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Alasiri A, Soltane R, Hegazy A, Khalil AM, Mahmoud SH, Khalil AA, Martinez-Sobrido L, Mostafa A. Vaccination and Antiviral Treatment against Avian Influenza H5Nx Viruses: A Harbinger of Virus Control or Evolution. Vaccines (Basel) 2023; 11:1628. [PMID: 38005960 PMCID: PMC10675773 DOI: 10.3390/vaccines11111628] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/11/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Despite the panzootic nature of emergent highly pathogenic avian influenza H5Nx viruses in wild migratory birds and domestic poultry, only a limited number of human infections with H5Nx viruses have been identified since its emergence in 1996. Few countries with endemic avian influenza viruses (AIVs) have implemented vaccination as a control strategy, while most of the countries have adopted a culling strategy for the infected flocks. To date, China and Egypt are the two major sites where vaccination has been adopted to control avian influenza H5Nx infections, especially with the widespread circulation of clade 2.3.4.4b H5N1 viruses. This virus is currently circulating among birds and poultry, with occasional spillovers to mammals, including humans. Herein, we will discuss the history of AIVs in Egypt as one of the hotspots for infections and the improper implementation of prophylactic and therapeutic control strategies, leading to continuous flock outbreaks with remarkable virus evolution scenarios. Along with current pre-pandemic preparedness efforts, comprehensive surveillance of H5Nx viruses in wild birds, domestic poultry, and mammals, including humans, in endemic areas is critical to explore the public health risk of the newly emerging immune-evasive or drug-resistant H5Nx variants.
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Affiliation(s)
- Ahlam Alasiri
- Department of Basic Sciences, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia; (A.A.); (R.S.)
| | - Raya Soltane
- Department of Basic Sciences, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia; (A.A.); (R.S.)
| | - Akram Hegazy
- Department of Agricultural Microbiology, Faculty of Agriculture, Cairo University, Giza District, Giza 12613, Egypt;
| | - Ahmed Magdy Khalil
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA;
- Department of Zoonotic Diseases, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44519, Egypt
| | - Sara H. Mahmoud
- Center of Scientific Excellence for Influenza Viruses, National Research Center, Giza 12622, Egypt;
| | - Ahmed A. Khalil
- Veterinary Sera and Vaccines Research Institute (VSVRI), Agriculture Research Center (ARC), Cairo 11435, Egypt;
| | | | - Ahmed Mostafa
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA;
- Center of Scientific Excellence for Influenza Viruses, National Research Center, Giza 12622, Egypt;
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2
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Detection and Characterization of an H9N2 Influenza A Virus in the Egyptian Rousette Bat in Limpopo, South Africa. Viruses 2023; 15:v15020498. [PMID: 36851712 PMCID: PMC9958621 DOI: 10.3390/v15020498] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
In recent years, bats have been shown to host various novel bat-specific influenza viruses, including H17N10 and H18N11 in the Americas and the H9N2 subtype from Africa. Rousettus aegyptiacus (Egyptian Rousette bat) is recognized as a host species for diverse viral agents. This study focused on the molecular surveillance of a maternal colony in Limpopo, South Africa, between 2017-2018. A pan-influenza hemi-nested RT-PCR assay targeting the PB1 gene was established, and influenza A virus RNA was identified from one fecal sample out of 860 samples. Genome segments were recovered using segment-specific amplification combined with standard Sanger sequencing and Illumina unbiased sequencing. The identified influenza A virus was closely related to the H9N2 bat-influenza virus, confirming the circulation of this subtype among Egyptian fruit bat populations in Southern Africa. This bat H9N2 subtype contained amino acid residues associated with transmission and virulence in either mammalian or avian hosts, though it will likely require additional adaptations before spillover.
