                         SEQUENCE LISTING

<110>  Massachusetts Institute of Technology
 
<120>  COMPOSITIONS AND METHODS FOR DOMINANT ANTIVIRAL THERAPY

<130>  MIT-040WO(01)

<150>  Not Yet Assigned
<151>  Herewith

<150>  63/160,219
<151>  2021-03-12

<160>  15    

<170>  PatentIn version 3.5

<210>  1
<211>  419
<212>  PRT
<213>  SARS-CoV-2

<400>  1

Met Ser Asp Asn Gly Pro Gln Asn Gln Arg Asn Ala Pro Arg Ile Thr 
1               5                   10                  15      


Phe Gly Gly Pro Ser Asp Ser Thr Gly Ser Asn Gln Asn Gly Glu Arg 
            20                  25                  30          


Ser Gly Ala Arg Ser Lys Gln Arg Arg Pro Gln Gly Leu Pro Asn Asn 
        35                  40                  45              


Thr Ala Ser Trp Phe Thr Ala Leu Thr Gln His Gly Lys Glu Asp Leu 
    50                  55                  60                  


Lys Phe Pro Arg Gly Gln Gly Val Pro Ile Asn Thr Asn Ser Ser Pro 
65                  70                  75                  80  


Asp Asp Gln Ile Gly Tyr Tyr Arg Arg Ala Thr Arg Arg Ile Arg Gly 
                85                  90                  95      


Gly Asp Gly Lys Met Lys Asp Leu Ser Pro Arg Trp Tyr Phe Tyr Tyr 
            100                 105                 110         


Leu Gly Thr Gly Pro Glu Ala Gly Leu Pro Tyr Gly Ala Asn Lys Asp 
        115                 120                 125             


Gly Ile Ile Trp Val Ala Thr Glu Gly Ala Leu Asn Thr Pro Lys Asp 
    130                 135                 140                 


His Ile Gly Thr Arg Asn Pro Ala Asn Asn Ala Ala Ile Val Leu Gln 
145                 150                 155                 160 


Leu Pro Gln Gly Thr Thr Leu Pro Lys Gly Phe Tyr Ala Glu Gly Ser 
                165                 170                 175     


Arg Gly Gly Ser Gln Ala Ser Ser Arg Ser Ser Ser Arg Ser Arg Asn 
            180                 185                 190         


Ser Ser Arg Asn Ser Thr Pro Gly Ser Ser Arg Gly Thr Ser Pro Ala 
        195                 200                 205             


Arg Met Ala Gly Asn Gly Gly Asp Ala Ala Leu Ala Leu Leu Leu Leu 
    210                 215                 220                 


Asp Arg Leu Asn Gln Leu Glu Ser Lys Met Ser Gly Lys Gly Gln Gln 
225                 230                 235                 240 


Gln Gln Gly Gln Thr Val Thr Lys Lys Ser Ala Ala Glu Ala Ser Lys 
                245                 250                 255     


Lys Pro Arg Gln Lys Arg Thr Ala Thr Lys Ala Tyr Asn Val Thr Gln 
            260                 265                 270         


Ala Phe Gly Arg Arg Gly Pro Glu Gln Thr Gln Gly Asn Phe Gly Asp 
        275                 280                 285             


Gln Glu Leu Ile Arg Gln Gly Thr Asp Tyr Lys His Trp Pro Gln Ile 
    290                 295                 300                 


Ala Gln Phe Ala Pro Ser Ala Ser Ala Phe Phe Gly Met Ser Arg Ile 
305                 310                 315                 320 


Gly Met Glu Val Thr Pro Ser Gly Thr Trp Leu Thr Tyr Thr Gly Ala 
                325                 330                 335     


Ile Lys Leu Asp Asp Lys Asp Pro Asn Phe Lys Asp Gln Val Ile Leu 
            340                 345                 350         


Leu Asn Lys His Ile Asp Ala Tyr Lys Thr Phe Pro Pro Thr Glu Pro 
        355                 360                 365             


