Combining spatial-temporal and phylogenetic analysis approaches for improved understanding on global H5N1 transmission

Background Since late 2003, the highly pathogenic influenza A H5N1 had initiated several outbreak waves that swept across the Eurasia and Africa continents. Getting prepared for reassortment or mutation of H5N1 viruses has become a global priority. Although the spreading mechanism of H5N1 has been studied from different perspectives, its main transmission agents and spread route problems remain unsolved. Methodology/Principal Findings Based on a compilation of the time and location of global H5N1 outbreaks from November 2003 to December 2006, we report an interdisciplinary effort that combines the geospatial informatics approach with a bioinformatics approach to form an improved understanding on the transmission mechanisms of H5N1 virus. Through a spherical coordinate based analysis, which is not conventionally done in geographical analyses, we reveal obvious spatial and temporal clusters of global H5N1 cases on different scales, which we consider to be associated with two different transmission modes of H5N1 viruses. Then through an interdisciplinary study of both geographic and phylogenetic analysis, we obtain a H5N1 spreading route map. Our results provide insight on competing hypotheses as to which avian hosts are responsible for the spread of H5N1. Conclusions/Significance We found that although South China and Southeast Asia may be the virus pool of avian flu, East Siberia may be the source of the H5N1 epidemic. The concentration of migratory birds from different places increases the possibility of gene mutation. Special attention should be paid to East Siberia, Middle Siberia and South China for improved surveillance of H5N1 viruses and monitoring of migratory birds.

Critical role of serpinB1 in regulating inflammatory responses in pulmonary influenza infection

Excessive inflammatory host response increases morbidity and mortality associated with seasonal respiratory influenza, and highly pathogenic virus strains are characterized by massive infiltration of monocytes and/or macrophages that produce a storm of injurious cytokines.

The ins and outs of biosecurity: bird 'flu in East Anglia and the spatial representation of risk

Avian influenza, or 'bird 'flu' arrived in Norfolk in April 2006 in the form of the low pathogenic strain H7N3. In February 2007 a highly pathogenic strain, H5N1, which can pose a risk to humans, was discovered in Suffolk. We examine how a local newspaper reported the outbreaks, focusing on the linguistic framing of biosecurity. Consistent with the growing concern with securitisation among policymakers, issues were discussed in terms of space (indoor–outdoor; local–global; national–international) and flows (movement, barriers and vectors) between spaces (farms, sheds and countries). The apportioning of blame along the lines of 'them and us'– Hungary and England – was tempered by the reporting on the Hungarian operations of the British poultry company. Explanations focused on indoor and outdoor farming and alleged breaches of biosecurity by the companies involved. As predicted by the idea of securitisation, risks were formulated as coming from outside the supposedly secure enclaves of poultry production.

Health, hygiene and biosecurity: tribal knowledge claims in the UK poultry industry

Since 1997 the world has been facing the threat of a human influenza pandemic that may be caused by an avian virus and the poultry industry around the globe has been grappling with the highly pathogenic strain of avian influenza H5N1, or in more informal terms bird flu. The UK poultry industry has lived with and through this threat and its consequences since 2005. This study investigates knowledge claims about health, hygiene and biosecurity as tools to ward off the threat from this virus. It takes a semi-ethnographic and discourse analytic approach to analyse a small corpus of semi-structured interviews carried out in the wake of one of the most publicised outbreaks of H5N1 in Suffolk in 2007. It reveals that claims about what best to do to protect flocks against the risk of disease are divided along lines imposed on the one hand by the structure of the industry and on the other by more 'tribal' lines drawn by knowledge and belief systems about purity and dirt, health and hygiene.

Anticipated behaviours of emergency prehospital medical care providers during an influenza pandemic

