of the coronavirus family and is a single-stranded positive enveloped RNA virus [26-28]. The viral genome is about 30 kb nucleotides in length and has a leader cap structure and an untranslated region (UTR) at the 5′ end and an UTR and a poly(A) tail at the 3′ end. Both UTR form highly specified RNA structures required for viral RNA translation, transcription, and replication. There are 14 open reading frames (ORF) within the viral genome, preceded by transcriptional regulatory sequences (TRS). The two main ORF's are ORF1a and ORF1b. ORF1a encodes a large polyprotein, which is cleaved into nonstructural proteins (NSP) 1-11. ORF1b is derived from the frameshift at the 3′ end of ORF1a and as result, encodes another large polyprotein, which is cleaved into NSP1-10 and NSP12-16. All these NSP make up the replication/transcription complex with distinct functions and are essential for viral RNA replication/transcription, which includes first synthesis of negative-stranded viral genomic RNA (gRNA) and subgenomic RNA (sgRNA) and subsequent synthesis positive-stranded gRNA and sgRNA. Four structural proteins: spike S, envelope E, membrane M, and nucleocaspid N, and nine accessory proteins: ORF3a/b, 6, 7a/b, 8, 9a/b and 10 are encoded by their corresponding sgRNA. Newly synthesized gRNA and structural proteins are assembled to form new infectious virions for the new round of infection. Because of the unique features and viral proteins (enzymes) involved, the RNA replication and transcription process affords the best targets to develop direct SARS2 targeting antiviral drugs.
Replicons have been the strategy of choice to screen and identify antiviral drugs for positive-stranded RNA viruses and to study molecular mechanisms of the viral replication process. They are constructed by reverse genetic engineering of partial viral genome and one or more structural genes so that the viral genome can replicate and persist in cells. Replicons have successfully been constructed in several families of positive-stranded RNA viruses including picornaviridae [29], caliciviridae [30], flaviviridae [31-36], and coronaviridae [37-41]. A great example is HCV replicons, which have been attributed to successful identification of several direct acting antivirals to treat HCV infections [42, 43]. All the replicons lack the envelope gene and other structural genes, and there are no infectious viruses produced from use of the replicons. Thus, replicons represent an ideal platform for identification of anti-SARS2 antiviral drugs and elucidation of molecular mechanisms of SARS2 replication for researchers, particularly for those who do not have access to a research facility of biosafety level 3 or higher required for working with SARS2.
The severe acute respiratory syndrome coronavirus-2 (SARS CoV-2, SARS2) remains a great global health threat and demands identification of more effective and SARS2-targeted antiviral drugs even with successful development of anti-SARS2 vaccines. Viral replicons have proven to be a rapid, safe and readily scalable platform for high throughput screening, identification and evaluation of antiviral drugs against positive-stranded RNA viruses.
This disclosure provides a unique robust SARS2 replicon with dual promoters HIV long terminal repeat (LTR) and T7 and with dual reporters luciferase and green fluorescent protein. Several other novel features were also incorporated into the design of the replicon, which together afford the replication fidelity of the replicon, maximized expression of the full-length replicon, and flexible monitoring of the replicon replication. These findings indicate that the replicon may provide a platform for rapid, sensitive, and safe screening and evaluation of the SARS2 replication inhibitors.
The genomic organization of the replicon was designed with features that were to ensure the replication fidelity of the replicon, to maximize the expression of the full-length replicon, and to offer the monitoring flexibility of the replicon replication. This disclosure demonstrates the success of the construction of the replicon and expression of reporter genes and SARS structural nucleocapsid N from the replicon DNA or the RNA that was in vitro transcribed from the replicon DNA. This disclosure demonstrates detection of the negative-stranded genomic RNA (gRNA) and subgenomic RNA (sgRNA) intermediates, a hallmark of replication of positive-stranded RNA viruses from the replicon. Lastly, this disclosure demonstrates expression of the reporter genes, nucleocapsid N gene, gRNA and sgRNA from the replicon was sensitive to inhibition by Remdesivir. Taken together, this disclosure supports the use of the replicon construct for identification of anti-SARS2 drugs and development of new anti-SARS strategies targeted at the step of the virus replication.
In one aspect, this disclosure provides a construct comprising a SARS-CoV-2 (SARS2) replicon, wherein the construct comprises 5′ to 3′:
In some embodiments, the construct further comprises a 5′ untranslated region (UTR) that is 5′ of the nucleic acid sequence encoding SARS2 non-structural protein 1. In some embodiments, the 5′ UTR is 5′ of the nucleic acid sequence encoding SARS2 non-structural protein 1, and is 3′ of the two or more promoter sequences. In some embodiments, the construct further comprises a 3′ untranslated region (UTR) that is 3′ of the nucleic acid sequence encoding SARS2 nucleocapsid protein. In some embodiments, the two or more promoters comprise a eukaryotic promoter and a prokaryotic promoter.
