Pathogenic Avian Influenza Subtype H5N1 Research Articles

Highly Pathogenic Avian Influenza Virus (H5N1) Clade 2.3.4.4b Introduced by Wild Birds, China, 2021.

Highly pathogenic avian influenza (HPAI) subtype H5N1 clade 2.3.4.4b virus has spread globally, causing unprecedented large-scale avian influenza outbreaks since 2020. In 2021, we isolated 17 highly pathogenic avian influenza H5N1 viruses from wild birds in China. To determine virus origin, we genetically analyzed 1,529 clade 2.3.4.4b H5N1 viruses reported globally since October 2020 and found that they formed 35 genotypes. The 17 viruses belonged to genotypes G07, which originated from eastern Asia, and G10, which originated from Russia. The viruses were moderately pathogenic in mice but were highly lethal in ducks. The viruses were in the same antigenic cluster as the current vaccine strain (H5-Re14) used in China. In chickens, the H5/H7 trivalent vaccine provided complete protection against clade 2.3.4.4b H5N1 virus challenge. Our data indicate that vaccination is an effective strategy for preventing and controlling the globally prevalent clade 2.3.4.4b H5N1 virus.

The health of influenza surveillance and pandemic preparedness in the wake of the COVID-19 pandemic.

The COVID-19 pandemic is the first to have emerged when Next Generation Sequencing was readily available and it has played the major role in following evolution of the causative agent, Severe Acute Respiratory Syndrome Coronavirus 2. Response to the pandemic was greatly facilitated though use of existing influenza surveillance networks: World Health Organization (WHO) Global Influenza Surveillance and Response System (GISRS), focussing largely on human influenza, and the OFFLU network of expertise on avian influenza established by the Food and Agricultural Organization of the United Nations (FAO) and the World Organization for Animal Health (WOAH). Data collection/deposition platforms associated with these networks, notably WHO's FluNet and the Global Initiative on Sharing All Influenza Data (GISAID) were/are being used intensely. Measures introduced to combat COVID-19 resulted in greatly decreased circulation of human seasonal influenza viruses for approximately 2 years, but circulation continued in the animal sector with an upsurge in the spread of highly pathogenic avian influenza subtype H5N1 with large numbers of wild bird deaths, culling of many poultry flocks and sporadic spill over into mammalian species, including humans, thereby increasing pandemic risk potential. While there are proposals/implementations to extend use of GISRS and GISAID to other infectious disease agents (e.g. Respiratory Syncytial Virus and Monkeypox), there is need to ensure that influenza surveillance is maintained and improved in both human and animal sectors in a sustainable manner to be truly prepared (early detection) for the next influenza pandemic.

Pathogenicity and pathogenesis of a recent highly pathogenic avian influenza subtype H5N8 in mule ducklings in Egypt.

In late 2017, an H5N8 highly pathogenic avian influenza (HPAI) virus, clade 2.3.4.4, was isolated from domestic ducks in Egypt, which was associated with high morbidity and low mortality. The pathogenicity increased due to the continuous circulation of virus in ducks. Thus, this study aimed to monitor the pathogenesis and pathogenicity of new H5N8 Avian influenza (AI) virus in mule ducklings. The lethal dose 50 (LD50) for this new local HPAI H5N8 isolate was calculated. Twenty ducklings were inoculated with 0.1 mL of dilution containing 10 LD50 HPAI per duck. The clinical signs and mortalities were recorded until 30 days post-infection (DPI) to confirm viral pathogenesis. Reverse transcription polymerase chain reaction was used to detect viral shedding from collected cloacal swabs after 3rd, 5th, 7th, 10th, 14th, 21st, and 30th DPI. The main histopathological lesions associated with the presence of HPAI virus were also recorded on the 3rd and 14th DPI. The result showed that the LD50 of the new HPAI H5N8 was 104 log10. Clinical signs were observed after 2nd DPI, but it was clinically severe on 3rd, 4th, and 5th DPI in the form of respiratory and gastric disorders, forming 90% of all diseased ducklings, whereas 30% of the infected ducks only showed nervous signs. The mortality rate peaked on 4th and 5th DPI with a cumulative mortality rate of 60% for the inoculated ducks, whereas no mortality was recorded after 6th DPI. Dead ducks showed typical postmortem lesions of AI disease. Necrosis and ecchymotic or petechial hemorrhages on the heart, pancreas, liver, and spleen were observed, whereas the lung showed pneumonia. With regard to viral shedding, infected ducklings shed the virus from its gut until 7th DPI, but the number of duck shedders gradually decreased until 14th DPI after viral shedding. The histopathological findings indicated that the spleen and thymus showed necrosis and hemorrhages, whereas the brain showed multifocal malacic foci and spread meningitis. Moreover, the lung had intrabronchial hyaline degeneration and fibrinous pneumonia on 3rd DPI. Furthermore, the liver showed multifocal necrotic foci and subcapsular hemorrhage, whereas the kidney showed remarkable tubular degeneration, mostly within the collecting tubules. Furthermore, the heart showed marked myocardiolysis of the cardiac muscle fibers. On 14th DPI, all histopathological lesions of the examined organs were restored to normal. The currently circulating HPAI H5N8 virus strain has high virulence, particularly for imported mule ducks that originated from non-vaccinated breeder ducks. Therefore, vaccination and quarantine measures must be applied on imported 1-day-old mule ducklings. Moreover, the pathogenesis must be reviewed and monitored for updating circulating AI strains caused by the continuous and rapid evolution of AI viruses.

