Lab of Neurogenetics and Precision Medicine

Publications

Early Detection of Novel SARS-CoV-2 Variants from Urban and Rural Wastewater through Genome Sequencing and Machine Learning
Apr 19 2024

Zhuang X, Vo V, Moshi MA, Dhede K, Ghani N, Akbar S, Chang CL, Young AK, Buttery E, Bendik, Zhang H, Afzal S, Moser, Cordes D, Lockett, Gerrity D, Kan HY, Oh EC.

Genome sequencing from wastewater has emerged as an accurate and cost-effective tool for identifying SARS-CoV-2 variants. However, existing methods for analyzing wastewater sequencing data are not designed to detect novel variants that have not been characterized in humans. Here, we present an unsupervised learning approach that clusters co-varying and time-evolving mutation patterns leading to the identification of SARS-CoV-2 variants. To build our model, we sequenced 3,659 wastewater samples collected over a span of more than two years from urban and rural locations in Southern Nevada. We then developed a multivariate independent component analysis (ICA)-based pipeline to transform mutation frequencies into independent sources with co-varying and time-evolving patterns and compared variant predictions to >5,000 SARS-CoV-2 clinical genomes isolated from Nevadans. Using the source patterns as data-driven reference “barcodes”, we demonstrated the model’s accuracy by successfully detecting the Delta variant in late 2021, Omicron variants in 2022, and emerging recombinant XBB variants in 2023. Our approach revealed the spatial and temporal dynamics of variants in both urban and rural regions; achieved earlier detection of most variants compared to other computational tools; and uncovered unique co-varying mutation patterns not associated with any known variant. The multivariate nature of our pipeline boosts statistical power and can support accurate and early detection of SARS-CoV-2 variants. This feature offers a unique opportunity for novel variant and pathogen detection, even in the absence of clinical testing.

Link to PubMed Article

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

Zhuang X, Moshi MA, Quinones O, Trenholm RA, Chang CL, Cordes D, Vanderford BJ, Vo V, Gerrity D, Oh EC.

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 measuring 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 increase over time in the level of stimulants such as cocaine (pFDR=1.40×10-10) and opioids, particularly norfentanyl (pFDR =1.66×10-12), 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=1.64×10-5). 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.

Link to PubMed Article

Science Education for the Youth (SEFTY): A Neuroscience Outreach Program for High School Students in Southern Nevada During the COVID-19 Pandemic

Ghani N, Baker H, Huntsinger A, Chen T, Familara TD, Itorralba JY, Vanderford F, Zhuang X, Chang CL, Vo V, Oh EC.

Laboratory outreach programs for K-12 students in the United States from 2020-2022 were suspended or delayed due to COVID-19 restrictions. While Southern Nevada also observed similar closures for onsite programs, we and others hypothesized that in-person laboratory activities could be prioritized after increasing vaccine doses were available to the public and masking was encouraged. Here, we describe how the Laboratory of Neurogenetics and Precision Medicine at the University of Nevada Las Vegas (UNLV) collaborated with administrators from a local school district to conduct training activities for high school students during the COVID-19 pandemic. The Science Education for the Youth (SEFTY) program’s curriculum was constructed to incorporate experiential learning, fostering collaboration and peer-to-peer knowledge exchange. Leveraging neuroscience tools from our UNLV laboratory, we engaged with 117 high school applicants from 2021-2022. Our recruitment efforts yielded a diverse cohort, with >41% Pacific Islander and Asian students, >9% African American students, and >12% multiracial students. We assessed the impact of the SEFTY program through pre- and post-assessment student evaluations, revealing a significant improvement of 20.3% in science proficiency ( p <0.001) after participating in the program. Collectively, our laboratory curriculum offers valuable insights into the capacity of an outreach program to actively foster diversity and cultivate opportunities for academic excellence, even in the challenging context of a global pandemic.

Link to PubMed Article

Environmental Surveillance of Flood Control Infrastructure Impacted by Unsheltered Individuals Leads to the Detection of SARS-CoV-2 and Novel Mutations in the Spike Gene

Harrington A, Vo V, Moshi M, Chang CL, Baker H, Ghani N, Itorralba JY, Papp K, Gerrity D, Moser D, Oh EC.

