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H5 highly pathogenic avian influenza viruses (HPAIVs) of the A/goose/Guangdong/1/1996 lineage have diversified into multiple clades, threatening wild birds and poultry worldwide. Clade 2.3.4.4b HPAIVs have been consistently isolated in [...]

MotivationThe potentially low precision associated with the geographic origin of sampled sequences represents an important limitation for spatially explicit (i.e. continuous) phylogeographic inference of fast-evolving pathogens such as RNA viruses. A substantial proportion of publicly available sequences is geo-referenced at broad spatial scale such as the administrative unit of origin, rather than more precise locations (e.g. geographic coordinates). Most frequently, such sequences are either discarded prior to continuous phylogeographic inference or arbitrarily assigned to the geographic coordinates of the centroid of their administrative area of origin for lack of a better alternative.ResultsWe here implement and describe a new approach that allows to incorporate heterogeneous prior sampling probabilities over a geographic area. External data, such as outbreak locations, are used to specify these prior sampling probabilities over a collection of sub-polygons. We apply this new method to the analysis of highly pathogenic avian influenza H5N1 clade data in the Mekong region. Our method allows to properly include, in continuous phylogeographic analyses, H5N1 sequences that are only associated with large administrative areas of origin and assign them with more accurate locations. Finally, we use continuous phylogeographic reconstructions to analyse the dispersal dynamics of different H5N1 clades and investigate the impact of environmental factors on lineage dispersal velocities.Availability and implementationOur new method allowing heterogeneous sampling priors for continuous phylogeographic inference is implemented in the open-source multi-platform software package BEAST 1.10.Supplementary informationSupplementary data are available at Bioinformatics online.

The European subtype of tick-borne encephalitis virus (TBEV-Eur; species Orthoflavivirus encephalitidis, family Flaviviridae) was the only tick-borne flavivirus present in central Europe known to cause neurologic disease in humans and several animal species. Here, we report a tick-borne flavivirus isolated from Alpine chamois (Rupicapra rupicapra rupicapra) with encephalitis and attached ticks, present over a wide area in the Alps. Cases were detected in 2017 in Salzburg, Austria, and 2023 in Lombardy and Piedmont, Italy. The virus strains exhibit 94.8–97.3% nucleotide identities to each other and are more closely related to Louping ill viruses (LIV; Orthoflavivirus loupingi; 90–92% identities) than to TBEV-Eur (less than 88%). The chamois-derived virus strains, tentatively termed "Alpine chamois encephalitis virus", form a well-supported independent genetic clade with Spanish goat encephalitis virus, clearly separated from other LIV. This supports its designation as a new virus subtype with the proposed shared taxonomic name "Spanish goat and Alpine chamois encephalitis virus subtype" within the species Orthoflavivirus loupingi. The zoonotic potential of this newly identified virus subtype as well as its host range in other animal species including farm animals needs to be further investigated. [ABSTRACT FROM AUTHOR]

Background A new strain of West Nile virus lineage 1 (WNV-1) emerged in the Veneto Region, northern Italy, in 2021, 8 years after the last WNV-1 outbreak in Italy. The virus, which co-circulates with West Nile virus lineage 2 (WNV-2), has become endemic in the region, where, in 2022, most human cases of neuroinvasive disease (WNND) reported in Europe have occurred. Methods Comparative analysis of the epidemiology and clinical presentation of WNV-1 and WNV-2 infection in humans, as well as the temporal and geographic distribution of WNV-1 and WNV-2 among wild birds and Culex pipiens mosquitoes in Veneto, from 16 May to 21 August 2022, to determine if the high number of WNND cases was associated with WNV-1. Results 222 human cases of WNV infection were confirmed by molecular testing, including 103 with West Nile fever (WNF) and 119 with WNND. The WNV lineage was determined in 201 (90.5%) cases, comprising 138 WNV-1 and 63 WNV-2 infections. In addition, 35 blood donors tested positive, including 30 in whom WNV lineage was determined (13 WNV-1 and 17 WNV-2). Comparative analysis of the distribution of WNV-1 and WNV-2 infections among WNND cases, WNF cases and WNV-positive blood donors showed that WNND patients were more likely to have WNV-1 infection than blood donors (odds ratio 3.44; 95% confidence interval: 1.54–8.24; P  = 0.0043). As observed in humans, in wild birds, WNV-1 had a higher infection rate (IR) and showed a more rapid expansion than WNV-2. At variance, the distribution of the two lineages was more even in mosquitoes, but with a trend of rapid increase of WNV-1 IR over WNV-2. Conclusions Comparative analysis of WNV-1 vs WNV-2 infection in humans, wild birds and mosquitos showed a rapid expansion of WNV-1 and suggested that WNV-1-infected patients might have an increased risk to develop severe disease. [ABSTRACT FROM AUTHOR]

