SN

Primer ID

Sequence (5′ → 3′)

Size (bp)

GC (%)

Tm (°G)

ΔG (kcal/mol)

Conserved domains
(Targets)

1

P1-F

TCCGTGGAGGAGGTCTTATC

20

55.00

58.44

-21.04

Nsp1

P1-R

ACACATAGGGCTGTTCAAGTT

21

42.86

58.00

-21.21

P1-Probe

TGGCACTTGTGGCTTAGTAGAAGTTGA

27

44.44

64.94

-28.35

2

P2-F

GAGGCTGTGTGTTCTCTTATGT

22

45.45

58.58

-22.17

Nsp2

P2-R
 

CCTTCTCCAACAACACCTGTAT

22

45.45

58.50

-21.99

P2-probe

AAGTGTGCCTATTGGGTTCCACGT

24

50.00

65.20

-26.62

3

P3-F

AAACTCAAACCCGTCCTTGAT

21

42.86

58.28

-21.33

Nsp2

P3-R

ACAATTTCCCAACCGTCTCTAA

22

40.91

58.15

-21.74

P3-Probe

TGGCTTGAAGAGAAGTTTAAGGAAGGTGT

29

41.38

65.11

-29.49

4

P4-F

TTCCCATCTGGTAAAGTTGAGG

22

45.45

58.21

-21.76

Nsp5

P4-R

CAGATCACATGTCTTGGACAGTA

23

43.48

58.45

-22.57

P4-probe

ACGGTCTTTGGCTTGATGACGTAGT

25

48.00

65.03

-27.39

5

P5-F

GCTATGAGGCCCAATTTCACTA

22

45.45

58.70

-22.10

Nsp5

P5-R

CTAAGTCTGTGCCAGCATGAA

21

47.62

58.80

-21.84

P5--probe

AGGGTTCATTCCTTAATGGTTCATGTGGT

29

41.38

65.24

-29.45

6

Env-F

GCACAAGCTGATGAGTACGA

20

50.00

58.50

-21.39

ORF3b
and
Cov_E

Env-R

GCAAGAATACCACGAAAGCAAG

22

45.45

59.00

-22.64

Env-Probe

TCGTTTCGGAAGAGACAGGTACGT

24

50.00

64.14

-26.35

7

RDRP-F

GCTGCCGGTACTACACAAA

19

52.63

58.27

-20.72

Nsp8

RDRP-R

TCGGATAACAGTGCAAGTACAA

22

40.91

58.25

-21.98

RDRP-probe

CTGCTTGCACTGATGACAATGCGT

24

50.00

65.19

-27.19

8

P8-F

ACTGACATAGCCAAGAAACCA

21

42.86

57.72

-21.07

Nsp15-NTD
and
Nsp11

P8-R

GAACACCATTACGGGCATTTC

21

47.62

58.35

-21.73

P8-probe

CTGAAACGATTTGTGCACCATCACTGT

27

44.44

65.14

-28.89

9

P9-F

GGTGTTATCACGCATGATGTTTC

23

43.48

59.16

-23.25

Nsp13-helicase

P9-R

TTTCTCCAAGCAGGGTTACG

20

50.00

58.31

-21.07

P9-probe

ACAGGCCACAAATAGGCGTGGTAA

24

50.00

65.25

-26.68

10

P10-F

GCACAAGCTTTAAACACGCT

20

45.00

58.36

-21.32

Spike_S1-S2_S2

P10-R

GTCTGCCTGTGATCAACCTATC

22

50.00

59.05

-22.51

P10-Probe

TCACGTCTTGACAAAGTTGAGGCTGA

26

46.15

65.24

-28.11

Pango

Sample

B.1.617.2 (Pango v.3.1.10), Delta (B.1.617.2-like) (Scorpio)

150

AY.3 (Pango v.3.1.9), Delta (B.1.617.2-like) (Scorpio)

29

AY.23 (Pango v.3.1.11 ), Delta (B.1.617.2-like) (Scorpio)

2

AY.4 (Pango v.3.1.11 2021-08-09), Delta (B.1.617.2-like) (Scorpio)

2

No

Conserved region

Conserved domains(Targets)

1

AAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTT

Nsp1 is a cleavage product of ORF1a.

