Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus in Europe

Estimating pathogen spread using structured coalescent and birth-death models: A quantitative comparison

Elucidating disease spread between subpopulations is crucial in guiding effective disease control efforts. Genomic epidemiology and phylodynamics have emerged as key principles to estimate such spread from pathogen phylogenies derived from molecular data. Two well-established structured phylodynamic methodologies - based on the coalescent and the birth-death model - are frequently employed to estimate viral spread between populations. Nonetheless, these methodologies operate under distinct assumptions whose impact on the accuracy of migration rate inference is yet to be thoroughly investigated. In this manuscript, we present a simulation study, contrasting the inferential outcomes of the structured coalescent model with constant population size and the multitype birth-death model with a constant rate. We explore this comparison across a range of migration rates in endemic diseases and epidemic outbreaks. The results of the epidemic outbreak analysis revealed that the birth-death model exhibits a superior ability to retrieve accurate migration rates compared to the coalescent model, regardless of the actual migration rate. Thus, to estimate accurate migration rates, the population dynamics have to be accounted for. On the other hand, for the endemic disease scenario, our investigation demonstrates that both models produce comparable coverage and accuracy of the migration rates, with the coalescent model generating more precise estimates. Regardless of the specific scenario, both models similarly estimated the source location of the disease. This research offers tangible modelling advice for infectious disease analysts, suggesting the use of either model for endemic diseases. For epidemic outbreaks, or scenarios with varying population size, structured phylodynamic models relying on the Kingman coalescent with constant population size should be avoided as they can lead to inaccurate estimates of the migration rate. Instead, coalescent models accounting for varying population size or birth-death models should be favoured. Importantly, our study emphasises the value of directly capturing exponential growth dynamics which could be a useful enhancement for structured coalescent models.

Detection and characterization of highly pathogenic avian influenza A (H5N1) clade 2.3.4.4b virus circulating in Argentina in 2023

In 2021, avian influenza A (H5N1) clade 2.3.4.4b virus spread to North America and then to Central and South America in October 2022, extending from Colombia to Chile in three months. During 2023, several countries, mostly in the Americas, reported outbreaks in poultry, wild birds and mammals, as well as the emergence of two cases in humans (one in Ecuador in January and one in Chile in March). As of September 20th, 2023, 17 countries in the Americas Region have recorded cases of A (H5N1) in birds and mammals. On February 14th, 2023, Argentina confirmed the first case of avian influenza in wild birds, which was later detected in backyard and commercial poultry, and in the South-American sea lion (Otaria flavescens) in Tierra del Fuego, in the south of the country. So far, 21 suspected cases have been recorded in humans; however, all of them tested negative for Influenza A virus. Hemagglutinin sequence data of animal viruses analyzed in this report showed that Argentinian viruses clustered together with those isolated in other countries of the region. Epidemiological data suggested the possibility of multiple simultaneous entries of the avian virus, highlighting the role of migratory avian populations in the introduction and dissemination of the disease in Argentina. Continued comprehensive surveillance of these viruses in animals and people worldwide, along with ongoing preparedness efforts, are critical to determine the public health risk.

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.

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.

Easier said than done! Organic farmers consider free-ranging important for laying hen welfare but outdoor areas need more shelter - important gaps between research and practice

1. The aim of the present study was to investigate the design and management of free-range areas and their use by birds on commercial organic laying hen farms in Sweden and to document farmers' perspectives on outdoor access for poultry.2. Eleven Swedish organic laying hen farms were visited. The farmers were interviewed about general farm management, bird health and behaviour and outdoor access. The free-range areas were assessed in terms of proportion covered by protective (high) vegetation and any artificial shelters provided. The numbers of hens ranging at different distances from the house were recorded twice during the day.3. The outdoor area within 250m from the house contained 0-5% vegetation cover on six of the farms and at least 80% pasture on seven farms. On 10 farms, no more than 13% of the flock was observed outdoors. Of the hens observed in the free-range area, the median proportion ranging within 20m from the house or veranda per observation event was 99% (IQR=55-100%), confirming reports by the farmers.4. Free-range access was considered important by all farmers, primarily for welfare reasons and most agreed that protective vegetation cover and/or artificial shelters were important in encouraging free-ranging. However, there was marked variation among the farmers in their suggestions on how to attract hens outside.

Evolution and Epidemic Spread of the Avian Infectious Bronchitis Virus (IBV) GI-23 in Brazil

Infectious bronchitis virus (IBV) is a pathogen affecting poultry flocks worldwide. GI-23 is an IBV lineage with a rapid spread into different continents of the world, and it was reported for the first time in South American/Brazilian broiler farms last year. This study aimed to investigate the recent introduction and epidemic spread of IBV GI-23 in Brazil. Ninety-four broiler flocks infected with this lineage were evaluated from October 2021 to January 2023. IBV GI-23 was detected using real-time RT-qPCR, and the S1 gene hypervariable regions 1 and 2 (HVR1/2) were sequenced. S1 complete and HVR1/2 nucleotide sequence datasets were used to carry out phylogenetic and phylodynamic analyses. Brazilian IBV GI-23 strains clustered into two specific subclades (SA.1 and SA.2), both in tree branches with IBV GI-23 from Eastern European poultry-producing countries, suggesting two independent and recent introductions (around 2018). Viral phylodynamic analysis showed that the IBV GI-23 population increased from 2020 to 2021, remaining constant for one year and declining in 2022. S1 amino acid sequences from Brazilian IBV GI-23 presented specific and characteristic substitutions in the HVR1/2 for subclades IBV GI-23 SA.1 and SA.2. This study brings new insights into the introduction and recent epidemiology of IBV GI-23 in Brazil.