Table 2 Primers released by WHO to detect SARS-CoV-2 using polymerase chain reaction.

From: Design and in silico validation of polymerase chain reaction primers to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

Location/primer or probe name

Sequence (5′ > 3′)

Length

Tm

GC (%)

SC

SC 3'

Target

Size

Specificity

No mis

10% mis

Germany (17 January 2020)

RdRP_SARSr-F2

GTGARATGGTCATGTGTGGCGG

22

63.25

57.14

5.5

1

RdRp

100

4

(0.001%)

210,600 (99.41%)

RdRP_SARSr-R1

CARATGTTAAASACACTATTAGCATA

26

54.25

25

5

4

RdRp

RdRP_SARSr-P2

FAM-CAGGTGGAACCTCATCAGGAGATGC-BBQ

25

64.89

56

6

5

RdRp

E_Sarbeco_F1

ACAGGTACGTTAATAGTTAATAGCGT

26

58.29

34.62

8

8

E

113

210,071

(99.16%)

210,610 (99.42%)

E_Sarbeco_R2

ATATTGCAGCAGTACGCACACA

22

60.93

45.45

7

1

E

E_Sarbeco_P1

FAM-ACACTAGCCATCCTTACTGCGCTTCG-BBQ

26

66.78

53.85

4

2

E

N_Sarbeco_F1

CACATTGGCACCCGCAATC

19

60.15

57.89

4

0

N

128

205,051 (96.79%)

209,594 (98.94%)

N_Sarbeco_R1

GAGGAACGAGAAGAGGCTTG

20

58

55

3

1

N

N_Sarbeco_P1

AM-ACTTCCTCAAGGAACAACATTGCCA-BBQ

25

63.15

44

8

3

N

Hong Kong (23 January 2020)

HKU-ORF1b-nsp14F

TGGGGYTTTACRGGTAACCT

20

47.07

50

7.5

4.5

ORF1b

132

209,633 (98.96%)

211,205 (99.70%)

HKU- ORF1b-nsp14R

AACRCGCTTAACAAAGCACTC

21

53.44

45

4

0

ORF1b

HKU-ORF1b-nsp141P

FAM-TAGTTGTGATGCWATCATGACTAG-TAMRA

24

54.86

39.13

10.5

6,5

ORF1b

HKU-NF

TAATCAGACAAGGAACTGATTA

22

52.27

31.82

7

7

N

110

207,359 (97.88%)

209,580 (98.93%)

HKU-NR

CGAAGGTGTGACTTCCATG

19

55.95

52.63

4

4

N

HKU-NP

FAM-GCAAATTGTGCAATTTGCGG-TAMRA

20

58.05

45

14

6

N

China (24 January 2020)

ORF1ab_F

CCCTGTGGGTTTTACACTTAA

21

55.7

42.86

4

4

ORF1ab

119

205,630 (97.07%)

206,591 (97.52%)

ORF1ab_R

ACGATTGTGCATCAGCTGA

19

57.46

47.37

8

8

ORF1ab

ORF1ab_P

FAM-CCGTCTGCGGTATGTGGAAAGGTTATGG-BHQ1

28

67.24

53.57

3

0

ORF1ab

N_F

GGGGAACTTCTCCTGCTAGAAT

22

59.23

50

7

2

N

99

124,314 (58.68%)

131,849 (62.24%)

N_R

CAGACATTTTGCTCTCAAGCTG

22

58.18

45.45

4

2

N

N_P

FAM-TTGCTGCTGCTTGACAGATT-TAMRA

20

58.39

45

4

1

N

Japan (24 January 2020)

NIID_WH-1_F501-F

TTCGGATGCTCGAACTGCACC

21

63.27

57.14

4

0

ORF1a

413

208,053 (98.21%)

210,374 (99.31%)

NIID_WH-1_R913-R

CTTTACCAGCACGTGCTAGAAGG

23

61.47

52.17

10

10

ORF1a

NIID_WH-1_F509-F

CTCGAACTGCACCTCATGG

19

58.24

57.89

4

2

ORF1a

346

206,148 (97.31%)

210,255 (99.25%)

NIID_WH-1_R854-R

CAGAAGTTGTTATCGACATAGC

22

55.05

40.91

4

3

ORF1a

NIID_WH-1_Seq_F519

ACCTCATGGTCATGTTATGG

20

54.79

45

6

1

ORF1a

322

206,749 (97.59%)

208,982 (98.65%)

NIID_WH-1_Seq_R840

GACATAGCGAGTGTATGCC

19

55.61

52.63

4

3

ORF1a

WuhanCoV-spk1-f

TTGGCAAAATTCAAGACTCACTTT

24

58.02

33.33

5

3

S

547

207,888 (98.13%)

209,802 (99.04%)

WuhanCoV-spk2-r

TGTGGTTCATAAAAATTCCTTTGTG

25

56.98

32

4

3

S

NIID_WH-1_F24381

TCAAGACTCACTTTCTTCCAC

21

55.48

42.86

4

0

S

493

207,271 (98.74%)

