Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection

The global evolution of SARS-CoV-2 depends in part upon the evolutionary dynamics within individual hosts with varying immune histories. To characterize the within-host evolution of acute SARS-CoV-2 infection, we sequenced saliva and nasal samples collected daily from vaccinated and unvaccinated individuals early during infection. We show that longitudinal sampling facilitates high-confidence genetic variant detection and reveals evolutionary dynamics missed by less-frequent sampling strategies. Within-host dynamics in both unvaccinated and vaccinated individuals appeared largely stochastic; however, in rare cases, minor genetic variants emerged to frequencies sufficient for forward transmission. Finally, we detected significant genetic compartmentalization of viral variants between saliva and nasal swab sample sites in many individuals. Altogether, these data provide a high-resolution profile of within-host SARS-CoV-2 evolutionary dynamics.IMPORTANCEWe detail the within-host evolutionary dynamics of SARS-CoV-2 during acute infection in 31 individuals using daily longitudinal sampling. We characterized patterns of mutational accumulation for unvaccinated and vaccinated individuals, and observed that temporal variant dynamics in both groups were largely stochastic. Comparison of paired nasal and saliva samples also revealed significant genetic compartmentalization between tissue environments in multiple individuals. Our results demonstrate how selection, genetic drift, and spatial compartmentalization all play important roles in shaping the within-host evolution of SARS-CoV-2 populations during acute infection.

Functional delineation of the luminal epithelial microenvironment in breast using cell-based screening in combinatorial microenvironments

Microenvironment signals are potent determinants of cell fate and arbiters of tissue homeostasis, however understanding how different microenvironment factors coordinately regulate cellular phenotype has been experimentally challenging. Here we used a high-throughput microenvironment microarray comprised of 2640 unique pairwise signals to identify factors that support proliferation and maintenance of primary human mammary luminal epithelial cells. Multiple microenvironment factors that modulated luminal cell number were identified, including: HGF, NRG1, BMP2, CXCL1, TGFB1, FGF2, PDGFB, RANKL, WNT3A, SPP1, HA, VTN, and OMD. All of these factors were previously shown to modulate luminal cell numbers in painstaking mouse genetics experiments, or were shown to have a role in breast cancer, demonstrating the relevance and power of our high-dimensional approach to dissect key microenvironmental signals. RNA-sequencing of primary epithelial and stromal cell lineages identified the cell types that express these signals and the cognate receptors in vivo. Cell-based functional studies confirmed which effects from microenvironment factors were reproducible and robust to individual variation. Hepatocyte growth factor (HGF) was the factor most robust to individual variation and drove expansion of luminal cells via cKit+ progenitor cells, which expressed abundant MET receptor. Luminal cells from women who are genetically high risk for breast cancer had significantly more MET receptor and may explain the characteristic expansion of the luminal lineage in those women. In ensemble, our approach provides proof of principle that microenvironment signals that control specific cellular states can be dissected with high-dimensional cell-based approaches.

A longitudinal study examining the associations between interpersonal trauma and romantic relationships among college students

We examined the associations between the developmental timing of interpersonal trauma exposure (IPT) and three indicators of involvement in and quality of romantic relationships in emerging adulthood: relationship status, relationship satisfaction, and partner alcohol use. We further examined whether these associations varied in a sex-specific manner. In a sample of emerging adult college students (N = 12,358; 61.5% female) assessed longitudinally across the college years, we found precollege IPT increased the likelihood of being in a relationship, while college-onset IPT decreased the likelihood. Precollege and college-onset IPT predicted lower relationship satisfaction, and college-onset IPT predicted higher partner alcohol use. There was no evidence that associations between IPT and relationship characteristics varied in a sex-specific manner. Findings indicate that IPT exposure, and the developmental timing of IPT, may affect college students' relationship status. Findings also suggest that IPT affects their ability to form satisfying relationships with prosocial partners.

Characteristics of Students Participating in Collegiate Recovery Programs and the Impact of COVID-19: An Updated National Longitudinal Study

The goals of the present study were to describe the development of the first national longitudinal study of collegiate recovery programs (CRP) students; provide an updated characterization of CRP students' demographics, past problem severity, and current recovery-related functioning; and examine the perceived impact of COVID-19 on CRP students' recovery. Universities and community colleges with CRPs across the United States and Ontario, Canada, were invited to partner on this project. Launched in fall 2020, three cohorts of participants were recruited. All participants who completed the baseline survey (N = 334 from 43 CRPs) were invited to complete follow-up surveys. The sample was composed of mostly undergraduate, White, cisgender women averaging 29 years old at baseline. They reported challenging backgrounds, including high levels of polysubstance use, alcohol/substance problem severity, mental health challenges, and involvement with the criminal legal system. Despite such adversity, they evidenced high levels of recovery-related functioning. Recovery capital and quality of life were high. Students reported an average of nearly four years in recovery, with most having between two and four years of abstinence from their primary substance of choice. COVID-19 represented a substantial source of stress for many, impacting some students' abstinence and recovery-related functioning. Results generally parallel findings from the only other national study of CRP students conducted a decade ago, providing a much-needed update and novel insights into CRP students. Findings can inform our understanding of the CRP student population and can be used to tailor CRP design and service offerings to students' backgrounds and needs.

Risk of Legionellosis in residential areas around farms irrigating with municipal wastewater

The conservation of freshwater is of both global and national importance, and in the United States, agriculture is one of the largest consumers of this resource. Reduction of the strain farming puts on local surface or groundwater is vital for ensuring resilience in the face of climate change, and one possible option is to irrigate with a combination of freshwater and reclaimed water from municipal wastewater treatment facilities. However, this wastewater can contain pathogens that are harmful to human health, such as Legionella pneumophila, which is a bacterium that can survive aerosolization and airborne transportation and cause severe pneumonia when inhaled. To assess an individual adult's risk of infection with L. pneumophila from a single exposure to agricultural spray irrigation, a quantitative microbial risk assessment was conducted for a scenario of spray irrigation in central Illinois, for the growing seasons in 2017, 2018, and 2019. The assessment found that the mean risk of infection for a single exposure exceeded the safety threshold of 10^-6 infections/exposure up to 1 km from a low-pressure irrigator and up to 2 km from a high-pressure irrigator, although no median risk exceeded the threshold for any distance or irrigator pressure. These findings suggest that spray irrigation with treated municipal wastewater could be a viable option for reducing freshwater consumption in Midwest farming, as long as irrigation on windy days is avoided and close proximity to the active irrigator is limited.

Abstract 4317: Comparison of Single-Molecule Flow (SiM-Flow) and qRT-PCR for detection of plasma miR-375 and miR-1290 in metastatic castrate-resistant prostate cancer (mCRPC)

Background: Plasma microRNA (miR)-375 and miR-1290 levels have been associated with poor survival and resistance to docetaxel chemotherapy. Detection of plasma miRs is typically performed using qRT-PCR, which is time-intensive and laborious. We developed a novel technique, SiM-Flow, that rapidly and accurately quantifies miRs from low blood volumes (~100 uL). SiM-Flow uses a fluorescence-based flow cytometer to digitally count nucleic acids that have been extended and fluorescently tagged. Our goal was to compare plasma miR detection using SiM-Flow with qRT-PCR assays and determine clinical outcomes in mCRPC stage.

Methods: Forty mCRPC patients undergoing state-specific treatment were enrolled prospectively. Uniform processing of plasma was performed on patient blood samples. Total RNA was extracted from 100 µL of plasma and qRT-PCR was performed using TaqMan miRNA assays for targets miR-375 and miR-1290, endogenous controls miR-30a-5p and miR-16, and exogenous control cel-miR-39. SiM-Flow was conducted using a commercial flow cytometer to count fluorescent barcoded rolling-circle-amplification-extended miR nanoparticles for the same targets. Target miR-375 and miR-1290 were normalized using the geometric means of endogenous controls miR-30a-5p, miR-16, and miR-39 and compared across the two assays by Spearman’s rank correlation analysis. Survival analysis was calculated from date of developing mCRPC to death using Cox Proportional Hazard Regression (CPHR) for association with mean of the miR targets normalized by miR-16.

Results: qRT-PCR assays were optimized to detect native targets, endogenous controls, and spike-in miRs from plasma with ≤100 aM limit of detection (LOD), while SiM-Flow was able to detect miRs from plasma with ≤10 aM LOD. After normalization, target miRs in plasma were detected in 26/40 mCRPC patients by qRT-PCR and in 31/40 patients by SiM-Flow. The Spearman Rho for normalized miR-375 was 0.738 and normalized miR-1290 was 0.130. Survival analysis showed a hazard ratio of 1.03 (95% CI 1.01, 1.05) for the mean of miR-375.