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

BackgroundIn 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.ResultsThe 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.ConclusionOur 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

Interpolation of Point Prevalence Rate of the Highly Pathogenic Avian Influenza Subtype H5N8 Second Phase Epidemic in South Korea.

Humans and animals are both susceptible to highly pathogenic avian influenza (HPAI) viruses. In the future, HPAI has the potential to be a source of zoonoses and pandemic disease drivers. It is necessary to identify areas of high risk that are more vulnerable to HPAI infections. In this study, we applied unbiased predictions based on known information to find points of localities with a high probability of point prevalence rate. To carry out such predictions, we utilized the inverse distance weighting (IDW) and kriging method, with the help of the R statistical computing program. The provinces of Jeollanam-do, Gyeonggi-do, Chungcheongbuk-do and Ulsan have high anticipated risk. This research might aid in the management of avian influenza threats associated with various potential risks.

Re-current Epizootics of Highly Pathogenic Avian Influenza in Nigeria: Status of Vaccination as Alternate control

Epizootic of Highly Pathogenic Avian Influenza subtype H5N1 in Nigeria was successfully contained during the first wave that lasted from 2006 to 2008 without the use of vaccine. Re-current and more severe outbreak was witnessed in 2015 and there are suspicions that some farmers may have resorted to vaccination to prevent infections in their flocks. We investigate evidence of vaccination in farms and the status of vaccination as alternate control for HPAI in Nigeria. The study was carried out in a cross section of 24 commercial poultry farms in four States in South West and North Central Nigeria. Five hundred and one sera collected randomly were screened by agar gel immunodiffusion (AGID) assay for antibody to group specific influenza A nucleoprotein. One hundred and eight sera obtained from five H5N1 infected poultry farms were also concurrently screened. Reactive sera were further analysed by Hemagglutinin Inhibition (HI) test against H5 antigen using 1% suspension of pooled washed chicken red blood cells. Only 8 out of 501 sera (1.6%) had evidence of influenza A antibody. All of the 8 samples were from one farm with 20 samples collected representing 40% seroconversion at farm level. Three out of those sera were positive for H5 at HI titer of 3log2. All other sera including those obtained from HPAI infected farms were negative for influenza antibody. This study confirms limited antibody response to avian influenza subtype H5 most likely due to vaccination in one commercial flock. Vaccination against avian influenza by farmers desperate to protect their investments may lead to unregulated and suboptimal application of vaccines requiring farmers’ and stakeholders’ engagement to forestall negative impact.
 Keywords: Avian influenza; Control measures; Recurrent outbreaks; Vaccination status.

