Decay of enveloped SARS-CoV-2 and non-enveloped PMMoV RNA in raw sewage from university dormitories DOI Creative Commons
Li Ye, Kurt T. Ash, Dominique C. Joyner

et al.

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: April 28, 2023

Introduction Although severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) RNA has been frequently detected in sewage from many university dormitories to inform public health decisions during the COVID-19 pandemic, a clear understanding of SARS-CoV-2 persistence site-specific raw is still lacking. To investigate persistence, field trial was conducted University Tennessee sewage, similar municipal wastewater. Methods The decay enveloped and non-enveloped Pepper mild mottle virus (PMMoV) investigated by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) at 4°C 20°C. Results Temperature, followed concentration level RNA, most significant factors that influenced first-order rate constants ( k ) RNA. mean values were 0.094 day −1 0.261 At high-, medium-, low-concentration levels 0.367, 0.169, 0.091 , respectively. Furthermore, there statistical difference between PMMoV different temperature conditions. Discussion first rates for both temperatures statistically comparable which showed sensitivity elevated but not This study provides evidence viral conditions levels.

Language: Английский

Comparison of high-frequency in-pipe SARS-CoV-2 wastewater-based surveillance to concurrent COVID-19 random clinical testing on a public U.S. university campus DOI
Jillian Wright, Erin M. Driver, Devin A. Bowes

et al.

The Science of The Total Environment, Journal Year: 2022, Volume and Issue: 820, P. 152877 - 152877

Published: Jan. 6, 2022

Language: Английский

Citations

50
A mixture model for determining SARS-Cov-2 variant composition in pooled samples DOI Open Access
Renan Valieris, Rodrigo D. Drummond, Alexandre Defelicibus

et al.

Bioinformatics, Journal Year: 2022, Volume and Issue: 38(7), P. 1809 - 1815

Published: Jan. 26, 2022

Abstract Motivation Despite of the fast development highly effective vaccines to control current COVID–19 pandemics, unequal distribution and availability these worldwide number people infected in world lead continuous emergence Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) variants concern. Therefore, it is likely that real-time genomic surveillance will be continuously needed as an unceasing monitoring tool, necessary follow spread disease evolution virus. In this context, new SARS-CoV-2, including refractory vaccines, makes programs tools utmost importance. Nevertheless, lack appropriate analytical quickly effectively access viral composition meta-transcriptomic sequencing data, environmental surveillance, represent possible challenges may impact adoption approach mitigate transmission viruses. Results We propose a statistical model for estimation relative frequencies SARS-CoV-2 pooled samples. This built by considering previously defined selection polymorphisms characterize variants. The methods described here support both raw reads polymorphisms-based markers calling predefined variant call format. obtained using simulated data show our method quite recovering correct proportions. Further, results longitudinal from wastewater samples two locations Switzerland agree well with those describing epidemiological COVID-19 clinical locations. Our can valuable tool tracking proportions complex mixtures such waste water Availability implementation http://github.com/rvalieris/LCS. Supplementary information are available at Bioinformatics online.

Language: Английский

Citations

46
Wastewater surveillance of SARS-CoV-2 and chemical markers in campus dormitories in an evolving COVID − 19 pandemic DOI Creative Commons
Sanjeeb Mohapatra,

Sumedha Bhatia,

Kavindra Yohan Kuhatheva Senaratna

et al.

Journal of Hazardous Materials, Journal Year: 2022, Volume and Issue: 446, P. 130690 - 130690

Published: Dec. 28, 2022

In this study, we report the implementation of a comprehensive wastewater surveillance testing program at university campus in Singapore to identify Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infected individuals and usage pharmaceuticals personal care products (PPCPs) as well other emerging contaminants (ECs). This unique co-monitoring simultaneously measured SARS-CoV-2 with chemical markers/contaminants COVID-19 situation evolved from pandemic endemic stages, following nationwide mass vaccination drive. RNA concentrations dormitories were using real-time reverse transcription-polymerase chain reaction (RT-qPCR) corroborated number symptomatic cases confirmed antigen rapid test (ART). Consistent results observed where detected increased proportionately residing on campus. Similarly, wide range ECs, including disinfectants antibiotics, through sensitive liquid chromatography tandem spectrometry (LC-MS/MS) techniques establish PPCPs consumption patterns during various stages Singapore. Statistical correlation was few ECs belonging disinfectants, PCPs antibiotics. A high concentration subsequent positive reported indicates that could serve marker such unprecedented times.

