Southward autumn migration of waterfowl facilitates cross-continental transmission of the highly pathogenic avian influenza H5N1 virus

Experimental infection of chickens, Pekin ducks, Eurasian wigeons and Barnacle geese with two recent highly pathogenic avian influenza H5N1 clade 2.3.4.4b viruses

Multiple genotypes of highly pathogenic avian influenza (HPAI) H5 clade 2.3.4.4b viruses have caused epizootics in wild birds and poultry. The HPAI H5N1 genotype C virus caused a modest epizootic, whereas the occurrence of the HPAI H5N1 genotype AB virus in 2021 resulted in the largest avian influenza epizootic in Europe to date. Here we studied the pathogenicity of two HPAI H5N1 viruses by experimentally infecting chickens, Pekin ducks, Eurasian wigeons and Barnacle geese. Our study demonstrates that pathogenicity of the H5N1-2021-AB virus is lower in Pekin ducks, Eurasian wigeons and Barnacle geese compared to the H5N1-2020-C virus, whereas virus shedding was high for both viruses. After inoculation with H5N1-2021-C viral antigen expression was higher in the brain of Pekin ducks, Eurasian wigeons and Barnacle geese, which caused higher mortality compared to inoculation with H5N1-2021-AB virus. Subclinical infections occurred in Pekin ducks and Eurasian wigeons and mortality was reduced in Barnacle geese after inoculation with H5N1-2021-AB virus while H5N1-2020-C virus caused high morbidity and mortality in these species. This H5N1-2021-AB virus trait may have contributed to efficient spread of the virus in wild bird populations. Therefore, high mortality, virus shedding and long-lasting viral antigen expression found in Barnacle geese may have increased the risk for introduction into poultry.

Surveillance for Avian Influenza in Wild Birds in the Lombardy Region (Italy) in the Period 2022-2024

Influenza A virus (AIV) circulation was investigated in the Lombardy region, during 2022-2024, in wild ducks (through hunting and sampling of faecal samples within natural parks) and wild birds found dead. Samples were analysed through real-time RT-PCRs for Influenza A virus, H5 and H7. Whole genome sequencing was performed on AIV-positive samples. Screening of 3497 hunted Anatidae revealed a total of 184 positive samples. Complete sequencing of 136 samples highlighted the presence of 21 different subtypes ranging from H1N1 to H12N5. The H5N1 HPAIV (high pathogenic AIV) subtype, clade 2.3.4.4b, was the most common during the 2022-2023 winter season (31.8%), while H5 LPAI (low pathogenic AIV) strains were the most prevalent (28.6%) in the 2023-2024 season. The molecular survey on wild birds found dead (n = 481) showed two positive buzzards (14%, 2/14), one grey heron (5.5%, 1/18) and one kestrel (7.6%, 1/13). Regarding the order of Charadriiformes, the dead gulls sampled in 2022 (17 birds) were all negative, whereas 85 out of 167 (51%) individuals were positive in 2023. All positives were caused by an H5N1 HPAIV clade 2.3.4.4b virus belonging to genotype BB. All the faecal samples (1699) received from passive surveillance in nature parks were analysed for AIV with negative results.

Novel Epidemiologic Features of High Pathogenicity Avian Influenza Virus A H5N1 2.3.3.4b Panzootic: A Review

Avian influenza is one of the most devastating avian diseases. The current high pathogenicity avian influenza (HPAI) A virus H5N1 clade 2.3.4.4b epizootic began in the 2020-2021 season, and has caused a panzootic, considered one of the worst ever reported. The present panzootic has novel epidemiological features that represent a challenge for its prevention and control. This review examines key epidemiological changes of the disease such as seasonality, geographic spread, and host range. The seasonality of the virus has changed, and contrary to previous avian influenza epizootics, this subclade was able to persist during boreal summer. Its geographic range has expanded, with reports in all continents except Australia. During this epizootic, HPAIV H5N1 has broadened its host range, infecting hundreds of bird species, and causing the death of thousands of wild birds and over 300 million poultry. The number and diversity of mammal species infected by H5N1 2.3.4.4b is unprecedented. Although considered low, this strain's potential to spillover to humans should not be underestimated, especially considering the current extremely high viral circulation in animals and increasing adaptation to mammals. Overall, HPAI A(H5N1) clade 2.3.4.4b represents an ongoing and growing threat to poultry, wildlife, and human health.

