Monkeypox virus (MPXV) is a zoonotic pathogen that has recently caused outbreaks in non-endemic areas. Wastewater-based surveillance (WBS) offers substantial potential for monitoring MPVX clades, and it can inform population-level disease dynamics. Here, we report a four-plex digital PCR assay to detect and quantify different clades and subclades of MPXV. The assay demonstrated specificity in distinguishing and quantifying MPXV by clade, which is advantageous for application in both clinical and wastewater settings.

The authors have declared no competing interest.

This project was funded by the Swiss National Science Foundation (SNSF Sinergia Grant Nr. CRSII5_205933).

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