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Abstract We report time resolved observations of the crystallization from liquid hydrogen, supercooled to temperatures below the melting point, using 11.2 keV X-ray diffraction from the Linac Coherent Light Source (LCLS). Changes to the metastable solid and liquid structure factors have been dynamically measured. This allows for a direct determination of the lowest energy crystal polymorphs, the stacking probabilities, as well as the liquid and solid densities and temperatures. Such measurements provide experimental evidence of an Arrhenius-like growth kinetics along the stacking direction during supercooling.

Abstract Background Clinical metagenomics involves the genomic sequencing of all microorganisms in clinical samples ideally after depletion of human DNA to increase sensitivity and reduce turnaround times. Current human DNA depletion methods preferentially preserve either DNA or RNA containing microbes, but not both simultaneously. Here we describe and present data using a practical and rapid mechanical host-depletion method allowing simultaneous detection of RNA and DNA microorganisms linked with nanopore sequencing. Methods The human cells from respiratory samples are lysed mechanically using 1.4 mm zirconium-silicate spheres and the human DNA is depleted using a nonspecific endonuclease. The RNA is converted to dsDNA to allow the simultaneous sequencing of DNA and RNA. Results The method decreases human DNA concentration by a median of eight Ct values while detecting a broad range of RNA & DNA viruses, bacteria, including atypical pathogens (Legionella, Chlamydia, Mycoplasma) and fungi (Candida, Pneumocystis, Aspergillus). The first automated reports are generated after 30 min sequencing from a 7 h end-to-end workflow. Sensitivity and specificity for bacterial detection are 90% and 100%, respectively, and viral detection are 92% and 100% after 2 h of sequencing. Prospective validation on 33 consecutive lower respiratory tract samples from ventilated patients with suspected pneumonia shows 60% concordance with routine testing, detection of additional pathogens in 21% of samples and pathogen genomic assembly achieve for 42% of viruses and 33% of bacteria. Conclusions Although further workflow refinement and validation on samples containing a broader range of pathogens is required, it holds promise as a clinically deployable workflow suitable for evaluation in routine microbiology laboratories.

Pathogenic Leptospira are spirochete bacteria which cause leptospirosis, a re-emerging zoonotic disease of global importance. Here, we use a recently described lineage of environmental-adapted leptospires, which are evolutionarily the closest relatives of the highly virulent Leptospira species, to explore the key phenotypic traits and genetic determinants of Leptospira virulence. Through a comprehensive approach integrating phylogenomic comparisons with in vitro and in vivo phenotyping studies, we show that the evolution towards pathogenicity is associated with both a decrease of the ability to survive in the environment and the acquisition of strategies that enable successful host colonization. This includes the evasion of the mammalian complement system and the adaptations to avoid activation of the innate immune cells by the highly-virulent Leptospira species (also called P1+ species), unlike other species belonging to the phylogenetically related P1- and P2 groups, as well as saprophytes. Moreover, our analysis reveals specific genetic determinants that have undergone positive selection during the course of evolution in Leptospira, contributing directly to virulence and host adaptation as demonstrated by gain-of-function and knock-down studies. Taken together, our findings define a new vision on Leptospira pathogenicity, identifying virulence attributes associated with clinically relevant species, and provide insights into the evolution and emergence of these life-threatening pathogens.

Summary: We investigated the dynamics of COVID-19 contacts subsequent conversion to SARS-CoV-2 infection in an inpatient setting across three National Health Service (NHS) Trusts. 9.2% (476/5,156) COVID-19 contacts met inclusion criteria, were typable and tested positive for COVID-19. There was no significant difference between Omicron and non-Omicron contacts overall conversion proportions. Omicron contacts converted faster than non-Omicron contacts (median 3 days vs 4 days, P=0.03), and had significantly greater proportions of early conversions at day 3, 5, and 7 timepoints.

Abstract Background Food diets are complex and a policy targeting one item of a person’s diet does not affect their nutritional intake in a solely additive or subtractive manner. Policies tackling unhealthy diets are more likely to be adopted by governments if there is robust evidence to support them. To evaluate dietary policies, it is important to understand the correlations and interdependencies between food groups, as these can lead to unintended negative consequences. We aimed to see whether reductions in consumption of a particular group is related to a net improvement in nutritional intake, after taking into account patterns of consumption and substitution across food groups. Methods Detailed dietary data was collected using a 24-h online dietary assessment from the UK Biobank and Oxford Web Q (n = 185,611). We used panel data fixed effects methods to estimate changes in energy, saturated fat, total sugar, and fibre following a 100gram reduction across 44 food groups. We compare these estimates against the average nutritional value of that food group from the UK National Diet and Nutrition Survey. Results We find evidence of variation in whether a food is compensated between the main confectionery products. Crisps, savoury snacks, and sugar confectionery are less likely to be compensated, whereas chocolate confectionery, biscuits, and buns/cakes/pastries and pies are compensated. The result is particularly striking for chocolate confectionery which shows that while chocolate confectionery often has a high energy content, eating less chocolate confectionery is not associated with an equal reduction in energy. Instead, we find individuals switch or compensate for their reduction in chocolate confectionery consumption with other high energy food items. Conclusions We find that sugar confectionery and crisps and savoury snacks are less likely to result in substitution than chocolate confectionery. This would suggest that food policies aiming to reduce the consumption of these food groups are more likely to result in overall lower consumption of unhealthy foods.

Species distribution models are useful conservation planning tools for at-risk species, especially if they are linked to planning efforts, conservation delivery, and a changing environment. The Dakota skipper (Hesperia dacotae) is an endemic butterfly of mixed and tallgrass prairie of the northern Great Plains that is listed as federally threatened in the United States and Canada. We modeled broad-scale habitat suitability for the Dakota skipper by relating occurrence observations collected via non-probabilistic population surveys and a stratified sample of pseudo-absences to environmental predictors using a machine learning approach (i.e. Random Forest classification model). Predictors were summarized at two local scales and one landscape scale to reflect a potential spatial hierarchy of settlement responses. We used recursive feature elimination to select the top 25 covariates from a suite of predictor variables related to climate, topography, vegetation cover, biomass, surface reflectance, disturbance history, and soil characteristics. The top model included six bioclimatic, one soil, and 18 local- and landscape-scale vegetation variables and indicated an association with undisturbed grasslands with higher perennial grass and forb cover and biomass. The model performed well, with kappa and AUC estimates of 0.92 and 0.99, respectively, for 20% of data withheld for validation. To understand how climate change might affect Dakota skipper distribution, we applied the model using future 30-year bioclimatic predictions. Predicted suitable habitat declined and the climate envelope associated with Dakota skipper occurrence shifted north into Canada. While it is unknown to what degree the bioclimatic relationships in the model are biologically meaningful or are simply correlative with our non-probabilistic sample of occurrences, our results present an urgency to improve data collection for Dakota skipper populations and better understand climatic relationships, as climate change could have profound effects on populations and conservation planning. Regardless of climate or model uncertainty, our results demonstrate the importance of maintaining sufficient quantities and quality of grass on the landscape to support populations of Dakota skipper.

