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Applications

Wastewater Epidemiology

Wastewater-based epidemiology (WBE) aims at measuring pathogens in wastewater at population scale.

 

This approach has proven to enable advanced warning ahead of clinical testing or hospitalizations, for public agencies and communities to better prepare for and prevent the spread of infectious diseases.


Hyperplex PCR™ is currently being used to monitor the spread of COVID variants in Sweden together with the Swedish Environmental Epidemiology Centre (SEEC) and is now available to be deployed world-wide.

Sewage Treatment Plant

Sites currently monitored in Sweden with hpPCR

18

Data points analyzed since Q4 2022

15 800+

Multiplex currently in panel

18

Why Hyperplex PCR for pandemic preparedness?

With multiplexing unleashed, Hyperplex PCR enables shorter time to action by enabling instant set-up and in real-time updating of panels with unparallaled specificity and sensitivity for routine monitoring and better pandemic preparedness systems.

What we measure

SARS-CoV-2
variant panel

18 mutations to discriminate 15 targets

PMMoV

XBB

XBB.1.5

EG.1

N3

CH.1.1

XBB.1.9

XBB.1.9.1/2

BA.2.75

EG.5

XBB.1.16

BA.2.86

BQ.1.1

EG.5.1

XBB.1.16.1

Other markers available or of importance to public health

Any target can be mix-and-matched into a new panel or on top of an existing panel

Influenza A

Influenza B

AMR sul1

Norovirus GII

HCoV NL63

Adenovirus 40/41

Influenza A H1

AMR mecA

AMR mefA

RSV A

HCoV 223E

Hepatitis A

Influenza A H3

AMR oxa-48

AMR 16s rRNA

RSV B

HCoV OC43

Rotavirus

Influenza A H5 (avian)

AMR tetA

Norovirus GI

Mpox virus

HCoV HKU1

Or add your own markers within 2 weeks

SARS-CoV-2 variants surveillance data

Together with the Swedish Environmental Epidemiology Center (SEEC), SARS-CoV-2 variants in Sweden are being monitored using Hyperplex PCR.

Up to 22 sites have been monitored with a 18-plex panel enabling monitoring unparallalled by other methods such as qPCR, dPCR and NGS.

The panel as been adapted to keep it up-to-date with relevant variants of concern by removing exting variants and swiftly add new mutations within 2 weeks from order. 

Read about some of the conclusions reached in our application note.

SEEC-sample-Figure-HeatMap_V2.png

Figure 1. Heatmap summary of SARS-CoV-2 VOC surveillance data generated with Hyperplex PCR over one year with an adaptable 18-plex panel for up to 22 sites in Sweden. Heatmap colors represent as following; blue (no signal detected), from green (low concentration) to pink (high concentration) of marker detected.

NGS-grade quantification of mutation frequency

Figure 2. A, B: Mutation frequency measured in wastewater with NGS (filled symbols) and hpPCR (open symbols). C: Linearity of mutation frequency measurements using hpPCR in a 10-plex target system (spiked targets). D: hpPCR vs NGS mutation frequency in WW samples.

4+ weeks earlier detection of emerging variants

Early_detection.png

Figure 3. Weekly measurement of S:F486P, characteristic of XBB 1.5 using hpPCR and NGS (Ion torrent). 8 wastewater collection sites were measured at each time point. Both measurements were performed on the same extracted nucleic acid sample.

Inhibitors problematic for wastewater samples

inhibitor_effect.png

Figure 4. Wastewater matrix contains inhibitors affecting the amplification in both qPCR and dPCR measurements. While dPCR may handle this better than qPCR, it is still subject to variance in analysis which has effect on the accuracy of analysis.

Negligible inhibitor effect with hpPCR

Inhibitor_effect_hpPCR.png

Figure 5. Intensity of N3 gene marker obtained after hpPCR on DNAse/RNAse-free water (pink) and 29 different wastewater samples (green). Signals from the control (pink) and wastewater samples show no significant difference, and both samples are well above the limit of detection (LoD) for signal detection of RCPs, making in particular mutation frequency analysis virtually not effected by inhibitors at all.

AMR analysis of low and high abundance targets

In this project, Hyperplex PCR was used for absolute quantification of AMR markers in wastewater samples, showcasing the read-out of targets as low as less than 10 copies/uL, combined with others as high as 105 copies/uL.


Expand the panel with more AMR markers and other pathogens of your choice while retaining absolute quantification.

AMR_quantification.png

Implement Hyperplex PCR for pandemic preparedness

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