                         SEQUENCE LISTING

<110>  The United States of America, as represented by the 
       Secretary, Department of Health and Human Services
       Nyan, Dougbeh-Chris
       Taylor, Deborah R.
       Swinson, Kevin L.
       Rios, Maria
       Ulitzky, Laura E.
 
<120>  METHODS FOR RAPID DETECTION AND IDENTIFICATION OF VIRAL NUCLEIC 
       ACIDS

<130>  4239-92838-02

<150>  US 61/979,446
<151>  2014-04-14

<160>  81    

<170>  PatentIn version 3.5

<210>  1
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HBV universal F3 primer

<400>  1
tcctcacaat accgcagagt                                                   20


<210>  2
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HBV universal R3 primer

<400>  2
gcagcaggat gaagaggaat                                                   20


<210>  3
<211>  46
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HBV universal FIP primer

<400>  3
gttggggact gcgaattttg gctttttaga ctcgtggtgg acttct                      46


<210>  4
<211>  44
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HBV universal RIP primer

<400>  4
tcactcacca acctcctgtc ctttttaaaa cgccgcagac acat                        44


<210>  5
<211>  23
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HBV universal LF primer

<400>  5
ggtgatcccc ctagaaaatt gag                                               23


<210>  6
<211>  22
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HBV universal LR primer

<400>  6
aatttgtcct ggttatcgct gg                                                22


<210>  7
<211>  22
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV universal set 1 F3 primer

<400>  7
gagtgttgta cagcctccag ga                                                22


<210>  8
<211>  18
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV universal set 1 R3 primer

<400>  8
attgggcggc ggttggtg                                                     18


<210>  9
<211>  44
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV universal set 1 FIP primer

<400>  9
ctcggctagc agtcttgcgg ttttgatgac cgggtccttt cttg                        44


<210>  10
<211>  44
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV universal set 1 RIP primer

<400>  10
tagtgttggg tcgcgaaagg cttttcacgg tctacgagac ctcc                        44


<210>  11
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV universal set 1 LF primer

<400>  11
gggcattgag cgggttaatc                                                   20


<210>  12
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV universal set 1 LR primer

<400>  12
ttgcggtact gcctgatagg                                                   20


<210>  13
<211>  18
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV universal set 2 F3 primer

<400>  13
cgggagagcc atagtggt                                                     18


<210>  14
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV universal set 2 F3 primer 2

<400>  14
ggcgacactc caccatagat                                                   20


<210>  15
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV universal set 2 R3 primer

<400>  15
cacggtctac gagacctcc                                                    19


<210>  16
<211>  44
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV universal set 2 FIP primer

<400>  16
ggcattgagc gggttgatcc aatttttgcg gaaccggtga gtac                        44


<210>  17
<211>  44
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV universal set 2 RIP primer

<400>  17
cgcgagactg ctagccgagt ttttacccta tcaggcagta ccac                        44


<210>  18
<211>  18
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV universal set 2 LF primer

<400>  18
tcgtcctggc aattccgg                                                     18


<210>  19
<211>  18
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV universal set 2 LR primer

<400>  19
gtgttgggtc gcgaaagg                                                     18


<210>  20
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV1 F3 primer

<400>  20
ggcgacactc caccatgaat                                                   20


<210>  21
<211>  22
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV1 R3 primer

<400>  21
ctatcaggca gtaccacaag gc                                                22


<210>  22
<211>  43
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV1 FIP primer

<400>  22
cactatggct ctcccgggag ttttcgtcta gccatggcgt tag                         43


<210>  23
<211>  44
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV1 RIP primer

<400>  23
ggaaccggtg agtacaccgg ttttcccaaa tctccaggca ttga                        44


<210>  24
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV1 LF primer

<400>  24
aggctgcacg acactcata                                                    19


<210>  25
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV1 LR primer

<400>  25
gaccgggtcc tttcttgga                                                    19


<210>  26
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV2 F3 primer

<400>  26
cgcagaaagc gtctagcca                                                    19


<210>  27
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV2 R3 primer

<400>  27
cgtactcgca agcaccctat c                                                 21


<210>  28
<211>  45
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV2 FIP primer

<400>  28
atgaccgggc atagagtggg tttttgtggt ctgcggaacc ggtga                       45


<210>  29
<211>  45
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV2 RIP primer

<400>  29
gcccccgcaa gactgctagc ttttctcgca agcaccctat caggc                       45


<210>  30
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV2 LF primer

<400>  30
aaaggaccca gtcttcccgg                                                   20


<210>  31
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV2 LR primer

<400>  31
agcgttgggt tgcgaaaggc c                                                 21


<210>  32
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV3 F3 primer

<400>  32
cccagaaatt tgggcgtgcc                                                   20


<210>  33
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV3 R3 primer

<400>  33
ggaacttgac gtcctgtgg                                                    19


<210>  34
<211>  44
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV3 FIP primer

<400>  34
gcaagcaccc tatcaggcag tattttcgcg agatcactag ccga                        44