In some embodiments, the eukaryotic promoter is selected from a HIV-1 long terminal repeat (LTR) promoter, a HIV-2 LTR promoter, a beta actin promoter, a cytomegalovirus (CMV) promoter, an human elongation factor-1 alpha (EF-1 alpha; EF1a) promoter, a phosphoglycerate kinase (PGK1) promoter, a simian virus 40 (SV40) promoter, a polyubiquitin C gene (UBC) promoter, a human T-lymphotropic virus type 1 (HTLV-1) LTR promoter, a human T-lymphotropic virus type 2 (HTLV-2) LTR promoter, a simian immunodeficiency virus (SIV) LTR promoter, a visna virus LTR promoter, a feline immunodeficiency virus (FIV) LTR promoter, an equine infectious anemia virus (EIAV) LTR promoter, a simian T-cell lymphoma virus (STLV) LTR promoter, a bovine leukemia virus (BLV) LTR promoter, a simian foamy virus (SFV) LTR promoter, and a bovine foamy virus (BFV) LTR promoter.
In some embodiments, the prokaryotic promoter is selected from a T7 promoter, a lac promoter, a Sp6 promoter, a tac promoter, a tet promoter, a trp promoter, a trc promoter, a T3 promoter, and a T5 promoter.
In some embodiments, the first reporter gene and the second reporter gene are optically detectable. In some embodiments, the first reporter gene and the second reporter gene are optically distinguishable.
In another aspect, this disclosure provides a construct comprising a SARS-CoV-2 (SARS2) replicon, wherein the construct comprises 5′ to 3′:
In some embodiments, the construct as disclosed herein comprises the sequence of SEQ ID NO:14.
In yet another aspect, this disclosure provides a method for screening a test compound for anti-SARS2 activity, wherein the method comprises: a) incubating the test compound with a cell line comprising the construct of claim 1; and b) assaying for the presence of expression of the first reporter gene or expression of the second reporter gene, wherein a decreased expression of the first reporter gene or a decreased expression of the second reporter gene compared to a control indicates that the test compound comprises anti-SARS2 activity.
In yet another aspect, this disclosure provides a kit for screening a test compound for anti-SARS2 activity, wherein the kit comprises the construct as disclosed herein. In some embodiments, the kit further comprises: one or more primer sets to detect one or more genes of the construct; one or more cell lines to be transfected with the construct; or reagents for detection and quantitation of the two or more reporter genes of the construct.
These and other features and advantages of the present disclosure will be more fully understood from the following detailed description taken together with the accompanying claims. It is noted that the scope of the claims is defined by the recitations therein and not by the specific discussion of features and advantages set forth in the present description.
Skilled artisans will appreciate that elements in the Figures are illustrated for simplicity and clarity and have not necessarily been drawn to scale. For example, the dimensions of some of the elements in the Figures can be exaggerated relative to other elements to help improve understanding of the embodiment(s) of the present disclosure.
Before describing the present disclosure in detail, a number of terms will be defined. Unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular. For example, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. It should be understood that the terms “a” and “an” as used herein refer to “one or more” of the enumerated components unless otherwise indicated or dictated by its context. The use of the alternative (e.g., “or”) should be understood to mean either one, both, or any combination thereof of the alternatives unless otherwise indicated.
In the present disclosure, any concentration range, percentage range, ratio range, or integer range is to be understood to include the value of any integer within the recited range and, when appropriate, fractions thereof (such as one tenth and one hundredth of an integer), unless otherwise indicated.
As used herein, the term “about” means ±10% of the indicated range, value, sequence, or structure, unless otherwise indicated.
It is noted that terms like “preferably,” “commonly,” and “typically” are not utilized herein to limit the scope of the claimed subject matter or to imply that certain features are critical, essential, or even important to the structure or function of the claimed subject matter. Rather, these terms are merely intended to highlight alternative or additional features that can or cannot be utilized in a particular embodiment of the present disclosure.
For the purposes of describing and defining the present disclosure it is noted that the term “substantially” is utilized herein to represent the inherent degree of uncertainty that can be attributed to any quantitative comparison, value, measurement, or other representation. The term “substantially” is also utilized herein to represent the degree by which a quantitative representation can vary from a stated reference without resulting in a change in the basic function of the subject matter at issue.
Unless expressly specified otherwise, the term “comprising” is used in the context of the present disclosure to indicate that further members may optionally be present in addition to the members of the list introduced by “comprising”. It is, however, contemplated as a specific embodiment of the present disclosure that the term “comprising” encompasses the possibility of no further members being present, i.e. for the purpose of this embodiment “comprising” is to be understood as having the meaning of “consisting of”.
As utilized in accordance with the present disclosure, unless otherwise indicated, all technical and scientific terms shall be understood to have the same meaning as commonly understood by one of ordinary skill in the art.
Methods well known to those skilled in the art can be used to construct genetic expression constructs and recombinant cells according to this disclosure. These methods include in vitro recombinant DNA techniques, synthetic techniques, in vivo recombination techniques, and polymerase chain reaction (PCR) techniques. See, for example, techniques as described in Green & Sambrook, 2012, MOLECULAR CLONING: A LABORATORY MANUAL, Fourth Edition, Cold Spring Harbor Laboratory, New York; Ausubel et al., 1989, CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, Greene Publishing Associates and Wiley Interscience, New York, and PCR Protocols: A Guide to Methods and Applications (Innis et al., 1990, Academic Press, San Diego, CA).
