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Emerg Microbes Infect. 2019;8(1):1370-1382. doi: 10.1080/22221751.2019.1663712.
Active surveillance and genetic evolution of avian influenza viruses in Egypt, 2016-2018.
Kandeil A1, Hicks JT2,3, Young SG4, El Taweel AN1, Kayed AS1, Moatasim Y1, Kutkat O1, Bagato O1, McKenzie PP5, Cai Z6, Badra R7, Kutkat M8, Bahl J2,3, Webby RJ5, Kayali G2,7, Ali MA1.
Author information
1 Center of Scientific Excellence for Influenza Viruses, Water Pollution Research Department, National Research Centre , Giza , Egypt. 2 University of Texas Health Sciences Center , Houston , TX , USA. 3 Center for the Ecology of Infectious Diseases, University of Georgia , Athens , USA. 4 University of Arkansas for Medical Sciences , Little Rock , AR , USA. 5 St. Jude Children's Research Hospital , Memphis , TN , USA. 6 Georgia State University , Atlanta , GA , USA. 7 Human Link , Hazmieh , Lebanon. 8 Poultry Diseases Department, National Research Centre , Giza , Egypt.
Abstract
Egypt is a hotspot for avian influenza virus (AIV) due to the endemicity of H5N1 and H9N2 viruses. AIVs were isolated from 329 samples collected in 2016-2018; 48% were H9N2, 37.1% were H5N8, 7.6% were H5N1, and 7.3% were co-infections with 2 of the 3 subtypes. The 32 hemagglutinin (HA) sequences of the H5N1 viruses formed a well-defined lineage within clade 2.2.1.2. The 10 HA sequences of the H5N8 viruses belonged to a subclade within 2.3.4.4. The 11 HA of H9N2 isolates showed high sequence homology with other Egyptian G1-like H9N2 viruses. The prevalence of H5N8 viruses in ducks (2.4%) was higher than in chickens (0.94%). Genetic reassortment was detected in H9N2 viruses. Antigenic analysis showed that H9N2 viruses are homogenous, antigenic drift was detected among H5N1 viruses. AI H5N8 showed higher replication rate followed by H9N2 and H5N1, respectively. H5N8 was more common in Southern Egypt, H9N2 in the Nile Delta, and H5N1 in both areas. Ducks and chickens played a significant role in transmission of H5N1 viruses. The endemicity and co-circulation of H5N1, H5N8, and H9N2 AIV coupled with the lack of a clear control strategy continues to provide avenues for further virus evolution in Egypt.
KEYWORDS:
Avian influenza; Egypt; genetic evolution; poultry; surveillance
PMID: 31526249 DOI: 10.1080/22221751.2019.1663712
Active surveillance and genetic evolution of avian influenza viruses in Egypt, 2016-2018.
Kandeil A1, Hicks JT2,3, Young SG4, El Taweel AN1, Kayed AS1, Moatasim Y1, Kutkat O1, Bagato O1, McKenzie PP5, Cai Z6, Badra R7, Kutkat M8, Bahl J2,3, Webby RJ5, Kayali G2,7, Ali MA1.
Author information
1 Center of Scientific Excellence for Influenza Viruses, Water Pollution Research Department, National Research Centre , Giza , Egypt. 2 University of Texas Health Sciences Center , Houston , TX , USA. 3 Center for the Ecology of Infectious Diseases, University of Georgia , Athens , USA. 4 University of Arkansas for Medical Sciences , Little Rock , AR , USA. 5 St. Jude Children's Research Hospital , Memphis , TN , USA. 6 Georgia State University , Atlanta , GA , USA. 7 Human Link , Hazmieh , Lebanon. 8 Poultry Diseases Department, National Research Centre , Giza , Egypt.
Abstract
Egypt is a hotspot for avian influenza virus (AIV) due to the endemicity of H5N1 and H9N2 viruses. AIVs were isolated from 329 samples collected in 2016-2018; 48% were H9N2, 37.1% were H5N8, 7.6% were H5N1, and 7.3% were co-infections with 2 of the 3 subtypes. The 32 hemagglutinin (HA) sequences of the H5N1 viruses formed a well-defined lineage within clade 2.2.1.2. The 10 HA sequences of the H5N8 viruses belonged to a subclade within 2.3.4.4. The 11 HA of H9N2 isolates showed high sequence homology with other Egyptian G1-like H9N2 viruses. The prevalence of H5N8 viruses in ducks (2.4%) was higher than in chickens (0.94%). Genetic reassortment was detected in H9N2 viruses. Antigenic analysis showed that H9N2 viruses are homogenous, antigenic drift was detected among H5N1 viruses. AI H5N8 showed higher replication rate followed by H9N2 and H5N1, respectively. H5N8 was more common in Southern Egypt, H9N2 in the Nile Delta, and H5N1 in both areas. Ducks and chickens played a significant role in transmission of H5N1 viruses. The endemicity and co-circulation of H5N1, H5N8, and H9N2 AIV coupled with the lack of a clear control strategy continues to provide avenues for further virus evolution in Egypt.
KEYWORDS:
Avian influenza; Egypt; genetic evolution; poultry; surveillance
PMID: 31526249 DOI: 10.1080/22221751.2019.1663712