In the United States, the growing number of people experiencing homelessness has become a socioeconomic crisis with public health ramifications, recently exacerbated by the COVID-19 pandemic. We hypothesized that the environmental surveillance of flood control infrastructure may be an effective approach to understand the prevalence of infectious disease. From December 2021 through July 2022, we tested for SARS-CoV-2 RNA from two flood control channels known to be impacted by unsheltered individuals residing in upstream tunnels. Using qPCR, we detected SARS-CoV-2 RNA in these environmental water samples when significant COVID-19 outbreaks were occurring in the surrounding community. We also performed whole genome sequencing to identify SARS-CoV-2 lineages. Variant compositions were consistent with those of geographically and temporally matched municipal wastewater samples and clinical specimens. However, we also detected 10 of 22 mutations specific to the Alpha variant in the environmental water samples collected during January 2022-one year after the Alpha infection peak. We also identified mutations in the spike gene that have never been identified in published reports. Our findings demonstrate that environmental surveillance of flood control infrastructure may be an effective tool to understand public health conditions among unsheltered individuals-a vulnerable population that is underrepresented in clinical surveillance data.

Link to PubMed Article

Wastewater surveillance of high risk substances in Southern Nevada: Sucralose normalization to translate data for potential public health action

Gerrity D, Crank K, Oh EC, Quinones O, Trenholm RA, Vanderford BJ.

The COVID-19 pandemic highlighted the value of wastewater surveillance in providing unbiased assessments of incidence/prevalence for infectious disease targets, ultimately leading to the development of local, state, and national programs across the United States. To address the growing epidemic of drug abuse, there have been calls to extend these programs to high risk substances (HRS) and metabolites, while leveraging the experience gained during the pandemic and from ongoing efforts in other countries. This study further advances the science of wastewater surveillance for HRS by (1) highlighting analytical and sewer transport considerations, (2) proposing sucralose normalization to adjust for varying human urine/fecal load and confounded population estimates (e.g., high tourism areas), and (3) characterizing temporal and geographic trends in HRS use. This one-year study across eight sewersheds in Southern Nevada (208 total samples) monitored concentrations of 17 pharmaceuticals and personal care products (PPCPs) and 22 HRS and metabolites, including natural, semi-synthetic, and synthetic opioids. The data indicated a ∼200 % increase in heroin and methamphetamine use since 2010, a stark increase in fentanyl consumption beginning in October 2022, and statistically significant differences in HRS consumption patterns between sewersheds and on certain dates. Notably, the latter outcome highlights the potential for wastewater surveillance data to be strategically translated into public health action to reduce and/or more rapidly respond to overdoses.

Link to PubMed Article

Correspondence on “The Environmental Microbiology Minimum Information (EMMI) Guidelines: qPCR and dPCR Quality and Reporting for Environmental Microbiology”

Crank K, Papp K, Barber C, Wang P, Bivins A, Gerrity D.

Real-time quantitative polymerase chain reaction (qPCR) and digital PCR (dPCR) methods have revolutionized environmental microbiology, yielding quantitative organism-specific data of nucleic acid targets in the environment. Such data are essential for characterizing interactions and processes of microbial communities, assessing microbial contaminants in the environment (water, air, fomites), and developing interventions (water treatment, surface disinfection, air purification) to curb infectious disease transmission. However, our review of recent qPCR and dPCR literature in our field of health-related environmental microbiology showed that many researchers are not reporting necessary and sufficient controls and methods, which would serve to strengthen their study results and conclusions. Here, we describe the application, utility, and interpretation of the suite of controls needed to make high quality qPCR and dPCR measurements of microorganisms in the environment. Our presentation is organized by the discrete steps and operations typical of this measurement process. We propose systematic terminology to minimize ambiguity and aid comparisons among studies. Example schemes for batching and combining controls for efficient work flow are demonstrated. We describe critical reporting elements for enhancing data credibility, and we provide an element checklist in the Supporting Information. Additionally, we present several key principles in metrology as context for laboratories to devise their own quality assurance and quality control reporting framework. Following the EMMI guidelines will improve comparability and reproducibility among qPCR and dPCR studies in environmental microbiology, better inform engineering and public health actions for preventing disease transmission through environmental pathways, and for the most pressing issues in the discipline, focus the weight of evidence in the direction toward solutions.