Introduction: Emergency prehospital medical care providers are frontline health workers during emergencies. However, little is known about their attitudes, perceptions, and likely behaviors during emergency conditions. Understanding these attitudes and behaviors is crucial to mitigating the psychological and operational effects of biohazard events such as pandemic influenza, and will support the business continuity of essential prehospital services. ----- ----- Problem: This study was designed to investigate the association between knowledge and attitudes regarding avian influenza on likely behavioral responses of Australian emergency prehospital medical care providers in pandemic conditions. ----- ----- Methods: Using a reply-paid postal questionnaire, the knowledge and attitudes of a national, stratified, random sample of the Australian emergency prehospital medical care workforce in relation to pandemic influenza were investigated. In addition to knowledge and attitudes, there were five measures of anticipated behavior during pandemic conditions: (1) preparedness to wear personal protective equipment (PPE); (2) preparedness to change role; (3) willingness to work; and likely refusal to work with colleagues who were exposed to (4) known and (5) suspected influenza. Multiple logistic regression models were constructed to determine the independent predictors of each of the anticipated behaviors, while controlling for other relevant variables. ----- ----- Results: Almost half (43%) of the 725 emergency prehospital medical care personnel who responded to the survey indicated that they would be unwilling to work during pandemic conditions; one-quarter indicated that they would not be prepared to work in PPE; and one-third would refuse to work with a colleague exposed to a known case of pandemic human influenza. Willingness to work during a pandemic (OR = 1.41; 95% CI = 1.0–1.9), and willingness to change roles (OR = 1.44; 95% CI = 1.04–2.0) significantly increased with adequate knowledge about infectious agents generally. Generally, refusal to work with exposed (OR = 0.48; 95% CI = 0.3–0.7) or potentially exposed (OR = 0.43; 95% CI = 0.3–0.6) colleagues significantly decreased with adequate knowledge about infectious agents. Confidence in the employer’s capacity to respond appropriately to a pandemic significantly increased employee willingness to work (OR = 2.83; 95% CI = 1.9–4.1); willingness to change roles during a pandemic (OR = 1.52; 95% CI = 1.1–2.1); preparedness to wear PPE (OR = 1.68; 95% CI = 1.1–2.5); and significantly decreased the likelihood of refusing to work with colleagues exposed to (suspected) influenza (OR = 0.59; 95% CI = 0.4–0.9). ----- ----- Conclusions:These findings indicate that education and training alone will not adequately prepare the emergency prehospital medical workforce for a pandemic. It is crucial to address the concerns of ambulance personnel and the perceived concerns of their relationship with partners in order to maintain an effective prehospital emergency medical care service during pandemic conditions.

Weather variability and influenza A (H7N9) transmission in Shanghai, China: A Bayesian spatial analysis

Abstract Background A novel avian influenza A (H7N9) virus was first found in humans in Shanghai, and infected over 433 patients in China. To date, very little is known about the spatiotemporal variability or environmental drivers of the risk of H7N9 infection. This study explored the spatial and temporal variation of H7N9 infection and assessed the effects of temperature and rainfall on H7N9 incidence. Methods A Bayesian spatial conditional autoregressive (CAR) model was used to assess the spatiotemporal distribution of the risk of H7N9 infection in Shanghai, by district and fortnight for the period 19th February–14th April 2013. Data on daily laboratory-confirmed H7N9 cases, and weather variability including temperature (°C) and rainfall (mm) were obtained from the Chinese Information System for Diseases Control and Prevention and Chinese Meteorological Data Sharing Service System, respectively, and aggregated by fortnight. Results High spatial variations in the H7N9 risk were mainly observed in the east and centre of Shanghai municipality. H7N9 incidence rate was significantly associated with fortnightly mean temperature (Relative Risk (RR): 1.54; 95% credible interval (CI): 1.22–1.94) and fortnightly mean rainfall (RR: 2.86; 95% CI: 1.47–5.56). Conclusion There was a substantial variation in the spatiotemporal distribution of H7N9 infection across different districts in Shanghai. Optimal temperature and rainfall may be one of the driving forces for H7N9.

Étude cas-témoins de l'épisode d'influenza aviaire hautement pathogène (H7N3) en Colombie-Britannique en 2004 utilisant des scores de biosécurité comme mesure de risque

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

Restrictions to the adaptation of influenza A virus H5 hemagglutinin to the human host

The binding specificities of a panel of avian influenza virus subtype H5 hemagglutinin (RA) proteins bearing mutations at key residues in the receptor binding site were investigated. The results demonstrate that two simultaneous mutations in the receptor binding site resulted in H5 RA binding in a pattern similar to that shown by human viruses. Coexpression of the ion channel protein, M2, from most avian and human strains tested protected H5 RA conformation during trafficking, indicating that no genetic barrier to the reassortment of the H5 surface antigen gene with internal genes of human viruses existed at this level.

A gel-capture assay for characterizing the sialyl-glycan selectivity of influenza viruses

