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Acocal-Juárez E, Márquez-Domínguez L, Vallejo-Ruíz V, Cedillo L, Santos-López G. Baloxavir Resistance Markers in Influenza A and B Viruses in the Americas. Drug Healthc Patient Saf 2024; 16:105-113. [PMID: 39296541 PMCID: PMC11410037 DOI: 10.2147/dhps.s470868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 07/20/2024] [Indexed: 09/21/2024] Open
Abstract
Aim Influenza control demands multifaceted strategies, including antiviral drugs. Baloxavir, a recent addition to influenza treatment, acts as an inhibitor of the Polymerase acid (PA) component of the viral polymerase. However, mutations associated with resistance have been identified. Purpose This study analyzed PA gene sequences of influenza A and B viruses (IAV and IBV, respectively) reported in the Americas, retrieved from databases published until May 2023, to identify primary markers of resistance to baloxavir. Patients and Methods PA gene sequences were obtained from the GISAID and NCBI databases, focusing on countries in the Americas with 500 or more sequences for IAV, and 50 or more sequences for IBV. Results Of the 58,816 PA sequences analyzed for IAV, only 55 (0.1%) harbored resistance markers, representing approximately 1 in 1000 occurrence. The most frequent markers were I38V (21 cases) and I38M (7 cases) at position 38 of PA, followed by E199G (9 cases) at position 199. For IBV, 14,684 sequences were analyzed, of which only eight presented a resistance marker (0.05%). Five sequences had the M34I marker, while the remaining three had the I38V marker. While frequency of resistance markers in PA is comparable to other regions, these results highlight the need for enhanced sequencing efforts, particularly in Latin America. Such efforts would serve to intensify influenza surveillance and inform public health interventions. Conclusion While baloxavir demonstrates efficacy against influenza, resistance markers have been identified, including pre-existing ones. Our study adds eight (IAV: six and IBV: two) new spontaneously occurring substitutions to the existing literature, highlighting the need for continued surveillance. Among these, I38M stands out due to its significant tenfold reduction in drug susceptibility. Therefore, vigilant monitoring of these resistance markers in IAV and IBV remains crucial for maintaining baloxavir's effectiveness and informing future public health interventions.
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Affiliation(s)
- Erick Acocal-Juárez
- Centro de Investigaciones en Ciencias Microbiológicas, Benemérita Universidad Autónoma de Puebla, Puebla Pue, Mexico
- Laboratorio de Biología Molecular y Virología, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Puebla, Mexico
- Centro de Detección Biomolecular, Benemérita Universidad Autónoma de Puebla México, Puebla Pue, Mexico
| | - Luis Márquez-Domínguez
- Laboratorio de Biología Molecular y Virología, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Verónica Vallejo-Ruíz
- Laboratorio de Biología Molecular y Virología, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Lilia Cedillo
- Centro de Detección Biomolecular, Benemérita Universidad Autónoma de Puebla México, Puebla Pue, Mexico
| | - Gerardo Santos-López
- Laboratorio de Biología Molecular y Virología, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Puebla, Mexico
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Giacinti JA, Signore AV, Jones MEB, Bourque L, Lair S, Jardine C, Stevens B, Bollinger T, Goldsmith D, Pybus M, Stasiak I, Davis R, Pople N, Nituch L, Brook RW, Ojkic D, Massé A, Dimitri-Masson G, Parsons GJ, Baker M, Yason C, Harms J, Jutha N, Neely J, Berhane Y, Lung O, French SK, Myers L, Provencher JF, Avery-Gomm S, Robertson GJ, Barychka T, Gurney KEB, Wight J, Rahman I, Hargan K, Lang AS, Montevecchi WA, Burt TV, Brown MGC, Pekarik C, Thompson T, McLaughlin A, Willie M, Wilson L, Flemming SA, Ross MV, Leafloor J, Baldwin F, Sharp C, Lewis H, Beaumont M, Hanson A, Ronconi RA, Reed E, Campbell M, Saunders M, Soos C. Avian influenza viruses in wild birds in Canada following incursions of highly pathogenic H5N1 virus from Eurasia in 2021-2022. mBio 2024; 15:e0320323. [PMID: 39012149 PMCID: PMC11323545 DOI: 10.1128/mbio.03203-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 05/24/2024] [Indexed: 07/17/2024] Open
Abstract
Following the detection of novel highly pathogenic avian influenza virus (HPAIV) H5N1 clade 2.3.4.4b in Newfoundland, Canada, in late 2021, avian influenza virus (AIV) surveillance in wild birds was scaled up across Canada. Herein, we present the results of Canada's Interagency Surveillance Program for Avian Influenza in Wild Birds during the first year (November 2021-November 2022) following the incursions of HPAIV from Eurasia. The key objectives of the surveillance program were to (i) identify the presence, distribution, and spread of HPAIV and other AIVs; (ii) identify wild bird morbidity and mortality associated with HPAIV; (iii) identify the range of wild bird species infected by HPAIV; and (iv) genetically characterize detected AIV. A total of 6,246 sick and dead wild birds were tested, of which 27.4% were HPAIV positive across 12 taxonomic orders and 80 species. Geographically, HPAIV detections occurred in all Canadian provinces and territories, with the highest numbers in the Atlantic and Central Flyways. Temporally, peak detections differed across flyways, though the national peak occurred in April 2022. In an additional 11,295 asymptomatic harvested or live-captured wild birds, 5.2% were HPAIV positive across 3 taxonomic orders and 19 species. Whole-genome sequencing identified HPAIV of Eurasian origin as most prevalent in the Atlantic Flyway, along with multiple reassortants of mixed Eurasian and North American origins distributed across Canada, with moderate structuring at the flyway scale. Wild birds were victims and reservoirs of HPAIV H5N1 2.3.4.4b, underscoring the importance of surveillance encompassing samples from sick and dead, as well as live and harvested birds, to provide insights into the dynamics and potential impacts of the HPAIV H5N1 outbreak. This dramatic shift in the presence and distribution of HPAIV in wild birds in Canada highlights a need for sustained investment in wild bird surveillance and collaboration across interagency partners. IMPORTANCE We present the results of Canada's Interagency Surveillance Program for Avian Influenza in Wild Birds in the year following the first detection of highly pathogenic avian influenza virus (HPAIV) H5N1 on the continent. The surveillance program tested over 17,000 wild birds, both sick and apparently healthy, which revealed spatiotemporal and taxonomic patterns in HPAIV prevalence and mortality across Canada. The significant shift in the presence and distribution of HPAIV in Canada's wild birds underscores the need for sustained investment in wild bird surveillance and collaboration across One Health partners.
