Ecology of avian influenza viruses in a changing world

Viral pathogen detection in U.S. game-farm mallard (Anas platyrhynchos) flags spillover risk to wild birds

The threat posed by emerging infectious diseases is a major concern for global public health, animal health and food security, and the role of birds in transmission is increasingly under scrutiny. Each year, millions of mass-reared game-farm birds are released into the wild, presenting a unique and a poorly understood risk to wild and susceptible bird populations, and to human health. In particular, the shedding of enteric pathogens through excrement into bodies of water at shared migratory stop-over sites, and breeding and wintering grounds, could facilitate multi-species long-distance pathogen dispersal and infection of high numbers of naive endemic birds annually. The Mallard (Anas platyrhynchos) is the most abundant of all duck species, migratory across much of its range, and an important game species for pen-rearing and release. Major recent population declines along the US Atlantic coast has been attributed to game-farm and wild mallard interbreeding and the introduction maladaptive traits into wild populations. However, pathogen transmission and zoonosis among game-farms Mallard may also impact these populations, as well as wildlife and human health. Here, we screened 16 game-farm Mallard from Wisconsin, United States, for enteric viral pathogens using metatranscriptomic data. Four families of viral pathogens were identified - Picobirnaviridae (Genogroup I), Caliciviridae (Duck Nacovirus), Picornaviridae (Duck Aalivirus) and Sedoreoviridae (Duck Rotavirus G). To our knowledge, this is the first report of Aalivirus in the Americas, and the first report of Calicivirus outside domestic chicken and turkey flocks in the United States. Our findings highlight the risk of viral pathogen spillover from peri-domestically reared game birds to naive wild bird populations.

The role of vaccination and environmental factors on outbreaks of high pathogenicity avian influenza H5N1 in Bangladesh

High Pathogenicity Avian Influenza (HPAI) H5N1 outbreaks continue to wreak havoc on the global poultry industry and threaten the health of wild bird populations, with sporadic spillover in humans and other mammals, resulting in widespread calls to vaccinate poultry. Bangladesh has been vaccinating poultry since 2012, presenting a prime opportunity to study the effects of vaccination on HPAI H5N1circulation in both poultry and wild birds. We investigated the efficacy of vaccinating commercial poultry against HPAI H5N1 along with climatic and socio-economic factors considered potential drivers of HPAI H5N1 outbreak risk in Bangladesh. Using a multivariate modeling approach, we estimated that the rate of outbreaks was 18 times higher before compared to after vaccination, with winter months having a three times higher chance of outbreaks than summer months. Variables resulting in small but significant increases in outbreak rate were relatively low ambient temperatures for the time of year, literacy rate, chicken and duck density, crop density, and presence of highways; this may be attributable to low temperatures supporting viral survival outside the host, higher literacy driving reporting rate, density of the host reservoir, and spread of the virus through increased connectivity. Despite the substantial impact of vaccination on outbreaks, we note that HPAI H5N1 is still enzootic in Bangladesh; vaccinated poultry flocks have high rates of H5N1 prevalence, and spillover to wild birds has increased. Vaccination in Bangladesh thus bears the risk of supporting "silent spread," where the vaccine only provides protection against disease and not also infection. Our findings underscore that poultry vaccination can be part of holistic HPAI mitigation strategies when accompanied by monitoring to avoid silent spread.

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.

Swine Backyard Production Systems in Central Chile: Characterizing Farm Structure, Animal Management, and Production Value Chain

Backyard production systems (BPS) are highly distributed in central Chile. While poultry BPS have been extensively characterized, there remains a notable gap in the characterization of swine BPS in central Chile. In addition, there is evidence that zoonotic pathogens, such as influenza A virus and Salmonella spp., are circulating in backyard poultry and pigs. A total of 358 BPS located in central Chile were evaluated between 2013 and 2015 by interviewing farm owners. Severe deficiencies in biosecurity measures were observed. The value chain of swine backyard production identified food, veterinary care (visits and products), and replacement or breeding animals as the primary inputs to the backyard. The most common origin of swine replacements was from outside the BPS (63%). The main outputs of the system were identified as meat and live animals, including piglets and breeding animals. In 16% of BPS, breeding animals were lent to other BPS, indicating the existence of animals and animal product movement in and out of backyard farms. Results from this study indicate that swine BPS in central Chile represents an animal-human interface that demands special attention for implementing targeted preventive measures to prevent the introduction and spread of animal pathogens and the emergence of zoonotic pathogens.

Ecogeographic Drivers of the Spatial Spread of Highly Pathogenic Avian Influenza Outbreaks in Europe and the United States, 2016-Early 2022

H5Nx highly pathogenic avian influenza (HPAI) viruses of clade 2.3.4.4 have caused outbreaks in Europe among wild and domestic birds since 2016 and were introduced to North America via wild migratory birds in December 2021. We examined the spatiotemporal extent of HPAI viruses across continents and characterized ecological and environmental predictors of virus spread between geographic regions by constructing a Bayesian phylodynamic generalized linear model (phylodynamic-GLM). The findings demonstrate localized epidemics of H5Nx throughout Europe in the first several years of the epizootic, followed by a singular branching point where H5N1 viruses were introduced to North America, likely via stopover locations throughout the North Atlantic. Once in the United States (US), H5Nx viruses spread at a greater rate between US-based regions as compared to prior spread in Europe. We established that geographic proximity is a predictor of virus spread between regions, implying that intercontinental transport across the Atlantic Ocean is relatively rare. An increase in mean ambient temperature over time was predictive of reduced H5Nx virus spread, which may reflect the effect of climate change on declines in host species abundance, decreased persistence of the virus in the environment, or changes in migratory patterns due to ecological alterations. Our data provide new knowledge about the spread and directionality of H5Nx virus dispersal in Europe and the US during an actively evolving intercontinental outbreak, including predictors of virus movement between regions, which will contribute to surveillance and mitigation strategies as the outbreak unfolds, and in future instances of uncontained avian spread of HPAI viruses.

Prevalence, Seroprevalence and Risk Factors of Avian Influenza in Wild Bird Populations in Korea: A Systematic Review and Meta-Analysis

Since the first recorded outbreak of the highly pathogenic avian influenza (HPAI) virus (H5N1) in South Korea in 2003, numerous sporadic outbreaks have occurred in South Korean duck and chicken farms, all of which have been attributed to avian influenza transmission from migratory wild birds. A thorough investigation of the prevalence and seroprevalence of avian influenza viruses (AIVs) in wild birds is critical for assessing the exposure risk and for directing strong and effective regulatory measures to counteract the spread of AIVs among wild birds, poultry, and humans. In this study, we performed a systematic review and meta-analysis, following the PRISMA guidelines, to generate a quantitative estimate of the prevalence and seroprevalence of AIVs in wild birds in South Korea. An extensive search of eligible studies was performed through electronic databases and 853 records were identified, of which, 49 fulfilled the inclusion criteria. The pooled prevalence and seroprevalence were estimated to be 1.57% (95% CI: 0.98, 2.51) and 15.91% (95% CI: 5.89, 36.38), respectively. The highest prevalence and seroprevalence rates were detected in the Anseriformes species, highlighting the critical role of this bird species in the dissemination of AIVs in South Korea. Furthermore, the results of the subgroup analysis also revealed that the AIV seroprevalence in wild birds varies depending on the detection rate, sample size, and sampling season. The findings of this study demonstrate the necessity of strengthening the surveillance for AIV in wild birds and implementing strong measures to curb the spread of AIV from wild birds to the poultry population.

