Climate change in the Arctic: Testing the poleward expansion of ticks and tick-borne diseases.

Climate change is most strongly felt in the polar regions of the world, with significant impacts on the species that live there. The arrival of parasites and pathogens from more temperate areas may become a significant problem for these populations, but current observations of parasite presence often lack a historical reference of prior absence. Observations in the high Arctic of the seabird tick Ixodes uriae suggested that this species expanded poleward in the last two decades in relation to climate change. As this tick can have a direct impact on the breeding success of its seabird hosts and vectors several pathogens, including Lyme disease spirochaetes, understanding its invasion dynamics is essential for predicting its impact on polar seabird populations. Here, we use population genetic data and host serology to test the hypothesis that I. uriae recently expanded into Svalbard. Both black-legged kittiwakes (Rissa tridactyla) and thick-billed murres (Uria lomvia) were sampled for ticks and blood in Kongsfjorden, Spitsbergen. Ticks were genotyped using microsatellite markers and population genetic analyses were performed using data from 14 reference populations from across the tick's northern distribution. In contrast to predictions, the Spitsbergen population showed high genetic diversity and significant differentiation from reference populations, suggesting long-term isolation. Host serology also demonstrated a high exposure rate to Lyme disease spirochaetes (Bbsl). Targeted PCR and sequencing confirmed the presence of Borrelia garinii in a Spitsbergen tick, demonstrating the presence of Lyme disease bacteria in the high Arctic for the first time. Taken together, results contradict the notion that I. uriae has recently expanded into the high Arctic. Rather, this tick has likely been present for some time, maintaining relatively high population sizes and an endemic transmission cycle of Bbsl. Close future observations of population infestation/infection rates will now be necessary to relate epidemiological changes to ongoing climate modifications.

Socioeconomic Disparities in Social Distancing During the COVID-19 Pandemic in the United States: Observational Study.

BACKGROUND: Eliminating disparities in the burden of COVID-19 requires equitable access to control measures across socio-economic groups. Limited research on socio-economic differences in mobility hampers our ability to understand whether inequalities in social distancing are occurring during the SARS-CoV-2 pandemic. OBJECTIVE: We aimed to assess how mobility patterns have varied across the United States during the COVID-19 pandemic and to identify associations with socioeconomic factors of populations. METHODS: We used anonymized mobility data from tens of millions of devices to measure the speed and depth of social distancing at the county level in the United States between February and May 2020, the period during which social distancing was widespread in this country. Using linear mixed models, we assessed the associations between social distancing and socioeconomic variables, including the proportion of people in the population below the poverty level, the proportion of Black people, the proportion of essential workers, and the population density. RESULTS: We found that the speed, depth, and duration of social distancing in the United States are heterogeneous. We particularly show that social distancing is slower and less intense in counties with higher proportions of people below the poverty level and essential workers; in contrast, we show that social distancing is intensely adopted in counties with higher population densities and larger Black populations. CONCLUSIONS: Socioeconomic inequalities appear to be associated with the levels of adoption of social distancing, potentially resulting in wide-ranging differences in the impact of the COVID-19 pandemic in communities across the United States. These inequalities are likely to amplify existing health disparities and must be addressed to ensure the success of ongoing pandemic mitigation efforts.

Exposure of breeding albatrosses to the agent of avian cholera: dynamics of antibody levels and ecological implications.