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3
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Yehia N, Salem HM, Mahmmod Y, Said D, Samir M, Mawgod SA, Sorour HK, AbdelRahman MAA, Selim S, Saad AM, El-Saadony MT, El-Meihy RM, Abd El-Hack ME, El-Tarabily KA, Zanaty AM. Common viral and bacterial avian respiratory infections: an updated review. Poult Sci 2023; 102:102553. [PMID: 36965253 PMCID: PMC10064437 DOI: 10.1016/j.psj.2023.102553] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 01/24/2023] [Accepted: 01/28/2023] [Indexed: 02/04/2023] Open
Abstract
Many pathogens that cause chronic diseases in birds use the respiratory tract as a primary route of infection, and respiratory disorders are the main leading source of financial losses in the poultry business. Respiratory infections are a serious problem facing the poultry sector, causing severe economic losses. Avian influenza virus, Newcastle disease virus, infectious bronchitis virus, and avian pneumovirus are particularly serious viral respiratory pathogens. Mycoplasma gallisepticum, Staphylococcus, Bordetella avium, Pasteurella multocida, Riemerella anatipestifer, Chlamydophila psittaci, and Escherichia coli have been identified as the most serious bacterial respiratory pathogens in poultry. This review gives an updated summary, incorporating the latest data, about the evidence for the circulation of widespread, economically important poultry respiratory pathogens, with special reference to possible methods for the control and prevention of these pathogens.
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Affiliation(s)
- Nahed Yehia
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza 12618, Egypt
| | - Heba M Salem
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | - Yasser Mahmmod
- Department of Veterinary Sciences, Faculty of Health Sciences, Higher Colleges of Technology, Al Ain 17155, United Arab Emirates
| | - Dalia Said
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza 12618, Egypt
| | - Mahmoud Samir
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza 12618, Egypt
| | - Sara Abdel Mawgod
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza 12618, Egypt
| | - Hend K Sorour
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza 12618, Egypt
| | - Mona A A AbdelRahman
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza 12618, Egypt
| | - Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72388, Saudi Arabia
| | - Ahmed M Saad
- Department of Biochemistry, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Mohamed T El-Saadony
- Department of Agricultural Microbiology, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Rasha M El-Meihy
- Department of Agricultural Microbiology, Faculty of Agriculture, Benha University, Moshtohor, Qaluybia 13736, Egypt
| | - Mohamed E Abd El-Hack
- Poultry Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Khaled A El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al Ain 15551, United Arab Emirates; Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain 15551, United Arab Emirates; Harry Butler Institute, Murdoch University, Murdoch 6150, Western Australia, Australia.
| | - Ali M Zanaty
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza 12618, Egypt
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4
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Machine Learning for the Prediction of Antiviral Compounds Targeting Avian Influenza A/H9N2 Viral Proteins. Symmetry (Basel) 2022. [DOI: 10.3390/sym14061114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Avian influenza subtype A/H9N2—which infects chickens, reducing egg production by up to 80%—may be transmissible to humans. In humans, this virus is very harmful since it attacks the respiratory system and reproductive tract, replicating in both. Previous attempts to find antiviral candidates capable of inhibiting influenza A/H9N2 transmission were unsuccessful. This study aims to better characterize A/H9N2 to facilitate the discovery of antiviral compounds capable of inhibiting its transmission. The Symmetry of this study is to apply several machine learning methods to perform virtual screening to identify H9N2 antivirus candidates. The parameters used to measure the machine learning model’s quality included accuracy, sensitivity, specificity, balanced accuracy, and receiver operating characteristic score. We found that the extreme gradient boosting method yielded better results in classifying compounds predicted to be suitable antiviral compounds than six other machine learning methods, including logistic regression, k-nearest neighbor analysis, support vector machine, multilayer perceptron, random forest, and gradient boosting. Using this algorithm, we identified 10 candidate synthetic compounds with the highest scores. These high scores predicted that the molecular fingerprint may involve strong bonding characteristics. Thus, we were able to find significant candidates for synthetic H9N2 antivirus compounds and identify the best machine learning method to perform virtual screenings.