Geospatial and Temporal Analysis of Avian Influenza Risk in Thailand: A GIS-Based Multi-Criteria Decision Analysis Approach for Enhanced Surveillance and Control

Avian influenza (AI) is a viral infection that profoundly affects global poultry production. This study aimed to identify the spatial and temporal factors associated with AI in Thailand, using a geographic information system (GIS)-based multi-criteria decision analysis (MCDA) approach. We discovered that high-risk areas for AI were primarily concentrated in the central and lower northern regions of the country, with fewer occurrences in the northeastern and southern regions. Model validation using historical outbreak data showed moderate agreement (AUC = 0.60, 95% CI = 0.58-0.61). This study provides valuable insights for planning national AI surveillance programs and aiding in disease prevention and control efforts. The efficiency and effectiveness of disease surveillance at the national level can be improved using this GIS-based MCDA, in conjunction with temporal risk factor analysis.

Dissemination of information in event-based surveillance, a case study of Avian Influenza

Event-Based Surveillance (EBS) tools, such as HealthMap and PADI-web, monitor online news reports and other unofficial sources, with the primary aim to provide timely information to users from health agencies on disease outbreaks occurring worldwide. In this work, we describe how outbreak-related information disseminates from a primary source, via a secondary source, to a definitive aggregator, an EBS tool, during the 2018/19 avian influenza season. We analysed 337 news items from the PADI-web and 115 news articles from HealthMap EBS tools reporting avian influenza outbreaks in birds worldwide between July 2018 and June 2019. We used the sources cited in the news to trace the path of each outbreak. We built a directed network with nodes representing the sources (characterised by type, specialisation, and geographical focus) and edges representing the flow of information. We calculated the degree as a centrality measure to determine the importance of the nodes in information dissemination. We analysed the role of the sources in early detection (detection of an event before its official notification) to the World Organisation for Animal Health (WOAH) and late detection. A total of 23% and 43% of the avian influenza outbreaks detected by the PADI-web and HealthMap, respectively, were shared on time before their notification. For both tools, national and local veterinary authorities were the primary sources of early detection. The early detection component mainly relied on the dissemination of nationally acknowledged events by online news and press agencies, bypassing international reporting to the WAOH. WOAH was the major secondary source for late detection, occupying a central position between national authorities and disseminator sources, such as online news. PADI-web and HealthMap were highly complementary in terms of detected sources, explaining why 90% of the events were detected by only one of the tools. We show that current EBS tools can provide timely outbreak-related information and priority news sources to improve digital disease surveillance.

A Generic Risk Assessment Model for Animal Disease Entry through Wildlife: The Example of Highly Pathogenic Avian Influenza and African Swine Fever in The Netherlands

Animal diseases can enter countries or regions through the movements of infected wildlife. A generic risk model would allow to quantify the risk of entry via this introduction route for different diseases and wildlife species, despite the vast variety in both, and help policy-makers to make informed decisions. Here, we propose such a generic risk assessment model and illustrate its application by assessing the risk of entry of African swine fever (ASF) through wild boar and highly pathogenic avian influenza (HPAI) through wild birds for the Netherlands between 2014-2021. We used disease outbreak data and abstracted movement patterns to populate a stochastic risk model. We found that the entry risk of HPAI fluctuated between the years, with a peak in 2021. In that year, we estimated the number of infected birds to reach the Dutch border by wild bird migration at 273 (95% uncertainty interval: 254-290). The probability that ASF outbreaks that occurred between 2014 and 2021 reached the Dutch border through wild boar movement was very low throughout the whole period; only the upper confidence bound indicated a small entry risk. On a yearly scale, the predicted entry risk for HPAI correlated well with the number of observed outbreaks. In conclusion, we present a generic and flexible framework to assess the entry risk of disease through wildlife. The model allows rapid and transparent estimation of the entry risk for diverse diseases and wildlife species. The modular structure of the model allows for adding nuance and complexity when required or when more data becomes available.

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.

