Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics.

The maturation of genomic surveillance in the past decade has enabled tracking of the emergence and spread of epidemics at an unprecedented level. During the COVID-19 pandemic, for example, genomic data revealed that local epidemics varied considerably in the frequency of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage importation and persistence, likely due to a combination of COVID-19 restrictions and changing connectivity. Here, we show that local COVID-19 epidemics are driven by regional transmission, including across international boundaries, but can become increasingly connected to distant locations following the relaxation of public health interventions. By integrating genomic, mobility, and epidemiological data, we find abundant transmission occurring between both adjacent and distant locations, supported by dynamic mobility patterns. We find that changing connectivity significantly influences local COVID-19 incidence. Our findings demonstrate a complex meaning of "local" when investigating connected epidemics and emphasize the importance of collaborative interventions for pandemic prevention and mitigation.

Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation.

Cohesin is important for 3D genome organization. Nevertheless, even the complete removal of cohesin has surprisingly little impact on steady-state gene transcription and enhancer activity. Here we show that cohesin is required for the core transcriptional response of primary macrophages to microbial signals, and for inducible enhancer activity that underpins inflammatory gene expression. Consistent with a role for inflammatory signals in promoting myeloid differentiation of hematopoietic stem and progenitor cells (HPSCs), cohesin mutations in HSPCs led to reduced inflammatory gene expression and increased resistance to differentiation-inducing inflammatory stimuli. These findings uncover an unexpected dependence of inducible gene expression on cohesin, link cohesin with myeloid differentiation, and may help explain the prevalence of cohesin mutations in human acute myeloid leukemia.

Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission.

As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing and/or sequencing capacity, which can also introduce biases1-3. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing4,5. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We developed and deployed improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detected emerging variants of concern up to 14 days earlier in wastewater samples, and identified multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.

Ronin governs the metabolic capacity of the embryonic lineage for post-implantation development.

During implantation, the murine embryo transitions from a "quiet" into an active metabolic/proliferative state, which kick-starts the growth and morphogenesis of the post-implantation conceptus. Such transition is also required for embryonic stem cells to be established from mouse blastocysts, but the factors regulating this process are poorly understood. Here, we show that Ronin plays a critical role in the process by enabling active energy production, and the loss of Ronin results in the establishment of a reversible quiescent state in which naïve pluripotency is promoted. In addition, Ronin fine-tunes the expression of genes that encode ribosomal proteins and is required for proper tissue-scale organisation of the pluripotent lineage during the transition from blastocyst to egg cylinder stage. Thus, Ronin function is essential for governing the metabolic capacity so that it can support the pluripotent lineage's high-energy demands for cell proliferation and morphogenesis.

Visualising three-dimensional genome organisation in two dimensions.

The three-dimensional organisation of the genome plays a crucial role in developmental gene regulation. In recent years, techniques to investigate this organisation have become more accessible to labs worldwide due to improvements in protocols and decreases in the cost of high-throughput sequencing. However, the resulting datasets are complex and can be challenging to analyse and interpret. Here, we provide a guide to visualisation approaches that can aid the interpretation of such datasets and the communication of biological results.

Feedforward regulation of Myc coordinates lineage-specific with housekeeping gene expression during B cell progenitor cell differentiation.

The differentiation of self-renewing progenitor cells requires not only the regulation of lineage- and developmental stage-specific genes but also the coordinated adaptation of housekeeping functions from a metabolically active, proliferative state toward quiescence. How metabolic and cell-cycle states are coordinated with the regulation of cell type-specific genes is an important question, because dissociation between differentiation, cell cycle, and metabolic states is a hallmark of cancer. Here, we use a model system to systematically identify key transcriptional regulators of Ikaros-dependent B cell-progenitor differentiation. We find that the coordinated regulation of housekeeping functions and tissue-specific gene expression requires a feedforward circuit whereby Ikaros down-regulates the expression of Myc. Our findings show how coordination between differentiation and housekeeping states can be achieved by interconnected regulators. Similar principles likely coordinate differentiation and housekeeping functions during progenitor cell differentiation in other cell lineages.