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El-Sayed MM, Arafa AS, Abdelmagid M, Youssef AI. Epidemiological surveillance of H9N2 avian influenza virus infection among chickens in farms and backyards in Egypt 2015-2016. Vet World 2021; 14:949-955. [PMID: 34083945 PMCID: PMC8167522 DOI: 10.14202/vetworld.2021.949-955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/02/2021] [Indexed: 11/29/2022] Open
Abstract
Background and Aim: LPAI H9N2 infection among the poultry population in Egypt constitutes an additional risk factor in the poultry industry. This study aimed to determine the prevalence of H9N2 avian influenza virus (AIV) in commercial and backyard chickens in Egypt. A 2-year survey of H9N2 AIV in chickens in farms and backyards was carried out in 2015 and 2016. Materials and Methods: Direct detection of H9N2 AIV was performed by detecting the virus in tracheal and cloacal swabs using real-time polymerase chain reaction assays. A total of 20,421 samples were collected from chickens in farms and backyards in 26 Egyptian governorates. Results: In 2015, cases positive for H9N2 AIV numbered 388 (3.9%) out of 10,016 examined cases. However, in 2016, the total positive cases numbered 447 (4.3%) out of 10,405 examined cases. The prevalence of H9N2 AIV among chickens on commercial farms was 4.6% out of the 16,666 chickens examined. The rates of positive cases in 2015 and 2016 were 4.4% (349/7884) and 4.7% (417/8782), respectively. The prevalence of H9N2 AIV in backyard chickens was 1.8% (69/3755). The rates of positive cases in backyard chickens were 1.8% (39/2132) in 2015 and again 1.8% (30/1623) in 2016. The highest positivity rate of H9N2 in chicken farms was in Beni-Suef (61.5%) (8/13), whereas the highest positivity rate in backyard chickens was in Fayoum (8.2%) (8/97). Conclusion: The analysis of H9N2 infections among chicken farms and in backyard chickens in the different governorates of Egypt over 2 years indicated widespread infection throughout the country. Thus, continuous surveillance and implementation of control programs are warranted.
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Affiliation(s)
- Moataz Mohamed El-Sayed
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, P.O. Box 264, Dokki, Giza 12618, Egypt
| | - Abdel Satar Arafa
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, P.O. Box 264, Dokki, Giza 12618, Egypt
| | - Marwa Abdelmagid
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, P.O. Box 264, Dokki, Giza 12618, Egypt
| | - Ahmed Ibrahim Youssef
- Animal Hygiene and Zoonoses, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, 41522, Egypt
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6
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Adel A, Mosaad Z, Shalaby AG, Selim K, Samy M, Abdelmagid MA, Hagag NM, Arafa AS, Hassan WM, Shahien MA. Molecular evolution of the hemagglutinin gene and epidemiological insight into low-pathogenic avian influenza H9N2 viruses in Egypt. Res Vet Sci 2021; 136:540-549. [PMID: 33887563 DOI: 10.1016/j.rvsc.2021.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 03/19/2021] [Accepted: 04/12/2021] [Indexed: 10/21/2022]
Abstract
Despite the low pathogenicity of the H9N2 avian influenza viruses, they can induce severe economic losses in various poultry sectors in conjunction with other factors. In Egypt, low-pathogenic avian influenza (LPAI) H9N2 became endemic in 2011 and has undergone continuous genetic evolution since then. The regular monitoring of the evolution of the virus is necessary to control its spread. During 2017-2020, there were 44 positive samples isolated, and these viruses were genetically sequenced to determine the hemagglutinin (HA) gene circulating in Egypt. The molecular analysis revealed at least nine changes in amino acid residues in comparison with the reference Egyptian strain from the original introduction in 2011 (A/qu/Egypt/113413v/2011), with a similarity of 95%-96%. Amino acid residues 180 and 216 are the most important residues in terms of positive selection pressure. Phylogenetically, the new Egyptian H9N2 viruses in 2017-2020 belonged to a new subcluster related to the strains that had been circulating since 2015. Comparative analysis of the HA gene of LPAI H9N2 viruses in Egypt from 2011 to 2020 supports a continuous evolution through the years with persistent markers.
