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Murashkina T, Sharshov K, Gadzhiev A, Petherbridge G, Derko A, Sobolev I, Dubovitskiy N, Loginova A, Kurskaya O, Kasianov N, Kabilov M, Mine J, Uchida Y, Tsunekuni R, Saito T, Alekseev A, Shestopalov A. Avian Influenza Virus and Avian Paramyxoviruses in Wild Waterfowl of the Western Coast of the Caspian Sea (2017-2020). Viruses 2024; 16:598. [PMID: 38675939 PMCID: PMC11054612 DOI: 10.3390/v16040598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
The flyways of many different wild waterfowl pass through the Caspian Sea region. The western coast of the middle Caspian Sea is an area with many wetlands, where wintering grounds with large concentrations of birds are located. It is known that wild waterfowl are a natural reservoir of the influenza A virus. In the mid-2000s, in the north of this region, the mass deaths of swans, gulls, and pelicans from high pathogenicity avian influenza virus (HPAIV) were noted. At present, there is still little known about the presence of avian influenza virus (AIVs) and different avian paramyxoviruses (APMVs) in the region's waterfowl bird populations. Here, we report the results of monitoring these viruses in the wild waterfowl of the western coast of the middle Caspian Sea from 2017 to 2020. Samples from 1438 individuals of 26 bird species of 7 orders were collected, from which 21 strains of AIV were isolated, amounting to a 1.46% isolation rate of the total number of samples analyzed (none of these birds exhibited external signs of disease). The following subtypes were determined and whole-genome nucleotide sequences of the isolated strains were obtained: H1N1 (n = 2), H3N8 (n = 8), H4N6 (n = 2), H7N3 (n = 2), H8N4 (n = 1), H10N5 (n = 1), and H12N5 (n = 1). No high pathogenicity influenza virus H5 subtype was detected. Phylogenetic analysis of AIV genomes did not reveal any specific pattern for viruses in the Caspian Sea region, showing that all segments belong to the Eurasian clades of classic avian-like influenza viruses. We also did not find the amino acid substitutions in the polymerase complex (PA, PB1, and PB2) that are critical for the increase in virulence or adaptation to mammals. In total, 23 hemagglutinating viruses not related to influenza A virus were also isolated, of which 15 belonged to avian paramyxoviruses. We were able to sequence 12 avian paramyxoviruses of three species, as follows: Newcastle disease virus (n = 4); Avian paramyxovirus 4 (n = 5); and Avian paramyxovirus 6 (n = 3). In the Russian Federation, the Newcastle disease virus of the VII.1.1 sub-genotype was first isolated from a wild bird (common pheasant) in the Caspian Sea region. The five avian paramyxovirus 4 isolates obtained belonged to the common clade in Genotype I, whereas phylogenetic analysis of three isolates of Avian paramyxovirus 6 showed that two isolates, isolated in 2017, belonged to Genotype I and that an isolate identified in 2020 belonged to Genotype II. The continued regular monitoring of AIVs and APMVs, the obtaining of data on the biological properties of isolated strains, and the accumulation of information on virus host species will allow for the adequate planning of epidemiological measures, suggest the most likely routes of spread of the virus, and assist in the prediction of the introduction of the viruses in the western coastal region of the middle Caspian Sea.
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Affiliation(s)
- Tatyana Murashkina
- Federal Research Center of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences (FRC FTM SB RAS), Novosibirsk 630060, Russia; (T.M.); (A.D.); (I.S.); (N.D.); (A.L.); (O.K.); (N.K.); (A.A.); (A.S.)
| | - Kirill Sharshov
- Federal Research Center of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences (FRC FTM SB RAS), Novosibirsk 630060, Russia; (T.M.); (A.D.); (I.S.); (N.D.); (A.L.); (O.K.); (N.K.); (A.A.); (A.S.)
| | - Alimurad Gadzhiev
- Faculty of Ecology and Sustainable Development, Dagestan State University, Makhachkala 367016, Russia;
| | - Guy Petherbridge
- Caspian Centre for Nature Conservation, International Institute of Ecology and Sustainable Development, Association of Universities and Research Centres of Caspian Region States, Makhachkala 367016, Russia;
| | - Anastasiya Derko
- Federal Research Center of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences (FRC FTM SB RAS), Novosibirsk 630060, Russia; (T.M.); (A.D.); (I.S.); (N.D.); (A.L.); (O.K.); (N.K.); (A.A.); (A.S.)
| | - Ivan Sobolev
- Federal Research Center of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences (FRC FTM SB RAS), Novosibirsk 630060, Russia; (T.M.); (A.D.); (I.S.); (N.D.); (A.L.); (O.K.); (N.K.); (A.A.); (A.S.)
| | - Nikita Dubovitskiy
- Federal Research Center of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences (FRC FTM SB RAS), Novosibirsk 630060, Russia; (T.M.); (A.D.); (I.S.); (N.D.); (A.L.); (O.K.); (N.K.); (A.A.); (A.S.)
| | - Arina Loginova
- Federal Research Center of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences (FRC FTM SB RAS), Novosibirsk 630060, Russia; (T.M.); (A.D.); (I.S.); (N.D.); (A.L.); (O.K.); (N.K.); (A.A.); (A.S.)
| | - Olga Kurskaya
- Federal Research Center of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences (FRC FTM SB RAS), Novosibirsk 630060, Russia; (T.M.); (A.D.); (I.S.); (N.D.); (A.L.); (O.K.); (N.K.); (A.A.); (A.S.)
| | - Nikita Kasianov
- Federal Research Center of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences (FRC FTM SB RAS), Novosibirsk 630060, Russia; (T.M.); (A.D.); (I.S.); (N.D.); (A.L.); (O.K.); (N.K.); (A.A.); (A.S.)
| | - Marsel Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia;
| | - Junki Mine
- Division of Transboundary Animal Disease, National Institute of Animal Health, Tsukuba 305-0856, Japan; (J.M.); (Y.U.); (R.T.); (T.S.)
| | - Yuko Uchida
- Division of Transboundary Animal Disease, National Institute of Animal Health, Tsukuba 305-0856, Japan; (J.M.); (Y.U.); (R.T.); (T.S.)
| | - Ryota Tsunekuni
- Division of Transboundary Animal Disease, National Institute of Animal Health, Tsukuba 305-0856, Japan; (J.M.); (Y.U.); (R.T.); (T.S.)
| | - Takehiko Saito
- Division of Transboundary Animal Disease, National Institute of Animal Health, Tsukuba 305-0856, Japan; (J.M.); (Y.U.); (R.T.); (T.S.)
| | - Alexander Alekseev
- Federal Research Center of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences (FRC FTM SB RAS), Novosibirsk 630060, Russia; (T.M.); (A.D.); (I.S.); (N.D.); (A.L.); (O.K.); (N.K.); (A.A.); (A.S.)
| | - Alexander Shestopalov
- Federal Research Center of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences (FRC FTM SB RAS), Novosibirsk 630060, Russia; (T.M.); (A.D.); (I.S.); (N.D.); (A.L.); (O.K.); (N.K.); (A.A.); (A.S.)
- Caspian Centre for Nature Conservation, International Institute of Ecology and Sustainable Development, Association of Universities and Research Centres of Caspian Region States, Makhachkala 367016, Russia;
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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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Rabalski L, Milewska A, Pohlmann A, Gackowska K, Lepionka T, Szczepaniak K, Swiatalska A, Sieminska I, Arent Z, Beer M, Koopmans M, Grzybek M, Pyrc K. Emergence and potential transmission route of avian influenza A (H5N1) virus in domestic cats in Poland, June 2023. Euro Surveill 2023; 28:2300390. [PMID: 37535471 PMCID: PMC10401914 DOI: 10.2807/1560-7917.es.2023.28.31.2300390] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 08/03/2023] [Indexed: 08/05/2023] Open
Abstract
In June 2023, a fatal disease outbreak in cats occurred in Poland. Most cases tested in Poland (29 of 47) were positive for highly pathogenic avian influenza (HPAI) A (H5N1) virus. Genetic analyses revealed clade 2.3.4.4b with point mutations indicative of initial mammalian hosts adaptations. Cat viral sequences were highly similar (n = 21), suggesting a potential common infection source. To investigate possible infection routes, our group tested food samples from affected households. HPAI H5N1 virus was detected in one poultry meat sample.
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Affiliation(s)
- Lukasz Rabalski
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, Gdansk, Poland
- Biological Threats Identification and Countermeasure Centre, Military Institute of Hygiene and Epidemiology, Pulawy, Poland
| | | | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Karolina Gackowska
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Tomasz Lepionka
- Biological Threats Identification and Countermeasure Centre, Military Institute of Hygiene and Epidemiology, Pulawy, Poland
| | - Klaudiusz Szczepaniak
- Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, Poland
| | | | | | | | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Maciej Grzybek
- Institute of Maritime and Tropical Medicine, Medical University of Gdańsk, Gdynia, Poland
| | - Krzysztof Pyrc
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
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Highly pathogenic avian influenza A (H5N1) virus infections in wild carnivores connected to mass mortalities of pheasants in Finland. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 111:105423. [PMID: 36889484 DOI: 10.1016/j.meegid.2023.105423] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/20/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023]
Abstract
Highly pathogenic avian influenza (HPAI) has caused widespread mortality in both wild and domestic birds in Europe during 2020-2022. Virus types H5N8 and H5N1 have dominated the epidemic. Isolated spill-over infections in mammals started to emerge as the epidemic continued. In autumn 2021, HPAI H5N1 caused a series of mass mortality events in farmed and released pheasants (Phasianus colchicus) in a restricted area in southern Finland. Later, in the same area, an otter (Lutra lutra), two red foxes (Vulpes vulpes) and a lynx (Lynx lynx) were found moribund or dead and infected with H5N1 HPAI virus. Phylogenetically, H5N1 strains from pheasants and mammals clustered together. Molecular analyses of the four mammalian virus strains revealed mutations in the PB2 gene segment (PB2-E627K and PB2-D701N) that are known to facilitate viral replication in mammals. This study revealed that avian influenza cases in mammals were spatially and temporally connected with avian mass mortalities suggesting increased infection pressure from birds to mammals.
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Berhane Y, Joseph T, Lung O, Embury-Hyatt C, Xu W, Cottrell P, Raverty S. Isolation and Characterization of Novel Reassortant Influenza A(H10N7) Virus in a Harbor Seal, British Columbia, Canada. Emerg Infect Dis 2022; 28:1480-1484. [PMID: 35731188 PMCID: PMC9239883 DOI: 10.3201/eid2807.212302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We isolated a novel reassortant influenza A(H10N7) virus from a harbor seal in British Columbia, Canada, that died from bronchointerstitial pneumonia. The virus had unique genome constellations involving lineages from North America and Eurasia and polymerase basic 2 segment D701N mutation, associated with adaptation to mammals.
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Fan M, Liang B, Zhao Y, Zhang Y, Liu Q, Tian M, Zheng Y, Xia H, Suzuki Y, Chen H, Ping J. Mutations of 127, 183 and 212 residues on the HA globular head affect the antigenicity, replication and pathogenicity of H9N2 avian influenza virus. Transbound Emerg Dis 2021; 69:e659-e670. [PMID: 34724348 DOI: 10.1111/tbed.14363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/04/2021] [Accepted: 09/29/2021] [Indexed: 11/27/2022]
Abstract
H9N2 avian influenza virus (AIV), one of the predominant subtypes devastating the poultry industry, has been circulating widely in the poultry population and causing huge economic losses. In this study, two H9N2 viruses with similar genetic backgrounds but different antigenicity were isolated from a poultry farm, namely A/chicken/Jiangsu/75/2018 (JS/75) and A/chicken/Jiangsu/76/2018 (JS/76). Sequence analysis revealed that their surface genes differed in three amino acid residues (127, 183 and 212) on the head of hemagglutinin (HA). To explore the differences between the two viruses in their biological features, six recombinant viruses, including the wild-type or mutant HA and NA of JS/75 and JS/76 were generated with A/Puerto Rico/8/1934 (PR8) backbone via reverse genetics. The chicken challenge study and HI assay data indicated that r-76/PR8 showed the most obvious antigen escape due to 127 and 183 amino acid substitutions in HA gene. Further studies verified that the 127N site was glycosylated in JS/76 and its mutants. Receptor-binding assays showed that all the recombination viruses were prone to bind the human-like receptors, except for the mutants which glycosylated 127N was deleted. Growth kinetics and mice challenge experiments indicated that 127N-glycosylated viruses showed less replication in A549 cells and lower pathogenicity in mice compared with wild-type viruses. Therefore, the glycosylation site and two amino acid alternations in the HA globular head were responsible for the differences in antigenicity and pathogenicity between the two H9N2 isolates. This study is significant in the research of the antigenic variation and vaccine updates for the H9N2 AIV. Also, highlighted the critical functions of glycosylation in the influenza virus on the pathogenicity against mammals.
