Optimising time-limited non-pharmaceutical interventions for COVID-19 outbreak control

Retrospective analyses of the non-pharmaceutical interventions (NPIs) used to combat the ongoing COVID-19 outbreak have highlighted the potential of optimizing interventions. These optimal interventions allow policymakers to manage NPIs to minimize the epidemiological and human health impacts of both COVID-19 and the intervention itself. Here, we use a susceptible-infectious-recovered (SIR) mathematical model to explore the feasibility of optimizing the duration, magnitude and trigger point of five different NPI scenarios to minimize the peak prevalence or the attack rate of a simulated UK COVID-19 outbreak. An optimal parameter space to minimize the peak prevalence or the attack rate was identified for each intervention scenario, with each scenario differing with regard to how reductions to transmission were modelled. However, we show that these optimal interventions are fragile, sensitive to epidemiological uncertainty and prone to implementation error. We highlight the use of robust, but suboptimal interventions as an alternative, with these interventions capable of mitigating the peak prevalence or the attack rate over a broader, more achievable parameter space, but being less efficacious than theoretically optimal interventions. This work provides an illustrative example of the concept of intervention optimization across a range of different NPI strategies. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'

Micro- and macroparasite species richness in birds:The role of host life history and ecology

Identifying the factors shaping variation in parasite diversity among host species is crucial to understand wildlife diseases. Although micro‐ and macroparasites may exert different selective pressures on their hosts, studies investigating the determinants of parasite species richness in animals have rarely considered this divide. Here, we investigated the role of host life history and ecology in explaining the species richness of helminths (macroparasites) and haemosporidians (microparasites) in birds world‐wide. We collated data from multiple global datasets on diverse bird traits (longevity, body mass, coloniality, migration distance/tendency, geographic range size and dietary and habitat breadths) and the species richness of their helminth and haemosporidian parasites. We tested predictors of helminth and haemosporidian parasite richness using phylogenetic generalized linear mixed models in a Bayesian framework. We found that, after controlling for research effort and host phylogeny, the richness of helminths, but not of haemosporidians, increased with host longevity, range size, migration distance and dietary breadth. Overall, these correlates were also important across different helminth groups (acanthocephalans, cestodes, nematodes and trematodes), and two additional ones (body mass, coloniality) emerged as important for cestodes and acanthocephalans. We propose that long life spans may promote the diversity of helminth parasite assemblages over evolutionary time, thus resulting in richer helminth faunas. Similarly, longer‐distance migrations, larger ranges and broader dietary breadths are likely to lead to greater encounter rates and the accumulation of trophically transmitted helminths. In contrast, vector‐borne haemosporidians may be influenced more by factors related to vector ecology than by the host traits included in the analyses. The lack of strong associations between haemosporidian species richness and host characteristics emphasizes the need to find appropriate traits to model the distribution and diversity of parasites with different environmental preferences in order to anticipate disease emergence risks associated with global change

A global risk assessment of primates under climate and land use/cover scenarios

Primates are facing an impending extinction crisis, driven by extensive habitat loss, land use change, and hunting. Climate change is an additional threat, which alone or in combination with other drivers, may severely impact those taxa unable to track suitable environmental conditions. Here, we investigate the extent of climate and land use/cover (LUC) change‐related risks for primates. We employed an analytical approach to objectively select a subset of climate scenarios, for which we then calculated changes in climatic and LUC conditions for 2050 across primate ranges (N=426 species) under a best‐ and a worst‐case scenario. Generalised linear models were used to examine whether these changes varied according to region, conservation status, range extent, and dominant habitat. Finally, we reclassified primate ranges based on different magnitudes of maximum temperature change, and quantified the proportion of ranges overall and of primate hotspots in particular that are likely to be exposed to extreme temperature increases. We found that, under the worst‐case scenario, 74% of Neotropical forest‐dwelling primates are likely to be exposed to maximum temperature increases up to 7°C. In contrast, 38% of Malagasy savanna primates will experience less pronounced warming of up to 3.5°C. About one quarter of Asian and African primates will face up to 50% crop expansion within their range. Primary land (undisturbed habitat) is expected to disappear across species’ ranges, whereas secondary land (disturbed habitat) will increase by up to 98%. With 86% of primate ranges likely to be exposed to maximum temperature increases >3°C, primate hotspots in the Neotropics are expected to be particularly vulnerable. Our study highlights the fundamental exposure risk of a large percentage of primate ranges to predicted climate and LUC changes. Importantly, our findings underscore the urgency with which climate change mitigation measures need to be implemented to avert primate extinctions on an unprecedented scale

