Highly Pathogenic Avian Influenza A(H5N1) Viruses from Multispecies Outbreak, Argentina, August 2023

We report full-genome characterization of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus from an outbreak among sea lions (August 2023) in Argentina and possible spillover to fur seals and terns. Mammalian adaptation mutations in virus isolated from marine mammals and a human in Chile were detected in mammalian and avian hosts.

Evolution and Current Status of Influenza A Virus in Chile: A Review

The influenza A virus (IAV) poses a significant global threat to public health and food security. Particularly concerning is the avian influenza virus (AIV) subtype H5N1, which has spread from Europe to North and Central/South America. This review presents recent developments in IAV evolution in birds, mammals, and humans in Chile. Chile's encounter with IAV began in 2002, with the highly pathogenic avian influenza (HPAI) H7N3 virus, derived from a unique South American low pathogenic avian influenza (LPAI) virus. In 2016-2017, LPAI H7N6 caused outbreaks in turkey, linked to wild birds in Chile and Bolivia. The pandemic influenza A (H1N1) 2009 (H1N1pdm09) virus in 2009 decreased egg production in turkeys. Since 2012, diverse IAV subtypes have emerged in backyard poultry and pigs. Reassortant AIVs, incorporating genes from both North and South American isolates, have been found in wild birds since 2007. Notably, from December 2022, HPAI H5N1 was detected in wild birds, sea lions, and a human, along Chile's north coast. It was introduced through Atlantic migratory flyways from North America. These findings emphasize the need for enhanced biosecurity on poultry farms and ongoing genomic surveillance to understand and manage AIVs in both wild and domestic bird populations in Chile.

Epidemiology and phylodynamics of multiple clades of H5N1 circulating in domestic duck farms in different production systems in Bangladesh

Waterfowl are considered to be natural reservoirs of the avian influenza virus (AIV). However, the dynamics of transmission and evolutionary patterns of AIV and its subtypes within duck farms in Bangladesh remain poorly documented. Hence, a cross-sectional study was conducted in nine districts of Bangladesh between 2019 and 2021, to determine the prevalence of AIV and its subtypes H5 and H9, as well as to identify risk factors and the phylodynamics of H5N1 clades circulating in domestic duck farms. The oropharyngeal and cloacal swab samples were tested for the AIV Matrix gene (M-gene) followed by H5, H7, and H9 subtypes using rRT-PCR. The exploratory analysis was performed to estimate AIV and its subtype prevalence in different production systems, and multivariable logistic regression model was used to identify the risk factors that influence AIV infection in ducks. Bayesian phylogenetic analysis was conducted to generate a maximum clade credibility (MCC) tree and the maximum likelihood method to determine the phylogenetic relationships of the H5N1 viruses isolated from ducks. AIV was detected in 40% (95% CI: 33.0-48.1) of the duck farms. The prevalence of AIV was highest in nomadic ducks (39.8%; 95% CI: 32.9-47.1), followed by commercial ducks (24.6%; 95% CI: 14.5-37.3) and backyard ducks (14.4%; 95% CI: 10.5-19.2). The H5 prevalence was also highest in nomadic ducks (19.4%; 95% CI: 14.0-25.7). The multivariable logistic regression model revealed that ducks from nomadic farms (AOR: 2.4; 95% CI: 1.45-3.93), juvenile (AOR: 2.2; 95% CI: 1.37-3.61), and sick ducks (AOR: 11.59; 95% CI: 4.82-32.44) had a higher risk of AIV. Similarly, the likelihood of H5 detection was higher in sick ducks (AOR: 40.8; 95% CI: 16.3-115.3). Bayesian phylogenetic analysis revealed that H5N1 viruses in ducks belong to two distinct clades, 2.3.2.1a, and 2.3.4.4b. The clade 2.3.2.1a (reassorted) has been evolving silently since 2015 and forming at least nine subgroups based on >90% posterior probability. Notably, clade 2.3.4.4b was introduced in ducks in Bangladesh by the end of the year 2020, which was genetically similar to viruses detected in wild birds in Japan, China, and Africa, indicating migration-associated transmission of an emerging panzootic clade. We recommend continuing AIV surveillance in the duck production system and preventing the intermingling of domestic ducks with migratory waterfowl in wetlands.