SEROPREVALENSI PENYAKIT AVIAN INFLUENZA SUBTIPE H5N1 PADA AYAM BURAS DI PASAR BERINGKIT DAN GALIRAN, BALI

Avian Influenza (AI) is a strategic communicable and zoonotic disease. The cause is a virus with Highly Pathogenic Avian Influenza (HPAI) subtype H5N1. The poultry market has important roles in the preservation, propagation, and spreads of the Avian Influenza (AI) virus from poultry to other species and humans. The purpose of this study was to determine the level of seroprevalence of Avian Influenza (H5N1) in free-range chickens at the Beringkit and Galiran market. A total of 120 free-range chickens were used as a sample. They have taken 60 serum samples per market. Serum removal is made from 5 merchants under the provisions of 3 samples from merchants who sell 6 to 10 free-range chickens. The sampling period is carried out for 2 months every 2 weeks 4 times. Sample testing was performed at the Denpasar Veterinary Centre with Haemagglutination (HA) and Haemagglutination Inhibition (HI) as barriers. The data titer of the antibodies obtained was analyzed by Non-Parametric Statistic Test Chi-Square (χ2) using IBM SPSS for windows. The results of the study showed that the AI subtype of the H5N1 subtype in both Beringkit Markets is 3.3% and Galiran Market is 6.7%, with seroprevalence in the two markets of 5.0% which is statistically not dissimilar (P<0.05). To prevent the transmissions of AI disease at the Beringkit Market and Galiran is recommended for vaccination and more attention to the market management and the free-range chicken maintenance system.

Outbreak of highly pathogenic avian influenza subtype H5N8 in two multi-age chicken farms in Jos, Plateau State, Nigeria

An outbreak of highly pathogenic avian influenza (HPAI) subtype H5N8 in two multi-age chicken flocks in Jos, Plateau State, Nigeria, is described. Diagnosis was made using tissue samples from the affected farms that were submitted to the Regional Lab for Animal Influenza and other Transboundary Animal Diseases, National Veterinary Research Institute, Vom. Pullets with broilers of 9 and 4 weeks of age respectively, from farm A (fA) and broilers, 4 weeks of age from farm B (fB) were submitted from flocks experiencing a drastic increase in mortality. The February 2019 outbreak resulted in10 – 60 % and 60 % mortality on fA and fB respectively. Clinical signs included anorexia, depression, hock sitting and sudden onset of increasing mortality. Gross lesions included edema of the head with cyanosis of comb and wattle; swollen abdomen due to ascites; generalized congestion of visceral organs with frank blood in the abdomen; congested mesenteric vessels with haemorrhages in the mucosa of small and large intestines; congested and frothy lungs with severe hemorrhagic tracheitis among others. In view of the clinical and gross pathology, HPAI was considered as the tentative diagnosis. Diagnosis of HPAI subtype H5N8 was confirmed by reverse transcriptase polymerase chain reaction and viral isolation in embryonated chicken eggs. The current outbreak has shown the presence of HPAI H5N8 in the country different from the H5N1 subtype that was introduced since 2006 in Nigeria. The co-circulation of these two subtypes if the current wave of infection is left unchecked will have adverse effects on poultry production, international trade and human health. Hence, the need for the re-evaluation and strengthening of the Government control policy to save the poultry industry from perennial economic loses.Keywords: Broilers, Highly pathogenic avian influenza (HPAI H5N8), Jos, Nigeria, Outbreaks, Pullets

Spatio-Temporal Analysis of Highly Pathogenic Avian Influenza outbreaks in Ghana.

