Persistence of highly pathogenic avian influenza viruses in natural ecosystems

Multifaceted analysis of temporal and spatial distribution and risk factors of global poultry HPAI-H5N1, 2005-2023

The purpose of this study was to analyze the characteristics of occurrence and spread of highly pathogenic avian influenza H5N1 (HPAI-H5N1) globally, understand its spatiotemporal characteristics, investigate the risk factors influencing outbreaks, and identify high-risk areas for disease occurrence. We collected the data on global poultry HPAI-H5N1 outbreaks from January 2005 to April 2023, and conducted a thorough analysis of the spatial and temporal characteristics of the disease through time series decomposition and directional distribution analysis. Additionally, an ecological niche model was established to explore the major factors influencing the occurrence of HPAI-H5N1 and to pinpoint high-risk areas. Our findings revealed that HPAI-H5N1 outbreaks were cyclical, and seasonal, exhibiting a rising trend, with a predominant northwest-southeast transmission direction. The ecological niche model highlighted that species factors and economic trade factors are critical in influencing the outbreak of HPAI-H5N1. Variables such as chicken and duck density, population density, isothermality, and road density, contributed to importantly risk of outbreaks. High-risk areas for HPAI-H5N1 occurrence were primarily identified in Europe, West Africa, Southeast Asia, and Southeast China. This study provided valuable insights into the spatial and temporal distribution characteristics and risk factors of global poultry HPAI-H5N1 outbreaks. The identification of high-risk areas provides essential information that can be used to develop more effective prevention and control policies.

Species-specific emergence of H7 highly pathogenic avian influenza virus is driven by intrahost selection differences between chickens and ducks

Highly pathogenic avian influenza viruses (HPAIVs) cause severe hemorrhagic disease in terrestrial poultry and are a threat to the poultry industry, wild life, and human health. HPAIVs arise from low pathogenic avian influenza viruses (LPAIVs), which circulate in wild aquatic birds. HPAIV emergence is thought to occur in poultry and not wild aquatic birds, but the reason for this species-restriction is not known. We hypothesized that, due to species-specific tropism and replication, intrahost HPAIV selection is favored in poultry and disfavored in wild aquatic birds. We tested this hypothesis by co-inoculating chickens, representative of poultry, and ducks, representative of wild aquatic birds, with a mixture of H7N7 HPAIV and LPAIV, mimicking HPAIV emergence in an experimental setting. Virus selection was monitored in swabs and tissues by RT-qPCR and immunostaining of differential N-terminal epitope tags that were added to the hemagglutinin protein. HPAIV was selected in four of six co-inoculated chickens, whereas LPAIV remained the major population in co-inoculated ducks on the long-term, despite detection of infectious HPAIV in tissues at early time points. Collectively, our data support the hypothesis that HPAIVs are more likely to be selected at the intrahost level in poultry than in wild aquatic birds and point towards species-specific differences in HPAIV and LPAIV tropism and replication levels as possible explanations.

Assessment of the spatiotemporal risk of avian influenza between waterfowl and poultry farms during the annual cycle: A spatial prediction study focused on seasonal distribution changes in resident waterfowl in South Korea

Previous studies and efforts to prevent and manage avian influenza (AI) outbreaks have mainly focused on the wintering season. However, outbreaks of AI have been reported in the summer, including the breeding season of waterfowl. Additionally, the spatial distribution of waterfowl can easily change during the annual cycle due to their life-cycle traits and the presence of both migrants and residents in the population. Thus, we assessed the spatiotemporal variation in AI exposure risk in poultry due to spatial distribution changes in three duck species included in both major residents and wintering migrants in South Korea, the mandarin, mallard and spot-billed duck, during wintering (October-March), breeding (April-June) and whole annual seasons. To estimate seasonal ecological niche variations among the three duck species, we applied pairwise ecological niche analysis using the Pianka index. Subsequently, seasonal distribution models were projected by overlaying the monthly ranges estimated by the maximum entropy model. Finally, we overlaid each seasonal distribution range onto a poultry distribution map of South Korea. We found that the mandarin had less niche overlap with the mallard and spot-billed duck during the wintering season than during the breeding season, whereas the mallard had less niche overlap with the mandarin and spot-billed duck during the breeding season than during the wintering season. Breeding and annual distribution ranges of the mandarin and spot-billed duck, but not the mallard, were similar or even wider than their wintering ranges. Similarly, the mandarin and spot-billed duck showed more extensive overlap proportions between poultry and their distributional ranges during both the breeding and annual seasons than during the wintering season. These results suggest that potential AI exposure in poultry can occur more widely in the summer than in winter, depending on sympatry with the host duck species. Future studies considering the population density and variable pathogenicity of AI are required.

Tropism of Highly Pathogenic Avian Influenza H5 Viruses from the 2020/2021 Epizootic in Wild Ducks and Geese

Highly pathogenic avian influenza (HPAI) outbreaks have become increasingly frequent in wild bird populations and have caused mass mortality in many wild bird species. The 2020/2021 epizootic was the largest and most deadly ever reported in Europe, and many new bird species tested positive for HPAI virus for the first time. This study investigated the tropism of HPAI virus in wild birds. We tested the pattern of virus attachment of 2020 H5N8 virus to intestinal and respiratory tissues of key bird species; and characterized pathology of naturally infected Eurasian wigeons (Mareca penelope) and barnacle geese (Branta leucopsis). This study determined that 2020 H5N8 virus had a high level of attachment to the intestinal epithelium (enterotropism) of dabbling ducks and geese and retained attachment to airway epithelium (respirotropism). Natural HPAI 2020 H5 virus infection in Eurasian wigeons and barnacle geese also showed a high level of neurotropism, as both species presented with brain lesions that co-localized with virus antigen expression. We concluded that the combination of respirotropism, neurotropism, and possibly enterotropism, contributed to the successful adaptation of 2020/2021 HPAI H5 viruses to wild waterbird populations.

Surveillance and control of SARS-CoV-2 in mustelids: An evolutionary perspective

The relevance of mustelids in SARS-CoV-2 transmission has become increasingly evident. Alongside experimental demonstration of airborne transmission among ferrets, the major animal model for human respiratory diseases, transmission of SARS-CoV-2 within- and/or between-commercial mink farms has occurred and continues to occur. The number of mink reared for the luxury fur trade is approximately 60.5 million, across 36 mustelid-farming countries. By July 2021, SARS-CoV-2 outbreaks have been reported in 12 of these countries, at 412 European and 20 North American mink farms. Reverse zoonotic transmission events (from humans to mink) have introduced the virus to farms with subsequent extensive mink-to-mink transmission as well as further zoonotic (mink-to-human) transmission events generating cases among both farm workers and the broader community. Overcrowded housing conditions inherent within intensive mink farms, often combined with poor sanitation and welfare, both guarantee spread of SARS-CoV-2 and facilitate opportunities for viral variants, thereby effectively representing biotic hubs for viral transmission and evolution of virulence. Adequate preventative, surveillance and control measures within the mink industry are imperative both for the control of the current global pandemic and to mitigate against future outbreaks.