An assessment of the highly pathogenic avian influenza resurgence at human-poultry-environment interface in North-central Nigeria: Sociocultural determinants and One Health implications

Highly pathogenic avian influenza H5N1 resurgence has occurred in Nigerian domestic bird flocks with public health concern. This study assessed poultry farmers' knowledge, perceptions, and biosecurity and biosafety practices regarding H5N1 resurgence, explore risk pathways for viral dissemination and associated socio-cultural and economic drivers in poultry flocks in Nigeria. A cross-sectional survey was carried out in randomly selected two poultry production systems, commercial intensive poultry production system and the backyard traditional free-range poultry production system. A One Health framework model was conceptualized to assess inter-links of biophysical, environmental, and sociocultural activities that interface to drive resurgence for better interventions. Descriptive and analytical statistical analyses were performed at 95% confidence level. Of the 422 recruited poultry farmers, 98.6% (n = 416) participated. Majorities of smallholder commercial farmers (93.5%) and backyard poultry keepers (97.7%) engaged in intensive and extensive management, respectively. Identified significant zoonotic risk pathways for H5N1 virus spread were through consumption of undercooked poultry meat and products, and contacts with infected birds and contaminated fomites. Separation of sick birds from apparently healthy ones, frequent cleaning and disinfection of equipment and premises, movement control of birds to nearby water bodies, use of personal protective equipment, and movement control of persons and vehicles into the flock settlements were significantly practiced biosecurity measures. Presence of nearby water bodies (ponds) close to flock settlements (p < 0.001), frequent contact of wild and domestic birds (p < 0.001), cultural practice of bird exchange between flocks (p < 0.001), and wild waterfowls' seasonal migrations (p < 0.001) significantly influenced resurgence. Understanding determinants interactions in the 'Conceptual One Health framework model' is required for better intercontinental intervention against HPAI H5N1. Reform of socio-cultural and economic activities using One Health approach will not only assure food safety and food security, but also guarantee public and environmental health.

Avian influenza spread and seabird movements between colonies

Seabirds have recently been experiencing high rates of mortality across wide scales due to highly pathogenic avian influenza (HPAI). During breeding, seabird populations are highly spatially structured, while over their lifetimes they spend much time at sea. This makes them unique systems in which to document how movement and interspecies interactions affect eco-epidemiological dynamics.

Highly Pathogenic Avian Influenza H5N1 Virus Infections in Wild Red Foxes (Vulpes vulpes) Show Neurotropism and Adaptive Virus Mutations

During the 2020 to 2022 epizootic of highly pathogenic avian influenza virus (HPAI), several infections of mammalian species were reported in Europe. In the Netherlands, HPAI H5N1 virus infections were detected in three wild red foxes (Vulpes vulpes) that were submitted with neurological symptoms between December of 2021 and February of 2022. A histopathological analysis demonstrated that the virus was mainly present in the brain, with limited or no detection in the respiratory tract or other organs. Limited or no virus shedding was observed in throat and rectal swabs. A phylogenetic analysis showed that the three fox viruses were not closely related, but they were related to HPAI H5N1 clade 2.3.4.4b viruses that are found in wild birds. This suggests that the virus was not transmitted between the foxes. A genetic analysis demonstrated the presence of the mammalian adaptation E627K in the polymerase basic two (PB2) protein of the two fox viruses. In both foxes, the avian (PB2-627E) and the mammalian (PB2-627K) variants were present as a mixture in the virus population, which suggests that the mutation emerged in these specific animals. The two variant viruses were isolated, and virus replication and passaging experiments were performed. These experiments showed that the mutation PB2-627K increases the replication of the virus in mammalian cell lines, compared to the chicken cell line, and at the lower temperatures of the mammalian upper respiratory tract. This study showed that the HPAI H5N1 virus is capable of adaptation to mammals; however, more adaptive mutations are required to allow for efficient transmission between mammals. Therefore, surveillance in mammals should be expanded to closely monitor the emergence of zoonotic mutations for pandemic preparedness. IMPORTANCE Highly pathogenic avian influenza (HPAI) viruses caused high mortality among wild birds from 2021 to 2022 in the Netherlands. Recently, three wild foxes were found to be infected with HPAI H5N1 viruses, likely due to the foxes feeding on infected birds. Although HPAI is a respiratory virus, in these foxes, the viruses were mostly detected in the brain. Two viruses isolated from the foxes contained a mutation that is associated with adaptation to mammals. We show that the mutant virus replicates better in mammalian cells than in avian cells and at the lower body temperature of mammals. More mutations are required before viruses can transmit between mammals or can be transmitted to humans. However, infections in mammalian species should be closely monitored to swiftly detect mutations that may increase the zoonotic potential of HPAI H5N1 viruses, as these may threaten public health.