Lys Lys Asp Lys Lys Lys Lys Ala Asp Glu Thr Gln Ala Leu Pro Gln 
    370                 375                 380                 


Arg Gln Lys Lys Gln Gln Thr Val Thr Leu Leu Pro Ala Ala Asp Leu 
385                 390                 395                 400 


Asp Asp Phe Ser Lys Gln Leu Gln Gln Ser Met Ser Ser Ala Asp Ser 
                405                 410                 415     


Thr Gln Ala 
            


<210>  2
<211>  12
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide

<400>  2

Gly Gly Ser Gly Gly Thr Gly Ser Gly Gly Ser Gly 
1               5                   10          


<210>  3
<211>  149
<212>  PRT
<213>  Staphylococcus aureus

<400>  3

Ala Thr Ser Thr Lys Lys Leu His Lys Glu Pro Ala Thr Leu Ile Lys 
1               5                   10                  15      


Ala Ile Asp Gly Asp Thr Val Lys Leu Met Tyr Lys Gly Gln Pro Met 
            20                  25                  30          


Thr Phe Arg Leu Leu Leu Val Asp Thr Pro Glu Thr Lys His Pro Lys 
        35                  40                  45              


Lys Gly Val Glu Lys Tyr Gly Pro Glu Ala Ser Ala Phe Thr Lys Lys 
    50                  55                  60                  


Met Val Glu Asn Ala Lys Lys Ile Glu Val Glu Phe Asp Lys Gly Gln 
65                  70                  75                  80  


Arg Thr Asp Lys Tyr Gly Arg Gly Leu Ala Tyr Ile Tyr Ala Asp Gly 
                85                  90                  95      


Lys Met Val Asn Glu Ala Leu Val Arg Gln Gly Leu Ala Lys Val Ala 
            100                 105                 110         


Tyr Val Tyr Lys Pro Asn Asn Thr His Glu Gln His Leu Arg Lys Ser 
        115                 120                 125             


Glu Ala Gln Ala Lys Lys Glu Lys Leu Asn Ile Trp Ser Glu Asp Asn 
    130                 135                 140                 


Ala Asp Ser Gly Gln 
145                 


<210>  4
<211>  580
<212>  PRT
<213>  Artificial sequence

<220>
<223>  Synthetic oligonucleotide

<400>  4

Met Ser Asp Asn Gly Pro Gln Asn Gln Arg Asn Ala Pro Arg Ile Thr 
1               5                   10                  15      


Phe Gly Gly Pro Ser Asp Ser Thr Gly Ser Asn Gln Asn Gly Glu Arg 
            20                  25                  30          


Ser Gly Ala Arg Ser Lys Gln Arg Arg Pro Gln Gly Leu Pro Asn Asn 
        35                  40                  45              


Thr Ala Ser Trp Phe Thr Ala Leu Thr Gln His Gly Lys Glu Asp Leu 
    50                  55                  60                  


Lys Phe Pro Arg Gly Gln Gly Val Pro Ile Asn Thr Asn Ser Ser Pro 
65                  70                  75                  80  


Asp Asp Gln Ile Gly Tyr Tyr Arg Arg Ala Thr Arg Arg Ile Arg Gly 
                85                  90                  95      


Gly Asp Gly Lys Met Lys Asp Leu Ser Pro Arg Trp Tyr Phe Tyr Tyr 
            100                 105                 110         


Leu Gly Thr Gly Pro Glu Ala Gly Leu Pro Tyr Gly Ala Asn Lys Asp 
        115                 120                 125             


Gly Ile Ile Trp Val Ala Thr Glu Gly Ala Leu Asn Thr Pro Lys Asp 
    130                 135                 140                 


His Ile Gly Thr Arg Asn Pro Ala Asn Asn Ala Ala Ile Val Leu Gln 
145                 150                 155                 160 


Leu Pro Gln Gly Thr Thr Leu Pro Lys Gly Phe Tyr Ala Glu Gly Ser 
                165                 170                 175     