Purpose: There is increasing recognition of monogenic aetiologies for kidney disease. We sought to identify whether genetic kidney disease (GKD) has distinct hospitalization patterns compared to other forms of chronic kidney disease (CKD). Methods: Health service utilization analysis was undertaken in a CKD cohort study across public hospital services in Queensland, Australia. CKD due to clinically coded potential monogenic causes was compared to all other causes in terms of annual frequency, cost, and type of hospital admission. Results: We analyzed 7 years of hospital admissions data (809,188 admissions) among 29,046 patients. Compared to non-genetic CKD, GKD was associated with a higher likelihood and cost of admissions. GKD had consistently more admissions (mean excess annual number of admissions increasing from 5.2 in year 1 to 13.4 in year 7) and more costly admissions (mean excess annual cost increasing from $5,265 in year 1 to $12,993 in year 7). This gap in hospitalization likelihood and cost increased over time for both surgical and medical admission episodes, but not for all (immunological, cancer) causes of admissions. Conclusion: Understanding the nature and extent of differences in healthcare needs between GKD and other CKD will enable better secondary prevention and inform resource allocation decisions to reduce healthcare system pressures attributable to knowable causes.

Background: We describe a case of a 55-year-old shepherd with history of mycotic aneurysm presenting with a chronic aortic endovascular graft infection caused by Nocardia nova and a newly identified Variovorax sp which we named ‘Variovorax durovernensis’. This is the first case of this Variovorax sp. causing human pathology. This organism was identified with whole-genome sequencing as a new species of Variovorax, with ‘Durovernum’ (the Latin name for Canterbury) suggested at our patients request; an ancient town where they work as a shepherd. Case Report: Our patient presented with a ruptured left common iliac mycotic aneurysm with Campylobacter fetus isolated, requiring emergent endovascular stenting. Seven months post-discharge they re-presented with headache, weight loss and back pain. A half-body fluorodeoxyglucose positron emission tomography (FDG-PET) scan showed aorto-bi-iliac graft uptake in the left periureteric region. The infected graft was explanted and revascularisation obtained with autologous harvested veins. Results: Graft samples grew Nocardia nova 3/5 samples on day 5 of incubation and yellow colonies of a gram-negative on 3/5 samples after 7 days. Identification of Variovorax genus was obtained using the Bruker MALDI-TOF Biotyper (Bruker Daltonics, Germany). Variovorax Sp. DNA was sequenced using Genomic DNA (SQK-LSK109 kit) on GridION (Oxford Nanopore Technologies). Sequence data was filtered and polished with genome Minimap2 and Nanopolish v0.8.4. Epi2Me identified a Variovorax sp.; in silico genomic analysis and in vitro phenotypic testing confirmed it as a new species. Conclusion: As diagnostic capabilities improve unusual clinical isolates can be reliably identified. The Bruker MALDI-TOF allowed identification of Variovorax Sp. causing clinical disease in this setting. This new species was defined with whole-genome sequencing allowing identification and recognition in international repositories.This case highlights the importance of an open mind interpreting results from clinical samples as more atypical infections from the environmental microbiome may be isolated.

Background: In Cape Town, the under-5 mortality rate has plateaued to 20 per 1000 live births, with 60% of child deaths occurring out of hospital. The southern subdistrict has the largest paediatric population in Metro West and accounts for 31% of deaths. This study aimed to uncover the access barriers and facilitators underlying this high burden of out-of-hospital deaths. Methods: An exploratory mixed-methods case study design employed three data collection strategies: a quantitative survey with randomly sampled community members, semi-structured interviews with purposively sampled caregivers whose children presented critically ill or deceased (January 2017 – December 2020) and a nominal group technique (NGT) to build solution-oriented consensus among purposively sampled health workers, representing different levels of care in the local health system. Results: A total of 62 community members were surveyed, 11 semi-structured caregiver interviews were conducted, and 11 health workers participated in the NGT. Community members (74%) experienced barriers in accessing care. Knowledge of basic home care for common conditions was limited. Thematic analysis of interviews showed affordability, acceptability, and access, household and facility factor barriers. The NGT suggested improvement in community-based services, transport access and lengthening service hours would facilitate access. Conclusion: While multiple barriers to accessing care were identified, facilitators addressing these barriers were explored. Healthcare planners should examine the barriers within their geographic areas of responsibility to reduce child deaths. Contribution: This study uncovers community perspectives on childhood out-of-hospital deaths and makes consensus-based recommendations for improvement.

Abstract Background The evidence for the clinical utility of pharmacogenomic (PGx) testing is growing, and guidelines exist for the use of PGx testing to inform prescribing of 13 antidepressants. Although previous randomised controlled trials of PGx testing for antidepressant prescribing have shown an association with remission of depression in clinical psychiatric settings, few trials have focused on the primary care setting, where most antidepressant prescribing occurs. Methods The PRESIDE Trial is a stratified double-blinded randomised controlled superiority trial that aims to evaluate the impact of a PGx-informed antidepressant prescribing report (compared with standard prescribing using the Australian Therapeutic Guidelines) on depressive symptoms after 12 weeks, when delivered in primary care. Six hundred seventy-two patients aged 18–65 years of general practitioners (GPs) in Victoria with moderate to severe depressive symptoms, measured using the Patient Health Questionnaire-9 (PHQ-9), will be randomly allocated 1:1 to each arm using a computer-generated sequence. Participants and GPs will be blinded to the study arm. The primary outcome is a difference between arms in the change of depressive symptoms, measured using the PHQ-9 after 12 weeks. Secondary outcomes include a difference between the arms in change in PHQ-9 score at 4, 8 and 26 weeks, proportion in remission at 12 weeks, a change in side effect profile of antidepressant medications, adherence to antidepressant medications, change in quality of life and cost-effectiveness of the intervention. Discussion This trial will provide evidence as to whether PGx-informed antidepressant prescribing is clinically efficacious and cost-effective. It will inform national and international policy and guidelines about the use of PGx to select antidepressants for people with moderate to severe depressive symptoms presenting in primary care. Trial registration Australian and New Zealand Clinical Trial Registry ACTRN12621000181808. Registered on 22 February 2021.