Conclusion: Target miR-375 levels detected with SiM-Flow had higher with qRT-PCR, at lower LOD for SiM-Flow. Mean Normalized miR-375 target levels also were associated with poor prognosis in mCRPC.

Citation Format: Manish Kohli, Siva Nalla, Chia-Wei Kuo, Claire Hanson, Matt Larsen, Anna Neibling, Jennifer Lloyd, Julia Batten, Neeraj Agarwal, Umang Swami, Benjamin Maughan, Sumati Gupta, Rebecca L. Smith, Andrew Smith. Comparison of Single-Molecule Flow (SiM-Flow) and qRT-PCR for detection of plasma miR-375 and miR-1290 in metastatic castrate-resistant prostate cancer (mCRPC). [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4317.

Current and Future Habitat Suitability Models for Four Ticks of Medical Concern in Illinois, USA

The greater U.S. Midwest is on the leading edge of tick and tick-borne disease (TBD) expansion, with tick and TBD encroachment into Illinois occurring from both the northern and the southern regions. To assess the historical and future habitat suitability of four ticks of medical concern within the state, we fit individual and mean-weighted ensemble species distribution models for Ixodes scapularis, Amblyomma americanum, Dermacentor variabilis, and a newly invading species, Amblyomma maculatum using a variety of landscape and mean climate variables for the periods of 1970-2000, 2041-2060, and 2061-2080. Ensemble model projections for the historical climate were consistent with known distributions of each species but predicted the habitat suitability of A. maculatum to be much greater throughout Illinois than what known distributions demonstrate. The presence of forests and wetlands were the most important landcover classes predicting the occurrence of all tick species. As the climate warmed, the expected distribution of all species became strongly responsive to precipitation and temperature variables, particularly precipitation of the warmest quarter and mean diurnal range, as well as proximity to forest cover and water sources. The suitable habitat for I. scapularis, A. americanum, and A. maculatum was predicted to significantly narrow in the 2050 climate scenario and then increase more broadly statewide in the 2070 scenario but at reduced likelihoods. Predicting where ticks may invade and concentrate as the climate changes will be important to anticipate, prevent, and treat TBD in Illinois.

Human biting mosquitoes and implications for West Nile virus transmission

BACKGROUND

West Nile virus (WNV), primarily vectored by mosquitoes of the genus Culex, is the most important mosquito-borne pathogen in North America, having infected thousands of humans and countless wildlife since its arrival in the USA in 1999. In locations with dedicated mosquito control programs, surveillance methods often rely on frequent testing of mosquitoes collected in a network of gravid traps (GTs) and CO2-baited light traps (LTs). Traps specifically targeting oviposition-seeking (e.g. GTs) and host-seeking (e.g. LTs) mosquitoes are vulnerable to trap bias, and captured specimens are often damaged, making morphological identification difficult.

METHODS

This study leverages an alternative mosquito collection method, the human landing catch (HLC), as a means to compare sampling of potential WNV vectors to traditional trapping methods. Human collectors exposed one limb for 15 min at crepuscular periods (5:00-8:30 am and 6:00-9:30 pm daily, the time when Culex species are most actively host-seeking) at each of 55 study sites in suburban Chicago, Illinois, for two summers (2018 and 2019).

RESULTS

A total of 223 human-seeking mosquitoes were caught by HLC, of which 46 (20.6%) were mosquitoes of genus Culex. Of these 46 collected Culex specimens, 34 (73.9%) were Cx. salinarius, a potential WNV vector species not thought to be highly abundant in upper Midwest USA. Per trapping effort, GTs and LTs collected > 7.5-fold the number of individual Culex specimens than HLC efforts.

CONCLUSIONS

The less commonly used HLC method provides important insight into the complement of human-biting mosquitoes in a region with consistent WNV epidemics. This study underscores the value of the HLC collection method as a complementary tool for surveillance to aid in WNV vector species characterization. However, given the added risk to the collector, novel mitigation methods or alternative approaches must be explored to incorporate HLC collections safely and strategically into control programs.

Urinary phthalate metabolite concentrations and hot flash outcomes: Longitudinal associations in the Midlife Women's Health Study

Midlife in women is an understudied time for environmental chemical exposures and menopausal outcomes. Recent cross-sectional research links phthalates with hot flashes, but little is known regarding such associations over time. Our objective was to estimate longitudinal associations between repeated measures of urinary phthalate metabolite concentrations and hot flash outcomes in midlife women. Using data from the Midlife Women's Health Study (MWHS), a prospective longitudinal study, we fit generalized linear mixed-effects models (GLMMs) and Cox proportional hazards regression models to repeated measures over a 4-year period. Recruitment occurred in Baltimore and surrounding counties, Maryland, USA between 2006 and 2015. Participants were premenopausal/perimenopausal women (n = 744) aged 45-54 years, who were not pregnant, not taking menopausal symptom medication or oral contraceptives, did not have hysterectomy/oophorectomy, and irrespective of hot flash experience. Baseline mean (SD) age was 48.4 (2.45), and 65% were premenopausal. Main outcome measures included adjusted odds ratios (ORs) for 4 self-reported hot flash outcomes (ever experienced, past 30 days experience, weekly/daily, and moderate/severe), and hazard ratios (HRs) for incident hot flashes. We observed mostly increased odds of certain hot flash outcomes with higher concentrations of metabolites of di (2-ethylhexyl) phthalate (DEHP), monoisobutyl phthalate (MiBP), and a molar summary measure of plasticizer phthalate metabolites (DEHP metabolites, mono-(3-carboxypropyl) phthalate (MCPP), monobenzyl phthalate (MBzP)). Some associations between exposures and outcomes indicated decreased odds. In conclusion, phthalate metabolites were associated with certain hot flash outcomes in midlife women. Midlife may be a sensitive period for higher phthalate metabolite concentrations with respect to menopausal symptoms.

Annexin A2 modulates phospholipid membrane composition upstream of Arp2 to control angiogenic sprout initiation

The intersection of protein and lipid biology is of growing importance for understanding how cells address structural challenges during adhesion and migration. While protein complexes engaged with the cytoskeleton play a vital role, support from the phospholipid membrane is crucial for directing localization and assembly of key protein complexes. During angiogenesis, dramatic cellular remodeling is necessary for endothelial cells to shift from a stable monolayer to invasive structures. However, the molecular dynamics between lipids and proteins during endothelial invasion are not defined. Here, we utilized cell culture, immunofluorescence, and lipidomic analyses to identify a novel role for the membrane binding protein Annexin A2 (ANXA2) in modulating the composition of specific membrane lipids necessary for cortical F-actin organization and adherens junction stabilization. In the absence of ANXA2, there is disorganized cortical F-actin, reduced junctional Arp2, excess sprout initiation, and ultimately failed sprout maturation. Furthermore, we observed reduced filipin III labeling of membrane cholesterol in cells with reduced ANXA2, suggesting there is an alteration in phospholipid membrane dynamics. Lipidomic analyses revealed that 42 lipid species were altered with loss of ANXA2, including an accumulation of phosphatidylcholine (16:0_16:0). We found that supplementation of phosphatidylcholine (16:0_16:0) in wild-type endothelial cells mimicked the ANXA2 knock-down phenotype, indicating that ANXA2 regulated the phospholipid membrane upstream of Arp2 recruitment and organization of cortical F-actin. Altogether, these data indicate a novel role for ANXA2 in coordinating events at endothelial junctions needed to initiate sprouting and show that proper lipid modulation is a critical component of these events.

Nocturnal Hot Flashes, but Not Serum Hormone Concentrations, as a Predictor of Insomnia in Menopausal Women: Results from the Midlife Women's Health Study

Background: Sleep disruptions are among the most common symptoms experienced during menopause and can be associated with depression, hot flashes, and fluctuating hormones. However, few studies have examined how such risk factors influence sleep in midlife women in a network-based approach that will establish the complex relationship between variables. Materials and Methods: We used a Bayesian network (BN) to examine the relationship between multiple factors known to influence sleep and depression in midlife women, including hormone concentrations, hot flashes, and menopause status among participants of the longitudinal Midlife Women's Health Study. In year 1, 762 women (45-54 years of age) answered questions regarding the frequency of insomnia, hot flashes, and depression; 389 of the same women answered similar questions at year 4. We measured serum hormones and calculated free estradiol index, free testosterone index, and ratios of estradiol:progesterone, and estradiol:testosterone. For our model, we calculated the change in frequency of insomnia, depression, and covariates (body mass index, menopause status, hot flashes at night, and present quality of life) from year 1 to 4. Results: Using a BN, we found that self-reported hot flashes at night, and no other factors, were direct predictors of self-reported insomnia in year 1. Surprisingly, we did not identify an association between hormone concentrations and self-reported insomnia. Frequency of insomnia in year 4 was only predicted by frequency of insomnia in year 1, whereas frequency of depression in year 4 was predicted by year 4 insomnia and frequency of depression in year 1. No other factors were direct predictors of insomnia or depression in our model. Conclusions: Therefore, hot flashes at night, previous insomnia, and depression are stronger predictors of how women will self-report frequency of sleep disruptions and treatment may reduce menopausal sleep complaints.