Despite critical implications for disease dynamics and surveillance in wild long-lived species, the immune response after exposure to potentially highly pathogenic bacterial disease agents is still poorly known. Among infectious diseases threatening wild populations, avian cholera, caused by the bacterium Pasteurella multocida, is a major concern. It frequently causes massive mortality events in wild populations, notably affecting nestlings of Indian yellow-nosed albatrosses (Thalassarche carteri) in the Indian Ocean. If adults are able to mount a long-term immune response, this could have important consequences regarding the dynamics of the pathogen in the local host community and the potential interest of vaccinating breeding females to transfer immunity to their offspring. By tracking the dynamics of antibodies against P. multocida during 4 years and implementing a vaccination experiment in a population of yellow-nosed albatrosses, we show that a significant proportion of adults were naturally exposed despite high annual survival for both vaccinated and non-vaccinated individuals. Adult-specific antibody levels were thus maintained long enough to inform about recent exposure. However, only low levels of maternal antibodies could be detected in nestlings the year following a vaccination of their mothers. A modification of the vaccine formulation and the possibility to re-vaccinate females 2 years after the first vaccination revealed that vaccines have the potential to elicit a stronger and more persistent response. Such results highlight the value of long-term observational and experimental studies of host exposure to infectious agents in the wild, where ecological and evolutionary processes are likely critical for driving disease dynamics.

Joint associations of blood plasma proteins with overwinter survival of a large mammal.

In many wild animal populations, hosts are at risk of parasites and malnutrition and resource costs of defence may be difficult to afford. We postulate that proteins, important in homeostasis and immunity, play a complex but central role in condition dependence and resource costs of mammalian immune defence. To test this, we measured plasma concentrations of albumin, total proteins. Self-reactive antibodies and parasite-specific IgG in female Soay sheep. Using a principal component analysis, we found a new metric of condition reflecting individual variation in acquisition, assimilation and/or recycling of plasma proteins that predicted overwinter survival. Controlling for this metric, an age-dependent trade-off between antibody titres and protein reserves emerged, indicating costs of mounting an antibody response: younger individuals survived best when prioritising immunity while older individuals fared better when maintaining high-protein nutritional plane. These findings suggest fascinating roles for protein acquisition and allocation in influencing survival in wild animal populations.

Integrating immune mechanisms to model nematode worm burden: an example in sheep.

Gastrointestinal nematodes represent important sources of economic losses in farmed ruminants, and the increasing frequency of anthelmintic resistance requires an increased ability to explore alternative strategies. Theoretical approaches at the crossroads of immunology and epidemiology are valuable tools in that context. In the case of Teladorsagia circumcincta in sheep, the immunological mechanisms important for resistance are increasingly well-characterized. However, despite the existence of a wide range of theoretical models, there is no framework integrating the characteristic features of this immune response into a tractable phenomenological model. Here, we propose to bridge that gap by developing a flexible modelling framework that allows for variability in nematode larval intake which can be used to track the variations in worm burdens. We parameterize this model using data from trickle infection of sheep and show that using simple immunological assumptions, our model can capture the dynamics of both adult worm burdens and nematode fecal egg counts. In addition, our analysis reveals interesting dose-dependent effects on the immune response. Finally, we discuss potential developments of this model and highlight how an improved cross-talk between empiricists and theoreticians would facilitate important advances in the study of infectious diseases.

Adaptive vibrational configuration interaction (A-VCI): A posteriori error estimation to efficiently compute anharmonic IR spectra.

A new variational algorithm called adaptive vibrational configuration interaction (A-VCI) intended for the resolution of the vibrational Schrödinger equation was developed. The main advantage of this approach is to efficiently reduce the dimension of the active space generated into the configuration interaction (CI) process. Here, we assume that the Hamiltonian writes as a sum of products of operators. This adaptive algorithm was developed with the use of three correlated conditions, i.e., a suitable starting space, a criterion for convergence, and a procedure to expand the approximate space. The velocity of the algorithm was increased with the use of a posteriori error estimator (residue) to select the most relevant direction to increase the space. Two examples have been selected for benchmark. In the case of H2CO, we mainly study the performance of A-VCI algorithm: comparison with the variation-perturbation method, choice of the initial space, and residual contributions. For CH3CN, we compare the A-VCI results with a computed reference spectrum using the same potential energy surface and for an active space reduced by about 90%.

Long antibody persistence and transgenerational transfer of immunity in a long-lived vertebrate.