As used herein, the terms “polynucleotide,” “nucleotide,” and “nucleic acid” can be used interchangeably to refer to nucleic acid comprising DNA, RNA, derivatives thereof, or combinations thereof, in either single-stranded or double-stranded embodiments depending on context as understood by the skilled worker. In the present disclosure, a “nucleic acid” molecule can include, DNA, cDNA and genomic DNA sequences, RNA, messenger RNA, and synthetic nucleic acid sequences. In some embodiments, the nucleic acid molecules are codon-optimized for expression. Thus, “nucleic acid” also encompasses embodiments in which analogs of DNA and RNA are employed. In some embodiments, the nucleic acid component may comprises one or more RNA molecules, such as viral RNA molecules or mRNA molecules that encode the protein of interest.
Disclosed herein is a novel non-infectious SARS2 replicon system. The SARS2 replicon construct comprises the following components in the direction from 5′ end to 3′ end: an HIV LTR promoter (for in vivo DNA transfection and efficient transcription of full-length RNA), a T7 promoter (for in vitro RNA transcription), a 5′ UTR (for RNA replication and anti-innate immunity), a P2A self cleaving sequence, a first reporter gene (e.g., firefly luciferase, which can be for replication monitoring by a luciferase assay, which is easy to scale up for high throughput screening), an IRES sequence (to facilitate efficient translation of the extremely large polyprotein), a TRS for GFP:Bsr subgenomic RNA transcription, GFP:Bsr (GFP offers the second sensitive monitoring of viral replication, blasticidin (Bsr) for stable replicon selection and long-term maintenance), a TRS for N subgenomic RNA transcription, N (for viral replication), orf10 3′ UTR (for RNA replication), poly-A) (polyadenylation signal), Rz at both 5′ end and 3′ end (ribozyme self-cleavage site to remove unwanted nucleotides from replicon RNA), and BGH poly-A (bovine growth hormone polyadenylation signal).
This platform will permit versatile, fast, easy, accurate and safe identification of anti-SARS2 inhibitors targeting various virus specific enzymes and different stages of virus replication and studies of basic virology of the virus.
The SARS2 replicon as described herein provides: (1) both delivery options of in vitro transcription RNA and recombinant DNA; (2) SARS2 non-structural genes, plus only structural N gene, therefore it is non-infectious (being safe, does not require BSL-3 or higher facility); (3) the HIV LTR promoter (in combination with Tat) allows abundant synthesis of the full-length RNA of about 28,000 nucleotides; (4) three reporters embedded in the system: luciferase, GFP and blasticidin, for fast, easy, and accurate monitoring of the surrogate virus replication; (5) an ECMV IRES, which will allow efficient translation of the polyprotein of about 7,000 amino acids. (6) a 5′ UTR-NSP1 and N-orf10 3′ UTR at the both ends of the SARS2 viral components of the construct, which allows for proper configuration of the RNA secondary structures within 5′ UTR and 3′ UTR for viral replication. (7) a Hammerhead virus ribozyme site at the 5′ end and a Hepatitis virus ribozyme site at the 3′ end that would allow production of RNA replicon with both 5′ and 3′ ends that are authentic to SARS2.
In one aspect, this disclosure provides a construct comprising a SARS-CoV-2 (SARS2) replicon, wherein the construct comprises 5′ to 3′:
As used herein, the terms “construct”, “vector” or “expression cassette”, refer to a nucleic acid construct that, when introduced into a host cell, results in transcription and/or translation of an RNA or polypeptide, respectively.
In some embodiments, the construct further comprises a 5′ untranslated region (UTR) that is 5′ of the nucleic acid sequence encoding SARS2 non-structural protein 1. In some embodiments, the 5′ UTR is 5′ of the nucleic acid sequence encoding SARS2 non-structural protein 1, and is 3′ of the two or more promoter sequences. In some embodiments, the construct further comprises a 3′ untranslated region (UTR) that is 3′ of the nucleic acid sequence encoding SARS2 nucleocapsid protein.
As used herein, the term “promoter,” refers to a polynucleotide sequence capable of driving transcription of a DNA sequence in a cell. Thus, promoters used in the constructs as disclosed herein, can include cis- and trans-acting transcriptional control elements and regulatory sequences that are involved in regulating or modulating the timing and/or rate of transcription of a gene in the construct. Reference to a promoter by name can include a wild type, native promoter as well as variants of the promoter that retain the ability to induce expression. Reference to a promoter by name is not restricted to a particular species, but also encompasses a promoter from a corresponding gene in other species.