Highly Pathogenic Avian Influenza Viruses at the Wild-Domestic Bird Interface in Europe: Future Directions for Research and Surveillance

Highly pathogenic avian influenza (HPAI) outbreaks in wild birds and poultry are no longer a rare phenomenon in Europe. In the past 15 years, HPAI outbreaks—in particular those caused by H5 viruses derived from the A/Goose/Guangdong/1/1996 lineage that emerged in southeast Asia in 1996—have been occuring with increasing frequency in Europe. Between 2005 and 2020, at least ten HPAI H5 incursions were identified in Europe resulting in mass mortalities among poultry and wild birds. Until 2009, the HPAI H5 virus outbreaks in Europe were caused by HPAI H5N1 clade 2.2 viruses, while from 2014 onwards HPAI H5 clade 2.3.4.4 viruses dominated outbreaks, with abundant genetic reassortments yielding subtypes H5N1, H5N2, H5N3, H5N4, H5N5, H5N6 and H5N8. The majority of HPAI H5 virus detections in wild and domestic birds within Europe coincide with southwest/westward fall migration and large local waterbird aggregations during wintering. In this review we provide an overview of HPAI H5 virus epidemiology, ecology and evolution at the interface between poultry and wild birds based on 15 years of avian influenza virus surveillance in Europe, and assess future directions for HPAI virus research and surveillance, including the integration of whole genome sequencing, host identification and avian ecology into risk-based surveillance and analyses.

Crossroads of highly pathogenic H5N1: overlap between wild and domestic birds in the Black Sea-Mediterranean impacts global transmission

Understanding transmission dynamics that link wild and domestic animals is a key element of predicting the emergence of infectious disease, an event that has highest likelihood of occurring wherever human livelihoods depend on agriculture and animal trade. Contact between poultry and wild birds is a key driver of the emergence of highly pathogenic avian influenza (HPAI), a process that allows for host switching and accelerated reassortment, diversification, and spread of virus between otherwise unconnected regions. This study addresses questions relevant to the spillover of HPAI at a transmission hotspot: what is the nature of the wild bird-poultry interface in Egypt and adjacent Black Sea-Mediterranean countries and how has this contributed to outbreaks occurring worldwide? Using a spatiotemporal model of infection risk informed by satellite tracking of waterfowl and viral phylogenetics, this study identified ecological conditions that contribute to spillover in this understudied region. Results indicated that multiple ducks (Northern Shoveler and Northern Pintail) hosted segments that shared ancestry with HPAI H5 from both clade 2.2.1 and clade 2.3.4 supporting the role of Anseriformes in linking viral populations in East Asia and Africa over large distances. Quantifying the overlap between wild ducks and H5N1-infected poultry revealed an increasing interface in late winter peaking in early spring when ducks expanded their range before migration, with key differences in the timing of poultry contact risk between local and long-distance migrants.

Emerging Diseases of Avian Wildlife

Climate change and the interaction with humans and domestic species influences disease in avian wildlife. This article provides updated information on emerging disease conditions such as the spread of an Asian tick, Haemaphysalis longicornis, and its associated diseases among migratory birds in the eastern United States; lymphoproliferative disease virus in wild turkeys in the United States; and salmonellosis, particularly among passerines, which has zoonotic potential. In addition, it includes updated information on West Nile virus, Wellfleet Bay virus, and avian influenza and is intended to serve as a complement to the current veterinary literature for veterinarians treating avian wildlife species.

Transmission of highly pathogenic avian influenza in the nomadic free-grazing duck production system in Viet Nam

The presence of free-grazing ducks (FGD) has consistently been shown to be associated with highly pathogenic avian influenza virus (HPAIV) H5N1 outbreaks in South-East Asia. However, the lack of knowledge about the transmission pathways limits the effectiveness of control efforts. To address this gap, we developed a probabilistic transmission model of HPAIV H5N1 in the nomadic FGD production system in Viet Nam, assuming different scenarios to address parameter uncertainty. Results suggested that HPAIV H5N1 could spread within the nomadic FGD production system, with an estimated flock-level effective reproduction number (r_e) ranging from 2.16 (95% confidence interval (CI): 1.39-3.49) to 6.10 (95%CI: 3.93-9.85) depending on the scenario. Indirect transmission via boats and trucks was shown to be the main transmission route in all scenarios. Results suggest that r_e could be reduced below one with 95% confidence if 86% of FGD flocks were vaccinated in the best-case scenario or 95% in the worst-case scenario. If vaccination was combined with cleaning and disinfection of transport vehicles twice a week, vaccination coverage could be lowered to 60% in the best-case scenario. These findings are of particular relevance for prioritising interventions for effective control of HPAIV in nomadic free-grazing duck production systems.

Fireworks-like surveillance approach: The case of HPAI H5N1 in wild birds in Europe

Highly pathogenic avian influenza (HPAI) risk management requires efficient surveillance of the infection in wild birds for early warning purposes. In this study, our aim was to describe the spread of continent-wide infection cases using a fireworks model and therefore improve current surveillance systems. The fireworks model is a metaphor illustrating the spread of HPAI as a point source epizootic. The approach is based on early detection of the outbreak seeds (sparks from the fireworks) and uses a predictive model of the probability of the occurrence of new cases following a seed introduction; this then determines the spatiotemporal perimeter for intense surveillance investigations. For a case study, we used surveillance data on HPAI H5N1 in wild birds across Europe between 2005 and 2010 to describe the outbreaks and determine the success of the case detection used to inform management of the disease. The fireworks description assumes simultaneous introductions of 'seeds' of cases, which then 'explode' in local foci but do not merge into a progressive disease wave. This model fits the data well. Using this predictive approach for HPAI cases in EU countries, we found that the investigation radius needed to achieve a detection level of 90% of new cases after an outbreak ranged from 10 km to more than 300 km, depending on the outbreak pattern. Based on these findings, the fireworks approach can be a valuable method for identifying the perimeters and risk areas to be targeted for enhanced surveillance. The rationale of the fireworks approach is quite generic and can easily be adapted to different situations and contexts.

Parasites of seabirds: A survey of effects and ecological implications

Parasites are ubiquitous in the environment, and can cause negative effects in their host species. Importantly, seabirds can be long-lived and cross multiple continents within a single annual cycle, thus their exposure to parasites may be greater than other taxa. With changing climatic conditions expected to influence parasite distribution and abundance, understanding current level of infection, transmission pathways and population-level impacts are integral aspects for predicting ecosystem changes, and how climate change will affect seabird species. In particular, a range of micro- and macro-parasites can affect seabird species, including ticks, mites, helminths, viruses and bacteria in gulls, terns, skimmers, skuas, auks and selected phalaropes (Charadriiformes), tropicbirds (Phaethontiformes), penguins (Sphenisciformes), tubenoses (Procellariiformes), cormorants, frigatebirds, boobies, gannets (Suliformes), and pelicans (Pelecaniformes) and marine seaducks and loons (Anseriformes and Gaviiformes). We found that the seabird orders of Charadriiformes and Procellariiformes were most represented in the parasite-seabird literature. While negative effects were reported in seabirds associated with all the parasite groups, most effects have been studied in adults with less information known about how parasites may affect chicks and fledglings. We found studies most often reported on negative effects in seabird hosts during the breeding season, although this is also the time when most seabird research occurs. Many studies report that external factors such as condition of the host, pollution, and environmental conditions can influence the effects of parasites, thus cumulative effects likely play a large role in how parasites influence seabirds at both the individual and population level. With an increased understanding of parasite-host dynamics it is clear that major environmental changes, often those associated with human activities, can directly or indirectly affect the distribution, abundance, or virulence of parasites and pathogens.