<210>  35
<211>  43
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV3 RIP primer

<400>  35
ggaggtctcg tagaccgtgc attttgcgac ggatggtgtt tct                         43


<210>  36
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV3 LF primer

<400>  36
ctttcgcgac ccaacacta                                                    19


<210>  37
<211>  25
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HCV3 LR primer

<400>  37
catgagcaca cttcctaaac ctcaa                                             25


<210>  38
<211>  22
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HIV1 F3 primer

<400>  38
acacagtggg gggacatcaa gc                                                22


<210>  39
<211>  23
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide- HIV1 R3 primer

<400>  39
gtcatccatg ctatttgttc ctg                                               23


<210>  40
<211>  24
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide- HIV1 R3 primer 2

<400>  40
tccatgctat ttgttcctga aggg                                              24


<210>  41
<211>  24
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide- HIV1 R3 primer 3

<400>  41
cctgaagggt actagtagtt cctg                                              24


<210>  42
<211>  44
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide- HIV1 FIP primer

<400>  42
gatgcaatct atcccattct gttttgccat gcaaatgtta aaag                        44


<210>  43
<211>  49
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide- HIV1 FIP primer 2

<400>  43
gatgcaatct atcccattct gttttgccat gcaaatgtta aaagagacc                   49


<210>  44
<211>  47
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide- HIV1 RIP primer

<400>  44
agtgcatgca gggcctattg cacttttgtt cctgctatgt cacttcc                     47


<210>  45
<211>  47
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide- HIV1 RIP primer 2

<400>  45
agtccatgga gggcctattg cacttttgtt cctgctatgt cacttcc                     47


<210>  46
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide- HIV1 LF primer

<400>  46
tcagcttcct cattgatggt c                                                 21


<210>  47
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide- HIV1 LF primer 2

<400>  47
cagcttcctc attgatggtc t                                                 21


<210>  48
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide- HIV1 LR primer

<400>  48
caggccagat gagagaacca a                                                 21


<210>  49
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HEV F3 primer

<400>  49
cggtggtttc tggggtgaca                                                   20


<210>  50
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HEV R3 primer

<400>  50
gagatagcag tcaacggcgc                                                   20


<210>  51
<211>  46
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HEV FIP primer

<400>  51
agggcgagct ccagccccgg ttttgccctt cgccctcccc tatatt                      46


<210>  52
<211>  44
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HEV RIP primer

<400>  52
ccagtcccag cgcccctccg ttttagctgg ggcagatcga cgac                        44


<210>  53
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HEV LF primer

<400>  53
tgtgaaacga catcggcggc                                                   20


<210>  54
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HEV LR primer

<400>  54
cgtcgatctg ccccagctgg                                                   20


<210>  55
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - WNV F3 primer

<400>  55
ggggccaata cgatttgtgt                                                   20


<210>  56
<211>  25
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - WNV F3 primer 2

<400>  56
cgatttgtgt tggctctctt ggcgt                                             25


<210>  57
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - WNV R3 primer

<400>  57
aggccaatca tgactgcaat                                                   20


<210>  58
<211>  46
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - WNV FIP primer

<400>  58
ctctccatcg atccagcact gcttttcttg gcgttcttca ggttca                      46


<210>  59
<211>  45
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - WNV RIP primer

<400>  59
actagggacc ttgaccagtg cttttttccg gtctttcctc ctctt                       45


<210>  60
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - WNV LF primer

<400>  60
cgggtcggag caattgctg                                                    19


<210>  61
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - WNV LR primer

<400>  61
tcaatcggcg gagctcaaaa c                                                 21


<210>  62
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - DENV F3 primer

<400>  62
agcttcatcg tggggatgt                                                    19


<210>  63
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - DENV R3 primer

<400>  63
ctctcccagc gtcaatatgc                                                   20


<210>  64
<211>  44
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - DENV FIP primer

<400>  64
ggaggggtct cctctaacca ctttttggct gcaacccatg gaag                        44


<210>  65
<211>  45
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - DENV RIP primer

<400>  65
caaaacataa cgcagcagcg ggttttgggg gtctcctcta acctc                       45


<210>  66
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - DENV LF primer

<400>  66
tgctacccca tgcgtacag                                                    19


<210>  67
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - DENV LR primer

<400>  67
caacaccagg ggaagctgt                                                    19


<210>  68
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - DENV set 2 F3 primer

<400>  68
atggaagctg tacgcatgg                                                    19


<210>  69
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - DENV set 2 R3 primer

<400>  69
gcgttctgtg cctggaatg                                                    19


<210>  70
<211>  45
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - DENV set 2 FIP primer

<400>  70
aggatacagc ttcccctggt gtttttgtgg ttagaggaga cccct                       45


<210>  71
<211>  45
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - DENV set 2 RIP primer

<400>  71
agaggttaga ggagaccccc gttttagcag gatctctggt ctctc                       45


<210>  72
<211>  18
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - DEN1 F3 primer

<400>  72
ggctgcaacc catggaag                                                     18