Airborne Avian Influenza Virus in Ambient Air in the Winter Habitats of Migratory Birds

Outbreaks of avian influenza virus (AIV) have raised public concerns recently. Airborne AIV has been evaluated in live poultry markets and case farms; however, no study has discussed airborne AIV in ambient air in the winter habitats of migratory birds. Therefore, this study aimed to evaluate airborne AIV, specifically H5, H7, and H9, in a critical winter habitat of migratory birds and assess the factors influencing airborne AIV transmission in ambient air to provide novel insights into the epidemiology of avian influenza. A total of 357 ambient air samples were collected in the Aogu Wetland, Taiwan, Republic of China, between October 2017 and December 2019 and analyzed using quantitative real-time polymerase chain reaction. The effects of environmental factors including air pollutants, meteorological factors, and the species of the observed migratory birds on the concentration of airborne AIV were also analyzed. To our knowledge, this is the first study to investigate the relationship between airborne AIV in ambient air and the influence factors in the winter habitats of migratory birds, demonstrating the benefits of environmental sampling for infectious disease epidemiology. The positive rate of airborne H7 (12%) was higher than that of H5 (8%) and H9 (10%). The daily mean temperature and daily maximum temperature had a significant negative correlation with influenza A, H7, and H9. Cold air masses and bird migration were significantly associated with airborne H9 and H7, respectively. In addition, we observed a significant correlation between AIV and the number of pintails, common teals, Indian spot-billed ducks, northern shovelers, Eurasian wigeons, tufted ducks, pied avocets, black-faced spoonbills, and great cormorants. In conclusion, we demonstrated the potential for alternative surveillance approaches (monitoring bird species) as an indicator for influenza-related risks and identified cold air masses and the presence of specific bird species as potential drivers of the presence and/or the airborne concentration of AIV.

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.

Divergent Reassortment and Transmission Dynamics of Highly Pathogenic Avian Influenza A(H5N8) Virus in Birds of China During 2021

Highly pathogenic influenza A(H5N8) viruses had caused several outbreaks among wild bird and poultry populations across the globe, and strikingly, caused human infection, posing serious public health concerns. In this study, we conducted influenza surveillance in China during 2021 to monitor the evolution of influenza viruses in poultry. A total of 35 influenza viruses were obtained in chickens, ducks, and geese, of which 30 H5N8 viruses, 3 H5N1 viruses, and 2 H5N6 viruses. Phylogenetic analysis suggested all of H5N1, H5N6, and H5N8 isolates were derived from clade 2.3.4.4b H5N8 viruses during 2020/21 season, and notably, the internal genes of H5N1 and H5N6 viruses shared different genetic heterogeneity with H5N8 viruses and had been reassorted with wild bird-origin H5N1 viruses from Europe. By contrast, almost all H5N8 viruses exhibited only one phylogenic cluster with wild bird-origin H5N8 viruses in China and Korea, indicating that H5N8 viruses in China were more stable. Besides, we found that Korea is the main output geographic location in the spread of these H5N8 viruses to northern and eastern China, and especially, the co-circulation of H5N8 viruses occurred within China, with central China acted as a seeding population during the H5N8 epidemic. The statistical support was strong for viral migration from wild birds to chickens and ducks, indicating that 2.3.4.4b poultry-origin H5N8 viruses during 2020–2021 were originated from wild birds. Our findings provide novel insights into evolution and transmission dynamics of H5 subtype influenza viruses among poultry after novel H5N8 viruses invaded China for nearly one year.

Connectivity dynamics in Irish mudflats between microorganisms including Vibrio spp., common cockles Cerastoderma edule, and shorebirds

Shellfish, including the key species the common cockle Cerastoderma edule, living and feeding in waters contaminated by infectious agents can accumulate them within their tissues. It is unknown if microbial pathogens and microparasites can subsequently be transmitted via concomitant predation to their consumers, including shorebirds. The objective of this study was to assess if pathogens associated with C. edule could be detected seasonally in the faeces of shorebirds that feed on C. edule and in the physical environment (sediment) in which C. edule reside, along the Irish and Celtic Seas. Two potentially pathogenic global groups, Vibrio and Haplosporidia, were detected in C. edule. Although Haplosporidia were not detected in the bird faeces nor in the sediment, identical strains of Vibrio splendidus were detected in C. edule and bird faecal samples at sites where the oystercatcher Haematopus ostralegus and other waders were observed to be feeding on cockles. Vibrio spp. prevalence was seasonal and increased in C. edule and bird faecal samples during the warmer months, possibly due to higher seawater temperatures that promote the replication of this bacteria. The sediment samples showed an overall higher prevalence of Vibrio spp. than the bird faecal and C. edule samples, and its detection remained consistently high through the sites and throughout the seasons, which further supports the role of the sediment as a Vibrio reservoir. Our findings shed light on the fact that not all pathogen groups are transmitted from prey to predator via feeding but bacteria such as V. splendidus can be. As most of the wading birds observed in this study are migratory, the results also indicate the potential for this bacterium to be dispersed over greater geographic distances, which will have consequences for areas where it may be introduced.

