Assessing different next-generation sequencing technologies for wastewater-based epidemiology DOI Creative Commons
Anika John, David Dreifuss,

S. Joh Kang

et al.

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

Published: May 22, 2024

Abstract Wastewater-based epidemiology has proven to be an important public health asset during the COVID-19 pandemic. It can provide less biassed and more cost-effective population-level monitoring of disease burden as compared clinical testing. An essential component SARS-CoV-2 wastewater is next-generation sequencing, providing genomic data identify quantify circulating viral strains rapidly. However, specific choice sequencing method influences quality timeliness generated hence its usefulness for wastewater-based pathogen surveillance. Here, we systematically benchmarked Illumina Novaseq 6000, Element Aviti, ONT R9.4.1 MinION flow cell, Flongle cell facilitate selection technology. Using a time series samples from influent six treatment plants throughout Switzerland, along with spike-in experiments, show that higher error rates Nanopore reduce accuracy estimates relative abundance variants, but overall trend in good concordance among all technologies. We find runtime cells reduced little five hours without significant impact on variant estimates. Our findings suggest tracking readily achievable tested technologies, albeit different tradeoffs terms cost, accuracy.

Language: Английский

Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data DOI Creative Commons
Steven G. Sutcliffe, Susanne A. Kraemer, Isaac Ellmen

et al.

Microbial Genomics, Journal Year: 2024, Volume and Issue: 10(5)

Published: May 24, 2024

Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during SARS-CoV-2 pandemic estimating community infection levels by qPCR. Sequencing pathogen genes genomes from wastewater adds information about genetic diversity, which can be used to identify viral lineages (including variants concern) that are circulating in local population. Capturing diversity sequencing not trivial, as samples often contain diverse mixture with real mutations errors, must deconvoluted computationally short reads. In this study we assess nine different computational tools have recently been developed address challenge. We simulated 100 sequence consisting BA.1, BA.2, Delta lineages, various mixtures, well Delta–Omicron recombinant synthetic ‘novel’ lineage. Most performed identifying true present their relative abundances were generally robust variation depth read length. While many identified down 1 % frequency, results more reliable above 5 threshold. The presence unknown lineage, represents unclassified increases error abundance estimates other but magnitude effect was small most tools. also varied how they labelled novel recombinants. our dataset just one possible use cases these methods, hope it helps users understand potential sources bias analysis appreciate commonalities differences methods.

Language: Английский

Citations

8
Assessment of Greywater Reuse in a University Building in a Hyper-Arid Region: Quantity, Quality, and Social Acceptance DOI Open Access
Teresa Margarita Lanchipa Ale, Ana Cruz-Baltuano, Nahuel Molero-Yañez

et al.

Sustainability, Journal Year: 2024, Volume and Issue: 16(7), P. 3088 - 3088

Published: April 8, 2024

Since Tacna is a hyper-arid region, greywater potential alternative water source. This study aimed to quantify and characterize in university building with 732 students, as well assess their perception of reuse. Water meters were used calculate quantity. To untreated quality, physical–chemical microbiological parameters analyzed. Questionnaires measure students’ acceptance regarding reuse using Likert scale. The quantity recorded this was 426.85 L/d, which less than reported previous global research. quality showed relatively low values parameters; however, microbial contamination higher compared international permissible limits for wastewater Furthermore, it found that the generated has little biodegradability (0.38). Students disclosed lower reusing 77.05% treated green areas. According characterization, biological treatment will not be enough ensure environmental protection user health; thus, also needed. produced quantities would generate 12.67% saving if toilet flushing. volume fulfills whole demand watering areas or roofs. assent greywater.

Language: Английский

Citations

3
Upconversion enabled innovation: Transfer of lab sensor to smartphone based field device DOI
Kamaljit Kaur, Navjeet Kaur,

Kanchan Swami

et al.

Food Research International, Journal Year: 2025, Volume and Issue: unknown, P. 116547 - 116547

Published: May 1, 2025

Language: Английский

Citations

0
Assessing different next-generation sequencing technologies for wastewater-based epidemiology DOI Creative Commons
Anika John, David Dreifuss,

S. Joh Kang

et al.

Water Research, Journal Year: 2024, Volume and Issue: 267, P. 122465 - 122465

Published: Sept. 19, 2024

Wastewater-based epidemiology has proven to be an important public health asset during the COVID-19 pandemic. It can provide less biassed and more cost-effective population-level monitoring of disease burden as compared clinical testing. An essential component SARS-CoV-2 wastewater is next-generation sequencing, providing genomic data identify quantify circulating viral strains rapidly. However, specific choice sequencing method influences quality timeliness generated hence its usefulness for wastewater-based pathogen surveillance. Here, we systematically benchmarked Illumina Novaseq 6000, Element Aviti, ONT R9.4.1 MinION flow cell, Flongle cell facilitate selection technology. Using a time series samples from influent six treatment plants throughout Switzerland, along with spike-in experiments, show that higher error rates Nanopore reduce accuracy estimates relative abundance variants, but overall trend in good concordance among all technologies. We find runtime cells reduced little five hours without significant impact on variant estimates. Our findings suggest tracking readily achievable tested technologies, albeit different tradeoffs terms cost, accuracy.

Language: Английский

Citations

1
Assessing different next-generation sequencing technologies for wastewater-based epidemiology DOI Creative Commons
Anika John, David Dreifuss,

S. Joh Kang

et al.

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

Published: May 22, 2024

Abstract Wastewater-based epidemiology has proven to be an important public health asset during the COVID-19 pandemic. It can provide less biassed and more cost-effective population-level monitoring of disease burden as compared clinical testing. An essential component SARS-CoV-2 wastewater is next-generation sequencing, providing genomic data identify quantify circulating viral strains rapidly. However, specific choice sequencing method influences quality timeliness generated hence its usefulness for wastewater-based pathogen surveillance. Here, we systematically benchmarked Illumina Novaseq 6000, Element Aviti, ONT R9.4.1 MinION flow cell, Flongle cell facilitate selection technology. Using a time series samples from influent six treatment plants throughout Switzerland, along with spike-in experiments, show that higher error rates Nanopore reduce accuracy estimates relative abundance variants, but overall trend in good concordance among all technologies. We find runtime cells reduced little five hours without significant impact on variant estimates. Our findings suggest tracking readily achievable tested technologies, albeit different tradeoffs terms cost, accuracy.

Language: Английский

Citations

0