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Affiliation(s)
- Jolene A. Giacinti
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Government of Canada, Winnipeg, Manitoba, Canada
| | - Anthony V. Signore
- Ecotoxicology and Wildlife Health Division, Science and Technology Branch, Environment and Climate Change Canada, Government of Canada, Ottawa, Ontario, Canada
| | - Megan E. B. Jones
- Canadian Wildlife Health Cooperative, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Laura Bourque
- Canadian Wildlife Health Cooperative, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Stéphane Lair
- Canadian Wildlife Health Cooperative, Faculté de médecine vétérinaire, Université de Montréal, St-Hyacinthe, Québec, Canada
| | - Claire Jardine
- Canadian Wildlife Health Cooperative, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Brian Stevens
- Canadian Wildlife Health Cooperative, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Trent Bollinger
- Canadian Wildlife Health Cooperative, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Dayna Goldsmith
- Canadian Wildlife Health Cooperative, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | | | - Margo Pybus
- Alberta Environment and Parks, Edmonton, Alberta, Canada
| | - Iga Stasiak
- Saskatchewan Ministry of Environment, Saskatoon, Saskatchewan, Canada
| | - Richard Davis
- Manitoba Department of Natural Resources and Northern Development, Wildlife Branch, Dauphin, Manitoba, Canada
| | - Neil Pople
- Veterinary Diagnostic Services, Manitoba Department of Agriculture, Winnipeg, Manitoba, Canada
| | - Larissa Nituch
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, Ontario, Canada
| | - Rodney W. Brook
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, Ontario, Canada
| | - Davor Ojkic
- Animal Health Laboratory, University of Guelph, Guelph, Ontario, Canada
| | - Ariane Massé
- Ministère de l’Environnement, de la Lutte contre les changements climatiques, de la Faune et des Parcs du Québec, Québec City, Québec, Canada
| | - Gabrielle Dimitri-Masson
- Ministère de l’Agriculture, des Pêcheries et de l’Alimentation du Québec, Québec City, Québec, Canada
| | - Glen J. Parsons
- Wildlife Division, Nova Scotia Department of Natural Resources and Renewables, Kentville, Nova Scotia, Canada
| | - Meghan Baker
- Animal Health Division, Department of Fisheries, Forestry and Agriculture, Government of Newfoundland and Labrador, St. John’s, Newfoundland and Labrador, Canada
| | - Carmencita Yason
- AVC Diagnostic Services, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Jane Harms
- Animal Health Unit, Environment Yukon, Government of Yukon, Whitehorse, Yukon, Canada
| | - Naima Jutha
- Wildlife Management Division, Department of Environment and Climate Change, Government of the Northwest Territories, Yellowknife, Northwest Territories, Canada
| | - Jon Neely
- Wildlife Operations Division, Department of Environment, Government of Nunavut, Iqaluit, Nunavut, Canada
| | - Yohannes Berhane
- Ecotoxicology and Wildlife Health Division, Science and Technology Branch, Environment and Climate Change Canada, Government of Canada, Ottawa, Ontario, Canada
| | - Oliver Lung
- Ecotoxicology and Wildlife Health Division, Science and Technology Branch, Environment and Climate Change Canada, Government of Canada, Ottawa, Ontario, Canada
| | - Shannon K. French
- Animal Health Strategic Planning and Research, Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Lawrna Myers
- Animal Health Strategic Planning and Research, Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Jennifer F. Provencher
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Government of Canada, Winnipeg, Manitoba, Canada
| | - Stephanie Avery-Gomm
- Wildlife Research Division, Science and Technology Branch, Environment and Climate Change Canada, Government of Canada, Mount Pearl, Newfoundland and Labrador, Canada
| | - Gregory J. Robertson
- Wildlife Research Division, Science and Technology Branch, Environment and Climate Change Canada, Government of Canada, Mount Pearl, Newfoundland and Labrador, Canada
| | - Tatsiana Barychka
- Wildlife Research Division, Science and Technology Branch, Environment and Climate Change Canada, Government of Canada, Mount Pearl, Newfoundland and Labrador, Canada
| | - Kirsty E. B. Gurney
- Ecotoxicology and Wildlife Health Division, Science and Technology Branch, Environment and Climate Change Canada, Government of Canada, Saskatoon, Saskatchewan, Canada
| | - Jordan Wight
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | - Ishraq Rahman
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | - Kathryn Hargan
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | - William A. Montevecchi
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
- Department of Psychology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | - Tori V. Burt
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
- Department of Psychology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | - Michael G. C. Brown
- Wildlife Management and Regulatory Affairs Division, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Gatineau, Québec, Canada
| | - Cynthia Pekarik
- Wildlife Management and Regulatory Affairs Division, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Gatineau, Québec, Canada
| | - Trevor Thompson
- Wildlife Management and Regulatory Affairs Division, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Gatineau, Québec, Canada
| | - Angela McLaughlin
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Government of Canada, Winnipeg, Manitoba, Canada
- Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Megan Willie
- Pacific Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Delta, British Columbia, Canada
| | - Laurie Wilson
- Pacific Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Delta, British Columbia, Canada
| | - Scott A. Flemming
- Pacific Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Delta, British Columbia, Canada
| | - Megan V. Ross
- Pacific Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Delta, British Columbia, Canada
| | - Jim Leafloor
- Prairie Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Winnipeg, Manitoba, Canada
| | - Frank Baldwin
- Prairie Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Winnipeg, Manitoba, Canada
| | - Chris Sharp
- Ontario Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Ottawa, Ontario, Canada
| | - Hannah Lewis
- Ontario Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Ottawa, Ontario, Canada
| | - Matthieu Beaumont
- Quebec Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Québec, Québec, Canada
| | - Al Hanson
- Atlantic Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Sackville, New Brunswick, Canada
| | - Robert A. Ronconi
- Atlantic Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Sackville, New Brunswick, Canada
| | - Eric Reed
- Northern Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Yellowknife, Northwest Territories, Canada
| | - Margaret Campbell
- Northern Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Whitehorse, Yukon, Canada
| | - Michelle Saunders
- Department of Lands and Natural Resources, Nunatsiavut Government, Nain, Newfoundland and Labrador, Canada
| | - Catherine Soos
- Ecotoxicology and Wildlife Health Division, Science and Technology Branch, Environment and Climate Change Canada, Government of Canada, Saskatoon, Saskatchewan, Canada
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Al-Shuhaib MBS, Alam S, Khan SA, Al-Shuhaib JMB, Chen YK, M Alshabrmi F. Hemagglutinin 3 and 8 can be the most efficient influenza subtypes for human host invasion; a comparative in silico approach. J Biomol Struct Dyn 2023:1-19. [PMID: 37965722 DOI: 10.1080/07391102.2023.2280674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/28/2023] [Indexed: 11/16/2023]
Abstract
The severity of the influenza virus infection is largely determined by its ability to invade the human host receptor. This critical step is conducted by utilizing hemagglutinin (HA) due to its binding with sialic acid 2,6 (SA). Though 18 subtypes (H1-H18) of HA have been identified, the most efficient one for conducting the host entry has not yet been resolved. This study aims to assess the severity of infections for HA variants by conducting a comparative docking of H1-H18 with the human SA receptor. Eighteen viral 3D structures were retrieved, minimized, and optimized for docking with human SA. In all retrieved structures, five conserved amino acid residues were selected for docking with human SA. Special protein grids were prepared by locating these five residues in the 18 selected subtypes. Results showed that H3 and H8 exerted the highest standard precision and extra precision docking scores, and the highest binding affinities with the human SA, respectively. Phylogenetic analyses confirmed the actual positioning of the selected 3D structures and showed these docked structures belonged to their usual classes due to the extremely close distances found in each docked subtype compared with its corresponding non-docked structures. H8-SA showed slightly better RMSD and SASA values than H3-SA, while H3-SIA showed more favourable radius of gyration scores than H8-SIA in the majority of the simulation period. Due to the highest affinity of binding of H3 and H8 with the human receptor, special caution should be exercised regarding any possible outbreak mediated by these subtypes in human populations. However, it is important to acknowledge a limitation inherent to the computational approach; it may hold relative rather than absolute significance. Further research is needed to deepen our understanding of the intricate interplay between HA variants and the host receptor, taking into account the broader context of viral infection dynamics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Sarfaraz Alam
- Tunneling Group Biotechnology Centre, Gliwice, Poland
| | | | | | - Yan-Kun Chen
- School of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Fahad M Alshabrmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
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4
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Bauer L, Benavides FFW, Veldhuis Kroeze EJB, de Wit E, van Riel D. The neuropathogenesis of highly pathogenic avian influenza H5Nx viruses in mammalian species including humans. Trends Neurosci 2023; 46:953-970. [PMID: 37684136 PMCID: PMC10591965 DOI: 10.1016/j.tins.2023.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/04/2023] [Indexed: 09/10/2023]
Abstract
Circulation of highly pathogenic avian influenza (HPAI) H5Nx viruses of the A/Goose/Guangdong/1/96 lineage in birds regularly causes infections of mammals, including humans. In many mammalian species, infections are associated with severe neurological disease, a unique feature of HPAI H5Nx viruses compared with other influenza A viruses. Here, we provide an overview of the neuropathogenesis of HPAI H5Nx virus infection in mammals, centered on three aspects: neuroinvasion, neurotropism, and neurovirulence. We focus on in vitro studies, as well as studies on naturally or experimentally infected mammals. Additionally, we discuss the contribution of viral factors to the neuropathogenesis of HPAI H5Nx virus infections and the efficacy of intervention strategies to prevent neuroinvasion or the development of neurological disease.