Although little studied in natural populations, the persistence of immunoglobulins may dramatically affect the dynamics of immunity and the ecology and evolution of host-pathogen interactions involving vertebrate hosts. By means of a multiple-year vaccination design against Newcastle disease virus, we experimentally addressed whether levels of specific antibodies can persist over several years in females of a long-lived procellariiform seabird-Cory's shearwater-and whether maternal antibodies against that antigen could persist over a long period in offspring several years after the mother was exposed. We found that a single vaccination led to high levels of antibodies for several years and that the females transmitted antibodies to their offspring that persisted for several weeks after hatching even 5 years after a single vaccination. The temporal persistence of maternally transferred antibodies in nestlings was highly dependent on the level at hatching. A second vaccination boosted efficiently the level of antibodies in females and thus their transfer to offspring. Overall, these results stress the need to consider the temporal dynamics of immune responses if we are to understand the evolutionary ecology of host-parasite interactions and trade-offs between immunity and other life-history characteristics, in particular in long-lived species. They also have strong implications for conservation when vaccination may be used in natural populations facing disease threats.

Heritable, heterogeneous, and costly resistance of sheep against nematodes and potential feedbacks to epidemiological dynamics.

Infected hosts may preserve fitness by resisting parasites (reducing parasite burden) and/or tolerating them (preventing or repairing infection-induced damage). Theory predicts that these individual-level defense strategies generate divergent population-level feedbacks that would maintain genetic heterogeneity for resistance but purge heterogeneity for tolerance. Because resistance reduces parasite abundance, selection for costly resistance traits will weaken as resistance becomes common. Such negative frequency-dependent selection contrasts with predictions for tolerance, which maintains parasite abundance and so is expected to generate positive frequency-dependent selection, unless, for example, tolerance trades off with resistance. Thus far, there have been few tests of this theory in natural systems. Here, we begin testing the predictions in a mammalian field system, using data on individual gastrointestinal nematode burdens, nematode-specific antibody titers (as a resistance metric), the slope of body weight on parasite burden (as a tolerance metric), and fitness from an unmanaged population of Soay sheep. We find that nematode resistance is costly to fitness and underpinned by genetic heterogeneity, and that resistance is independent of tolerance. Drawing upon empirical metrics such as developed here, future work will elucidate how resistance and tolerance feedbacks interact to generate population-scale patterns in the Soay sheep and other field systems.

Strategic vaccine stockpiles for regional epidemics of emerging viruses: A geospatial modeling framework.

Multinational epidemics of emerging infectious diseases are increasingly common, due to anthropogenic pressure on ecosystems and the growing connectivity of human populations. Early and efficient vaccination can contain outbreaks and prevent mass mortality, but optimal vaccine stockpiling strategies are dependent on pathogen characteristics, reservoir ecology, and epidemic dynamics. Here, we model major regional outbreaks of Nipah virus and Middle East respiratory syndrome, and use these to develop a generalized framework for estimating vaccine stockpile needs based on spillover geography, spatially-heterogeneous healthcare capacity and spatially-distributed human mobility networks. Because outbreak sizes were highly skewed, we found that most outbreaks were readily contained (median stockpile estimate for MERS-CoV: 2,089 doses; Nipah: 1,882 doses), but the maximum estimated stockpile need in a highly unlikely large outbreak scenario was 2-3 orders of magnitude higher (MERS-CoV: ∼87,000 doses; Nipah âˆ¼ 1.1 million doses). Sensitivity analysis revealed that stockpile needs were more dependent on basic epidemiological parameters (i.e., death and recovery rate) and healthcare availability than any uncertainty related to vaccine efficacy or deployment strategy. Our results highlight the value of descriptive epidemiology for real-world modeling applications, and suggest that stockpile allocation should consider ecological, epidemiological, and social dimensions of risk.

Evolution of the temporal persistence of immune protection.

