Paradox of vaccination: is vaccination really effective against avian flu epidemics?

Association of poultry vaccination with interspecies transmission and molecular evolution of H5 subtype avian influenza virus

The effectiveness of poultry vaccination in preventing the transmission of highly pathogenic avian influenza viruses (AIVs) has been debated, and its impact on wild birds remains uncertain. Here, we reconstruct the movements of H5 subtype AIV lineages among vaccinated poultry, unvaccinated poultry, and wild birds, worldwide, from 1996 to 2023. We find that there is a time lag in viral transmission among different host populations and that movements from wild birds to unvaccinated poultry were more frequent than those from wild birds to vaccinated poultry. Furthermore, our findings suggest that the HA (hemagglutinin) gene of the AIV lineage that circulated predominately in Chinese poultry experienced greater nonsynonymous divergence and adaptive fixation than other lineages. Our results indicate that the epidemiological, ecological, and evolutionary consequences of widespread AIV vaccination in poultry may be linked in complex ways and that much work is needed to better understand how such interventions may affect AIV transmission to, within, and from wild birds.

Evolution of H7N9 highly pathogenic avian influenza virus in the context of vaccination

Human infections with the H7N9 influenza virus have been eliminated in China through vaccination of poultry; however, the H7N9 virus has not yet been eradicated from poultry. Carefully analysis of H7N9 viruses in poultry that have sub-optimal immunity may provide a unique opportunity to witness the evolution of highly pathogenic avian influenza virus in the context of vaccination. Between January 2020 and June 2023, we isolated 16 H7N9 viruses from samples we collected during surveillance and samples that were sent to us for disease diagnosis. Genetic analysis indicated that these viruses belonged to a single genotype previously detected in poultry. Antigenic analysis indicated that 12 of the 16 viruses were antigenically close to the H7-Re4 vaccine virus that has been used since January 2022, and the other four viruses showed reduced reactivity with the vaccine. Animal studies indicated that all 16 viruses were nonlethal in mice, and four of six viruses showed reduced virulence in chickens upon intranasally inoculation. Importantly, the H7N9 viruses detected in this study exclusively bound to the avian-type receptors, having lost the capacity to bind to human-type receptors. Our study shows that vaccination slows the evolution of H7N9 virus by preventing its reassortment with other viruses and eliminates a harmful characteristic of H7N9 virus, namely its ability to bind to human-type receptors.

A systemic review on medicinal plants and their bioactive constituents against avian influenza and further confirmation through in-silico analysis

Background

Avian influenza or more commonly known as bird flu is a widespread infectious disease in poultry. This review aims to accumulate information of different natural plant sources that can aid in combating this disease. Influenza virus (IV) is known for its ability to mutate and infect different species (including humans) and cause fatal consequences.

Methods

Total 33 plants and 4 natural compounds were identified and documented. Molecular docking was performed against the target viral protein neuraminidase (NA), with some plant based natural compounds and compared their results with standard drugs Oseltamivir and Zanamivir to obtain novel drug targets for influenza in chickens.

Results

It was seen that most extracts exhibit their action by interacting with viral hemagglutinin or neuraminidase and inhibit viral entry or release from the host cell. Some plants also interacted with the viral RNA replication or by reducing proinflammatory cytokines. Ethanol was mostly used for extraction. Among all the plants Theobroma cacao, Capparis Sinaica Veil, Androgarphis paniculate, Thallasodendron cillatum, Sinularia candidula, Larcifomes officinalis, Lenzites betulina, Datronia molis, Trametes gibbose exhibited their activity with least concentration (below 10 μg/ml). The dockings results showed that some natural compounds (5,7- dimethoxyflavone, Aloe emodin, Anthocyanins, Quercetin, Hemanthamine, Lyocrine, Terpenoid EA showed satisfactory binding affinity and binding specificity with viral neuraminidase compared to the synthetic drugs.

Conclusion

This review clusters up to date information of effective herbal plants to bolster future influenza treatment research in chickens. The in-silico analysis also suggests some potential targets for future drug development but these require more clinical analysis.

Evaluation of vaccination strategies to control an avian influenza outbreak in French poultry production networks using EVACS tool