Spatiotemporal analysis of highly pathogenic avian influenza (H5N1) outbreaks in poultry in Egypt (2006 to 2017)

Background

In Egypt, the highly pathogenic avian influenza (HPAI) subtype H5N1 is endemic and possesses a severe impact on the poultry. To provide a better understanding of the distributional characteristics of HPAI H5N1 outbreaks in Egypt, this study aimed to explore the spatiotemporal pattern and identify clusters of HPAI H5N1 outbreaks in Egypt from 2006 to 2017.

Results

The Epidemic curve (EC) was constructed through time series analysis; in which six epidemic waves (EWs) were revealed. Outbreaks mainly started in winter peaked in March and ended in summer. However, newly emerged thermostable clades (2.2.1.1 and 2.2.1.2) during the 4th EW enabled the virus to survive and cause infection in warmer months with a clear alteration in the seasonality of the epidemic cycle in the 5th EW. The endemic situation became more complicated by the emergence of new serotypes. As a result, the EC ended up without any specific pattern since the 6th EW to now. The spatial analysis showed that the highest outbreak density was recorded in the Nile Delta considering it as the ‘Hot spot’ region. By the 6th EW, the outbreak extended to include the Nile valley. From spatiotemporal cluster epidemics, clustering in the Delta was a common feature in all EWs with primary clusters consistently detected in the hot-spot region, but the location and size varied with each EW. The highest Relative Risk (RR) regions in an EW were noticed to contain the primary clusters of the next EW and were found to include stopover sites for migratory wild birds. They were in Fayoum, Dakahlia, Qalyobiya, Sharkia, Kafr_Elsheikh, Giza, Behera, Menia, and BeniSuef governorates. Transmission of HPAI H5N1 occurred from one location to another directly resulted in a series of outbreaks forming neighboring secondary clusters. The absence of geographical borders between the governorates in addition to non-restricted movements of poultry and low vaccination and surveillance coverage contributed to the wider spread of infection all over Egypt and to look like one epidemiological unit.

Conclusion

Our findings can help in better understanding of the characteristics of HPAI H5N1 outbreaks and the distribution of outbreak risk, which can be used for effective disease control strategies.

Graphical abstract

A Systematic Evaluation of Measures Against Highly Pathogenic Avian Influenza (HPAI) in Indonesia