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Affiliation(s)
- Lisa Bauer
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | | | | | - Emmie de Wit
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Debby van Riel
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands.
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5
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Yin R, Luo Z, Zhuang P, Zeng M, Li M, Lin Z, Kwoh CK. ViPal: A framework for virulence prediction of influenza viruses with prior viral knowledge using genomic sequences. J Biomed Inform 2023; 142:104388. [PMID: 37178781 PMCID: PMC10602211 DOI: 10.1016/j.jbi.2023.104388] [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: 01/24/2023] [Revised: 04/30/2023] [Accepted: 05/07/2023] [Indexed: 05/15/2023]
Abstract
Influenza viruses pose great threats to public health and cause enormous economic losses every year. Previous work has revealed the viral factors associated with the virulence of influenza viruses in mammals. However, taking prior viral knowledge represented by heterogeneous categorical and discrete information into account to explore virus virulence is scarce in the existing work. How to make full use of the preceding domain knowledge in virulence study is challenging but beneficial. This paper proposes a general framework named ViPal for virulence prediction in mice that incorporates discrete prior viral mutation and reassortment information based on all eight influenza segments. The posterior regularization technique is leveraged to transform prior viral knowledge into constraint features and integrated into the machine learning models. Experimental results on influenza genomic datasets validate that our proposed framework can improve virulence prediction performance over baselines. The comparison between ViPal and other existing methods shows the computational efficiency of our framework with comparable or superior performance. Moreover, the interpretable analysis through SHAP (SHapley Additive exPlanations) identifies the scores of constraint features contributing to the prediction. We hope this framework could provide assistance for the accurate detection of influenza virulence and facilitate flu surveillance.
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Affiliation(s)
- Rui Yin
- Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, USA; School of Computer Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore.
| | - Zihan Luo
- School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, China
| | - Pei Zhuang
- Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Min Zeng
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Min Li
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Zhuoyi Lin
- School of Computer Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Chee Keong Kwoh
- School of Computer Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
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Mettier J, Prompt C, Bruder E, Da Costa B, Chevalier C, Le Goffic R. Comparison of PB1-F2 Proximity Interactomes Reveals Functional Differences between a Human and an Avian Influenza Virus. Viruses 2023; 15:v15020328. [PMID: 36851542 PMCID: PMC9961899 DOI: 10.3390/v15020328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/13/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023] Open
Abstract
Most influenza viruses express the PB1-F2 protein which is regarded as a virulence factor. However, PB1-F2 behaves differently in avian and mammalian hosts, suggesting that this protein may be involved in the species barrier crossings regularly observed in influenza viruses. To better understand the functions associated with this viral protein, we decided to compare the BioID2-derived proximity interactome of a human PB1-F2 from an H3N2 virus with that of an avian PB1-F2 from an H7N1 strain. The results obtained reveal that the two proteins share only a few interactors and thus common functions. The human virus protein is mainly involved in signaling by Rho GTPases while the avian virus protein is mainly involved in ribonucleoprotein complex biogenesis. PB1-F2 H3N2 interactors include several members of the 14-3-3 protein family, a family of regulatory proteins involved in many signaling pathways. We then validated the interaction with 14-3-3 proteins and were able to show that the association of H3N2-PB1-F2 with YWHAH increased the activity of the antiviral sensor MDA5, while H7N1-PB1-F2 had no effect. Collectively, these results show that PB1-F2 can associate with a large range of protein complexes and exert a wide variety of functions. Furthermore, PB1-F2 interactome differs according to the avian or human origin of the protein.
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Liu M, Liu K, Cheng D, Zheng B, Li S, Mo Z. The regulatory role of NLRX1 in innate immunity and human disease. Cytokine 2022; 160:156055. [DOI: 10.1016/j.cyto.2022.156055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/01/2022] [Accepted: 09/20/2022] [Indexed: 11/03/2022]
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Molecular Characteristics, Receptor Specificity, and Pathogenicity of Avian Influenza Viruses Isolated from Wild Ducks in Russia. Int J Mol Sci 2022; 23:ijms231810829. [PMID: 36142740 PMCID: PMC9502348 DOI: 10.3390/ijms231810829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Avian influenza viruses (AIV) of wild ducks are known to be able to sporadically infect domestic birds and spread along poultry. Regular surveillance of AIV in the wild is needed to prepare for potential outbreaks. During long-year monitoring, 46 strains of AIV were isolated from gulls and mallards in Moscow ponds and completely sequenced. Amino acid positions that affect the pathogenicity of influenza viruses in different hosts were tested. The binding affinity of the virus for receptors analogs typical for different hosts and the pathogenicity of viruses for mice and chickens were investigated. Moscow isolates did not contain well-known markers of pathogenicity and/or adaptation to mammals, so as a polybasic cleavage site in HA, substitutions of 226Q and 228G amino acids in the receptor-binding region of HA, and substitutions of 627E and 701D amino acids in the PB2. The PDZ-domain ligand in the NS protein of all studied viruses contains the ESEV or ESEI sequence. Although several viruses had the N66S substitution in the PB1-F2 protein, all Moscow isolates were apathogenic for both mice and chickens. This demonstrates that the phenotypic manifestation of pathogenicity factors is not absolute but depends on the genome context.
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Wu W, Alexander JS, Metcalf JP. In Vivo and In Vitro Studies of Cigarette Smoke Effects on Innate Responses to Influenza Virus: A Matter of Models? Viruses 2022; 14:1824. [PMID: 36016446 PMCID: PMC9415757 DOI: 10.3390/v14081824] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/05/2022] [Accepted: 08/17/2022] [Indexed: 11/26/2022] Open
Abstract
Cigarette smoke (CS) is a significant public health problem and a leading risk factor for the development of chronic obstructive pulmonary disease (COPD) in the developed world. Respiratory viral infections, such as the influenza A virus (IAV), are associated with acute exacerbations of COPD and are more severe in cigarette smokers. To fight against viral infection, the host has developed an innate immune system, which has complicated mechanisms regulating the expression and activation of cytokines and chemokines to maximize the innate and adaptive antiviral response, as well as limiting the immunopathology that leads to exaggerated lung damage. In the case of IAV, responders include airway and alveolar epithelia, lung macrophages and dendritic cells. To achieve a successful infection, IAV must overcome these defenses. In this review, we summarize the detrimental role of CS in influenza infections. This includes both immunosuppressive and proinflammatory effects on innate immune responses during IAV infection. Some of the results, with respect to CS effects in mouse models, appear to have discordant results, which could be at least partially addressed by standardization of animal viral infection models to evaluate the effect of CS exposure in this context.
