Recombination events are concentrated in the spike protein region of Betacoronaviruses.

The Betacoronaviruses comprise multiple subgenera whose members have been implicated in human disease. As with SARS, MERS and now SARS-CoV-2, the origin and emergence of new variants are often attributed to events of recombination that alter host tropism or disease severity. In most cases, recombination has been detected by searches for excessively similar genomic regions in divergent strains; however, such analyses are complicated by the high mutation rates of RNA viruses, which can produce sequence similarities in distant strains by convergent mutations. By applying a genome-wide approach that examines the source of individual polymorphisms and that can be tested against null models in which recombination is absent and homoplasies can arise only by convergent mutations, we examine the extent and limits of recombination in Betacoronaviruses. We find that recombination accounts for nearly 40% of the polymorphisms circulating in populations and that gene exchange occurs almost exclusively among strains belonging to the same subgenus. Although experimental studies have shown that recombinational exchanges occur at random along the coronaviral genome, in nature, they are vastly overrepresented in regions controlling viral interaction with host cells.

Discriminating arboviral species.

Mosquito-borne arboviruses, including a diverse array of alphaviruses and flaviviruses, lead to hundreds of millions of human infections each year. Current methods for species-level classification of arboviruses adhere to guidelines prescribed by the International Committee on Taxonomy of Viruses (ICTV), and generally apply a polyphasic approach that might include information about viral vectors, hosts, geographical distribution, antigenicity, levels of DNA similarity, disease association and/or ecological characteristics. However, there is substantial variation in the criteria used to define viral species, which can lead to the establishment of artificial boundaries between species and inconsistencies when inferring their relatedness, variation and evolutionary history. In this study, we apply a single, uniform principle - that underlying the Biological Species Concept (BSC) - to define biological species of arboviruses based on recombination between genomes. Given that few recombination events have been documented in arboviruses, we investigate the incidence of recombination within and among major arboviral groups using an approach based on the ratio of homoplastic sites (recombinant alleles) to non-homoplastic sites (vertically transmitted alleles). This approach supports many ICTV-designations but also recognizes several cases in which a named species comprises multiple biological species. These findings demonstrate that this metric may be applied to all lifeforms, including viruses, and lead to more consistent and accurate delineation of viral species.

Oral or Topical Exposure to Glyphosate in Herbicide Formulation Impacts the Gut Microbiota and Survival Rates of Honey Bees.

Honey bees are important agricultural pollinators that rely on a specific gut microbiota for the regulation of their immune system and defense against pathogens. Environmental stressors that affect the bee gut microbial community, such as antibiotics and glyphosate, can indirectly compromise bee health. Most of the experiments demonstrating these effects have been done under laboratory conditions with pure chemicals. Here, we investigated the oral and topical effects of various concentrations of glyphosate in a herbicide formulation on the honey bee gut microbiota and health under laboratory and field conditions. Under all of these conditions, the formulation, dissolved in sucrose syrup or water, affected the abundance of beneficial bacteria in the bee gut in a dose-dependent way. Mark-recapture experiments also demonstrated that bees exposed to the formulation were more likely to disappear from the colony, once reintroduced after exposure. Although no visible effects were observed for hives exposed to the formulation in field experiments, challenge trials with the pathogen Serratia marcescens, performed under laboratory conditions, revealed that bees from hives exposed to the formulation exhibited increased mortality compared with bees from control hives. In the field experiments, glyphosate was detected in honey collected from exposed hives, showing that worker bees transfer xenobiotics to the hive, thereby extending exposure and increasing the chances of exposure to recently emerged bees. These findings show that different routes of exposure to glyphosate-based herbicide can affect honey bees and their gut microbiota.IMPORTANCE The honey bee gut microbial community plays a vital role in immune response and defense against opportunistic pathogens. Environmental stressors, such as the herbicide glyphosate, may affect the gut microbiota, with negative consequences for bee health. Glyphosate is usually sprayed in the field mixed with adjuvants, which enhance herbicidal activity. These adjuvants may also enhance undesired effects in nontargeted organisms. This seems to be the case for glyphosate-based herbicide on honey bees. As we show in this study, oral exposure to either pure glyphosate or glyphosate in a commercial herbicide formulation perturbs the gut microbiota of honey bees, and topical exposure to the formulation also has a direct effect on honey bee health, increasing mortality in a dose-dependent way and leaving surviving bees with a perturbed microbiota. Understanding the effects of herbicide formulations on honey bees may help to protect these important agricultural pollinators.