Over the past years, many different control measures have been implemented to prevent HPAI infection. The national plan with numerous measures lead to problems in terms of prioritization and budget allocation. Our study objectives are to (i) establish an inventory of measures on HPAI control in Indonesia since the first actions were taken in 2004, (ii) evaluate preferences for different HPAI control measures applied in the West Java province at the district level during 2013–2017, and (iii) establish a basis for further qualitative and quantitative research to improve control for an endemic HPAI in Indonesia. This research was carried out according to the following five steps (i) development of an HPAI management framework for an endemic state, (ii) inventorization of measures directed at HPAI and description of the development of HPAI in Indonesia, (iii) development of a questionnaire for the experts involved, (iv) systematic evaluation of preferences for short- and long-term HPAI strategies and measures applied in the West Java Province based on expert opinion, and (v) data analysis. The study systematically evaluated in total 27 measures. The results of this study show that the animal disease management framework is helpful as a systematic structure to distinguish and evaluate strategies and measures. In our framework, we defined the following strategies: prevention, monitoring, control, mitigation, eradication, and human protection. The findings of our research show that the primary aims of the government were to safeguard humans from HPAI transmission by mitigating HPAI disease in livestock. The measures with the highest priority were preventive vaccination of poultry, biosecurity, and stamping-out infected flocks. This showed that the government predominantly chose a vaccination-based HPAI mitigation strategy. However, the chosen strategy has a low implementation feasibility. A collaboration between the responsible stakeholders farmers may increase the feasibility of the chosen strategy in the future. Furthermore, our findings provide a basis for research into the motivation of farmers to implement different measures as well as into the expected impact of different measures to develop an effective and efficient mitigation approach.

Highly pathogenic avian influenza A/H5N1 Clade 2.3.2.1c virus in poultry in Cameroon, 2016-2017

In May 2016, highly pathogenic avian influenza virus of the subtype A/H5N1 was detected in Cameroon in an industrial poultry farm at Mvog-Betsi, Yaoundé (Centre region), with a recorded sudden increase of deaths among chickens, and an overall mortality rate of 75%. The virus spread further and caused new outbreaks in some parts of the country. In total, 21 outbreaks were confirmed from May 2016 to March 2017 (six in the Centre, six in the West, eight in the South and one in the Adamaoua regions). This resulted in an estimated total loss of 138,252 birds (44,451 deaths due to infection and 93,801 stamped out). Only domestic birds (chickens, ducks and geese) were affected in farms as well as in poultry markets. The outbreaks occurred in three waves, the first from May to June 2016, the second in September 2016 and the last wave in March 2017. The topology of the phylogeny based on the haemagglutinin gene segment indicated that the causative H5N1 viruses fall within the genetic clade 2.3.2.1c, within the same group as the A/H5N1 viruses collected in Niger in 2015 and 2016. More importantly, the gene constellation of four representative viruses showed evidence of H5N1/H9N2 intra-clade reassortment. Additional epidemiological and genetic data from affected countries in West Africa are needed to better trace the origin, spread and evolution of A/H5N1 in Cameroon. RESEARCH HIGHLIGHTS HPAI A/H5N1 was detected in May 2016 in domestic chickens in Yaoundé-Cameroon. Twenty-one outbreaks in total were confirmed from May 2016 to March 2017. The causative H5N1 viruses fall within the genetic clade 2.3.2.1c. The viral gene constellation showed evidence of H5N1/H9N2 intra-clade reassortment.

A two dose immunization with an inactivated reassortant H5N2 virus protects chickens against lethal challenge with homologous 2.3.2.1 clade and heterologous 2.2 clade highly pathogenic avian influenza H5N1 viruses

The present study was aimed at generating a reassortant vaccine candidate virus with clade 2.3.2.1 Hemagglutinin (HA) and its evaluation in a challenge study for protection against homologous (2.3.2.1 clade) and heterologous (2.2 clade) highly pathogenic avian influenza (HPAI) H5N1 viruses. Plasmid-based reverse genetics technique was used to rescue a 5 + 3 reassortant H5N2 strain containing the modified HA of H5N1 (clade 2.3.2.1), the Neuraminidase (NA) of H9N2, the Matrix (M) of H5N1 and the internal genes of A/WSN/33 H1N1. In addition, another 6 + 2 reassortant virus containing modified HA from H5N1 (clade 2.3.2.1), the NA from H9N2 and the internal genes of A/WSN/33 H1N1 was also rescued. The 5 + 3 reassortant H5N2 virus could grow to a higher titer in both MDCK cells and chicken eggs compared to the 6 + 2 reassortant H5N2 virus. The vaccine containing the inactivated 5 + 3 reassortant H5N2 virus was used in a two-dose immunization regime which protected specific pathogen free (SPF) chickens against two repeated challenges with homologous 2.3.2.1 clade and heterologous 2.2 clade HPAI H5N1 viruses. The 5 + 3 reassortant H5N2 virus based on clade 2.3.2.1 generated in this study can be effective in protecting chickens in the case of an outbreak caused by antigenically different clade 2.2 HPAI H5N1 viruses and opens the way to explore its applicability as potential vaccine candidate especially in the Asian countries reporting these clades frequently. The study also indicates that sequential immunization can broaden protection level against antigenically diverse strains of H5N1 viruses.