Survivability of highly pathogenic avian influenza virus (H5N1) in naturally preened duck feathers at different temperatures

Ducks are the "Trojan Horses" for Asian H5N1 avian influenza viruses (AIV) and attain carrier status without displaying overt infection. These birds help in the spread of the virus among the poultry and human population through direct or indirect contact. Preen oil is the secretion of preen gland of water birds such as ducks. In a process called preening, the water birds spread preen oil across their feather and body. Preen oil has been known to play a significant role in the accumulation of various pathogens including Highly Pathogenic Avian Influenza (HPAI) from water onto feathers. However, the studies are scarce on the role of preen oil in the survivability of HPAIV. We conducted a simulative study to analyse the effect of preen oil on the survivability of the HPAI virus (H5N1) on duck feathers. Duck feather samples along with relevant controls were spiked with the H5N1 virus at two different initial concentrations (10⁴ EID₅₀ and 10⁶ EID₅₀ ), stored at 37°C, 25°C and 10°C temperatures and tested at regular intervals for percent infectivity by egg culture method and qRT-PCR. The infectivity and viral load were significantly higher in naturally preened duck feathers in comparison to the three preen oil deficit controls at both low and high initial concentrations of virus (10⁴ EID₅₀ and 10⁶ EID₅₀ ). Maximum persistence was seen at 10°C in naturally preened duck feathers spiked with 10⁶ EID₅₀ concentration of viruses. It was also seen that depletion of preen oil from duck feathers reduced the persistence of the virus. These results demonstrate that preen oil plays a significant role in survivability and protection of HPAIV on duck feathers. This study herein will present new avenues in understanding one of the epidemiological niches of HPAIV.

Long-term avian influenza virus epidemiology in a small Spanish wetland ecosystem is driven by the breeding Anseriformes community

During 2007-2009 and 2012-2014, avian influenza virus (AIV) was studied in a wild avian community of a northern Spanish wetland using non-invasive sampling methods and host identification by COI barcoding. The aim of this longitudinal study was to evaluate AIV dynamics in a natural wetland ecosystem, taking into account both virological aspects and ecological traits of hosts. Global AIV prevalence decreased significantly during the second sampling period (0.3%) compared to the first (6.6%). Circulating subtype distributions were also different between periods, with a noteworthy H5 and H7 subtype richness during the first sampling period. Mallard Anas platyrhynchos was identified as the main AIV host, although not all positive samples could be ascribed to the host. We modelled AIV prevalence with regard to the avian host community composition and meteorological data from the wetland. Statistical analysis revealed seasonal differences in AIV detection, with higher prevalence during the breeding season compared to other phenological events. The model also shows that the lower AIV prevalence during the second study period was associated with a significant reduction of breeding Anseriformes in the wetland, revealing a long-term fluctuation of AIV prevalence driven by the breeding Anseriformes community. This longitudinal study on AIV epidemiology in a natural ecosystem reveals that although prevalence follows seasonal and annual patterns, long-term prevalence fluctuation is linked to the breeding community composition and size. These results are relevant to understanding the influence of host ecology on pathogen transmission for preventing and managing influenza emergence.

Influenza Virus Segment Composition Influences Viral Stability in the Environment

The transmission routes of Influenza A viruses (IAVs) submit virus particles to a wide range of environmental conditions that affect their transmission. In water, temperature, salinity, and pH are important factors modulating viral persistence in a strain-dependent manner, and the viral factors driving IAV persistence remain to be described. We used an innovative method based on a real-time cell system analysis to quantify viral decay in an environmental model. Thus, we identified the viral hemagglutinin (HA) and neuraminidase (NA) as the main proteins driving the environmental persistence by comparing the inactivation slopes of several reassortant viruses. We also introduced synonymous and non-synonymous mutations in the HA or in the NA that modulated IAV persistence. Our results demonstrate that HA stability and expression level, as well as calcium-binding sites of the NA protein, are molecular determinants of viral persistence. Finally, IAV particles could not trigger membrane fusion after environmental exposure, stressing the importance of the HA and the NA for environmental persistence.

Potential Biological and Climatic Factors That Influence the Incidence and Persistence of Highly Pathogenic H5N1 Avian Influenza Virus in Egypt

Highly pathogenic H5N1 avian influenza virus (A/H5N1) of clade 2.2.1 is endemic in poultry in Egypt where the highest number of human infections worldwide was reported. During the last 12 years the Egyptian A/H5N1 evolved into several genotypes. In 2007-2014 vaccinated poultry suffered from antigenic drift variants of clade 2.2.1.1 and in 2014/2015 an unprecedented upsurge of A/H5N1 clade 2.2.1.2 occurred in poultry and humans. Factors contributing to the endemicity or re-emergence of A/H5N1 in poultry in Egypt remain unclear. Here, three potential factors were studied: climatic factors (temperature, relative humidity, and wind speed), biological fitness in vitro, and pathogenicity in domestic Pekin and Muscovy ducks. Statistical analyses using negative binomial regression models indicated that ambient temperature in winter months influenced the spread of A/H5N1 in different geographic areas analyzed in this study. In vitro, at 4 and 56°C 2.2.1.1 and recent 2.2.1.2 viruses were more stable than other viruses used in this study. Further, Pekin ducks were more resistant than Muscovy ducks and the viruses were excreted for up to 2 weeks post-infection assuming a strong role as a reservoir. Taken together, ambient temperature in winter months potentially contributes to increasing outbreaks in some regions in Egypt. Heat stability of clade 2.2.1.1 and recent 2.2.1.2 viruses probably favors their persistence at elevated temperatures. Importantly, asymptomatically infected Pekin ducks may play an important role in the spread of avian and human-like A/H5N1 in Egypt. Therefore, control measures including targeted surveillance and culling of silently infected Pekin ducks should be considered.

Modeling the spread of avian influenza viruses in aquatic reservoirs: A novel hydrodynamic approach applied to the Rhône delta (southern France)

Wild aquatic birds represent a natural reservoir of avian influenza viruses (AIV) that can be spread to poultry. AIV epizootics were associated with huge economic impacts during the last decades and are still of major concern. Within aquatic bird populations AIV are transmitted either by direct contact or through the ingestion of water that has been contaminated by infected individuals. This second route involving environmental transmission is of utmost importance in AIV dynamics, yet it has received far less attention than direct bird-to-bird contamination. Our objective was to combine a hydrodynamic model with data on mallard abundance and AIV infection rate within the population, so as to characterize virus dissemination within a complex wetland network. We chose the Vaccarès hydrosystem as a wetland model since it represents a large part of the Camargue region, which is a major wintering site for a large diversity of aquatic birds including AIV hosts. We aimed to identify the environmental parameters that drive AIV dynamics within this system and the spatio-temporal pattern of dispersion and persistence of viruses. Our results show that in a complex hydrosystem we can expect a great heterogeneity in AIV risk among wetlands. Our simulations underline how a simple "homogeneous box" approach could in the case of deltaic ecosystems minimize the expected risk by diluting it in the whole system. Moreover, such undermining of the risk perception could affect the predictions relative to risk duration. We present a new approach to identify hotspots of virus concentrations within deltaic areas that could take advantage of the duck count data, AIV surveys and hydrodynamic models that may already be available in several major duck wintering areas comprised of complex hydrosystems, such as the large European deltas. Our method could be of particular interest to optimize surveillance strategies in the current context of highly pathogenic AIV diffusion within wild bird populations.

Are Poultry or Wild Birds the Main Reservoirs for Avian Influenza in Bangladesh?

Avian influenza viruses (AIV) are of great socioeconomic and health concern, notably in Southeast Asia where highly pathogenic strains, such as highly pathogenic avian influenza (HPAI) H5N1 and other H5 and H7 AIVs, continue to occur. Wild bird migrants are often implicated in the maintenance and spread of AIV. However, little systematic surveillance of wild birds has been conducted in Southeast Asia to evaluate whether the prevalence of AIV in wild birds is higher than in other parts of the world where HPAI outbreaks occur less frequently. Across Bangladesh, we randomly sampled a total of 3585 wild and domestic birds to assess the prevalence of AIV and antibodies against AIV and compared these with prevalence levels found in other endemic and non-endemic countries. Our study showed that both resident and migratory wild birds in Bangladesh do not have a particularly elevated AIV prevalence and AIV sero-prevalence compared to wild birds from regions in the world where H5N1 is not endemic and fewer AIV outbreaks in poultry occur. Like elsewhere, notably wild birds of the orders Anseriformes were identified as the main wild bird reservoir, although we found exceptionally high sero-prevalence in one representative of the order Passeriformes, the house crow (Corvus splendens), importantly living on offal from live bird markets. This finding, together with high sero- and viral prevalence levels of AIV in domestic birds, suggests that wild birds are not at the base of the perpetuation of AIV problems in the local poultry sector, but may easily become victim to AIV spill back from poultry into some species of wild birds, potentially assisting in further spread of the virus.