COVID and college: how the pandemic impacted alcohol use disorder status among students

Objective: Alcohol consumption patterns during the COVID-19 pandemic have varied notably. Participants: We examined the acute impact of the pandemic on alcohol use disorder (AUD) in a generalizable sample of college students who were surveyed pre-pandemic and re-surveyed in May 2020. Method: Items assessed pre-pandemic included DSM-5 AUD and mental health symptoms. A COVID-19 impacts questionnaire was administered, and alcohol and mental health items re-assessed. Results: AUD symptoms decreased from pre-pandemic to during the pandemic, demonstrating a change in trajectory compared to prior cohorts. Students with persistent AUD reported greater concurrent symptoms of PTSD, depression, and alcohol consumption than those with remitted AUD (ps ≤ .02), but not increased COVID-19 impact. Persistent AUD status was predicted by higher sensation seeking and alcohol consumption. Conclusions: Students with concurrent mental health problems are at continued risk for persistent AUD. Findings highlight the impact of the college environment and social context for drinking on AUD.

A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses

The phenotype of a cell and its underlying molecular state is strongly influenced by extracellular signals, including growth factors, hormones, and extracellular matrix proteins. While these signals are normally tightly controlled, their dysregulation leads to phenotypic and molecular states associated with diverse diseases. To develop a detailed understanding of the linkage between molecular and phenotypic changes, we generated a comprehensive dataset that catalogs the transcriptional, proteomic, epigenomic and phenotypic responses of MCF10A mammary epithelial cells after exposure to the ligands EGF, HGF, OSM, IFNG, TGFB and BMP2. Systematic assessment of the molecular and cellular phenotypes induced by these ligands comprise the LINCS Microenvironment (ME) perturbation dataset, which has been curated and made publicly available for community-wide analysis and development of novel computational methods ( synapse.org/LINCS_MCF10A ). In illustrative analyses, we demonstrate how this dataset can be used to discover functionally related molecular features linked to specific cellular phenotypes. Beyond these analyses, this dataset will serve as a resource for the broader scientific community to mine for biological insights, to compare signals carried across distinct molecular modalities, and to develop new computational methods for integrative data analysis.

An Interdisciplinary Approach to One Health: Course Design, Development, and Delivery

One Health is an approach to studying health by recognizing the interconnections between people, animals, plants, and their shared environment. This article describes the process of designing a new course on One Health at the University of Illinois at Urbana-Champaign (UIUC). We brought together faculty and students from across campus to develop a multidisciplinary course dedicated to One Health and infectious diseases. This group met over 9 months to brainstorm course goals, objectives, and ideas. The group also organized a workshop to explore One Health's existing knowledge and ongoing work on the UIUC campus. We solicited the help of experts throughout the university to co-teach the course. The course curriculum and course materials included 13 unique case studies. The course was offered in fall 2019, and its goals were to add to the existing training and coursework on One Health at the University of Illinois campus, offer a course that would be suitable for students from all fields of study, and develop helpful case studies to be made available to other educators. Student feedback highlights the course's successes as well as areas for future improvement. This article describes this entire process of course development, provides recommendations to guide improvements in the next offering of the course, and details our contributions to the field of One Health education.

Integrative analysis of drug response and clinical outcome in acute myeloid leukemia

Acute myeloid leukemia (AML) is a cancer of myeloid-lineage cells with limited therapeutic options. We previously combined ex vivo drug sensitivity with genomic, transcriptomic, and clinical annotations for a large cohort of AML patients, which facilitated discovery of functional genomic correlates. Here, we present a dataset that has been harmonized with our initial report to yield a cumulative cohort of 805 patients (942 specimens). We show strong cross-cohort concordance and identify features of drug response. Further, deconvoluting transcriptomic data shows that drug sensitivity is governed broadly by AML cell differentiation state, sometimes conditionally affecting other correlates of response. Finally, modeling of clinical outcome reveals a single gene, PEAR1, to be among the strongest predictors of patient survival, especially for young patients. Collectively, this report expands a large functional genomic resource, offers avenues for mechanistic exploration and drug development, and reveals tools for predicting outcome in AML.

Use of Space by black-and-gold howler monkeys (Alouatta caraya) in an urban environment in Paraguay

As urbanisation continues to reduce the available habitat for wildlife, some species, including the black-and-gold howler monkey (Alouatta caraya) in Pilar, southwest Paraguay, are making their homes in anthropogenic environments. Understanding an animal’s home range is an important step to understanding its ecological needs, and an essential requirement for the creation of robust conservation plans. In this study, we determined the home ranges and core areas of five groups of urban dwelling A. caraya using Minimum Convex Polygon (MCP) and Kernel Density Estimation (KDE) Analysis. We used a Spearman’s Correlation to explore the relationship between home range size and group size. All five groups had home ranges of less than 10 ha and used core areas of less than 1 ha. Group size had no significant relationship to home range size. We provide the first estimates of home range for A. caraya in an urban environment in Paraguay. Though the home ranges of the urban A. caraya in Pilar, Paraguay fall at the smaller end of the spectrum of range sizes in Alouatta, they are not abnormal for a species in this genus.

Knowledge, attitudes, and practices of Illinois medical professionals related to ticks and tick-borne disease

Background

The rising incidence of tick-borne disease (TBD) underscores the importance of proficiency in TBD diagnosis. Clinicians' knowledge about vector ticks and TBDs in their area may influence whether patients are questioned about potential tick exposure and the consideration of diagnostic testing for TBDs.

Objective

Our objective was to assess the knowledge, attitudes, and practices of Illinois clinicians towards ticks and TBDs. The study aimed to 1) identify predictors associated with knowledge, 2) identify knowledge gaps, and 3) evaluate attitudes and practices related to TBDs.

Methods

A web-based knowledge, attitudes, and practices survey about Illinois ticks and TBDs was disseminated to physicians, mid-level practitioners, and nurses between August 2020 and February 2022. Poisson regression analysis was conducted to identify predictors of higher scores.

Results

Of 346 respondents, 80% correctly identified Lyme disease as endemic to Illinois, and 95% were familiar with diagnostic testing for Lyme. Knowledge of other TBDs present in the state was highest among physicians, yet only 26% of physicians believed Rocky Mountain spotted fever (RMSF) to be present in Illinois, and only 17% believed ehrlichiosis to be endemic. Only 32% of physicians knew the cause of Alpha-gal syndrome and fewer than 18% were aware of available diagnostic testing. Tick or TBD-related education within the past two years was the most significant predictor of higher scores, increasing overall knowledge scores by 26% (RR 1.26, 95% CI 1.13–1.41) and increasing scores specific to TBDs by 42% (RR 1.42, 95% CI 1.19–1.69).

Conclusion

Illinois clinicians were informed about Lyme disease but lacked knowledge of other TBDs endemic to the state, including RMSF, ehrlichiosis, and Alpha-gal syndrome. The strongest predictor of knowledge was tick/TBD training in the previous two years, highlighting the importance of frequent region-specific training on ticks and TBDs.

Longitudinal Analysis of SARS-CoV-2 Vaccine Breakthrough Infections Reveals Limited Infectious Virus Shedding and Restricted Tissue Distribution

Background

The global effort to vaccinate people against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during an ongoing pandemic has raised questions about how vaccine breakthrough infections compare with infections in immunologically naive individuals and the potential for vaccinated individuals to transmit the virus.

Methods

We examined viral dynamics and infectious virus shedding through daily longitudinal sampling in 23 adults infected with SARS-CoV-2 at varying stages of vaccination, including 6 fully vaccinated individuals.

Results

The durations of both infectious virus shedding and symptoms were significantly reduced in vaccinated individuals compared with unvaccinated individuals. We also observed that breakthrough infections are associated with strong tissue compartmentalization and are only detectable in saliva in some cases.

Conclusions

Vaccination shortens the duration of time of high transmission potential, minimizes symptom duration, and may restrict tissue dissemination.

A Scoping Review of Species Distribution Modeling Methods for Tick Vectors

Background

Globally, tick-borne disease is a pervasive and worsening problem that impacts human and domestic animal health, livelihoods, and numerous economies. Species distribution models are useful tools to help address these issues, but many different modeling approaches and environmental data sources exist.

Objective

We conducted a scoping review that examined all available research employing species distribution models to predict occurrence and map tick species to understand the diversity of model strategies, environmental predictors, tick data sources, frequency of climate projects of tick ranges, and types of model validation methods.

