RNA-Seq of untreated wastewater to assess COVID-19 and emerging and endemic viruses for public health surveillance

Stockdale, Stephen R.; Blanchard, Adam A.; Nayak, Amit R.; Husain, Aliabbas A.; Nashine, Rupam; Dudani, Hemanshi; McClure, C. Patrick; Tarr, Alexander W.; Nag, Aditi; Meena, Ekta; Sinha, Vikky; Shrivastava, Sandeep; Hill, Colin; Singer, Andrew C.; Gomes, Rachel L.; Acheampong, Edward; Babu, Chidambaram Saravana; Bhatnagar, Tarun; Vetrivel, Umashankar; Arora, Sudipti; Kashyap, Rajpal S.; Monaghan, Tanya

doi:10.1016/j.lansea.2023.100205

Cited by 6 publications

(2 citation statements)

References 62 publications

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“…Public health surveillance can also benefit from non-targeted applications of RNA sequencing. Stockdale et al (2023) demonstrated its potential for monitoring COVID-19 and other viruses in untreated wastewater [ 77 ]. This approach can provide early warnings of outbreaks and inform public health interventions.…”

Section: The Universality Of Applications For Nucleic Acid-based Non-...mentioning

confidence: 99%

Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases

Spatz,

Afonso

2024

Veterinary Sciences

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Metagenomics offers the potential to replace and simplify classical methods used in the clinical diagnosis of human and veterinary infectious diseases. Metagenomics boasts a high pathogen discovery rate and high specificity, advantages absent in most classical approaches. However, its widespread adoption in clinical settings is still pending, with a slow transition from research to routine use. While longer turnaround times and higher costs were once concerns, these issues are currently being addressed by automation, better chemistries, improved sequencing platforms, better databases, and automated bioinformatics analysis. However, many technical options and steps, each producing highly variable outcomes, have reduced the technology’s operational value, discouraging its implementation in diagnostic labs. We present a case for utilizing non-targeted RNA sequencing (NT-RNA-seq) as an ideal metagenomics method for the detection of infectious disease-causing agents in humans and animals. Additionally, to create operational value, we propose to identify best practices for the “core” of steps that are invariably shared among many human and veterinary protocols. Reference materials, sequencing procedures, and bioinformatics standards should accelerate the validation processes necessary for the widespread adoption of this technology. Best practices could be determined through “implementation research” by a consortium of interested institutions working on common samples.

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Section: The Universality Of Applications For Nucleic Acid-based Non-...mentioning

confidence: 99%

Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases

Spatz,

Afonso

2024

Veterinary Sciences

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“…In response to COVID-19, wastewater monitoring programs have gained renewed importance as a method for tracking public health threats, providing real-time insights through the analysis of community sewage [10][11][12] . This method can detect a wide range of substances, from pharmaceuticals 2,13,14 to pathogens [15][16][17][18][19][20][21] , thereby reflecting the health behaviors and exposures of a population. Such analysis reveals important trends in drug usage, dietary habits, and the presence of environmental contaminants-key indicators of social determinants like economic status, healthcare access, and environmental risks.…”

Section: Introductionmentioning

confidence: 99%

Spatial and Temporal Drug Usage Patterns in Wastewater Correlate with Socioeconomic and Demographic Indicators in Southern Nevada

