Genomic Analysis and Surveillance of Respiratory Syncytial Virus (RSV) Using Wastewater-Based Epidemiology (WBE).

Respiratory syncytial virus (RSV) causes severe infections in infants, immunocompromised or elderly individuals resulting in annual epidemics of respiratory disease. Currently, limited clinical surveillance and the lack of predictable seasonal dynamics limits the public health response. Wastewater-based epidemiology (WBE) has recently been used globally as a key metric in determining prevalence of SARS-CoV-2 in the community but its application to other respiratory viruses is limited. In this study, we present an integrated genomic WBE approach, applying RT-qPCR and partial G-gene sequencing to track RSV levels and variants in the community. We report increasing detection of RSV in wastewater concomitant with increasing numbers of positive clinical cases. Analysis of wastewater-derived RSV sequences permitted identification of distinct circulating lineages within and between seasons. Altogether, our genomic WBE platform has the potential to complement ongoing global surveillance and aid the management of RSV by informing the timely deployment of pharmaceutical and non-pharmaceutical interventions.

Using a Multi-Site RCT to Predict Impacts for a Single Site: Do Better Data and Methods Yield More Accurate Predictions?

Multi-site randomized controlled trials (RCTs) provide unbiased estimates of the average impact in the study sample. However, their ability to accurately predict the impact for individual sites outside the study sample, to inform local policy decisions, is largely unknown. To extend prior research on this question, we analyzed six multi-site RCTs and tested modern prediction methods-lasso regression and Bayesian Additive Regression Trees (BART)-using a wide range of moderator variables. The main study findings are that: (1) all of the methods yielded accurate impact predictions when the variation in impacts across sites was close to zero (as expected); (2) none of the methods yielded accurate impact predictions when the variation in impacts across sites was substantial; and (3) BART typically produced "less inaccurate" predictions than lasso regression or than the Sample Average Treatment Effect. These results raise concerns that when the impact of an intervention varies considerably across sites, statistical modelling using the data commonly collected by multi-site RCTs will be insufficient to explain the variation in impacts across sites and accurately predict impacts for individual sites.

Improved recovery of SARS-CoV-2 from wastewater through application of RNA and DNA stabilising agents.

Wastewater Based Epidemiology (WBE) has become an integral part of the public health effort to track the levels of SARS-CoV-2 within communities. Detection of SARS-CoV-2 in wastewater can be challenging due to relatively low levels of virus within the sample. The wastewater matrix is also comprised of commercial and domestically derived contaminants, as well as RNases, all of which can adversely affect RT-qPCR analysis. To improve SARS-CoV-2 detection within wastewater samples we investigated both the effect of template dilution (as a means to reduce RT-qPCR inhibition) and sample stabilisation via addition of DNA/RNA Shield™ and/or RNA Later™ (to prevent RNA degradation via RNases) as a means to improve viral fragment detection. Using both methodologies, a significant improvement in SARS-CoV-2 detection from wastewater samples was observed. No adverse effects of stabilising agent addition on downstream Next-Generation Sequencing workflows were detected.

Detection of human adenovirus F41 in wastewater and its relationship to clinical cases of acute hepatitis of unknown aetiology.

As of 8 July 2022, the World Health Organization (WHO) have reported 1010 probable cases of acute hepatitis of unknown aetiology in children worldwide, including approximately 250 cases in the United Kingdom (UK). Clinical presentations have often been severe, with liver transplantation a frequent clinical outcome. Human adenovirus F41 (HAdV-F41) has been detected in most children with acute hepatitis, but its role in the pathogenesis of this infection has yet to be established. Wastewater-based epidemiology (WBE) has become a well-established tool for monitoring the community spread of SARS-CoV-2, as well as other pathogens and chemicals. In this study, we adopted a WBE approach to monitoring levels of HAdV-F40/41 in wastewater before and during an acute hepatitis outbreak in Northern Ireland. We report increasing detection of HAdV-F40/41 in wastewater, concomitant with increasing numbers of clinical cases. Amplicon whole genome sequencing further classified the wastewater-derived HAdV as belonging to the F41 genotype which in turn was homologous to clinically derived sequences. We propose that WBE has the potential to inform community surveillance of HAdV-F41 and can further contribute to the ongoing global discussion supporting HAdV-F41 involvement in acute hepatitis cases.

Decision rules for determining terrestrial movement and the consequences for filtering high-resolution global positioning system tracks: a case study using the African lion (Panthera leo).

