Key Advantages Nanotrap Particles enable simple, automated methods for bio-surveillance of a broad spectrum of infectious diseases, including hepatitis A. The automated Nanotrap Particle method is compatible with several large-volume sample types, including produced wash water and wastewater. The automated Nanotrap Particle method offers equivalent or better hepatitis A viral detection from wastewater samples, as compared to an HA filtration method. Introduction Hepatitis A is an acute inflammatory liver disease which results from infection by the hepatitis A virus (HAV). It is faeco-orally spread, and its severity is age dependent. Recently, cases of acute hepatitis of unknown origin among young children have been reported from 12 countries around the world. Routine food safety testing can be used to effectively identify HAV present on foods, while wastewater surveillance for HAV can provide an indication of infection levels and affected geographical locations. Municipal wastewater harbors a variety of pathogenic viruses. Extensive research has been conducted on the persistence of human enteric viruses, which are transmitted via the fecal-oral route, in wastewater and in the aquatic environment. Wastewater surveillance is appealing because a single sample can ‘test’ a large population, it can enable detection from both asymptomatic and symptomatic individuals, and it can provide an indication of changing trends in population infection levels about 7 days ahead of clinical testing. CDC and HHS, in collaboration with agencies throughout the federal government, implemented the National Wastewater Surveillance System (NWSS) in response to the COVID-19 pandemic as a resource to help public health officials and communities utilize wastewater data to guide community level response and decision making. There is an interest in using the infrastructure in place to detect and monitor other common and potentially deadly pathogens. Nanotrap Particles have demonstrated sensitive, rapid, and easy-to-use automated and manual methods for wastewater SARS-CoV-2 testing. In this application note, we show that Nanotrap® Microbiome A Particles can also capture HAV from wastewater samples and from simulated agricultural produce wash samples. Nanotrap Microbiome A Particles outperformed the HA Filtration method for HAV capture and concentration in two spiked wastewater samples. APPLICATION NOTE SKU 10XXX SKU 44XXX

Mass-spectrometry-based proteomic analysis of biological samples is a powerful tool for the identification of potential biomarkers. Cerebrospinal fluid (CSF) is a common sample type used in proteomic analyses because of its clinical relevance and low protein complexity. However, high abundances of albumin and immunoglobin proteins can mask the detection of lower abundance proteins. (1) In this application note, we demonstrate how to use the Nanotrap® Protein Enrichment Affinity Kits (PEAK) to manually process CSF samples. We compare the number of unique protein identifications obtained from a CSF sample using different Nanotrap Protein Particle workflows to the same CSF sample processed without using the Nanotrap PEAK. We also compare the overlap of unique protein identifications for these different workflows. The Venn diagram illustrates the overlap of unique protein identifications (protein IDs) for the 1-particle Method using each of the three different Nanotrap Protein Particle types. APPLICATION NOTE SKU # 34XXX Lit. # CSF-AN31394

Droplet digital PCR is an attractive choice for rare mutation detection during liquid biopsy studies due to its powerful sensitivity, ease of use and data analysis, and generally lower price point than other common detection technologies such as next-generation sequencing. In this study, the NEAT Liquid Biopsy Kit was compared to a competitor kit using Bio-Rad ddPCR™ KRAS G12/G13 Screening Kit to detect KRAS mutations in plasma spiked with liquid biopsy standards at varying allele frequency. Figure 1. Number of Droplets Positive for KRAS G12/G13 Mutations from 4 mL Spiked Plasma TECHNICAL NOTE SKU 77XXX

In this application note, we use Sypro-Ruby staining of protein gels to demonstrate that each of the three Nanotrap Protein Particle types captures and concentrates proteins from K2EDTA plasma samples and reduces the presence of the highly abundant albumin protein. Sypro-Ruby staining images demonstrate that Nanotrap Protein Particles A, B, and C capture proteins across different size ranges and reduce the abundance of high molecular weight proteins. APPLICATION NOTE SKU # 34XXX

In this application note, we investigate the compatibility of Nanotrap® Particles with wastewater samples treated with Wastewater Stabilization Buffer. Additionally, we studied the claimed seven-day stability at room temperature for wastewater samples treated with Wastewater Stabilization Buffer using Nanotrap Particles for viral and bacterial target concentration. Confirming the stability supports the development of robust and efficient workflows for environmental monitoring and public health surveillance, particularly in the context of detecting and analyzing pathogens in wastewater. Demonstrating compatibility of Zymo Research’s Wastewater Stabilization Buffer with Nanotrap Particles for both viral and bacterial targets. APPLICATION NOTE SKU 44XXX, 65XXX

