Evaluating Nanotrap Microbiome Particles as A Wastewater Viral Concentration Method

Food and Environmental Virology, Год журнала: 2025, Номер 17(1)

Опубликована: Янв. 4, 2025

Abstract Wastewater-based surveillance has emerged as a powerful approach to monitoring infectious diseases within community. Typically, wastewater samples are concentrated before viral analyses improve sensitivity. Current concentration methods vary in time requirements, costs, and efficiency. Here, we evaluated the efficiency bias of novel approach, Nanotrap Microbiome Particles (NMP), wastewater. NMP was target-specific, with significantly lower concentrations bacterial indicator HF183 Carjivirus (formerly crAssphage) relative direct extraction (1.2 × 10 5 vs. 3.4 GC/mL 2.0 1.2 GC/mL, respectively), but higher fecal Pepper Mild Mottle Virus (PMMoV) (1.4 8.4 3 GC/mL). Targeted metagenomic sequencing showed that resulted more unique species reads per sample than extractions ( p < 0.001) by detecting went undetected extractions. Key families identified high abundances were Adenoviridae, Caliciviridae, Herpesviridae, Papillomaviridae, Polyomaviridae. differential ability for concentrating clinically relevant families, suggesting technology should be optimized specific targets implementation.

Язык: Английский

---

Novel Workflows for Separate Isolation of Pathogen RNA or DNA from Wastewater: Detection by Innovative and Conventional qPCR

BIO-PROTOCOL, Год журнала: 2025, Номер 15(1365)

Опубликована: Янв. 1, 2025

Wastewater-based surveillance (WBS) can provide a wealth of information regarding the health status communities from measurements nucleic acids found in wastewater. Processing workflows for WBS typically include sample collection, primary concentration step, and lysis microbes to release acids, followed by acid purification molecular-based quantification. This manuscript provides beginning end with an emphasis on filtration-based approaches coupled specific extraction processes. Here, two processing are presented, one focusing RNA-specific pathogens other focused DNA-specific within wastewater: 1) The approach, employed analyzing RNA viruses like severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) couples electronegative filtration wastewater placement filter buffer direct extraction. 2) DNA Candida auris, uses size selection membranes during filtration, subsequently buffer, bead-beating, Separate versus isolations have advantage improving detection target pathogen. A novel aspect workflow is lysates, which shows enhanced recoveries, whereas approach requires bead beating prior Novelty also provided new qPCR called Volcano 2nd Generation (V2G), polymerase capable using as template, bypassing reverse transcriptase step normally required qPCR. Key features • Membrane concentrating suspended solids After concentration, optimized separate recovery DNA. Unique utilized perform analysis, foregoing transcription, RNA. Sample products use molecular techniques (e.g., sequencing) generate high-quality, concentrated extracts minimal inhibitors. Validated through COVID-19 where >1,000 samples >3,000 concentrates produced these been created analyzed, published results. complete protocol was used in: J Biomol Tech (2023), DOI: 10.7171/3fc1f5fe.dfa8d906.

Язык: Английский

---

The Impact of Viral Concentration Method on Quantification and Long Amplicon Nanopore Sequencing of SARS-CoV-2 and Noroviruses in Wastewater

Microorganisms, Год журнала: 2025, Номер 13(2), С. 229 - 229

Опубликована: Янв. 22, 2025

Wastewater-based surveillance has gained attention in the four years following start of COVID-19 pandemic. Accurate pathogen detection, quantification and characterisation rely on selection appropriate methodologies. Here, we explore impact viral concentration method RT-qPCR inhibition norovirus genogroups I II (GI GII), crAssphage, phi6 SARS-CoV-2. Additionally, their long amplicon sequencing for typing noroviruses whole-genome (WGS) SARS-CoV-2 was explored. each significantly different apart from two ultrafiltration methods, InnovaPrep® concentrating pipette (IP) Vivaspin® (VS) centrifugal concentrators. Using an reduced by 62.0% to 96.0% compared ammonium sulphate (AS) polyethylene glycol (PEG) precipitation-based methods. Viral impacted with highest concentrations (copies/L) observed VS 7.2- 83.2-fold differences AS depending target. Norovirus showed genotype-dependent IP performing best GI GII although performance gains were relatively small. outperformed across all metrics during WGS. Overall, performed when considering areas investigation.

Язык: Английский

---

SARS-CoV-2 epidemiology, kinetics, and evolution: A narrative review

Virulence, Год журнала: 2025, Номер 16(1)

Опубликована: Апрель 8, 2025

Since winter 2019, SARS-CoV-2 has emerged, spread, and evolved all around the globe. We explore 4 y of evolutionary epidemiology this virus, ranging from applied public health challenges to more conceptual biology perspectives. Through review, we first present spread lethality infections it causes, starting its emergence in Wuhan (China) initial epidemics world, compare virus other betacoronaviruses, focus on airborne transmission, containment strategies ("zero-COVID" vs. "herd immunity"), explain phylogeographical tracking, underline importance natural selection epidemics, mention within-host population dynamics. Finally, discuss how pandemic transformed (or should transform) surveillance prevention viral respiratory identify perspectives for research COVID-19.