Zhuang,

Moshi,

Quinones

et al. 2024

Preprint

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Evaluating drug use within populations in the United States poses significant challenges due to various social, ethical, and legal constraints, often impeding the collection of accurate and timely data. Here, we aimed to overcome these barriers by conducting a comprehensive analysis of drug consumption trends and their association with socioeconomic and demographic factors. From May 2022 to April 2023, we analyzed 208 wastewater samples from eight sampling locations across six wastewater treatment plants in Southern Nevada, covering a population of 2.4 million residents with 50 million annual tourists. Using bi-weekly influent wastewater samples, we employed mass spectrometry to detect 39 analytes, including pharmaceuticals and personal care products (PPCPs) and high risk substances (HRS). Our results revealed a significant temporal rise in stimulants such as cocaine (pFDR=1.40x10-10) and opioids, particularly norfentanyl (pFDR =1.66x10-12), while PPCPs exhibited seasonal variation such as peak usage of DEET, an active ingredient in insect repellents, during the summer (pFDR =0.05). Wastewater from socioeconomically disadvantaged or rural areas, as determined by Area Deprivation Index (ADI) and Rural-Urban Commuting Area Codes (RUCA) scores, demonstrated distinct overall usage patterns, such as higher usage/concentration of HRS, including cocaine (p=0.05) and norfentanyl (p=1.64x10-5). Our approach offers a near real-time, comprehensive tool to assess drug consumption and personal care product usage at a community level, linking wastewater patterns to socioeconomic and demographic factors. This approach has the potential to significantly enhance public health monitoring strategies in the United States.

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Drug Use Patterns in Wastewater and Socioeconomic and Demographic Indicators

Zhuang,

Moshi,

Quinones

et al. 2024

JAMA Netw Open

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ImportanceMeasuring drug use behaviors in individuals and across large communities presents substantial challenges, often complicated by socioeconomic and demographic variables.ObjectivesTo detect spatial and temporal changes in community drug use by analyzing concentrations of analytes in influent wastewater and exploring their associations with area-based socioeconomic and sociodemographic metrics like the area deprivation index (ADI) and rural-urban commuting area (RUCA) codes.Design, Setting, and ParticipantsThis longitudinal, cross-sectional wastewater study was performed from May 2022 to April 2023 and included biweekly influent wastewater samples of 39 analytes from 8 sampling locations across 6 wastewater treatment plants in southern Nevada. Statistical analyses were conducted in December 2023.Main Outcomes and MeasuresIt was hypothesized that wastewater monitoring of pharmaceuticals and personal care products (PPCPs) and high-risk substances (HRSs) could reveal true spatial and temporal drug use patterns in near–real time. Data collection of samples for PPCPs and HRSs was performed using mass spectrometry. Both ADI and RUCA scores were utilized to characterize neighborhood contexts in the analysis. The false discovery rate (FDR) method was utilized to correct for multiple comparisons (PFDR).ResultsOver the 12-month wastewater monitoring period, 208 samples for PPCPs and HRSs were collected, and analysis revealed an increase in the consumption of HRSs and the seasonal variation in PPCP use in southern Nevada. There was a significant increase in levels of stimulant-associated analytes, such as cocaine (β = 9.17 × 10−4; SE = 1.29 × 10−4; PFDR = 1.40 × 10−10), and opioids or their metabolites, notably norfentanyl (β = 1.48 × 10−4; SE = 1.88 × 10−4; PFDR = 1.66 × 10−12). In contrast, DEET, an active ingredient in mosquito and tick repellents, demonstrated a seasonal use pattern (β = −4.85 × 10−4; SE = 2.09 × 10−4; PFDR = 4.87 × 10−2). Wastewater from more disadvantaged or rural neighborhoods, as assessed through ADI and RUCA scores, was more likely to show a significant positive correlation with HRSs, such as cocaine (β = 0.075; SE = 0.038; P = .05) and norfentanyl (β = 0.004; SE = 0.001; P = 1.64 × 10−5).Conclusions and RelevanceThese findings suggest that wastewater monitoring of PPCPs and HRSs offers a complementary method to existing public health tools, providing timely data for tracking substance use behaviors and use of PPCPs at a population level.

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RNA-Seq of untreated wastewater to assess COVID-19 and emerging and endemic viruses for public health surveillance

Cited by 6 publications

References 62 publications

Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases

Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases

Spatial and Temporal Drug Usage Patterns in Wastewater Correlate with Socioeconomic and Demographic Indicators in Southern Nevada

Drug Use Patterns in Wastewater and Socioeconomic and Demographic Indicators

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