Between October 2021 and April 2022, 317 outbreaks caused by highly pathogenic avian influen-za (HPAI) H5N1 viruses were notified in poultry farms in the northeastern Italian Regions. The complete genomes of 214 strains were used to estimate the genetic network based on the virus similarity. An exponential random graph model (ERGM) was used to assess the effect of at-risk contacts, same owners, in-bound/out-bound risk windows overlap, genetic differences, geograph-ic distances, same species and poultry company, on the probability of observing a link within the genetic network, which can be interpreted as the potential propagation of the epidemic via lateral spread or a common source of infection. The variables same poultry company (Est.=0.548, C.I.=[0.179;0.918]) and risk windows overlap (Est.=0.339, C.I.=[0.309;0.368]) were associated with a higher probability of link formation, while the genetic differences (Est.=-0.563, C.I.=[-0.640;-0.486]) and geographic distances (Est.=-0.058, C.I.=[-0.078;-0.038]) indicated a re-duced probability. The integration of epidemiological data with genomic analyses allows moni-toring the epidemic evolution and helps explain the dynamics of lateral spreads suggesting the potential diffusion routes. The 2021-2022 epidemic stresses the need to further strengthen the bi-osecurity measures, and to encourage the reorganisation of the poultry production sector to mini-mize the impact of future epidemics.

In 2021/2022, the re-emergence of highly pathogenic avian influenza (HPAI) occurred in Europe. The outbreak was seeded from two sources, resident and reintroduced viruses, which is unprecedented in the recorded history of avian influenza. The dominating subtype was H5N1, representing a reversion to the original A/goose/Guangdong/1/1996-like subtype combination. In this study, we present a whole genome sequence and a phylogenetic analysis of 57 H5N1 HPAI and two low pathogenic avian influenza (LPAI) H5N1 strains collected in the Czech Republic during 2021/2022. Phylogenetic analysis revealed close relationships between H5N1 genomes from poultry and wild birds and secondary transmission in commercial geese. The genotyping showed considerable genetic heterogeneity among Czech H5N1 viruses with six different HPAI genotypes, three of which were apparently unique. In addition, second-order reassortment relationships were observed with the direct involvement of co-circulating H5N1 LPAI strains. The genetic distance between Czech H5N1 HPAI and the closest LPAI segments available in the database illustrates the profound gaps in our knowledge of circulating LPAI strains. The changing dynamics of HPAI in the wild may increase the likelihood of future HPAI outbreaks and present new challenges in poultry management, biosecurity, and surveillance.

In 2020-2021, the second massive dissemination of a highly-pathogenic avian influenza (HPAI) of H5Nx subtype occurred in Europe. During this period, the virus caused numerous outbreaks in poultry, including in the Czech Republic. In the present study, we provide an insight into the genetic variability of the Czech/2021 (CZE/2021) H5N8 viruses to determine the relationships between strains from wild and domestic poultry and to infer transmission routes between the affected flocks of commercial poultry. For this purpose, whole genome sequencing and phylogenetic analysis of 70 H5N8 HPAI genomes representing 79.7% of the cases were performed. All CZE/2021 H5N8 viruses belonged to the 2.3.4.4b H5 lineage and circulated without reassortment, retaining the A/chicken/Iraq/1/2020 H5N8-like genotype constellation. Phylogenetic analysis suggested frequent local transmission of H5N8 HPAI from wild birds to minor poultry and extensive farm-to-farm spread among commercial poultry farms. In addition, the analysis suggested one cross-border transmission event. Indirect transmission via contaminated materials was considered the most likely source of infection. Improved biosecurity and increased collaboration between the field veterinarians and the laboratory are essential to limit the local spread of the virus and to reveal and interrupt critical routes of infection.

Concurrent waves of Coronavirus disease, Ebola virus disease, avian influenza A and black fungus are jeopardizing the lives in some parts of Africa and Asia. From this point of view, this review aims to summarize both socio-economic and public health implications of these parallel outbreaks along with their best possible management approaches. Various online databases were used to collect the necessary information regarding these outbreaks. Based on the reports published and analyses done so far, the long-lasting damages caused by these simultaneous outbreaks on global socio-economical and public health status can be conceived from the past experiences of outbreaks, especially the COVID-19 pandemic. Moreover, prolonged restrictions by the local government may lead to food insecurity, global recession, and an enormous impact on the mental health of people of all ages, specifically in developing countries. Such overwhelming effects already have been reported to be declining national growth of the economy as well as increasing political insecurity and shortage of basic needs. Although various actions have already been taken including vaccination, clinical management, and further research, social distancing, and lockdown, etc. to improve the situation, the emerging variants and associated genetic mutations may make the containment difficult worsening the situation again. Considering the current mutational dynamics of the pathogens and the past experiences, perpetual preparedness along with updated clinical management backed by epidemiological studies and innovating scientific effort are inevitable to combat the simultaneous waves of multiple infectious diseases.

The Influenza A virus (IAV) is a highly infectious virus that poses a significant threat to global public health and food supplies. The current subtype of avian influenza virus (AIV), H5N1, is being closely monitored worldwide due to its unprecedented spread from Europe to North America and now to Central and South America. This review summarizes recent updates on the evolution of the different IAV subtypes in birds and mammals including humans, in Chile. The distribution and spread of AIV H5N1 in Chile indicated a complex interplay between ecological and human factors in that it was negatively correlated with distance to the closest urban center and precipitation and temperature seasonality. It is evident that highly pathogenic avian influenza (HPAI) H5N1 in Chile was introduced from North America via the Atlantic migratory flyways as opposed to local transmission from other countries in South America. The presence of these viruses in Chile underscores the need for increased biosecurity on poultry farms and continuous genomic surveillance approaches to understand and control AIVs in both wild and domestic bird populations in Chile.