Microclimate–forage growth linkages across two strongly contrasting precipitation years in a Mediterranean catchment

Given the complex topography of California rangelands, contrasting microclimates affect forage growth at catchment scales. However, documentation of microclimate–forage growth associations is limited, especially in Mediterranean regions experiencing pronounced climate change impacts. To better understand microclimate–forage growth linkages, we monitored forage productivity and root-zone soil temperature and moisture (0–15 and 15–30 cm) in 16 topographic positions in a 10-ha annual grassland catchment in California's Central Coast Range. Data were collected through two strongly contrasting growing seasons, a wet year (2016–17) with 287-mm precipitation and a dry year (2017–18) with 123-mm precipitation. Plant-available soil water storage (0–30 cm) was more than half full for most of the wet year; mean peak standing forage was 2790 kg ha−1 (range: 1597–4570 kg ha−1). The dry year had restricted plant-available water and mean peak standing forage was reduced to 970 kg ha−1 (range: 462–1496 kg ha−1). In the wet year, forage growth appeared energy limited (light and temperature): warmer sites produced more forage across a 3–4°C soil temperature gradient but late season growth was associated with moister sites spanning this energy gradient. In the dry year, the warmest topographic positions produced limited forage across a 10°C soil temperature gradient until late season rainfall in March. Linear models accounting for interactions between soil moisture and temperature explained about half of rapid, springtime forage growth variance. These findings reveal dynamic but clear microclimate–forage growth linkages in complex terrain, and thus, have implications for rangeland drought monitoring and dryland ecosystems modeling under climate change

Genome-wide Association Study for Beta-glucan Concentration in Elite North American Oat

Genome-wide association studies (GWAS) can be a useful approach to detect quantitative trait loci (QTL) controlling complex traits in crop plants. Oat (Avena sativa L.) β-glucan is a soluble dietary fiber and has been shown to have positive health benefits. We report a GWAS involving 446 elite oat breeding lines from North America genotyped with 1005 diversity arrays technology (DArT) markers and with phenotypic data from both historical and balanced 2-yr data. Association analyses accounting for pair-wise relationships and population structure were conducted using single-marker tests and least absolute shrinkage and selection operator (LASSO). Single-marker tests yielded six and 15 significant markers for the historical and balanced data sets, respectively. The LASSO method selected 24 and 37 markers as the most important in explaining β-glucan concentration for the historical and balanced data sets, respectively. Comparisons of genetic location showed that 15 of the markers in our study were found on the same linkage groups as QTL identified in previous studies. Four of the markers colocalized to within 4 cM of three previously detected QTL, suggesting concordance between QTL detected in our study and previous studies. Two of the significant markers were also adjacent to a β-glucan candidate gene in the rice (Oryza sativa L.) genome. Our findings suggest that GWAS can be used for QTL detection for the purpose of gene discovery and for marker-assisted selection to improve β-glucan concentration in elite oat

Research review: the relationship between social anxiety and social cognition in children and adolescents: a systematic review and meta‐analysis

Childhood Social Anxiety Disorder (SAD) is common and impairing. The recommended treatment is a disorder specific form of cognitive behavioural therapy (CBT) that includes social skills training and, whilst they appear to be more effective than more general treatments, it is not clear whether social skills training is the critical component involved in improved outcomes, particularly given that evidence for the relationship between social anxiety and social skills deficits in children is inconsistent. This may be partly due to an overlap in their observable features, and because the nature of the association may vary in different contexts (e.g. according to child age). An alternative approach is to examine the association between social anxiety and the social cognitive capacities that underpin social skills. This paper aims to examine the association between social anxiety and social cognition in children and adolescents, and examine conceptual and methodological moderators of this relationship. Methods Papers published between 1980 and 2019 were screened systematically. Fifty studies were identified from which an effect size could be calculated for the relationship between social anxiety and social cognition, including 15,411 children and adolescents. Results An overall significant, but moderate effect (r = −.15) was identified, where increased social anxiety was associated with lower social cognitive ability. Moderation analyses revealed specific associations within studies examining social anxiety among participants with and without ASD who were older than 7 years old, and studies assessing the relationship between social anxiety and specific aspects of Theory of Mind (ToM). No significant association was identified between social anxiety and emotion recognition. Conclusions Significant associations between social anxiety and social cognitive abilities appear to be accounted for by elevated social anxiety among children with ASD, and those with difficulties in specific aspects of ToM but not broader social skills, such as emotion recognition. This reinforces the importance of accurately identifying and treating social anxiety within ASD populations. In addition, treatments for social anxiety among neurotypical populations may benefit from targeting particular aspects of ToM rather than emotion recognition and other broad social skills