Over 200,000 new lung cancer patients are diagnosed every year, with over 150,000 deaths from the disease, making it one of the most lethal cancers. (1) Non-small cell lung cancer (NSCLC) makes up 85% of lung cancer patients in the US, with lung adenocarcinomas being the most common histological subtype of NSCLC. Lung adenocarcinomas are frequently characterized by KRAS mutations, which appear to correlate with disease aggressiveness. KRAS is also useful for predicting therapeutic response.(2) KRAS mutations can arise at any point during cancer progression, and detection of mutations as they appear is crucial to understanding the disease. Liquid biopsy of patient plasma is often used to understand disease progression in NSCLC patients, as mutations present in solid tumors can often be detected in plasma samples in low amounts. This non-invasive approach allows for more frequent sampling than traditional tissue biopsies but requires the detection of very low-frequency alleles. In this study, plasma from six NSCLC patients with known KRAS mutations was extracted by two different methods and the digital PCR (dPCR) results were compared. Quantification of wild-type KRAS in clinical plasma samples. APPLICATION NOTE SKU 77XXX

Recent research underscores the need for surveillance of waterborne pathogens in tap water systems. Studies have demonstrated that pathogens like Legionella pneumophila and Pseudomonas aeruginosa can persist in tap water systems and pose significant health risks, especially to immunocompromised individuals. Legionella, which is known to cause Legionnaires’ disease, thrives in complex water system environments, including those in urban settings, where it can become a significant public health concern due to its ability to survive chlorination and other disinfection methods. (4,5) We oftentimes detect microbes in environmental samples 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 ten days of incubation. (6) The Nanotrap® Microbiome A and Nanotrap® Microbiome B Particles capture and concentrate multiple Legionella species and, when evaluated on a per-volume basis, exhibit superior capture efficiency, outperforming both HA filtration and centrifugation methods. Beyond Legionella species, our methodology efficiently captures a broader spectrum of waterborne pathogens, including Mycobacterium abscessus and Pseudomonas aeruginosa , offering a versatile solution in the surveillance and control of microbial threats in water systems. The Nanotrap technology offers an efficient, scalable, and easily automatable method for monitoring pathogens in tap water. APPLICATION NOTE SKU 10XXX SKU 44XXX

Food and Environmental Virology (2025) 17:10 https://doi.org/10.1007/s12560-024-09628-w Authors: Marlee Shaffer, Devin North, Kyle Bibby Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, USA Article Wastewater-based surveillance has emerged as a powerful approach to monitoring infectious diseases within a community. Typically, wastewater samples are concentrated before viral analyses to improve sensitivity. Current concentration methods vary in time requirements, costs, and efficiency. Here, we evaluated the concentration efficiency and bias of a novel viral concentration approach, Nanotrap Microbiome Particles (NMP), in wastewater. dPCR Comparison of Carjivirus, HF 183, and PMMoV for Nanotrap Particles and Direct Extraction Methods.

Read the article Abstract BLOODPAC is a public-private consortium that develops best practices, coordinates clinical and translational research, and manages the BLOODPAC Data Commons to broadly support the liquid biopsy community and accelerate regulatory review to aid patient accessibility. BLOODPAC previously recommended 11 preanalytical minimal technical data elements (MTDEs) for BLOODPAC-sponsored studies and data submitted to BLOODPAC Data Commons. The current landscape analysis evaluates the overlap of the BLOODPAC MTDEs with current best practices, guidelines, and standards documents related to clinical and research liquid biopsy applications. Our findings indicate an existing high degree of concordance among these documents. Where differences exist, the BLOODPAC preanalytical MTDEs can be considered a minimal practicable set for organizations to utilize. These MTDEs were developed following extensive examination of best practices and iterative conversations with the U.S. FDA. BLOODPAC recommends the use of these MTDEs in submissions to data commons and to support liquid biopsy clinical trials and research globally.

