Impact of the implementation of rest days in live bird markets on the dynamics of H5N1 highly pathogenic avian influenza

Live bird markets (LBMs) act as a network ‘hub’ and potential reservoir of infection for domestic poultry. They may therefore be responsible for sustaining H5N1 highly pathogenic avian influenza (HPAI) virus circulation within the poultry sector, and thus a suitable target for implementing control strategies. We developed a stochastic transmission model to understand how market functioning impacts on the transmission dynamics. We then investigated the potential for rest days—periods during which markets are emptied and disinfected—to modulate the dynamics of H5N1 HPAI within the poultry sector using a stochastic meta-population model. Our results suggest that under plausible parameter scenarios, HPAI H5N1 could be sustained silently within LBMs with the time spent by poultry in markets and the frequency of introduction of new susceptible birds'' dominant factors determining sustained silent spread. Compared with interventions applied in farms (i.e. stamping out, vaccination), our model shows that frequent rest days are an effective means to reduce HPAI transmission. Furthermore, our model predicts that full market closure would be only slightly more effective than rest days to reduce transmission. Strategies applied within markets could thus help to control transmission of the disease.     

Detection of mortality clusters associated with highly pathogenic avian influenza in poultry: a theoretical analysis

Rapid detection of infectious disease outbreaks is often crucial for their effective control. One example is highly pathogenic avian influenza (HPAI) such as H5N1 in commercial poultry flocks. There are no quantitative data, however, on how quickly the effects of HPAI infection in poultry flocks can be detected. Here, we study, using an individual-based mathematical model, time to detection in chicken flocks. Detection is triggered when mortality, food or water intake or egg production in layers pass recommended thresholds suggested from the experience of past HPAI outbreaks. We suggest a new threshold for caged flocks—the cage mortality detection threshold—as a more sensitive threshold than current ones. Time to detection is shown to depend nonlinearly on R₀ and is particularly sensitive for R₀<10. It also depends logarithmically on flock size and number of birds per cage. We also examine how many false alarms occur in uninfected flocks when we vary detection thresholds owing to background mortality. The false alarm rate is shown to be sensitive to detection thresholds, dependent on flock size and background mortality and independent of the length of the production cycle. We suggest that current detection thresholds appear sufficient to rapidly detect the effects of a high R₀ HPAI strain such as H7N7 over a wide range of flock sizes. Time to detection of the effects of a low R₀ HPAI strain such as H5N1 can be significantly improved, particularly for large flocks, by lowering detection thresholds, and this can be accomplished without causing excessive false alarms in uninfected flocks. The results are discussed in terms of optimizing the design of disease surveillance programmes in general.     

Predictive ethoinformatics reveals the complex migratory behaviour of a pelagic seabird,the Manx Shearwater

Understanding the behaviour of animals in the wild is fundamental to conservation efforts. Advances in bio-logging technologies have offered insights into the behaviour of animals during foraging, migration and social interaction. However, broader application of these systems has been limited by device mass, cost and longevity. Here, we use information from multiple logger types to predict individual behaviour in a highly pelagic, migratory seabird, the Manx Shearwater (Puffinus puffinus). Using behavioural states resolved from GPS tracking of foraging during the breeding season, we demonstrate that individual behaviours can be accurately predicted during multi-year migrations from low cost, lightweight, salt-water immersion devices. This reveals a complex pattern of migratory stopovers: some involving high proportions of foraging, and others of rest behaviour. We use this technique to examine three consecutive years of global migrations, revealing the prominence of foraging behaviour during migration and the importance of highly productive waters during migratory stopover.     