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Affiliation(s)
- Menglu Fan
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, P. R. China
| | - Bing Liang
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, P. R. China
| | - Yongzhen Zhao
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, P. R. China
| | - Yaping Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Qingzheng Liu
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, P. R. China
| | - Miao Tian
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, P. R. China
| | - Yiqing Zheng
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, P. R. China
| | - Huizhi Xia
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, P. R. China
| | - Yasuo Suzuki
- College of Life and Health Sciences, Chubu University, Aichi, Japan
| | - Hualan Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Jihui Ping
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, P. R. China
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Xu G, Wang F, Li Q, Bing G, Xie S, Sun S, Bian Z, Sun H, Feng Y, Peng X, Jiang H, Zhu L, Fan X, Qin Y, Ding J. Mutations in PB2 and HA enhanced pathogenicity of H4N6 avian influenza virus in mice. J Gen Virol 2021; 101:910-920. [PMID: 31081750 DOI: 10.1099/jgv.0.001192] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The H4 subtype avian influenza virus (AIV) continues to circulate in both wild birds and poultry, and occasionally infects mammals (e.g. pigs). H4-specific antibodies have also been detected in poultry farm workers, which suggests that H4 AIV poses a potential threat to public health. However, the molecular mechanism by which H4 AIVs could gain adaptation to mammals and whether this has occurred remain largely unknown. To better understand this mechanism, an avirulent H4N6 strain (A/mallard/Beijing/21/2011, BJ21) was serially passaged in mice and mutations were characterized after passaging. A virulent mouse-adapted strain was generated after 12 passages, which was tentatively designated BJ21-MA. The BJ21-MA strain replicated more efficiently than the parental BJ21, both in vivo and in vitro. Molecular analysis of BJ21-MA identified four mutations, located in proteins PB2 (E158K and E627K) and HA (L331I and G453R, H3 numbering). Further studies showed that the introduction of E158K and/or E627K substitutions into PB2 significantly increased polymerase activity, which led to the enhanced replication and virulence of BJ21-MA. Although individual L331I or G453R substitutions in HA did not change the pathogenicity of BJ21 in mice, both mutations significantly enhanced virulence. In conclusion, our data presented in this study demonstrate that avian H4 virus can adapt to mammals by point mutations in PB2 or HA, which consequently poses a potential threat to public health.
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Affiliation(s)
- Guanlong Xu
- National Reference Laboratory for Animal Brucellosis, China Institute of Veterinary Drug Control, Beijing 100081, PR China
| | - Fang Wang
- National Reference Laboratory for Animal Brucellosis, China Institute of Veterinary Drug Control, Beijing 100081, PR China
| | - Qiuchen Li
- National Reference Laboratory for Animal Brucellosis, China Institute of Veterinary Drug Control, Beijing 100081, PR China.,College of Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018 Shandong, PR China
| | - Guoxia Bing
- China Animal Disease Control Center, Beijing 100125, PR China
| | - Shijie Xie
- National Reference Laboratory for Animal Brucellosis, China Institute of Veterinary Drug Control, Beijing 100081, PR China
| | - Shijing Sun
- National Reference Laboratory for Animal Brucellosis, China Institute of Veterinary Drug Control, Beijing 100081, PR China
| | - Zengjie Bian
- National Reference Laboratory for Animal Brucellosis, China Institute of Veterinary Drug Control, Beijing 100081, PR China
| | - HaoJie Sun
- National Reference Laboratory for Animal Brucellosis, China Institute of Veterinary Drug Control, Beijing 100081, PR China
| | - Yu Feng
- National Reference Laboratory for Animal Brucellosis, China Institute of Veterinary Drug Control, Beijing 100081, PR China
| | - Xiaowei Peng
- National Reference Laboratory for Animal Brucellosis, China Institute of Veterinary Drug Control, Beijing 100081, PR China
| | - Hui Jiang
- National Reference Laboratory for Animal Brucellosis, China Institute of Veterinary Drug Control, Beijing 100081, PR China
| | - Liangquan Zhu
- National Reference Laboratory for Animal Brucellosis, China Institute of Veterinary Drug Control, Beijing 100081, PR China
| | - Xuezheng Fan
- National Reference Laboratory for Animal Brucellosis, China Institute of Veterinary Drug Control, Beijing 100081, PR China
| | - Yuming Qin
- National Reference Laboratory for Animal Brucellosis, China Institute of Veterinary Drug Control, Beijing 100081, PR China
| | - Jiabo Ding
- National Reference Laboratory for Animal Brucellosis, China Institute of Veterinary Drug Control, Beijing 100081, PR China
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Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. Int J Mol Sci 2020; 21:ijms21072353. [PMID: 32231159 PMCID: PMC7178042 DOI: 10.3390/ijms21072353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 02/02/2023] Open
Abstract
Highly pathogenic (HP) avian influenza viruses (AIVs) are naturally restricted to H5 and H7 subtypes with a polybasic cleavage site (CS) in hemagglutinin (HA) and any AIV with an intravenous pathogenicity index (IVPI) ≥ 1.2. Although only a few non-H5/H7 viruses fulfill the criteria of HPAIV; it remains unclear why these viruses did not spread in domestic birds. In 2012, a unique H4N2 virus with a polybasic CS 322PEKRRTR/G329 was isolated from quails in California which, however, was avirulent in chickens. This is the only known non-H5/H7 virus with four basic amino acids in the HACS. Here, we investigated the virulence of this virus in chickens after expansion of the polybasic CS by substitution of T327R (322PEKRRRR/G329) or T327K (322PEKRRKR/G329) with or without reassortment with HPAIV H5N1 and H7N7. The impact of single mutations or reassortment on virus fitness in vitro and in vivo was studied. Efficient cell culture replication of T327R/K carrying H4N2 viruses increased by treatment with trypsin, particularly in MDCK cells, and reassortment with HPAIV H5N1. Replication, virus excretion and bird-to-bird transmission of H4N2 was remarkably compromised by the CS mutations, but restored after reassortment with HPAIV H5N1, although not with HPAIV H7N7. Viruses carrying the H4-HA with or without R327 or K327 mutations and the other seven gene segments from HPAIV H5N1 exhibited high virulence and efficient transmission in chickens. Together, increasing the number of basic amino acids in the H4N2 HACS was detrimental for viral fitness particularly in vivo but compensated by reassortment with HPAIV H5N1. This may explain the absence of non-H5/H7 HPAIV in poultry.
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Sharshov K, Mine J, Sobolev I, Kurskaya O, Dubovitskiy N, Kabilov M, Alikina T, Nakayama M, Tsunekuni R, Derko A, Prokopyeva E, Alekseev A, Shchelkanov M, Druzyaka A, Gadzhiev A, Uchida Y, Shestopalov A, Saito T. Characterization and Phylodynamics of Reassortant H12Nx Viruses in Northern Eurasia. Microorganisms 2019; 7:microorganisms7120643. [PMID: 31816947 PMCID: PMC6956379 DOI: 10.3390/microorganisms7120643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 11/19/2019] [Accepted: 11/30/2019] [Indexed: 11/16/2022] Open
Abstract
Wild waterfowl birds are known to be the main reservoir for a variety of avian influenza viruses of different subtypes. Some subtypes, such as H2Nx, H8Nx, H12Nx, and H14Nx, occur relatively rarely in nature. During 10-year long-term surveillance, we isolated five rare H12N5 and one H12N2 viruses in three different distinct geographic regions of Northern Eurasia and studied their characteristics. H12N2 from the Far East region was a double reassortant containing hemagglutinin (HA), non-structural (NS) and nucleoprotein (NP) segments of the American lineage and others from the classical Eurasian avian-like lineage. H12N5 viruses contain Eurasian lineage segments. We suggest a phylogeographical scheme for reassortment events associated with geographical groups of aquatic birds and their migration flyways. The H12N2 virus is of particular interest as this subtype has been found in common teal in the Russian Far East region, and it has a strong relation to North American avian influenza virus lineages, clearly showing that viral exchange of segments between the two continents does occur. Our results emphasize the importance of Avian Influenza Virus (AIV) surveillance in Northern Eurasia for the annual screening of virus characteristics, including the genetic constellation of rare virus subtypes, to understand the evolutionary ecology of AIV.
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Affiliation(s)
- Kirill Sharshov
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (I.S.); (O.K.); (N.D.); (E.P.); (A.A.); (A.S.)
- Correspondence: ; Tel.: +7-960-794-2136; Fax: +7-383-333-6456
| | - Junki Mine
- Division of Transboundary Animal Disease, National Institute of Animal Health, Tsukuba, Ibaraki 305-0856, Japan; (J.M.); (M.N.); (R.T.); (Y.U.); (T.S.)
| | - Ivan Sobolev
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (I.S.); (O.K.); (N.D.); (E.P.); (A.A.); (A.S.)
| | - Olga Kurskaya
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (I.S.); (O.K.); (N.D.); (E.P.); (A.A.); (A.S.)
| | - Nikita Dubovitskiy
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (I.S.); (O.K.); (N.D.); (E.P.); (A.A.); (A.S.)
| | - Marsel Kabilov
- Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia; (M.K.); (T.A.)
| | - Tatiana Alikina
- Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia; (M.K.); (T.A.)
| | - Momoko Nakayama
- Division of Transboundary Animal Disease, National Institute of Animal Health, Tsukuba, Ibaraki 305-0856, Japan; (J.M.); (M.N.); (R.T.); (Y.U.); (T.S.)
| | - Ryota Tsunekuni
- Division of Transboundary Animal Disease, National Institute of Animal Health, Tsukuba, Ibaraki 305-0856, Japan; (J.M.); (M.N.); (R.T.); (Y.U.); (T.S.)
| | - Anastasiya Derko
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (I.S.); (O.K.); (N.D.); (E.P.); (A.A.); (A.S.)
| | - Elena Prokopyeva
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (I.S.); (O.K.); (N.D.); (E.P.); (A.A.); (A.S.)
| | - Alexander Alekseev
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (I.S.); (O.K.); (N.D.); (E.P.); (A.A.); (A.S.)
| | - Michael Shchelkanov
- School of Biomedicine, Far Eastern Federal University, 690091 Vladivostok, Russia;
- Laboratory of Virology, Federal Scientific Center of East Asia Terrestrial Biodiversity, 690022 Vladivostok, Russia
- Laboratory of marine microbiota, National Scientific Center o Marine Biology, 690041 Vladivostok, Russia
| | - Alexey Druzyaka
- Laboratory of behavioral ecology, Institute of Animal Systematics and Ecology, 630091 Novosibirsk, Russia;
| | - Alimurad Gadzhiev
- Department of Ecology, Dagestan State University, 367000 Makhachkala, Russia;
| | - Yuko Uchida
- Division of Transboundary Animal Disease, National Institute of Animal Health, Tsukuba, Ibaraki 305-0856, Japan; (J.M.); (M.N.); (R.T.); (Y.U.); (T.S.)
| | - Alexander Shestopalov
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (I.S.); (O.K.); (N.D.); (E.P.); (A.A.); (A.S.)
| | - Takehiko Saito
- Division of Transboundary Animal Disease, National Institute of Animal Health, Tsukuba, Ibaraki 305-0856, Japan; (J.M.); (M.N.); (R.T.); (Y.U.); (T.S.)
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10
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Suttie A, Deng YM, Greenhill AR, Dussart P, Horwood PF, Karlsson EA. Inventory of molecular markers affecting biological characteristics of avian influenza A viruses. Virus Genes 2019; 55:739-768. [PMID: 31428925 PMCID: PMC6831541 DOI: 10.1007/s11262-019-01700-z] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 08/09/2019] [Indexed: 12/20/2022]
Abstract
Avian influenza viruses (AIVs) circulate globally, spilling over into domestic poultry and causing zoonotic infections in humans. Fortunately, AIVs are not yet capable of causing sustained human-to-human infection; however, AIVs are still a high risk as future pandemic strains, especially if they acquire further mutations that facilitate human infection and/or increase pathogenesis. Molecular characterization of sequencing data for known genetic markers associated with AIV adaptation, transmission, and antiviral resistance allows for fast, efficient assessment of AIV risk. Here we summarize and update the current knowledge on experimentally verified molecular markers involved in AIV pathogenicity, receptor binding, replicative capacity, and transmission in both poultry and mammals with a broad focus to include data available on other AIV subtypes outside of A/H5N1 and A/H7N9.
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Affiliation(s)
- Annika Suttie
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, 5 Monivong Blvd, PO Box #983, Phnom Penh, Cambodia
- School of Health and Life Sciences, Federation University, Churchill, Australia
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Yi-Mo Deng
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Andrew R Greenhill
- School of Health and Life Sciences, Federation University, Churchill, Australia
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, 5 Monivong Blvd, PO Box #983, Phnom Penh, Cambodia
| | - Paul F Horwood
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
| | - Erik A Karlsson
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, 5 Monivong Blvd, PO Box #983, Phnom Penh, Cambodia.
