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Rabalski L, Kosinski M, Cybulski P, Stadejek T, Lepek K. Genetic Diversity of Type A Influenza Viruses Found in Swine Herds in Northwestern Poland from 2017 to 2019: The One Health Perspective. Viruses 2023; 15:1893. [PMID: 37766299 PMCID: PMC10536349 DOI: 10.3390/v15091893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Influenza A viruses (IAV) are still a cause of concern for public health and veterinary services worldwide. With (-) RNA-segmented genome architecture, influenza viruses are prone to reassortment and can generate a great variety of strains, some capable of crossing interspecies barriers. Seasonal IAV strains continuously spread from humans to pigs, leading to multiple reassortation events with strains endemic to swine. Due to its high adaptability to humans, a reassortant strain based on "human-like" genes could potentially be a carrier of avian origin segments responsible for high virulence, and hence become the next pandemic strain with unseen pathogenicity. The rapid evolution of sequencing methods has provided a fast and cost-efficient way to assess the genetic diversity of IAV. In this study, we investigated the genetic diversity of swine influenza viruses (swIAVs) collected from Polish farms. A total of 376 samples were collected from 11 farms. The infection was confirmed in 112 cases. The isolates were subjected to next-generation sequencing (NGS), resulting in 93 full genome sequences. Phylogenetic analysis classified 59 isolates as genotype T (H1avN2g) and 34 isolates as genotype P (H1pdmN1pdm), all of which had an internal gene cassette (IGC) derived from the H1N1pdm09-like strain. These data are consistent with evolutionary trends in European swIAVs. The applied methodology proved to be useful in monitoring the genetic diversity of IAV at the human-animal interface.
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Affiliation(s)
- Lukasz Rabalski
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
- Biological Threats Identification and Countermeasure Center of the General Karol Kaczkowski Military Institute of Hygiene and Epidemiology, Lubelska 4 St, 24-100 Pulawy, Poland
| | - Maciej Kosinski
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Piotr Cybulski
- Goodvalley Agro S.A., Dworcowa 25, 77-320 Przechlewo, Poland
| | - Tomasz Stadejek
- Department of Pathology and Veterinary Diagnostic, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, 02-776 Warsaw, Poland
| | - Krzysztof Lepek
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
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AbuBakar U, Amrani L, Kamarulzaman FA, Karsani SA, Hassandarvish P, Khairat JE. Avian Influenza Virus Tropism in Humans. Viruses 2023; 15:833. [PMID: 37112812 PMCID: PMC10142937 DOI: 10.3390/v15040833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/12/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023] Open
Abstract
An influenza pandemic happens when a novel influenza A virus is able to infect and transmit efficiently to a new, distinct host species. Although the exact timing of pandemics is uncertain, it is known that both viral and host factors play a role in their emergence. Species-specific interactions between the virus and the host cell determine the virus tropism, including binding and entering cells, replicating the viral RNA genome within the host cell nucleus, assembling, maturing and releasing the virus to neighboring cells, tissues or organs before transmitting it between individuals. The influenza A virus has a vast and antigenically varied reservoir. In wild aquatic birds, the infection is typically asymptomatic. Avian influenza virus (AIV) can cross into new species, and occasionally it can acquire the ability to transmit from human to human. A pandemic might occur if a new influenza virus acquires enough adaptive mutations to maintain transmission between people. This review highlights the key determinants AIV must achieve to initiate a human pandemic and describes how AIV mutates to establish tropism and stable human adaptation. Understanding the tropism of AIV may be crucial in preventing virus transmission in humans and may help the design of vaccines, antivirals and therapeutic agents against the virus.