Infectious dose-dependent accumulation of live highly pathogenic avian influenza H5N1 virus in chicken skeletal muscle-implications for public health

Highly pathogenic avian influenza viruses (HPAIV) of H5N1 subtype are a major global threat to poultry and public health. Export of poultry products, such as chicken and duck meat, is a known source for the cross-boundary spread of HPAI H5N1 viruses. Humans get infected with HPAI H5N1 viruses either by close contact with infected poultry or through consumption of fresh/undercooked poultry meat. Skeletal muscle is the largest soft tissue in chicken that has been shown to contain virus during systemic HPAIV infection and supports productive virus infection. However, the time between infection of a chicken with H5N1 virus and presence of virus in muscle tissue is not yet known. Further, it is also not clear whether chicken infected with low doses of H5N1 virus that cause non-fatal subclinical infections continue to accumulate virus in skeletal muscle. We investigated the amount and duration of virus detection in skeletal muscle of chicken experimentally infected with different doses (10² , 10³ and 10⁴ EID₅₀ ) of a HPAI H5N1 virus. Influenza viral antigen could be detected as early as 6 hr after infection and live virus was recovered from 48 hr after infection. Notably, chicken infected with lower levels of HPAI H5N1 virus (i.e., 10² EID₅₀ ) did not die acutely, but continued to accumulate high levels of H5N1 virus in skeletal muscle until 6 days post-infection. Our data suggest that there is a potential risk of human exposure to H5N1 virus through meat from clinically healthy chicken infected with a low dose of virus. Our results highlight the need to implement rigorous monitoring systems to screen poultry meat from H5N1 endemic countries to limit the global spread of H5N1 viruses.

Awareness and mitigation measures on highly pathogenic avian influenza in pastoral poultry flocks of North-central Nigeria: any challenging gap?

Village poultry closely interact with wild birds and other livestock in extensively managed poultry flocks, a practice common in pastoral communities of Nigeria. This practice provides sustained dissemination of avian viruses, such as highly pathogenic avian influenza (HPAI) H5N1 virus. The objectives of this study were to assess their knowledge/awareness, risks identification and biosecurity measures on HPAI H5N1 in pastoral poultry flocks. A questionnaire-based cross-sectional survey was conducted in systematically selected pastoral households of North-central Nigeria between May 2015 and June 2016. A total of 422 pastoralists participated in the study. Mean age of the respondents was 54.7 ± 11.4 SD years and 36.0% of them were in age group 50-59 years. The majority (81.3%) of respondents were of the Fulani tribe. Also, 64.9% of the respondents had no formal education and only 6.9% had tertiary education. About 30.8% of the nomadic and 81.0% of sedentary pastoralists significantly mentioned avian influenza to be a zoonotic disease. Very few nomadic (10.9%) and sedentary (26.1%) pastoralists significantly reported restriction of birds' movement to nearby water bodies as biosecurity measure. Only 7.6% of the nomadic and 16.1% of sedentary pastoralists practiced keeping of birds according to species. Sedentary pastoralists were more likely to have significant knowledge about HPAI H5N1 than the nomadic (OR: 1.76; 94% CI: 1.19-2.61). Female pastoralists were more likely to practice significant biosecurity measures against HPAI H5N1 than the males (OR: 1.99; 95% CI: 1.28-3.09). The majority of pastoralists neither possessed adequate knowledge about avian influenza nor applied adequate biosecurity measures against it, which are the most challenging gaps. Education of pastoralists on HPAI virus infection, specifically on information about clinical signs of avian influenza in birds, transmission dynamics among different species of birds, flyways of migrating wild birds and adequate mitigation measures are recommended.

