The new coronavirus (2019-nCoV) was first detected in Wuhan City, Hubei Province China. Tens of thousands of infections with 2019-nCoV have been reported in China. The virus is spreading from person-to-person in parts of the world. Coronaviruses are a large family of viruses that are common in many animals, including camels, cattle, cats, and bats. However, some animal coronaviruses can infect people and spread between people, for example MERS, SARS, and now with 2019-nCoV {CDC}.
Corona virus outbreaks in January 2020.
Source: Wikimedia Commons
The following is a list of primers and probes for the detection of the new 2019 coronavirus (2019-nCoV) in human clinical specimens. Please use indicated concentrations as a guide. Actual concentrations used should be experimentally verified.
!! Primers and probes for the detection of the new 2019 coronavirus are available from BSI !!
Genome: Wuhan seafood market pneumonia virus isolate 2019-nCoV/USA-AZ1/2020, complete genome Sequence ID: MN997409.1 Length: 29882
Note: A, Adenine; C, Cytosine; G, Guanine; T, Thymine; U, Uracil; R, A or G; Y, C or T; S, G or C; W, A or T; K, G or T; M, A or C; B, C or G or T; D, A or G or T; V, A or C or G; N, any base.
Name | Label 5’ | Oligonucleotide Sequence (5’>3’) | Label 3’ | Working Conc. [μM] |
| | N Protein | | |
2019-nCoV_N1-F |
| GACCCCAAAATCAGCGAAAT 28287------------28306 |
|
|
2019-nCoV_N1-R |
| TCTGGTTACTGCCAGTTGAATCTG 28358---------------28335 |
| 20 |
2019-nCoV_N1-P | FAM | ACCCCGCATTACGTTTGGTGGACC 28309---------------28332 | BHQ1 | 5 |
2019-nCoV_N2-F |
| TTACAAACATTGGCCGCAAA 29164-------------29183 |
| 20 |
2019-nCoV_N2-R |
| GCGCGACATTCCGAAGAA 29230------------29213 |
| 20 |
2019-nCoV_N2-P | FAM | ACAATTTGCCCCCAGCGCTTCAG 29188---------------29210 | BHQ1 | 5 |
2019-nCoV_N3-F |
| GGGAGCCTTGAATACACCAAAA 28681--------------28702 |
| 20 |
2019-nCoV_N3-R |
| TGTAGCACGATTGCAGCATTG 28752--------------28732 |
| 20 |
2019-nCoV_N3-P | FAM | AYCACATTGGCACCCGCAATCCTG 28706--------------28727 | BHQ1 | 5 |
Name | Label 5’ | Oligonucleotide Sequence (5’>3’) | Label 3’ | Working Conc. [μM] |
| | RNAse Protein | | |
RP-F |
| AGATTTGGACCTGCGAGCG |
| 20 |
RP-R |
| GAGCGGCTGTCTCCACAAGT |
|
|
RP-P RNAse P | FAM | TTCTGACCTGAAGGCTCTGCGCG | BHQ-1 | 5 |
Name | Label 5’ | Oligonucleotide Sequence (5’>3’) | Label 3’ | Working Conc. [μM] |
| | ORF1ab | | |
2019-nCoV-OFP |
| CCCTGTGGGTTTTACACTTAA 13342------------13362 |
| 0.6 |
2019-nCoV-ORP |
| ACGATTGTGCATCAGCTGA 13460------------13442 |
| 0.8 |
2019-nCoV-OP | FAM | CCGTCTGCGGTATGTGGAAAGGTTATGG 13377-------------------13404 | BBQ1 | 0.1 |
|
| Nucleoprotein- protein N |
|
|
2019-nCoV-NFP |
| GGGGAACTTCTCCTGCTAGAAT 28881-------------28902 |
| 0.6 |
2019-nCoV-NRP |
| CAGACATTTTGCTCTCAAGCTG 28979-------------28958 |
| 0.8 |
2019-nCoV-NP | FAM | TTGCTGCTGCTTGACAGATT 28934-------------28953 | TAMRA | 0.1 |
|
| ORF1b-nsp14 |
|
|
HKU-ORF1b-nsp14F |
| TGGGGYTTTACRGGTAACCT 18778-----------18797 |
| 0.6 |
HKU- ORF1b-nsp14R |
| AACRCGCTTAACAAAGCACTC 18909-------------18889 |
| 0.8 |
HKU-ORF1b-nsp141P | FAM | TAGTTGTGATGCWATCATGACTAG 18849---------------18872 | TAMRA | 0.1 |
|
| Nucleoprotein – Protein N |
|
|
HKU-NF |
| TAATCAGACAAGGAACTGATTA 29145--------------29166 |
| 0.6 |
HKU-NR |
| CGAAGGTGTGACTTCCATG 29254-----------29236 |
| 0.8 |
HKU-NP | FAM | GCAAATTGTGCAATTTGCGG 29196------------29177 | TAMRA | 0.1 |
Positive Control for insertion into plasmid |
AGTTGACTTCGCAGTGGCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTG AAGAGAAGTTTAAGGAAGGTGTAGAGACCCTGTGGGTTTTACACTTAAAAACACAGTCTGTACCGTCTGCGGTAT GTGGAAAGGTTATGGCTGTAGTTGTGATCAACTCCGCGAACCCATGCTTCAGTCAGCTGATGCACAATCGTTTTT ACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCAATGGCGGTGATGCTGCT |
Name | Label 5’ | Oligonucleotide Sequence (5’>3’) | Label 3’ | Working Conc. [μM] |
|
| RNA-dependent RNA polymerase |
|
|
RdRP_SARSr-F2 |
| GTGARATGGTCATGTGTGGCGG 15431-------------15452 2019-nCoV genome |
| 0.6 |
RdRP_SARSr-R1 |
| CARATGTTAAASACACTATTAGCATA 15460-----------------15435 Coronavirus BtRs-BetaCoV/YN2018D, complete genome. Sequence ID: MK211378.1 Length: 30213 |
| 0.8 |
RdRP_SARSr-P1 | FAM | CCAGGTGGWACRTCATCMGGTGATGC 145---------------------170 Bat coronavirus isolate B18-171 RNA-dependent RNA polymerase (RdRp) gene, partial cds. Sequence ID: MK991947.1 Length: 387 | BBQ1 | 0.1 |
RdRP_SARSr-P2 | FAM | CAGGTGGAACCTCATCAGGAGATGC 15470----------------15494 Specific for 2019-nCoV, will not detect SARSCoV. Wuhan seafood market pneumonia virus isolate 2019-nCoV/USA-AZ1/2020, complete genome Sequence ID: MN997409.1Length: 29882 | BBQ1 | 0.1 |
Reference
https://www.who.int/docs/default-source/coronaviruse/peiris-protocol-16-1-20.pdf?sfvrsn=af1aac73_4
Liu G, Li H, Zhao S, Lu R, Niu P, Tan W. Viral and Bacterial Etiology of Acute Febrile Respiratory Syndrome among Patients in Qinghai, China.Biomed Environ Sci. 2019 Jun;32(6):438-445. https://www.sciencedirect.com/science/article/pii/S0895398819301230
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