Avian influenza H5N1 viral and bird migration networks in Asia

Spatiotemporal genotype replacement of H5N8 avian influenza viruses contributed to H5N1 emergence in 2021/2022 panzootic

Since 2020, clade 2.3.4.4b highly pathogenic avian influenza H5N8 and H5N1 viruses have swept through continents, posing serious threats to the world. Through comprehensive analyses of epidemiological, genetic, and bird migration data, we found that the dominant genotype replacement of the H5N8 viruses in 2020 contributed to the H5N1 outbreak in the 2021/2022 wave. The 2020 outbreak of the H5N8 G1 genotype instead of the G0 genotype produced reassortment opportunities and led to the emergence of a new H5N1 virus with G1's HA and MP genes. Despite extensive reassortments in the 2021/2022 wave, the H5N1 virus retained the HA and MP genes, causing a significant outbreak in Europe and North America. Furtherly, through the wild bird migration flyways investigation, we found that the temporal-spatial coincidence between the outbreak of the H5N8 G1 virus and the bird autumn migration may have expanded the H5 viral spread, which may be one of the main drivers of the emergence of the 2020-2022 H5 panzootic.IMPORTANCESince 2020, highly pathogenic avian influenza (HPAI) H5 subtype variants of clade 2.3.4.4b have spread across continents, posing unprecedented threats globally. However, the factors promoting the genesis and spread of H5 HPAI viruses remain unclear. Here, we found that the spatiotemporal genotype replacement of H5N8 HPAI viruses contributed to the emergence of the H5N1 variant that caused the 2021/2022 panzootic, and the viral evolution in poultry of Egypt and surrounding area and autumn bird migration from the Russia-Kazakhstan region to Europe are important drivers of the emergence of the 2020-2022 H5 panzootic. These findings provide important targets for early warning and could help control the current and future HPAI epidemics.

Synchrony of Bird Migration with Global Dispersal of Avian Influenza Reveals Exposed Bird Orders

Highly pathogenic avian influenza virus (HPAIV) A H5, particularly clade 2.3.4.4, has caused worldwide outbreaks in domestic poultry, occasional spillover to humans, and increasing deaths of diverse species of wild birds since 2014. Wild bird migration is currently acknowledged as an important ecological process contributing to the global dispersal of HPAIV H5. However, this mechanism has not been quantified using bird movement data from different species, and the timing and location of exposure of different species is unclear. We sought to explore these questions through phylodynamic analyses based on empirical data of bird movement tracking and virus genome sequences of clade 2.3.4.4 and 2.3.2.1. First, we demonstrate that seasonal bird migration can explain salient features of the global dispersal of clade 2.3.4.4. Second, we detect synchrony between the seasonality of bird annual cycle phases and virus lineage movements. We reveal the differing exposed bird orders at geographical origins and destinations of HPAIV H5 clade 2.3.4.4 lineage movements, including relatively under-discussed orders. Our study provides a phylodynamic framework that links the bird movement ecology and genomic epidemiology of avian influenza; it highlights the importance of integrating bird behavior and life history in avian influenza studies.

Evolution and Spread of Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Virus in Wild Birds, South Korea, 2022-2023

During October 2022-March 2023, highly pathogenic avian influenza (HPAI) A(H5N1) clade 2.3.4.4b virus caused outbreaks in South Korea, including 174 cases in wild birds. To understand the origin and role of wild birds in the evolution and spread of HPAI viruses, we sequenced 113 HPAI isolates from wild birds and performed phylogenetic analysis. We identified 16 different genotypes, indicating extensive genetic reassortment with viruses in wild birds. Phylodynamic analysis showed that the viruses were most likely introduced to the southern Gyeonggi-do/northern Chungcheongnam-do area through whooper swans (Cygnus cygnus) and spread southward. Cross-species transmission occurred between various wild bird species, including waterfowl and raptors, resulting in the persistence of HPAI in wild bird populations and further geographic spread as these birds migrated throughout South Korea. Enhanced genomic surveillance was an integral part of the HPAI outbreak response, aiding in timely understanding of the origin, evolution, and spread of the virus.

Detection of clade 2.3.4.4 highly pathogenic avian influenza H5 viruses in healthy wild birds in the Hadeji-Nguru wetland, Nigeria 2022

Background

The introduction of multiple avian influenza virus (AIV) subtypes into Nigeria has resulted in several poultry outbreaks purportedly linked to trade and wild birds. The role of wild birds in perpetuating AIV in Nigeria was, therefore, elucidated.

Methods

A cross-sectional study was conducted among wild aquatic bird species at the Hadejia-Nguru wetlands in Northeastern Nigeria between March and April 2022. A total of 452 swabs (226 cloacae and 226 oropharyngeal) were collected using a mist net to capture the birds. These samples were tested by RT-qPCR, followed by sequencing.

Results

Highly pathogenic AIV of the H5N1 subtype was identified in clinically healthy wild bird species, namely, African jacana, ruff, spur-winged goose, squared-tailed nightjar, white-faced whistling ducks, and white stork. A prevalence of 11.1% (25/226) was recorded. Phylogenetic analysis of the complete HA gene segment indicated the presence of clade 2.3.4.4b. However, these H5N1 viruses characterized from these wild birds cluster separately from the H5N1 viruses characterized in Nigerian poultry since early 2021. Specifically, the viruses form two distinct genetic groups both linked with the Eurasian H5N1 gene pool but likely resulting from two distinct introductions of the virus in the region. Whole-genome characterization of the viruses reveals the presence of mammalian adaptive marker E627K in two Afro-tropical resident aquatic ducks. This has zoonotic potential.

Conclusion

Our findings highlight the key role of surveillance in wild birds to monitor the diversity of viruses in this area, provide the foundations of epidemiological understanding, and facilitate risk assessment.

Phylodynamic approaches to studying avian influenza virus

Avian influenza viruses can cause severe disease in domestic and wild birds and are a pandemic threat. Phylodynamics is the study of how epidemiological, evolutionary, and immunological processes can interact to shape viral phylogenies. This review summarizes how phylodynamic methods have and could contribute to the study of avian influenza viruses. Specifically, we assess how phylodynamics can be used to examine viral spread within and between wild or domestic bird populations at various geographical scales, identify factors associated with virus dispersal, and determine the order and timing of virus lineage movement between geographic regions or poultry production systems. We discuss factors that can complicate the interpretation of phylodynamic results and identify how future methodological developments could contribute to improved control of the virus.

Functional traits explain waterbirds' host status, subtype richness, and community-level infection risk for avian influenza

Species functional traits can influence pathogen transmission processes, and consequently affect species' host status, pathogen diversity, and community-level infection risk. We here investigated, for 143 European waterbird species, effects of functional traits on host status and pathogen diversity (subtype richness) for avian influenza virus at species level. We then explored the association between functional diversity and HPAI H5Nx occurrence at the community level for 2016/17 and 2021/22 epidemics in Europe. We found that both host status and subtype richness were shaped by several traits, such as diet guild and dispersal ability, and that the community-weighted means of these traits were also correlated with community-level risk of H5Nx occurrence. Moreover, functional divergence was negatively associated with H5Nx occurrence, indicating that functional diversity can reduce infection risk. Our findings highlight the value of integrating trait-based ecology into the framework of diversity-disease relationship, and provide new insights for HPAI prediction and prevention.