The ecology of avian influenza viruses in wild dabbling ducks (Anas spp.) in Canada

Avian influenza virus (AIV) occurrence and transmission remain important wildlife and human health issues in much of the world, including in North America. Through Canada’s Inter-Agency Wild Bird Influenza Survey, close to 20,000 apparently healthy, wild dabbling ducks (of seven species) were tested for AIV between 2005 and 2011. We used these data to identify and evaluate ecological and demographic correlates of infection with low pathogenic AIVs in wild dabbling ducks (Anas spp.) across Canada. Generalized linear mixed effects model analyses revealed that risk of AIV infection was higher in hatch-year birds compared to adults, and was positively associated with a high proportion of hatch-year birds in the population. Males were more likely to be infected than females in British Columbia and in Eastern Provinces of Canada, but more complex relationships among age and sex cohorts were found in the Prairie Provinces. A species effect was apparent in Eastern Canada and British Columbia, where teal (A. discors and/or A. carolinensis) were less likely to be infected than mallards (A. platyrhynchos). Risk of AIV infection increased with the density of the breeding population, in both Eastern Canada and the Prairie Provinces, and lower temperatures preceding sampling were associated with a higher probability of AIV infection in Eastern Canada. Our results provide new insights into the ecological and demographic factors associated with AIV infection in waterfowl.

Competition between low and high pathogenicity avian influenza in a two-patch system

Over the last decade, the epidemiology of avian influenza has undergone a significant transformation. Not only have we seen an increase in the number of outbreaks of the deadly strain known as highly pathogenic avian influenza (HPAI), but the number of birds infected, and the cost of control has risen drastically. Live poultry markets play a huge role in the bird to bird transmission of avian influenza. We develop a two patch model to determine the competition between low pathogenic avian influenza (LPAI) and HPAI strains when migration is present. We define the two patches as live poultry markets in which the patches are connected through migration. We use a system of differential equations to analyze the existence-stability of the LPAI and HPAI equilibria and established results for the critical threshold R₀. We observed that in general migration in both directions increases the abundance of poultry infected with the HPAI strain. Migration promotes the coexistence in Patch 2 while in Patch 1 the region of coexistence fluctuates when migration is active between both patches.

The ecology and adaptive evolution of influenza A interspecies transmission

Since 2013, there have been several alarming influenza-related events; the spread of highly pathogenic avian influenza H5 viruses into North America, the detection of H10N8 and H5N6 zoonotic infections, the ongoing H7N9 infections in China and the continued zoonosis of H5N1 viruses in parts of Asia and the Middle East. The risk of a new influenza pandemic increases with the repeated interspecies transmission events that facilitate reassortment between animal influenza strains; thus, it is of utmost importance to understand the factors involved that promote or become a barrier to cross-species transmission of Influenza A viruses (IAVs). Here, we provide an overview of the ecology and evolutionary adaptations of IAVs, with a focus on a review of the molecular factors that enable interspecies transmission of the various virus gene segments.

Culling and the Common Good: Re-evaluating Harms and Benefits under the One Health Paradigm

One Health (OH) is a novel paradigm that recognizes that human and non-human animal health is interlinked through our shared environment. Increasingly prominent in public health responses to zoonoses, OH differs from traditional approaches to animal-borne infectious risks, because it also aims to promote the health of animals and ecological systems. Despite the widespread adoption of OH, culling remains a key component of institutional responses to the risks of zoonoses. Using the threats posed by highly pathogenic avian influenza viruses to human and animal health, economic activity and food security as a case exemplar, we explore whether culling and other standard control measures for animal-borne infectious disease might be justified as part of OH approaches. Our central premise is that OH requires us to reformulate 'health' as universal good that is best shared across species boundaries such that human health and well-being are contingent upon identifying and meeting the relevant sets of human and non-human interests and shared dependencies. Our purpose is to further nascent discussions about the ethical dimensions of OH and begin to describe the principles around which a public health agenda that truly seeks to co-promote human and non-human health could potentially begin to be implemented.

The enigma of the apparent disappearance of Eurasian highly pathogenic H5 clade 2.3.4.4 influenza A viruses in North American waterfowl

One of the major unresolved questions in influenza A virus (IAV) ecology is exemplified by the apparent disappearance of highly pathogenic (HP) H5N1, H5N2, and H5N8 (H5Nx) viruses containing the Eurasian hemagglutinin 2.3.4.4 clade from wild bird populations in North America. The introduction of Eurasian lineage HP H5 clade 2.3.4.4 H5N8 IAV and subsequent reassortment with low-pathogenic H?N2 and H?N1 North American wild bird-origin IAVs in late 2014 resulted in widespread HP H5Nx IAV infections and outbreaks in poultry and wild birds across two-thirds of North America starting in November 2014 and continuing through June 2015. Although the stamping out strategies adopted by the poultry industry and animal health authorities in Canada and the United States-which included culling, quarantining, increased biosecurity, and abstention from vaccine use-were successful in eradicating the HP H5Nx viruses from poultry, these activities do not explain the apparent disappearance of these viruses from migratory waterfowl. Here we examine current and historical aquatic bird IAV surveillance and outbreaks of HP H5Nx in poultry in the United States and Canada, providing additional evidence of unresolved mechanisms that restrict the emergence and perpetuation of HP avian influenza viruses in these natural reservoirs.

Widespread detection of highly pathogenic H5 influenza viruses in wild birds from the Pacific Flyway of the United States

A novel highly pathogenic avian influenza virus belonging to the H5 clade 2.3.4.4 variant viruses was detected in North America in late 2014. Motivated by the identification of these viruses in domestic poultry in Canada, an intensive study was initiated to conduct highly pathogenic avian influenza surveillance in wild birds in the Pacific Flyway of the United States. A total of 4,729 hunter-harvested wild birds were sampled and highly pathogenic avian influenza virus was detected in 1.3% (n = 63). Three H5 clade 2.3.4.4 subtypes were isolated from wild birds, H5N2, H5N8, and H5N1, representing the wholly Eurasian lineage H5N8 and two novel reassortant viruses. Testing of 150 additional wild birds during avian morbidity and mortality investigations in Washington yielded 10 (6.7%) additional highly pathogenic avian influenza isolates (H5N8 = 3 and H5N2 = 7). The geographically widespread detection of these viruses in apparently healthy wild waterfowl suggest that the H5 clade 2.3.4.4 variant viruses may behave similarly in this taxonomic group whereby many waterfowl species are susceptible to infection but do not demonstrate obvious clinical disease. Despite these findings in wild waterfowl, mortality has been documented for some wild bird species and losses in US domestic poultry during the first half of 2015 were unprecedented.

One Health: Lessons Learned from East Africa

Africa is faced with many of the most daunting challenges of our time. It comprises roughly 15% of the world's human population, and most of its countries are perpetually ranked "Low" on the United Nations' Human Development Index. On the other hand, Africa has arguably the largest proportion of intact natural ecosystems, biodiversity, and sociocultural capital and the lowest impact on global warming of any continent. Thus, African leaders are faced with competing demands and values among a multitude of complex issues, such as high human population growth, extreme poverty, food insecurity, land use policy, climate change, and biodiversity conservation. In this context, building sustainable national systems for human and/or animal health is one of the grand challenges of this generation. Today's complex global health and development challenges require long-term commitment and a range of approaches that are too broad for any one discipline, institution, or country to implement on its own. The One Health concept recognizes the interconnectedness of global health issues and, as such, promotes the importance of and need for international, interdisciplinary, and cross-sectoral communication and collaboration at local, national, and international levels. By taking advantage of natural cultural tendencies for shared leadership, resource allocation, and community values, African leaders are currently proactively demonstrating the principles of One Health, and thus becoming a model for this global vision. And by focusing on partnerships rather than donor-recipient relationships, they are fostering the development of shared priorities and are increasingly driving their own health agenda to fulfill their own needs.