Design

Following the PRISMA-ScR checklist, we searched scientific databases for eligible articles, their references, and explored related publications through a graphical tool (www.connectedpapers.com). Two independent reviewers performed article selection and characterization using a priori criteria.

Results

We describe data collected from 107 peer-reviewed articles that met our inclusion criteria. The literature reflects that tick species distributions have been modeled predominantly in North America and Europe and have mostly modeled the habitat suitability for Ixodes ricinus (n = 23; 21.5%). A wide range of bioclimatic databases and other environmental correlates were utilized among models, but the WorldClim database and its bioclimatic variables 1–19 appeared in 60 (56%) papers. The most frequently chosen modeling approach was MaxEnt, which also appeared in 60 (56%) of papers. Despite the importance of ensemble modeling to reduce bias, only 23 papers (21.5%) employed more than one algorithm, and just six (5.6%) used an ensemble approach that incorporated at least five different modeling methods for comparison. Area under the curve/receiver operating characteristic was the most frequently reported model validation method, utilized in nearly all (98.9%) included studies. Only 21% of papers used future climate scenarios to predict tick range expansion or contraction. Regardless of the representative concentration pathway, six of seven genera were expected to both expand and retract depending on location, while Ornithodoros was predicted to only expand beyond its current range.

Conclusion

Species distribution modeling techniques are useful and widely employed tools for predicting tick habitat suitability and range movement. However, the vast array of methods, data sources, and validation strategies within the SDM literature support the need for standardized protocols for species distribution and ecological niche modeling for tick vectors.

Mitigation of SARS-CoV-2 transmission at a large public university

In Fall 2020, universities saw extensive transmission of SARS-CoV-2 among their populations, threatening health of the university and surrounding communities, and viability of in-person instruction. Here we report a case study at the University of Illinois at Urbana-Champaign, where a multimodal “SHIELD: Target, Test, and Tell” program, with other non-pharmaceutical interventions, was employed to keep classrooms and laboratories open. The program included epidemiological modeling and surveillance, fast/frequent testing using a novel low-cost and scalable saliva-based RT-qPCR assay for SARS-CoV-2 that bypasses RNA extraction, called covidSHIELD, and digital tools for communication and compliance. In Fall 2020, we performed >1,000,000 covidSHIELD tests, positivity rates remained low, we had zero COVID-19-related hospitalizations or deaths amongst our university community, and mortality in the surrounding Champaign County was reduced more than 4-fold relative to expected. This case study shows that fast/frequent testing and other interventions mitigated transmission of SARS-CoV-2 at a large public university.

Mitigation of SARS-CoV-2 transmission at a large public university

In Fall 2020, universities saw extensive transmission of SARS-CoV-2 among their populations, threatening health of the university and surrounding communities, and viability of in-person instruction. Here we report a case study at the University of Illinois at Urbana-Champaign, where a multimodal “SHIELD: Target, Test, and Tell” program, with other non-pharmaceutical interventions, was employed to keep classrooms and laboratories open. The program included epidemiological modeling and surveillance, fast/frequent testing using a novel low-cost and scalable saliva-based RT-qPCR assay for SARS-CoV-2 that bypasses RNA extraction, called covidSHIELD, and digital tools for communication and compliance. In Fall 2020, we performed >1,000,000 covidSHIELD tests, positivity rates remained low, we had zero COVID-19-related hospitalizations or deaths amongst our university community, and mortality in the surrounding Champaign County was reduced more than 4-fold relative to expected. This case study shows that fast/frequent testing and other interventions mitigated transmission of SARS-CoV-2 at a large public university.

Safely opening university campuses has been a major challenge during the COVID-19 pandemic. Here, the authors describe a program of public health measures employed at a university in the United States which, combined with other non-pharmaceutical interventions, allowed the university to stay open in fall 2020 with limited evidence of transmission.

Early sonographic response to a new medical therapy is associated with future treatment response or failure in patients with inflammatory bowel disease

OBJECTIVE

Gastrointestinal ultrasound (GIUS) accurately assesses inflammation and is responsive to changes in inflammatory bowel disease. This study aimed to determine the prognostic utility of sonographic response in the first 14 weeks of a newly-instituted therapy with therapeutic response at 46 weeks and to compare its performance with standard clinical assessment tools.

METHODS

Patients with sonographic evidence of inflammation were assessed by GIUS, clinical activity, serum C-reactive protein and faecal calprotectin again 2, 6 and 14 weeks after commencing a new biologic or thiopurine. Treatment failure was defined as undergoing surgery, hospitalisation, escalation of dosage or introduction of new medication over 46-weeks' follow-up. Sonographic response was defined as a decrease in bowel wall thickness and improved vascularity.

RESULTS

In 31 patients (median age 49 years, 74% Crohn's disease), sonographic response at 14 weeks [OR 19.3, 95% confidence interval (CI), 3.23-101.10; P = 0.0054] and faecal calprotectin (P = 0.018), but no clinical disease activity or C-reactive protein, were predictive of subsequent treatment response. Sonographic response alone was predictive at week 6 (P = 0.016), but not week 2. 16% reduction in bowel wall thickness at 6 weeks (area-under-the-receiver-operator-curve=0.86; P = 0.002; sensitivity 72%, specificity 90%), with similar performance for 10% at 14 weeks, was associated with treatment response.

CONCLUSION

Sonographic response as early as 6 weeks after initiation of a new therapy may accurately predict treatment outcomes over 46 weeks and is superior to other markers used to monitor disease activity.

Adherence to a priori-Defined Diet Quality Indices Throughout the Early Disease Course Is Associated With Survival in Head and Neck Cancer Survivors: An Application Involving Marginal Structural Models

No studies, to date, have scrutinized the role of a priori dietary patterns on prognosis following a head and neck squamous cell carcinoma (HNSCC) diagnosis. The purpose of this analysis was to evaluate the associations between adherence to six a priori defined diet quality indices (including AHEI-2010, aMED, DASH, and three low-carbohydrate indices) throughout the first 3 years of observation and all-cause and cancer-specific mortalities in 468 newly diagnosed HNSCC patients from the University of Michigan Head and Neck Specialized Program of Research Excellence (UM-SPORE). The dietary intake data were measured using a food frequency questionnaire administered at three annual time points commencing at study entry. Deaths and their causes were documented throughout the study using various data sources. Marginal structural Cox proportional hazards models were used to evaluate the role of diet quality, as a time-varying covariate, on mortality. There were 93 deaths from all causes and 74 cancer-related deaths adjudicated throughout the observation period. There was a strong inverse association between adherence to the AHEI-2010, all-cause mortality (HR_Q5–Q1:0.07, 95% CI:0.01–0.43, p_trend:0.04), and cancer-specific mortality (HR_Q5–Q1:0.15, 95% CI:0.02–1.07, p_trend:0.04). Other more modest associations were noted for the low-carbohydrate indices. In sum, higher adherence to the AHEI-2010 and a plant-based low-carbohydrate index throughout the first 3 years since diagnosis may bolster survival and prognosis in newly diagnosed patients with HNSCC.

Nonspecific ileitis: Impact of histopathology and gastrointestinal ultrasound in achieving the diagnosis of Crohn's disease

Background and Aim

Nonspecific ileitis is inflammation of the ileum without specific diagnostic features. A minority may go on to develop Crohn's disease, but optimal pathways of further investigation have not been established. This study aimed to identify a cohort of patients with nonspecific ileitis and to determine the value of ileal histology and gastrointestinal ultrasound in identifying/excluding Crohn's disease.

Patients and Methods

In a retrospective analysis, all patients having nonspecific ileitis at colonoscopy from January 2010 to August 2021 were identified. Clinical associations with those subsequently diagnosed with Crohn's disease were examined with specific reference to ileal histology and gastrointestinal ultrasound.

Results

Of 29 638 procedures, 147 patients (0.5%) had nonspecific ileitis. Crohn's disease was subsequently diagnosed in 8 patients (5.4%) at a median of 148 (range 27–603) days after colonoscopy. The presence of chronic inflammation on ileal biopsies was more common in those subsequently diagnosed with Crohn's disease (63% vs 20%; P = 0.0145). On gastrointestinal ultrasound, none of the 26 patients with normal bowel wall thickness (<3 mm) were subsequently diagnosed with Crohn's disease, and repeat ultrasound in 15 patients 1 year later showed no change. Of the nine patients with abnormal sonographic findings, three were diagnostic for Crohn's disease. Repeat ultrasound revealed Crohn's disease in two, while four had resolution of the abnormal findings.

Conclusion

Although ileal histology was of limited value in identifying patients with nonspecific ileitis who were subsequently diagnosed with Crohn's disease, gastrointestinal ultrasound was highly informative. Prospective studies are needed to confirm the value of gastrointestinal ultrasound as a diagnostic and monitoring tool in this setting.

