ChapterDx Monkeypox virus (MPXV) NGS Kit 

Amplifying and sequencing 21 diverse loci spanning MPXV genome. The combination of sequences for those loci enables differentiating MPXV from other mammalian poxviruses, distinguishing MPXVs at different lineages,  and discriminating MPXVs at the same lineage such as those responsible for 2022 outbreak. The assay also targets GAPDH (internal control) and varicella-zoster virus (VZV), the causative agent for chickenpox and shingles.



ChapterDx MPXV NGS assay amplifies and sequences 21 MPXV loci, and provides genotyping results to the subtype level. The assay is designed for tracking the source of infection (viral surveillance). This assay can differentiate MPXV from other mammalian poxviruses, can distinguish MPXVs at different lineages,  and can also discriminate MPXVs at the same lineage such as those responsible for 2022 outbreak. The assay requires low amounts of nucleic acid material, has a relatively fast turnaround time, and is suitable for low, medium and high-throughput sample scales. The assay has a simple and user-friendly workflow and is easy to automate. The analysis software is included in the kit. 


ChapterDx MPXV NGS assay consists of the following steps:

  1. DNA extraction (not provided)

  2. Multiplex PCR

  3. Pooling and purification

  4. Next-generation sequencing

In the PCR reaction, both amplification and indexing/barcoding of each specimen occurs simultaneously. After PCR reaction, amplicons for different samples are pooled in one tube. The following procedures deal with only one tube regardless of how many samples. After the cleanup step, the library is sequenced on an Illumina sequencing platform. The entire workflow takes about 24 hours, of which about 3 hours is benchwork/incubation time and 17 hours of sequencing. It takes less than half hour to complete data analysis.


  • Analyze sequences at 21 most polymorphic loci spanning poxvirus genome

  • Loci are at diverse sites including intergenic regions

  • Unaffected by ongoing mutations

  • Differentiate MPXVs from poxviruses infecting other mammals

  • Distinguish MPXVs at different lineages

  • Discriminate MPXVs at same lineage

  • Single-tube and single-step PCR reaction 

  • User-friendly,  easy-to-automate workflow

  • Cost-efficient and suitable for low, medium and high throughput scales

  • Data analysis software is included


Location of Amplicons in MPXV Genome (click to enlarge)

Monkeypox Loci Genome.png
Red color highlights the location of loci in MPXV assay

ChapterDx MPXV NGS Assay Workflow

MPXV workflow.png

Cat No./ Size     C7228A /96 rxns (includes 96 indexing)

                          C7228B /192 rxns (includes 192 indexing)

For Research Use Only (RUO)

Patent Pending