#Genetic characterization of highly pathogenic avian #influenza #H5N8 virus isolated from commercial #poultry #farms in #Egypt reveals zoonotic potential

 

Abstract

Highly pathogenic avian influenza (HPAI) H5N8 virus, first identified in late 2016 in Egypt, continues to circulate and has replaced the previously dominant HPAI H5N1 virus of clade 2.2.1. In this study, HPAI H5N8 was detected on 23 commercial poultry farms in Egypt. Complete genome sequences of three isolates collected in 2021 were obtained using next-generation sequencing (NGS) and subjected to genetic characterization. Phylogenetic analysis showed these isolates to belong to clade 2.3.4.4b, comprising two genotypes: EA-2021-Q and EA-2020-A. Molecular analysis of the haemagglutinin (HA) protein revealed the presence of T156A and V538A substitutions in the duck isolate and an N183S substitution in the chicken isolate. Several additional nonsynonymous mutations were identified, including 147I and 504V in the PB2 protein, 127V, 672L, and 550L in the PA protein, 64F and 69P in the M2 protein, and 42S in the NS1 protein. Comparative analysis of HA antigenic sites between these isolates and the human vaccine against H5N8 revealed four nonsynonymous mutations: S141P, A154N, D45N, and V174I. Notably, the HA sequences of the studied isolates shared 98.7–99.4% amino acid sequence identity, and the NA sequences shared 96.1–97.1% identity to those of the 2.3.4.4b candidate human H5N8 vaccine strain (CVV) A/Astrakhan/3212/2020-like. These findings underscore the importance of continuous monitoring of the genetic evolution of avian influenza viruses to guide updates of candidate vaccine strains. Furthermore, the high similarity between the detected isolates and a zoonotic Russian H5N8 wild-type strain highlights the potential risk of cross-species transmission and possible human infection.

Source: 

Link: https://link.springer.com/article/10.1007/s00705-025-06479-z

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Local and introduced #lineages drive #MERS-CoV #recombination in Egyptian #camels

 

ABSTRACT

Dromedary camels are the primary reservoir for Middle East respiratory syndrome coronavirus (MERS-CoV), a zoonotic coronavirus responsible for sporadic human infections. While clade B predominates in the Arabian Peninsula and is frequently linked to zoonotic outbreaks and household secondary transmission, clade C circulates primarily in African camels, with limited evidence of human infections. The extent of MERS-CoV transmission, genetic diversity, and cross-species potential in North Africa remains poorly characterized. Here, we investigate MERS-CoV incidence, seroprevalence, and genomic recombination in dromedary camels and sympatric livestock across slaughterhouses and farms in Egypt. MERS-CoV was detected in 12% of camels sampled at slaughterhouses, with no evidence of infection in cattle, buffalo, sheep, or goats. Seroprevalence was higher in slaughtered camels (79%) than camels on farms (12%). Phylogenetic analyses of MERS-CoV genomes obtained from dromedary camels revealed an introduction of clade B into Egypt, originating from the Arabian Peninsula. Furthermore, we identified recombination events between clades B and C, in addition to events within each clade. This included at least one clade C virus that acquired multiple genomic regions from the newly introduced clade B viruses. These findings suggest that newly introduced MERS-CoV strains can recombine with locally circulating viruses, generating novel variants with potential zoonotic implications and challenging assumptions of limited cross-regional exchange. Enhanced surveillance, targeted control measures, and a One Health approach are crucial to mitigating MERS-CoV transmission and the emergence of recombinant strains.

IMPORTANCE

This study highlights the importance of monitoring Middle East respiratory syndrome coronavirus (MERS-CoV) in dromedary camels, which are the main animal source of this virus that can occasionally infect humans. While most human cases have been linked to strains in the Arabian Peninsula, this research focused on Egypt, where the virus is less understood. Among surveyed dromedary camels and associated livestock, a significant number of camels at slaughterhouses were infected, and many had antibodies showing past exposure. Importantly, we discovered that a strain common in the Arabian Peninsula had recently entered Egypt and mixed genetically with local strains. This mixing, or recombination, can lead to new virus versions that may pose new risks to humans. The findings challenge the belief that MERS-CoV strains in different regions do not interact and highlight the need for stronger monitoring and prevention strategies. A One Health approach, linking animal, human, and environmental health, is key to managing future risks.