Link to ACS Article

Identification and genome sequencing of an influenza H3N2 variant in wastewater from elementary schools during a surge of influenza A cases in Las Vegas, Nevada

Vo V, Harrington A, Chang CL, Baker H, Ghani N, Basinew, N, Itorralba JY, Tillett RL, Moshi M, Dahlmann, Familara T, Ghani M, Boss S, Vanderford F, Tang A, Gu R, Papp K, Khan E, Koutras C, Kan HY, Lockett C, Gerrity D, Oh EC

Real-time surveillance of infectious diseases at schools or in communities is often hampered by delays in reporting due to resource limitations and infrastructure issues. By incorporating quantitative PCR and genome sequencing, wastewater surveillance has been an effective complement to public health surveillance at the community and building-scale for pathogens such as poliovirus, SARS-CoV-2, and even the monkeypox virus. In this study, we asked whether wastewater surveillance programs at elementary schools could be leveraged to detect RNA from influenza viruses shed in wastewater. We monitored for influenza A and B viral RNA in wastewater from six elementary schools from January to May 2022. Quantitative PCR led to the identification of influenza A viral RNA at three schools, which coincided with the lifting of COVID-19 restrictions and a surge in influenza A infections in Las Vegas, Nevada, USA. We performed genome sequencing of wastewater RNA, leading to the identification of a 2021-2022 vaccine-resistant influenza A (H3N2) 3C.2a1b.2a.2 subclade. We next tested wastewater samples from a treatment plant that serviced the elementary schools, but we were unable to detect the presence of influenza A/B RNA. Together, our results demonstrate the utility of near-source wastewater surveillance for the detection of local influenza transmission in schools, which has the potential to be investigated further with paired school-level influenza incidence data.

Link to PubMed Article

Candida auris Discovery through Community Wastewater Surveillance during Healthcare Outbreak, Nevada, USA

Rossi A, Chavez J, Iverson T, Hergert J, Oakeson K, LaCross N, Njoku C, Gorzalski A, Gerrity D

Candida auris transmission is steadily increasing across the United States. We report culture-based detection of C. auris in wastewater and the epidemiologic link between isolated strains and southern Nevada, USA, hospitals within the sampled sewershed. Our results illustrate the potential of wastewater surveillance for containing C. auris.

Link to PubMed Article

Community-Scale Wastewater Surveillance of Candida auris during an Ongoing Outbreak in Southern Nevada

Barber C, Crank K, Papp K, Innes GK, Schmitz BW, Chavez J, Rossi A, Gerrity D

Candida auris is an opportunistic fungal pathogen and an emerging global public health threat, given its high mortality among infected individuals, antifungal resistance, and persistence in healthcare environments. This study explored the applicability of wastewater surveillance for C. auris in a metropolitan area with reported outbreaks across multiple healthcare facilities. Influent or primary effluent samples were collected over 10 weeks from seven sewersheds in Southern Nevada. Pelleted solids were analyzed using an adapted quantitative polymerase chain reaction (qPCR) assay targeting the ITS2 region of the C. auris genome. Positive detection was observed in 72 of 91 samples (79%), with higher detection frequencies in sewersheds serving healthcare facilities involved in the outbreak (94 vs 20% sample positivity). Influent wastewater concentrations ranged from 2.8 to 5.7 log10 gene copies per liter (gc/L), and primary clarification achieved an average log reduction value (LRV) of 1.24 ± 0.34. Presumptive negative surface water and wastewater controls were non-detect. These results demonstrate that wastewater surveillance may assist in tracking the spread of C. auris and serve as an early warning tool for public health action. These findings provide the foundation for future application of wastewater-based epidemiology (WBE) to community- or facility-level surveillance of C. auris and other high consequence, healthcare-associated infectious agents.

Link to PubMed Article

Detection of the Omicron BA.1 Variant of SARS-CoV-2 in Wastewater From a Las Vegas Tourist Area