Cell-cultured, live attenuated, X-31ca-based H5N1 pre-pandemic influenza vaccine

The manufacture of influenza vaccines has traditionally depended upon a method using embryonated hen's eggs. However, concerns regarding the potential shortage of the influenza substrate in the event of a pandemic has led to the development of cell culture-derived vaccines, which offers shorter lead-in times and greater production flexibility. We examined optimal conditions for the production of reassortant X-31ca-based H5N1 cold-adapted live attenuated influenza vaccine (rH5N1ca) cultured in mammalian cell lines. During ten passages in MDCK cells, the rH5N1ca vaccine maintained cold-adapted and temperature-sensitive phenotypes, and no mutations occurred in the hemagglutinin and neuraminidase surface antigens, demonstrating genetic and phenotypic stability. Single immunization in mice with the rH5N1ca induced robust antibody responses and protected the mice against lethal challenge. Stable maintenance of attenuation phenotypes and immunogenicity of the rH5N1ca from cell-culture suggest that they can be produced as a stockpile for pandemic preparedness as an alternative to current egg-based production.

H7N9 and H5N1 avian influenza suitability models for China: accounting for new poultry and live-poultry markets distribution data

In the last two decades, two important avian influenza viruses infecting humans emerged in China, the highly pathogenic avian influenza (HPAI) H5N1 virus in the late nineties, and the low pathogenic avian influenza (LPAI) H7N9 virus in 2013. China is home to the largest population of chickens (4.83 billion) and ducks (0.694 billion), representing, respectively 23.1 and 58.6% of the 2013 world stock, with a significant part of poultry sold through live-poultry markets potentially contributing to the spread of avian influenza viruses. Previous models have looked at factors associated with HPAI H5N1 in poultry and LPAI H7N9 in markets. However, these have not been studied and compared with a consistent set of predictor variables. Significant progress was recently made in the collection of poultry census and live-poultry market data, which are key potential factors in the distribution of both diseases. Here we compiled and reprocessed a new set of poultry census data and used these to analyse HPAI H5N1 and LPAI H7N9 distributions with boosted regression trees models. We found a limited impact of the improved poultry layers compared to models based on previous poultry census data, and a positive and previously unreported association between HPAI H5N1 outbreaks and the density of live-poultry markets. In addition, the models fitted for the HPAI H5N1 and LPAI H7N9 viruses predict a high risk of disease presence for the area around Shanghai and Hong Kong. The main difference in prediction between the two viruses concerned the suitability of HPAI H5N1 in north-China around the Yellow sea (outlined with Tianjin, Beijing, and Shenyang city) where LPAI H7N9 has not spread intensely.

An evaluation of biosecurity compliance levels and assessment of associated risk factors for highly pathogenic avian influenza H5N1 infection of live-bird-markets, Nigeria and Egypt

Live bird market (LBM) is integral component in the perpetuation of HPAI H5N1, while biosecurity is crucial and key to the prevention and control of infectious diseases. Biosecurity compliance level and risk factor assessments in 155LBMs was evaluated in Nigeria and Egypt through the administration of a 68-item biosecurity checklist, scored based on the modifications of previous qualitative data, and analysed for degree of compliance. LBMs were scored as "complied with a biosecurity item" if they had good-very good scores (4). All scores were coded and analysed using descriptive statistics and risk or protective factors were determined using univariable and multivariable logistic regression at p≤0.05. Trading of wild birds and other animal in the LBMs (Odd Ratio (OR)=34.90; p=0.01) and claims of hand disinfection after slaughter (OR=31.16; p=0.03) were significant risk factors while mandatory routine disinfection of markets (OR=0.13; p≤0.00), fencing and gates for live bird market (OR=0.02; p≤0.01) and hand washing after slaughter (OR=0.41; p≤0.05) were protective factors for and against the infection of Nigerian and Egyptian LBMs with the HPAI H5N1 virus. Almost all the LBMs complied poorly with most of the variables in the checklist (p≤0.05), but pathways to improved biosecurity in the LBMs existed. We concluded that the LBM operators play a critical role in the disruption of transmission of H5N1 virus infection through improved biosecurity and participatory epidemiology and multidisciplinary approach is needed.