Source: 

Link: https://journals.asm.org/doi/full/10.1128/jvi.00641-25?af=R

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History of Mass Transportation: The Henschel & Co. Diesel Locomotive on Egyptian National Railways

By Abdelrhman 1990 - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=130430126

Henschel locomotive on Egyptian National Railways

Source: 

Link: https://en.wikipedia.org/wiki/Henschel_%26_Son

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#Genomic #surveillance and #evolution of co-circulating avian #influenza #H5N1 and #H5N8 viruses in #Egypt, 2022–2024

 

ABSTRACT

For over two decades, avian influenza virus (AIV) has significantly impacted the Egyptian poultry population, with multiple subtypes and genotypes contributing to significant economic and agricultural losses. As part of an ongoing national surveillance effort, this study aimed to monitor and genetically characterize AIV circulation across various poultry sectors in Egypt. Between 2022 and 2024, a total of 446,790 swab samples were collected, representing commercial farms (n = 25,057), backyard flocks (n = 403), and live bird markets “LBM” (n = 1250) to assess the prevalence and genetic diversity of circulating AIV strains. A total of 173 sampling units were found positive for high pathogenicity (HP) AIV H5, including farms (n = 17), backyards (n = 11), and LBMs (n = 145). The HPAIV of H5N8 subtype was dominant (n = 75) over the H5N1 (n = 27) subtypes among all sectors and bird species (chickens, ducks, turkeys). Whole genome sequence analysis of positive H5 samples revealed high similarity with HPAIVs of clade 2.3.4.4b, which has been confirmed phylogenetically. Two distinct subtypes H5N1 (EA-2021-AB genotype) and H5N8 (EA-2020-A genotype) were identified, with two variants detected within the H5N8 viruses. Evolutionary analyses indicate that Egyptian H5N8 viruses are under strong selection pressure and exhibit a higher nucleotide substitution rate compared to the Egyptian H5N1 viruses of clade 2.3.4.4b. With the evolving HPAI H5 virus’s situation in different locations around the globe, including Egypt, this study underlines the importance of active surveillance in the timely detection of emerging AIV genotypes, monitoring virus evolution, and refining risk assessments.

Source: Emerging Microbes and Infections, https://www.tandfonline.com/doi/full/10.1080/22221751.2025.2562046#abstract

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Isolation, characterization and phylogenetic analyses of avian #influenza A #H9N2 viruses isolated from #poultry between 2019 and 2023 in #Egypt

Abstract

The current study aimed to investigate the genetic characterization and evolution of low pathogenic avian influenza virus H9N2 in Egypt. Ten H9N2 viruses were recently isolated from samples collected between 2019 and 2023. Phylogenetic analysis of the haemagglutinin (HA) gene segment of the H9N2 isolates showed a relatedness with G1 H9 4.2 lineage and clustered within genotype III of the Egyptian strains identified earlier in 2018. The majority of H9N2 strains had seven and eight glycosylation sites in HA and neuraminidase (NA) respectively. All strains carried H191 and L234 residues in their hemagglutinin which are markers facilitating avian-to-human cross species barrier transmission. No stalk deletions were detected in NA gene. In addition, genetic analysis of the NA and M encoding proteins revealed the absence of substitutions associated with resistance to oseltamivir and amantadine. The NA showed S372A and R403W substitutions which were previously detected in H3N2 and H1N2 viruses that were reported in previous influenza pandemics in 1975 and 2001 respectively. Many mutations associated with virulence and mammalian infection were detected in internal proteins such as PB2(V504), PB1-F2(N66), PA (V127, L672, and L550), M2(S64), and NS1(42S). Analysis showed the presence of full-length PB1-F2 with 227PDZ230 motif which is associated with virus virulence and pathogenesis. Mammalian associated mutations such as PB2 (I 667, T64), PB1-P13, PB1-F2-S82, NP-K214, NP-Q398 and M1-I15 were detected. The HA gene was under positive selection pressure especially at sites 198 and 235 of RBS, while other internal genes were under negative selection pressure. The study highlights the importance of continuous monitoring of H9N2 virus to enable timely implementation of control measures in poultry populations in Egypt.