France recently faced two epizootic waves of highly pathogenic avian influenza (HPAI) in poultry (H5N6 in 2015-2016 and H5N8 in 2016-2017), mainly in the fattening duck production sector. Vaccination against avian influenza (AI) is currently not authorised in France even though its potential benefits were discussed during these epizootic events. The objective of this work was to evaluate the potential efficiency of different vaccination strategies that could be applied against AI in France. The EVACS tool, which is a decision support tool developed to evaluate vaccination strategies, was applied in several French poultry production sectors: broiler, layer, turkey, duck and guinea fowl. EVACS was used to simulate the performance of vaccination strategies in terms of vaccination coverage, immunity levels and spatial distribution of the immunity level. A cost-benefit analysis was then applied based on EVACS results to identify the most efficient strategy. For each sector, vaccination protocols were tested according to the production type (breeders/production, indoor/outdoor), the integration level (integrated/independent) and the type of vaccine (hatchery vaccination using a recombinant vaccine/farm vaccination using an inactivated vaccine). The most efficient protocols for each sector were then combined to test different overall vaccination strategies at the national level. Even if it was not possible to compare vaccination protocols with the two vaccines types in "foie gras" duck, meat duck and guinea fowl production sectors as no hatchery vaccine currently exist for these species, these production sectors were also described and included in this simulation. Both types of vaccination (at hatchery and farm level) enabled protective immunity levels for the control of AI, but higher poultry population immunity level was reached (including independent farms) using hatchery vaccination. We also showed that hatchery vaccination was more efficient (higher benefit-cost ratio) than farm vaccination. Sufficient and homogeneously spatially distributed protective levels were reached in the overall poultry population with vaccination strategies targeting breeders, chicken layers and broilers and turkeys, without the need to include ducks and guinea fowls. However, vaccination strategies involving the highest number of species and production types were the most efficient in terms of cost-benefit. This study provides critical information on the efficiency of different vaccination strategies to support future decision making in case vaccination was applied to prevent and control HPAI in France.

Models to predict the public health impact of vaccine resistance: A systematic review

Pathogen evolution is a potential threat to the long-term benefits provided by public health vaccination campaigns. Mathematical modeling can be a powerful tool to examine the forces responsible for the development of vaccine resistance and to predict its public health implications. We conducted a systematic review of existing literature to understand the construction and application of vaccine resistance models. We identified 26 studies that modeled the public health impact of vaccine resistance for 12 different pathogens. Most models predicted that vaccines would reduce overall disease burden in spite of evolution of vaccine resistance. Relatively few pathogens and populations for which vaccine resistance may be problematic were covered in the reviewed studies, with low- and middle-income countries particularly under-represented. We discuss the key components of model design, as well as patterns of model predictions.

Population-level mathematical modeling of antimicrobial resistance: a systematic review

BACKGROUND

Mathematical transmission models are increasingly used to guide public health interventions for infectious diseases, particularly in the context of emerging pathogens; however, the contribution of modeling to the growing issue of antimicrobial resistance (AMR) remains unclear. Here, we systematically evaluate publications on population-level transmission models of AMR over a recent period (2006-2016) to gauge the state of research and identify gaps warranting further work.

METHODS

We performed a systematic literature search of relevant databases to identify transmission studies of AMR in viral, bacterial, and parasitic disease systems. We analyzed the temporal, geographic, and subject matter trends, described the predominant medical and behavioral interventions studied, and identified central findings relating to key pathogens.

RESULTS

We identified 273 modeling studies; the majority of which (> 70%) focused on 5 infectious diseases (human immunodeficiency virus (HIV), influenza virus, Plasmodium falciparum (malaria), Mycobacterium tuberculosis (TB), and methicillin-resistant Staphylococcus aureus (MRSA)). AMR studies of influenza and nosocomial pathogens were mainly set in industrialized nations, while HIV, TB, and malaria studies were heavily skewed towards developing countries. The majority of articles focused on AMR exclusively in humans (89%), either in community (58%) or healthcare (27%) settings. Model systems were largely compartmental (76%) and deterministic (66%). Only 43% of models were calibrated against epidemiological data, and few were validated against out-of-sample datasets (14%). The interventions considered were primarily the impact of different drug regimens, hygiene and infection control measures, screening, and diagnostics, while few studies addressed de novo resistance, vaccination strategies, economic, or behavioral changes to reduce antibiotic use in humans and animals.

CONCLUSIONS

The AMR modeling literature concentrates on disease systems where resistance has been long-established, while few studies pro-actively address recent rise in resistance in new pathogens or explore upstream strategies to reduce overall antibiotic consumption. Notable gaps include research on emerging resistance in Enterobacteriaceae and Neisseria gonorrhoeae; AMR transmission at the animal-human interface, particularly in agricultural and veterinary settings; transmission between hospitals and the community; the role of environmental factors in AMR transmission; and the potential of vaccines to combat AMR.

