Longer amplicons provide better sensitivity for electrochemical sensing of viral nucleic acid in water samples using PCB electrodes DOI Creative Commons

Shruti Ahuja,

Manish Kumar, Ruchira Nandeshwar

et al.

Scientific Reports, Journal Year: 2022, Volume and Issue: 12(1)

Published: May 25, 2022

Abstract The importance of monitoring environmental samples has gained a lot prominence since the onset COVID-19 pandemic, and several surveillance efforts are underway using gold standard, albeit expensive qPCR-based techniques. Electrochemical DNA biosensors could offer potential cost-effective solution suitable for water in lower middle income countries. In this work, we demonstrate electrochemical detection amplicons as long $${503}\,\hbox {bp}$$ 503 bp obtained from Phi6 bacteriophage (a popular surrogate SARS-CoV-2) isolated spiked lake samples, ENIG finish PCB electrodes with no surface modification. sensor response is thoroughly characterised two fragments different lengths ( $${117}\,\hbox 117 ), impact salt PCR master mix on methylene blue (MB)-DNA interactions studied. Our findings establish that length fragment significantly determines sensitivity, ability to detect without gel purification products demonstrated work bodes well realisation fully-automated solutions situ measurement viral load samples.

Language: Английский

Wastewater-Based Detection of Two Influenza Outbreaks DOI Creative Commons
Marlene K. Wolfe,

Dorothea Duong,

Kevin M. Bakker

et al.

Environmental Science & Technology Letters, Journal Year: 2022, Volume and Issue: 9(8), P. 687 - 692

Published: July 5, 2022

Traditional influenza surveillance informs control strategies but can lag behind outbreak onset and undercount cases. Wastewater is effective for monitoring near real-time dynamics of outbreaks has not been attempted influenza. We quantified A virus (IAV) RNA in wastewater during two active on university campuses different parts the United States times year using case data from an investigation high-quality student athletes. In both cases, IAV concentrations were strongly associated with reported incidence rates (Kendall's τ values 0.58 0.67 University Michigan Stanford University, respectively). Furthermore, reflected patterns magnitudes. For outbreak, evidence sequencing indicated same circulating strain identified cases outbreak. The results demonstrate that effectively detect will therefore be a valuable supplement to traditional forms surveillance.

Language: Английский

Citations

147
Application of digital PCR for public health-related water quality monitoring DOI
Ananda Tiwari, Warish Ahmed, Sami Oikarinen

et al.

The Science of The Total Environment, Journal Year: 2022, Volume and Issue: 837, P. 155663 - 155663

Published: May 4, 2022

Language: Английский

Citations

78
Recent progress on wastewater-based epidemiology for COVID-19 surveillance: A systematic review of analytical procedures and epidemiological modeling DOI Open Access
Stéfano Ciannella, Cristina González-Fernández, Jenifer Gómez‐Pastora

et al.

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 878, P. 162953 - 162953

Published: March 21, 2023

Language: Английский

Citations

60
State-space modelling using wastewater virus and epidemiological data to estimate reported COVID-19 cases and the potential infection numbers DOI
Syun-suke Kadoya, Yubing Li, Yilei Wang

et al.

Journal of The Royal Society Interface, Journal Year: 2025, Volume and Issue: 22(222)

Published: Jan. 1, 2025

The current situation of COVID-19 measures makes it difficult to accurately assess the prevalence SARS-CoV-2 due a decrease in reporting rates, leading missed initial transmission events and subsequent outbreaks. There is growing recognition that wastewater virus data assist estimating potential infections, including asymptomatic unreported infections. Understanding hidden behind reported cases critical for decision-making when choosing appropriate social intervention measures. However, models implicitly assume homogeneity human behaviour, such as shedding patterns within population, making challenging predict emergence new variants variant-specific or parameters. This can result predictions with considerable uncertainty. In this study, we established state-space model based on viral load both infection numbers. Our using showed high goodness-of-fit case numbers despite dataset waves two distinct variants. Furthermore, successfully provided estimates infection, reflecting superspreading nature transmission. study supports notion surveillance modelling have effectively

Language: Английский

Citations

2
SARS-CoV-2 RNA is enriched by orders of magnitude in primary settled solids relative to liquid wastewater at publicly owned treatment works DOI Creative Commons
Sooyeol Kim, Lauren C. Kennedy, Marlene K. Wolfe

et al.

Environmental Science Water Research & Technology, Journal Year: 2022, Volume and Issue: 8(4), P. 757 - 770

Published: Jan. 1, 2022

We compared SARS-CoV-2 RNA concentrations in primary settled solids and raw wastewater samples matched date to investigate the relationship between two matrices.