Eating disorders and COVID-19 - different or just more?

BACKGROUND: COVID-19 saw an increase in child mental health presentations internationally. Clinicians analogised the exponential increase in anorexia nervosa to a 'tsunami' or 'outbreak', raising parallel concerns regarding medical and psychological risks (Marsh in The Guardian, 2021; Leask in NZ Herald, 2021; Monteleone et al. in Eat Weight Disord 26(8):2443-2452, 2021) . It is unclear whether Ireland emulated this picture of increased referrals with increased medical compromise. AIMS: This paper examines both rates and clinical profiles of child eating disorder presentations in the Republic of Ireland (ROI), across different clinical settings. METHODS: Following ethical approval, retrospective chart reviews were conducted in a community eating disorder service and in two paediatric hospital settings. The time frame of the different studies ranged from January 2016 to December 2022. RESULTS: Community eating disorder services saw significantly higher referral rates post COVID-19 (3.78/month vs. 2.31/month, p = 0.02), with a shorter duration of illness (4.8 months vs. 7.4 months, p = 0.001), but no significant difference in ideal body weight % (IBW%) at referral (85.32% vs. 83.7%, p = 0.1). Both paediatric hospitals witnessed significantly increased referrals post-COVID-19 (hospital 1; 4.38/month vs. 1.93/month, p = 0.0001; hospital 2; 2.8/month vs. 0.92/month, p < 0.0001), but no significant difference in IBW% at assessment (hospital 1; 82.7% vs. 81.39%, p = 0.673; hospital 2; 81.5% vs. 83%, p = 0.563). There was no significant difference in clinical profile, management, or duration of hospital stay. CONCLUSIONS: This study supports the growing consensus of a pandemic specific increase in eating disorder referrals to both medical and psychiatry services. However, there was little to indicate a change in clinical profile or severity. Ongoing monitoring of referrals is necessary to ensure adequate service availability and expertise.

Using display technologies to identify macrocyclic peptide antibiotics.

Antibiotic resistant bacterial infections are now a leading cause of global mortality. While drug resistance continues to spread, the clinical antibiotic pipeline has become bare. This discord has focused attention on developing new strategies for antimicrobial discovery. Natural macrocyclic peptide-based products have provided novel antibiotics and antibiotic scaffolds targeting several essential bacterial cell envelope processes, but discovery of such natural products remains a slow and inefficient process. Synthetic strategies employing peptide display technologies can quickly screen large libraries of macrocyclic sequences for specific target binding and general antibacterial potential providing alternative approaches for new antibiotic discovery. Here we review cell envelope processes that can be targeted with macrocyclic peptide therapeutics, outline important macrocyclic peptide display technologies, and discuss future strategies for both library design and screening.

Generation of Synthetic Acinetobacter baumannii-Specific Nanobodies.

The bacterial pathogen Acinetobacter baumannii is a leading cause of drug-resistant infections. Here, we investigated the potential of developing nanobodies that can recognize A. baumannii over other Gram-negative bacteria. Through generation and panning of a synthetic nanobody library, we identified several potential lead candidates. We demonstrate how incorporation of next-generation sequencing analysis can aid in the selection of lead candidate nanobodies. Using monoclonal phage display, we validated the binding of lead nanobodies to A. baumannii. Subsequent purification and biochemical characterization revealed one particularly robust nanobody that specifically bound select A. baumannii strains compared to other common drug-resistant pathogens. These findings support the potential for nanobodies to selectively target A. baumannii and the identification of lead candidates for future investigation.

Adapting antibacterial display to identify serum-active macrocyclic peptide antibiotics.

The lack of available treatments for many antimicrobial-resistant infections highlights the critical need for antibiotic discovery innovation. Peptides are an underappreciated antibiotic scaffold because they often suffer from proteolytic instability and toxicity toward human cells, making in vivo use challenging. To investigate sequence factors related to serum activity, we adapt an antibacterial display technology to screen a library of peptide macrocycles for antibacterial potential directly in human serum. We identify dozens of new macrocyclic peptide antibiotic sequences and find that serum activity within our library is influenced by peptide length, cationic charge, and the number of disulfide bonds present. Interestingly, an optimized version of our most active lead peptide permeates the outer membrane of Gram-negative bacteria without strong inner-membrane disruption and kills bacteria slowly while causing cell elongation. This contrasts with traditional cationic antimicrobial peptides, which kill rapidly via lysis of both bacterial membranes. Notably, this optimized variant is not toxic to mammalian cells and retains its function in vivo, suggesting therapeutic promise. Our results support the use of more physiologically relevant conditions when screening peptides for antimicrobial activity which retain in vivo functionality.

