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

The purpose of this study was to showcase the effectiveness of Nanotrap® Extraction Advanced Technologies (NEAT) Liquid Biopsy Particles in capturing shorter DNA fragments. The data provided evidence of the NEAT Kit’s capability to efficiently capture DNA fragments ranging from 50 to 800 base pairs, which are characteristic of cell-free DNA (cfDNA), while effectively excluding longer DNA fragments of 800+ base pairs, which typically represent genomic DNA (gDNA). TECHNICAL NOTE - SKU 77XXX

This study evaluated the recovery of cell-free DNA (cfDNA), as determined by cfDNA concentration and purity, in samples extracted with the NEAT Liquid Biopsy Kit, competitor Kit 1, and competitor Kit 2. Samples were processed with the NEAT Liquid Biopsy Kit and the two competitor kits across multiple sample volumes, on different sample processing systems, and from different blood collection tubes. The data demonstrates the consistent improvement of both cfDNA concentration and cfDNA purity (as measured by the percentage of the eluent that is cfDNA vs the total cfDNA and gDNA in the eluent) in samples processed with NEAT Liquid Biopsy Kit, Kit 1, and Kit 2. The NEAT Liquid Biopsy Kit improved cfDNA concentration by an average of 8.0-fold over Kit 1 and by an average of 2.19-fold over Kit 2. The NEAT Liquid Biopsy Kit also improved percent cfDNA by an average of 23% over Kit 1 and by an average of 8% over Kit 2. The NEAT Liquid Biopsy Kit is a robust, dependable, and flexible cfDNA extraction kit that provides scalable solutions for laboratories. TECHNICAL NOTE SKU 77XXX

This study evaluated the detection of EGFR L858R and T790M cancer mutations in 4 mL non-small cell lung cancer (NSCLC) diagnostic remnant plasma samples collected in K2EDTA tubes, deidentified and acquired from Discovery Life Sciences and Precision for Medicine. The NEAT Liquid Biopsy Kit was used for sample extraction on the KingFisher™ Apex System, followed by analysis on the QIAGEN QIAcuity Digital PCR System with LNA mutation assays. These samples were identified as EGFR mutation-positive by examining treatment data gathered at the time of blood collection. Samples 1, 3, and 4 were expected to be positive for EGFR T790M with other potential EGFR mutations, and Sample 2 was expected to be positive for EGFR L858R but not T790M. The data showed that all four samples characterized as true positive from patients with NSCLC were positive for the T790M mutation, and two of these samples were also positive for the L858R mutation. The simultaneous occurrence of mutations may be significant in a clinical setting, suggesting a possible specific disease pattern or subtype within the studied group. Additionally, all four control samples from healthy donors tested negative, demonstrating the kit’s reliability in correctly identifying true negative samples within the sample set described above. Collectively, these initial findings suggest that the NEAT Liquid Biopsy Kit will enable accurate cancer mutation detection in NSCLC samples for research use. TECHNICAL NOTE SKU 77XXX

The primary objective of this study was to illustrate the scalability of the Nanotrap® Extraction Advanced Technology (NEAT) Liquid Biopsy Kit on both KingFisher™ Apex and KingFisher™ Flex systems. The data demonstrates that the NEAT Liquid Biopsy Kit exhibits outstanding reliability and linear scalability (R2 = 0.9), consistently achieving higher concentrations of cell-free DNA (cfDNA) when compared to both Kit 1 and Kit 2 across 1 mL, 2 mL, and 4 mL plasma samples. TECHNICAL NOTE SKU 77XXX

This study aimed to determine whether the NEAT Liquid Biopsy Kit is suitable for use with PAXgene® Blood ccfDNA Tubes, effectively extracting cell-free DNA (cfDNA) under varied storage conditions specified by the manufacturer. The data underscores the superior performance of the NEAT Liquid Biopsy Kit compared to its competitor, Kit 2, in the extraction of cfDNA. These findings suggest that the NEAT Liquid Biopsy Kit is a dependable and efficient method for cfDNA extraction. TECHNICAL NOTE SKU 77XXX

The purpose of this study was to demonstrate that the NEAT Liquid Biopsy Kit-Streck BCT is suitable for use with the Streck Cell-Free DNA BCT®, effectively capturing and concentrating cell-free DNA (cfDNA) under varied storage conditions specified by the manufacturer. The data underscore the superior performance of the NEAT Kit compared to a competitor, Kit 2, in the cfDNA capture and concentration. These findings confirm that the NEAT Liquid Biopsy Kit is a dependable and efficient method for cfDNA capture and concentration. Blood samples from three donors were drawn into Streck Cell- Free DNA BCT. The tubes were stored at room temperature (19°C-23°C). After days two and seven, plasma was collected per tube manufacturer’s instructions. cfDNA was isolated from 4 mL of plasma sample using competitor Kit 2 (automated, magnetic silica bead-based method) and the NEAT Liquid Biopsy Kit - Streck BCT. Samples were processed using the KingFisher™ Apex System. cfDNA was analyzed using the Agilent Cell-Free DNA ScreenTape on the 4200 TapeStation. Bars represent the concentrations of the average of three technical replicates and error bars indicate one standard deviation. TECHNICAL NOTE SKU 77XXX

This application note demonstrates that the NEAT Liquid Biopsy Kit can be combined with GT Molecular dPCR EGFR Actionable Mutations Panel Assay Kit for the Bio-Rad QX200™ Droplet Digital™ PCR System for highly-sensitive detection of the EGFR T790M mutation. The NEAT Liquid Biopsy Kit’s ability to improve cfDNA and ctDNA concentrations in combination with the exclusion of gDNA can improve detection of variant alleles, which increases sensitivity and reduces the risk of false negatives. APPLICATION NOTE SKU 77XXX

Next-generation sequencing (NGS) is often used in liquid biopsy research to detect a wide range of genes or whole genome sequencing. Targeted sequencing, while limited to detecting a specific set of mutations, offers higher sensitivity compared to whole genome sequencing. This makes tools like the Trusight Myeloid Sequencing Panel highly effective for clinical research studies. In this Tech Note, see how the NEAT Liquid Biopsy Kit shows compatibility with the Illumina Trusight Myeloid Sequencing Panel, demonstrating its potential as an effective tool for identifying specific mutations in liquid biopsies through NGS. TECHNICAL NOTE SKU 77XXX

Liquid biopsy represents a highly sensitive, non-invasive approach to detect cancer biomarkers early and monitor response to treatments.  However, detecting biomarkers in circulating tumor DNA and cell-free DNA (cfDNA) is challenging, as cfDNA is often fragmented or present at very low levels and requires highly sensitive mutation detection technology. In this application note, we demonstrate that the NEAT Liquid Biopsy Kit captures and concentrates low-abundance cfDNA from plasma samples with limited binding of larger genomic DNA, increasing opportunities for cfDNA and liquid biopsy to be used in precision oncology. The NEAT Liquid Biopsy Kit can concentrate low-abundant KRAS G12C, a common mutation found in cancers including non-small-cell lung cancer and colorectal cancer. Coupled with the GT-Digital KRAS G12C;G12 Assay Kit and highly sensitive droplet digital PCR (ddPCR), the NEAT Liquid Biopsy Kit allows for the detection of 0.1% KRAS G12C from plasma, exhibiting similar performance to competitor approaches. The data presented within highlights an end-to-end solution for monitoring mutant KRAS G12C. APPLICATION NOTE SKU 77XXX