Projections of wastewater as an indicator of COVID-19 cases in corrections facilities: a modelling study (preprint)

BackgroundAlthough prison facilities are not fully isolated from the communities they are located within, the majority of the population is confined and requires high levels of health vigilance and protection. This study sought to examine the dynamic relationship between facility level wastewater viral RNA concentration and probability of at least one positive COVID-19 case within the facility. MethodsThe study period was January 11, 2021 through May 12, 2023. Wastewater samples were collected and analyzed for SARS-CoV-2 (N1) and pepper mild mottle virus (PMMoV) three times per week across 14 prison facilities in Kentucky (USA). Confirmed positive clinical case reports were also provided. A hierarchical Bayesian spatial-temporal model with a latent lagged process was developed. FindingsWe modeled a facility-specific SARS-CoV-2 (N1) normalized by PMMoV wastewater ratio associated with at least one COVID-19 facility case with an 80% probability. The ratio differs among facilities. Across the 14 facilities, our model demonstrates an average capture rate of 94{middle dot}95% via the N1/PMMoV threshold with pts [≥] 0{middle dot}5. However, it is noteworthy as the pts threshold is set higher, such as at 0{middle dot}9 or above, the models average capture rate reduces to 60%. This robust performance underscores the models effectiveness in accurately detecting the presence of positive COVID-19 cases of incarcerated people. InterpretationThe findings of this study provide a correction facility-specific threshold model for public health response based on frequent wastewater surveillance.

SARS-CoV-2 wastewater concentration and linked longitudinal seroprevalence: a spatial analysis of strain mutation, post-COVID-19 vaccination effect, and hospitalization burden forecasting (preprint)

Background Since early in the COVID-19 pandemic, SARS-CoV-2 wastewater concentration has been measured as a surrogate for community prevalence. However, our knowledge remains limited regarding wastewater concentration and effects of the COVID-19 vaccination on overall disease burden as measured by hospitalization rates. Methods We used weekly SARS-CoV-2 wastewater concentration with a stratified random sampling of seroprevalence, and spatially linked vaccination and hospitalization data, from April to August 2021. Our susceptible (S), vaccinated (V), variant-specific infected (I1 and I2), recovered (R), and seropositive (T) model (SVI2RT) tracked prevalence longitudinally. This was related to wastewater concentration for a spatial analysis of strain mutation, vaccination effect, and overall hospitalization burden. Findings We found strong linear association between wastewater concentration and estimated community prevalence (r=0.916). Based on the corresponding regression model, the 64% county vaccination rate translated into about 57% decrease in SARS-CoV-2 incidence. During the study period, the estimated effect of SARS-CoV-2 Delta variant emergence was seen as an over 7-fold increase of infection counts, which corresponded to over 12-fold increase in wastewater concentration. Hospitalization burden and wastewater concentration had the strongest correlation (r=0.963) at 1 week lag time. We estimated the community vaccination campaign resulted in about 63% reduction in the number of daily admissions over the study period. This protective effect was counteracted by the emergence of SARS-CoV-2 Delta strain mutation. Interpretation Wastewater samples can be used to estimate the effects of vaccination and hospitalization burden. Our study underscores the importance of continued environmental surveillance post-vaccine and provides a proof of concept for environmental epidemiology monitoring.

Combining community wastewater genomic surveillance with state clinical surveillance: A framework for SARS-CoV-2 public health practice (preprint)

Study objectiveTo garner a framework for combining community wastewater surveillance with state clinical surveillance that influence confirmation of SARS-CoV-2 variants within the community, and recommend how the flow of such research evidence could be expanded and employed for public health response. Design, setting, and participantsThis work involved analyzing wastewater samples collected weekly from 17 geographically resolved locations in Louisville/Jefferson County, Kentucky from February 10 to November 29, 2021. Genomic surveillance and RT-qPCR platforms were used as screening to identify SARS-CoV-2 in wastewater, and state clinical surveillance was used for confirmation. Main resultsThe results demonstrate increased epidemiological value of combining community wastewater genomic surveillance and RT-qPCR with conventional case auditing methods. The spatial scale and temporal frequency of wastewater sampling provides promising sensitivity and specificity to be useful to gain public health screening insights about community emergence, seeding, and spread. ConclusionsBetter national surveillance systems are needed for future pathogens and variants, and wastewater-based genomic surveillance represents opportune coupling. This paper presents current evidence that complementary wastewater and clinical testing is enhanced cost-effectively when linked; making a strong case for a joint public health framework. The findings suggest significant potential for rapid progress to be made in extending this work to consider pathogens of interest as a whole within wastewater, which could be examined in either a targeted fashion as we currently do with SARS-CoV-2 or in terms of a global monitoring of all pathogens found, and developing evidence based public health practice to best support community health. Thumbnail BoxO_ST_ABSWhat is already known on this subject?C_ST_ABSThe primary approach for the genomic surveillance of SARS-CoV-2 relies on the sequencing of clinical COVID-19 samples. Variants of SARS-CoV-2 can also be tracked in community wastewater. What this study adds?We propose that, for comprehensive community surveillance, the first line of community pathogen screening should involve geographically-resolved wastewater samples collected at a regular frequency and employ both Next Generation Sequencing (NGS) and RT-qPCR. These results could then be compared with state clinical surveillance. This framework is a more comprehensive and cost-effective approach for surveillance in practice to catch community emergence, seeding, and spread. Policy implicationsOur results present a framework that could support the implementation of better surveillance policies directed to solve future community pathogen and variant detection. We anticipate this work can help public health officials implement rational community sampling schemes and develop sensible coordination with other clinical surveillance. The utility of this for COVID-19 extends to many other infectious disease models and other public health hazards such as toxic exposures.