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11
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Butler J, Middleton D, Haining J, Layton R, Rockman S, Brown LE, Sapats S. Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. Viruses 2019; 11:v11100915. [PMID: 31590265 PMCID: PMC6832663 DOI: 10.3390/v11100915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/06/2019] [Accepted: 09/10/2019] [Indexed: 12/27/2022] Open
Abstract
Circulating avian influenza viruses pose a significant threat, with human infections occurring infrequently but with potentially severe consequences. To examine the dynamics and locale of the adaptation process of avian influenza viruses when introduced to a mammalian host, we infected ferrets with H5N1 viruses. As expected, all ferrets infected with the human H5N1 isolate A/Vietnam/1203/2004 showed severe disease and virus replication outside the respiratory tract in multiple organs including the brain. In contrast infection of ferrets with the avian H5N1 virus A/Chicken/Laos/Xaythiani-26/2006 showed a different collective pattern of infection; many ferrets developed and cleared a mild respiratory infection but a subset (25–50%), showed extended replication in the upper respiratory tract and developed infection in distal sites. Virus from these severely infected ferrets was commonly found in tissues that included liver and small intestine. In most instances the virus had acquired the common virulence substitution PB2 E627K but, in one case, a previously unidentified combination of two amino acid substitutions at PB2 S489P and NP V408I, which enhanced polymerase activity, was found. We noted that virus with high pathogenicity adaptations could be dominant in an extra-respiratory site without being equally represented in the nasal wash. Further ferret passage of these mutated viruses resulted in high pathogenicity in all ferrets. These findings illustrate the remarkable ability of avian influenza viruses that avoid clearance in the respiratory tract, to mutate towards a high pathogenicity phenotype during just a single passage in ferrets and also indicate a window of less than 5 days in which treatment may curtail systemic infection.
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Affiliation(s)
- Jeffrey Butler
- The Commonwealth Scientific and Industrial Research Organisation, Australian Animal Health Laboratory (CSIRO-AAHL), Geelong 3219, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute of Infection and Immunity, Melbourne 3000, Victoria, Australia
| | - Deborah Middleton
- The Commonwealth Scientific and Industrial Research Organisation, Australian Animal Health Laboratory (CSIRO-AAHL), Geelong 3219, Victoria, Australia
| | - Jessica Haining
- The Commonwealth Scientific and Industrial Research Organisation, Australian Animal Health Laboratory (CSIRO-AAHL), Geelong 3219, Victoria, Australia
| | - Rachel Layton
- The Commonwealth Scientific and Industrial Research Organisation, Australian Animal Health Laboratory (CSIRO-AAHL), Geelong 3219, Victoria, Australia
| | - Steven Rockman
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute of Infection and Immunity, Melbourne 3000, Victoria, Australia
- Seqirus, 63 Poplar Rd, Parkville 3052, Victoria, Australia
| | - Lorena E Brown
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute of Infection and Immunity, Melbourne 3000, Victoria, Australia.
| | - Sandra Sapats
- The Commonwealth Scientific and Industrial Research Organisation, Australian Animal Health Laboratory (CSIRO-AAHL), Geelong 3219, Victoria, Australia
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12
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Long GS, Hussen M, Dench J, Aris-Brosou S. Identifying genetic determinants of complex phenotypes from whole genome sequence data. BMC Genomics 2019; 20:470. [PMID: 31182025 PMCID: PMC6558885 DOI: 10.1186/s12864-019-5820-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/21/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND A critical goal in biology is to relate the phenotype to the genotype, that is, to find the genetic determinants of various traits. However, while simple monofactorial determinants are relatively easy to identify, the underpinnings of complex phenotypes are harder to predict. While traditional approaches rely on genome-wide association studies based on Single Nucleotide Polymorphism data, the ability of machine learning algorithms to find these determinants in whole proteome data is still not well known. RESULTS To better understand the applicability of machine learning in this case, we implemented two such algorithms, adaptive boosting (AB) and repeated random forest (RRF), and developed a chunking layer that facilitates the analysis of whole proteome data. We first assessed the performance of these algorithms and tuned them on an influenza data set, for which the determinants of three complex phenotypes (infectivity, transmissibility, and pathogenicity) are known based on experimental evidence. This allowed us to show that chunking improves runtimes by an order of magnitude. Based on simulations, we showed that chunking also increases sensitivity of the predictions, reaching 100% with as few as 20 sequences in a small proteome as in the influenza case (5k sites), but may require at least 30 sequences to reach 90% on larger alignments (500k sites). While RRF has less specificity than random forest, it was never <50%, and RRF sensitivity was significantly higher at smaller chunk sizes. We then used these algorithms to predict the determinants of three types of drug resistance (to Ciprofloxacin, Ceftazidime, and Gentamicin) in a bacterium, Pseudomonas aeruginosa. While both algorithms performed well in the case of the influenza data, results were more nuanced in the bacterial case, with RRF making more sensible predictions, with smaller errors rates, than AB. CONCLUSIONS Altogether, we demonstrated that ML algorithms can be used to identify genetic determinants in small proteomes (viruses), even when trained on small numbers of individuals. We further showed that our RRF algorithm may deserve more scrutiny, which should be facilitated by the decreasing costs of both sequencing and phenotyping of large cohorts of individuals.
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Affiliation(s)
- George S Long
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Mohammed Hussen
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Jonathan Dench
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Stéphane Aris-Brosou
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada. .,Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada.
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13
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The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Viruses 2019; 11:v11030292. [PMID: 30909490 PMCID: PMC6480796 DOI: 10.3390/v11030292] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/21/2019] [Accepted: 03/22/2019] [Indexed: 12/27/2022] Open
Abstract
Significantly higher numbers of human infections with H5N1 virus have occurred in Indonesia and Egypt, compared with other affected areas, and it is speculated that there are specific viral factors for human infection with avian H5N1 viruses in these locations. We previously showed PB2-K526R is present in 80% of Indonesian H5N1 human isolates, which lack the more common PB2-E627K substitution. Testing the hypothesis that this mutation may prime avian H5N1 virus for human infection, we showed that: (1) K526R is rarely found in avian influenza viruses but was identified in H5N1 viruses 2–3 years after the virus emerged in Indonesia, coincident with the emergence of H5N1 human infections in Indonesia; (2) K526R is required for efficient replication of Indonesia H5N1 virus in mammalian cells in vitro and in vivo and reverse substitution to 526K in human isolates abolishes this ability; (3) Indonesian H5N1 virus, which contains K526R-PB2, is stable and does not further acquire E627K following replication in infected mice; and (4) virus containing K526R-PB2 shows no fitness deficit in avian species. These findings illustrate an important mechanism in which a host adaptive mutation that predisposes avian H5N1 virus towards infecting humans has arisen with the virus becoming prevalent in avian species prior to human infections occurring. A similar mechanism is observed in the Qinghai-lineage H5N1 viruses that have caused many human cases in Egypt; here, E627K predisposes towards human infections. Surveillance should focus on the detection of adaptation markers in avian strains that prime for human infection.
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14
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Attenuation of highly pathogenic avian influenza A(H5N1) viruses in Indonesia following the reassortment and acquisition of genes from low pathogenicity avian influenza A virus progenitors. Emerg Microbes Infect 2018; 7:147. [PMID: 30131494 PMCID: PMC6104089 DOI: 10.1038/s41426-018-0147-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 06/06/2018] [Accepted: 06/23/2018] [Indexed: 12/13/2022]
Abstract
The highly pathogenic avian influenza (HPAI) A(H5N1) virus is endemic in Indonesian poultry and has caused sporadic human infection in Indonesia since 2005. Surveillance of H5N1 viruses in live bird markets (LBMs) during 2012 and 2013 was carried out to provide epidemiologic and virologic information regarding viral circulation and the risk of human exposure. Real-time RT-PCR of avian cloacal swabs and environmental samples revealed influenza A-positive specimens, which were then subjected to virus isolation and genomic sequencing. Genetic analysis of specimens collected at multiple LBMs in Indonesia identified both low pathogenicity avian influenza (LPAI) A(H3N8) and HPAI A(H5N1) viruses belonging to clade 2.1.3.2a. Comparison of internal gene segments among the LPAI and HPAI viruses revealed that the latter had acquired the PB2, PB1, and NS genes from LPAI progenitors and other viruses containing a wild type (wt) genomic constellation. Comparison of murine infectivity of the LPAI A(H3N8), wt HPAI A(H5N1) and reassortant HPAI A(H5N1) viruses showed that the acquisition of LPAI internal genes attenuated the reassortant HPAI virus, producing a mouse infectivity/virulence phenotype comparable to that of the LPAI virus. Comparison of molecular markers in each viral gene segment suggested that mutations in PB2 and NS1 may facilitate attenuation. The discovery of an attenuated HPAI A(H5N1) virus in mice that resulted from reassortment may have implications for the capability of these viruses to transmit and cause disease. In addition, surveillance suggests that LBMs in Indonesia may play a role in the generation of reassortant A(H5) viruses and should be monitored.
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15
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A Dual Motif in the Hemagglutinin of H5N1 Goose/Guangdong-Like Highly Pathogenic Avian Influenza Virus Strains Is Conserved from Their Early Evolution and Increases both Membrane Fusion pH and Virulence. J Virol 2018; 92:JVI.00778-18. [PMID: 29899102 DOI: 10.1128/jvi.00778-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 06/02/2018] [Indexed: 12/27/2022] Open
Abstract
Zoonotic highly pathogenic avian influenza viruses (HPAIV) have raised serious public health concerns of a novel pandemic. These strains emerge from low-pathogenic precursors by the acquisition of a polybasic hemagglutinin (HA) cleavage site, the prime virulence determinant. However, required coadaptations of the HA early in HPAIV evolution remained uncertain. To address this question, we generated several HA1/HA2 chimeras and point mutants of an H5N1 clade 2.2.2 HPAIV and an H5N1 low-pathogenic strain. Initial surveys of 3,385 HPAIV H5 HA sequences revealed frequencies of 0.5% for the single amino acids 123R and 124I but a frequency of 97.5% for the dual combination. This highly conserved dual motif is still retained in contemporary H5 HPAIV, including the novel H5NX reassortants carrying neuraminidases of different subtypes, like the H5N8 and the zoonotic H5N6 strains. Remarkably, the earliest Asian H5N1 HPAIV, the Goose/Guangdong strains from 1996/1997, carried 123R only, whereas 124I appeared later in 1997. Experimental reversion in the HPAIV HA to the two residues 123S and124T, characteristic of low-pathogenic strains, prevented virus rescue, while the single substitutions attenuated the virus in both chicken and mice considerably, accompanied by a decreased HA fusion pH. This increased pH sensitivity of H5 HPAIV enables HA-mediated membrane fusion at a higher endosomal pH. Therefore, this HA adaptation may permit infection of cells with less-acidic endosomes, e.g., within the respiratory tract, resulting in an extended organ tropism. Taken together, HA coadaptation to increased acid sensitivity promoted the early evolution of H5 Goose/Guangdong-like HPAIV strains and is still required for their zoonotic potential.IMPORTANCE Zoonotic highly pathogenic avian influenza viruses (HPAIV) have raised serious public health concerns of a novel pandemic. Their prime virulence determinant is the polybasic hemagglutinin (HA) cleavage site. However, required coadaptations in the HA (and other genes) remained uncertain. Here, we identified the dual motif 123R/124I in the HA head that increases the activation pH of HA-mediated membrane fusion, essential for virus genome release into the cytoplasm. This motif is extremely predominant in H5 HPAIV and emerged already in the earliest 1997 H5N1 HPAIV. Reversion to 123S or 124T, characteristic of low-pathogenic strains, attenuated the virus in chicken and mice, accompanied by a decreased HA activation pH. This increased pH sensitivity of H5 HPAIV extends the viral tropism to cells with less-acidic endosomes, e.g., within the respiratory tract. Therefore, early HA adaptation to increased acid sensitivity promoted the emergence of H5 Goose/Guangdong-like HPAIV strains and is required for their zoonotic potential.