Summary: Innate lymphoid cells (ILCs) are tissue-resident effector cells with roles in tissue homeostasis, protective immunity, and inflammatory disease. Group 3 ILCs (ILC3s) are classically defined by the master transcription factor RORγt. However, ILC3 can be further subdivided into subsets that share type 3 effector modules that exhibit significant ontological, transcriptional, phenotypic, and functional heterogeneity. Notably lymphoid tissue inducer (LTi)-like ILC3s mediate effector functions not typically associated with other RORγt-expressing lymphocytes, suggesting that additional transcription factors contribute to dictate ILC3 subset phenotypes. Here, we identify Bcl6 as a subset-defining transcription factor of LTi-like ILC3s in mice and humans. Deletion of Bcl6 results in dysregulation of the LTi-like ILC3 transcriptional program and markedly enhances expression of interleukin-17A (IL-17A) and IL-17F in LTi-like ILC3s in a manner in part dependent upon the commensal microbiota—and associated with worsened inflammation in a model of colitis. Together, these findings redefine our understanding of ILC3 subset biology.

ABSTRACT Despite the success of COVID-19 vaccines in preventing infection and/or severe disease, there has been an increase in SARS-CoV-2 infections in vaccinated individuals owing to the waning vaccine-derived immunity, and the emergence of new variants which encode escape mutations in Spike. Following breakthrough infection in vaccinated individuals, an increase in neutralization breadth has been observed in sera/plasma. However, how exposure to a heterologous Spike broadens the neutralizing response at the monoclonal antibody (mAb) level is not fully understood. Through isolation of 119 mAbs from three individuals receiving two doses of BNT162b2 vaccine before becoming Delta or Omicron/BA.1 infected, we show that serum breadth occurs due to the presence of somatically mutated mAbs with broad neutralization activity indicative of re-activation and maturation of B cells generated through previous COVID-19 vaccination. Isolated mAbs frequently show reduced neutralization of current circulating variants including BA.2.75.2, XBB, XBB.1.5, and BQ.1.1 confirming continuous selective pressure on Spike to evolve and evade neutralization. However, isolation of mAbs that display effective cross-neutralization against all variants indicates the presence of conserved epitopes on the receptor binding domain and a lesser extent the N-terminal domain. These findings have implications for the selection of Spike antigens for next-generation COVID-19 vaccines. IMPORTANCE With the emergence of SARS-CoV-2 viral variants, there has been an increase in infections in vaccinated individuals. Here, we isolated monoclonal antibodies (mAbs) from individuals experiencing a breakthrough infection (Delta or BA.1) to determine how exposure to a heterologous Spike broadens the neutralizing antibody response at the monoclonal level. All mAbs isolated had reactivity to the Spike of the vaccine and infection variant. While many mAbs showed reduced neutralization of current circulating variants, we identified mAbs with broad and potent neutralization of BA.2.75.2, XBB, XBB.1.5, and BQ.1.1 indicating the presence of conserved epitopes on Spike. These results indicate that variant-based vaccine boosters have the potential to broaden the vaccine response.

Microbial biofilm build-up in water distribution systems can pose a risk to human health and pipe material integrity. The impact is more devastating in space stations and to astronauts due to the isolation from necessary replacement parts and medical resources. As a result, there is a need for coatings to be implemented onto the inner region of the pipe to minimize the adherence and growth of biofilms. Lubricant-infused surfaces has been one such interesting material for anti-biofouling applications in which their slippery property promotes repellence to many liquids and thus prevents bacterial adherence. Textured and porous films are suitable substrate candidates to infuse and contain the lubricant. However, there is little investigation in utilizing a nanoparticulate thin film as the substrate material for lubricant infusion. A nanoparticulate film has high porosity within the structure which can promote greater lubricant infusion and retention. The implementation as a thin film structure aids to reduce material consumption and cost. In our study, we utilized a well-studied nanoporous thin film fabricated via layer-by-layer assembly of polycations and colloid silica and then calcination for greater stability. The film was further functionalized to promote fluorinated groups and improve affinity with a fluorinated lubricant. The pristine nanoporous film was characterized to determine its morphology, thickness, wettability, and porosity. The lubricant-infused film was then tested for its lubricant layer stability upon various washing conditions and its performance against bacterial biofilm adherence as a result of its slippery property. Overall, the modified silica nanoparticulate thin film demonstrated potential as a base substrate for lubricant-infused surface fabrication that repelled against ambient aqueous solvents and as an anti-biofouling coating that demonstrated low biofilm coverage and colony forming unit values. Further optimization to improve lubricant retention or incorporation of a secondary function can aid in developing better coatings for biofilm mitigation.

Abstract Introduction Randomised controlled trials have shown that steroids reduce the risk of dying in patients with severe Coronavirus disease 2019 (COVID-19), whilst many real-world studies have failed to replicate this result. We aim to investigate real-world effectiveness of steroids in severe COVID-19. Methods Clinical, demographic, and viral genome data extracted from electronic patient record (EPR) was analysed from all SARS-CoV-2 RNA positive patients admitted with severe COVID-19, defined by hypoxia at presentation, between March 13th 2020 and May 27th 2021. Steroid treatment was measured by the number of prescription-days with dexamethasone, hydrocortisone, prednisolone or methylprednisolone. The association between steroid > 3 days treatment and disease outcome was explored using multivariable cox proportional hazards models with adjustment for confounders (including age, gender, ethnicity, co-morbidities and SARS-CoV-2 variant). The outcome was in-hospital mortality. Results 1100 severe COVID-19 cases were identified having crude hospital mortality of 15.3%. 793/1100 (72.1%) individuals were treated with steroids and 513/1100 (46.6%) received steroid ≤ 3 days. From the multivariate model, steroid > 3 days was associated with decreased hazard of in-hospital mortality (HR: 0.47 (95% CI: 0.31–0.72)). Conclusion The protective effect of steroid treatment for severe COVID-19 reported in randomised clinical trials was replicated in this retrospective study of a large real-world cohort.

The epithelial protein Coxsackievirus Adenovirus Receptor (CAR) is a virus receptor but may have other functions. Here the authors show that deletion of CAR in mice leads to reduced house dust mite-induced lung inflammation, reduced neutrophil accumulation and alterations in airway remodelling.

Precise Doppler studies of extrasolar planets require fine-grained control of observational cadence, i.e., the timing of and spacing between observations. We present a novel framework for scheduling a set of Doppler campaigns with different cadence requirements at the W. M. Keck Observatory. For a set of observing programs and allocated nights on an instrument, our software optimizes the timing and ordering of ∼1000 observations within a given observing semester. We achieve a near-optimal solution in real-time using a hierarchical Integer Linear Programming framework. Our scheduling formulation optimizes over the roughly 10 ^3000 possible orderings. A top level optimization finds the most regular sequence of allocated nights by which to observe each host star in the request catalog based on a frequency specified in the request. A second optimization scheme minimizes the slews and downtime of the instrument. We have assessed our algorithms performance with simulated data and with the real suite of Doppler observations of the California Planet Search in 2023.

