In this paper, we describe results from a high-pathogenic H5N1 avian influenza virus (AIV) surveillance program in previously H5-vaccinated commercial and family-backyard poultry flocks that was conducted from 2007 to 2008 by the Egyptian National Laboratory for Veterinary Quality Control on Poultry Production. The real-time reverse transcription PCR assay was used to detect the influenza A virus matrix gene and detection of the H5 and N1 subtypes was accomplished using a commercially available kit real-time reverse transcription PCR assay. The virus was detected in 35/3,610 (0.97%) and 27/8,682 (0.31%) of examined commercial poultry farms and 246/816 (30%) and 89/1,723 (5.2%) of backyard flocks in 2007 and 2008, respectively. Positive flocks were identified throughout the year, with the highest frequencies occurring during the winter months. Anti-H5 serum antibody titers in selected commercial poultry ranged from <2 (negative) to 9.6 log(2) when determined in the hemagglutination inhibition test using a H5 AIV antigen. In conclusion, despite the nationwide vaccination strategy of poultry in Egypt to combat H5N1 AIV, continuous circulation of the virus in vaccinated commercial and backyard poultry was reported and the efficacy of the vaccination using a challenge model with the current circulating field virus should be revised.
A distinct cluster of highly pathogenic avian influenza viruses of subtype A(H5N1) has been found to emerge within clade 2.2.1.2 in poultry in Egypt since summer 2014 and appears to have quickly become predominant. Viruses of this cluster may be associated with increased incidence of human influenza A(H5N1) infections in Egypt over the last months.
BackgroundHighly pathogenic avian influenza (HPAI) viruses of the H5N1 subtype are widely distributed within poultry populations in Egypt and have caused multiple human infections. Linking the epidemiological and sequence data is important to understand the transmission, persistence and evolution of the virus. This work describes the phylogenetic dynamics of H5N1 based on molecular characterization of the hemagglutinin (HA) gene of isolates collected from February 2006 to May 2014.MethodsFull-length HA sequences of 368 H5N1 viruses were generated and were genetically analysed to study their genetic evolution. They were collected from different poultry species, production sectors, and geographic locations in Egypt. The Bayesian Markov Chain Monte Carlo (BMCMC) method was applied to estimate the evolutionary rates among different virus clusters; additionally, an analysis of selection pressures in the HA gene was performed using the Single Likelihood Ancestor Counting (SLAC) method.ResultsThe phylogenetic analysis of the H5 gene from 2006–14 indicated the presence of one virus introduction of the classic clade (2.2.1) from which two main subgroups were originated, the variant subgroup which was further subdivided into 2 sub-divisions (2.2.1.1 and 2.2.1.1a) and the endemic subgroup (2.2.1.2). The clade 2.2.1.2 showed a high evolution rate over a period of 6 years (6.9 × 10−3 sub/site/year) in comparison to the 2.2.1.1a variant cluster (7.2 × 10−3 over a period of 4 years). Those two clusters are under positive selection as they possess 5 distinct positively selected sites in the HA gene. The mutations at 120, 154, and 162 HA antigenic sites and the other two mutations (129∆, I151T) that occurred from 2009–14 were found to be stable in the 2.2.1.2 clade. Additionally, 13 groups of H5N1 HPAI viruses were identified based on their amino acid sequences at the cleavage site and “EKRRKKR” became the dominant pattern beginning in 2013.ConclusionsContinuous evolution of H5N1 HPAI viruses in Egypt has been observed in all poultry farming and production systems in almost all regions of the country. The wide circulation of the 2.2.1.2 clade carrying triple mutations (120, 129∆, I151T) associated with increased binding affinity to human receptors is an alarming finding of public health importance.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-016-0477-7) contains supplementary material, which is available to authorized users.
Olive (Olea europaea) is host of 13 different viruses but, it is possible that other viruses, which are either non mechanically transmissible or occur in low concentration in plant tissues, are present in nature. This likelihood is supported by the widespread occurrence of double-stranded RNAs (dsRNAs) in plants negative to biological tests. As very little information is available on the geographical distribution of olive-infecting, investigations were conducted for gathering information on the prevalence and distribution of olive viruses in the Mediterranean basin based on the presence of double stranded RNA (dsRNA). A total of 527 samples were collected throughout the surveys covering 10 countries and 83 locations. Out of 286 tested samples collected from 6 Italian regions, 210 (73.4%) were dsRNA positive, whereas the average of viral infections in the Mediterranean basin was 64.5%. Molecular hybridisation tests, on 25 % of dsRNA-positive samples collected in Apulia, revealed the presence of the three nepoviruses (ArMV, CLRV and SLRSV), OLYaV and OLV-1.
Highly pathogenic avian influenza (HPAI) virus of the H5N1 subtype has been enzootic in the Egyptian poultry with significant human infections since 2008. This work evaluates the epidemiological and virological information from February 2006 to May 2015 in spatial and temporal terms. Only data with confirmed HPAI H5N1 sub-type were collected, and matched with the epidemiological data from various spatially and temporally-dispersed surveillances implemented between 2006 and 2015. Spatio-temporal analysis was conducted on a total of 3338 confirmed H5N1 HPAI poultry disease outbreaks and outputs described based on transmission patterns, poultry species, production types affected, trade, geographic and temporal distributions in Egypt. The H5N1 virus persists in the Egyptian poultry displaying a seasonal pattern with peak prevalence between January and March. There was no specific geographic pattern, but chickens and ducks were more affected. However, relatively higher disease incidences were recorded in the Nile Delta. Phylogenetic studies of the haemagglutinin gene sequences of H5N1 viruses indicated that multiple clusters circulated between 2006 and 2015, with significant deviations in circulation. Epidemiological dynamics of HPAI has changed with the origins of majority of outbreaks shifted to household poultry. The persistence of HPAI H5N1 in poultry with recurrent and sporadic infections in humans can influence virus evolution spatio-temporally. Household poultry plays significant roles in the H5N1 virus transmission to poultry and humans, but the role of commercial poultry needs further clarifications. While poultry trading supports the persistence and transmission of H5N1, the role of individual species may warrant further investigation. Surveillance activities, applying a multi-sectoral approach, are recommended.
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