Association of prenatal substance use with prenatal and postpartum care: Evidence from the Pregnancy Risk Assessment Monitoring System, 2016-2019.

The objective of this study was to build on existing qualitative research to estimate the association of prenatal substance use with prenatal and postpartum care. We used data from the 2016-2019 Pregnancy Risk Assessment Monitoring System for 9 states. We conducted adjusted linear regression to compare month of gestation of first prenatal visit and adjusted logistic regression to compare receipt of adequate prenatal care and a postpartum healthcare visit among women who reported prenatal use of any opioids, prescription opioids, marijuana, and illicit drugs to those who did not report use of each substance. Women who reported prenatal use of any opioids (Risk Difference(RD) = 0.16; 95% Confidence Interval (CI) = 0.04, 0.28), prescription opioids (RD = 0.16; 95% CI = 0.04, 0.28), marijuana (RD = 0.25; 95% CI = 0.10, 0.41) and illicit drugs (RD = 0.52; 95% CI = 0.09, 0.95) initiated prenatal care later than those who did not report use of each substance. Women who reported prenatal use of any opioid (Odds Ratio (OR) = 0.82; 95% CI = 0.68, 1.00), prescription opioids (OR = 0.84; 95% CI = 0.69, 1.02), marijuana (OR = 0.59; 95% CI = 0.48, 0.73) and illicit drugs (OR = 0.29; 95% CI = 0.20, 0.42) were less likely to receive adequate prenatal care. Women who reported prenatal use of any opioid (OR = 0.82, 95% CI = 0.65, 1.04), prescription opioids (OR = 0.83; 95% CI = 0.66, 1.05), marijuana (OR = 0.65; 95% CI = 0.51, 0.82) and illicit drugs (OR = 0.47; 95% CI = 0.30, 0.72) had a lower likelihood of a postpartum visit than those who did not report use of each substance. Results indicate potential intervention points for pregnant women who use substances.

Real-time Feedback to Improve HIV Treatment Adherence in Pregnant and Postpartum Women in Uganda: A Randomized Controlled Trial.

We assessed an intervention aimed at improving adherence to antiretroviral therapy (ART) among pregnant and postpartum women living with HIV (PPWLH). We randomized 133 pregnant women initiating ART in Uganda to receive text reminders generated by real time-enabled electronic monitors and data-informed counseling through 3 months postpartum (PPM3) or standard care. Intention-to-treat analyses found low adherence levels and no intervention impact. Proportions achieving ≥95% adherence in PPM3 were 16.4% vs. 9.1% (t = -1.14, p = 0.26) in intervention vs. comparison groups, respectively; 30.9% vs. 29.1% achieved ≥80% adherence. Additional analyses found significant adherence declines after delivery, and no effect on disease progression (CD4-cell count, viral load), though treatment interruptions were significantly fewer in intervention participants. Per-protocol analyses encompassing participants who used adherence monitors as designed experienced better outcomes, suggesting potential benefit for some PPWLH. The study was registered on ClinicalTrials.Gov (NCT02396394).

Seasonal trends and maternal characteristics as predictors of maternal undernutrition and low birthweight in Eastern Maharashtra, India.

Few studies have assessed whether women and infants in rural and peri-urban communities in South Asia experience seasonal fluctuations in nutritional status; however, a handful of studies have documented seasonal variability in risk factors for undernutrition including food availability, physical activity and infections. We used data from the Maternal and Newborn Health (MNH) registry, a population-based pregnancy and birth registry in Eastern Maharashtra, India, to analyse seasonal trends in birthweight and maternal nutritional status-body mass index (BMI) and haemoglobin-in the first trimester of pregnancy. We plotted monthly and seasonal trends in birthweight, and maternal BMI and haemoglobin, and used multivariable regression models to identify seasonal and maternal characteristics that predicted each outcome. Between October 2014 and January 2018, MNH included 29,253 livebirths with recorded birthweight. BMI was assessed in 15,252 women less than 12 weeks of gestation and haemoglobin in 18,278 women less than 13 weeks of gestation. Maternal characteristics (age, education, parity and height) were significantly associated with nutritional status; however, there were minimal seasonal fluctuations in birthweight or maternal nutrition. There were significant secular trends in maternal haemoglobin; between 2014 and 2018, the prevalence of maternal anaemia decreased from 91% to 79% and moderate or severe anaemia from 53% to 37%. The prevalence of maternal underweight (45.3%) and overweight (9.8%) and low birthweight (19.1%) remained relatively constant over the study period. Our findings highlight that in some rural and peri-urban areas in South Asia, tackling systemic drivers of malnutrition may be more effective than targeted interventions based on season.