Whereas traditional histology and light microscopy require multiple steps of formalin fixation, paraffin embedding, and sectioning to generate images for pathologic diagnosis, Microscopy using Ultraviolet Surface Excitation (MUSE) operates through UV excitation on the cut surface of tissue, generating images of high resolution without the need to fix or section tissue and allowing for potential use for downstream molecular tests. Here, we present the first study of the use and suitability of MUSE microscopy for neuropathological samples. MUSE images were generated from surgical biopsy samples of primary and metastatic brain tumor biopsy samples (n = 27), and blinded assessments of diagnoses, tumor grades, and cellular features were compared to corresponding hematoxylin and eosin (H&E) images. A set of MUSE-treated samples subsequently underwent exome and targeted sequencing, and quality metrics were compared to those from fresh frozen specimens. Diagnostic accuracy was relatively high, and DNA and RNA integrity appeared to be preserved for this cohort. This suggests that MUSE may be a reliable method of generating high-quality diagnostic-grade histologic images for neuropathology on a rapid and sample-sparing basis and for subsequent molecular analysis of DNA and RNA.

Vaccines against the SARS-CoV-2 virus were authorized for use by the Food and Drug Administration (FDA) in the United States and have proven effective for the prevention of morbidity and death from COVID-19. Certain immunosuppressant medications prevent the development of protective immunity following COVID-19 vaccination. In December 2021, the FDA issued an emergency use authorization (EUA) for a monoclonal-antibody combination of tixagevimab and cilgavimab, under the brand name Evusheld, for pre-exposure prophylaxis (PrEP) against COVID-19 for individuals with moderate-to-severe immune compromise. While a 77% reduction in symptomatic COVID-19 was observed in the PROVENT study, the trial was conducted prior to emergence of the B.1.1.529 Omicron variant. We suspected reduced efficacy of PrEP against Omicron subvariants. We conducted a retrospective cohort study comparing the prevalence of symptomatic COVID-19 infections between 1 January 2022 and 1 July 2022 in eligible patients treated with PrEP versus untreated using a questionnaire administered with the REDCap survey tool. Responses from 235 participants were included in the final analysis, with 176 untreated respondents and 59 in the PrEP cohort. Symptomatic COVID-19 infections were reported in 50 (28.4%) untreated participants and only 9 (15.3%) of those who received PrEP (p = 0.0557; OR 0.4536; 95% CI 0.2046 to 0.9599). Only two participants were hospitalized for COVID-19 infection, both in the untreated cohort. The reduction in COVID-19 infections did not achieve statistical significance, indicating diminished efficacy against Omicron variants.

Prolonged eosinophilia is characteristic of trichinellosis. To determine the optimal eosinophil threshold for reflex Trichinella testing, we examined all 43 cases in Nunavik, Quebec, Canada, during 2009–2019. Using receiver operating characteristic analysis, we determined that eosinophil counts >0.8 × 109 cells/L should prompt consideration of trichinellosis and testing to rapidly identify potential outbreaks.

Abstract Background Urinary tract infections (UTI) caused by Escherichia coli and Enterococcus spp., which are frequently coisolated in polymicrobial UTI, cause morbidity among dogs and warrant antimicrobial therapy. Objectives To evaluate clinical features of dogs with polymicrobial E. coli and Enterococcal UTI. Animals Forty‐four client‐owned dogs with polymicrobial bacteriuria and groups of 100 client‐owned dogs with E. coli and Enterococcal monomicrobial bacteriuria. Methods Retrospective cohort study of medical records of dogs at a university teaching hospital from 2014 to 2019. Prevalence of recurrent UTI and isolate antimicrobial resistance were determined. Clinical outcomes of dogs with recurrent UTI from groups including cost and hospital visits were compared. Results Recurrent UTI was more prevalent (P = .05) in dogs with polymicrobial bacteriuria (57%, 95% confidence interval [95% CI]: 42%‐70%) compared to the Enterococcal monomicrobial group (40%, 95% CI: 31%‐50%). Escherichia coli from polymicrobial bacteriuria were more frequently resistant to doxycycline (P

Objective Although a high‐resolution computed tomography (HRCT) scan of the chest is the gold standard test for the detection of interstitial lung disease (ILD), there is no consensus among rheumatologists regarding the use of HRCT to screen for ILD in their patients with systemic sclerosis (SSc). The aims of this study were to describe the HRCT ordering practices at SSc centers in the United States and to determine which patient characteristics are associated with HRCT performance. Methods We performed a prospective cohort study of patients with SSc enrolled in the US‐based Collaborative National Quality and Efficacy Registry (CONQUER). We performed univariate logistic regression followed by multivariable logistic regression to determine which patient characteristics were associated with HRCT performance. Results Of the 356 patients with SSc enrolled in CONQUER, 286 (80.3%) underwent HRCT at some point during their disease course. On multivariable analyses, missing total lung capacity percent predicted (odds ratio [OR] 3.26, 95% confidence interval [CI]: 1.53‐7.41, P = 0.007) was positively associated with ever having undergone HRCT, whereas a positive anti‐centromere antibody (OR 0.27, 95% CI: 0.12‐0.61, P = 0.008) and missing forced vital capacity percent predicted (OR 0.29, 95% CI: 0.10‐0.80, P = 0.005) were negatively associated with ever having undergone HRCT. There was a trend toward a positive association between crackles on pulmonary exam and ever having undergone HRCT (OR 2.28, 95% CI: 0.97‐6.05, P = 0.058), although this relationship did not reach statistical significance. Conclusion The majority of patients with SSc enrolled in CONQUER underwent HRCT. A positive anti‐centromere antibody was the key clinical variable inversely associated with performance of HRCT.

Abstract Transferrin receptor (TFRC) is the major mediator for iron entry into a cell. Under excessive iron conditions, TFRC is expected to be reduced to lower iron uptake and toxicity. However, the mechanism whereby TFRC expression is maintained at high levels in iron‐enriched cancer cells and the contribution of TFRC to cancer development are enigmatic. Here the work shows TFRC is induced by adenomatous polyposis coli (APC) gene loss‐driven β‐catenin activation in colorectal cancer, whereas TFRC‐mediated intratumoral iron accumulation potentiates β‐catenin signaling by directly enhancing the activity of tankyrase. Disruption of TFRC leads to a reduction of colonic iron levels and iron‐dependent tankyrase activity, which caused stabilization of axis inhibition protein 2 (AXIN2) and subsequent repression of the β‐catenin/c‐Myc/E2F Transcription Factor 1/DNA polymerase delta1 (POLD1) axis. POLD1 knockdown, iron chelation, and TFRC disruption increase DNA replication stress, DNA damage response, apoptosis, and reduce colon tumor growth. Importantly, a combination of iron chelators and DNA damaging agents increases DNA damage response and reduces colon tumor cell growth. TFRC‐mediated iron import is at the center of a novel feed‐forward loop that facilitates colonic epithelial cell survival. This discovery may provide novel strategies for colorectal cancer therapy.

