Patent Publication Number: US-2023151367-A1

Title: Therapeutic interfering particles for corona virus

Description:
PRIORITY APPLICATIONS 
     This application claims the benefit of priority of U.S. Provisional Application Ser. No. 63/014,394, filed Apr. 23, 2020, the content of which is specifically incorporated herein by reference in its entirety. 
    
    
     GOVERNMENT SUPPORT 
     This invention was made with government support under 1-DP2-OD006677-01 awarded by the National Institutes of Health and under D17AC00009 awarded by DOD/DARPA. The government has certain rights in the invention. 
    
    
     INCORPORATION BY REFERENCE OF SEQUENCE LISTING PROVIDED BY AS A TEXT FILE 
     A Sequence Listing is provided herewith as a text file, “2135793.txt” created on Apr. 23, 2021 and having a size of 143,360 bytes. The contents of the text file are incorporated by reference herein in their entirety. 
     BACKGROUND 
     The World Health Organization has declared Covid-19 a global pandemic. A highly infectious coronavirus, officially called SARS-CoV-2, causes the Covid-19 disease. Even with the most effective containment strategies, the spread of the Covid-19 respiratory disease has only been slowed. While effective vaccines exist for current strain of SARS-CoV-2, new variants and mutant strains continue to develop. Hence, there is a need for treatments that interfere with infection as well and/or new vaccines that can facilitate recovery from infection and put an end to the SARS-CoV-2 pandemic. 
     SUMMARY 
     Provided are defective SARS-CoV-2 constructs and methods for generating defective SARS-CoV-2 constructs that can interfere with or block infection of uninfected cells. The methods and compositions are useful for treatment of SARS-CoV-2 infections. 
     The defective SARS-CoV-2 constructs described herein are SARS-CoV-2 recombinant deletion mutants. Such recombinant SARS-CoV-2 deletion mutants can be interfering and/or conditionally replicating SARS-CoV-2 deletion mutants. Even without non-SARS-CoV-2 nucleic acids the SARS-CoV-2 constructs can be therapeutic interfering particles or therapeutic interfering nucleic acids. 
     These constructs can include cis-acting elements comprising a 5′ untranslated region (5′ UTR), a 3′ untranslated region (3′ UTR), a poly-A tail, or a combination thereof; and SARS-CoV-2 genomic nucleic acid segments. Typically, the SARS-CoV-2 genomic nucleic acid segments have substantial deletions relative to the wild type SARS-CoV-2 genome. Hence, the therapeutic interfering SARS-CoV-2 nucleic acids and particles can be incapable of replication and production of virus on their own, and can, for example, require replication-competent SARS-CoV-2 to act as a helper virus. 
     Examples of such therapeutic interfering particles, defective SARS-CoV-2 constructs, and therapeutic interfering nucleic acids can include any of the 5′ SARS-CoV-2 truncated sequences such as any of those with SEQ ID NO:28, 30, 32 or 33 and/or any of the 3′ SARS-CoV-2 truncated sequences such as any of those with SEQ ID NO:31 or 32. The 3′ SARS-CoV-2 sequences can include extended poly A sequences. For example, the extended poly-A sequences can have at least 100 adenine nucleotides to 250 adenine nucleotides. Such extended poly-A sequences can, for example, extend the half-life of the mRNA. 
     The SARS-CoV-2 therapeutic interfering particles can therefore include an RNA transcription signals, translation initiation sites, extended poly-A tails, or a combination thereof. In addition, to the deletions, the SARS-CoV-2 genomic nucleic acid segments can have one or more nucleotide sequence alterations compared to a wild type or native SARS-CoV-2 genomic nucleotide sequence. 
     Also described herein are one or more inhibitors of transcription regulating sequences (TRSs): TRS1-L: 5′-cuaaac-3′ (SEQ ID NO:36), TRS2-L: 5′-acgaac-3′ (SEQ ID NO:37), and TRS3-L, 5′-cuaaacgaac-3′ (SEQ ID NO:38), and compositions thereof. The TRS inhibitors can be used alone or in conjunction with therapeutic interfering particles SARS-CoV-2 constructs to inhibit and/or interfere with SARS-CoV-2 infection. 
     The therapeutic interfering SARS-CoV-2 nucleic acids and/or the TRS inhibitors can, for example, block wild type SARS-CoV-2 cellular entry, compete for structural proteins that mediate viral particle assembly, reduce the reproduction of wild type SARS-CoV-2, produce proteins that inhibit assembly of viral particles, inhibit transcription/replication of SARS-CoV-2 nucleic acids, or a combination thereof. 
     Methods are also described herein that include making and using a SARS-CoV-2 deletion library. In some embodiments, a subject method includes: (a) inserting transposon cassette comprising a target sequence for a sequence specific DNA endonuclease into a population of circular SARS-CoV-2 DNAs to generate a population of transposon-inserted circular SARS-CoV-2 DNAs; (b) contacting the population of transposon-inserted circular SARS-CoV-2 DNAs with the sequence specific DNA endonuclease to generate a population of cleaved linear SARS-CoV-2 DNAs; (c) contacting the population of cleaved linear SARS-CoV-2 DNAs with one or more exonucleases to generate a population of SARS-CoV-2 deletion DNAs; and (d) circularizing the SARS-CoV-2 deletion DNAs to generate a library of circularized SARS-CoV-2 deletion DNAs. 
     In some cases, the transposon cassette includes a first recognition sequence positioned at or near one end of the transposon cassette and a second recognition sequence positioned at or near the other end of the transposon cassette. 
     In some such cases, the method further includes introducing members of the library of circularized SARS-CoV-2 deletion DNAs into mammalian cells and assaying for viral infectivity. For example, the SARS-CoV-2 deletion DNAs can be introduced to epithelial cells, or alveolar cells (e.g., human alveolar type II cells). In some cases, the method further includes sequencing members of the library of circularized SARS-CoV-2 deletion DNAs to identify defective SARS-CoV-2 interfering particles (DIPs). 
     In some cases, the sequence specific DNA endonuclease is selected from: a meganuclease, a CRISPR/Cas endonuclease, a zinc finger nuclease, or a TALEN. In some cases, the one or more exonucleases includes T4 DNA polymerase. In some cases, the one or more exonucleases includes a 3′ to 5′ exonuclease and a 5′ to 3′ exonuclease. In some cases, the one or more exonucleases includes RecJ. In some cases, a subject method includes inserting a barcode sequence prior to or simultaneous with step (d). 
     In some cases, the step of contacting the population of cleaved linear SARS-CoV-2 DNAs with one or more exonucleases is performed in the presence of a single strand binding protein (SSB). 
     Also provided are methods of generating and identifying a defective SARS-CoV-2 interfering particle (DIP). In some cases, the methods include (a) inserting a target sequence for a sequence specific DNA endonuclease into a population of circular SARS-CoV-2 viral DNAs, each comprising a viral genome, to generate a population of sequence-inserted SARS-CoV-2 viral DNAs; (b) contacting the population of sequence-inserted SARS-CoV-2 viral DNAs with the sequence specific DNA endonuclease to generate a population of cleaved linear SARS-CoV-2 viral DNAs; (c) contacting the population of cleaved linear SARS-CoV-2 viral DNAs with an exonuclease to generate a population of deletion DNAs; (d) circularizing the SARS-CoV-2 deletion DNAs to generate a library of circularized SARS-CoV-2 deletion viral DNAs; and (e) sequencing members of the library of circularized deletion SARS-CoV-2 viral DNAs to identify SARS-CoV-2 deletion interfering particles (DIPs). In some cases, the method includes inserting a barcode sequence prior to or simultaneous with step (d). 
     In some cases, the method includes introducing members of the generated library of circularized SARS-CoV-2 deletion DNAs into cells, for example, mammalian cells, and assaying for viral infectivity. In some cases, the inserting of step (a) includes inserting a transposon cassette into the population of circular SARS-CoV-2 viral DNAs, where the transposon cassette includes the target sequence for the sequence specific DNA endonuclease, and wherein said generated population of sequence-inserted SARS-CoV-2 viral DNAs is a population of transposon-inserted viral DNAs. In some cases, the method includes, after step (d), infecting cells, for example, mammalian cells in culture with members of the library of circularized deletion SARS-CoV-2 viral DNAs at a high multiplicity of infection (MOI), culturing the infected cells for a period of time ranging from 12 hours to 2 days, adding naive cells to the to the culture, and harvesting virus from the cells in culture. In some cases, the method includes, after step (d), infecting cells, for example, mammalian cells in culture with members of the library of circularized deletion viral DNAs at a low multiplicity of infection (MOI), culturing the infected cells in the presence of an inhibitor of viral replication for a period of time ranging from 1 day to 6 days, infecting the cultured cells with functional virus at a high MOI, culturing the infected cells for a period of time ranging from 12 hours to 4 days, and harvesting virus from the cultured cells. 
    
    
     
       DESCRIPTION OF THE FIGURES 
         FIG.  1    shows a schematic diagram of the SARS-CoV-2 genome and encoded open reading frames (ORFs). 
         FIG.  2 A- 2 B  illustrate infection of cells by wild type and defective SARS-CoV-2.  FIG.  2 A  shows a schematic representation of infection by a wildtype SARS-CoV-2 genome. After integration into a cellular genome (DNA at left), SARS-CoV-2 RNAs are generated that ultimately produce the packaging proteins that form the virus capsid. Infective SARS-CoV-2 can escape their original host cell and infect new cells if they have the needed (functional wild type) surface recognition proteins.  FIG.  2 B  shows a schematic of infection when defective SARS-CoV-2 particles (referred to as Therapeutic Interfering Particles, TIPs) are present with viable SARS-CoV-2. The defective SARS-CoV-2 particles have pared-down versions of the SARS-CoV-2 genome engineered to carry a packaging signal, and other viral cis elements required for packaging. The defective SARS-CoV-2 RNA can thus only be made by cells that also express SARS-CoV-2 proteins. The defective SARS-CoV-2 particles are engineered to produce substantially more defective SARS-CoV-2 genomic RNA copies than wild type SARS-CoV-2 in dually infected cells. With disproportionately more defective SARS-CoV-2 genomic RNA than wild type SARS-CoV-2 genomic RNA, the SARS-CoV-2 packaging materials are mainly wasted enclosing defective SARS-CoV-2 genomic RNA. The defective SARS-CoV-2 particles lower the wild type SARS-CoV-2 burst size and convert infected cells from producing wild type SARS-CoV-2 into producing mostly defective SARS-CoV-2 particles, thereby lowering the wild type SARS-CoV-2 viral load. 
         FIG.  3    schematically illustrates a method for constructing a randomized, barcoded deletion library for making defective SARS-CoV-2 particles. The schematic cycle method for constructing a barcoded TIP candidate library from a molecular clone involves: [1] in vitro introduction of a retrotransposition into circular SARS-CoV-2 double stranded DNA, [2] exonuclease-mediated excision of the randomly inserted retrotransposon, [3] enzymatic chew back to create a deletion (A) in the circular SARS-CoV-2, and [4] circularizing and barcoding during re-ligation to generate the barcoded TIP candidate library (see, e.g., WO201811225 by Weinberger et al. and WO/2014/151771 by Weinberger et al., which are both incorporated herein by reference in their entireties). 
         FIG.  4    a schematic diagram illustrating molecular details and steps for one embodiment of a method of generating a deletion library. In step (a) the meganuclease (e.g., 1-Sce1 or 1-Ceu1) cleaves the SARS-CoV-2 double stranded DNA. In step (b) the cleaved ends of the SARS-CoV-2 DNA are chewed back. In step (c), the chewed back ends are repaired. Thus, a deleted gap (A) is present between the ends. In step (d) the 5′ phosphate is removed by alkaline phosphatase (AP) and a dA tail is generated with Klenow. In step (e), the ends are ligated to a barcode cassette, thereby generating numerous circular, barcoded deletion SARS-CoV-2 mutants. 
         FIG.  5 A- 5 C  illustrate methods for generating and analyzing random deletion libraries of SARS-CoV-2 deletion mutants.  FIG.  5 A  schematically illustrates generation of a random deletion library (RDL) for a 30 kb SARS-CoV-2 molecular clone. Three 10 kb fragments are shown that were used for RDL sub-libraries, where the three fragments were different segments of the SARS-CoV-2 genome. The ends of the three fragments were chewed back (e.g., as described in  FIG.  4   ), and the barcodes (shaded circles) were inserted as the deleted SARS-CoV-2 DNA fragments were ligated. Hence, the barcodes will be at different positions along the fragments. Because the barcodes include sites for primer initiation, sequencing readily identified where the deletions reside in the different SARS-CoV-2 deletion mutants.  FIG.  5 B  graphically illustrates illumina deep sequencing landscapes of barcode positions in the three random deletion sub-libraries. Such sequencing showed that the sub-libraries contain more than 587,000 unique SARS-CoV-2 deletion mutants.  FIG.  5 C  shows gels of electrophoretically separated DNA from the ligated RDL libraries illustrating that there are bands of about 30 kb as well as lower molecular weight bands (ladder is in left lane: the 3 additional lanes are triplicates). 
         FIG.  6 A- 6 D  illustrate the ‘viroreactor’ strategy used to generate SARS-CoV-2 therapeutic interfering particles (TIPs).  FIG.  6 A  schematically illustrates VeroE6 cells that were immobilized on beads, grown in suspension under gentle agitation, and infected with SARS-CoV-2 at the indicated MOI. 50% of the cells and media were harvested and replaced every other day.  FIG.  6 B  shows flow cytometry plots of harvested cells stained for Propidium Iodide, a cell death marker.  FIG.  6 C  graphically illustrates the percentage cell viability following SARS-CoV-2 infection at a MOI of 0.5.  FIG.  6 D  graphically illustrates the cell viability (%) following SARS-CoV-2 infection at a MOI of 5.0. As shown in  FIG.  6 C- 6 D , the percentage of viable free cells (circular symbols) and viable immobilized cells (triangular symbols) exhibit an initial dip in cell viability, but the cultures recover by day 14 post infection. 
         FIG.  7 A- 7 B  schematically illustrate the structures of two therapeutic interfering particles constructs for SARS-CoV-2, TIP1 and TIP2.  FIG.  7 A  shows an example of the TIP1 construct structure.  FIG.  7 B  shows an example of the TIP2 construct structure. The schematics show that TIP1 and TIP2 encode portions of the 5′ and 3′ untranslated regions (UTRs) of SARS-CoV-2. TIP1 encodes 450nt of 5′UTR and 330nt of 3′UTR. TIP2 includes the 5′UTR region and a larger portion of SARS-CoV-2 ORF1a (i.e., TIP2 encodes a deletion of ORF1a). Hence, TIP1 and TIP2 include the packaging signal but cannot express a functional copy of the viral ORF1a gene. The 3′UTR that is encoded by the TIP2 extends upstream 413nt into the SARS-COV-2 N gene but TIP2 does not encode a functional form of the N gene (i.e., it encodes a deletion of part of the N gene). To facilitate analysis, the cassettes also include an IRES-mCherry reporter for flow cytometry analysis. 
         FIG.  8 A- 8 C  graphically illustrate that four different types of therapeutic interfering particles (TIPs) reduce SARS-CoV-2 replication by more than 50-fold.  FIG.  8 A  graphically illustrates the fold change in with SARS-CoV-2 RNA when various therapeutic interfering particles (TIPs) are present. Cells were transfected with mRNA of TIP1 (T1), TIP1* (T1*), TIP2 (T2) or TIP2* (T2*) and the cells were infected with SARS-CoV-2 (MOI=0.005). Yield-reduction of SARS-CoV-2 replication was assessed by measuring the fold-reduction in SARS-CoV-2 mRNA (E gene) at 48 hrs post infection. mRNA was quantified by RT-qPCR with primers specific to 5′-end of N gene and the E gene that are not present in TIPs. The fold-reduction in SARS-CoV-2 mRNA as detected by E gene primers is shown. TIP2 exhibits the greatest interference with SARS-CoV-2.  FIG.  8 B  graphically illustrates the relative Log 10 amounts of SARS-CoV-2 genome when TIP1 and TIP2 therapeutic interfering particles are incubated for about 24 hours with the SARS-CoV-2 genome, as compared to control without the therapeutic interfering particles.  FIG.  8 C  graphically illustrates the relative Log 10 amounts of SARS-CoV-2 genome when TIP1 and TIP2 therapeutic interfering particles are incubated for about 48 hours with the SARS-CoV-2 genome, as compared to control without the therapeutic interfering particles. 
         FIG.  9 A- 9 B  illustrate that TIP candidates are mobilized by SARS-CoV-2 and transmit together with SARS-CoV-2.  FIG.  9 A  shows flow cytometry analysis of mCherry expression by Vero cells that received supernatant transferred from SARS-CoV-2 infected cells incubated with TIP1 and TIP2 therapeutic interfering particles compared to control cells receiving supernatant from naïve uninfected cells that were incubated with the TIP1 and TIP2 particles. As shown, mCherry-expressing cells were detected when the TIP1 or TIP2 particles were present but essentially no mCherry-expressing cells were detected in the control cells.  FIG.  9 B  graphically illustrates the log 10 amount of SARS-CoV-2 genome when TIP1 and TIP2 therapeutic interfering particles were incubated with cells that were infected with SARS-CoV-2 for 24 hours compared to controls that were not infected by SARS-CoV-2.  FIG.  9 C  graphically illustrates the log 10 amount of SARS-CoV-2 genome when TIP1 and TIP2 therapeutic interfering particles were incubated with cells that were infected with SARS-CoV-2 for 48 hours compared to controls that were not infected by SARS-CoV-2. 
         FIG.  10    schematically illustrates a method for interfering with SARS-CoV-2 transcription by transfection with antisense Transcription Regulating Sequences (TRS). 
         FIGS.  11 A- 11 C  graphically illustrate that antisense Transcription Regulating Sequences (TRS) can reduce SARS-CoV-2 plaque forming units (pfus).  FIG.  11 A  graphically illustrates the SARS-CoV-2 pfu after transfection with antisense TRS1 (ACGAACCUAAACACGAACCUAAAC (SEQ ID NO:25)).  FIG.  11 B  graphically illustrates the SARS-CoV-2 pfu after transfection with antisense TRS2 (ACGAACACGAACACGAACACGAAC (SEQ ID NO:26)).  FIG.  11 C  graphically illustrates the SARS-CoV-2 pfu after transfection with antisense TRS3 (CUAAACCUAAACCUAAACCUAAAC (SEQ ID NO:27)). 
         FIG.  12    graphically illustrates that the combination of the TRS with either the TIP1 or the TIP2 significantly reduced the SARS-CoV-2 genome numbers compared to the TRS alone. 
         FIG.  13 A- 13 C  illustrate that TIP1 and TIP2 therapeutic interfering particles significantly reduce the replication of different SARS-CoV-2 strains, including South African and U.K. strains of SARS-CoV-2.  FIG.  13 A  illustrates that TIP1 and TIP2 significantly reduce the replication of South African 501Y.V2.HV delta variant of SARS-CoV-2.  FIG.  13 B  illustrates that TIP1 and TIP2 significantly reduce the replication of South African 501Y.V2.HV variant of SARS-CoV-2.  FIG.  13 C  illustrates that TIP1 and TIP2 significantly reduce the replication of U.K B.1.1.7 variant of SARS-CoV-2. 
     
    
    
     DETAILED DESCRIPTION 
     Described herein are methods for making defective SARS-CoV-2 particles that can interfere with SARS-CoV-2 infection (SARS-CoV-2 therapeutic interfering particles), and compositions of such interfering therapeutic particles useful for reducing SARS-CoV-2 infection. 
     As shown herein, SARS-CoV-2 therapeutic interfering particles (TIPs) can reduce SARS-CoV-2 replication by more than 50-fold. The SARS-CoV-2 TIPs can include segments of the 5′ and 3′ ends of the SARS-CoV-2 genome. For example, the SARS-CoV-2 TIPs can include segments of the 5′-UTR and the 3′-UTR of SARS-CoV-2. In some cases, a detectable marker and/or a barcode can be present between the 5′ and 3′ segments of the SARS-CoV-2 genome. Examples of SARS-CoV-2 therapeutic interfering particles (TIPs) include the TIP1, TIP2, TIP1*, and TIP2* constructs described herein. 
     The 5′ SARS-CoV-2 sequences in TIP1 are as shown below (SEQ ID NO:28). 
                      1 ATTAAAGGTT TATACCTTCC CAGGTAACAA ACCAACCAAC                41 TTTCGATCTC TTGTAGATCT GTTCTCTAAA CGAACTTTAA                81 AATCTGTGTG GCTGTCACTC GGCTGCATGC TTAGTGCACT               121 CACGCAGTAT AATTAATAAC TAATTAGTGT CGTTGACAGG               161 ACACGAGTAA CTCGTCTATC TTCTGCAGGC TGCTTACGGT               201 TTCGTCCGTG TTGCAGCCGA TCATCAGCAC ATCTAGGTTT               241    C   GTCCGGGTG TGACCGAAAG GTAAGATGGA GAGCCTTGTC               281 CCTGGTTTCA ACGAGAAAAC ACACGTCCAA CTCAGTTTGC               321 CTGTTTTACA GGTTCGCGAC GTGCTCGTAC GTGGCTTTGG               361 AGACTCCGTG GAGGAGGTCT TATCAGAGGC ACGTCAACAT               401 CTTAAAGATG GCACTTGTGG CTTAGTAGAA GTTGAAAAAG               411 gcgttttgcc            
The 3′ SARS-CoV-2 sequences in TIP1 are shown below as SEQ ID NO:29.
 
                      1 GACCACACAA GGCAGATGGG CTATATAAAC GTTTTCGCTT                41 TTCCGTTTAC GATATATAGT CTACTCTTGT GCAGAATGAA                81 TTCTCGTAAC TACATAGCAC AAGTAGATGT AGTTAACTTT               121 AATCTCACAT AGCAATCTTT AATCAGTGTG TAACATTAGG               161 GAGGACTTGA AAGAGCCACC ACATTTTCAC CGAGGCCACG               201 CGGAGTACGA TCGAGTGTAC AGTGAACAAT GCTAGGGAGA               241 GCTGCCTATA TGGAAGAGCC CTAATGTGTA AAATTAATTT               281 TAGTAGTGCT ATCCCCATGT GATTTTAATA GCTTCTTAGG               321 AGAATGACAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA               361 A            
The 5′ SARS-CoV-2 sequences in TIP2 are as shown below (SEQ ID NO:30).
 
                       1 ATTAAAGGTT TATACCTTCC CAGGTAACAA ACCAACCAAC                 41 TTTCGATCTC TTGTAGATCT GTTCTCTAAA CGAACTTTAA                 81 AATCTGTGTG GCTGTCACTC GGCTGCATGC TTAGTGCACT                121 CACGCAGTAT AATTAATAAC TAATTACTGT CGTTGACAGG                161 ACACGAGTAA CTCGTCTATC TTCTGCAGGC TGCTTACGGT                201 TTCGTCCGTG TTGCAGCCGA TCATCAGCAC ATCTAGGTTT                241    C   GTCCGGGTG TGACCGAAAG GTAAGATGGA GAGCCTTGTC                281 CCTGGTTTCA ACGAGAAAAC ACACGTCCAA CTCAGTTTGC                321 CTGTTTTACA GGTTCGCGAC GTGCTCGTAC GTGGCTTTGG                361 AGACTCCGTG GAGGAGGTCT TATCAGAGGC ACGTCAACAT                401 CTTAAAGATG GCACTTGTGG CTTAGTAGAA GTTGAAAAAG                441 GCGTTTTGCC TCAACTTGAA CAGCCCTATG TGTTCATCAA                481 ACGTTCGGAT GCTCGAACTG CACCTCATGG TCATGTTATG                521 GTTGAGCTGG TAGCAGAACT CGAAGGCATT CAGTACGGTC                561 GTAGTGGTGA GACACTTGGT GTCCTTGTCC CTCATGTGGG                601 CGAAATACCA GTGGCTTACC GCAAGGTTCT TCTTCGTAAG                641 AACGGTAATA AAGGAGCTGG TGGCCATAGT TACGGCGCCG                681 ATCTAAAGTC ATTTGACTTA GGCGACGAGC TTGGCACTGA                721 TCCTTATGAA GATTTTCAAG AAAACTGGAA CACTAAACAT                761 AGCAGTGGTG TTACCCGTGA ACTCATGCGT GAGCTTAACG                801 GAGGGGCATA CACTCGCTAT GTCGATAACA ACTTCTGTGG                841 CCCTGATGGC TACCCTCTTG AGTGCATTAA AGACCTTCTA                881 GCACGTGCTG GTAAAGCTTC ATGCACTTTG TCCGAACAAC                921 TGGACTTTAT TGACACTAAG AGGGGTGTAT ACTGCTGCCG                961 TGAACATGAG CATGAAATTG CTTGGTACAC GGAACGTTCT               1001 GAAAAGAGCT ATGAATTGCA GACACCTTTT GAAATTAAAT               1041 TGGCAAAGAA ATTTGACACC TTCAATGGGG AATGTCCAAA               1081 TTTTGTATTT CCCTTAAATT CCATAATCAA GACTATTCAA               1121 CCAAGGGTTG AAAAGAAAAA GCTTGATGGC TTTATGGGTA               1161 GAATTCGATC TGTCTATCCA GTTGCGTCAC CAAATGAATG               1201 CAACCAAATG TGCCTTTCAA CTCTCATGAA GTGTGATCAT               1241 TGTGGTGAAA CTTCATGGCA GACGGGCGAT TTTGTTAAAG               1281 CCACTTGCGA ATTTTGTGGC ACTGAGAATT TGACTAAAGA               1321 AGGTGCCACT ACTTGTGGTT ACTTACCCCA AAATGCTGTT               1361 GTTAAAATTT ATTGTCCAGC ATGTCACAAT TCAGAAGTAG               1401 GACCTGAGCA TAGTCTTGCC GAATACCATA ATGAATCTGG               1441 CTTGAAAACC ATTCTTCGTA AGGGTGGTCG CACTATTGCC               1481 TTTGGAGGCT GTGTGTTCTC TTATGTTGGT TGCCATAACA               1521 AGTGTGCCTA TTGGGTTCCA gaattagatc tctcgaggtt               1561 aacgaattct gctatacgaa gttatccctc             
The 3′ SARS-CoV-2 sequences in TIP2 are as shown below (SEQ ID NO:31).
 
     
       
         
           
               
            
               
                   1 ATTTGCCCCC AGCGCTTCAG CGTTCTTCGG AATGTCGCGC 
               
               
                   
               
               
                  41 ATTGGCATGG AAGTCACACC TTCGGGAACG TGGTTGACCT 
               
               
                   
               
               
                  81 ACACAGGTGC CATCAAATTG GATGACAAAG ATCCAAATTT 
               
               
                   
               
               
                 121 CAAAGATCAA GTCATTTTGC TGAATAAGCA TATTGACGCA 
               
               
                   
               
               
                 161 TACAAAACAT TCCCACCAAC AGAGCCTAAA AAGGACAAAA 
               
               
                   
               
               
                 201 AGAAGAAGGC TGATGAAACT CAAGCCTTAG CGCAGAGACA 
               
               
                   
               
               
                 241 GAAGAAACAG CAAACTGTGA CTCTTCTTCC TGCTGCAGAT 
               
               
                   
               
               
                 281 TTGGATGATT TCTCCAAACA ATTGCAACAA TCCATGAGCA 
               
               
                   
               
               
                 321 GTGCTGACTC AACTCAGGCC TAAACTCATG CAGACCACAC 
               
               
                   
               
               
                 361 AAGGCAGATG GGCTATATAA ACGTTTTCGC TTTTCCGTTT 
               
               
                   
               
               
                 401 ACGATATATA GTCTACTCTT GTGCAGAATG AATTCTCGTA 
               
               
                   
               
               
                 441 ACTACATAGC ACAAGTAGAT GTAGTTAACT TTAATCTCAC 
               
               
                   
               
               
                 481 ATAGCAATCT TTAATCAGTG TGTAACATTA GGGAGGACTT 
               
               
                   
               
               
                 521 GAAAGAGCCA CCACATTTTC ACCGAGGCCA CGCGGAGTAC 
               
               
                   
               
               
                 561 GATCGAGTGT ACAGTGAACA ATGCTAGGGA GAGCTGCCTA 
               
               
                   
               
               
                 601 TATGGAAGAG CCCTAATGTG TAAAATTAAT TTTAGTAGTG 
               
               
                   
               
               
                 641 CTATCCCCAT GTGATTTTAA TAGCTTCTTA GGAGAATGAC 
               
               
                   
               
               
                 681 AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAA 
               
            
           
         
       
     
     Two additional TIP variants were also cloned TIP11* and TIP2*, these contain the common C-241-T mutation within the 5′ UTR. This C241T UTR mutation co-transmits across populations together with the spike protein D614G mutation. 
     Hence, the 5′ SARS-CoV-2 sequences in TIP1* are as shown below (SEQ ID NO:32). 
                      1 ATTAAAGGTT TATACCTTCC CAGGTAACAA ACCAACCAAC                41 TTTCGATCTC TTGTAGATCT GTTCTCTAAA CGAACTTTAA                81 AATCTGTGTG GCTGTCACTC GGCTGCATGC TTAGTGCACT               121 CACGCAGTAT AATTAATAAC TAATTAGTGT CGTTGACAGG               161 ACACGAGTAA CTCGTCTATC TTCTGCAGGC TGCTTACGGT               201 TTCGTCCGTG TTGCAGCCGA TCATCAGCAC ATCTAGGTTT               241    T   GTCCGGGTG TGACCGAAAG GTAAGATGGA GAGCCTTGTC               281 CCTGGTTTCA ACGAGAAAAC ACACGTCCAA CTCAGTTTGC               321 CTGTTTTACA GGTTCGCGAC GTGCTCGTAC GTGGCTTTGG               361 AGACTCCGTG GAGGAGGTCT TATCAGAGGC ACGTCAACAT               401 CTTAAAGATG GCACTTGTGG CTTAGTAGAA GTTGAAAAAG               411 GCGTTTTGCC            
Similarly, the 5′ SARS-CoV-2 sequences in TIP2* are as shown below (SEQ ID NO:33).
 