Habitat‐dependent occupancy and movement in a migrant songbird highlights the importance of mangroves and forested lagoons in Panama and Colombia

Climate change is predicted to impact tropical mangrove forests due to decreased rainfall, sea‐level rise, and increased seasonality of flooding. Such changes are likely to influence habitat quality for migratory songbirds occupying mangrove wetlands during the tropical dry season. Overwintering habitat quality is known to be associated with fitness in migratory songbirds, yet studies have focused primarily on territorial species. Little is known about the ecology of nonterritorial species that may display more complex movement patterns within and among habitats of differing quality. In this study, we assess within‐season survival and movement at two spatio‐temporal scales of a nonterritorial overwintering bird, the prothonotary warbler (Protonotaria citrea), that depends on mangroves and tropical lowland forests. Specifically, we (a) estimated within‐patch survival and persistence over a six‐week period using radio‐tagged birds in central Panama and (b) modeled abundance and occupancy dynamics at survey points throughout eastern Panama and northern Colombia as the dry season progressed. We found that site persistence was highest in mangroves; however, the probability of survival did not differ among habitats. The probability of warbler occupancy increased with canopy cover, and wet habitats were least likely to experience local extinction as the dry season progressed. We also found that warbler abundance is highest in forests with the tallest canopies. This study is one of the first to demonstrate habitat‐dependent occupancy and movement in a nonterritorial overwintering migrant songbird, and our findings highlight the need to conserve intact, mature mangrove, and lowland forests

Complex transboundary movements of marine megafauna in the Western Indian Ocean

Transboundary marine species have an increased risk of overexploitation as management regimes and enforcement can vary among states. The complex geopolitical layout of exclusive economic zones (EEZs) in the Western Indian Ocean (WIO) introduces the potential for migratory species to cross multiple boundaries, consequently a lack of scientific data could complicate regional management. In the current study, we highlight both the relative lack of spatial data available in the WIO, and the prevalence of transboundary movements in species that have previously been studied in the region. Five tiger sharks Galeocerdo cuvier were tracked with near real‐time positioning (SPOT) satellite tags to determine individual shark movements relative to EEZs within the WIO. Concurrently, a literature search was performed to identify all satellite telemetry studies conducted to date in the WIO for marine megafaunal species, and the results compared to global satellite telemetry effort. Finally, the satellite tracks of all marine species monitored in the WIO were extracted and digitized to examine the scale of transboundary movements that occur in the region. Tiger sharks exhibited both coastal and oceanic movements, with one individual crossing a total of eight EEZs. Satellite telemetry effort in the WIO has not matched the global increase, with only 4.7% of global studies occurring in the region. Species in the WIO remained within the EEZ in which they were tagged in only three studies, while all other species demonstrated some level of transboundary movement. This study demonstrates the lack of spatial data available for informed regional management in an area where transboundary movements by marine megafauna are highly prevalent. Without more dedicated funding and research, the rich biodiversity of the WIO is at risk of overexploitation from the diverse threats present within the various political regions

Migration distance does not predict blood parasitism in a migratory songbird

Migration can influence host–parasite dynamics in animals by increasing exposure to parasites, by reducing the energy available for immune defense, or by culling of infected individuals. These mechanisms have been demonstrated in several comparative analyses; however, few studies have investigated whether conspecific variation in migration distance may also be related to infection risk. Here, we ask whether autumn migration distance, inferred from stable hydrogen isotope analysis of summer‐grown feathers (δ 2Hf) in Europe, correlates with blood parasite prevalence and intensity of infection for willow warblers (Phylloscopus trochilus ) wintering in Zambia. We also investigated whether infection was correlated with individual condition (assessed via corticosterone, scaled mass index, and feather quality). We found that 43% of birds were infected with Haemoproteus palloris (lineage WW1). Using generalized linear models, we found no relationship between migration distance and either Haemoproteus infection prevalence or intensity. There was spatial variation in breeding ground origins of infected versus noninfected birds, with infected birds originating from more northern sites than noninfected birds, but this difference translated into only slightly longer estimated migration distances (~214 km) for infected birds. We found no relationship between body condition indices and Haemoproteus infection prevalence or intensity. Our results do not support any of the proposed mechanisms for migration effects on host–parasite dynamics and cautiously suggest that other factors may be more important for determining individual susceptibility to disease in migratory bird species