The evolution of resistance to parasites has been the focus of numerous theoretical studies and several mechanisms, ranging from innate to acquired immune responses, have been considered. Life-history theory predicts that long-lived species should invest more resources into maintenance and immunity than short-lived species. Here, we provide further theoretical and empirical support for this hypothesis. First, an analysis of the evolution of the persistence of immune protection in a theoretical framework accounting for maternal transfer of immunity reveals that longer-lived hosts are expected to invest in more persistent intragenerational and transgenerational immune responses. Controlling for phylogenetic structure and for the confounding effect of catabolic activity, we further showed that immunoglobulin half-life and longevity are positively correlated in mammal species. Our study confirms that persistence of immunity has evolved as part of elaborate anti-parasitic defence strategies.

Shaving Waivers in the United States Air Force and Their Impact on Promotions of Black/African-American Members.

INTRODUCTION: Regulations of the United States Air Force (USAF) prohibit male members from growing beards. Shaving waivers can be issued to airmen who are not able to shave due to various medical conditions such as pseudofolliculitis barbae, a condition that predominantly affects Blacks/African-Americans. Beard growth has been anecdotally associated with a negative impact on career progression. This study sought to establish if shaving waivers are associated with delays in promotion and, if present, if this association leads to racial bias. MATERIALS AND METHODS: An online survey that collected information relating to shaving waivers and demographic data was emailed to all air force male members at 12 randomly selected air force bases. Generalized linear models were conducted to test the waiver group difference in promotion time controlling for rank and the covariates of race/ethnicity, level of education, professional military education completion, and disciplinary action. RESULTS: A total of 51,703 survey invitations were emailed to members, and 10,383 complete responses were received (20.08% response rate). The demographics of the study cohort closely matched that of the USAF. Shaving waivers were associated with a longer time to promotion (P = .0003). The interaction between race and waiver status was not significant, indicating that shaving waivers are associated with a similarly longer time to promotion in individuals of all races. However, 64.18% of those in the waiver group were Black/African-American despite only being 12.85% of the study cohort. CONCLUSIONS: This study found an association between shaving waivers and delayed promotions. The majority of the waiver group was Black/African-American, which may lead to a racially discriminatory effect of the male grooming standards of the USAF.

Spatiotemporal-social association predicts immunological similarity in rewilded mice.

Environmental influences on immune phenotypes are well-documented, but our understanding of which elements of the environment affect immune systems, and how, remains vague. Behaviors, including socializing with others, are central to an individual's interaction with its environment. We therefore tracked behavior of rewilded laboratory mice of three inbred strains in outdoor enclosures and examined contributions of behavior, including associations measured from spatiotemporal co-occurrences, to immune phenotypes. We found extensive variation in individual and social behavior among and within mouse strains upon rewilding. In addition, we found that the more associated two individuals were, the more similar their immune phenotypes were. Spatiotemporal association was particularly predictive of similar memory T and B cell profiles and was more influential than sibling relationships or shared infection status. These results highlight the importance of shared spatiotemporal activity patterns and/or social networks for immune phenotype and suggest potential immunological correlates of social life.

[Modelling the spread of influenza A]. / Circulation des virus influenza A : apports de la modélisation.

The mathematical models used to produce a simplified description of reality appear as important modern epidemiology tools. Indeed, a goal in epidemiology is to understand how pathogens are transmitted between individuals. This would predict epidemics and their extent in time and space. The models can provide a guide to public health practitioners, through comparison of different strategies in disease management. Also, it improves our understanding of pathogen transmission. Here, we focused on some of these models to emphasize their practical value in understanding the influenza viruses' circulation. First, we present a simple epidemiological model that provides an understandable approach to follow in order to build a model. Second, we show how to use such simple models to include the epidemic process in a more global scale. Finally, we explain how modeling can help investigate the extent to which a pathogen can trigger an epidemic or the effects of public health measures on evolving influenza viruses.

Socio-economic disparities in social distancing during the COVID-19 pandemic in the United States.