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Affiliation(s)
- Umarqayum AbuBakar
- Institute of Biological Sciences (ISB), Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Lina Amrani
- Institute of Biological Sciences (ISB), Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Farah Ayuni Kamarulzaman
- Institute of Biological Sciences (ISB), Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Saiful Anuar Karsani
- Institute of Biological Sciences (ISB), Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Pouya Hassandarvish
- Tropical Infectious Diseases Research and Education Center, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Jasmine Elanie Khairat
- Institute of Biological Sciences (ISB), Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
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Martins de Camargo M, Caetano AR, Ferreira de Miranda Santos IK. Evolutionary pressures rendered by animal husbandry practices for avian influenza viruses to adapt to humans. iScience 2022; 25:104005. [PMID: 35313691 PMCID: PMC8933668 DOI: 10.1016/j.isci.2022.104005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Commercial poultry operations produce and crowd billions of birds every year, which is a source of inexpensive animal protein. Commercial poultry is intensely bred for desirable production traits, and currently presents very low variability at the major histocompatibility complex. This situation dampens the advantages conferred by the MHC’s high genetic variability, and crowding generates immunosuppressive stress. We address the proteins of influenza A viruses directly and indirectly involved in host specificities. We discuss how mutants with increased virulence and/or altered host specificity may arise if few class I alleles are the sole selective pressure on avian viruses circulating in immunocompromised poultry. This hypothesis is testable with peptidomics of MHC ligands. Breeding strategies for commercial poultry can easily and inexpensively include high variability of MHC as a trait of interest, to help save billions of dollars as a disease burden caused by influenza and decrease the risk of selecting highly virulent strains.
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Cellular 5'-3' mRNA Exoribonuclease XRN1 Inhibits Interferon Beta Activation and Facilitates Influenza A Virus Replication. mBio 2021; 12:e0094521. [PMID: 34311580 PMCID: PMC8406323 DOI: 10.1128/mbio.00945-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Cellular 5′-3′ exoribonuclease 1 (XRN1) is best known for its role as a decay factor, which by degrading 5′ monophosphate RNA after the decapping of DCP2 in P-bodies (PBs) in Drosophila, yeast, and mammals. XRN1 has been shown to degrade host antiviral mRNAs following the influenza A virus (IAV) PA-X-mediated exonucleolytic cleavage processes. However, the mechanistic details of how XRN1 facilitates influenza A virus replication remain unclear. In this study, we discovered that XRN1 and nonstructural protein 1 (NS1) of IAV are directly associated and colocalize in the PBs. Moreover, XRN1 downregulation impaired viral replication while the viral titers were significantly increased in cells overexpressing XRN1, which suggest that XRN1 is a positive regulator in IAV life cycle. We further demonstrated that the IAV growth curve could be suppressed by adenosine 3′,5′-bisphosphate (pAp) treatment, an inhibitor of XRN1. In virus-infected XRN1 knockout cells, the phosphorylated interferon regulatory factor 3 (p-IRF3) protein, interferon beta (IFN-β) mRNA, and interferon-stimulated genes (ISGs) were significantly increased, resulting in the enhancement of the host innate immune response and suppression of viral protein production. Our data suggest a novel mechanism by which the IAV hijacks the cellular XRN1 to suppress the host innate immune response and to facilitate viral replication.
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Li X, Zhang L, Liu Y, Ma L, Zhang N, Xia C. Structures of the MHC-I molecule BF2*1501 disclose the preferred presentation of an H5N1 virus-derived epitope. J Biol Chem 2020; 295:5292-5306. [PMID: 32152225 PMCID: PMC7170506 DOI: 10.1074/jbc.ra120.012713] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/06/2020] [Indexed: 01/05/2023] Open
Abstract
Lethal infections by strains of the highly-pathogenic avian influenza virus (HPAIV) H5N1 pose serious threats to both the poultry industry and public health worldwide. A lack of confirmed HPAIV epitopes recognized by cytotoxic T lymphocytes (CTLs) has hindered the utilization of CD8+ T-cell-mediated immunity and has precluded the development of effectively diversified epitope-based vaccination approaches. In particular, an HPAIV H5N1 CTL-recognized epitope based on the peptide MHC-I-β2m (pMHC-I) complex has not yet been designed. Here, screening a collection of selected peptides of several HPAIV strains against a specific pathogen-free pMHC-I (pBF2*1501), we identified a highly-conserved HPAIV H5N1 CTL epitope, named HPAIV-PA123-130 We determined the structure of the BF2*1501-PA123-130 complex at 2.1 Å resolution to elucidate the molecular mechanisms of a preferential presentation of the highly-conserved PA123-130 epitope in the chicken B15 lineage. Conformational characteristics of the PA123-130 epitope with a protruding Tyr-7 residue indicated that this epitope has great potential to be recognized by specific TCRs. Moreover, significantly increased numbers of CD8+ T cells specific for the HPAIV-PA123-130 epitope in peptide-immunized chickens indicated that a repertoire of CD8+ T cells can specifically respond to this epitope. We anticipate that the identification and structural characterization of the PA123-130 epitope reported here could enable further studies of CTL immunity against HPAIV H5N1. Such studies may aid in the development of vaccine development strategies using well-conserved internal viral antigens in chickens.
