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

S. Joh Kang

и другие.

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

Опубликована: Май 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.

Язык: Английский

Nanopore Environmental Analysis DOI Creative Commons
Xiaofeng Lu, Xiaoyu Du, Dong Zhong

и другие.

JACS Au, Год журнала: 2025, Номер unknown

Опубликована: Апрель 1, 2025

Язык: Английский

Процитировано

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

S. Joh Kang

и другие.

Water Research, Год журнала: 2024, Номер 267, С. 122465 - 122465

Опубликована: Сен. 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.

Язык: Английский

Процитировано

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

S. Joh Kang

и другие.

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

Опубликована: Май 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.

Язык: Английский

Процитировано

0