The NIH Comparative Genomics Resource: addressing the promises and challenges of comparative genomics on human health

Comparative genomics is the comparison of genetic information within and across organisms to understand the evolution, structure, and function of genes, proteins, and non-coding regions (Sivashankari and Shanmughavel, Bioinformation 1:376-8, 2007). Advances in sequencing technology and assembly algorithms have resulted in the ability to sequence large genomes and provided a wealth of data that are being used in comparative genomic analyses. Comparative analysis can be leveraged to systematically explore and evaluate the biological relationships and evolution between species, aid in understanding the structure and function of genes, and gain a better understanding of disease and potential drug targets. As our knowledge of genetics expands, comparative genomics can help identify emerging model organisms among a broader span of the tree of life, positively impacting human health. This impact includes, but is not limited to, zoonotic disease research, therapeutics development, microbiome research, xenotransplantation, oncology, and toxicology. Despite advancements in comparative genomics, new challenges have arisen around the quantity, quality assurance, annotation, and interoperability of genomic data and metadata. New tools and approaches are required to meet these challenges and fulfill the needs of researchers. This paper focuses on how the National Institutes of Health (NIH) Comparative Genomics Resource (CGR) can address both the opportunities for comparative genomics to further impact human health and confront an increasingly complex set of challenges facing researchers.

Decision-support tools to build climate resilience against emerging infectious diseases in Europe and beyond

Climate change is one of several drivers of recurrent outbreaks and geographical range expansion of infectious diseases in Europe. We propose a framework for the co-production of policy-relevant indicators and decision-support tools that track past, present, and future climate-induced disease risks across hazard, exposure, and vulnerability domains at the animal, human, and environmental interface. This entails the co-development of early warning and response systems and tools to assess the costs and benefits of climate change adaptation and mitigation measures across sectors, to increase health system resilience at regional and local levels and reveal novel policy entry points and opportunities. Our approach involves multi-level engagement, innovative methodologies, and novel data streams. We take advantage of intelligence generated locally and empirically to quantify effects in areas experiencing rapid urban transformation and heterogeneous climate-induced disease threats. Our goal is to reduce the knowledge-to-action gap by developing an integrated One Health-Climate Risk framework.

Spatio-temporal distribution & seasonality of highly pathogenic avian influenza H5N1 & H5N8 outbreaks in India, 2006-2021

Background & objectives

The highly pathogenic avian influenza (HPAI) H5N1 and H5N8 viruses have been one of the leading causes of avian diseases worldwide, resulting in severe economic losses and posing potential zoonotic risk. There are no reports on the correlation of the seasonality of H5N1 and H5N8 viruses with the migratory bird season in India, along with the species affected. The present report describes the distribution and seasonality of HPAI outbreaks in India from 2006 to 2021.

Methods

The data on the occurrence and locations of outbreaks in India and affected bird species were collated from the Food and Agriculture Organization of the United Nations database and grouped by month and year. The distribution and seasonality of HPAI H5N1 and H5N8 viruses were analyzed.

Results

A total of 284 H5N1 outbreaks were reported since 2006, with a surge in 2021. The initial outbreaks of H5N1 were predominantly in poultry. Since 2016, 57 outbreaks of H5N8 were also reported, predominantly in wild birds. Most of the outbreaks of HPAI were reported from post monsoon onwards till pre-summer season (i.e. between October and March) with their peak in winter, in January. Apart from poultry, the bird species such as owl, Indian peafowl, lesser adjutant, crows and wild migratory birds such as demoiselle crane, northern pintail and bar-headed goose were positive for HPAI.

Interpretation & conclusions

Such studies on the seasonality of HPAI outbreaks would help in the development of prevention and control strategies. The recent human infections of H5N1 and H9N2 viruses highlight the need to strengthen surveillance in wild, resident, migratory birds and in poultry along with One Health studies in India.

Potential cross-species transmission of highly pathogenic avian influenza H5 subtype (HPAI H5) viruses to humans calls for the development of H5-specific and universal influenza vaccines

In recent years, highly pathogenic avian influenza H5 subtype (HPAI H5) viruses have been prevalent around the world in both avian and mammalian species, causing serious economic losses to farmers. HPAI H5 infections of zoonotic origin also pose a threat to human health. Upon evaluating the global distribution of HPAI H5 viruses from 2019 to 2022, we found that the dominant strain of HPAI H5 rapidly changed from H5N8 to H5N1. A comparison of HA sequences from human- and avian-derived HPAI H5 viruses indicated high homology within the same subtype of viruses. Moreover, amino acid residues 137A, 192I, and 193R in the receptor-binding domain of HA1 were the key mutation sites for human infection in the current HPAI H5 subtype viruses. The recent rapid transmission of H5N1 HPAI in minks may result in the further evolution of the virus in mammals, thereby causing cross-species transmission to humans in the near future. This potential cross-species transmission calls for the development of an H5-specific influenza vaccine, as well as a universal influenza vaccine able to provide protection against a broad range of influenza strains.

H9N2 avian influenza virus dispersal along Bangladeshi poultry trading networks

Avian influenza virus subtype H9N2 is endemic in Bangladesh's poultry population. The subtype affects poultry production and poses a potential zoonotic risk. Insufficient understanding of how the poultry trading network shapes the dissemination of avian influenza viruses has hindered the design of targeted interventions to reduce their spread. Here, we use phylodynamic analyses of haemagglutinin sequences to investigate the spatial spread and dispersal patterns of H9N2 viruses in Bangladesh's poultry population, focusing on its two largest cities (Dhaka and Chattogram) and their poultry production and distribution networks. Our analyses suggest that H9N2 subtype avian influenza virus lineage movement occurs relatively less frequently between Bangladesh's two largest cities than within each city. H9N2 viruses detected in single markets are often more closely related to viruses from other markets in the same city than to each other, consistent with close epidemiological connectivity between markets. Our analyses also suggest that H9N2 viruses may spread more frequently between chickens of the three most commonly sold types (sunali-a cross-bred of Fayoumi hen and Rhode Island Red cock, deshi-local indigenous, and exotic broiler) in Dhaka than in Chattogram. Overall, this study improves our understanding of how Bangladesh's poultry trading system impacts avian influenza virus spread and should contribute to the design of tailored surveillance that accommodates local heterogeneity in virus dispersal patterns.

Emerging Highly Pathogenic Avian Influenza (H5N8) Virus in Podiceps nigricollis in Northwest China in 2021

Three highly pathogenic avian influenza (H5N8) viruses were detected in the migratory bird Podiceps nigricollis in Northwest China in June 2021. Phylogenetic analysis indicated that these H5N8 isolates belonged to clade 2.3.4.4b, which were highly homologous to strains isolated in China and South Korea. In this study, H5N8 virus infection in Podiceps nigricollis was detected using Oxford Nanopore Technologies sequencing technology and caused pathological changes in multiple organs.