Outbreaks of H5N1 in poultry in Thailand: the relative role of poultry production types in sustaining transmission and the impact of active surveillance in control

H5N1, highly pathogenic avian influenza, continues to pose a public health risk in the countries of southeast Asia where it has become endemic. However, in Thailand, which experienced two of the largest recorded epidemics in 2004–2005, the disease has been successfully reduced to very low levels. We fitted a spatio-temporal model of the spread of infection to outbreak data collected during the second wave of outbreaks to assess the extent to which different poultry types were responsible for propagating infection. Our estimates suggest that the wave of outbreaks would not have been possible without the contribution of backyard flocks to the susceptibility of a sub-district. However, we also estimated that outbreaks involving commercial poultry, a much larger sector in Thailand than in neighbouring countries, were disproportionately infectious, a factor which was also crucial in sustaining the wave. As a result, implemented measures that aim to reduce the role of commercial farms in the spread of infection, such as the drive to bring aspects of the supply chain ‘in house’, may help to explain the subsequent success in controlling H5N1 in Thailand. We also found that periods of active surveillance substantially improved the rate of outbreak detection.     

Optimizing the early detection of low pathogenic avian influenza H7N9 virus in live bird markets

In Southeast Asia, surveillance at live bird markets (LBMs) has been identified as crucial for detecting avian influenza viruses (AIV) and reducing the risk of human infections. However, the design of effective surveillance systems in LBMs remains complex given the rapid turn-over of poultry. We developed a deterministic transmission model to provide guidance for optimizing AIV surveillance efforts. The model was calibrated to fit one of the largest LBMs in northern Vietnam at high risk of low pathogenic H7N9 virus introduction from China to identify the surveillance strategy that optimizes H7N9 detection. Results show that (i) using a portable diagnostic device would slightly reduce the number of infected birds leaving the LBM before the first detection, as compared to a laboratory-based diagnostic strategy, (ii) H7N9 detection could become more timely by sampling birds staying overnight, just before new susceptible birds are introduced at the beginning of a working day, and (iii) banning birds staying overnight would represent an effective intervention to reduce the risk of H7N9 spread but would decrease the likelihood of virus detection if introduced. These strategies should receive high priority in Vietnam and other Asian countries at risk of H7N9 introduction.     

Differential effects of magnetic pulses on the orientation of naturally migrating birds

In migratory passerine birds, strong magnetic pulses are thought to be diagnostic of the remagnetization of iron minerals in a putative sensory system contained in the beak. Previous evidence suggests that while such a magnetic pulse affects the orientation of migratory birds in orientation cages, no effect was present when pulse-treated birds were tested in natural migration. Here we show that two migrating passerine birds treated with a strong magnetic pulse, designed to alter the magnetic sense, migrated in a direction that differed significantly from that of controls when tested in natural conditions. The orientation of treated birds was different depending on the alignment of the pulse with respect to the magnetic field. These results can aid in advancing understanding of how the putative iron-mineral-based receptors found in birds'' beaks may be used to detect and signal the intensity and/or direction of the Earth''s magnetic field.     

An avian influenza model with latency and vaccination

Avian influenza, caused by influenza A viruses, has received worldwide attention in recent years. The viruses can spread from birds to humans as well as transmit among human hosts. In this study, we formulate a mathematical model for avian influenza that includes bird-human interaction and that incorporates the effects of infection latency and human vaccination. We investigate the essential dynamics of the model through an equilibrium analysis. Meanwhile, we explore effective vaccination strategy to control avian influenza outbreaks using optimal control theory. Our results indicate that strategically deployed human vaccination can significantly reduce the numbers of exposed and infectious people.     

Modelling the propagation of social response during a disease outbreak

Epidemic trajectories and associated social responses vary widely between populations, with severe reactions sometimes observed. When confronted with fatal or novel pathogens, people exhibit a variety of behaviours from anxiety to hoarding of medical supplies, overwhelming medical infrastructure and rioting. We developed a coupled network approach to understanding and predicting social response. We couple the disease spread and panic spread processes and model them through local interactions between agents. The social contagion process depends on the prevalence of the disease, its perceived risk and a global media signal. We verify the model by analysing the spread of disease and social response during the 2009 H1N1 outbreak in Mexico City and 2003 severe acute respiratory syndrome and 2009 H1N1 outbreaks in Hong Kong, accurately predicting population-level behaviour. This kind of empirically validated model is critical to exploring strategies for public health intervention, increasing our ability to anticipate the response to infectious disease outbreaks.     

