Wastewater Surveillance Testing for Infectious Diseases

Explore tools and resources for wastewater surveillance testing

Wastewater surveillance is a useful tool for monitoring the regional spread of infectious diseases before an outbreak occurs. With the emergence of SARS-CoV-2 infections, multiple organizations worldwide are working on SARS-CoV-2 surveillance methods using wastewater to monitor regional or city-level spread of the virus, analyze individual dorms on campuses to identify asymptomatic carriers, capture emerging mutations, and respond to possible infections. Methods of detection and surveillance for SARS-CoV-2 are outlined in this webpage and can potentially be adapted for all other pathogens, including viruses and bacteria.

Wastewater surveillance testing workflow

Wastewater concentration workflow icon

Wastewater concentration

Wastewater samples must be concentrated and then extracted for improved detection and analysis. Concentration steps can range from precipitation, ultracentrifugation, to the most efficient and advanced, virus enrichment through Dynabeads.

Automated sample processing workflow icon

Automated sample processing

KingFisher instruments paired with MagMAX wastewater kits allow for a completely automated nucleic acid isolation format without inconvenient centrifugation, filtration, or bead beating steps.

Nucleic acid purification workflow icon

Nucleic acid purification

From the eluate containing concentrated viral particles, viral nucleic acid can be purified using the Applied Biosystems MagMAX Wastewater Ultra Nucleic Acid Isolation Kit. 

Viral pathogen detection via a wide range of qPCR instruments

Viral pathogen detection

These can be detected using Applied Biosystems QuantStudio Real-Time PCR Systems. Amplification curves are generated with supporting software. Downstream analysis via dPCR and NGS.

Resources and tools

Nucleic acid purification

Flexibility

  • Choose your preferred concentration method and protocol
  • Pre-concentrate samples from large volumes using ultracentrifugation, precipitation, or filtration
  • Use the Dynabeads option for automated viral enrichment of up to 10 mL volume
  • Directly isolate from 1 mL of wastewater without concentration
  • Manual and automated protocols available

Whole workflow solution—Purchase the whole workflow from sample collection to analysis with one supplier. We can help you get started on a wastewater testing program.

Scalability—These automation compatible kits can help streamline your process to set up sampling across the scale of your organization. Automation-ready protocols written for KingFisher Flex, KingFisher APEX, and KingFisher Duo systems.

MagMAX Wastewater Ultra Nucleic Acid Isolation Kit

Product information

 
MagMAX Wastewater Ultra Nucleic Acid Isolation Kit

MagMAX Wastewater Ultra Nucleic Acid Isolation Kit, with Virus Enrichment
Who should use?Wastewater research and surveillance/community testing
Sample typesPre-concentrated wastewater and sludgeWastewater
Research needs
  • Flexibility—works with a variety of concentration protocols
  • Scalability—automatable technology
  • Total workflow—products from collection to analysis
  • Efficiency—concentration protocol and Dynabeads already included
  • Scalability—automatable technology
  • Total workflow—products from collection to analysis
Downstream compatibility
  • qRT-PCR, NGS and digital PCR
  • Automation-ready protocols for KingFisher Flex, APEX, and Duo Prime
  • Manual protocols available
Format20–100 preps depending on input volume
KingFisher instrument run time28 minutes for MagMAX Wastewater Ultra73 minutes for MagMAX Wastewater Ultra with VE
Total time per run with hands-on time45 minutes for nucleic acid isolation90 minutes for virus enrichment + nucleic acid isolation
Cat. No.A52606A52610

Wastewater concentration

Concentration of wastewater through Dynabeads viral enrichment

The benefits of the Dynabeads Wastewater Virus Enrichment in MagMAX Wastewater Ultra Nucleic Acid Isolation Kit include:

  • Fast isolation kinetics (~10 min)
  • Easy release (~10 min)
  • Easy to automate with Thermo Scientific Kingfisher instruments
  • Can be used on other negatively charged enveloped viruses, vesicles, and proteins

Large volumes of wastewater must be concentrated before extraction to enable detection and analysis. Samples can be concentrated via precipitation, filtration, or ultracentrifugation, and efficient virus enrichment can be performed using Dynabeads Wastewater Virus Enrichment beads. All concentration methods are compatible with the MagMAX Wastewater Ultra Kit.