Retention in HIV Care Among HIV-Seropositive Pregnant and Postpartum Women in Uganda: Results of a Randomized Controlled Trial.

We tested an intervention that aimed to increase retention in antiretroviral therapy (ART) among HIV-positive pregnant and postpartum women, a population shown to be vulnerable to poor ART outcomes. 133 pregnant women initiating ART at 2 hospitals in Uganda used real time-enabled wireless pill monitors (WPM) for 1 month, and were then randomized to receive text message reminders (triggered by late dose-taking) and data-informed counseling through 3 months postpartum or standard care. We assessed "full retention" (proportion attending all monthly clinic visits and delivering at a study facility; "visit retention" (proportion of clinic visits attended); and "postpartum retention" (proportion retained at 3 months postpartum). Intention-to-treat and per protocol analyses found that retention was relatively low and similar between groups, with no significant differences. Retention declined significantly post-delivery. The intervention was unsuccessful in this population, which experiences suboptimal ART retention and is in urgent need of effective interventions.

Assessing coverage of essential maternal and child health interventions using health-facility data in Uganda.

BACKGROUND: Nationally representative household surveys are the gold standard for tracking progress in coverage of life-saving maternal and child interventions, but often do not provide timely information on coverage at the local and health facility level. Electronic routine health information system (RHIS) data could help provide this information, but there are currently concerns about data quality. This analysis seeks to improve the usability of and confidence in electronic RHIS data by using adjustments to calculate more accurate numerators and denominators for essential interventions. METHODS: Data from three sources (Ugandan Demographic and Health (UDHS) survey, electronic RHIS, and census) were used to provide estimates of essential maternal (> 4 antenatal care visits (ANC), skilled delivery, and postnatal care visit (PNC)) and child health interventions (diphtheria, pertussis, tetanus, and hepatitis B and Haemophilus influenzae type b and polio vaccination series, measles vaccination, and vitamin A). Electronic RHIS data was checked for quality and both numerators and denominators were adjusted to improve accuracy. Estimates were compared between the three sources. RESULTS: Estimates of maternal health interventions from adjusted electronic RHIS data were lower than those of the UDHS, while child intervention estimates were typically higher. Adjustment of electronic RHIS data generally improved accuracy compared with no adjustment. There was considerable agreement between estimates from adjusted, electronic RHIS data, and UDHS for skilled delivery and first dose of childhood vaccination series, but lesser agreement for ANC visits and second and third doses of childhood vaccinations. CONCLUSIONS: Nationally representative household surveys will likely continue being the gold standard of coverage estimates of maternal and child health interventions, but this analysis shows that current approaches to adjusting health facility estimate works better for some indications than others. Further efforts to improve accuracy of estimates from RHIS sources are needed.

Evaluating the effect of care around labor and delivery practices on early neonatal mortality in the Global Network's Maternal and Newborn Health Registry.