Source: BMC Veterinary Research, https://bmcvetres.biomedcentral.com/articles/10.1186/s12917-025-04514-4

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#Phylogenetic Analysis and Spread of HPAI #H5N1 in Middle Eastern Countries Based on #Hemagglutinin and #Neuraminidase Gene Sequences

Abstract

Highly pathogenic avian influenza (HPAI) A/H5N1 viruses threaten animal and human health worldwide. The first documented cases in the Middle East were reported in 2005; however, despite extensive phylogenetic studies, there is limited information on the transmission dynamics of the virus within this region. We analyzed HA and NA gene sequences from various hosts to address this gap and to understand the virus’s spread and evolution in the Middle East. We hypothesized that H5N1 transmission exhibits host-specific or geographically influenced clade structures in this region. This study traced transmission pathways of HPAI A/H5N1 through a phylogenetic and amino acid sequence analysis of HA and NA gene segments from isolates across different hosts in Middle Eastern countries, using the MUSCLE algorithm for alignments and MEGA11 software for phylogenetic analysis. Sequences were selected from NCBI’s virus database based on geographic and host diversity, including those from birds, humans, and other mammals, and were collected at different time points, predominantly after the early 2000s. An amino acid phylogenetic tree was also constructed to examine the conservation of key HA and NA protein residues, identifying distinct clades linked to specific countries and host species, suggesting a possible interspecies transmission and cross-border spread distinct between Egypt and neighboring countries. These findings underscore the role of migratory birds in regional transmission and point to the need for more targeted surveillance and biosecurity efforts, offering more genomic insights into the spread of HPAI A/H5N1 and contributing valuable information for future prevention strategies.

Source: Viruses, https://www.mdpi.com/1999-4915/17/5/734

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Emergence of a novel #reassortant highly pathogenic avian #influenza clade 2.3.4.4b A(#H5N2) Virus, 2024

ABSTRACT

Reassortant highly pathogenic avian influenza A(H5N2) clade 2.3.4.4.b viruses were detected from ducks and environmental samples in Egypt, June 2024. Genomic and phylogenetic analyses revealed a novel genotype produced by the reassortment of an A(H5N1) clade 2.3.3.4b virus with an A(H9N2) G1-like virus. Monitoring the spread of this virus is important.

Source: Emerging Microbes and Infections, https://www.tandfonline.com/doi/full/10.1080/22221751.2025.2455601#abstract

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Spatio-temporal #dynamics and #risk cluster #analysis of highly pathogenic avian #influenza (#H5N1) in #poultry: Advancing #outbreak #management through customized regional strategies in #Egypt

ABSTRACT 

Background: 

Highly pathogenic avian influenza (HPAI) (H5N1) has been endemic in Egypt for almost two decades, profoundly impacting both the poultry industry and public health. Egypt stands as a prominent epicenter for HPAI H5N1 outbreaks in Africa, marked by the highest number of positive human cases. Despite continuous governmental efforts, prior research underscored the inadequacy of strategies in controlling the virus spread. 

Aim: 

This study identified spatiotemporal patterns and high-risk clusters of HPAI H5N1 outbreaks at the subdistrict level. 

Methods: 

This study involved trial tracking of HPAI H5N1 endemicity dynamics, enabling tailored interventions at a regional level based on robust epidemiological investigations to address the persistent challenge of HPAI H5N1 in Egypt. This study illuminated spatiotemporal outbreak dynamics, with specific attention on Menofia governorate. 

Results: 

Despite the region’s early poultry impacts, initial outbreaks did not originate from Menofia in studied epidemic waves (EWs). Outbreak risk spatial distribution displayed an escalating pattern at the northern border, followed by risk reduction through the sixth EW. The predominant hot spot region was localized within rural districts, particularly villages, while urbanization coincided with lower outbreak density. Observed smoothed densities revealed epidemic propagation within urban centers, preceding its transition to new areas and establishing direct connections with neighboring cities. Primary cluster prognostication was plausible, occurring in regions previously hosting elevated relative risk clusters during preceding EWs. Identification of enduring pinpoint clusters, persistent for extended durations, indicated close contact dynamics and localized viral circulation within populations. 

Conclusion: 

This study highlights the significance of customized regional interventions based on the rigorous epidemiological framework. This approach is pivotal in the profound comprehension of endemicity dynamics, efficiently limits geographical infection spread, and contains outbreaks within delineated areas.

Source: Open Veterinary Journal, https://doi.org/10.5455/OVJ.2024.v14.i11.20

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