Bidirectional Movement of Emerging H5N8 Avian Influenza Viruses Between Europe and Asia via Migratory Birds Since Early 2020

Migratory birds play a critical role in the rapid spread of highly pathogenic avian influenza (HPAI) H5N8 virus clade 2.3.4.4 across Eurasia. Elucidating the timing and pattern of virus transmission is essential therefore for understanding the spatial dissemination of these viruses. In this study, we surveyed >27,000 wild birds in China, tracked the year-round migration patterns of 20 bird species across China since 2006, and generated new HPAI H5N8 virus genomic data. Using this new data set, we investigated the seasonal transmission dynamics of HPAI H5N8 viruses across Eurasia. We found that introductions of HPAI H5N8 viruses to different Eurasian regions were associated with the seasonal migration of wild birds. Moreover, we report a backflow of HPAI H5N8 virus lineages from Europe to Asia, suggesting that Europe acts as both a source and a sink in the global HPAI virus transmission network.

Taurolidine improved protection against highly pathogenetic avian influenza H5N1 virus lethal-infection in mouse model by regulating the NF-κB signaling pathway

Taurolidine (TRD), a derivative of taurine, has anti-bacterial and anti-tumor effects by chemically reacting with cell-walls, endotoxins and exotoxins to inhibit the adhesion of microorganisms. However, its application in antiviral therapy is seldom reported. Here, we reported that TRD significantly inhibited the replication of influenza virus H5N1 in MDCK cells with the half-maximal inhibitory concentration (EC₅₀) of 34.45 ​μg/mL. Furthermore, the drug inhibited the amplification of the cytokine storm effect and improved the survival rate of mice lethal challenged with H5N1 (protection rate was 86%). Moreover, TRD attenuated virus-induced lung damage and reduced virus titers in mice lungs. Administration of TRD reduced the number of neutrophils and increased the number of lymphocytes in the blood of H5N1 virus-infected mice. Importantly, the drug regulated the NF-κB signaling pathway by inhibiting the separation of NF-κB and IκBa, thereby reducing the expression of inflammatory factors. In conclusion, our findings suggested that TRD could act as a potential anti-influenza drug candidate in further clinical studies.

Emergence of H5N8 avian influenza virus in domestic geese in a wild bird habitat, Yishui Lake, north central China

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H5N8 viruses emerged in the wild bird habitat at Yishui Lake.

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The homology between HG12 and a Russian human strain was over 99%.

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HG12 can be transmitted through direct contact between guinea pigs.

Scaling migrations to communities: An empirical case of migration network in the Arctic

Seasonal migrants transport energy, nutrients, contaminants, parasites and diseases, while also connecting distant food webs between communities and ecosystems, which contributes to structuring meta-communities and meta-ecosystems. However, we currently lack a framework to characterize the structure of the spatial connections maintained by all migratory species reproducing or wintering in a given community. Here, we use a network approach to represent and characterize migratory pathways at the community level and provide an empirical description of this pattern from a High-Arctic terrestrial community. We define community migration networks as multipartite networks representing different biogeographic regions connected with a focal community through the seasonal movements of its migratory species. We focus on the Bylot Island High-Arctic terrestrial community, a summer breeding ground for several migratory species. We define the non-breeding range of each species using tracking devices, or range maps refined by flyways and habitat types. We show that the migratory species breeding on Bylot Island are found across hundreds of ecoregions on several continents during the non-breeding period and present a low spatial overlap. The migratory species are divided into groups associated with different sets of ecoregions. The non-random structure observed in our empirical community migration network suggests evolutionary and geographic constraints as well as ecological factors act to shape migrations at the community level. Overall, our study provides a simple and generalizable framework as a starting point to better integrate migrations at the community level. Our framework is a far-reaching tool that could be adapted to address the seasonal transport of energy, contaminants, parasites and diseases in ecosystems, as well as trophic interactions in communities with migratory species.

Integrating Citizen Scientist Data into the Surveillance System for Avian Influenza Virus, Taiwan

The continuing circulation and reassortment with low-pathogenicity avian influenza Gs/Gd (goose/Guangdong/1996)-like avian influenza viruses (AIVs) has caused huge economic losses and raised public health concerns over the zoonotic potential. Virologic surveillance of wild birds has been suggested as part of a global AIV surveillance system. However, underreporting and biased selection of sampling sites has rendered gaining information about the transmission and evolution of highly pathogenic AIV problematic. We explored the use of the Citizen Scientist eBird database to elucidate the dynamic distribution of wild birds in Taiwan and their potential for AIV exchange with domestic poultry. Through the 2-stage analytical framework, we associated nonignorable risk with 10 species of wild birds with >100 significant positive results. We generated a risk map, which served as the guide for highly pathogenic AIV surveillance. Our methodologic blueprint has the potential to be incorporated into the global AIV surveillance system of wild birds.

An early warning system for highly pathogenic viruses borne by waterbird species and related dynamics of climate change in the Caspian Sea region: Outlines of a concept

Aim. Formulation of the outlines of the concept of ViEW (Viral Early Warning) which is intended as a long term system of multidisciplinary transboundary cooperation between specialist institutions of all five Caspian region states to research, regularly monitor and share data about the generation, transmission and epidemiology of avian‐borne pathogens and their vectors in the region, and the ways climate change may affect these processes.

Material and Methods. The concept is based on the multidisciplinary experience of the authors in researching the processes incorporated in the ViEW concept and on an in‐depth survey of the literature involved.

Results. The outlines of the ViEW concept are presented in this study for review and comment by interested parties and stakeholders.

Conclusion. Review of activities and opinions of specialists and organizations with remits relating to the development, establishment and maintenance of ViEW, indicates that such a system is a necessity for global animal and human health because of the role that the Caspian region plays in the mass migration of species of waterbird known as vectors for avian influenza and the already evident impacts of climate change on their phenologies. Waterbirds frequenting the Caspian Sea littorals and their habitats together constitute a major potential global hotspot or High Risk region for the generation and transmission of highly pathogenic avian influenza viruses and other dangerous zoonotic diseases.

High pathogenicity avian influenza: targeted active surveillance of wild birds to enable early detection of emerging disease threats

Avian influenza (AI) is an important disease that has significant implications for animal and human health. High pathogenicity AI (HPAI) has emerged in consecutive seasons within the UK to cause the largest outbreaks recorded. Statutory measures to control outbreaks of AI virus (AIV) at poultry farms involve disposal of all birds on infected premises. Understanding of the timing of incursions into the UK could facilitate decisions on improved responses. During the autumnal migration and wintering period (autumn 2019- spring 2020), three active sampling approaches were trialled for wild bird species considered likely to be involved in captive AI outbreaks with retrospective laboratory testing undertaken to define the presence of AIV.Faecal sampling of birds (n = 594) caught during routine and responsive mist net sampling failed to detect AIV. Cloacal sampling of hunter-harvested waterfowl (n = 146) detected seven positive samples from three species with the earliest detection on the 17 October 2020. Statutory sampling first detected AIV in wild and captive birds on 3 November 2020. We conclude that hunter sourced sampling of waterfowl presents an opportunity to detect AI within the UK in advance of outbreaks on poultry farms and allow for early intervention measures to protect the national poultry flock.