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Affiliation(s)
- Wenxin Wu
- Pulmonary, Critical Care & Sleep Medicine, Department of Medicine, the University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Jeremy S. Alexander
- Pulmonary, Critical Care & Sleep Medicine, Department of Medicine, the University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Jordan P. Metcalf
- Pulmonary, Critical Care & Sleep Medicine, Department of Medicine, the University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Department of Microbiology and Immunology, the University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Veterans Affairs Medical Center, Oklahoma City, OK 73104, USA
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Quirós-González V, Maderuelo-Fernández JÁ, Haro-Pérez AM, González-Calle D, Barreales-Rodríguez V, Eiros JM. Influenza complications: Reporting cardiac events through a hospital surveillance system. Rev Clin Esp 2022; 222:S2254-8874(22)00070-4. [PMID: 35843784 DOI: 10.1016/j.rceng.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/01/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND AND AIMS The aim of this study was to determine the complications of influenza in all adults hospitalized with this disease and, specifically, to analyze the characteristics of post-infection cardiovascular events. METHODS This work is observational descriptive study of adults hospitalized with influenza during the 2017-2018 and 2018-2019 seasons using the specific registry of a tertiary hospital. The complications analyzed were pneumonia, multiple organ dysfunction syndrome, septic shock, acute respiratory distress syndrome, and cardiac events. RESULTS A total of 928 adults with influenza required hospitalization and 303 (32.7%) presented with one or more complications. A post-influenza cardiac event occurred in 2.5% of patients; they had a higher probability of ICU admission and higher mortality. Influenza vaccination was a protective factor for cardiac events (OR 0.32; 95%CI 0.13-0.83). CONCLUSIONS Influenza can lead to important complications in hospitalized patients. The high mortality rate associated with post-infection cardiac events means that preventive measures, including annual influenza vaccination, need to be emphasized.
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Affiliation(s)
- V Quirós-González
- Dirección de Planificación, Hospital Universitario 12 de Octubre, Madrid, Spain.
| | - J Á Maderuelo-Fernández
- Unidad de Investigación en Atención Primaria de Salamanca (APISAL), Instituto de investigación Biomédica de Salamanca (IBSAL), Gerencia de Atención Primaria de Salamanca, Gerencia Regional de Salud de Castilla y León (SACyL), Spain
| | - A M Haro-Pérez
- Servicio de Medicina Preventiva, Complejo Asistencial Universitario de Salamanca, Salamanca, Spain
| | - D González-Calle
- Servicio de Cardiología, Complejo Asistencial Universitario de Salamanca, Salamanca, Spain
| | - V Barreales-Rodríguez
- Servicio de Medicina Interna, Complejo Asistencial Universitario de Salamanca, Salamanca, Spain
| | - J M Eiros
- Servicio de Microbiología, Hospital Universitario Río Hortega, Valladolid, Spain
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11
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Li B, Su G, Xiao C, Zhang J, Li H, Sun N, Lao G, Yu Y, Ren X, Qi W, Wang X, Liao M. The PB2 co-adaptation of H10N8 avian influenza virus increases the pathogenicity to chickens and mice. Transbound Emerg Dis 2022; 69:1794-1803. [PMID: 34008327 DOI: 10.1111/tbed.14157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/06/2021] [Accepted: 05/14/2021] [Indexed: 12/18/2022]
Abstract
Avian influenza (AI) is an important zoonotic disease, which can be transmitted across species barriers to other hosts, especially humans, posing a serious threat to the poultry industry and public health. In recent years, human cases infected with the H10N8, H9N2, and H7N9 of avian influenza viruses (AIVs) have been identified frequently as have the internal genes of H7N9 and H10N8, which are derived from H9N2 viruses. The adaptive mutation of the PB2 gene is an important way for the H10N8, H9N2, and H7N9 AIVs to spread across species to adapt to new hosts. Several well-known adaptive mutations in the PB2 gene, such as E627K, D701N, and A588V, significantly enhanced the virulence of the AIVs in mammals. However, the co-adaptation of AIVs to avian and mammalian hosts is rarely studied. In this study, we found that the mutations of PB2-I292V, PB2-R389K, PB2-A588V, PB2-T598M/V, PB2-L648V, and PB2-T676M substitutions significantly increased after 2012. In addition, in our previous studies, we found that the human-origin and avian-origin of H10N8 AIVs with very high homology also have these six mutation differences in PB2 gene, and the avian-origin H10N8 strain known as JX102 with all the key amino acids on the PB2 protein in the pre-evolutionary stage, so JX102 was chosen as a model strain. Among them, PB2-A588V significantly enhanced the activity of polymerase in avian and mammalian cells. Notably, animal experiments showed that PB2-A588V substitution increased the pathogenicity and transmissibility in chickens and the virulence of mice. The combined mutations of PB2-F6 (including PB2-I292V, PB2-R389K, PB2-A588V, PB2-T598M, PB2-L648V, and PB2-T676M) obtained higher adaptability of AIVs in avians and mammals than that of the single mutation of PB2-A588V, which suggested that the PB2 588 site is a key co-adaptation site and that synergies with other mutation sites can further enhance this co-adaptability. The results of this study show that the emergence of co-adaptation not only increases the threat to avians and mammals but may also contribute to a pandemic among avians and cross the interspecies barrier to mammals.
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Affiliation(s)
- Bo Li
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Zoonoses, Ministry of Agricultural and Rural Affairs of the People's Republic of China, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, National Development and Reform Commission of the People's Republic of China, Guangzhou, China
- Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou, China
| | - Guanming Su
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Chencheng Xiao
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jiahao Zhang
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Zoonoses, Ministry of Agricultural and Rural Affairs of the People's Republic of China, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, National Development and Reform Commission of the People's Republic of China, Guangzhou, China
- Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou, China
| | - Huanan Li
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Zoonoses, Ministry of Agricultural and Rural Affairs of the People's Republic of China, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, National Development and Reform Commission of the People's Republic of China, Guangzhou, China
- Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou, China
| | - Na Sun
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Guangjie Lao
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yuandi Yu
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xingxing Ren
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Wenbao Qi
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Zoonoses, Ministry of Agricultural and Rural Affairs of the People's Republic of China, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, National Development and Reform Commission of the People's Republic of China, Guangzhou, China
- Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou, China
| | - Xiuhui Wang
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Hebei Province Poultry Engineering Technology Research Center, Hebei University of Engineering, Handan, People's Republic of China
| | - Ming Liao
- National Avian Influenza Para-Reference Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Zoonoses, Ministry of Agricultural and Rural Affairs of the People's Republic of China, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, National Development and Reform Commission of the People's Republic of China, Guangzhou, China
- Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou, China
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12
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Quirós-González V, Maderuelo-Fernández J, Haro-Pérez A, González-Calle D, Barreales-Rodríguez V, Eiros J. Complicaciones de la gripe: información sobre eventos cardíacos a través de un sistema de vigilancia hospitalario. Rev Clin Esp 2022. [DOI: 10.1016/j.rce.2022.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Xu Z, Liu X, Ma X, Zou W, Chen Q, Chen F, Deng X, Liang J, Dong C, Lan K, Wu S, Zhou HB. Discovery of oseltamivir-based novel PROTACs as degraders targeting neuraminidase to combat H1N1 influenza virus. CELL INSIGHT 2022; 1:100030. [PMID: 37193052 PMCID: PMC10120310 DOI: 10.1016/j.cellin.2022.100030] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/06/2022] [Accepted: 05/06/2022] [Indexed: 05/16/2023]
Abstract
Annual and sporadic influenza outbreaks pose a great threat to human health and the economy worldwide. Moreover, the frequent mutation of influenza viruses caused by antigen drift complicates the application of antiviral therapeutics. As such, there is an urgent need for novel antiviral agents to tackle the problem of insufficient efficacy of licensed drugs. Inspired by the success of the newly emerged PROTACs (PROteolysis TArgeting Chimeras) strategy, we report herein the design and synthesis of novel PROTAC molecules based on an oseltamivir scaffold to combat severe annual influenza outbreaks. Among these, several compounds showed good anti-H1N1 activity and efficient influenza neuraminidase (NA) degradation activity. The best compound, 8e, effectively induced influenza NA degradation in a dose-dependent manner and relied on the ubiquitin-proteasome pathway. Moreover, Compound 8e exhibited potent antiviral activity toward both wild-type H1N1 virus and an oseltamivir-resistant strain (H1N1, H274Y). A molecular docking study demonstrated that Compound 8e had good hydrogen-bonding and hydrophobic interactions with both the active sites of NA and Von Hippel-Lindau (VHL) proteins, which could effectively drive the favorable interaction of these two proteins. Thus, as the first report of a successful anti-influenza PROTAC, this proof of concept will greatly widen the application range of the PROTAC technique to antiviral drug discovery.