The combined use of global positioning system (GPS) technology and motion sensors within the discipline of movement ecology has increased over recent years. This is particularly the case for instrumented wildlife, with many studies now opting to record parameters at high (infra-second) sampling frequencies. However, the detail with which GPS loggers can elucidate fine-scale movement depends on the precision and accuracy of fixes, with accuracy being affected by signal reception. We hypothesized that animal behaviour was the main factor affecting fix inaccuracy, with inherent GPS positional noise (jitter) being most apparent during GPS fixes for non-moving locations, thereby producing disproportionate error during rest periods. A movement-verified filtering (MVF) protocol was constructed to compare GPS-derived speed data with dynamic body acceleration, to provide a computationally quick method for identifying genuine travelling movement. This method was tested on 11 free-ranging lions (Panthera leo) fitted with collar-mounted GPS units and tri-axial motion sensors recording at 1 and 40 Hz, respectively. The findings support the hypothesis and show that distance moved estimates were, on average, overestimated by greater than 80% prior to GPS screening. We present the conceptual and mathematical protocols for screening fix inaccuracy within high-resolution GPS datasets and demonstrate the importance that MVF has for avoiding inaccurate and biased estimates of movement.

How often should dead-reckoned animal movement paths be corrected for drift?

BACKGROUND: Understanding what animals do in time and space is important for a range of ecological questions, however accurate estimates of how animals use space is challenging. Within the use of animal-attached tags, radio telemetry (including the Global Positioning System, 'GPS') is typically used to verify an animal's location periodically. Straight lines are typically drawn between these 'Verified Positions' ('VPs') so the interpolation of space-use is limited by the temporal and spatial resolution of the system's measurement. As such, parameters such as route-taken and distance travelled can be poorly represented when using VP systems alone. Dead-reckoning has been suggested as a technique to improve the accuracy and resolution of reconstructed movement paths, whilst maximising battery life of VP systems. This typically involves deriving travel vectors from motion sensor systems and periodically correcting path dimensions for drift with simultaneously deployed VP systems. How often paths should be corrected for drift, however, has remained unclear. METHODS AND RESULTS: Here, we review the utility of dead-reckoning across four contrasting model species using different forms of locomotion (the African lion Panthera leo, the red-tailed tropicbird Phaethon rubricauda, the Magellanic penguin Spheniscus magellanicus, and the imperial cormorant Leucocarbo atriceps). Simulations were performed to examine the extent of dead-reckoning error, relative to VPs, as a function of Verified Position correction (VP correction) rate and the effect of this on estimates of distance moved. Dead-reckoning error was greatest for animals travelling within air and water. We demonstrate how sources of measurement error can arise within VP-corrected dead-reckoned tracks and propose advancements to this procedure to maximise dead-reckoning accuracy. CONCLUSIONS: We review the utility of VP-corrected dead-reckoning according to movement type and consider a range of ecological questions that would benefit from dead-reckoning, primarily concerning animal-barrier interactions and foraging strategies.

Rosin Soap Exhibits Virucidal Activity.

Chemical methods of virus inactivation are used routinely to prevent viral transmission in both a personal hygiene capacity but also in at-risk environments like hospitals. Several virucidal products exist, including hand soaps, gels, and surface disinfectants. Resin acids, which can be derived from tall oil, produced from trees, have been shown to exhibit antibacterial activity. However, whether these products or their derivatives have virucidal activity is unknown. Here, we assessed the capacity of rosin soap to inactivate a panel of pathogenic mammalian viruses in vitro. We show that rosin soap can inactivate human enveloped viruses: influenza A virus (IAV), respiratory syncytial virus, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). For IAV, rosin soap could provide a 100,000-fold reduction in infectivity. However, rosin soap failed to affect the nonenveloped encephalomyocarditis virus (EMCV). The inhibitory effect of rosin soap against IAV infectivity was dependent on its concentration but not on the incubation time or temperature. In all, we demonstrate a novel chemical inactivation method against enveloped viruses, which could be of use for preventing virus infections in certain settings. IMPORTANCE Viruses remain a significant cause of human disease and death, most notably illustrated through the current coronavirus disease 2019 (COVID-19) pandemic. Control of virus infection continues to pose a significant global health challenge to the human population. Viruses can spread through multiple routes, including via environmental and surface contamination, where viruses can remain infectious for days. Methods for inactivating viruses on such surfaces may help mitigate infection. Here, we present evidence identifying a novel virucidal product, rosin soap, which is produced from tall oil from coniferous trees. Rosin soap was able to rapidly and potently inactivate influenza virus and other enveloped viruses.

Animal lifestyle affects acceptable mass limits for attached tags.