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16
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Young SG, Kitchen A, Kayali G, Carrel M. Unlocking pandemic potential: prevalence and spatial patterns of key substitutions in avian influenza H5N1 in Egyptian isolates. BMC Infect Dis 2018; 18:314. [PMID: 29980172 PMCID: PMC6035396 DOI: 10.1186/s12879-018-3222-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/28/2018] [Indexed: 11/10/2022] Open
Abstract
Background Avian influenza H5N1 has a high human case fatality rate, but is not yet well-adapted to human hosts. Amino acid substitutions currently circulating in avian populations may enhance viral fitness in, and thus viral adaptation to, human hosts. Substitutions which could increase the risk of a human pandemic (through changes to host specificity, virulence, replication ability, transmissibility, or drug susceptibility) are termed key substitutions (KS). Egypt represents the epicenter of human H5N1 infections, with more confirmed cases than any other country. To date, however, there have not been any spatial analyses of KS in Egypt. Methods Using 925 viral samples of H5N1 from Egypt, we aligned protein sequences and scanned for KS. We geocoded isolates using dasymetric mapping, then carried out geospatial hot spot analyses to identify spatial clusters of high KS detection rates. KS prevalence and spatial clusters were evaluated for all detected KS, as well as when stratified by phenotypic consequence. Results A total of 39 distinct KS were detected in the wild, including 17 not previously reported in Egypt. KS were detected in 874 samples (94.5%). Detection rates varied by viral protein with most KS observed in the surface hemagglutinin (HA) and neuraminidase (NA) proteins, as well as the interior non-structural 1 (NS1) protein. The most frequently detected KS were associated with increased viral binding to mammalian cells and virulence. Samples with high overall detection rates of KS exhibited statistically significant spatial clustering in two governorates in the northwestern Nile delta, Alexandria and Beheira. Conclusions KS provide a possible mechanism by which avian influenza H5N1 could evolve into a pandemic candidate. With numerous KS circulating in Egypt, and non-random spatial clustering of KS detection rates, these findings suggest the need for increased surveillance in these areas.
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Affiliation(s)
- Sean G Young
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
| | - Andrew Kitchen
- Department of Anthropology, University of Iowa, Iowa City, IA, USA
| | - Ghazi Kayali
- Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas Health Sciences Center, Houston, TX, USA.,Department of Scientific Research, Human Link, Hazmieh, Lebanon
| | - Margaret Carrel
- Department of Geographical and Sustainability Sciences, University of Iowa, Iowa City, IA, USA.,Department of Epidemiology, University of Iowa, Iowa City, IA, USA
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17
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Samir M, Hamed M, Abdallah F, Kinh Nguyen V, Hernandez-Vargas EA, Seehusen F, Baumgärtner W, Hussein A, Ali AAH, Pessler F. An Egyptian HPAI H5N1 isolate from clade 2.2.1.2 is highly pathogenic in an experimentally infected domestic duck breed (Sudani duck). Transbound Emerg Dis 2018; 65:859-873. [PMID: 29363279 DOI: 10.1111/tbed.12816] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Indexed: 01/26/2023]
Abstract
The highly pathogenic avian influenza (HPAI) H5N1 viruses continue to cause major problems in poultry and can, although rarely, cause human infection. Being enzootic in domestic poultry, Egyptian isolates are continuously evolving, and novel clades vary in their pathogenicity in avian hosts. Considering the importance of domestic ducks as natural hosts of HPAI H5N1 viruses and their likelihood of physical contact with other avian hosts and humans, it is of utmost importance to characterize the pathogenicity of newly emerged HPAI strains in the domestic duck. The most recently identified Egyptian clade 2.2.1.2 HPAI H5N1 viruses have been isolated from naturally infected pigeons, turkeys and humans. However, essentially nothing is known about their pathogenicity in domestic ducks. We therefore characterized the pathogenicity of an Egyptian HPAI H5N1 isolate A/chicken/Faquos/amn12/2011 (clade 2.2.1.2) in Sudani duck, a domestic duck breed commonly reared in Egypt. While viral transcription (HA mRNA) was highest in lung, heart and kidney peaking between 40 and 48 hpi, lower levels were detected in brain. Weight loss of infected ducks started at 16 hpi and persisted until 120 hpi. The first severe clinical signs were noted by 32 hpi and peaked in severity at 72 and 96 hpi. Haematological analyses showed a decline in total leucocytes, granulocytes, platelets and granulocyte/lymphocyte ratio, but lymphocytosis. Upon necropsy, lesions were obvious in heart, liver, spleen and pancreas and consisted mainly of necrosis and petechial haemorrhage. Histologically, lungs were the most severely affected organs, whereas brain only showed mild neuronal degeneration and gliosis at 48 hpi despite obvious neurological clinical signs. Taken together, our results provide first evidence that this HPAI H5N1 isolate (clade 2.2.1.2) is highly pathogenic to Sudani ducks and highlight the importance of this breed as potential reservoir and disseminator of HPAI strains from this clade.
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Affiliation(s)
- M Samir
- TWINCORE, Center for Experimental and Clinical Infection Research, Hannover, Germany.,Department of Zoonoses, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - M Hamed
- Marsa matrouh branch, Animal Health Research Institute, Dokki, Giza, Egypt
| | - F Abdallah
- Department of Virology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - V Kinh Nguyen
- Systems Medicine of Infectious Diseases, Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - E A Hernandez-Vargas
- Systems Medicine of Infectious Diseases, Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - F Seehusen
- Department of Pathology, University of Veterinary Medicine, Hannover, Germany
| | - W Baumgärtner
- Department of Pathology, University of Veterinary Medicine, Hannover, Germany
| | - A Hussein
- Department of Avian and Rabbit Medicine, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - A A H Ali
- Department of Virology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - F Pessler
- TWINCORE, Center for Experimental and Clinical Infection Research, Hannover, Germany.,Helmholtz Centre for Infection Research, Braunschweig, Germany
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18
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Genomic signature analysis of the recently emerged highly pathogenic A(H5N8) avian influenza virus: implying an evolutionary trend for bird-to-human transmission. Microbes Infect 2017; 19:597-604. [PMID: 28889970 DOI: 10.1016/j.micinf.2017.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 08/14/2017] [Accepted: 08/18/2017] [Indexed: 11/20/2022]
Abstract
In early 2014, a novel subclade (2.3.4.4) of the highly pathogenic avian influenza (HPAI) A(H5N8) virus caused the first outbreak in domestic ducks and migratory birds in South Korea. Since then, it has spread to 44 countries and regions. To date, no human infections with A(H5N8) virus have been reported, but the possibility cannot be excluded. By analyzing the genomic signatures of A(H5N8) strains, we found that among the 47 species-associated signature positions, three positions exhibited human-like signatures (HLS), including PA-404S, PB2-613I and PB2-702R and that mutation trend of host signatures of avian A(H5N8) is different before and after 2014. About 82% of A(H5N8) isolates collected after January of 2014 carried the 3 HLS (PA-404S/PB2-613I/PB2-702R) in combination, while none of isolates collected before 2014 had this combination. Furthermore, the HA protein had S137A and S227R substitutions in the receptor-binding site and A160T in the glycosylation site, potentially increasing viral ability to bind human-type receptors. Based on these findings, the newly emerged HPAI A(H5N8) isolates show an evolutionary trend toward gaining more HLS and, along with it, the potential for bird-to-human transmissibility. Therefore, more extensive surveillance of this rapidly spreading HPAI A(H5N8) and preparedness against its potential pandemic are urgently needed.
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19
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Chen W, Xu Q, Zhong Y, Yu H, Shu J, Ma T, Li Z. Genetic variation and co-evolutionary relationship of RNA polymerase complex segments in influenza A viruses. Virology 2017; 511:193-206. [PMID: 28866238 DOI: 10.1016/j.virol.2017.07.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 07/18/2017] [Accepted: 07/20/2017] [Indexed: 11/19/2022]
Abstract
The RNA polymerase complex (RNApc) in influenza A viruses (IVs) is composed of the PB2, PB1 and PA subunits, which are encoded by the three longest genome segments (Seg1-3) and are responsible for the replication of vRNAs and transcription of viral mRNAs. However, the co-evolutionary relationships of the three segments from the known 126 subtypes IVs are unclear. In this study, we performed a detailed analysis based on a total number of 121,191 nucleotide sequences. Three segment sequences were aligned before the repeated, incomplete and mixed sequences were removed for homologous and phylogenetic analyses. Subsequently, the estimated substitution rates and TMRCAs (Times for Most Recent Common Ancestor) were calculated by 175 representative IVs. Tracing the cladistic distribution of three segments from these IVs, co-evolutionary patterns and trajectories could be inferred. The further correlation analysis of six internal protein coding segments reflect the RNApc segments have the closer correlation than others during continuous reassortments. This global approach facilitates the establishment of a fast antiviral strategy and monitoring of viral variation.
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Affiliation(s)
- Wentian Chen
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an 710069, PR China
| | - Qi Xu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an 710069, PR China
| | - Yaogang Zhong
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an 710069, PR China
| | - Hanjie Yu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an 710069, PR China
| | - Jian Shu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an 710069, PR China
| | - Tianran Ma
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an 710069, PR China
| | - Zheng Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an 710069, PR China.
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20
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Richard M, Herfst S, van den Brand JMA, de Meulder D, Lexmond P, Bestebroer TM, Fouchier RAM. Mutations Driving Airborne Transmission of A/H5N1 Virus in Mammals Cause Substantial Attenuation in Chickens only when combined. Sci Rep 2017; 7:7187. [PMID: 28775271 PMCID: PMC5543172 DOI: 10.1038/s41598-017-07000-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/22/2017] [Indexed: 12/12/2022] Open
Abstract
A/H5N1 influenza viruses pose a threat to human and animal health. A fully avian A/H5N1 influenza virus was previously shown to acquire airborne transmissibility between ferrets upon accumulation of five or six substitutions that affected three traits: polymerase activity, hemagglutinin stability and receptor binding. Here, the impact of these traits on A/H5N1 virus replication, tissue tropism, pathogenesis and transmission was investigated in chickens. The virus containing all substitutions associated with transmission in mammals was highly attenuated in chickens. However, single substitutions that affect polymerase activity, hemagglutinin stability and receptor binding generally had a small or negligible impact on virus replication, morbidity and mortality. A virus carrying two substitutions in the receptor-binding site was attenuated, although its tissue tropism in chickens was not affected. This data indicate that an A/H5N1 virus that is airborne-transmissible between mammals is unlikely to emerge in chickens, although individual mammalian adaptive substitutions have limited impact on viral fitness in chickens.
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Affiliation(s)
- Mathilde Richard
- Department of Viroscience, Postgraduate School Molecular Medicine, Erasmus MC, Rotterdam, The Netherlands.
| | - Sander Herfst
- Department of Viroscience, Postgraduate School Molecular Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Judith M A van den Brand
- Department of Viroscience, Postgraduate School Molecular Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Dennis de Meulder
- Department of Viroscience, Postgraduate School Molecular Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Pascal Lexmond
- Department of Viroscience, Postgraduate School Molecular Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Theo M Bestebroer
- Department of Viroscience, Postgraduate School Molecular Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Postgraduate School Molecular Medicine, Erasmus MC, Rotterdam, The Netherlands
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21
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Zhao H, Chu H, Zhao X, Shuai H, Wong BHY, Wen L, Yuan S, Zheng BJ, Zhou J, Yuen KY. Novel residues in the PA protein of avian influenza H7N7 virus affect virulence in mammalian hosts. Virology 2016; 498:1-8. [PMID: 27525812 DOI: 10.1016/j.virol.2016.08.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 08/02/2016] [Accepted: 08/04/2016] [Indexed: 01/21/2023]
Abstract
To evaluate the pathogenicity, a highly pathogenic avian influenza H7N7 virus (A/Netherlands/219/03) isolated from human was passaged in mice. A mutant virus (mH7N7) with attenuated virulence was isolated from mouse lung, which had a 3-log higher MLD50 than the wild-type virus (wH7N7). Sequence analysis and reverse genetics study revealed that mutations in PA account for the compromised viral replication in mammalian cells and mice. A mini-genome assay demonstrated that PA mutations P103H and S659L can cooperatively decrease polymerase activity. Actually, PA with double mutation P103H-S659L cannot sustain the generation of live virus by reverse genetics. Interestingly, the prior infection of mH7N7 virus provided mice with cross-protection against lethal challenge of other subtypes of influenza A virus including H1N1, H5N1 and H7N9. In conclusion, we demonstrated that PA mutations P103H and S659L can cooperatively reduce polymerase activity and viral replication in mammalian cells and attenuate pathogenicity in mice.
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Affiliation(s)
- Hanjun Zhao
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Hin Chu
- Department of Microbiology, The University of Hong Kong, Hong Kong; State Key Laboratory of Emerging Infectious Diseases, Hong Kong; Research Centre of Infection and Immunology, Hong Kong
| | - Xiaoyu Zhao
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Huiping Shuai
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | | | - Lei Wen
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Shuofeng Yuan
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Bo-Jian Zheng
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Jie Zhou
- Department of Microbiology, The University of Hong Kong, Hong Kong; State Key Laboratory of Emerging Infectious Diseases, Hong Kong; Research Centre of Infection and Immunology, Hong Kong.
| | - Kwok-Yung Yuen
- Department of Microbiology, The University of Hong Kong, Hong Kong; State Key Laboratory of Emerging Infectious Diseases, Hong Kong; Research Centre of Infection and Immunology, Hong Kong; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong.