Arg Gly Gly Ser Gln Ala Ser Ser Arg Ser Ser Ser Arg Ser Arg Asn 
            180                 185                 190         


Ser Ser Arg Asn Ser Thr Pro Gly Ser Ser Arg Gly Thr Ser Pro Ala 
        195                 200                 205             


Arg Met Ala Gly Asn Gly Gly Asp Ala Ala Leu Ala Leu Leu Leu Leu 
    210                 215                 220                 


Asp Arg Leu Asn Gln Leu Glu Ser Lys Met Ser Gly Lys Gly Gln Gln 
225                 230                 235                 240 


Gln Gln Gly Gln Thr Val Thr Lys Lys Ser Ala Ala Glu Ala Ser Lys 
                245                 250                 255     


Lys Pro Arg Gln Lys Arg Thr Ala Thr Lys Ala Tyr Asn Val Thr Gln 
            260                 265                 270         


Ala Phe Gly Arg Arg Gly Pro Glu Gln Thr Gln Gly Asn Phe Gly Asp 
        275                 280                 285             


Gln Glu Leu Ile Arg Gln Gly Thr Asp Tyr Lys His Trp Pro Gln Ile 
    290                 295                 300                 


Ala Gln Phe Ala Pro Ser Ala Ser Ala Phe Phe Gly Met Ser Arg Ile 
305                 310                 315                 320 


Gly Met Glu Val Thr Pro Ser Gly Thr Trp Leu Thr Tyr Thr Gly Ala 
                325                 330                 335     


Ile Lys Leu Asp Asp Lys Asp Pro Asn Phe Lys Asp Gln Val Ile Leu 
            340                 345                 350         


Leu Asn Lys His Ile Asp Ala Tyr Lys Thr Phe Pro Pro Thr Glu Pro 
        355                 360                 365             


Lys Lys Asp Lys Lys Lys Lys Ala Asp Glu Thr Gln Ala Leu Pro Gln 
    370                 375                 380                 


Arg Gln Lys Lys Gln Gln Thr Val Thr Leu Leu Pro Ala Ala Asp Leu 
385                 390                 395                 400 


Asp Asp Phe Ser Lys Gln Leu Gln Gln Ser Met Ser Ser Ala Asp Ser 
                405                 410                 415     


Thr Gln Ala Gly Gly Ser Gly Gly Thr Gly Ser Gly Gly Ser Gly Ala 
            420                 425                 430         


Thr Ser Thr Lys Lys Leu His Lys Glu Pro Ala Thr Leu Ile Lys Ala 
        435                 440                 445             


Ile Asp Gly Asp Thr Val Lys Leu Met Tyr Lys Gly Gln Pro Met Thr 
    450                 455                 460                 


Phe Arg Leu Leu Leu Val Asp Thr Pro Glu Thr Lys His Pro Lys Lys 
465                 470                 475                 480 


Gly Val Glu Lys Tyr Gly Pro Glu Ala Ser Ala Phe Thr Lys Lys Met 
                485                 490                 495     


Val Glu Asn Ala Lys Lys Ile Glu Val Glu Phe Asp Lys Gly Gln Arg 
            500                 505                 510         


Thr Asp Lys Tyr Gly Arg Gly Leu Ala Tyr Ile Tyr Ala Asp Gly Lys 
        515                 520                 525             


Met Val Asn Glu Ala Leu Val Arg Gln Gly Leu Ala Lys Val Ala Tyr 
    530                 535                 540                 


Val Tyr Lys Pro Asn Asn Thr His Glu Gln His Leu Arg Lys Ser Glu 
545                 550                 555                 560 


Ala Gln Ala Lys Lys Glu Lys Leu Asn Ile Trp Ser Glu Asp Asn Ala 
                565                 570                 575     