ObjectiveThe purpose of the study was to characterize the spatial distribution and temporal patterns of laboratory confirmed H5N1 outbreaks from January 2007 to December 2017 in Ghana.IntroductionHighly pathogenic avian influenza (HPAI) subtype H5N1 virus causes a highly contagious disease in poultry with up to 100% mortality and occasionally causes sporadic human infection. The first outbreak of HPAI H5N1 in Africa was reported in Nigeria in 2006 and has since been reported in seven other African countries with confirmed human cases and outbreaks in poultry. Since the emergence of Highly Pathogenic Avian Influenza (HPAI), virus subtype H5N1 in Ghana in 2007, outbreaks in poultry have led to dire economic consequences for the poultry sector, resulting from mass destruction of affected flocks. An economy heavily dependent on agriculture, the persistence of outbreaks threaten the livelihood of farmers who depend on poultry production for survival.Despite significant efforts made in HPAI-H5N1 control and prevention in Ghana, outbreaks persist and continue to spread to new areas. It is uncertain to what extent different pathways contribute to the introduction and the dissemination of the virus in Ghana. There is a need to understand the complex nature of the interactions between local and migratory fowl, the risk of transmission due to human endeavor and trade mechanisms that increase the likelihood of HPAI-H5N1 outbreaks in Ghana.MethodsData for the study was sourced from national outbreak records at the Veterinary Services Directorate.The study analyzed outbreak data for the years 2007-2017. Data retrieved from outbreak reports included the date of onset of outbreak, location and geographic coordinates, type and number of poultry species affected, natural deaths of birds and type of farming system on outbreak farms. We calculated frequency distributions for the types of poultry species affected, the type of farming system and mortality rates on affected premises.We described the distribution of HPAI-H5N1 outbreaks using coordinate maps in ArcGIS and displayed relevant sites of waterfowl and wild bird habitation. To describe the temporal pattern of HPAI-H5N1 outbreaks in Ghana for the period, we created an epidemic curve by plotting the monthly number of outbreaks for the period January 2007 to December 2017 in Excel. We used space-time scan statistics to determine significant local clusters.ResultsA total of sixty-six (66) outbreaks of HPAI-H5N1 occurred in Ghana from January 2007 to December 2017. The outbreak sites were distributed in seven (7) out of ten (10) regions in Ghana. The affected regions are located in the southern and middle belt of Ghana. Most of the outbreaks (74.2%) occurred in densely populated areas of the Greater Accra region. Overall, layer flocks were mostly affected with 56% of affected premises constituting layer farms. Commercial farms and backyard farms made up the majority of affected farms (50% and 42.4%). Free ranging birds were the least affected farm type (7.6%). Two epidemic waves were identified for H5N1 in Ghana; the first wave with 6 outbreaks, lasted a period of four (4) months from April to July 2007, and the second with 60 outbreaks, spanned a period of 2 years from April 2015 to November 2016. Temporal distribution of the outbreaks showed that the outbreak peaked in May 2007 for the first wave and in July 2017 for the second wave with minor peaks observed in April and July 2016. The decrease in the number of the outbreaks after July in both waves is attributed to the onset of slaughter and trade restrictions for poultry in affected areas. Space-time scan statistics identified significant primary clusters of H5N1 outbreaks in the coastal belt of the Greater Accra region, characterized by major commercial activities and the presence of wetlands of relevance to wild birds and migratory waterfowl.ConclusionsTwo (2) major waves of H5N1 outbreaks occurred in Ghana between 2007 and 2017. The distribution of outbreaks and poultry species in both waves, show that the epidemiology of H5N1 virus in Ghana is changing. The findings highlight the importance of reviewing existing control and preventive measures as well as strengthening avian influenza surveillance in proposed high- risk areas.ReferencesForeign Animal Diseases. Revised 2008 Seventh Edition. Committee on foreign and emerging diseases of the United States Animal Health Association.Avian Influenza, OIE terrestrial manual 2015To K.K.W.et al. Avian influenza A H5N1 virus: a continuous threat to humans. Emerging Microbes Infections (2012) 1, e25.Watanabe Y. et al. The changing nature of avian influenza A virus (H5N1). Trends Microbiol. 2012 Jan; 20 (1):11-20. doi: 10.1016/j.tim.2011.10.003. Epub 2011 Dec 5

Migratory waterfowls from Europe as potential source of highly pathogenic avian influenza infection to Nigeria poultry

Highly pathogenic avian influenza H5N1 was detected for the first time in Nigeria and Africa in 2006. The source of the outbreak was not immediately clear, but scientific opinions favoured multiple introductions. The need to evaluate available epidemiological and virological data to demonstrate most probable source of introduction is important for focused control efforts. In this study, we described ten years (2006-2016) scientific observations available through ecology, epidemio-surveillance and molecular virology of avian influenza in Nigeria. Nigeria is geographically located in the tropical humid region with abundant wetlands presenting ideal ambience for birdlife. Ornithological evidence also showed that the country lies in the path of two major migratory flyways from Europe and Asia providing opportunities for co-mingling of different species and age of wild birds with resident birds. Genomic characterization including phylogenetic analysis revealed a high degree of homology among virus strains isolated in Nigeria and those detected in migratory birds from Europe suggesting common source epidemic. This study agreed with postulation that migratory wild birds from Europe may be responsible for the introduction of highly pathogenic avian influenza subtype H5N1 to Nigeria. Feral waterfowls around water bodies thereafter bridge transmission to domestic poultry holdings whereas local trade and movement of poultry and poultry products may further spread infection locally. In the light of this understanding, routine risk based sentinel surveillance for avian influenza in domestic waterfowls in ecological hotspots is recommended for early detection and response thereby saving economic losses and mitigating public health emergencies. Keywords: Avian influenza, Migratory waterfowls, Nigeria, Poultry

Dynamics of the 2004 avian influenza H5N1 outbreak in Thailand: The role of duck farming, sequential model fitting and control