Cross-protective efficacies of highly-pathogenic avian influenza H5N1 vaccines against a recent H5N8 virus

To investigate cross-protective vaccine efficacy of highly-pathogenic avian influenza H5N1 viruses against a recent HPAI H5N8 virus, we immunized C57BL/6 mice and ferrets with three alum-adjuvanted inactivated whole H5N1 vaccines developed through reverse-genetics (Rg): [Vietnam/1194/04xPR8 (clade 1), Korea/W149/06xPR8 (clade 2.2), and Korea/ES223N/03xPR8 (clade 2.5)]. Although relatively low cross-reactivities (10-40 HI titer) were observed against heterologous H5N8 virus, immunized animals were 100% protected from challenge with the 20 mLD50 of H5N8 virus, with the exception of mice vaccinated with 3.5μg of Rg Vietnam/1194/04xPR8. Of note, the Rg Korea/ES223N/03xPR8 vaccine provided not only effective protection, but also markedly inhibited viral replication in the lungs and nasal swabs of vaccine recipients within five days of HPAI H5N8 virus challenge. Further, we demonstrated that antibody-dependent cell-mediated cytotoxicity (ADCC) of an antibody-coated target cell by cytotoxic effector cells also plays a role in the heterologous protection of H5N1 vaccines against H5N8 challenge.

An Alternative Vaccination Approach for The Prevention of Highly Pathogenic Avian Influenza Subtype H5N1 in The Red River Delta, Vietnam -A Geospatial-Based Cost-Effectiveness Analysis

This study addresses the tradeoff between Vietnam's national poultry vaccination program, which implemented an annual two-round HPAI H5N1 vaccination program for the entire geographical area of the Red River Delta during the period from 2005-2010, and an alternative vaccination program which would involve vaccination for every production cycle at the recommended poultry age in high risk areas within the Delta. The ex ante analysis framework was applied to identify the location of areas with high probability of HPAI H5N1 occurrence for the alternative vaccination program by using boosted regression trees (BRT) models, followed by weighted overlay operations. Cost-effectiveness of the vaccination programs was then estimated to measure the tradeoff between the past national poultry vaccination program and the alternative vaccination program. Ex ante analysis showed that the focus areas for the alternative vaccination program included 1137 communes, corresponding to 50.6% of total communes in the Delta, and located primarily in the coastal areas to the east and south of Hanoi. The cost-effectiveness analysis suggested that the alternative vaccination program would have been more successful in reducing the rate of disease occurrence and the total cost of vaccinations, as compared to the national poultry vaccination program.

Development of Disease-specific, Context-specific Surveillance Models: Avian Influenza (H5N1)-Related Risks and Behaviours in African Countries

Avian influenza virus (H5N1) is a rapidly disseminating infection that affects poultry and, potentially, humans. Because the avian virus has already adapted to several mammalian species, decreasing the rate of avian-mammalian contacts is critical to diminish the chances of a total adaptation of H5N1 to humans. To prevent the pandemic such adaptation could facilitate, a biology-specific disease surveillance model is needed, which should also consider geographical and socio-cultural factors. Here, we conceptualized a surveillance model meant to capture H5N1-related biological and cultural aspects, which included food processing, trade and cooking-related practices, as well as incentives (or disincentives) for desirable behaviours. This proof of concept was tested with data collected from 378 Egyptian and Nigerian sites (local [backyard] producers/live bird markets/village abattoirs/commercial abattoirs and veterinary agencies). Findings revealed numerous opportunities for pathogens to disseminate, as well as lack of incentives to adopt preventive measures, and factors that promoted epidemic dissemination. Supporting such observations, the estimated risk for H5N1-related human mortality was higher than previously reported. The need for multidimensional disease surveillance models, which may detect risks at higher levels than models that only measure one factor or outcome, was supported. To develop efficient surveillance systems, interactions should be captured, which include but exceed biological factors. This low-cost and easily implementable model, if conducted over time, may identify focal instances where tailored policies may diminish both endemicity and the total adaptation of H5N1 to the human species.