Neglected parasite reservoirs in wetlands: Prevalence and diversity of avian haemosporidians in waterbird communities in Northeast China

The diversity of waterbirds is threatened, and haemosporidian parasite infection is considered one of the most important causative factors. However, to date, only a few studies focusing on specific parasite species have been carried out, which cannot reflect the general patterns at the community level. To test whether the reported haemosporidian diversity in waterbirds is underestimated, we estimated the prevalence and lineage diversity of avian haemosporidian parasites in 353 waterbirds from 26 species in the Tumuji National Nature Reserve, Northeast China, as well as the host-parasite associations. According to the molecular analysis of cytochrome b (cyt b) barcode sequences, 28.3% of the birds were infected by 49 distinct parasite lineages, including 11 Plasmodium, 12 Haemoproteus, and 26 Leucocytozoon lineages, of which 39 were novel. The highest prevalence was contributed by Leucocytozoon (13.31%), followed by Plasmodium (13.03%) and Haemoproteus (4.25%), which suggested that waterbirds were infected to a lesser extent by Haemoproteus than by the other two genera. Among the most sampled birds, species belonging to Anatidae appeared to be susceptible to Leucocytozoon but resistant to Plasmodium, while Rallidae presented the opposite pattern. On the phylogenetic tree, most of the Leucocytozoon lineages detected in Anatidae clustered together and formed two well-supported clades, while lineages restricted to Gruidae were distantly related to other parasites in all three genera. SW5 was the most abundant lineage and therefore might be a major threat to waterbirds; among the hosts, the common coot harboured the highest diversity of parasite lineages and thus could act as a reservoir for potential transmission. This is the first study of avian haemosporidian infections in a wild waterbird community in Asia. Our findings have doubled the number of lineages recorded in waterbirds, broadened our understanding of host-parasite associations, and addressed the importance of studying haemosporidian infections in wild waterbird conservation.

One health pathogen surveillance demonstrated the dissemination of gut pathogens within the two coastal regions associated with intensive farming

BACKGROUND

Intensive aquaculture farming has caused significant degradation of coastal wetlands and has been proposed as a reservoir for pathogenic Vibrio spp.

RESULTS

Gut pathogens including Vibrio spp., Salmonella spp., and Klebsiella spp. were isolated from bird feces, shrimp and wetland water in two typical coastal regions of China in 2015 and 2017 and were subsequently subjected to whole-genome sequencing. Meanwhile, local patient isolates were also selected to confirm the epidemiological links. Bacterial community composition analyses of the sediments that were sampled in 2015 and 2017 were conducted by the hypervariable region 4 of the 16S rRNA gene. Together with the local clinical isolates, we observed highly related Vibrio isolates from waterbirds, wetlands and shrimp. Phylogenetic genome comparisons also demonstrated that sequence types ST3 and ST2414 Vibrio parahaemolyticus isolates obtained from aquatic animals were clonally related to patient isolates. Likewise, three Salmonella typhimurium isolates were also genomically related to one clinical strain. The results showed that farming activities significantly altered the community composition and resulted in the emergence of several pathogens, including Acinetobacter, Mycobacterium and Legionella.

CONCLUSIONS

In conclusion, our results demonstrated that intensive shrimp farming in wetlands has two devastating impacts: pathogen dissemination from aquatic animals into migratory birds and transmission of foodborne pathogens into local communities.