Asp Ser Gly Gln 
            580 


<210>  5
<211>  1743
<212>  DNA
<213>  Artificial sequence

<220>
<223>  Synthetic oligonucleotide

<400>  5
atgtccgaca acggcccgca gaatcaacga aacgctcccc gaattacatt cggtggtcca       60

tcagactcca ctggaagtaa tcagaatggg gaacggtcag gcgccagatc aaagcaacgg      120

cgaccgcagg gtctcccgaa taataccgct tcctggttta ccgccctcac ccagcatggc      180

aaagaagacc tgaagtttcc aaggggtcag ggggtaccca ttaatactaa ttcctcccca      240

gacgaccaga ttggctacta tcggcgagcg accaggcgca tacggggtgg tgatgggaaa      300

atgaaggatc tttcacctag atggtatttt tactatctgg gtacgggtcc ggaagcgggt      360

ctgccctacg gcgccaacaa ggacggtata atatgggttg caactgaagg agctttgaat      420

acacctaagg accacattgg cactcgaaat cccgccaaca atgcagccat cgttttgcag      480

ctgccgcagg gtactacact tccaaagggt ttctatgccg agggatctag aggcgggtca      540

caggcatcct cccggtcaag ttcaagatct cgaaattcat ctcgcaacag taccccaggc      600

tcttctagag gtacctcacc ggcccggatg gccggcaacg gtggcgatgc tgctctcgcg      660

ctcctcctcc tggaccgcct taatcagctg gaaagtaaga tgtccgggaa gggacaacaa      720

caacaaggcc agacagtaac taaaaagagc gcggcagaag cgtcaaagaa gccccgacaa      780

aaaaggactg ctacaaaggc atataatgtc acccaggctt tcggccgcag aggcccagag      840

cagacccagg gcaactttgg tgatcaagag ttgatccggc agggcactga ctataaacac      900

tggccccaga tcgcccaatt cgcaccaagt gcgagcgcat ttttcgggat gtctaggatt      960

ggaatggaag tcactccatc tggtacctgg ttgacataca caggtgcgat aaagctggac     1020

gacaaggatc cgaactttaa agatcaggtt attttgctca acaaacacat cgatgcttac     1080

aagactttcc cccctactga acccaaaaag gataaaaaga agaaagcgga cgaaacacag     1140

gcgttgccgc agagacagaa aaaacagcaa actgtgactc ttcttccggc ggcagacttg     1200

gatgatttct ctaagcaact gcagcagagt atgtcctctg ctgactcaac gcaagccggc     1260

gggagtggtg gtacgggaag cgggggcagc ggcgctacat caacaaagaa actgcacaag     1320

gaaccagcta ctcttatcaa agctattgac ggcgatactg tgaaacttat gtacaaaggg     1380

caaccaatga catttcggct tttgctggta gatactccag aaacaaagca tcctaagaag     1440

ggggtagaga aatacggccc ggaggcgtct gcatttacaa aaaaaatggt cgaaaatgct     1500

aagaaaattg aagtcgagtt cgataaaggt cagcggacgg acaagtatgg aaggggattg     1560

gcttatatat atgccgacgg aaaaatggta aatgaagcat tggtgcgcca ggggttggca     1620

aaagtggcct acgtctacaa accgaataac acccatgaac agcatttgag aaaatctgaa     1680

gcccaggcga agaaagagaa actcaacatc tggtcagaag ataatgctga cagtggacaa     1740

taa                                                                   1743


<210>  6
<211>  127
<212>  PRT
<213>  SARS-CoV-2

<400>  6

Thr Ala Ser Trp Phe Thr Ala Leu Thr Gln His Gly Lys Glu Asp Leu 
1               5                   10                  15      


Lys Phe Pro Arg Gly Gln Gly Val Pro Ile Asn Thr Asn Ser Ser Pro 
            20                  25                  30          


Asp Asp Gln Ile Gly Tyr Tyr Arg Arg Ala Thr Arg Arg Ile Arg Gly 
        35                  40                  45              


Gly Asp Gly Lys Met Lys Asp Leu Ser Pro Arg Trp Tyr Phe Tyr Tyr 
    50                  55                  60                  