Vo V, Tillett RL, Papp K, Chang CL, Harrington A, Moshi M, Oh EC

Importance: Interpretation of wastewater surveillance data is potentially confounded in communities with mobile populations, so it is important to account for this issue when conducting wastewater-based epidemiology (WBE).
Objectives: To leverage spatial and temporal differences in wastewater whole-genome sequencing (WGS) data to quantify relative SARS-CoV-2 contributions from visitors to southern Nevada.
Design, setting, and participants: This cross-sectional wastewater surveillance study was performed during the COVID-19 pandemic (March 2020 to February 2022) and included weekly influent wastewater samples that were analyzed by reverse transcription-quantitative polymerase chain reaction to quantify SARS-CoV-2 RNA and WGS for identification of variants of concern. This study was conducted in the Las Vegas, Nevada, metropolitan area, which is a semi-urban area with approximately 2.3 million residents and nearly 1 million weekly visitors. Samples were collected from 7 wastewater treatment plant (WWTP) locations that collectively serve the vast majority of southern Nevada (excluding the small number of septic systems) and 1 manhole serving the southern portion of the Las Vegas Strip. With Las Vegas tourism returning to prepandemic levels in 2021, it was hypothesized that visitors were contributing a disproportionate fraction of SARS-CoV-2 RNA to the largest WWTP in southern Nevada, potentially confounding efforts to estimate COVID-19 incidence in the local community through WBE.
Main outcomes and measures: Relative SARS-CoV-2 load and variants from visitors vs the local population.
Results: The Omicron BA.1 VOC was detected in the Las Vegas Strip manhole approximately 1 week before its detection at the WWTP locations (December 13, 2021) and by clinical testing (December 14, 2021). On December 13, Omicron-specific mutations represented a mean (SD) of 48.0% (4.2%) of all genomes from the Las Vegas Strip manhole and 4.1% (1.4%) of all genomes at facilities 2 and 3; by December 20, Omicron-specific mutations represented means (SD) of 82.0% (3.0%) of all genomes at the Las Vegas Strip manhole and 48.0% (2.8%) of all genomes at facilities 2 and 3, respectively. During this time, it was estimated that visitors contributed more than 60% of the SARS-CoV-2 load to the sewershed serving the Las Vegas Strip and that Omicron prevalence among visitors was 40% to 60% on December 13 and 80% to 100% on December 20th.
Conclusions and relevance: Wastewater surveillance is a valuable complement to clinical tools and can provide time-sensitive data for decision-makers and policy makers. This study represents a novel approach for quantifying the confounding effects of mobile populations on wastewater surveillance data, thereby allowing for modification of an existing WBE framework for estimating COVID-19 incidence in southern Nevada.

Link to PubMed Article

Longitudinal monitoring of SARS-CoV-2 in wastewater using viral genetic markers and the estimation of unconfirmed COVID-19 cases

Li L, Mazurowski L, Dewan A, Carine M, Haak L, Guarin TC, Dastjerdi NG, Gerrity D, Mentzer C, Pagilla KR

In this study, wastewater-based surveillance was carried out to establish the correlation between SARS-CoV-2 viral RNA concentrations in wastewater and the incidence of corona virus disease 2019 (COVID-19) from clinical testing. The influent wastewater of three major water reclamation facilities (WRFs) in Northern Nevada, serving a population of 390,750, was monitored for SARS-CoV-2 viral RNA gene markers, N1 and N2, from June 2020 through September 2021. A total of 614 samples were collected and analyzed. The SARS-CoV-2 concentrations in wastewater were observed to peak twice during the study period. A moderate correlation trend between coronavirus disease 2019 (COVID-19) incidence data from clinical testing and SARS-CoV-2 viral RNA concentrations in wastewater was observed (Spearman r = 0.533). This correlation improved when using weekly average SARS-CoV-2 marker concentrations of wastewater and clinical case data (Spearman r = 0.790), presumably by mitigating the inherent variability of the environmental dataset and the effects of clinical testing artifacts (e.g., reporting lags). The research also demonstrated the value of wastewater-based surveillance as an early warning signal for early detection of trends in COVID-19 incidence. This was accomplished by identifying that the reported clinical cases had a stronger correlation to SARS-CoV-2 wastewater monitoring data when they were estimated to lag 7-days behind the wastewater data. The results aided local decision makers in developing strategies to manage COVID-19 in the region and provide a framework for how wastewater-based surveillance can be applied across localities to enhance the public health monitoring of the ongoing pandemic.