Efficacy of scallop shell powders and slaked lime for inactivating avian influenza virus under harsh conditions

The efficacy and stability of scallop shell powder (SSP) were investigated, in terms of its capacity to inactivate avian influenza virus (AIV), and compared with slaked lime (SL). An environmental simulation was conducted by emulating sunlight and wet-dry conditions. The powders were collected at consecutive 2-week intervals under sunlight and upon every resuspension. These materials were tested by mixing them with AIV and incubating the mixture for 3 min or 20 h, followed by AIV titration. At the same time, a pH buffering test was conducted by neutralization with Tris-HCl. The results revealed that SSP and SL have high alkalinity and excellent ability to inactivate AIV. In a simulated harsh environment, SSP and SL retained a satisfactory ability to inactivate AIV within 20 h throughout the experimental procedure. However, SSP was able to inactivate AIV during a short contact period (3 min), even under harsh conditions, and it was more resistant than SL to neutralization.

Virological evaluation of avian influenza virus persistence in natural and anthropic ecosystems of Western Siberia (Novosibirsk Region, summer 2012)

BACKGROUND

Wild aquatic birds, reservoir of low-pathogenicity (LP) avian influenza viruses (AIVs), congregate in huge numbers in Western Siberia wetlands, where major intra- and inter-continental bird flyways overlap. In 2005 and 2006, highly pathogenic (HP) AIV H5N1 epizootics affected wild and domestic birds in the Novosibirsk Region. In 2012, we evaluated AIV persistence in Siberian natural and anthropic ecosystems.

METHODOLOGY/PRINCIPAL FINDINGS

In Novosibirsk Region, 166 wild birds ecologically linked to aquatic environments and 152 domestic waterfowl were examined for AIV isolation in embryonating chicken eggs. Biological samples were obtained by integrating the conventional cloacal swab collection with the harvesting of samples from birds' plumage. Haemagglutinating allantoic fluids were further characterized by serological and molecular methods. In August-September 2012, 17 AIVs, including three H3N8, eight H4N6, two H4N?, one H2N?, one H?N2, and two unsubtyped LPAIVs, were isolated from 15 wild ducks. Whereas comparable proportions of wild Anseriformes (n.118) tested virus isolation (VI)-positive from cloaca and feathers (5.9% vs 8.5%) were detected, the overall prevalence of virus isolation, obtained from both sampling methods, was 2.4 times higher than that calculated on results from cloacal swab examination only (14.4% vs 5.9%). Unlike previously described in this area, the H4N6 antigenic subtype was found to be the prevalent one in 2012. Both cloacal and feather samples collected from domestic waterfowl tested VI-negative.

CONCLUSION/SIGNIFICANCE

We found lack of evidence for the H5N1 HPAIV circulation, explainable by the poor environmental fitness of HPAIVs in natural ecosystems. Our LPAIV isolation data emphasise the importance of Siberia wetlands in influenza A virus ecology, providing evidence of changes in circulation dynamics of HN antigenic subtypes harboured in wild bird reservoirs. Further studies of isolates, based on bioinformatic approaches to virus molecular evolution and phylogenesis, will be needed to better elucidate mechanisms involved in AIV perpetuation in this area.

Reassortment patterns of avian influenza virus internal segments among different subtypes

Background

The segmented RNA genome of avian Influenza viruses (AIV) allows genetic reassortment between co-infecting viruses, providing an evolutionary pathway to generate genetic innovation. The genetic diversity (16 haemagglutinin and 9 neuraminidase subtypes) of AIV indicates an extensive reservoir of influenza viruses exists in bird populations, but how frequently subtypes reassort with each other is still unknown. Here we quantify the reassortment patterns among subtypes in the Eurasian avian viral pool by reconstructing the ancestral states of the subtypes as discrete states on time-scaled phylogenies with respect to the internal protein coding segments. We further analyzed how host species, the inferred evolutionary rates and the d_N/d_S ratio varied among segments and between discrete subtypes, and whether these factors may be associated with inter-subtype reassortment rate.

Results

The general patterns of reassortment are similar among five internal segments with the exception of segment 8, encoding the Non-Structural genes, which has a more divergent phylogeny. However, significant variation in rates between subtypes was observed. In particular, hemagglutinin-encoding segments of subtypes H5 to H9 reassort at a lower rate compared to those of H1 to H4, and Neuraminidase-encoding segments of subtypes N1 and N2 reassort less frequently than N3 to N9. Both host species and d_N/d_S ratio were significantly associated with reassortment rate, while evolutionary rate was not associated. The d_N/d_S ratio was negatively correlated with reassortment rate, as was the number of negatively selected sites for all segments.

Conclusions

These results indicate that overall selective constraint and host species are both associated with reassortment rate. These results together identify the wild bird population as the major source of new reassortants, rather than domestic poultry. The lower reassortment rates observed for H5N1 and H9N2 may be explained by the large proportion of strains derived from domestic poultry populations. In contrast, the higher rates observed in the H1N1, H3N8 and H4N6 subtypes could be due to their primary origin as infections of wild birds with multiple low pathogenicity strains in the large avian reservoir.

Neurologic aspects of influenza viruses

Although influenza A and B viruses are primarily known as respiratory viruses and mainly infected only the upper respiratory tract in humans, patients with influenza often develop signs and symptoms that are not due to the respiratory system. Frequently individuals with influenza develop headaches, meningismus, and even seizures in addition to their typical respiratory symptoms. In the past decades, influenza viruses have also been associated with serious non-respiratory signs. The famous 1918 strain of influenza was associated with von Economo's encephalitis lethargica and postencephalitic parkinsonism. In the 1960s influenza virus infections in children were associated with Reye's syndrome characterized often by fatty non-inflammatory hepatic disease and an encephalopathy with marked non-inflammatory cerebral edema. Intermittently children with influenza develop focal myalgia and myositis. Guillain–Barré syndrome was epidemiologically associated with the 1978 killed influenza vaccine but not subsequent vaccines. Although occasional children with influenza have developed encephalopathy, from 2000 through 2004 there was an increase in the number of serious cases of acute necrotizing encephalopathy accompanying infection with the influenza A 2009 strain. The current H5N1 strain of bird influenza occasionally infects humans with a high mortality rate and some appear to have central nervous signs. This chapter explores what is known about these influenza neurologic associations.

Will the damage be done before we feel the heat? Infectious disease emergence and human response

The global political economy is facing extreme challenges against a backdrop of large-scale expansion of human and domestic animal populations and related impacts on the biosphere. Significant global socio-ecological changes have occurred in the period of a single lifetime, driven by increased technology and access to physical and biological resources through open markets and globalization. Current resource consumption rates are not sustainable and ecological tipping points are being reached and one of the indicators of these may be a changing balance between hosts and pathogens. A period of extraordinary progress in reducing infection risk and disease impact on humans and domestic animals in the 20th Century is reversing in the 21st, but not always and not everywhere. Drivers for this shift are discussed in terms of demographics, agroecology, biodiversity decline and loss of resilience in ecosystems, climate change and increasing interconnectedness between species globally. Causality of disease emergence remains highly speculative, but patterns and data are emerging to commend a precautionary approach, while reassessing our global political, social and economic systems.