Public awareness and support for use of wastewater for SARS-CoV-2 monitoring: A community survey in Louisville, Kentucky (preprint)

The majority of sewer systems in the United States and other countries, are operated by public utilities. In the absence of any regulation, public perception of monitoring wastewater for population health biomarkers is an important consideration for a public utility commission when allocating resources for this purpose. In August 2021, we conducted a survey as part of an ongoing COVID-19 community prevalence study in Louisville/Jefferson County, KY. The survey comprised of seven questions about awareness of and privacy concerns and was sent to 32,000 households randomly distributed within the county. A total of 1,220 sampled adults participated in the probability sample, and 981 were used in analysis. A total of 2,444 adults additionally responded in the convenience sample, and 1,751 were used in analysis. The samples were weighted to produce estimates representative of all adults in the county. Public awareness of tracking COVID-19 virus in the sewers was low. Opinions about how data from this activity are shared strongly supported public disclosure of monitoring results. Responses showed more support for measuring the largest areas (>30,000 to 50,000 households) typically representing population levels found in a community or regional wastewater treatment plant. Those who had a history of COVID-19 infection were more likely to support highly localized monitoring. Understanding wastewater surveillance strategies and thresholds of privacy concerns requires in-depth, comprehensive analysis of public opinion for continued success and efficacy of public health monitoring.

A rapid assessment of wastewater for genomic surveillance of SARS-CoV-2 variants at sewershed scale in Louisville, KY (preprint)

The successful viral detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater at various pooled scales (1-4) and discovery in the USA of B.1.1.7 , B.1.351 and P.1 variants (5), has led to an interest in developing reliable population-level wastewater viral genomic surveillance. The diversity of SARS-CoV-2 sequences reported to be circulating in the USA, have been determined by sequencing clinical samples; however, these variants can also be surveilled by sequencing wastewater samples (6-9). As of March 2021, the variants of concern - B.1.1.7, B.1.351, and P.1 have been widely detected in clinical samples from 47 states in the USA. In Kentucky, only five clinical cases have been linked to the presence of these variants (5),which could indicate incomplete surveillance. Broadening the application of genomic surveillance using wastewater in the community could enhance SARS-CoV-2 variant population monitoring. In this communication, we report on the genomic surveillance of SARS-CoV-2 using wastewater samples in Jefferson County, KY. Samples were collected from manholes and treatment facilities, covering populations of 8,000 to 350,000 people (Table 1). RNA isolated from wastewater samples was used to quantify SARS-CoV-2 and analyze the genetic variation through high-throughput sequencing (See Supplementary Methods). Bioinformatics approaches were used to rapidly identify single nucleotide genetic alterations, which were compared with known variants of interest and concern. In February 2021, we analyzed seven wastewater samples for SARS-CoV-2 genomic surveillance (Figure 1). We did not detect genetic variations indicative of any current variant of concern, beyond the widespread D614G spike protein mutation (Supplementary Methods Tables 2-5). In all samples, we identified at least four of ten mutations consistent with the presence of the variant of interest B.1.429, and one sample contained seven of ten mutations (Table 2). The B.1.429 variant was confirmed in patient samples in Kentucky in January 2021 (10), and a single patient in the study area was reported to be positive for B.1.1.7 on February 9, 2021 (11). With our current metrics we flagged sites 833, 891, and Treatment plant #2 for potential presence of variant B.1.429 (3/7 sites). Differences in the scale of sample pooling in the community revealed unanticipated inconsistencies in variant representation. Specifically, variants observed in smaller catchment areas, such as neighborhood manhole locations, were not observed in downstream treatment plants, suggesting catchment size or population could impact the ability to detect diversity. Given the highly variable viral genome sequence coverage recovered from wastewater samples, there is an urgent need to develop a set of consistent thresholds constituting positive/negative presence of a variant. Monitoring SARS-CoV-2 variants in wastewater may warn of an emerging variant of concern and identify variant dominance occurring when a new variant is introduced in a community. Wastewater genetic monitoring may be particularly useful in the context of limited clinical sample sequencing capacity because a broad perspective on the genetic diversity can be obtained from a few samples. To develop comprehensive epidemiological frameworks required to guide policy, population-level wastewater surveillance of viral genetic diversity should be complemented by clinical sample testing.

Wastewater sample site selection to estimate geographically-resolved community prevalence of COVID-19: A research protocol (preprint)

Background: Wastewater monitoring for virus infections within communities can complement conventional clinical surveillance. Currently, most SARS-CoV-2 testing is performed during clinical encounters with symptomatic individuals, and therefore likely underrepresents actual population prevalence. Randomized testing on a regular basis to estimate population-level infection rates is prohibitively costly and is hampered by a range of barriers associated with participation in clinical research. In comparison, community-level fecal monitoring can be performed through wastewater surveillance and can effectively surveil communities with less temporal lag than other surveillance methods. However, epidemiologically-defined protocols for wastewater sample site selection are lacking. Methods: Herein we describe methods for developing a geographically-resolved population-level wastewater sampling approach in Jefferson County, Kentucky which may have general applicability for cities throughout the United States. This approach was developed by the selection of sampling locations along sewer lines transporting raw wastewater from geographically and demographically distinct areas that correspond with locations where random testing of residents occurs. Conclusions: Development of this protocol for population-level sampling for SARS-CoV-2 prevalence in wastewater can be utilized to inform consistent wastewater monitoring among cities for up-to-date and geographically-resolved information on COVID-19 prevalence within communities. This information could substantially supplement public health surveillance of COVID-19 and thus serve to better guide targeted mitigation strategies throughout the United States.