Deriving a Measure of Social Recovery Capital From the Important People and Activities Instrument: Construction and Psychometric Properties

AIM

This study presents a measure of Social Recovery Capital (SRC) derived from the Important People and Activities instrument (IPA).

METHODS

The sample comprised young adults who participated in the Collaborative Study on the Genetics of Alcoholism, a high-risk family study of alcohol use disorder (N = 2472). Exploratory and confirmatory factor analysis identified influential items and factor structure, adjusting for family relatedness. The final scale was tested for reliability and validity.

RESULTS

Factor analysis retained 10 items loading on three factors (Network Abstinence Behaviors, Basic Network Structure and Network Importance) that together explained 42% of the variance in SRC. The total model showed adequate fit (Comparative Fit Index = 0.95; Tucker Lewis Index = 0.93; Root Mean Square Error of Approximation = 0.06; Standardized Root Mean Squared Residual = 0.05) and acceptable reliability (α = 0.60; McDonald's ω = 0.73) and correlated with validation measures mostly in the weak to moderate range. Due to variable factor scores for reliability and validity, we only recommend using the total score.

CONCLUSION

The SRC-IPA is a novel measure of SRC derived from the IPA that captures social network data and has applications in research and clinical work. Secondary data analyses using the SRC-IPA in studies that collected the IPA can further demonstrate the interaction of SRC with a wide variety of clinical indicators and demographic characteristics, making it a valuable addition to other measures of SRC.

Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness

The dynamics of SARS-CoV-2 replication and shedding in humans remain poorly understood. We captured the dynamics of infectious virus and viral RNA shedding during acute infection through daily longitudinal sampling of 60 individuals for up to 14 days. By fitting mechanistic models, we directly estimated viral expansion and clearance rates and overall infectiousness for each individual. Significant person-to-person variation in infectious virus shedding suggests that individual-level heterogeneity in viral dynamics contributes to 'superspreading'. Viral genome loads often peaked days earlier in saliva than in nasal swabs, indicating strong tissue compartmentalization and suggesting that saliva may serve as a superior sampling site for early detection of infection. Viral loads and clearance kinetics of Alpha (B.1.1.7) and previously circulating non-variant-of-concern viruses were mostly indistinguishable, indicating that the enhanced transmissibility of this variant cannot be explained simply by higher viral loads or delayed clearance. These results provide a high-resolution portrait of SARS-CoV-2 infection dynamics and implicate individual-level heterogeneity in infectiousness in superspreading.

Knowledge, attitudes, and practices of veterinary professionals towards ticks and tick-borne diseases in Illinois

Objective

A lack of standardized surveillance or reporting of tick-borne diseases (TBDs) in Illinois creates uncertainty for veterinarians regarding TBDs occurring within their practice geography or which TBDs may be encroaching on their area from neighboring territories. Therefore, the objective of this study was to gauge the knowledge, attitudes, and practices of veterinary professionals in Southern and Central Illinois to establish a foundation for targeting educational and outreach programs that address knowledge gaps.

Sample

72 veterinary professionals in Central and Southern Illinois.

Procedures

An online knowledge, attitudes, and practices survey was distributed to veterinary professionals in Southern and Central Illinois. Poisson regression analyses were conducted to determine factors associated with knowledge scores and the estimated number of TBD cases diagnosed.

Results

Knowledge scores were significantly higher among veterinary practitioners with recent (within the last 5 years) training on TBD. The number of cases of TBD diagnosed was higher among those reporting concern about TBD, and among those who routinely test for TBDs. The types of diseases diagnosed were heavily influenced by the diagnostic method used.

Clinical relevance

This study paints a cohesive picture of human factors associated with diagnosing veterinary diseases and TBD prevalence in Southern and Central Illinois. Our results highlight the importance and practical value of veterinary continuing education on ticks and TBDs for both companion animals and public health. Building capacity for training veterinarians in parasitology using partnerships between academia and industry may strengthen the knowledge and understanding of ticks and tick-borne pathogens in the veterinary community.

Effects of Climate on the Variation in Abundance of Three Tick Species in Illinois

The range of ticks in North America has been steadily increasing likely, in part, due to climate change. Along with it, there has been a rise in cases of tick-borne disease. Among those medically important tick species of particular concern are Ixodes scapularis Say (Acari: Ixodidae), Dermacentor variabilis Say (Acari: Ixodidae), and Amblyomma americanum Linneaus (Acari: Ixodidae). The aim of this study was to determine if climate factors explain existing differences in abundance of the three aforementioned tick species between two climatically different regions of Illinois (Central and Southern), and if climate variables impact each species differently. We used both zero-inflated regression approaches and Bayesian network analyses to assess relationships among environmental variables and tick abundance. Results suggested that the maximum average temperature and total precipitation are associated with differential impact on species abundance and that this difference varied by region. Results also reinforced a differential level of resistance to desiccation among these tick species. Our findings help to further define risk periods of tick exposure for the general public, and reinforce the importance of responding to each tick species differently.

Preliminary findings reveal that phthalate exposure is associated with both subjective and objective measures of sleep in a small population of midlife women

Phthalates are endocrine-disrupting chemicals that influence endogenous hormones. Few studies have examined the link between phthalates and menopause. A recent secondary analysis revealed that phthalates were associated with self-reported sleep measures in perimenopausal women. However, the associations between phthalate exposure and additional measures of sleep remain unknown. We recruited a population of 27 midlife women (aged 45-54) to study the relationship between phthalate exposure and both subjective and objective measures of sleep. Preliminary results indicate that women with higher phthalate exposure have reduced sleep quality, more frequent sleep disruptions, and more restless sleep compared to women with lower exposure.

Dietary plasticity of a understudied primate (Sapajus cay) in a biodiversity hotspot: applying ecological traits to habitat conservation in the Upper Paraná Atlantic Forest

One of the main threats to wild primates is habitat alteration, fragmentation and destruction. Therefore it is crucial to understand the ability of those species to adapt to human-induced habitat changes to prevent extirpation. Key to this is a species diet plasticity. In Paraguay over 91% of the Upper Paraná Atlantic Forest has been destroyed to expand agricultural land. We determined the diet composition of three Sapajus cay groups in degraded and near-pristine Atlantic Forest in eastern Paraguay to assess whether the diet composition of this species changes with habitat degradation. We accounted for diet variability associated with demographic traits and forest characteristics using multinomial linear models. Once the effect of age, sex, and season were accounted for, we found that the diet of capuchins was plastic and shifted to adapt to studied degraded forest conditions. The results showed that (as expected) the capuchins have a generalist and flexible diet, including opportunistically taking advantage of crop plants, particularly Slash Pine plantations, when the risks were lower. The capuchins ability to adjust their diet in different habitat fragments demonstrates that small islands of Paraguayan Atlantic Forest are valuable for their persistence. This insight can be used to create applied conservation strategies, such as using the existing Payment for Ecosystem Services (PES) legislation to provide an opportunity to begin reconnecting fragments using native trees bordered by Slash Pine plantations. Using the capuchins as an umbrella species would increase public support of the program, while compensation through the PES scheme and profiting from the timber would encourage landowner participation.

Effects of tick surveillance education on knowledge, attitudes, and practices of local health department employees

Background

The number of cases of tick-borne diseases in humans is increasing rapidly within Illinois. The responsibility for increased surveillance of tick-borne disease cases and tick vectors is being placed on local health departments throughout the United States, but they often lack the funding, time, and/or training needed to perform said surveillance. The aims of this study were to develop, deliver, and determine the effectiveness of tick surveillance training workshops for local health department employees within Illinois.

Methods

We developed and delivered in-person training at local health department offices in each of six Illinois Department of Public Health Environmental Health Regions between April–May of 2019. Pre-, post-, and six-month follow-up questionnaires on knowledge, attitudes, and practices with regards to tick surveillance were administered to training participants. Paired student’s t-test or Wilcoxon signed-rank test were used to compare knowledge, attitudes, and practices scores between questionnaires with Cohen’s d being used to calculate effect sizes associated with t-tests. McNemar’s and McNemar-Bowker tests were used to evaluate individual questions. Spearman’s rank correlation was used to evaluate the relationship between knowledge, attitudes, and practices at pre-, post-, and six-month follow-up.

Results

Seventy-six employees from 40 local health departments that represent 44% (45/102) of Illinois counties attended at least one training workshop. Of these attendees, 81.5% (62/76) participated in at least one survey, 79% (60/76) in the in-person pre-training survey, 74% (56/76) in the in-person post-training survey, and 22% (17/76) in the online six-month follow-up survey. The average knowledge score was significantly increased by 8.21 (95% CI:7.28–9.14) points from pre-training to post-training. The average overall attitude score significantly increased by 5.29 (95% CI: 3.91–6.66) points from pre- to post-training. There were no significant differences in practice scores.