Link to PubMed Article

Identification of a rare SARS-CoV-2 XL hybrid variant in wastewater and the subsequent discovery of two infected individuals in Nevada

Vo V, Harrington A, Afzal S, Papp K, Chang CL, Baker H, Aguilar P, Buttery E, Picker MA, Lockett C, Gerrity D, Kan HY, Oh EC

The identification of novel SARS-CoV-2 variants can predict new patterns of COVID-19 community transmission and lead to the deployment of public health resources. However, increased access to at-home antigen tests and reduced free PCR tests have recently led to data gaps for the surveillance of evolving SARS-CoV-2 variants. To overcome such limitations, we asked whether wastewater surveillance could be leveraged to detect rare variants circulating in a community before local detection in human cases. Here, we performed whole genome sequencing (WGS) of SARS-CoV-2 from a wastewater treatment plant serving Las Vegas, Nevada in April 2022. Using metrics that exceeded 100× depth at a coverage of >90 % of the viral genome, we identified a variant profile similar to the XL recombinant lineage containing 26 mutations found in BA.1 and BA.2 and three private mutations. Prompted by the discovery of this rare lineage in wastewater, we analyzed clinical COVID-19 sequencing data from Southern Nevada and identified two cases infected with the XL lineage. Taken together, our data highlight how wastewater genome sequencing data can be used to discover rare SARS-CoV-2 lineages in a community and complement local public health surveillance.

Link to PubMed Article

Urban monitoring of antimicrobial resistance during a COVID-19 surge through wastewater surveillance

Harrington A, Vo V, Papp K, Tillett RL, Chang CL, Baker H, Shen S, Amei A, Lockett C, Gerrity D, Oh EC

During the early phase of the COVID-19 pandemic, infected patients presented with symptoms similar to bacterial pneumonias and were treated with antibiotics before confirmation of a bacterial or fungal co-infection. We reasoned that wastewater surveillance could reveal potential relationships between reduced antimicrobial stewardship, specifically misprescribing antibiotics to treat viral infections, and the occurrence of antimicrobial resistance (AMR) in an urban community. Here, we analyzed microbial communities and AMR profiles in sewage samples from a wastewater treatment plant (WWTP) and a community shelter in Las Vegas, Nevada during a COVID-19 surge in December 2020. Using a respiratory pathogen and AMR enrichment next-generation sequencing panel, we identified four major phyla in the wastewater, including Actinobacteria, Firmicutes, Bacteroidetes and Proteobacteria. Consistent with antibiotics that were reportedly used to treat COVID-19 infections (e.g., fluoroquinolones and beta-lactams), we also measured a significant spike in corresponding AMR genes in the wastewater samples. AMR genes associated with colistin resistance (mcr genes) were also identified exclusively at the WWTP, suggesting that multidrug resistant bacterial infections were being treated during this time. We next compared the Las Vegas sewage data to local 2018–2019 antibiograms, which are antimicrobial susceptibility profile reports about common clinical pathogens. Similar to the discovery of higher levels of beta-lactamase resistance genes in sewage during 2020, beta-lactam antibiotics accounted for 51 ± 3 % of reported antibiotics used in antimicrobial susceptibility tests of 2018–2019 clinical isolates. Our data highlight how wastewater-based epidemiology (WBE) can be leveraged to complement more traditional surveillance efforts by providing community-level data to help identify current and emerging AMR threats.

Link to PubMed Article

Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance

Ahmed W, Simpson SL, Bertsch PM, Bibby K, Bivins A, Blackall LL, Bofill-Mas S, Bosch A, Brandão J, Choi PM, Ciesielski M, Donner E, D’Souza N, Farnleitner AH, Gerrity D, Gonzalez R, Griffith JF, Gyawali P, Haas CN, Hamilton KA, Hapuarachchi HC, Harwood VJ, Haque R, Jackson G, Khan SJ, Khan W, Kitajima M, Korajkic A, La Rosa G, Layton BA, Lipp E, McLellan SL, McMinn B, Medema G, Metcalfe S, Meijer WG, Mueller JF, Murphy H, Naughton CC, Noble RT, Payyappat S, Petterson S, Pitkänen T, Rajal VB, Reyneke B, Roman FA Jr, Rose JB, Rusiñol M, Sadowsky MJ, Sala-Comorera L, Setoh YX, Sherchan SP, Sirikanchana K, Smith W, Steele JA, Sabburg R, Symonds EM, Thai P, Thomas KV, Tynan J, Toze S, Thompson J, Whiteley AS, Wong JCC

Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world’s environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results’ reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases.