209,820 (99.04%)

NIID_WH-1_R24873

ATTTGAAACAAAGACACCTTCAC

23

56.13

34.78

5

0

S

NIID_WH-1_Seq_F24383

AAGACTCACTTTCTTCCACAG

21

55.47

42.86

4

1

S

483

207,222 (97.82%)

209,803 (99.04%)

NIID_WH-1_Seq_R24865

CAAAGACACCTTCACGAGG

19

55.88

52.63

3

2

S

NIID_2019-nCOV_N_F2

AAATTTTGGGGACCAGGAAC

20

56.09

45

6

1

N

108

0

(0%)

209,526 (98.91%)

NIID_2019-nCOV_N_R2

TGGCAGCTGTGTAGGTCAAC

20

60.25

55

6

2

N

NIID_2019-nCOV_N_P2

FAM-ATGTCGCGCATTGGCATGGA-BHQ

20

63.5

55

6

0

N

Thailand (23 January 2020)

WH-NIC N-F

CGTTTGGTGGACCCTCAGAT

20

59.68

55

4

2

N

57

207,825 (98.10%)

211,075 (99.64%)

WH-NIC N-R

CCCCACTGCGTTCTCCATT

19

60

57.89

3

1

N

WH-NIC N-P

FAM-CAACTGGCAGTAACCA- BQH1

16

50.27

50

7

1

N

USA (24 January 2020)

2019-nCoV_N1-F

GACCCCAAAATCAGCGAAAT

20

56.67

45

2

2

N

72

208,464 (98.40%)

211,123 (99.66%)

2019-nCoV_N1-R

TCTGGTTACTGCCAGTTGAATCTG

24

60.8

45.83

7

5

N

2019-nCoV_N1-P

FAM-ACCCCGCATTACGTTTGGTGGACC-BHQ1

24

67.48

58.33

4

4

N

2019-nCoV_N2-F

TTACAAACATTGGCCGCAAA

20

57.11

40

5

5

N

67

204,237 (96.41%)

209,575 (98.93%)

2019-nCoV_N2-R

GCGCGACATTCCGAAGAA

18

58.53

55.56

5

2

N

2019-nCoV_N2-P

FAM-ACAATTTGCCCCCAGCGCTTCAG-BHQ1

23

66.45

56.52

6

2

N

2019-nCoV_N3-F

GGGAGCCTTGAATACACCAAAA

22

58.84

45.45

4

0

N

72

208,807 (98.57%)

210,931 (99.57%)

2019-nCoV_N3-R

TGTAGCACGATTGCAGCATTG

21

59.87

47.62

5

3

N

2019-nCoV_N3-P

FAM-AYCACATTGGCACCCGCAATCCTG-BHQ1

24

65.21

56.52

4

1

N

RP-F

AGATTTGGACCTGCGAGCG

19

60.45

57.89

3

2

RNAse P

0

0

(0%)

0

(0%)

RP-R

GAGCGGCTGTCTCCACAAGT

20

62.44

60

5

2

RNAse P

RP-P

FAM-TTCTGACCTGAAGGCTCTGCGCG-BHQ1

23

67.21

60.87

4

4

RNAse P

Paris (2 March 2020)

nCoV_IP2-12669Fw

ATGAGCTTAGTCCTGTTG

18

51.11

44.44

4

0

RdRp

108

209,365 (98.83%)

210,516 (99.37%)

nCoV_IP2-12759Rv

CTCCCTTTGTTGTGTTGT

18

52.57

44.44

1

0

RdRp

nCoV_IP2-12696bProbe( +)

HEX-AGATGTCTTGTGCTGCCGGTA-BHQ-1

21

61.78

52.38

4

4

RdRp

nCoV_IP4-14059Fw

GGTAACTGGTATGATTTCG

19

50.65

42.11

3

2

RdRp

107

210,158 (99.20%)

211,239 (99.71%)

nCoV_IP4-14146Rv

CTGGTCAAGGTTAATATAGG

20

49.98

40

4

0

RdRp

nCoV_IP4-14084Probe( +)

FAM-TCATACAAACCACGCCAGG-BHQ-1

19

57.76

52.63

3

3

RdRp

E_Sarbeco_F1

ACAGGTACGTTAATAGTTAATAGCGT

26

58.29

34.62

8

8

E

113

210,071 (99.16%)

210,610 (99.42%)

E_Sarbeco_R2

ATATTGCAGCAGTACGCACACA

22

60.93

45.45

7

1

E

E_Sarbeco_P1

FAM-ACACTAGCCATCCTTACTGCGCTTCG-BHQ-1

26

66.78

53.85

4

2

E

  1. The percentage of the total number of sequences that annel without mismatches or allowing 10% mismatches are shown in parentheses.
  2. F forward primer; R reverse primer; P probe; Tm melting temperature; GC% G + C percentage; SC self complementarity; SC 3’ self 3’-complementarity; No mis number of sequences that anneal to the primer without mismatches; 10% mis number of sequences that anneal to the primer allowing 10% mismatches.
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