Adapting antibacterial display to identify serum active macrocyclic peptide antibiotics.

The lack of available treatments for many antimicrobial resistant infections highlights the critical need for antibiotic discovery innovation. Peptides are an underappreciated antibiotic scaffold because they often suffer from proteolytic instability and toxicity towards human cells, making in vivo use challenging. To investigate sequence factors related to serum activity, we adapt an antibacterial display technology to screen a library of peptide macrocycles for antibacterial potential directly in human serum. We identify dozens of new macrocyclic peptide antibiotic sequences and find that serum activity within our library is influenced by peptide length, cationic charge, and the number of disulfide bonds present. Interestingly, an optimized version of our most active lead peptide permeates the outer membrane of gram-negative bacteria without strong inner membrane disruption and kills bacteria slowly while causing cell elongation. This contrasts with traditional cationic antimicrobial peptides, which kill rapidly via lysis of both bacterial membranes. Notably, this optimized variant is not toxic to mammalian cells and retains its function in vivo , suggesting therapeutic promise. Our results support the use of more physiologically relevant conditions when screening peptides for antimicrobial activity which retain in vivo functionality. Significance: Traditional methods of natural antibiotic discovery are low throughput and cannot keep pace with the development of antimicrobial resistance. Synthetic peptide display technologies offer a high-throughput means of screening drug candidates, but rarely consider functionality beyond simple target binding and do not consider retention of function in vivo . Here, we adapt a function-based, antibacterial display technology to screen a large library of peptide macrocycles directly for bacterial growth inhibition in human serum. This screen identifies an optimized non-toxic macrocyclic peptide antibiotic retaining in vivo function, suggesting this advancement could increase clinical antibiotic discovery efficiency.

Studies in haemoglobin E beta-thalassaemia.

Haemoglobin E beta-thalassaemia is the commonest form of severe thalassaemia in many Asian countries, but little is known about its natural history, the reasons for its clinical diversity, or its optimal management. Despite its frequency, haemoglobin E beta-thalassaemia is often managed in an ill-defined and haphazard way, usually by demand transfusion. We studied a cohort of Sri Lankan patients with haemoglobin E beta-thalassaemia over 5 years, and identified several genetic and environmental factors possibly contributing to the phenotypic diversity of the disorder. These included modifiers of haemoglobin F production, malaria and age-related changes in adaptation to anaemia. Our findings suggest that in many patients, haemoglobin E beta-thalassaemia can be managed without transfusion, even with low haemoglobin levels. Age-related changes in the pattern of adaptation to anaemia suggest that more cost-effective approaches to management should be explored.

Southeast Asian ovalocytosis and pregnancy in a malaria-endemic region of Papua New Guinea.

The band 3 deletion for southeast Asian ovalocytosis (SAO) occurs commonly in southeast Asia and the western Pacific. Southeast Asian ovalocytosis is associated with protection against cerebral malaria in children and therefore could reduce sequestration of erythrocytes parasitized by Plasmodium falciparum in the brain microvasculature. Sequestration of parasitized erythrocytes in the placenta accounts for much of the pathology of malaria during pregnancy. Therefore, we investigated the effect of SAO on malaria during pregnancy in the malaria-hyperendemic north coastal region of Papua New Guinea. The frequency of SAO in 927 women attending hospital for delivery was 8.7% (95% confidence interval = 6.9-10.5). Markers of fertility, the frequency of miscarriages and stillbirths, maternal anemia, placental and peripheral malaria at delivery, and birth weight were similar in women with and without SAO. In summary, although we can not exclude an interaction between SAO and malaria during pregnancy, we found no evidence that it provided a clinical benefit in this population.

Field dependence and stimulus complexity in a figure copying task.

