Two major epidemics of highly pathogenic avian influenza virus H5N8 and H5N1 in domestic poultry in France, 2020-2022

Are all avian influenza outbreaks in poultry the same? The predicted impact of poultry species and virus subtype

AIMS

Outbreaks of avian influenza in poultry farms are currently increasing in frequency, with devastating consequences for animal welfare, farmers and supply chains. Some studies have documented the direct spread of the avian influenza virus between farms. Prevention of spread between farms relies on biosecurity surveillance and control measures. However, the evolution of an outbreak on a farm might vary depending on the virus strain and poultry species involved; this would have important implications for surveillance systems, epidemiological investigations and control measures.

METHODS AND RESULTS

In this study, we utilized existing parameter estimates from the literature to evaluate the predicted course of an epidemic in a standard poultry flock with 10,000 birds. We used a stochastic SEIR simulation model to simulate outbreaks in different species and with different virus subtypes. The simulations predicted large differences in the duration and severity of outbreaks, depending on the virus subtypes. For both turkeys and chickens, outbreaks with HPAI were of shorter duration than outbreaks with LPAI. In outbreaks involving the infection of chickens with different virus subtypes, the shortest epidemic involved H7N7 and HPAIV H5N1 (median duration of 9 and 17 days, respectively) and the longest involved H5N2 (median duration of 68 days). The most severe outbreaks (number of chickens infected) were predicted for H5N1, H7N1 and H7N3 virus subtypes, and the least severe for H5N2 and H7N7, in which outbreaks for the latter subtype were predicted to develop most slowly.

CONCLUSIONS

These simulation results suggest that surveillance of certain subtypes of avian influenza virus, in chicken flocks in particular, needs to be sensitive and timely if infection is to be detected with sufficient time to implement control measures. The variability in the predictions highlights that avian influenza outbreaks are different in severity, speed and duration, so surveillance and disease response need to be nuanced and fit the specific context of poultry species and virus subtypes.

Enzootic Circulation, Massive Gull Mortality and Poultry Outbreaks during the 2022/2023 High-Pathogenicity Avian Influenza H5N1 Season in the Czech Republic

In 2022/2023, Europe experienced its third consecutive season of high-pathogenicity avian influenza. During this period, the Czech Republic was again severely affected. For the first time, the number of culled birds approached one million, which was three times higher than in previous seasons. In parallel to the outbreaks in poultry, mass die-offs of gulls were also observed. In the present study, we performed whole-genome sequencing and phylogenetic analysis of 137 H5N1 strains collected in the Czech Republic in 2022/2023 (94.6% of all outbreaks or locations). The analysis revealed four distinct genotypes: AB, CH, BB and AF. Phylogenetic analysis suggested that the AF genotype persisted from the previous H5N1 season without reassortment. In addition, the genotype BB, which was detected mainly in gulls, showed a noticeable strain diversity at the local level. This virus was also responsible for a single outbreak in commercially bred turkeys. Finally, an interesting spatio-temporal cluster with three co-circulating H5N1 genotypes, AB, CH and AF, was identified with no evidence of intrasubtype reassortment. Highly sensitive molecular surveillance and the timely sharing of genomic sequences and associated metadata could greatly assist in tracking the spread and detecting molecular changes associated with the increased virulence of this potentially zoonotic pathogen.

New Patterns for Highly Pathogenic Avian Influenza and Adjustment of Prevention, Control and Surveillance Strategies: The Example of France

From 2020 up to summer 2023, there was a substantial change in the situation concerning the high pathogenic avian influenza (HPAI) virus in Europe. This change concerned mainly virus circulation within wildlife, both in wild birds and wild mammals. It involved the seasonality of HPAI detections, the species affected, excess mortality events, and the apparent increased level of contamination in wild birds. The knock-on effect concerned new impacts and challenges for the poultry sector, which is affected by repeated annual waves of HPAI arriving with wild migratory birds and by risks due to viral circulation within resident wild birds across the year. Indeed, exceeding expectations, new poultry sectors and production areas have been affected during the recent HPAI seasons in France. The HPAI virus strains involved also generate considerable concern about human health because of enhanced risks of species barrier crossing. In this article, we present these changes in detail, along with the required adjustment of prevention, control, and surveillance strategies, focusing specifically on the situation in France.

Vaccination of poultry against highly pathogenic avian influenza - part 1. Available vaccines and vaccination strategies

Several vaccines have been developed against highly pathogenic avian influenza (HPAI), mostly inactivated whole-virus vaccines for chickens. In the EU, one vaccine is authorised in chickens but is not fully efficacious to stop transmission, highlighting the need for vaccines tailored to diverse poultry species and production types. Off-label use of vaccines is possible, but effectiveness varies. Vaccines are usually injectable, a time-consuming process. Mass-application vaccines outside hatcheries remain rare. First vaccination varies from in-ovo to 6 weeks of age. Data about immunity onset and duration in the target species are often unavailable, despite being key for effective planning. Minimising antigenic distance between vaccines and field strains is essential, requiring rapid updates of vaccines to match circulating strains. Generating harmonised vaccine efficacy data showing vaccine ability to reduce transmission is crucial and this ability should be also assessed in field trials. Planning vaccination requires selecting the most adequate vaccine type and vaccination scheme. Emergency protective vaccination is limited to vaccines that are not restricted by species, age or pre-existing vector-immunity, while preventive vaccination should prioritise achieving the highest protection, especially for the most susceptible species in high-risk transmission areas. Model simulations in France, Italy and The Netherlands revealed that (i) duck and turkey farms are more infectious than chickens, (ii) depopulating infected farms only showed limitations in controlling disease spread, while 1-km ring-culling performed better than or similar to emergency preventive ring-vaccination scenarios, although with the highest number of depopulated farms, (iii) preventive vaccination of the most susceptible species in high-risk transmission areas was the best option to minimise the outbreaks' number and duration, (iv) during outbreaks in such areas, emergency protective vaccination in a 3-km radius was more effective than 1- and 10-km radius. Vaccine efficacy should be monitored and complement other surveillance and preventive efforts.