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Affiliation(s)
- Zhichao Xu
- State Key Laboratory of Virology, Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Xinjin Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiaoyu Ma
- State Key Laboratory of Virology, Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Wenting Zou
- State Key Laboratory of Virology, Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Qi Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Feifei Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiaofei Deng
- State Key Laboratory of Virology, Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Jinsen Liang
- State Key Laboratory of Virology, Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Chune Dong
- State Key Laboratory of Virology, Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Ke Lan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430071, China
| | - Shuwen Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Hai-Bing Zhou
- State Key Laboratory of Virology, Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430071, China
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14
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Wang Q, Wang Z, Zhang J, Zhang Q, Zheng M, Wen J, Zhao G, Li Q. Dual RNA-Seq of H5N1 Avian Influenza Virus and Host Cell Transcriptomes Reveals Novel Insights Into Host-Pathogen Cross Talk. Front Microbiol 2022; 13:828277. [PMID: 35495687 PMCID: PMC9039741 DOI: 10.3389/fmicb.2022.828277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
H5N1 avian influenza virus (AIV) is a highly pathogenic influenza virus that poses a substantial threat to poultry production and public health. A comprehensive understanding of host-pathogen interactions for AIV requires knowledge of gene expression changes in both the pathogen and the host upon infection. We report the use of dual RNA sequencing technology to uncover trends in gene expression in H5N1 AIV and chickens (DF1 cells) during the course of infection. The expression of all viral genes increased continuously from 0 to 20 h post infection. We also identified 2,762 differentially expressed host genes during infection. Pathway analysis found that genes related to the signaling pathways of DNA replication, T cell activation, NF-kappa B signaling pathway, and RNA degradation were significantly enriched. We demonstrated that the cis-acting lncRNA MSTRG.14019.1 targeted CSE1L and may affect virus replication. This study provides a more comprehensive and detailed understanding of host-virus interactions at the RNA level during the course of H5N1 AIV infection.
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Affiliation(s)
- Qiao Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zixuan Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jin Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qi Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Maiqing Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Wen
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guiping Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qinghe Li
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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15
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Zhang M, Liu M, Bai S, Zhao C, Li Z, Xu J, Zhang X. Influenza A Virus-Host Specificity: An Ongoing Cross-Talk Between Viral and Host Factors. Front Microbiol 2021; 12:777885. [PMID: 34803997 PMCID: PMC8602901 DOI: 10.3389/fmicb.2021.777885] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022] Open
Abstract
One big threat from influenza A viruses (IAVs) is that novel viruses emerge from mutation alongside reassortment. Some of them have gained the capability to transmit into human from the avian reservoir. Understanding the molecular events and the involved factors in breaking the cross-species barrier holds important implication for the surveillance and prevention of potential influenza outbreaks. In this review, we summarize recent progresses, including several ground-breaking findings, in how the interaction between host and viral factors, exemplified by the PB2 subunit of the influenza virus RNA polymerase co-opting host ANP32 protein to facilitate transcription and replication of the viral genome, shapes the evolution of IAVs from host specificity to cross-species infection.
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Affiliation(s)
- Miaomiao Zhang
- Scientific Research Center, Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Veterinary Research Institute, Chinese Academic of Agricultural Sciences & Animal Influenza Virus Evolution and Pathogenesis Innovation Team of the Agricultural Science and Technology Innovation Team, Shanghai, China
| | - Mingbin Liu
- Scientific Research Center, Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shimeng Bai
- Scientific Research Center, Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chen Zhao
- Scientific Research Center, Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zejun Li
- Shanghai Veterinary Research Institute, Chinese Academic of Agricultural Sciences & Animal Influenza Virus Evolution and Pathogenesis Innovation Team of the Agricultural Science and Technology Innovation Team, Shanghai, China
| | - Jianqing Xu
- Scientific Research Center, Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaoyan Zhang
- Scientific Research Center, Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Medical College, Fudan University, Shanghai, China
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16
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Wang Q, Zhang Q, Zheng M, Wen J, Li Q, Zhao G. Viral-Host Interactome Analysis Reveals Chicken STAU2 Interacts With Non-structural Protein 1 and Promotes the Replication of H5N1 Avian Influenza Virus. Front Immunol 2021; 12:590679. [PMID: 33968009 PMCID: PMC8098808 DOI: 10.3389/fimmu.2021.590679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 02/22/2021] [Indexed: 12/29/2022] Open
Abstract
As a highly pathogenic influenza virus, H5N1 avian influenza virus (AIV) poses a great threat to poultry production and public health. H5N1 AIV has a small genome and, therefore, relies heavily on its host cellular machinery to replicate. To develop a comprehensive understanding of how H5N1 AIV rewires host cellular machinery during the course of infection, it is crucial to identify which host proteins and complexes come into physical contact with the viral proteins. Here, we utilized affinity purification mass spectrometry (AP-MS) to systematically determine the physical interactions of 11 H5N1 AIV proteins with host proteins in chicken DF1 cells. We identified with high confidence 1,043 H5N1 AIV–chicken interactions involving 621 individual chicken proteins and uncovered a number of host proteins and complexes that were targeted by the viral proteins. Specifically, we revealed that chicken Staufen double-stranded RNA-binding protein 2 interacts with AIV non-structural protein 1 (NS1) and promotes the replication of the virus by enhancing the nuclear export of NS1 mRNA. This dataset facilitates a more comprehensive and detailed understanding of how the host machinery is manipulated during the course of H5N1 AIV infection.
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Affiliation(s)
- Qiao Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qi Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Maiqing Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Wen
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qinghe Li
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guiping Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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17
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Pickering RJ, Booty LM. NLR in eXile: Emerging roles of NLRX1 in immunity and human disease. Immunology 2020; 162:268-280. [PMID: 33314068 DOI: 10.1111/imm.13291] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/02/2020] [Accepted: 11/10/2020] [Indexed: 02/06/2023] Open
Abstract
NLRX1 is a member of the NOD-like receptor family, a set of pattern recognition receptors associated with innate immunity. Interestingly, NLRX1 exists in somewhat of an exile from its NLR counterparts with unique features that mediate atypical functions compared with traditional NOD-like receptors (NLRs). Aside from a mitochondrial targeting sequence, the N-terminal region is yet to be characterized. Mitochondrially located, NLRX1 sits within a subgroup of regulatory NLRs responsible for negatively regulating cellular inflammatory signalling. As well as modulating pathogen response, emerging evidence is implicating NLRX1 as a central homeostatic gatekeeper between mitochondrial biology and immunological response. More recently, NLRX1 has been implicated in a wide range of disease, both pathogen-driven and otherwise. Emerging links of NLRX1 in cancer biology, autoimmunity and other inflammatory conditions are raising the potential of targeting NLRX1 therapeutically, with recent studies in inflammatory bowel disease showing great promise. Within this review, we address the unique features of NLRX1, its roles in innate immune signalling and its involvement in a range of inflammatory, metabolic and oncology disease indications with a focus on areas that could benefit from therapeutic targeting of NLRX1.