     
       
         
           
               
            
               
                    1 ATTAAAGGTT TATACCTTCC CAGGTAACAA ACCAACCAAC 
               
               
                   
               
               
                   41 TTTCGATCTC TTGTAGATCT GTTCTCTAAA CGAACTTTAA 
               
               
                   
               
               
                   81 AATCTGTGTG GCTGTCACTC GGCTGCATGC TTAGTGCACT 
               
               
                   
               
               
                  121 CACGCAGTAT AATTAATAAC TAATTACTGT CGTTGACAGG 
               
               
                   
               
               
                  161 ACACGAGTAA CTCGTCTATC TTCTGCAGGC TGCTTACGGT 
               
               
                   
               
               
                  201 TTCGTCCGTG TTGCAGCCGA TCATCAGCAC ATCTAGGTTT 
               
               
                   
               
               
                  241    T   GTCCGGGTG TGACCGAAAG GTAAGATGGA GAGCCTTGTC 
               
               
                   
               
               
                  281 CCTGGTTTCA ACGAGAAAAC ACACGTCCAA CTCAGTTTGC 
               
               
                   
               
               
                  321 CTGTTTTACA GGTTCGCGAC GTGCTCGTAC GTGGCTTTGG 
               
               
                   
               
               
                  361 AGACTCCGTG GAGGAGGTCT TATCAGAGGC ACGTCAACAT 
               
               
                   
               
               
                  401 CTTAAAGATG GCACTTGTGG CTTAGTAGAA GTTGAAAAAG 
               
               
                   
               
               
                  441 GCGTTTTGCC TCAACTTGAA CAGCCCTATG TGTTCATCAA 
               
               
                   
               
               
                  481 ACGTTCGGAT GCTCGAACTG CACCTCATGG TCATGTTATG 
               
               
                   
               
               
                  521 GTTGAGCTGG TAGCAGAACT CGAAGGCATT TCATGTTATG 
               
               
                   
               
               
                  561 GTAGTGGTGA GACACTTGGT GTCCTTGTCC CTCATGTGGG 
               
               
                   
               
               
                  601 CGAAATACCA GTGGCTTACC GCAAGGTTCT TCTTCGTAAG 
               
               
                   
               
               
                  641 AACGGTAATA AAGGAGCTGG TGGCCATAGT TACGGCGCCG 
               
               
                   
               
               
                  681 ATCTAAAGTC ATTTGACTTA GGCGACGAGC TTGGCACTGA 
               
               
                   
               
               
                  721 TCCTTATGAA GATTTTCAAG AAAACTGGAA CACTAAACAT 
               
               
                   
               
               
                  761 AGCAGTGGTG TTACCCGTGA ACTCATGCGT GAGCTTAACG 
               
               
                   
               
               
                  801 GAGGGGCATA CACTCGCTAT GTCGATAACA ACTTCTGTGG 
               
               
                   
               
               
                  841 CCCTGATGGC TACCCTCTTG AGTGCATTAA AGACCTTCTA 
               
               
                   
               
               
                  881 GCACGTGCTG GTAAAGCTTC ATGCACTTTG TCCGAACAAC 
               
               
                   
               
               
                  921 TGGACTTTAT TGACACTAAG AGGGGTGTAT ACTGCTGCCG 
               
               
                   
               
               
                  961 TGAACATGAG CATGAAATTG CTTGGTACAC GGAACGTTCT 
               
               
                   
               
               
                 1001 GAAAAGAGCT ATGAATTGCA GACACCTTTT GAAATTAAAT 
               
               
                   
               
               
                 1041 TGGCAAAGAA ATTTGACACC TTCAATGGGG AATGTCCAAA 
               
               
                   
               
               
                 1081 TTTTGTATTT CCCTTAAATT CCATAATCAA GACTATTCAA 
               
               
                   
               
               
                 1121 CCAAGGGTTG AAAAGAAAAA GCTTGATGGC TTTATGGGTA 
               
               
                   
               
               
                 1161 GAATTCGATC TGTCTATCCA GTTGCGTCAC CAAATGAATG 
               
               
                   
               
               
                 1201 CAACCAAATG TGCCTTTCAA CTCTCATGAA GTGTGATCAT 
               
               
                   
               
               
                 1241 TGTGGTGAAA CTTCATGGCA GACGGGCGAT TTTGTTAAAG 
               
               
                   
               
               
                 1281 CCACTTGCGA ATTTTGTGGC ACTGAGAATT TGACTAAAGA 
               
               
                   
               
               
                 1321 AGGTGCCACT ACTTGTGGTT ACTTAGCCCA AAATGCTGTT 
               
               
                   
               
               
                 1361 GTTAAAATTT ATTGTCCAGC ATGTCACAAT TCAGAAGTAG 
               
               
                   
               
               
                 1401 GACCTGAGCA TAGTCTTGCC GAATAGCATA ATGAATCTGG 
               
               
                   
               
               
                 1441 CTTGAAAACC ATTCTTCGTA AGGGTGGTCG CACTATTGCC 
               
               
                   
               
               
                 1481 TTTGGAGGCT GTGTGTTCTC TTATGTTGGT TGCCATAACA 
               
               
                   
               
               
                 1521 AGTGTGCCTA TTGGGTTCCA gaaatagatc tctcgaggtt 
               
               
                   
               
               
                 1561 aacgaattct gctatacgaa gttatccctc  
               
            
           
         
       