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22
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Fang S, Wang X, Dong F, Jin T, Liu G, Lu X, Peng B, Wu W, Liu H, Kong D, Tang X, Qin Y, Mei S, Xie X, He J, Ma H, Zhang R, Cheng J. Genomic characterization of influenza A (H7N9) viruses isolated in Shenzhen, Southern China, during the second epidemic wave. Arch Virol 2016; 161:2117-32. [PMID: 27169600 DOI: 10.1007/s00705-016-2872-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 04/24/2016] [Indexed: 10/21/2022]
Abstract
There were three epidemic waves of human infection with avian influenza A (H7N9) virus in 2013-2014. While many analyses of the genomic origin, evolution, and molecular characteristics of the influenza A (H7N9) virus have been performed using sequences from the first epidemic wave, genomic characterization of the virus from the second epidemic wave has been comparatively less reported. In this study, an in-depth analysis was performed with respect to the genomic characteristics of 11 H7N9 virus strains isolated from confirmed cases and four H7N9 virus strains isolated from environmental samples in Shenzhen during the second epidemic wave. Phylogenetic analysis demonstrated that six internal segments of the influenza A (H7N9) virus isolated from confirmed cases and environmental samples in Shenzhen were clustered into two different clades and that the origin of the influenza A (H7N9) virus isolated from confirmed cases in Shenzhen was different from that of viruses isolated during the first wave. In addition, H9N2 viruses, which were prevalent in southern China, played an important role in the reassortment of the influenza A (H7N9) virus isolated in Shenzhen. HA-R47K and -T122A, PB2-V139I, PB1-I397M, and NS1-T216P were the signature amino acids of the influenza A (H7N9) virus isolated from confirmed cases in Shenzhen. We found that the HA, NA, M, and PA genes of the A(H7N9) viruses underwent positive selection in the human population. Therefore, enhanced surveillance should be carried out to determine the origin and mode of transmission of the novel influenza A (H7N9) virus and to facilitate the formulation of effective policies for prevention and containment of a human infection epidemics.
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Affiliation(s)
- Shisong Fang
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Xin Wang
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Fangyuan Dong
- College of Medicine, Jinan University, 601 Huangpu Avenue West, Guangzhou, China
| | - Tao Jin
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Guang Liu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xing Lu
- Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Bo Peng
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Weihua Wu
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Hui Liu
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Dongfeng Kong
- Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Xiujuan Tang
- Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Yanmin Qin
- Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Shujiang Mei
- Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Xu Xie
- Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Jianfan He
- Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Hanwu Ma
- Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Renli Zhang
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China.
| | - Jinquan Cheng
- Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China.
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23
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Hu T, Zhao H, Zhang Y, Zhang W, Kong Q, Zhang Z, Cui Q, Qiu W, Deng B, Fan Q, Zhang F. Fatal influenza A (H5N1) virus Infection in zoo-housed Tigers in Yunnan Province, China. Sci Rep 2016; 6:25845. [PMID: 27162026 PMCID: PMC4861906 DOI: 10.1038/srep25845] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 04/25/2016] [Indexed: 01/12/2023] Open
Abstract
From 2014 to 2015, three cases of highly pathogenic avian influenza infection occurred in zoo-housed north-east China tigers (Panthera tigris ssp.altaica) and four tigers died of respiratory distress in succession in Yunnan Province, China. We isolated and characterized three highly pathogenic avian influenza A(H5N1) viruses from these tigers. Phylogenetic analysis indicated that A/tiger /Yunnan /tig1404 /2014(H5N1) belongs to the provisional subclade 2.3.4.4e which were novel reassortant influenza A (H5N1) viruses with six internal genes from avian influenza A (H5N2) viruses. The HA gene of the isolated A/tiger /Yunnan /tig1412 /2014(H5N1) virus belongs to the subclade 2.3.2.1b. The isolated A/tiger /Yunnan /tig1508/2015 (H5N1) virus was a novel reassortant influenza A (H5N1) virus with three internal genes (PB2, PB1 and M) from H9N2 virus and belongs to the subclade 2.3.2.1c.
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Affiliation(s)
- Tingsong Hu
- Centre for Disease Control and Prevention, Chengdu Military Region, Kunming 650118, China
| | - Huanyun Zhao
- Centre for Animal Disease Control and Prevention, Yunnan Province, Kunming 650051, China
| | - Yan Zhang
- Department of Biochemistry and Molecular Biology, Fudan University Shanghai Medical College, Shanghai 200030, China
| | - Wendong Zhang
- Centre for Animal Disease Control and Prevention, Yunnan Province, Kunming 650051, China
| | - Qiang Kong
- Centre for Animal Disease Control and Prevention, Yunnan Province, Kunming 650051, China
- Yunnan Agriculture University, Kunming 650223, China
| | - Zhixiao Zhang
- Centre for Disease Control and Prevention, Chengdu Military Region, Kunming 650118, China
| | - Qinghua Cui
- Centre for Disease Control and Prevention, Chengdu Military Region, Kunming 650118, China
| | - Wei Qiu
- Centre for Disease Control and Prevention, Chengdu Military Region, Kunming 650118, China
| | - Bo Deng
- Centre for Disease Control and Prevention, Chengdu Military Region, Kunming 650118, China
| | - Quanshui Fan
- Centre for Disease Control and Prevention, Chengdu Military Region, Kunming 650118, China
| | - Fuqiang Zhang
- Centre for Disease Control and Prevention, Chengdu Military Region, Kunming 650118, China
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24
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Influenza virus polymerase: Functions on host range, inhibition of cellular response to infection and pathogenicity. Virus Res 2015; 209:23-38. [DOI: 10.1016/j.virusres.2015.03.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Revised: 03/25/2015] [Accepted: 03/26/2015] [Indexed: 01/06/2023]
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25
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Thor SW, Nguyen H, Balish A, Hoang AN, Gustin KM, Nhung PT, Jones J, Thu NN, Davis W, Ngoc TNT, Jang Y, Sleeman K, Villanueva J, Kile J, Gubareva LV, Lindstrom S, Tumpey TM, Davis CT, Long NT. Detection and Characterization of Clade 1 Reassortant H5N1 Viruses Isolated from Human Cases in Vietnam during 2013. PLoS One 2015; 10:e0133867. [PMID: 26244768 PMCID: PMC4526568 DOI: 10.1371/journal.pone.0133867] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/03/2015] [Indexed: 02/03/2023] Open
Abstract
Highly pathogenic avian influenza (HPAI) H5N1 is endemic in Vietnamese poultry and has caused sporadic human infection in Vietnam since 2003. Human infections with HPAI H5N1 are of concern due to a high mortality rate and the potential for the emergence of pandemic viruses with sustained human-to-human transmission. Viruses isolated from humans in southern Vietnam have been classified as clade 1 with a single genome constellation (VN3) since their earliest detection in 2003. This is consistent with detection of this clade/genotype in poultry viruses endemic to the Mekong River Delta and surrounding regions. Comparison of H5N1 viruses detected in humans from southern Vietnamese provinces during 2012 and 2013 revealed the emergence of a 2013 reassortant virus with clade 1.1.2 hemagglutinin (HA) and neuraminidase (NA) surface protein genes but internal genes derived from clade 2.3.2.1a viruses (A/Hubei/1/2010-like; VN12). Closer analysis revealed mutations in multiple genes of this novel genotype (referred to as VN49) previously associated with increased virulence in animal models and other markers of adaptation to mammalian hosts. Despite the changes identified between the 2012 and 2013 genotypes analyzed, their virulence in a ferret model was similar. Antigenically, the 2013 viruses were less cross-reactive with ferret antiserum produced to the clade 1 progenitor virus, A/Vietnam/1203/2004, but reacted with antiserum produced against a new clade 1.1.2 WHO candidate vaccine virus (A/Cambodia/W0526301/2012) with comparable hemagglutination inhibition titers as the homologous antigen. Together, these results indicate changes to both surface and internal protein genes of H5N1 viruses circulating in southern Vietnam compared to 2012 and earlier viruses.
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Affiliation(s)
- Sharmi W. Thor
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Hieu Nguyen
- Institute Pasteur-Ho Chi Minh City, National Influenza Center-2, Ho Chi Minh City, Vietnam
| | - Amanda Balish
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Anh Nguyen Hoang
- Institute Pasteur-Ho Chi Minh City, National Influenza Center-2, Ho Chi Minh City, Vietnam
| | - Kortney M. Gustin
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Pham Thi Nhung
- Institute Pasteur-Ho Chi Minh City, National Influenza Center-2, Ho Chi Minh City, Vietnam
| | - Joyce Jones
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Ngoc Nguyen Thu
- Institute Pasteur-Ho Chi Minh City, National Influenza Center-2, Ho Chi Minh City, Vietnam
| | - William Davis
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Thao Nguyen Thi Ngoc
- Institute Pasteur-Ho Chi Minh City, National Influenza Center-2, Ho Chi Minh City, Vietnam
| | - Yunho Jang
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Katrina Sleeman
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Julie Villanueva
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - James Kile
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Influenza Program, Centers for Disease Control and Prevention- Vietnam, Hanoi, Vietnam
| | - Larisa V. Gubareva
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Stephen Lindstrom
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Terrence M. Tumpey
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - C. Todd Davis
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail: (NTL); (CTD)
| | - Nguyen Thanh Long
- Institute Pasteur-Ho Chi Minh City, National Influenza Center-2, Ho Chi Minh City, Vietnam
- * E-mail: (NTL); (CTD)
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26
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Rapid emergence of a PB2-E627K substitution confers a virulent phenotype to an H9N2 avian influenza virus during adoption in mice. Arch Virol 2015; 160:1267-77. [PMID: 25782865 DOI: 10.1007/s00705-015-2383-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 02/25/2015] [Indexed: 10/23/2022]
Abstract
The worldwide circulation of H9N2 avian influenza virus in poultry, the greater than 2.3 % positive rate for anti-H9 antibodies in poultry-exposed workers, and several reports of human infection indicate that H9N2 virus is a potential threat to human health. Here, we found three mutations that conferred high virulence to H9N2 virus in mice after four passages. The PB2-E627K substitution rapidly appeared at the second passage and played a decisive role in virulence. Polymerase complexes possessing PB2-E627K displayed 16.1-fold higher viral polymerase activity when compared to the wild-type virus, which may account for enhanced virulence of this virus. The other two substitutions (HA-N313D and HA-N496S) enhanced binding to both α2,3-linked and α2,6-linked sialic acid receptors; however, the HA-N313D and N496S substitutions alone decreased the virulence of mouse-adapted virus. Furthermore, this mouse-adapted virus was still not transmissible among guinea pigs by direct contact (0/3 pairs). Our findings show that adaption in mice enhanced the viral polymerase activity and receptor-binding ability, which resulted in a virulent phenotype in mice but not a transmissible phenotype in guinea pigs, indicating that host factors play an important role in adaptive evolution of influenza in new hosts.
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27
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Zhang X, Chen S, Jiang Y, Huang K, Huang J, Yang D, Zhu J, Zhu Y, Shi S, Peng D, Liu X. Hemagglutinin glycosylation modulates the pathogenicity and antigenicity of the H5N1 avian influenza virus. Vet Microbiol 2014; 175:244-56. [PMID: 25544041 DOI: 10.1016/j.vetmic.2014.12.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 12/09/2014] [Accepted: 12/11/2014] [Indexed: 10/24/2022]
Abstract
The location and number of glycosylation in HA proteins exhibit large variations among H5 subtype avian influenza viruses (AIVs). To investigate the effect of glycosylation in the globular head of HA on the pathogenicity and antigenicity of H5N1 AIVs, seven rescued AIVs differing in their glycosylation patterns (144N, 158N and 169N) within the HA globular head of A/Mallard/Huadong/S/2005 were generated using site directed mutagenesis. Results showed that loss of glycosylation 158N was the prerequisite for H5 AIV binding to the α2,6-linked receptor. Only in conjunction with the removal of the 158N glycosylation, the H5 AIVs harboring both 144N and 169N glycosylations obtained an optimal binding preference to the α2,6-linked receptor. Compared with the wild-type virus, growth of viruses lacking glycosylation at either 158N or 169N was significantly reduced both in MDCK and A549 cells, while replication of viruses with additional glycosylation 144N was significantly promoted. Mutant viruses with loss of 158N or 169N glycosylation sites showed increased pathogenicity, systemic spread and pulmonary inflammation in mice compared to the wild-type H5N1 virus. In addition, chicken studies demonstrated that inactivated de-glycosylation 169N mutant induced cross-reaction HI and neutralization antibody against various clades of H5N1 AIVs. Moreover, this type of glycan pattern vaccine virus provided better cross-protection in chickens compared to wild-type vaccine virus. Thus, the glycosylation alteration of HA should be considered in the global surveillance and vaccine design of H5 subtype AIVs.