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Affiliation(s)
- Robert J Pickering
- Immunology Network, Adaptive Immunity Research Unit, GlaxoSmithKline, Stevenage, UK.,Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - Lee M Booty
- Immunology Network, Adaptive Immunity Research Unit, GlaxoSmithKline, Stevenage, UK
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18
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Improvement of PR8-Derived Recombinant Clade 2.3.4.4c H5N6 Vaccine Strains by Optimization of Internal Genes and H103Y Mutation of Hemagglutinin. Vaccines (Basel) 2020; 8:vaccines8040781. [PMID: 33419331 PMCID: PMC7766170 DOI: 10.3390/vaccines8040781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 12/04/2022] Open
Abstract
Clade 2.3.4.4c H5N6 avian influenza A viruses (AIVs) may have originally adapted to infect chickens and have caused highly pathogenic avian influenza (HPAI) in poultry and human fatalities. Although A/Puerto Rico/8/1934 (H1N1) (PR8)-derived recombinant clade 2.3.4.4c H5N6 vaccine strains have been effective in embryonated chicken eggs-based vaccine production system, they need to be improved in terms of immunogenicity and potential mammalian pathogenicity. We replaced the PB2 gene alone or the PB2 (polymerase basic protein 2), NP (nucleoprotein), M (matrix protein) and NS (non-structural protein) genes together in the PR8 strain with corresponding genes from AIVs with low pathogenicity to remove mammalian pathogenicity and to match CD8+ T cell epitopes with contemporary HPAI viruses, respectively, without loss of viral fitness. Additionally, we tested the effect of the H103Y mutation of hemagglutinin (HA) on antigen productivity, mammalian pathogenicity and heat/acid stability. The replacement of PB2 genes and the H103Y mutation reduced the mammalian pathogenicity but increased the antigen productivity of the recombinant vaccine strains. The H103Y mutation increased heat stability but unexpectedly decreased acid stability, probably resulting in increased activation pH for HA. Interestingly, vaccination with inactivated recombinant virus with replaced NP, M and NS genes halted challenge virus shedding earlier than the recombinant vaccine without internal genes replacement. In conclusion, we successfully generated recombinant clade 2.3.4.4c H5N6 vaccine strains that were less pathogenic to mammals and more productive and heat stable than conventional PR8-derived recombinant strains by optimization of internal genes and the H103Y mutation of HA.
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19
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Abdelrahman Z, Li M, Wang X. Comparative Review of SARS-CoV-2, SARS-CoV, MERS-CoV, and Influenza A Respiratory Viruses. Front Immunol 2020; 11:552909. [PMID: 33013925 PMCID: PMC7516028 DOI: 10.3389/fimmu.2020.552909] [Citation(s) in RCA: 262] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/24/2020] [Indexed: 12/28/2022] Open
Abstract
The 2019 novel coronavirus (SARS-CoV-2) pandemic has caused a global health emergency. The outbreak of this virus has raised a number of questions: What is SARS-CoV-2? How transmissible is SARS-CoV-2? How severely affected are patients infected with SARS-CoV-2? What are the risk factors for viral infection? What are the differences between this novel coronavirus and other coronaviruses? To answer these questions, we performed a comparative study of four pathogenic viruses that primarily attack the respiratory system and may cause death, namely, SARS-CoV-2, severe acute respiratory syndrome (SARS-CoV), Middle East respiratory syndrome (MERS-CoV), and influenza A viruses (H1N1 and H3N2 strains). This comparative study provides a critical evaluation of the origin, genomic features, transmission, and pathogenicity of these viruses. Because the coronavirus disease 2019 (COVID-19) pandemic caused by SARS-CoV-2 is ongoing, this evaluation may inform public health administrators and medical experts to aid in curbing the pandemic's progression.
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MESH Headings
- Animals
- Betacoronavirus/genetics
- Betacoronavirus/pathogenicity
- Birds/virology
- COVID-19
- Coronavirus Infections/epidemiology
- Coronavirus Infections/transmission
- Coronavirus Infections/virology
- Genome, Viral
- Humans
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/pathogenicity
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/pathogenicity
- Influenza in Birds/epidemiology
- Influenza in Birds/transmission
- Influenza in Birds/virology
- Influenza, Human/epidemiology
- Influenza, Human/transmission
- Influenza, Human/virology
- Middle East Respiratory Syndrome Coronavirus/genetics
- Middle East Respiratory Syndrome Coronavirus/pathogenicity
- Pandemics
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/transmission
- Pneumonia, Viral/virology
- Severe acute respiratory syndrome-related coronavirus/genetics
- Severe acute respiratory syndrome-related coronavirus/pathogenicity
- SARS-CoV-2
- Severe Acute Respiratory Syndrome/epidemiology
- Severe Acute Respiratory Syndrome/transmission
- Severe Acute Respiratory Syndrome/virology
- Virulence/immunology
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Affiliation(s)
- Zeinab Abdelrahman
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
- Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Mengyuan Li
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
- Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
- Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
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20
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Murri S, Madrières S, Tatard C, Piry S, Benoit L, Loiseau A, Pradel J, Artige E, Audiot P, Leménager N, Lacôte S, Vulin J, Charbonnel N, Marianneau P, Castel G. Detection and Genetic Characterization of Puumala Orthohantavirus S-Segment in Areas of France Non-Endemic for Nephropathia Epidemica. Pathogens 2020; 9:pathogens9090721. [PMID: 32882953 PMCID: PMC7559001 DOI: 10.3390/pathogens9090721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/15/2020] [Accepted: 08/22/2020] [Indexed: 12/30/2022] Open
Abstract
Puumala virus (PUUV) in Europe causes nephropathia epidemica (NE), a mild form of hemorrhagic fever with renal syndrome (HFRS). The incidence of NE is highly heterogeneous spatially, whereas the geographic distribution of the wild reservoir of PUUV, the bank vole, is essentially homogeneous. Our understanding of the processes driving this heterogeneity remains incomplete due to gaps in knowledge. Little is known about the current distribution and genetic variation of PUUV in the areas outside the well-identified zones of NE endemicity. We trapped bank voles in four forests in French regions in which NE is considered non-endemic, but sporadic NE cases have been reported recently. We tested bank voles for anti-PUUV IgG and characterized the S segment sequences of PUUV from seropositive animals. Phylogenetic analyses revealed specific amino-acid signatures and genetic differences between PUUV circulating in non-endemic and nearby NE-endemic areas. We also showed, in temporal surveys, that the amino-acid sequences of PUUV had undergone fewer recent changes in areas non-endemic for NE than in endemic areas. The evolutionary history of the current French PUUV clusters was investigated by phylogeographic approaches, and the results were considered in the context of the history of French forests. Our findings highlight the need to monitor the circulation and genetics of PUUV in a larger array of bank vole populations, to improve our understanding of the risk of NE.
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Affiliation(s)
- Séverine Murri
- ANSES—Laboratoire de Lyon, Unité Virologie, 69007 Lyon, France; (S.M.); (S.M.); (S.L.); (J.V.); (P.M.)
| | - Sarah Madrières
- ANSES—Laboratoire de Lyon, Unité Virologie, 69007 Lyon, France; (S.M.); (S.M.); (S.L.); (J.V.); (P.M.)