Avian influenza H5N1 viral and bird migration networks in Asia

The spatial spread of the highly pathogenic avian influenza virus H5N1 and its long-term persistence in Asia have resulted in avian influenza panzootics and enormous economic losses in the poultry sector. However, an understanding of the regional long-distance transmission and seasonal patterns of the virus is still lacking. In this study, we present a phylogeographic approach to reconstruct the viral migration network. We show that within each wild fowl migratory flyway, the timing of H5N1 outbreaks and viral migrations are closely associated, but little viral transmission was observed between the flyways. The bird migration network is shown to better reflect the observed viral gene sequence data than other networks and contributes to seasonal H5N1 epidemics in local regions and its large-scale transmission along flyways. These findings have potentially far-reaching consequences, improving our understanding of how bird migration drives the periodic reemergence of H5N1 in Asia.

Tracking the Evolution in Phylogeny, Structure and Function of H5N1 Influenza Virus PA Gene

Highly pathogenic avian influenza (HPAI) H5N1 viruses have severely affected the poultry industry of Vietnam and Indonesia. The outbreaks of HPAI H5N1 viruses continue to pose a serious threat to public health, which have profound impacts on public health. In this study, we presented phylogenetic evidences for five reassortants among HPAI H5N1 viruses sampled from Vietnam and Indonesia during 2003-2013 and found that reassortment events occurred more frequently in the three gene segments (PB1, PA and HA) than in the remaining five gene segments (PB2, NA, NP, NS and MP). The sequence-based analyses have revealed that the PA protein displays high levels of DNA sequence polymorphism and variability than other internal proteins. Seven positive selection sites were detected in PA proteins, which ranked second only to the surface glycoproteins. Structure-based comparative analysis of PA proteins showed a remarkable sequence conservation between the high-pathogenic, low-pathogenic and reassortant viruses, indicating that PA appears to be a potential antiviral target. Furthermore, by analysing the published data, we compared the differential expression of genes involved in RIG-I- and MAVS-mediated intracellular type I interferon (IFN)-inducing pathway between the VN3028IIcl2-infected, IDN3006-infected and IDN3006/PA-infected groups. Our analyses indicated that the inhibitory effect of the PA protein on MAVS was not strong. In addition, transcriptional levels of 33 mitochondrial proteins involved in the induction of apoptosis have significantly increased, suggesting that PA may play an important role in apoptosis signalling pathway.

Evolutionary and Ecological Dynamics of Transboundary Disease Caused by H5N1 Virus in Southeast Asia

Southeast Asia has been the breeding ground for many emerging diseases in the past decade, and it is in this region that new genetic variants of HPAI H5N1 viruses have been emerging. Cross-border movement of animals accelerates the spread of H5N1, and the changing environmental conditions also exert strong selective pressure on the viruses. The transboundary zoonotic diseases caused by H5N1 pose a serious and continual threat to global economy and public health. Here, we divided the H5N1 viruses isolated in Southeast Asia during 2003-2009 into four groups according to their phylogenetic relationships among HA gene sequences. Molecular evolution analysis suggests populations in expansion rather than a positive selection for group 2 and group 3, yet group 4 is under strong positive selection. Site 193 was found to be a potential glycosylation site and located in receptor-binding domain. Note that site 193 tends to appear in avian isolates instead of human strains. Population dynamics analysis reveals that the effective population size of infections in Southeast Asia has undergone three obvious increases, and the results are consistent with the epidemiological analysis. Ecological and phylogeographical analyses show that agro-ecological environments, migratory birds, domestic waterfowl, especially free-ranging ducks, are crucial in the occurrence, maintenance and spread of H5N1 virus. The epidemiological links between Indonesia and Suphanburi observed suggest that viruses in Indonesia were originated from multiple introductions.