Avian Influenza in Wild Birds and Poultry: Dissemination Pathways, Monitoring Methods, and Virus Ecology

Avian influenza is one of the largest known threats to domestic poultry. Influenza outbreaks on poultry farms typically lead to the complete slaughter of the entire domestic bird population, causing severe economic losses worldwide. Moreover, there are highly pathogenic avian influenza (HPAI) strains that are able to infect the swine or human population in addition to their primary avian host and, as such, have the potential of being a global zoonotic and pandemic threat. Migratory birds, especially waterfowl, are a natural reservoir of the avian influenza virus; they carry and exchange different virus strains along their migration routes, leading to antigenic drift and antigenic shift, which results in the emergence of novel HPAI viruses. This requires monitoring over time and in different locations to allow for the upkeep of relevant knowledge on avian influenza virus evolution and the prevention of novel epizootic and epidemic outbreaks. In this review, we assess the role of migratory birds in the spread and introduction of influenza strains on a global level, based on recent data. Our analysis sheds light on the details of viral dissemination linked to avian migration, the viral exchange between migratory waterfowl and domestic poultry, virus ecology in general, and viral evolution as a process tightly linked to bird migration. We also provide insight into methods used to detect and quantify avian influenza in the wild. This review may be beneficial for the influenza research community and may pave the way to novel strategies of avian influenza and HPAI zoonosis outbreak monitoring and prevention.

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.

GPS-telemetry unveils the regular high-elevation crossing of the Himalayas by a migratory raptor: implications for definition of a "Central Asian Flyway"

Remote technologies are producing leapfrog advances in identifying the routes and connectivity of migratory species, which are still unknown for hundreds of taxa, especially Asian ones. Here, we used GPS-telemetry to uncover the migration routes and breeding areas of the massive population of migratory Black-eared kites wintering around the megacity of Delhi-India, which hosts the largest raptor concentration of the world. Kites migrated for 3300-4800 km along a narrow corridor, crossing the Himalayas at extremely high elevations (up to > 6500 m a.s.l.) by the K2 of the Karakoram Range and travelled long periods at elevations above 3500 m. They then crossed/circumvented the Taklamakan Desert and Tian Shan Range to reach their unknown breeding quarters at the intersection between Kazakhstan, Russia, China and Mongolia. Route configuration seemed to be shaped by dominant wind support and barrier avoidance. Wintering ranges were smaller than breeding ranges and concentrated around Delhi, likely in response to massive human food-subsidies. Our results illustrate that high-elevation crossings by soaring migrants may be more common than previously appreciated and suggest the delineation of a hitherto poorly-appreciated "Central Asian Flyway", which must funnel hundreds of thousands of migrants from central Asia into the Indian subcontinent via multiple modes of the Himalayan crossing.

Population genomics of louping ill virus provide new insights into the evolution of tick-borne flaviviruses

The emergence and spread of tick-borne arboviruses pose an increased challenge to human and animal health. In Europe this is demonstrated by the increasingly wide distribution of tick-borne encephalitis virus (TBEV, Flavivirus, Flaviviridae), which has recently been found in the United Kingdom (UK). However, much less is known about other tick-borne flaviviruses (TBFV), such as the closely related louping ill virus (LIV), an animal pathogen which is endemic to the UK and Ireland, but which has been detected in other parts of Europe including Scandinavia and Russia. The emergence and potential spatial overlap of these viruses necessitates improved understanding of LIV genomic diversity, geographic spread and evolutionary history. We sequenced a virus archive composed of 22 LIV isolates which had been sampled throughout the UK over a period of over 80 years. Combining this dataset with published virus sequences, we detected no sign of recombination and found low diversity and limited evidence for positive selection in the LIV genome. Phylogenetic analysis provided evidence of geographic clustering as well as long-distance movement, including movement events that appear recent. However, despite genomic data and an 80-year time span, we found that the data contained insufficient temporal signal to reliably estimate a molecular clock rate for LIV. Additional analyses revealed that this also applied to TBEV, albeit to a lesser extent, pointing to a general problem with phylogenetic dating for TBFV. The 22 LIV genomes generated during this study provide a more reliable LIV phylogeny, improving our knowledge of the evolution of tick-borne flaviviruses. Our inability to estimate a molecular clock rate for both LIV and TBEV suggests that temporal calibration of tick-borne flavivirus evolution should be interpreted with caution and highlight a unique aspect of these viruses which may be explained by their reliance on tick vectors.

