An outbreak of HPAIV H5N1 in Nakhon Sawan province, Thailand, in 2004 caused sporadic deaths of Asian openbill storks ( Anastomus oscitans). An investigation was undertaken to determine if this virus occurs and circulates in wild birds in Nakhon Sawan province. Following the outbreak, a widespread serosurvey was conducted using the hemagglutination inhibition assay and microneutralization assay to detect antibodies against AIV H5. From 2007 to 2014, blood was collected from a total of 753 wild birds, representing 10 orders and 44 species. The results reveal that 10 serum samples were positive for AIV H5 antibodies. These seropositive results, found in the orders Ciconiiformes and Anseriformes, demonstrate that waterfowl serve as a reservoir host of AIV. Moreover, the seroprevalences in streak-eared bulbul showed habitat sharing with waterfowl or duck.

Haemagglutinin (HA) and neuraminidase (NA) are two vital surface glycoproteins of influenza virus. The HA of H5N6 highly pathogenic avian influenza virus is divided into Major/H5 and Minor/H5, and its NA consists of short stalk NA and full-length stalk NA. The strain combined with Major/H5 and short stalk NA account for 76.8% of all strains, and the proportion was 23.0% matched by Minor/H5 and full-length stalk NA. Our objective was to investigate the influence of HA-NA matching on the biological characteristics and the effects of the epidemic trend of H5N6 on mice and chickens. Four different strains combined with two HAs and two NAs of the represented H5N6 viruses with the fixed six internal segments were rescued and analyzed. Plaque formation, NA activity of infectious particles, and virus growth curve assays, as well as a saliva acid receptor experiment, with mice and chickens were performed. We found that all the strains can replicate well on Madin-Darby canine kidney (MDCK) cells and chicken embryo fibroblasts (CEF) cells, simultaneously, mice and infection group chickens were complete lethal. However, the strain combined with Major/H5 and short stalk N6 formed smaller plaque on MDCK, showed a moderate replication ability in both MDCK and CEF, and exhibited a higher survival rate among the contact group of chickens. Conversely, strains with opposite biological characters which combined with Minor/H5 and short stalk N6 seldom exist in nature. Hence, we drew the conclusion that the appropriate combination of Major/H5 and short stalk N6 occur widely in nature with appropriate biological characteristics for the proliferation and transmission, whereas other combinations of HA and NA had a low proportion and even have not yet been detected.

Wild birds are natural hosts of avian influenza viruses (AIV) and can transmit viruses to poultry and other species. To monitor the prevalence of AIV antibodies, 211 eggs from wild Mallards ( Anas platyrhynchos) and 177 from wild White-winged Terns ( Chlidonias leucopterus) were collected from Zhalong Wetland and Xianghai Wetland in northeastern Republic of China from April to September, 2016. A hemagglutinin inhibition test detected the presence of H1, H3, H5, and H7 subtype-specific antibodies. The prevalences of AIV antibodies of subtypes H1 and H3 were relatively high while the prevalences of H5 and H7 AIV subtype antibody were low. In Zhalong Wetland, the prevalence of H1 AIV subtype antibody in Mallards was the highest, with a percentage of 11.0%. Prevalence of all AIV subtype-specific antibodies in Mallard was higher than those in White-winged Terns.

In recent past, the respiratory infection has emerged as a great challenge to the poultry farmers. Various pathogens including Avian pneumovirus (APV), Avian influenza virus (AIV), Infectious bronchitis virus (IBV) and Newcastle disease virus (NDV), Avibacterium paragallinarum, Ornithobacterium rhinotracheale (ORT), Mycoplasma synoviae (MS), Mycoplasma gallisepticum (MG) and Avian pathogenic Escherichia coli (APEC) are involved in the respiratory disease complex in birds [1], [2] (Bradbury, 1984; Roussan et al., 2008). Hence, respiratory disease complex is the most serious disease affecting to poultry and causes heavy economic losses in the poultry industry worldwide [3] (Murthy et al., 2008). In recent years, metagenomics is powerful analyzing tool for detection of pathogens directly from clinical samples without any prior knowledge of the organism in a given sample [4], [5] (Schuster, 2008; Pereira et al., 2010). High throughput Next-Generation-Sequencing technology was used for sequencing the isolated genomic DNA. These data provides an insight about taxonomic and functional status of microorganisms responsible for causing respiratory infection in broiler. The data of these metagenome are available in the BioSample Submission Portal as Bioproject PRJNA339659 and SRA accession number SRR5997823, SRR5992854, SRR6037376, SRR6024702, SRR6012248 and SRR6008913.