The Highly Pathogenic Avian Influenza (HPAI) subtype H5N1 virus persists in many countries and has been circulating in poultry, wild birds. In addition, the virus has emerged in other species and frequent zoonotic spillover events indicate that there remains a significant risk to human health. It is crucial to understand the dynamics of the disease in the poultry industry to develop a more comprehensive knowledge of the risks of transmission and to establish a better distribution of resources when implementing control. In this paper, we develop a set of mathematical models that simulate the spread of HPAI H5N1 in the poultry industry in Thailand, utilising data from the 2004 epidemic. The model that incorporates the intensity of duck farming when assessing transmision risk provides the best fit to the spatiotemporal characteristics of the observed outbreak, implying that intensive duck farming drives transmission of HPAI in Thailand. We also extend our models using a sequential model fitting approach to explore the ability of the models to be used in “real time” during novel disease outbreaks. We conclude that, whilst predictions of epidemic size are estimated poorly in the early stages of disease outbreaks, the model can infer the preferred control policy that should be deployed to minimise the impact of the disease.

Morphological Differences of Pancreatic Lesions in Mute Swans and Hens Naturally Infected with Highly Pathogenic Avian Influenza Virus H5N8

Abstract During the epizootic of highly pathogenic avian influenza subtype H5N8 in Serbia in the winter of 2016-2017, the highest percent of mortality due to this infection was recorded in mute swans (Cygnus olor). Besides mute swans, avian influenza virus subtype H5N8 was also diagnosed in a small number of hens in rural households. Pancreatic tissues from avian influenza H5N8 positive mute swans and hens that died during this outbreak were collected to determine the character of morphological lesions and the distribution of the viral antigen in this organ. Macroscopic examination of the pancreas of mute swans revealed hemorrhages as well as necrosis, while there were no macroscopic visible lesions in the pancreas of infected hens. Despite the different macroscopic finding, microscopic examination of the pancreas of both infected bird species revealed lesions in the form of acute pancreatitis and multifocal acinar necrosis. The viral antigen was abundantly expressed in the cytoplasm and nucleus of necrotic cells, as well as in macrophages in both examined bird species. Immunohistochemical expression of the viral antigen in the pancreas was strongly consistent with histological lesions. According to the above described findings, it could be concluded that highly pathogenic avian influenza virus H5N8 has a high affinity to pancreatic tissue in both mute swans and hens and the distribution and the character of the lesions in the pancreas are similar in both bird species.

Risk factors associated with highly pathogenic avian influenza subtype H5N8 outbreaks on broiler duck farms in South Korea.

Highly Pathogenic Avian Influenza (HPAI) subtype H5N8 outbreaks occurred in poultry farms in South Korea in 2014 resulting in significant damage to the poultry industry. Between 2014 and 2016, the pandemic disease caused significant economic loss and social disruption. To evaluate the risk factors for HPAI infection in broiler duck farms, we conducted a retrospective case-control study on broiler duck farms. Forty-three farms with confirmed laboratories on premises were selected as the case group, and 43 HPAI-negative farms were designated as the control group. Control farms were matched based on farm location and were within a 3-km radius from the case premises. Spatial and environmental factors were characterized by site visit and plotted through a geographic information system (GIS). Univariable and multivariable logistic regression models were developed to assess possible risk factors associated with HPAI broiler duck farm infection. Four final variables were identified as risk factors in a final multivariable logistic model: "Farms with ≥7 flocks" (odds ratio [OR]=6.99, 95% confidence interval [CI] 1.34-37.04), "Farm owner with ≥15years of raising poultry career" (OR=7.91, 95% CI 1.69-37.14), "Presence of any poultry farms located within 500m of the farm" (OR=6.30, 95% CI 1.08-36.93) and "Not using a faecal removal service" (OR=27.78, 95% CI 3.89-198.80). This highlights that the HPAI H5N8 outbreaks in South Korea were associated with farm owner education, number of flocks and facilities and farm biosecurity. Awareness of these factors may help to reduce the spread of HPAI H5N8 across broiler duck farms in Korea during epidemics. Greater understanding of the risk factors for H5N8 may improve farm vulnerability to HPAI and other subtypes and help to establish policies to prevent re-occurrence. These findings are relevant to global prevention recommendations and intervention protocols.

