In this application note, we show that Nanotrap® Microbiome A Particles with the MagMAX™ Wastewater Ultra Nucleic Acid Isolation Kit is compatible with the Clear Dx™ FlexPro: Wastewater (SARS-CoV-2) and leads to higher genome coverage than a competitor method. Wastewater-based epidemiology (WBE) increased in prevalence during the pandemic as a way to measure disease load in a community cheaply and easily. It can be used to track disease at both a species and variant level; PCR applications are commonly used to measure different species and known variants, whereas sequencing is required to detect novel variants. Accurate and complete sequencing from wastewater requires clean and concentrated nucleic acid samples, so it is very dependent on the quality of sample preparation. Concentration methods need to concentrate microbes without concentrating inhibitors that are present in the sample matrix, and extraction methods need to purify the nucleic acid enough for adequate enzymatic activity during library preparation. The Clear Dx FlexPro: Wastewater (SARS-CoV-2) WGS Reagent and Automation Bundle uses targeted sequencing to identify SARS-CoV-2 strains in a system that provides a fully automated workflow for library prep and sequencing.

Legionella, a genus of pathogenic bacteria endemic to natural freshwater sources like lakes, rivers, and groundwater, are capable of colonizing human-engineered water systems, including cooling towers, hospital/hotel water networks, and hot water tanks, putting humans at risk for legionellosis infections. Legionella is oftentimes detected in the environment via the plate culture method, but this method has sensitivity, time, and throughput limitations. Recent advancements have introduced alternative testing methods, including lateral flow devices and liquid culture, yet these techniques still demand either a significant number of viable cells or up to seven days of incubation. In this poster, read how the Nanotrap® Microbiome A and B Particles capture and concentrate multiple Legionella species, and when evaluated on a per-volume basis, exhibit superior concentration efficiency, outperforming both HA filtration and centrifugation methods.

Most Nanotrap Microbiome Particle automated wastewater testing protocols for the KingFisher™ System involve two serial runs on the KingFisher System – the first run captures and concentrates the microbes from the wastewater and the second run extracts the nucleic acids from the concentrated microbes. These protocols combine the output from four separate 24-sample concentration runs into a single 96-well plate for an extraction run. In labs processing 24 samples or fewer at a time, a protocol that combines capture, concentration, and extraction into one run in a 24-well format is more efficient. This protocol integrates wastewater capture, concentration, and nucleic acid extraction into one KingFisher System run, reducing plate types from five to two compared to the standard protocol (Figures 1 and 2). This study demonstrates equivalent sensitivity between the one-run protocol and two-run protocol for bacterial and viral targets across diverse wastewater samples. APPLICATION NOTE SKU 10XXX SKU 44XXX

As wastewater-based epidemiology expands from SARS-CoV-2 to additional pathogen targets, the suitability of a process control as a control for additional pathogens must also be considered. Bovine coronavirus (BCoV) and bovine respiratory syncytial virus (BRSV) have been used as process controls for other RNA viruses, such as respiratory syncytial virus (RSV) and influenza A and B. In this application note, we show that: A process control can be used to correct for sample loss during processing. Intact viral particles can be used as process controls with Nanotrap® Microbiome A Particles. APPLICATION NOTE SKU 10XXX SKU 44XXX