The particular promoter employed to control the expression of a nucleic acid sequence of interest is not believed to be important, so long as it is capable of directing the expression of the polynucleotide in the targeted cell. Thus, where a human cell is targeted the nucleic acid sequence-coding region may, for example, be placed adjacent to and under the control of a promoter that is capable of being expressed in a human cell. Generally speaking, such a promoter might include either a human or viral promoter. The use of other viral or mammalian cellular or bacterial phage promoters which are well known in the art to achieve expression of a coding sequence of interest is contemplated as well, provided that the levels of expression are sufficient for a given purpose. By employing a promoter with well-known properties, the level and pattern of expression of the protein of interest following transfection or transformation can be optimized. In some embodiments, the two or more promoters of the construct as disclosed herein, comprise a eukaryotic promoter and a prokaryotic promoter. In some embodiments, the eukaryotic promoter is selected from a HIV-1 long terminal repeat (LTR) promoter, a HIV-2 LTR promoter, a beta actin promoter, a cytomegalovirus (CMV) promoter, an human elongation factor-1 alpha (EF-1 alpha; EF1a) promoter, a phosphoglycerate kinase (PGK1) promoter, a simian virus 40 (SV40) promoter, a polyubiquitin C gene (UBC) promoter, a human T-lymphotropic virus type 1 (HTLV-1) LTR promoter, a human T-lymphotropic virus type 2 (HTLV-2) LTR promoter, a simian immunodeficiency virus (SIV) LTR promoter, a visna virus LTR promoter, a feline immunodeficiency virus (FIV) LTR promoter, an equine infectious anemia virus (EIAV) LTR promoter, a simian T-cell lymphoma virus (STLV) LTR promoter, a bovine leukemia virus (BLV) LTR promoter, a simian foamy virus (SFV) LTR promoter, and a bovine foamy virus (BFV) LTR promoter. In some embodiments, the eukaryotic promoter is a HIV-1 long terminal repeat (LTR) promoter. In some embodiments, the prokaryotic promoter is selected from a T7 promoter, a lac promoter, a Sp6 promoter, a tac promoter, a tet promoter, a trp promoter, a trc promoter, a T3 promoter, and a T5 promoter. In some embodiments, the prokaryotic promoter is a T7 promoter.
In some embodiments, the two or more promoters are operably linked to one or more genes in the construct. As used herein, the term “operably linked” refers to a functional relationship between two or more nucleic acid sequences of the construct. Typically, it refers to the functional relationship of a transcriptional regulatory promoter sequence to a transcribed gene sequence. For example, a promoter is operably linked to a DNA or RNA sequence if it stimulates or modulates the transcription of the DNA or RNA sequence in an appropriate host cell or other expression system. Generally, promoter transcriptional regulatory sequences that are operably linked to a transcribed gene sequence are physically contiguous to the transcribed sequence.
As used herein, a “reporter gene” refers to a nucleic acid sequence encoding a protein product that can generate, under appropriate conditions, a detectable signal that allows detection for indicating the presence and/or quantity of the reporter gene protein product. In some embodiments, the first reporter gene or the second reporter gene is a nucleic acid sequence encoding a protein that allows a cell to present a detectable signal. Examples of such a protein capable of generating a detectable signal include a protein that generates a fluorescence signal or a phosphorescence signal, a protein that is detectable in an assay, or a protein exhibiting an enzyme activity. Examples of a protein encoded by the first reporter gene or the second reporter gene can include fluorescent proteins such as a green fluorescent protein (GFP), a humanized Renilla green fluorescent protein (hrGEP), a blue fluorescent protein (BFP), a cyan fluorescent protein (CFP), a yellow fluorescent protein (YFP), a red fluorescent protein (RFP or DsRed), and enhanced or modified versions thereof. Additional examples of a protein encoded by the first reporter gene or the second reporter gene can include bioluminescent proteins such as firefly luciferase and Renilla luciferase. Further examples of a protein encoded by such a reporter gene include enzymes for converting chemiluminescent substrates, such as alkaline phosphatase, peroxidase, chloramphenicol acetyltransferase, and β-galactosidase. In some embodiments, a reporter gene detected by a light signal such as a fluorescence signal or a phosphorescence signal can correlate to the expression level of the reporter gene. This can be observed in a state in which a cell is maintained, and a cell used for evaluation can be easily selected, while the cell is alive. The reporter gene can be used in an experiment in which a test substance is continuously administered, and a change over time in the expression level of the reporter gene can be pursued in a real time.
In some embodiments, the first reporter gene and the second reporter gene are optically detectable. In some embodiments, the first reporter gene and the second reporter gene are optically distinguishable. In some embodiments, the first reporter gene and the second reporter gene are different reporter genes.
In some embodiments, the construct as disclosed herein comprises a polyadenylation signal (e.g. a poly-A tail) to effect proper polyadenylation of the gene transcript. Any poly-A sequence can be employed such as human or bovine growth hormone and SV40 polyadenylation signals and LTR polyadenylation signals. In an embodiment, the construct as disclosed herein comprises the polyadenylation signal from bovine growth hormone.
In certain embodiments, the construct as disclosed herein comprises an internal ribosome entry sites (IRES) element to create multigene, or polycistronic messages. IRES elements are able to bypass the ribosome-scanning model of 5′ methylated cap-dependent translation and begin translation at internal sites. IRES elements can be linked to heterologous open reading frames. Multiple open reading frames can be transcribed together, each separated by an IRES, creating polycistronic messages. By virtue of the IRES element, each open reading frame is accessible to ribosomes for efficient translation. Multiple genes can be efficiently expressed using a single promoter/enhancer to transcribe a single message. In an embodiment, the construct as disclosed herein comprises an IRES element from encephalomarcarditis virus.
The SARS2 replicon construct as described herein addresses the need for anti-SARS2 drug discovery and research on SARS2 and other viruses.