2

CCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCACGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACAACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGAATCGCCATTATTTTGGCAT

Nsp2
N-Terminal

3

TATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTTAAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAATTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAA

Nsp2- which is 100% preserved and fit for more genetic studies.

4

CTCTATCACCTCAGCTGTTTTGCAGAGTGGTTTTAGAAAAATGGCATTCCCATCTGGTAAAGTTGAGGGTTGTATGGTACAAGTAACTTGTGGTACAACTACACTTAACGGTCTTTGGCTTGATGACGTAGTTTACTGTCCAAGACATGTGATCTGCACCTCTGAAGACATGCTTAACCCTAATTATGAAGATTTACTCATTCGTAAGTCTAATCATAATTT

Nsp5- called the prime protease (Mpro or 3C-like protease 3CLpro) dominant enzyme.

5

AGGACAGACTTTTTCAGTGTTAGCTTGTTACAATGGTTCACCATCTGGTGTTTACCAATGTGCTATGAGGCCCAATTTCACTATTAAGGGTTCATTCCTTAATGGTTCATGTGGTAGTGTTGGTTTTAACATAGATTATGACTGTGTCTCTTTTTGTTACATGCACCATATGGAATTACCAACTGGAGTTCATGCTGGCACAGACTTAGAAGGTAACTTTTATGGACCTTTTGTTGACAGGCAAACAGCACAAGCAGCTGGTACGGACACAACTATTACAGTTAATGTTTTAGCTTGGTTGTACGCTGCTGTTATAAATGGAGACAGGTGGTTTCTCAATCGATTTACCACAACTCTTAATGACTTTAACCTTGTGG

Nsp5- in this procedure also building it a peak value target for the circumstances of anti-coronavirus therapeutics.

6

CCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTATTCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGTGAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTC

Coronavirus envelope (E) proteins -that are highly pathogenic SARS-CoV-2.
Also accessory protein ORF3b- that blocks IFN synthesis, signaling and stops spreading to the nucleus in transfected cells.

7

AACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTACACAAACTGCTTGCACTGATGACAATGCGTTAGCTTACTACAACACAACAAAGGGAGGTAGGTTTGTACTTGCACTGTTATCCGATTTACAGGATTTGAAATGGGCTAGATTCCCTAAGAGTGATGGAACTGGTACTATCTATA

Nsp8 grants processivity on RNA-dependent RNA polymerase. Key component Nsp9 constantly seizes other proteins in the replicase complex to moderate efficient virus transcription and replication. Oligomerization of Porcine Delta Coronavirus (PDCoV).

8

ATCTGGGACTACAAAAGAGATGCTCCAGCACATATATCTACTATTGGTGTTTGTTCTATGACTGACATAGCCAAGAAACCAACTGAAACGATTTGTGCACCATCACTGTCTTTTTTGATGGTAGAGTTGATGGTCAAGTAGACTTATTTAGAAATGCCCGTAATGGTGTTCTTATTACAGAAGGTAGTGTTAAAGGTTTACAACCATCTGTAGGTCCCAAACAAGCTAGTCTTAATGGAGTCACATTAATTGGAGAAGCCGTAAAAACACAGTTCAATTATTATAAGAAAGTTGATGGTGTTGT

Nsp15-NTD
Nsp15 diverges from that of further coronavirus members and has been shown to exist as a dimer and a monomer in solution. Nsp11 from the product of enveloped positive-strand RNA virus PRRSV performs as a dimer.

9

GGCGTTGTCCTGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGATAATAAGCTTAAAGCACATAAAGACAAATCAGCTCAATGCTTTAAAATGTTTTATAAGGGTGTTATCACGCATGATGTTTCATCTGCAATTAACAGGCCACAAATAGGCGTGGTAAGAGAATTCCTTACACGTAACCCTGCTTGGAGAAA

The helicase domain Nsp13 from delta coronavirus, along with pathogenic human viruses (SARS-CoV-2).

10

ATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTA

 S1/S2 cleavage region and the S2 fusion subunit of the spike (S) glycoprotein SARS-CoV-2 depict a central role in viral entry by inaugurating fusion of the viral and cellular membranes.