Prevalence and Predictors of Seasonal Influenza Vaccine Uptake in Saudi Arabia Post COVID-19: A Web-Based Online Cross-Sectional Study

In the fall of 2022, the number of influenza-like illnesses (ILIs) and severe acute respiratory infections (SARIs) in Saudi Arabia had significantly increased compared with the corresponding period in previous years. Concerns regarding the population's seasonal influenza vaccine (SIV) uptake rates have emerged. In particular, the SIV uptake rates may have dropped post the COVID-19 pandemic compared with rates prior to the COVID-19 era. In this study, we aimed to estimate the prevalence and predictors of SIV uptake in Saudi Arabia post the COVID-19 pandemic. We conducted a cross-sectional study utilizing an online survey platform. We mainly collected sociodemographic information and determined whether the respondent was a healthcare professional or had a chronic disease. The overall SIV uptake prevalence was 31.8%. A lower SIV uptake was observed among those aged 55 years or older, females, residents of the central region, non-health practitioners, and those without chronic diseases. Several factors were associated with SIV uptake. Those aged 35-44 were over three-fold more likely to receive an SIV than those aged 55 years or older (OR: 3.66; 95% CI: 1.33-10.05). In addition, males had 73% higher odds of SIV uptake than females (OR: 1.73; 95% CI: 1.18-2.55). Health practitioners were more likely to receive an SIV than non-health practitioners (OR: 2.11; 95% CI: 1.45-3.06). Similarly, those with chronic diseases had 86% higher odds of SIV uptake than those without chronic diseases (OR: 1.86; 95% CI: 1.18-2.95). These findings can provide insights into the low prevalence and predictors of SIV uptake in Saudi Arabia. Future studies should be conducted to further explore the potential factors associated with such a low prevalence of SIV uptake post COVID-19 in Saudi Arabia.

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.

Exploring surface water as a transmission medium of avian influenza viruses - systematic infection studies in mallards

Mallards (Anas platyrhynchos) are an abundant anseriform migratory wild bird species worldwide and an important reservoir for the maintenance of low pathogenicity (LP) avian influenza viruses (AIV). They have also been implicated in the spread of high pathogenicity (HP) AIV after spill-over events from HPAIV-infected poultry. The spread of HPAIV within wild water bird populations may lead to viral contamination of natural habitats. The role of small shallow water bodies as a transmission medium of AIV among mallards is investigated here in three experimental settings. (i) Delayed onset but rapid progression of infection seeded by two mallards inoculated with either LP or HP AIV to each eight sentinel mallards was observed in groups with access to a small 100 L water pool. In contrast, groups with a bell drinker as the sole source of drinking water showed a rapid onset but lengthened course of infection. (ii) HPAIV infection also set off when virus was dispersed in the water pool; titres as low as 10² TCID₅₀ L^-1 (translating to 0.1 TCID₅₀ mL^-1) proved to be sufficient. (iii) Substantial loads of viral RNA (and infectivity) were also found on the surface of the birds' breast plumage. "Unloading" of virus infectivity from contaminated plumage into water bodies may be an efficient mechanism of virus spread by infected mallards. However, transposure of HPAIV via the plumage of an uninfected mallard failed. We conclude, surface water in small shallow water bodies may play an important role as a mediator of AIV infection of aquatic wild birds.

Public health response to outbreaks of highly pathogenic avian influenza (H5N1) among poultry in Northeast of Ireland, November 2021 to January 2022

OBJECTIVES

Human infections from highly pathogenic avian influenza (HPAI) H5N1 are associated with significant morbidity and mortality internationally. This study aimed to use routinely available data to examine key strategies to prevent H5N1 transmission to humans during outbreaks in poultry in residents in Cavan, Louth, Meath and Monaghan.

STUDY DESIGN

This was a cross-sectional based study.

METHODS

Data were obtained from Health Protection Team in the Department of Public Health, HSE North East and Department of Agriculture, Food, and the Marine (DAFM). Data entry and analyses were conducted using Microsoft Excel 2016.

RESULTS

The public health response focussed on contact tracing, monitoring and follow-up for household, farm workers and DAFM staff exposed on the affected farms. A total of 157 contact episodes were identified. Contacts received advice about active monitoring from their last exposure. A total of 111 (80%) were recommended chemoprophylaxis for exposure to HPAI H5N1. During the active monitoring period, two contacts developed acute respiratory symptoms, and parainfluenza 3 and rhino/enterovirus were identified in these individuals, respectively.

CONCLUSIONS

The findings of this study, using routinely gathered data, highlighted that collaboration between public health and DAFM at regional and national levels was key to rapid response to these outbreaks of HPAI in domesticated poultry. In addition, the public health response appears to have been successful in preventing H5N1 transmission from domesticated birds to humans.

Risky business in Georgia's wild birds: Contact rates between wild birds and backyard chickens is influenced by supplemental feed

Backyard chickens are increasingly popular, and their husbandry varies widely. How backyard chickens are housed may influence the accessibility of chicken feed and water to wild birds, and thus, the contact rates between both groups. Increased contacts have implications for pathogen transmission; for instance, Newcastle disease virus or avian influenza virus may be transmitted to and from backyard chickens from contaminated water or feed. Given this potentially increased pathogen risk to wild birds and backyard chickens, we examined which wild bird species are likely to encounter backyard chickens and their resources. We performed a supplemental feeding experiment followed by observations at three sites associated with backyard chickens in North Georgia, USA. At each site, we identified the species of wild birds that: (a) shared habitat with the chickens, (b) had a higher frequency of detection relative to other species and (c) encountered the coops. We identified 14 wild bird species that entered the coops to consume supplemental feed and were considered high-risk for pathogen transmission. Our results provide evidence that contact between wild birds and backyard chickens is frequent and more common than previously believed, which has crucial epidemiological implications for wildlife managers and backyard chicken owners.

Novel Low Pathogenic Avian Influenza H6N1 in Backyard Chicken in Easter Island (Rapa Nui), Chilean Polynesia

Little is known about the prevalence of avian influenza viruses (AIV) in wildlife and domestic animals in Polynesia. Here, we present the results of active AIV surveillance performed during two sampling seasons in 2019 on Easter Island (Rapa Nui). Tracheal and cloacal swabs as well as sera samples were obtained from domestic backyard poultry, while fresh faeces were collected from wild birds. In addition to detecting antibodies against AIV in 46% of the domestic chickens in backyard production systems tested, we isolated a novel low pathogenic H6N1 virus from a chicken. Phylogenetic analysis of all genetic segments revealed that the virus was closely related to AIV’s circulating in South America. Our analysis showed different geographical origins of the genetic segments, with the PA, HA, NA, NP, and MP gene segments coming from central Chile and the PB2, PB1, and NS being closely related to viruses isolated in Argentina. While the route of introduction can only be speculated, our analysis shows the persistence and independent evolution of this strain in the island since its putative introduction between 2015 and 2016. The results of this research are the first evidence of AIV circulation in domestic birds on a Polynesian island and increase our understanding of AIV ecology in region, warranting further surveillance on Rapa Nui and beyond.

Phylodynamic Study of the Conserved RNA Structure Encompassing the Hemagglutinin Cleavage Site Encoding Region of H5 and H7 Low Pathogenic Avian Influenza Viruses

Highly Pathogenic Avian Influenza Viruses (HPAIV) evolve from Low Pathogenic Avian Influenza Viruses (LPAIV) of the H5 and H7 subtypes. This evolution is characterized by the acquisition of a multi-basic cleavage site (MBCS) motif in the hemagglutinin (HA) that leads to an extended viral tropism and severe disease in poultry. One key unanswered question is whether the risk of transition to HPAIV is similar for all LPAIV H5 or H7 strains, or whether specific determinants in the HA sequence of some H5 or H7 LPAIV strains correlate with a higher risk of transition to HPAIV. Here we determined if specific features of the conserved RNA stem loop located at the hemagglutinin cleavage site-encoding region could be detected along the LPAIV to HPAIV evolutionary pathway. Analysis of the thermodynamic stability of the predicted RNA structures showed no specific patterns common to HA sequences leading to HPAIV and distinct from those remaining LPAIV. However, RNA structure clustering analysis revealed that most of the American lineage ancestors leading to H7 emergences via recombination shared the same vRNA structure topology at the HA1/HA2 boundary region. Our study thus identified predicted secondary RNA structures present in the HA of H7 viruses, which could promote genetic recombination and acquisition of a MBCS.