BACKGROUND: Neonatal deaths in first 28-days of life represent 47% of all deaths under the age of five years globally and are a focus of the United Nation's (UN's) Sustainable Development Goals. Pregnant women are delivering in facilities but that does not indicate quality of care during delivery and the postpartum period. The World Health Organization's Essential Newborn Care (ENC) package reduces neonatal mortality, but lacks a simple and valid composite index that measures its effectiveness. METHODS: Data on 5 intra-partum and 3 post-partum practices (indicators) recommended as part of ENC, routinely collected in NICHD's Global Network's (GN) Maternal Newborn Health Registry (MNHR) between 2010 and 2013, were included. We evaluated if all 8 practices (Care around Delivery - CAD), combined as an index was associated with reduced early neonatal mortality rates (days 0-6 of life). RESULTS: A total of 150,848 live births were included in the analysis. The individual indicators varied across sites. All components were present in 19.9% births (range 0.4 to 31% across sites). Present indicators (8 components) were associated with reduced early neonatal mortality [adjusted RR (95% CI):0.81 (0.77, 0.85); p < 0.0001]. Despite an overall association between CAD and early neonatal mortality (RR < 1.0 for all early mortality): delivery by skilled birth attendant; presence of fetal heart and delayed bathing were associated with increased early neonatal mortality. CONCLUSIONS: Present indicators (8 practices) of CAD were associated with a 19% reduction in the risk of neonatal death in the diverse health facilities where delivery occurred within the GN MNHR. These indicators could be monitored to identify facilities that need to improve compliance with ENC practices to reduce preventable neonatal deaths. Three of the 8 indicators were associated with increased neonatal mortality, due to baby being sick at birth. Although promising, this composite index needs refinement before use to monitor facility-based quality of care in association with early neonatal mortality. Trial registration The identifier of the Maternal Newborn Health Registry at ClinicalTrials.gov is NCT01073475.

Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin.

In addition to mediating sister chromatid cohesion during the cell cycle, the cohesin complex associates with CTCF and with active gene regulatory elements to form long-range interactions between its binding sites. Genome-wide chromosome conformation capture had shown that cohesin's main role in interphase genome organization is in mediating interactions within architectural chromosome compartments, rather than specifying compartments per se. However, it remains unclear how cohesin-mediated interactions contribute to the regulation of gene expression. We have found that the binding of CTCF and cohesin is highly enriched at enhancers and in particular at enhancer arrays or "super-enhancers" in mouse thymocytes. Using local and global chromosome conformation capture, we demonstrate that enhancer elements associate not just in linear sequence, but also in 3D, and that spatial enhancer clustering is facilitated by cohesin. The conditional deletion of cohesin from noncycling thymocytes preserved enhancer position, H3K27ac, H4K4me1, and enhancer transcription, but weakened interactions between enhancers. Interestingly, ∼ 50% of deregulated genes reside in the vicinity of enhancer elements, suggesting that cohesin regulates gene expression through spatial clustering of enhancer elements. We propose a model for cohesin-dependent gene regulation in which spatial clustering of enhancer elements acts as a unified mechanism for both enhancer-promoter "connections" and "insulation."

Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments.

Chromosome conformation capture approaches have shown that interphase chromatin is partitioned into spatially segregated Mb-sized compartments and sub-Mb-sized topological domains. This compartmentalization is thought to facilitate the matching of genes and regulatory elements, but its precise function and mechanistic basis remain unknown. Cohesin controls chromosome topology to enable DNA repair and chromosome segregation in cycling cells. In addition, cohesin associates with active enhancers and promoters and with CTCF to form long-range interactions important for gene regulation. Although these findings suggest an important role for cohesin in genome organization, this role has not been assessed on a global scale. Unexpectedly, we find that architectural compartments are maintained in noncycling mouse thymocytes after genetic depletion of cohesin in vivo. Cohesin was, however, required for specific long-range interactions within compartments where cohesin-regulated genes reside. Cohesin depletion diminished interactions between cohesin-bound sites, whereas alternative interactions between chromatin features associated with transcriptional activation and repression became more prominent, with corresponding changes in gene expression. Our findings indicate that cohesin-mediated long-range interactions facilitate discrete gene expression states within preexisting chromosomal compartments.

GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data.