Language: Английский

Citations

41
Wastewater-based monitoring of SARS-CoV-2 at UK airports and its potential role in international public health surveillance DOI Creative Commons
Kata Farkas,

Rachel Williams,

Natasha Alex-Sanders

et al.

PLOS Global Public Health, Journal Year: 2023, Volume and Issue: 3(1), P. e0001346 - e0001346

Published: Jan. 19, 2023

It is well established that air travel plays a key role in the global spread of many enteric and respiratory diseases, including COVID-19. Even with restrictions (e.g. mask wearing, negative COVID-19 test prior to departure), SARS-CoV-2 may be transmitted by asymptomatic or pre-symptomatic individuals carrying virus. Due limitation current clinical surveillance approaches, complementary methods need developed allow estimation frequency entry across international borders. Wastewater-based epidemiology (WBE) represents one such approach, allowing unbiased sampling carriage passenger cohorts entering via airports. In this study, we monitored sewage samples from terminals (n = 150) aircraft 32) at three major airports UK for 1–3 weeks March 2022. As raw were more turbid than typical municipal wastewater, used beef extract treatment followed polyethylene glycol (PEG) precipitation concentrate viruses, reverse transcription quantitative PCR (RT-qPCR) detection faecal indicator virus, crAssphage. All taken sewers arrival Heathrow Bristol airports, 85% sites Edinburgh airport, positive SARS-CoV-2. This suggests high prevalence among passengers and/or airport staff members. Samples derived also showed 93% positivity. No difference viral was found before after lifted. Our results suggest WBE useful tool monitoring transfer rate human pathogens other disease-causing agents borders should form part wider efforts monitor contain future disease outbreaks.

Language: Английский

Citations

35
Monitoring of SARS‐CoV‐2 concentration and circulation of variants of concern in wastewater of Leuven, Belgium DOI
Annabel Rector, Mandy Bloemen, Marijn Thijssen

et al.

Journal of Medical Virology, Journal Year: 2023, Volume and Issue: 95(2)

Published: Feb. 1, 2023

Wastewater surveillance plays an important role in the management of coronavirus disease 2019 (COVID-19) pandemic all over world. Using different wastewater collection points Leuven, we wanted to investigate use as early warning system for uprise infections and a tool follow circulation specific variants concern (VOCs) particular geographic areas. samples were collected from local neighborhood sewers large regional treatment plant (WWTP) area Belgium. After virus concentration, severe acute respiratory syndrome 2 (SARS-CoV-2) RNA was quantified by real-time quantitative polymerase chain reaction (RT-qPCR) normalized with human fecal indicator pepper mild mottle (PMMoV). A combination multiplex RT-qPCR assays used detect signature mutations circulating VOCs. Fecal shedding SARS-CoV-2 measured feces hospitalized patients. In two residential sampling sites, rise concentration preceded peaks positive cases. WWTP, viral load seen concomitant consecutive waves cases caused original Wuhan strain subsequent During Omicron BA.1 wave, increased lesser degree, even after normalization using PMMoV. This might be attributable lower level excretion this variant. Circulation VOCs Alpha, Delta, BA1/BA.2, BA.4/BA.5 could detected based on presence key mutations. The shift noticeable wastewater, being present simultaneously during transition period. Wastewater-based is sensitive monitor levels larger regions. times reduced test capacity, can prove highly valuable. Differences various should however taken into account when population.

Language: Английский

Citations

29
A multistate assessment of population normalization factors for wastewater-based epidemiology of COVID-19 DOI Creative Commons
Andrew Rainey,

Song Liang,

Joseph H. Bisesi

et al.