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Affiliation(s)
- Xiaojian Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, Jiangsu 225009, PR China; Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, Jiangsu 225009, PR China
| | - Sujuan Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, Jiangsu 225009, PR China; Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, Jiangsu 225009, PR China
| | - Yi Jiang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, Jiangsu 225009, PR China; Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, Jiangsu 225009, PR China
| | - Kai Huang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, Jiangsu 225009, PR China; Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, Jiangsu 225009, PR China
| | - Jun Huang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, Jiangsu 225009, PR China; Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, Jiangsu 225009, PR China
| | - Da Yang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, Jiangsu 225009, PR China; Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, Jiangsu 225009, PR China
| | - Jingjing Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, Jiangsu 225009, PR China; Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, Jiangsu 225009, PR China
| | - Yinbiao Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, Jiangsu 225009, PR China; Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, Jiangsu 225009, PR China
| | - Shaohua Shi
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, Jiangsu 225009, PR China; Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, Jiangsu 225009, PR China
| | - Daxin Peng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, Jiangsu 225009, PR China; Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, Jiangsu 225009, PR China.
| | - Xiufan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, Jiangsu 225009, PR China; Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, Jiangsu 225009, PR China
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28
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Contemporary avian influenza A virus subtype H1, H6, H7, H10, and H15 hemagglutinin genes encode a mammalian virulence factor similar to the 1918 pandemic virus H1 hemagglutinin. mBio 2014; 5:e02116. [PMID: 25406382 PMCID: PMC4251996 DOI: 10.1128/mbio.02116-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Zoonotic avian influenza virus infections may lead to epidemics or pandemics. The 1918 pandemic influenza virus has an avian influenza virus-like genome, and its H1 hemagglutinin was identified as a key mammalian virulence factor. A chimeric 1918 virus expressing a contemporary avian H1 hemagglutinin, however, displayed murine pathogenicity indistinguishable from that of the 1918 virus. Here, isogenic chimeric avian influenza viruses were constructed on an avian influenza virus backbone, differing only by hemagglutinin subtype expressed. Viruses expressing the avian H1, H6, H7, H10, and H15 subtypes were pathogenic in mice and cytopathic in normal human bronchial epithelial cells, in contrast to H2-, H3-, H5-, H9-, H11-, H13-, H14-, and H16-expressing viruses. Mouse pathogenicity was associated with pulmonary macrophage and neutrophil recruitment. These data suggest that avian influenza virus hemagglutinins H1, H6, H7, H10, and H15 contain inherent mammalian virulence factors and likely share a key virulence property of the 1918 virus. Consequently, zoonotic infections with avian influenza viruses bearing one of these hemagglutinins may cause enhanced disease in mammals. Influenza viruses from birds can cause outbreaks in humans and may contribute to the development of pandemics. The 1918 pandemic influenza virus has an avian influenza virus-like genome, and its main surface protein, an H1 subtype hemagglutinin, was identified as a key mammalian virulence factor. In a previous study, a 1918 virus expressing an avian H1 gene was as virulent in mice as the reconstructed 1918 virus. Here, a set of avian influenza viruses was constructed, differing only by hemagglutinin subtype. Viruses with the avian H1, H6, H7, H10, and H15 subtypes caused severe disease in mice and damaged human lung cells. Consequently, infections with avian influenza viruses bearing one of these hemagglutinins may cause enhanced disease in mammals, and therefore surveillance for human infections with these subtypes may be important in controlling future outbreaks.
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He S, Shi J, Qi X, Huang G, Chen H, Lu C. Lethal infection by a novel reassortant H5N1 avian influenza A virus in a zoo-housed tiger. Microbes Infect 2014; 17:54-61. [PMID: 25461468 DOI: 10.1016/j.micinf.2014.10.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 09/22/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
Abstract
In early 2013, a Bengal tiger (Panthera tigris) in a zoo died of respiratory distress. All specimens from the tiger were positive for HPAI H5N1, which were detected by real-time PCR, including nose swab, throat swab, tracheal swab, heart, liver, spleen, lung, kidney, aquae pericardii and cerebrospinal fluid. One stain of virus, A/Tiger/JS/1/2013, was isolated from the lung sample. Pathogenicity experiments showed that the isolate was able to replicate and cause death in mice. Phylogenetic analysis indicated that HA and NA of A/Tiger/JS/1/2013 clustered with A/duck/Vietnam/OIE-2202/2012 (H5N1), which belongs to clade 2.3.2.1. Interestingly, the gene segment PB2 shared 98% homology with A/wild duck/Korea/CSM-28/20/2010 (H4N6), which suggested that A/Tiger/JS/1/2013 is a novel reassortant H5N1 subtype virus. Immunohistochemical analysis also confirmed that the tiger was infected by this new reassortant HPAI H5N1 virus. Overall, our results showed that this Bengal tiger was infected by a novel reassortant H5N1, suggesting that the H5N1 virus can successfully cross species barriers from avian to mammal through reassortment.
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Affiliation(s)
- Shang He
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210095, China; OIE Reference Laboratory for Swine Streptococcosis, Nanjing 210095, China
| | - Jianzhong Shi
- Division of Animal Influenza, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China
| | - Xian Qi
- Institute of the Prevention of Acute Disease, Jiangsu Province Center for Disease Control and Prevention, Nanjing 210009, China
| | - Guoqing Huang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Hualan Chen
- Division of Animal Influenza, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China
| | - Chengping Lu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210095, China; OIE Reference Laboratory for Swine Streptococcosis, Nanjing 210095, China.
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Chin AWH, Li OTW, Mok CKP, Ng MKW, Peiris M, Poon LLM. Influenza A viruses with different amino acid residues at PB2-627 display distinct replication properties in vitro and in vivo: revealing the sequence plasticity of PB2-627 position. Virology 2014; 468-470:545-555. [PMID: 25262472 DOI: 10.1016/j.virol.2014.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 08/23/2014] [Accepted: 09/08/2014] [Indexed: 11/26/2022]
Abstract
Sequence analyses of influenza PB2 sequences indicate that the 627 position almost exclusively contains either lysine (K) or glutamic acid (E), suggesting a high sequence constraint at this genetic marker. Here, we used a site-directed random mutagenesis method to demonstrate that PB2-627 position has a high sequence plasticity. Recombinant viruses carrying various amino acid residues at this position are viable in cell cultures. These PB2-627 mutants showed various polymerase activities and replication kinetics in mammalian and avian cells as well as pathogenicity in mice. Serially passaging these mutants in MDCK cells generated some compensatory PB2 mutations that can restore polymerase activities of the PB2-627 mutants. Of these, PB2-D309N was identified as a novel one. Besides showing that influenza virus can tolerate a wide range of amino acid residues at the PB2-627 position, this study also demonstrates a potential strategy to identify novel mutations that can enhance viral polymerase.
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Affiliation(s)
- Alex W H Chin
- Centre of Influenza Research & School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Olive T W Li
- Centre of Influenza Research & School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Chris K P Mok
- Centre of Influenza Research & School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong; The HKU-Pasteur Research Pole & School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Miko K W Ng
- Centre of Influenza Research & School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Malik Peiris
- Centre of Influenza Research & School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong; The HKU-Pasteur Research Pole & School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Leo L M Poon
- Centre of Influenza Research & School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong.
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Mutations to PB2 and NP proteins of an avian influenza virus combine to confer efficient growth in primary human respiratory cells. J Virol 2014; 88:13436-46. [PMID: 25210184 DOI: 10.1128/jvi.01093-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED Influenza pandemics occur when influenza A viruses (IAV) adapted to other host species enter humans and spread through the population. Pandemics are relatively rare due to host restriction of IAV: strains adapted to nonhuman species do not readily infect, replicate in, or transmit among humans. IAV can overcome host restriction through reassortment or adaptive evolution, and these are mechanisms by which pandemic strains arise in nature. To identify mutations that facilitate growth of avian IAV in humans, we have adapted influenza A/duck/Alberta/35/1976 (H1N1) (dk/AB/76) virus to a high-growth phenotype in differentiated human tracheo-bronchial epithelial (HTBE) cells. Following 10 serial passages of three independent lineages, the bulk populations showed similar growth in HTBE cells to that of a human seasonal virus. The coding changes present in six clonal isolates were determined. The majority of changes were located in the polymerase complex and nucleoprotein (NP), and all isolates carried mutations in the PB2 627 domain and regions of NP thought to interact with PB2. Using reverse genetics, the impact on growth and polymerase activity of individual and paired mutations in PB2 and NP was evaluated. The results indicate that coupling of the mammalian-adaptive mutation PB2 E627K or Q591K to selected mutations in NP further augments the growth of the corresponding viruses. In addition, minimal combinations of three (PB2 Q236H, E627K, and NP N309K) or two (PB2 Q591K and NP S50G) mutations were sufficient to recapitulate the efficient growth in HTBE cells of dk/AB/76 viruses isolated after 10 passages in this substrate. IMPORTANCE Influenza A viruses adapted to birds do not typically grow well in humans. However, as has been seen recently with H5N1 and H7N9 subtype viruses, productive and virulent infection of humans with avian influenza viruses can occur. The ability of avian influenza viruses to adapt to new host species is a consequence of their high mutation rate that supports their zoonotic potential. Understanding of the adaptation of avian viruses to mammals strengthens public health efforts aimed at controlling influenza. In particular, it is critical to know how readily and through mutation to which functional components avian influenza viruses gain the ability to grow efficiently in humans. Our data show that as few as three mutations, in the PB2 and NP proteins, support robust growth of a low-pathogenic, H1N1 duck isolate in primary human respiratory cells.
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Abstract
The influenza A virus causes a highly contagious respiratory disease that significantly impacts our economy and health. Its replication and transcription is catalyzed by the viral RNA polymerase. This enzyme is also crucial for the virus, because it is involved in the adaptation of zoonotic strains. It is thus of major interest for the development of antiviral therapies and is being intensively studied. In this article, we will discuss recent advances that have improved our knowledge of the structure of the RNA polymerase and how mutations in the polymerase help the virus to spread effectively among new hosts.
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Affiliation(s)
- Thomas M Stubbs
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK ; Babraham Institute, Brabraham Research Campus, Cambridge, CB22 3AT, UK
| | - Aartjan Jw Te Velthuis
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
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Cauldwell AV, Long JS, Moncorgé O, Barclay WS. Viral determinants of influenza A virus host range. J Gen Virol 2014; 95:1193-1210. [DOI: 10.1099/vir.0.062836-0] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Typical avian influenza A viruses are restricted from replicating efficiently and causing disease in humans. However, an avian virus can become adapted to humans by mutating or recombining with currently circulating human viruses. These viruses have the potential to cause pandemics in an immunologically naïve human population. It is critical that we understand the molecular basis of host-range restriction and how this can be overcome. Here, we review our current understanding of the mechanisms by which influenza viruses adapt to replicate efficiently in a new host. We predominantly focus on the influenza polymerase, which remains one of the least understood host-range barriers.
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Affiliation(s)
- Anna V. Cauldwell
- Imperial College London, Faculty of Medicine, Division of Infectious Disease, Norfolk Place, London W2 1PG, UK
| | - Jason S. Long
- Imperial College London, Faculty of Medicine, Division of Infectious Disease, Norfolk Place, London W2 1PG, UK
| | - Olivier Moncorgé
- Imperial College London, Faculty of Medicine, Division of Infectious Disease, Norfolk Place, London W2 1PG, UK
| | - Wendy S. Barclay
- Imperial College London, Faculty of Medicine, Division of Infectious Disease, Norfolk Place, London W2 1PG, UK
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Lim K, Kim M, Lee MK, Ko J, Hong S, Choi BS. Biophysical characterization of sites of host adaptive mutation in the influenza A virus RNA polymerase PB2 RNA-binding domain. Int J Biochem Cell Biol 2014; 53:237-45. [PMID: 24875650 DOI: 10.1016/j.biocel.2014.05.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 04/15/2014] [Accepted: 05/16/2014] [Indexed: 11/19/2022]
Abstract
Influenza RNA polymerase is composed of three subunits, PA, PB1, and PB2, which interact with each other for transcription and replication of the viral RNA genome in the nucleus of infected cells. PB2 RNA-binding 627-domain (residues 535-693), located in the C-terminus, presents a highly basic surface around residue lysine 627 and has been proposed to interact with viral or cellular factors, resulting in host adaptation. However, the function of this domain is not yet characterized in detail. In this study, we identified RNA-binding activity and RNA-binding surfaces in both the N-terminal and basic C-terminal regions of PB2 627-domain using NMR experiments. Through mutagenesis studies, we confirmed which residues directly interact with RNA and mapped their locations on the RNA-binding surface. In addition, by luciferase activity assays, we showed that influenza virus polymerase activity may correlate with the interaction between PB2 and RNA. Representative host adaptive mutations (residues 591 and 627) were found to be located on the RNA-binding surface and were confirmed to directly interact with RNA and to affect polymerase activity. From these results, we suggest that influenza virus polymerase activity may be regulated through the interaction between PB2 627-domain and RNA and that consequently host adaptation of the virus may be influenced.