Effects of circulation weather types on influenza hospital admissions in Spain

In this study, we use a statistical approach based on generalized additive models, linking atmospheric circulation and the number of influenza-related hospital admissions in the Spanish Iberian Peninsula during 2003-2013. The relative risks are estimated for administrative units in the Spanish territory, which is politically structured into 15 regions called autonomous communities. A catalog of atmospheric circulation types is defined for this purpose. The relationship between the exposure and response variables is modeled using a distributed lag nonlinear model (DLNM). Types from southwest and anticyclonic are significant in terms of the probability of having more influenza-related hospital admissions for all of Spain. The heterogeneity of the results is very high. The relative risk is also estimated for each autonomous community and weather type, with the maximum number of influenza-related hospital admissions associated with circulation types from the southwest and the south. We identify six specific situations where relative risk is considered extreme and twelve with a high risk of increasing influenza-related hospital admissions. The rest of the situations present a moderate risk. Atmospheric local conditions become a key factor for understanding influenza spread in each spatial unit of the Peninsula. Further research is needed to understand how different weather variables (temperature, humidity, and sun radiation) interact and promote the spread of influenza.

A patho-microbiological study of tissue samples of the Greater Adjutant Leptoptilos dubius (Aves: Ciconiiformes: Ciconiidae) that died in Deeporbeel Wildlife Sanctuary, Assam, India

The Greater Adjutant is an IUCN Red List ‘Endangered’ scavenging stork.  This study reports the findings of post-mortem, histopathology, and a series of microbiological tests conducted on the Greater Adjutant that died in Deeporbeel Wildlife Sanctuary, Assam.  A post-mortem examination revealed extensive nodule forming parasitic (Balfouria monogama) infestations in the stomach and intestine.  Generalised congestion and haemorrhages in multiple organs were also revealed by the histopathological findings.  Bacteriological culture detected the presence of Escherichia coli, Enterococcus sp., and Clostridium perfringens (C. perfringens was confirmed by cpa gene PCR).  Virus detection tests like HA and HI test for NDV and rapid antigen detection test for Avian Influenza virus were found to be negative; however, PCR of tissue samples from two Greater Adjutants for Flavivirus was found to be positive.  Greater Adjutants may carry the above bacteria as commensals in their GI tract and may possibly act as a reservoir of Flavivirus.  The actual cause of deaths, however, were confirmed by the forensic report to be due to organophosphorus toxicity.

The socioeconomic and environmental drivers of the COVID-19 pandemic: A review

In recent decades, there has been an intensification of the socioeconomic and environmental drivers of pandemics, including ecosystem conversion, meat consumption, urbanization, and connectivity among cities and countries. This paper reviews how these four systemic drivers help explain the dynamics of the COVID-19 pandemic and other recent emerging infectious diseases, and the policies that can be adopted to mitigate their risks. Land-use change and meat consumption increase the likelihood of pathogen spillover from animals to people. The risk that such zoonotic outbreaks will then spread to become pandemics is magnified by growing urban populations and the networks of trade and travel within and among countries. Zoonotic spillover can be mitigated through habitat protection and restrictions on the wildlife trade. Containing infectious disease spread requires a high degree of coordination among institutions across geographic jurisdictions and economic sectors, all backed by international investment and cooperation.

Probability of a zoonotic spillover with seasonal variation

Zoonotic infectious diseases are spread from animals to humans. It is estimated that over 60% of human infectious diseases are zoonotic and 75% of them are emerging zoonoses. The majority of emerging zoonotic infectious diseases are caused by viruses including avian influenza, rabies, Ebola, coronaviruses and hantaviruses. Spillover of infection from animals to humans depends on a complex transmission pathway, which is influenced by epidemiological and environmental processes. In this investigation, the focus is on direct transmission between animals and humans and the effects of seasonal variations on the transmission and recovery rates. Fluctuations in transmission and recovery, besides being influenced by physiological processes and behaviors of pathogen and host, are driven by seasonal variations in temperature, humidity or rainfall. A new time-nonhomogeneous stochastic process is formulated for infectious disease spread from animals to humans when transmission and recovery rates are time-periodic. A branching process approximation is applied near the disease-free state to predict the probability of the first spillover event from animals to humans. This probability is a periodic function of the time when infection is introduced into the animal population. It is shown that the highest risk of a spillover depends on a combination of animal to human transmission, animal to animal transmission and animal recovery. The results are applied to a stochastic model for avian influenza with spillover from domestic poultry to humans.

Molecular identification and phylogenetic characterization of influenza A virus at a wildlife-livestock interface in Mexico

Influenza A virus (IAV) outbreaks constitute a constant threat to public health and pose a remarkable impact on socio-economic systems worldwide. Interactions between wild and domestic birds, humans and swine can lead to spillover events. Backyard livestock systems in proximity to wetlands represent high-risk areas for viral spread. However, some gaps remain in our knowledge of IAV transmission at the wildlife-livestock interface in Mexico. Hence, the study aimed at molecular identification and phylogenetic characterization of IAV in the wild duck-backyard livestock interface at a wetland of Mexico. A total of 875 animals were tested by real-time RT-PCR (qRT-PCR). We detected IAV in 3.68% of the wild ducks sampled during the winter season 2016-2017. Nonetheless, the samples obtained from backyard poultry and swine tested negative. The highest IAV frequency (11.10%) was found in the Mexican duck (Anas diazi). Subtypes H1N1, H3N2 and H5N2 were detected. Phylogenetic analyses revealed that IAV detected in wild birds from the Lerma wetlands was mostly related to swine and poultry IAV strains previously isolated in the United States and Mexico. Except, the UIFMVZ377/H5N2 related to North American waterbirds. In conclusion, the co-circulation of three IAV subtypes in wild ducks close to backyard farms in Mexico, as well as the local identification of influenza viruses genetically related to Mexican and North American IAV strains, highlights the importance of the Lerma marshes for influenza surveillance given the close interaction among wild birds, poultry, pigs and humans.

Virus-like Particle Vaccines: A Prospective Panacea Against an Avian Influenza Panzootic

Epizootics of highly pathogenic avian influenza (HPAI) have resulted in the deaths of millions of birds leading to huge financial losses to the poultry industry worldwide. The roles of migratory wild birds in the harbouring, mutation, and transmission of avian influenza viruses (AIVs), and the lack of broad-spectrum prophylactic vaccines present imminent threats of a global panzootic. To prevent this, control measures that include effective AIV surveillance programmes, treatment regimens, and universal vaccines are being developed and analysed for their effectiveness. We reviewed the epidemiology of AIVs with regards to past avian influenza (AI) outbreaks in birds. The AIV surveillance programmes in wild and domestic birds, as well as their roles in AI control were also evaluated. We discussed the limitations of the currently used AI vaccines, which necessitated the development of a universal vaccine. We evaluated the current development of AI vaccines based upon virus-like particles (VLPs), particularly those displaying the matrix-2 ectodomain (M2e) peptide. Finally, we highlighted the prospects of these VLP vaccines as universal vaccines with the potential of preventing an AI panzootic.