In some embodiments, the replicons described herein can be used for drug discovery. In other embodiments, the replicons described herein can be used as a surrogate platform for live SARS2 virus infection to understand the basics of SARS2 virology. Because of non-infectious nature of the replicon, it would be of great value to scientists who do not have access to the BSL3 facility that is required for working with SARS2.
In another aspect, this disclosure provides a method for screening a test compound for anti-SARS2 activity, wherein the method comprises: a) incubating the test compound with a cell line comprising the construct as described herein; and b) assaying for the presence of expression of the first reporter gene or expression of the second reporter gene, wherein a decreased expression of the first reporter gene or a decreased expression of the second reporter gene compared to a control indicates that the test compound comprises anti-SARS2 activity.
In order to determine the effect of a test compound on the SARS2 replicon construct, it will be necessary to transfer the SARS2 replicon construct as disclosed herein into a cell. Such transfer may employ viral or non-viral methods of gene transfer. A transformed cell comprising the SARS2 replicon construct is generated by introducing the SARS2 replicon construct into the cell. Suitable methods for polynucleotide delivery for transformation of an organelle, a cell, a tissue or an organism for use with the current methods include virtually any method by which a polynucleotide (e.g., DNA) can be introduced into an organelle, a cell, a tissue or an organism. A eukaryotic cell can be used as a recipient for the SARS2 replicon construct. Numerous cell lines and cultures are available for use as a host cell, and they can be obtained through the American Type Culture Collection (ATCC).
Any appropriate method may be used to transfect or transform the cells, or to administer the SARS2 replicon construct as disclosed herein. In some embodiments, examples of construct delivery into a cell can include methods such as delivery using cationic polymers and lipid like molecules.
The method for screening for a test compound for anti-SARS2 activity can comprise screening a test compound for its ability to inhibit or block the expression or function of the SARS2 replicon as disclosed herein. In the screening method as disclosed herein, a test compound having an ability to inhibit or block the expression or function of one or more SARS2 genes of the construct may be screened. When a substance having an effect of inhibiting the expression of one or more SARS2 genes of the construct, the test compound is capable of reducing the expression level of the one or more SARS2 genes of the construct by about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95% or more.
The cells to be used for screening are preferably cells of a biological species that is a host for SARS2 virus. In some embodiments, the cells are cultured cell lines of mammals and birds. In some embodiments, the cells are human cells. In some embodiments, the cells are avian cells.
The change in the expression level of the SARS2 genes of the construct can be evaluated using the reporter genes of the construct, or at the mRNA level or at the protein level. For example, the expression level of the SARS2 genes of the construct can be quantitatively compared by a nucleic acid amplification reaction such as RT-PCR method, immunohistochemistry method, or western blot (Western blot) method.
In another aspect, the disclosure also provides for a kit for use in screening a test compound for anti-SARS2 activity. In some embodiments, the kit comprises the replicon construct as disclosed herein. In certain embodiments, the kit comprises a replicon construct having the sequence of SEQ ID NO:14. In some embodiments, the kit can further comprise one or more primer/probe sets that provides a detectable signal on the occurrence on the transcription of one or more of the genes of the SARS2 replicon construct provided herein. In some embodiments, the kit can further comprise one or more cell lines to be transfected with the construct. In some embodiments, the kit further comprises one or more reagents for detection and quantitation of the two or more reporter genes of the replicon construct disclosed herein.
The design and organization of the replicon of the present disclosure can be used as a replicon for other viruses besides SARS2.
Materials and Methods
Cells, transfection, and Remdesivir treatment. 293T and Vero were purchased from American Tissue Culture Collection (Manassas, VA) and were maintained in DMEM (Sigma-Aldrich, Burlington, MA) supplied with 10% FBS (Atlanta Biologicals, Flowery, GA) and penicillion/streptomycin in a 37° C., 5% CO2 incubator. Cells were transfected with Lipofectamin 3000 (ThermoFisher Scientific, Waltham, MA) according to the manufacturer's protocol. For experiments involving Remdesivir treatment, the cells were treated with Remdesivir for 1 hour before transfection, continued with Remdesivir treatment for 24 hours following cell transfection with DNA or RNA, and harvested for the luciferase reporter gene assay, Western blotting, and RT-PCR analysis. Remdesivir was purchased from Cayman Chemical Company (Ann Arbor, MI) and dissolved in DMSO.