Public health concerns of highly pathogenic avian influenza H5N1 endemicity in Africa

Highly pathogenic avian influenza virus (HPAIV) H5N1 was first officially reported in Africa in 2006; thereafter this virus has spread rapidly from Nigeria to 11 other African countries. This study was aimed at utilizing data from confirmed laboratory reports to carry out a qualitative evaluation of the factors responsible for HPAI H5N1 persistence in Africa and the public health implications; and to suggest appropriate control measures. Relevant publications were sought from data banks and repositories of FAO, OIE, WHO, and Google scholars. Substantiated data on HPAI H5N1 outbreaks in poultry in Africa and in humans across the world were mined. HPAI H5N1 affects poultry and human populations, with Egypt having highest human cases (346) globally. Nigeria had a reinfection from 2014 to 2015, with outbreaks in Côte d'Ivoire, Ghana, Niger, Nigeria, and Burkina Faso throughout 2016 unabated. The persistence of this virus in Africa is attributed to the survivability of HPAIV, ability to evolve other subtypes through genetic reassortment, poor biosecurity compliance at the live bird markets and poultry farms, husbandry methods and multispecies livestock farming, poultry vaccinations, and continuous shedding of HPAIV, transboundary transmission of HPAIV through poultry trades; and transcontinental migratory birds. There is, therefore, the need for African nations to realistically reassess their status, through regular surveillance and be transparent with HPAI H5N1 outbreak data. Also, it is important to have an understanding of HPAIV migration dynamics which will be helpful in epidemiological modeling, disease prevention, control and eradication measures.

Vaccines against influenza A viruses in poultry and swine: Status and future developments

Influenza A viruses are important pathogens with a very broad host spectrum including domestic poultry and swine. For preventing clinical disease and controlling the spread, vaccination is one of the most efficient tools. Classical influenza vaccines for domestic poultry and swine are conventional inactivated preparations. However, a very broad range of novel vaccine types ranging from (i) nucleic acid-based vaccines, (ii) replicon particles, (iii) subunits and virus-like particles, (iv) vectored vaccines, or (v) live-attenuated vaccines has been described, and some of them are now also used in the field. The different novel approaches for vaccines against avian and swine influenza virus infections are reviewed, and additional features like universal vaccines, novel application approaches and the "differentiating infected from vaccinated animals" (DIVA)-strategy are summarized.

AVIAN FLU: MODELING AND IMPLICATIONS FOR CONTROL

At present, H5N1 avian influenza (AI) is a zoonotic disease where the transmission to humans occurs from infected domestic birds. Since 2003, more than 500 people have been infected and nearly 60% of them have died. If the H5N1 virus becomes efficiently human-to-human transmittable, a pandemic will occur with potentially high mortality. A mathematical model of AI, which involves human influenza, is introduced to better understand the complex epidemiology of AI and the emergence of a pandemic strain. Demographic and epidemiological data on birds and humans are used for the parameterization of the model. The differential equation system faithfully projects the cumulative number of H5N1 human cases and captures the dynamics of the yearly cases. The model is used to rank the efficacy of the current control measures used to prevent the emergence of a pandemic strain. We find that culling without re-population and vaccination are the two most efficient control measures each giving 22% decrease in the number of H5N1 infected humans for each 1% change in the affected parameters (μb, νb for culling and βb, νb for vaccination). Control measures applied to humans, such as wearing protective gear, are not very efficient, giving less than 1% decrease in the number of H5N1 infected humans for each 1% decrease in βY, the bird-to-human transmission coefficient of H5N1. Furthermore, we find that should a pandemic strain emerge, it will invade, possibly displacing the human influenza virus in circulation at that time. Moreover, higher prevalence levels of human influenza will obstruct the invasion capabilities of the pandemic H5N1 strain. This effect is not very pronounced, as we find that 1% increase in human influenza prevalence will decrease the invasion capabilities of the pandemic strain with 0.006%.

A mathematical model of avian influenza with half-saturated incidence

The widespread impact of avian influenza viruses not only poses risks to birds, but also to humans. The viruses spread from birds to humans and from human to human In addition, mutation in the primary strain will increase the infectiousness of avian influenza. We developed a mathematical model of avian influenza for both bird and human populations. The effect of half-saturated incidence on transmission dynamics of the disease is investigated. The half-saturation constants determine the levels at which birds and humans contract avian influenza. To prevent the spread of avian influenza, the associated half-saturation constants must be increased, especially the half-saturation constant H m for humans with mutant strain. The quantity H m plays an essential role in determining the basic reproduction number of this model. Furthermore, by decreasing the rate β m at which human-to-human mutant influenza is contracted, an outbreak can be controlled more effectively. To combat the outbreak, we propose both pharmaceutical (vaccination) and non-pharmaceutical (personal protection and isolation) control methods to reduce the transmission of avian influenza. Vaccination and personal protection will decrease β m, while isolation will increase H m. Numerical simulations demonstrate that all proposed control strategies will lead to disease eradication; however, if we only employ vaccination, it will require slightly longer to eradicate the disease than only applying non-pharmaceutical or a combination of pharmaceutical and non-pharmaceutical control methods. In conclusion, it is important to adopt a combination of control methods to fight an avian influenza outbreak.