Language: Английский

Citations

69
SARS-CoV-2 RNA surveillance in large to small centralized wastewater treatment plants preceding the third COVID-19 resurgence in Bangkok, Thailand DOI Creative Commons
Jatuwat Sangsanont, Surapong Rattanakul, Akechai Kongprajug

et al.

The Science of The Total Environment, Journal Year: 2021, Volume and Issue: 809, P. 151169 - 151169

Published: Oct. 25, 2021

Wastewater surveillance for SARS-CoV-2 RNA has been a successful indicator of COVID-19 outbreaks in populations prior to clinical testing. However, this mostly conducted high-income countries, which means there is dearth performance investigations low- and middle-income countries with different socio-economic settings. This study evaluated the applicability monitoring wastewater (n = 132) inform infection city Bangkok, Thailand using CDC N1 N2 RT-qPCR assays. influents 112) effluents 20) were collected from 19 centralized treatment plants (WWTPs) comprising four large, medium, 11 small WWTPs during seven sampling events January April 2021 third resurgence that was officially declared 2021. The assay showed higher detection rates lower Ct values than N2. first detected at event when new reported cases low. Increased positive preceded an increase number newly increased over time incidence. (both viral loads) strongest correlation daily 22-24 days lag (Spearman's Rho 0.85-1.00). Large (serving 432,000-580,000 population) exhibited similar trends loads those all WWTPs, emphasizing routine large could provide sufficient information city-scale dynamics. Higher frequency fewer sites, i.e., representative therefore suggested especially subsiding period outbreak indicate prevalence infection, acting as early warning resurgence.

Language: Английский

Citations

58
A wastewater-based epidemiology tool for COVID-19 surveillance in Portugal DOI Open Access
Sílvia Monteiro,

Daniela Rente,

Mónica V. Cunha

et al.

The Science of The Total Environment, Journal Year: 2021, Volume and Issue: 804, P. 150264 - 150264

Published: Sept. 11, 2021

Language: Английский

Citations

56
Sensitivity of wastewater-based epidemiology for detection of SARS-CoV-2 RNA in a low prevalence setting DOI
Joanne Hewitt, Sam Trowsdale, Bridget Armstrong

et al.

Water Research, Journal Year: 2022, Volume and Issue: 211, P. 118032 - 118032

Published: Jan. 2, 2022

Language: Английский

Citations

55
Direct comparison of RT-ddPCR and targeted amplicon sequencing for SARS-CoV-2 mutation monitoring in wastewater DOI Creative Commons
Esther G. Lou, Nicolae Sapoval, Camille McCall

et al.

The Science of The Total Environment, Journal Year: 2022, Volume and Issue: 833, P. 155059 - 155059

Published: April 6, 2022

Language: Английский

Citations

48
Long-term monitoring of SARS-CoV-2 variants in wastewater using a coordinated workflow of droplet digital PCR and nanopore sequencing DOI Creative Commons
Katie Vigil, Nishita Dsouza,

Julia Bazner

et al.

Water Research, Journal Year: 2024, Volume and Issue: 254, P. 121338 - 121338

Published: Feb. 18, 2024

Quantitative polymerase chain reaction (PCR) and genome sequencing are important methods for wastewater surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The reverse transcription-droplet digital PCR (RT-ddPCR) is a highly sensitive method quantifying SARS-CoV-2 RNA in samples to track the trends viral activity levels but cannot identify new variants. It also takes time develop PCR-based assays targeting variants interest. Whole (WGS) can be used monitor known variants, it generally not quantitative. Several short-read techniques expensive might experience delayed turnaround times when outsourced due inadequate in-house resources. Recently, portable nanopore system offers an affordable real-time wastewater. This technology has potential enable swift response disease outbreaks without relying on clinical results. In addressing concerns related rapid accurate variant analysis, both RT-ddPCR were employed emergence was conducted at 23 sewer maintenance hole sites five treatment plants Michigan from 2020 2022. 2020, dominated by parental (20A, 20C 20G), followed 20I (Alpha, B.1.1.7) early 2021 Delta concern (VOC) late 2021. For year 2022, Omicron dominated. Nanopore validate suspected cases that initially undetermined assays. concordance rate between identifying clade-level 76.9%. Notably, instances disagreement two most prominent identification We showed with N gene concentrations >104 GC/100ml as measured improve recovery coverage depth using MinION device. better detecting key spike protein mutations A67V, del69-70, K417N, L452R, N501Y, N679K, R408S (p-value <0.05) compared sequencing. suggested should coordinated where preliminary quantification confirmatory detection or reported here adopted reliable analysis community level public health response.

Language: Английский

Citations

11