Tick-borne pathogens represent a major emerging threat to public health and in recent years have been expanding into new areas. LIV is a neglected virus endemic to the UK and Ireland (though it has been detected in Scandinavia and Russia) which is closely related to the major human pathogen TBEV, but predominantly causes disease in sheep and grouse. The recent detection of TBEV in the UK, which has also emerged elsewhere in Europe, requires more detailed understanding of the spread and sequence diversity of LIV. This could be important for diagnosis and vaccination, but also to improve our understanding of the evolution and emergence of these tick-borne viruses. Here we describe the sequencing of 22 LIV isolates which have been sampled from several host species across the past century. We have utilised this dataset to investigate the evolutionary pressures that LIV is subjected to and have explored the evolution of LIV using phylogenetic analysis. Crucially we were unable to estimate a reliable molecular clock rate for LIV and found that this problem also extends to a larger phylogeny of TBEV sequences. This work highlights a previously unknown caveat of tick-borne flavivirus evolutionary analysis which may be important for understanding the evolution of these important pathogens.

Effects of migration network configuration and migration synchrony on infection prevalence in geese

Migration can influence dynamics of pathogen-host interactions. However, it is not clearly known how migration pattern, in terms of the configuration of the migration network and the synchrony of migration, affects infection prevalence. We therefore applied a discrete-time SIR model, integrating environmental transmission and migration, to various migration networks, including networks with serial, parallel, or both serial and parallel stopover sites, and with various levels of migration synchrony. We applied the model to the infection of avian influenza virus in a migratory geese population. In a network with only serial stopover sites, increasing the number of stopover sites reduced infection prevalence, because with every new stopover site, the amount of virus in the environment was lower than that in the previous stopover site, thereby reducing the exposure of the migratory population. In a network with parallel stopover sites, both increasing the number and earlier appearance of the stopover sites led to an earlier peak of infection prevalence in the migratory population, because the migratory population is exposed to larger total amount of virus in the environment, speeding-up the infection accumulation. Furthermore, higher migration synchrony reduced the average number of cumulative infection, because the majority of the population can fly to a new stopover site where the amount of virus is still relatively low and has not been increased due to virus shedding of infected birds. Our simulations indicate that a migration pattern with multiple serial stopover sites and with highly synchronized migration reduces the infection prevalence.

Long-distance transmission of pathogenic Vibrio species by migratory waterbirds: a potential threat to the public health

A potential mechanism for the global distribution of waterborne pathogens is through carriage by the migratory waterbirds. However, this mode of transmission has yet been confirmed epidemiologically. Here, we conducted whole genome sequencing of Vibrio spp. collected from waterbirds, sediments, and mollusks in the estuary of the Liaohe River in China to investigate this transmission mode. We found that a V. parahaemolyticus strain isolated from a waterbird was clonally related to the other V. parahaemolyticus strains obtained from the sediments and mollusks, and three V. mimicus strains isolated from bird feces were genomically related to those found in the mollusks and upstream groundwater, suggesting that the bird-carried Vibrio strains were acquired through the direct predation of the local mollusks. Surprisingly, two bird-carried V. parahaemolyticus strains belonging to the same clone were identified in Panjin and Shanghai, which are over 1,150 km apart, and another two were found at two locations 50 km apart, further supporting that waterbirds are capable of carrying and disseminating these pathogens over long distances. Our results provide the first evidence of direct transmission from mollusks to waterbirds and confirm that waterbirds act as disseminating vehicles of waterborne pathogens. Effective surveillance of migratory waterbirds along their routes will be valuable for predicting future epidemics of infectious diseases.

Review of Emerging Japanese Encephalitis Virus: New Aspects and Concepts about Entry into the Brain and Inter-Cellular Spreading

Japanese encephalitis virus (JEV) is an emerging flavivirus of the Asia-Pacific region. More than two billion people live in endemic or epidemic areas and are at risk of infection. Recently, the first autochthonous human case was recorded in Africa, and infected birds have been found in Europe. JEV may spread even further to other continents. The first section of this review covers established and new information about the epidemiology of JEV. The subsequent sections focus on the impact of JEV on humans, including the natural course and immunity. Furthermore, new concepts are discussed about JEV’s entry into the brain. Finally, interactions of JEV and host cells are covered, as well as how JEV may spread in the body through latently infected immune cells and cell-to-cell transmission of virions or via other infectious material, including JEV genomic RNA.

