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Initial assessment of the ability of published coronavirus primers sets to detect the Wuhan coronavirus

Used primer sets

Pan-CoV:

Luna et al. Journal of clinical microbiology, 2007, p 1049-1052

panCoV_fwd1           TTATGGGTTGGGATTATC

panCoV_fwd2           TGATGGGATGGGACTATC

panCoV_rev1            TCATCACTCAGAATCATCA

panCoV_rev2            TCATCAGAAAGAATCATCA

panCoV_rev3            TCGTCGGACAAGATCATCA

panCoV_ne_fwd1        CTTATGGGTTGGGATTATCCTAAGTGTGA

panCoV_ne_fwd2        CTTATGGGTTGGGATTATCCCAAATGTGA

panCov_ne_re          CACACAACACCTTCATCAGATAGAATCATCA

Chu et al. Avian coronavirus in wild aquatic birds. J Virol. 2011 Dec;85(23):12815-20

Chu_pan-CoV_1st_F GGKTGGGAYTAYCCKAARTG

Chu_pan-CoV_1st_R TGYTGTSWRCARAAYTCRTG

Chu_pan-CoV_2nd_F        GGTTGGGACTATCCTAAGTGTGA

Chu_pan-CoV_2nd_R        CCATCATCAGATAGAATCATCAT

MERS-CoV:

Corman et al. Euro Surveill. 2012;17(39):pii=20285. (screening)

UpE

emcE-fwd  GCAACGCGCGATTCAGTT

emcE-probe      CTCTTCACATAATCGCCCCGAGCTCG

emcE-rev   GCCTCTACACGGGACCCATA

ORF1b

ORF1b-Fwd       TTCGATGTTGAGGGTGCTCAT),

ORF1b-Prb       CCCGTAATGCATGTGGCACCAATGT

ORF1b-Rev       TCACACCAGTTGAAAATCCTAATTG)

Corman et al. Euro Surveill. 2012;17(49):pii=20334 (confirmation)

ORF1a-Fwd     CCACTACTCCCATTTCGTCAG

ORF1a-Prb      TTGCAAATTGGCTTGCCCCCACT

ORF1a-Rev       CAGTATGTGTAGTGCGCATATAAGCA

Confirmation assay EMC

emcN-fwd GGGTGTACCTCTTAATGCCAATTC

emcN-probe      ACCCCTGCGCAAAATGCTGGG

emcN-rev  TCTGTCCTGTCTCCGCCAAT

SARS

Kuiken T, et al, Newly disc.coronavirus as the primary cause of SARS, lancet 2003;362(9380);263-70

SARS NP fwd1   caaacattggccgcaaatt

SARS NP probe cacaatttgctccaagtgcctctgca

SARS NP rev1    caatgcgtgacattccaaaga

Poon et al. . JCV 28(3), https://doi.org/10.1016/j.jcv.2003.08.004

ORF1b

F CAGAACGCTGTAGCTTCAAAAATCT

P TCTGCGTAGGCAATCC

R       TCAGAACCCTGTGATGAATCAACAG

Human Coronoviruses NL63, 229E, OC43, HKU1, EMC Viroscience primers

hCoV-229E

229E-fwd-TM    cgcaagaattcagaaccagag

229E-probe       ccacacttcaatcaaaagctcccaaatg

229E-rev-TM     gggagtcaggttcttcaacaa

hCoV-OC-43

OC43TM_fwd1 CGATGAGGCTATTCCGACTAGGT

OC43TM_prb1  TCCGCCTGGCACGGTACTCCCT

OC43TM_rev1  CCTTCCTGAGCCTTCAATATAGTAACC

hCoV-NL63

NL63-fwd  GAA GCG TGT TCC TAC CAG AGA

NL63-probe       AAA TGT TAT TCA GTG CTT TGG TCC TCG TGA

NL63-rev   GAA TCC CCC ATA TTG TGA TTA AA

hCoV-HKU1

HKU1_fwd agttcccattgctttcggagta

HKU1_rev  ccggctgtgtctataccaatatcc

HKU1-probe      ccccttctgaagcaa (MGB)

Human Coronoviruses NL63, 229E, OC43, HKU1, AMC primers

Jansen et al. J Clin Virol. 2011 Jul;51(3):179-85. doi: 10.1016/j.jcv.2011.04.010. Epub 2011 May 14.

NL63+229E

HCoV2-F             GCT RAG CAT GAT TTC TTT ACT TGG

HCoV-P              CAG ART CAT TTA TGG TAA TGT TAG TAG ACA

HCoV2-R             CAR TYT TKT TCA TCA AAG TTA CGC A

OC43+HKU1

HCoV1-F           GGT GGY TGG GAY GAT ATG TTA CG

HCov2-P    ATG TTG ACA AYC CTG TWC TTA TGG GTT GGG

HCoV1-R            KRT TTG GCATAG CAC GAT CAC A


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