     
     The TIP constructs used in the experiments described herein included a marker (mCherry) encoded between the 5′ and 3′ SARS-CoV-2 nucleic acids. Expression of such a marker allowed replication the TIP constructs to be detected in cells transfected with the TIP constructs. Inclusion of such markers is useful for monitoring the TIPs but the marker may not be needed or included in therapeutic interfering particles that are administered as treatment of a patient or subject infected with SARS-CoV-2. 
     In general, the methods for making SARS-CoV-2 therapeutic interfering particles involve cleaving a population of circular SARS-CoV-2 DNA at different positions in the DNA circle to generate a library of cleaved (linearized) SARS-CoV-2 DNAs where members of the library are cut at different locations. One or more exonucleases are then used to ‘chew back’ the end(s) of the cut site and the ‘chewed ends’ are then ligated to reform circular DNA. This generates a deletion library. There are numerous ways to achieve each of the steps (e.g., the cleavage step at different positions for the members of the library), and there are optional steps that can be performed prior to the circularizing (e.g., ligation) step. As discussed in more detail below, more than one round of library generation can be performed, and thus the subject methods can be used the generate complex deletion libraries in which members of the library include more than one deletion. 
     Generating a Library of Cleaved (Linearized) SARS-CoV-2 DNAs 
     The methods described herein include generating a library of cleaved (linearized) SARS-CoV-2 DNAs from a population of circular SARS-CoV-2 DNAs. In some cases, the position of cleavage of the SARS-CoV-2 DNA population is random. For example, a transposon cassette can be inserted at random positions into a population of SARS-CoV-2 DNAs, where the transposon cassette includes a target sequence (recognition sequence) for a sequence specific DNA endonuclease. In such a case, the transposon cassette is being used as a vehicle for inserting a recognition sequence into the population of SARS-CoV-2 DNAs (at random positions). A sequence specific DNA endonuclease (one that recognizes the recognition sequence) can then be used to cleave the SARS-CoV-2 DNAs, thereby generating a library of cleaved (linearized) SARS-CoV-2 DNAs where members of the library are cut at different locations. 
     The term “transposon cassette” is used herein to mean a nucleic acid molecule that includes a ‘sequence of interest’ flanked by sequences that can be used by a transposon to insert the sequence of interest into a SARS-CoV-2 DNA. Thus, in some cases, the ‘sequence of interest’ is flanked by transposon compatible inverted terminal repeats (ITRs), i.e., ITRs that are recognized and utilized by a transposon. In cases where a transposon cassette is used as a vehicle for inserting one or more target sequences (for one or more sequence specific DNA endonucleases) into SARS-CoV-2 DNAs, the sequence of interest can include the one or more recognition sequences. 
     In some cases, the sequence of interest includes a selectable marker gene, for example, a nucleotide sequence encoding a selectable marker such as a gene encoding a protein that provides for drug resistance, for example, antibiotic resistance. In some cases, a sequence of interest includes a first copy and a second copy of a recognition sequence for a first sequence specific DNA endonuclease (e.g., a first meganuclease). In some cases, a sequence of interest includes a selectable marker gene flanked by a first and second recognition sequence for a sequence specific DNA endonuclease (e.g., meganuclease). In some such cases, the first recognition sequence and the second recognition sequence are identical and can be considered a first copy and a second copy of a recognition sequence. In some such cases, the first recognition sequence is different than the second recognition sequence. In some cases, the first recognition sequence and second recognition sequence (e.g., first and second copies of a recognition sequence) flank a selectable marker gene, for example, one that encodes a drug resistance protein such as an antibiotic resistance protein. In some embodiments, a subject transposon cassette includes a first copy and a second copy of a recognition sequence for a first meganuclease; and a first copy and a second copy of a recognition sequence for a second meganuclease. 
     In any of the above scenarios, in some cases, the first and/or second recognition sequence is a site for 1-Sce1 meganuclease (e.g., aactataacggtcctaa{circumflex over ( )}ggtagcgaa (SEQ ID NO:34)). In some cases, the first and/or second recognition sequence is a site for 1-Ceu1 meganuclease (e.g., aactataacggtcctaa{circumflex over ( )}ggtagcgaa (SEQ ID NO:35)). See.  FIG.  4   . In some cases, a first recognition sequence is a site for 1-Sce1 and a second recognition sequence is a site for 1-Ceu1. In some cases a first and/or second recognition sequence is a recognition sequence for a meganuclease, for example, selected from: a LAGLIDADG meganuclease (LMNs), 1-Sce1, 1-Ceu1, 1-Cre1, 1-Dmo1, 1-Chu1, 1-Dir1, 1-Flmu1, 1-Flmu11, 1-Ani1, 1-Sce1V, 1-Csm1, 1-Pan1, 1-Pan11, 1-PanMI, 1-Sce11, I-Ppo1, 1-Sce111, 1-Ltd, 1-Gpi1, 1-GZe1, 1-Onu1, 1-HjeMI, I-Mso1, 1-Tev1, 1-Tev11, 1-Tev111, P1-Mie1, P1-Mtu1, P1-Psp1, P1-Tli I, P1-Tli II, and P1-SceV. 
     As noted above, a subject transposon cassette includes a sequence of interest flanked by transposase compatible inverted terminal repeats (ITRs). The ITRs can be compatible with any desired transposase, for example, a bacterial transposase such as Tn3, Tn5, Tn7, Tn9, Tn10, Tn903, Tn1681, and the like; and eukaryotic transposases such as Tc1/mariner super family transposases, piggyBac superfamily transposases, hAT superfamily transposases, Sleeping Beauty, Frog Prince, Minos, Himari, and the like. In some cases, the transposase compatible ITRs are compatible with (i.e., can be recognized and utilized by) a Tn5 transposase. Some of the methods provided herein include a step of inserting a transposase cassette into a SARS-CoV-2 DNA. Such a step includes contacting the SARS-CoV-2 DNA and the transposon cassette with a transposase. In some cases, this contacting occurs inside of a cell such as a bacterial cell, and in some cases this contacting occurs in vitro outside of a cell. As the transposase compatible ITRs listed above are suitable for compositions and methods disclosed herein, so too are the transposases. As such, suitable transposases include but are not limited to bacterial transposases such as Tn3, Tn5, Tn7, Tn9, Tn10, Tn903, Tn1681, and the like; and eukaryotic transposases such as Tc1/mariner super family transposases, piggyBac superfamily transposases, hAT superfamily transposases, Sleeping Beauty, Frog Prince, Minos, Himarl, and the like. In some cases, the transposase is a Tn5 transposase. 
     In some embodiments, a subject method includes a step of inserting a target sequence (e.g., one or more target sequences) for a sequence specific DNA endonuclease (e.g., one or more sequence specific DNA endonucleases) into a population of circular SARS-CoV-2 DNAs, thereby generating a population of sequence-inserted circular SARS-CoV-2 DNAs. In some cases, the inserting step is carried out by inserting a transposon cassette that includes the target sequence (e.g., the one or more target sequences), thereby generating a population of transposon-inserted circular SARS-CoV-2 DNAs. In some cases, the transposon cassette includes a single recognition sequence (e.g., in the middle or near one end of the transposon cassette) and can therefore be used to introduce a single recognition sequence into the population of SARS-CoV-2 DNAs. In some cases, the transposon cassette includes more than one recognition sequences (e.g., a first and a second recognition sequence). In some such cases, the first and second recognition sequences are positioned at or near the ends of the transposon cassette (e.g., within 20 bases, 30 bases, 50 bases, 60 bases, 75 bases, or 100 bases of the end) such that cleavage of the first and second recognition sequences effectively removes the transposon cassette (or most of the transposon cassette) from the SARS-CoV-2 DNA, while simultaneously generating a linearized SARS-CoV-2 DNA, and therefore generating the desired library of cleaved (linearized) SARS-CoV-2 DNAs where members of the library are cut at different locations. 
     In some cases when the transposon cassette include first and second recognition sequences, the first and second recognition sequences are the same, and are therefore first and second copies of a given recognition sequence. In some such cases, the same sequence specific DNA endonuclease (e.g., restriction enzyme, meganuclease, programmable genome editing nuclease) can then be used to cleave at both sites. 
     In some embodiments, the transposon cassette includes a first and a second recognition sequence where the first and second recognition sequences are not the same. In some such cases, a different sequence specific DNA endonuclease (e.g., restriction enzyme, meganuclease, programmable genome editing nuclease) is used to cleave the two sites (e.g., the library of transposon-inserted SARS-CoV-2 DNAs can be contacted with two sequence specific DNA endonucleases). However, in some cases one sequence specific DNA endonuclease can still be used. For example, in some cases two different guide RNAs can be used with the same CRISPR/Cas protein. As another example, in some cases a given sequence specific DNA endonuclease can recognize both recognition sequences. 
     In some cases, the population of circular SARS-CoV-2 DNAs (e.g., plasmids) are present inside of host cells (e.g., bacterial host cells such as  E. coli ) and the step of inserting a transposon cassette takes place inside of the host cell. For example, the methods can include introducing a transposase and/or a nucleic acid encoding a transposase into a selected cell or expression of a transposase within the cell from an existing expression cassette that encodes the transposase, and the like. In some such cases, a subject method can include a selection/growth step in the host cell. For example, if the transposon cassette includes a drug resistance marker, the host cells can be grown in the presence of drug to select for those cells harboring a transposon-inserted circular target DNA. 
     Once a population of transposon-inserted circular SARS-CoV-2 DNAs is generated (and in some cases after a selection/growth step in the host cells), the population can be isolated/purified from the host cells prior to the next step (e.g., prior to contacting them with a sequence specific DNA endonuclease). 
     Because the circular SARS-CoV-2 DNAs can be small circular DNAs (e.g., less than 50 kb), a selection and growth step in bacteria can in some cases be avoided through the use of in vitro rolling circle amplification (RCA). For example, after repair of nicked target DNA post-transposition, a highly-processive and strand-displacing polymerase (e.g., phi29 DNA polymerase), along with primers specific to the inserted transposon cassette, can be used to selectively amplify insertion mutants from the pool of circular plasmids. In other words, such a step can circumvent amplifying DNA through bacterial transformation. Use of RCA can decrease the time required for growth/selection of bacteria and can avoid biasing the library towards clones that do not impede bacterial growth. 
     Non-Random Cleavage 
     As noted above, in some cases the position of cleavage of the SARS-CoV-2 DNA population is random, however in some cases the position of cleavage is not random. For example, a population of SARS-CoV-2 DNAs can be distributed (e.g., aliquoted) into different vessels (e.g., different tubes, different wells of a multi-well plate etc.). If a specific sequence of interest is selected within the SARS-CoV-2 genomic sequence, then that sequence of interest can be cleaved within the circular SARS-CoV-2 DNAs. Separate aliquots of circular SARS-CoV-2 DNAs can be placed within different vessels (e.g., wells of the multi-well plate) and the different aliquots of circular SARS-CoV-2 DNAs can be cleaved at different pre-determined locations by using a programmable sequence specific endonuclease. For example, if a CRISPR/Cas endonuclease (e.g., Cas9, Cpf1, and the like) is used, guide RNAs can readily be designed to target any desired sequence within the SARS-CoV-2 genome (e.g., while taking protospacer adjacent motif (PAM) sequence requirements into account in some cases). For example, guide RNAs can be tiled at any desired spacing along the circular SARS-CoV-2 DNAs (e.g., every 5 nucleotides (nt), every 10 nt, every 20 nt, every 50nt—overlapping, non-overlapping, and the like). The circular SARS-CoV-2 DNAs in each vessel (e.g., each well) can be contacted with one of the guide RNAs in addition to the CRISPR/Cas endonuclease. In this way, a library of cleaved SARS-CoV-2 DNAs can be generated where members of the library are separated from one another because they are in separate vessels. As would be understood by one of ordinary skill in the art, in some cases, one would take PAM sequences into account when designing guide RNAs, and therefore the spacing between guide RNA target sites can be a function of PAM sequence constraints, and consistent spacing across a given target sequence would not necessarily be possible in some cases. However, different CRISPR/Cas endonucleases (e.g., even the same protein, such as Cas9, isolated from different species) can have different PAM requirements, and thus, the use of more than one CRISPR/Cas endonuclease can in some cases relieve at least some of the constraints imposed by PAM requirements on available target sites. Further steps of the method can then be carried out separately (e.g., in separate vessels, in separate wells of a multi-well plate), or at any step, members can be pooled and treated together in one vessel. 
     As an illustrative but non-limiting example, one could use 96 different guide RNAs (or 384 different guide RNAs) to cleave aliquots of circular SARS-CoV-2 DNAs in 96 different wells of a 96-well plate (or 384 different wells of a 384 well plate), to generate 96 members (or 384 members) of a library where each member is cleaved at a different site. The cleavage sites can be designed by the user prior to starting the method. The exonuclease step (chew back) can then be performed in separate wells (e.g., by aliquoting exonuclease to each well), or two more wells can be pooled prior to adding exonuclease to the pool. 
     Circular SARS-CoV-2 DNAs 
     A circular SARS-CoV-2 DNA of a population of circular SARS-CoV-2 DNAs can be any circular SARS-CoV-2 DNA and can be generated from any isolate of SARS-CoV-2. In some cases, the circular SARS-CoV-2 DNAs are plasmid DNAs. For example, in some cases, the circular SARS-CoV-2 DNAs include an origin of replication (ORI). In some cases, the circular SARS-CoV-2 DNAs include a drug resistance marker (e.g., a nucleotide sequence encoding a protein that provides for drug resistance). In some embodiments, a population of circular SARS-CoV-2 DNAs are generated from a population of linear DNA molecules (e.g., via intramolecular ligation). For example, a subject method can include a step of circularizing a population of linear SARS-CoV-2 DNA molecules (e.g., a population of PCR products, a population of linear viral SARS-CoV-2 genomes, a population of products from a restriction digest, etc.) to generate a population of circular SARS-CoV-2 DNAs. In some cases, members of such a population are identical (e.g., many copies of a PCR product or restriction digest can be used to generate a population of SARS-CoV-2 DNAs, where each circular DNA is identical). In some cases, members of such a population of circular SARS-CoV-2 DNAs can be different from one another. For example, the population of circular SARS-CoV-2 DNAs can be generated from two or more different SARS-CoV-2 isolates or be generated from different SARS-CoV-2 PCR products or be generated from different restriction digest products of SARS-CoV-2. 
     In some cases, the population of circular SARS-CoV-2 DNAs can itself be a deletion library. For example, the population of circular SARS-CoV-2 DNAs can be a library of known deletion mutants (e.g., known viral deletion mutants). As another example, if two rounds of a subject method are performed, the starting population of SARS-CoV-2 DNAs for the second round can be a deletion library (e.g., generated during a first round of deletion) where members of the library include deletions of different sections of DNA relative to other members of the library. Such a library can serve as a population of circular SARS-CoV-2 DNAs, e.g., a transposon cassette can still be introduced into the population. Performing a second round of deletion in this manner can therefore generate constructs with deletions at multiple different entry points. As an illustrative example, for a SARS-CoV-2 DNA of about 29-30 kb (kilobases) in length, the first round of deletion might have deleted bases 2000 through 2650 for a one member (of the library that was generated), of which multiple copies would likely be present. A second round of deletion might generate two new members, both of which are generated from copies of the same deletion member. Thus, for example, one new member might be generated with bases 3500 through 3650 deleted (in addition to bases 2000 through 2650), while a second new member might be generated with bases 1500 through 1580 deleted (in addition to bases 2000 through 2650). Thus, multiple rounds of deletion (e.g., 2, 3, 4, 5, etc.) can produce complex deletion libraries. In some cases, more than one round of library generation is performed where the second round includes the insertion of a transposon cassette, e.g., as described above. 
     For example, in some cases, a first round of deletion is performed using a CRISPR/Cas endonuclease to generate the cleaved linear SARS-CoV-2 DNAs by targeting the CRISPR/Cas endonuclease to pre-selected sites within the population of circular SARS-CoV-2 DNAs (e.g., by designing guide RNAs, e.g., at pre-selected spacing, to target one or more SARS-CoV-2 sequences of interest). After exonuclease treatment and circularization to generate a first library of circularized deletion DNAs, the library of circularized deletion DNAs is used as input (as a population of circular SARS-CoV-2 DNAs) for a second round of deletion. Thus, one or more target sequences for one or more sequence specific DNA endonucleases (e.g., one or more meganucleases) is inserted (e.g., at random positions via a transposon cassette) into the library of circularized SARS-CoV-2 deletion DNAs to generate a population of transposon-inserted circular SARS-CoV-2 DNAs, and the method is continued. In some such cases, the first round of deletion might only target a small number of locations of interest for deletion (one location, e.g., using only one guide RNA that targets a particular location; or a small number of locations, e.g., using a small number of guide RNAs to target a small number of locations), while the second round is used to generate deletion constructs that include the first deletion plus a second deletion. 
     In some cases, the circular SARS-CoV-2 DNAs include the whole viral genome. In other cases, the circular SARS-CoV-2 DNAs include a partial SARS-CoV-2 viral genome. Thus, in some cases the subject methods are used to generate a library of viral deletion mutants. In some such cases, a library of generated viral deletion mutants can be considered a library of potential defective interfering particles (DIPs). DIPs are mutant versions of SARS-CoV-2 viruses that include genomic deletions such that they are unable to replicate except when complemented by wild-type virus replicating within the same cell. Defective interfering particles (DIPs) can arise naturally because viral genomes encode both cis-acting and trans-acting elements. Trans-acting elements (trans-elements) code for gene products, such as capsid proteins or transcription factors, and cis-acting elements (cis-elements) are regions of the viral genome that interact with trans-element products to achieve productive viral replication including viral genome amplification, encapsidation, and viral egress. In other words, the SARS-CoV-2 viral genome of a DIP can still be copied and packaged into viral particles if the missing (deleted) trans-elements are provided in trans (e.g., by a co-infecting virus). In some cases, a DIP can be used therapeutically to reduce viral infectivity of a co-infecting virus, e.g., by competing for and therefore diluting out the available trans-elements. In such cases, where a SARS-CoV-2 DIP can be used as a therapeutic (e.g., as a treatment for Covid-19 infections), that SARS-CoV-2 DIP can be referred to as a therapeutic interfering particle (TIP). 
     While DIPs may arise naturally, methods of this disclosure can be used to generate useful types of SARS-CoV-2 DIPs, for example, by generating a deletion library of viral SARS-CoV-2 genomes. DIPs can then be identified from such a deletion library by sequencing the library members to identify those predicted to be DIPs. Alternatively, or additionally, a generated deletion library can be screened. For example, a library of SARS-CoV-2 DIPs can be introduced into cells, to identify those members with viral genomes having the desired function. Additional description of DIPs and TIPs and uses thereof is provided in U.S. Patent Application Publication No. 20160015759, the disclosure of which is incorporated by reference herein in its entirety. 
     Thus, in some cases a subject method includes introducing members of a library of generated SARS-CoV-2 deletion constructs into a target cell (e.g., a eukaryotic cell, such as a mammalian cell, such as a human cell) and assaying for infectivity. In some such cases, the assaying step also includes complementation of the library members with a co-infecting SARS-CoV-2 virus. 
     Such introducing is meant herein to encompass any form of introduction of nucleic acids into cells (e.g., electroporation, transfection, lipofection, nanoparticle delivery, viral delivery, and the like). For example, such ‘introduction’ encompasses infecting mammalian cells in culture (e.g., with members of a generated library of circularized SARS-CoV-2 deletion viral DNAs that can be encapsulated as viral particles that contain viral genomes encoded by the members of the generated library of circularized deletion viral DNAs). 
     In some cases, a method includes generating from a library of SARS-CoV-2 deletion DNAs, at least one of: linear double stranded DNA (dsDNA) products, linear single stranded DNA (ssDNA) products, linear single stranded RNA (ssRNA) products, and linear double stranded RNA (dsRNA) products. Thus in some such cases, a subject method includes introducing such linear dsDNA products, linear ssDNA products, linear ssRNA products, and/or linear dsRNA products into mammalian cells (e.g., via any convenient method for introducing nucleic acids into cells, including but not limited to electroporation, transfection, lipofection, nanoparticle delivery, viral delivery, and the like). 
     Such methods can also include assaying for viral infectivity. Assaying for viral infectivity can be performed using any convenient method. Assaying for viral infectivity can be performed on the cells into which the members of the library of circularized SARS-CoV-2 deletion DNAs (and/or at least one of: linear double stranded DNA (dsDNA) products, linear single stranded DNA (ssDNA) products, linear single stranded RNA (ssRNA) products, and linear double stranded RNA (dsRNA) products generated from the library of circularized deletion DNAs) are introduced. For example, in some cases the members and/or products are introduced as encapsulated particles. In some cases, members of the library of circularized SARS-CoV-2 deletion DNAs (and/or at least one of: linear dsDNA products, linear ssDNA products, linear ssRNA products, and linear dsRNA products generated from the library of circularized SARS-CoV-2 deletion DNAs) are introduced into a first population of cells (e.g., mammalian cells) in order to generate viral particles, and the viral particles are then used to contact a second population of cells (e.g., mammalian cells). Thus, as used herein, unless otherwise explicitly described, the phrase “assaying for viral infectivity” encompasses both of the above scenarios (e.g., encompasses assaying for infectivity in the cells into which the members and/or products were introduced, and also encompasses assaying the second population of cells as described above). 
     In some embodiments a subject method (e.g., a method of generating and identifying a DIP) includes, after generating a deletion library (e.g., a library of circularized SARS-CoV-2 deletion DNAs), a high multiplicity of infection (MOI) screen (e.g., utilizing a MOI of &gt;2). As used herein, a “high MOI” is a MOI of 2 or more (e.g., 2.5 or more, 3 or more, 5 or more, etc.). In some cases, a subject method uses a high MOI. Thus, in some cases, a subject method uses a MOI (a high MOI) of 2 or more, 3 or more, or 5 or more. In some cases, a subject method uses a MOI (a high MOI) in a range of from 2-150 (e.g., from 2-100, 2-80, 2-50, 2-30, 3-150, 3-100, 3-80, 3-50, 3-30, 5-150, 5-100, 5-80, 5-50, or 5-30). In some cases, a subject method uses a MOI (a high MOI) in a range of from 3-100 (e.g., 5-100). At high MOI, many (if not all) cells are infected by more than one virus, which allows for complementation of defective viruses by wildtype counterparts. Repeated passaging of deletion mutant libraries at high-MOI can select for mutants that can be mobilized effectively by a wild type SARS-CoV-2. For example, in some cases the method includes infecting mammalian cells in culture with members of the library of circularized SARS-CoV-2 deletion viral DNAs at a high multiplicity of infection (MOI), culturing the infected cells for a period of time ranging from 12 hours to 2 days (e.g., from 12 hours to 36 hours or 12 hours to 24 hours), adding naive cells to the to the culture, and harvesting virus from the cells in culture. However, this screening step can in some cases select for DIPs/TIPs which can be mobilized effectively by the wildtype virus but are cytopathic in the absence of the wildtype coinfection. 
     Thus, in some embodiments a subject method (e.g., a method of generating and identifying a DIP) includes a more stringent screen (referred to herein as a “low multiplicity of infection (MOI) screen”). As used herein, a “low MOI” includes use of a MOI of less than 1 (e.g., less than 0.8, less than 0.6, etc.). In some cases, a subject method uses a low MOI. Thus, in some cases, a subject method uses a MOI (a low MOI) of less than 1 (e.g., less than 0.8, less than 0.6). In some cases, a subject method uses a MOI (a low MOI) in a range of from 0.001-0.8 (e.g., from 0.001-0.6, 0.001-0.5, 0.005-0.8, 0.005-0.6, 0.01-0.8, or 0.01-0.5). In some cases, a subject method uses a MOI (a low MOI) in a range of from 0.01-0.5. For example, a low-MOI infection of target cells with a deletion library (e.g., utilizing a MOI of &lt;1) can be alternated with a high-MOI infection of the transduced population with wildtype virus (e.g., SARS-CoV-2) to mobilize DIPs to naive cells. 
     In some cases, cells with one or more SARS-CoV-2 or one or more SARS-CoV-2 deletion DNAs can be propagated in the presence of a drug to test whether further rounds of replication occur. During the recovery period, cells infected with wild type virus (e.g., SARS-CoV-2 infected cells) will be killed, but cells transduced by well-behaving mutants (which do not produce cell-killing trans-factors) will be maintained. In this fashion, mutants can be selected that do not kill their transduced host-cell but that can mobilize during wildtype virus coinfection. Thus, in some cases a subject method includes infecting mammalian cells in culture with members of the library of circularized deletion SARS-CoV-2 viral DNAs at a low multiplicity of infection (MOI), culturing the infected cells in the presence of an inhibitor of viral replication for a period of time ranging from 1 day to 6 days (e.g., from 1 day to 5 days, from 1 day to 4 days, from 1 day to 3 days, or from 1 day to 2 days), infecting the cultured cells with functional SARS-CoV-2 virus at a high MOI, culturing the infected cells for a period of time ranging from 12 hours to 4 days (e.g., 12 hours to 72 hours, 12 hours to 48 hours, or 12 hours to 24 hours), and harvesting virus from the cultured cells. 
     In some embodiments, a subject method includes (a) inserting a target sequence for a sequence specific DNA endonuclease into a population of circular SARS-CoV-2 viral DNAs, to generate a population of sequence-inserted SARS-CoV-2 DNAs; (b) contacting the population of sequence-inserted SARS-CoV-2 DNAs with the sequence specific DNA endonuclease to generate a population of cleaved linear SARS-CoV-2 DNAs; (c) contacting the population of cleaved linear viral DNAs with an exonuclease to generate a population of SARS-CoV-2 deletion DNAs; (d) circularizing (e.g., via ligation) the SARS-CoV-2 deletion DNAs to generate a library of circularized SARS-CoV-2 deletion DNAs; and (e) sequencing members of the library of circularized SARS-CoV-2 deletion DNAs to identify deletion interfering particles (DIPs). In some cases, the method includes inserting a barcode sequence prior to or simultaneous with step (d). 
     In some cases, the inserting of step (a) includes inserting a transposon cassette into the population of circular SARS-CoV-2 viral DNAs, wherein the transposon cassette includes the target sequence for the sequence specific DNA endonuclease, and where the generated population of sequence-inserted SARS-CoV-2 DNAs is a population of transposon-inserted viral DNAs. In some cases (e.g., in some cases when using a CRISPR/Cas endonuclease), a subject method does not include step (a), and the first step of the method is instead cleaving members of the library in different locations relative to one another, which step can be followed by the exonuclease step. 
     Target Sequence and Sequence Specific DNA Endonucleases 
     In some cases, a target sequence for a sequence specific DNA endonuclease is inserted into a SARS-CoV-2 DNA, for example, using a transposon cassette. The ‘target sequence’ is also referred to herein as a recognition sequence or recognition site. The term sequence specific endonuclease is used herein to refer to a DNA endonuclease that binds to and/or recognizes the target sequence in a SARS-CoV-2 DNA and cleaves the SARS-CoV-2 DNA. In other words, a sequence specific DNA endonuclease recognizes a specific sequence (a recognition sequence) within a SARS-CoV-2 DNA molecule and cleaves the molecule based on that recognition. In some cases, the sequence specific DNA endonuclease cleaves the SARS-CoV-2 DNA within the recognition sequence and in some cases it cleaves outside of the recognition sequence (e.g., in the case of type US restriction endonucleases). 
     The term sequence specific DNA endonuclease encompasses can include, for example, restriction enzymes, meganucleases, and programmable genome editing nucleases. Examples of sequence specific endonucleases include but are not limited to: restriction endonucleases such as EcoRI, EcoRV, BamHI, etc.; meganucleases such as LAGLI DADG meganucleases (LMNs), 1-Sce1, 1-Ceu1, 1-Cre1, 1-Dmo1, 1-Chu1, 1-Dir1, 1-Flmu1, 1-Flmu11, 1-Ani1, 1-Sce1V, 1-Csm1, 1-Pan1, 1-Pan11, 1-PanMI, 1-Sce11, 1-Ppo1, 1-Sce111, 1-Ltr1, 1-Gpi1, 1-GZe1, 1-Onu1, 1-HjeMI, 1-Mso1, 1-Tev1, 1-Tev11, 1-Tev111, P1-Mle1, P1-Mtu1, P1-Psp1, PI-TIi I, PI-TIi II, P1-SceV, and the like; and programmable gene editing endonucleases such as Zinc Finger Nucleases (ZFNs), transcription activator like effector nuclease (TALENs), and CRISPR/Cas endonucleases. In some cases, the sequence specific endonuclease of a subject composition and/or method is selected from: a meganuclease and a programmable gene editing endonuclease. In some cases, the sequence specific endonuclease of a subject composition and/or method is selected from: a meganuclease, a ZFN, a TALEN, and a CRISPR/Cas endonuclease (e.g., Cas9, Cpf1, and the like). 
     In some cases, the sequence specific endonuclease of a subject composition and/or method is a meganuclease. In some cases the meganuclease is selected from: LAGLIDADG meganucleases (LMNs), 1-Sce1, 1-Ceu1, 1-Cre1, 1-Dmo1, 1-Chu1, 1-Dir1, 1-Flmu1, 1-Flmu11, 1-Ani1, I-Sce1V, 1-Csm1, 1-Pan1, 1-Pan11, 1-PanMI, 1-Sce11, 1-Ppo1, 1-Sce111, 1-Ltr1, 1-Gpi1, 1-GZe1, 1-Onu1, I-HjeMI, 1-Mso1, 1-Tev1, 1-Tev11, 1-Tev111, P1-Mle1, P1-Mtu1, P1-Psp1, PI-TIi I, PI-TIi II, and P1-SceV. In some cases, the meganuclease 1-Sce1 is used. In some cases, the meganuclease 1-Ceu1 is used. In some cases, the meganucleases 1-Sce1 and 1-Ceu1 are used. 
     In some cases, the sequence specific DNA endonuclease is a programmable genome editing nuclease. The term “programmable genome editing nuclease” is used herein to refer to endonucleases that can be targeted to different sites (recognition sequences) within a SARS-CoV-2 DNA. Examples of suitable programmable genome editing nucleases include but are not limited to zinc finger nucleases (ZFNs), TAL-effector DNA binding domain-nuclease fusion proteins (transcription activator-like effector nucleases (TALENs)), and CRISPR/Cas endonucleases (e.g., class 2 CRISPR/Cas endonucleases such as a type II, type V, or type VI CRISPR/Cas endonucleases). Thus, in some embodiments, a programmable genome editing nuclease is selected from: a ZFN, a TALEN, and a CRISPR/Cas endonuclease (e.g., a class 2 CRISPR/Cas endonuclease such as a type II, type V, or type VI CRISPR/Cas endonuclease). In some cases, the sequence specific endonuclease of a subject composition and/or method is a CRISPR/Cas endonuclease (e.g., Cas9, Cpf1, and the like). In some cases, the sequence specific endonuclease of a subject composition and/or method is selected from: a meganuclease, a ZFN, and a TALEN. 
     Information related to class 2 type II CRISPR/Cas endonuclease Cas9 proteins and Cas9 guide RNAs (as well as methods of their delivery) (as well as information regarding requirements related to protospacer adjacent motif (PAM) sequences present in SARS-CoV-2 nucleic acids) can be found, for example, in the following Jinek et al., Science. 2012 Aug. 17; 337(6096):816-21; Chylinski et al., RNA Biol. 2013 May; 10(5): 726-37; Ma et al., Biomed Res Int. 2013; 2013:270805; Hou et al., Proc Natl Acad Sci USA. 2013 Sep. 24; 1 10(39): 15644-9; Jinek et al., Elife. 2013; 2:e00471; Pattanayak et al., Nat Biotechnol. 2013 September; 31 (9):839-43; Qi et al, Cell. 2013 Feb. 28; 152(5): 1173-83; Wang et al., Cell. 2013 May 9; 153(4):910-8; Auer et. al., Genome Res. 2013 Oct. 31; Chen et. al., Nucleic Acids Res. 2013 Nov. 1; 41 (20):e19; Cheng et. al., Cell Res. 2013 October; 23(10): 1 163-71; Cho et. al., Genetics. 2013 November; 195(3): 1 177-80; DiCarlo et al., Nucleic Acids Res. 2013 April; 41 (7):4336-43; Dickinson et. al., Nat Methods. 2013 October; 10(10): 1028-34; Ebina et. al., Sci Rep. 2013; 3:2510; Fujii et. al, Nucleic Acids Res. 2013 Nov. 1; 41 (20):e187; Hu et. al., Cell Res. 2013 November; 23(1 1): 1322-5; Jiang et. al., Nucleic Acids Res. 2013 Nov. 1; 41 (20):e188; Larson et. al., Nat Protoc. 2013 November; 8(1 1):2180-96; Mali et. at., Nat Methods. 2013 October; 10(10):957-63; Nakayama et. al., Genesis. 2013 December; 51 (12):835-43; Ran et. al., Nat Protoc. 2013 November; 8(1 1):2281-308; Ran et. al., Cell. 2013 Sep. 12; 154(6): 1380-9; Upadhyay et. al., G3 (Bethesda). 2013 Dec. 9; 3(12):2233-8; Walsh et. al., Proc Natl Acad Sci USA. 2013 Sep. 24; 110(39): 15514-5; Xie et. al., Mol Plant. 2013 Oct. 9; Yang et. al., Cell. 2013 Sep. 12; 154(6): 1370-9; Briner et al., Mol Cell. 2014 Oct. 23; 56(2):333-9; and U.S. patents and patent applications: U.S. Pat. Nos. 8,906,616; 8,895,308; 8,889,418; 8,889,356; 8,871,445; 8,865,406; 8,795,965; 8,771,945; 8,697,359; 20140068797; 20140170753; 20140179006; 20140179770; 20140186843; 20140186919; 20140186958; 20140189896; 20140227787; 20140234972; 20140242664; 20140242699; 20140242700; 20140242702; 20140248702; 20140256046; 20140273037; 20140273226; 20140273230; 20140273231; 20140273232; 20140273233; 20140273234; 20140273235; 20140287938; 20140295556; 20140295557; 20140298547; 20140304853; 20140309487; 20140310828; 20140310830; 20140315985; 20140335063; 20140335620; 20140342456; 20140342457; 20140342458; 20140349400; 20140349405; 20140356867; 20140356956; 20140356958; 20140356959; 20140357523; 20140357530; 20140364333; and 20140377868; all of which are hereby incorporated by reference in their entirety. Examples and guidance related to type V CRISPR/Cas endonucleases (e.g., Cpf1) or type VI CRISPR/Cas endonucleases and guide RNAs (as well as information regarding requirements related to protospacer adjacent motif (PAM) sequences present in SARS-CoV-2 nucleic acids) can be found in the art, for example, see Zetsche et al, Cell. 2015 Oct. 22; 163(3):759-71; Makarova et al, Nat Rev Microbiol. 2015 November; 13(11):722-36; and Shmakov et al., Mol Cell. 2015 Nov. 5; 60(3):385-97. 
     Useful designer zinc finger modules include those that recognize various GNN and ANN triplets (Dreier, et al., (2001) J Biol Chem 276:29466-78; Dreier, et al., (2000) J Mol Biol 303:489-502; Liu, et al., (2002) J Biol Chem 277:3850-6), as well as those that recognize various CNN or TNN triplets (Dreier, et al., (2005) J Biol Chem 280:35588-97; Jamieson, et al., (2003) Nature Rev Drug Discov 2:361-8). See also, Durai, et al., (2005) Nucleic Acids Res 33:5978-90; Segal, (2002) Methods 26:76-83; Porteus and Carroll, (2005) Nat Biotechnol 23:967-73; Pabo, et al., (2001) Ann Rev Biochem 70:313-40; Wolfe, et al., (2000) Ann Rev Biophys Biomol Struct 29: 183-212; Segal and Barbas, (2001) Curr Opin Biotechnol 12:632-7; Segal, et al., (2003) Biochemistry 42:2137-48; Beerli and Barbas, (2002) Nat Biotechnol 20: 135-41; Carroll, et al., (2006) Nature Protocols 1:1329; Ordiz, et al., (2002) Proc Natl Acad Sci USA 99: 13290-5; Guan, et al., (2002) Proc Natl Acad Sci USA 99: 13296-301. 
     For more information on ZFNs and TALENs (as well as methods of their delivery), refer to Sanjana et al., Nat Protoc. 2012 Jan. 5; 7(1): 171-92 as well as international patent applications WO2002099084; WO00/42219, WO02/42459; WO2003062455; WO03/080809; WO05/014791; WO05/084190; WO08/021207; WO09/042186; WO09/054985; WO10/079430; and WO10/065123; U.S. Pat. Nos. 8,685,737; 6,140,466; 6,511,808; and 6,453,242; and US Patent Application Nos. 2011/0145940, 2003/0059767, and 2003/0108880; all of which are hereby incorporated by reference in their entirety. 
     In some cases (e.g., in the case of restriction enzymes), the recognition sequence is a constant (does not change) for the given protein (e.g., the recognition sequence for the BamHI restriction enzyme is G{circumflex over ( )}GATCC). In some cases, the sequence specific DNA endonuclease is ‘programmable’ in the sense that the protein (or its associated RNA in the case of CRISPR/Cas endonucleases) can be modified/engineered to recognize a desired recognition sequence. In some cases (e.g., in cases where the sequence specific DNA endonuclease is a meganuclease and/or in cases where the sequence specific DNA endonuclease is a CRISPR/Cas endonuclease), the recognition sequence has a length of 14 or more nucleotides (nt) (e.g., 15 or more, 16 or more, 17 or more, 18 or more, 19 or more, or 20 or more nt). In some cases, the recognition sequence has a length in a range of from 14-40 nt (e.g., 14-35, 14-30, 14-25, 15-40, 15-35, 15-30, 15-25, 16-40, 16-35, 16-30, 16-25, 17-40, 17-35, 17-30, or 17-25 nt). In some cases, the recognition sequence has a length of 14 or more base pairs (bp) (e.g., 15 or more, 16 or more, 17 or more, 18 or more, 19 or more, or 20 or more bp). In some cases, the recognition sequence has a length in a range of from 14-40 bp (e.g., 14-35, 14-30, 14-25, 15-40, 15-35, 15-30, 15-25, 16-40, 16-35, 16-30, 16-25, 17-40, 17-35, 17-30, or 17-25 bp). 
     When referring above to the lengths of a recognition sequence, the double-stranded helix and the recognition sequence can be thought of in terms of base pairs (bp), while in some cases (e.g., in the case of CRISPR/Cas endonucleases) the recognition sequence is recognized in single stranded form (e.g., a guide RNA of a CRISPR/Cas endonuclease can hybridize to the SARS-CoV-2 DNA) and the recognition sequence can be thought of in terms of nucleotides (nt). However, when using ‘bp’ or‘nt’ herein when referring to a recognition sequence, this terminology is not intended to be limiting. As an example, if a particular method or composition described herein encompasses both types of sequence specific DNA endonuclease (those that recognize ‘bp’ and those that recognize ‘nt’), either of the terms ‘nt’ or ‘bp’ can be used without limiting the scope of the sequence specific DNA endonuclease, because one of ordinary skill in the art would readily understand which term (‘nt’ or ‘bp’) would appropriately apply, and would understand that this depends on which protein is chosen. In the case of a length limitation of the recognition sequence, one of ordinary skill in the art would understand that the length limitation being discussed equally applies regardless of whether the term ‘nt’ or‘bp’ is used. 
     Chew Back (Exonuclease Digestion) 
     After the circular SARS-CoV-2 DNAs are cleaved, generating a population of cleaved linear SARS-CoV-2 DNAs, the open ends of the linear SARS-CoV-2 DNAs are digested (chewed back) by exonucleases. Many different exonucleases will be known to one of ordinary skill in the art and any convenient exonuclease can be used. In some cases, a 5′ to 3′ exonuclease is used. In some cases, a 3′ to 5′ exonuclease is used. In some cases, an exonuclease is used that has both 5′ to 3′ and 3′ to 5′ exonuclease activity. In some cases, more than one exonuclease is used (e.g., 2 exonucleases). In some cases, the population of cleaved linear SARS-CoV-2 DNAs is contacted with a 5′ to 3′ exonuclease and a 3′ to 5′ exonuclease (e.g., simultaneously or one before the other). 
     In some cases, a T4 DNA polymerase is used as a 3′ to 5′ exonuclease (in the absence of dNTPs, T4 DNA polymerase has 3′ to 5′ exonuclease activity). In some cases, RecJ is used as a 5′ to 3′ exonuclease. In some cases, T4 DNA polymerase (in the absence of dNTPs) and RecJ are used. Examples of exonucleases include but are not limited to: DNA polymerase (e.g., T4 DNA polymerase) (in the absence of dNTPs), lambda exonuclease (5′-&gt;3′), T5 exonuclease (5′-&gt;3′), exonuclease III (3′-&gt;5′), exonuclease V (5′-&gt;3′ and 3′-&gt;5′), T7 exonuclease (5′-&gt;3′), exonuclease T, exonuclease VII (truncated) (5′-&gt;3′), and RecJ exonuclease (5′-&gt;3′). 
     The rate of DNA digestion (chew back) is sensitive to temperature, thus the size of the desired deletion can be controlled by regulating the temperature during exonuclease digestion. For example, in the examples section below when using T4 DNA polymerase (in the absence of dNTPs) and RecJ as the exonucleases, the double-end digestion rate (chew back rate) proceeded at a rate of 50 bp/min at 37° C. and at a reduced rate at lower temperatures (e.g., as discussed in the examples section below). Thus, temperature can be decreased or increased and/or digestion time can be decreased or increased to control the size of deletion (i.e., the amount of exonuclease digestion). For example, in some cases, the temperature and time are adjusted so that exonuclease digestion causes a deletion in a desired size range. As an illustrative example, if a deletion in a range of from 500-1000 base pairs (bp) is desired, the time and temperature of digestion can be adjusted so that 250-500 nucleotides are removed from each end of the linearized (cut) SARS-CoV-2 DNA, i.e., the size of the deletion is the sum of the number of nucleotides removed from each end of the linearized SARS-CoV-2 DNA. In some cases, the temperature and time are adjusted so that exonuclease digestion causes a deletion having a size in a range of from 20-1000 bp (e.g., from 20-50, 40-80, 20-100, 40-100, 20-200, 40-200, 60-100, 60-200, 80-150, 80-250, 100-250, 150-350, 100-500, 200-500, 200-700, 300-800, 400-800, 500-1000, 700-1000, 20-800, 50-1000, 100-1000, 250-1000, 50-1000, 50-750, 100-1000, or 100-750 bp). 
     In some cases, contacting with an exonuclease (one or more exonucleases) is performed at a temperature in a range of from room temperature (e.g., 25° C.) to 40° C. (e.g., from 25-37° C., 30-37° C., 32-40° C., or 30-40° C.). In some cases, contacting with an exonuclease is performed at 37° C. In some cases, contacting with an exonuclease is performed at 32° C. In some cases, contacting with an exonuclease is performed at 30° C. In some cases, contacting with an exonuclease is performed at 25° C. In some cases, contacting with an exonuclease is performed at room temperature. 
     In some cases, the SARS-CoV-2 DNA is contacted with an exonuclease (one or more exonucleases) for a period of time in a range of from 10 seconds to 40 minutes (e.g., from 10 seconds to 30 minutes, 10 seconds to 20 minutes, 10 seconds to 15 minutes, 10 seconds to 10 minutes, 30 seconds to 30 minutes, 30 seconds to 20 minutes, 30 seconds to 15 minutes, 30 seconds to 12 minutes, 30 seconds to 10 minutes, 1 to 40 minutes, 1 to 30 minutes, 1 to 20 minutes, 1 to 15 minutes, 1 to 10 minutes, 3 to 40 minutes, 3 to 30 minutes, 3 to 20 minutes, 3 to 15 minutes, 3 to 12 minutes, or 3 to 10 minutes). In some cases, the contacting is for a period of time in a range of from 20 seconds to 15 minutes. 
     After DNA digestion (chew back), the remaining overhanging DNA ends can be repaired (e.g., using T4 DNA Polymerase plus dNTPs) or in some cases the single stranded overhangs can be removed (e.g., using a nuclease such as mung bean nuclease that cleaves single stranded DNA but not double stranded DNA). For example, if only a 5′ to 3′ or 3′ to 5′ exonuclease is used, a nuclease specific for single stranded DNA (i.e., that does not cut double stranded DNA) (e.g., mung bean nuclease) can be used to remove the overhang. 
     The step of contacting with one or more exonucleases (i.e., chew back) can be carried out in the presence or absence of a single strand binding protein (SSB protein). An SSB is a protein that binds to exposed single stranded DNA ends, which can achieve numerous results, including but not limited to: (i) helping stabilize the DNA by preventing nucleases from accessing the DNA, and (ii) preventing hairpin formation within the single stranded DNA. Examples of SSB proteins include but are not limited to a eukaryotic SSB protein (e.g., replication protein A (RPA)); bacterial SSB protein; and viral SSB proteins. In some cases, the step of contacting with one or more exonucleases is performed in the presence of an SSB. In some cases, the step of contacting with one or more exonucleases is performed in the absence of an SSB. 
     Barcode 
     In some embodiments, the members of a library are ‘tagged’ by adding a barcode to the SARS-CoV-2 DNAs after exonuclease digestion (and after remaining overhanging DNA ends are repaired/removed). The addition of a barcode can be performed prior to or simultaneously with re-circularizing (ligation). As used herein, term “barcode” is used to mean a stretch of nucleotides having a sequence that uniquely tags members of the library for future identification. For example, in some cases, a barcode cassette (from a pool of random barcode cassettes) can be added and the library sequenced so that it is known which barcode sequence is associated with which particular member, i.e., with which particular deletion (e.g., a lookup table can be created such that each member of a deletion library has a unique barcode). In this way, members of a deletion library can be tracked and accounted for by virtue of presence of the barcode (instead of having to identify the members by determining the location of deletion). Identifying the presence of a short stretch of nucleotides using any convenient assay can easily be accomplished. Use of such barcodes is easier than isolating and sequencing individual members (in order to determine location of deletion) each time the library is used for a given experiment. For example, one can readily determine which library members are present before an experiment (e.g., before introducing library members into cells to assay for viral infectivity), and compare this to which members are present after the experiment by simply assaying for the presence of the barcode before and after, e.g., using high throughput sequencing, a microarray, PCR, qPCR, or any other method that can detect the presence/absence of a barcode sequence. 
     In some cases, a barcode is added as a cassette. A barcode cassette is a stretch of nucleotides that have at least one constant region (a region shared by all members receiving the cassette) and a barcode region (i.e., a barcode sequence—a region unique to the members that receive the barcode such that the barcode uniquely marks the members of the library). For example, a barcode cassette can include (i) a constant region that is a primer site, which site is in common among the barcode cassettes used, and (ii) a barcode sequence that is a unique tag, e.g., can be a stretch of random sequence. In some cases, a barcode cassette includes a barcode region flanked by two constant regions (e.g., two different primer sites). As an illustrative example, in some cases a barcode cassette is a 60 bp cassette that includes a 20 bp random barcode flanked by 20 bp primer binding sites (e.g., see  FIG.  4   ). 
     A barcode sequence can have any convenient length and is preferably long enough so that it uniquely marks the members of a given library of interest. In some cases, the barcode sequence has a length of from 15 bp to 40 bp (e.g., from 15-35 bp, 15-30 bp, 15-25 bp, 17-40 bp, 17-35 bp, 17-30 bp, or 17-25 bp). In some cases, the barcode sequence has a length of 20 bp. Likewise, a barcode cassette can have any convenient length, and this length depends on the length of the barcode sequence plus the length of the constant region(s). In some cases, the barcode cassette has a length of from 40 bp to 100 bp (e.g., from 40-80 bp, 45-100 bp, 45-80 bp, 45-70 bp, 50-100 bp, 50-80 bp, or 50-70 bp). In some cases, the barcode cassette has a length of 60 bp. 
     A barcode or barcode cassette can be added using any convenient method. For example, a linear SARS-CoV-2 DNA can be recircularized by ligation to a 3′-dT-tailed barcode cassette drawn from a pool of random barcode cassettes. The nicked hemiligation product can then be sealed and transformed into a host cell, e.g., a bacterial cell. 
     Generating a Product 
     In some cases, a subject method includes a step of generating (e.g., from a generated library of circularized SARS-CoV-2 deletion DNAs) at least one of: linear double stranded DNA (dsDNA) products (e.g., via cleavage of the circular DNA, via PCR, etc.), linear single stranded DNA (ssDNA) products (e.g., via transcription and reverse transcription), linear single stranded RNA (ssRNA) products (e.g., via transcription), and linear double stranded RNA (dsRNA) products. If so desired, the linear SARS-CoV-2 products can then be introduced into a cell (e.g., mammalian cell). For example, a common technique for RNA viruses is to perform in vitro transcription from a dsDNA template (circular or linear) to make RNA, and then to introduce this RNA into cells (e.g., via electroporation, chemical methods, etc.) to generate viral stocks. 
     Also, within the scope of the disclosure are kits. For example, in some cases a subject kit can include one or more of (in any combination): (i) a population of circular SARS-CoV-2 DNAs as described herein, (ii) a transposon cassette as described herein, (iii) a sequence specific DNA endonuclease as described herein, (iv) one or more guide RNAs for a CRISPR/Cas endonuclease as described herein, (v) a population of barcodes and/or barcode cassettes as described herein, and (vi) a population of host cells, e.g., for propagation of the library, for assaying for viral infectivity, etc., as described herein. In some cases, a subject kit can include instructions for use. Kits typically include a label indicating the intended use of the contents of the kit. The term label includes any writing, or recorded material supplied on or with the kit, or which otherwise accompanies the kit. 
     SARS-CoV-2 Virus 
     The SARS-CoV-2 virus has a single-stranded RNA genome with about 29891 nucleotides, that encode about 9860 amino acids. A SARS-CoV-2 selected RNA genome can be copied and made into a DNA by reverse transcription and formation of a cDNA. A linear SARS-CoV-2 DNA can be circularized by ligation of SARS-CoV-2 DNA ends. 
     A DNA sequence for the SARS-CoV-2 genome, with coding regions, is available as accession number NC_045512.2 from the NCBI website (provided as SEQ ID NO:1 herein). 
                        1 ATTAAAGGTT TATACCTTCC CAGGTAACAA ACCAACCAAC                  41 TTTCGATCTC TTGTAGATCT GTTCTCTAAA CGAACTTTAA                  81 AATCTGTGTG GCTGTCACTC GGCTGCATGC TTAGTGCACT                 121 CACGCAGTAT AATTAATAAC TAATTACTGT CGTTGACAGG                 161 ACACGAGTAA CTCGTCTATC TTCTGCAGGC TGCTTACGGT                 201 TTCGTCCGTG TTGCAGCCGA TCATCAGCAC ATCTAGGTTT                 241 CGTCCGGGTG TGACCGAAAG GTAAGATGGA GAGCCTTGTC                 281 CCTGGTTTCA ACGAGAAAAC ACACGTCCAA CTCAGTTTGC                 321 CTGTTTTACA GGTTCGCGAC GTGCTCGTAC GTGGCTTTGG                 361 AGACTCCGTG GAGGAGGTCT TATCAGAGGC ACGTCAACAT                 401 CTTAAAGATG GCACTTGTGG CTTAGTAGAA GTTGAAAAAG                 441 SCGTTTTGCC TCAACTTGAA CAGCCCTATG TGTTCATCAA                 481 ACGTTCGGAT GCTCGAACTG CACCTCATGG TCATGTTATG                 521 GTTGAGCTGG TAGCAGAACT CGAAGGCATT CAGTACGGTC                 561 GTAGTGGTGA GAGACTTGGT GTCCTTGTCC CTCATGTGGG                 601 CGAAATACCA GTGGCTTACC GCAAGGTTCT TCTTCGTAAG                 641 AACGGTAATA AAGGAGCTGG TGGCCATAGT TACGGCGCCG                 681 ATCTAAAGTC ATTTGACTTA GGCGACGAGC TTGGCACTGA                 721 TCCTTATGAA GATTTTCAAG AAAACTGGAA CACTAAACAT                 761 AGCAGTGGTG TTACCCGTGA ACTCATGCGT GAGCTTAACG                 801 GAGGGGCATA CACTCGCTAT GTCGATAACA ACTTCTGTGG                 841 CCCTGATGGC TACCCTCTTG AGTGCATTAA AGACCTTCTA                 881 GCACGTGCTG GTAAAGCTTC ATGCACTTTG TCCGAACAAC                 921 TGGACTTTAT TGACACTAAG AGGGGTGTAT ACTGCTGCCG                 961 TGAACATGAG CATGAAATTG CTTGGTACAC GGAACGTTCT                1001 GAAAAGAGCT ATGAATTGCA GACACCTTTT GAAATTAAAT                1041 TGGCAAAGAA ATTTGACACC TTCAATGGGG AATGTCCAAA                1081 TTTTGTATTT CCCTTAAATT CCATAATCAA GACTATTCAA                1121 CCAAGGGTTG AAAAGAAAAA GCTTGATGGC TTTATGGGTA                1161 GAATTCGATC TGTCTATCCA GTTGCGTCAC CAAATGAATG                1201 CAACCAAATG TGCCTTTCAA CTCTCATGAA GTGTGATCAT                1241 TGTGGTGAAA CTTCATGGCA GACGGGCGAT TTTGTTAAAG                1281 CCACTTGCGA ATTTTGTGGC ACTGAGAATT TGACTAAAGA                1321 AGGTGCCACT ACTTGTGGTT ACTTACCCCA AAATGCTGTT                1361 GTTAAAATTT ATTGTCCAGC ATGTCACAAT TCAGAAGTAG                1401 GACCTGAGCA TAGTCTTGCC GAATACCATA ATGAATCTGG                1441 CTTGAAAACC ATTCTTCGTA AGGGTGGTCG CACTATTGCC                1481 TTTGGAGGCT GTGTGTTCTC TTATGTTGGT TGCCATAACA                1521 AGTGTGCCTA TTGGGTTCCA CGTGCTAGCG CTAACATAGG                1561 TTGTAACCAT ACAGGTGTTG TTGGAGAAGG TTCCGAAGGT                1601 CTTAATGACA ACCTTCTTGA AATACTCCAA AAAGAGAAAG                1641 TCAACATCAA TATTGTTGGT GACTTTAAAC TTAATGAAGA                1681 GATCGCCATT ATTTTGGCAT CTTTTTCTGC TTCCACAAGT                1721 GCTTTTGTGG AAACTGTGAA AGGTTTGGAT TATAAAGCAT                1761 TCAAACAAAT TGTTGAATCC TGTGGTAATT TTAAAGTTAC                1801 AAAAGGAAAA GCTAAAAAAG GTGCCTGGAA TATTGGTGAA                1841 CAGAAATCAA TACTGAGTCC TCTTTATGCA TTTGCATCAG                1881 AGGCTGCTCG TGTTGTACGA TCAATTTTCT CCCGCACTCT                1921 TGAAACTGCT CAAAATTCTG TGCGTGTTTT ACAGAAGGCC                1961 GCTATAACAA TACTAGATGG AATTTCACAG TATTCACTGA                2001 GAGTCATTGA TGCTATGATG TTCACATCTG ATTTGGCTAC                2041 TAACAATCTA GTTGTAATGG CCTACATTAC AGGTGGTGTT                2081 GTTCAGTTGA CTTCGCAGTG GCTAACTAAC ATCTTTGGCA                2121 CTGTTTATGA AAAACTCAAA CCCGTCCTTG ATTGGCTTGA                2161 AGAGAAGTTT AAGGAAGGTG TAGAGTTTCT TAGAGACGGT                2201 TGGGAAATTG TTAAATTTAT CTCAACCTGT GCTTGTGAAA                2241 TTGTCGGTGG ACAAATTGTC ACCTGTGCAA AGGAAATTAA                2281 GGAGAGTGTT CAGACATTCT TTAAGCTTGT AAATAAATTT                2321 TTGGCTTTGT GTGCTGACTC TATCATTATT GGTGGAGCTA                2361 AACTTAAAGC CTTGAATTTA GGTGAAACAT TTGTCACGCA                2401 CTCAAAGGGA TTGTACAGAA AGTGTGTTAA ATCCAGAGAA                2441 GAAACTGGCC TACTCATGCC TCTAAAAGCC CCAAAAGAAA                2481 TTATCTTCTT AGAGGGAGAA ACACTTCCCA CAGAAGTGTT                2521 AACAGAGGAA GTTGTCTTGA AAACTGGTGA TTTACAACCA                2561 TTAGAACAAC CTACTAGTGA AGCTGTTGAA GCTCCATTGG                2601 TTGGTACACC AGTTTGTATT AACGGGCTTA TGTTGCTCGA                2641 AATCAAAGAC ACAGAAAAGT ACTGTGCCCT TGCACCTAAT                2681 ATGATGGTAA CAAACAATAC CTTCACACTC AAAGGCGGTG                2721 CACCAACAAA GGTTACTTTT GGTGATGACA CTGTGATAGA                2761 AGTGLAAGGT TACAAGAGTG TGAATATCAC TTTTGAACTT                2801 GATGAAAGGA TTGATAAAGT ACTTAATGAG AAGTGCTCTG                2841 CCTATACAGT TGAACTCGGT ACAGAAGTAA ATGAGTTCGC                2881 CTGTGTTGTG GCAGATGCTG TCATAAAAAC TTTGCAACCA                2921 GTATCTGAAT TACTTACACC ACTGGGCATT GATTTAGATG                2961 AGTGGAGTAT GGCTACATAC TACTTATTTG ATGAGTCTGG                3001 TGAGTTTAAA TTGGCTTCAC ATATGTATTG TTCTTTCTAC                3041 CCTCCAGATG AGGATGAAGA AGAAGGTGAT TGTGAAGAAG                3081 AAGAGTTTGA GCCATCAACT CAATATGAGT ATGGTACTGA                3121 AGATGATTAC CAAGGTAAAC CTTTGGAATT TGGTGCCACT                3161 TCTGCTGCTC TTCAACCTGA AGAAGAGCAA GAAGAAGATT                3201 GGTTAGATGA TGATAGTCAA CAAACTGTTG GTCAACAAGA                3241 CGGCAGTGAG GACAATCAGA CAACTACTAT TCAAACAATT                3281 GTTGAGGTTC AACCTCAATT AGAGATGGAA CTTACACCAG                3321 TTGTTCAGAC TATTGAAGTG AATAGTTTTA GTGGTTATTT                3361 AAAACTTACT GACAATGTAT ACATTAAAAA TGCAGACATT                3401 GTGGAAGAAG CTAAAAAGGT AAAACCAACA GTGGTTGTTA                3441 ATGCAGCCAA TGTTTACCTT AAACATGGAG GAGGTGTTGC                3481 AGGAGCCTTA AATAAGGCTA CTAACAATGC CATGCAAGTT                3521 GAATCTGATG ATTACATAGC TACTAATGGA CCACTTAAAG                3561 TGGGTGGTAG TTGTGTTTTA AGCGGACACA ATCTTGCTAA                3601 ACACTGTCTT CATGTTGTCG GCCCAAATGT TAACAAAGGT                3641 GAAGACATTC AACTTCTTAA GAGTGCTTAT GAAAATTTTA                3681 ATCAGCACGA AGTTCTACTT GCACCATTAT TATCAGCTGG                3721 TATTTTTGGT GCTGACCCTA TACATTCTTT AAGAGTTTGT                3761 GTAGATACTG TTCGCACAAA TGTCTACTTA GCTGTCTTTG                3801 ATAAAAATCT CTATGACAAA CTTGTTTCAA GCTTTTTGGA                3841 AATGAAGAGT GAAAAGCAAG TTGAACAAAA GATCGCTGAG                3881 ATTCCTAAAG AGGAAGTTAA GCCATTTATA ACTGAAAGTA                3921 AACCTTCAGT TGAACAGAGA AAACAAGATG ATAAGAAAAT                3961 CAAAGCTTGT GTTGAAGAAG TTACAACAAC TCTGGAAGAA                4001 ACTAAGTTCC TCACAGAAAA CTTGTTACTT TATATTGACA                4041 TTAATGGCAA TCTTCATCCA GATTCTGCCA CTCTTGTTAG                4081 TGACATTGAC ATCACTTTCT TAAAGAAAGA TGCTCCATAT                4121 ATAGTGGGTG ATGTTGTTCA AGAGGGTGTT TTAACTGCTG                4161 TGGTTATACC TACTAAAAAG GCTGGTGGCA CTACTGAAAT                4201 GCTAGCGAAA GCTTTGAGAA AAGTGCCAAC AGACAATTAT                4241 ATAACCACTT ACCCGGGTCA GGGTTTAAAT GGTTACACTG                4281 TAGAGGAGEC AAAGACAGTG CTTAAAAAGT GTAAAAGTGC                4321 CTTTTACATT CTACCATCTA TTATCTCTAA TGAGAAGCAA                4361 GAAATTCTTG GAACTGTTTC TTGGAATTTG CGAGAAATGC                4401 TTGCACATGC AGAAGAAACA CGCAAATTAA TGCCTGTCTG                4441 TGTGGAAACT AAAGCCATAG TTTCAACTAT ACAGCGTAAA                4481 TATAAGGGTA TTAAAATACA AGAGGGTGTG GTTGATTATG                4521 GTGCTAGATT TTACTTTTAC ACCAGTAAAA CAACTGTAGC                4561 GTCACTTATC AACACACTTA ACGATCTAAA TGAAACTCTT                4601 GTTACAATGC CACTTGGCTA TGTAACACAT GGCTTAAATT                4641 TGGAAGAAGC TGCTCGGTAT ATGAGATCTC TCAAAGTGCC                4681 AGCTACAGTT TCTGTTTCTT CACCTGATGC TGTTACAGCG                4721 TATAATGGTT ATCTTACTTC TTCTTCTAAA ACACCTGAAG                4761 AACATTTTAT TGAAACCATC TCACTTGCTG GTTCCTATAA                4801 AGATTGGTCC TATTCTGGAC AATCTACACA ACTAGGTATA                4841 GAATTTCTTA AGAGAGGTGA TAAAAGTGTA TATTACACTA                4881 GTAATCCTAC CACATTCCAC CTAGATGGTG AAGTTATCAC                4921 CTTTGACAAT CTTAAGACAC TTCTTTCTTT GAGAGAAGTG                4961 AGGAGTATTA AGGTGTTTAG AACAGTAGAC AACATTAACC                5001 TCCACACGCA AGTTGTGGAC ATGTCAATGA CATATGGACA                5041 AGAGTTTGGT CCAACTTATT TGGATGGAGC TGATGTTACT                5081 AAAATAAAAC CTCATAATTC AGATGAAGGT AAAACATTTT                5121 ATGTTTTAGC TAATGATGAG ACTCTACGTG TTGAGGCTTT                5161 TGAGTAGTAC CACACAACTG ATCCTAGTTT TCTGGGTAGG                5201 TACATGTCAG CATTAAATCA CACTAAAAAG TGGAAATACC                5241 CACAAGTTAA TGGTTTAACT TCTATTAAAT GGGCAGATAA                5281 CAACTGTTAT CTTGCCACTG CATTGTTAAC ACTCCAACAA                5321 ATAGAGTTGA AGTTTAATCC ACCTGCTCTA CAAGATGCTT                5361 ATTACAGAGC AAGGGCTGGT GAAGCTGCTA ACTTTTGTGC                5401 ACTTATCTTA GCCTACTGTA ATAAGACAGT AGGTGAGTTA                5441 GGTGATGTTA GAGAAACAAT GAGTTACTTG TTTCAACATG                5481 CCAATTTAGA TTCTTGCAAA AGAGTCTTGA ACGTGGTGTG                5521 TAAAACTTGT GGACAACAGC AGACAACCCT TAAGGGTGTA                5561 GAAGCTGTTA TGTACATGGG CACACTTTCT TATGAACAAT                5601 TTAAGAAAGG TGTTCAGATA CCTTGTACGT GTGGTAAACA                5641 AGCTACAAAA TATCTAGTAG AACAGGAGTC ACCTTTTGTT                5681 ATGATGTCAG CACCACCTGC TCAGTATGAA CTTAAGCATG                5721 GTACATTTAC TTGTGCTAGT GAGTACACTG GTAATTACCA                5761 GTGTGGTCAC TATAAACATA TAACTTCTAA AGAAACTTTG                5801 TATTGCATAG ACGGTGCTTT ACTTACAAAG TCCTCAGAAT                5841 ACAAAGGTCC TATTACGGAT GTTTTCTACA AAGAAAACAG                5881 TTACACAACA ACCATAAAAC CAGTTACTTA TAAATTGGAT                5921 GGTGTTGTTT GTACAGAAAT TGACCCTAAG TTGGACAATT                5961 ATTATAAGAA AGACAATTCT TATTTCACAG AGCAACCAAT                6001 TGATCTTGTA CCAAACCAAC CATATCCAAA CGCAAGCTTC                6041 GATAATTTTA AGTTTGTATG TGATAATATC AAATTTGCTG                6081 ATGATTTAAA CCAGTTAACT GGTTATAAGA AACCTGCTTC                6121 AAGAGAGCTT AAAGTTACAT TTTTCCCTGA CTTAAATGGT                6161 GATGTGGTGG CTATTGATTA TAAACACTAG ACACCCTCTT                6201 TTAAGAAAGG AGCTAAATTG TTACATAAAC CTATTGTTTG                6241 GCATGTTAAC AATGCAACTA ATAAAGCCAC GTATAAACCA                6281 AATACCTGGT GTATACGTTG TCTTTGGAGC ACAAAACGAG                6321 TTGAAACATC AAATTCGTTT GATGTACTGA AGTCAGAGGA                6361 CGCGCAGGGA ATGGATAATC TTGCCTGCGA AGATCTAAAA                6401 CCAGTCTCTG AAGAAGTAGT GGAAAATCCT ACCATACAGA                6441 AAGACGTTCT TGAGTGTAAT GTGAAAACTA CCGAAGTTGT                6481 AGGAGALATT ATACTTAAAC CAGCAAATAA TAGTTTAAAA                6521 ATTACAGAAG AGGTTGGCCA CACAGATCTA ATGGCTGCTT                6561 ATGTAGACAA TTCTAGTCTT ACTATTAAGA AACCTAATGA                6601 ATTATCTAGA GTATTAGGTT TGAAAACCCT TGCTACTCAT                6641 GGTTTAGCTG CTGTTAATAG TGTCCCTTGG GATACTATAG                6681 CTAATTATGC TAAGCCTTTT CTTAACAAAG TTGTTAGTAC                6721 AACTACTAAC ATAGTTACAC GGTGTTTAAA CCGTGTTTGT                6761 ACTAATTATA TGCCTTATTT CTTTACTTTA TTGCTACAAT                6801 TGTGTACTTT TACTAGAAGT ACAAATTCTA GAATTAAAGC                6841 ATCTATGCCG ACTACTATAG CAAAGAATAC TGTTAAGAGT                6881 GTCGGTAAAT TTTGTCTAGA GGCTTCATTT AATTATTTGA                6921 AGTCACCTAA TTTTTCTAAA CTGATAAATA TTATAATTTG                6961 GTTTTTACTA TTAAGTGTTT GCCTAGGTTC TTTAATCTAC                7001 TCAACCGCTG CTTTAGGTGT TTTAATGTCT AATTTAGGCA                7041 TGCCTTCTTA CTGTACTGGT TACAGAGAAG GCTATTTGAA                7081 CTCTACTAAT GTCACTATTG CAACCTACTG TACTGGTTCT                7121 ATACCTTGTA GTGTTTGTCT TAGTGGTTTA GATTCTTTAG                7161 ACACCTATCC TTCTTTAGAA ACTATACAAA TTACCATTTC                7201 ATCTTTTAAA TGGGATTTAA CTGCTTTTGG CTTAGTRGCA                7241 GAGTGGTTTT TGGCATATAT TCTTTTCACT AGGTTTTTCT                7281 ATGTACTTGG ATTGGCTGCA ATCATGCAAT TGTTTTTCAG                7321 CTATTTTGCA GTACATTTTA TTAGTAATTC TTGGCTTATG                7361 TGGTTAATAA TTAATCTTGT ACAAATGGCC CCGATTTCAG                7401 CTATGGTTAG AATGTACATC TTCTTTGCAT CATTTTATTA                7441 TGTATGGAAA AGTTATGTGC ATGTTGTAGA CGGTTGTAAT                7481 TCATCAACTT GTATGATGTG TTACAAACGT AATAGAGCAA                7521 CAAGAGTCGA ATGTACAACT ATTGTTAATG GTGTTAGAAG                7561 GTCCTTTTAT GTCTATGCTA ATGGAGGTAA AGGCTTTTGC                7601 AAACTACACA ATTGGAATTG TGTTAATTGT GATACATTCT                7641 GTGCTGGTAG TACATTTATT AGTGATGAAG TTGCGAGAGA                7681 CTTGTCACTA CAGTTTAAAA GACCAATAAA TCCTACTGAC                7721 CAGTCTTCTT ACATCGTTGA TAGTGTTACA GTGAAGAATG                7761 GTTCCATCCA TCTTTACTTT GATAAAGCTG GTCAAAAGAC                7801 TTATGAAAGA CATTCTCTCT CTCATTTTGT TAACTTAGAC                7841 AACCTGAGAG CTAATAACAC TAAAGGTTCA TTGCCTATTA                7881 ATGTTATAGT TTTTGATGGT AAATCAAAAT GTGAAGAATC                7921 ATCTGCAAAA TCAGCGTCTG TTTACTACAG TCAGCTTATG                7961 TGTCAACCTA TACTGTTACT AGATCAGGCA TTAGTGTCTG                8001 ATGTTGGTGA TAGTGCGGAA GTTGCAGTTA AAATGTTTGA                8041 TGCTTACGTT AATACGTTTT CATCAACTTT TAACGTACCA                8081 ATGGAAAAAC TCAAAACACT AGTTGCAACT GCAGAAGCTG                8121 AACTTGCAAA GAATGTGTCC TTAGACAATG TCTTATCTAC                8161 TTTTATTTCA GCAGCTCGGC AAGGGTTTGT TGATTCAGAT                8201 GTAGAAACTA AAGATGTTGT TGAATGTCTT AAATTGTCAC                8241 ATCAATCTGA CATAGAAGTT ACTGGCGATA GTTGTAATAA                8281 CTATATGCTC ACCTATAACA AAGTTGAAAA CATGACACCC                8321 CGTGACCTTG GTGCTTGTAT TGACTGTAGT GCGCGTCATA                8361 TTAATGCGCA GGTAGCAAAA AGTCACAACA TTGCTTTGAT                8401 ATGGAACGTT AAAGATTTCA TGTCATTGTC TGAACAACTA                8441 CGAAAACAAA TACGTAGTGC TGCTAAAAAG AATAACTTAC                8481 CTTTTAAGTT GACATGTGCA ACTACTAGAC AAGTTGTTAA                8321 TGTTGTAACA ACAAAGATAG CACTTAAGGG TGGTAAAATT                8561 GTTAATAATT GGTTGAAGCA GTTAATTAAA GTTACACTTG                8601 TGTTCCTTTT TGTTGCTGCT ATTTTCTATT TAATAACACC                8641 TGTTCATGTC ATGTCTAAAC ATACTGACTT TTCAAGTGAA                8681 ATCATAGGAT ACAAGGCTAT TGATGGTGGT GTCACTCGTG                8721 ACATAGCATC TACAGATACT TGTTTTGCTA ACAAACATGC                8761 TGATTTTGAC ACATGGTTTA GCCAGCGTGG TGGTAGTTAT                8801 ACTAATGACA AAGCTTGCCC ATTGATTGCT GCAGTCATAA                8841 CAAGAGAAGT GGGTTTTGTC GTGCCTGGTT TGCCTGGCAC                8881 GATATTACGC ACAACTAATG GTGACTTTTT GCATTTCTTA                8921 CCTAGAGTTT TTAGTGCAGT TGGTAACATC TGTTACACAC                8961 CATCAAAACT TATAGAGTAC ACTGACTTTG CAACATCAGC                9001 TTGTGTTTTG GCTGCTGAAT GTACAATTTT TAAAGATGCT                9041 TCTGGTAAGC CAGTACCATA TTGTTATGAT ACCAATGTAC                9081 TAGAAGGTTC TGTTGCTTAT GAAAGTTTAC GCCCTGACAC                9121 ACGTTATGTG CTCATGGATG GCTCTATTAT TCAATTTCCT                9161 AACACCTACC TTGAAGGTTC TGTTAGAGTG GTAACAACTT                9201 TTGATTCTGA GTACTGTAGG CACGGCACTT GTGAAAGATC                9241 AGAAGCTGGT GTTTGTGTAT CTACTAGTGG TAGATGGGTA                9281 CTTAACAATG ATTATTACAG ATCTTTACCA GGAGTTTTCT                9321 GTGGTGTAGA TGCTGTAAAT TTACTTACTA ATATGTTTAC                9361 ACCACTAATT CAACCTATTG GTGCTTTGGA CATATCAGCA                9401 TCTATAGTAG CTGGTGGTAT TGTAGCTATC GTAGTAACAT                9441 GCCTTGCCTA CTATTTTATG AGGTTTAGAA GAGCTTTTGG                9481 TGAATACAGT CATGTAGTTG CCTTTAATAC TTTACTATTC                9521 CTTATGTCAT TCACTGTACT CTGTTTAACA CCAGTTTACT                9561 cattcttacc TGGTGTTTAT TCTGTTATTT ACTTGTACTT                9601 GACATTTTAT CTTACTAATG ATGTTTCTTT TTTAGCACAT                9641 ATTCAGTGGA TGGTTATGTT CACACCTTTA GTACCTTTCT                9681 GGATAACAAT TGCTTATATC ATTTGTATTT CCACAAAGCA                9721 TTTCTATTGG TTOTTTAGTA ATTAGGTAAA GAGACGTGTA                9761 GTCTTTAATG GTGTTTCCTT TAGTACTTTT GAAGAAGCTG                9801 CGCTGTGCAC CTTTTTGTTA AATAAAGAAA TGTATCTAAA                9841 GTTGCGTAGT GATGTGCTAT TACCTCTTAC GCAATATAAT                9881 AGATACTTAG CTCTTTATAA TAAGTACAAG TATTTTAGTG                9921 GAGCAATGGA TACAACTAGC TACAGAGAAG CTGCTTGTTG                9961 TCATCTCGCA AAGGCTCTCA ATGACTTCAG TAACTCAGGT               10001 TCTGATGTTC TTTACCAACC ACCACAAACC TCTATCACCT               10041 CAGCTGTTTT GCAGAGTGGT TTTAGAAAAA TGGCATTCCC               10081 ATCTGGTAAA GTTGAGGGTT GTATGGTACA AGTAACTTGT               10121 GGTACAACTA CACTTAACGG TCTTTGGCTT GATGAGGTAG               10161 TTTACTGTCC AAGACATGTG ATCTGCACCT CTGAAGACAT               10201 GCTTAACCCT AATTATGAAG ATTTACTCAT TCGTAAGTCT               10241 AATCATAATT TCTTGGTACA GGCTGGTAAT GTTCAACTCA               10281 GGGTTATTGG ACATTCTATG CAAAATTGTG TACTTAAGCT               10321 TAAGGTTGAT ACAGCCAATC CTAAGACACC TAAGTATAAG               10361 TTTGTTCGCA TTCAACCAGG ACAGACTTTT TCAGTGTTAG               10401 CTTGTTACAA TGGTTCACCA TCTGGTGTTT ACCAATGTGC               10441 TATGAGGCCC AATTTCACTA TTAAGGGTTC ATTCCTTAAT               10481 GGTTCATGTG GTAGTGTTGG TTTTAACATA GATTATGACT               10521 GTGTCTCTTT TTGTTACATG CACCATATGG AATTACCAAC               10561 TGGAGTTCAT GCTGGCACAG ACTTAGAAGG TAACTTTTAT               10601 GGACCTTTTG TTGACAGGCA AACAGCACAA GCAGCTGGTA               10641 CGGACACAAC TATTAGAGTT AATGTTTTAG CTTGGTTGTA               10681 CGCTGCTGTT ATAAATGGAG ACAGGTGGTT TCTCAATCGA               10721 TTTACCACAA CTCTTAATGA CTTTAACCTT GTGGCTATGA               10761 AGTACAATTA TGAACCTCTA ACACAAGACC ATGTTGACAT               10801 ACTAGGACCT CTTTCTGCTC AAACTGGAAT TGCCGTTTTA               10841 GATATGTGTG CTTCATTAAA AGAATTACTG CAAAATGGTA               10881 TGAATGGACG TACCATATTG GGTAGTGCTT TATTAGAAGA               10921 TGAATTTACA CCTTTTGATG TTGTTAGAGA ATGCTCAGGT               10961 GTTACTTTCC AAAGTGCAGT GAAAAGAACA ATCAAGGGTA               11001 CACACCACTG GTTGTTACTC ACAATTTTGA CTTCACTTTT               11041 AGTTTTAGTC CAGAGTACTC AATGGTCTTT GTTCTTTTTT               11081 TTGTATGAAA ATGCCTTTTT ACCTTTTGCT ATGGGTATTA               11121 TTGCTATGTC TGCTTTTGCA ATGATGTTTG TCAAACATAA               11161 GCATGCATTT CTCTGTTTGT TTTTGTTACC TTCTCTTGCC               11201 ACTGTAGCTT ATTTTAATAT GGTCTATATG CCTGCTAGTT               11241 GGGTGATGCG TATTATGACA TGGTTGGATA TGGTTGATAC               11281 TAGTTTGTCT GGTTTTAAGC TAAAAGACTG TGTTATGTAT               11321 GCATCAGCTG TAGTGTTACT AATCCTTATG ACAGCAAGAA               11361 CTGTGTATGA TGATGGTGCT AGGAGAGTGT GGACACTTAT               11401 GAATGTCTTG ACACTCGTTT ATAAAGTTTA TTATGGTAAT               11441 GCTTTAGATC AAGCCATTTC CATGTGGGCT CTTATAATCT               11481 CTGTTACTTC TAACTACTCA GGTGTAGTTA CAACTGTCAT               11521 GTTTTTGGCC AGAGGTATTG TTTTTATGTG TGTTGAGTAT               11561 TGCCCTATTT TCTTCATAAC TGGTAATACA CTTCAGTGTA               11601 TAATGCTAGT TTATTGTTTC TTAGGCTATT TTTGTACTTG               11641 TTACTTTGGC CTCTTTTGTT TACTCAACCG CTACTTTAGA               11681 CTGACTCTTG GTGTTTATGA TTACTTAGTT TCTACACAGG               11721 AGTTTAGATA TATGAATTCA CAGGGACTAG TCCCACCCAA               11761 GAATAGCATA GATGCCTTCA AACTCAACAT TAAATTGTTG               11801 GGTGTTGGTG GCAAACCTTG TATCAAAGTA GCCACTGTAC               11841 AGTCTAAAAT GTCAGATGTA AAGTGCACAT CAGTAGTCTT               11881 ACTCTCAGTT TTGCAACAAC TCAGAGTAGA ATCATCATCT               11921 AAATTGTGGG CTCAATGTGT CCAGTTACAC AATGACATTC               11961 TCTTAGCTAA AGATACTACT GAAGCCTTTG AAAAAATGGT               12001 TTCACTACTT TCTGTTTTGC TTTCCATGCA GGGTGCTGTA               12041 GACATAAACA AGCTTTGTGA AGAAATGCTG GACAACAGGG               12081 CAACCTTACA AGCTATAGCC TCAGAGTTTA GTTCCCTTCC               12121 ATCATATGCA GCTTTTGCTA CTGCTCAAGA AGCTTATGAG               12161 CAGGCTGTTG CTAATGGTGA TTCTGAAGTT GTTCTTAAAA               12201 AGTTGAAGAA GTCTTTGAAT GTGGCTAAAT CTGAATTTGA               12241 CCGTGATGCA GCCATGCAAC GTAAGTTGGA AAAGATGGCT               12281 GATCAAGCTA TGACCCAAAT GTATAAACAG GCTAGATCTG               12321 AGGACAAGAG GGCAAAAGTT ACTAGTGCTA TGCAGACAAT               12361 GCTTTTCACT ATGCTTAGAA AGTTGGATAA TGATGCACTC               12401 AACAACATTA TCAACAATGC AAGAGATGGT TGTGTTCCCT               12441 TGAACATAAT ACCTCTTACA ACAGCAGCCA AACTAATGGT               12481 TGTCATACCA GACTATAACA CATATAAAAA TACGTGTGAT               12521 GGTACAACAT TTACTTATGC ATCAGCATTG TGGGAAATCC               12561 AACAGGTTGT AGATGCAGAT AGTAAAATTG TTCAACTTAG               12601 TGAAATTAGT ATGGACAATT CACCTAATTT AGCATGGCCT               12641 CTTATTGTAA CAGCTTTAAG GGCCAATTCT GCTGTCAAAT               12681 TACAGAATAA TGAGCTTAGT CCTGTTGCAC TACGACAGAT               12721 GTCTTGTGCT GCCGGTACTA CACAAACTGC TTGCACTGAT               12761 GACAATGCGT TAGCTTACTA CAACACAACA AAGGGAGGTA               12801 GGTTTGTACT TGCACTGTTA TCCGATTTAC AGGATTTGAA               12841 ATGGGCTAGA TTCCCTAAGA GTGATGGAAC TGGTACTATC               12881 TATACAGAAC TGGAACCACC TTGTAGGTTT GTTACAGACA               12921 CACCTAAAGG TCCTAAAGTG AAGTATTTAT ACTTTATTAA               12961 AGGATTAAAC AACCTAAATA GAGGTATGGT ACTTGGTAGT               13001 TTAGCTGCCA CAGTACGTCT ACAAGCTGGT AATGCAACAG               13041 AAGTGCCTGC CAATTCAACT GTATTATCTT TCTGTGCTTT               13081 TGCTGTAGAT GCTGCTAAAG CTTACAAAGA TTATCTAGCT               13121 AGTGGGGGAC AACCAATCAC TAATTGTGTT AAGATGTTGT               13161 GTACACACAC TGGTACTGGT CAGGCAATAA CAGTTAGACC               13201 GGAAGCCAAT ATGGATCAAG AATCCTTTGG TGGTGCATCG               13241 TGTTGTCTGT ACTGCCGTTG CCACATAGAT CATCCAAATC               13281 CTAAAGGATT TTGTGACTTA AAAGGTAAGT ATGTACAAAT               13321 ACCTACAACT TGTGCTAATG ACCCTGTGGG TTTTACACTT               13361 AAAAACACAG TCTGTACCGT CTGCGGTATG TGGAAAGGTT               13401 ATGGCTGTAG TTGTGATCAA CTCCGCGAAC CCATGCTTCA               13441 GTCAGCTGAT GCACAATCGT TTTTAAACGG GTTTGCGGTG               13481 TAAGTGCAGC CCGTCTTACA CCGTGCGGCA CAGGCACTAG               13521 TACTGATGTC GTATACAGGG CTTTTGACAT CTACAATGAT               13561 AAAGTAGCTG GTTTTGCTAA ATTCCTAAAA ACTAATTGTT               13601 GTCGCTTCCA AGAAAAGGAC GAAGATGACA ATTTAATTGA               13641 TTCTTACTTT GTAGTTAAGA GACACACTTT CTCTAACTAC               13681 CAACATGAAG AAACAATTTA TAATTTACTT AAGGATTGTC               13721 CAGCTGTTGC TAAACATGAC TTCTTTAAGT TTAGAATAGA               13761 CGGTGACATG GTACCACATA TATCACGTCA ACGTCTTACT               13801 AAATACACAA TGGCAGACCT CGTCTATGCT TTAAGGCATT               13841 TTGATGAAGG TAATTGTGAC ACATTAAAAG AAATACTTGT               13881 CACATACAAT TGTTGTGATG ATGATTATTT CAATAAAAAG               13921 GACTGGTATG ATTTTGTAGA AAACCCAGAT ATATTACGCG               13961 TATACGCCAA CTTAGGTGAA CGTGTACGCC AAGCTTTGTT               14001 AAAAACAGTA CAATTCTGTG ATGCCATGCG AAATGCTGGT               14041 ATTGTTGGTG TACTGACATT AGATAATCAA GATCTCAATG               14081 GTAACTGGTA TGATTTCGGT GATTTCATAC AAACCACGCC               14121 AGGTAGTGGA GTTCCTGTTG TAGATTCTTA TTATTCATTG               14161 TTAATGCCTA TATTAACCTT GACCAGGGCT TTAACTGCAG               14201 AGTCACATGT TGACACTGAC TTAACAAAGC CTTACATTAA               14241 GTGGGATTTG TTAAAATATG ACTTCACGGA AGAGAGGTTA               14281 AAACTCTTTG ACCGTTATTT TAAATATTGG GATCAGACAT               14321 ACCACCCAAA TTGTGTTAAC TGTTTGGATG ACAGATGCAT               14361 TCTGCATTGT GCAAACTTTA ATGTTTTACT CTCTACAGTG               14401 TTCCCACCTA CAAGTTTTGG ACCACTAGTG AGAAAAATAT               14441 TTGTTGATGG TGTTCCATTT GTAGTTTCAA CTGGATACCA               14481 CTTCAGAGAG CTAGGTGTTG TACATAATCA GGATGTAAAC               14521 TTACATAGCT CTAGACTTAG TTTTAAGGAA TTACTTGTGT               14561 ATGCTGCTGA CCCTGCTATG CACGCTGCTT CTGGTAATCT               14601 ATTACTAGAT AAACGCACTA CGTGCTTTTC AGTAGCTGCA               14641 CTTACTAACA ATCTTGCTTT TCAAACTGTC AAACCCGGTA               14681 ATTTTAACAA AGACTTCTAT GACTTTGCTG TGTCTAAGGG               14721 TTTCTTTAAG GAAGGAAGTT CTGTTGAATT AAAACACTTC               14761 TTCTTTGCTC AGGATGGTAA TGCTGCTATC AGCGATTATG               14801 ACTAGTATCG TTATAATCTA CCAACAATGT GTGATATCAG               14841 ACAACTACTA TTTGTAGTTG AAGTTGTTGA TAAGTACTTT               14881 GATTGTTACG ATGGTGGCTG TATTAATGCT AACCAAGTCA               14921 TCGTCAACAA CCTAGACAAA TCAGCTGGTT TTCCATTTAA               14961 TAAATGGGGT AAGGCTAGAC TTTATTATGA TTCAATGAGT               15001 TATGAGGATC AAGATGCACT TTTCGCATAT ACAAAACGTA               15041 ATGTCATCCC TACTATAACT CAAATGAATC TTAAGTATGC               15081 CATTAGTGCA AAGAATAGAG CTCGCACCGT AGLTGGTGTC               15121 TCTATCTGTA GTACTATGAC CAATAGACAG TTTCATCAAA               15161 AATTATTGAA ATCAATAGCC GCCACTAGAG GAGCTACTGT               15201 AGTAATTGGA ACAAGCAAAT TCTATGGTGG TTGGCACAAC               15241 ATGTTAAAAA CTGTTTATAG TGATGTAGAA AACCCTCACC               15281 TTATGGGTTG GGATTATCCT AAATGTGATA GAGCCATGCC               15321 TAACATGCTT AGAATTATGG CCTCACTTGT TCTTGCTCGC               15361 AAACATACAA CGTGTTGTAG CTTGTCACAC CGTTTCTATA               15401 GATTAGCTAA TGAGTGTGCT CAAGTATTGA GTGAAATGGT               15441 CATGTGTGGC GGTTCACTAT ATGTTAAACC AGGTGGAACC               15481 TCATCAGGAG ATGCCACAAC TGCTTATGCT AATAGTGTTT               15521 TTAACATTTG TCAAGCTGTC ACGGCCAATG TTAATGCACT               15561 TTTATCTACT GATGGTAACA AAATTGCCGA TAAGTATGTC               15601 CGCAATTTAC AACACAGACT TTATGAGTGT CTCTATAGAA               15641 ATAGAGATGT TGACACAGAC TTTGTGAATG AGTTTTACGC               15681 ATATTTGCGT AAACATTTCT CAATGATGAT ACTCTCTGAC               15721 GATGCTGTTG TGTGTTTCAA TAGCACTTAT GCATCTCAAG               15761 GTCTAGTGGC TAGCATAAAG AACTTTAAGT CAGTTCTTTA               15801 TTATCAAAAC AATGTTTTTA TGTCTGAAGC AAAATGTTGG               15841 ACTGAGACTG ACCTTACTAA AGGACCTCAT GAATTTTGCT               15881 CTCAACATAC AATGCTAGTT AAACAGGGTG ATGATTATGT               15921 GTACCTTCCT TACCCAGATC CATCAAGAAT CCTAGGGGCC               15961 GGCTGTTTTG TAGATGATAT CGTAAAAACA GATGGTACAC               16001 TTATGATTGA ACGGTTCGTG TCTTTAGCTA TAGATGCTTA               16041 CCCACTTACT AAACATCCTA ATCAGGAGTA TGCTGATGTC               16081 TTTCATTTGT ACTTACAATA CATAAGAAAG CTACATGATG               16121 AGTTAACAGG ACACATGTTA GACATGTATT CTGTTATGCT               16161 TAGTAATGAT AACAGTTCAA GGTATTGGGA ACCTGAGTTT               16201 TATGAGGCTA TGTACACACC GCATACAGTC TTACAGGCTG               16241 TTGGGGCTTG TGTTCTTTGC AATTCACAGA CTTCATTAAG               16281 ATGTGGTGCT TGCATACGTA GACCATTCTT ATGTTGTAAA               16321 TGCTGTTACG ACCATGTCAT ATCAACATCA CATAAATTAG               16361 TCTTGTCTGT TAATCCGTAT GTTTGCAATG CTCCAGGTTG               16401 TGATGTCACA GATGTGACTC AACTTTACTT AGGAGGTATG               16441 AGCTATTATT GTAAATGAGA TAAACCACCC ATTAGTTTTC               16481 CATTGTGTGC TAATGGACAA GTTTTTGGTT TATATAAAAA               16521 TACATGTGTT GGTAGCGATA ATGTTACTGA CTTTAATGCA               16561 ATTGLAACAT GTGACTGGAC AAATGCTGGT GATTACATTT               16601 TAGCTAACAC CTGTACTGAA AGACTCAAGC TTTTTGCAGC               16641 AGAAACGCTC AAAGCTAGTG AGGAGACATT TAAACTGTCT               16681 TATGGTATTG CTACTGTACG TGAAGTGCTG TCTGACAGAG               16721 AATTACATCT TTCATGGGAA GTTGGTAAAC CTAGACCACC               16161 ACTTAACCGA AATTATGTCT TTACTGGTTA TCGTGTAACT               16801 AAAAACAGTA AAGTACAAAT AGGAGAGTAC ACCTTTGAAA               16841 AAGGTGAGTA TGGTGATGCT GTTGTTTACC GAGGTACAAC               16881 AACTTACAAA TTAAATGTTG GTGATTATTT TGTGCTGACA               16921 TCACATACAG TAATGCCATT AAGTGCACCT ACACTAGTGC               16961 CACAAGAGCA CTATGTTAGA ATTACTGGCT TATACCCAAC               17001 ACTCAATATC TCAGATGAGT TTTCTAGCAA TGTTGCAAAT               17041 TATCAAAAGG TTGGTATGCA AAAGTATTCT ACACTCCAGG               17081 GACCACCTGG TACTGGTAAG AGTCATTTTG CTATTGGCCT               17121 AGCTCTCTAC TACCCTTCTG CTCGCATAGT GTATACAGCT               17161 TGCTCTCATG CCGCTGTTGA TGCACTATGT GAGAAGGCAT               17201 TAAAATATTT GCCTATAGAT AAATGTAGTA GAATTATACC               17241 TGCACGTGCT CGTGTAGAGT GTTTTGATAA ATTCAAAGTG               17281 AATTCAACAT TAGAACAGTA TGTCTTTTGT ACTGTAAATG               17321 CATTGCCTGA GACGACAGCA GATATAGTTG TCTTTGATGA               17361 AATTTCAATG GCCACAAATT ATGATTTGAG TGTTGTCAAT               17401 GCCAGATTAC GTGCTAAGCA CTATGTGTAC ATTGGCGACC               17441 CTGCTCAATT ACCTGCACCA CGCACATTGC TAACTAAGGG               17481 CACACTAGAA CCAGAATATT TCAATTCAGT GTGTAGACTT               17521 ATGAAAACTA TAGGTCCAGA CATGTTCCTC GGAACTTGTC               17561 GGCGTTGTCC TGCTGAAATT GTTGACACTG TGAGTGCTTT               17601 GGTTTATGAT AATAAGCTTA AAGCACATAA AGACAAATCA               17641 GCTCAATGCT TTAAAATGTT TTATAAGGGT GTTATCACGC               17681 ATGATGTTTC ATCTGCAATT AACAGGCCAC AAATAGGCGT               17721 GGTAAGAGAA TTCCTTACAC GTAACCCTGC TTGGAGAAAA               17761 GCTGTCTTTA TTTCACCTTA TAATTCACAG AATGCTGTAG               17801 CCTCAAAGAT TTTGGGACTA CCAACTCAAA CTGTTGATTC               17841 ATCACAGGGC TCAGAATATG ACTATGTCAT ATTCACTCAA               17881 ACCACTGAAA CAGCTCACTC TTGTAATGTA AACAGATTTA               17921 ATGTTGCTAT TACCAGAGCA AAAGTAGGCA TACTTTGCAT               17961 AATGTCTGAT AGAGAGCTTT ATGACAAGTT GCAATTTACA               18001 AGTCTTGAAA TTCCACGTAG GAATGTGGCA ACTTTACAAG               18041 CTGAAAATGT AACAGGACTC TTTAAAGATT GTAGTAAGGT               18081 AATCACTGGG TTACATCCTA CACAGGCACC TACACACCTC               18121 AGTGTTGACA CTAAATTCAA AACTGAAGGT TTATGTGTTG               18161 ACATACCTGG CATACCTAAG GACATGACCT ATAGAAGACT               18201 CATCTCTATG ATGGGTTTTA AAATGAATTA TCAAGTTAAT               18241 GGTTACCCTA ACATGTTTAT CACCCGCGAA GAAGCTATAA               18281 GACATGTACG TGCATGGATT GGCTTCGATG TCGAGGGGTG               18321 TCATGCTACT AGAGAAGGTG TTGGTACCAA TTTACCTTTA               18361 CAGCTAGGTT TTTCTACAGG TGTTAACCTA GTTGCTGTAC               18401 CTACAGGTTA TGTTGATACA CCTAATAATA CAGATTTTTC               18441 CAGAGTTAGT GCTAAACCAC CGCCTGGAGA TCAATTTAAA               18481 CACCTCATAC CAGTTATGTA CAAAGGACTT CCTTGGAATG               18521 TAGTGCGTAT AAAGATTGTA CAAATGTTAA GTGACACACT               18561 TAAAAATCTC TGTGAGAGAG TCGTATTTGT CTTATGGGCA               18601 CATGGCTTTG AGTTGACATC TATGAAGTAT TTTGTGAAAA               18641 TAGGACCTGA GCGCACCTGT TGTCTATGTG ATAGACGTGC               18681 CACATGCTTT TCCACTGCTT CAGACACTTA TGCCTGTTGG               18721 CATCATTCTA TTGGATTTGA TTACGTCTAT AATCCGTTTA               18761 TGATTGATGT TCAACAATGG GGTTTTACAG GTAACCTACA               18801 AAGCAACCAT GATCTGTATT GTCAAGTCCA TGGTAATGCA               18841 CATGTAGCTA GTTGTGATGC AATCATGACT AGGTGTCTAG               18881 CTGTCCACGA GTGCTTTGTT AAGCGTGTTG ACTGGACTAT               18921 TGAATATCCT ATAATTGGTG ATGAACTGAA GATTAATGCG               18961 GCTTGTAGAA AGGTTCAACA CATGGTTGTT AAAGCTGCAT               19001 TATTAGCAGA CAAATTCCCA GTTCTTCACG ACATTGGTAA               19041 CCCTAAAGCT ATTAAGTGTG TACCTCAAGC TGATGTAGAA               19081 TGGAAGTTCT ATGATGCACA GCCTTGTAGT GACAAAGCTT               19121 ATAAAATAGA AGAATTATTC TATTCTTATG CCACACATTC               19161 TGACAAATTC AGAGATGGTG TATGCCTATT TTGGAATTGC               19201 AATGTCGATA GATATCCTGC TAATTCCATT GTTTGTAGAT               19241 TTGACACTAG AGTGCTATCT AACCTTAACT TGCCTGGTTG               19281 TGATGGTGGC AGTTTGTATG TAAATAAACA TGCATTCCAC               19321 ACACCAGCTT TTGATAAAAG TGCTTTTGTT AATTTAAAAC               19361 AATTACCATT TTTCTATTAC TCTGACAGTC CATGTGAGTC               19401 TCATGGAAAA CAAGTAGTGT GAGATATAGA TTATGTACCA               19441 CTAAAGTCTG CTACGTGTAT AACACGTTGC AATTTAGGTG               19481 GTGCTGTCTG TAGACATCAT GCTAATGAGT ACAGATTGTA               19521 TCTCGATGCT TATAACATGA TGATCTCAGC TGGCTTTAGC               19561 TTGTGGGTTT ACAAACAATT TGATACTTAT AACCTCTGGA               19601 ACACTTTTAG AAGACTTCAG AGTTTAGAAA ATGTGGCTTT               19641 TAATGTTGTA AATAAGGGAC ACTTTGATGG ACAACAGGGT               19681 GAAGTACCAG TTTCTATCAT TAATAACACT GTTTACACAA               19721 AAGTTGATGG TGTTGATGTA GAATTGTTTG AAAATAAAAC               19761 AACATTACCT GTTAATGTAG CATTTGAGCT TTGGGCTAAG               19801 CGCAACATTA AACCAGTACC AGAGGTGAAA ATACTCAATA               19841 ATTTGGGTGT GGACATTGCT GCTAATACTG TGATCTGGGA               19881 CTACAAAAGA GATGCTCCAG CACATATATC TACTATTGGT               19921 GTTTGTTCTA TGACTGACAT AGCCAAGAAA CCAACTGAAA               19961 CGATTTGTGC ACCACTCACT GTCTTTTTTG ATGGTAGAGT               20001 TGATGGTCAA GTAGACTTAT TTAGAAATGC CCGTAATGGT               20041 GTTCTTATTA CAGAAGGTAG TGTTAAAGGT TTACAACCAT               20081 CTGTAGGTCC CAAACAAGCT AGTCTTAATG GAGTGAGATT               20121 AATTGGAGAA GCCGTAAAAA CACAGTTCAA TTATTATAAG               20161 AAAGTTGATG GTGTTGTCCA ACAATTACCT GAAACTTACT               20201 TTACTCAGAG TAGAAATTTA CAAGAATTTA AACCCAGGAG               20241 TCAAATGGAA ATTGATTTCT TAGAATTAGC TATGGATGAA               20281 TTCATTGAAC GGTATAAATT AGAAGGCTAT GCCTTCGAAC               20321 ATATCGTTTA TGGAGATTTT AGTCATAGTC AGTTAGGTGG               20361 TTTACATCTA CTGATTGGAC TAGCTAAACG TTTTAAGGAA               20401 TCACCTTTTG AATTAGAAGA TTTTATTCCT ATGGACAGTA               20441 CAGTTAAAAA CTATTTCATA ACAGATGCGC AAACAGGTTC               20481 ATCTAAGTGT GTGTGTTCTG TTATTGATTT ATTAGTTGAT               20521 GATTTTGTTG AAATAATAAA ATCCCAAGAT TTATCTGTAG                20561 TTTCTAAGGT TGTCAAAGTG ACTATTGACT ATACAGAAAT               20601 TTCATTTATG CTTTGGTGTA AAGATGGCCA TGTAGAAACA                20641 TTTTACCCAA AATTACAATC TAGTCAAGCG TGGCAACCGG                20681 GTGTTGCTAT GCCTAATCTT TACAAAATGC AAAGAATGCT               20721 ATTAGAAAAG TGTGACCTTC AAAATTATGG TGATAGTGCA                20761 ACATTACCTA AAGGCATAAT GATGAATGTC GCAAAATATA                20801 CTCAACTGTG TCAATATTTA AACACATTAA CATTAGCTGT               20841 ACCCTATAAT ATGAGAGTTA TACATTTTGG TGCTGGTTCT               20881 GATAAAGGAG TTGCACCAGG TACAGCTGTT TTAAGACAGT               20921 GGTTGCCTAC GGGTACGCTG CTTGTCGATT CAGATCTTAA                20961 TGACTTTGTC TCTGATGCAG ATTCAACTTT GATTGGTGAT               21001 TGTGCAACTG TACATACAGC TAATAAATGG GATCTCATTA                21041 TTAGTGATAT GTACGACCCT AAGACTAAAA ATGTTACAAA               21081 AGAAAATGAC TCTAAAGAGG GTTTTTTCAC TTACATTTGT               21121 GGGTTTATAC AACAAAAGCT AGCTCTTGGA GGTTCCGTGG                21161 CTATAAAGAT AACAGAACAT TCTTGGAATG CTGATCTTTA                21201 TAAGCTCATG GGACACTTCG CATGGTGGAC AGCCTTTGTT               21241 ACTAATGTGA ATGCGTCATC ATCTGAAGCA TTTTTAATTG                21281 GATGTAATTA TCTTGGCAAA CCACGCGAAC AAATAGATGG                21321 TTATGTCATG CATGCAAATT ACATATTTTG GAGGAATACA                21361 AATCCAATTC AGTTGTCTTC CTATTCTTTA TTTGACATGA                21401 GTAAATTTCC CCTTAAATTA AGGGGTACTG CTGTTATGTC               21441 TTTAAAAGAA GGTCAAATCA ATGATATGAT TTTATCTCTT               21481 CTTAGTAAAG GTAGACTTAT AATTAGAGAA AACAACAGAG                21521 TTGTTATTTC TAGTGATGTT CTTGTTAACA ACTAAACGAA                21561 CAATGTTTGT TTTTCTTGTT TTATTGCCAC TAGTCTCTAG                21601 TCAGTGTGTT AATCTTACAA CCAGAACTCA ATTAGCCCCT               21641 GCATACACTA ATTCTTTCAC ACGTGGTGTT TATTACCCTG                21681 ACAAAGTTTT CAGATCCTCA GTTTTAGATT CAACTCAGGA                21721 CTTGTTCTTA CCTTTCTTTT CCAATGTTAC TTGGTTCCAT               21761 GCTATACATG TCTCTGGGAC CAATGGTACT AAGAGGTTTG                21801 ATAACCCTGT CCTACCATTT AATGATGGTG TTTATTTTGC               21841 TTCCACTGAG AAGTCTAACA TAATAAGAGG CTGGATTTTT               21881 GGTACTACTT TAGATTCGAA GACCCAGTCC CTACTTATTG                21921 TTAATAACGC TACTAATGTT GTTATTAAAG TCTGTGAATT               21961 TCAATTTTGT AATGATCCAT TTTTGGGTGT TTATTAGCAC               22001 AAAAACAACA AAAGTTGGAT GGAAAGTGAG TTCAGAGTTT               22041 ATTCTAGTGC GAATAATTGC ACTTTTGAAT ATGTCTCTCA                22081 GCCTTTTCTT ATGGACCTTG AAGGAAAACA GGGTAATTTC               22121 AAAAATCTTA GGGAATTTGT GTTTAAGAAT ATTGATGGTT               22161 ATTTTAAAAT ATATTCTAAG CACACGCCTA TTAATTTAGT               22201 GCGTGATCTC CCTCAGGGTT TTTCGGCTTT AGAACCATTG                22241 GTAGATTTGC CAATAGGTAT TAACATCACT AGGTTTCAAA                22281 CTTTACTTGC TTTACATAGA AGTTATTTGA CTCCTGGTGA                22321 TTCTTCTTCA GGTTGGACAG CTGGTGCTGC AGCTTATTAT               22361 GTGGGTTATC TTCAACCTAG GACTTTTCTA TTAAAATATA                22401 ATGAAAATGG AACCATTACA GATGCTGTAG ACTGTGCACT               22441 TGACCCTCTC TCAGAAACAA AGTGTACGTT GAAATCCTTC               22481 ACTGTAGAAA AAGGAATCTA TCAAACTTCT AACTTTAGAG                22521 TCCAACCAAC AGAATCTATT GTTAGATTTC CTAATATTAC               22561 AAACTTGTGC CCTTTTGGTG AAGTTTTTAA CGCCACCAGA                22601 TTTGCATCTG TTTATGCTTG GAACAGGAAG AGAATCAGCA                22641 ACTGTGTTGC TGATTATTCT GTCCTATATA ATTCCGCATC               22681 ATTTTCCACT TTTAAGTGTT ATGGAGTGTC TCCTACTAAA                22721 TTAAATGATC TCTGCTTTAC TAATGTCTAT GCAGATTCAT               22761 TTGTAATTAG AGGTGATGAA GTCAGACAAA TCGCTCCAGG                22801 GCAAACTGGA AAGATTGCTG ATTATAATTA TAAATTACCA                22841 GATGATTTTA CAGGCTGCGT TATAGCTTGG AATTCTAACA                22881 ATCTTGATTC TAAGGTTGGT GGTAATTATA ATTACCTGTA                22921 TAGATTGTTT AGGAAGTCTA ATCTCAAACC TTTTGAGAGA                22961 GATATTTCAA CTGAAATCTA TCAGGCCGGT AGCACACCTT               23001 GTAATGGTGT TGAAGGTTTT AATTGTTACT TTCCTTTACA                23041 ATCATATGGT TTCCAACCCA CTAATGGTGT TGGTTACCAA               23081 CCATACAGAG TAGTAGTACT TTCTTTTGAA CTTCTACATG               23121 CACCAGCAAC TGTTTGTGGA CCTAAAAAGT CTACTAATTT               23161 GGTTAAAAAC AAATGTGTCA ATTTCAACTT CAATGGTTTA               23201 ACAGGCACAG GTGTTCTTAC TGAGTCTAAC AAAAAGTTTC               23241 TGCCTTTCCA ACAATTTGGC AGAGACATTG CTGACACTAC               23281 TGATGCTGTC CGTGATCCAC AGACACTTGA GATTCTTGAC               23321 ATTAGACCAT GTTCTTTTGG TGGTGTCAGT GTTATAACAC               23361 CAGGAACAAA TACTTCTAAC CAGGTTGCTG TTCTTTATCA               23401 GGATGTTAAC TGCACAGAAG TCCCTGTTGC TATTCATGCA               23441 GATCAACTTA CTCCTACTTG GCGTGTTTAT TCTACAGGTT               23481 CTAATGTTTT TCAAACACGT GCAGGCTGTT TAATAGGGGC               23521 TGAACATGTC AACAACTCAT ATGAGTGTGA CATACCCATT               23561 GGTGCAGGTA TATGCGCTAG TTATCAGACT CAGACTAATT               23601 CTCCTCGGCG GGCACGTAGT GTAGCTAGTC AATCCATCAT               23641 TGCCTACACT ATGTCACTTG GTGCAGAAAA TTCAGTTGCT               23681 TACTCTAATA ACTCTATTGC CATACCCACA AATTTTACTA               23721 TTAGTGTTAC CACAGAAATT CTACCAGTGT CTATGACCAA               23761 GACATCAGTA GATTGTACAA TGTACATTTG TGGTGATTCA               23801 ACTGAATGCA GCAATCTTTT GTTGCAATAT GGCAGTTTTT               23841 GTACACAATT AAACCGTGCT TTAACTGGAA TAGCTGTTGA               23881 ACAAGACAAA AACACCLAAG AAGTTTTTGC ACAAGTCAAA               23921 CAAATTTACA AAACACCACC AATTAAAGAT TTTGGTGGTT               23961 TTAATTTTTC ACAAATATTA CCAGATCCAT CAAAACCAAG               24001 CAAGAGGTCA TTTATTGAAG ATCTACTTTT CAACAAAGTG               24041 ACACTTGCAG ATGCTGGCTT CATCAAACAA TATGGTGATT               24081 GCCTTGGTGA TATTGCTGCT AGAGACCTCA TTTGTGCACA               24121 AAAGTTTAAC GGCCTTACTG TTTTGCCACC TTTGCTCACA               24161 GATGAAATGA TTGCTCAATA CACTTCTGCA CTGTTAGCGG               24201 GTACAATCAC TTCTGGTTGG ACCTTTGGTG CAGGTGCTGC               24241 ATTACAAATA CCATTTGCTA TGCAAATGGC TTATAGGTTT               24281 AATGGTATTG GAGTTAGACA GAATGTTCTC TATGAGAACC               24321 AAAAATTGAT TGCCAACCAA TTTAATAGTG CTATTGGCAA               24361 AATTCAAGAC TCACTTTCTT CCACAGCAAG TGCACTTGGA               24401 AAACTTCAAG ATGTGGTCAA CCAAAATGCA CAAGCTTTAA               24441 ACACGCTTGT TAAACAACTT AGCTCCAATT TTGGTGCAAT               24481 TTCAAGTGTT TTAAATGATA TCCTTTCACG TCTTGACAAA               24521 GTTGAGGCTG AAGTGCAAAT TGATAGGTTG ATCACAGGCA               24561 GACTTCAAAG TTTGCAGACA TATGTGACTC AACAATTAAT               24601 TAGAGCTGCA GAAATCAGAG CTTCTGCTAA TCTTGCTGCT               24641 ACTAAAATGT CAGAGTGTGT ACTTGGACAA TCAAAAAGAG               24681 TTGATTTTTG TGGAAAGGGC TATCATCTTA TGTCCTTCCC               24721 TCAGTCAGCA CCTCATGGTG TAGTCTTCTT GCATGTGACT               24761 TATGTCCCTG CACAAGAAAA GAACTTCACA ACTGCTCCTG               24801 CCATTTGTCA TGATGGAAAA GCACACTTTC CTCGTGAAGG               24841 TGTCTTTGTT TCAAATGGCA CACACTGGTT TGTAACACAA               24881 AGGAATTTTT ATGAACCACA AATCATTACT ACAGACAACA               24921 CATTTGTGTC TGGTAACTGT GATGTTGTAA TAGGAATTGT               24961 CAACAACACA GTTTATGATC CTTTGCAACC TGAATTAGAC               25001 TCATTCAAGG AGGAGTTAGA TAAATATTTT AAGAATCATA               25041 CATCACCAGA TGTTGATTTA GGTGACATCT CTGGCATTAA               25081 TGCTTCAGTT GTAAACATTC AAAAAGAAAT TGACCGCCTC               25121 AATGAGGTTG CCAAGAATTT AAATGAATCT CTCATCGATC               25161 TCCAAGAACT TGGAAAGTAT GAGCAGTATA TAAAATGGCC               25201 ATGGTACATT TGGCTAGGTT TTATAGCTGG CTTGATTGCC               25241 ATAGTAATGG TGACAATTAT GCTTTGCTGT ATGACCAGTT               25281 GCTGTAGTTG TCTCAAGGGC TGTTGTTCTT GTGGATCCTG               25321 CTGCAAATTT GATGAAGACG ACTCTGAGCC AGTGCTCAAA               25361 GGAGTCAAAT TACATTACAC ATAAACGAAC TTATGGATTT               25401 GTTTATGAGA ATCTTCACAA TTGGAACTGT AACTTTGAAG               25441 CAAGGTGAAA TCAAGGATGC TACTCCTTCA GATTTTGTTC               25481 GCGCTACTGC AACGATAGCG ATACAAGCCT CACTCCCTTT               25521 CGGATGGCTT ATTGTTGGCG TTGCACTTCT TGCTGTTTTT               25561 CAGAGCGCTT CCAAAATCAT AACCCTCAAA AAGAGATGGC               25601 AACTAGCACT CTCCAAGGGT GTTCACTTTG TTTGCAACTT               25641 GCTGTTGTTG TTTGTAACAG TTTACTCAGA CCTTTTGCTC               25681 GTTGCTGCTG GCCTTGAAGC CCCTTTTCTC TATCTTTATG               25721 CTTTAGTCTA CTTCTTGCAG AGTATAAACT TTGTAAGAAT               25761 AATAATGAGG CTTTGGCTTT GCTGGAAATG CCGTTCCAAA               25801 AACCCATTAG TTTATGATGC CAACTATTTT CTTTGCTGGC               25841 ATACTAATTG TTACGACTAT TGTATACCTT ACAATAGTGT               25881 AACTTCTTCA ATTGTCATTA CTTCAGGTGA TGGCACAACA               25921 AGTCCTATTT CTGAACATGA CTACCAGATT GGTGGTTATA               25961 CTGAAAAATG GGAATCTGGA GTAAAAGACT GTGTTGTATT               26001 ACACAGTTAC TTCACTTCAG ACTATTACCA GCTGTACTCA               26041 ACTCAATTGA GTACAGACAC TGGTGTTGAA CATGTTACCT               26081 TCTTCATCTA CAATAAAATT GTTGATGAGC CTGAAGAACA               26121 TGTCCAAATT CACACAATCG ACGGTTCATC CGSAGTTGTT               26161 AATCCAGTAA TGGAACCAAT TTATGATGAA CCAACGACGA               26201 CTACTAGCGT GCCTTTGTAA GCACAAGCTG ATAAGTACGA               26241 ACTTATGTAG TCATTCGTTT CGGAAGAGAC AGGTACGTTA               26281 ATAGTTAATA GCGTACTTCT TTTTCTTGCT TTCGTGGTAT               26321 TCTTGCTAGT TACACTAGCC ATCCTTACTG CGCTTCGATT               26361 GTGTGCGTAC TGCTGCAATA TTGTTAACGT GAGTCTTGTA               26401 AAACCTTCTT TTTACGTTTA CTCTCGTGTT AAAAATCTGA               26441 ATTCTTCTAG AGTTCCTGAT CTTCTGGTCT AAACGAACTA               26481 AATATTATAT TAGTTTTTCT GTTTGGAACT TTAATTTTAG               26521 CCATGGCAGA TTCCAACGGT ACTATTACCG TTGAAGAGCT               26561 TAAAAAGCTC CTTGAACAAT GGAACCTAGT AATAGGTTTC               26601 CTATTCCTTA CATGGATTTG TCTTCTACAA TTTGCCTATG               26641 CCAACAGGAA TAGGTTTTTG TATATAATTA AGTTAATTTT               26681 CCTCTGGCTG TTATGGCCAG TAACTTTAGC TTCTTTTGTG               26721 CTTGCTGCTG TTTACAGAAT AAATTGGATC ACCGGTGGAA               26761 TTGCTATCGC AATGGCTTGT CTTGTAGGCT TGATGTGGCT               26801 CAGCTACTTC ATTGCTTCTT TCAGACTGTT TGCGCGTACG               26841 CGTTCCATGT GGTCATTCAA TCCAGAAACT AACATTCTTC               26881 TCAACGTGCC ACTCCATGGC ACTATTCTGA CCAGACCGCT               26921 TCTAGAAAGT GAACTCGTAA TCGGAGCTGT GATCCTTCGT               26961 GGACATCTTC GTATTGCTGG ACACCATCTA GGACGCTGTG               27001 ACATCAAGGA CCTGCCTAAA GAAATCACTG TTGCTACATC               27041 ACGAACGCTT TCTTATTACA AATTGGGAGC TTCGCAGCGT               27081 GTAGCAGGTG ACTCAGGTTT TGCTGCATAC AGTCGCTACA               27121 GGATTGGCAA CTATAAATTA AACACAGACC ATTCCAGTAG               27161 CAGTGACAAT ATTGCTTTGC TTGTACAGTA AGTGACAACA               27201 GATGTTTCAT CTCGTTGACT TTCAGGTTAC TATAGCAGAG               27241 ATATTACTAA TTATTATGAG GACTTTTAAA GTTTCCATTT               27281 GGAATCTTGA TTACATCATA AACCTCATAA TAAAAAATTT               27321 ATCTAAGTCA CTAACTGAGA ATAAATATTC TCAATTAGAT               27361 GAAGAGCAAC CAATGGAGAT TGATTAAACG AACATGAAAA               27401 TTATTCTTTT CTTGGCACTG ATAACACTCG CTACTTGTGA               27441 GCTTTATCAC TAGCAAGAGT GTGTTAGAGG TACAACAGTA               27481 CTTTTAAAAG AACCTTGCTC TTCTGGAACA TACGAGGGCA               27521 ATTCACCATT TCATCCTCTA GCTGATAACA AATTTGCACT               27561 GACTTGCTTT AGGACTCAAT TTGCTTTTGC TTGTCCTGAC               27601 GGCGTAAAAC ACGTCTATCA GTTACGTGCC AGATCAGTTT               27641 CACCTAAACT GTTCATGAGA CAAGAGGAAG TTCAAGAACT               27681 TTACTCTCCA ATTTTTCTTA TTGTTGCGGC AATAGTGTTT               27721 ATAACACTTT GCTTCACACT CAAAAGAAAG ACAGAATGAT               2/iol TGAACTTTCA TTAATTGACT TCTATTTGTG CTTTTTAGCC               27801 TTTCTGCTAT TCCTTGTTTT AATTATGCTT ATTATCTTTT               27841 GGTTCTCACT TGAACTGCAA GATCATAATG AAACTTGTCA               27881 CGCCTAAACG AACATGAAAT TTCTTGTTTT CTTAGGAATC               27921 ATCACAACTG TAGCTGCATT TCACCAAGAA TGTAGTTTAC               27961 AGTCATGTAG TCAACATCAA CCATATGTAG TTGATGACCC               28001 GTGTCCTATT CACTTCTATT CTAAATGGTA TATTAGAGTA               28041 GGAGCTAGAA AATCAGCACC TTTAATTGAA TTGTGCGTGG               28081 ATGAGGCTGG TTCTAAATCA CCCATTCAGT ACATCGATAT               28121 CGGTAATTAT ACAGTTTCCT GTTTACCTTT TAAAATTAAT               28161 TGCCAGGAAC CTAAATTGGG TAGTCTTGTA GTGCGTTGTT               28201 CGTTCTATGA AGACTTTTTA GAGTATCATG ACGTTCGTGT               28241 TGTTTTAGAT TTCATCTAAA CGAACAAACT AAAATGTCTG               28281 ATAATGGACC CCAAAATCAG CGAAATGCAC CCCGCATTAC               28321 GTTTGGTGGA CCCTCAGATT CAACTGGCAG TAACCAGAAT               28361 GGAGAACGCA GTGGGGCGCG ATCAAAACAA CGTCGGCCCC               28401 AAGGTTTACC CAATAATACT GCGTCTTGGT TCACCGCTCT               28441 CACTCAACAT GGCAAGGAAG ACCTTAAATT CCCTCGAGGA               28481 CAAGGCGTTC CAATTAACAC CAATAGCAGT CCAGATGACC               28521 AAATTGGCTA CTAGCGAAGA GCTACCAGAC GAATTCGTGG               28561 TGGTGACGGT AAAATGAAAG ATCTCAGTCC AAGATGGTAT               28601 TTCTACTACC TAGGAACTGG GCCAGAAGCT GGACTTCCCT               28641 ATGGTGCTAA CAAAGACGGC ATCATATGGG TTGCAACTGA               28681 GGGAGCCTTG AATACACCAA AAGATCACAT TGGCACCCGC               28721 AATCCTGCTA ACAATGCTGC AATCGTGCTA CAACTTCCTC               28761 AAGGAACAAC ATTGCCAAAA GGCTTCTACG CAGAAGGGAG               28801 CAGAGGCGGC AGTCAAGCCT CTTCTCGTTC CTCATCACGT               28841 AGTCGCAACA GTTCAAGAAA TTCAACTCCA GGCAGCAGTA               28881 GGGGAACTTC TCCTGCTAGA ATGGCTGGCA ATGGCGGTGA               28921 TGCTGCTCTT GCTTTGCTGC TGCTTGACAG ATTGAACCAG               28961 CTTGAGAGCA AAATGTCTGG TAAAGGCCAA CAACAACAAG               29001 GCCAAACTGT CACTAAGAAA TCTGCTGCTG AGGCTTCTAA               29041 GAAGCCTCGG CAAAAACGTA CTGCCACTAA AGCATACAAT               29081 GTAACACAAG CTTTCGGCAG ACGTGGTCCA GAACAAACCC               29121 AAGGAAATTT TGGGGACCAG GAACTAATCA GACAAGGAAC               29161 TGATTAGAAA CATTGGCCGC AAATTGCACA ATTTGCCCCC               29201 AGCGCTTCAG CGTTCTTCGG AATGTCGCGC ATTGGCATGG               29241 AAGTCACACC TTCGGGAACG TGGTTGACCT ACACAGGTGG               29281 CATCAAATTG GATGACAAAG ATCCAAATTT CAAAGATCAA               29321 GTCATTTTGC TGAATAAGCA TATTGACGCA TACAAAACAT               29361 TCCCACCAAC AGAGCCTAAA AAGGACAAAA AGAAGAAGGC               29401 TGATGAAACT CAAGCCTTAC CGCAGAGACA GAAGAAACAG               29441 CAAACTGTGA CTCTTCTTCC TGCTGCAGAT TTGGATGATT               29481 TCTCCAAACA ATTGCAACAA TCCATGAGCA GTGCTGACTC               29521 AACTCAGGCC TAAACTCATG CAGACCACAC AAGGCAGATG               29561 GGCTATATAA ACGTTTTCGC TTTTCCGTTT ACGATATATA               29601 GTCTACTCTT GTGCAGAATG AATTCTCGTA ACTACATAGC               29641 ACAAGTAGAT GTAGTTAACT TTAATCTCAC ATAGCAATCT               29681 TTAATCAGTG TGTAACATTA GGGAGGACTT GAAAGAGCCA               29721 CCACATTTTC ACCGAGGCCA CGCGGAGTAC GATCGAGTGT               29761 ACAGTGAACA ATGCTAGGGA GAGCTGCCTA TATGGAAGAG               29801 CCCTAATGTG TAAAATTAAT TTTAGTAGTG CTATCCCCAT               29841 GTGATTTTAA TAGCTTCTTA GGAGAATGAC AAAAAAAAAA               29881 AAAAAAAAAA AAAAAAAAAA AAA            
The SARS-CoV-2 can have a 5′ untranslated region (5′ UTR; also known as a leader sequence or leader RNA) at positions 1-265 of the SEQ CD NO:1 sequence. Such a 5′ UTR can include the region of an mRNA that is directly upstream from the initiation codon. The 5′ UTR and 3′ UTR may also facilitate packaging of SARS-CoV-2.
 