Synthesis of replicon fragments and construction of recombinant non-infectious SARS2 replicon DNA. The full-length SARS2 DNA replicon is 27,952 nucleotides (nt). It was synthesized in five fragments onto the pMX vector (for F2-5) or pMK vector (for F1/6) and sequenced by ThermoFisher Scientific. The sizes of the fragments were as follows: F2—nt 3583-8945; F3—nt 8942-15011; F4—nt 15007-21092; F5—nt 21078-24749; F1/6—nt 1-1642/nt 24689-27952. The fragments were designed with either BsaI or SalI restriction sites for subsequent cloning. Fragment F2-5 on pMX were ligated together at the unique BsaI sites using a Golden Gate Assembly kit (New England Biolabs, Ipswich, MA). Specifically, a ligation reaction (20 μl) containing 200 ng each of the four constructs (pMX.F2, 3, 4, or 5), T4 DNA ligase buffer and Golden Gate Enzyme Mix was set up and incubated at 37° C. for 1 hour to obtain the ligated product containing fragment 2-5 of the replicon on the pMX vector (pMX.F2-5). The ligated product was gel purified, digested with SalI, and gel purified to obtain fragment F2-5. pMK.F1/6 was digested with SalI and annealed with SalI-digested F2-5 through a pre-designed 50-nucleotide homolog overhang using a Gibson Assembly kit (New England Biolabs). Specifically, a reaction (20 μl) containing fragment F2-5, SalI-digested pMK.F1/6, and Gibson Assembly Master Mix was set up and incubated at 50° C. for 1 hour. An aliquot of the reaction was transformed into B10 competent E. coli (New England Biolabs). The final replicon DNA construct pMK.F1-6 was verified by PCR with 5 pairs of primers spanning each of the five adjacent junctions: 5′-aag atc gcc gtg taa gaa ttc cg-3 (nt 3315-3337; SEQ ID NO:01) and 5′-tgc ccg cgg tta tca tcg tgt t-3′ (nt 3919-3898; SEQ ID NO:02) for F1/F2; 5′-tgc ata gac ggt gct tta ctt ac-3′ (nt 8915-8937; SEQ ID NO:03) and 5′-ggt aca aga tca att ggt tgc tc-3′ (nt 9123-9101; SEQ ID NO:04) for F2/F3; 5′-ggt ggc aaa cct tgt atc aaa g-3′ (nt 14918-14939; SEQ ID NO:05) and 5′-gag gct ata gct tgt aag gtt gc-3′ (nt 15213-15191; SEQ ID NO:06) for F3/F4; 5′-cag ggc tca gaa tat gac tat g-3′ (nt 20956-20977; SEQ ID NO:07) and 5′-gtg tag gtg cct gtg tag gat-3′ (nt 21223-21206; SEQ ID NO:08) for F4/F5; 5′-ctt tgg ggt act gct gtt atg t-3′ (nt 24533-24554; SEQ ID NO:09) and 5′-cat ctc ctt cac ctt cac cag a-3′ (nt 24793-24772; SEQ ID NO:10) for F5/F6.
Purification of the SARS2 replicon plasmid DNA pMK.F1-6 and in vitro RNA transcription. A single colony was selected from the B10-transformed E. coli plate above, inoculated in 2 ml Amp+LB medium, and cultured at room temperature overnight at a shaker speed of 30 rpm. The 2 ml culture was transferred to 100 ml Amp+LB medium and continued to culture for 48 hours. The culture was pelleted and suspended 2 ml of 50 mM glucose, 50 mM Tris, pH 8.0, 10 mM EDTA, pH 8.0, and 50 μg/ml DNase-free RNase A, added 4 ml of 0.1 M NaOH and 1% SDS, incubated at room temperature for 3 minutes, added 3 ml of 1.5 M potassium acetate, pH 5.5, incubated at room temperature for 10 minutes. Mixing throughout the process had to be extremely gentle to avoid shearing of the large size plasmid DNA. Then, the mixture was spun at 3000 g for 10 minutes, the clear supernatant was recovered, added 2 volumes of isopropanol, incubated at −20° C. for 10 minutes, and spun at 10000 g for 10 minutes. The DNA pellet was rinsed with 75% ethanol, suspend in TE buffer containing 50 μg/ml DNase-free RNase A, incubated at room temperature for 30 minutes, and extracted with phenol/chloroform/isoamyl for 2-3 minutes. RNase A treatment and phenol/chloroform/isoamyl extraction were repeated two more times. The aqueous phase was added 2 volumes of isopropanol and spun at 10000 g for 10 minutes. The DNA pellet was rinsed with 75% ethanol, dried, and suspended in TE as the replicon plasmid pMK.F1-6 DNA. Throughout the process, all mixing steps had to be extremely gentle to avoid shearing of the plasmid DNA. For in vitro transcription, replicon RNA was synthesized using 10 μg replicon DNA/100 μl reaction and a T7 RoboMAX Express large-scale RNA synthesis kit (Promega, Madison, WI) in which Ribo m7G Cap analog (Promega) was included. The reaction was performed at 25° C. for 24 hours, treated with RQ1 RNase-Free DNase (Promega) at 37° C. 15 minutes, and extracted with phenol:chloroform:isoamyl once and chloroform:isoamyl once. The aqueous phase was added 2 volumes of isopropanol and spun at 10000 g for 10 minutes. The RNA pellet was rinsed with 75% ethanol, dried, and suspended in TE as replicon RNA.
Luciferase Reporter Gene Assay. 293T (1.5×105 cells/well) and Vero (1.5×105 cells/well) were plated in a 24-well plate, transfected with a total of 0.4 μg DNA or 0.3 μg RNA, cultured for 6-72 hours, harvested, and washed with PBS. The cells were lyzed and assayed for the luciferase activity using the Firefly Luciferase Assay system (Promega) according to the manufacturer's instructions and an Opticomp Luminometer (MGM Instruments, Hamden, CT).
