
                                SEQUENCE LISTING

<110> ChemGenes Corporation
      Srivastava, Suresh C.

<120> RT-qPCR Molecular Detection and
  Diagnosis

<130> 5802.1001002

<150> 17/073,281          
<151> 2020-10-16  

<150> 16/874,647          
<151> 2020-05-14  

<160> 63

<170> FastSEQ for Windows Version 4.0

<210> 1
<211> 25
<212> DNA
<213> Artificial Sequence

<220> 
<223> Probe-1

<220> 
<221> misc_feature   
<222> 1
<223> cytosine is modified with a 6-FAM

<220> 
<221> misc_feature   
<222> 25
<223> thymine is modified with a IQ-4

<400> 1
catcattcac ccttggcaca ggtgt                                       25

<210> 2
<211> 25
<212> DNA
<213> Artificial Sequence

<220> 
<223> Probe-2

<220> 
<221> misc_feature   
<222> 1
<223> cytosine is modified with a 6-FAM

<220> 
<221> misc_feature   
<222> 25
<223> thymine is modified with a BHQ2

<400> 2
catcattcac ccttggcaca ggtgt                                       25

<210> 3
<211> 20
<212> DNA
<213> Artificial Sequence

<220> 
<223> Forward Primer

<400> 3
cccatgttcg tcatgggtgt                                             20

<210> 4
<211> 24
<212> DNA
<213> Artificial Sequence

<220> 
<223> N1 Probe

<400> 4
accccgcatt acgtttggtg gacc                                        24

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

<220> 
<223> N2 Probe

<400> 5
acaatttgcc cccagcgctt cag                                         23

<210> 6
<211> 24
<212> DNA
<213> Artificial Sequence

<220> 
<223> N3 Probe

<400> 6
aycacattgg cacccgcaat cctg                                        24

<210> 7
<211> 20
<212> DNA
<213> Artificial Sequence

<220> 
<223> N1 Forward Primer

<400> 7
gaccccaaaa tcagcgaaat                                             20

<210> 8
<211> 24
<212> DNA
<213> Artificial Sequence

<220> 
<223> N1 Reverse Primer

<400> 8
tctggttact gccagttgaa tctg                                        24

<210> 9
<211> 20
<212> DNA
<213> Artificial Sequence

<220> 
<223> N2 Forward Primer

<400> 9
ttacaaacat tggccgcaaa                                             20

<210> 10
<211> 18
<212> DNA
<213> Artificial Sequence

<220> 
<223> N2 Reverse Primer

<400> 10
gcgcgacatt ccgaagaa                                               18

<210> 11
<211> 22
<212> DNA
<213> Artificial Sequence

<220> 
<223> N3 Forward Primer

<400> 11
gggagccttg aatacaccaa aa                                          22

<210> 12
<211> 21
<212> DNA
<213> Artificial Sequence

<220> 
<223> N3 Reverse Primer

<400> 12
tgtagcacga ttgcagcatt g                                           21

<210> 13
<211> 22
<212> DNA
<213> Artificial Sequence

<220> 
<223> Reverse Primer

<400> 13
ggtcatgagt ccttccacga ta                                          22

<210> 14
<211> 25
<212> DNA
<213> Artificial Sequence

<220> 
<223> Probe-1

<220> 
<221> misc_feature   
<222> 1
<223> cytosine is modified with a 6-FAM

<220> 
<221> misc_feature   
<222> 25
<223> cytosine is modified with a IQ-4

<400> 14
ctgcaccacc aactgcttag caccc                                       25

<210> 15
<211> 25
<212> DNA
<213> Artificial Sequence

<220> 
<223> Probe-2

<220> 
<221> misc_feature   
<222> 1
<223> cytosine is modified with a 6-FAM

<220> 
<221> misc_feature   
<222> 25
<223> cytosine is modified with a BHQ1

<400> 15
ctgcaccacc aactgcttag caccc                                       25

<210> 16
<211> 25
<212> DNA
<213> Artificial Sequence

<220> 
<223> Probe-3

<220> 
<221> misc_feature   
<222> 1
<223> cytosine is modified with a 6-FAM

<220> 