MagMAX Wastewater Ultra Nucleic Acid Isolation Kit

Wastewater surveillance experimental workflow

Wastewater surveillance experimental workflow

Protocols included in kit

Wastewater starting volume

Sample detailsKit reagents sufficient forKingFisher scripts availableProtocol timePurchase this kit
10 mLConcentration of 10 mL wastewater using Dynabeads followed by nucleic acid isolation100 prepsFlex, Duo Prime, APEX90 minutesMagMAX Wastewater Ultra Nucleic Acid Isolation Kit, with Virus EnrichmentA52610
200 μL200 μL wastewater pre-concentrated using a preferred method, e.g., ultracentrifugation100 prepsFlex, Duo Prime, APEX45 minutesMagMAX Wastewater Ultra Nucleic Acid Isolation KitA52606
1 mL*

A. 1 mL non-concentrated wastewater

B. Wastewater pre-concentrated to 1 mL volume using a preferred method, e.g., precipitation

20 prepsFlex, Duo Prime, APEX45 minutes
50–500 mLConcentration of 50–500 mL wastewater using filtration followed by nucleic acid isolation20 prepsFlex, Duo Prime, APEX90 minutes
Sludge200 mg sludge20 prepsFlex, Duo Prime, APEX45 minutes
*works for 1-2 mL, but 1 mL is the most sensitive

Automated sample processing

Enable high throughput wastewater testing with KingFisher systems

The benefits of KingFisher Instruments include:

  • Various throughputs—process 6–96 samples per run depending on the instrument model
  • Interchangeable formats—choose 24- or 96-well plates so you can process a wide range of input volumes
  • Protocol customization—easily edit, modify, or create new protocols
  • Optimized reagents—compatible with multiple magnetic-bead reagents

Ask a specialist Request a demo

Product information

KingFisher instrument
Duo Prime

Flex

Apex

Presto
Instrument sizeCompact benchtopBenchtopBenchtopBenchtop—integrates with robotic liquid handler
Throughput levelLow to mediumMedium to highMedium to highUltrahigh
Processing volume range 
  • 50-1,000 μL: 12-pin magnet head
  • 200-5,000 μL: 6-pin magnet head
  • 20-100 μL: 96-well PCR plate, skirted*
  • 20-200 μL: 96-well plate
  • 50-1,000 μL: 96 deep-well plate
  • 200-5,000 μL: 24 deep-well plate
  • 15-1,000 μL: 96 deep-well plate
  • 15-200 μL: 96-well KingFisher standard plate
  • 10-80 μL: 96-well PCR plate
  • 30-5,000 μL: 24 deep-well plate
  • 30-200 μL: 96 storage tubes
  • 200-1,000 μL: 24 storage tubes
  • 50-1,000 μL: 96 deep-well plate
  • 200-5,000 μL; 24 deep-well plate
  • 50-150 μL: 96-well KingFisher standard plate
Samples per run6 or 1224 or 9624 or 9624 or 96
Customizable protocolsYes, with PC softwareYes, with PC softwareYes, with touchscreen or PC softwareYes, with PC software
Heating/cooling
  • 10°C to 75°C (plate row block A)
  • 4°C to 75°C (elution strip block)
  • From 5°C above ambient temperature to 115°C
  • From 4°C above ambient temperature to 100°C
  • Cooling down to 4°C
  • From 5°C above ambient temperature to 115°C
Ultraviolet lamp8 watts (up to 16 hr)No2 UV lamps, max 23 h 59 minNo
Ordering information
  • KingFisher Duo Prime Purification System 5400110
  • KingFisher Flex Purification System with 96 PCR Head 5400610 
  • KingFisher Flex Purification System with 96 
  • KingFisher Head 5400620 
  • KingFisher Flex Purification System with 24 Deep-Well Head 5400640 
  • KingFisher Flex Purification System with 96 Deep-Well Head 5400630
 