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Affiliation(s)
- Xiaoying Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100094, People's Republic of China; School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, People's Republic of China
| | - Lijie Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100094, People's Republic of China
| | - Yanjie Liu
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100094, People's Republic of China; Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture, Institute of Apiculture, Chinese Academy of Agricultural Sciences, Beijing 100093, People's Republic of China
| | - Lizhen Ma
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100094, People's Republic of China
| | - Nianzhi Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100094, People's Republic of China
| | - Chun Xia
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100094, People's Republic of China; Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, China Agricultural University, Beijing 100094, People's Republic of China.
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Martelli P, Teng JLL, Lee FK, Yeong KY, Fong JYH, Hui SW, Chan KH, Lau SKP, Woo PCY. Influenza A(H1N1)pdm09 Virus Infection in a Captive Giant Panda, Hong Kong. Emerg Infect Dis 2020; 25:2303-2306. [PMID: 31742520 PMCID: PMC6874238 DOI: 10.3201/eid2512.191143] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
We report influenza A(H1N1)pdm09 virus infection in a captive giant panda in Hong Kong. The viral load peaked on day 1 and became undetectable on day 5, and an antibody response developed. Genome analysis showed 99.3%-99.9% nucleotide identity between the virus and influenza A(H1N1)pdm09 virus circulating in Hong Kong.
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Elhakim M, Hafiz Rasooly M, Fahim M, Sheikh Ali S, Haddad N, Cherkaoui I, Hjaija D, Nadeem S, Assiri A, Aljifri A, Elkholy A, Barakat A, Shrestha B, Abubakar A, Malik SMMR. Epidemiology of severe cases of influenza and other acute respiratory infections in the Eastern Mediterranean Region, July 2016 to June 2018. J Infect Public Health 2020; 13:423-429. [PMID: 31281105 PMCID: PMC7102678 DOI: 10.1016/j.jiph.2019.06.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 06/11/2019] [Accepted: 06/12/2019] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Influenza surveillance systems in the Eastern Mediterranean Region have been strengthened in the past few years and 16 of the 19 countries in the Region with functional influenza surveillance systems report their influenza data to the EMFLU Network. This study aimed to investigate the epidemiology of circulating influenza viruses, causing SARI, and reported to the EMFLU during July 2016 to June 2018. METHODS Data included in this study were collected by 15 countries of the Region from 110 SARI sentinel surveillance sites over two influenza seasons. RESULTS A total of 40,917 cases of SARI were included in the study. Most cases [20,551 (50.2%)] were less than 5years of age. Influenza virus was detected in 3995 patients, 2849 (11.8%) were influenza A and 1146 (4.8%) were influenza B. Influenza A(H1N1)pdm09 was the predominant circulating subtype with 1666 cases (58.5%). Other than influenza, respiratory syncytial virus was the most common respiratory infection circulating, with 277 cases (35.9%). CONCLUSION Influenza viruses cause a high number of severe respiratory infections in EMR. It is crucial for the countries to continue improving their influenza surveillance capacity in order detect any unusual influenza activity or new strain that may cause a pandemic.