The Impact of a Six-Year Climate Anomaly on the "Spanish Flu" Pandemic and WWI

The H1N1 "Spanish influenza" pandemic of 1918-1919 caused the highest known number of deaths recorded for a single pandemic in human history. Several theories have been offered to explain the virulence and spread of the disease, but the environmental context remains underexamined. In this study, we present a new environmental record from a European, Alpine ice core, showing a significant climate anomaly that affected the continent from 1914 to 1919. Incessant torrential rain and declining temperatures increased casualties in the battlefields of World War I (WWI), setting the stage for the spread of the pandemic at the end of the conflict. Multiple independent records of temperature, precipitation, and mortality corroborate these findings.

Mathematically modeling spillovers of an emerging infectious zoonosis with an intermediate host

Modeling the behavior of zoonotic pandemic threats is a key component of their control. Many emerging zoonoses, such as SARS, Nipah, and Hendra, mutated from their wild type while circulating in an intermediate host population, usually a domestic species, to become more transmissible among humans, and this transmission route will only become more likely as agriculture and trade intensifies around the world. Passage through an intermediate host enables many otherwise rare diseases to become better adapted to humans, and so understanding this process with accurate mathematical models is necessary to prevent epidemics of emerging zoonoses, guide policy interventions in public health, and predict the behavior of an epidemic. In this paper, we account for a zoonotic disease mutating in an intermediate host by introducing a new mathematical model for disease transmission among three species. We present a model of these disease dynamics, including the equilibria of the system and the basic reproductive number of the pathogen, finding that in the presence of biologically realistic interspecies transmission parameters, a zoonotic disease with the capacity to mutate in an intermediate host population can establish itself in humans even if its R₀ in humans is less than 1. This result and model can be used to predict the behavior of any zoonosis with an intermediate host and assist efforts to protect public health.

The Emergence of H7N7 Highly Pathogenic Avian Influenza Virus from Low Pathogenicity Avian Influenza Virus Using an in ovo Embryo Culture Model

Outbreaks of highly pathogenic avian influenza virus (HPAIV) often result in the infection of millions of poultry, causing up to 100% mortality. HPAIV has been shown to emerge from low pathogenicity avian influenza virus (LPAIV) in field outbreaks. Direct evidence for the emergence of H7N7 HPAIV from a LPAIV precursor with a rare di-basic cleavage site (DBCS) was identified in the UK in 2008. The DBCS contained an additional basic amino acid compared to commonly circulating LPAIVs that harbor a single-basic amino acid at the cleavage site (SBCS). Using reverse genetics, outbreak HPAIVs were rescued with a DBCS (H7N7_DB), as seen in the LPAIV precursor or an SBCS representative of common H7 LPAIVs (H7N7_SB). Passage of H7N7_DB in chicken embryo tissues showed spontaneous evolution to a HPAIV. In contrast, deep sequencing of extracts from embryo tissues in which H7N7_SB was serially passaged showed retention of the LPAIV genotype. Thus, in chicken embryos, an H7N7 virus containing a DBCS appears naturally unstable, enabling rapid evolution to HPAIV. Evaluation in embryo tissue presents a useful approach to study AIV evolution and allows a laboratory-based dissection of molecular mechanisms behind the emergence of HPAIV.

Prevalence and Diversity of Avian Influenza Virus Hemagglutinin Sero-Subtypes in Poultry and Wild Birds in Bangladesh

Highly pathogenic avian influenza H5 viruses have pandemic potential, cause significant economic losses and are of veterinary and public health concerns. This study aimed to investigate the distribution and diversity of hemagglutinin (HA) subtypes of avian influenza virus (AIV) in poultry and wild birds in Bangladesh. We conducted an avian influenza sero-surveillance in wild and domestic birds in wetlands of Chattogram and Sylhet in the winter seasons 2012-2014. We tested serum samples using a competitive enzyme-linked immunosorbent assay (c-ELISA), and randomly selected positive serum samples (170 of 942) were tested using hemagglutination inhibition (HI) to detect antibodies against the 16 different HA sero-subtypes. All AIV sero-subtypes except H7, H11, H14 and H15 were identified in the present study, with H5 and H9 dominating over other subtypes, regardless of the bird species. The diversity of HA sero-subtypes within groups ranged from 3 (in household chickens) to 10 (in migratory birds). The prevalence of the H5 sero-subtype was 76.3% (29/38) in nomadic ducks, 71.4% (5/7) in household chicken, 66.7% (24/36) in resident wild birds, 65.9% (27/41) in migratory birds and 61.7% (29/47) in household ducks. Moreover, the H9 sero-subtype was common in migratory birds (56%; 23/41), followed by 38.3% (18/47) in household ducks, 36.8% (14/38) in nomadic ducks, 30.6% (11/66) in resident wild birds and 28.5% (2/7) in household chickens. H1, H4 and H6 sero-subtypes were the most common sero-subtypes (80%; 8/10, 70%; 7/10 and 70%; 7/10, respectively) in migratory birds in 2012, H9 in resident wild birds (83.3%; 5/6) and H2 in nomadic ducks (73.9%; 17/23) in 2013, and the H5 sero-subtype in all types of birds (50% to 100%) in 2014. The present study demonstrates that a high diversity of HA subtypes circulated in diverse bird species in Bangladesh, and this broad range of AIV hosts may increase the probability of AIVs' reassortment and may enhance the emergence of novel AIV strains. A continued surveillance for AIV at targeted domestic-wild bird interfaces is recommended to understand the ecology and evolution of AIVs.

Risk factors and spatial relative risk assessment for influenza A virus in poultry and swine in backyard production systems of central Chile

Backyard production systems (BPS) are a common form of poultry and swine production worldwide. The limited implementation of biosecurity standards in these operations makes BPS a potential source for the emergence of pathogens that have an impact on both animal and public health. Information regarding circulation of influenza A virus (IAV) in poultry and swine raised in BPS is scarce; particularly in South American countries. The objective of this study was to estimate prevalence and seroprevalence of IAV in BPS in central Chile, identify subtype diversity, evaluate risk factors and spatial relative risk for IAV. Samples were collected from 329 BPS from central Chile. Seroprevalence at BPS level was 34.7% (95% CI: 23.1%–46.2%), 19.7% (95% CI: 9.9%–30.6%) and 11.7% (95% CI: 7.2%–16.4%), whereas prevalence at BPS level was 4.2% (95% CI: 0.0%–8.8%), 8.2% (95% CI: 0.8%–14.0%) and 9.2% (95% CI: 4.8%–13.1%), for the Metropolitan, Valparaiso and LGB O’Higgins regions, respectively. Spatial analysis revealed that central‐western area of Metropolitan region and the southern province of Valparaiso region could be considered as high‐risk areas for IAV (spatial relative risk = 2.2, p < .05). Logistic regression models identified the practice of breeding both poultry and pigs at the BPS as a risk factor (95% CI 1.06–3.75). From 75 IAV ELISA‐positive sera, 20 chicken sera had haemagglutination inhibition titres ranging from 20 to 160, and of these, 11 had microneutralization titres ranging from 40 to 960 for one or more IAV subtypes. Identified subtypes were H1, H3, H4, H9, H10 and H12. Results from this study highlight the need for further IAV surveillance programmes in BPS in Chile. Early detection of IAV strains circulating in backyard animals, especially in regions with large human populations, could have an enormous impact on animal and public health.