Real-Time Video-Microscopy of Migrating Immune Cells in Altered Gravity During Parabolic Flights

In our project we developed a technical equipment which allows to visualize migration of cells in real-time video-microscopy during altered gravity conditions of NOVESPACE Airbus A300 ZERO-G parabolic flights. For validation of the experimental device we have used fast moving human neutrophils as example, because their migration is fundamental to keep the organism under immunological surveillance. Their migration is indispensable for immune effector function, where the cells leave the blood vessels and navigate to places of infection to fulfill their main task of phagocytosis. Thereby, we have analyzed if their migration is affected during altered gravity conditions and if pharmacological modification of cytoskeletal dynamics influences neutrophil migratory activity. Whereas we detected no change in neutrophil locomotory behaviour in microgravity, we found a significant inhibitory influence of hypergravity, irrespective of the chemical stimulus used. Our results suggest that hypergravity, following a microgravity environment, could represent a hazard to the human immune system function. Thus, our cell migration assay offers an optimum experimental device for studying the migratory activity and underlying signal transduction mechanisms of neutrophils to assess the immunological fitness of humans in space to fight infection, but also for investigating the locomotion of other cell types or unicellular organisms such as ciliates.     

Identification of A/H5N1 influenza viruses using a single gene diagnostic microarray

In previous work, a simple diagnostic DNA microarray that targeted only the matrix gene segment of influenza A (MChip) was developed and evaluated with patient samples. In this work, the analytical utility of the MChip for detection and subtyping of an emerging virus was evaluated with a diverse set of A/H5N1 influenza viruses. A total of 43 different highly pathogenic A/H5N1 viral isolates that were collected from diverse geographic locations, including Vietnam, Nigeria, Indonesia, and Kazakhstan, representing human, feline, and a variety of avian infections spanning the time period 2003-2006 were used in this study. A probabilistic artificial neural network was developed for automated microarray image interpretation through pattern recognition. The microarray assay and subsequent subtype assignment by the artificial neural network resulted in correct identification of 24 "unknown" A/H5N1 positive samples with no false positives. Analysis of a data set composed of A/H5N1, A/H3N2, and A/H1N1 positive samples and negative controls resulted in a clinical sensitivity of 97% and a clinical specificity of 100%.     

Preventable H5N1 avian influenza epidemics in the British poultry industry network exhibit characteristic scales

Epidemics are frequently simulated on redundantly wired contact networks, which have many more links between sites than are minimally required to connect all. Consequently, the modelled pathogen can travel numerous alternative routes, complicating effective containment strategies. These networks have moreover been found to exhibit ‘scale-free’ properties and percolation, suggesting resilience to damage. However, realistic H5N1 avian influenza transmission probabilities and containment strategies, here modelled on the British poultry industry network, show that infection dynamics can additionally express characteristic scales. These system-preferred scales constitute small areas within an observed power law distribution that exhibit a lesser slope than the power law itself, indicating a slightly increased relative likelihood. These characteristic scales are here produced by a network-pervading intranet of so-called hotspot sites that propagate large epidemics below the percolation threshold. This intranet is, however, extremely vulnerable; targeted inoculation of a mere 3–6% (depending on incorporated biosecurity measures) of the British poultry industry network prevents large and moderate H5N1 outbreaks completely, offering an order of magnitude improvement over previously advocated strategies affecting the most highly connected ‘hub’ sites. In other words, hotspots and hubs are separate functional entities that do not necessarily coincide, and hotspots can make more effective inoculation targets. Given the ubiquity and relevance of networks (epidemics, Internet, power grids, protein interaction), recognition of this spreading regime elsewhere would suggest a similar disproportionate sensitivity to such surgical interventions.     