The ongoing SARS-CoV-2 pandemic demonstrates the utility of real-time sequence analysis in monitoring and surveillance of pathogens. However, cost-effective sequencing requires that samples be PCR amplified and multiplexed via barcoding onto a single flow cell, resulting in challenges with maximising and balancing coverage for each sample. To address this, we developed a real-time analysis pipeline to maximise flow cell performance and optimise sequencing time and costs for any amplicon based sequencing. We extended our nanopore analysis platform MinoTour to incorporate ARTIC network bioinformatics analysis pipelines. MinoTour predicts which samples will reach sufficient coverage for downstream analysis and runs the ARTIC networks Medaka pipeline once sufficient coverage has been reached. We show that stopping a viral sequencing run earlier, at the point that sufficient data has become available, has no negative effect on subsequent down-stream analysis. A separate tool, SwordFish, is used to automate adaptive sampling on Nanopore sequencers during the sequencing run. This enables normalisation of coverage both within (amplicons) and between samples (barcodes) on barcoded sequencing runs. We show that this process enriches under-represented samples and amplicons in a library as well as reducing the time taken to obtain complete genomes without affecting the consensus sequence.

Self-structural health monitoring (SHM) functionalities for fiber-reinforced polymer composites have become highly sought after to ensure the structural safety of newly advancing components in the automotive, civil, mechanical, and aerospace industries. This paper introduces a self-damage detection and memory (SDDM) hybrid composite material, where the structural carbon fiber tow is transformed into a piezoresistive sensor network, and the structural glass fiber operates as electrical insulation. In this study, SDDM specimens were fabricated, and tensile and impact tests were performed. The tensile tests of SDDM specimens find two distinct loading peaks: first where the carbon fiber fails, and second where the glass fiber fails. A linear correlation was observed between the carbon fiber resistance and composite strain up to a threshold, beyond which a sharp nonlinear increase in resistance occurred. The resistance then approached infinity, coinciding with the first loading peak and failure of the carbon fiber elements. This demonstrates the potential for a damage early warning threshold. Additionally, the effect of stitching the sensor tow in a zig-zag pattern over a large area was investigated using tailored fiber placement (TFP) of 1-loop, 3-loop, and 5-loop specimens. Tensile testing found that increasing the number of loops improved the sensor’s accuracy for strain sensing. Furthermore, impact tests were conducted, and as the impact energy progressively increased, the sensor resistance permanently increased. This illustrates a capability for self-memory of microdamage throughout the life cycle of the structure, potentially useful for predicting the remaining life of the composite.

The purpose of this manuscript is to describe the ways that preservice teachers, in their first mathematics education course, understood race in mathematics classrooms. Through a qualitative document analysis of course assignments, we identify three ways students wrote about race: using race-evasive maneuvers to avoid discussion of race in mathematics education, skimming past racial issues in ways that reduced their importance, and directly engaging with race in the active pursuit of racial competence. Our results suggest ways that critical mathematics topics can encourage students to begin this pursuit and underscore the need for intentionally antiracist-oriented mathematics teacher education.

Abstract Background Clinical metagenomics (CMg) has the potential to be translated from a research tool into routine service to improve antimicrobial treatment and infection control decisions. The SARS-CoV-2 pandemic provides added impetus to realise these benefits, given the increased risk of secondary infection and nosocomial transmission of multi-drug-resistant (MDR) pathogens linked with the expansion of critical care capacity. Methods CMg using nanopore sequencing was evaluated in a proof-of-concept study on 43 respiratory samples from 34 intubated patients across seven intensive care units (ICUs) over a 9-week period during the first COVID-19 pandemic wave. Results An 8-h CMg workflow was 92% sensitive (95% CI, 75–99%) and 82% specific (95% CI, 57–96%) for bacterial identification based on culture-positive and culture-negative samples, respectively. CMg sequencing reported the presence or absence of β-lactam-resistant genes carried by Enterobacterales that would modify the initial guideline-recommended antibiotics in every case. CMg was also 100% concordant with quantitative PCR for detecting Aspergillus fumigatus from 4 positive and 39 negative samples. Molecular typing using 24-h sequencing data identified an MDR-K. pneumoniae ST307 outbreak involving 4 patients and an MDR-C. striatum outbreak involving 14 patients across three ICUs. Conclusion CMg testing provides accurate pathogen detection and antibiotic resistance prediction in a same-day laboratory workflow, with assembled genomes available the next day for genomic surveillance. The provision of this technology in a service setting could fundamentally change the multi-disciplinary team approach to managing ICU infections. The potential to improve the initial targeted treatment and rapidly detect unsuspected outbreaks of MDR-pathogens justifies further expedited clinical assessment of CMg.

Background: Viral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings. Methods: We conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data collection period, followed by intervention periods comprising 8 weeks of ‘rapid’ (

More than 170 subspecies are listed as threatened or endangered under the US Endangered Species Act. Most of these subspecies were described decades ago on the basis of geographical variation in morphology using relatively primitive taxonomic methods. The US Fish and Wildlife Service defaults to subspecies descriptions by taxonomists working with specific groups of organisms, but there is no single definition of subspecies across plants and animals. Valid tests today usually entail molecular analyses of variation within and among populations, although there is no reason that behavioral, ecological or molecular characters could not be used, and include tests for significant differences between samples of the putative endangered subspecies and its nearest geographic relatives. We evaluated data gathered since subspecies listed under the ESA were described finding about one-third are valid (distinct evolutionary taxa), one-third are not, and one-third have not been tested. Therefore, it should not be assumed that because a subspecies occurs in a checklist, it is taxonomically valid. If the US Fish and Wildlife Service intends to continue listing subspecies, we suggest that they convene taxonomic experts representing various groups of organisms to provide a minimal set of criteria for a subspecies to be listed under the ESA.

Inflammatory bowel disease (IBD) is an idiopathic condition characterized by chronic relapsing inflammation in the intestine. While the precise etiology of IBD remains unknown, genetics, the gut microbiome, environmental factors, and the immune system have all been shown to contribute to the disease pathophysiology. In recent years, attention has shifted towards the role that innate lymphoid cells (ILCs) may play in the dysregulation of intestinal immunity observed in IBD. ILCs are a group of heterogenous immune cells which can be found at mucosal barriers. They act as critical mediators of the regulation of intestinal homeostasis and the orchestration of its inflammatory response. Despite helper-like type 1 ILCs (ILC1s) constituting a particularly rare ILC population in the intestine, recent work has suggested that an accumulation of intestinal ILC1s in individuals with IBD may act to exacerbate its pathology. In this review, we summarize existing knowledge on helper-like ILC1 plasticity and their classification in murine and human settings. Moreover, we discuss what is currently understood about the roles that ILC1s may play in the progression of IBD pathogenesis.

