Wastewater-based epidemiology: deriving a SARS-CoV-2 data validation method to assess data quality and to improve trend recognition

Frontiers in Public Health, Journal Year: 2024, Volume and Issue: 12

Published: Dec. 12, 2024

Introduction Accurate and consistent data play a critical role in enabling health officials to make informed decisions regarding emerging trends SARS-CoV-2 infections. Alongside traditional indicators such as the 7-day-incidence rate, wastewater-based epidemiology can provide valuable insights into concentration changes. However, wastewater compositions systems are rather complex. Multiple effects precipitation events or industrial discharges might affect quantification of concentrations. Hence, analysing from more than 150 treatment plants (WWTP) Germany necessitates an automated reliable method evaluate validity, identify potential extreme events, and, if possible, improve overall quality. Methods We developed that first categorises quality WWTPs corresponding laboratories based on number outliers reproduction rate well implausible inflection points within time series. Subsequently, we scrutinised statistical several standard control parameters (QCP) routinely collected during analysis process flow electrical conductivity, surrogate viruses like pepper mild mottle virus. Furthermore, investigated ratio analysed gene segments indicate laboratory errors. To success our method, measure degree accordance between identified QCP curves. Results discussion Our reveals segment ratios typically best at identifying curve albeit variations across laboratories. The exclusion datapoints plausibility checks predominantly improves derived categories good with visual assessments. Conclusion Good is crucial for trend recognition, both WWTP level when aggregating regional national trends. model help context health-related monitoring be optimised each individual account large diversity among WWTPs.

Language: Английский

Novel dPCR-Based Approach for SARS-CoV-2 Variant Detection and Monitoring in Wastewater: A Multi-State Comparison with Clinical Genotyping and GISAID Sequencing Data

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 8, 2024

Abstract Wastewater testing has emerged as an effective tool for monitoring levels of SARS-CoV-2 infection in sewered communities. As July 2024, PCR-based methods continue to be the most widely used wastewater surveillance (1–3). Data from is usually available public health authorities near real time, typically within 5 7 days after waste enters sewer (4,5). Unfortunately, while these can accurately detect and quantify SARS-CoV-2, they are not differentiate between multitude variants, including variants that classified Variants High Consequence (VOHC) Concern (VOC) (6). Currently, identify extracted nucleic acids must analyzed using resource-intensive sequencing-based methods. Moreover, every lab access sequencing technology, so availability equipment expertise also a roadblock besides These costly time-consuming methods, informative, diminish some early warning benefits provided by surveillance. creating additional barriers due expertise. In response analytical shortcomings, we developed assessed alternative approach variant customizable dPCR-based genotyping assays. This expansion previously described method analyzing clinical samples utilizing qPCR-based genotyping. Relative sequencing, this cost-effective, fast, easily implemented. We combined along with well-established Nanotrap Ⓡ Particles virus concentration part processing protocol perform five labs across multiple regions United States. The results displayed on public-facing dashboard alongside GISAID data (see https://tracker.rosalind.bio ). Despite conducting fewer than samples, our effectively detected signals emerging trends community, similar analyses. For instance, Georgia, rapid rise dominance Unknown BA.2.86*/JN* 2024 were consistently observed closely matched database. Similarly, EG.5* FL* showed elevated before detection, highlighting potential testing. Detailed analysis datasets various states revealed consistency fall genotyping, data. demonstrates prevalence matches settings, underscoring capability wastewater-based provide extended circulating often preceding detections several weeks. further calculating positive percent agreement detection four (JN, EG.5, FL, XBB) whole genome set 129 both ranged 54% FL 97% JN, average 76% all variants. Additionally, estimate collecting dPCR significantly less expensive compared next-generation sequencing. Labs outsource face much higher costs longer delays. Transitioning multiplex could reduce cost turnaround time. Finally, discuss challenges lessons learned development, validation, implementation findings support use complementary surveillance, offering broader more inclusive picture transmission community.

Language: Английский

Automated Protocol for Monitoring Droplets and Fomites on Surfaces

Microbiology Research, Journal Year: 2023, Volume and Issue: 15(1), P. 120 - 136

Published: Dec. 27, 2023

During the COVID-19 pandemic, extensive efforts focused on developing a better understanding of indirect transmission routes, environmental monitoring fomites, and suitable surveillance strategies, providing new perspectives to also face other communicable diseases. Rapid methods for contamination are strongly needed support risk assessment, epidemiological prevent infections from spreading. We optimized automatized protocol based fomite detection by qPCR, using microbial-signature approach marker genes belonging microbiota droplets or different biological fluids. The procedure was implemented exploiting available tools developed SARS-CoV-2 tracing, such as flocked swab sampling, real-time PCR equipment automatic extraction nucleic acids. This allowed scaling up, simplifying, speeding up step swabs, processing at least 48 samples within 45 min vs. 90 about 24 manual protocols. A comparison microflora data Next-Generation Sequencing (NGS) supports effectiveness this semiautomated procedure, good quality DNA with comparable representation species shown biodiversity indexes. Today, qPCR is widely relatively inexpensive; therefore may represent promising tool hospital hygiene in surveilling fomites associated pathogen’s transmission.

Language: Английский