Silicon-nanowire-based CMOS-compatible field-effect transistor nanosensors for ultrasensitive electrical detection of nucleic acids

We herein report the design of a novel semiconducting silicon nanowire field-effect transistor (SiNW-FET) biosensor array for ultrasensitive label-free and real-time detection of nucleic acids. Highly responsive SiNWs with narrow sizes and high surface-to-volume-ratios were "top-down" fabricated with a complementary metal oxide semiconductor compatible anisotropic self-stop etching technique. When SiNWs were covalently modified with DNA probes, the nanosensor showed highly sensitive concentration-dependent conductance change in response to specific target DNA sequences. This SiNW-FET nanosensor revealed ultrahigh sensitivity for rapid and reliable detection of 1 fM of target DNA and high specificity single-nucleotide polymorphism discrimination. As a proof-of-concept for multiplex detection with this small-size and mass producible sensor array, we demonstrated simultaneous selective detection of two pathogenic strain virus DNA sequences (H1N1 and H5N1) of avian influenza.     

A dynamic,ensemble learning approach to forecast dengue fever epidemic years in Brazil using weather and population susceptibility cycles

Transmission of dengue fever depends on a complex interplay of human, climate and mosquito dynamics, which often change in time and space. It is well known that its disease dynamics are highly influenced by multiple factors including population susceptibility to infection as well as by microclimates: small-area climatic conditions which create environments favourable for the breeding and survival of mosquitoes. Here, we present a novel machine learning dengue forecasting approach, which, dynamically in time and space, identifies local patterns in weather and population susceptibility to make epidemic predictions at the city level in Brazil, months ahead of the occurrence of disease outbreaks. Weather-based predictions are improved when information on population susceptibility is incorporated, indicating that immunity is an important predictor neglected by most dengue forecast models. Given the generalizability of our methodology to any location or input data, it may prove valuable for public health decision-making aimed at mitigating the effects of seasonal dengue outbreaks in locations globally.     

It wasn't supposed to be a coronavirus: The quest for an influenza A(H5N1)-derived vaccine and the limits of pandemic preparedness

The COVID-19 pandemic has raised questions about what efforts were made across the world to prepare governments and healthcare systems for such an event. This spotlight article looks at developments made in “pre-pandemic preparedness planning” following a number of outbreaks of influenza type A virus in 1997. At that time, a specific avian influenza subtype, referred to as A(H5N1), wreaked havoc among fowl but also infected humans through direct transmission. The potential for slight genetic mutations that could make A(H5N1) more infectious, allowing human-to-human transmission, presented the threat of a deadly influenza pandemic. As a result, the U.S. government (and others coordinating through the World Health Organization) launched a pandemic preparation plan, including strategies to develop vaccines against A(H5N1) and its genetic lineages each year. This spotlight article discusses the events that led to the specific concern about A(H5N1) among public health officials, as well as early efforts to derive and stockpile an appropriate vaccine to protect against a possible pandemic. This perspective presents the challenges the world has faced, in recent history, in striving to keep one step ahead of pandemic threats.     

Quantifying year-round nocturnal bird migration with a fluid dynamics model

To understand the influence of biomass flows on ecosystems, we need to characterize and quantify migrations at various spatial and temporal scales. Representing the movements of migrating birds as a fluid, we applied a flow model to bird density and velocity maps retrieved from the European weather radar network, covering almost a year. We quantified how many birds take-off, fly, and land across Western Europe to (1) track bird migration waves between nights, (2) cumulate the number of birds on the ground and (3) quantify the seasonal flow into and out of the study area through several regional transects. Our results identified several migration waves that crossed the study area in 4 days only and included up to 188 million (M) birds that took-off in a single night. In spring, we estimated that 494 M birds entered the study area, 251 M left it, and 243 M birds remained within the study area. In autumn, 314 M birds entered the study area while 858 M left it. In addition to identifying fundamental quantities, our study highlights the potential of combining interdisciplinary data and methods to elucidate the dynamics of avian migration from nightly to yearly time scales and from regional to continental spatial scales.     