Leu Gly Thr Gly Pro Glu Ala Gly Leu Pro Tyr Gly Ala Asn Lys Asp 
65                  70                  75                  80  


Gly Ile Ile Trp Val Ala Thr Glu Gly Ala Leu Asn Thr Pro Lys Asp 
                85                  90                  95      


His Ile Gly Thr Arg Asn Pro Ala Asn Asn Ala Ala Ile Val Leu Gln 
            100                 105                 110         


Leu Pro Gln Gly Thr Thr Leu Pro Lys Gly Phe Tyr Ala Glu Gly 
        115                 120                 125         


<210>  7
<211>  119
<212>  PRT
<213>  SARS-CoV-2

<400>  7

Thr Lys Lys Ser Ala Ala Glu Ala Ser Lys Lys Pro Arg Gln Lys Arg 
1               5                   10                  15      


Thr Ala Thr Lys Ala Tyr Asn Val Thr Gln Ala Phe Gly Arg Arg Gly 
            20                  25                  30          


Pro Glu Gln Thr Gln Gly Asn Phe Gly Asp Gln Glu Leu Ile Arg Gln 
        35                  40                  45              


Gly Thr Asp Tyr Lys His Trp Pro Gln Ile Ala Gln Phe Ala Pro Ser 
    50                  55                  60                  


Ala Ser Ala Phe Phe Gly Met Ser Arg Ile Gly Met Glu Val Thr Pro 
65                  70                  75                  80  


Ser Gly Thr Trp Leu Thr Tyr Thr Gly Ala Ile Lys Leu Asp Asp Lys 
                85                  90                  95      


Asp Pro Asn Phe Lys Asp Gln Val Ile Leu Leu Asn Lys His Ile Asp 
            100                 105                 110         


Ala Tyr Lys Thr Phe Pro Pro 
        115                 


<210>  8
<211>  55
<212>  PRT
<213>  SARS-CoV-2

<400>  8

Pro Thr Glu Pro Lys Lys Asp Lys Lys Lys Lys Ala Asp Glu Thr Gln 
1               5                   10                  15      


Ala Leu Pro Gln Arg Gln Lys Lys Gln Gln Thr Val Thr Leu Leu Pro 
            20                  25                  30          


Ala Ala Asp Leu Asp Asp Phe Ser Lys Gln Leu Gln Gln Ser Met Ser 
        35                  40                  45              


Ser Ala Asp Ser Thr Gln Ala 
    50                  55  


<210>  9
<211>  49
<212>  PRT
<213>  SARS-CoV-2

<400>  9

Met Ser Asp Asn Gly Pro Gln Asn Gln Arg Asn Ala Pro Arg Ile Thr 
1               5                   10                  15      


Phe Gly Gly Pro Ser Asp Ser Thr Gly Ser Asn Gln Asn Gly Glu Arg 
            20                  25                  30          


Ser Gly Ala Arg Ser Lys Gln Arg Arg Pro Gln Gly Leu Pro Asn Asn 
        35                  40                  45              


Thr 
    


<210>  10
<211>  73
<212>  PRT
<213>  SARS-CoV-2

<400>  10

Gly Ser Arg Gly Gly Ser Gln Ala Ser Ser Arg Ser Ser Ser Arg Ser 
1               5                   10                  15      


Arg Asn Ser Ser Arg Asn Ser Thr Pro Gly Ser Ser Arg Gly Thr Ser 
            20                  25                  30          


Pro Ala Arg Met Ala Gly Asn Gly Gly Asp Ala Ala Leu Ala Leu Leu 
        35                  40                  45              


Leu Leu Asp Arg Leu Asn Gln Leu Glu Ser Lys Met Ser Gly Lys Gly 
    50                  55                  60                  


Gln Gln Gln Gln Gly Gln Thr Val Thr 
65                  70              


<210>  11
<211>  28
<212>  PRT
<213>  SARS-CoV-2

<400>  11

Pro Thr Glu Pro Lys Lys Asp Lys Lys Lys Lys Ala Asp Glu Thr Gln 
1               5                   10                  15      