<221> misc_feature   
<222> 25
<223> cytosine is modified with a BHQ2

<400> 16
ctgcaccacc aactgcttag caccc                                       25

<210> 17
<211> 24
<212> DNA
<213> Artificial Sequence

<220> 
<223> Probe-1

<220> 
<221> misc_feature   
<222> 1
<223> adenine is modified with a 6-FAM

<220> 
<221> misc_feature   
<222> 24
<223> cytosine is modified with a IQ-4

<400> 17
accccgcatt acgtttggtg gacc                                        24

<210> 18
<211> 24
<212> DNA
<213> Artificial Sequence

<220> 
<223> Probe-2

<220> 
<221> misc_feature   
<222> 1
<223> adenine is modified with a 6-FAM

<220> 
<221> misc_feature   
<222> 24
<223> cytosine is modified with a BHQ1

<400> 18
accccgcatt acgtttggtg gacc                                        24

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

<220> 
<223> Probe-3

<220> 
<221> misc_feature   
<222> 1
<223> adenine is modified with a 6-FAM

<220> 
<221> misc_feature   
<222> 24
<223> cytosine is modified with a BHQ2

<400> 19
accccgcatt acgtttggtg gacc                                        24

<210> 20
<211> 23
<212> DNA
<213> Artificial Sequence

<220> 
<223> Probe-1

<220> 
<221> misc_feature   
<222> 1
<223> adenine is modified with a 6-FAM

<220> 
<221> misc_feature   
<222> 23
<223> guanine is modified with a IQ-4

<400> 20
acaatttgcc cccagcgctt cag                                         23

<210> 21
<211> 23
<212> DNA
<213> Artificial Sequence

<220> 
<223> Probe-2

<220> 
<221> misc_feature   
<222> 1
<223> adenine is modified with a 6-FAM

<220> 
<221> misc_feature   
<222> 23
<223> guanine is modified with a BHQ1

<400> 21
acaatttgcc cccagcgctt cag                                         23

<210> 22
<211> 23
<212> DNA
<213> Artificial Sequence

<220> 
<223> Probe-3

<220> 
<221> misc_feature   
<222> 1
<223> adenine is modified with a 6-FAM

<220> 
<221> misc_feature   
<222> 23
<223> guanine is modified with a BHQ2

<400> 22
acaatttgcc cccagcgctt cag                                         23

<210> 23
<211> 24
<212> DNA
<213> Artificial Sequence

<220> 
<223> Probe-1

<220> 
<221> misc_feature   
<222> 1
<223> adenine is modified with a 6-FAM

<220> 
<221> misc_feature   
<222> 24
<223> guanine is modified with a IQ-4

<400> 23
aycacattgg cacccgcaat cctg                                        24

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

<220> 
<223> Probe-2

<220> 
<221> misc_feature   
<222> 1
<223> adenine is modified with a 6-FAM

<220> 
<221> misc_feature   
<222> 24
<223> guanine is modified with a BHQ1

<400> 24
aycacattgg cacccgcaat cctg                                        24

<210> 25
<211> 24
<212> DNA
<213> Artificial Sequence

<220> 
<223> Probe-3

<220> 
<221> misc_feature   
<222> 1
<223> adenine is modified with a 6-FAM

<220> 
<221> misc_feature   
<222> 24
<223> guanine is modified with a BHQ2

<400> 25
aycacattgg cacccgcaat cctg                                        24

<210> 26
<211> 22
<212> DNA
<213> Artificial Sequence

<220> 
<223> Forward Primer

<400> 26
acagctgtgt ggtgcttctg tg                                          22

<210> 27
<211> 22
<212> DNA
<213> Artificial Sequence

<220> 
<223> Reverse Primer

<400> 27
cattgtcctc tgtccaggca tc                                          22

<210> 28
<211> 25
<212> DNA
<213> Artificial Sequence

<220> 
<223> Inf A Forward 1

<400> 28
caagaccaat cytgtcacct ctgac                                       25

<210> 29
<211> 25
<212> DNA
<213> Artificial Sequence

<220> 
<223> Inf A Forward 2