On December 23, 2020, a single poultry farm composed of 4 barns of laying hens having a total of 102,000 birds in Pout, Thies Region, Senegal, reported increased deaths (mortality [...]

Background: Since its discovery in 1926, Newcastle disease (ND) is still emerging in many avian species worldwide causing severe economic losses due to high mortality. Aim: This article aims to discuss the challenge of virulent ND in poultry in Libya, focusing on recent outbreaks investigated in Alzintan, Alrayaina, Nalut, and Surman, cities located in the western region of Libya. Methods: Clinical signs and lesions were recorded. Tissues, as well as tracheal and cloacal swabs, were collected. RNA extraction was performed for confirmation using PCR and sequencing. Results: Mortality, in general, reached 50%-100% in vaccinated flocks with respiratory distress, diarrhea, swelling of the face, and nasal discharges. Necropsy revealed severe hemorrhages in the proventriculus, necrosis, and hemorrhages in the intestine and cecal tonsils. All tested samples were positive for avian orthoavulavirus 1 (AOAV-1) using rRTPCR and genetic analysis. The sequences obtained are referable to AOAV-1, which is the same strain in all tested samples. The amino acid sequences deduced from the cleavage site of the F protein are referable to a velogenic strain of AOAV-1 belonging to genotype VII.2. The detected strains in the current study revealed 86%-91% identity with European isolates identified between 2020 and 2022 and isolates from Asia and Africa and 97% identity to the previous isolated Libyan strains in 2013 and 2016. It is slightly different by the presence of amino acid lycine at position 111 on the cleavage site of the F0 gene as compared to previous Libyan strains in which arginine was found in the same position. The nucleotide sequence at this position changed from (aga) in AOAV-1 strains of years 2013 and 2016 to (aag) of the year 2023. Conclusion: ND remains a significant threat to the poultry industry in Libya. Therefore, there is an urgent need to conduct an epidemiological study with a representative number of samples from all regions of the country, alongside the implementation of an inactivated vaccine targeting genotype VII. [ABSTRACT FROM AUTHOR]

We isolated highly pathogenic avian influenza (HPAI) H5N5 and H5N1 viruses from crows in Hokkaido, Japan, during winter 2023–24. They shared genetic similarity with HPAI H5N5 viruses from northern Europe but differed from those in Asia. Continuous monitoring and rapid information sharing between countries are needed to prevent HPAI virus transmission. [ABSTRACT FROM AUTHOR]

Influenza A/H9 viruses circulate worldwide in wild and domestic avian species, continuing to evolve and posing a zoonotic risk. A substantial increase in human infections with A/H9N2 subtype avian influenza viruses (AIVs) and the emergence of novel reassortants carrying A/H9N2-origin internal genes has occurred in recent years. Different names have been used to describe the circulating and emerging A/H9 lineages. To address this issue, an international group of experts from animal and public health laboratories, endorsed by the WOAH/FAO Network of Expertise on Animal Influenza, has created a practical lineage classification and nomenclature system based on the analysis of 10,638 hemagglutinin sequences from A/H9 AIVs sampled worldwide. This system incorporates phylogenetic relationships and epidemiologic characteristics designed to trace emerging and circulating lineages and clades. To aid in lineage and clade assignment, an online tool has been created. This proposed classification enables rapid comprehension of the global spread and evolution of A/H9 AIVs. [ABSTRACT FROM AUTHOR]