Link to PubMed Article

Pathogen Peak “Averaging” in Potable Reuse Systems: Lessons Learned from Wastewater Surveillance of SARS-CoV-2

Gerrity D, Papp K, Pecson BM

This study describes wastewater concentrations of SARS-CoV-2 at seven different sampling locations in Southern Nevada (ranging from 4.2 to 8.7 log10 gc/L) and highlights several key variables affecting those concentrations, including COVID-19 incidence, sample type, and service area population. This information is important for implementing wastewater-based epidemiology, but it also provides insight relevant to the design and regulation of potable reuse systems. Specifically, smaller systems may be more prone to influent concentration spikes that can drive enteric pathogen risk during disease outbreaks. It may be possible to leverage reactor hydraulics to achieve peak “averaging” in these scenarios, although it then becomes important to consider how elevated risks at the lower percentiles potentially offset benefits at the upper percentiles. Informed by SARS-CoV-2 concentration dynamics, the current study simulated relative risk for a hypothetical enteric pathogen. Simulated reactor hydraulics (i.e., dispersion) increased pathogen concentrations by up to 2.6 logs at lower percentiles but also decreased concentrations by up to 1.1 logs at the upper percentiles that sometimes drive public health risk. Collectively, these data highlight the importance of considering outbreak conditions, pathogen spikes, and peak “averaging” in the design and operation of treatment systems and in the development of regulatory frameworks.

Link to PubMed Article

Use of wastewater surveillance for early detection of Alpha and Epsilon SARS-CoV-2 variants of concern and estimation of overall COVID-19 infection burden

Vo V, Tillett RL, Papp K, Shen S, Gu R, Gorzalski A, Siao D, Markland R, Chang CL, Baker H, Chen J, Schiller M, Betancourt WQ, Buttery E, Pandori M, Picker MA, Gerrity D, Oh EC

A decline in diagnostic testing for SARS-CoV-2 is expected to delay the tracking of COVID-19 variants of concern and interest in the United States. We hypothesize that wastewater surveillance programs provide an effective alternative for detecting emerging variants and assessing COVID-19 incidence, particularly when clinical surveillance is limited. Here, we analyzed SARS-CoV-2 RNA in wastewater from eight locations across Southern Nevada between March 2020 and April 2021. Trends in SARS-CoV-2 RNA concentrations (ranging from 4.3 log10 gc/L to 8.7 log10 gc/L) matched trends in confirmed COVID-19 incidence, but wastewater surveillance also highlighted several limitations with the clinical data. Amplicon-based whole genome sequencing (WGS) of 86 wastewater samples identified the B.1.1.7 (Alpha) and B.1.429 (Epsilon) lineages in December 2020, but clinical sequencing failed to identify the variants until January 2021, thereby demonstrating that ‘pooled’ wastewater samples can sometimes expedite variant detection. Also, by calibrating fecal shedding (11.4 log10 gc/infection) and wastewater surveillance data to reported seroprevalence, we estimate that ~38% of individuals in Southern Nevada had been infected by SARS-CoV-2 as of April 2021, which is significantly higher than the 10% of individuals confirmed through clinical testing. Sewershed-specific ascertainment ratios (i.e., X-fold infection undercounts) ranged from 1.0 to 7.7, potentially due to demographic differences. Our data underscore the growing application of wastewater surveillance in not only the identification and quantification of infectious agents, but also the detection of variants of concern that may be missed when diagnostic testing is limited or unavailable.

Link to PubMed Article

SARS-CoV-2 variant detection at a university dormitory using wastewater genomic tools

Vo V, Tillett RL, Chang CL, Gerrity D, Betancourt WQ, Oh EC

In the Fall of 2020, university campuses in the United States resumed on-campus instruction and implemented wastewater monitoring for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). While quantitative polymerase chain reaction (qPCR) tests were deployed successfully to detect viral RNA in wastewater across campuses, the feasibility of detecting viral variants from a residential building like a dormitory was unclear. Here, we demonstrate that wastewater surveillance from a dormitory with at least three infected students could lead to the identification of viral genomes with more than 95% coverage. Our results indicate that viral variant detection from wastewater is achievable at a dormitory and that coronavirus disease 2019 (COVID-19) wastewater surveillance programs will benefit from the implementation of viral whole genome sequencing at universities.