<400> 29
caagaccaat yctgtcacct ytgac                                       25

<210> 30
<211> 23
<212> DNA
<213> Artificial Sequence

<220> 
<223> Inf A Reverse 1

<400> 30
gcattytgga caaavcgtct acg                                         23

<210> 31
<211> 23
<212> DNA
<213> Artificial Sequence

<220> 
<223> Inf A Reverse 2

<400> 31
gcattttgga taaagcgtct acg                                         23

<210> 32
<211> 22
<212> DNA
<213> Artificial Sequence

<220> 
<223> Inf B Forward

<400> 32
tcctcaaytc actcttcgag cg                                          22

<210> 33
<211> 21
<212> DNA
<213> Artificial Sequence

<220> 
<223> Inf B Reverse

<400> 33
cggtgctctt gaccaaattg g                                           21

<210> 34
<211> 23
<212> DNA
<213> Artificial Sequence

<220> 
<223> SC2 Forward

<400> 34
ctgcagattt ggatgatttc tcc                                         23

<210> 35
<211> 25
<212> DNA
<213> Artificial Sequence

<220> 
<223> SC2 Reverse

<400> 35
ccttgtgtgg tctgcatgag tttag                                       25

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

<220> 
<223> RnaseP Forward

<400> 36
agatttggac ctgcgagcg                                              19

<210> 37
<211> 20
<212> DNA
<213> Artificial Sequence

<220> 
<223> RnaseP Reverse

<400> 37
gagcggctgt ctccacaagt                                             20

<210> 38
<211> 24
<212> DNA
<213> Artificial Sequence

<220> 
<223> Inf A Probe

<400> 38
tgcagtcctc gctcactggg cacg                                        24

<210> 39
<211> 27
<212> DNA
<213> Artificial Sequence

<220> 
<223> Inf B Probe

<400> 39
ccaattcgag cagctgaaac tgcggtg                                     27

<210> 40
<211> 30
<212> DNA
<213> Artificial Sequence

<220> 
<223> SC2 Probe

<400> 40
attgcaacaa tccatgagca gtgctgactc                                  30

<210> 41
<211> 23
<212> DNA
<213> Artificial Sequence

<220> 
<223> Rnase P Probe

<400> 41
ttctgacctg aaggctctgc gcg                                         23

<210> 42
<211> 24
<212> DNA
<213> Artificial Sequence

<220> 
<223> N1 Probe-3

<220> 
<221> misc_feature   
<222> 1
<223> adenine is modified with a Hex

<220> 
<221> misc_feature   
<222> (9)...(10)
<223> a AmC7-IQ4 is between nucleotides 9 and 10

<220> 
<221> misc_feature   
<222> 24
<223> cytosine is modified with a IQ4

<400> 42
accccgcatt acgtttggtg gacc                                        24

<210> 43
<211> 24
<212> DNA
<213> Artificial Sequence

<220> 
<223> N1 Probe-4

<220> 
<221> misc_feature   
<222> 1
<223> adenine is modified with a Hex

<220> 
<221> misc_feature   
<222> (9)...(10)
<223> a AmC7-IQ4 is between nucleotides 9 and 10

<220> 
<221> misc_feature   
<222> 24
<223> cytosine is modified with a phosphate

<400> 43
accccgcatt acgtttggtg gacc                                        24

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

<220> 
<223> N2 Probe

<220> 
<221> misc_feature   
<222> 1
<223> adenine is modified with a FAM

<220> 
<221> misc_feature   
<222> (6)...(7)
<223> a AmC7-IQ4 is between nucleotides 6 and 7

<220> 
<221> misc_feature   
<222> 23
<223> guanine is modified with a phosphate

<400> 44
acaatttgcc cccagcgctt cag                                         23

<210> 45
<211> 24
<212> DNA
<213> Artificial Sequence

<220> 
<223> N1 Probe-5

<220> 
<221> misc_feature   
<222> 1
<223> adenine is modified with a Hex

<220> 
<221> misc_feature   
<222> 24
<223> n = 3'-OCH3 cytidine modified at the 2' position
      with IQ-4

