Disentangling the role of Africa in the global spread of H5 highly pathogenic avian influenza

The role of Africa in the dynamics of the global spread of a zoonotic and economicallyimportant virus, such as the highly pathogenic avian influenza (HPAI) H5Nx of the Gs/GD lineage, remains unexplored. Here we characterise the spatiotemporal patterns of virus diffusion during three HPAI H5Nx intercontinental epidemic waves and demonstrate that Africa mainly acted as an ecological sink of the HPAI H5Nx viruses. A joint analysis of host dynamics and continuous spatial diffusion indicates that poultry trade as well as wild bird migrations have contributed to the virus spreading into Africa, with West Africa acting as a crucial hotspot for virus introduction and dissemination into the continent. We demonstrate varying paths of avian influenza incursions into Africa as well as virus spread within Africa over time, which reveal that virus expansion is a complex phenomenon, shaped by an intricate interplay between avian host ecology, virus characteristics and environmental variables.USAID under the OSRO/GLO/501/USA and OSRO/GLO/507/USA projects and by European Union’s Horizon 2020 research and innovation programme under grant agreement No 727922 (DELTAFLU). The European Research Council under the European Unionʼs Horizon 2020 research and innovation programme (grant agreement no. 725422-ReservoirDOCS). P.L. acknowledges support by the Research Foundation – Flanders FWO, G066215N, G0D5117N and G0B9317N). B.V. is a postdoctoral research fellow supported by the FWO.http://www.nature.com/naturecommunicationsam2020Microbiology and Plant Patholog

Characterization and Genotyping of Avian Infectious Bronchitis Virus in Egypt from 2019 to 2022

Avian infectious bronchitis virus (IBV) causes a major problem in broiler chickens due to increasing mortality and lowering body weight. This group of gammacorona viruses has the ability to emerge frequent new variants. In the present study, 18 broiler chicken farms from 7 Egyptian governorates that showed respiratory signs were sampled from 2019 to 2022. There were 11 farms positive for detection of IBV with real time RT-PCR. The samples were inoculated in specific pathogen free (SPF) embryos for three successive blind passages and the obtained viruses were sequenced for hypervariable region of spike protein (S1) to study their genetic diversity. The results showed that the S1 gene was clustered into two major groups, the first group has only one virus belong to classical vaccine strain of GI-1 lineage and the second group contain nine viruses belong to genotype GI-23 (variant II). They are further separated in two subgroups, first subgroup GI-23.2.1, contains 8 viruses, second subgroup contain one virus belong to genotype GI-23.2.2. The selection pressure analysis revealed episodic diversifying selection on multiple sites, with positive selection observed at five amino acid residues of the S1 protein, as demonstrated by FEL models. The recombination analysis of the S1 gene reveled two viruses with recombination events. The F1282-7-IB-2022 exhibited a slight recombination from IS/1494/2006 and a larger recombination from M41-2004. Meanwhile, the F1282-8-IB-2022 had a minor recombination of strain 4/91-1998 and a larger recombination from the Egyptian strain IBV-D1344/2/4/10-EG. The 3D structural models of hypervariable region HVR of S1 protein also showed that the recent viruses in this study from subgroup GI-23.2.1 (F1282-6-IB-2022) have high structural similarity with vaccine strain D274 and local vaccine seed virus IBV-EG/1212B-2012 than classic or variant GI-23.2.2 subgroup. These results can support efforts to compare the efficacy of local and imported vaccines both in-vivo and in-vitro and to help in controlling the disease

Characterization and Genotyping of Avian Infectious Bronchitis Virus in Egypt from 2019 to 2022

Avian infectious bronchitis virus (IBV) causes a major problem in broiler chickens due to increasing mortality and lowering body weight. This group of gammacorona viruses has the ability to emerge frequent new variants. In the present study, 18 broiler chicken farms from 7 Egyptian governorates that showed respiratory signs were sampled from 2019 to 2022. There were 11 farms positive for detection of IBV with real time RT-PCR. The samples were inoculated in specific pathogen free (SPF) embryos for three successive blind passages and the obtained viruses were sequenced for hypervariable region of spike protein (S1) to study their genetic diversity. The results showed that the S1 gene was clustered into two major groups, the first group has only one virus belong to classical vaccine strain of GI-1 lineage and the second group contain nine viruses belong to genotype GI-23 (variant II). They are further separated in two subgroups, first subgroup GI-23.2.1, contains 8 viruses, second subgroup contain one virus belong to genotype GI-23.2.2. The selection pressure analysis revealed episodic diversifying selection on multiple sites, with positive selection observed at five amino acid residues of the S1 protein, as demonstrated by FEL models. The recombination analysis of the S1 gene reveled two viruses with recombination events. The F1282-7-IB-2022 exhibited a slight recombination from IS/1494/2006 and a larger recombination from M41-2004. Meanwhile, the F1282-8-IB-2022 had a minor recombination of strain 4/91-1998 and a larger recombination from the Egyptian strain IBV-D1344/2/4/10-EG. The 3D structural models of hypervariable region HVR of S1 protein also showed that the recent viruses in this study from subgroup GI-23.2.1 (F1282-6-IB-2022) have high structural similarity with vaccine strain D274 and local vaccine seed virus IBV-EG/1212B-2012 than classic or variant GI-23.2.2 subgroup. These results can support efforts to compare the efficacy of local and imported vaccines both in-vivo and in-vitro and to help in controlling the disease