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Affiliation(s)
- Kyungeun Lim
- Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Meehyein Kim
- Virus Research and Testing Group, KRICT, Sinseongno, Yuseong-gu, Daejeon 305-600, Republic of Korea
| | - Mi-Kyung Lee
- Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Junsang Ko
- Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Sungwoo Hong
- Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Byong-Seok Choi
- Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
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Mok CKP, Lee HHY, Lestra M, Nicholls JM, Chan MCW, Sia SF, Zhu H, Poon LLM, Guan Y, Peiris JSM. Amino acid substitutions in polymerase basic protein 2 gene contribute to the pathogenicity of the novel A/H7N9 influenza virus in mammalian hosts. J Virol 2014; 88:3568-76. [PMID: 24403592 PMCID: PMC3957932 DOI: 10.1128/jvi.02740-13] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 01/02/2014] [Indexed: 02/04/2023] Open
Abstract
UNLABELLED A novel avian-origin influenza A/H7N9 virus emerged in 2013 to cause more than 130 cases of zoonotic human disease, with an overall case fatality rate of around 30% in cases detected. It has been shown that an E-to-K amino acid change at residue 627 of polymerase basic protein 2 (PB2) occurred frequently in the H7N9 isolates obtained from humans but not in viruses isolated from poultry. Although this mutation has been reported to confer increased mammalian pathogenicity in other avian influenza subtypes, it has not been experimentally investigated in the H7N9 virus. In this study, we determined the contribution of PB2-E627K in H7N9 virus to its pathogenicity in mammalian hosts. In addition, the compensatory role of the PB2 mutations T271A, Q591K, and D701N in H7N9 virus was investigated. We characterized the activity of polymerase complexes with these PB2 mutations and found that they enhance the polymerase activity in human 293T cells. The rescued mutants enhanced growth in mammalian cells in vitro. Mice infected with the H7N9 mutant containing the avian signature protein PB2-627E showed a marked decrease in disease severity (weight loss) and pathology compared to mice infected with the wild-type strain (PB2-627K) or other PB2 mutants. Also, mutants with PB2-627E showed lower virus replication and proinflammatory cytokine responses in the lungs of the virus-infected mice, which may contribute to pathogenicity. Our results suggest that these amino acid substitutions contribute to mouse pathogenicity and mammalian adaptation. IMPORTANCE A novel avian H7N9 influenza A virus emerged in east China in 2013 to cause zoonotic human disease associated with significant mortality. It is important to understand the viral genetic markers of mammalian adaptation and disease severity in this H7N9 virus. Since many human (but not avian) H7N9 virus isolates have an amino acid substitution at position E627K in the polymerase basic protein 2 (PB2) gene, we investigated the role of this and other functionally related mutations for polymerase activity in vitro, virus replication competence, and pathogenicity in the mouse model. We found that E627K and functionally related mutations are associated with increased polymerase activity, increased viral replication competence, and increased disease severity in mice.
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Affiliation(s)
- Chris Ka Pun Mok
- Centre of Influenza Research, School of Public Health, HKU Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
- HKU-Pasteur Research Pole, School of Public Health, HKU Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Horace Hok Yeung Lee
- Centre of Influenza Research, School of Public Health, HKU Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
- HKU-Pasteur Research Pole, School of Public Health, HKU Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Maxime Lestra
- HKU-Pasteur Research Pole, School of Public Health, HKU Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - John Malcolm Nicholls
- Department of Pathology, HKU Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Michael Chi Wai Chan
- Centre of Influenza Research, School of Public Health, HKU Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Sin Fun Sia
- Centre of Influenza Research, School of Public Health, HKU Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Huachen Zhu
- Centre of Influenza Research, School of Public Health, HKU Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Leo Lit Man Poon
- Centre of Influenza Research, School of Public Health, HKU Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Yi Guan
- Centre of Influenza Research, School of Public Health, HKU Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Joseph Sriyal Malik Peiris
- Centre of Influenza Research, School of Public Health, HKU Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
- HKU-Pasteur Research Pole, School of Public Health, HKU Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
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Kreibich A, Stech O, Hundt J, Ziller M, Mettenleiter TC, Stech J. Avian influenza virus h3 hemagglutinin may enable high fitness of novel human virus reassortants. PLoS One 2013; 8:e79165. [PMID: 24265752 PMCID: PMC3827155 DOI: 10.1371/journal.pone.0079165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 09/20/2013] [Indexed: 11/18/2022] Open
Abstract
Reassortment of influenza A virus genes enables antigenic shift resulting in the emergence of pandemic viruses with novel hemagglutinins (HA) acquired from avian strains. Here, we investigated whether historic and contemporary avian strains with different replication capacity in human cells can donate their hemagglutinin to a pandemic human virus. We performed double-infections with two avian H3 strains as HA donors and a human acceptor strain, and determined gene compositions and replication of HA reassortants in mammalian cells. To enforce selection for the avian virus HA, we generated a strictly elastase-dependent HA cleavage site mutant from A/Hong Kong/1/68 (H3N2) (Hk68-Ela). This mutant was used for co-infections of human cells with A/Duck/Ukraine/1/63 (H3N8) (DkUkr63) or the more recent A/Mallard/Germany/Wv64-67/05 (H3N2) (MallGer05) in the absence of elastase but presence of trypsin. Among 21 plaques analyzed from each assay, we found 12 HA reassortants with DkUkr63 (4 genotypes) and 14 with MallGer05 (10 genotypes) that replicated in human cells comparable to the parental human virus. Although DkUkr63 replicated in mammalian cells at a reduced level compared to MallGer05 and Hk68, it transmitted its HA to the human virus, indicating that lower replication efficiency of an avian virus in a mammalian host may not constrain the emergence of viable HA reassortants. The finding that HA and HA/NA reassortants replicated efficiently like the human virus suggests that further HA adaptation remains a relevant barrier for emergence of novel HA reassortants.
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Affiliation(s)
- Anne Kreibich
- Friedrich-Loeffler-Institut, Institute of Molecular Biology, Greifswald-Insel Riems, Germany
| | - Olga Stech
- Friedrich-Loeffler-Institut, Institute of Molecular Biology, Greifswald-Insel Riems, Germany
| | - Jana Hundt
- Friedrich-Loeffler-Institut, Institute of Molecular Biology, Greifswald-Insel Riems, Germany
| | - Mario Ziller
- Friedrich-Loeffler-Institut, Biomathematics Working Group, Greifswald-Insel Riems, Germany
| | - Thomas C. Mettenleiter
- Friedrich-Loeffler-Institut, Institute of Molecular Biology, Greifswald-Insel Riems, Germany
| | - Juergen Stech
- Friedrich-Loeffler-Institut, Institute of Molecular Biology, Greifswald-Insel Riems, Germany
- * E-mail:
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Liu Q, Liu DY, Yang ZQ. Characteristics of human infection with avian influenza viruses and development of new antiviral agents. Acta Pharmacol Sin 2013; 34:1257-69. [PMID: 24096642 PMCID: PMC3791557 DOI: 10.1038/aps.2013.121] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 08/01/2013] [Indexed: 12/21/2022] Open
Abstract
Since 1997, several epizootic avian influenza viruses (AIVs) have been transmitted to humans, causing diseases and even deaths. The recent emergence of severe human infections with AIV (H7N9) in China has raised concerns about efficient interpersonal viral transmission, polygenic traits in viral pathogenicity and the management of newly emerging strains. The symptoms associated with viral infection are different in various AI strains: H5N1 and newly emerged H7N9 induce severe pneumonia and related complications in patients, while some H7 and H9 subtypes cause only conjunctivitis or mild respiratory symptoms. The virulence and tissue tropism of viruses as well as the host responses contribute to the pathogenesis of human AIV infection. Several preventive and therapeutic approaches have been proposed to combat AIV infection, including antiviral drugs such as M2 inhibitors, neuraminidase inhibitors, RNA polymerase inhibitors, attachment inhibitors and signal-transduction inhibitors etc. In this article, we summarize the recent progress in researches on the epidemiology, clinical features, pathogenicity determinants, and available or potential antivirals of AIV.
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Affiliation(s)
- Qiang Liu
- State Key Laboratory of Virology/Institute of Medical Virology, School of Medicine, Wuhan University, Wuhan 430071, China
- The First College of Clinical Medical Science, China Three Gorges University/Yichang Central People's Hospital, Yichang 443000, China
| | - Dong-ying Liu
- State Key Laboratory of Virology/Institute of Medical Virology, School of Medicine, Wuhan University, Wuhan 430071, China
- Department of Microbiology, School of Medicine, Wuhan University, Wuhan 430071, China
| | - Zhan-qiu Yang
- State Key Laboratory of Virology/Institute of Medical Virology, School of Medicine, Wuhan University, Wuhan 430071, China
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Polymerase complex with lysine at position 627 of the PB2 of influenza virus A/Hong Kong/483/97 (H5N1) efficiently transcribes and replicates virus genes in mouse cells. Virus Res 2013; 178:404-10. [PMID: 24070983 DOI: 10.1016/j.virusres.2013.09.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 08/04/2013] [Accepted: 09/06/2013] [Indexed: 11/23/2022]
Abstract
Influenza virus A/Hong Kong/483/97 (H5N1) (HK483-K) has the PB2 with lysine at position 627 (PB2-627K) and is highly pathogenic in chickens and mice. On the other hand, the pathogenicity of mutant virus (HK483-E), which was generated by substituting lysine with glutamic acid at the position of the PB2, is lower than that of HK483-K in mice, but is highly pathogenic in chickens. The PB2 is one of the components of heterotrimeric polymerase complex, which plays roles in the transcription and replication of virus genes. Cell-free polymerase assay revealed that intrinsic transcription activity of the polymerase complex with PB2-627K is higher than that of glutamic acid (PB2-627E). In chicken cells, transcription efficiency of the polymerase complex with PB2-627E was not lower than those with PB2-627K, indicating that transcription of virus genes is modulated by some host factors in chicken cells, resulting in high growth. Polymerase complex with PB2-627K efficiently transcribes and replicates virus polymerase genes in mouse cells, leading to high growth of HK483-K compared with that of HK483-E. The results of our experiments clearly suggest that efficient transcription and replication of virus genes by polymerase complex result in the higher pathogenicity in mice.
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Evaluation of phenotypic markers in full genome sequences of avian influenza isolates from California. Comp Immunol Microbiol Infect Dis 2013; 36:521-36. [DOI: 10.1016/j.cimid.2013.06.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 06/14/2013] [Accepted: 06/19/2013] [Indexed: 12/20/2022]
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The effect of the PB2 mutation 627K on highly pathogenic H5N1 avian influenza virus is dependent on the virus lineage. J Virol 2013; 87:9983-96. [PMID: 23843645 DOI: 10.1128/jvi.01399-13] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clade 2.2 Eurasian-lineage H5N1 highly pathogenic avian influenza viruses (HPAIVs) were first detected in Qinghai Lake, China, in 2005 and subsequently spread through Asia, Europe, and Africa. Importantly, these viruses carried a lysine at amino acid position 627 of the PB2 protein (PB2 627K), a known mammalian adaptation motif. Previous avian influenza virus isolates have carried glutamic acid in this position (PB2 627E), commonly described to restrict virus polymerase function in the mammalian host. We sought to examine the effect of PB2 627K on viral maintenance in the avian reservoir. Viruses constructed by reverse genetics were engineered to contain converse PB2 627K/E mutations in a Eurasian H5N1 virus (A/turkey/Turkey/5/2005 [Ty/05]) and, for comparison, a historical pre-Asian H5N1 HPAIV that naturally bears PB2 627E (A/turkey/England/50-92/1991 [50-92]). The 50-92 PB2 627K was genetically unstable during virus propagation, resulting in reversion to PB2 627E or the accumulation of the additional mutation PB2 628R and/or a synonymous mutation from an A to a G nucleotide at nucleotide position 1869 (PB2 A1869G). Intriguingly, PB2 628R and/or A1869G appeared to improve the genetic stability of 50-92 PB2 627K. However, the replication of 50-92 PB2 627K in conjunction with these stabilizing mutations was significantly restricted in experimentally infected chickens, where reversion to PB2 627E occurred. In contrast, no significant effects on viral fitness were observed for Ty/05 PB2 627E or 627K in in vitro or in vivo experiments. Our observations suggest that PB2 627K is supported in Eurasian-lineage viruses; in contrast, PB2 627K carries a significant fitness cost in the historical pre-Asian 50-92 virus.