<400> 45
accccgcatt acgtttggtg gacn                                        24

<210> 46
<211> 24
<212> DNA
<213> Artificial Sequence

<220> 
<223> N1 Probe-6

<220> 
<221> misc_feature   
<222> 1
<223> adenine is modified with a R6G-AmC6

<220> 
<221> misc_feature   
<222> 24
<223> cytosine is modified with a IQ4

<400> 46
accccgcatt acgtttggtg gacc                                        24

<210> 47
<211> 24
<212> DNA
<213> Artificial Sequence

<220> 
<223> N1 Probe-1

<220> 
<221> misc_feature   
<222> 1
<223> adenine is modified with a Hex

<220> 
<221> misc_feature   
<222> 24
<223> cytosine is modified with a IQ4

<400> 47
accccgcatt acgtttggtg gacc                                        24

<210> 48
<211> 24
<212> DNA
<213> Artificial Sequence

<220> 
<223> N1 Probe-2

<220> 
<221> misc_feature   
<222> 1
<223> adenine is modified with a ATTO425

<220> 
<221> misc_feature   
<222> 24
<223> cytosine is modified with a IQ4

<400> 48
accccgcatt acgtttggtg gacc                                        24

<210> 49
<211> 24
<212> DNA
<213> Artificial Sequence

<220> 
<223> N3 Probe

<220> 
<221> misc_feature   
<222> 1
<223> adenine is modified with a  ROX

<220> 
<221> misc_feature   
<222> 2
<223> N = A, T, C or G

<220> 
<221> misc_feature   
<222> 24
<223> guanine is modified with a IQ-4

<400> 49
ancacattgg cacccgcaat cctg                                        24

<210> 50
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Forward primer

<400> 50
aatgatccat ttttgggtgt ttattacc                                    28

<210> 51
<211> 22
<212> DNA
<213> Artificial Sequence

<220> 
<223> Reverse primer

<400> 51
ggtccataag aaaaggctga ga                                          22

<210> 52
<211> 26
<212> DNA
<213> Artificial Sequence

<220> 
<223> S Probe-1

<220> 
<221> misc_feature   
<222> 1
<223> adenine is modified with FAM

<220> 
<221> misc_feature   
<222> 26
<223> cytosine is modified with IQ4

<400> 52
agtgagttca gagtttattc tagtgc                                      26

<210> 53
<211> 26
<212> DNA
<213> Artificial Sequence

<220> 
<223> S Probe-2

<220> 
<221> misc_feature   
<222> 1
<223> adenine is modified with R6G

<220> 
<221> misc_feature   
<222> 26
<223> cytosine is modified with IQ4

<400> 53
agtgagttca gagtttattc tagtgc                                      26

<210> 54
<211> 132
<212> DNA
<213> Artificial Sequence

<220> 
<223> Template DNA version of virus RNA S gene (wild
      type)

<400> 54
gtaatgatcc atttttgggt gtttattacc acaaaaacaa caaaagttgg atggaaagtg 60
agttcagagt ttattctagt gcgaataatt gcacttttga atatgtctct cagccttttc 120
ttatggacct tg                                                     132

<210> 55
<211> 126
<212> DNA
<213> Artificial Sequence

<220> 
<223> Template DNA version of virus RNA S-delta 157/158
      gene (contains 6-base deletion)

<400> 55
gtaatgatcc atttttgggt gtttattacc acaaaaacaa caaaagttgg atggaaagtg 60
aggtttattc tagtgcgaat aattgcactt ttgaatatgt ctctcagcct tttcttatgg 120
accttg                                                            126

<210> 56
<211> 26
<212> DNA
<213> Artificial Sequence

<220> 
<223> S Probe

<400> 56
agtgagttca gagtttattc tagtgc                                      26

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

<220> 
<223> S-delta 157/158 Probe

<400> 57
agtgaggttt attctagtgc                                             20

<210> 58
<211> 20
<212> DNA
<213> Artificial Sequence

<220> 
<223> ORF1a delta-3675-3677 Forward Primer

<400> 58
tgcctgctag ttgggtgatg                                             20

<210> 59
<211> 25
<212> DNA
<213> Artificial Sequence

<220> 
<223> ORF1a delta-3675-3677 Reverse Primer

<400> 59
tgctgtcata aggattagta acact                                       25

<210> 60
<211> 31
<212> DNA
<213> Artificial Sequence

<220> 
<223> ORF1a delta-3675-3677 Probe

<220> 
<221> misc_feature   
<222> 1
<223> guanine is modified with FAM

<220> 
<221> misc_feature   
<222> 31
<223> B is modified with IQ41

<220> 
<221> misc_feature   
<222> 31
<223> B is C, G or T

<400> 60
gtttgtctgg ttttaagcta aaagactgtg b                                31

<210> 61
<211> 24
<212> DNA
<213> Artificial Sequence

<220> 
<223> S delta-69-70 Forward Primer

<400> 61
tcaactcagg acttgttctt acct                                        24

<210> 62
<211> 22
<212> DNA
<213> Artificial Sequence

<220> 
<223> S delta-69-70 Reverse Primer

<400> 62
tggtaggaca gggttatcaa ac                                          22

<210> 63
<211> 25
<212> DNA
<213> Artificial Sequence

<220> 
<223> S delta-69-70 Probe

<220> 
<221> misc_feature   
<222> 1
<223> thymine is modified with ROX

<220> 
<221> misc_feature   
<222> 25
<223> adenine is modified with IQ4

<400> 63
ttccatgcta tacatgtctc tggga                                       25