     Similarly, the SARS-CoV-2 can have a 3′ untranslated region (3′ UTR) at positions 29675-29903. In positive strand RNA viruses, the 3′-UTR can play a role in viral RNA replication because the origin of the minus-strand RNA replication intermediate is at the 3′-end of the genome. 
     The SARS-CoV-2 genome encodes four major structural proteins: the spike (S) protein, nucleocapsid (N) protein, membrane (M) protein, and the envelope (E) protein. Some of these proteins are part of a large polyprotein, which is at positions 266-21555 of the SEQ ID NO:1 sequence, where this open reading frame is referred to as ORFlab polyprotein and has SEQ ID NO:2, shown below. 
                       1 MESLVPGENE KTHVQLSLPV LQVRDVLVRG FGDSVEEVLS                 41 EARQHLKDGT CGLVEVEKGV LPQLEQPYVF IKRSDARTAP                 81 HGHVMVELVA ELEGIQYGRS GETLGVLVPH VGEIPVAYRK                121 VLLRKNGNKG AGGHSYGADL KSFDLGDELG TDPYEDFQEN                161 WNTKHSSGVT RELMRELNGG AYTRYVDNNF CGPDGYPLEC                201 IKDLLARAGK ASCTLSEOLD FIDTKRGVYC CREHEHEIAW                241 YTERSEKSYE LQTPFEIKLA KKFDTFNGEC PNFVFPLNST                281 IKTIQPRVEK KKLDGFMGRI RSVYPVASPN ECNQMCLSTL                321 MKCDHCGETS WQTGDFVKAT CEFCGTENLT KEGATTCGYL                361 PQNAVVKIYC PACHNSEVGP EHSLAEYHNE SGLKTILRKG                401 GRTIAFGGCV FSYVGCHNKC AYWVPRASAN IGCNHTGVVG                441 EGSEGLNDNL LEILQKEKVN INIVGDFKLN EEIAIILASF                481 SASTSAFVET VKGLDYKAFK QIVESCGNFK VTKGKAKKGA                521 WNIGEQKSIL SPLYAFASEA ARVVRSIFSR TLETAQNSVR                561 VLQKAAITIL DGISQYSLRL IDAMMFTSDL ATNNLVVMAY                601 ITGGVVQLTS QWLTNIFGTV YEKLKPVLDW LEEKFKEGVE                641 FLRDGWEIVK FISTCACEIV GGQIVTCAKE IKESVQTFFK                681 LVNKFLALCA DSIIIGGAKL KALNLGETFV THSKGLYRKC                721 VKSREETGLL MPLKAPKEII FLEGETLPTE VLTEEVVLKT                761 GDLQPLEQPT SEAVEAPLVG TPVCINGLML LEIKDTEKYC                801 ALAPNMMVTN NTFTLKGGAP TKVTFGDDTV IEVQGYKSVN                841 ITFELDERID KVLNEKCSAY TVELGTEVNE FACVVADAVI                881 KTLQPVSELL TPLGIDLDEW SMATYYLFDE SGEFKLASHM                921 YCSFYPPDED EEEGDCEEEE FEPSTQYEYG TEDDYQGKPL                961 EFGATSAALQ PEEEQEEDWL DDDSQQTVGQ QDGSEDNQTT               1001 TIQTIVEVQP QLEMELTPVV QTTEVNSFSG YLKLTDNVYI               1041 KNADIVEEAK KVKPTVVVNA ANVYLKHGGG VAGALNKATN               1081 NAMQVESDDY IATNGPLKVG GSCVLSGHNL AKHCLHVVGP               1121 NVNKGEDIQL LKSAYENFNQ HEVLLAPLLS AGIFGADPIH               1161 SLRVCVDTVR TNVYLAVFDK NLYDKLVSSF LEMKSEKQVE               1201 QKIAEIPKEE VKPFITESKP SVEQRKQDDK KIKACVEEVT               1241 TTLEETKFLT ENLLLYIDIN GNLHPDSATL VSDIDITFLK               1281 KDAPYIVGDV VQEGVLTAVV IPTKKAGGTT EMLAKALRKV               1321 PTDNYITTYP GQGLNGYTVE EAKTVLKKCK SAFYILPSII               1361 SNEKQEILGT VSWNLREMLA HAEETRKLMP VCVETKAIVS               1401 TIQRKYKGIK IQEGVVDYGA RFYFYTSKTT VASLINTLND               1441 LNETLVTMPL GYVTHGLNLE EAARYMRSLK VPATVSVSSP               1481 DAVTAYNGYL TSSSKTPEEH FIETISLAGS YKDWSYSGQS               1521 TQLGIEFLKR GDKSVYYTSN PTTFHLDGEV ITFDNLKTLL               1581 SLREVRTIKV FTTVDNINLH TQVVDMSMTY GQQFGPTYLD               1601 GADVTKIKPH NSHEGKTFYV LPNDDTLRVE AFEYYHTTDP               1641 SFLGRYMSAL NHTKKWKYPQ VNGLTSIKWA DNNCYLATAL               1681 LTLQQIELKF NPPALQDAYY RARAGEAANF CALILAYCNK               1721 TVGELGDVRE TMSYLFQHAN LDSCKRVLNV VCKTCGQQQT               1761 TLKGVEAVMY MGTLSYEQFK KGVQIPCTCG KQATKYLVQQ               1801 ESPFVMMSAP PAQYELKHGT FTCASEYTGN YQCGHYKHIT               1841 SKETLYCIDG ALLTKSSEYK GPITDVFYKE NSYTTTIKPV               1881 TYKLDGVVCT EIDPKLDNYY KKDNSYFTEQ PIDLVPNQPY               1921 PNASFDNFKF VCDNIKFADD LNOLTGYKKP ASRELKVTFF               1961 PDLNGDVVAI DYKHYTPSFK KGAKLLHKPI VWHVNNATNK               2001 ATYKPNTWCI RCLWSTKPVE TSNSFDVLKS EDAQGMDNLA               2041 CEDLKPVSEE VVENPTIQKD VLECNVKTTE VVGDIILKPA               2081 NNSLKITEEV GHTDLMAAYV DNSSLTIKKP NELSRVLGLK               2121 TLATHGLAAV NSVPWDTIAN YAKPFLNKVV STTTNTVTRC               2161 LNRVCTNYMP IFFTLLLQLC TFTRSTNSRI KASMPTTIAK               2201 NTVKSVGKFC LEASFNYLKS PNFSKLINII IWFLLLSVCL               2241 GSLIYSTAAL GVLMSNLGMP SYCTGYREGY LNSTNVTIAT               2281 YCTGSIPCSV CLSGLDSLDT YPSLETIQIT ISSFKWDLTA               2321 FGLVAEWFLA YILFTRFFYV LGLAAIMQLF FSYFAVHFIS               2361 NSWLMWLIIN LVOMAPISAM VRMYIFFASF YYVWKSYVHV               2401 VDGCNSSTCM MCYKRNRATR VECTTIVNGV RRSFYVYANG               2441 GKGFCKLHNW NCVNCDTFCA GSTFISDEVA RDLSLQFKRP               2481 INPTDQSSYI VDSVTVKNGS IHLYFDKAGQ KTYERHSLSH               2521 FVNLDNLRAN NTKGSLPINV IVFDGKSKCE ESSAKSASVY               2561 YSOLMCOPIL LLDQALVSDV GDSAEVAVKM FDAYVNTFSS               2601 TFNVPMEKLK TLVATAEAEL AKNVSLDNVL STFISAARQG               2641 FVDSDVETKD VVECLKLSHQ SDIEVTGDSC NNYMLTYNKV               2481 ENMTPRDLGA CIDCSAREIN AQVAKSHNIA LIWNVKDFMS               2521 LSEQLRKQIR SAAKKNNLPF KLTCATTRQV VNVVTTKIAL               2561 KGGKIVNNWL KQLIKVTLVF LFVAAIFYLI TPVHVMSKHT               2601 DFSSEIIGYK AIDGGVTRDI ASTDTCFANK HADFDTWFSQ               2641 RGGSYTNDKA CPLIAAVITR EVGFVVPGLP GTILRTTNGD               2681 FLHFLPRVFS AVGNICYTPS KLIEYTDFAT SACVLAAECT               2721 IFKDASGKPV PYCYDTNVLE GSVAYESLRP DTRYVLMDGS               2761 IIQFPNTYLE GSVRVVTTFD SEYCRHGTCE RSEAGVCVST               2801 SGRWVLNNDY YRSLPGVFCG VDAVNLLTNM FTPLIQPIGA               2841 LDISASIVAG GIVAIVVTCL AYYFMRFRRA FGEYSHVVAF               2881 NTLLFLMSFT VLCLTPVYSF LPGVYSVIYL YLTFYLTNDV               2921 SFLAHIQWMV MFTPLVPFW1 TIAYIICIST KHFYWFFSNY               2961 LKRRVVFNGV SFSTFEEAAL CTFLLNKEMY LKLRSDVLLP               3001 LTQYNRYLAL YNKYKYFSGA MDTTSYREAA CCHLAKALND               3041 FSNSGSDVLY QPPQTSITSA VLQSGFRKMA FPSGKVEGCM               3081 VQVTCGTTTL NGLWLDDVVY CPRHVICTSE DMLNPNYEDL               3121 LIRKSNHNFL VQAGNVQLRV IGHSMQNCVL KLKVDTANPK               3161 TPKYKFVRIQ PGQTFSVLAC YNGSPSGVYQ CAMRPNFTIK               3201 GSFLNGSCGS VGFNIDYDCV SFCYMHHMEL PTGVHAGTDL               3241 EGNFYGPFVD RQTAQAAGTD TTiTVNVLAW LYAAVINGDK               3281 WFLNRFTTTL NDFNLVAMKY NYEPLTQDHV DILGPLSAQT               3321 GIAVLDMCAS LKELLQNGMN GRTILGSALL EDEFTPFDVV               3361 RQCSGVTFQS AVKRTIKGTH HWLLLTILTS LLVLVQSTQW               3401 SLFFFLYENA FLPFAMGIIA MSAFAMMFVK HKHAFLCLFL               3441 LPSLATVAYE NMVYMPASWV MRIMTWLDMV DTSLSGFKLK               3481 DCVMYASAVV LLILMTARTV YDDGARRVWT LMNVLTLVYK               3521 VYYGNALDQA ISMWALIISV TSNYSGVVTT VMFLARGIVE               3561 MCVEYCPIFF ITGNTLQCIM LVYCFLGYFC TCYFGLFCLL               3601 NRYFRLTLGV YDYLVSTQEF RYMNSQGLLP PKNSIDAFKL               3641 NIKLLGVGGK PCIKVATVOS KMSDVKCTSV VLLSVLQQLR               3681 VESSSKLWAQ CVQLHNDILL AKDTTEAFEK MVSLLSVLLS               3721 MQGAVDINKL CEEMLDNRAT LQAIASEFSS LPSYAAFATA               3761 QEAYEQAVAN GDSEVVLKKL KKSLNVAKSE FDRDAAMQRK               3801 LEKMADQAMT QMYKQARSED KRAKVTSAMQ TMLFTMLRKL               3841 DNDALNNIIN NARDGCVPLN IIPLTTAAKL MVVTPDYNTY               3881 KNTCDGTTFT YASALWEIQQ VVDADSKIVQ LSEISMDNSP               3921 NLAWPLIVTA LRANSAVKLQ NNELSPVALR QMSCAAGTTQ               3961 TACTDDNALA YYNTTKGGRF VLALLSDLOD LKWARFPKSD               4001 GTGTIYTELE PPCRFVTDTP KGPKVKYLYF IKGLNNLNRG               4041 MVLGSLAATV RLQAGNATEV PANSTVLSEC AFAVDAAKAY               4081 KDYLASGGQP ITNCVKMLCT HTGTGQAITV TPEANMDQES               4121 FGGASCCLYC RCHTDHPNPK GFCDLKGKYV QTPTTCANDP               4161 VGFTLKNTVC TVCGMWKGYG CSCDQLREPM LQSADAQSFL               4201 NG FAV            
In some cases, the constructs and therapeutic interfering particles described herein can have a deletion of the SARS-CoV-2 genome that includes portions of the genome that encode SEQ ID NO:2. Such deletions can inactivate the SEQ ID NO:2 protein.
 
