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Monkeypox PCR

Assays for monkeypox detection

Your partner for monkeypox research

Research is an essential factor in addressing the evolving monkeypox public health emergency. To do their part, labs need tools to study the disease. QIAGEN is ready to help. We offer three different assay options for monkeypox virus (MPXV) testing.

Monkeypox assay options

Each assay option provides hydrolysis probe-based assays to detect MPXV and differentiation between Congo Basin, also now referred to as Clade I (CB) and West African (WA), now referred to as Clade II (Clade IIa and Clade IIb). 

View further details in the protocols found below.

These assays are intended for molecular biology applications for epidemiological research using digital PCR and real-time PCR.

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Details & specifications

Three different designs are available:

MPXV-CDC assays are based on published US CDC assays designs (1)

  • The WA assay targets the TNF receptor gene at the terminal inverted repeat region and covers both subvariants Clade IIa and IIb
  • The CB Assay, covering Clade I, detects the complement binding protein (C3L) gene

LNA-enhanced QIAGEN assays are based on QIAGEN’s own expert designs using LNA technology for increased specificity

  • The WA assay targets approximately 200 nt upstream of the gene R1R and covers both clade subvariants IIa and IIb
  • The CB assay covers the 5’-end of the surface glycoprotein gene B21R and upstream

Wastewater testing assays using LNA-enhanced assays for dPCR

  • The WA assay targets approximately 200 nt upstream of the gene R1R and covers both clade subvariants IIa and IIb
  • The CB assay covers the 5’-end of the surface glycoprotein gene B21R and upstream 
All assay options are available with a range of different dyes for multiplexing and also offer an RNase P assay for sampling- and in-process control.

dPCR US CDC

Individual primer pairs and probes
(available for 100 or 1000 reactions)		 Cat. no. GG-ID Component(s) Suggested dye for multiplexing*
1_MPXV-CDC_WA-f 338303 CDM00008 1 Primer
1_MPXV-CDC_WA-r 338303 CDM00009 1 Primer
1_MPXV-CDC_WA 338300 CDP00027 Probe FAM
1_MPXV-CDC_CB-f 338303 CDM00010 1 Primer
1_MPXV-CDC_CB-r 338303 CDM00011 1 Primer
1_MPXV-CDC_CB 338300 CDP00028 Probe Cy5 or ROX
1_RNAse-P(g)_f 338303 CDM00006 1 Primer
1_RNAse-P(g)_r 338303 CDM00007 1 Primer
1_Rnase-P(g) 338300 CDP00029 Probe HEX
*Available dyes:
Dye FAM HEX TAMRA ROX CY5
Key F H M R C

dPCR LNA-enhanced

Individual primer pairs and probes
(available for 100 or 1000 reactions)		 Cat. no. GG-ID Component(s) Suggested dye for multiplexing*
3_MPXV_WA-f 338303 CDM00016 1 Primer
3_MPXV_WA-r 338303 CDM00017 1 Primer
3_MPXV_WA 338300 CDP00032 Probe FAM
2_MPXV_CB-f 338303 CDM00014 1 Primer
2_MPXV_CB-r 338303 CDM00015 1 Primer
2_MPXV_CB 338300 CDP00031 Probe Cy5 or ROX
1_RNAse-P(g)_f 338303 CDM00006 1 Primer
1_RNAse-P(g)_r 338303 CDM00007 1 Primer
1_Rnase-P(g) 338300 CDP00029 Probe HEX

*Available dyes:
Dye FAM HEX TAMRA ROX CY5
Key F H M R C

dPCR wastewater

Individual primer pairs and probes
(available for 100 or 1000 reactions)		 Cat. no. GG-ID Component(s) Suggested dye for multiplexing*
3_MPXV_WA-f 338303 CDM00016 1 Primer
3_MPXV_WA-r 338303 CDM00017 1 Primer
3_MPXV_WA 338300 CDP00032 1 Probe FAM
2_MPXV_CB-f 338303 CDM00014 1 Primer
2_MPXV_CB-r 338303 CDM00015 1 Primer
2_MPXV_CB 338300 CDP00031 1 Probe HEX
1_HF183L_f 338303 CDM00032 1 Primer
1_HF183L_r 338303 CDM00033 1 Primer
1_HF183L 338300 CDP00044 1 Probe ROX
4_PMMoV_f 338303 CDM00034 1 Primer
4_PMMoV_r 338303 CDM00035 1 Primer
4_PMMoV 338300 CDP00045 1 Probe Cy5