Background: The global death toll from coronavirus disease 2019 (COVID-19) has exceeded 2 million, and treatments to decrease mortality are needed urgently. Objectives: To examine the probabilities of a clinically meaningful reduction in mortality for remdesivir and systemic corticosteroids. Design, setting and participants: This was a probabilistic re-analysis of clinical trial data for corticosteroids and remdesivir in the treatment of hospitalized patients with COVID-19 using a Bayesian random effects meta-analytic approach. Studies were identified from existing meta-analyses performed by the World Health Organization. Main outcomes and measures: Posterior probabilities of an absolute decrease in mortality compared with control patients, by subgroups based on oxygen requirements, were calculated for corticosteroids and remdesivir. Probabilities of ≥1%, ≥2% and ≥5% absolute decrease in mortality were quantified. Results: For patients needing mechanical ventilation, the probability of ≥1% absolute decrease in mortality was 4% for remdesivir and 93% for corticosteroids. For patients needing supplemental oxygen without mechanical ventilation, the probability of ≥1% absolute decrease in mortality was 81% for remdesivir and 93% for dexamethasone. Finally, for patients who did not need oxygen support, the probability of ≥1% absolute decrease in mortality was 29% for remdesivir and 4% for dexamethasone. Conclusions and relevance: Using a Bayesian analytic approach, remdesivir had low probability of achieving a clinically meaningful reduction in mortality, except for patients needing supplemental oxygen without mechanical ventilation. Corticosteroids were more promising for patients needing oxygen support, especially mechanical ventilation. While awaiting more definitive studies, this probabilistic interpretation of the evidence will help to guide treatment decisions for clinicians, as well as guideline and policy makers.

Abstract Trazodone (TRZ) is a commonly prescribed antidepressant with significant off-label use for insomnia. A recent drug screening revealed that TRZ interferes with sterol biosynthesis, causing elevated levels of sterol precursor 7-dehydrocholesterol (7-DHC). Recognizing the well-documented, disruptive effect of 7-DHC on brain development, we designed a study to analyze TRZ effects during pregnancy. Utilizing an in vivo model and human biomaterial, our studies were designed to also account for drug interactions with maternal or offspring Dhcr7 genotype. In a maternal exposure model, we found that TRZ treatment increased 7-DHC and decreased desmosterol levels in brain tissue in newborn pups. We also observed interactions between Dhcr7 mutations and maternal TRZ exposure, giving rise to the most elevated toxic oxysterols in brains of Dhcr7 +/− pups with maternal TRZ exposure, independently of the maternal Dhcr7 genotype. Therefore, TRZ use during pregnancy might be a risk factor for in utero development of a neurodevelopmental disorder, especially when the unborn child is of DHCR7 +/− genotype. The effects of TRZ on 7-DHC was corroborated in human serum samples. We analyzed sterols and TRZ levels in individuals with TRZ prescriptions and found that circulating TRZ levels correlated highly with 7-DHC. The abundance of off-label use and high prescription rates of TRZ might represent a risk for the development of DHCR7 heterozygous fetuses. Thus, TRZ use during pregnancy is potentially a serious public health concern.

Acetylcholine (ACh) from neuronal and non-neuronal sources plays an important role in the regulation of immune responses and is associated with the development of several disease pathologies. We have previously demonstrated that group 2 innate lymphoid cell (ILC2)-derived ACh is required for optimal type 2 responses to parasitic infection and therefore sought to determine whether this also plays a role in allergic inflammation. RoraCre+ChatLoxP mice (in which ILC2s cannot synthesize ACh) were exposed to an allergenic extract of the fungus Alternaria alternata, and immune responses in the airways and lung tissues were analyzed. Airway neutrophilia and expression of the neutrophil chemoattractants CXCL1 and CXCL2 were enhanced 24 h after exposure, suggesting that ILC2-derived ACh plays a role in limiting excessive pulmonary neutrophilic inflammation. The effect of non-selective depletion of ACh was examined by intranasal administration of a stable parasite-secreted acetylcholinesterase. Depletion of airway ACh in this manner resulted in a more profound enhancement of neutrophilia and chemokine expression, suggesting multiple cellular sources for the release of ACh. In contrast, depletion of ACh inhibited Alternaria-induced activation of ILC2s, suppressing the expression of IL-5, IL-13, and subsequent eosinophilia. Depletion of ACh reduced macrophages with an alternatively activated M2 phenotype and an increase in M1 macrophage marker expression. These data suggest that ACh regulates allergic airway inflammation in several ways, enhancing ILC2-driven eosinophilia but suppressing neutrophilia through reduced chemokine expression.

Cardiovascular diseases (CVDs) are responsible for most pre-mature deaths worldwide, contributing significantly to the global burden of disease and its associated costs to individuals and healthcare systems. Obesity and associated metabolic inflammation underlie development of several major health conditions which act as direct risk factors for development of CVDs. Immune system responses contribute greatly to CVD development and progression, as well as disease resolution. Innate lymphoid cells (ILCs) are a family of helper-like and cytotoxic lymphocytes, typically enriched at barrier sites such as the skin, lung, and gastrointestinal tract. However, recent studies indicate that most solid organs and tissues are home to resident populations of ILCs - including those of the cardiovascular system. Despite their relative rarity, ILCs contribute to many important biological effects during health, whilst promoting inflammatory responses during tissue damage and disease. This mini review will discuss the evidence for pathological and protective roles of ILCs in CVD, and its associated risk factor, obesity.

ABSTRACT Numerous studies have shown that a prior SARS-CoV-2 infection can greatly enhance the antibody response to COVID-19 vaccination, with this so called “hybrid immunity” leading to greater neutralization breadth against SARS-CoV-2 variants of concern. However, little is known about how breakthrough infection (BTI) in COVID-19-vaccinated individuals will impact the magnitude and breadth of the neutralizing antibody response. Here, we compared neutralizing antibody responses between unvaccinated and COVID-19-double-vaccinated individuals (including both AZD1222 and BNT162b2 vaccinees) who have been infected with the Delta (B.1.617.2) variant. Rapid production of spike-reactive IgG was observed in the vaccinated group, providing evidence of effective vaccine priming. Overall, potent cross-neutralizing activity against current SARS-CoV-2 variants of concern was observed in the BTI group compared to the infection group, including neutralization of the Omicron (B.1.1.529) variant. This study provides important insights into population immunity where transmission levels remain high and in the context of new or emerging variants of concern. IMPORTANCE COVID-19 vaccines have been vital in controlling SARS-CoV-2 infections and reducing hospitalizations. However, breakthrough SARS-CoV-2 infections (BTI) occur in some vaccinated individuals. Here, we study how BTI impacts on the potency and the breadth of the neutralizing antibody response. We show that a Delta infection in COVID-19-vaccinated individuals provides potent neutralization against the current SARS-CoV-2 variants of concern, including the Omicron variant.