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Affiliation(s)
- Amany Adel
- Reference Laboratory for Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza 12618, Egypt.
| | - Zienab Mosaad
- Reference Laboratory for Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza 12618, Egypt
| | - Azhar G Shalaby
- Reference Laboratory for Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza 12618, Egypt
| | - Karim Selim
- Reference Laboratory for Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza 12618, Egypt
| | - Mohamed Samy
- Reference Laboratory for Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza 12618, Egypt
| | - Marwa A Abdelmagid
- Reference Laboratory for Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza 12618, Egypt
| | - Naglaa M Hagag
- Reference Laboratory for Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza 12618, Egypt
| | - Abdel Satar Arafa
- Reference Laboratory for Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza 12618, Egypt
| | - Wafaa M Hassan
- Reference Laboratory for Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza 12618, Egypt
| | - Momtaz A Shahien
- Reference Laboratory for Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza 12618, Egypt
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7
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Zhang X, Zhao Q, Wu C, Xie Z, Ci X, Li H, Lin W, Zhang H, Xie Q. Nitrate Is Crucial for the Proliferation of Gut Escherichia coli Caused by H9N2 AIV Infection and Effective Regulation by Chinese Herbal Medicine Ageratum-Liquid. Front Microbiol 2020; 11:555739. [PMID: 33193136 PMCID: PMC7662154 DOI: 10.3389/fmicb.2020.555739] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 10/12/2020] [Indexed: 12/12/2022] Open
Abstract
H9N2 avian influenza virus (AIV) infection in chickens is often accompanied by secondary bacterial infection, but the mechanism is unclear. The aim of the present study was to reveal that mechanism and explore non-antibiotic treatment. 16s rRNA sequencing and metabonomics were performed in the intestinal contents of chickens infected with H9N2 AIV or H9N2 AIV and fed with ageratum-liquid (AL) to reveal the metabolite that promote intestinal Escherichia coli (E. coli) proliferation caused by H9N2 AIV, as well as to determine the regulatory effect of AL. It was found that H9N2 AIV infection led E. coli to become the dominant gut microbe and promoted E. coli translocation from the intestinal tract to the visceral tissue through the damaged intestinal barrier. H9N2 AIV infection induces inflammation in the intestinal mucosa and promotes the secretion and release of nitrate from the host intestinal epithelium. In addition, nitrate promoted E. coli proliferation in the inflamed intestinal tract following H9N2 AIV infection. Furthermore, Chinese herbal medicine AL can restore intestinal homeostasis, inhibit the production of nitrate in the intestinal epithelium and effectively prevent the proliferation and translocation of E. coli in the intestines. This is the first report on the mechanism of E. coli secondary infection induced by H9N2 AIV, where herbal medicine AL was shown to have a good preventive effect on the secondary infection.
