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Monkeypox PCR

Assays for mpox 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 (CB), also now referred to as clade I (clade Ia and Ib) and West African (WA), now referred to as -clade II (-clade IIa and -clade IIb). 

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 (clade Ia only)

LNA-enhanced QIAGEN assays are based on QIAGEN 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 (due to the placement of the assay, it targets both the clade Ia and Ib)**

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 (due to the placement of the assay, it targets both the clade Ia and Ib)**
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.
Available MPXV assays:
Name Cat. No GG-ID Target Platform  Application/Comments



clade Ia  clade Ib  clade II 

3_MPXV_WA  338304  CDB00022  no  no**  yes dPCR   
1_4_MPXV_C2  338304  CDB00974  no  no**  yes  dPCR  Alternative design to 3_MPXV_WA,
in-silico design not tested in multiplex 
1_MPXV-CDC_CB  338304  CDB00018  yes  no**  no  dPCR   
2_MPXV_CB  338304  CDB00021  yes  yes**  no  dPCR   
1_4_MPXV_C1  338304  CDB00975  yes  yes**  no  dPCR  Alternative design to 2_MPXV_CB,
in-silico design not tested in multiplex 
3_MPXV_WA  338324  CQB00036  no  no**  yes  qPCR   
1_4_MPXV_C2  338324  CQB00100  no  no**  yes  qPCR  Alternative design to 3_MPXV_WA,
in-silico design not tested in multiplex 
1_MPXV-CDC_CB  338324  CQB00031  yes  no**  no  qPCR   
2_MPXV_CB  338324  CQB00034  yes  yes**  no  qPCR   
1_4_MPXV_C1  338324  CQB00101  yes  yes**  no  qPCR  Alternative design to 2_MPXV_CB,
in-silico design not tested in multiplex 
Available control assays:
Name  Cat. No  GG-ID  Target  Platform  Application/Comments 
1_Rnase-P(g)  338304  CDB00019  human RNAseP  dPCR  Reference Assay Human samples 
1_HF183L  338304  CDB00033  Bacteroides cluster  dPCR  Reference Assay WasteWater 
1_Rnase-P(g)  338324  CQB00033  human RNAseP  qPCR  Reference Assay Human samples 

How to prepare for an order

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

  1. What assay (cat. no. and GG-ID) you want to order
  2. Preferred dye
  3. Number of reactions: 1000 reactions for dPCR and 4000 reaction for qPCR

Example assay configuration for complete qPCR MPXV assay “1_MPXV-CDC_CB” with FAM in 4000-reaction scale: CQB00031-F4000

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

Suggested Multiplexes for different applications

Multiplex for human samples (dPCR)*:
Name  Cat. No  GG-ID  Target Platform  Recommended Dye 
      clade 1A  clade 1B  clade 2     
1_MPXV-CDC_CB  338304  CDB00018  yes  no**  no  dPCR  Cy5 
2_MPXV_CB  338304  CDB00021  yes  yes**  no  dPCR  FAM 
 1_Rnase-P(g)  338304  CDB00019  human RNAseP  dPCR  HEX 

Multiplex for Wastewater samples (dPCR)*:
Name  Cat. No  GG-ID  Target  Platform  Recommended Dye 
      clade 1A  clade 1B  clade 2     
1_MPXV-CDC_CB  338304  CDB00018  yes  no**  no  dPCR  CY5 
2_MPXV_CB  338304  CDB00021  yes  yes**  no  dPCR  FAM 
1_HF183L  338304  CDB00033  Bacteroides cluster  dPCR  HEX 

Multiplex for human samples (qPCR)*:
Name  Cat. No  GG-ID  Target  Platform  Recommended Dye 
      clade 1A  clade 1B  clade 2     
1_MPXV-CDC_CB  338324  CQB00031  yes  no**  no  qPCR  Cy5 
2_MPXV_CB  338324  CQB00034  yes  yes**  no  qPCR  FAM 
1_Rnase-P(g)  338324  CQB00033  human RNAseP  qPCR  HEX 

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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.