Assessing potential pathogenicity of novel highly pathogenic avian influenza (H5N6) viruses isolated from Mongolian wild duck feces using a mouse model

Several novel highly pathogenic avian influenza (HPAIVs) A(H5N6) viruses were reported in Mongolia in 2020, some of which included host-specific markers associated with mammalian infection. However, their pathogenicity has not yet been investigated. Here, we isolated and evaluate two novel genotypes of A(H5N6) subtype in Mongolia during 2018–2019 (A/wildDuck/MN/H5N6/2018-19). Their evolution pattern and molecular characteristics were evaluated using gene sequencing and their pathogenicity was determined using a mouse model. We also compared their antigenicity with previous H5 Clade 2.3.4.4 human isolates by cross-hemagglutination inhibition (HI). Our data suggests that A/wildDuck/MN/H5N6/2018-19 belongs to clade 2.3.4.4h, and maintains several residues associated with mammal adaptation. In addition, our evaluations revealed that their isolates are less virulent in mice than the previously identified H5 human isolates. However, their antigenicity is distinct from other HPAIVs H5 clade 2.3.4.4, thus supporting their continued evaluation as potential infection risks and the preparation of novel candidate vaccines for their neutralization.

A unified global genotyping framework of dengue virus serotype-1 for a stratified coordinated surveillance strategy of dengue epidemics

Background

Dengue is the fastest spreading arboviral disease, posing great challenges on global public health. A reproduceable and comparable global genotyping framework for contextualizing spatiotemporal epidemiological data of dengue virus (DENV) is essential for research studies and collaborative surveillance.

Methods

Targeting DENV-1 spreading prominently in recent decades, by reconciling all qualified complete E gene sequences of 5003 DENV-1 strains with epidemiological information from 78 epidemic countries/areas ranging from 1944 to 2018, we established and characterized a unified global high-resolution genotyping framework using phylogenetics, population genetics, phylogeography, and phylodynamics.

Results

The defined framework was discriminated with three hierarchical layers of genotype, subgenotype and clade with respective mean pairwise distances 2–6%, 0.8–2%, and ≤ 0.8%. The global epidemic patterns of DENV-1 showed strong geographic constraints representing stratified spatial-genetic epidemic pairs of Continent-Genotype, Region-Subgenotype and Nation-Clade, thereby identifying 12 epidemic regions which prospectively facilitates the region-based coordination. The increasing cross-transmission trends were also demonstrated. The traditional endemic countries such as Thailand, Vietnam and Indonesia displayed as persisting dominant source centers, while the emerging epidemic countries such as China, Australia, and the USA, where dengue outbreaks were frequently triggered by importation, showed a growing trend of DENV-1 diffusion. The probably hidden epidemics were found especially in Africa and India. Then, our framework can be utilized in an accurate stratified coordinated surveillance based on the defined viral population compositions. Thereby it is prospectively valuable for further hampering the ongoing transition process of epidemic to endemic, addressing the issue of inadequate monitoring, and warning us to be concerned about the cross-national, cross-regional, and cross-continental diffusions of dengue, which can potentially trigger large epidemics.

Conclusions

The framework and its utilization in quantitatively assessing DENV-1 epidemics has laid a foundation and re-unveiled the urgency for establishing a stratified coordinated surveillance platform for blocking global spreading of dengue. This framework is also expected to bridge classical DENV-1 genotyping with genomic epidemiology and risk modeling. We will promote it to the public and update it periodically.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s40249-022-01024-5.

Health in poultry- immunity and microbiome with regard to a concept of one health

The overall concept of OneHealth focuses on health and infectious disease in the context of the relationship between humans, animals, and the environment. In poultry production, there are many opportunities to implement OneHealth by organizing work and introducing appropriate engineering solutions. It is recommended that future research directions include designing and testing solutions to improve air quality and the elimination of antibiotics in the poultry industry. For this to be possible, it is essential to understand the indigenous microbiota of poultry, which plays a crucial role in nutrients, but also restricts the growth of pathogenic organisms. In poultry production, the most important thing is disease control in the herd, high product quality, and product efficiency. Food safety is key for consumers, as some zoonoses are transmitted through the food chain. Moreover, antibiotic resistance of bacteria is becoming a growing threat. For this reason, it is essential to maintain the proper immune status in the herd. Virus disease control in poultry is based on vaccination programs and the maintenance of biosecurity. This chapter aims to present the current state of knowledge in the field of immunity and microbiome of poultry in the context of the OneHealth concept.

Habitat loss exacerbates pathogen spread: An Agent-based model of avian influenza infection in migratory waterfowl

Habitat availability determines the distribution of migratory waterfowl along their flyway, which further influences the transmission and spatial spread of avian influenza viruses (AIVs). The extensive habitat loss in the East Asian-Australasian Flyway (EAAF) may have potentially altered the virus spread and transmission, but those consequences are rarely studied. We constructed 6 fall migration networks that differed in their level of habitat loss, wherein an increase in habitat loss resulted in smaller networks with fewer sites and links. We integrated an agent-based model and a susceptible-infected-recovered model to simulate waterfowl migration and AIV transmission. We found that extensive habitat loss in the EAAF can 1) relocate the outbreaks northwards, responding to the distribution changes of wintering waterfowl geese, 2) increase the outbreak risk in remaining sites due to larger goose congregations, and 3) facilitate AIV transmission in the migratory population. In addition, our modeling output was in line with the predictions from the concept of "migratory escape", i.e., the migration allows the geese to "escape" from the location where infection risk is high, affecting the pattern of infection prevalence in the waterfowl population. Our modeling shed light on the potential consequences of habitat loss in spreading and transmitting AIV at the flyway scale and suggested the driving mechanisms behind these effects, indicating the importance of conservation in changing spatial and temporal patterns of AIV outbreaks.

Role of wild birds in the spread of clade 2.3.4.4e H5N6 highly pathogenic avian influenza virus into South Korea and Japan

H5Nx highly pathogenic avian influenza viruses (HPAIVs) have caused transboundary epizootics in poultry and wild birds. In 2016, the H5N6 subtype of clade 2.3.4.4e HPAIVs caused multiple outbreaks in Asia, including China, Japan, Korea, and Vietnam. However, the geographical spread pattern of 2.3.4.4e H5N6 HPAIV has not been clearly identified. To better understand the emergence and transmission history of 2.3.4.4e H5N6 HPAIV, we investigated the underlying epidemiologic processes associated with this viral spread by performing a Bayesian phylogeography analysis. The results revealed that wild waterfowl played a central role in the transboundary spread of clade 2.3.4.4e H5N6 HPAIV into both endemic and non-endemic countries, causing multiple incursions of the 2.3.4.4e H5N6 HPAIV into South Korea, Japan, and Vietnam. In our analysis, Guangdong province, China was estimated to be the most probable site where 2.3.4.4e H5N6 HPAIVs emerged prior to the transboundary transmissions. Continued genomic surveillance in both wild birds and poultry would be necessary for monitoring of HPAIV incursions. In addition, enhanced biosecurity would be key to preventing the HPAIV spread by minimizing contact between domestic poultry and wild birds.