Importance: Eliminating disparities in the burden of COVID-19 requires equitable access to control measures across socio-economic groups. Limited research on socio-economic differences in mobility hampers our ability to understand whether inequalities in social distancing are occurring during the SARS-CoV-2 pandemic. Objective: To assess how mobility patterns have varied across the United States during the COVID-19 pandemic, and identify associations with socio-economic factors of populations. Design Setting and Participants: We used anonymized mobility data from tens of millions of devices to measure the speed and depth of social distancing at the county level between February and May 2020. Using linear mixed models, we assessed the associations between social distancing and socio-economic variables, including the proportion of people below the poverty level, the proportion of Black people, the proportion of essential workers, and the population density. Main outcomes and Results: We find that the speed, depth, and duration of social distancing in the United States is heterogeneous. We particularly show that social distancing is slower and less intense in counties with higher proportions of people below the poverty level and essential workers; and in contrast, that social distancing is intense in counties with higher population densities and larger Black populations. Conclusions and relevance: Socio-economic inequalities appear to be associated with the levels of adoption of social distancing, potentially resulting in wide-ranging differences in the impact of COVID-19 in communities across the United States. This is likely to amplify existing health disparities, and needs to be addressed to ensure the success of ongoing pandemic mitigation efforts.

The landscape of childhood vaccine exemptions in the United States.

Once-eliminated vaccine-preventable childhood diseases, such as measles, are resurging across the United States. Understanding the spatio-temporal trends in vaccine exemptions is crucial to targeting public health intervention to increase vaccine uptake and anticipating vulnerable populations as cases surge. However, prior available data on childhood disease vaccination is either at too rough a spatial scale for this spatially-heterogeneous issue, or is only available for small geographic regions, making general conclusions infeasible. Here, we have collated school vaccine exemption data across the United States and provide it at the county-level for all years included. We demonstrate the fine-scale spatial heterogeneity in vaccine exemption levels, and show that many counties may fall below the herd immunity threshold. We also show that vaccine exemptions increase over time in most states, and non-medical exemptions are highly prevalent where allowed. Our dataset also highlights the need for greater data sharing and standardized reporting across the United States.

Getting Personal: How Childhood Vaccination Policies Shape the Landscape of Vaccine Exemptions.

BACKGROUND: State-mandated school entry immunization requirements in the United States play an important role in achieving high vaccine coverage, but variations in vaccine exemption policies result in a patchwork of vaccine coverage across the country. METHODS: In this study, we evaluate epidemiological effects and spatial variations in nonmedical exemption (NME) rates in the context of vaccine policies. We first analyze the correlation between NME rates and vaccine coverage for 3 significant childhood vaccinations. Furthermore, we assess the effects of policy changes in a subset of states, using a correlative approach at the state level and performing a clustering analysis at the county level. RESULTS: We find that higher rates of exemptions are associated with lower vaccination rates of school-aged children in all cases. In a subset of states where exemption policy has recently changed, we show that the effects on statewide NME rates vary widely and that decreases in NMEs can lead to an increase in other types of exemptions. Finally, our clustering analysis in California, Illinois, and Connecticut shows that policy changes affect the spatial distribution of NMEs. CONCLUSIONS: Our work suggests that vaccination policies have significant impacts on patterns of herd immunity. Our findings can be used to develop evidence-based vaccine legislation.

Next-generation serology: integrating cross-sectional and capture-recapture approaches to infer disease dynamics.

Two approaches have been classically used in disease ecology to estimate epidemiological parameters from field studies: cross-sectional sampling from unmarked individuals and longitudinal capture-recapture setups, which generally involve more limited numbers of marked individuals due to cost and logistical constraints. Although the benefits of longitudinal setups are increasingly acknowledged in the disease ecology community, cross-sectional data remain largely overrepresented in the literature, probably because of the inherent costs of longitudinal surveys. In this context, we used simulated data to compare the performances of cross-sectional and longitudinal designs to estimate the force of infection (i.e., the rate at which susceptible individuals become infected). Then, inspired from recent method developments in quantitative ecology, we explore the benefits of integrating both cross-sectional (seroprevalences) and longitudinal (individuals histories) data sets. In doing so, we investigate the effects of host species life history, antibody persistence, and degree of a priori knowledge and uncertainty on demographic and epidemiological parameters, as those are expected to affect in different ways the level of inference possible from the data. Our results highlight how those elements are important to consider in determining optimal sampling designs. In the case of long-lived species exposed to infectious agents resulting in persistent antibody responses, integrated designs are especially valuable as they benefit from the performances of longitudinal designs even with relatively small longitudinal sample sizes. As an illustration, we apply this approach to a combination of empirical and simulated data inspired from a case of bats exposed to a rabies virus. Overall, this work highlights that serology field studies could greatly benefit from the opportunity of integrating cross-sectional and longitudinal designs.