Objectives Nosocomial transmission of SARS-CoV-2 has been a significant cause of mortality in National Health Service (NHS) hospitals during the COVID-19 pandemic. The COG-UK Consortium Hospital-Onset COVID-19 Infections (COG-UK HOCI) study aims to evaluate whether the use of rapid whole-genome sequencing of SARS-CoV-2, supported by a novel probabilistic reporting methodology, can inform infection prevention and control (IPC) practice within NHS hospital settings.Design Multicentre, prospective, interventional, superiority study.Setting 14 participating NHS hospitals over winter–spring 2020/2021 in the UK.Participants Eligible patients must be admitted to hospital with first-confirmed SARS-CoV-2 PCR-positive test result >48 hour from time of admission, where COVID-19 diagnosis not suspected on admission. The projected sample size is 2380 patients.Intervention The intervention is the return of a sequence report, within 48 hours in one phase (rapid local lab processing) and within 5–10 days in a second phase (mimicking central lab), comparing the viral genome from an eligible study participant with others within and outside the hospital site.Primary and secondary outcome measures The primary outcomes are incidence of Public Health England (PHE)/IPC-defined SARS-CoV-2 hospital-acquired infection during the baseline and two interventional phases, and proportion of hospital-onset cases with genomic evidence of transmission linkage following implementation of the intervention where such linkage was not suspected by initial IPC investigation. Secondary outcomes include incidence of hospital outbreaks, with and without sequencing data; actual and desirable changes to IPC actions; periods of healthcare worker (HCW) absence. Health economic analysis will be conducted to determine cost benefit of the intervention. A process evaluation using qualitative interviews with HCWs will be conducted alongside the study.Trial registration number ISRCTN50212645. Pre-results stage. This manuscript is based on protocol V.6.0. 2 September 2021.

BackgroundHealth care workers (HCW), particularly immigrants and ethnic minorities are at increased risk for SARS-CoV-2 infection. Outcomes during a COVID-19 associated hospitalization are not well described among HCW. We aimed to describe the characteristics of HCW admitted with COVID-19 including immigrant status and ethnicity and the associated risk factors for Intensive Care unit (ICU) admission and death.MethodsAdults with laboratory-confirmed community-acquired COVID-19 hospitalized from March 1 to June 30, 2020, at four tertiary-care hospitals in Montréal, Canada were included. Demographics, comorbidities, occupation, immigration status, country of birth, ethnicity, workplace exposures, and hospital outcomes (ICU admission and death) were obtained through a chart review and phone survey. A Fine and Gray competing risk proportional hazards model was used to estimate the risk of ICU admission among HCW stratified by immigrant status and region of birth.ResultsAmong 1104 included persons, 150 (14%) were HCW, with a phone survey participation rate of 68%. HCWs were younger (50 vs 64 years; pConclusionImmigrant HCW were particularly exposed to COVID-19 infection in the first wave of the pandemic in Quebec. Despite being young and healthy, one third of all HCW required ICU admission, highlighting the importance of preventing workplace transmission through strong infection prevention and control measures, including high COVID-19 vaccination coverage.

The size and complexity of modern astronomical surveys has grown to the point where, in many cases, traditional human scheduling of observations are tedious at best and impractical at worst. Automated scheduling algorithms present an opportunity to save human effort and increase scientific productivity. A common scheduling challenge involves determining the optimal ordering of a set of targets over a night subject to timing constraints and time-dependent slew overheads. We present a solution to the “traveling telescope problem” that uses mixed-integer linear programming. This algorithm is fast enough to enable dynamic schedule generation in many astronomical contexts. It can determine the optimal solution for 100 observations within 10 minutes on a modern workstation, reducing slew overheads by a factor of 5 compared to random ordering. We also provide a heuristic method that can return a near-optimal solution at significantly reduced computational cost. As a case study, we explore our algorithm’s suitability to automatic schedule generation for Doppler planet searches.

Summary: We identify amino acid variants within dominant SARS-CoV-2 T cell epitopes by interrogating global sequence data. Several variants within nucleocapsid and ORF3a epitopes have arisen independently in multiple lineages and result in loss of recognition by epitope-specific T cells assessed by IFN-γ and cytotoxic killing assays. Complete loss of T cell responsiveness was seen due to Q213K in the A∗01:01-restricted CD8+ ORF3a epitope FTSDYYQLY207-215; due to P13L, P13S, and P13T in the B∗27:05-restricted CD8+ nucleocapsid epitope QRNAPRITF9-17; and due to T362I and P365S in the A∗03:01/A∗11:01-restricted CD8+ nucleocapsid epitope KTFPPTEPK361-369. CD8+ T cell lines unable to recognize variant epitopes have diverse T cell receptor repertoires. These data demonstrate the potential for T cell evasion and highlight the need for ongoing surveillance for variants capable of escaping T cell as well as humoral immunity.

Chronic kidney disease (CKD) is one of the most common chronic diseases in the western world. In Australia, around 1.7 million Australians aged 18 years and over (about one in ten) have indicators of CKD, and 1.8 million hospitalisations were associated with CKD in 2017–18. There is currently very little understanding of the impact of CKD on health service utilisation and costs. Understanding the disease pathways of CKD and its effects on service utilisation and patient outcomes is essential to predicting the course of the disease in the future, its effects on health services utilisation and capacity to better manage the burden of premature deaths or the need for dialysis that results from CKD. We describe the establishment of a data linkage framework to study hospital admissions of CKD patients in the public renal services in the Australian state of Queensland, and its potential to advance understanding of their course and outcomes. Seven years of retrospective data (2011–2018) on hospital-based health services utilisation were provided by Queensland Health for all 7,341 patients who enrolled in the CKD.QLD Registry up to Jan 2019. The data were supplied from three datasets: the Queensland Hospital Admitted Patient Data Collection, the Queensland Registrar General deaths, and the Activity Based Funding Model Output data. In addition, data were supplied from two cohorts of de-identified patients admitted to hospital in the same interval (22,023 patients each), who were not in the CKD.QLD Registry, the first with CKD and the second without CKD as indicated by International Classification of Diseases and Related Health Problems, Tenth Revision, Australian Modification. The comprehensive and multifaceted data via the data linkage will enable us to identify opportunities for efficiencies in management of patients with CKD and for interventions that improve their outcomes.

Innate lymphoid cells (ILC) play a significant role in the intestinal immune response and T-bet+ CD127+ group 1 cells (ILC1) have been linked to the pathogenesis of human inflammatory bowel disease (IBD). However, the functional importance of ILC1 in the context of an intact adaptive immune response has been controversial. In this report we demonstrate that induced depletion of T-bet using a Rosa26-Cre-ERT2 model resulted in the loss of intestinal ILC1, pointing to a post-developmental requirement of T-bet expression for these cells. In contrast, neither colonic lamina propria (cLP) ILC2 nor cLP ILC3 abundance were altered upon induced deletion of T-bet. Mechanistically, we report that STAT1 or STAT4 are not required for intestinal ILC1 development and maintenance. Mice with induced deletion of T-bet and subsequent loss of ILC1 were protected from the induction of severe colitis in vivo. Hence, this study provides support for the clinical development of an IBD treatment based on ILC1 depletion via targeting T-bet or its downstream transcriptional targets.