Язык: Английский

---

Considerations and Opportunities for Probe Capture Enrichment Sequencing of Emerging Viruses from Wastewater

Environmental Science & Technology, Год журнала: 2024, Номер 58(19), С. 8161 - 8168

Опубликована: Май 1, 2024

Until recently, wastewater-based monitoring for pathogens of public health concern primarily used PCR-based quantification methods and targeted sequencing specific (e.g., SARS-CoV-2). In the past three years, researchers have expanded to monitor a broad range pathogens, applying probe capture enrichment wastewater. The goals those studies included (1) expanding fundamental knowledge disease dynamics known (2) evaluating potential early detection emerging diseases resulting from zoonotic spillover or novel viral variants. Several using off-the-shelf panels designed clinical environmental surveillance reported that increased virus relative abundance but did not recover complete genomes most nonenteric viruses. Based on our experience recent results by others these wastewater, clinical, synthetic samples, we discuss challenges technical factors affect rates false positive negative results. We identify trade-offs opportunities throughout workflow, including in wastewater sample processing, panel design, bioinformatic analysis. suggest tailored concentration background removal, carefully panels, multithresholded bioinformatics

Язык: Английский

---

RBD amplicon sequencing of wastewater reveals patterns of variant emergence and evolution

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июль 12, 2024

Abstract Rapid evolution of SARS-CoV-2 has resulted in the emergence numerous variants, posing significant challenges to public health surveillance. Clinical genome sequencing, while valuable, limitations capturing full epidemiological dynamics circulating variants general population. This study utilized receptor-binding domain (RBD) amplicon sequencing wastewater samples monitor community and El Paso, TX. Over 17 months, we identified 91 observed waves dominant transitioning from BA.2 BA.2.12.1, BA.4&5, BQ.1, XBB.1.5. Our findings demonstrated early detection identification unreported outbreaks, showing strong consistency with clinical data at local, state, national levels. Alpha diversity analyses revealed periodical variations, highest winter outbreak lag phases, likely due lower competition among before growth phase. The underscores importance low transmission periods for rapid mutation variant evolution. highlights effectiveness integrating RBD surveillance tracking viral evolution, understanding emergence, enhancing preparedness.

Язык: Английский

---

Multiplexed detection, partitioning, and persistence of wild type and vaccine strains of measles, mumps, and rubella viruses in wastewater

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Май 24, 2024

Abstract Wastewater surveillance of vaccine-preventable diseases may provide early warning outbreaks and identify areas to target for immunization. To advance wastewater monitoring measles, mumps, rubella viruses, we developed validated a multiplexed RT-ddPCR assay the detection their RNA. Because measles-mumps-rubella (MMR) vaccine is an attenuated live virus vaccine, also that distinguishes between wild-type strains measles in it using sample collected from facility with active outbreak. We evaluated partitioning behavior viruses liquid solid fractions influent wastewater. found assaying fraction resulted more sensitive despite fact viral RNA was enriched due low solids content Finally, investigated stability samples spiked over 28 days at two different concentrations temperatures (4°C room temperature) observed limited decay. Our study supports feasibility population-level surveillance.

Язык: Английский

---

Revealing patterns of SARS-CoV-2 variant emergence and evolution using RBD amplicon sequencing of wastewater

Journal of Infection, Год журнала: 2024, Номер 89(5), С. 106284 - 106284

Опубликована: Сен. 26, 2024

Rapid evolution of SARS-CoV-2 has resulted in the emergence numerous variants, posing significant challenges to public health surveillance. Clinical genome sequencing, while valuable, limitations capturing full epidemiological dynamics circulating variants general population. This study aimed monitor variant community and using receptor-binding domain (RBD) amplicon sequencing wastewater samples.

Язык: Английский

---

Multiplexed Detection, Partitioning, and Persistence of Wild-Type and Vaccine Strains of Measles, Mumps, and Rubella Viruses in Wastewater

Environmental Science & Technology, Год журнала: 2024, Номер unknown

Опубликована: Дек. 9, 2024

Wastewater surveillance of vaccine-preventable diseases may provide early warning outbreaks and identify areas to target for immunization. To advance wastewater monitoring measles, mumps, rubella viruses, we developed validated a multiplexed RT-ddPCR assay the detection their RNA. Because measles-mumps-rubella (MMR) vaccine is an attenuated live virus vaccine, also that distinguishes between wild-type strains measles in it using sample collected from facility with active outbreak. We evaluated partitioning behavior viruses liquid solid fractions influent wastewater. found assaying fraction resulted more sensitive despite fact viral RNA was enriched due low solids content Finally, investigated stability samples spiked over 28 days at two different concentrations temperatures (4 °C room temperature) through freeze-thaw observed limited decay. Our study supports feasibility population-level surveillance.

Язык: Английский

---

Genomic surveillance of Canadian airport wastewater samples allows early detection of emerging SARS-CoV-2 lineages

Scientific Reports, Год журнала: 2024, Номер 14(1)

Опубликована: Ноя. 3, 2024

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 viral lineages which arrive by many routes transmission including via transportation hubs. In Canadian province Ontario, numerous municipal treatment plants (WWTPs) participate in WW infectious disease targets such as SARS-CoV-2 qPCR and whole genome sequencing (WGS). Greater Toronto Airports Authority (GTAA), operator Pearson International Airport (Toronto Pearson), been participating since January 2022. As a major international airport Canada largest national hub, this is ideal location for globally emerging variants concern (VOCs). study, collected from Pearson’s two terminals pooled aircraft sewage was processed WGS using tiled-amplicon approach targeting virus genome. Data generated analyzed monitor trends lineage frequencies. Initial detections were compared between samples, samples surrounding regions, Ontario clinical data published Public Health Ontario. Results enabled early detection VOCs individual mutations On average, novel at preceded 1–4 weeks, up 16 weeks one case. This project illustrates efficacy transitory hubs sets example that could applied other viruses part preparedness strategy provide monitoring on mass scale.

Язык: Английский

---