     An RNA-dependent RNA polymerase is encoded at positions 13442-13468 and 13468-16236 of the SARS-CoV-2 SEQ ID NO:1 nucleic acid. This RNA-dependent RNA polymerase has been assigned NCBI accession number YP_009725307 and has the following sequence (SEQ ID NO:3). 
                      1 SADAQSFLNR VCGVSAARLT PCGTGTSTDV VYRAFDIYND                41 KVAGFAKFLK TNCCRFQEKD EDDNLIDSYF VVKRHTFSNY                81 QHEETIYNLL KDCPAVAKHD FFKFRIDGDM VPHISRQRLT               121 KYTMADLVYA LRHFDEGNCD TLKEILVTYN CCDDDYFNKK               161 DWYDFVENPD ILRVYANLGE RVRQALLKTV QFCDAMRNAG               201 IVGVLTLDNQ DLNGNWYDFG DFTQTTPGSG VPVVDSYYSL               241 LMPILTLTRA LTAESHVDTD LIKPYIKWDL LKYDFTEERL               281 KLFDRYFKYW DQTYHPNCVN CLDDRCILHC ANFNVLFSTV               321 FPPTSFGPLV RKIFVDGVPF VVSTGYHFRE LGVVHNQDVN               361 LHSSRLSFKE LLVYAADPAM HAASGNLLLD KRTTCFSVAA               401 LTNNVAFQTV KPGNFNKDFY DFAVSKGFFK EGSSVELKHF               441 FFAQDGNAAI SDYDYYRYNL PTMCDIRQLL FVVEVVDKYF               481 DCYDGGC1NA NQVIVNNLDK SAGFPFNKWG KARLYYDSMS               521 YEDODALFAY TKRNVIPTIT QMNLKYAISA KNRARTVAGV               561 SICSTMTNRQ FHQKLLKSIA ATRGATVVIG TSKFYGGWHN               601 MLKTVYSDVE NPHLMGWDYP KCDRAMPNML RIMASLVLAR               641 KHTTCCSLSH RFYRLANECA QVLSEMVMCG GSLYVKPGGT               681 SSGDATTAYA NSVFNICQAV TANVNALLST DGNKIADKYV               721 RNLQHRLYEC LYRNRDVDTD FVNEFYAYLR KHFSMMILSD               761 DAVVCFNSTY ASQGLVASIK NFKSVLYYON NVFMSEAKCW               801 TETDLTKGPH EFCSQHTMLV KQGDDYVYLP YPDPSRILGA               841 GCFVDDIVKT DGTLMIERFV SLAIDAYPLT KHPNQEYADV               881 FHLYLQYIRK LHDELTGHML DMYSVMLTND NTSRYWEPEF               921 YEAMYTPHTV LQ            
In some cases, the constructs and therapeutic interfering particles described herein can have a deletion of the SARS-CoV-2 genome that includes portions of the genome that encode SEQ ID NO:3. Such deletions can inactivate the SEQ ID NO:3 protein.
 