Evolution of scaling emergence in large-scale spatial epidemic spreading

Background

Zipf's law and Heaps' law are two representatives of the scaling concepts, which play a significant role in the study of complexity science. The coexistence of the Zipf's law and the Heaps' law motivates different understandings on the dependence between these two scalings, which has still hardly been clarified.

Methodology/Principal Findings

In this article, we observe an evolution process of the scalings: the Zipf's law and the Heaps' law are naturally shaped to coexist at the initial time, while the crossover comes with the emergence of their inconsistency at the larger time before reaching a stable state, where the Heaps' law still exists with the disappearance of strict Zipf's law. Such findings are illustrated with a scenario of large-scale spatial epidemic spreading, and the empirical results of pandemic disease support a universal analysis of the relation between the two laws regardless of the biological details of disease. Employing the United States domestic air transportation and demographic data to construct a metapopulation model for simulating the pandemic spread at the U.S. country level, we uncover that the broad heterogeneity of the infrastructure plays a key role in the evolution of scaling emergence.

Conclusions/Significance

The analyses of large-scale spatial epidemic spreading help understand the temporal evolution of scalings, indicating the coexistence of the Zipf's law and the Heaps' law depends on the collective dynamics of epidemic processes, and the heterogeneity of epidemic spread indicates the significance of performing targeted containment strategies at the early time of a pandemic disease.

The influenza pandemic of 2009: lessons and implications

Influenza is a moving target, which evolves in unexpected directions and is recurrent annually. The 2009 influenza A/H1N1 pandemic virus was unlike the 2009 seasonal virus strains and originated in pigs prior to infecting humans. Three strains of viruses gave rise to the pandemic virus by antigenic shift, reassortment, and recombination, which occurred in pigs as 'mixing vessels'. The three strains of viruses had originally been derived from birds, pigs, and humans. The influenza hemagglutinin (HA) and neuraminidase (NA) external proteins are used to categorize and group influenza viruses. The internal proteins (PB1, PB1-F2, PB2, PA, NP, M, and NS) are involved in the pathogenesis of influenza infection. A major difference between the 1918 and 2009 pandemic viruses is the lack of the pathogenic protein PB1-F2 in the 2009 pandemic strains, which was present in the more virulent 1918 pandemic strains. We provide an overview of influenza infection since 1847 and the advent of influenza vaccination since 1944. Vaccines and chemotherapy help reduce the spread of influenza, reduce morbidity and mortality, and are utilized by the global rapid-response organizations associated with the WHO. Immediate identification of impending epidemic and pandemic strains, as well as sustained vigilance and collaboration, demonstrate continued success in combating influenza.

Ecology of avian influenza viruses in a changing world

Influenza A virus infections result in approximately 500,000 human deaths per year and many more sublethal infections. Wild birds are recognized as the ancestral host of influenza A viruses, and avian viruses have contributed genetic material to most human viruses, including subtypes H5N1 and H1N1. Thus, influenza virus transmission in wild and domestic animals and humans is intimately connected. Here we review how anthropogenic change, including human population growth, land use, climate change, globalization of trade, agricultural intensification, and changes in vaccine technology may alter the evolution and transmission of influenza viruses. Evidence suggests that viral transmission in domestic poultry, spillover to other domestic animals, wild birds and humans, and the potential for subsequent pandemic spread, are all increasing. We highlight four areas in need of research: drivers of viral subtype dynamics; ecological and evolutionary determinants of transmissibility and virulence in birds and humans; the impact of changing land use and climate on hosts, viruses, and transmission; and the impact of influenza viruses on wild bird hosts, including their ability to migrate while shedding virus.

A geographical spread of vaccine-resistance in avian influenza epidemics

Vaccination can be a useful tool for control of avian influenza outbreaks in poultry, but its use is reconsidered in most of the countries worldwide because of its negative effects on the disease control. One of the most important negative effects is the potential for emergence of vaccine-resistant viruses. Actually, in the vaccination program in China and Mexico, several vaccine-resistant strains were confirmed. Vaccine-resistant strains usually cause a loss of the protection effectiveness of vaccination. Therefore, a vaccination program that engenders the emergence of the resistant strain might promote the spread of the resistant strain and undermine the control of the infectious disease, even if the vaccination protects against the transmission of a vaccine-sensitive strain. We designed and analyzed a deterministic patch-structured model in heterogeneous areas (with or without vaccination) illustrating transmission of vaccine-sensitive and vaccine-resistant strains during a vaccination program. We found that the vaccination program can eradicate the vaccine-sensitive strain but lead to a prevalence of vaccine-resistant strain. Further, interestingly, the replacement of viral strain could occur in another area without vaccination through a migration of non-infectious individuals due to an illegal trade of poultry. It is also a novel result that only a complete eradication of both strains in vaccination area can achieve the complete eradication in another areas. Thus we can obtain deeper understanding of an effect of vaccination for better development of vaccination strategies to control avian influenza spread.