  • KingFisher Presto Purification System with 24 Deep-Well Head. 5400840 
  • KingFisher Presto Purification System with 96 Deep-Well Head. 5400830

Wastewater concentration resources

Protocols for wastewater sample concentration flyer cover image

Flyer: Protocols for wastewater sample concentration

Optimized protocol for the enrichment of SARS-CoV-2 in wastewater samples. Large sample volumes of wastewater are dilute. Thus, they must be enriched for intact viral presence for pathogen detection via qPCR. Applied Biosystems MagMAX Wastewater Ultra Nucleic Acid Isolation Kits offer a whole host of advantages over traditional wastewater surveillance methods. Isolate nucleic acids from concentrated wastewater in as little as 45 minutes. Our viral enrichment protocol using magnetic beads helps enable concentration and nucleic acid isolation in less than 2 hours.

Read more

Podcast on detection of SARS-CoV-2 in wastewater

Podcast: Infectious pathogen detection and surveillance

Infectious pathogen surveillance from wastewater and fecal samples has been recently adopted as a method for monitoring emergence and re-emergence of infectious pathogens. This method allows public health agencies, universities, hospitals, cruise lines, and more to detect a pathogen and respond before there is a community outbreak. Thermo Fisher Scientific has partnered with many labs globally to implement new wastewater testing systems and optimize existing wastewater monitoring processes. Listen in to learn about the importance of wastewater.

Download now

Automated sample processing resources

New Asset Image

Study: Multiple workflow options for detection of SARS-CoV-2 in wastewater

Five robust workflows were developed for rapid concentration and qPCR analysis of SARS-CoV-2 from different volumes of wastewater: low (1 mL), medium (10 mL), and large (50 mL). The protocols described here are extensions of those developed in previous studies and have been optimized for processing multiple sample types. The protocols include a fully automated workflow to enable high-throughput processing; this workflow has been successfully used in the field.

Read more

Webinar: From wastewater surveillance to human sample analysis

Webinar: Infectious pathogen detection from human samples

Learn more about methods for wastewater detection from Thermo Fisher Scientific scientists Alexandre “Sasha” Vlassov, Madhu Jasti, and Emily Zeringer at American Science Microbe 2021. In which, the team describes protocols for fecal sample, rectal swab, and wastewater detection for SARS-CoV-2. Additionally, molecular workflows for detection and monitoring of pathogens and microbiota are outlined. The common issues of user time consumption and inconsistent results in sample preparation are addressed and resolved with automated workflows. These workflows allow for increased sensitivity, significant time savings, and increased productivity.

Download now

Streamlined SARS-CoV-2 Wastewater Monitoring infographic

Infographic: Streamlined SARS-CoV-2 wastewater monitoring

Untreated wastewater or primary sludge can be used as samples for wastewater monitoring workflows, but there are advantages and drawbacks to each. This infographic describes processes involved in both primary sludge and untreated wastewater sample processing.

Download now

Infectious pathogen detection from wastewater samples analysis cover image

Slide deck: Infectious pathogen detection from wastewater sample analysis

This slide deck covers protocols and workflows from Thermo Fisher Scientific for SARS-CoV-2 detection from wastewater samples. It additionally includes sources for organizations worldwide that have developed SARS-CoV-2 wastewater detection methods. Workflows include sample collection, concentration, nucleic acid extraction, pathogen detection, and analysis. Additional viral targets have been tested including Adenovirus, Flu A, Enterovirus, and Norovirus. Both large volume (centrifugation/ultrafiltration) and low volume (direct) methodologies are covered in the slide deck. Published literature is additionally cited.

Download now

Nucleic acid purification resources

Podcast on wastewater testing and analysis of SARS-CoV-2

Podcast: New infectious pathogen detection technologies

This 10-minute podcast covers SARS-CoV-2 molecular testing, from human sample analysis to wastewater surveillance. In which, Dr. Alexander ”Sasha“ Vlassov, Senior Manager of Research and Development at Thermo Fisher Scientific, discusses wastewater surveillance as a useful tool for monitoring the regional spread of viral pathogens, as well as three different testing options for SARS-CoV-2: detection of viral proteins or antigens, detection of viral nucleic acid by PCR, and detection of virus-specific antibodies in the blood.