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Caroline Tatard
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Sylvain Piry
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Laure Benoit
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Anne Loiseau
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Julien Pradel
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Emmanuelle Artige
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Philippe Audiot
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Nicolas Leménager
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Sandra Lacôte
- ANSES—Laboratoire de Lyon, Unité Virologie, 69007 Lyon, France; (S.M.); (S.M.); (S.L.); (J.V.); (P.M.)
| | - Johann Vulin
- ANSES—Laboratoire de Lyon, Unité Virologie, 69007 Lyon, France; (S.M.); (S.M.); (S.L.); (J.V.); (P.M.)
| | - Nathalie Charbonnel
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Philippe Marianneau
- ANSES—Laboratoire de Lyon, Unité Virologie, 69007 Lyon, France; (S.M.); (S.M.); (S.L.); (J.V.); (P.M.)
| | - Guillaume Castel
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
- Correspondence:
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Yu J, Sun X, Goie JYG, Zhang Y. Regulation of Host Immune Responses against Influenza A Virus Infection by Mitogen-Activated Protein Kinases (MAPKs). Microorganisms 2020; 8:microorganisms8071067. [PMID: 32709018 PMCID: PMC7409222 DOI: 10.3390/microorganisms8071067] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 12/12/2022] Open
Abstract
Influenza is a major respiratory viral disease caused by infections from the influenza A virus (IAV) that persists across various seasonal outbreaks globally each year. Host immune response is a key factor determining disease severity of influenza infection, presenting an attractive target for the development of novel therapies for treatments. Among the multiple signal transduction pathways regulating the host immune activation and function in response to IAV infections, the mitogen-activated protein kinase (MAPK) pathways are important signalling axes, downstream of various pattern recognition receptors (PRRs), activated by IAVs that regulate various cellular processes in immune cells of both innate and adaptive immunity. Moreover, aberrant MAPK activation underpins overexuberant production of inflammatory mediators, promoting the development of the “cytokine storm”, a characteristic of severe respiratory viral diseases. Therefore, elucidation of the regulatory roles of MAPK in immune responses against IAVs is not only essential for understanding the pathogenesis of severe influenza, but also critical for developing MAPK-dependent therapies for treatment of respiratory viral diseases. In this review, we will summarise the current understanding of MAPK functions in both innate and adaptive immune response against IAVs and discuss their contributions towards the cytokine storm caused by highly pathogenic influenza viruses.
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Affiliation(s)
- Jiabo Yu
- Integrative Biomedical Sciences Programme, University of Edinburgh Institute, Zhejiang University, International Campus Zhejiang University, Haining 314400, China; (J.Y.); (X.S.)
| | - Xiang Sun
- Integrative Biomedical Sciences Programme, University of Edinburgh Institute, Zhejiang University, International Campus Zhejiang University, Haining 314400, China; (J.Y.); (X.S.)
| | - Jian Yi Gerald Goie
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore;
- The Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
| | - Yongliang Zhang
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore;
- The Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
- Correspondence: ; Tel.: +65-65166407
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22
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Chen LJ, Guo JJ, Guo WW, Shen EX, Wang X, Li KJ, Yan J, Shi M, Li YR, Hou W. Molecular Epidemiology and Vaccine Compatibility Analysis of Seasonal Influenza Viruses in Wuhan, 2016-2019. Virol Sin 2020; 35:556-565. [PMID: 32394327 DOI: 10.1007/s12250-020-00225-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/07/2020] [Indexed: 10/24/2022] Open
Abstract
Influenza viruses (FLUV) cause high morbidity and mortality annually in the world and pose a serious threat to the public health. Wuhan, as an important transportation hub in China, has a dense population and suitable climate, which also lays a major hidden danger for the outbreak of influenza. To survey and characterize the seasonal FLUV in Wuhan during 2016-2019, we collected 44,738 throat swabs, among which 15.5% were influenza A (FLUAV) positive, 6.1% influenza B (FLUBV) and 0.3% co-infection. By monitoring FLUV in each month from June 2016 to May 2019, different with the previously seasonality pattern, only a single influenza peak was appeared in winter of 2017-2018 and 2018-2019, respectively. These data indicated that the complex circulation pattern of seasonal influenza in Wuhan. In addition, we found the age group was skewed towards 5-14 years group whose activity were mostly school based, which suggested school may be an important place for influenza outbreaks. Meanwhile, phylogenic analysis revealed that two subtypes (subclade 3C.2a2 and 3C.2a1b) of A(H3N2) were circulating in Wuhan and there was an obvious transition in 2018 because the two subclades were detected simultaneously. Furthermore, by estimating the vaccine effectiveness, we found that the vaccine strain of FLUAV didn't seem to match very well the current epidemic strain, especially A(H3N2). Hence, more accurate prediction of seasonal outbreak is essential for vaccine design. Taken together, our results provided the current information about seasonal FLUV in Wuhan which form the basis for vaccine updating.
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Affiliation(s)
- Liang-Jun Chen
- Department of Laboratory Medicine, Zhongnan Hospital, State Key Laboratory of Virology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Jing-Jing Guo
- Department of Laboratory Medicine, Zhongnan Hospital, State Key Laboratory of Virology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Wei-Wei Guo
- Department of Laboratory Medicine, Zhongnan Hospital, State Key Laboratory of Virology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - E-Xiang Shen
- Department of Laboratory Medicine, Zhongnan Hospital, State Key Laboratory of Virology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Xin Wang
- Department of Laboratory Medicine, Zhongnan Hospital, State Key Laboratory of Virology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Kai-Ji Li
- Department of Laboratory Medicine, Zhongnan Hospital, State Key Laboratory of Virology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Jie Yan
- Department of Laboratory Medicine, Zhongnan Hospital, State Key Laboratory of Virology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Mang Shi
- School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.,Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Yi-Rong Li
- Department of Laboratory Medicine, Zhongnan Hospital, State Key Laboratory of Virology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China.
| | - Wei Hou
- Department of Laboratory Medicine, Zhongnan Hospital, State Key Laboratory of Virology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China.
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23
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Influenza A virus PB1‐F2 protein: An ambivalent innate immune modulator and virulence factor. J Leukoc Biol 2020; 107:763-771. [DOI: 10.1002/jlb.4mr0320-206r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 12/14/2022] Open
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24
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de Freitas CS, Rocha MEN, Sacramento CQ, Marttorelli A, Ferreira AC, Rocha N, de Oliveira AC, de Oliveira Gomes AM, Dos Santos PS, da Silva EO, da Costa JP, de Lima Moreira D, Bozza PT, Silva JL, Barroso SPC, Souza TML. Agathisflavone, a Biflavonoid from Anacardium occidentale L., Inhibits Influenza Virus Neuraminidase. Curr Top Med Chem 2020; 20:111-120. [PMID: 31854280 DOI: 10.2174/1568026620666191219150738] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/31/2019] [Accepted: 11/25/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND Neuraminidase inhibitors (NAIs) are the only class of antivirals in clinical use against influenza virus approved worldwide. However, approximately 1-3% of circulating strains present resistance mutations to oseltamivir (OST), the most used NAI. Therefore, it is important to catalogue new molecules to inhibit influenza virus, especially OST-resistant strains. Natural products from tropical plants used for human consumption represent a worthy class of substances. Their use could be stimulated in resource-limited setting where the access to expensive antiviral therapies is restricted. METHODS We evaluated the anti-influenza virus activity of agathisflavone derived from Anacardium occidentale L. RESULTS The neuraminidase (NA) activity of wild-type and OST-resistant influenza virus was inhibited by agathisflavone, with IC50 values ranging from 20 to 2.0 µM, respectively. Agathisflavone inhibited influenza virus replication with EC50 of 1.3 µM. Sequential passages of the virus in the presence of agathisflavone revealed the emergence of mutation R249S, A250S and R253Q in the NA gene. These changes are outside the OST binding region, meaning that agathisflavone targets this viral enzyme at a region different than conventional NAIs. CONCLUSION Altogether our data suggest that agathisflavone has a promising chemical structure for the development of anti-influenza drugs.