Ecological divergence of wild birds drives avian influenza spillover and global spread

The diversity of influenza A viruses (IAV) is primarily hosted by two highly divergent avian orders: Anseriformes (ducks, swans and geese) and Charadriiformes (gulls, terns and shorebirds). Studies of IAV have historically focused on Anseriformes, specifically dabbling ducks, overlooking the diversity of hosts in nature, including gull and goose species that have successfully adapted to human habitats. This study sought to address this imbalance by characterizing spillover dynamics and global transmission patterns of IAV over 10 years at greater taxonomic resolution than previously considered. Furthermore, the circulation of viral subtypes in birds that are either host-adapted (low pathogenic H13, H16) or host-generalist (highly pathogenic avian influenza—HPAI H5) provided a unique opportunity to test and extend models of viral evolution. Using Bayesian phylodynamic modelling we uncovered a complex transmission network that relied on ecologically divergent bird hosts. The generalist subtype, HPAI H5 was driven largely by wild geese and swans that acted as a source for wild ducks, gulls, land birds, and domestic geese. Gulls were responsible for moving HPAI H5 more rapidly than any other host, a finding that may reflect their long-distance, pelagic movements and their immuno-naïve status against this subtype. Wild ducks, long viewed as primary hosts for spillover, occupied an optimal space for viral transmission, contributing to geographic expansion and rapid dispersal of HPAI H5. Evidence of inter-hemispheric dispersal via both the Pacific and Atlantic Rims was detected, supporting surveillance at high latitudes along continental margins to achieve early detection. Both neutral (geographic expansion) and non-neutral (antigenic selection) evolutionary processes were found to shape subtype evolution which manifested as unique geographic hotspots for each subtype at the global scale. This study reveals how a diversity of avian hosts contribute to viral spread and spillover with the potential to improve surveillance in an era of rapid global change.

Our study provides novel insights into the biology of influenza A virus (IAV), which is timely in view of the unusually large number of animal and human cases of highly pathogenic avian influenza (HPAI) H5 across Europe, Asia, Africa and North America. Currently we face challenges with predicting how the avian reservoir will influence IAV spread because the mechanisms by which different subtypes disperse are not well understood. Our study sought to address this knowledge gap by systematically comparing the evolutionary dynamics that drive IAV transmission across subtypes and bird hosts with the goal of identifying spillover pathways at the wild-domestic interface. By analyzing the evolution of IAV over 10 years at greater taxonomic resolution than previously considered, we uncovered a complex transmission network that relied on ecologically divergent bird hosts. Domestic birds were responsible for slow but steady range expansion of HPAI H5, while wild birds such as geese, swans, gulls and ducks contibuted to rapid but episodic dispersal via uniquely different pathways. By assessing how virus-host systems are coupled, findings from this study have the potential to refine and enhance global surveillance and outbreak prediction.

Biological Earth observation with animal sensors

Space-based tracking technology using low-cost miniature tags is now delivering data on fine-scale animal movement at near-global scale. Linked with remotely sensed environmental data, this offers a biological lens on habitat integrity and connectivity for conservation and human health; a global network of animal sentinels of environmental change.

Interpolation of Point Prevalence Rate of the Highly Pathogenic Avian Influenza Subtype H5N8 Second Phase Epidemic in South Korea

Humans and animals are both susceptible to highly pathogenic avian influenza (HPAI) viruses. In the future, HPAI has the potential to be a source of zoonoses and pandemic disease drivers. It is necessary to identify areas of high risk that are more vulnerable to HPAI infections. In this study, we applied unbiased predictions based on known information to find points of localities with a high probability of point prevalence rate. To carry out such predictions, we utilized the inverse distance weighting (IDW) and kriging method, with the help of the R statistical computing program. The provinces of Jeollanam-do, Gyeonggi-do, Chungcheongbuk-do and Ulsan have high anticipated risk. This research might aid in the management of avian influenza threats associated with various potential risks.

Association between climate variables and dengue incidence in Nakhon Si Thammarat Province, Thailand

The tropical climate of Thailand encourages very high mosquito densities in certain areas and is ideal for dengue transmission, especially in the southern region where the province Nakhon Si Thammarat is located. It has the longest dengue fever transmission duration that is affected by some important climate predictors, such as rainfall, number of rainy days, temperature and humidity. We aimed to explore the relationship between weather variables and dengue and to analyse transmission hotspots and coldspots at the district-level. Poisson probability distribution of the generalized linear model (GLM) was used to examine the association between the monthly weather variable data and the reported number of dengue cases from January 2002 to December 2018 and geographic information system (GIS) for dengue hotspot analysis. Results showed a significant association between the environmental variables and dengue incidence when comparing the seasons. Temperature, sea-level pressure and wind speed had the highest coefficients, i.e. β=0.17, β= -0.12 and β= -0.11 (P<0.001), respectively. The risk of dengue incidence occurring during the rainy season was almost twice as high as that during monsoon. Statistically significant spatial clusters of dengue cases were observed all through the province in different years. Nabon was identified as a hotspot, while Pak Phanang was a coldspot for dengue fever incidence, explained by the fact that the former is a rubber-plantation hub, while the agricultural plains of the latter lend themselves to the practice of pisciculture combined with rice farming. This information is imminently important for planning apt sustainable control measures for dengue epidemics.

Emerging and Re-emerging Vector-Borne Infectious Diseases and the Challenges for Control: A Review

Vector-borne emerging and re-emerging diseases pose considerable public health problem worldwide. Some of these diseases are emerging and/or re-emerging at increasing rates and appeared in new regions in the past two decades. Studies emphasized that the interactions among pathogens, hosts, and the environment play a key role for the emergence or re-emergence of these diseases. Furthermore, social and demographic factors such as human population growth, urbanization, globalization, trade exchange and travel and close interactions with livestock have significantly been linked with the emergence and/or re-emergence of vector-borne diseases. Other studies emphasize the ongoing evolution of pathogens, proliferation of reservoir populations, and antimicrobial drug use to be the principal exacerbating forces for emergence and re-emergence of vector-borne infectious diseases. Still other studies equivocally claim that climate change has been associated with appearance and resurgence of vector-borne infectious diseases. Despite the fact that many important emerging and re-emerging vector-borne infectious diseases are becoming better controlled, our success in stopping the many new appearing and resurging vector-borne infectious diseases that may happen in the future seems to be uncertain. Hence, this paper reviews and synthesizes the existing literature to explore global patterns of emerging and re-emerging vector-borne infections and the challenges for their control. It also attempts to give insights to the epidemiological profile of major vector-borne diseases including Zika fever, dengue, West Nile fever, Crimean-Congo hemorrhagic fever, Chikungunya, Yellow fever, and Rift Valley fever.