Download now

Isolating SARS-CoV-2 from wastewater flyer cover image

Flyer: Protocols for wastewater nucleic acid purification

This automated protocol has been optimized for the concentration of SARS-CoV-2 and other viral targets in wastewater samples since these samples are highly diluted and pre-enrichment is needed to improve the detection of pathogens. The method we describe here can be used for downstream nucleic acid extraction after enrichment for viral/pathogen targets with Applied Biosystems MagMAX Wastewater kits and requires just 90 minutes of processing time. Using Applied Biosystems Dynabeads Wastewater Virus Enrichment beads for SARS-CoV-2 and other viral targets from wastewater samples followed by bead-based nucleic acid extraction is designed to be simple, fast, and reliable.

Read more

Nucleic acid purification

Flexibility

  • Choose your preferred concentration method and protocol
  • Pre-concentrate samples from large volumes using ultracentrifugation, precipitation, or filtration
  • Use the Dynabeads option for automated viral enrichment of up to 10 mL volume
  • Directly isolate from 1 mL of wastewater without concentration
  • Manual and automated protocols available

Whole workflow solution—Purchase the whole workflow from sample collection to analysis with one supplier. We can help you get started on a wastewater testing program.

Scalability—These automation compatible kits can help streamline your process to set up sampling across the scale of your organization. Automation-ready protocols written for KingFisher Flex, KingFisher APEX, and KingFisher Duo systems.

MagMAX Wastewater Ultra Nucleic Acid Isolation Kit

Product information

 
MagMAX Wastewater Ultra Nucleic Acid Isolation Kit

MagMAX Wastewater Ultra Nucleic Acid Isolation Kit, with Virus Enrichment
Who should use?Wastewater research and surveillance/community testing
Sample typesPre-concentrated wastewater and sludgeWastewater
Research needs
  • Flexibility—works with a variety of concentration protocols
  • Scalability—automatable technology
  • Total workflow—products from collection to analysis
  • Efficiency—concentration protocol and Dynabeads already included
  • Scalability—automatable technology
  • Total workflow—products from collection to analysis
Downstream compatibility
  • qRT-PCR, NGS and digital PCR
  • Automation-ready protocols for KingFisher Flex, APEX, and Duo Prime
  • Manual protocols available
Format20–100 preps depending on input volume
KingFisher instrument run time28 minutes for MagMAX Wastewater Ultra73 minutes for MagMAX Wastewater Ultra with VE
Total time per run with hands-on time45 minutes for nucleic acid isolation90 minutes for virus enrichment + nucleic acid isolation
Cat. No.A52606A52610

Wastewater concentration

Concentration of wastewater through Dynabeads viral enrichment

The benefits of the Dynabeads Wastewater Virus Enrichment in MagMAX Wastewater Ultra Nucleic Acid Isolation Kit include:

  • Fast isolation kinetics (~10 min)
  • Easy release (~10 min)
  • Easy to automate with Thermo Scientific Kingfisher instruments
  • Can be used on other negatively charged enveloped viruses, vesicles, and proteins

Large volumes of wastewater must be concentrated before extraction to enable detection and analysis. Samples can be concentrated via precipitation, filtration, or ultracentrifugation, and efficient virus enrichment can be performed using Dynabeads Wastewater Virus Enrichment beads. All concentration methods are compatible with the MagMAX Wastewater Ultra Kit.

MagMAX Wastewater Ultra Nucleic Acid Isolation Kit

Wastewater surveillance experimental workflow

Wastewater surveillance experimental workflow

Protocols included in kit

Wastewater starting volume

Sample detailsKit reagents sufficient forKingFisher scripts availableProtocol timePurchase this kit
10 mLConcentration of 10 mL wastewater using Dynabeads followed by nucleic acid isolation100 prepsFlex, Duo Prime, APEX90 minutesMagMAX Wastewater Ultra Nucleic Acid Isolation Kit, with Virus EnrichmentA52610
200 μL200 μL wastewater pre-concentrated using a preferred method, e.g., ultracentrifugation100 prepsFlex, Duo Prime, APEX45 minutesMagMAX Wastewater Ultra Nucleic Acid Isolation KitA52606
1 mL*