Novel reassortant avian influenza H7N9 virus and pandemic 2009 H1N1 (H1N1pdm) virus cause human infections, while avian H7N2 and swine H1N1 virus mainly infect birds and pigs, respectively. There is no robust in vitro model for assessing the infectivity of emerging viruses in humans. Based on a recently established method, we generated long-term expanding 3D human airway organoids which accommodate four types of airway epithelial cells: ciliated, goblet, club, and basal cells. We report differentiation conditions which increase ciliated cell numbers to a nearly physiological level with synchronously beating cilia readily discernible in every organoid. In addition, the differentiation conditions induce elevated levels of serine proteases, which are essential for productive infection of human influenza viruses and low-pathogenic avian influenza viruses. We also established improved 2D monolayer culture conditions for the differentiated airway organoids. To demonstrate the ability of differentiated airway organoids to identify human-infective virus, 3D and 2D differentiated airway organoids are applied to evaluate two pairs of viruses with known distinct infectivity in humans, H7N9/Ah versus H7N2 and H1N1pdm versus an H1N1 strain isolated from swine (H1N1sw). The human-infective H7N9/Ah virus replicated more robustly than the poorly human-infective H7N2 virus; the highly human-infective H1N1pdm virus replicated to a higher titer than the counterpart H1N1sw. Collectively, we developed differentiated human airway organoids which can morphologically and functionally simulate human airway epithelium. These differentiated airway organoids can be applied for rapid assessment of the infectivity of emerging respiratory viruses to human.

Airborne transmission of H5N1 highly pathogenic avian influenza (HPAI) viruses has occurred among poultry and from poultry to humans during home or live-poultry market slaughter of infected poultry, and such transmission has been experimentally reproduced. In this study, we investigated simple, practical changes in the processing of H5N1 virus-infected chickens to reduce infectious airborne particles and their transmission. Our findings suggest that containing the birds during the killing and bleeding first step by using a disposable plastic bag, a commonly available cooking pot widely used in Egypt (halla), or a bucket significantly reduces generation of infectious airborne particles and transmission to ferrets. Similarly, lack of infectious airborne particles was observed when processing vaccinated chickens that had been challenged with HPAI virus. Moreover, the use of a mechanical defeatherer significantly increased total number of particles in the air compared to manual defeathering. This study confirms that simple changes in poultry processing can efficiently mitigate generation of infectious airborne particles and their transmission to humans.

Highly pathogenic avian influenza virus (HPAIV) H5N1 has been reported in Asia, including Indonesia since 2003. Although several risk factors related to the HPAIV outbreaks in poultry in Indonesia have been identified, little is known of the contact structure of farms of different poultry production types (backyard chickens, broilers, layers, and ducks). This study aims to quantify the contact rates associated with the movement of people, and movements of live birds and products and equipment that affect the risk of HPAIV H5N1 transmission between poultry farms in Indonesia. On 124 poultry farms in 6 districts in West Java, logbooks were distributed to record the movements of farmers/staff and visitors and their poultry contacts. Most movements in backyard chicken, commercial native chicken, broiler and duck farms were visits to and from other poultry farms, whilst in layer farms visits to and from poultry companies, visits to egg collection houses and visit from other poultry farms were most frequent. Over 75% of persons visiting backyard chicken and duck farms had previously visited other poultry farms on the same day. Visitors of backyard chicken farms had the highest average contact rate, either direct contact with poultry on other farms before the visits (1.35 contact/day) or contact during their visits in the farms (10.03 contact/day). These results suggest that backyard chicken farms are most at risk for transmission of HPAIV compared to farms of the other poultry production types. Since visits of farm-to-farm were high, backyard farms could also a potential source for HPAIV transmission to commercial poultry farms.