Deciphering transmission dynamics and spillover of avian influenza viruses from avian species to swine populations globally

Genome sequences of eleven avian influenza virus (AIV) subtypes have been reported in swine populations from seven countries until August 2020. To unravel the transmission dynamics and spillover events of AIVs from avian reservoirs to swine, full-length hemagglutinin (HA) sequences of AIV subtypes (n = 11) reported from various avian species and swine were retrieved from the ‘Influenza Research Database’. Phylogenetic analysis identified closely related avian and swine AIV sequences suggesting potential spillover events from multiple domestic and wild avian species, including chicken, duck, pigeon, goose, quail, and aquatic birds to swine. Furthermore, N-linked glycosylation analysis of these closely related AIV sequences supported the possibility of multiple spillover events of highly pathogenic H5N1 and low pathogenic H9N2 viruses from various avian species to swine. The principal coordinate analysis further validated these findings for H5N1 and H9N2 viruses; however, spillover events of the other nine AIV subtypes were limited. Interestingly, the presence of potential mammalian adaptation markers, particularly in some of the swine H5N1, H7N9, and H9N2 viruses, suggested that these viruses may have already adapted in swine. The occurrence and circulation of these AIVs in swine, especially the H5N1 and H9N2 viruses with numerous spillover events from the avian reservoirs to swine, pose a significant threat in terms of their reassortment with endemic swine viruses or circulating human influenza viruses within the swine which may facilitate the emergence of a novel influenza virus strain with pandemic potential.

The COVID-19 pandemic and its implications on the environment

The emerging threat posed by COVID-19 pandemic has strongly modified our lifestyle, making urgent to re-consider the humans-environment relationships and stimulating towards more sustainable choices in our daily behavior. Scientific evidences showed that the onset of new viral pathogens with a high epidemic-pandemic potential is often the result of complex interactions between animals, humans and environment. In this context, the interest of the scientific community has also been attracted towards the potential interactions of SARS-CoV-2 with environmental compartments. Many issues, ranging from the epidemiology and persistence of SARS-CoV-2 in water bodies to the potential implications of lockdown measures on environmental quality status are here reviewed, with a special reference to marine ecosystems. Due to current sanitary emergence, the relevance of pilot studies regarding the interactions between SARS-CoV-2 spread and the direct and indirect environmental impacts of the COVID-19 pandemic, that are still a matter of scientific debate, is underlined.

Rainfall driven and wild-bird mediated avian influenza virus outbreaks in Australian poultry

Globally, outbreaks of Avian Influenza Virus (AIV) in poultry continue to burden economies and endanger human, livestock and wildlife health. Wild waterbirds are often identified as possible sources for poultry infection. Therefore, it is important to understand the ecological and environmental factors that directly influence infection dynamics in wild birds, as these factors may thereby indirectly affect outbreaks in poultry. In Australia, where large parts of the country experience erratic rainfall patterns, intense rainfalls lead to wild waterfowl breeding events at temporary wetlands and increased proportions of immunologically naïve juvenile birds. It is hypothesized that after breeding, when the temporary wetlands dry, increasing densities of immunologically naïve waterbirds returning to permanent water bodies might strongly contribute to AIV prevalence in wild waterfowl in Australia. Since rainfall has been implicated as an important environmental driver in AIV dynamics in wild waterbirds in southeast Australia and wild waterbirds are identified globally to have a role in virus spillover into poultry, we hypothesise that rainfall events have an indirect effect on AIV outbreaks in poultry in southeast Australia. In this study we investigated this hypothesis by examining the correlation between the timing of AIV outbreaks in poultry in and near the Murray-Darling basin in relation to temporal patterns in regional rainfall since 1970. Our findings support our hypothesis and suggest that the risk of AIV outbreaks in poultry increases after a period of high rainfall, with peak AIV risk two years after the onset of the high-rainfall period. This is presumably triggered by increased rates of waterbird breeding and consequent higher proportions of immunologically naïve juvenile waterbirds entering the population directly after major rainfall events, which subsequently aggregate near permanent water bodies when the landscape dries out.

Transboundary Animal Diseases, an Overview of 17 Diseases with Potential for Global Spread and Serious Consequences

Animals provide food and other critical resources to most of the global population. As such, diseases of animals can cause dire consequences, especially disease with high rates of morbidity or mortality. Transboundary animal diseases (TADs) are highly contagious or transmissible, epidemic diseases, with the potential to spread rapidly across the globe and the potential to cause substantial socioeconomic and public health consequences. Transboundary animal diseases can threaten the global food supply, reduce the availability of non-food animal products, or cause the loss of human productivity or life. Further, TADs result in socioeconomic consequences from costs of control or preventative measures, and from trade restrictions. A greater understanding of the transmission, spread, and pathogenesis of these diseases is required. Further work is also needed to improve the efficacy and cost of both diagnostics and vaccines. This review aims to give a broad overview of 17 TADs, providing researchers and veterinarians with a current, succinct resource of salient details regarding these significant diseases. For each disease, we provide a synopsis of the disease and its status, species and geographic areas affected, a summary of in vitro or in vivo research models, and when available, information regarding prevention or treatment.

Do contrasting patterns of migration movements and disease outbreaks between congeneric waterfowl species reflect differing immunity?

Long-distance migrations influence the dynamics of hostpathogen interactions and understanding the role of migratory waterfowl in the spread of the highly pathogenic avian influenza viruses (HPAIV) is important. While wild geese have been associated with outbreak events, disease ecology of closely related species has not been studied to the same extent. The swan goose (Anser cygnoides) and the bar-headed goose (Anser indicus) are congeneric species with distinctly different HPAIV infection records; the former with few and the latter with numerous records. We compared movements of these species, as well as the more distantly related whooper swan (Cygnus cygnus) through their annual migratory cycle to better understand exposure to HPAIV events and how this compares within and between congeneric and noncongeneric species. In spite of their record of fewer infections, swan geese were more likely to come in contact with disease outbreaks than bar-headed geese. We propose two possible explanations: i) frequent prolonged contact with domestic ducks increases innate immunity in swan geese, and/or ii) the stress of high-elevation migration reduces immunity of bar-headed geese. Continued efforts to improve our understanding of species-level pathogen response is critical to assessing disease transmission risk.