A. 1 mL non-concentrated wastewater

B. Wastewater pre-concentrated to 1 mL volume using a preferred method, e.g., precipitation

20 prepsFlex, Duo Prime, APEX45 minutes
50–500 mLConcentration of 50–500 mL wastewater using filtration followed by nucleic acid isolation20 prepsFlex, Duo Prime, APEX90 minutes
Sludge200 mg sludge20 prepsFlex, Duo Prime, APEX45 minutes
*works for 1-2 mL, but 1 mL is the most sensitive

Automated sample processing

Enable high throughput wastewater testing with KingFisher systems

The benefits of KingFisher Instruments include:

  • Various throughputs—process 6–96 samples per run depending on the instrument model
  • Interchangeable formats—choose 24- or 96-well plates so you can process a wide range of input volumes
  • Protocol customization—easily edit, modify, or create new protocols
  • Optimized reagents—compatible with multiple magnetic-bead reagents

Ask a specialist Request a demo

Product information

KingFisher instrument
Duo Prime

Flex

Apex

Presto
Instrument sizeCompact benchtopBenchtopBenchtopBenchtop—integrates with robotic liquid handler
Throughput levelLow to mediumMedium to highMedium to highUltrahigh
Processing volume range 
  • 50-1,000 μL: 12-pin magnet head
  • 200-5,000 μL: 6-pin magnet head
  • 20-100 μL: 96-well PCR plate, skirted*
  • 20-200 μL: 96-well plate
  • 50-1,000 μL: 96 deep-well plate
  • 200-5,000 μL: 24 deep-well plate
  • 15-1,000 μL: 96 deep-well plate
  • 15-200 μL: 96-well KingFisher standard plate
  • 10-80 μL: 96-well PCR plate
  • 30-5,000 μL: 24 deep-well plate
  • 30-200 μL: 96 storage tubes
  • 200-1,000 μL: 24 storage tubes
  • 50-1,000 μL: 96 deep-well plate
  • 200-5,000 μL; 24 deep-well plate
  • 50-150 μL: 96-well KingFisher standard plate
Samples per run6 or 1224 or 9624 or 9624 or 96
Customizable protocolsYes, with PC softwareYes, with PC softwareYes, with touchscreen or PC softwareYes, with PC software
Heating/cooling
  • 10°C to 75°C (plate row block A)
  • 4°C to 75°C (elution strip block)
  • From 5°C above ambient temperature to 115°C
  • From 4°C above ambient temperature to 100°C
  • Cooling down to 4°C
  • From 5°C above ambient temperature to 115°C
Ultraviolet lamp8 watts (up to 16 hr)No2 UV lamps, max 23 h 59 minNo
Ordering information
  • KingFisher Duo Prime Purification System 5400110
  • KingFisher Flex Purification System with 96 PCR Head 5400610 
  • KingFisher Flex Purification System with 96 
  • KingFisher Head 5400620 
  • KingFisher Flex Purification System with 24 Deep-Well Head 5400640 
  • KingFisher Flex Purification System with 96 Deep-Well Head 5400630
 
  • KingFisher Presto Purification System with 24 Deep-Well Head. 5400840 
  • KingFisher Presto Purification System with 96 Deep-Well Head. 5400830

Wastewater concentration resources

Protocols for wastewater sample concentration flyer cover image

Flyer: Protocols for wastewater sample concentration

Optimized protocol for the enrichment of SARS-CoV-2 in wastewater samples. Large sample volumes of wastewater are dilute. Thus, they must be enriched for intact viral presence for pathogen detection via qPCR. Applied Biosystems MagMAX Wastewater Ultra Nucleic Acid Isolation Kits offer a whole host of advantages over traditional wastewater surveillance methods. Isolate nucleic acids from concentrated wastewater in as little as 45 minutes. Our viral enrichment protocol using magnetic beads helps enable concentration and nucleic acid isolation in less than 2 hours.