Field dependence is often associated with studies of cognitive style from Witkin's laboratory but Piaget also considered the concept a fundamental factor in the development of visuoperceptual analysis. Assessment has traditionally relied on two measures, the Rod-and-Frame Test and the Embedded Figures Test. A new task was developed, based on the Rod-and-Frame Test, in which a target stimulus is drawn within a misleading frame. Misleading frames significantly influenced the orientation of drawings created by 36 kindergartners in Exp. 1, and the drawing of more complex stimulus figures was influenced by the frames for a group of 65 adults in Exp. 2. Field-dependent behavior is related to the complexity of the task and to age. The correlation of scores on the Embedded Figures Test with performance on this task was low for both groups.

Emerging insights in the management of hemoglobin E beta thalassemia.

Globally, hemoglobin (Hb) E beta thalassemia accounts for approximately half the severe forms of beta thalassemia. Because of its wide clinical diversity and the ability of patients with this condition to adapt unusually well to low hemoglobin levels, the management of Hb E beta thalassemia, particularly the decision to instigate regular blood transfusion, is particularly difficult. Here, we present a summary of our work in patients with this condition, which attempts to define clinical, adaptive, and genetic factors of possible value in determining the early management of this condition.

The acute phase response in children with mild and severe malaria in Papua New Guinea.

The production of acute phase proteins during infection is an important part of innate immunity and limits inflammation. However, little is known of the acute phase response in malaria. We measured acute phase proteins in plasma in children attending clinics and admitted to hospital with acute malaria in Papua New Guinea. Plasma ferritin concentration increased progressively with disease severity with markedly elevated levels in the most severely ill children. Plasma ferritin was >500 ng/ml in 7/99 (7.1%) outpatients with uncomplicated malaria, 22/100 (22.0%) hospital non-severe cases, 64/175 (36.6%) severe malaria cases who survived and 7/9 (77.8%) severe malaria deaths (P<0.001). The greatest concentration of ferritin (3561 ng/ml) was observed in a child who died. By contrast, C-reactive protein concentration was markedly increased in 153 children with uncomplicated malaria [median 203 (interquartile range 51-365) microg/ml] but, surprisingly, was only moderately increased in 135 children with one or more severe manifestations of malaria [47 (17-97) microg/ml; P<0.001] and in 6 children who died [41 (22-280) microg/ml]. Excessive free-radical damage resulting from a combination of iron-induced oxidant stress and reduced levels of C-reactive protein may be an important pathological mechanism in severe malaria and amenable to therapeutic intervention.

Age-related changes in adaptation to severe anemia in childhood in developing countries.

Severe forms of anemia in children in the developing countries may be characterized by different clinical manifestations at particular stages of development. Whether this reflects developmental changes in adaptation to anemia or other mechanisms is not clear. The pattern of adaptation to anemia has been assessed in 110 individuals with hemoglobin (Hb) E beta-thalassemia, one of the commonest forms of inherited anemia in Asia. It has been found that age and Hb levels are independent variables with respect to erythropoietin response and that there is a decline in the latter at a similar degree of anemia during development. To determine whether this finding is applicable to anemia due to other causes, a similar study has been carried out on 279 children with severe anemia due to Plasmodium falciparum malaria; the results were similar to those in the patients with thalassemia. These observations may have important implications both for the better understanding of the pathophysiology of profound anemia in early life and for its more logical and cost-effective management.

A human complement receptor 1 polymorphism that reduces Plasmodium falciparum rosetting confers protection against severe malaria.

Parasitized red blood cells (RBCs) from children suffering from severe malaria often adhere to complement receptor 1 (CR1) on uninfected RBCs to form clumps of cells known as "rosettes." Despite a well documented association between rosetting and severe malaria, it is controversial whether rosetting is a cause or a correlate of parasite virulence. CR1-deficient RBC show greatly reduced rosetting; therefore, we hypothesized that, if rosetting is a direct cause of malaria pathology, CR1-deficient individuals should be protected against severe disease. In this study, we show that RBC CR1 deficiency occurs in up to 80% of healthy individuals from the malaria-endemic regions of Papua New Guinea. This RBC CR1 deficiency is associated with polymorphisms in the CR1 gene and, unexpectedly, with alpha-thalassemia, a common genetic disorder in Melanesian populations. Analysis of a case-control study demonstrated that the CR1 polymorphisms and alpha-thalassemia independently confer protection against severe malaria. We have therefore identified CR1 as a new malaria resistance gene and provided compelling evidence that rosetting is an important parasite virulence phenotype that should be a target for drug and vaccine development.