Genomic evolution, transmission dynamics, and pathogenicity of avian influenza A (H5N8) viruses emerging in China, 2020

Multiple recent outbreaks of highly pathogenic H5N8 viruses originating in aquatic birds frequently occurred in most European countries, Russia, South Korea, and Japan during the winter of 2020–21, and one zoonotic event of poultry workers infected with novel H5N8 viruses were reported in Russia. Strikingly, these novel H5N8 viruses had emerged and been co-circulating in wild birds and poultry in multiple provinces of China during 2020–21. In China, the population of aquatic birds has risen significantly in the past twenty years, and China is regarded as the largest reservoir for influenza viruses carried in aquatic birds across the globe. Hence, the co-circulation of these novel H5N8 viruses poses an alarming threat to not only poultry industry but also human health. In this study, we sequenced full-length genomes of these H5N8 viruses circulating in China. Phylogenetic analysis demonstrated that poultry-origin H5N8 viruses in China fell within wild birds-origin clade 2.3.4.4b H5N8 viruses from Europe during 2020–21, and notably, were genetically closely related to human-infecting H5N8 viruses in Russia. Moreover, they possessed several molecular markers associated with mammalian adaption. Bayesian coalescent analysis showed that these H5N8 viruses might have introduced into China during June–September 2020, suggesting that these H5N8 viruses might have introduced via wild bird migration or poultry trade. Besides, we also found that the effective population size of clade 2.3.4.4b H5N8 viruses dramatically increased during the winter season of 2020/21, as is consistent with previous increase of genetic diversity during the winter seasons of 2013/14 and 2016/17, which indicated that the wild bird migration accelerates the genetic diversity of these H5N8 viruses during the winter season of 2020/21. Notably, these novel H5N8 viruses were lethal to chickens and mice, highly transmissible to ducks, and were antigenically distinct from 2.3.4.4h H5 viruses circulating in China, posing considerable threats to public health. Our findings offer novel insights into the evolution and risk assessment of H5N8 viruses during the winter season of 2020–21.

Development of a Dissemination Platform for Spatiotemporal and Phylogenetic Analysis of Avian Infectious Bronchitis Virus

Infecting large portions of the global poultry populations, the avian infectious bronchitis virus (IBV) remains a major economic burden in North America. With more than 30 serotypes globally distributed, Arkansas, Connecticut, Delaware, Georgia, and Massachusetts are among the most predominant serotypes in the United States. Even though vaccination is widely used, the high mutation rate exhibited by IBV is continuously triggering the emergence of new viral strains and hindering control and prevention measures. For that reason, targeted strategies based on constantly updated information on the IBV circulation are necessary. Here, we sampled IBV-infected farms from one US state and collected and analyzed 65 genetic sequences coming from three different lineages along with the immunization information of each sampled farm. Phylodynamic analyses showed that IBV dispersal velocity was 12.3 km/year. The majority of IBV infections appeared to have derived from the introduction of the Arkansas DPI serotype, and the Arkansas DPI and Georgia 13 were the predominant serotypes. When analyzed against IBV sequences collected across the United States and deposited in the GenBank database, the most likely viral origin of our sequences was from the states of Alabama, Georgia, and Delaware. Information about vaccination showed that the MILDVAC-MASS+ARK vaccine was applied on 26% of the farms. Using a publicly accessible open-source tool for real-time interactive tracking of pathogen spread and evolution, we analyzed the spatiotemporal spread of IBV and developed an online reporting dashboard. Overall, our work demonstrates how the combination of genetic and spatial information could be used to track the spread and evolution of poultry diseases, providing timely information to the industry. Our results could allow producers and veterinarians to monitor in near-real time the current IBV strain circulating, making it more informative, for example, in vaccination-related decisions.

Continental-scale dynamics of avian influenza in U.S. waterfowl are driven by demography, migration, and temperature

Emerging diseases of wildlife origin are increasingly spilling over into humans and domestic animals. Surveillance and risk assessments for transmission between these populations are informed by a mechanistic understanding of the pathogens in wildlife reservoirs. For avian influenza viruses (AIV), much observational and experimental work in wildlife has been conducted at local scales, yet fully understanding their spread and distribution requires assessing the mechanisms acting at both local, (e.g., intrinsic epidemic dynamics), and continental scales, (e.g., long-distance migration). Here, we combined a large, continental-scale data set on low pathogenic, Type A AIV in the United States with a novel network-based application of bird banding/recovery data to investigate the migration-based drivers of AIV and their relative importance compared to well-characterized local drivers (e.g., demography, environmental persistence). We compared among regression models reflecting hypothesized ecological processes and evaluated their ability to predict AIV in space and time using within and out-of-sample validation. We found that predictors of AIV were associated with multiple mechanisms at local and continental scales. Hypotheses characterizing local epidemic dynamics were strongly supported, with age, the age-specific aggregation of migratory birds in an area and temperature being the best predictors of infection. Hypotheses defining larger, network-based features of the migration processes, such as clustering or between-cluster mixing explained less variation but were also supported. Therefore, our results support a role for local processes in driving the continental distribution of AIV.

Ecological and Conservation Significance of Herpesvirus Infection in Neotropical Bats

Bats are the second most diverse order of mammals and key species for ecosystem functioning, providing a wide range of ecosystem services, from pest control to seed dispersal. Chiropterans are known for hosting a large diversity of viruses, in some cases with little or no effect to their health. Here, we report on the results of a screening for DNA (Herpesviridae) and RNA viruses (Rhabdovirus and Pneumovirus), finding a high prevalence and wide diversity of both Beta- and Gamma-Herpesvirus in insectivorous and hematophagous bats of the southern cone of South America. Our findings suggest that bats in the southern neotropics harbor a high diversity of herpesviruses and, at least in some cases, the viral community in the bat species is more strongly associated with ecological traits of the hosts, rather than their taxonomy. The presence of a separate clade into the Gammaherpesvirinae subfamily in the common vampire bat suggests the independent circulation of herpesviruses in hematophagous and insectivorous bats and highlights the properness of these viruses to track vampire bats' population structure for rabies studies. Hence, we suggest that as other pathogens viruses may be used to track the population dynamics of their hosts, including movement and demographics.

Preparing for Emerging Zoonotic Viruses

The risk of emergence and spread of novel human pathogens originating from an animal reservoir has increased in the past decades. However, the unpredictable nature of disease emergence makes surveillance and preparedness challenging. Knowledge of general risk factors for emergence and spread, combined with local level data is needed to develop a risk-based methodology for early detection. This involves the implementation of the One Health approach, integrating human, animal and environmental health sectors, as well as social sciences, bioinformatics and more. Recent technical advances, such as metagenomic sequencing, will aid the rapid detection of novel pathogens on the human-animal interface.

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.

Highly Pathogenic Avian Influenza Clade 2.3.4.4b Subtype H5N8 Virus Isolated from Mandarin Duck in South Korea, 2020

In October 2020, a highly pathogenic avian influenza (HPAI) subtype H5N8 virus was identified from a fecal sample of a wild mandarin duck (Aix galericulata) in South Korea. We sequenced all eight genome segments of the virus, designated as A/Mandarin duck/Korea/K20-551-4/2020(H5N8), and conducted genetic characterization and comparative phylogenetic analysis to track its origin. Genome sequencing and phylogenetic analysis show that the hemagglutinin gene belongs to H5 clade 2.3.4.4 subgroup B. All genes share high levels of nucleotide identity with H5N8 HPAI viruses identified from Europe during early 2020. Enhanced active surveillance in wild and domestic birds is needed to monitor the introduction and spread of HPAI via wild birds and to inform the design of improved prevention and control strategies.