     A helicase is encoded at positions 16237-18039 of the SARS-CoV-2 SEQ ID NO:1 nucleic acid. This helicase has been assigned NCBI accession number YP_009725308.1 and has the following sequence (SEQ ID NO:4). 
                      1 AVGACVLCNS QTSLRCGACI RRPFLCCKCC YDHVISTSHK                41 LVLSVNPYVC NAPGCDVTDV TQLYLGGMSY YCKSHKPPIS                81 FPLCANGQVF GLYKNTCVGS DNVTDFNAIA TCDWTNAGDY               121 ILANTCTERL KLFAAETLKA TEETFKLSYG IATVREVLSD               161 RELHLSWEVG KPRPPLNRNY VFTGYRVTKN SKVQIGEYTE               201 EKGDYGDAVV YRGTTTYKLN VGDYFVLTSH TVMPLSAPTL               241 VPQEHYVRIT GLYPTLNISD EFSSNVANYQ KVGMQKYSTL               281 QGPPGTGKSH FAIGLALYYP SARIVYTAGS HAAVDALCEK               321 ALKYLPIDKC SRIIPARARV ECFDKFKVNS TLEQYVFCTV               361 NALPETTADI VVFDEISMAT NYDLSVVNAR LRAKHYVYIG               401 DPAQLPAPRT LLTKGTLEPE YFNSVCRLMK TIGPDMFLGT               441 CRRCPAEIVD TVSALVYDNK LKAHKDKSAQ CFKMFYKGVI               481 THDVSSAINR PQIGVVREFL TRNPAWRKAV FISPYNSQNA               521 VASKILGLPT QTVDSSQGSE YDYVIFTQTT ETAHSCNVNR               561 FNVAITRAKV GILCIMSDRD LYDKLQFTSL EIPRRNVATL               601 Q            
In some cases, the constructs and therapeutic interfering particles described herein can have a deletion of the SARS-CoV-2 genome that includes portions of the genome that encode SEQ ID NOA4 Such deletions can inactivate the SEQ ID NOA4 protein.
 
     The SARS-CoV-2 can have an open reading frame at positions 21563-25384 (gene 5) of the SEQ ID NO:1 sequence that can be referred to as GU280_gp02, where this open reading frame encodes a surface glycoprotein or a spike glycoprotein (SEQ ID NO:5, shown below). 
                        1   MEVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD               41   KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD               81   NPVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV               121   NNATNVVIKV CEFQFCNDPF LGVYYHKNNK SWMESEFRVY               161   SSANNCTFEY VSQPFLMDLE GKQGNFKNLR EFVFKNIDGY               201   FKIYSKHTPI NLVRDLPQGE SALEPLVDLP IGINITRFQT               241   LLALHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN               281   ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV               321   QPTESIVRFP NITNLCPFGE VFNATRFASV YAWNRKRISN               361   CVADYSVLYN SASFSTFKCY GVSPTKLNDL CFTNVYADSF               401   VIRGDEVRQI APGQTGKIAD YNYKLPDDFT GCVIAWNSNN               441   LDSKVGGNYN YLYRLFRKSN LKPFERDIST E1YQAGSTPC               481   NGVEGFNCYF PLQSYGFQPT NGVGYQPYRV VVLSFELLHA               521   PATVCGPKKS TNLVKNKCVN FNFNGLTGTG VLTESNKKIL               561   PFQQFGRDIA DTTDAVRDPQ TLEILDITPC SFGGVSVITP               601   GTNTSNQVAV LYQDVNCTEV PVAIHADQLT PTWRVYSTGS               641   NVFQTRAGCL IGAEHVNNSY ECDIPIGAGI CASYQTQTNS               681   PRRARSVASQ SIIAYTMSLG AENSVAYSNN SIAIPTNFTI               721   SVTTEILPVS MTKTSVDCTM YICGDSTECS NLLLQYGSFC               761   TQLNRALTGI AVEQDKNTQE VFAQVKQIYK TPPIKDFGGF               801   NFSQILPDPS KPSKRSFIED LLFNKVTLAD AGFTKQYGDC               841   LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG               881   TITSGWTFGA GAALQIPFAM QMAYRFNGIG VTQNVLYENQ               921   KLIANQFNSA IGKIQDSLSS TASALGKLQD VVNQNAQALN               961   TLVKQLSSNF GAISSVLND1 LSRLDKVEAE VQIDRLITGR               1001   LQSLQTYVTQ QLIRAAEIRA SANLAATKMS ECVLGQSKRV               1041   DFCGKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA               1081   ICHDGKAHFP REGVFVSNGT HWFVTQKNFY EPQIITTDNT               1121   FVSGNCDVVI GIVNNTVYDP LQPELDSFKE ELDKYFKNHT               1161   SPDVDLGDIS GINASVVNIQ KEIDRLNEVA KNLNESLIDL               1201   QELGKYEQYI KWPWYIWLGF IAGLIAIVMV TIMLCCMTSC               1241   CSCLKGCCSC GSCCKFDEDD SEPVLKGVKL HYT                    
In some cases, the constructs and therapeutic interfering particles described herein can have a deletion of the SARS-CoV-2 genome that includes portions of the genome that encode SEQ ID NO:5. Such deletions can inactivate the SEQ ID NO:5 protein.
 
     The S or spike protein is responsible for facilitating entry of the SARS-CoV-2 into cells. It is composed of a short intracellular tail, a transmembrane anchor, and a large ectodomain that consists of a receptor binding S1 subunit and a membrane-fusing S2 subunit. The spike receptor binding domain can reside at amino acid positions 330-583 of the SEQ ID NO:5 spike protein (shown below as SEQ ID NO:6). 
                    330          P NITNLCPFGE VFNATRFASV YAWNRKRISN               361 CVADYSVLYN SASFSTEKCY GVSPTKLNDL CFTNVYADSE               401 VIRGDEVRQI APGQTGKIAD YNYKLPDDFT GCVIAWNSNN               441 LDSKVGGNYN YLYRLFRKSN LKPFERDIST EIYQAGSTPC               481 NGVEGFNCYF PLQSYGFQPT NGVGYQPYRV VVLSFELLHA               521 PATVCGPKKS TNLVKNKCVN FNFNGLTGTG VLTESNKKFL               561 PFQQFGRDIA DTTDAVRDPQ TLE            
Analysis of this receptor binding motif (RBM) in the spike protein showed that most of the amino acid residues essential for receptor binding were conserved between SARS-CoV and SARS-CoV-2, suggesting that the 2 CoV strains use the same host receptor for cell entry. The entry receptor utilized by SARS-CoV is the angiotensin-converting enzyme 2 (ACE-2).
 
     In some cases, the constructs and therapeutic interfering particles described herein can have a deletion of the SARS-CoV-2 genome that includes portions of the genome that encode SEQ ID NO:6. Such deletions can inactivate the SEQ ID NO:6 protein. 
     The SARS-CoV-2 spike protein membrane-fusing S2 domain can be at positions 662-1270 of the SEQ ID NO:5 spike protein (shown below as SEQ ID NO:7). 
     
       
         
           
               
            
               
                  662             CDIPIGAGI CASYQTQTNS 
               
               
                   
               
               
                  681 PRRARSVASQ SIIAYTMSLG AENSVAYSNN SIAIPTNFTI 
               
               
                   
               
               
                  721 SVTTEILPVS MTKTSVDCTM YICGDSTECS NLLLQYGSFC 
               
               
                   
               
               
                  761 TQLNRALTGI AVEQDKNTQE VFAQVKQIYK TPPIKDFGGF 
               
               
                   
               
               
                  801 NFSQILPDPS KPSKRSFTED LLFNKVTLAD AGFIKQYGDC 
               
               
                   
               
               
                  841 LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG 
               
               
                   
               
               
                  881 TITSGWTFGA GAALQIPFAM QMAYRFNGIG VTQNVLYENQ 
               
               
                   
               
               
                  921 KLIANQFNSA IGKIQDSLSS TASALGKLQD VVNQNAQALN 
               
               
                   
               
               
                  961 TLVKQLSSNF GAISSVLNDI LSRLDKVEAE VQIDRLITGR 
               
               
                   
               
               
                 1001 LQSLQTYVTQ QLIRAAEIRA SANLAATKMS ECVLGQSKRV 
               
               
                   
               
               
                 1041 DFCGKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA 
               
               
                   
               
               
                 1081 ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTDNT 
               
               
                   
               
               
                 1121 FVSGNCDVVI GIVNNTVYDP LQPELDSFKE ELDKYFKNHT 
               
               
                   
               
               
                 1161 SPDVDLGDIS GINASVVNIQ KEIDRLNEVA KNLNESLIDL 
               
               
                   
               
               
                 1201 QELGKYEQYI KWPWYIWLGF IAGLIAIVMV TIMLCCMTSC 
               
               
                   
               
               
                 1241 CSCLKGCCSC GSCCKFDEDD SEPVLKGVKL H 
               
            
           
         
       
     
     The SARS-CoV-2 can have an open reading frame at positions 2720-8554 of the SEQ ID NO:1 sequence that can be referred to as nsp3, which includes transmembrane domain 1 (TM1). This nsp3 open reading frame with transmembrane domain 1 has NCBI accession no. YP_009725299.1 and is shown below as SEQ ID NO:8. 
                        1   APTKVTFGDD TVIEVQGYKS VNITFELDER IDKVLNEKCS               41   AYTVELGTEV NEFACVVADA VIKTLQPVSE LLTPLGIDLD               81   EWSMATYYLF DESGEFKLAS HMYCSFYPPD EDEEEGDCEE               121   EEFEPSTQYE YGTEDDYQGK PLEFGATSAA LQPEEEQEED               161   WLDDDSQQTV GQQDGSEDNQ TTTIQTIVEV QPQLEMELTP               201   VVQTIEVNSF SGYLKLTDNV YIKNADIVEE AKKVKPTVVV               241   NAANVYLKHG GGVAGALNKA TNNAMQVESD DYIATNGPLK               281   VGGSCVLSGH NLAKHCLHVV GPNVNKGEDI QLLKSAYENF               321   NQHEVLLAPL LSAGIFGADP IHSLRVCVDT VRTNVYLAVF               361   DKNLYDKLVS SFLEMKSEKQ VEQKIAEIPK EEVKPFITES               401   KPSVEQRKQD DKKIKACVEE VTTTLEETKF LTENLLLYID               441   INGNLHPDSA TLVSDIDITF LKKDAPYIVG DVVQEGVLTA               481   VVIPTKKAGG TTEMLAKALR KVPTDNYITT YPGQGLNGYT               521   VEEAKTVLKK CKSAFYILPS IISNEKQEIL GTVSWNLREM               561   LAHAEETRKL MPVCVETKAI VSTIQRKYKG IKIQEGVVDY               601   GARFYFYTSK TTVASLINTL NDLNETLVTM PLGYVTHGLN               641   LEEAARYMRS LKVPATVSVS SPDAVTAYNG YLTSSSKTPE               681   EHFIETISLA GSYKDWSYSG QSTQLGIEFL KRGDKSVYYT               721   SNPTTFHLDG EVITFDNLKT LLSLREVRTI KVFTTVDNIN               761   LHTQVVDMSM TYGQQFGPTY LDGADVTKIK PHNSHEGKTF               801   YVLPNDDTLR VEAFEYYHTT DPSFLGRYMS ALNHTKKWKY               841   PQVNGLTSIK WADNNCYLAT ALLTLQQIEL KFNPPALQDA               881   YYRARAGEAA NFCALILAYC NKTVGELGDV RETMSYLFQH               921   ANLDSCKRVL NVVCKTCGQQ QTTLKGVEAV MYMGTLSYEQ               961   FKKGVQIPCT CGKQATKYLV QQESPFVMMS APPAQYELKH               1001   GTFTCASEYT GNYQCGHYKH ITSKETLYCI DGALLTKSSE               1041   YKGPITDVFY KENSYTTTIK PVTYKLDGVV CTEIDPKLDN               1081   YYKKDNSYFT EQPIDLVPNQ PYPNASFDNF KFVCDNIKFA               1121   DDLNQLTGYK KPASRELKVT FFPDLNGDVV AIDYKHYTPS               1161   FKKGAKLLHK PIVWHVNNAT NKATYKPNTW CIRCLWSTKP               1201   VETSNSFDVL KSEDAQGMDN LACEDLKPVS EEVVENPTIQ               1241   KDVLECNVKT TEVVGDITLK PANNSLKITE EVGHTDLMAA               1281   YVDNSSLTIK KPNELSRVLG LKTLATHGLA AVNSVPWDTI               1321   ANYAKPFLNK VVSTTTNIVT RCLNRVCTNY MPYFFTLLLQ               1361   LCTFTRSTNS RIKASMPTTI AKNTVKSVGK FCLEASFNYL               1401   KSPNFSKLIN IIIWFLLLSV CLGSLIYSTA ALGVLMSNLG               1441   MPSYCTGYRE GYLNSTNVTI ATYCTGSIPC SVCLSGLDSL               1481   DTYPSLETIQ ITISSFKWDL TAFGLVAEWF LAYILFTRFF               1521   YVLGLAAIMQ LFFSYFAVHF ISNSWLMWLI INLVQMAPIS               1561   AMVRMYIFFA SFYYVWKSYV HVVDGCNSST CMMCYKRNRA               1601   TRVECTTIVN GVRRSFYVYA NGGKGFCKLH NWNCVNCDTF               1641   CAGSTFISDE VARDLSLQFK RPINPTDQSS YIVDSVTVKN               1681   GSIHLYFDKA GQKTYERHSL SHFVNLDNLR ANNTKGSLPI               1721   NVIVFDGKSK CEESSAKSAS VYYSQLMCQP ILLLDQALVS               1761   DVGDSAEVAV KMFDAYVNTF SSTFNVPMEK LKTLVATAEA               1801   ELAKNVSLDN VLSTFISAAR QGFVDSDVET KDVVECLKLS               1841   HQSDIEVTGD SCNNYMLTYN KVENMTPRDL GACIDCSARH               1881   INAQVAKSHN IALIWNVKDF MSLSEQLRKQ IRSAAKKNNL               1921   PFKLTCATTR QVVNVVTTKI ALKGG            
The nsp3 protein has additional conserved domains including an N-terminal acidic (Ac), a predicted phosphoesterase, a papain-like proteinase, Y-domain, transmembrane domain 1 (TM1), and an adenosine diphosphate-ribose 1″-phosphatase (ADRP).
 
     In some cases, the constructs and therapeutic interfering particles described herein can have a deletion of the SARS-CoV-2 genome that includes portions of the genome that encode SEQ ID NO:8. Such deletions can inactivate the SEQ ID NO:8 protein. 
     The SARS-CoV-2 can have an open reading frame at positions 8555-10054 of the SEQ ID NO:1 sequence that can be referred to as nsp4B_TM, which includes transmembrane domain 2 (TM2). This nsp4B_TM open reading frame with transmembrane domain 2 has NCBI accession no. YP_009725300 and is shown below as SEQ ID NO:9. 
                      1 KIVNNWLKQL IKVTLVFLEV AAIFYLITPV HVMSKHTDFS                41 SEIIGYKAID GGVTRDIAST DTCFANKHAD FDTWFSQRGG                81 SYTNDKACPL IAAVITREVG FVVPGLPGTI LRTTNGDFLH               121 FLPRVFSAVG NICYTPSKLI EYTDFATSAC VLAAECTIFK               161 DASGKPVPYC YDTNVLEGSV AYESLRPDTR YVLMDGSIIQ               201 FPNTYLEGSV RVVTTFDSEY CRHGTCERSE AGVCVSTSGR               241 WVLNNDYYRS LPGVFCGVDA VNLLTNMFTP LIQPIGALDI               281 SASIVAGGIV AIVVTCLAYY FMRFRRAFGE YSHVVAFNTL               321 LFLMSFTVLC LTPVYSFLPG VYSVIYLYLT FYTTNDVSFL               361 AHIQWMVMFT PLVPFWITIA YIICISTKHF YWFFSNYLKR               401 RVVFNGVSFS TFEEAALCTF LLNKEMYLKL RSDVLLPLTQ               441 YNRYLALYNK YKYFSGAMDT TSYREAACCH LAKALNDFSN               481 SGSDVLYQPP QTSITSAVLQ            
In some cases, the constructs and therapeutic interfering particles described herein can have a deletion of the SARS-CoV-2 genome that includes portions of the genome that encode SEQ ID NO:9. Such deletions can inactivate the SEQ ID NO:9 protein.
 
     The SARS-CoV-2 can have an open reading frame at positions 25393-26220 (ORF3a) of the SEQ ID NO:1 sequence that can be referred to as GU280_gp03 (SEQ ID NO:10, shown below). 
     
       
         
           
               
            
               
                   1 MDLEMRIFTI GTVTLKQGEI KDATPSDFVR ATATIPIQAS 
               
               
                   
               
               
                  41 LPFGWLIVGV ALLAVFQSAS KIITLKKRWQ LALSKGVHFV 
               
               
                   
               
               
                  81 CNLLLLFVTV YSHLLLVAAG LEAPFLYLYA LVYFLQSINF 
               
               
                   
               
               
                 121 VRIIMRLWLC WKCRSKNPLL YDANYFLCWH TNCYDYCIPY 
               
               
                   
               
               
                 161 NSVTSSIVIT SGDGTTSPIS EHDYQIGGYT EKWESGVKDC 
               
               
                   
               
               
                 201 VVTHSYFTST YYQLYSTQLS TDTGVEHVTF FIYNKIVDEP 
               
               
                   
               
               
                 241 EEHVQIHTID GSSGVVNPVM EPIYDEPTTT TSVPL 
               
            
           
         
       
     
     In some cases, the constructs and therapeutic interfering particles described herein can have a deletion of the SARS-CoV-2 genome that includes portions of the genome that encode SEQ ID NO:10. Such deletions can inactivate the SEQ ID NO:10 protein. 
     The SARS-CoV-2 can have an open reading frame at positions 26245-26472 (gene E) of the SEQ ID NO:1 sequence that can be referred to as GU280_gp04 (SEQ ID NO: 11, shown below). 
                             1 MYSFVSEETG TLIVNSVLLF LAFVVFLLVT LAILTALRLC                       41 AYCCNIVNVS LVKPSFYVYS RVKNLNSSRV PDLLV            
The SEQ ID NO: 11 protein is a structural protein, for example, an envelope protein. In some cases, the constructs and therapeutic interfering particles described herein can have a deletion of the SARS-CoV-2 genome that includes portions of the genome that encode SEQ ID NO:11. Such deletions can inactivate the SEQ ID NO:11 protein.
 
     The SARS-CoV-2 can have an open reading frame at positions 27202-27191 (M protein gene; ORF5) of the SEQ ID NO:1 sequence that can be referred to as GU280_gp05 (SEQ ID NO:12, shown below). 
                      1 MADSNGTITV EELKKLLEQ WNLVIGFLFLT WICLLQFAYA                41 NRNRFLYIIK LIFLWLLWP VTLACFVLAAV YRINWITGGI               121 A1AMACLVGL MWLSYFIAS FRLFARTRSMW SFNPETNILL               161 NVPLHGTILT RPLLESELV IGAVILRGHLR IAGHHLGRCD               201 IKDLPKEITV ATSRTLSYY KLGASQRVAGD SGFAAYSRYR               241 IGNYKLNTDH SSSSDNIA               121 LLVQ            
The SEQ ID NO:12 protein is a structural protein, for example, a membrane glycoprotein. In some cases, the constructs and therapeutic interfering particles described herein can have a deletion of the SARS-CoV-2 genome that includes portions of the genome that encode SEQ ID NO:12. Such deletions can inactivate the SEQ ID NO:12 protein.
 
     The SARS-CoV-2 can have an open reading frame at positions 27202-27387 (ORF6) of the SEQ ID NO:1 sequence that can be referred to as GU280_gp06 (SEQ ID NO:13, shown below). 
                     1 MFHLVDFQVT IAEILLIIMR  TFKVSIWNLD YIINLIIKNL               41 SKSLTENKYS QLDEEQPMEI D            
In some cases, the constructs and therapeutic interfering particles described herein can have a deletion of the SARS-CoV-2 genome that includes portions of the genome that encode SEQ ID NO:13. Such deletions can inactivate the SEQ ID NO:13 protein.
 
     The SARS-CoV-2 can have an open reading frame at positions 27394-27759 (ORF7a) of the SEQ ID NO:1 sequence that can be referred to as GU280_gp07 (SEQ ID NO:14, shown below). 
                      1 MKIILFLALI TLATCELYHY QECVRGTTVL LKEPCSSGTY                41 EGNSPFHPLA DNKFALTCFS TQFAFACPDG VKHVYQLRAR               121 SVSPKLFIRQ EEVQELYSPI FLIVAAIVFI TLCFTLKRKT               161 E             
In some cases, the constructs and therapeutic interfering particles described herein can have a deletion of the SARS-CoV-2 genome that includes portions of the genome that encode SEQ ID NO:14. Such deletions can inactivate the SEQ ID NO:14 protein.
 
     The SARS-CoV-2 can have an open reading frame at positions 27756-27887 (ORF7b) of the SEQ ID NO:1 sequence that can be referred to as GU280_gp08 (SEQ ID NO:15, shown below). 
                             1 MIELSLIDFY LCFLAFLLFL VLIMLIIFWF SLELQDHNET                       41 CHA            
In some cases, the constructs and therapeutic interfering particles described herein can have a deletion of the SARS-CoV-2 genome that includes portions of the genome that encode SEQ ID NO:15. Such deletions can inactivate the SEQ ID NO:15 protein.
 
     The SARS-CoV-2 can have an open reading frame at positions 27894-28259 (ORF8) of the SEQ ID NO:1 sequence that can be referred to as GU280_gp09 (SEQ ID NO:16, shown below). 
                      1 MKFTVFLGII TTVAAFHQEC SLQSCTQHQP YVVDDPCPIH                41 FYSKWYIRVG ARKSAPLIEL CVDEAGSKSP IQYIDIGNYT               121 VSCLPFTINC QEPKLGSLVV RCSFYEDFLE YHDVRVVLDF               161            
In some cases, the constructs and therapeutic interfering particles described herein can have a deletion of the SARS-CoV-2 genome that includes portions of the genome that encode SEQ ID NO:16. Such deletions can inactivate the SEQ ID NO:16 protein.
 
     The SARS-CoV-2 can have an open reading frame at positions 28274-29533 (gene N; ORF9) of the SEQ ID NO:1 sequence that can be referred to as GU280_gp10 (SEQ ID NO:17, shown below). 
                      1 MSDNGPQNQR NAPRITFGGP SDSTGSNQNG ERSGARSKQR                41 RPQGLPNNTA SWFTALTQHG KEDLKFPRGQ GVPINTNSSP               121 DDQIGYYRRA TRRIRGGDGK MKDLSPRWYF YYLGTGPEAG               161 LPYGANKDGI 1WVATEGALN TPKDHIGTRN PANNAAIVLQ               201 LPQGTTLPKG FYAEGSRGGS QASSRSSSRS RNSSRNSTPG               241 SSRGTSPARM AGNGGDAALA LLLLDRLNQL ESKMSGKGQQ               281 QQGQTVTKKS AAEASKKPRQ KRTATKAYNV TQAFGRRGPE               521 QTQGNFGDQE LIRQGTDYKH WPQIAQFAPS ASAFFGMSRI               561 GMEVTPSGTW LTYTGAIKLD DKDPNFKDQV ILLNKHIDAY               601 KTFPPTEPKK DKKKKADETQ ALPQRQKKQQ TVTLLPAADL               641 DDFSKQLQQS MSSADSTQA            
The SEQ ID NO 17 protein is a structural protein, for example, a nucleocapsid phosphoprotein. In some cases, the constructs and therapeutic interfering particles described herein can have a deletion of the SARS-CoV-2 genome that includes portions of the genome that encode SEQ ID NO:17. Such deletions can inactivate the SEQ ID NO:17 protein.
 
     The SARS-CoV-2 can have an open reading frame at positions 29558-29674 (ORF10) of the SEQ ID NO:1 sequence that can be referred to as GU280_gp11 (SEQ ID NO:19, shown below). 
                            1 MGYINVFAFP FTIYSLLLCR MNSRNYIAQV DWNFNLT            
In some cases, the constructs and therapeutic interfering particles described herein can have a deletion of the SARS-CoV-2 genome that includes portions of the genome that encode SEQ ID NO:19. Such deletions can inactivate the SEQ ID NO:19 protein.
 
     The SARS-CoV-2 can have a stem-loops at positions 29609-29644 and 29629-29657, which is within the encoded GU280_gp11. For example, the SARS-CoV-2 stem-loop at positions 29609-29644 is shown below as SEQ ID NO:20. 
                            29601 TT GTGCAGAATG AATTCTCGTA ACTACATAGC                       29641 ACAA            
For example, the SARS-CoV-2 stem-loop at positions 29629-29657 is shown below as SEQ ID NO:21.
 
                            29629 TA ACTACATAGC ACAAGTAGAT GTAGTTA            
In some cases, the constructs and therapeutic interfering particles described herein can have a deletion of the SARS-CoV-2 genome that includes portions of the genome that encode SEQ ID NO:20 and/or 21. Such deletions can inactivate the SEQ ID NO:20 and/or 21 protein.
 
     The SARS-CoV-2 can have an open reading frame at positions 12686-13024 (nsp9) of the SEQ ID NO:1 sequence that encodes a ssRNA-binding protein with NCBI accession number YP_009725305.1, which has the following sequence (SEQ ID NO:22). 
                             1 NNELSPVALR QMSCAAGTTQ TACTDDNALA YYNTTKGGRF                       41 VLALLSDLQD LKWARFPKSD GTGTIYTELE PPCRFVTDTP                       81 KGPKVKYLYF IKGLNNLNRG MVLGSLAATV RLQ            
In some cases, the constructs and therapeutic interfering particles described herein can have a deletion of the SARS-CoV-2 genome that includes portions of the genome that encode SEQ ID NO:22. Such deletions can inactivate the SEQ ID NO:22 protein.
 
