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
Long endemicity of the Highly Pathogenic Avian Influenza (HPAI) H5N1 subtype in Egypt poses a lot of threats to public health. Contrary to what is previously known, outbreaks have been circulated continuously in the poultry sectors all year round without seasonality. These changes call the need for epidemiological studies to prove or deny the influence of climate variability on outbreak occurrence, which is the aim of this study. This work proposes a modern approach to examine the degree to which the HPAI-H5N1disease event is being influenced by climate variability as a potential risk factor using generalized estimating equations (GEEs). GEE model revealed that the effect of climate variability differs according to the timing of the outbreak occurrence. Temperature and relative humidity could have both positive and negative effects on disease events. During the cold seasons especially in the first quarter, higher minimum temperatures, consistently show higher risks of disease occurrence, because this condition stimulates viral activity, while lower minimum temperatures support virus survival in the other quarters of the year with the highest negative effect in the third quarter. On the other hand, relative humidity negatively affects the outbreak in the first quarter of the year as the humid weather does not support viral circulation, while the highest positive effect was found in the second quarter during which low humidity favors the disease event.
Background The poultry industry in Egypt has been suffering from endemic highly pathogenic avian influenza (HPAI) virus, subtype H5N1 since 2006. However, the emergence of H9N2, H5N8, and H5N2 in 2011, 2016, and 2019 respectively, has aggravated the situation. Our objective was to evaluate how effective are the mitigation strategies by a Quantitative Risk Assessment (QRA) model which used daily outbreak data of HPAI-H5N1 subtype in Egypt, stratified by different successive epidemic waves from 2006 to 2016. Results By applying the epidemiologic problem-oriented approach methodology, a conceptual scenario tree was drawn based on the knowledgebase. Monte Carlo simulations of QRA parameters based on outbreak data were performed using @Risk software based on a scenario-driven decision tree. In poultry farms, the expected probability of HPAI H5N1 prevalence is 48% due to failure of mitigation strategies in 90% of the time during Monte Carlo simulations. Failure of efficacy of these mitigations will raise prevalence to 70% with missed vaccination, while failure in detection by surveillance activities will raise it to 99%. In backyard poultry farms, the likelihood of still having a high HPAI-H5N1 prevalence in different poultry types due to failure of passive and active surveillance varies between domestic, mixed and reservoir. In mixed poultry, the probability of HPAI-H5N1 not detected by surveillance was the highest with a mean and a SD of 16.8 × 10–3 and 3.26 × 10–01 respectively. The sensitivity analysis ranking for the likelihood of HPAI-H5N1 in poultry farms due to missed vaccination, failure to be detected by passive and active surveillance was examined. Among poultry farms, increasing vaccination by 1 SD will decrease the prevalence by 14%, while active and passive surveillance decreases prevalence by 12, and 6%, respectively. In backyard, the active surveillance had high impact in decreasing the prevalence by 16% in domestic chicken. Whereas the passive surveillance had less impact in decreasing prevalence by 14% in mixed poultry and 3% in domestic chicken. Conclusion It could be concluded that the applied strategies were not effective in controlling the spread of the HPAI-H5N1 virus. Public health officials should take into consideration the evaluation of their control strategies in their response.
Highly Pathogenic Avian Influenza (HPAI) H5N1 virus is widely circulated between poultry flocks in Egypt. The present study described the spatiotemporal dynamics of HPAI H5N1 in five Nile Delta governorates, Egypt (Dakhlia, Qalyobia, Sharkia, Gharbia, and Menofia) where most cases were reported for the years 2006 to 2016. Moreover, this study explored the impact of climate variability in outbreaks occurrence using the statistical generalized estimating equation model. The highest prevalence rate was recorded in Dakhlia and Qalyobia governorates, while Menofia governorate had the lowest one. From 2006 to 2009, the classic clade 2.2.1 was predominant and remained stable. It was demonstrated that new unreported clades had been evolved from classic clades after the vaccination pressure until 2010 resulted in raising the PR sharply. The stability of PR from 2012 to 2014 could be attributed to the adaptation of 2.2.1.2 endemic clade. The generalized estimating equation model revealed that a one-unit increase in maximum and minimum temperature decreased the risk of a poultry outbreak by about 6% and 4%, respectively. According to the obtained results, it seems that the virus circulates and causes infection throughout the year, indicating changes in virus epidemiology and temporal patterns.
BackgroundThe poultry industry in Egypt has been suffering from endemic highly pathogenic avian influenza (HPAI) virus, subtype H5N1 since 2006. However, the emergence of H9N2, H5N8, and H5N2 in 2011, 2016, and 2019 respectively, has aggravated the situation. Our objective was to evaluate how effective are the mitigation strategies by a Quantitative Risk Assessment (QRA) model utilizing daily outbreak data of HPAI-H5N1stratified by different epidemic waves from 2006 to 2016 are in Egypt. ResultsUtilizing the epidemiologic problem-oriented approach methodology, a conceptual scenario tree was drawn based on the knowledgebase. Monte Carlo simulations of QRA parameters were ran utilizing @Risk software. In poultry farms, the likelihood of poultry still having a high Prevalence Rate (PR) after failure of mitigation strategies such as vaccination, passive, and active surveillance, in 90% of the time, these mitigations will fail 48% of the time. Failure of efficacy of these mitigations will raise PR to 70% with missed vaccination, while failure in detection by surveillance will raise it to 99%. In backyard poultry, the likelihood of still having a high HPAI-H5N1 PR in three different poultry types due to failure of passive and active surveillance varies between domestic, mixed and reservoir. In mixed poultry, the probability of HPAI-H5N1 not detected by surveillance was higher with a mean and a SD of 16.8 x 10-3 and 3.26 x 10-01 respectively. The sensitivity analysis ranking for the likelihood of HPAI-H5N1 in poultry farms due to missed vaccination, failure to be detected by passive and active surveillance was examined. In poultry farms, increasing vaccination by 1 SD will decrease the PR by 14%, in active surveillance by 12% and in passive surveillance by 6%, respectively. while in backyard, the active surveillance had high impact in decreasing the PR by 16% in domestic poultry. Whereas the passive surveillance had less impact in decreasing PR by 14% in mixed poultry and 3% in domestic poultry. ConclusionIt could be concluded that the applied strategies were not efficient in controlling the spread of the HPAI-H5N1 virus. Public health officials should take into consideration the evaluation of their control strategies in their response.
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