In Vitro Antiviral Activity of Commercial Products of Herbal Extracts Against Highly Pathogenic Avian Influenza (H5N1) Virus

Three commercial products of herbal extracts (Amphiflu-Ex®, Fyto-immune Plus® and Viu-Vet®) were tested for antiviral activity against two Egyptian highly pathogenic avian influenza subtype H5N1 isolates (isolated form backyard poultry) and upon sequencing and phylogenetic analysis, they belonged to clade 2.2.1.2., This antiviral assay for the products done by using chicken embryo fibroblast (CEF) cell culture through cytopathic effect (CPE) inhibition assay in two different layouts to elucidate post-exposure and pre-exposure antiviral activity of the products. The Amphiflu-Ex® at conc. 50 µl/ml showed significant virucidal activity (100% inhibition) in post-exposure assay for both viral isolates which was further confirmed by quantitative real time RT-PCR method showed 100% reduction in virus titers for both isolates and further investigation done on The Amphiflu-Ex® on conc. 20 µl/ml, the virus titers were decreased by 2.72-2.8 logs (Log 10 virus titers) and on conc 10 µl/ml, the virus titers were decreased by 1-1.27 logs for both isolates, The maximum non-toxic concentration (MNTC) for the three products estimated by cytotoxicity assay was 50 µl/ml and TCID50 used for both isolates were 106 copy/100 µl.

Estimating the between-farm transmission rates for highly pathogenic avian influenza subtype H5N1 epidemics in Bangladesh between 2007 and 2013.

Highly Pathogenic Avian Influenza (HPAI) is classified by the World Organization for Animal Health as one of the notifiable diseases. Its occurrence is associated with severe socio-economic impacts and is also zoonotic. Bangladesh HPAI epidemic data for the period between 2007 and 2013 were obtained and split into epidemic waves based on the time lag between outbreaks. By assuming the number of newly infected farms to be binomially distributed, we fit a Generalized Linear Model to the data to estimate between-farm transmission rates (β). These parameters are then used together with the calculated infectious periods to estimate the respective basic reproduction numbers (R0 ). The change in β and R0 with time during the course of each epidemic wave was explored. Finally, sensitivity analyses of the effects of reducing the delay in detecting infection on a farm as well as extended infectiousness of a farm beyond the day of culling were assessed. The point estimates obtained for β ranged from 0.08 (95% CI: 0.06-0.10) to 0.11 (95% CI: 0.08-0.20) per infectious farm per day while R0 ranged from 0.85 (95% CI: 0.77-1.02) to 0.96 (95% CI: 0.72-1.20). Sensitivity analyses reveal that the estimates are quite robust to changes in the assumptions about the day in reporting infection and extended infectiousness. In the analysis allowing for time-varying transmission parameters, the rising and declining phases observed in the epidemic data were synchronized with the moments when R0 was greater and less than one, respectively. From an epidemiological perspective, the consistency of these estimates and their magnitude (R0 ≈1) indicate that the effectiveness of the deployed control measures was largely invariant between epidemic waves and the trend of the time-varying R0 supports the hypothesis of sustained farm-to-farm transmission that is possibly initiated by a few unique introductions.

Southward autumn migration of waterfowl facilitates cross-continental transmission of the highly pathogenic avian influenza H5N1 virus.

The highly pathogenic avian influenza subtype H5N1 (HPAI H5N1) is a worldwide zoonotic infectious disease, threatening humans, poultry and wild birds. The role of wild birds in the spread of HPAI H5N1 has previously been investigated by comparing disease spread patterns with bird migration routes. However, the different roles that the southward autumn and northward spring migration might play in virus transmission have hardly been explored. Using direction analysis, we analyze HPAI H5N1 transmission directions and angular concentration of currently circulating viral clades, and compare these with waterfowl seasonal migration directions along major waterfowl flyways. Out of 22 HPAI H5N1 transmission directions, 18 had both a southward direction and a relatively high concentration. Differences between disease transmission and waterfowl migration directions were significantly smaller for autumn than for spring migration. The four northward transmission directions were found along Asian flyways, where the initial epicenter of the virus was located. We suggest waterfowl first picked up the virus from East Asia, then brought it to the north via spring migration, and then spread it to other parts of world mainly by autumn migration. We emphasize waterfowl autumn migration plays a relatively important role in HPAI H5N1 transmission compared to spring migration.

Turnover of Village Chickens Undermines Vaccine Coverage to Control HPAI H5N1.