     The constructs and/or therapeutic interfering particles described herein can have portions of the SARS-CoV-2 genome, where the deletions of the genome include at least 100, at least 500, at least 1000, at least 1500, at least 2000, at least 2500, at least 3000, at least 4000, at least 5000, at least 6000, at least 7000, at least 8000, at least 9000, at least 10,000, at least 11,000, at least 12,000, at least 13,000, at least 14,000, at least 15,000, at least 16,000, at least 17,000, at least 18,000, at least 19,000, at least 20,000, at least 21,000, at least 22,000, at least 23,000, at least 24,000, at least 25,000, at least 26,000, at least 27,000, at least 27500, or at least 28000 nucleotides of the SARS-CoV-2 genome. 
     The foregoing sequences are DNA sequences. The SARS-CoV-2 nucleic acids used in the compositions and methods described herein can be DNA or RNA versions of such sequences. The 3′ SARS-CoV-2 nucleic acids can include extended poly A sequences. For example, the extended poly-A sequences can have at least 100 adenine nucleotides to 250 adenine nucleotides. Such extended poly-A sequences can, for example, extend the half-life of the mRNA. 
     In addition, the SARS-CoV-2 genome can naturally have structural variations that are reflections of sequence variations. Hence, the SARS-CoV-2 used in the compositions and methods described herein can, for example, have one or more nucleotide or amino acid differences from the sequences shown as SEQ ID NO:1-35. In some cases, the SARS-CoV-2 used in the compositions and methods described herein can, for example, have two, three, four, five, six, seven, eight, nine, ten, fifteen, twenty, twenty-five, thirty, or more nucleotide or amino acid differences from the sequences shown as SEQ ID NO:1-35. Hence, prior to deletion any of the SARS-CoV-2 nucleic acids used in the methods and compositions described herein can be a DNA or RNA with at least 70%, or at least 75%, or at least 80%, or at least 85%, or at least 90%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or at least 99.5% sequence identity to any of SEQ ID NO:1-35. 
     SARS-CoV-2 Deletion Mutants 
     The present disclosure provides SARS-CoV-2 deletion mutants, for example, interfering, conditionally replicating, SARS-CoV-2 deletion mutants, and related constructs. For example, the present disclosure provides SARS-CoV-2 deletion mutants have one or more of the deletions relative to the wild type SARS-CoV-2 sequence. 
     The present disclosure therefore also provides SARS-CoV-2 deletion mutants. Such SARS-CoV-2 deletion mutants can have one or more deletions, for example at any location in SEQ ID NO:1. Such deletions can truncate or eliminate the sequence of any of the encoded polypeptides. For example, such deletions can truncate or delete the amino acid sequences identified by SEQ ID NOs: 2-19 or 22. For example, such deletions of SARS-CoV-2 nucleic acids can reduce or eliminate the expression of any of the polypeptides encoded by the SARS-CoV-2 nucleic acids. However, in some cases certain regions of the SARS-CoV-2 genome should be retained (e.g., portions of the 5′UTR and/or the 3′UTR) and not be deleted. 
     The present disclosure identifies specific regions of the SARS-CoV-2 genome that should be retained and specific regions of the SARS-CoV-2 genome that can be deleted in order to provide interfering, conditionally replicating, SARS-CoV-2 deletion mutants and related constructs. For example, in order to function as therapeutic interfering particles (TIPs), SARS-CoV-2 deletion mutants can retain cis-acting elements such as, for example, the 5′ UTR and the 3′ UTR. In addition to retaining cis-acting elements, the interfering SARS-CoV-2 particles can, in some cases, retain portions of some of the SARS-CoV-2 proteins, such as the N protein or the spike receptor binding S1 subunit (e.g., SEQ ID NO:6). 
     Interfering SARS-CoV-2 particles that exhibit interference with wild type SARS-CoV-2 may, for example, compete for structural proteins that mediate viral particle assembly, or produce proteins that inhibit assembly of viral particles. For example, interfering SARS-CoV-2 particles that exhibit interference can have a deletion in the membrane-fusing S2 subunit of the spike protein (e.g., SEQ ID NO:7). In some cases, interfering SARS-CoV-2 particles that exhibit interference can have one or more deletions in the RNA-dependent RNA polymerase (e.g., SEQ ID NO:3). In some cases, interfering SARS-CoV-2 particles that exhibit interference can have one or more deletions in the M protein (membrane glycoprotein)(e.g., SEQ ID NO:12). In some cases, interfering SARS-CoV-2 particles that exhibit interference can have one or more deletions in the ssRNA-binding protein (e.g., SEQ ID NO:22). 
     Also described herein are methods of generating a variant interfering, conditionally replicating, SARS-CoV-2 construct. The method generally involves: a) introducing an interfering construct as described above into a first host cell population or a first individual; b) obtaining a biological sample from a second cell population or a second individual to whom the interfering construct has been transmitted from the first host cell population or first individual (either directly or via one or more intervening cells/individuals), wherein the construct present in the second cell population or second individual is a variant of the interfering construct introduced into the first host cell population or first individual, and c) cloning the variant construct from the second host cell population or second individual. 
     The deletion sizes of the SARS-CoV-2 deletion mutants and interfering, conditionally replicating, SARS-CoV-2 construct can vary. For example, the SARS-CoV-2 deletion mutants and interfering, conditionally replicating, SARS-CoV-2 construct can have one or more deletions, where each deletion has at least 1 bp, at least 2 bp, at least 3 bp, at least 4 bp, at least 5 bp, at least 6 bp, at least 7 bp, at least 8 bp, at least 9 bp, at least 10 bp, at least 12 bp, at least 15 bp, at least 20 bp, at least 25 bp, at least 30 bp, at least 40 bp of deletion. 
     In some cases, the deletion size can range, for example, from about 10 bp to about 5000 bp; from about 800 bp to about 2500 bp; from about 900 bp to about 2400 bp; from about 1000 bp to about 2300 bp; from about 1100 bp to about 2200 bp; from about 1200 bp to about 2100 bp; from about 1300 bp to about 2000 bp; from about 1400 bp to about 1900 bp; from about 1500 bp to about 1800 bp; or from about 1600 bp to about 1700 bp. 
     The present disclosure provides an interfering, conditionally replicating SARS-CoV-2 construct. For simplicity, the interfering, conditionally replicating SARS-CoV-2 constructs are referred to as SARS-CoV-2 “interfering constructs” or “TIPs.” A subject interfering construct can be conditionally replicating. For example, a subject interfering construct, when present in a mammalian host, cannot, in the absence of a wild-type SARS-CoV-2, form infectious particles containing copies of itself. A subject interfering construct can be packaged into an infectious particle in vitro in a laboratory (e.g., in an in vitro cell culture) when the appropriate polypeptides required for packaging are provided. The infectious particle can deliver the interfering construct into a host cell, for example, an in vivo host cell. Once inside an in vivo host cell (a host cell in a mammalian subject), the interfering construct can integrate into the genome of the host cell or the interfering construct can remain cytoplasmic. The interfering construct can in some cases replicate in the in vivo host cell only in the presence of a wildtype SARS-CoV-2. When an in vivo host cell with an interfering construct is infected by a wildtype SARS-CoV-2, the interfering construct can replicate (e.g., is transcribed and packaged). In some cases, the interfering construct can replicate substantially more efficiently than the wildtype SARS-CoV-2, thereby outcompeting the wildtype SARS-CoV-2. As a result, the SARS-CoV-2 viral load is substantially reduced in the individual. 
     An interfering construct can be an RNA construct, or a DNA construct (e.g., a DNA copy of an RNA). 
     In some cases, an interfering construct does not include any heterologous nucleotide sequences not derived from SARS-CoV-2. “Heterologous” refers to a nucleotide sequence that is not normally present in a wild-type SARS-CoV-2 in nature. For example, in some cases an interfering construct may not include any heterologous nucleotide sequences that encode a gene product. Gene products include polypeptides and RNA. 
     In some cases an interfering construct can include heterologous nucleotide sequences not derived from SARS-CoV-2. For example, an interfering construct can include one or more barcode sequences, one or more segments encoding a detectable marker, one or more promoters, one or more RNA transcription or translation initiation sites, one or more termination signals, or a combination thereof. The constructs can also include an origin of replication. 
     An interfering construct can include SARS-CoV-2 cis-acting elements; and can include an alteration in the SARS-CoV-2 nucleotide sequence such that alteration renders one or more encoded SARS-CoV-2 trans-acting polypeptides non-functional. By “non-functional” is meant that the SARS-CoV-2 trans-activating polypeptide does not carry out its normal function, for example, due to truncation of or internal deletion within the encoded polypeptide, or due to lack of the polypeptide altogether. “Alteration” of a SARS-CoV-2 nucleotide sequence includes deletion of one or more nucleotides and/or substitution of one or more nucleotides. 
     In some cases, an interfering construct, when present in a host cell (e.g., in a host cell in an individual) that is infected with a wildtype SARS-CoV-2, replicates at a rate that is at least about 10%, at least about 20%, at least about 30%, at least about 40/6, at least about 50%, at least about 75%, at least about 2-fold, at least about 2.5-fold, at least about 5-fold, at least about 10-fold, or greater than 10-fold, higher than the rate of replication of the wildtype SARS-CoV-2 in a host cell of the same type that does not comprise a subject interfering construct. 
     In some cases, an interfering construct, when present in a host cell (e.g., in a host cell in an individual) that is infected with a wildtype SARS-CoV-2, reduces the amount of wildtype SARS-CoV-2 transcripts in the cell by at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, or at least about 90%, compared to the amount of wildtype SARS-CoV-2 transcripts in a host cell that is infected with wildtype SARS-CoV-2, but does not comprise a subject interfering construct. 
     In some cases, an interfering construct, when present in a host cell (e.g., in a host cell in an individual) that is infected with a wildtype SARS-CoV-2, results in production of interfering construct-encoded RNA such that the ratio (by weight, e.g., μg:μg) of interfering construct-encoded RNA to wild-type SARS-CoV-2-encoded RNA in the cytoplasm of the host cell is greater than 1. In some cases, an interfering construct, when present in a host cell (e.g., in a host cell in an individual) that is infected with a wildtype SARS-CoV-2, results in production of interfering construct-encoded RNA such that the ratio (by weight, e.g., μg:μg) of interfering construct-encoded RNA to wild-type SARS-CoV-2-encoded RNA in the cytoplasm of the host cell is from at least about 1.5:1 to at least about 102:1 or greater than 102:1, e.g., from about 1.5:1 to about 2:1, from about 2:1 to about 5:1, from about 5:1 to about 10:1, from about 10:1 to about 25:1, from about 25:1 to about 50:1, from about 50:1 to about 75:1, from about 75:1 to about 100:1, or greater than 100:1. 
     In some cases, an interfering construct, when present in a host cell (e.g., in a host cell in an individual) that is infected with a wildtype SARS-CoV-2, results in production of interfering construct-encoded RNA such that the ratio (e.g., molar ratio) of interfering construct-encoded RNA to wild-type SARS-CoV-2-encoded RNA in the cytoplasm of the host cell is greater than 1. In some cases, an interfering construct, when present in a host cell (e.g., in a host cell in an individual) that is infected with a wildtype SARS-CoV-2, results in production of interfering construct-encoded RNA such that the ratio (e.g., molar ratio) of interfering construct-encoded RNA to wild-type SARS-CoV-2-encoded RNA in the cytoplasm of the host cell is from at least about 1.5:1 to at least about 102:1 or greater than 102:1, e.g., from about 1.5:1 to about 2:1, from about 2:1 to about 5:1, from about 5:1 to about 10:1, from about 10:1 to about 25:1, from about 25:1 to about 50:1, from about 50:1 to about 75:1, from about 75:1 to about 100:1, or greater than 100:1. 
     A subject interfering construct can exhibit a basic reproductive ratio (R 0 ) (also referred to as the “basic reproductive number”) that is greater than 1. R 0  is the number of cases one case generates on average over the course of its infectious period. When R 0  is &gt;1, the infection will be able to spread in a population (of cells or individuals). Thus, a subject interfering construct has the capacity to spread from one cell to another or from one individual to another in a population. In some cases, the subject interfering construct (or a subject interfering particle) has an R 0  from about 2 to about 5, from about 5 to about 7, from about 7 to about 10, from about 10 to about 15, or greater than 15. 
     Any convenient method can be used to measure the ratio of interfering construct-encoded RNA to wild-type SARS-CoV-2-encoded RNA in the cytoplasm of the host cell. Suitable methods can include, for example, measuring transcript number directly via qRT-PCR (e.g., single-cell qRT-PCR) of both an interfering construct-encoded RNA and a wild-type SARS-CoV-2-encoded RNA; measuring levels of a protein encoded by the interfering construct-encoded RNA and the wild-type SARS-CoV-2-encoded RNA (e.g., via western blot, ELISA, mass spectrometry, etc.); and measuring levels of a detectable label associated with the interfering construct-encoded RNA and the wild-type SARS-CoV-2-encoded RNA (e.g., fluorescence of a fluorescent protein that is encoded by the RNA and is fused to a protein that is translated from the RNA). Such measurements can be performed, for example, after co-transfection, using any convenient cell type. 
     In some embodiments, the interfering construct-encoded RNA is packaged. In some embodiments, the interfering construct-encoded RNA is unpackaged. In some cases, the interfering construct-encoded RNA includes both packaged and unpackaged RNA. 
     Treatment 
     The present disclosure provides a method of reducing SARS-CoV-2 viral load in an individual. The method generally involves administering to the individual an effective amount of a subject interfering nucleic acid construct, a pharmaceutical formulation comprising a subject interfering nucleic acid construct, a subject interfering particle, or a pharmaceutical formulation comprising a subject interfering particle. 
     In some cases, a subject method involves administering to an individual in need thereof an effective amount of a SARS-CoV-2 interfering particle, or a pharmaceutical formulation comprising a subject interfering particle. In some cases, an effective amount of a subject interfering particle is an amount that, when administered to an individual in one or more doses, in monotherapy or in combination therapy, is effective to reduce SARS-CoV-2 virus load in the individual by at least about 10%, at least about 20%, at least about 25%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, or greater than 80%, compared to the SARS-CoV-2 virus load in the individual in the absence of treatment with the interfering particle. 
     In some cases, a subject method involves administering to an individual in need thereof an effective amount of a subject interfering particle. In some embodiments, an “effective amount” of a subject interfering particle is an amount that, when administered to an individual in one or more doses, in monotherapy or in combination therapy, is effective to reduce symptoms of SARS-CoV-2 in the individual by at least about 20%, at least about 25%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 2-fold, at least about 2.5-fold, at least about 3-fold, at least about 5-fold, at least about 10-fold, or greater than 10-fold, compared to the individual in the absence of treatment with the interfering particle. 
     Any of a variety of methods can be used to determine whether a treatment method is effective. For example, determining whether the methods are effective can include evaluating whether the wild type SARS-CoV-2 viral load is reduced, determining whether the infected subject is producing antibodies against SARS-CoV-2, determining whether the infected subject is breathing without assistance, and/or determining whether the temperature of the infected subject is returning to normal. Measuring viral load can be by measuring the amount of SARS-CoV-2 in a biological sample, for example, using a polymerase chain reaction (PCR) with primers specific SARS-CoV-2 polynucleotide sequence; detecting and/or measuring a polypeptide encoded by SARS-CoV-2; using an immunological assay such as an enzyme-linked immunosorbent assay (ELISA) with an antibody specific for a SARS-CoV-2 polypeptide; or a combination thereof. 
     Formulations, Dosages, and Routes of Administration 
     Prior to introduction into a host, an interfering construct or an interfering particle can be formulated into various compositions for use in therapeutic and prophylactic treatment methods. In particular, the interfering construct or interfering particle can be made into a pharmaceutical composition by combination with appropriate pharmaceutically acceptable carriers or diluents and can be formulated to be appropriate for either human or veterinary applications. For simplicity, a subject interfering construct and a subject interfering particle are collectively referred to below as “active agent” or “active ingredient.” 
     Thus, a composition for use in a subject treatment method can comprise a SARS-CoV-2 interfering construct or SARS-CoV-2 interfering particle in combination with a pharmaceutically acceptable carrier. A variety of pharmaceutically acceptable carriers can be used that are suitable for administration. The choice of carrier will be determined, in part, by the particular vector, as well as by the particular method used to administer the composition. One skilled in the art will also appreciate that various routes of administering a composition are available, and, although more than one route can be used for administration, a particular route can provide a more immediate and more effective reaction than another route. Accordingly, there are a wide variety of suitable formulations of a subject interfering construct composition or a subject interfering particle composition. 
     A composition a subject interfering construct or subject interfering particle, alone or in combination with other antiviral compounds, can be made into a formulation suitable for parenteral administration. Such a formulation can include aqueous and nonaqueous, isotonic sterile injection solutions, which can contain antioxidants, buffers, bacteriostats, and solutes that render the formulation isotonic with the blood of the intended recipient, and aqueous and nonaqueous sterile suspensions that can include suspending agents, solubilizers, thickening agents, stabilizers, and preservatives. The formulations can be provided in unit dose or multidose sealed containers, such as ampules and vials, and can be stored in a freeze-dried (lyophilized) condition requiring only the addition of the sterile liquid carrier, for example, water, for injections, immediately prior to use. Injectable solutions and suspensions can be prepared from sterile powders, granules, and tablets, as described herein. 
     An aerosol formulation suitable for administration via inhalation also can be made. The aerosol formulation can be placed into a pressurized acceptable propellant, such as dichlorodifluoromethane, propane, nitrogen, and the like. 
     A formulation suitable for oral administration can be a liquid solution, such as an effective amount of a subject interfering construct or a subject interfering particle dissolved in diluents, such as water, saline, or fruit juice; capsules, sachets or tablets, each containing a predetermined amount of the active agent (a subject interfering construct or subject interfering particle), as solid or granules; solutions or suspensions in an aqueous liquid; and oil-in-water emulsions or water-in-oil emulsions. Tablet forms can include one or more of lactose, mannitol, corn starch, potato starch, microcrystalline cellulose, acacia, gelatin, colloidal silicon dioxide, croscarmellose sodium, talc, magnesium stearate, stearic acid, and other excipients, colorants, diluents, buffering agents, moistening agents, preservatives, flavoring agents, and pharmacologically compatible carriers. 
     Similarly, a formulation suitable for oral administration can include lozenge forms, that can comprise the active ingredient in a flavor, usually sucrose and acacia or tragacanth; pastilles comprising the active ingredient (a subject interfering construct or subject interfering particle) in an inert base, such as gelatin and glycerin, or sucrose and acacia; and mouthwashes comprising the active agent in a suitable liquid carrier; as well as creams, emulsions, gels, and the like containing, in addition to the active agent, such carriers as are available in the art. 
     A formulation for rectal administration can be presented as a suppository with a suitable base comprising, for example, cocoa butter or a salicylate. A formulation suitable for vaginal administration can be presented as a pessary, tampon, cream, gel, paste, foam, or spray formula containing, in addition to the active ingredient, such carriers as are known in the art to be appropriate. Similarly, the active ingredient can be combined with a lubricant as a coating on a condom. 
     The dose administered to an animal, particularly a human, in the context of the present invention should be sufficient to effect a therapeutic response in the infected individual over a reasonable time frame. The dose will be determined by the potency of the particular interfering construct or interfering particle employed for treatment, the severity of the disease state, as well as the body weight and age of the infected individual. The size of the dose also will be determined by the existence of any adverse side effects that can accompany the use of the particular interfering construct or interfering particle employed. It is always desirable, whenever possible, to keep adverse side effects to a minimum. 
     The dosage can be in unit dosage form, such as a tablet, a capsule, a unit volume of a liquid formulation, etc. The term “unit dosage form” as used herein refers to physically discrete units suitable as unitary dosages for human and animal subjects, each unit containing a predetermined quantity of an interfering construct or an interfering particle, alone or in combination with other antiviral agents, calculated in an amount sufficient to produce the desired effect in association with a pharmaceutically acceptable diluent, carrier, or vehicle. The specifications for the unit dosage forms of the present disclosure depend on the particular construct or particle employed and the effect to be achieved, as well as the pharmacodynamics associated with each construct or particle in the host. The dose administered can be an “antiviral effective amount” or an amount necessary to achieve an “effective level” in the individual patient. 
     Generally, an amount of a subject interfering construct or a subject interfering particle sufficient to achieve a tissue concentration of the administered construct or particle of from about 50 mg/kg to about 300 mg/kg of body weight per day can be administered, e.g., an amount of from about 100 mg/kg to about 200 mg/kg of body weight per day. In certain applications, e.g., topical, ocular or vaginal applications, multiple daily doses can be administered. Moreover, the number of doses will vary depending on the means of delivery and the particular interfering construct or interfering particle administered. 
     In some embodiments, a subject interfering construct or interfering particle (or composition comprising same) is administered in combination therapy with one or more additional therapeutic agents. Suitable additional therapeutic agents include agents that inhibit one or more functions of SARS-CoV-2 virus, agents that treat or ameliorate a symptom of SARS-CoV-2 virus infection; agents that treat an infection that may occur secondary to SARS-CoV-2 virus infection; and the like. 
     Kits, Containers, Devices, Delivery Systems 
     Kits are described herein that include unit doses of the active agent (SARS-CoV-2 interfering particles or SARS-CoV-2 deletion nucleic acids). The unit doses can be formulated for nasal, oral, transdermal, or injectable (e.g., for intramuscular, intravenous, or subcutaneous injection) administration. In such kits, in addition to the containers containing the unit doses will be an informational package insert describing the use and attendant benefits of the drugs in treating SARS-CoV-2 infection. Suitable active agents (a subject interfering construct or a subject interfering particle) and unit doses are those described herein above. 
     In many embodiments, a subject kit will further include instructions for practicing the subject methods or means for obtaining the same (e.g., a website URL directing the user to a webpage which provides the instructions), where these instructions are typically printed on a substrate, which substrate may be one or more of: a package insert, the packaging, formulation containers, and the like. 
     In some embodiments, a subject kit includes one or more components or features that increase patient compliance, e.g., a component or system to aid the patient in remembering to take the active agent at the appropriate time or interval. Such components include, but are not limited to, a calendaring system to aid the patient in remembering to take the active agent at the appropriate time or interval. 
     The present invention provides a delivery system comprising an active agent. In some embodiments, the delivery system is a delivery system that provides for injection of a formulation comprising an active agent subcutaneously, intravenously, or intramuscularly. In other embodiments, the delivery system is a vaginal or rectal delivery system. 
     In some embodiments, an active agent is packaged for oral administration. The present invention provides a packaging unit comprising daily dosage units of an active agent. For example, the packaging unit is in some embodiments a conventional blister pack or any other form that includes tablets, pills, and the like. The blister pack will contain the appropriate number of unit dosage forms, in a sealed blister pack with a cardboard, paperboard, foil, or plastic backing, and enclosed in a suitable cover. Each blister container may be numbered or otherwise labeled, e.g., starting with day 1. 
     In some embodiments, a subject delivery system comprises an injection device. Exemplary, non-limiting drug delivery devices include injections devices, such as pen injectors, and needle/syringe devices. In some embodiments, the invention provides an injection delivery device that is pre-loaded with a formulation comprising an effective amount of a subject active agent. For example, a subject delivery device comprises an injection device pre-loaded with a single dose of a subject active agent. A subject injection device can be re-usable or disposable. 
     Pen injectors are available. Exemplary devices which can be adapted for use in the present methods are any of a variety of pen injectors from Becton Dickinson, e.g., BD™ Pen, BD™ Pen II, BD™ Auto-Injector: a pen injector from Innoject, Inc.; any of the medication delivery pen devices discussed in U.S. Pat. Nos. 5,728,074, 6,096,010, 6,146,361, 6,248,095, 6,277,099, and 6,221,053; and the like. The medication delivery pen can be disposable, or reusable and refillable. 
     In some embodiments, a subject delivery system comprises a device for delivery to nasal passages or lungs. For example, the compositions described herein can be formulated for delivery by a nebulizer, an inhaler device, or the like. 
     Bioadhesive microparticles constitute still another drug delivery system suitable for use in the context of the present disclosure. This system is a multi-phase liquid or semi-solid preparation that preferably does not seep from the nasal passages. The substances can cling to the nasal wall and release the drug over a period of time. Many of these systems were designed for nasal use (e.g. U.S. Pat. No. 4,756,907). The system may comprise microspheres with an active agent; and a surfactant for enhancing uptake of the drug. The microparticles have a diameter of 10-100 μm and can be prepared from starch, gelatin, albumin, collagen, or dextran. 
     Another system is a container comprising a subject formulation (e.g., a tube) that is adapted for use with an applicator. The active agent is incorporated into liquids, creams, lotions, foams, paste, ointments, and gels which can be applied to the vagina or rectum using an applicator. Processes for preparing pharmaceuticals in cream, lotion, foam, paste, ointment and gel formats can be found throughout the literature. An example of a suitable system is a standard fragrance-free lotion formulation containing glycerol, ceramides, mineral oil, petrolatum, parabens, fragrance and water such as the product sold under the trademark JERGENS™ (Andrew Jergens Co., Cincinnati, Ohio). Suitable nontoxic pharmaceutically acceptable systems for use in the compositions of the present invention will be apparent to those skilled in the art of pharmaceutical formulations and examples are described in Remington&#39;s Pharmaceutical Sciences, 19th Edition, A. R. Gennaro, ed., 1995. The choice of suitable carriers will depend on the exact nature of the particular vaginal or rectal dosage form desired, e.g., whether the active ingredient(s) is/are to be formulated into a cream, lotion, foam, ointment, paste, solution, or gel, as well as on the identity of the active ingredient(s). Other suitable delivery devices are those described in U.S. Pat. No. 6,476,079. 
     Subjects to be Treated 
     The methods of the present disclosure are suitable for treating individuals who are suspected of having SARS-CoV-2 infection, and individuals who have SARS-CoV-2 infection, e.g., who have been diagnosed as having SARS-CoV-2 infection. The methods of the present disclosure are also suitable for use in individuals who have not been diagnosed as having SARS-CoV-2 infection (e.g., individuals who have been tested for SARS-CoV-2 and who have tested negative for SARS-CoV-2; and individuals who have not been tested), and who are considered at greater risk than the general population of contracting an SARS-CoV-2 infection (e.g., “at risk” individuals). 
     The methods of the present disclosure are suitable for treating individuals who are suspected of having SARS-CoV-2 infection, individuals who have SARS-CoV-2 infection (e.g., who have been diagnosed as having SARS-CoV-2 infection), and individuals who are considered at greater risk than the general population of contracting SARS-CoV-2 infection. Such individuals include, but are not limited to, individuals with healthy, intact immune systems, but who are at risk for becoming SARS-CoV-2 infected (“at-risk” individuals). In addition, such individuals include, but are not limited to, individuals that do not appear to have SARS-CoV-2 infection, but who may have reduced immune responses, heart disease, reduced lung capacity or a combination thereof (“at-risk” individuals). At-risk individuals include, but are not limited to, individuals who have a greater likelihood than the general population of becoming SARS-CoV-2 infection infected. Individuals at risk for becoming SARS-CoV-2 infected include, but are not limited to, essential services personnel such as medical personnel, emergency medical personnel, law enforcement, ambulance drivers, and public service drivers. Individuals at risk for becoming SARS-CoV-2 infected include, but are not limited to, older individuals (e.g., older than 65), immunocompromised individuals, individuals with heart disease, obese individuals, and individuals with other viral or bacterial infections. Individuals suitable for treatment therefore include individuals infected with, or at risk of becoming infected with SARS-CoV-2 or any variant thereof. 
     Definitions 
     A “wild-type strain of a virus” is a strain that does not comprise any of the human-made mutations as described herein, i.e., a wild-type virus is any virus that can be isolated from nature (e.g., from a human infected with the virus). A wild-type virus can be cultured in a laboratory, but still, in the absence of any other virus, is capable of producing progeny genomes or virions like those isolated from nature. 
     As used herein, the terms “treatment,” “treating,” and the like, refer to obtaining a desired pharmacologic and/or physiologic effect. The effect may be prophylactic in terms of completely or partially preventing a disease or symptom thereof and/or may be therapeutic in terms of a partial or complete cure for a disease and/or adverse effect attributable to the disease. “Treatment,” as used herein, covers any treatment of a disease in a mammal, particularly in a human, and includes: (a) preventing the disease from occurring in a subject which may be predisposed to the disease but has not yet been diagnosed as having it; (b) inhibiting the disease, i.e., arresting its development; and (c) relieving the disease, i.e., causing regression of the disease. 
     The terms “individual,” “subject,” “host,” and “patient,” used interchangeably herein, refer to a mammal, including, but not limited to, murines (rats, mice), non-human primates, humans, canines, felines, ungulates (e.g., equines, bovines, ovines, porcines, caprines), etc. 
     A “therapeutically effective amount” or “efficacious amount” refers to the amount of an agent (e.g., a construct, a particle, etc., as described herein) that, when administered to a mammal (e.g., a human) or other subject for treating a disease, is sufficient to effect such treatment for the disease. The “therapeutically effective amount” can vary depending on the compound or the cell, the disease and its severity and the age, weight, etc., of the subject to be treated. 
     The terms “co-administration” and “in combination with” include the administration of two or more therapeutic agents either simultaneously, concurrently or sequentially within no specific time limits. In one embodiment, the agents are present in the cell or in the subject&#39;s body at the same time or exert their biological or therapeutic effect at the same time. In one embodiment, the therapeutic agents are in the same composition or unit dosage form. In other embodiments, the therapeutic agents are in separate compositions or unit dosage forms. In certain embodiments, a first agent can be administered prior to (e.g., minutes, 15 minutes, 30 minutes, 45 minutes, 1 hour, 2 hours, 4 hours, 6 hours, 12 hours, 24 hours, 48 hours, 72 hours, 96 hours, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 8 weeks, or 12 weeks before), concomitantly with, or subsequent to (e.g., 5 minutes, 15 minutes, 30 minutes, 45 minutes, 1 hour, 2 hours, 4 hours, 6 hours, 12 hours, 24 hours, 48 hours, 72 hours, 96 hours, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 8 weeks, or 12 weeks after) the administration of a second therapeutic agent. 
     As used herein, a “pharmaceutical composition” is meant to encompass a composition suitable for administration to a subject, such as a mammal, e.g., a human. In general a “pharmaceutical composition” is sterile and is free of contaminants that are capable of eliciting an undesirable response within the subject (e.g., the compound(s) in the pharmaceutical composition is pharmaceutical grade). Pharmaceutical compositions can be designed for administration to subjects or patients in need thereof via a number of different routes of administration including oral, buccal, rectal, parenteral, intraperitoneal, intradermal, intratracheal and the like. 
     All numerical designations, for example, temperature, time, concentration, viral load, and molecular weight, including ranges, are approximations which are varied (+) or (−) by increments of 0.1 or 1.0, where appropriate. It is to be understood, although not always explicitly stated that all numerical designations are preceded by the term “about.” It also is to be understood, although not always explicitly stated, that the reagents described herein are merely exemplary and that in some cases equivalents may be available in the art. 
     Also, as used herein, “and/or” refers to and encompasses any and all possible combinations of one or more of the associated listed items, as well as the lack of combinations when interpreted in the alternative (“or”). 
     It must be noted that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “an interfering particle” includes a plurality of such particles and reference to “the cis-acting element” includes reference to one or more cis-acting elements and equivalents thereof known to those skilled in the art, and so forth. It is further noted that the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as “solely,” “only” and the like in connection with the recitation of claim elements or use of a “negative” limitation. 
     Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range, is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges, and are also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention. 
     The following examples illustrate some of the experimental work performed in the development of the invention. 
     Example 1: Generating SARS-CoV-2 Random Deletion Libraries (RDLs) 
     To systematically identify regions of SARS-CoV-2 required for efficient mobilization, a randomized deletion screen was utilized similar to that described by Weinberger and Notton (2017), which created and index random-deletion libraries of HIV NL4-3. 
     Briefly, plasmid DNA was subjected to transposon-mediated random insertion, followed by excision of the transposon and exonuclease-mediated digestion of the exposed ends to create deletions centered at a random genetic position, each of variable size. The plasmid was then re-ligated together with a cassette containing a 20-nucleotide random DNA barcode to ‘index’ the deletion. Indexing allows a deleted region to be easily identified (by the junction of genomic sequence and the barcode) and tracked/quantified by deep sequencing. This process is schematically illustrated in  FIGS.  1 - 4   .  FIG.  5 A  further illustrates this process. 
     The deletion sites in the members of the libraries were sequenced. Deletion depth plots illustrated in  FIG.  5 B  show that the sub-libraries contained over 587,000 deletions. The sub-libraries were ligated to form full-length libraries, the SARS-CoV-2 inserts were in vitro transcribed into RNA and the RNA was transfected into VeroE6 cells. The transfected cells were then infected with wild-type SARS-CoV-2 virus to test for mobilization of the deletion mutants. After three virus passages, RNA was extracted from cells and the presence of deletion barcodes was analyzed. 
     SARS-CoV-2 Viroreactor 
     A SARS-CoV-2 viroreactor was set up using VeroE6 cells growing on silicone beads in suspension that can be infected with the SARS-CoV-2 deletion mutants, thereby creating a dynamic system to improve infection and ultimately evolution of SARS-CoV-2 therapeutic interfering particles (TIPs). The conditions used for the SARS-CoV-2 viroreactor were adapted from the protocol used to isolate an HIV TIP (described by Weinberger and Notton (2017)). 
     As illustrated in  FIG.  6 A , when the VeroE6 cells reached steady-state density, they were infected with the SARS-CoV-2 deletion mutants at a MOI of either 0.5 or 5, under gentle agitation. Half of the culture was removed from the reactor every day and replaced with fresh cells and media. Samples removed from the reactor were centrifugated, supernatants were frozen for later analysis and cell viability was measured by flow cytometry using a propidium iodine staining protocol ( FIG.  6 B ). Cell viability was low (35-60%) at 2 days post infection (dpi) ( FIG.  6 C- 6 D ) but started recovering as soon as 4 days post-infection (dpi) and stayed stable (60-805) until 12 dpi. At day 13, the cultures recovered to over 90% of cell viability. 
     Example 2: SARS-CoV-2 Therapeutic Interfering Particles (TIPs) 
     Minimal TIP constructs, TIP1 and TIP2, with the structures shown in  FIG.  7 A- 7 B  were designed and cloned. The TIP1 and TIP2 constructs encode varying portions of the 5′ and 3′ UTRs of SARS-CoV-2 and express an mCherry reporter protein driven from an IRES. The plasmid constructs were sequence verified. 
     The 5′ SARS-CoV-2 sequences in TIP1 are as shown below (SEQ ID NO:28). 
                      1 ATTAAAGGTT TATACCTTCC CAGGTAACAA ACCAACCAAC                41 TTTCGATCTC TTGTAGATCT GTTCTCTAAA CGAACTTTAA                81 AATCTGTGTG GCTGTCACTC GGCTGCATGC TTAGTGCACT               121 CACGCAGTAT AATTAATAAC TAATTACTGT CGTTGACAGG               161 ACACGAGTAA CTCGTCTATC TTCTGCAGGC TGCTTACGGT               201 TTCGTCCGTG TTGCAGCCGA TCATCAGCAC ATCTAGGTTT               241    C   GTCCGGGTG TGAGCGAAAG GTAAGATGGA GAGCCTTGTC               281 CCTGGTTTCA ACGAGAAAAC ACACGTCCAA CTCAGTTTGC               321 CTGTTTTACA GGTTCGCGAC GTGCTCGTAC GTGGCTTTGG               361 AGACTCCGTG GAGGAGGTCT TATCAGAGGC ACGTCAACAT               401 CTTAAAGATG GCACTTGTGG CTTAGTAGAA GTTGAAAAAG               411 GCGTTTTGCC            
The 3′ SARS-CoV-2 sequences in TIP1 are shown below as SEQ ID NO:29.
 
                      1 ATTAAAGGTT TATACCTTCC CAGGTAACAA ACCAACCAAC                41 TTTCGATCTC TTGTAGATCT GTTCTCTAAA CGAACTTTAA                81 AATCTGTGTG GCTGTCACTC GGCTGCATGC TTAGTGCACT               121 CACGCAGTAT AATTAATAAC TAATTACTGT CGTTGACAGG               161 ACACGAGTAA CTCGTCTATC TTCTGCAGGC TGCTTACGGT               201 TTCGTCCGTG TTGCAGCCGA TCATCAGCAC ATCTAGGTTT               241    C   GTCCGGGTG TGACCGAAAG GTAAGATGGA GAGCCTTGTC               281 CCTGGTTTCA ACGAGAAAAC ACACGTCCAA CTCAGTTTGC               321 CTGTTTTACA GGTTCGCGAC GTGCTCGTAC GTGGCTTTGG               361 AGACTCCGTG GAGGAGGTCT TATCAGAGGC ACGTCAACAT               401 CTTAAAGATG GCACTTGTGG CTTAGTAGAA GTTGAAAAAG               411 GCGTTTTGCC             
The 5′ SARS-CoV-2 sequences in TIP2 are as shown below (SEQ ID NO:30).
 