Summary: Background: Lateral flow devices (LFDs) for rapid antigen testing are set to become a cornerstone of SARS-CoV-2 mass community testing, although their reduced sensitivity compared with PCR has raised questions of how well they identify infectious cases. Understanding their capabilities and limitations is, therefore, essential for successful implementation. We evaluated six commercial LFDs and assessed their correlation with infectious virus culture and PCR cycle threshold (Ct) values. Methods: In a single-centre, laboratory evaluation study, we did a head-to-head comparison of six LFDs commercially available in the UK: Innova Rapid SARS-CoV-2 Antigen Test, Spring Healthcare SARS-CoV-2 Antigen Rapid Test Cassette, E25Bio Rapid Diagnostic Test, Encode SARS-CoV-2 Antigen Rapid Test Device, SureScreen COVID-19 Rapid Antigen Test Cassette, and SureScreen COVID-19 Rapid Fluorescence Antigen Test. We estimated the specificities and sensitivities of the LFDs using stored naso-oropharyngeal swabs collected at St Thomas' Hospital (London, UK) for routine diagnostic SARS-CoV-2 testing by real-time RT-PCR (RT-rtPCR). Swabs were from inpatients and outpatients from all departments of St Thomas' Hospital, and from health-care staff (all departments) and their household contacts. SARS-CoV-2-negative swabs from the same population (confirmed by RT-rtPCR) were used for comparative specificity determinations. All samples were collected between March 23 and Oct 27, 2020. We determined the limit of detection (LOD) for each test using viral plaque-forming units (PFUs) and viral RNA copy numbers of laboratory-grown SARS-CoV-2. Additionally, LFDs were selected to assess the correlation of antigen test result with RT-rtPCR Ct values and positive viral culture in Vero E6 cells. This analysis included longitudinal swabs from five infected inpatients with varying disease severities. Furthermore, the sensitivities of available LFDs were assessed in swabs (n=23; collected from Dec 4, 2020, to Jan 12, 2021) confirmed to be positive (RT-rtPCR and whole-genome sequencing) for the B.1.1.7 variant, which was the dominant genotype in the UK at the time of study completion. Findings: All LFDs showed high specificity (≥98·0%), except for the E25Bio test (86·0% [95% CI 77·9–99·9]), and most tests reliably detected 50 PFU/test (equivalent SARS-CoV-2 N gene Ct value of 23·7, or RNA copy number of 3 × 106/mL). Sensitivities of the LFDs on clinical samples ranged from 65·0% (55·2–73·6) to 89·0% (81·4–93·8). These sensitivities increased to greater than 90% for samples with Ct values of lower than 25 for all tests except the SureScreen fluorescence (SureScreen-F) test. Positive virus culture was identified in 57 (40·4%) of 141 samples; 54 (94·7%) of the positive cultures were from swabs with Ct values lower than 25. Among the three LFDs selected for detailed comparisons (the tests with highest sensitivity [Innova], highest specificity [Encode], and alternative technology [SureScreen-F]), sensitivity of the LFDs increased to at least 94·7% when only including samples with detected viral growth. Longitudinal studies of RT-rtPCR-positive samples (tested with Innova, Encode, and both SureScreen-F and the SureScreen visual [SureScreen-V] test) showed that most of the tests identified all infectious samples as positive. Test performance (assessed for Innova and SureScreen-V) was not affected when reassessed on swabs positive for the UK variant B.1.1.7. Interpretation: In this comprehensive comparison of antigen LFDs and virus infectivity, we found a clear relationship between Ct values, quantitative culture of infectious virus, and antigen LFD positivity in clinical samples. Our data support regular testing of target groups with LFDs to supplement the current PCR testing capacity, which would help to rapidly identify infected individuals in situations in which they would otherwise go undetected. Funding: King's Together Rapid COVID-19, Medical Research Council, Wellcome Trust, Huo Family Foundation, UK Department of Health, National Institute for Health Research Comprehensive Biomedical Research Centre.

Virulent strains of Salmonella enterica subsp. enterica serovar Enteritidis (SE) harbored by poultry can cause disease in poultry flocks and potentially result in human foodborne illness. Two broiler flocks grown a year apart on the same premises experienced mortality throughout the growing period due to septicemic disease caused by SE. Gross lesions predominantly consisted of polyserositis followed by yolk sacculitis, arthritis, osteomyelitis, and spondylitis. Tissues with lesions were cultured yielding 59 SE isolates. These were genotyped by Rep-PCR followed by whole-genome sequencing (WGS) of 15 isolates which were clonal. The strain, SE_TAU19, was further characterized for antimicrobial susceptibility and virulence in a broiler embryo lethality assay. SE_TAU19 was resistant to nalidixic acid and sulfadimethoxine and was virulent to embryos with 100% mortality of all challenged broiler embryos within 3.5 days. Screening the SE_TAU19 whole-genome sequence revealed seven antimicrobial resistance (AMR) genes, 120 virulence genes, and two IncF plasmid replicons corresponding to a single, serovar-specific pSEV virulence plasmid. The pef, spv, and rck virulence genes localized to the plasmid sequence assembly. We report phenotypic and genomic features of a virulent SE strain from persistently infected broiler flocks and present a workflow for SE characterization from isolate collection to genome assembly and sequence analysis. Further SE surveillance and investigation of SE virulence in broiler chickens is warranted.

Summary: We report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike ΔH69/V70 in multiple independent lineages, often occurring after acquisition of receptor binding motif replacements such as N439K and Y453F, known to increase binding affinity to the ACE2 receptor and confer antibody escape. In vitro, we show that, although ΔH69/V70 itself is not an antibody evasion mechanism, it increases infectivity associated with enhanced incorporation of cleaved spike into virions. ΔH69/V70 is able to partially rescue infectivity of spike proteins that have acquired N439K and Y453F escape mutations by increased spike incorporation. In addition, replacement of the H69 and V70 residues in the Alpha variant B.1.1.7 spike (where ΔH69/V70 occurs naturally) impairs spike incorporation and entry efficiency of the B.1.1.7 spike pseudotyped virus. Alpha variant B.1.1.7 spike mediates faster kinetics of cell-cell fusion than wild-type Wuhan-1 D614G, dependent on ΔH69/V70. Therefore, as ΔH69/V70 compensates for immune escape mutations that impair infectivity, continued surveillance for deletions with functional effects is warranted.