Rapid evolution of Mexican H7N3 highly pathogenic avian influenza viruses in poultry

Highly pathogenic avian influenza (HPAI) virus subtype H7N3 has been circulating in poultry in Mexico since 2012 and vaccination has been used to control the disease. In this study, eight Mexican H7N3 HPAI viruses from 2015–2017 were isolated and fully sequenced. No evidence of reassortment was detected with other avian influenza (AI) viruses, but phylogenetic analyses show divergence of all eight gene segments into three genetic clusters by 2015, with 94.94 to 98.78 percent nucleotide homology of the HA genes when compared to the index virus from 2012. The HA protein of viruses from each cluster showed a different number of basic amino acids (n = 5–7) in the cleavage site, and six different patterns at the predicted N-glycosylation sites. Comparison of the sequences of the Mexican lineage H7N3 HPAI viruses and American ancestral wild bird AI viruses to characterize the virus evolutionary dynamics showed that the nucleotide substitution rates in PB2, PB1, PA, HA, NP, and NS genes greatly increased once the virus was introduced into poultry. The global nonsynonymous and synonymous ratios imply strong purifying selection driving the evolution of the virus. Forty-nine positively selected sites out of 171 nonsynonymous mutations were identified in the Mexican H7N3 HPAI viruses, including 7 amino acid changes observed in higher proportion in North American poultry origin AI viruses isolates than in wild bird-origin viruses. Continuous monitoring and molecular characterization of the H7N3 HPAI virus is important for better understanding of the virus evolutionary dynamics and further improving control measures including vaccination.

Low pathogenic avian influenza (H7N6) virus causing an outbreak in commercial Turkey farms in Chile

In late 2016, an H7N6 low pathogenic avian influenza virus outbreak occurred in domestic turkeys in Central Chile. We characterized the genetic and antigenic properties of the outbreak virus and its experimental transmission in chickens. Our studies demonstrate that the outbreak virus is a reassortment of genes identified from Chilean wild bird viruses between 2013 and 2017 and displays molecular adaptations to poultry and antiviral resistance to adamantanes. Further, these wild bird viruses are also able to transmit in experimentally infected chickens highlighting the need for continued surveillance and improvement of biosecurity in poultry farms.

Effective control measures considering spatial heterogeneity to mitigate the 2016-2017 avian influenza epidemic in the Republic of Korea

During the winter of 2016-2017, an epidemic of highly pathogenic avian influenza (HPAI) led to high mortality in poultry and put a serious burden on the poultry industry of the Republic of Korea. Effective control measures considering spatial heterogeneity to mitigate the HPAI epidemic is still a challenging issue. Here we develop a spatial-temporal compartmental model that incorporates the culling rate as a function of the reported farms and farm density in each town. The epidemiological and geographical data of two species, chickens and ducks, from the farms in the sixteen towns in Eumseong-gun and Jincheon-gun are used to find the best-fitted parameters of the metapopulation model. The best culling radius to maximize the final size of the susceptible farms and minimize the total number of culled farms is calculated from the model. The local reproductive number using the next generation method is calculated as an indicator of virus transmission in a given area. Simulation results indicate that this parameter is strongly influenced not only by epidemiological factors such as transmissibility and/or susceptibility of poultry species but also by geographical and demographical factors such as the distribution of poultry farms (or density) and connectivity (or distance) between farms. Based on this result, we suggest the best culling radius with respect to the local reproductive number in a targeted area.

Emerging human infectious diseases and the links to global food production

Infectious diseases are emerging globally at an unprecedented rate while global food demand is projected to increase sharply by 2100. Here, we synthesize the pathways by which projected agricultural expansion and intensification will influence human infectious diseases and how human infectious diseases might likewise affect food production and distribution. Feeding 11 billion people will require substantial increases in crop and animal production that will expand agricultural use of antibiotics, water, pesticides and fertilizer, and contact rates between humans and both wild and domestic animals, all with consequences for the emergence and spread of infectious agents. Indeed, our synthesis of the literature suggests that, since 1940, agricultural drivers were associated with >25% of all - and >50% of zoonotic - infectious diseases that emerged in humans, proportions that will likely increase as agriculture expands and intensifies. We identify agricultural and disease management and policy actions, and additional research, needed to address the public health challenge posed by feeding 11 billion people.

B cell epitopes in the intrinsically disordered regions of neuraminidase and hemagglutinin proteins of H5N1 and H9N2 avian influenza viruses for peptide-based vaccine development

Avian influenza viruses (AIV) are very active in several parts of the globe and are the cause of huge economic loss for the poultry industry and also human fatalities. Three dimensional modeling was carried out for neuraminidase (NA) and hemagglutinin (HA) proteins of AIV. The C-score, estimated TM-Score, and estimated root-mean-square deviation (RMSD) score for NA of H5N1 were -1.18, 0.57 ± 0.15, and 9.8 ± 7.6, respectively. The C-score, estimated TM-Score, and estimated RMSD score for NA of H9N2 were -1.43, 0.54 ± 0.15, and 10.5 ± 4.6, respectively. The C-score, estimated TM-Score, and estimated RMSD score for HA of H5N1 were -0.03, 0.71 ± 0.12, and 7.7 ± 4.3, respectively. The C-score, estimated TM-Score, and estimated RMSD score for HA of H9N2 were -0.57, 0.64 ± 0.13, and 8.9 ± 4.6, respectively. Intrinsically disordered regions were identified for the NA and HA proteins of H5N1 and H9N2 with the use of PONDR program. Linear B cell epitope was predicted using BepiPred 2 program for NA and HA of H5N1 and H9N2 avian influenza strains. Discontinuous epitopes were predicted by Discotope 2 program. The linear epitopes that were considered likely to be immunogenic and within the intrinsically disordered region for the NA of H5N1 was TKSTNSRSGFEMIWDPNGWTGTDSSFSVK, and for H9N2 it was VGDTPRNDDSSSSSNCRDPNNERGAP. In the case of HA of H5N1, it was QRLVPKIATRSKVNGQSG and ATGLRNSPQRERRRKK; for H9N2 it was INRTFKPLIGPRPLVNGLQG and SLKLAVGLRNVPARSSR. The discontinuous epitopes of NA of H5N1 and H9N2 were identified at various regions of the protein structure spanning from amino acid residue positions 90 to 449 and 107 to 469, respectively. Similarly, the discontinuous epitopes of HA of H5N1 and H9N2 were identified in the amino acid residue positions 27 to 517 and 136 to 521, respectively. This study has identified potential and highly immunogenic linear and conformational B-cell epitopes towards developing a vaccine against AIV both for human and poultry use.

Intercontinental spread of Asian-origin H7 avian influenza viruses by captive bird trade in 1990's

Wild bird migration and illegal trade of infected poultry, eggs, and poultry products have been associated with the spread of avian influenza viruses (AIV). During 1992-1996, H7N1 and H7N8 low pathogenic AIV (LPAIV) were identified from captive wild birds; such as Pekin robin (Leiothrix lutea), magpie robin (Copsychus saularis), flycatcher sp. (genus Empidonax), a species of softbill and parakeet, sun conure (Aratinga solstitialis), painted conure (Pyrrhura picta), fairy bluebird (Irena puella), and common iora (Aegithina tiphia), kept in aviaries or quarantine stations in England, The Netherlands, Singapore and the United States (U.S.). In this study, we sequenced these H7 viruses isolated from quarantine facilities and aviaries using next-generation sequencing and conducted a comparative phylogenetic analysis of complete genome sequences to elucidate spread patterns. The complete genome sequencing and phylogenetic analysis suggested that H7 viruses originated from a common source, even though they were obtained from birds in distant geographical regions. All H7N1 and H7N8 viruses were LPAIV, except a H7N1 highly pathogenic AIV (HPAIV), A/Pekin robin/California/30412/1994(H7N1) virus. Our results support the continued need for regulation of the captive wild bird trade to reduce the risk of introduction and dissemination of both LPAIV and HPAIV throughout the world.