Molecular characterization of full fusion protein (F) of Newcastle disease virus genotype VIId isolated from Egypt during 2012-2016

Aim: The aim of this work was to study the sequence F gene of Newcastle disease virus (NDV) in regard to pathotyping and genotyping and to study the evolution of this NDV in Egypt. Materials and Methods: The present study was conducted using samples from seven suspected NDV flocks of vaccinated chickens during 2012-2016 from six governorates in Egypt. The NDV was successfully isolated from pathological specimens through inoculation in specific pathogen-free embryonated chicken eggs. Results: Pathogenicity of the NDV isolates has been estimated through intracerebral pathogenicity index and ranged from 1.66 to 1.73 which indicates the velogenic type of NDV isolates. Pathotyping and genotyping of these isolates were done through sequencing of full-length F gene. Results indicated that the seven NDV isolates showed characteristic cleavage site motif (112RRQKRF117) for the velogenic strains of NDV. Phylogenetic analysis of the F gene clustered these isolates within Group I of genotype VIId within Israeli strains NDV/IS/2015, NDV-Ch/SD883, and most of the Middle East strains. Six of seven sequenced isolates have six potential N-linked glycosylation sites. The neutralization epitope on the five antigenic sites of fusion is conserved in all Egyptian strains of this study except NDV-KFR-B7-2012 which has a substitution at D 170 N in epitope A4. In all our strains, 10 cysteine residues are recorded, except one loss of cysteine at residue 370 in both NDV-EG-35-2014 and NDV-GHB-328F-2016. Conclusion: All viruses in this study have 52 amino acid substitutions within fusion gene in compared with Lasota strain that reveals importance for its antigenic and structural function. The present work highlights the important need to sequence F gene of NDV genotype VIId to investigate the evolution of this NDV in Egypt

Predominance and geo-mapping of avian influenza H5N1 in poultry sectors in Egypt

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.The United States Agency for International Development (USAID) (grant number AID-263-IO-11-00001, Mod.#3) in the framework of OSRO/EGY/501/USA, through projects jointly implemented by the FAO, General Organization for Veterinary Services and NLQP.http://www.sherpa.ac.uk/romeo/issn/1827-1987/am2017Production Animal StudiesVeterinary Tropical Disease

Additional file 1: Figure S1. of Phylodynamics of avian influenza clade 2.2.1 H5N1 viruses in Egypt

Schematic diagram showing the distribution and dynamic pattern of different H5N1 clusters on the Map of Egypt. (GIF 67 kb

Predominance and geo-mapping of avian influenza H5N1 in poultry sectors in Egypt

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

Efficacy of a locally prepared live clone vaccine against Newcastle disease virus genotype IV and genotype VIId in Egypt

Vaccines against the virulent Newcastle disease virus (NDV) are broadly existing and can provide protection; nevertheless, better immunization practices are required to avoid clinical disease and limit virus circulation. This study evaluating the immunogenicity and protective efficiency of locally prepared clone 30 live-attenuated vaccine against the challenge impact of virulent NDV genotype IV and genotype VIId prevalent in Egypt in comparison with the commercially prepared live Lasota vaccine as a positive control group. The efficacy of the vaccine was evaluated based on the antibody titer, protection rate, oropharyngeal, and cloacal shedding. Therefore, 150 one day old specific pathogen free chicks (SPF) were divided in to three groups 50 bird per group (G).G1and G2 received 100 µl containing 6 log 10 EID50 via the oculo-nasal route of clone 30 vaccine and lasota vaccine in order, while G3 (un vaccinated) received sterile saline at the same route and dose. On day 21 post vaccination (pv) 40 bird from each group were challenged with a dose of 6.5 log10/ml EID50 intramuscular per bird for both genotype IV and genotype VIId (20 bird /genotype virus),the other 10 birds left from each group were kept separate for antibody level monitoring for the 6th  week pv. Results revealed that, during vaccine preparation, the clone 30 virus showed a high virus titer when propagated in SPF embryonating chicken eggs (SPF-ECEs), which reached 1012/EID50/ml. The protection rate due to the clone 30 vaccine and the lasota vaccine was alike and showed 75% and 70% against challenge with genotype IV and genotype VIId, respectively, there were no significant differences (p > 0.05) between the antibody titer produced by the clone 30 vaccinated group and lasota group. Both the clone 30 and lasota vaccines showed nearly similar levels of oropharyngeal and cloacal shedding. The results clarify that, although there were no detected differences between the immune response and the protective efficacy of clone 30 vaccine and lasota vaccine but, the use of clone 30 vaccine is still advantageous for its superior immunogenicity and low post-vaccinal reaction, which will make the clone 30 vaccine suggestive for primary immunization, especially in immunologically naive birds. In conclusion, the prepared Clone 30 vaccine in the current study is safe for chicks and can be used as an effective vaccine against the circulating NDV