                        1   ATTAAAGGTT TATACCTTCC CAGGTAACAA ACCAACCAAC               41   TTTCGATCTC TTGTAGATCT GTTCTCTAAA CGAACTTTAA               81   AATCTGTGTG GCTGTCACTC GGCTGCATGC TTAGTGCACT               121   CACGCAGTAT AATTAATAAC TAATTACTGT CGTTGACAGG               101   ACACGAGTAA CTCGTCTATC TTCTGCAGGC TGCTTACGGT               201   TTCGTCCGTG TTGCAGCCGA TCATCAGCAC ATCTAGGTTT               241       C   GTCCGGGTG TGACCGAAAG GTAAGATGGA GAGCCTTGTC               281   CCTGGTTTCA ACGAGAAAAC ACACGTCCAA CTCAGTTTGC               321   CTGTTTTACA GGTTCGCGAC GTGCTCGTAC GTGGCTTTGG               361   AGACTCCGTG GAGGAGGTCT TATCAGAGGC ACGTCAACAT               401   CTTAAAGATG GCACTTGTGG CTTAGTAGAA GTTGAAAAAG               441   GCGTTTTGCC TCAACTTGAA CAGCCCTATG TGTTCATCAA               481   ACGTTCGGAT GCTCGAACTG CACCTCATGG TCATGTTATG               521   GTTGAGCTGG TAGCAGAACT CGAAGGCATT CAGTACGGTC               561   GTAGTGGTGA GACACTTGGT GTCCTTGTCC CTCATGTGGG               601   CGAAATACCA GTGGCTTACC GCAAGGTTCT TCTTCGTAAG               641   AACGGTAATA AAGGAGCTGG TGGCCATAGT TACGGCGCCG               681   ATCTAAAGTC ATTTGACTTA GGCGACGAGC TTGGCACTGA               721   TCCTTATGAA GATTTTCAAG AAAACTGGAA CACTAAACAT               761   AGCAGTGGTG TTACCCGTGA ACTCATGCGT GAGCTTAACG               801   GAGGGGCATA CACTCGCTAT GTCGATAACA ACTTCTGTGG               841   CCCTGATGGC TACCCTCTTG AGTGCATTAA AGACCTTCTA               881   GCACGTGCTG GTAAAGCTTC ATGCACTTTG TCCGAACAAC               921   TGGACTTTAT TGACACTAAG AGGGGTGTAT ACTGCTGCCG               961   TGAACATGAG CATGAAATTG CTTGGTACAC GGAACGTTCT               1001   GAAAAGAGCT ATGAATTGCA GACACCTTTT GAAATTAAAT               1041   TGGCAAAGAA ATTTGACACC TTCAATGGGG AATGTCCAAA               1081   TTTTGTATTT CCCTTAAATT CCATAATCAA GACTATTCAA               1121   CCAAGGGTTG AAAAGAAAAA GCTTGATGGC TTTATGGGTA               1161   GAATTCGATC TGTCTATCCA GTTGCGTCAC CAAATGAATG               1201   CAACCAAATG TGCCTTTCAA CTCTCATGAA GTGTGATCAT               1241   TGTGGTGAAA CTTCATGGCA GACGGGCGAT tttgttaaag               1281   CCACTTGCGA ATTTTGTGGC ACTGAGAATT TGACTAAAGA               1321   AGGTGCCACT ACTTGTGGTT AC1TAGCCCA AAATGCTGTT               1361   GTTAAAATTT ATTGTCCAGC ATGTCACAAT TCAGAAGTAG               1401   GACCTGAGCA TAGTCTTGCC GAATACCATA ATGAATCTGG               1441   CTTGAAAACC ATTCTTCGTA AGGGTGGTCG CACTATTGCC               1481   TTTGGAGGCT GTGTGTTCTC TTATGTTGGT TGCCATAACA               1521   AGTGTGCCTA TTGGGTTCCA gaattagatc tctcgaggtt               1561   aacgaattct gctatacgaa gttatccctc            
The 3′ SARS-CoV-2 sequences in TIP2 are as shown below (SEQ ID NO:31).
 
     
       
         
           
               
            
               
                   1 ATTTGCCCCC AGCGCTTCAG CGTTCTTCGG AATGTCGCGC 
               
               
                   
               
               
                  41 ATTGGCATGG AAGTCACACC TTCGGGAACG TGGTTGACCT 
               
               
                   
               
               
                  81 ACACAGGTGC CATCAAATTG GATGACAAAG ATCCAAATTT 
               
               
                   
               
               
                 121 CAAAGATCAA GTCATTTTGC TGAATAAGCA TATTGACGCA 
               
               
                   
               
               
                 161 TACAAAACAT TCCCACCAAC AGAGCCTAAA AAGGACAAAA 
               
               
                   
               
               
                 201 AGAAGAAGGC TGATGAAACT CAAGCCTTAC CGUAGAGACA 
               
               
                   
               
               
                 241 GAAGAAACAG CAAACTGTGA CTCTTCTTCC TGCTGCAGAT 
               
               
                   
               
               
                 281 TTGGATGATT TCTCCAAACA ATTGCAACAA TCCATGAGCA 
               
               
                   
               
               
                 321 GTGCTGACTC AACTCAGGCC TAAACTCATG CAGACCACAC 
               
               
                   
               
               
                 361 AAGGCAGATG GGCTATATAA ACGTTTTCGC TTTTCCGTTT 
               
               
                   
               
               
                 401 ACGATATATA GTCTACTCTT GTGCAGAATG AATTCTCGTA 
               
               
                   
               
               
                 441 ACTAGATAGC ACAAGTAGAT GTAGTTAACT TTAATCTCAC 
               
               
                   
               
               
                 481 ATAGCAATCT TTAATCAGTG TGTAACATTA GGGAGGACTT 
               
               
                   
               
               
                 521 GAAAGAGCCA CCACATTTTC ACCGAGGCCA CGCGGAGTAC 
               
               
                   
               
               
                 561 GATCGAGTGT AGAGTGAACA ATGCTAGGGA GAGCTGCCTA 
               
               
                   
               
               
                 601 TATGGAAGAG CCCTAATGTG TAAAATTAAT TTTAGTAGTG 
               
               
                   
               
               
                 641 CTATCCCCAT GTGATTTTAA TAGCTTCTTA GGAGAATGAC 
               
               
                   
               
               
                 681 AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAA 
               
            
           
         
       
     
     Two additional TIP variants were also cloned TIP11* and TIP2*, these contain the common C-241-T mutation within the 5′ UTR. This C241T UTR mutation co-transmits across populations together with the spike protein D614G mutation. 
     Hence, the 5′ SARS-CoV-2 sequences in TIP1* are as shown below (SEQ ID NO:32). 
                      1 ATTAAAGGTT TATACCTTCC CAGGTAACAA ACCAACCAAC                41 TTTCGATCTC TTGTAGATCT GTTCTCTAAA CGAACTTTAA                81 AATCTGTGTG GCTGTCACTC GGCTGCATGC TTAGTGCACT               121 CACGCAGTAT AATTAATAAC TAATTACTGT CGTTGACAGG               161 ACACGAGTAA CTCGTCTATC TTCTGCAGGC TGCTTACGGT               201 TTCGTCCGTG TTGCAGCCGA TCATCAGCAC ATCTAGGTTT               241    T   GTCCGGGTG TGACCGAAAG GTAAGATGGA GAGCCTTGTC               281 CCTGGTTTCA ACGAGAAAAC ACACGTCCAA CTCAGTTTGC               321 CTGTTTTACA GGTTCGCGAC GTGCTCGTAC GTGGCTTTGG               361 AGACTCCGTG GAGGAGGTCT TATCAGAGGC ACGTCAACAT               401 CTTAAAGATG GCACTTGTGG CTTAGTAGAA GTTGAAAAAG               411 GCGTTTTGCC            
Similarly, the SARS-CoV-2 sequences in TIP2* are as shown below (SEQ ID NO:33).
 
     
       
         
           
               
            
               
                    1 ATTAAAGGTT TATACCTTCC CAGGTAACAA ACCAACCAAC 
               
               
                   
               
               
                  201 TTCGTCCGTG TTGCAGCCGA TCATCAGCAC ATCTAGGTTT 
               
               
                   
               
               
                  241    T   GTCCGGGTG TGACCGAAAG GTAAGATGGA GAGCCTTGTC 
               
               
                   
               
               
                  281 CCTGGTTTCA ACGAGAAAAC ACACGTCCAA CTCAGTTTGC 
               
               
                   
               
               
                  321 CTGTTTTACA GGTTCGCGAC GTGCTCGTAC GTGGCTTTGG 
               
               
                   
               
               
                  361 AGACTCCGTG GAGGAGGTCT TATCAGAGGC ACGTCAACAT 
               
               
                   
               
               
                  401 CTTAAAGATG GCACTTGTGG CTTAGTAGAA GTTGAAAAAG 
               
               
                   
               
               
                  441 GCGTTTTGCC 7CAACTTGAA CAGCCCTATG TGTTCATCAA 
               
               
                   
               
               
                  481 ACGTTCGGAT GCTCGAACTG CACCTCATGG TCATGTTATG 
               
               
                   
               
               
                  521 GTTGAGCTGG TAGCAGAACT CGAAGGCATT CAGTACGGTC 
               
               
                   
               
               
                  561 GTAGTGGTGA GACACTTGGT GTCCTTGTCC CTCATGTGGG 
               
               
                   
               
               
                  601 CGAAATACCA GTGGCTTACC GCAAGGTTCT TCTTCGTAAG 
               
               
                   
               
               
                  641 AACGGTAATA AAGGAGCTGG TGGCCATAGT TACGGCGCCG 
               
               
                   
               
               
                  681 ATCTAAAGTC ATTTGACTTA GGCGACGAGC TTGGCACTGA 
               
               
                   
               
               
                  721 TCCTTATGAA GATTTTCAAG AAAACTGGAA CACTAAACAT 
               
               
                   
               
               
                  761 AGCAGTGGTG TTACCCGTGA ACTCATGCGT GAGCTTAACG 
               
               
                   
               
               
                  801 GAGGGGCATA CACTCGCTAT GTCGATAACA ACTTCTGTGG 
               
               
                   
               
               
                  841 CCCTGATGGC TACCCTCTTG AGTGCATTAA AGACCTTCTA 
               
               
                   
               
               
                  881 GCACGTGCTG GTAAAGCTTC ATGCACTTTG TCCGAACAAC 
               
               
                   
               
               
                  921 TGGACTTTAT TGACACTAAG AGGGGTGTAT ACTGCTGCCG 
               
               
                   
               
               
                  961 TGAACATGAG CATGAAATTG CTTGGTACAC GGAACGTTCT 
               
               
                   
               
               
                 1001 GAAAAGAGCT ATGAATTGCA GACACCTTTT GAAATTAAAT 
               
               
                   
               
               
                 1041 TGGCAAAGAA ATTTGACACC TTCAATGGGG AATGTCCAAA 
               
               
                   
               
               
                 1081 TTTTGTATTT CCCTTAAATT CCATAATCAA GACTATTCAA 
               
               
                   
               
               
                 1121 CCAAGGGTTG AAAAGAAAAA GCTTGATGGC TTTATGGGTA 
               
               
                   
               
               
                 1161 GAATTCGATC TGTCTATCCA GTTGCGTCAC CAAATGAATG 
               
               
                   
               
               
                 1201 CAACCAAATG TGCCTTTCAA ctctcatgaa GTGTGATCAT 
               
               
                   
               
               
                 1241 TGTGGTGAAA CTTCATGGCA GACGGGCGAT TTTGTTAAAG 
               
               
                   
               
               
                 1281 CCACTTGCGA ATTTTGTGGC ACTGAGAATT TGACTAAAGA 
               
               
                   
               
               
                 1321 AGGTGCCACT ACTTGTGGTT ACTTACCCCA AAATGCTGTT 
               
               
                   
               
               
                 1361 GTTAAAATTT ATTGTCCAGC ATGTCACAAT TCAGAAGTAG 
               
               
                   
               
               
                 1401 GACCTGAGCA TAGTCTTGCC GAATACCATA ATGAATCTGG 
               
               
                   
               
               
                 1441 CTTGAAAACC ATTCTTCGTA AGGGTGGTCG CACTATTGCC 
               
               
                   
               
               
                 1481 TTTGGAGGCT GTGTGTTCTC TTATGTTGGT TGCCATAACA 
               
               
                   
               
               
                 1521 AGTGTGCCTA TTGGGTTCCA gaattagatc tctcgaggtt 
               
               
                   
               
               
                 1561 aacgaattct gctatacgaa gttatccctc  
               
            
           
         
       
     
     To test whether TIP constructs can reduce SARS-CoV-2 replication, mRNA from the four TIP constructs was generated by in vitro transcription from a T7 promoter operably linked upstream of the TIP in each plasmid. The different preparations of in vitro transcribed TIP mRNA were transfected into Vero E6 cells (TIP1, TIP1, TIP2, or TIP2*), and the cells were infected with SARS-CoV-2 (WA strain) at an MOI=0.005. At 48 hrs post-infection samples were harvested and a yield-reduction assay was conducted (see  FIG.  8   ). Yield-reduction assays were measured by fold-reduction in SARS-CoV-2 mRNA (E gene) at 48 hrs post infection because the SARS-CoV-2 E (envelope) gene does not occur in the TIP sequences. 
     As shown in  FIG.  8   , all of the TIP constructs reduced SARS-CoV-2 viral replication but the TIP2 construct exhibited the greatest interference with SARS-CoV-2. 
     Example 3: SARS-CoV-2 TIPs are Mobilized by SARS-CoV-2 and Transmit Together with SARS-CoV-2 
     Supernatant transfer experiments were performed to test the ability of the candidate TIPs to be mobilized by SARS-CoV-2 and transmitted together with SARS-CoV-2. 
     SARS-CoV-2-infected Vero E6 cells were transfected with various TIP candidates having the structures shown in  FIGS.  7 A- 7 B . Analysis for mCherry expression could therefore be used as a measure of TIP replication. Supernatant was collected from this first population of cells at 96 hours post-infection and the supernatant was transferred to a second population of fresh Vero cells. As a first control, supernatant was transferred from naïve uninfected cells to Vero cells, and as a second control supernatant was transferred from SARS-CoV-2 infected cells that were not transfected with TIPs. Flow cytometry was performed to analyze mCherry expression of the second population of cells at 48 hours after supernatant transfer. 
     As shown in  FIG.  9   , the first and second controls showed no mCherry expression ( FIG.  9 A- 9 B ). However, the supernatant from cells transfected with TIP candidate mRNA and infected with SARS-CoV-2 did generate mCherry producing cells, indicating that functional viral-like particles (VLPs) were being generated by SARS-CoV-2 helper virus ( FIG.  9 C- 9 I ). In general, we found that mRNA transfection yielded better mobilization ( FIG.  9 G- 9 H ) than DNA transfection ( FIG.  9 C- 9 F ). This was consistent with results from the yield reduction assay by RT-qPCR where mRNA transfection also yielded better interference with SARS-CoV-2 than did DNA transfection (not shown). 
     Example 4: Transcription Regulating Sequences (TRS) for Antiviral Intervention Against SARS-CoV-2 
     This Example describes use of antisense RNAs to intervene or interfere with SARS-CoV-2 infection. 
     Transcription initiation is regulated in coronaviruses by several types of consensus transcription regulating sequences (TRSs): TRS1-L: 5′-cuaaac-3′ (SEQ ID NO:36), TRS2-L: 5′-acgaac-3′ (SEQ ID NO:37), and TRS3-L, 5′-cuaaacgaac-3′ (SEQ ID NO:38). 
     To evaluate whether transcription can be inhibited from these transcriptional initiation sites, the following antisense TRS RNAs were developed: 
     
       
         
           
               
               
            
               
                   
                 TRS1- 
               
               
                   
                 (SEQ ID NO: 25) 
               
               
                   
                 ACGAACCUAAACACGAACCUAAAC; 
               
               
                   
                   
               
               
                   
                 TRS2- 
               
               
                   
                 (SEQ ID NO: 26) 
               
               
                   
                 (ACGAACACGAACACGAACACGAAC; 
               
               
                   
                 and 
               
               
                   
                   
               
               
                   
                 TRS3- 
               
               
                   
                 (SEQ ID NO :27) 
               
               
                   
                 CUAAACCUAAACCUAAACCUAAAC. 
               
            
           
         
       
     
     Vero cells were transfected with the antisense TRS RNAs and then infected with SARS-CoV-2 (MOI 0.01 or 0.05). As controls, cells were transfected with a scrambled RNA (instead of a TRS RNA) and then infected with SARS-CoV-2 (MOI 0.01 or 0.05). The titers of SARS-CoV-2 were determined by quantitative PCR and western blots were prepared at 24, 48, and 72 hours. 
     As shown in  FIG.  11 A- 11 C , use of the TRS2 antisense reduced SARS-CoV-2 titers to the greatest extent ( FIG.  11 B ). 
     Vero cells were then incubated with combination of a TRS2 antisense with either TIP1 or TIP2, and then the cells were infected with SARS-CoV-2. The fold changes in SARS-CoV-2 genome numbers were then determined. 
     As shown in  FIG.  12   , the combination of the TRS2 antisense with either the TIP1 or TIP2 significantly reduced the SARS-CoV-2 genome numbers compared to the TRS alone. 
     Example 5: SARS-CoV-2 TIPs Reduce Replication of Different SARS-CoV-2 Strains 
     This Example describes use of therapeutic interfering particles (TIP1 and TIP2) to intervene or interfere with different SARS-CoV-2 strains. 
     Vero cells were pretreated with lipid nanoparticles encapsulating therapeutic interfering particles (TIP1 or TIP2 at 0.3 ng/μl or 0.003 ng/μl), or a control RNA. At two hours post-treatment the cells were infected (MOI 0.005) with one of the following SARS-CoV-2 strains:
         The 501Y.V2.HV variant of SARS-CoV-2, colloquially known as a South African variant;   The 501Y.V2.HV delta variant of SARS-CoV-2, colloquially known as a South African variant; and   The B.1.1.7 variant, colloquially known as a U.K. variant.
 
Supernatant from the infected cultures was harvested at 48 hours post-infection and the SARS-CoV-2 viral titer was quantified.
       

       FIG.  13 A- 13 C  illustrate that TIP1 and TIP2 significantly reduce the replication of SARS-CoV-2 in a dose-dependent manner. 
     The following statements provide a summary of some aspects of the inventive nucleic acids and methods described herein. 
     Statements: 
     1. A recombinant SARS-CoV-2 construct, the construct comprising: cis-acting elements comprising at least 100 nucleotides of a SARS-CoV-2 5′ untranslated region (5′ UTR), at least 100 nucleotides of a 3′ untranslated region (3′ UTR), or a combination thereof.
 
2. The construct of statement 1, which interferes with SARS-CoV-2 replication.
 
3. The construct of statement 1 or 2, which cannot replicate.
 
4. The construct of any one of statements 1-3, which replicates in the presence of infective SARS-CoV-2.
 
5. The construct of any one of statements 1-4, wherein the construct is incapable of replication and production of virus on its own but requires replication-competent SARS-CoV-2 to act as a helper virus.
 
6. The construct of any one of statements 1-5, which can be transmitted between cells in the presence of infective SARS-CoV-2.
 
7. The construct of any one of statements 1-6, comprising a packaging signal for SARS-CoV-2.
 
8. The construct of any one of statements 1-7, comprising deletion of portions of the SARS-CoV-2 genome encoding portions of any of SEQ ID NO:1-22.
 
9. The construct of statement 8, wherein the portions deleted from the genome comprise at least 10 to at least 27,000 nucleotides.
 
10. The construct of statement 8 or 9, wherein the portions deleted from the genome comprise at least 100, at least 500, at least 1000, at least 1500, at least 2000, at least 2500, at least 3000, at least 4000, at least 5000, at least 6000, at least 7000, at least 8000, at least 9000, at least 10,000, at least 11,000, at least 12,000, at least 13,000, at least 14,000, at least 15,000, at least 16,000, at least 17,000, at least 18,000, at least 19,000, at least 20,000, at least 21,000, at least 22,000, at least 23,000, at least 24,000, at least 25,000, at least 26,000, at least 27,000, at least 27500, or at least 28000 nucleotides of the SARS-CoV-2 genome.
 
11. The construct of any one of statements 1-10, wherein the SARS-CoV-2 construct blocks wild type SARS-CoV-2 cellular entry, competes for structural proteins that mediate viral particle assembly, exhibits reduced reproduction of the SARS-CoV-2 construct in vivo, produces proteins that inhibit assembly of viral particles, or a combination thereof.
 
12. The construct of statement 11, wherein SARS-CoV-2 genomic nucleic acids with one or more nucleotide sequence alterations compared to a wild type or native SARS-CoV-2 genomic nucleotide sequence;
 
13. The construct of statement 11 or 12, comprising one or more nucleotide sequence alterations in a spike protein membrane-fusing S2 subunit, an RNA-dependent RNA polymerase, a M protein (membrane glycoprotein), a ssRNA-binding protein, or a combination thereof in the SARS-CoV-2 construct genomic nucleic acids.
 
14. The construct of any of statements 1-13, wherein the SARS-CoV-2 construct genomic RNA is produced at a higher rate than wild-type SARS-CoV-2 genomic RNA when present in a host cell infected with a wild-type SARS-CoV-2, such that the ratio of the construct SARS-CoV-2 genomic RNA to the wild-type SARS-CoV-2 genomic RNA is greater than 1 in the cell.
 
15. The construct of any of statements 1-14, wherein the construct has a higher transmission frequency than the wild-type SARS-CoV-2.
 
16. The construct of any of statements 1-15, wherein the construct has a basic reproductive ratio (R0)&gt;1.
 
17. The construct of any of statements 1-16, wherein the construct is packaged with the same or a higher efficiency than wild-type SARS-CoV-2 when present in a host cell infected with a wild-type SARS-CoV-2.
 
18. The construct of any of statements 1-17, wherein the construct comprises at least a 1-20 nucleotide deletion within positions 1-265, 266-805, 806-2719, 2720-8554, 8555-10054, 10055-10972, 10973-11842, 11843-12091, 12092-12685, 12686-13024, 13025-13441, 13442-13468, 13468-16236, 16237-18039, 18040-19620, 19621-20658, 20659-21552, 21563-25384, 266-13483, or a combination thereof, wherein the position numbers are relative to reference SARS-CoV-2 sequence SEQ ID NO:1.
 
19. The construct of any of statements 1-18, wherein the construct comprises at least a 1-20 nucleotide deletion within positions 21563-25384 of a spike glycoprotein coding region, within positions numbered 13442-16236 of an RNA-dependent RNA polymerase coding region, positions 26523-27191 of an M protein (membrane glycoprotein) coding region, positions 12686-13024 of a ssRNA-binding protein coding region, or a combination thereof, wherein the position numbers are relative to reference SARS-CoV-2 sequence SEQ ID NO:1.
 
20. The construct of any of statements 1-19, wherein the construct comprises deletion of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160 170, 180, 190, 200, 225, 250, 300, 350, 400, 450 or 500 nucleotides.
 
21. The construct of any of statements 1-20, wherein the construct comprises 5′ SARS-CoV-2 truncated sequences having any of SEQ ID NO:28, 30, 32 or 33.
 
22. The construct of any of statements 1-21, wherein the construct comprises 3′ SARS-CoV-2 truncated sequences such as any of those with SEQ ID NO:31 or 32.
 
23. The construct of any of statements 1-22 wherein the construct comprises extended poly A sequences.
 
24. The construct of statement 23, wherein the extended poly A sequences extend the half-life of the mRNA.
 
25. The construct of any of statements 23 or 24, wherein the extended poly A sequences, comprise at least 100 adenine nucleotides, at least 120 adenine nucleotides, at least 140 adenine nucleotides, at least 150 adenine nucleotides, at least 170 adenine nucleotides, at least 180 adenine nucleotides, at least 200 adenine nucleotides, at least 225 adenine nucleotides, or at least 250 adenine nucleotides.
 
26. The construct of any of statements 1-25, wherein the construct comprises a segment encoding a detectable marker.
 
27. A particle comprising the construct of any one of statements 1-26 and a viral envelope protein.
 
28. A pharmaceutical composition comprising the construct of any of statements 1-26 or the particle of statement 27 and a pharmaceutically acceptable excipient.
 
29. An inhibitor of SARS-CoV-2 transcription regulating sequences (TRSs) that can bind to one of more of: TRS1-L: 5′-cuaaac-3′ (SEQ ID NO:36), TRS2-L: 5′-acgaac-3′ (SEQ ID NO:37), TRS3-L, 5′-cuaaacgaac-3′ (SEQ ID NO:38), or a combination thereof.
 
30. The inhibitor of statement 29, comprising a sequence comprising or consisting essentially of:
 
     TRS1-ACGAACCUAAACACGAACCUAAAC (SEQ ID NO:25); 
     TRS2-ACGAACACGAACACGAACACGAAC (SEQ ID NO:26); 
     TRS3-CUAAACCUAAACCUAAACCUAAAC (SEQ ID NO:27); or 
     a combination thereof. 
     31. A pharmaceutical composition comprising the inhibitor of statement 29 or 30 and a pharmaceutically acceptable excipient.
 
32. A pharmaceutical composition comprising a pharmaceutically acceptable excipient and the inhibitor of statement 29 or 30, the construct of any of statements 1-26, the particle of statement 27, or a combination thereof.
 
33. A method comprising administering the composition of statement 28, 31, or 32 to a subject.
 
34. The method of statement 33, wherein the subject is an experimental animal infected with SARS-CoV-2.
 
35. The method of statement 33, wherein the subject is a human.
 
36. The method of statement 33 or 35, wherein the subject is a human suspected of being infected with SARS-CoV-2, wherein the subject is a human who tested positive for SARS-CoV-2.
 
37. The method of any one of statements 33-36, wherein the subject has a medical condition, a pre-existing condition, or a condition that reduces heart, lung, brain or immune system function.
 
38. An isolated cell comprising the construct of any of statements 1-26 or the particle of statement 27.
 
39. A method of generating a deletion library, comprising:
         (a) inserting a transposon cassette comprising a target sequence for a sequence specific DNA endonuclease into a population of circular SARS-CoV-2 DNAs to generate a population of transposon-inserted circular SARS-CoV-2 DNAs;   (b) contacting the population of transposon-inserted circular SARS-CoV-2 DNAs with the sequence specific DNA endonuclease to generate a population of cleaved linear SARS-CoV-2 DNAs;   (c) contacting the population of cleaved linear SARS-CoV-2 DNAs with one or more exonucleases to generate a population of deletion DNAs; and   (d) circularizing the deletion DNAs to generate a library of circularized SARS-CoV-2 deletion DNAs.
 
40. The method of statement 39, wherein the circular SARS-CoV-2 DNAs are plasmids that comprise a SARS-CoV-2 genome.
 
41. The method of statement 39 or 40, wherein the method further comprises introducing members of the library of circularized SARS-CoV-2 deletion DNAs into mammalian cells and assaying for SARS-CoV-2 viral infectivity.
 
42. The method of one any of statements 39-41, wherein the method further comprises sequencing members of the library of circularized deletion DNAs to identify SARS-CoV-2 defective interfering particles (DIPs).
 
43. The method of any one of statements 39-42, wherein the sequence specific DNA endonuclease is selected from: a meganuclease, a CRISPR/Cas endonuclease, a zinc finger nuclease, or a TALEN.
 
44. The method of any one of statements 39-43 wherein the method comprises inserting a barcode sequence prior to or simultaneous with step (d).
 
45. The method of any one of statements 39-44, wherein the one or more exonucleases comprises T4 DNA polymerase.
 
46. The method of any one of statements 39-45, wherein the one or more exonucleases comprises a 3′ to 5′ exonuclease and a 5′ to 3′ exonuclease.
 
47. The method of any one of statements 39-46, wherein the step of contacting the population of cleaved linear SARS-CoV-2 DNAs with one or more exonucleases is performed in the presence of a single strand binding protein (SSB).
 
48. The method of any one of statements 39-47, wherein the transposon cassette comprises a first recognition sequence positioned at or near one end of the transposon cassette and a second recognition sequence positioned at or near the other end of the transposon cassette.
 
49. The method of any one of statements 39-48, further comprising, prior to step (a), circularizing a population of SARS-CoV-2 linear DNA molecules to generate said population of circular SARS-CoV-2 DNAs.
 
50. The method of statement 49, wherein the population of linear SARS-CoV-2 DNA molecules comprises one or more PCR products, one or more linear viral genomes, and/or one or more restriction digest products.
 
51. The method of any one of statements 39-50, further comprising introducing members of the library of circularized SARS-CoV-2 deletion DNAs into mammalian cells.
 
52. The method of any one of statements 39-51, further comprising generating from the library of circularized SARS-CoV-2 deletion DNAs, at least one of: linear double stranded DNA (dsDNA) products, linear single stranded DNA (ssDNA) products, linear single stranded RNA (ssRNA) products, and linear double stranded RNA (dsRNA) products.
 
53. The method of statement 52, further comprising introducing said linear dsDNA products, linear ssDNA products, linear ssRNA products, and/or linear dsRNA products into mammalian cells.
 
54. A method of generating and identifying a defective interfering particle (DIP), comprising:
   (a) inserting a target sequence for a sequence specific DNA endonuclease into a population of circular SARS-CoV-2 viral DNAs, each SARS-CoV-2 viral DNA comprising a SARS-CoV-2 viral genome, to generate a population of sequence-inserted viral DNAs;   (b) contacting the population of sequence-inserted viral DNAs with the sequence specific DNA endonuclease to generate a population of cleaved linear viral DNAs;   (c) contacting the population of cleaved linear viral DNAs with an exonuclease to generate a population of deletion DNAs;   (d) circularizing the deletion DNAs to generate a library of circularized deletion viral DNAs; and   (e) sequencing members of the library of circularized deletion viral DNAs to identify deletion interfering particles (DIPs).
 
55. The method of statement 54, comprising, prior to step (a), circularizing a population of linear DNA molecules to generate said population of circular SARS-CoV-2 viral DNAs.
 
56. The method of statement 54 or 55, wherein the population of linear DNA molecules comprises one or more PCR products, one or more linear viral genomes, and/or one or more restriction digest products.
 
57. The method of any one of statements 54-56, wherein the method comprises inserting a barcode sequence prior to or simultaneous with step (d).
 
58. The method of any one of statements 54-57, further comprising (i) introducing members of the library of circularized SARS-CoV-2 deletion viral DNAs into mammalian cells; and (ii) assaying for viral infectivity.
 
59. The method of any one of statements 54-58, further comprising: generating from the library of circularized SARS-CoV-2 deletion viral DNAs, at least one of: linear double stranded DNA (dsDNA) products, linear single stranded DNA (ssDNA) products, linear single stranded RNA (ssRNA) products, and linear double stranded RNA (dsRNA) products.
 
60. The method of statement 59, further comprising:
   introducing said linear dsDNA products, linear ssDNA products, linear ssRNA products, and/or linear dsRNA products into mammalian cells; and assaying for viral infectivity.
 
61. The method of any of statements 39-60, wherein the inserting of step (a) comprises inserting a transposon cassette into the population of circular SARS-CoV-2 viral DNAs, wherein the transposon cassette comprises the target sequence for the sequence specific DNA endonuclease, and wherein said generated population of sequence-inserted viral DNAs is a population of transposon-inserted viral DNAs.
 
62. The method of any one of statements 39-61, wherein the method comprises, after step (d), infecting mammalian cells in culture with members of the library of circularized deletion viral DNAs at a high multiplicity of infection (MOI), culturing the infected cells for a period of time ranging from 12 hours to 2 days, adding naive cells to the to the culture, and harvesting virus from the cells in culture.
 
63. The method of any one of statements 39-62, wherein the method comprises, after step (d), infecting mammalian cells in culture with members of the library of circularized deletion viral DNAs at a low multiplicity of infection (MOI), culturing the infected cells in the presence of an inhibitor of viral replication for a period of time ranging from 1 day to 6 days, infecting the cultured cells with functional virus at a high MOI, culturing the infected cells for a period of time ranging from 12 hours to 4 days, and harvesting virus from the cultured cells.
 
64. A method of treating an individual suspected of being infected with SARS-CoV-2 virus, the method comprising administering a therapeutically effective amount of the construct of any of statements 1-26, the particle of statement 27, or the pharmaceutical composition of statement 28 to the individual.
 
65. The method of statement 64, further comprising administering a therapeutically effective amount of the composition of statement 31 or 32 to the individual.
 
66. The method of statement 64 or 65, which reduces SARS-CoV-2 viral load in the individual.
 
67. The method of any one of statements 64-66, wherein the individual has been diagnosed with SARS-CoV-2 infection or is considered to be at higher risk than the general population of becoming infected with SARS-CoV-2.
 
68. A kit for treating an infection by SARS-CoV-2 virus comprising a container comprising of the construct of any of statements 1-26, the particle of statement 27, the pharmaceutical composition of statement 28, or the composition of statement 31 or 32 to the individual.
 
69. The kit of statement 68, wherein the container is a syringe or a devise for administration to lungs or nasal passages.
 
70. An isolated biological fluid comprising the construct of one of statements 1-26.
 
71. The isolated biological fluid of statement 65, wherein the biological fluid is blood or plasma.
 
72. A method of generating a particle, the method comprising transfecting a cell infected with SARS-CoV-2 virus with the construct of any of statements 1-26 and incubating the cell under conditions suitable for packaging the construct in the particle.
       

     It is to be understood that while the invention has been described in conjunction with the above embodiments, that the foregoing description and examples are intended to illustrate and not limit the scope of the invention. Other aspects, advantages and modifications within the scope of the invention will be apparent to those skilled in the art to which the invention pertains. 
     Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the present invention, the preferred methods and materials are now described. All publications mentioned herein are incorporated herein by reference to disclose and describe the methods and/or materials in connection with which the publications are cited. 
     It is to be understood that this invention is not limited to particular embodiments described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only by the appended claims. Under no circumstances may the patent be interpreted to be limited by any statement made by any Examiner or any other official or employee of the Patent and Trademark Office unless such statement is specifically and without qualification or reservation expressly adopted in a responsive writing by Applicants. 
     In addition, where the features or aspects of the invention are described in terms of Markush groups, those skilled in the art will recognize that the invention is also thereby described in terms of any individual member or subgroup members of the Markush group.