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Liu Q, Lu L, Sun Z, Chen GW, Wen Y, Jiang S. Genomic signature and protein sequence analysis of a novel influenza A (H7N9) virus that causes an outbreak in humans in China. Microbes Infect 2013; 15:432-9. [DOI: 10.1016/j.micinf.2013.04.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 04/18/2013] [Indexed: 01/12/2023]
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Gabriel G, Czudai-Matwich V, Klenk HD. Adaptive mutations in the H5N1 polymerase complex. Virus Res 2013; 178:53-62. [PMID: 23732876 DOI: 10.1016/j.virusres.2013.05.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 04/04/2013] [Accepted: 05/20/2013] [Indexed: 12/28/2022]
Abstract
Adaptation of the viral polymerase to host factors plays an important role in interspecies transmission of H5N1 viruses. Several adaptive mutations have been identified that, in general, determine not only host range, but also pathogenicity and transmissibility of the virus. The available evidence indicates that most of these mutations are found in the PB2 subunit of the polymerase. Particularly prominent mutations are located in the C-terminal domain of PB2 involving the amino acid exchanges E627K and D701N. Both mutations, that are also responsible for the adaptation of other avian viruses to mammalian hosts, have been described in human H5N1 isolates. In animal models, it could be demonstrated that they enhance pathogenicity in mice and induce contact transmission in guinea pigs. Mutation E627K has also been identified as a determinant of air-borne H5N1 transmission in ferrets. We are only beginning to understand the underlying mechanisms at the molecular level. Thus, mutation D701N promotes importin-α mediated nuclear transport in mammalian cells. Mutation E627K also enhances the replication rate in an importin-α dependent fashion in mammalian cells, yet without affecting nuclear entry of PB2. Numerous other adaptive mutations, some of which compensate for the lack of PB2 E627K, have been observed in PB2 as well as in the polymerase subunit PB1, the nucleoprotein NP, and the nuclear export protein NEP (NS2).
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Affiliation(s)
- Gülsah Gabriel
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
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An MDCK cell culture-derived formalin-inactivated influenza virus whole-virion vaccine from an influenza virus library confers cross-protective immunity by intranasal administration in mice. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2013; 20:998-1007. [PMID: 23637045 DOI: 10.1128/cvi.00024-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
It is currently impossible to predict the next pandemic influenza virus strain. We have thus established a library of influenza viruses of all hemagglutinin and neuraminidase subtypes and their genes. In this article, we examine the applicability of a rapid production model for the preparation of vaccines against emerging pandemic influenza viruses. This procedure utilizes the influenza virus library, cell culture-based vaccine production, and intranasal administration to induce a cross-protective immune response. First, an influenza virus reassortant from the library, A/duck/Hokkaido/Vac-3/2007 (H5N1), was passaged 22 times (P22) in Madin-Darby canine kidney (MDCK) cells. The P22 virus had a titer of >2 ×10(8) PFU/ml, which was 40 times that of the original strain, with 4 point mutations, which altered amino acids in the deduced protein sequences encoded by the PB2 and PA genes. We then produced a formalin-inactivated whole-virion vaccine from the MDCK cell-cultured A/duck/Hokkaido/Vac-3/2007 (H5N1) P22 virus. Intranasal immunization of mice with this vaccine protected them against challenges with lethal influenza viruses of homologous and heterologous subtypes. We further demonstrated that intranasal immunization with the vaccine induced cross-reactive neutralizing antibody responses against the homotypic H5N1 influenza virus and its antigenic variants and cross-reactive cell-mediated immune responses to the homologous virus, its variants within a subtype, and even an influenza virus of a different subtype. These results indicate that a rapid model for emergency vaccine production may be effective for producing the next generation of pandemic influenza virus vaccines.
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Adaptation of avian influenza A virus polymerase in mammals to overcome the host species barrier. J Virol 2013; 87:7200-9. [PMID: 23616660 DOI: 10.1128/jvi.00980-13] [Citation(s) in RCA: 170] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Avian influenza A viruses, such as the highly pathogenic avian H5N1 viruses, sporadically enter the human population but often do not transmit between individuals. In rare cases, however, they establish a new lineage in humans. In addition to well-characterized barriers to cell entry, one major hurdle which avian viruses must overcome is their poor polymerase activity in human cells. There is compelling evidence that these viruses overcome this obstacle by acquiring adaptive mutations in the polymerase subunits PB1, PB2, and PA and the nucleoprotein (NP) as well as in the novel polymerase cofactor nuclear export protein (NEP). Recent findings suggest that synthesis of the viral genome may represent the major defect of avian polymerases in human cells. While the precise mechanisms remain to be unveiled, it appears that a broad spectrum of polymerase adaptive mutations can act collectively to overcome this defect. Thus, identification and monitoring of emerging adaptive mutations that further increase polymerase activity in human cells are critical to estimate the pandemic potential of avian viruses.
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Belser JA, Tumpey TM. H5N1 pathogenesis studies in mammalian models. Virus Res 2013; 178:168-85. [PMID: 23458998 DOI: 10.1016/j.virusres.2013.02.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 12/14/2012] [Accepted: 02/06/2013] [Indexed: 12/21/2022]
Abstract
H5N1 influenza viruses are capable of causing severe disease and death in humans, and represent a potential pandemic subtype should they acquire a transmissible phenotype. Due to the expanding host and geographic range of this virus subtype, there is an urgent need to better understand the contribution of both virus and host responses following H5N1 virus infection to prevent and control human disease. The use of mammalian models, notably the mouse and ferret, has enabled the detailed study of both complex virus-host interactions as well as the contribution of individual viral proteins and point mutations which influence virulence. In this review, we describe the behavior of H5N1 viruses which exhibit high and low virulence in numerous mammalian species, and highlight the contribution of inoculation route to virus pathogenicity. The involvement of host responses as studied in both inbred and outbred mammalian models is discussed. The roles of individual viral gene products and molecular determinants which modulate the severity of H5N1 disease in vivo are presented. This research contributes not only to our understanding of influenza virus pathogenesis, but also identifies novel preventative and therapeutic targets to mitigate the disease burden caused by avian influenza viruses.
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Affiliation(s)
- Jessica A Belser
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, United States
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Liu Y, Qin K, Meng G, Zhang J, Zhou J, Zhao G, Luo M, Zheng X. Structural and functional characterization of K339T substitution identified in the PB2 subunit cap-binding pocket of influenza A virus. J Biol Chem 2013; 288:11013-23. [PMID: 23436652 DOI: 10.1074/jbc.m112.392878] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Influenza virus RNA-dependent RNA polymerase is a heterotrimer composed of PA, PB1, and PB2 subunits. RNA-dependent RNA polymerase is required for both transcription and replication of influenza viral RNA taking place in the nucleus of infected cells. A "cap-snatching" mechanism is used to generate a 5'-capped primer for transcription in which the cap-binding domain of PB2 (PB2cap) captures the 5' cap of the host pre-mRNA. Our statistical analysis of PB2 sequences showed that residue Lys(339) located in the cap-binding pocket of H5N1 PB2cap was gradually replaced by Thr(339) over the past decade. To understand the role of this amino acid polymorphism, we solved the crystal structures of PB2cap with or without a pre-mRNA cap analog, m(7)GTP, in the presence of Lys(339) or Thr(339). The structures showed that Lys(339) contributes to binding the γ-phosphate group of m(7)GTP, and the replacement of Lys(339) by Thr eliminates this interaction. Isothermal titration calorimetry analysis showed that Thr(339) attenuated the PB2cap cap binding activity in vitro compared with Lys(339). Further functional studies confirmed that Thr(339)-PB2-containing ribonucleoprotein complex has a reduced influenza polymerase activity and RNA synthesis activity, and a reconstituted H5N1 virus containing the Thr(339) substitution exhibited a lower virulence to mice but more active replication in Madin-Darby canine kidney cells. The K339T substitution in the cap-binding pocket of PB2 modulates the polymerase activity and virulence by regulating the cap binding activity. It is informative to track variations in the cap-binding pocket of PB2 in surveillance of the evolution and spread of influenza virus.
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Affiliation(s)
- Yong Liu
- State Key Lab of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
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Wang J, Sun Y, Xu Q, Tan Y, Pu J, Yang H, Brown EG, Liu J. Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. PLoS One 2012; 7:e40752. [PMID: 22808250 PMCID: PMC3393695 DOI: 10.1371/journal.pone.0040752] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 06/12/2012] [Indexed: 11/18/2022] Open
Abstract
H9N2 influenza viruses have been circulating worldwide in multiple avian species and have repeatedly infected humans to cause typical disease. The continued avian-to-human interspecies transmission of H9N2 viruses raises concerns about the possibility of viral adaption with increased virulence for humans. To investigate the genetic basis of H9N2 influenza virus host range and pathogenicity in mammals, we generated a mouse-adapted H9N2 virus (SD16-MA) that possessed significantly higher virulence than wide-type virus (SD16). Increased virulence was detectable after 8 sequential lung passages in mice. Five amino acid substitutions were found in the genome of SD16-MA compared with SD16 virus: PB2 (M147L, V250G and E627K), HA (L226Q) and M1 (R210K). Assessments of replication in mice showed that all of the SD16-MA PB2, HA and M1 genome segments increased virus replication; however, only the mouse-adapted PB2 significantly increased virulence. Although the PB2 E627K amino acid substitution enhanced viral polymerase activity and replication, none of the single mutations of mouse adapted PB2 could confer increased virulence on the SD16 backbone. The combination of M147L and E627K significantly enhanced viral replication ability and virulence in mice. Thus, our results show that the combination of PB2 amino acids at position 147 and 627 is critical for the increased pathogenicity of H9N2 influenza virus in mammalian host.
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Affiliation(s)
- Jingjing Wang
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yipeng Sun
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Qi Xu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yuanyuan Tan
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Juan Pu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Hanchun Yang
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Earl G. Brown
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Emerging Pathogens Research Centre, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Jinhua Liu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
- The Shandong Animal Disease Control Center, Jinan, China
- * E-mail:
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Analysis by single-gene reassortment demonstrates that the 1918 influenza virus is functionally compatible with a low-pathogenicity avian influenza virus in mice. J Virol 2012; 86:9211-20. [PMID: 22718825 DOI: 10.1128/jvi.00887-12] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The 1918-1919 "Spanish" influenza pandemic is estimated to have caused 50 million deaths worldwide. Understanding the origin, virulence, and pathogenic properties of past pandemic influenza viruses, including the 1918 virus, is crucial for current public health preparedness and future pandemic planning. The origin of the 1918 pandemic virus has not been resolved, but its coding sequences are very like those of avian influenza virus. The proteins encoded by the 1918 virus differ from typical low-pathogenicity avian influenza viruses at only a small number of amino acids in each open reading frame. In this study, a series of chimeric 1918 influenza viruses were created in which each of the eight 1918 pandemic virus gene segments was replaced individually with the corresponding gene segment of a prototypical low-pathogenicity avian influenza (LPAI) H1N1 virus in order to investigate functional compatibility of the 1918 virus genome with gene segments from an LPAI virus and to identify gene segments and mutations important for mammalian adaptation. This set of eight "7:1" chimeric viruses was compared to the parental 1918 and LPAI H1N1 viruses in intranasally infected mice. Seven of the 1918 LPAI 7:1 chimeric viruses replicated and caused disease equivalent to the fully reconstructed 1918 virus. Only the chimeric 1918 virus containing the avian influenza PB2 gene segment was attenuated in mice. This attenuation could be corrected by the single E627K amino acid change, further confirming the importance of this change in mammalian adaptation and mouse pathogenicity. While the mechanisms of influenza virus host switch, and particularly mammalian host adaptation are still only partly understood, these data suggest that the 1918 virus, whatever its origin, is very similar to avian influenza virus.
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Abstract
Two studies of H5N1 avian influenza viruses that had been genetically engineered to render them transmissible between ferrets have proved highly controversial. Divergent opinions exist about the importance of these studies of influenza transmission and about potential 'dual use' research implications. No consensus has developed yet about how to balance these concerns. After not recommending immediate full publication of earlier, less complete versions of the studies, the United States National Science Advisory Board for Biosecurity subsequently recommended full publication of more complete manuscripts; however, controversy about this and similar research remains.
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Sequence in the influenza A virus nucleoprotein required for viral polymerase binding and RNA synthesis. J Virol 2012; 86:7292-7. [PMID: 22532672 DOI: 10.1128/jvi.00014-12] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many proposed mechanisms for influenza A viral RNA synthesis include an interaction of the nucleoprotein (NP) with the viral polymerase. To identify an NP sequence required for this interaction, we used the cryoelectron microscopic structure of an influenza virus miniribonucleoprotein as a guide for choosing promising surface-exposed sequences. We show that three amino acids (R204, W207, and R208) located in a loop at the top of the head domain of NP are required for functional interaction with the viral polymerase. Quantitative reverse transcription-PCR (RT-PCR) measurements of RNAs synthesized in minigenome assays established that each of these NP amino acids is required for viral RNA synthesis. The mutation of these three amino acids does not affect nuclear localization or RNA-binding and oligomerization activities of NP. In vitro binding experiments with purified virus polymerase and NPs established that these three amino acids are required for NP binding to the viral polymerase.
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