Live bird markets (LBM) are important for trading poultry in many developing countries where they are being considered hotspots of Avian Influenza Virus (AIV) prevalence and contamination. An active surveillance for Avian Influenza Virus (AIV) was conducted on four species of LBM birds (chickens, ducks, quails and pigeons) from 10 of the largest LBM in Chittagong, Bangladesh, and two species of peri-domestic wild birds (house crow and Asian pied starling) in their direct vicinity from November 2012 until September 2016. Our aim was to identify the scale and annual pattern of AIV circulation in both the LBM birds and the two per-domestic wild bird species living in close proximity of the LBM. In the latter two species, the annual pattern in AIV antibody prevalence was additionally investigated. A total of 4770 LBM birds and 1119 peri-domestic wild birds were sampled. We used rt-PCR for detection of the AIV M-gene and AIV subtypes H5, H7 and H9 from swab samples. We used c-ELISA for AIV antibody detection from serum samples of peri-domestic wild birds. Average AIV prevalence among the four LBM species varied between 16 and 28%, whereas no AIV was detected in peri-domestic wild birds by rt-PCR. In all LBM species we found significantly higher AIV prevalence in winter compared to summer. A similar pattern was found in AIV antibody prevalence in peri-domestic wild birds feeding in the direct vicinity of LBM. For the subtypes of AIV investigated, we found a significantly higher proportion of AIV H5 in LBM chickens and H9 in LBM ducks. No H7 was detected in any of the investigated samples. We conclude that AIV and notably AIV H5 and H9 were circulating in the investigated LBM of Bangladesh with clear seasonality that matched the prevalence of AIV antibodies of peri-domestic wild birds. These patterns show great resemblance to the annual outbreak patterns in Bangladeshi poultry industry. Our data suggest considerable exchange of AIV within and among the four LBM bird species and peri-domestic wild birds, which likely contributes to the maintenance of the AIV problems in Bangladesh. Increasing biosecurity and notably reducing the direct and indirect mixing of various domestic bird species and peri-domestic wild birds and developing all-in-all-out selling systems with regular use of disinfectant are likely to reduce the risk of transmission and spread of AIV, including HPAI.

Objective: To understand characteristics of demographic, seasonal and spatial distribution of H5N1 cases in major countries of Asia (Indonesia, Cambodia, Vietnam, China) and Africa (Egypt). Methods: Through searching public data resource and published papers, we collected cases information in five countries from May 1st, 1997 to November 6th, 2017, including general characteristics, diagnosis, onset and exposure history, etc. Different characteristics of survived and death cases in different countries were described and χ(2) test was used to compare the differences among death cases and odds ratio (OR) and 95%CI value was used to compare death risk in different countries. Results: A total of 856 cases were reported in five countries with Egypt had the most cases (44.3%). The highest number of cases were reported in 2015 (18.3%). 53% cases were reported from January to March, and 96.1% of cases had the history of poultry exposure. 64.2% (43 cases) cases in China had live poultry market exposure, but the sick/dead poultry exposure was the major exposure for cases in other four countries. 452 death cases were reported in five countries, and the fatality rate was 52.8%. With Egypt as the reference group, the highest death risk was seen in Indonesia (OR (95%CI): 11.52 (7.46-17.77)), followed by Cambodia (OR (95%CI): 4.27(2.37-7.69)) and China (OR (95%CI): 2.87 (1.73-4.74)). The age distribution of death cases among 5 countries was statistically significant, and the highest fatality rate was in 15-54 years group in Egypt (83.6%, 102 cases), while in Cambodia the highest fatality rate was in 0-14 years group (76.9%, 30 cases). The highest number of deaths were reported in 2006, and 48.3% were reported from January to March. There was difference in exposure routes among 5 countries (χ(2)=43.85, P=0.001), 63.2% (24 cases) of the death cases in China had live poultry market exposure. 92.9% (79 cases), 83.3% (40 cases) and 100.0% (38 cases) death cases in Indonesia, Vietnam and Camodia had sick/dead poultry exposure, respectively;and 81.6% (31 cases) of the death cases in Egypt had backyard poultry exposure. Conclusion: The geographical distribution, seasonal age, gender, exposure matter and outcome of H5N1 cases in five countries were different.

This work aimed to analyze the herd immunity to influenza among a Russian population living in regions with an increased risk of emergence of viruses with pandemic potential, and to isolate and investigate virus strains from severe influenza cases, including fatal cases, during the 2016-2017 epidemic season. In November 2016 - March 2017 highly pathogenic influenza outbreaks were registered in Russia among wild birds and poultry. No cases of human infection were registered. Analysis of 760 sera from people who had contact with infected or perished birds revealed the presence of antibodies to A(H5N1) virus of clade 2.3.2.1c and A(H5N8) virus of clade 2.3.4.4. The 2016-2017 influenza epidemic season in Russia began in weeks 46-47 of 2016 with predominant circulation of influenza A(H3N2) viruses. Strains isolated from severe influenza cases mainly belonged to 3C.2a.2 and 3C.2a.3 genetic groups. Up to the 8th week of 2017 severe influenza cases were often caused by influenza B viruses which belonged to 1A genetic group with antigenic properties similar to B/Brisbane/60/2008. All influenza A and B virus strains isolated in the 2016-2017 epidemic season were sensitive to oseltamivir and zanamivir.