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Affiliation(s)
- Mohamed Elhakim
- Infectious Hazard Management Unit, Department of Health Emergencies, World Health Organization, Regional Office for the Eastern Mediterranean, Cairo, Egypt.
| | - Mohammad Hafiz Rasooly
- Surveillance/National Influenza Coordinator, EHIS DG, Surveillance Department, Ministry of Public Health, Kabul, Afghanistan
| | - Manal Fahim
- Department of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and Population, Cairo, Egypt
| | - Sami Sheikh Ali
- Data Analysis Division, Influenza Surveillance Focal Point, Communicable Diseases Directorate, Ministry of Health, Amman, Jordan
| | - Nadine Haddad
- Epidemiological Surveillance Program, Ministry of Public Health, Beirut, Lebanon
| | - Imad Cherkaoui
- Influenza Surveillance Focal Point, Directorate of Epidemiology, Ministry of Health, Rabat, Morocco
| | - Diaa Hjaija
- Palestinian Ministry of Health, Ramallah, occupied Palestinian territory
| | - Shazia Nadeem
- Public Health Department, Ministry of Public Health, Doha, Qatar
| | | | - Alanoud Aljifri
- Influenza Surveillance Focal Point, Adult Infectious Disease Consultant, Ministry of Health, Riyadh, Saudi Arabia
| | - Amgad Elkholy
- Infectious Hazard Management Unit, Department of Health Emergencies, World Health Organization, Regional Office for the Eastern Mediterranean, Cairo, Egypt
| | - Amal Barakat
- Infectious Hazard Management Unit, Department of Health Emergencies, World Health Organization, Regional Office for the Eastern Mediterranean, Cairo, Egypt
| | - Bhagawan Shrestha
- Infectious Hazard Management Unit, Department of Health Emergencies, World Health Organization, Regional Office for the Eastern Mediterranean, Cairo, Egypt
| | - Abdinasir Abubakar
- Infectious Hazard Management Unit, Department of Health Emergencies, World Health Organization, Regional Office for the Eastern Mediterranean, Cairo, Egypt
| | - Sk Md Mamunur R Malik
- Infectious Hazard Management Unit, Department of Health Emergencies, World Health Organization, Regional Office for the Eastern Mediterranean, Cairo, Egypt
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Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. Pathogens 2019; 8:pathogens8040194. [PMID: 31635227 PMCID: PMC6963832 DOI: 10.3390/pathogens8040194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 09/27/2019] [Accepted: 10/01/2019] [Indexed: 01/16/2023] Open
Abstract
The hemagglutinin (HA) is a major influenza virus antigen, which, once recognized by antibodies and substitutions in HA genes, helps virus in escaping the human immune response. It is therefore critical to perform genetic and phylogenetic analysis of HA in circulating influenza viruses. We performed phylogenetic and genetic analysis of isolates from Ukraine, the vaccine strain and reference strains were used to phylogenetically identify trends in mutation locations and substitutions. Ukrainian isolates were collected between 2009–2017 and clustered in the influenza genetic groups 2, 6, 7, and 8. Genetic changes were observed in each of the antigenic sites: Sa – S162T, K163Q, K163I; Sb – S185T, A186T, S190G, S190R; Ca1 – S203T, R205K, E235V, E235D, S236P; Ca2 – P137H, H138R, A141T, D222G, D222N; Cb – A73S, S74R, S74N. In spite of detected mutations in antigenic sites, Ukrainian isolates retained similarity to the vaccine strain A/California/07/09 circulated during 2009–2017. However, WHO recommended a new vaccine strain A/Michigan/45/2015 for the Southern Hemisphere after the emergence of the new genetic groups 6B.1 and 6B.2. Our study demonstrated genetic variability of HA protein of A(H1N1)pdm09 viruses isolated in 2009–2017 in Ukraine. Influenza surveillance is very important for understanding epidemiological situations.
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