Water Research, Год журнала: 2023, Номер 241, С. 120116 - 120116
Опубликована: Май 23, 2023
Язык: Английский
Nature Water, Год журнала: 2023, Номер unknown
Опубликована: Фев. 9, 2023
Язык: Английский
Процитировано
33
PLoS ONE, Год журнала: 2023, Номер 18(4), С. e0284370 - e0284370
Опубликована: Апрель 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
Язык: Английский
Процитировано
29
The Journal of Applied Laboratory Medicine, Год журнала: 2024, Номер 9(1), С. 124 - 137
Опубликована: Янв. 1, 2024
Abstract Background Digital polymerase chain reaction (dPCR) is an accurate and sensitive molecular method that can be used in clinical diagnostic, prognostic, predictive tests. The key component of the dPCR partitioning a single into many thousands droplets, nanochannels or other nano- picoliter-sized reactions. This results high enough sensitivity to detect rare nucleic acid targets provides absolute quantification target sequences alleles compared PCR-based methods. Content An increasing number platforms have been introduced commercially recent years more are being developed. These differ partitioning, degree automation, multiplexing capabilities but all similar ways for highly variety targets. Currently, applications include oncology, microbiology infectious disease, genetics, prenatal/newborn screening. Commercially available tests developed variants with therapeutic significance specific disease types. Summary power technology relies on reactions increased accuracy qPCR. More recently, has applied detection known cell-free DNA circulating tumor DNA. Future liquid biopsy, treatment resistance detection, screening minimal residual monitoring allograft engraftment transplanted patients.
Язык: Английский
Процитировано
11
The Science of The Total Environment, Год журнала: 2025, Номер 970, С. 178939 - 178939
Опубликована: Март 1, 2025
Multiplex digital PCR (dPCR) approaches are commonly employed in wastewater-based epidemiology (WBE) studies. However, optimizing the dPCR workflow is a critical step to ensure its reliability and accuracy before application. In this study, 6-plex Crystal Digital PCR® (cdPCR) was optimized for simultaneous detection of six epidemiologically important pathogens, including three enteric viruses, noroviruses genogroups I II (NoV-GI GII) enteroviruses (EnV), respiratory severe acute syndrome coronavirus 2 (SARS-CoV-2), which causative agent disease 2019 (COVID-19), influenza A virus (InfA), syncytial B (RSVB), wastewater. Four cDNA input ratios (20 %-70 %) two extraction kits were evaluated optimization, with 30 % AllPrep PowerViral DNA/RNA Kit (Qiagen) exhibiting optimal performance. The cdPCR assay applied year-long wastewater surveillance study Japan (n = 52), revealing distinct trends prevalence viruses. NoV-GII detected 96 samples highest mean concentration (6.1 ± 0.6 log10 copies/L), while SARS-CoV-2 InfA 60 50 samples, respectively, reflected circulation these pathogens within community. Notably, RSVB less frequently (25 %), line fewer cases reported during period. concentrations EnV showed significant positive correlations hand foot mouth herpangina cases, respectively. no observed RSV COVID-19, possibly due testing RSVA more prevalent also cluster outbreaks. These findings demonstrated utility detecting provided insights into community trends, representing an advancement WBE.
Язык: Английский
Процитировано
1
The Science of The Total Environment, Год журнала: 2022, Номер 859, С. 160072 - 160072
Опубликована: Ноя. 7, 2022
In this study, two virus concentration methods, namely Adsorption-Extraction (AE) and Nanotrap® Magnetic Virus Particles (NMVP) along with commercially available extraction kits were used to quantify endogenous pepper mild mottle (PMMoV) severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in nucleic acid extracted from 48 wastewater samples collected over six events eight treatment plants (WWTPs). The main aim was determine which workflow (i.e., methods) produces greater concentrations of PMMoV SARS-CoV-2 gene copies (GC) comparison each other. Turbidity total suspended solids (TSS) within among the WWTPs highly variable (41–385 NTU 77–668 mg/L TSS). 58 % individual samples, log10 GC by NMVP compared AE workflow. Paired measurements GC/10 mL across all weakly correlated (r = 0.455, p 0.001) demonstrated a poor linear relationship (r2 0.207). 69 contrast PMMoV, derived counts strongly 0.859, < strong 0.738). general, achieved decreased increasing turbidity, but did not appear be as sensitive either turbidity or TSS levels. These findings suggest that sample concentration, intended target for analysis should considered when validating an optimal surveillance viruses.