Co-circulation of genetically distinct highly pathogenic avian influenza A clade 2.3.4.4 (H5N6) viruses in wild waterfowl and poultry in Europe and East Asia, 2017-18

Highly pathogenic avian influenza (HPAI) H5 clade 2.3.4.4 viruses were first introduced into Europe in late 2014 and re-introduced in late 2016, following detections in Asia and Russia. In contrast to the 2014–15 H5N8 wave, there was substantial local virus amplification in wild birds in Europe in 2016–17 and associated wild bird mortality, with evidence for occasional gene exchange with low pathogenic avian influenza (LPAI) viruses. Since December 2017, several European countries have again reported events or outbreaks with HPAI H5N6 reassortant viruses in both wild birds and poultry, respectively. Previous phylogenetic studies have shown that the two earliest incursions of HPAI H5N8 viruses originated in Southeast Asia and subsequently spread to Europe. In contrast, this study indicates that recent HPAI H5N6 viruses evolved from the H5N8 2016–17 viruses during 2017 by reassortment of a European HPAI H5N8 virus and wild host reservoir LPAI viruses. The genetic and phenotypic differences between these outbreaks and the continuing detections of HPAI viruses in Europe are a cause of concern for both animal and human health. The current co-circulation of potentially zoonotic HPAI and LPAI virus strains in Asia warrants the determination of drivers responsible for the global spread of Asian lineage viruses and the potential threat they pose to public health.

H7N6 low pathogenic avian influenza outbreak in commercial turkey farms in Chile caused by a native South American Lineage

In December 2016, low pathogenic avian influenza (LPAI) caused by an H7N6 subtype was confirmed in a grow-out turkey farm located in Valparaiso Region, Chile. Depopulation of exposed animals, zoning, animal movement control and active surveillance were implemented to contain the outbreak. Two weeks later, a second grow-out turkey farm located 70 km north of the first site was also infected by H7N6 LPAI, which subsequently spilled over to one backyard poultry flock. The virus involved in the outbreak shared a close genetic relationship with Chilean aquatic birds' viruses collected in previous years. The A/turkey/Chile/2017(H7N6) LPAI virus belonged to a native South American lineage. Based on the H7 and most of the internal genes' phylogenies, these viruses were also closely related to the ones that caused a highly pathogenic avian influenza outbreak in Chile in 2002. Results from this study help to understand the regional dynamics of influenza outbreaks, highlighting the importance of local native viruses circulating in the natural reservoir hosts.

The Impact of Climate Change on Raw and Untreated Wastewater Use for Agriculture, Especially in Arid Regions: A Review

Climate change is one of the major challenges of our time that pose unprecedented stress to the environment and threats to human health. The global impacts of climate change are vast, spanning from extreme weather events to changes in patterns and distribution of infectious diseases. Lack of rainfall associated with higher temperatures has a direct influence on agricultural production. This is compounded by a growing population forecasted to expand further with increasing needs for food and water. All this has led to the increasing use of wastewater worldwide. In this review, we more specifically discuss the use of untreated wastewater in agriculture in the Middle East and North Africa (MENA) countries, the most arid region in the world. This presents challenges for agriculture with respect to water availability and increasing wastewater use in agri-food chain. This in turn exerts pressures on the safety of food raised from such irrigated crops. Current practices in the MENA region indicate that ineffective water resource management, lack of water quality policies, and slow-paced wastewater management strategies continue to contribute to a decline in water resources and an increased unplanned use of black and graywater in agriculture. Radical actions are needed in the region to improve water and wastewater management to adapt to these impacts. In this regard, the 2006 WHO guidelines for the use of wastewater contain recommendations for the most effective solutions. They provide a step-by-step guide for series of appropriate health protection measures for microbial reduction targets of 6 log units for viral, bacterial, and protozoan pathogens, but these need to be combined with new varieties of crops that are drought and pest resistant. More research into economic local treatment procedures for wastewater in the region is warranted.

Avian influenza virus ecology and evolution through a climatic lens

Avian influenza virus (AIV) is a major health threat to both avian and human populations. The ecology of the virus is driven by numerous factors, including climate and avian migration patterns, yet relatively little is known about these drivers. Long-distance transport of the virus is tied to inter- and intra-continental bird migration, while enhanced viral reassortment is linked to breeding habitats in Beringia shared by migrant species from North America and Asia. Furthermore, water temperature, pH, salinity, and co-existing biota all impact the viability and persistence of the virus in the environment. Changes in climate can potentially alter the ecology of AIV through multiple pathways. Warming temperatures can change the timing and patterns of bird migration, creating novel assemblages of species and new opportunities for viral transport and reassortment. Water temperature and chemistry may also be altered, resulting in changes in virus survival. In this review, we explain how these shifts have the potential to increase viral persistence, pathogenicity, and transmissibility and amplify the threat of pandemic disease in animal and human hosts. Better understanding of climatic influences on viral ecology is essential to developing strategies to limit adverse health effects in humans and animals.

Identification, sequence analysis, and infectivity of H9N2 avian influenza viruses isolated from geese

The subtype H9N2 avian influenza virus greatly threatens the Chinese poultry industry, even with annual vaccination. Waterfowl can be asymptomatically infected with the H9N2 virus. In this study, three H9N2 virus strains, designated A/Goose/Jiangsu/YZ527/2011 (H9N2, Gs/JS/YZ527/11), A/Goose/Jiangsu/SQ119/2012 (H9N2, Gs/JS/SQ119/12), and A/Goose/Jiangsu/JD564/2012 (H9N2, Gs/JS/JD564/12), were isolated from domestic geese. Molecular characterization of the three isolates showed that the Gs/JS/YZ527/11 virus is a double-reassortant virus, combining genes of A/Quail/Hong Kong/G1/97 (H9N2, G1/97)-like and A/Chicken/Shanghai/F/98 (H9N2, F/98)-like; the Gs/JS/SQ119/12 virus is a triple-reassortant virus combining genes of G1/97-like, F/98-like, and A/Duck/Shantou/163/2004 (H9N2, ST/163/04)-like. The sequences of Gs/JS/JD564/12 share high homology with those of the F/98 virus, except for the neuraminidase gene, whereas the internal genes of Gs/JS/YZ527/11 and Gs/JS/SQ119/12 are closely related to those of the H7N9 viruses. An infectivity analysis of the three isolates showed that Gs/JS/SQ119/12 and Gs/JS/YZ527/11 replicated well, with seroconversion, in geese and chickens, the Gs/JS/JD564/12 did not infect well in geese or chickens, and the F/98 virus only infected chickens, with seroconversion. Emergence of these new reassortant H9N2 avian influenza viruses indicates that these viruses can infect both chicken and goose and can produce different types of lesions in each species.

Genetic and biological characterization of H9N2 avian influenza viruses isolated in China from 2011 to 2014

The genotypes of the H9N2 avian influenza viruses have changed since 2013 when almost all H9N2 viruses circulating in chickens in China were genotype 57 (G57) with the fittest lineage of each gene. To characterize the H9N2 variant viruses from 2011 to 2014, 28 H9N2 influenza viruses were isolated from live poultry markets in China from 2011–2014 and were analyzed by genetic and biological characterization. Our findings showed that 16 residues that changed antigenicity, two potential N-linked glycosylation sites, and one amino acid in the receptor binding site of the HA protein changed significantly from 2011–2014. Moreover, the HA and NA genes in the phylogenetic tree were mainly clustered into two independent branches, A and B, based on the year of isolation. H9N2 virus internal genes were related to those from the human-infected avian influenza viruses H5N1, H7N9, and H10N8. In particular, the NS gene in the phylogenetic tree revealed genetic divergence of the virus gene into three branches labeled A, B, and C, which were related to the H9N2, H10N8, and H7N9 viruses, respectively. Additionally, the isolates also showed varying levels of infection and airborne transmission. These results indicated that the H9N2 virus had undergone an adaptive evolution and variation from 2011–2014.