Animal-attached devices have transformed our understanding of vertebrate ecology. To minimize any associated harm, researchers have long advocated that tag masses should not exceed 3% of carrier body mass. However, this ignores tag forces resulting from animal movement. Using data from collar-attached accelerometers on 10 diverse free-ranging terrestrial species from koalas to cheetahs, we detail a tag-based acceleration method to clarify acceptable tag mass limits. We quantify animal athleticism in terms of fractions of animal movement time devoted to different collar-recorded accelerations and convert those accelerations to forces (acceleration × tag mass) to allow derivation of any defined force limits for specified fractions of any animal's active time. Specifying that tags should exert forces that are less than 3% of the gravitational force exerted on the animal's body for 95% of the time led to corrected tag masses that should constitute between 1.6% and 2.98% of carrier mass, depending on athleticism. Strikingly, in four carnivore species encompassing two orders of magnitude in mass (ca 2-200 kg), forces exerted by '3%' tags were equivalent to 4-19% of carrier body mass during moving, with a maximum of 54% in a hunting cheetah. This fundamentally changes how acceptable tag mass limits should be determined by ethics bodies, irrespective of the force and time limits specified.

What Interventions Work Best for Families Who Experience Homelessness? Impact Estimates from the Family Options Study.

What housing and service interventions work best to reduce homelessness for families in the United States? The Family Options Study randomly assigned 2,282 families recruited in homeless shelters across 12 sites to priority access to one of three active interventions or to usual care in their communities. The interventions were long-term rent subsidies, short-term rent subsidies, and transitional housing in supervised programs with intensive psychosocial services. In two waves of follow-up data collected 20and 37 months later, priority access to long-term rent subsidies reduced homelessness sand food insecurity and improved other aspects of adult and child well-being relative to usual care, at a cost 9 percent higher. The other interventions had little effect. The study provides support for the view that homelessness for most families is an economic problem that long-term rent subsidies resolve and does not support the view that families must address psychosocial problems to succeed in housing. It has implications for focusing government resources on this important social problem.

A Summer Nutrition Benefit Pilot Program and Low-income Children's Food Security.

BACKGROUND: Federal summer meals programs serve less than one-sixth of children that receive free or reduced-price meals during the school year. To address this gap in food assistance for school-aged children, the Summer Electronic Benefits Transfer for Children (SEBTC) Demonstrations provided summer food assistance in the form of electronic benefits transfer cards to households with school-aged children certified for free or reduced-price meals during the school year. METHODS: Over 2011-2013, the SEBTC demonstrations were evaluated by using a random assignment design. Households were randomly assigned a monthly $60-per-child benefit, a monthly $30-per-child benefit, or no benefit, depending on the study year. Key outcomes included children's food security and consumption of foods and food groups related to a healthful diet (diet quality). At baseline (in the spring) and again in the summer, the evaluation surveyed ∼52 000 households over the course of the 3 years of the impact study. RESULTS: SEBTC reduced the prevalence of very low food security among children by one-third. It also had positive impacts on 6 of the 8 child nutrition outcomes measured (amounts of fruits and vegetables; whole grains; dairy foods; and added sugars). CONCLUSIONS: SEBTC is a promising model to improve food security and the dietary quality of low-income school-aged children in the summer months.

Characteristics of School Districts That Participate in Rigorous National Educational Evaluations.

Given increasing interest in evidence-based policy, there is growing attention to how well the results from rigorous program evaluations may inform policy decisions. However, little attention has been paid to documenting the characteristics of schools or districts that participate in rigorous educational evaluations, and how they compare to potential target populations for the interventions that were evaluated. Utilizing a list of the actual districts that participated in 11 large-scale rigorous educational evaluations, we compare those districts to several different target populations of districts that could potentially be affected by policy decisions regarding the interventions under study. We find that school districts that participated in the 11 rigorous educational evaluations differ from the interventions' target populations in several ways, including size, student performance on state assessments, and location (urban/rural). These findings raise questions about whether, as currently implemented, the results from rigorous impact studies in education are likely to generalize to the larger set of school districts-and thus schools and students-of potential interest to policymakers, and how we can improve our study designs to retain strong internal validity while also enhancing external validity.

External Validity in Policy Evaluations that Choose Sites Purposively.

Evaluations of the impact of social programs are often carried out in multiple "sites," such as school districts, housing authorities, local TANF offices, or One-Stop Career Centers. Most evaluations select sites purposively following a process that is nonrandom. Unfortunately, purposive site selection can produce a sample of sites that is not representative of the population of interest for the program. In this paper, we propose a conceptual model of purposive site selection. We begin with the proposition that a purposive sample of sites can usefully be conceptualized as a random sample of sites from some well-defined population, for which the sampling probabilities are unknown and vary across sites. This proposition allows us to derive a formal, yet intuitive, mathematical expression for the bias in the pooled impact estimate when sites are selected purposively. This formula helps us to better understand the consequences of selecting sites purposively, and the factors that contribute to the bias. Additional research is needed to obtain evidence on how large the bias tends to be in actual studies that select sites purposively, and to develop methods to increase the external validity of these studies.