Язык: Английский
Процитировано
32
Biomedical Engineering Advances, Год журнала: 2023, Номер 6, С. 100092 - 100092
Опубликована: Май 18, 2023
Digital polymerase chain reaction (dPCR) is an emerging technique for the absolute quantification of target nucleic acids. dPCR got attention as a precise tool in preclinical research, particularly when used to detect genetic mutations and result highly measurements. In dPCR, statistic Poisson distribution was followed random molecules different partitions, which essential quantification. Amplified sequences partitions are identified by fluorescence each partition functions separate PCR microreactor. Without need calibration, percentage PCR-positive sufficient estimate concentration sequence. The present revolution digital made possible advancements microfluidics, provided effective partitioning techniques. this paper, contrast underlying ideas quantitative real-time with measurement acids quantity Polymerase (q-PCR). This review study briefly introduced background compared types PCR, qPCR PCR. fundamental concept also explained compares advantages over analyzes applications diagnostic cancer viral species.
Язык: Английский
Процитировано
22
Viruses, Год журнала: 2023, Номер 15(1), С. 206 - 206
Опубликована: Янв. 11, 2023
Multiple lineages of SARS-CoV-2 have been identified featuring distinct sets genetic changes that confer to the virus higher transmissibility and ability evade existing immunity. The continuous evolution may pose challenges for current treatment options diagnostic tools. In this study, we first evaluated performance 14 WHO-recommended real-time reverse transcription (RT)-PCR assays currently in use detection found only one assay has reduced against Omicron. We then developed a new duplex RT-PCR based on amplification two ultra-conserved elements present within genome. successfully detects all tested variants concern (including Omicron sub-lineages BA.4 BA.5) from both clinical wastewater samples with high sensitivity specificity. also functions as one-step droplet digital assay. This assay, addition testing, could be adopted surveillance programs routine monitoring SARS-CoV-2's presence population samples. Positive results our conjunction negative an Omicron-specific provide timely indication emergence novel variant certain community thereby aid public health interventions.
Язык: Английский
Процитировано
21
The Science of The Total Environment, Год журнала: 2023, Номер 913, С. 169746 - 169746
Опубликована: Дек. 28, 2023
Язык: Английский
Процитировано
20
Scientific Reports, Год журнала: 2024, Номер 14(1)
Опубликована: Фев. 14, 2024
Abstract Wastewater surveillance of coronavirus disease 2019 (COVID-19) commonly applies reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to quantify severe acute respiratory syndrome 2 (SARS-CoV-2) RNA concentrations in wastewater over time. In most applications worldwide, maximal sensitivity and specificity RT-qPCR has been achieved, part, by monitoring two or more genomic loci SARS-CoV-2. Ontario, Canada, the provincial Surveillance Initiative reports average copies CDC N1 N2 normalized fecal biomarker pepper mild mottle virus. November 2021, emergence Omicron variant concern, harboring a C28311T mutation within probe region, challenged accuracy consensus between measurements this study, we developed applied novel real-time dual quality assurance control framework based on relative difference City Ottawa dataset identify loss assay period from July 10, 2022 January 31, 2023. Further analysis via sequencing allele-specific revealed high proportion mutations C28312T A28330G during study period, both across province. It is hypothesized that nucleotide especially A28330G, led inefficient annealing, resulting reduction assay. This highlights importance implementing criteria continually evaluate, near real-time, signal produced rely detection pathogens whose genomes undergo rates mutation.
Язык: Английский
Процитировано
9
FEMS Microbes, Год журнала: 2024, Номер 5
Опубликована: Янв. 1, 2024
Abstract Wastewater-based epidemiology is now widely used in many countries for the routine monitoring of SARS-CoV-2 and other viruses at a community level. However, efficient sample processing technologies are still under investigation. In this study, we compared performance novel Nanotrap® Microbiome Particles (NMP) concentration method to commonly polyethylene glycol (PEG) precipitation concentrating from wastewater their subsequent quantification sequencing. For this, first spiked with SARS-CoV-2, influenza measles norovirus found that NMP recovered 0.4%–21% them depending on virus type, providing consistent reproducible results. Using PEG methods, monitored A B viruses, RSV, enteroviruses GI GII crAssphage using quantitative PCR (qPCR)-based methods next-generation Good viral recoveries were observed highly abundant both methods; however, was more successful recovery low-abundance present wastewater. Furthermore, samples processed successfully sequenced than those method. Virus enhanced by high volumes when applied. Overall, our results suggest rapid easy targets wastewater, whereas may be suited analysis next generation
Язык: Английский
Процитировано
7