BACKGROUND: Precise quantitative and spatiotemporal control of gene expression is necessary to ensure proper cellular differentiation and the maintenance of homeostasis. The relationship between gene expression and the spatial organisation of chromatin is highly complex, interdependent and not completely understood. The development of experimental techniques to interrogate both the higher-order structure of chromatin and the interactions between regulatory elements has recently lead to important insights on how gene expression is controlled. The ability to gain these and future insights is critically dependent on computational tools for the analysis and visualisation of data produced by these techniques. RESULTS AND CONCLUSION: We have developed GenomicInteractions, a freely available R/Bioconductor package designed for processing, analysis and visualisation of data generated from various types of chromosome conformation capture experiments. The package allows the easy annotation and summarisation of large genome-wide datasets at both the level of individual interactions and sets of genomic features, and provides several different methods for interrogating and visualising this type of data. We demonstrate this package's utility by showing example analyses performed on interaction datasets generated using Hi-C and ChIA-PET.

Using Audience Response Systems to Enhance Chronic, Noncancer Pain Knowledge Acquisition Among Veterans.

BACKGROUND: Educating patients on factual information related to chronic pain and self-management improves knowledge, pain outcomes, and compliance. The current study assesses changes in pain knowledge among veterans who attended a 12-week "Pain Education School" and examines whether or not the addition of an active learning component (i.e., use of an audience response system [ARS]) leads to greater increases in pain knowledge. MATERIALS AND METHODS: A sample of 102 veterans 24-84 years of age who elected to participate in the 12-week pain education program was evaluated. Only a subgroup of veterans (n=69) had access to the ARS. RESULTS: A 2×2 repeated-measures multivariate analyses of variance was conducted to examine changes in pain knowledge, pain beliefs, stage of readiness to adopt a self-management approach, and depressive symptoms over time and to explore the impact of ARS use on pain knowledge acquisition. Participants reported a statistically significant difference between their pre- and posttest measures of pain beliefs (p=0.04), stage of readiness to adopt a self-management approach (p=0.00), and depressive symptoms (p=0.00). Veterans who used the ARS demonstrated significantly greater increases in pain knowledge acquisition after completing the pain education program than those who did not (p=0.03). CONCLUSIONS: Findings provide support for the incorporation of ARS in pain education programming to facilitate active learning and to increase knowledge acquisition. Findings also provide evidence for the effectiveness of pain education programs in improving veterans' attitudes about their pain, increasing readiness to engage in self-management, and decreasing depressive symptoms.

Kernel machine SNP-set testing under multiple candidate kernels.

Joint testing for the cumulative effect of multiple single-nucleotide polymorphisms grouped on the basis of prior biological knowledge has become a popular and powerful strategy for the analysis of large-scale genetic association studies. The kernel machine (KM)-testing framework is a useful approach that has been proposed for testing associations between multiple genetic variants and many different types of complex traits by comparing pairwise similarity in phenotype between subjects to pairwise similarity in genotype, with similarity in genotype defined via a kernel function. An advantage of the KM framework is its flexibility: choosing different kernel functions allows for different assumptions concerning the underlying model and can allow for improved power. In practice, it is difficult to know which kernel to use a priori because this depends on the unknown underlying trait architecture and selecting the kernel which gives the lowest P-value can lead to inflated type I error. Therefore, we propose practical strategies for KM testing when multiple candidate kernels are present based on constructing composite kernels and based on efficient perturbation procedures. We demonstrate through simulations and real data applications that the procedures protect the type I error rate and can lead to substantially improved power over poor choices of kernels and only modest differences in power vs. using the best candidate kernel.

Different in different ways: A network-analysis approach to voice and prosody in Autism Spectrum Disorder.

The current study investigated whether the difficulty in finding group differences in prosody between speakers with autism spectrum disorder (ASD) and neurotypical (NT) speakers might be explained by identifying different acoustic profiles of speakers which, while still perceived as atypical, might be characterized by different acoustic qualities. We modelled the speech from a selection of speakers (N = 26), with and without ASD, as a network of nodes defined by acoustic features. We used a community-detection algorithm to identify clusters of speakers who were acoustically similar and compared these clusters with atypicality ratings by naïve and expert human raters. Results identified three clusters: one primarily composed of speakers with ASD, one of mostly NT speakers, and one comprised of an even mixture of ASD and NT speakers. The human raters were highly reliable at distinguishing speakers with and without ASD, regardless of which cluster the speaker was in. These results suggest that community-detection methods using a network approach may complement commonly-employed human ratings to improve our understanding of the intonation profiles in ASD.