Read the article: https://rdcu.be/d3mV3 Overton, A.K., Knapp, J.J., Lawal, O.U. et al. Genomic surveillance of Canadian airport wastewater samples allows early detection of emerging SARS-CoV-2 lineages. Sci Rep 14 , 26534 (2024). https://doi.org/10.1038/s41598-024-76925-6 Abstract The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has shown wastewater (WW) surveillance to be an effective means of tracking the emergence of viral lineages which arrive by many routes of transmission including via transportation hubs. In the Canadian province of Ontario, numerous municipal wastewater treatment plants (WWTPs) participate in WW surveillance of infectious disease targets such as SARS-CoV-2 by qPCR and whole genome sequencing (WGS). The Greater Toronto Airports Authority (GTAA), operator of Toronto Pearson International Airport (Toronto Pearson), has been participating in WW surveillance since January 2022. As a major international airport in Canada and the largest national hub, this airport is an ideal location for tracking globally emerging SARS-CoV-2 variants of concern (VOCs). In this study, WW collected from Toronto Pearson’s two terminals and pooled aircraft sewage was processed for WGS using a tiled-amplicon approach targeting the SARS-CoV-2 virus genome. Data generated was analyzed to monitor trends of SARS-CoV-2 lineage frequencies. Initial detections of emerging lineages were compared between Toronto Pearson WW samples, municipal WW samples collected from the surrounding regions, and Ontario clinical data as published by Public Health Ontario. Results enabled the early detection of VOCs and individual mutations emerging in Ontario. On average, the emergence of novel lineages at the airport preceded clinical detections by 1–4 weeks and up to 16 weeks in one case. This project illustrates the efficacy of WW surveillance at transitory transportation hubs and sets an example that could be applied to other viruses as part of a pandemic preparedness strategy and to provide monitoring on a mass scale.

Das, Amaresh, Joseph Gutkoska, Yadata Tadassa, and Wei Jia. 2024. "Enhanced Recovery and Detection of Highly Infectious Animal Disease Viruses by Virus Capture Using Nanotrap® Microbiome A Particles" Viruses  16, no. 11: 1657. https://doi.org/10.3390/v16111657 Abstract This study reports the use of Nanotrap® Microbiome A Particles (NMAPs) to capture and concentrate viruses from diluted suspensions to improve their recovery and sensitivity to detection by real-time PCR/RT-PCR (qPCR/RT-qPCR). Five highly infectious animal disease viruses including goatpox virus (GTPV), sheeppox virus (SPPV), lumpy skin disease virus (LSDV), peste des petits ruminants virus (PPRV), and African swine fever virus (ASFV) were used in this study. After capture, the viruses remained viable and recoverable by virus isolation (VI) using susceptible cell lines. To assess efficacy of recovery, the viruses were serially diluted in phosphate-buffered saline (PBS) or Eagle’s Minimum Essential Medium (EMEM) and then subjected to virus capture using NMAPs. The NMAPs and the captured viruses were clarified on a magnetic stand, reconstituted in PBS or EMEM, and analyzed separately by VI and virus-specific qPCR/RT-qPCR. The PCR results showed up to a 100-fold increase in the sensitivity of detection of the viruses following virus capture compared to the untreated viruses from the same dilutions. Experimental and clinical samples were subjected to virus capture using NMAPs and analyzed by PCR to determine diagnostic sensitivity (DSe) that was comparable (100%) to that determined using untreated (-NMAPs) samples. NMAPs were also used to capture spiked viruses from EDTA whole blood (EWB). Virus capture from EWB was partially blocked, most likely by hemoglobin (HMB), which also binds NMAPs and outcompetes the viruses. The effect of HMB could be removed by either dilution (in PBS) or using HemogloBind™ (Biotech Support Group; Monmouth Junction, NJ, USA), which specifically binds and precipitates HMB. Enhanced recovery and detection of viruses using NMAPs can be applicable to other highly pathogenic animal viruses of agricultural importance.

In this application note, plasma samples from three individual donors were processed (4 mL per sample) using the NEAT Liquid Biopsy Kit and two competitor kits (Kit 1 and Kit 2). The elution products from all three extraction kits were analyzed for quantification and purity data with the Agilent TapeStation 4200, Cell-Free DNA ScreenTape. The NEAT Liquid Biopsy Kit provided an average of 3-fold improvement in cfDNA concentration when compared to Kit 1. The NEAT Liquid Biopsy Kit workflow provided an average of 1.3-fold improvement in cfDNA concentration when compared to Kit 2. APPLICATION NOTE SKU 77XXX