PubMed: https://pubmed.ncbi.nlm.nih.gov/38534222/ Authors: Vishnu Sharma, Hitomi Takamura, Manish Biyani, Ryo Honda Abstract Wastewater-based epidemiology (WBE) is an effective and efficient tool for the early detection of infectious disease outbreaks in a community. However, currently available methods are laborious, costly, and time-consuming due to the low concentration of viruses and the presence of matrix chemicals in wastewater that may interfere with molecular analyses. In the present study, we designed a highly sensitive "Quick Poop (wastewater with fecal waste) Sensor" (termed, QPsor) using a joint approach of Nanotrap microbiome particles and RICCA (RNA Isothermal Co-Assisted and Coupled Amplification). Using QPsor, the WBE study showed a strong correlation with standard PEG concentrations and the qPCR technique. Using a closed format for a paper-based lateral flow assay, we were able to demonstrate the potential of our assay as a real-time, point-of-care test by detecting the heat-inactivated SARS-CoV-2 virus in wastewater at concentrations of 100 copies/mL and within one hour. As a proof-of-concept demonstration, we analyzed the presence of viral RNA of the SARS-CoV-2 virus and PMMoV in raw wastewater samples from wastewater treatment plants on-site and within 60 min. The results show that the QPsor method can be an effective tool for disease outbreak detection by combining an AI-enabled case detection model with real-time on-site viral RNA extraction and amplification, especially in the absence of intensive clinical laboratory facilities. The lab-free, lab-quality test capabilities of QPsor for viral prevalence and transmission in the community can contribute to the efficient management of pandemic situations. Figure 1 A schematic layout of the QPsor system to monitor SARS-CoV-2 viruses in wastewater. Possible results (test line positive or negative) are highlighted by red box in step-6.

Wastewater-based epidemiology (WBE) to monitor SARS-CoV-2 has rapidly expanded across the globe as data has shown that WBE trends correlate with clinical case trends1,2. The success of WBE with SARS-CoV-2 has led to interest in monitoring additional pathogens, such as those that cause sexually transmitted infections (STI)3. STIs pose significant public health risks and are generally underreported as individuals are often hesitant to get tested. The Centers for Disease Control and Prevention estimated over 2.5 million cases of chlamydia, gonorrhea, and syphilis in 20214. Surveillance of these microorganisms’ prevalence within wastewater could provide public health officials with a tool to alert them when there is a rise in STIs within the population. Read the poster to learn about capturing and concentrating three common STI causing pathogens: Chlamydia trachomatis, Neisseria gonorrhoeae, and Mycoplasma genitalium from wastewater.

Presently, both DNA and RNA commercial extraction kits use a common method in which a crowding agent or alcohol induces a conformational change in the nucleic acid. The nucleic acid then binds with silica beads/columns or carboxylated beads, facilitating its separation from the remainder of the sample. The effectiveness of this method is dependent on component concentrations, and it is most efficient with larger DNA/RNA.1 Ceres Nanosciences developed the patented Nanotrap® Particle technology that uses magnetic hydrogel particles with bound affinity baits to capture and concentrate low-abundance analytes. We have had success with our Microbiome Particles, particularly for wastewater testing, and recently developed Nanotrap Particles that bind small DNA fragments. These particles are incorporated into our new Nanotrap Extraction Advanced Technologies (NEAT) Liquid Biopsy Kit. Blood contains small amounts of circulating cell free DNA (cfDNA) originating from cells around the body. This cfDNA provides insights into the genetics of somatic cells and is particularly valuable in detecting tumor mutations. Traditionally, a biopsy of the tumor itself had to be tested to determine the tumor genetics, which can be invasive and often constrained by the limited number of biopsy procedures. However, by examining these tumor mutations in blood, testing becomes more frequent, allowing for enhanced diagnostic and therapeutic interventions. Detecting cfDNA poses challenges due to low concentrations and difficulty in capturing smaller fragments with existing DNA extraction technology. The NEAT Liquid Biopsy Kit is specifically designed to capture small DNA fragments while excluding larger genomic DNA, which is unlikely to contain cancer mutations. This size selection provides more targeted DNA capture, resulting in a higher fraction of the DNA of interest and ultimately improving downstream results. In this proof-of-concept study, two prevalent cancer mutations, namely EGFR T790M and KRAS G12C were used. KRAS G12C is the most frequently observed mutation in human cancers2 and EGFR T790M is the most common mutation responsible for resistance to tyrosine kinase inhibitor therapy.