Validation of an RNAscope assay for the detection of avian influenza A virus

Highly pathogenic avian influenza (HPAI) is an acute viral disease associated with high mortality and great economic losses. Immunohistochemistry (IHC) is a common diagnostic and research tool for the demonstration of avian influenza A virus (AIAV) antigens within affected tissues, supporting etiologic diagnosis and assessing viral distribution in both naturally and experimentally infected birds. RNAscope in situ hybridization (ISH) has been used successfully for the identification of a variety of viral nucleic acids within histologic samples. We validated RNAscope ISH for the detection of AIAV in formalin-fixed, paraffin-embedded (FFPE) tissues. RNAscope ISH targeting the AIAV matrix gene and anti-IAV nucleoprotein IHC were performed on 61 FFPE tissue sections obtained from 3 AIAV-negative, 16 H5 HPAIAV, and 1 low pathogenicity AIAV naturally infected birds, including 7 species sampled between 2009 and 2022. All AIAV-negative birds were confirmed negative by both techniques. All AIAVs were detected successfully by both techniques in all selected tissues and species. Subsequently, H-score comparison was assessed through computer-assisted quantitative analysis on a tissue microarray comprised of 132 tissue cores from 9 HPAIAV-infected domestic ducks. Pearson correlation of r = 0.95 (0.94-0.97), Lin concordance coefficient of ρc = 0.91 (0.88-0.93), and Bland-Altman analysis indicated high correlation and moderate concordance between the 2 techniques. H-score values were significantly higher with RNAscope ISH compared to IHC for brain, lung, and pancreatic tissues (p ≤ 0.05). Overall, our results indicate that RNAscope ISH is a suitable and sensitive tool for in situ detection of AIAV in FFPE tissues.

Impact of palmiped farm density on the resilience of the poultry sector to highly pathogenic avian influenza H5N8 in France

We analysed the interplay between palmiped farm density and the vulnerability of the poultry production system to highly pathogenic avian influenza (HPAI) H5N8. To do so, we used a spatially-explicit transmission model, which was calibrated to reproduce the observed spatio-temporal distribution of outbreaks in France during the 2016-2017 epidemic of HPAI. Six scenarios were investigated, in which the density of palmiped farms was decreased in the municipalities with the highest palmiped farm density. For each of the six scenarios, we first calculated the spatial distribution of the basic reproduction number (R₀), i.e. the expected number of farms a particular farm would be likely to infect, should all other farms be susceptible. We also ran in silico simulations of the adjusted model for each scenario to estimate epidemic sizes and time-varying effective reproduction numbers. We showed that reducing palmiped farm density in the densest municipalities decreased substantially the size of the areas with high R₀ values (> 1.5). In silico simulations suggested that reducing palmiped farm density, even slightly, in the densest municipalities was expected to decrease substantially the number of affected poultry farms and therefore provide benefits to the poultry sector as a whole. However, they also suggest that it would not have been sufficient, even in combination with the intervention measures implemented during the 2016-2017 epidemic, to completely prevent the virus from spreading. Therefore, the effectiveness of alternative structural preventive approaches now needs to be assessed, including flock size reduction and targeted vaccination.

Prevalence of the H5N8 influenza virus in birds: Systematic review with meta-analysis

INTRODUCTION

Avian influenza viruses are members of the Orthomyxoviridae family, considered highly pathogenic (HPAI). They result from genetic variations from their low virulence predecessors. HPAI is a global problem. Large outbreaks of HAPI have significant health and economic impacts.

OBJECTIVE

The objective of this study was to assess the prevalence of the H5N8 Influenza virus in birds, as well as to assess its variability according to the countries and years.

METHODS

A systematic review of the literature was carried out in six databases (Web of Sciences, Scopus, PubMed, SciELO, Lilacs and Google Scholar) to evaluate the proportion of birds infected with the H5N8 Influenza virus, by molecular and immunological techniques. A meta-analysis was performed using a random-effects model to calculate the pooled prevalence, 95% confidence intervals (95%CI). A 2-tailed 5% alpha level was used for hypothesis testing. Measures of heterogeneity were estimated and reported, including the Cochrane Q statistic, the I² index, and the tau-squared test. In addition, bird species performed subgroup analyzes.

RESULTS

152 data groups were analyzed, a combined prevalence of 1.6% (95% CI 1.3-1.9%) was found for molecular studies, and the ELISA study yielded a seroprevalence of 66.7%; those results of molecular detection varied by year, from 0.2% in 2014 to 52.6% in 2020 and 96.9% in 2015.

CONCLUSION

The combined prevalence was substantial because large outbreaks have caused severe economic repercussions. In addition, it is considered a serious concern for public health due to its possible zoonotic activity.