Evolution of influenza A virus H7 and N9 subtypes, Eastern Asia

Influenza A viruses are a threat to poultry and human health. We investigated evolution of influenza A virus H7 and N9 subtypes in wild and domestic birds. Influenza A(H7N9) virus probably emerged after a long silent circulation in live poultry markets in eastern Asia.

Emerging and reemerging diseases of avian wildlife

Of the many important avian wildlife diseases, aspergillosis, West Nile virus, avipoxvirus, Wellfleet Bay virus, avian influenza, and inclusion body disease of cranes are covered in this article. Wellfleet Bay virus, first identified in 2010, is considered an emerging disease. Avian influenza and West Nile virus have recently been in the public eye because of their zoonotic potential and links to wildlife. Several diseases labeled as reemerging are included because of recent outbreaks or, more importantly, recent research in areas such as genomics, which shed light on the mechanisms whereby these adaptable, persistent pathogens continue to spread and thrive.

Connecting the study of wild influenza with the potential for pandemic disease

Continuing outbreaks of pathogenic (H5N1) and pandemic (SOIVH1N1) influenza have underscored the need to understand the origin, characteristics, and evolution of novel influenza A virus (IAV) variants that pose a threat to human health. In the last 4-5years, focus has been placed on the organization of large-scale surveillance programs to examine the phylogenetics of avian influenza virus (AIV) and host-virus relationships in domestic and wild animals. Here we review the current gaps in wild animal and environmental surveillance and the current understanding of genetic signatures in potentially pandemic strains.

Infectious disease emergence and global change: thinking systemically in a shrinking world

BACKGROUND

Concern intensifying that emerging infectious diseases and global environmental changes that could generate major future human pandemics.

METHOD

A focused literature review was undertaken, partly informed by a forthcoming report on environment, agriculture and infectious diseases of poverty, facilitated by the Special Programme for Tropical Diseases.

RESULTS

More than ten categories of infectious disease emergence exist, but none formally analyse past, current or future burden of disease. Other evidence suggests that the dominant public health concern focuses on two informal groupings. Most important is the perceived threat of newly recognised infections, especially viruses that arise or are newly discovered in developing countries that originate in species exotic to developed countries, such as non-human primates, bats and rodents. These pathogens may be transmitted by insects or bats, or via direct human contact with bushmeat. The second group is new strains of influenza arising from intensively farmed chickens or pigs, or emerging from Asian "wet markets" where several bird species have close contact. Both forms appear justified because of two great pandemics: HIV/AIDS (which appears to have originated from bushmeat hunting in Africa before emerging globally) and Spanish influenza, which killed up to 2.5% of the human population around the end of World War I. Insufficiently appreciated is the contribution of the milieu which appeared to facilitate the high disease burden in these pandemics. Additionally, excess anxiety over emerging infectious diseases diverts attention from issues of greater public health importance, especially: (i) existing (including neglected) infectious diseases and (ii) the changing milieu that is eroding the determinants of immunity and public health, caused by adverse global environmental changes, including climate change and other components of stressed life and civilisation-supporting systems.

CONCLUSIONS

The focus on novel pathogens and minor forms of anti-microbial resistance in emerging disease literature is unjustified by their burden of disease, actual and potential, and diverts attention from far more important health problems and determinants. There is insufficient understanding of systemic factors that promote pandemics. Adverse global change could generate circumstances conducive to future pandemics with a high burden of disease, arising via anti-microbial and insecticidal resistance, under-nutrition, conflict, and public health breakdown.

Proteomic analysis of the lungs of mice infected with different pathotypes of H5N1 avian influenza viruses

The virulence of influenza virus is determined by viral and host factors. Data on the genetic basis of the virulence of H5N1 influenza viruses have increased over the past decade; however, the contributions of host factors to the outcomes of H5N1 infection remain largely unknown. Here, we tested two chicken H5N1 viruses in mice and found that A/chicken/VN1214/2007 was nonlethal in mice and only replicated in the lung, whereas A/chicken/VN1180/2006 was highly lethal and replicated systemically in mice. To investigate the host response against these two different virus infections, we performed proteomic analysis by using 2D DIGE on the lung tissues of mice collected on days 1 and 3 postinoculation with different viruses or PBS as a control. Thirty-nine differentially expressed (DE) proteins related to "immune and stimulus response," "macromolecular biosynthesis and metabolism," and "cellular component and cytoskeleton" were identified in the virus-inoculated groups. Moreover, 13 DE proteins were identified between the two virus-inoculated groups, implying that these proteins may play important roles in the different outcomes of infection with these two viruses. Our data provide important information regarding the host response to mild and lethal H5N1 influenza virus infection.

Risks of emerging infectious diseases: evolving threats in a changing area, the mediterranean basin

The Mediterranean basin is a biodiversity hotspot; it has historically had a large human presence that has shaped ecosystems for millennia. As the cradle of many civilizations, the area was one of the main theatres for transitions that punctuated both human and pathogen histories, which are intimately linked. Today we are living through another great historical transition summarized in the expression 'global changes'. In this context, we are witnessing a rise in the emergence of pathogens widely associated with aforementioned global changes. The Mediterranean basin might be especially vulnerable to this phenomenon due to the acute consequences global changes will have in this key intercontinental interface region. In addition, Arab revolutions and European economic crisis are creating both sanitary issues and presenting new opportunities to improve infectious disease control and prevention in the region. The aim of this review is to identify the impacts that ongoing changes might have on the risk of infectious disease emergence in the Mediterranean basin. We focussed on three key domains undergoing transformations: (i) resources, namely safe drinking water and animal products, (ii) socio-economic factors including health inequalities within countries and poor sanitary conditions linked to ongoing conflicts and (iii) movements of people and goods that are reshaped by current changes and are intimately linked to the risk of disease proliferation. Building on recent examples, we try to identify upcoming challenges and discuss ways to meet them in the light of existing international human and veterinary health guidelines and their possible improvements.

Model to track wild birds for avian influenza by means of population dynamics and surveillance information

Design, sampling and data interpretation constitute an important challenge for wildlife surveillance of avian influenza viruses (AIV). The aim of this study was to construct a model to improve and enhance identification in both different periods and locations of avian species likely at high risk of contact with AIV in a specific wetland. This study presents an individual-based stochastic model for the Ebre Delta as an example of this appliance. Based on the Monte-Carlo method, the model simulates the dynamics of the spread of AIV among wild birds in a natural park following introduction of an infected bird. Data on wild bird species population, apparent AIV prevalence recorded in wild birds during the period of study, and ecological information on factors such as behaviour, contact rates or patterns of movements of waterfowl were incorporated as inputs of the model. From these inputs, the model predicted those species that would introduce most of AIV in different periods and those species and areas that would be at high risk as a consequence of the spread of these AIV incursions. This method can serve as a complementary tool to previous studies to optimize the allocation of the limited AI surveillance resources in a local complex ecosystem. However, this study indicates that in order to predict the evolution of the spread of AIV at the local scale, there is a need for further research on the identification of host factors involved in the interspecies transmission of AIV.