Migratory hosts can maintain the high-dose/refuge effect in a structured host-parasite system: The case of sea lice and salmon

Migration can reduce parasite burdens in migratory hosts, but it connects populations and can drive disease dynamics in domestic species. Farmed salmon are infested by sea louse parasites, often carried by migratory wild salmonids, resulting in a costly problem for industry and risk to wild populations when farms amplify louse numbers. Chemical treatment can control lice, but resistance has evolved in many salmon-farming regions. Resistance has, however, been slow to evolve in the north-east Pacific Ocean, where large wild-salmon populations harbour large sea louse populations. Using a mathematical model of host-macroparasite dynamics, we explored the roles of domestic, wild oceanic and connective migratory host populations in maintaining treatment susceptibility in associated sea lice. Our results show that a large wild salmon population, unexposed to direct infestation by lice from farms; high levels of on-farm treatment; and a healthy migratory host population are all critical to slowing or stopping the evolution of treatment resistance. Our results reproduce the "high-dose/refuge effect," from the agricultural literature, with the added requirement of a migratory host population to maintain treatment susceptibility. This work highlights the role that migratory hosts may play in shared wildlife/livestock disease, where evolution can occur in ecological time.

Highly Pathogenic Avian Influenza (H5N1) Landscape Suitability Varies by Wetland Habitats and the Degree of Interface between Wild Waterfowl and Poultry in India

Highly pathogenic avian influenza (HPAI) virus, subtype H5N1, constitutes one of the world's most important health and economic concerns given the catastrophic impact of epizootics on the poultry industry, the high mortality attending spillover in humans, and its potential as a source subtype for a future pandemic. Nevertheless, we still lack an adequate understanding of HPAI H5N1 epidemiology and infection ecology. The nature of the wild waterfowl-poultry interface, and the sharing of diverse wetland habitat among these birds, currently underscore important knowledge gaps. India has emerged as a global hotspot for HPAI H5N1, while also providing critical wintering habitat for many species of migratory waterfowl and year-round habitat for several resident waterfowl species. The current study sought to examine the extent to which the wild waterfowl-poultry interface, varied wetland habitat, and climate influence HPAI H5N1 epizootics in poultry in India. Using World Organisation for Animal Health reported outbreaks, this study showed that the wild waterfowl-poultry interface and lacustrine, riparian, and coastal marsh wetland systems were strongly associated with landscape suitability, and these relationships varied by scale. Although increasing poultry density was associated with increasing risk, this was only the case in the absence of wild waterfowl habitat, and only at a local scale. In landscapes increasingly shared between wild waterfowl and poultry, suitability was greater among lower density poultry, again at a local scale only. These findings provide further insight into the occurrence of HPAI H5N1 in India and suggest important landscape targets for blocking the waterfowl-poultry interface to interrupt virus transmission and prevent future outbreaks.

A review on prediction of seasonal diseases based on climate change using big data

Big Data occupies an important place in the prediction of diseases that happen due to climate change. In each aspect of human life, the weather plays a major role. It directly affects human society or human life. Because of an extreme weather condition creates various diseases among humans. Such as Vector-borne diseases (Malaria, dengue and chikungunya fever), Water-borne diseases (Cholera, Typhoid), Air-borne diseases (Chicken Pox, influenza and small Pox) and Food-borne diseases (Diarrhoea and Salmonella) etc. This survey presents an overview for a climate variable such as extreme temperature, precipitation, humidity and how unexpected climate conditions can affect the disease and living organism.

Characterization of H3 subtype avian influenza viruses isolated from poultry in Vietnam

To date, avian influenza viruses (AIVs) have persisted in domestic poultry in wet markets in East Asian countries. We have performed ongoing virus surveillance in poultry populations in Vietnam since 2011, with the goal of controlling avian influenza. Throughout this study, 110 H3 AIVs were isolated from 2760 swab samples of poultry in markets and duck farms. H3 hemagglutinin (HA) genes of the isolates were phylogenetically classified into eight groups (I-VIII). Genetic diversity was also observed in the other seven gene segments. Groups I-IV also included AIVs from wild waterbirds. The epidemic strains in poultry switched from groups I-III and VI to groups I, IV, V, and VIII around 2013. H3 AIVs in groups I and V were maintained in poultry until at least 2016, which likely accompanied their dissemination from the northern to the southern regions of Vietnam. Groups VI-VIII AIVs were antigenically distinct from the other groups. Some H3 AIV isolates had similar N6 neuraminidase and matrix genes as H5 highly pathogenic avian influenza viruses (HPAIVs). These results reveal that genetically and antigenically different H3 AIVs have been co-circulating in poultry in Vietnam. Poultry is usually reared outside in this country and is at risk of infection with wild waterbird-originating AIVs. In poultry flocks, the intruded H3 AIVs must have experienced antigenic drift/shift and genetic reassortment, which could contribute to the emergence of H5 HPAIVs with novel gene constellations.

Avian Influenza Virus Prevalence and Subtype Diversity in Wild Birds in Shanghai, China, 2016-2018

From 2016 to 2018, surveillance of influenza A viruses in wild birds was conducted in Shanghai, located at the East Asian-Australian flyway, China. A total of 5112 samples from 51 species of wild birds were collected from three different wetlands. The total three-year prevalence of influenza A viruses among them was 8.8%, as assessed using real-time polymerase chain reaction (PCR) methods, and the total prevalence was higher in Anseriformes (26.3%) than in the Charadriiformes (2.3%) and the other orders (2.4%) in the Chongmin wetlands. Anseriformes should be the key monitoring group in future surveillance efforts. The peak prevalence of influenza A viruses in Charadriiformes were in April and September, and in other bird orders, the peaks were in November and December. Twelve subtypes of haemagglutinin (HA; H1-H12) and eight subtypes of neuraminidase (NA; N1, N2, N4-N9) were identified in 21 different combinations. The greatest subtype diversity could be found in common teal, suggesting that this species of the bird might play an important role in the ecology and epidemiology of influenza A viruses in Shanghai. These results will increase our understanding of the ecology and epidemiology of influenza A viruses in wild bird hosts in eastern China, and provide references for subsequent surveillance of influenza A virus in wild birds in this area.

MaxEnt Modeling of Dermacentor marginatus (Acari: Ixodidae) Distribution in Xinjiang, China

Dermacentor marginatus Sulkzer is a common tick species found in the Xinjiang Uygur Autonomous Region (XUAR) of China, and is a vector for a variety of pathogens. To determine the potential distribution of this tick species in Xinjiang, a metadata containing 84 D. marginatus presence records combined with four localities from field collection were used for MaxEnt modeling to predict potential distribution of this tick species. Identification of tick samples showed 756 of 988 (76%) were D. marginatus. MaxEnt modeling results indicated that the potential distribution of this tick species was mainly confined to northern XUAR. Highly suitable areas included west side of Altay mountain, west rim of Junggar basin, and Yili River valley in the study area. The model showed an AUC value of 0.838 ± 0.063 (SD), based on 10-fold cross-validation. Although tick presence records used for modeling were limited, this is the first regional tick distribution model for D. marginatus in Xinjiang. The model will be helpful in assessing the risk of tick-borne diseases to human and animals in the region.