Conclusions

Our study found the training was effective in increasing the knowledge of ticks, tick-borne diseases, and surveillance as well as promoting positive attitudes related to surveillance. While the training, by itself, was not associated with increases in surveillance practices, we were able to empower local public health officials with the knowledge and positive attitudes needed to enact change.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12889-022-12667-2.

Effects of low-intensity cattle ranching on amphibians in the Ñeembucú Wetland Complex, Paraguay

ABSTRACT Cattle in wetlands impact water quality through waste excretion, which deposits excess nutrients, as well as decreasing the biomass and height of vegetation through trampling and herbivory. Amphibians are sensitive to these changes due to their porous skin and reliance on vegetated microhabitats. Previous studies examining the effect of cattle on amphibians in wetlands report conflicting results, exemplifying the need to avoid overgeneralizations and instead examine specific environments. In the Ñeembucú Wetland Complex in Paraguay, low-intensity cattle ranching is a common practice. This study seeks to understand how the presence of cattle in these operations impacts water chemistry and amphibian species richness, as well as determining which cattle effects (eutrophication, nutrient loading, and decreased vegetation height diversity) have the greatest impact on amphibian communities. We anticipated that increased cattle presence would negatively impact wetland condition, and consequentially lower amphibian species richness. Data was collected over seven weeks at Estancia Santa Ana, a low-intensity cattle ranch in Pilar, Paraguay. Cattle presence was measured through cow footprints and feces densities, while a vegetation survey and water quality testing (nitrate, phosphate, and dissolved oxygen) served as environmental metrics. Pitfall trapping was used to gather information on amphibian species richness and community composition. A Pearson parametric correlation test and Factor Analysis of Mixed Data in R were then used to understand the relationship between variables. Very few statistically relationships were found between variables, and those that existed showed a very weak correlation. This suggests that cow presence does not have as strong of an impact on water quality or amphibian species richness as expected. Terrestrial and aquatic vegetation were found to explain much of the variation among the data, which verifies the importance of amphibians’ microhabitats. While future research comparing generalist and specialist species in the area is necessary, these initial results suggest a hopeful future for collaboration on environmental efforts with low-intensity cattle ranchers.

Urinary phthalate metabolite concentrations and serum hormone levels in pre- and perimenopausal women from the Midlife Women's Health Study

BACKGROUND

Phthalate exposure is associated with altered reproductive function, but little is known about associations between phthalate and hormone levels in midlife women.

METHODS

This cross-sectional analysis includes 45-54-year-old pre- and perimenopausal women from Baltimore, MD and its surrounding counties enrolled in the Midlife Women's Health Study (n = 718). Serum and urine samples were collected from participants once a week for four consecutive weeks to span the menstrual cycle. Serum samples were assayed for estradiol, testosterone, progesterone, sex hormone binding globulin (SHBG), follicle-stimulating hormone (FSH), and anti-Müllerian hormone (AMH), and geometric means were calculated for each hormone across all four weeks. Urine samples were analyzed for nine phthalate metabolites from pools of one-to-four urine samples. Phthalate metabolite concentrations were specific gravity-adjusted and assessed as individual metabolites or as molar sums of metabolites from common parents (di(2-ethylhexyl) phthalate metabolites, ∑DEHP), exposure sources (plastic, ∑Plastics; personal care products, ∑PCP), biological activity (anti-androgenic, ∑AA), and sum of all metabolites (∑Phthalates). We used linear regression models to assess overall associations of phthalate metabolites with hormones, controlling for important demographic, lifestyle, and health factors. We also explored whether associations differed by menopause status, body mass index (BMI), and race/ethnicity.

RESULTS

Most participants were non-Hispanic white (67%) or black (29%), college-educated (65%), employed (80%), and had somewhat higher mean urinary phthalate metabolite concentrations than other U.S. women. Overall, the following positive associations were observed between phthalate metabolites and hormones: ∑DEHP (%Δ: 4.9; 95%CI: 0.5, 9.6), ∑Plastics (%Δ: 5.1; 95%CI: 0.3, 10.0), and ∑AA (%Δ: 7.8; 95%CI: 2.3, 13.6) with estradiol; MiBP (%Δ: 6.6; 95%CI: 1.5, 12.1) with testosterone; ∑DEHP (%Δ: 8.3; 95%CI: 1.5, 15.6), ∑Plastics (%Δ: 9.8; 95%CI: 2.4, 17.7), MEP (%Δ: 4.6; 95%CI: 0.1, 9.2), ∑PCP (%Δ: 6.0; 95%CI: 0.2, 12.2), ∑Phthalates (%Δ: 9.0; 95%CI: 2.1, 16.5), and ∑AA (%Δ: 12.9; 95%CI: 4.4, 22.1) with progesterone; and MBP (%Δ: 8.5; 95%CI: 1.2, 16.3) and ∑AA (%Δ: 9.0; 95%CI: 1.3, 17.4) with AMH. Associations of phthalate metabolites with hormones differed by menopause status (strongest in premenopausal women for estradiol, progesterone, and FSH), BMI (strongest in obese women for progesterone), and race/ethnicity (strongest in non-Hispanic white women for estradiol and AMH).

CONCLUSIONS

We found that phthalate metabolites were positively associated with several hormones in midlife women, and that some demographic and lifestyle characteristics modified these associations. Future longitudinal studies are needed to corroborate these findings in more diverse midlife populations.

A longitudinal study of the moderating effects of romantic relationships on the associations between alcohol use and trauma in college students

BACKGROUND AND AIMS

College students report high levels of alcohol use, which can be exacerbated by interpersonal trauma exposure (IPT). Romantic relationships may represent salient contexts for moderating associations between IPT and alcohol use. We examined whether relationship status, partner alcohol use and relationship satisfaction moderated associations between IPT and alcohol use, and whether these associations varied in a sex-specific manner.

DESIGN

University-wide longitudinal survey of college students.

SETTING

Large, urban public university in mid-Atlantic United States.

PARTICIPANTS

We used two subsets of participants (n = 5673 and 3195) from the Spit for Science project, a longitudinal study of college students. Participants completed baseline assessments during the autumn of their freshman year and were invited to complete follow-up assessments every spring thereafter. Participants were included in the present study if they completed surveys at baseline and at least one follow-up assessment (meanfollow-ups  = 1.70, range = 1-4).

MEASUREMENTS

Predictors included precollege and college-onset IPT, relationship status, partner alcohol use, relationship satisfaction and sex. Alcohol consumption was the primary outcome of interest. Pre-college IPT was measured at baseline and all other measures were assessed at each follow-up.

FINDINGS

Individuals with pre-college IPT consumed more alcohol than those without IPT, but this was mitigated for those in relationships (β = -0.15, P = 0.046, 95% confidence interval (CI) = -0.29, 0.00). Individuals with college-onset IPT consumed more alcohol than those without IPT, and this was more pronounced for those with higher partner alcohol use (β = -0.18, P = 0.001, 95% CI = -0.29, -0.07). Relationship satisfaction was not a significant moderator of the associations between IPT and alcohol use (Ps > 0.05 and 95% CIs include 0).

CONCLUSIONS

Involvement in relationships, but not relationship satisfaction, appears to reduce the effects of interpersonal trauma exposure (IPT) on alcohol use among US college students, while high partner alcohol use appears to exacerbate it. The moderating effects of relationship characteristics depend on the developmental timing of IPT.

A new measure to understand the role of science in US Congress: lessons learned from the Legislative Use of Research Survey (LURS)

BACKGROUND

There is growing interest in and recognition of the need to use scientific evidence to inform policymaking. However, many of the existing studies on the use of research evidence (URE) have been largely qualitative, and the majority of existing quantitative measures are underdeveloped or were tested in regional or context-dependent settings. We are unaware of any quantitative measures of URE with national policymakers in the US.

AIMS AND OBJECTIVES

Explore how to measure URE quantitatively by validating a measure of congressional staff's attitudes and behaviors regarding URE, the Legislative Use of Research Survey (LURS), and by discussing the lessons learned through administering the survey.

METHODS

A 68-item survey was administered to 80 congressional staff to measure their reported research use, value of research, interactions with researchers, general information sources, and research information sources. Confirmatory factor analyses were conducted on each of these five scales. We then trimmed the number of items, based on a combination of poor factor loadings and theoretical rationale, and ran the analyses on the trimmed subscales.

FINDINGS

We substantially improved our model fits for each scale over the original models and all items had acceptable factor loadings with our trimmed 35-item survey. We also describe the unique set of challenges and lessons learned from surveying congressional staff.

DISCUSSION AND CONCLUSIONS

This work contributes to the transdisciplinary field of URE by offering a tool for studying the mechanisms that can bridge research and policy and shedding light into best practices for measuring URE with national policymakers in the US.