Live bird markets in Bangladesh as a potentially important source for Avian Influenza Virus transmission

Live bird markets (LBM) are important for trading poultry in many developing countries where they are being considered hotspots of Avian Influenza Virus (AIV) prevalence and contamination. An active surveillance for Avian Influenza Virus (AIV) was conducted on four species of LBM birds (chickens, ducks, quails and pigeons) from 10 of the largest LBM in Chittagong, Bangladesh, and two species of peri-domestic wild birds (house crow and Asian pied starling) in their direct vicinity from November 2012 until September 2016. Our aim was to identify the scale and annual pattern of AIV circulation in both the LBM birds and the two per-domestic wild bird species living in close proximity of the LBM. In the latter two species, the annual pattern in AIV antibody prevalence was additionally investigated. A total of 4770 LBM birds and 1119 peri-domestic wild birds were sampled. We used rt-PCR for detection of the AIV M-gene and AIV subtypes H5, H7 and H9 from swab samples. We used c-ELISA for AIV antibody detection from serum samples of peri-domestic wild birds. Average AIV prevalence among the four LBM species varied between 16 and 28%, whereas no AIV was detected in peri-domestic wild birds by rt-PCR. In all LBM species we found significantly higher AIV prevalence in winter compared to summer. A similar pattern was found in AIV antibody prevalence in peri-domestic wild birds feeding in the direct vicinity of LBM. For the subtypes of AIV investigated, we found a significantly higher proportion of AIV H5 in LBM chickens and H9 in LBM ducks. No H7 was detected in any of the investigated samples. We conclude that AIV and notably AIV H5 and H9 were circulating in the investigated LBM of Bangladesh with clear seasonality that matched the prevalence of AIV antibodies of peri-domestic wild birds. These patterns show great resemblance to the annual outbreak patterns in Bangladeshi poultry industry. Our data suggest considerable exchange of AIV within and among the four LBM bird species and peri-domestic wild birds, which likely contributes to the maintenance of the AIV problems in Bangladesh. Increasing biosecurity and notably reducing the direct and indirect mixing of various domestic bird species and peri-domestic wild birds and developing all-in-all-out selling systems with regular use of disinfectant are likely to reduce the risk of transmission and spread of AIV, including HPAI.

Low Pathogenic Avian Influenza Exposure Risk Assessment in Australian Commercial Chicken Farms

This study investigated the pathways of exposure to low pathogenic avian influenza (LPAI) virus among Australian commercial chicken farms and estimated the likelihood of this exposure occurring using scenario trees and a stochastic modeling approach following the World Organization for Animal Health methodology for risk assessment. Input values for the models were sourced from scientific literature and an on-farm survey conducted during 2015 and 2016 among Australian commercial chicken farms located in New South Wales and Queensland. Outputs from the models revealed that the probability of a first LPAI virus exposure to a chicken in an Australian commercial chicken farms from one wild bird at any point in time is extremely low. A comparative assessment revealed that across the five farm types (non-free-range meat chicken, free-range meat chicken, cage layer, barn layer, and free range layer farms), free-range layer farms had the highest probability of exposure (7.5 × 10^-4; 5% and 95%, 5.7 × 10^-4-0.001). The results indicate that the presence of a large number of wild birds on farm is required for exposure to occur across all farm types. The median probability of direct exposure was highest in free-range farm types (5.6 × 10^-4 and 1.6 × 10^-4 for free-range layer and free-range meat chicken farms, respectively) and indirect exposure was highest in non-free-range farm types (2.7 × 10^-4, 2.0 × 10^-4, and 1.9 × 10^-4 for non-free-range meat chicken, cage layer, and barn layer farms, respectively). The probability of exposure was found to be lowest in summer for all farm types. Sensitivity analysis revealed that the proportion of waterfowl among wild birds on the farm, the presence of waterfowl in the range and feed storage areas, and the prevalence of LPAI in wild birds are the most influential parameters for the probability of Australian commercial chicken farms being exposed to avian influenza (AI) virus. These results highlight the importance of ensuring good biosecurity on farms to minimize the risk of exposure to AI virus and the importance of continuous surveillance of LPAI prevalence including subtypes in wild bird populations.

Towards an eco-phylogenetic framework for infectious disease ecology

Identifying patterns and drivers of infectious disease dynamics across multiple scales is a fundamental challenge for modern science. There is growing awareness that it is necessary to incorporate multi-host and/or multi-parasite interactions to understand and predict current and future disease threats better, and new tools are needed to help address this task. Eco-phylogenetics (phylogenetic community ecology) provides one avenue for exploring multi-host multi-parasite systems, yet the incorporation of eco-phylogenetic concepts and methods into studies of host pathogen dynamics has lagged behind. Eco-phylogenetics is a transformative approach that uses evolutionary history to infer present-day dynamics. Here, we present an eco-phylogenetic framework to reveal insights into parasite communities and infectious disease dynamics across spatial and temporal scales. We illustrate how eco-phylogenetic methods can help untangle the mechanisms of host-parasite dynamics from individual (e.g. co-infection) to landscape scales (e.g. parasite/host community structure). An improved ecological understanding of multi-host and multi-pathogen dynamics across scales will increase our ability to predict disease threats.

Global genetic variation and transmission dynamics of H9N2 avian influenza virus

The H9N2 influenza viruses are extensively circulating in the poultry population, and variable genotypes can be generated through mutation, recombination and reassortment, which may be better adapted to infect a new host, resist drug treatment or escape immune pressure. The LPAI H9N2 viruses have the potential to evolve towards high levels of virulence in human. Some studies about the regional dispersal were reported, but global dissemination and the drivers of the virus are poorly understood, particularly at the genome scale. Here, we have analysed all eight gene segments of 168 H9N2 genomes sampled randomly aiming to provide a panoramic framework for better understanding the genesis and genetic variation of the viruses, and utilized phylogeography and spatial epidemiology approaches to uncover the effects of the genetic variation, predictors and spread of H9N2 viruses. We found that more frequent reassortment events involve segments PA, NP and NS, and 21 isolates have possible mosaic structure resulting from recombination events. Estimates of gene-specific global dN/dS ratios showed that all genes were subject to purifying selection. However, a total of 13 sites were detected under positive selection by at least two of three methods, which located within segments HA, NA, M2, NS1 and PA. Additionally, we inferred that NA segment has the highest rate of nucleotide substitution, and its tMRCA estimate is the youngest than the remaining segments' inference. About the spatial history, air transportation of human was identified as the predominant driver of global viral migration using GLM analysis, and economic factors and geographical distance were the modest predictors. Higher migration rates were estimated between five pairs of regions (>0.01) indicating the frequent migration of the viruses between discrete geographical locations. Further, our Markov jumps analysis showed that viral migration is more frequent between Southern China and Northern China, and high rate of gene flow was observed between America and East Asia. Moreover, the America together with Southeast Asia acted as the primary hubs of global transmission, forming the trunk of evolutionary tree. These findings suggested a complex interaction between virus evolution, epidemiology and human behaviour.