Western blotting. 293T (4×106 cells) were plated in a 10 cm plate, transfected with a total of 10 μg DNA or 7.5 μg RNA, cultured for 4-72 hours, harvested, and washed with PBS. The cells were lyzed in RIPA buffer (50 mM Tris-HCl, pH 7.4, 150 mM NaCl, 1% Triton X-100, 1% sodium deoxycholate, 0.1% SDS, 2 mm PMSF, and 1× protease inhibitor mixture (Roche, Indianapolis, IN) and incubated on ice for 20 minutes. The whole cell lysates (40 μg) were run 10% SDS-PAGE gel, blotted for direct detection of the GFP signal at 488 nm, or blotted against SARS2 nucleocapsid antibody (1:500; BEI Resources, Manassas, VA), followed by ECL visualization (ThermoFisher Scientific). Blots were stripped for re-probing against an anti-β-actin antibody (Sigma-Aldrich).
RT-PCR determination of (+) and (−) strand SARS2 replicon genomic RNA (gRNA) or N subgenomic RNA (sgRNA). 293T (6.5×105 cells/well) were plated in a 6-well plate, transfected with a total of 1.5 μg DNA or 1.2 μg RNA, cultured for 24 hours, harvested, and washed with PBS. Total RNA was isolated from cells using a Trizol Reagents kit (ThermoFisher) according to the manufacturer's instructions, treated with RQ1 RNase-free DNase in 1×RQ1 DNase reaction buffer (Promega) at 37° C. 10 minutes, and extracted with an equal volume of acidic phenol (ThermoFisher Scientific). The aqueous phase was added 2 volumes of isopropanol and spun at 10000 g for 10 minutes. The RNA pellet was rinsed with 75% ethanol and suspended in RNase-free water (ThermoFisher Scientific). Primer TRS-L5′ was used to reverse transcribe (−) strand RNA to cDNA, while primer N3′ was used to reverse transcribe (+) strand RNA to cDNA. Primer pair N5′/N3′ was used to PCR amplify the full-length N gene (1260 bp) from both (+) and (−) strand gRNA and sgRNA-derived cDNA. Primer pair TRS-L5′/N3′ was used to PCR amplify both (+) and (−) strand sgRNA-derived cDNA. The sequences of the primers were as follows: TRS-L5′: 5′-atc tct tgt aga tct gtt ctc taa acg aac aaa cta aa-3′ (nt 845-874; SEQ ID NO:11); N-5′: 5′-atg tct gat aat gga ccc ca-3′ (nt 28274-29291; SEQ ID NO:12); N-3′: 5-tta ggc ctg agt tga gtc ag-3′ (nt 295534-29512; SEQ ID NO:13).
Using as the reference the Wuhan-Hu-1 isolate SARS2 genome (GenBank: NC_045512.2,
Hammerhead virus ribozyme site (HHV Rz) and Hepatitis Delta virus ribozyme site (HDV Rz) were inserted immediately before 5′ end and after the 3′ end of SARS2, respectively, to allow removal of extra nucleotides at both 5′ and 3′ ends from the nascent RNA transcribed from the replicon DNA either by cellular transcription machinery or the RNA from in vitro transcription, so that the RNA replicon with authentic 5′ and 3′ ends were produced to faithfully recapitulate RNA replication and transcription. For the same reason, NSP1 and ORF10 adjacent to the 5′ end and 3′ end were kept in the replicon design. HDV Rz would also allow direct use of the DNA replicon for in vitro transcription without linearizing. The firefly luciferase reporter gene (fLuc) was inserted between NSP1 and NSP2-16 to monitor translation and replication/transcription of the replicon, while the GFP::Bsr fusion gene was inserted between NSP16 and nucleocapsid N gene to monitor replication/transcription of the replicon and selection of stable cell replicons. The nucleocapsid N gene and its transcriptional regulatory sequence (TRS) were kept for efficient SARS gRNA and N sgRNA replication and N protein expression [40]. The TRS of the S gene was inserted before the GFP::Bsr fusion gene for GFP::Bsr sgRNA replication and GFP::Bsr protein expression. Porcine teschovirus-1 self-cleaving peptide 2A (P2A) was inserted between NSP1 and fLuc to ensure proper processing of NSP1 and fLuc. Encephalomarcarditis virus internal ribozyme entry site (IRES) was inserted before the NSP2-16 gene to facilitate translation of the large polypeptide NSP2-16 from the RNA replicon. Bovine growth hormone polyadenylation signal (BGH pA) was added to the a end to stabilize the RNA.