Sialic acids (SA) usually linked to galactose (Gal) in an α2,6- or α2,3-configuration are considered the main cell receptors for influenza viruses, in particular for their hemagglutinins (HA). The typing of influenza virus HA receptor selectivity is relevant for understanding the transmissibility of avian and swine viruses to the human population. In this study we developed a simple and inexpensive gel-capture assay (GCA) of the influenza virus HA receptor-binding selectivity. Its principle is the binding of soluble influenza virus to pentasaccharide analogs, representatives of receptors of human and avian influenza viruses, immobilized on a gel resin. The human and avian analogs consisted of a sialyllactose-N-tetraose c (LSTc) [Neu5Ac(α2,6)Gal(β1-3)GlcNAc(β1-3)Gal(β1-4)Glc] and a sialyllactose-N-tetraose a (LSTa) [Neu5Ac(α2,3)Gal(β1-3)GlcNAc(β1-3)Gal(β1-4)Glc], respectively. Following equilibration, the unbound virus is washed away and the bound one is assayed via HA by densitometry as a function of the analog concentration. Using GCA, the receptor selectivity of three influenza viruses of different HA subtype was investigated. The results showed that the egg-adapted A/California/07/2009 (H1N1) virus exhibited an avian α2,3-linked LSTa selectivity, however, it retained the ability to bind to the α2,6-linked LSTc human receptor analog. Influenza B virus B/Florida/4/2006 showed α2,6-linked LSTc selectivity and a poor α2,3-linked LSTa avidity. The H3N2 virus A/Wisconsin/15/2009 displayed almost comparable avidity for both receptor analogs with a marginally greater α2,3-linked LSTa avidity. The described assay protocol provides a simple and rapid method for the characterization of influenza virus HA receptor binding selectivity. Keywords: influenza virus; hemagglutinin; receptor; sialyllactose-N-tetraose; gel-capture assay.

Drought-rainfall cycles as potential environmental drivers of fowl plague and Newcastle disease uutbreaks in Australian poultry

Climatic conditions in Australia are erratic and characterised by periods of intense rainfall followed by periods of intense drought. This has considerable impact on the population dynamics and ecology of many Australian species of waterfowl, which are thought to form the reservoir of avian influenza viruses (AIV) but may also be important carriers (and possibly reservoirs) of other diseases (e.g. bursal disease, Newcastle disease). During the wet, waterfowl numbers increase with many serologically naive juveniles entering the population. During the subsequent period of drought, bird densities increase in the few remaining wetlands. We hypothesise that it is during this period of increasing densities of naive birds that the population’s viral prevalence of some infectious diseases may increase dramatically. Indeed, there exists a remarkable and suggestive coincidence between outbreaks of fowl plaque and Newcastle disease in Australian poultry farms and the periods of drought following a very wet period. In other words, we suspect a link between increased risk for disease outbreaks in poultry farms and the hypothesised high in the prevalences of the viruses causing these diseases in waterfowl. Given that poultry farms may provide ideal conditions for development of high-pathogenic strains, there is also a reciprocal risk for wildlife involved during these periods.

Estudo da eficácia de espuma para a depopulação de aves para situações de emergência sanitaria

There are several difficulties in the control of quick spreading and highly contagious poultry diseases such as avian influenza and Newcastle disease, which require large numbers of poultry to be rapidly killed inside the poultry houses in order to minimize human exposure and disease spreading. We have built and tested an equipment that uses a waterbased foam from high expansion fire detergent that induces poultry anoxia measured by sensorial signs, time to death, lethality and macro and microscopically lesions. Two hundred 78-weeks old hens were divided into ten groups and exposed to different times of death according to exposure to water-foam varying from 5min30s to 8min15s. All poultry died after six minutes of water-foam cover. Foam bubbles were observed in oral cavity and trachea of all poultry at each time of exposure to foam, revealing physical asphyxia. Macroscopically, congestion in oral cavity and in trachea mucosa was observed. Histopathology revealed diffuse and moderate hemorrhage in lungs and no lesion in trachea. The efficacy of water-foam procedure for poultry depopulation was demonstrated validating its recommendation in case of emergency.

Presence of antibodies against H5, H7 and H9 influenza a virus in wild birds in the state of São Paulo, Brazil

Although the natural reservoirs of the avian influenza (AI) virus have been extensively studied in many countries, there is a clear lack of information on this subject in South America, particularly in Brazil. The objective of this study was to conduct a serological survey for H5, H7 and H9 antibodies to AI-subtype viruses in wild birds in the state of São Paulo, Brazil. Serum samples were tested using the hemagglutination-inhibition assay. Out of the 31 wild birds sampled between January and December of 2006, seven (22.58%), were seropositive for H5, H7 and H9; four (12.90%) were seropositive for H5 and H7; 13 (41.94%), were seropositive only for H7; three (9.7%), were seropositive only for H9; and four (12.90%) were negative for all three hemagglutinin subtypes. These results indicate that AI viruses belonging to H5, H7 and H9 subtypes circulate among wild birds in the state of São Paulo in the form of either concurrent or consecutive infections. This study contributes to the knowledge of AI epidemiology in Brazil, and stresses the need of further detailed and long-term epidemiological and ecological investigation to determine the current status of this virus.

Evaluación preliminar del impacto en México de la influenza AH1N1: documento elaborado por el equipo conjunto CEPAL

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Imunocaptura do vírus de Influenza aviária para dia diagnóstico em RT-PCR em tempo real

Pós-graduação em Microbiologia Agropecuária - FCAV