Global estimates of mammalian viral diversity accounting for host sharing.

Present estimates suggest there are over 1 million virus species found in mammals alone, with about half a million posing a possible threat to human health. Although previous estimates assume linear scaling between host and virus diversity, we show that ecological network theory predicts a non-linear relationship, produced by patterns of host sharing among virus species. To account for host sharing, we fit a power law scaling relationship for host-virus species interaction networks. We estimate that there are about 40,000 virus species in mammals (including ~10,000 viruses with zoonotic potential), a reduction of two orders of magnitude from present projections of viral diversity. We expect that the increasing availability of host-virus association data will improve the precision of these estimates and their use in the sampling and surveillance of pathogens with pandemic potential. We suggest host sharing should be more widely included in macroecological approaches to estimating biodiversity.

What is stirring in the reservoir? Modelling mechanisms of henipavirus circulation in fruit bat hosts.

Pathogen circulation among reservoir hosts is a precondition for zoonotic spillover. Unlike the acute, high morbidity infections typical in spillover hosts, infected reservoir hosts often exhibit low morbidity and mortality. Although it has been proposed that reservoir host infections may be persistent with recurrent episodes of shedding, direct evidence is often lacking. We construct a generalized SEIR (susceptible, exposed, infectious, recovered) framework encompassing 46 sub-models representing the full range of possible transitions among those four states of infection and immunity. We then use likelihood-based methods to fit these models to nine years of longitudinal data on henipavirus serology from a captive colony of Eidolon helvum bats in Ghana. We find that reinfection is necessary to explain observed dynamics; that acute infectious periods may be very short (hours to days); that immunity, if present, lasts about 1-2 years; and that recurring latent infection is likely. Although quantitative inference is sensitive to assumptions about serology, qualitative predictions are robust. Our novel approach helps clarify mechanisms of viral persistence and circulation in wild bats, including estimated ranges for key parameters such as the basic reproduction number and the duration of the infectious period. Our results inform how future field-based and experimental work could differentiate the processes of viral recurrence and reinfection in reservoir hosts. This article is part of the theme issue 'Dynamic and integrative approaches to understanding pathogen spillover'.

Support for viral persistence in bats from age-specific serology and models of maternal immunity.

Spatiotemporally-localised prediction of virus emergence from wildlife requires focused studies on the ecology and immunology of reservoir hosts in their native habitat. Reliable predictions from mathematical models remain difficult in most systems due to a dearth of appropriate empirical data. Our goal was to study the circulation and immune dynamics of zoonotic viruses in bat populations and investigate the effects of maternally-derived and acquired immunity on viral persistence. Using rare age-specific serological data from wild-caught Eidolon helvum fruit bats as a case study, we estimated viral transmission parameters for a stochastic infection model. We estimated mean durations of around 6 months for maternally-derived immunity to Lagos bat virus and African henipavirus, whereas acquired immunity was long-lasting (Lagos bat virus: mean 12 years, henipavirus: mean 4 years). In the presence of a seasonal birth pulse, the effect of maternally-derived immunity on virus persistence within modelled bat populations was highly dependent on transmission characteristics. To explain previous reports of viral persistence within small natural and captive E. helvum populations, we hypothesise that some bats must experience prolonged infectious periods or within-host latency. By further elucidating plausible mechanisms of virus persistence in bat populations, we contribute to guidance of future field studies.