High influenza a virus infection rates in Mallards bred for hunting in the Camargue, South of France

During the last decade, the role of wildlife in emerging pathogen transmission to domestic animals has often been pointed out. Conversely, far less attention has been paid to pathogen transmission from domestic animals to wildlife. Here, we focus on the case of game restocking, which implies the release of millions of animals worldwide each year. We conducted a 2-year study in the Camargue (Southern France) to investigate the influence of hand-reared Mallard releases on avian influenza virus dynamics in surrounding wildlife. We sampled Mallards (cloacal swabs) from several game duck facilities in 2009 and 2010 before their release. A very high (99%) infection rate caused by an H10N7 strain was detected in the game bird facility we sampled in 2009. We did not detect this strain in shot ducks we sampled, neither during the 2008/2009 nor the 2009/2010 hunting seasons. In 2010 infection rates ranged from 0 to 24% in hand-reared ducks. The 2009 H10N7 strain was fully sequenced. It results from multiple reassortment events between Eurasian low pathogenic strains. Interestingly, H10N7 strains had previously caused human infections in Egypt and Australia. The H10 and N7 segments we sequenced were clearly distinct from the Australian ones but they belonged to the same large cluster as the Egyptian ones. We did not observe any mutation linked to increased virulence, transmission to mammals, or antiviral resistance in the H10N7 strain we identified. Our results indicate that the potential role of hand-reared Mallards in influenza virus epizootics must be taken into account given the likely risk of viral exchange between game bird facilities and wild habitats, owing to duck rearing conditions. Measures implemented to limit transmission from wildlife to domestic animals as well as measures to control transmission from domestic animals to wild ones need to be equally reinforced.

Reassortant influenza A viruses in wild duck populations: effects on viral shedding and persistence in water

Wild ducks of the genus Anas represent the natural hosts for a large genetic diversity of influenza A viruses. In these hosts, co-infections with different virus genotypes are frequent and result in high rates of genetic reassortment. Recent genomic data have provided information regarding the pattern and frequency of these reassortant viruses in duck populations; however, potential consequences on viral shedding and maintenance in the environment have not been investigated. On the basis of full-genome sequencing, we identified five virus genotypes, in a wild duck population in northwestern Minnesota (USA), that naturally arose from genetic reassortments. We investigated the effects of influenza A virus genotype on the viral shedding pattern in Mallards (Anas platyrhynchos) and the duration of infectivity in water, under different temperature regimens. Overall, we found that variation in the viral genome composition of these isolates had limited effects on duration, extent and pattern of viral shedding, as well as on the reduction of infectivity in water over time. These results support that, in wild ducks, functionally equivalent gene segments could be maintained in virus populations with no fitness costs when genetic reassortments occur.

Consecutive natural influenza a virus infections in sentinel mallards in the evident absence of subtype-specific hemagglutination inhibiting antibodies

Dabbling ducks, particularly Mallards (Anas platyrhynchos) have been frequently and consistently reported to play a pivotal role as a reservoir of low pathogenic avian influenza viruses (AIV). From October 2006 to November 2008, hand-raised Mallard ducks kept at a pond in an avifaunistically rich area of Southern Germany served as sentinel birds in the AIV surveillance programme in Germany. The pond was regularly visited by several species of dabbling ducks. A flock of sentinel birds, consisting of the same 16 individual birds during the whole study period, was regularly tested virologically and serologically for AIV infections. Swab samples were screened by RT-qPCR and, if positive, virus was isolated in embryonated chicken eggs. Serum samples were tested by the use of competitive ELISA and hemagglutinin inhibition (HI) assay. Sequences of full-length hemagglutinin (HA) and neuraminidase (NA) genes were phylogenetically analysed. Four episodes of infections with Eurasian-type AIV occurred in August (H6N8), October/November (H3N2, H2N3) 2007, in January (H3N2) and September (H3N8) 2008. The HA and NA genes of the H3N2 viruses of October 2007 and January 2008 were almost identical rendering the possibility of a re-introduction of that virus from the environment of the sentinel flock highly likely. The HA of the H3N8 virus of September 2008 belonged to a different cluster. As a correlate of the humoral immune response, titres of nucleocapsid protein-specific antibodies fluctuated in correlation with the course of AIV infection episodes. However, no specific systemic response of hemagglutination inhibiting antibodies could be demonstrated even if homologous viral antigens were used. Besides being useful as early indicators for the circulation of influenza viruses in a specific region, the sentinel ducks also contributed to gaining insights into the ecobiology of AIV infection in aquatic wild birds.

Highly pathogenic influenza A(H5N1) virus survival in complex artificial aquatic biotopes

Background

Very little is known regarding the persistence of Highly Pathogenic Avian Influenza (HPAI) H5N1 viruses in aquatic environments in tropical countries, although environmental materials have been suggested to play a role as reservoirs and sources of transmission for H5N1 viruses.

Methodology/Principal Findings

The survival of HPAI H5N1 viruses in experimental aquatic biotopes (water, mud, aquatic flora and fauna) relevant to field conditions in Cambodia was investigated. Artificial aquatic biotopes, including simple ones containing only mud and water, and complex biotopes involving the presence of aquatic flora and fauna, were set up. They were experimentally contaminated with H5N1 virus. The persistence of HPAI H5N1 virus (local avian and human isolates) was determined by virus isolation in embryonated chicken eggs and by real-time reverse-polymerase chain reaction. Persistence of infectious virus did not exceed 4 days, and was only identified in rain water. No infectious virus particles were detected in pond and lake water or mud even when high inoculum doses were used. However, viral RNA persisted up to 20 days in rain water and 7 days in pond or lake water. Viral RNA was also detected in mud samples, up to 14 days post-contamination in several cases. Infectious virus and viral RNA was detected in few cases in the aquatic fauna and flora, especially in bivalves and labyrinth fish, although these organisms seemed to be mostly passive carriers of the virus rather than host allowing virus replication.

Conclusions/Significance

Although several factors for the survival and persistence of HPAI viruses in the environment are still to be elucidated, and are particularly hard to control in laboratory conditions, our results, along with previous data, support the idea that environmental surveillance is of major relevance for avian influenza control programs.

Ecological determinants of highly pathogenic avian influenza (H5N1) outbreaks in Bangladesh

Background

The agro-ecology and poultry husbandry of the south Asian and south-east Asian countries share common features, however, with noticeable differences. Hence, the ecological determinants associated with risk of highly pathogenic avian influenza (HPAI-H5N1) outbreaks are expected to differ between Bangladesh and e.g., Thailand and Vietnam. The primary aim of the current study was to establish ecological determinants associated with the risk of HPAI-H5N1 outbreaks at subdistrict level in Bangladesh. The secondary aim was to explore the performance of two different statistical modeling approaches for unmeasured spatially correlated variation.

Methodology/Principal Findings

An ecological study at subdistrict level in Bangladesh was performed with 138 subdistricts with HPAI-H5N1 outbreaks during 2007–2008, and 326 subdistricts with no outbreaks. The association between ecological determinants and HPAI-H5N1 outbreaks was examined using a generalized linear mixed model. Spatial clustering of the ecological data was modeled using 1) an intrinsic conditional autoregressive (ICAR) model at subdistrict level considering their first order neighbors, and 2) a multilevel (ML) model with subdistricts nested within districts. Ecological determinants significantly associated with risk of HPAI-H5N1 outbreaks at subdistrict level were migratory birds' staging areas, river network, household density, literacy rate, poultry density, live bird markets, and highway network. Predictive risk maps were derived based on the resulting models. The resulting models indicate that the ML model absorbed some of the covariate effect of the ICAR model because of the neighbor structure implied in the two different models.

Conclusions/Significance

The study identified a new set of ecological determinants related to river networks, migratory birds' staging areas and literacy rate in addition to already known risk factors, and clarified that the generalized concept of free grazing duck and duck-rice cultivation interacted ecology are not significant determinants for Bangladesh. These findings will refine current understanding of the HPAI-H5N1 epidemiology in Bangladesh.

Environment: a potential source of animal and human infection with influenza A (H5N1) virus

BACKGROUND

Very little is known regarding the persistence of highly pathogenic avian influenza H5N1 viruses in natural settings during outbreaks in tropical countries, although environmental factors may well play a role in the persistence and in the transmission of H5N1 virus.

OBJECTIVE

To investigate various environmental compartments surrounding outbreak areas as potential sources for H5N1 virus transmission.