Ala Leu Pro Gln Arg Gln Lys Lys Gln Gln Thr Val 
            20                  25              


<210>  12
<211>  28
<212>  PRT
<213>  SARS-CoV-2

<400>  12

Val Thr Leu Leu Pro Ala Ala Asp Leu Asp Asp Phe Ser Lys Gln Leu 
1               5                   10                  15      


Gln Gln Ser Met Ser Ser Ala Asp Ser Thr Gln Ala 
            20                  25              


<210>  13
<211>  149
<212>  PRT
<213>  Staphylococcus aureus

<400>  13

Ala Thr Ser Thr Lys Lys Leu His Lys Glu Pro Ala Thr Leu Ile Lys 
1               5                   10                  15      


Ala Ile Asp Gly Asp Thr Val Lys Leu Met Tyr Lys Gly Gln Pro Met 
            20                  25                  30          


Thr Phe Arg Leu Leu Leu Val Asp Thr Pro Ser Thr Lys His Pro Lys 
        35                  40                  45              


Lys Gly Val Glu Lys Tyr Gly Pro Glu Ala Ser Ala Phe Thr Lys Lys 
    50                  55                  60                  


Met Val Glu Asn Ala Lys Lys Ile Glu Val Glu Phe Asp Lys Gly Gln 
65                  70                  75                  80  


Arg Thr Asp Lys Tyr Gly Gly Gly Leu Ala Tyr Ile Tyr Ala Asp Gly 
                85                  90                  95      


Lys Met Val Asn Glu Ala Leu Val Arg Gln Gly Leu Ala Lys Val Ala 
            100                 105                 110         


Tyr Val Tyr Lys Pro Asn Asn Thr His Glu Gln His Leu Arg Lys Ser 
        115                 120                 125             


Glu Ala Gln Ala Lys Lys Glu Lys Leu Asn Ile Trp Ser Glu Asp Asn 
    130                 135                 140                 


Ala Asp Ser Gly Gln 
145                 


<210>  14
<211>  8
<212>  RNA
<213>  Artificial sequence

<220>
<223>  Synthetic oligonucleotide

<400>  14
uuuuuuuu                                                                 8


<210>  15
<211>  173
<212>  PRT
<213>  SARS-CoV-2

<400>  15

Thr Lys Lys Ser Ala Ala Glu Ala Ser Lys Lys Pro Arg Gln Lys Arg 
1               5                   10                  15      


Thr Ala Thr Lys Ala Tyr Asn Val Thr Gln Ala Phe Gly Arg Arg Gly 
            20                  25                  30          


Pro Glu Gln Thr Gln Gly Asn Phe Gly Asp Gln Glu Leu Ile Arg Gln 
        35                  40                  45              


Gly Thr Asp Tyr Lys His Trp Pro Gln Ile Ala Gln Phe Ala Pro Ser 
    50                  55                  60                  


Ala Ser Ala Phe Phe Gly Met Ser Arg Ile Gly Met Glu Val Thr Pro 
65                  70                  75                  80  


Ser Gly Thr Trp Leu Thr Tyr Thr Gly Ala Ile Lys Leu Asp Asp Lys 
                85                  90                  95      


Asp Pro Asn Phe Lys Asp Gln Val Ile Leu Leu Asn Lys His Ile Asp 
            100                 105                 110         


Ala Tyr Lys Thr Phe Pro Pro Thr Glu Pro Lys Lys Asp Lys Lys Lys 
        115                 120                 125             


Lys Ala Asp Glu Thr Gln Ala Leu Pro Gln Arg Gln Lys Lys Gln Gln 
    130                 135                 140                 


Thr Val Thr Leu Leu Pro Ala Ala Asp Leu Asp Asp Phe Ser Lys Gln 
145                 150                 155                 160 


Leu Gln Gln Ser Met Ser Ser Ala Asp Ser Thr Gln Ala 
                165                 170             