Linking social and spatial networks to viral community phylogenetics reveals subtype-specific transmission dynamics in African lions

Heterogeneity within pathogen species can have important consequences for how pathogens transmit across landscapes; however, discerning different transmission routes is challenging. Here, we apply both phylodynamic and phylogenetic community ecology techniques to examine the consequences of pathogen heterogeneity on transmission by assessing subtype-specific transmission pathways in a social carnivore. We use comprehensive social and spatial network data to examine transmission pathways for three subtypes of feline immunodeficiency virus (FIV_Ple ) in African lions (Panthera leo) at multiple scales in the Serengeti National Park, Tanzania. We used FIV_Ple molecular data to examine the role of social organization and lion density in shaping transmission pathways and tested to what extent vertical (i.e., father- and/or mother-offspring relationships) or horizontal (between unrelated individuals) transmission underpinned these patterns for each subtype. Using the same data, we constructed subtype-specific FIV_Ple co-occurrence networks and assessed what combination of social networks, spatial networks or co-infection best structured the FIV_Ple network. While social organization (i.e., pride) was an important component of FIV_Ple transmission pathways at all scales, we find that FIV_Ple subtypes exhibited different transmission pathways at within- and between-pride scales. A combination of social and spatial networks, coupled with consideration of subtype co-infection, was likely to be important for FIV_Ple transmission for the two major subtypes, but the relative contribution of each factor was strongly subtype-specific. Our study provides evidence that pathogen heterogeneity is important in understanding pathogen transmission, which could have consequences for how endemic pathogens are managed. Furthermore, we demonstrate that community phylogenetic ecology coupled with phylodynamic techniques can reveal insights into the differential evolutionary pressures acting on virus subtypes, which can manifest into landscape-level effects.

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.

Ecological determinants of health: food and environment on human health

Human health and diseases are determined by many complex factors. Health threats from the human-animal-ecosystems interface (HAEI) and zoonotic diseases (zoonoses) impose an increasing risk continuously to public health, from those emerging pathogens transmitted through contact with animals, food, water and contaminated environments. Immense challenges forced on the ecological perspectives on food and the eco-environments, including aquaculture, agriculture and the entire food systems. Impacts of food and eco-environments on human health will be examined amongst the importance of human interventions for intended purposes in lowering the adverse effects on the biodiversity. The complexity of relevant conditions defined as factors contributing to the ecological determinants of health will be illuminated from different perspectives based on concepts, citations, examples and models, in conjunction with harmful consequential effects of human-induced disturbances to our environments and food systems, together with the burdens from ecosystem disruption, environmental hazards and loss of ecosystem functions. The eco-health literacy should be further promoting under the "One Health" vision, with "One World" concept under Ecological Public Health Model for sustaining our environments and the planet earth for all beings, which is coincidentally echoing Confucian's theory for the environmental ethics of ecological harmony.

Viral factors in influenza pandemic risk assessment

The threat of an influenza A virus pandemic stems from continual virus spillovers from reservoir species, a tiny fraction of which spark sustained transmission in humans. To date, no pandemic emergence of a new influenza strain has been preceded by detection of a closely related precursor in an animal or human. Nonetheless, influenza surveillance efforts are expanding, prompting a need for tools to assess the pandemic risk posed by a detected virus. The goal would be to use genetic sequence and/or biological assays of viral traits to identify those non-human influenza viruses with the greatest risk of evolving into pandemic threats, and/or to understand drivers of such evolution, to prioritize pandemic prevention or response measures. We describe such efforts, identify progress and ongoing challenges, and discuss three specific traits of influenza viruses (hemagglutinin receptor binding specificity, hemagglutinin pH of activation, and polymerase complex efficiency) that contribute to pandemic risk.

Persistence of Low Pathogenic Influenza A Virus in Water: A Systematic Review and Quantitative Meta-Analysis

Avian influenza viruses are able to persist in the environment, in-between the transmission of the virus among its natural hosts. Quantifying the environmental factors that affect the persistence of avian influenza virus is important for influencing our ability to predict future outbreaks and target surveillance and control methods. We conducted a systematic review and quantitative meta-analysis of the environmental factors that affect the decay of low pathogenic avian influenza virus (LPAIV) in water. Abiotic factors affecting the persistence of LPAIV have been investigated for nearly 40 years, yet published data was produced by only 26 quantitative studies. These studies have been conducted by a small number of principal authors (n = 17) and have investigated a narrow range of environmental conditions, all of which were based in laboratories with limited reflection of natural conditions. The use of quantitative meta-analytic techniques provided the opportunity to assess persistence across a greater range of conditions than each individual study can achieve, through the estimation of mean effect-sizes and relationships among multiple variables. Temperature was the most influential variable, for both the strength and magnitude of the effect-size. Moderator variables explained a large proportion of the heterogeneity among effect-sizes. Salinity and pH were important factors, although future work is required to broaden the range of abiotic factors examined, as well as including further diurnal variation and greater environmental realism generally. We were unable to extract a quantitative effect-size estimate for approximately half (50.4%) of the reported experimental outcomes and we strongly recommend a minimum set of quantitative reporting to be included in all studies, which will allow robust assimilation and analysis of future findings. In addition we suggest possible means of increasing the applicability of future studies to the natural environment, and evaluating the biological content of natural waterbodies.

Presence of Vaccine-Derived Newcastle Disease Viruses in Wild Birds

Our study demonstrates the repeated isolation of vaccine-derived Newcastle disease viruses from different species of wild birds across four continents from 1997 through 2014. The data indicate that at least 17 species from ten avian orders occupying different habitats excrete vaccine-derived Newcastle disease viruses. The most frequently reported isolates were detected among individuals in the order Columbiformes (n = 23), followed in frequency by the order Anseriformes (n = 13). Samples were isolated from both free-ranging (n = 47) and wild birds kept in captivity (n = 7). The number of recovered vaccine-derived viruses corresponded with the most widely utilized vaccines, LaSota (n = 28) and Hitchner B1 (n = 19). Other detected vaccine-derived viruses resembled the PHY-LMV2 and V4 vaccines, with five and two cases, respectively. These results and the ubiquitous and synanthropic nature of wild pigeons highlight their potential role as indicator species for the presence of Newcastle disease virus of low virulence in the environment. The reverse spillover of live agents from domestic animals to wildlife as a result of the expansion of livestock industries employing massive amounts of live virus vaccines represent an underappreciated and poorly studied effect of human activity on wildlife.

Intense circulation of A/H5N1 and other avian influenza viruses in Cambodian live-bird markets with serological evidence of sub-clinical human infections

Surveillance for avian influenza viruses (AIVs) in poultry and environmental samples was conducted in four live-bird markets in Cambodia from January through November 2013. Through real-time RT-PCR testing, AIVs were detected in 45% of 1048 samples collected throughout the year. Detection rates ranged from 32% and 18% in duck and chicken swabs, respectively, to 75% in carcass wash water samples. Influenza A/H5N1 virus was detected in 79% of samples positive for influenza A virus and 35% of all samples collected. Sequence analysis of full-length haemagglutinin (HA) and neuraminidase (NA) genes from A/H5N1 viruses, and full-genome analysis of six representative isolates, revealed that the clade 1.1.2 reassortant virus associated with Cambodian human cases during 2013 was the only A/H5N1 virus detected during the year. However, multiplex reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of HA and NA genes revealed co-circulation of at least nine low pathogenic AIVs from HA1, HA2, HA3, HA4, HA6, HA7, HA9, HA10 and HA11 subtypes. Four repeated serological surveys were conducted throughout the year in a cohort of 125 poultry workers. Serological testing found an overall prevalence of 4.5% and 1.8% for antibodies to A/H5N1 and A/H9N2, respectively. Seroconversion rates of 3.7 and 0.9 cases per 1000 person-months participation were detected for A/H5N1 and A/H9N2, respectively. Peak AIV circulation was associated with the Lunar New Year festival. Knowledge of periods of increased circulation of avian influenza in markets should inform intervention measures such as market cleaning and closures to reduce risk of human infections and emergence of novel AIVs.