<210>  73
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - DEN1 R3 primer

<400>  73
tgcctggaat gatgctgtag                                                   20


<210>  74
<211>  44
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - DEN1 FIP primer

<400>  74
cgctgctgcg ttatgttttg ggttttctgt acgcatgggg tagc                        44


<210>  75
<211>  45
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - DEN1 RIP primer

<400>  75
agaggttaga ggagaccccc gttttagcag gatctctggt ctctc                       45


<210>  76
<211>  360
<212>  DNA
<213>  Hepatitis B virus

<400>  76
aatctcctcg aggactgggg accctgcacc gaacatggag aacatcacat caggattcct       60

aggacccctg ctcgtgttac aggcggggtt tttcttgttg acaagaatcc tcacaatacc      120

gcagagtcta gactcgtggt ggacttctct caattttcta gggggatcac ccgtgtgtct      180

tggccaaaat tcgcagtccc caacctccaa tcactcacca acctcctgtc ctccaatttg      240

tcctggttat cgctggatgt gtctgcggcg ttttatcata ttcctcttca tcctgctgct      300

atgcctcatc ttcttattgg ttcttctgga ttatcagggt atgttgcccg tttgtcctct      360


<210>  77
<211>  420
<212>  DNA
<213>  Hepatitis C virus

<400>  77
ttcacgcaga aagcgtctag ccatggcgtt agtatgagtg ttgtacagcc tccaggaccc       60

cccctcccgg gagagccata gtggtcttcg gaaccggtga gtacaccgga atcgccggga      120

tgaccgggtc ctttcttgga ttaacccgct caatgcccgg aaatttgggc gtgcccccgc      180

aagactgcta gccgagtagt gttgggtcgc gaaaggcctt gcggtactgc ctgatagggt      240

gcttgcgagt gccccgggag gtctcgtaga ccgtgcacca tgagcacgaa tcctaaacct      300

caaagaaaaa ccaaacgtaa caccaaccgc cgcccaatgg acgttaagtt cccgggtggt      360

ggccagatcg ttggcggagt ttacttgttg ccgcgcaggg gccccagatt gggtgtgcgc      420


<210>  78
<211>  420
<212>  DNA
<213>  Hepatitis C virus

<400>  78
gccagccccc tgatgggggc gacactccac catgaatcac tcccctgtga ggaactactg       60

tcttcacgca gaaagcgtct agccatggcg ttagtatgag tgtcgtgcag cctccaggac      120

cccccctccc gggagagcca tagtggtctg cggaaccggt gagtacaccg gaattgccag      180

gacgaccggg tcctttcttg gataaacccg ctcaatgcct ggagatttgg gcgtgccccc      240

gcaagactgc tagccgagta gtgttgggtc gcgaaaggcc ttgtggtact gcctgatagg      300

gtgcttgcga gtgccccggg aggtctcgta gaccgtgcac catgagcacg aatcctaaac      360

ctcaaagaaa aaccaaacgt aacaccaacc gtcgcccaca ggacgtcaag ttcccgggtg      420


<210>  79
<211>  420
<212>  DNA
<213>  Hepatitis C virus

<400>  79
acccgcccct aataggggcg acactccgcc atgaaccact cccctgtgag gaactactgt       60

cttcacgcag aaagcgtcta gccatggcgt tagtatgagt gtcgtacagc ctccaggccc      120

ccccctcccg ggagagccat agtggtctgc ggaaccggtg agtacaccgg aattgccggg      180

aagactgggt cctttcttgg ataaacccac tctatgcccg gtcatttggg cgtgcccccg      240

caagactgct agccgagtag cgttgggttg cgaaaggcct tgtggtactg cctgataggg      300

tgcttgcgag tgccccggga ggtctcgtag accgtgcacc atgagcacaa atcctaaacc      360

tcaaagaaaa accaaaagaa acaccaaccg tcgcccacaa gacgttaagt ttccgggcgg      420


<210>  80
<211>  420
<212>  DNA
<213>  Hepatitis C virus

<400>  80
acctgcctct tacgaggcga cactccacca tggatcactc ccctgtgagg aacttctgtc       60

ttcacgcgga aagcgcctag ccatggcgtt agtacgagtg tcgtgcagcc tccaggaccc      120

cccctcccgg gagagccata gtggtctgcg gaaccggtga gtacaccgga atcgctgggg      180

tgaccgggtc ctttcttgga gcaacccgct caatacccag aaatttgggc gtgcccccgc      240

gagatcacta gccgagtagt gttgggtcgc gaaaggcctt gtggtactgc ctgatagggt      300

gcttgcgagt gccccgggag gtctcgtaga ccgtgcaaca tgagcacact tcctaaacct      360

caaagaaaaa ccaaaagaaa caccatccgt cgcccacagg acgtcaagtt cccgggtggc      420


<210>  81
<211>  22
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic oligonucleotide - HIV1 F3 primer 2

<400>  81
aacaccatgc taaacacagt gg                                                22