To construct the two-in-one dual reporter SARS2 DNA replicon construct (27,952 nucleotides), the replicon was divided to 5 fragments (F1/6 and F2, F3, F4, and F5,
Gene expression from the new replicon was tested. The first reporter gene fLuc was inserted between NSP1 and NSP2-16. So the fLuc expression could be used as an indicator of translation of positive-stranded RNA that was either transcribed from the replicon DNA, the in vitro transcribed replicon RNA, or gRNA resulting from replication of these initial transcribed RNA. First, the luciferase (fLuc) expression in cells transfected with the replicon construct was tested and effects of HIV Tat expression on the fLuc expression. fLuc expression, measured by the fLuc activity, was detected in 293T transfected with the replicon DNA alone and increased in 293T co-transfected with Tat expression plasmid pc3.Tat in a dose-dependent manner (
The second reporter gene GFP was inserted as a fusion protein with Blasticidin (Bsr) between NSP2-16 and N gene, and the GFP gene was preceded with the authentic transcriptional regulatory sequences (TRS) of SARS2 S gene. Thus, GFP expression would represent replication of gRNA and GFP sgRNA and translation of GFP sgRNA. GFP expression was detected in 293T transfected with the replicon DNA at 4 hours post transfection, increased up to 48 hours and then decreased (
The full-length SARS2 replicon RNA could be derived from in vitro transcription of the replicon DNA or transcription of the replicon DNA in cells by cellular transcription machinery, and serve as the template for translation and expression of NSP1-16 and for synthesis of negative-stranded gRNA and sgRNA intermediates, which in turn served as the templates for subsequent synthesis positive-stranded gRNA and sgRNA (
The effects of Remdesivir was tested on expression of these two reporter genes and SARS nucleocapsid N gene from the replicon. 293T were transfected with the replicon and treated with different concentrations of Remdesivir. Remdesivir inhibited the fLuc gene expression in a concentration-dependent manner (
This disclosure provides the engineering, construction and characterization of a dual promoter-driven and dual reporter-expressing SARS2 replicon. This replicon construct contained the genomic organization from 5′ end to 3′ end: LTR-T7-HHD Rz-5′UTR-NSP1-P2A-fLuc-IRES-NSP2-16-TRS-GFP::Bsr-TRS-N-ORF10-3′UTR-HDV Rz-BGH pA. Over the past two years, several SARS-CoV-2 replicons have been developed [58-67]. The general genomic composition of these SARS-CoV-2 replicons includes 5′UTR, ORF1a/1b, a Luc gene or green fluorescence protein (GFP) reporter gene, N, and 3′UTR from 5′ end to 3′ end. But they differ in how the replicon RNA is produced. Some replicons have a T7 promoter at the 5′ end, the replicon RNA has to be synthesized in vitro [58-63]. Other replicons have the human cytomegalovirus (CMV) immediate-early enhance and promoter at the 5′ end, the replicon RNA is transcribed from the replicon DNA that is introduced into cells by transfection [64-67]. There were several main features that still remained unique to the replicon as disclosed herein. These included efficient full-length RNA transcription under the HIV LTR promoter and its transactivation by Tat co-expression, production of the replicon RNA with 5′ and 3′ ends that are identical to the native SARS2, fLuc insertion within the NSP genes as the indicator for translation and replication/transcription of the replicon RNA, placement of IRES before NSP2-16 to facilitate NSP2-16 translation and expression, and one cassette 5UTR-NSP1 at the 5′ end and one cassette ORF10-3′UTR at the 3′ end to maintain the native RNA secondary structure for RNA translation, replication and transcription.
The replicon construct presented herein, when transfected into cells in the form of DNA, or RNA that was transcribed from the DNA, showed successful expression of reporter genes fLuc, GFP, and SARS2 structural gene N in 293T and Vero6. The construct also demonstrated expression of negative-stranded gRNA and SARS2 N sgRNA, which provided additional evidence to support expression and replication of the replicon in these cells. Lastly, the construct demonstrated that an RNA-dependent RNA polymerase inhibitor that has been used to treat SARS2 infection inhibited expression of reporter genes fLuc, GFP, and SARS2 structural gene N and negative- and positive-stranded gRNA and SARS2 N sgRNA in 293T and Vero6. Two other cell lines Hela and Huh7 were also tested in this study and obtained similar results (data not shown). All the findings together support the notion that the new replicon could be used as a surrogate system for screening and identifying anti-SARS2 antiviral drugs and for studying the molecular mechanisms of the host and viral control of SARS2 replication and transcription.
The reporter gene GFP was introduced as an indicator to monitor RNA replication/transcription from the replicon. Surprisingly, only GFP expression was detected on Western blots and only very weak signal under the fluorescence microscope. This phenomenon did appear to be cell type-dependent, as brighter GFP was detected in Vero6 than 293T. This may be due to conformational changes of GFP in the GFP-Bsr fusion protein. Establishing stable cells comprising the replicon construct was attempted, by single cell or bulking cloning with inclusion of Bsr in the culture medium and passages, using different cell lines, and using both the replicon DNA transfection and the replicon RNA transfection; however, attempts were unsuccessful. Thus, these studies were performed using the transient replicon by transfection. Nevertheless, of note is that among all 10 published SARS2 replicons so far, only two SARS2 replicons lead to creation of stable replicon cells [58, 67], and the other eight all appear to be transient replicons [59-66]. Further understanding of the design and organizational differences between these two groups of SARS2 replicons may lead to identification of viral and host factors necessary for SARS2 replication as well as help construct better SARS2 replicons for anti-SARS2 drug screening and evaluation.
Having described the subject matter of the disclosure in detail and by reference to specific embodiments thereof, it will be apparent that modifications and variations are possible without departing from the scope of the claimed subject matter. More specifically, although some aspects of the present disclosure are identified herein as particularly advantageous, it is contemplated that the present subject matter is not necessarily limited to these particular aspects of the claimed subject matter.
This application is a non-provisional application of U.S. Provisional Application 63/323,788, filed Mar. 25, 2022, the disclosure of which is incorporated by reference in its entirety.
| Number | Date | Country | |
|---|---|---|---|
| 63323788 | Mar 2022 | US |