METHODS

Environmental specimens were collected following outbreaks of avian influenza in Cambodia between April 2007 and February 2010. The methods used to concentrate H5N1 virus from water samples were based either on agglutination of the virus with chicken red blood cells or on adsorption on glass wool, followed by an elution-concentration step. An elution-concentration method was used for mud specimens. All samples that tested positive by real-time RT-PCRs (qRT-PCRs) targeting the HA5, M and NA1 genes were inoculated into embryonated hen eggs for virus isolation.

RESULTS

Of a total of 246 samples, 46 (19%) tested positive for H5N1 by qRT-PCRs. Viral RNA was frequently detected in dust, mud and soil samples from the farms' environment (respectively, 46%, 31% and 15%). Samples collected from ponds gave a lower proportion of positive samples (6%) as compared to those collected from the farms (24%). In only one sample, infectious virus particles were successfully isolated.

CONCLUSION

During H5N1 virus outbreaks, numerous environmental samples surrounding outbreak areas are contaminated by the virus and may act as potential sources for human and/or animal contamination.

Eco-virological approach for assessing the role of wild birds in the spread of avian influenza H5N1 along the Central Asian Flyway

A unique pattern of highly pathogenic avian influenza (HPAI) H5N1 outbreaks has emerged along the Central Asia Flyway, where infection of wild birds has been reported with steady frequency since 2005. We assessed the potential for two hosts of HPAI H5N1, the bar-headed goose (Anser indicus) and ruddy shelduck (Tadorna tadorna), to act as agents for virus dispersal along this 'thoroughfare'. We used an eco-virological approach to compare the migration of 141 birds marked with GPS satellite transmitters during 2005-2010 with: 1) the spatio-temporal patterns of poultry and wild bird outbreaks of HPAI H5N1, and 2) the trajectory of the virus in the outbreak region based on phylogeographic mapping. We found that biweekly utilization distributions (UDs) for 19.2% of bar-headed geese and 46.2% of ruddy shelduck were significantly associated with outbreaks. Ruddy shelduck showed highest correlation with poultry outbreaks owing to their wintering distribution in South Asia, where there is considerable opportunity for HPAI H5N1 spillover from poultry. Both species showed correlation with wild bird outbreaks during the spring migration, suggesting they may be involved in the northward movement of the virus. However, phylogeographic mapping of HPAI H5N1 clades 2.2 and 2.3 did not support dissemination of the virus in a northern direction along the migration corridor. In particular, two subclades (2.2.1 and 2.3.2) moved in a strictly southern direction in contrast to our spatio-temporal analysis of bird migration. Our attempt to reconcile the disciplines of wild bird ecology and HPAI H5N1 virology highlights prospects offered by both approaches as well as their limitations.

Study of influenza A virus in wild boars living in a major duck wintering site

Wild birds, which are reservoirs of influenza viruses, are believed to be the original source of new influenza viruses-including highly pathogenic ones-that can be transmitted to domestic animals as well as humans and represent a potential epizootic and/or pandemic threat. Despite increasing knowledge on influenza A virus dynamics in wild birds, the viral circulation in wild boars remains largely unknown. This is of particular interest since pigs can be infected with both human and avian viruses; upon co-infection, they can act as a mixing vessel through reassortment, a mechanism that resulted in the emergence of the pandemic H1N1 virus in 2009. The Camargue (Southern France) appears as an ideal study area to investigate inter-species transmission of influenza A viruses from wild birds and possibly humans to wild boars. Indeed, the important local wild boar population shares wetland use with humans and the largest concentration of wintering ducks in France, that are both susceptible to infection by influenza A viruses. Additionally, wild boars occasionally prey on ducks. We conducted a virological and serological survey on wild boars in the Camargue (Southern France) between September 2009 and November 2010. No influenza A virus was detected in the collected nasal swabs (n=315) and no influenza specific antibodies were observed in the serological samples (n=20). As the study was mainly focused on viral excretion, which is limited in time, we cannot exclude that low or occasional influenza A virus circulation took place during the study period. Although, wild boars did not seem to be a key element in the dynamics of influenza A virus circulation in the Camargue, wild boar influenza A virus infections should be more widely studied to determine if the pattern observed here represents the normal situation or an exceptional one.

Migratory flyway and geographical distance are barriers to the gene flow of influenza virus among North American birds

Despite the importance of migratory birds in the ecology and evolution of avian influenza virus (AIV), there is a lack of information on the patterns of AIV spread at the intra-continental scale. We applied a variety of statistical phylogeographic techniques to a plethora of viral genome sequence data to determine the strength, pattern and determinants of gene flow in AIV sampled from wild birds in North America. These analyses revealed a clear isolation-by-distance of AIV among sampling localities. In addition, we show that phylogeographic models incorporating information on the avian flyway of sampling proved a better fit to the observed sequence data than those specifying homogeneous or random rates of gene flow among localities. In sum, these data strongly suggest that the intra-continental spread of AIV by migratory birds is subject to major ecological barriers, including spatial distance and avian flyway.

Prevalence of Buggy Creek virus (Togaviridae: Alphavirus) in insect vectors increases over time in the presence of an invasive avian host

Invasive species can disrupt natural disease dynamics by altering pathogen transmission among native hosts and vectors. The relatively recent occupancy of cliff swallow (Petrochelidon pyrrhonota) nesting colonies in western Nebraska by introduced European house sparrows (Passer domesticus) has led to yearly increases in the prevalence of an endemic arbovirus, Buggy Creek virus (BCRV), in its native swallow bug (Oeciacus vicarius) vector at sites containing both the invasive sparrow host and the native swallow host. At sites without the invasive host, no long-term changes in prevalence have occurred. The percentage of BCRV isolates exhibiting cytopathicity in Vero-cell culture assays increased significantly with year at sites with sparrows but not at swallow-only sites, suggesting that the virus is becoming more virulent to vertebrates in the presence of the invasive host. Increased BCRV prevalence in bug vectors at mixed-species colonies may reflect high virus replication rates in house sparrow hosts, resulting in frequent virus transmission between sparrows and swallow bugs. This case represents a rare empirical example of a pathogen effectively switching to an invasive host, documented in the early phases of the host's arrival in a specialized ecosystem and illustrating how an invasive species can promote long-term changes in host-parasite transmission dynamics.

Spatio-temporal magnitude and direction of highly pathogenic avian influenza (H5N1) outbreaks in Bangladesh

BACKGROUND

The number of outbreaks of HPAI-H5N1 reported by Bangladesh from 2007 through 2011 placed the country among the highest reported numbers worldwide. However, so far, the understanding of the epidemic progression, direction, intensity, persistence and risk variation of HPAI-H5N1 outbreaks over space and time in Bangladesh remains limited.

METHODOLOGY/PRINCIPAL FINDINGS

To determine the magnitude and spatial pattern of the highly pathogenic avian influenza A subtype H5N1 virus outbreaks over space and time in poultry from 2007 to 2009 in Bangladesh, we applied descriptive and analytical spatial statistics. Temporal distribution of the outbreaks revealed three independent waves of outbreaks that were clustered during winter and spring. The descriptive analyses revealed that the magnitude of the second wave was the highest as compared to the first and third waves. Exploratory mapping of the infected flocks revealed that the highest intensity and magnitude of the outbreaks was systematic and persistent in an oblique line that connects south-east to north-west through the central part of the country. The line follows the Brahmaputra-Meghna river system, the junction between Central Asian and East Asian flyways, and the major poultry trading route in Bangladesh. Moreover, several important migratory bird areas were identified along the line. Geostatistical analysis revealed significant latitudinal directions of outbreak progressions that have similarity to the detected line of intensity and magnitude.

CONCLUSION/SIGNIFICANCE

The line of magnitude and direction indicate the necessity of mobilizing maximum resources on this line to strengthen the existing surveillance.