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Affiliation(s)
- Xinheng Zhang
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China.,Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China.,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Qiqi Zhao
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China.,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Che Wu
- College of Animal Science, South China Agricultural University, Guangzhou, China.,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Zi Xie
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China.,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Xiaotong Ci
- College of Animal Science, South China Agricultural University, Guangzhou, China.,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Hongxin Li
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China.,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Wencheng Lin
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China.,Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China.,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Huanmin Zhang
- USDA, Agriculture Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI, United States
| | - Qingmei Xie
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China.,Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China.,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
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Immunization of turkeys with a DNA vaccine expressing the haemagglutinin gene of low pathogenic avian influenza virus subtype H9N2. J Virol Methods 2020; 284:113938. [PMID: 32663531 DOI: 10.1016/j.jviromet.2020.113938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/22/2020] [Accepted: 07/09/2020] [Indexed: 01/25/2023]
Abstract
Low pathogenic avian influenza H9N2 is still circulating in the Middle East causing respiratory manifestations and severe economic losses in poultry. In the present study, an H9 plasmid-based DNA vaccine targeting the HA gene of H9N2 A/CK/Egypt/SCU8/2014 was developed and evaluated in turkeys. The full length of HA was cloned into vector plasmids under the control of a cytomegalovirus promoter. The in-vitro expression of the recombinant HA was demonstrated in HeLa cells transfected with the plasmids pVAX1-H9 or pCR-H9 using western blot and Immunofluorescent assay (IFA). The efficacy of pVAX-H9 and pCR- H9, naked or saponin-adjuvanted, was evaluated in turkey poults at 3 weeks and challenged with A/CK/Egypt/SCU8/2014 (106 EID50/bird at 3 weeks post-vaccination. The efficacy was assesses based on virus shedding, oropharyngeal and cloacal, as well as seroconversion using haemagglutination inhibition (HI) test. All immunized birds showed high HI antibody titers (7-8 log2) at 3 weeks post-vaccination. None of the birds vaccinated with naked or saponin-adjuvanted pVAX-H9 or pCR-H9 showed any clinical signs. The pVAX-H9 and pCR-H9 alone did not prevent cloacal and oropharyngeal virus shedding, however, saponin-adjuvanted pVAX1-H9 and pCR-H9 prevented cloacal and oropharyngeal virus shedding at 3 and 5 days post challenge, respectively. In conclusion, DNA vaccination with pVAX1-H9 and pCR-H9 could protect turkey from the H9N2 virus, but vaccination regimes need to be improved.
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9
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Li R, Adel A, Bohlin J, Lundkvist Å, Olsen B, Pettersson JHO, Naguib MM. Phylogeographic Dynamics of Influenza A(H9N2) Virus Crossing Egypt. Front Microbiol 2020; 11:392. [PMID: 32265861 PMCID: PMC7105594 DOI: 10.3389/fmicb.2020.00392] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 02/25/2020] [Indexed: 11/23/2022] Open
Abstract
Low pathogenic avian influenza (LPAI) virus of subtype H9N2 is the most frequently detected subtype among domestic poultry and is a public health concern because of its zoonotic potential. Due to the multiple and complex routes of LPAIV H9N2 between geographic regions, little is known about the spatial diffusion of H9N2 virus to, within, and from Egypt, where it is endemic among poultry since 2011. Using close to 800 publicly available hemagglutinin (HA) segment nucleotide sequences, associated location and temporal data, we conducted a Bayesian discrete phylogeographic analysis. Here, we reconstructed and traced the origin, spread and principal transmission routes of H9N2 across large geographical regions, in addition to the transmission between Egypt and the rest of the world and between different Egyptian governorates. Our analysis suggests that during the last few decades, H9N2 has been introduced back and forth continuously between the countries where it is endemic. Amongst these regions, Saudi Arabia, United Arab Emirates and Iraq act as main distribution hubs and drive the viral migration worldwide, with bi-directional and long-distance diffusions. It is noteworthy that H9N2 was introduced once to Egypt via Israel in mid 2009, and that the descendants of the Egyptian LAIVs H9N2 were back-transmitted to Israel in 2015. Additionally, governorates in middle Egypt (Giza, Fayoum and Bani Souwaif) are major hubs in the LPAIV H9N2 transmission network in Egypt. This knowledge highlights that H9N2 is both a global and a national concern and can aid in updating the surveillance program and vaccine strain selection.
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Affiliation(s)
- Ruiyun Li
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Amany Adel
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Jon Bohlin
- Department of Infectious Disease Epidemiology and Modelling, Domain for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Åke Lundkvist
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Björn Olsen
- Department of Medical Sciences, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - John H-O Pettersson
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden.,Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life & Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Mahmoud M Naguib
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt.,Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
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