Development and application of multiplex PCR method for simultaneous detection of seven viruses in ducks

BACKGROUND

Major viruses, including duck-origin avian influenza virus, duck-origin Newcastle disease virus, novel duck parvovirus, duck hepatitis A virus, duck Tembusu virus, fowl adenovirus, and duck enteritis virus, pose great harm to ducks and cause enormous economic losses to duck industry. This study aims to establish a multiplex polymerase chain reaction (m-PCR) method for simultaneous detection of these seven viruses.

RESULTS

Specific primers were designed and synthesized according to the conserved region of seven viral gene sequences. Then, seven recombinant plasmids, as the positive controls, were reconstructed in this study. Within the study, D-optimal design was adopted to optimize PCR parameters. The optimum parameters for m-PCR were annealing temperature at 57 °C, Mg²⁺ concentration at 4 mM, Taq DNA polymerase concentration at 0.05 U/μL, and dNTP concentration at 0.32 mM. With these optimal parameters, the m-PCR method produced neither cross-reactions among these seven viruses nor nonspecific reactions with other common waterfowl pathogens. The detection limit of m-PCR for each virus was 1 × 10⁴ viral DNA copies/μL. In addition, the m-PCR method could detect a combination of several random viruses in co-infection analysis. Finally, the m-PCR method was successfully applied to clinical samples, and the detection results were consistent with uniplex PCR.

CONCLUSION

Given its rapidity, specificity, sensitivity, and convenience, the established m-PCR method is feasible for simultaneous detection of seven duck-infecting viruses and can be applied to clinical diagnosis of viral infection in ducks.

The development of biodiversity conservation measures in China's hydro projects: A review

The hydropower capacity of China ranks first in the world and accounts for approximately 20% of the total energy production in the country. While hydropower has substantially contributed to meeting China's renewable energy targets and providing clean energy to rural areas, the development of hydropower in China has been met with significant controversy. Ecologically, hydro projects alter the landscape, with potential impacts to the country's aquatic biodiversity. Over the past four decades in China, various mainstream opinions and misunderstandings have been presented concerning how to alleviate the negative impacts of hydro projects on aquatic ecosystems. This article reviews research concerning potential mitigation measures to enhance aquatic biodiversity conservation in hydro projects in China. Based on the academic attention such research has attracted, three technical measures for aquatic biodiversity conservation are considered: (1) fish passages, (2) restocking efforts and (3) river and lake renovations. This article provides a historical comparison of these three practices in China to demonstrate the advantages and disadvantages of each method. The article also reviews the relevant legislation, regulations and technical guidelines concerning China's hydro projects dating back to 1979. The dynamics in research, publications, and patents concerning these three mitigation measures are summarized to demonstrate their technological developments in the context of legislative and policy advances. Data were gathered through the China Knowledge Resource Integrated Database and the State Intellectual Property Office of the People's Republic of China. Based on the analysis provided, the article recommends an expansion of China's environmental certification system for hydro projects, more robust regional legislation to bolster the national framework, the cooperation between upstream and downstream conservation mechanisms, and better monitoring to determine the efficacy of mitigation measures.

Haematospirillum and insect Wolbachia DNA in avian blood

In this study, blood samples of 259 Acrocephalus sp. warblers were molecularly analysed for Anaplasmataceae and Rhodospirillaceae based on PCR amplification of 16S rRNA gene fragments. One bird blood sample (from Reed Warbler, Acrocephalus scirpaceus) yielded a sequence with 99.8% identity to Haematospirillum jordaniae. This is the first molecular evidence for the occurrence of this species in the blood of any vertebrate other than human. Another bird blood sample (from Marsh Warbler: Acrocephalus palustris) yielded a Wolbachia sequence, closely related to a moth endosymbiont with 99.8% identity. A nematode origin of Wolbachia DNA detected here in avian blood can be excluded, because results of phylogenetic analysis showed its closest alignment with insect wolbachiae. This is the first finding of insect Wolbachia DNA in the circulatory system of birds, which can be explained either by the inoculation of wolbachiae by blood-sucking vectors, or passing of Wolbachia DNA from the gut into the blood of this insectivorous bird species.