Highly pathogenic avian influenza (HPAI) subtype H5N1 remains an enzootic disease of village chickens in Indonesia, posing ongoing risk at the animal-human interface. Previous modelling showed that the fast natural turnover of chicken populations might undermine herd immunity after vaccination, although actual details of how this effect applies to Indonesia's village chicken population have not been determined. We explored the turnover effect in Indonesia's scavenging and mixed populations of village chickens using an extended Leslie matrix model parameterized with data collected from village chicken flocks in Java region, Indonesia. Population dynamics were simulated for 208weeks; the turnover effect was simulated for 16weeks after vaccination in two 'best case' scenarios, where the whole population (scenario 1), or birds aged over 14days (scenario 2), were vaccinated. We found that the scavenging and mixed populations have different productive traits. When steady-state dynamics are reached, both populations are dominated by females (54.5%), and 'growers' and 'chicks' represent the most abundant age stages with 39% and 38% in the scavenging, and 60% and 25% in the mixed population, respectively. Simulations showed that the population turnover might reduce the herd immunity below the critical threshold that prevents the re-emergence of HPAI H5N1 4-8weeks (scavenging) and 6-9weeks (mixed population) after vaccination in scenario 1, and 2-6weeks (scavenging) and 4-7weeks (mixed population) after vaccination in scenario 2. In conclusion, we found that Indonesia's village chicken population does not have a unique underlying population dynamic and therefore, different turnover effects on herd immunity may be expected after vaccination; nonetheless, our simulations carried out in best case scenarios highlight the limitations of current vaccine technologies to control HPAI H5N1. This suggests that the improvements and complementary strategies are necessary and must be explored.

The Landscape Epidemiology of Seasonal Clustering of Highly Pathogenic Avian Influenza (H5N1) in Domestic Poultry in Africa, Europe and Asia.

Highly pathogenic avian influenza subtype H5N1 (H5N1) has contributed to substantial economic loss for backyard and large-scale poultry farmers each year since 1997. While the distribution of domestic H5N1 outbreaks across Africa, Europe and Asia is extensive, those features of the landscape conferring greatest risk remain uncertain. Furthermore, the extent to which influential landscape features may vary by season has been inadequately described. The current investigation used World Organization for Animal Health surveillance data to (i) delineate areas at greatest risk of H5N1 epizootics among domestic poultry, (ii) identify those abiotic and biotic features of the landscape associated with outbreak risk and (iii) examine patterns of epizootic clustering by season. Inhomogeneous point process models were used to predict the intensity of H5N1 outbreaks and describe the spatial dependencies between them. During October through March, decreasing precipitation, increasing isothermality and the presence of H5N1 in wild birds were significantly associated with the increased risk of domestic H5N1 epizootics. Conversely, increasing precipitation and decreasing isothermality were associated with the increased risk during April through September. Increasing temperature during the coldest quarter, domestic poultry density and proximity to surface water were associated with the increased risk of domestic outbreaks throughout the year. Spatial dependencies between outbreaks appeared to vary seasonally, with substantial clustering at small and large scales identified during October through March even after accounting for inhomogeneity due to landscape factors. In contrast, during April to September, H5N1 outbreaks exhibited no clustering at small scale once accounting for landscape factors. This investigation has identified seasonal differences in risk and clustering patterns of H5N1 outbreaks in domestic poultry and may suggest strategies in high-risk areas with features amenable to intervention such as controlling domestic bird movement in areas of high poultry density or preventing contact between poultry and wild birds and/or surface water features.

Widespread of H5N1 infections in apparently healthy backyard poultry.

Highly pathogenic avian influenza subtype H5N1 represents a threat to the poultry industry and human health worldwide. Inapparently infected birds are suspected to play an essential role in the spread of avian influenza virus. In the current study, a total of 25,646 samples (16,185 chicken, 4696 ducks, 1633 geese and 3132 turkeys) from apparently healthy birds were screened for the presence of positive samples for H5N1 during 2009-2014. The samples were examined by reverse transcriptase real-time polymerase chain reaction (rRT-PCR) for M, H5 and N1 genes of avian influenza viruses. The results revealed that the HPAI H5N1 existed in an inapparent manner in ducks (4.68%), geese (4.10%), chickens (2.48%) and turkeys (2.29%). The current finding highlights the serious impact of such type on birds in the epidemiology of H5N1 in birds, animals and humans. It also highlights the existence of another reason other than vaccination that contributes to the widespread of inapparent infection of H5N1 in Egypt.

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.