Read more

Podcast on detection of SARS-CoV-2 in wastewater

Podcast: Infectious pathogen detection and surveillance

Infectious pathogen surveillance from wastewater and fecal samples has been recently adopted as a method for monitoring emergence and re-emergence of infectious pathogens. This method allows public health agencies, universities, hospitals, cruise lines, and more to detect a pathogen and respond before there is a community outbreak. Thermo Fisher Scientific has partnered with many labs globally to implement new wastewater testing systems and optimize existing wastewater monitoring processes. Listen in to learn about the importance of wastewater.

Download now

Automated sample processing resources

New Asset Image

Study: Multiple workflow options for detection of SARS-CoV-2 in wastewater

Five robust workflows were developed for rapid concentration and qPCR analysis of SARS-CoV-2 from different volumes of wastewater: low (1 mL), medium (10 mL), and large (50 mL). The protocols described here are extensions of those developed in previous studies and have been optimized for processing multiple sample types. The protocols include a fully automated workflow to enable high-throughput processing; this workflow has been successfully used in the field.

Read more

Webinar: From wastewater surveillance to human sample analysis

Webinar: Infectious pathogen detection from human samples

Learn more about methods for wastewater detection from Thermo Fisher Scientific scientists Alexandre “Sasha” Vlassov, Madhu Jasti, and Emily Zeringer at American Science Microbe 2021. In which, the team describes protocols for fecal sample, rectal swab, and wastewater detection for SARS-CoV-2. Additionally, molecular workflows for detection and monitoring of pathogens and microbiota are outlined. The common issues of user time consumption and inconsistent results in sample preparation are addressed and resolved with automated workflows. These workflows allow for increased sensitivity, significant time savings, and increased productivity.

Download now

Streamlined SARS-CoV-2 Wastewater Monitoring infographic

Infographic: Streamlined SARS-CoV-2 wastewater monitoring

Untreated wastewater or primary sludge can be used as samples for wastewater monitoring workflows, but there are advantages and drawbacks to each. This infographic describes processes involved in both primary sludge and untreated wastewater sample processing.

Download now

Infectious pathogen detection from wastewater samples analysis cover image

Slide deck: Infectious pathogen detection from wastewater sample analysis

This slide deck covers protocols and workflows from Thermo Fisher Scientific for SARS-CoV-2 detection from wastewater samples. It additionally includes sources for organizations worldwide that have developed SARS-CoV-2 wastewater detection methods. Workflows include sample collection, concentration, nucleic acid extraction, pathogen detection, and analysis. Additional viral targets have been tested including Adenovirus, Flu A, Enterovirus, and Norovirus. Both large volume (centrifugation/ultrafiltration) and low volume (direct) methodologies are covered in the slide deck. Published literature is additionally cited.

Download now

Nucleic acid purification resources

Podcast on wastewater testing and analysis of SARS-CoV-2

Podcast: New infectious pathogen detection technologies

This 10-minute podcast covers SARS-CoV-2 molecular testing, from human sample analysis to wastewater surveillance. In which, Dr. Alexander ”Sasha“ Vlassov, Senior Manager of Research and Development at Thermo Fisher Scientific, discusses wastewater surveillance as a useful tool for monitoring the regional spread of viral pathogens, as well as three different testing options for SARS-CoV-2: detection of viral proteins or antigens, detection of viral nucleic acid by PCR, and detection of virus-specific antibodies in the blood.

Download now

Isolating SARS-CoV-2 from wastewater flyer cover image

Flyer: Protocols for wastewater nucleic acid purification

This automated protocol has been optimized for the concentration of SARS-CoV-2 and other viral targets in wastewater samples since these samples are highly diluted and pre-enrichment is needed to improve the detection of pathogens. The method we describe here can be used for downstream nucleic acid extraction after enrichment for viral/pathogen targets with Applied Biosystems MagMAX Wastewater kits and requires just 90 minutes of processing time. Using Applied Biosystems Dynabeads Wastewater Virus Enrichment beads for SARS-CoV-2 and other viral targets from wastewater samples followed by bead-based nucleic acid extraction is designed to be simple, fast, and reliable.

Read more