In January 2020, increased mortality was reported in a small broiler breeder flock in County Fermanagh, Northern Ireland. Gross pathological findings included coelomitis, oophoritis, salpingitis, visceral gout, splenomegaly, and renomegaly. Clinical presentation included inappetence, pronounced diarrhoea, and increased egg deformation. These signs, in combination with increased mortality, triggered a notifiable avian disease investigation. High pathogenicity avian influenza virus (HPAIV) was not suspected, as mortality levels and clinical signs were not consistent with HPAIV. Laboratory investigation demonstrated the causative agent to be a low-pathogenicity avian influenza virus (LPAIV), subtype H6N1, resulting in an outbreak that affected 15 premises in Northern Ireland. The H6N1 virus was also associated with infection on 13 premises in the Republic of Ireland and six in Great Britain. The close genetic relationship between the viruses in Ireland and Northern Ireland suggested a direct causal link whereas those in Great Britain were associated with exposure to a common ancestral virus. Overall, this rapidly spreading outbreak required the culling of over 2 million birds across the United Kingdom and the Republic of Ireland to stamp out the incursion. This report demonstrates the importance of investigating LPAIV outbreaks promptly, given their substantial economic impacts. [ABSTRACT FROM AUTHOR]

Avian influenza viruses (AIV) remain prevalent among wild bird populations in the European Union and European Economic Area (EU/EEA), leading to significant illness and mortality of birds. Transmission between bird and mammal species has been observed, particularly in fur animal farms, where outbreaks have been reported. While transmission from infected birds to humans is rare, there have been instances of exposure to these viruses since 2020 without any symptomatic infections reported in the EU/EEA. However, these viruses continue to evolve globally, and with the migration of wild birds, new strains carrying potential mutations for mammalian adaptation could be selected. If avian A(H5N1) influenza viruses acquire the ability to spread efficiently among humans, large‐scale transmission could occur due to the lack of immune defences against H5 viruses in humans. The emergence of AIV capable of infecting mammals, including humans, can be facilitated by various drivers. Some intrinsic drivers are related to virus characteristics or host susceptibility. Other drivers are extrinsic and may increase exposure of mammals and humans to AIV thereby stimulating mutation and adaptation to mammals. Extrinsic drivers include the ecology of domestic and wild host species, human activities like farming practices and the use of natural resources, climatic and environmental factors. One Health measures to mitigate the risk of AIV adapting to mammals and humans focus on limiting exposure and preventing spread. Key options for actions include enhancing surveillance targeting humans and animals, ensuring access to rapid diagnostics, promoting collaboration between animal and human sectors, and considering the implementation of preventive measures such as vaccination of poultry. Effective communication to different target audiences should be emphasised, as well as strengthening veterinary infrastructure, enforcing biosecurity measures at farms, and reducing wildlife contact with domestic animals. Careful planning of poultry and fur animal farming, especially in areas with high waterfowl density, is essential for effective risk reduction. [ABSTRACT FROM AUTHOR]

Highly pathogenic avian influenza (HPAI) is a zoonotic notifiable disease that can cause high mortality rates in most domestic poultry and in some wild bird species. Since 2003, HPAI H5 [...]

In spring 2016, highly pathogenic avian influenza (HPAI) outbreaks caused by the H5N8 subtype of clade 2.3.4.4 (group B) were reported in migratory wild birds in Qinghai Lake, China (1), [...]

The SARS-CoV-2 Delta variant of concern (VOC) was often associated with serious clinical course of the COVID-19 disease. Herein, we investigated the selective pressure, gene flow and evaluation on the frequencies of mutations causing amino acid substitutions in the Delta variant in three Italian regions. A total of 1500 SARS-CoV-2 Delta genomes, collected in Italy from April to October 2021 were investigated, including a subset of 596 from three Italian regions. The selective pressure and the frequency of amino acid substitutions and the prediction of their possible impact on the stability of the proteins were investigated. Delta variant dataset, in this study, identified 68 sites under positive selection: 16 in the spike (23.5%), 11 in nsp2 (16.2%) and 10 in nsp12 (14.7%) genes. Three of the positive sites in the spike were located in the receptor-binding domain (RBD). In Delta genomes from the three regions, 6 changes were identified as very common (>83.7%), 4 as common (>64.0%), 21 at low frequency (2.1%–25.0%) and 29 rare (≤2.0%). The detection of positive selection on key mutations may represent a model to identify recurrent signature mutations of the virus. [ABSTRACT FROM AUTHOR]

In December 2014, a strain of highly pathogenic avian influenza (HPAI) A(H5N1) virus responsible for deaths among poultry was detected in southwestern Nigeria, specifically in a live bird market in [...]