National chlorhexidine coverage and factors associated with newborn umbilical cord care in Bangladesh and Nepal: a cross-sectional analysis using household data.

BACKGROUND: Preventable newborn deaths are a global tragedy with many of these deaths concentrated in the first week and day of life. A simple low-cost intervention, chlorhexidine cleansing of the umbilical cord, can prevent deaths from omphalitis, an infection of the umbilical cord. Bangladesh and Nepal have national policies promoting chlorhexidine use, as well as routinely collected household survey data, which allows for an assessment of coverage and predictors of the intervention. METHODS: We used data from the 2017-2018 Bangladesh Demographic and Health Survey and the 2016 Nepal Demographic and Health Survey, two large-scale nationally representative household surveys. We studied coverage of single application of chlorhexidine to the umbilical cord of newborns born in the past year using descriptive, bivariate and multivariable analyses. Key predictors of newborns receiving chlorhexidine cleansing, including socio-economic factors, healthcare related factors and the application of harmful and nonharmful substances, were explored in this study. RESULTS: Coverage of chlorhexidine cleansing was 15.0% in Bangladesh and 50.7% in Nepal, while the application of a harmful substance was 16.9% in Bangladesh and 22.6% in Nepal. Results from the multivariable analyses indicated that delivery in a health facility was strongly associated with a newborn's receipt of chlorhexidine in both countries (Bangladesh: OR = 2.23, p = 0.002; Nepal: OR = 5.01, p = 0.000). In Bangladesh, delivery by Cesarean section and application of another non-harmful substance were significantly and positively associated with the receipt of chlorhexidine. In Nepal antenatal care was significantly and positively associated with chlorhexidine, while application of a harmful substance was significantly and negatively associated with receipt of chlorhexidine. Maternal education, urban/rural residence, religion and sex were not significant in the multivariable analysis. Wealth was not a significant factor in Bangladesh, but in Nepal newborns in the two highest wealth quintiles were significantly less likely to receive chlorhexidine than newborns in the lowest wealth quintile. CONCLUSION: As Bangladesh and Nepal continue to scale-up chlorhexidine for newborn umbilical cord care, additional focus on newborns born in non-facility environments may be warranted. Chlorhexidine cleansing may have the potential to be an equitable intervention, as newborns from the poorest wealth quintiles and whose mothers had less education were not disadvantaged in receiving the intervention in these two settings.

Estimating the effects of COVID-19 on essential health services utilization in Uganda and Bangladesh using data from routine health information systems.

Background: Since March 2020, the coronavirus disease 2019 (COVID-19) pandemic has been a major shock to health systems across the world. We examined national usage patterns for selected basic, essential health services, before and during the COVID-19 pandemic in Uganda and Bangladesh, to determine whether COVID-19 affected reporting of service utilization and the use of health services in each country. Methods: We used routine health information system data since January 2017 to analyze reporting and service utilization patterns for a variety of health services. Using time series models to replicate pre-COVID-19 trajectories over time we estimated what levels would have been observed if COVID-19 had not occurred during the pandemic months, starting in March 2020. The difference between the observed and predicted levels is the COVID-19 effect on health services. Results: The time trend models for Uganda and Bangladesh closely replicated the levels and trajectories of service utilization during the 38 months prior to the COVID-19 pandemic. Our results indicate that COVID-19 had severe effects across all services, particularly during the first months of the pandemic, but COVID-19 impacts on health services and subsequent recovery varied by service type. In general, recovery to expected levels was slow and incomplete across the most affected services. Conclusion: Our analytical approach based on national information system data could be very useful as a form of surveillance for health services disruptions from any cause leading to rapid responses from health service managers and policymakers.