Semi-Automated Arbovirus Detection in Wastewater with Nanotrap Microbiome Particles and the Nanotrap PRIME Extraction Kit

Poster: Saunders, Ceres Nanosciences, IWA World Water Congress & Exhibition (2026)

Overview

This study evaluated Nanotrap® Microbiome A and B Particles combined with the Nanotrap® PRIME Extraction Kit for concentrating, extracting, and detecting mosquito-borne arboviruses from wastewater. Wastewater samples were spiked with West Nile virus, dengue virus, Zika virus, chikungunya virus, and yellow fever virus to assess multi-pathogen capture, sensitivity, reproducibility across wastewater matrices, and compatibility with qPCR and digital PCR (dPCR). The objective was to determine whether a rapid, semi-automated Nanotrap workflow could detect arboviruses at concentrations relevant to wastewater-based epidemiology (WBE) and outbreak surveillance.

Key Findings

Detection of multiple arboviruses with a single Nanotrap workflow

• Nanotrap Microbiome A and B Particles successfully captured West Nile, dengue, Zika, chikungunya, and yellow fever viruses from wastewater.

• West Nile, dengue, and Zika were simultaneously recovered from four unique wastewater samples spiked at 10⁴ copies/mL, demonstrating multi-target capture across different wastewater matrices.

• Consistent detection across the four samples suggests that the workflow can tolerate variability in wastewater composition.

Detection at concentrations relevant to wastewater surveillance

• Chikungunya and yellow fever were detected across concentrations ranging from 10 to 1,000 copies/mL by both qPCR and dPCR.

• Reported endogenous chikungunya concentrations in wastewater are approximately 100–1,300 copies/mL, placing the demonstrated Nanotrap detection range within concentrations observed during real-world surveillance.

• Yellow fever was detectable at 10 copies/mL, approaching modeled wastewater concentrations expected from relatively small numbers of infections.

Integrated concentration and nucleic acid extraction

• Microbial capture and concentration were performed with Nanotrap Microbiome A and B Particles, followed by nucleic acid purification using the Nanotrap PRIME Extraction Kit.

• The poster's workflow illustrates an integrated process from wastewater collection → Nanotrap concentration → extraction → detection → analysis, reducing the need for separate concentration and extraction approaches.

• The workflow processed 10 mL wastewater samples in the experiments shown, while the authors note that 10–35 mL inputs are appropriate for native arbovirus isolation based on reported wastewater concentrations.

Compatible with qPCR and digital PCR

• Nanotrap-enriched nucleic acids were successfully analyzed using both Bio-Rad CFX96 qPCR and QIAGEN QIAcuity® One dPCR platforms.

• Chikungunya and yellow fever were detected across the tested concentration range with both platforms, demonstrating flexibility for laboratories using different downstream molecular detection technologies.

Implications for Nanotrap Technology

This proof-of-concept expands the demonstrated utility of the Nanotrap Microbiome workflow into arbovirus wastewater surveillance. A particularly important feature is the ability to concentrate several arboviruses with the same A+B particle chemistry and PRIME extraction workflow, potentially allowing laboratories to monitor emerging mosquito-borne diseases without developing a separate sample preparation process for each virus. The workflow is also described as compatible with respiratory virus and bacterial detection, supporting its potential as a multi-pathogen wastewater surveillance platform.

Conclusion

The study demonstrates that Nanotrap Microbiome Particles combined with the Nanotrap PRIME Extraction Kit can capture and enable detection of five medically important arboviruses from wastewater, including chikungunya and yellow fever at concentrations as low as 10 copies/mL under the tested conditions. The workflow is faster than previously described arbovirus wastewater concentration methods and can be performed in automated or semi-automated formats, supporting higher-throughput surveillance. As a proof-of-concept based primarily on contrived wastewater samples, further validation with endogenous arbovirus-positive wastewater will be important to establish real-world recovery, sensitivity, and limits of detection.

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