Diagnostics 2022 ABSTRACT: Infectious uveitis is a sight-threatening infection commonly caused by herpesviruses. Vitreous humor is often collected for molecular confirmation of the causative agent during vitrectomy and mixed in large volumes of buffered saline, diluting the pathogen load. Here, we explore affinity-capture hydrogel particles (Nanotrap®) to concentrate low abundant herpesviruses from diluted vitreous. Simulated samples were prepared using porcine vitreous spiked with HSV-1, HSV-2, VZV and CMV at 105 copies/mL. Pure undiluted samples were used to test capturing capability of three custom Nanotrap particles (red, white and blue) in a vitreous matrix. We found that all particles demonstrated affinity to the herpesviruses, with the Red Particles having both good capture capability and ease of handling for all herpesviruses. To mimic diluted vitrectomy specimens, simulated-infected vitreous were then serially diluted in 7 mL TE buffer. Diluted samples were subjected to an enrichment protocol using the Nanotrap Red particles. Sensitivity of pathogen detection by qPCR in diluted vitreous increased anywhere between 2.3 to 26.5 times compared to non-enriched specimens. This resulted in a 10-fold increase in the limit of detection for HSV-1, HSV-2 and VZV. These data demonstrated that Nanotrap particles can capture and concentrate HSV-1, HSV-2, VZV and CMV in a vitreous matrix.

The Nanotrap® Microbiome A and B Particles capture and concentrate multiple Legionella species, offering improved performance over current standard Legionella concentration methods. The Nanotrap Microbiome Particle method enables the detection of L. pneumophila serogroup 1 at a concentration of 0.1 cell / mL in environmental water. APPLICATION NOTE SKU 10XXX SKU 44XXX

In this application note, we show how the Nanotrap® Microbiome A and B Particles: Capture and concentrate STI-causing bacteria from wastewater samples across a wide range of bacterial concentrations Improve detection of those bacteria by processing a larger sample volume Improve detection of those bacteria compared to an alternative sample processing method Are compatible with multiplex digital PCR (dPCR) assays on the QIAcuity One 5plex Device APPLICATION NOTE SKU 10XXX SKU 44XXX

Morbidity and Mortality Weekly Report (MMWR) Weekly / January 18, 2024 / 73(2);37–43 Read the entire article Abstract In October 2022, CDC’s National Wastewater Surveillance System began routine testing of U.S. wastewater for Monkeypox virus. Wastewater surveillance sensitivity, positive predictive value (PPV), and negative predictive value (NPV) for Monkeypox virus were evaluated by comparing wastewater detections (Monkeypox virus detected versus not detected) to numbers of persons with mpox in a county who were shedding virus. Case ascertainment was assumed to be complete, and persons with mpox were assumed to shed virus for 25 days after symptom onset. A total of 281 cases and 3,492 wastewater samples from 89 sites in 26 counties were included in the analysis. Wastewater surveillance in a single week, from samples representing thousands to millions of persons, had a sensitivity of 32% for detecting one or more persons shedding Monkeypox virus, 49% for detecting five or more persons shedding virus, and 77% for detecting 15 or more persons shedding virus. Weekly PPV and NPV for detecting persons shedding Monkeypox virus in a county were 62% and 80%, respectively. An absence of detections in counties with wastewater surveillance signified a high probability that a large number of cases were not present. Results can help to guide the public health response to Monkeypox virus wastewater detections. A single, isolated detection likely warrants a limited public health response. An absence of detections, in combination with no reported cases, can give public health officials greater confidence that no cases are present. Wastewater surveillance can serve as a useful complement to case surveillance for guiding the public health response to an mpox outbreak.

The purpose of this study was to compare low-frequency, rare variant allele detection by digital PCR in Streck Cell-Free DNA BCT samples processed by the NEAT Liquid Biopsy Kit with competitor Kit 2. The data demonstrates that the NEAT Liquid Biopsy Kit increases the concentration of mutant alleles in these DNA samples, which improves the reliability of detection across replicates. In other words, the NEAT Liquid Biopsy Kit has fewer non-detects than competitor Kit 2. This data highlights the performance of the NEAT Liquid Biopsy Kit compared to its competitor, Kit 2, in the detection of rare variant alleles in difficult samples for cfDNA extraction. TECHNICAL NOTE - SKU 10XXX SKU 55XXX