Link to PubMed Article

  1. Zhuang X, Vo V, Moshi MA, Dhede K, Ghani N, Akbar S, Chang CL, Young AK, Buttery E, Bendik, Zhang H, Afzal S, Moser, Cordes D, Lockett, Gerrity D, Kan HY, Oh EC. Early Detection of Novel SARS-CoV-2 Variants from Urban and Rural Wastewater through Genome Sequencing and Machine Learning – medRxiv. 2024 Apr 19 doi.org/10.1101/2024.04.18.24306052.
  2. Zhuang X, Moshi MA, Quinones O, Trenholm RA, Chang CL, Cordes D, Vanderford BJ, Vo V, Gerrity D, Oh EC. Spatial and Temporal Drug Usage Patterns in Wastewater Correlate with Socioeconomic and Demographic Indicators in Southern Nevada – medRxiv. 2024 Feb 4:2024.02.02.24302241. doi: 10.1101/2024.02.02.24302241.
  3. Ghani N, Baker H, Huntsinger A, Chen T, Familara TD, Itorralba JY, Vanderford F, Zhuang X, Chang CL, Vo V, Oh EC. Science Education for the Youth (SEFTY): A Neuroscience Outreach Program for High School Students in Southern Nevada During the COVID-19 Pandemic. eNeuro. 2024 Apr 5;11(4):ENEURO.0039-24.2024. doi: 10.1523/ENEURO.0039-24.2024. Print 2024 Apr.
  4. Harrington A, Vo V, Chang CL, Baker H, Ghani N, Moshi M, Itorralba JY, Papp K, Gerrity D, Moser D, Oh EC. Environmental surveillance of flood control infrastructure impacted by unsheltered individuals leads to the detection of SARS-CoV-2 and novel mutations in the spike gene. Environ. Sci Technol. Lett. 2024 May 14;11(5):410-417. doi: 10.1021/acs.estlett.3c00938. Epub 2024 Apr 3.
  5. Gerrity D, Crank K, Oh EC, Quinones O, Trenholm RA, Vanderford BJ. Wastewater surveillance of high risk substances in Southern Nevada: Sucralose normalization to translate data for potential public health action. Sci Total Environ 2024 Jan 15:908:168369. doi: 10.1016/j.scitotenv.2023.168369. Epub 2023 Nov 10.
  6. Crank K, Papp K, Barber C, Wang P, Bivins A, Gerrity D. Correspondence on “The Environmental Microbiology Minimum Information (EMMI) Guidelines: qPCR and dPCR Quality and Reporting for Environmental Microbiology”. Environ Sci Technol. 2023 Dec 5;57(48):20448-20449. doi: 10.1021/acs.est.3c07968. Epub 2023 Nov 10.
  7. Mehrotra A, Munakata N, Maal-Bared R, Gerrity D, Sabater J, Bessler S. Wastewater-Based Surveillance Does Not Belong in a Regulatory Framework Designed to Protect Waters That Receive Treated Wastewater. Comment on Wright, T.; Adhikari, A. Utilizing a National Wastewater Monitoring Program to Address the U.S. Opioid Epidemic: A Focus on Metro Atlanta, Georgia. Int. J. Environ. Res. Public Health 2023, 20, 5282. Int J Environ Res Public Health. 2023 Aug 24;20(17):6636. doi: 10.3390/ijerph20176636.
  8. Vo V, Harrington A, Chang CL, Baker H, Ghani N, Basinew, N, Itorralba JY, Tillett RL, Moshi M, Dahlmann, Familara T, Ghani M, Boss S, Vanderford F, Tang A, Gu R, Papp K, Khan E, Koutras C, Kan HY, Lockett C, Gerrity D, Oh EC. Detection and genome sequencing of an influenza H3N2 variant in wastewater from elementary schools during a surge of influenza A cases in Las Vegas, Nevada. Sci Total Environ. 2023 Feb 8;872:162058. doi: 10.1016/j.scitotenv.2023.162058.
  9. Rossi A, Chavez J, Iverson T, Hergert J, Oakeson K, LaCross N, Njoku C, Gorzalski A, Gerrity D. Candida auris Discovery through Community Wastewater Surveillance during Healthcare Outbreak, Nevada, USA, 2022. Emerg Infect Dis. 2023 Feb;29(2):422-425. doi: 10.3201/eid2902.221523.