Origin of grain boundary motion during diffusion bonding by hot pressing

The microstructural changes during diffusion bonding of Al₂O₃ fibres with boron-doped Ni₃Al plates by hot pressing were investigated. Particular attention was paid to the conversion of the bonding surfaces to an interior grain boundary and its migration during the hot-pressing treatment. The microstructure changes were found to depend on the grain size of the matrix material prior to hot pressing. Fine-grained matrix material led to a fast migration of the bonded interface in order to establish force equilibrium at grain boundary junctions at the prior surfaces. In coarse-grained material, the bonded interface moved after much larger hot pressing time by strain-induced boundary migration due to the accumulated plastic-strain during prolonged hot-pressing treatment. The fibres were found to strongly impede migration of the bonded interface, which can interfere with the perfection of the bonding process.     

Injectable and Pathogen‐Mimicking Hydrogels for Enhanced Protective Immunity against Emerging and Highly Pathogenic Influenza Virus

Seasonal emerging infectious diseases such as influenza A impose substantial risk and need new translational strategies to achieve active immunomodulation. Here, a novel injectable pathogen‐mimicking hydrogel (iPMH) that can enhance both cellular and humoral immune responses is suggested. By the help of poly(γ‐glutamic acid) that has abundant carboxylate groups and dispersion helper function, hydrophobic immunostimulatory 3‐O‐desacyl‐4′‐monophosphoryl lipid A (MPLA) molecules and viral antigens (PR8, W150) can be successfully combined as pathogen‐mimicking adjuvants. Polyelectrolyte complex between the poly(γ‐glutamic acid)‐based adjuvants and collagens generate in situ gel‐forming hydrogel at physiological temperature. When the iPMH are immunized, they act as a pathogen‐mimicking (MPLA, H1N1, H5N1) immune priming center and a depot for continuous stimulation of immune system, resulting in the induction of high levels (8.5 times higher) of antigen‐specific IgG titers in the sera of mice and the increased number of IFN‐γ‐producing cells (7.3 times higher) compared with those in the groups immunized with antigen plus clinically used aluminum gels. Following the intranasal infection of the mouse adapted virus (emerging infectious 2009 H1N1 and highly pathogenic 2006 H5N1) at 50 times the 50% lethal dose, the mice immunized with viral antigens plus iPMH exhibit 100% protective immunity against lethal virus challenge.     

No apparent effect of a magnetic pulse on free-flight behaviour in northern wheatears (Oenanthe oenanthe) at a stopover site

Naïve migrants reach their wintering grounds following a clock-and-compass strategy. During these inaugural migrations, birds internalise, among others, cues from the Earth''s magnetic field to create a geomagnetic map, with which they navigate to destinations familiar to them on subsequent migrations. Geomagnetic map cues are thought to be sensed by a magnetic-particle-based receptor, which can be specifically affected by a magnetic pulse. Indeed, the orientation of experienced but not naïve birds was compromised after magnetic pulsing, indicating geomagnetic map use. Little is known about the importance of this putative magnetoreceptor for navigation and decision-making in free-flying migrants. Therefore, we studied in unprecedented detail how a magnetic pulse would affect departure probability, nocturnal departure timing, departure direction and consistency in flight direction over 50–100 km in experienced and naïve long-distant migrant songbirds using a large-scale radio-tracking system. Contrary to our expectations and despite a high sample size (n_total = 137) for a free-flight study, we found no significant after-effect of the magnetic pulse on the migratory traits, suggesting the geomagnetic map is not essential for the intermediate autumn migration phase. These findings warrant re-thinking about perception and use of geomagnetic maps for migratory decisions within a sensory and ecological context.