PLoS ONE, Journal Year: 2023, Volume and Issue: 18(4), P. e0284370 - e0284370

Published: April 12, 2023

Wastewater-based epidemiology (WBE) has become a valuable tool for monitoring SARS-CoV-2 infection trends throughout the COVID-19 pandemic. Population biomarkers that measure relative human fecal contribution to normalize wastewater concentrations are needed improved analysis and interpretation of community trends. The Centers Disease Control Prevention National Wastewater Surveillance System (CDC NWSS) recommends using flow rate or indicators as population normalization factors. However, there is no consensus on which factor performs best. In this study, we provided first multistate assessment effects (crAssphage, F+ Coliphage, PMMoV) correlation cases CDC NWSS dataset 182 communities across six U.S. states. Flow normalized produced strongest with cases. from three were significantly lower than rate. Additionally, reverse transcription droplet digital polymerase chain reaction (RT-ddPCR) values over samples analyzed real-time quantitative (rRT-qPCR). Our shows utilizing RT-ddPCR generate between

Language: Английский

Citations

29
COVID-19 monitoring with sparse sampling of sewered and non-sewered wastewater in urban and rural communities DOI Creative Commons
Dhammika Leshan Wannigama, Mohan Amarasiri, Parichart Hongsing

et al.

iScience, Journal Year: 2023, Volume and Issue: 26(7), P. 107019 - 107019

Published: June 9, 2023

Language: Английский

Citations

26
Structured Ethical Review for Wastewater-Based Testing in Support of Public Health DOI Creative Commons
Devin A. Bowes, Amanda Darling, Erin M. Driver

et al.

Environmental Science & Technology, Journal Year: 2023, Volume and Issue: 57(35), P. 12969 - 12980

Published: Aug. 23, 2023

Wastewater-based testing (WBT) for SARS-CoV-2 has rapidly expanded over the past three years due to its ability provide a comprehensive measurement of disease prevalence independent clinical testing. The development and simultaneous application WBT measured biomarkers research activities pursuit public health goals, both areas with well-established ethical frameworks. Currently, practitioners do not employ standardized review process, introducing potential adverse outcomes professionals community members. To address this deficiency, an interdisciplinary workshop developed framework structured WBT. employed consensus approach create as set 11 questions derived from primarily guidance. This study retrospectively applied these monitoring programs covering emergent phase pandemic (3/2020-2/2022 (

Language: Английский

Citations

23
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
Examining the stability of viral RNA and DNA in wastewater: Effects of storage time, temperature, and freeze-thaw cycles DOI Creative Commons
Rachel C. Williams, William Bernard Perry, Kathryn Lambert-Slosarska

et al.

Water Research, Journal Year: 2024, Volume and Issue: 259, P. 121879 - 121879

Published: June 3, 2024

Wastewater-based epidemiology (WBE) has been demonstrably successful as a relatively unbiased tool for monitoring levels of SARS-CoV-2 virus circulating in communities during the COVID-19 pandemic. Accumulated biobanks wastewater samples allow retrospective exploration spatial and temporal trends public health indicators such chemicals, viruses, antimicrobial resistance genes, possible emergence novel human or zoonotic pathogens. We investigated resilience to time, temperature, freeze-thaw cycles, plus optimal storage conditions maintain stability genetic material (RNA/DNA) viral +ssRNA (Envelope - E, Nucleocapsid N Spike protein S genes SARS-CoV-2), dsRNA (Phi6 phage) circular dsDNA (crAssphage) wastewater. Samples consisted (i) processed extracted samples, (ii) distilled water (iii) raw, unprocessed samples. were stored at -80 °C, -20 4 20 °C 10 days, going through up cycles (once per day). Sample was measured using reverse transcription quantitative PCR, automated electrophoresis, short-read whole genome sequencing. Exploring different areas demonstrated that gene showed greater sensitivity than E genes. Investigating surrogate normalisation viruses Phi6 remains stable comparison laboratory setting crAssphage resilient temperature variation. Recovery raw significantly when which supported by sequencing data all both time negatively impacted metrics. Historical extracts re-quantified 12, 14 16 months after original quantification no major changes. This study highlights importance fast processing extraction following are robust range temperatures.

Language: Английский

Citations

10