  10. Barber C, Crank K, Papp K, Innes GK, Schmitz BW, Chavez J, Rossi A, Gerrity D. Community-Scale Wastewater Surveillance of Candida auris during an Ongoing Outbreak in Southern Nevada.Environ Sci Technol. 2023 Jan 31;57(4):1755-1763. doi: 10.1021/acs.est.2c07763. Epub 2023 Jan 19.
  11. Vo V, Tillett RL, Papp K, Chang CL, Harrington A, Moshi M, Oh EC, Gerrity D. Detection of the Omicron BA.1 variant of SARS-CoV-2 in wastewater from a Las Vegas Tourist Area. JAMA Netw Open 2023 Feb 1;6(2):e230550. doi: 10.1001/jamanetworkopen.2023.0550.
  12. Li L, Mazurowski L, Dewan A, Carine M, Haak L, Guarin TC, Dastjerdi NG, Gerrity D, Mentzer C, Pagilla KR. Longitudinal monitoring of SARS-CoV-2 in wastewater using viral genetic markers and the estimation of unconfirmed COVID-19 cases. Sci Total Environ. 2022 Apr 15;817:152958. doi: 10.1016/j.scitotenv.2022.152958. Epub 2022 Jan 10.
  13. Vo V, Harrington A, Afzal S, Papp K, Chang CL, Baker H, Aguilar P, Buttery E, Picker MA, Lockett C, Gerrity D, Kan HY, Oh EC. Identification of a rare SARS-CoV-2 XL hybrid variant in wastewater and the subsequent discovery of two infected individuals in Nevada. Sci Total Environ. 2023 Feb 1;858(Pt 3):160024. doi: 10.1016/j.scitotenv.2022.160024. Epub 2022 Nov 8.
  14. Harrington A, Vo V, Papp K, Tillett RL, Chang CL, Baker H, Shen S, Amei A, Lockett C, Gerrity D, Oh EC. Urban monitoring of antimicrobial resistance during a COVID-19 surge through wastewater surveillance. Sci Total Environ. 2022 Sep 7;853:158577. doi: 10.1016/j.scitotenv.2022.158577.
  15. Ahmed W, Simpson SL, Bertsch PM, Bibby K, Bivins A, Blackall LL, Bofill-Mas S, Bosch A, Brandão J, Choi PM, Ciesielski M, Donner E, D’Souza N, Farnleitner AH, Gerrity D, Gonzalez R, Griffith JF, Gyawali P, Haas CN, Hamilton KA, Hapuarachchi HC, Harwood VJ, Haque R, Jackson G, Khan SJ, Khan W, Kitajima M, Korajkic A, La Rosa G, Layton BA, Lipp E, McLellan SL, McMinn B, Medema G, Metcalfe S, Meijer WG, Mueller JF, Murphy H, Naughton CC, Noble RT, Payyappat S, Petterson S, Pitkänen T, Rajal VB, Reyneke B, Roman FA Jr, Rose JB, Rusiñol M, Sadowsky MJ, Sala-Comorera L, Setoh YX, Sherchan SP, Sirikanchana K, Smith W, Steele JA, Sabburg R, Symonds EM, Thai P, Thomas KV, Tynan J, Toze S, Thompson J, Whiteley AS, Wong JCC, Sano D, Wuertz S, Xagoraraki I, Zhang Q, Zimmer-Faust AG, Shanks OC. Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance. Sci Total Environ. 2022 Jan 20;805:149877. doi: 10.1016/j.scitotenv.2021.149877. Epub 2021 Aug 25.
  16. Gerrity D, Papp K, Pecson BM. Pathogen Peak “Averaging” in Potable Reuse Systems: Lessons Learned from Wastewater Surveillance of SARS-CoV-2. ACS ES T Water. 2022 Jan 12;2(11):1863-1870. doi: 10.1021/acsestwater.1c00378. eCollection 2022 Nov 11.
  17. Vo V, Tillett RL, Papp K, Shen S, Gu R, Gorzalski A, Siao D, Markland R, Chang CL, Baker H, Chen J, Schiller M, Betancourt WQ, Buttery E, Pandori M, Picker MA, Gerrity D, Oh EC. Use of wastewater surveillance for early detection of Alpha and Epsilon SARS-CoV-2 variants of concern and estimation of overall COVID-19 infection burden. Sci Total Environ. 2022 Apr 22;835:155410. doi: 10.1016/ j.scitotenv.2022.155410. Online ahead of print.
  18. Vo V, Tillett RL, Chang CL, Gerrity D, Betancourt WQ, Oh EC. SARS-CoV-2 variant detection at a university dormitory using wastewater genomic tools. Sci Total Environ. 2022 Jan 20;805:149930. Epub 2021 Sep 7.