Interrater reliability of the assessment of disease activity by gastrointestinal ultrasound in a prospective cohort of patients with inflammatory bowel disease

OBJECTIVE

Gastrointestinal ultrasound is a radiological investigation for monitoring patients with inflammatory bowel disease. However, the reliability of the findings depends on the reproducibility of results between different operators. Thus, the study aim was to assess the interrater reliability of gastrointestinal ultrasound in individuals with inflammatory bowel disease between gastroenterologists with varying GIUS experience. .

METHODS

Patients were prospectively recruited at the commencement of a new medical therapy for a baseline assessment, with a second assessment at the end of treatment induction (3 months). Consecutive, blinded ultrasounds were performed by two operators for every test. Gastrointestinal ultrasound examination included assessment of bowel wall thickness, vascularity, wall stratification assessment, mesenteric hyperechogenicity and lymphadenopathy.

RESULTS

Forty-nine patients were recruited (Crohn's n = 27, ulcerative colitis n = 22) with 35 returning for a repeat assessment at 3 months. At baseline, the intraclass coefficient for bowel wall thickness was near perfect (0.882). By bowel segment, the closest correlation was in the terminal ileum and differences in bowel wall thickness were similar by disease subtype. All other ultrasound indices of disease activity demonstrated substantial to near-perfect agreement with Gwet's agreement coefficient: vascularity (0.681), wall stratification (0.685), mesenteric hyperechogenicity (0.841) and lymphadenopathy (0.633). Similar findings were seen at 3 months.

CONCLUSION

There is substantial agreement between operators of varying experience in gastrointestinal ultrasound findings in patients with Crohn's disease or ulcerative colitis and this is repeatedly demonstrated over time. Thus, a well-trained operator should be sufficient to assess disease activity in patients with inflammatory bowel disease.

Duration of skin desensitisation following palmar digital nerve blocks with lidocaine, bupivacaine, mepivacaine and prilocaine

Objective comparative evidence of the time to onset and duration of effect provided by local anaesthetic (LA) agents for perineural blocks in the horse is lacking. Clear knowledge of these properties is required to guide clinically appropriate agent selection and aid interpretation of response to diagnostic blocks for lameness examinations. An interventional study, with complete, randomised crossover design was used to compare time to onset and duration of skin desensitisation provided by four LA agents applied to palmar digital nerve blocks in 12 horses. Effect at each time point was determined using a pressure gauge to measure the mechanical nociceptive threshold (MNT) over the heel bulbs. Complete desensitisation was defined when MNT was greater than four times the pre-block baseline. Onset and duration of complete desensitisation were recorded and compared across agents using a mixed linear model. When significant (P ≤ 0.05), post-hoc paired comparisons between agents were performed against a Tukey's corrected P ≤ 0.05. Onset of complete skin desensitisation for each agent was <5 min. Duration for lidocaine (mean 25 min; 95% confidence interval [CI] 9-42) was shorter than bupivacaine (53 min; 95% CI 39-65), which was shorter than both prilocaine (102 min; 95% CI 81-123) and mepivacaine (107 min; 95% CI 92-121), which were not different. Although onset of complete skin desensitisation was not different for the LA agents tested, duration varied from 25 min to nearly 2 h. Prilocaine and mepivacaine provided the most prolonged duration of effect, both exceeding bupivacaine.

Longitudinal Assessment of Diagnostic Test Performance Over the Course of Acute SARS-CoV-2 Infection

BACKGROUND

Serial screening is critical for restricting spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by facilitating timely identification of infected individuals to interrupt transmission. Variation in sensitivity of different diagnostic tests at different stages of infection has not been well documented.

METHODS

In a longitudinal study of 43 adults newly infected with SARS-CoV-2, all provided daily saliva and nasal swabs for quantitative reverse transcription polymerase chain reaction (RT-qPCR), Quidel SARS Sofia antigen fluorescent immunoassay (FIA), and live virus culture.

RESULTS

Both RT-qPCR and Quidel SARS Sofia antigen FIA peaked in sensitivity during the period in which live virus was detected in nasal swabs, but sensitivity of RT-qPCR tests rose more rapidly prior to this period. We also found that serial testing multiple times per week increases the sensitivity of antigen tests.

CONCLUSIONS

RT-qPCR tests are more effective than antigen tests at identifying infected individuals prior to or early during the infectious period and thus for minimizing forward transmission (given timely results reporting). All tests showed >98% sensitivity for identifying infected individuals if used at least every 3 days. Daily screening using antigen tests can achieve approximately 90% sensitivity for identifying infected individuals while they are viral culture positive.

Longitudinal analysis of SARS-CoV-2 vaccine breakthrough infections reveal limited infectious virus shedding and restricted tissue distribution

The global effort to vaccinate people against SARS-CoV-2 in the midst of an ongoing pandemic has raised questions about the nature of vaccine breakthrough infections and the potential for vaccinated individuals to transmit the virus. These questions have become even more urgent as new variants of concern with enhanced transmissibility, such as Delta, continue to emerge. To shed light on how vaccine breakthrough infections compare with infections in immunologically naive individuals, we examined viral dynamics and infectious virus shedding through daily longitudinal sampling in a small cohort of adults infected with SARS-CoV-2 at varying stages of vaccination. The durations of both infectious virus shedding and symptoms were significantly reduced in vaccinated individuals compared with unvaccinated individuals. We also observed that breakthrough infections are associated with strong tissue compartmentalization and are only detectable in saliva in some cases. These data indicate that vaccination shortens the duration of time of high transmission potential, minimizes symptom duration, and may restrict tissue dissemination.

A proposed framework for the development and qualitative evaluation of West Nile virus models and their application to local public health decision-making

West Nile virus (WNV) is a globally distributed mosquito-borne virus of great public health concern. The number of WNV human cases and mosquito infection patterns vary in space and time. Many statistical models have been developed to understand and predict WNV geographic and temporal dynamics. However, these modeling efforts have been disjointed with little model comparison and inconsistent validation. In this paper, we describe a framework to unify and standardize WNV modeling efforts nationwide. WNV risk, detection, or warning models for this review were solicited from active research groups working in different regions of the United States. A total of 13 models were selected and described. The spatial and temporal scales of each model were compared to guide the timing and the locations for mosquito and virus surveillance, to support mosquito vector control decisions, and to assist in conducting public health outreach campaigns at multiple scales of decision-making. Our overarching goal is to bridge the existing gap between model development, which is usually conducted as an academic exercise, and practical model applications, which occur at state, tribal, local, or territorial public health and mosquito control agency levels. The proposed model assessment and comparison framework helps clarify the value of individual models for decision-making and identifies the appropriate temporal and spatial scope of each model. This qualitative evaluation clearly identifies gaps in linking models to applied decisions and sets the stage for a quantitative comparison of models. Specifically, whereas many coarse-grained models (county resolution or greater) have been developed, the greatest need is for fine-grained, short-term planning models (m-km, days-weeks) that remain scarce. We further recommend quantifying the value of information for each decision to identify decisions that would benefit most from model input.

Using a developmental perspective to examine the moderating effects of marriage on heavy episodic drinking in a young adult sample enriched for risk

Many studies demonstrate that marriage protects against risky alcohol use and moderates genetic influences on alcohol outcomes; however, previous work has not considered these effects from a developmental perspective or in high-risk individuals. These represent important gaps, as it cannot be assumed that marriage has uniform effects across development or in high-risk samples. We took a longitudinal developmental approach to examine whether marital status was associated with heavy episodic drinking (HED), and whether marital status moderated polygenic influences on HED. Our sample included 937 individuals (53.25% female) from the Collaborative Study on the Genetics of Alcoholism who reported their HED and marital status biennially between the ages of 21 and 25. Polygenic risk scores (PRS) were derived from a genome-wide association study of alcohol consumption. Marital status was not associated with HED; however, we observed pathogenic gene-by-environment effects that changed across young adulthood. Among those who married young (age 21), individuals with higher PRS reported more HED; however, these effects decayed over time. The same pattern was found in supplementary analyses using parental history of alcohol use disorder as the index of genetic liability. Our findings indicate that early marriage may exacerbate risk for those with higher polygenic load.

The Associations of Polygenic Scores for Risky Behaviors and Parenting Behaviors with Adolescent Externalizing Problems

The current study focused on longitudinal effects of genetics and parental behaviors and their interplay on externalizing behaviors in a panel study following individuals from adolescence to young adulthood. The nationally representative sample of Add Health participants of European ancestry included N = 4142 individuals, measured on three occasions. Parenting was operationalized as experiences with child maltreatment and maternal closeness. Externalizing problems were operationalized as alcohol use, cannabis use, and antisocial behaviors. Genetic effects were operationalized as a polygenic score (PGS) of risky behaviors. The results showed significant effects for child maltreatment, maternal closeness, and PGS, above and beyond other factors and previous levels of externalizing behaviors. Furthermore, maternal closeness was found to negatively correlate with PGS. No significant interaction effects of parenting and PGS were found. The results underscore the joint independent effects of parenting and genetics on the change in externalizing behaviors from adolescence to young adulthood.