*Available dyes:
Dye FAM HEX TAMRA ROX CY5
Key F H M R C

qPCR US CDC

Individual primer pairs and probes
(available for 400 or 4000 reactions)		 Cat. no. GG-ID Component(s) Suggested dye for multiplexing*
1_MPXV-CDC_WA-f 338323 CQM00005 1 Primer
1_MPXV-CDC_WA-r 338323 CQM00006 1 Primer
1_MPXV-CDC_WA 338320 CQP00035 Probe FAM
1_MPXV-CDC_CB-f 338323 CQM00007 1 Primer
1_MPXV-CDC_CB-r 338323 CQM00008 1 Primer
1_MPXV-CDC_CB 338320 CQP00034 Probe Cy5 or ROX
1_RNAse-P(g)_f 338323 CQM00003 1 Primer
1_RNAse-P(g)_r 338323 CQM00004 1 Primer
1_Rnase-P(g) 338320 CQP00036 Probe HEX

*Available dyes:
Dye FAM TET JOE YAKYE HEX CY3 ATTO55 TAMRA ROX TxRed CY35 ATTO647N CY5 CY55 ATTO680
Key F T J Y H D A M R X E B C G I

qPCR LNA-enhanced

Individual primer pairs and probes
(available for 400 or 4000 reactions)		 Cat. no. GG-ID Component(s) Suggested dye for multiplexing*
3_MPXV_WA-f 338323 CQM00013 1 Primer
3_MPXV_WA-r 338323 CQM00014 1 Primer
3_MPXV_WA 338320 CQP00039 Probe FAM
2_MPXV_CB-f 338323 CQM00011 1 Primer
2_MPXV_CB-r 338323 CQM00012 1 Primer
2_MPXV_CB 338320 CQP00037 Probe CY5 or ROX
1_RNAse-P(g)_f 338323 CQM00003 1 Primer
1_RNAse-P(g)_r 338323 CQM00004 1 Primer
1_Rnase-P(g) 338320 CQP00036 Probe HEX

*Available dyes:
Dye FAM TET JOE YAKYE HEX CY3 ATTO55 TAMRA ROX TxRed CY35 ATTO647N CY5 CY55 ATTO680
Key F T J Y H D A M R X E B C G I

How to prepare for an order

Our early-access ordering setup is going via our Genomic Services. When preparing to place an assay order, it helps to keep a few questions in mind:

  1. What assay (cat. no. and GG-ID) do you want to order?
  2. Dye preference for individual probe or complete assay
  3. What is the reaction number needed? 100 or 1000 reactions for dPCR or 400 or 4000 reactions for qPCR
  4. Finally, add “MP” for all monkeypox assays

Example assay configuration for complete qPCR MPXV assay “1_MPXV-CDC_WA” with FAM in 4000-reaction scale: CQB00032-F4000MP

Please note: Assays should be ordered with different dyes for multiplexing, for example, Assay1 (FAM) + Assay2 (CY5) + Assay3 (HEX)

dPCR and qPCR protocols

Monkeypox virus wastewater testing using dPCR

Monkeypox virus CDC probe PCR assay – dPCR 

Monkeypox virus CDC probe PCR assay – qPCR 

Monkeypox virus LNA-enhanced probe PCR assay – dPCR

Monkeypox virus LNA-enhanced probe PCR assay – qPCR

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References:
  1. Li, Y., Zhao H., Wilkins K., Hughes, C., and Damon I.K. (2010) Real-time PCR assays for the specific detection of monkeypox virus West African and Congo Basin strain DNA. J. Virol. Methods 169, 223–227.