A Survey of Tick Surveillance and Control Practices in the United States

Tickborne diseases are an increasing public health threat in the United States. Prevention and diagnosis of tickborne diseases are improved by access to current and accurate information on where medically important ticks and their associated human and veterinary pathogens are present, their local abundance or prevalence, and when ticks are actively seeking hosts. The true extent of tick and tickborne pathogen expansion is poorly defined, in part because of a lack of nationally standardized tick surveillance. We surveyed 140 vector-borne disease professionals working in state, county, and local public health and vector control agencies to assess their 1) tick surveillance program objectives, 2) pathogen testing methods, 3) tick control practices, 4) data communication strategies, and 5) barriers to program development and operation. Fewer than half of respondents reported that their jurisdiction was engaged in routine, active tick surveillance, but nearly two-thirds reported engaging in passive tick surveillance. Detection of tick presence was the most commonly stated current surveillance objective (76.2%). Most of the programs currently supporting tick pathogen testing were in the Northeast (70.8%), Upper and Central Midwest (64.3%), and the West (71.4%) regions. The most common pathogens screened for were Rickettsia spp. (Rickettsiales: Rickettsiaceae) and bacterial and viral agents transmitted by Ixodes (Acari: Ixodidae) ticks. Only 12% of respondents indicated their jurisdiction directly conducts or otherwise financially supports tick control. Responses indicated that their ability to expand the capacity of tick surveillance and control programs was impeded by inconsistent funding, limited infrastructure, guidance on best practices, and institutional capacity to perform these functions.

Comparing Contributions of Passive and Active Tick Collection Methods to Determine Establishment of Ticks of Public Health Concern Within Illinois

In Illinois, between 1990 and 2017, tick-borne diseases in humans increased 10-fold, yet we have insufficient information on when and where people are exposed to vector ticks (Ixodida: Ixodidae). The aims of our research were to compare contributions of passive and active tick collection methods in determining establishment of ticks of public health concern and obtain information on tick distributions within Illinois. We used three surveillance strategies within the Illinois Tick Inventory Collaboration Network to gather information about the ticks of public health concern: 1) passive collection (voluntary submission by the public); 2) systematic collection (biweekly active surveillance); and 3) special collections (active collections in locations of special interest). Of collected adult and nymphal ticks, 436 were from passive collections, 142 from systematic collections, and 1,270 from special collections. Tick species distribution status changed in 36 counties. Our data provide noteworthy updates to distribution maps for use by public health agencies to develop prevention and control strategies. Additionally, the program built a network of collaborations and partnerships to support future tick surveillance efforts within Illinois and highlighted how the combination of the three surveillance strategies can be used to determine geographic spread of ticks, pinpoint locations in need of more surveillance, and help with long-term efforts that support phenology studies.

Daily sampling of early SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness

The dynamics of SARS-CoV-2 replication and shedding in humans remain poorly understood. We captured the dynamics of infectious virus and viral RNA shedding during acute infection through daily longitudinal sampling of 60 individuals for up to 14 days. By fitting mechanistic models, we directly estimate viral reproduction and clearance rates, and overall infectiousness for each individual. Significant person-to-person variation in infectious virus shedding suggests that individual-level heterogeneity in viral dynamics contributes to superspreading. Viral genome load often peaked days earlier in saliva than in nasal swabs, indicating strong compartmentalization and suggesting that saliva may serve as a superior sampling site for early detection of infection. Viral loads and clearance kinetics of B.1.1.7 and non-B.1.1.7 viruses in nasal swabs were indistinguishable, however B.1.1.7 exhibited a significantly slower pre-peak growth rate in saliva. These results provide a high-resolution portrait of SARS-CoV-2 infection dynamics and implicate individual-level heterogeneity in infectiousness in superspreading.

Quantification and Comparison of Risks Associated with Wastewater Use in Spray Irrigation

In the U.S., spray irrigation is the most common method used in agriculture and supplementing with animal wastewater has the potential to reduce water demands. However, this could expose individuals to respiratory pathogens such as Legionella pneumophila and nontuberculosis Mycobacteria (NTM). Disinfection with methods like anaerobic digestion is an option but can increase concentrations of cytotoxic ammonia (personal communication). Our study aimed to model the annual risks of infection from these bacterial pathogens and the air concentrations of ammonia and determine if anaerobically digesting this wastewater is a safe option. Air dispersion modeling, conducted in AERMOD, generated air concentrations of water during the irrigation season (May-September) for the years 2013-2018. These values fed into the quantitative microbial risk assessments for the bacteria and allowed calculation of ammonia air concentrations. The outputs of these models were compared to the safety thresholds of 10^-4 infections/year and 0.5 mg/m³ , respectively, to determine their potential for negative health outcomes. It was determined that infection from NTM was not a concern for individuals near active spray irrigators, but that infection with L. pneumophila could be a concern, with a maximum predicted annual risk of infection of 3.5 × 10^-3 infections/year and 25.2% of parameter combinations exceeding the established threshold. Ammonia posed a minor risk, with 1.5% of parameter combinations surpassing the risk threshold of 0.5 mg/m³ . These findings suggest that animal wastewater should be anaerobically digested prior to use in irrigation to remove harmful pathogens.

Risk awareness of black-and-gold howler monkeys living in an urban environment in south-west Paraguay

As urbanisation increases, wild primates are exposed to urban environments which come with a distinct and often novel set of risks. Urban habitats can form a matrix of forest fragments and anthropogenic structures, including buildings, electric cables and roads, which can limit movement and force species to live in hazardous areas. We studied five groups of urban black and gold howler monkey (Alouatta caraya) in Pilar, Paraguay, to investigate whether the monkeys are aware of anthropogenic risks based on their patterns of self-scratching behaviour, an indicator of stress, and how they used the space available to them. Using a Risk Index created for the study, we ranked the level of risk attributed to different zones of their home range, awarding each zone with a hazard score. Using Quantum GIS and kernel density estimation, we determined the relationship between habitat use and hazard score. Using a Spearman’s rank correlation, we found nonsignificant relationships between the hazard score and self-scratching behaviour for four groups, suggesting a lack of awareness. However, there was a significant negative relationship between the hazard score and home range use for four groups, indicating that they spent more time in areas with lower levels of anthropogenic risk.

Early Assessment With Gastrointestinal Ultrasound in Patients Hospitalised for a Flare of Ulcerative Colitis and Predicting the Need for Salvage Therapy: A Pilot Study

Approximately 30% of patients hospitalised with severe ulcerative colitis do not respond to corticosteroids, but the decision to introduce salvage therapy is delayed to at least the third day of treatment, according to the widely applied Oxford criteria to assess response. This pilot study aimed to determine if gastrointestinal ultrasound performed on admission can predict steroid-refractory disease. In 10 consecutive patients with severe ulcerative colitis, gastrointestinal ultrasound was performed within 24 h of admission. Six patients failed corticosteroids and required infliximab salvage therapy. Colonic bowel wall thickness was a median of 4.6 mm (range 4.2-5.6 mm) in those responding to steroids compared with 6.2 mm (6-7.9 mm) in those requiring salvage therapy (p = 0.009). Any colonic segment with a bowel wall thickness of >6 mm was associated with the need for salvage therapy (p = 0.033). Gastrointestinal ultrasound may provide an early indication of poor corticosteroid response and enable a timelier introduction of salvage therapy in patients with severe ulcerative colitis.

Longitudinal assessment of diagnostic test performance over the course of acute SARS-CoV-2 infection

What is already known about this topic?

Diagnostic tests and sample types for SARS-CoV-2 vary in sensitivity across the infection period.

What is added by this report?

We show that both RTqPCR (from nasal swab and saliva) and the Quidel SARS Sofia FIA rapid antigen tests peak in sensitivity during the period in which live virus can be detected in nasal swabs, but that the sensitivity of RTqPCR tests rises more rapidly in the pre-infectious period. We also use empirical data to estimate the sensitivities of RTqPCR and antigen tests as a function of testing frequency.

What are the implications for public health practice?

RTqPCR tests will be more effective than rapid antigen tests at identifying infected individuals prior to or early during the infectious period and thus for minimizing forward transmission (provided results reporting is timely). All modalities, including rapid antigen tests, showed >94% sensitivity to detect infection if used at least twice per week. Regular surveillance/screening using rapid antigen tests 2-3 times per week can be an effective strategy to achieve high sensitivity (>95%) for identifying infected individuals.