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Affiliation(s)
- Caroline S de Freitas
- Laboratorio de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundacao Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Diseases of Neglected Populations (INCT/IDNP), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Marco E N Rocha
- Laboratorio de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundacao Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Diseases of Neglected Populations (INCT/IDNP), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil.,Laboratório de Química de Produtos Naturais 5, Farmanguinhos, Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carolina Q Sacramento
- Laboratorio de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundacao Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Diseases of Neglected Populations (INCT/IDNP), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Andressa Marttorelli
- Laboratorio de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundacao Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Diseases of Neglected Populations (INCT/IDNP), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - André C Ferreira
- Laboratorio de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundacao Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Diseases of Neglected Populations (INCT/IDNP), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Natasha Rocha
- Laboratorio de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundacao Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Diseases of Neglected Populations (INCT/IDNP), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Andrea Cheble de Oliveira
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto Nacional de Ciencia e Tecnologia de Biologia Estrutural e Bioimagem, Brazil
| | - Andre Marco de Oliveira Gomes
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto Nacional de Ciencia e Tecnologia de Biologia Estrutural e Bioimagem, Brazil
| | - Patrícia Souza Dos Santos
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto Nacional de Ciencia e Tecnologia de Biologia Estrutural e Bioimagem, Brazil
| | - Edilene Oliveira da Silva
- Instituto Nacional de Ciencia e Tecnologia de Biologia Estrutural e Bioimagem, Brazil.,Universidade Federal do Pará, Instituto de Ciências Biológicas, Laboratório de Biologia Estrutural, Belém, Pará, Brazil
| | - Josineide Pantoja da Costa
- Instituto Nacional de Ciencia e Tecnologia de Biologia Estrutural e Bioimagem, Brazil.,Universidade Federal do Pará, Instituto de Ciências Biológicas, Laboratório de Biologia Estrutural, Belém, Pará, Brazil
| | - Davyson de Lima Moreira
- Laboratório de Química de Produtos Naturais 5, Farmanguinhos, Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Patrícia T Bozza
- Laboratorio de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundacao Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Jerson L Silva
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto Nacional de Ciencia e Tecnologia de Biologia Estrutural e Bioimagem, Brazil
| | - Shana Priscila Coutinho Barroso
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto Nacional de Ciencia e Tecnologia de Biologia Estrutural e Bioimagem, Brazil.,Instituto de Pesquisas Biomédicas, Hospital Naval Marcílio Dias, Marinha do Brasil, Brazil
| | - Thiago Moreno L Souza
- Laboratorio de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundacao Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Diseases of Neglected Populations (INCT/IDNP), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
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Sila-On D, Chertchinnapa P, Shinkai Y, Kojima T, Nakano H. Development of a dual monoclonal antibody sandwich enzyme-linked immunosorbent assay for the detection of swine influenza virus using rabbit monoclonal antibody by Ecobody technology. J Biosci Bioeng 2020; 130:217-225. [PMID: 32284304 DOI: 10.1016/j.jbiosc.2020.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 02/26/2020] [Accepted: 03/03/2020] [Indexed: 10/24/2022]
Abstract
A dual monoclonal antibody sandwich enzyme-linked immunosorbent assay (mAb sandwich ELISA) has been developed using rabbit monoclonal antibodies generated by Ecobody technology, which includes the isolation of single B cells binding to a specific antigen, amplification of the heavy and light chains of these immunoglobulins, and expression of the fragment of antigen binding (Fab) by cell-free protein synthesis (CFPS). A rabbit was immunized with swine influenza virus (SIV) vaccine, from which single B cells binding to the antigen were isolated. Then, immunoglobulin mRNA was amplified from single cells by reverse transcription-polymerase chain reaction, followed by the attachment of a T7 promoter, appropriate tags, and a T7 terminator for the expression of the Fab portion by CFPS. By taking advantage of two different peptide tags fused to the same Fab, optimal combinations for coating Fab on assay plates and detecting Fab, both synthesized by CFPS, were investigated for mAb sandwich ELISA. Pairs of Fab detected 0.5 ng SIV in the assay. In summary, this result showed the applicability of Ecobody technology for a variety of immunodetection kits for high throughput analyses.
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Affiliation(s)
- Daorung Sila-On
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Phornnaphat Chertchinnapa
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yusuke Shinkai
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Takaaki Kojima
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Hideo Nakano
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
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Viral Determinants in H5N1 Influenza A Virus Enable Productive Infection of HeLa Cells. J Virol 2020; 94:JVI.01410-19. [PMID: 31776276 DOI: 10.1128/jvi.01410-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/04/2019] [Indexed: 12/14/2022] Open
Abstract
Influenza A virus (IAV) is a human respiratory pathogen that causes yearly global epidemics, as well as sporadic pandemics due to human adaptation of pathogenic strains. Efficient replication of IAV in different species is, in part, dictated by its ability to exploit the genetic environment of the host cell. To investigate IAV tropism in human cells, we evaluated the replication of IAV strains in a diverse subset of epithelial cell lines. HeLa cells were refractory to the growth of human H1N1 and H3N2 viruses and low-pathogenic avian influenza (LPAI) viruses. Interestingly, a human isolate of the highly pathogenic avian influenza (HPAI) H5N1 virus successfully propagated in HeLa cells to levels comparable to those in a human lung cell line. Heterokaryon cells generated by fusion of HeLa and permissive cells supported H1N1 virus growth, suggesting the absence of a host factor(s) required for the replication of H1N1, but not H5N1, viruses in HeLa cells. The absence of this factor(s) was mapped to reduced nuclear import, replication, and translation, as well as deficient viral budding. Using reassortant H1N1:H5N1 viruses, we found that the combined introduction of nucleoprotein (NP) and hemagglutinin (HA) from an H5N1 virus was necessary and sufficient to enable H1N1 virus growth. Overall, this study suggests that the absence of one or more cellular factors in HeLa cells results in abortive replication of H1N1, H3N2, and LPAI viruses, which can be circumvented upon the introduction of H5N1 virus NP and HA. Further understanding of the molecular basis of this restriction will provide important insights into the virus-host interactions that underlie IAV pathogenesis and tropism.IMPORTANCE Many zoonotic avian influenza A viruses have successfully crossed the species barrier and caused mild to life-threatening disease in humans. While human-to-human transmission is limited, there is a risk that these zoonotic viruses may acquire adaptive mutations enabling them to propagate efficiently and cause devastating human pandemics. Therefore, it is important to identify viral determinants that provide these viruses with a replicative advantage in human cells. Here, we tested the growth of influenza A virus in a subset of human cell lines and found that abortive replication of H1N1 viruses in HeLa cells can be circumvented upon the introduction of H5N1 virus HA and NP. Overall, this work leverages the genetic diversity of multiple human cell lines to highlight viral determinants that could contribute to H5N1 virus pathogenesis and tropism.
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Yin R, Zhou X, Rashid S, Kwoh CK. HopPER: an adaptive model for probability estimation of influenza reassortment through host prediction. BMC Med Genomics 2020; 13:9. [PMID: 31973709 PMCID: PMC6979075 DOI: 10.1186/s12920-019-0656-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 12/26/2019] [Indexed: 12/29/2022] Open
Abstract
Background Influenza reassortment, a mechanism where influenza viruses exchange their RNA segments by co-infecting a single cell, has been implicated in several major pandemics since 19th century. Owing to the significant impact on public health and social stability, great attention has been received on the identification of influenza reassortment. Methods We proposed a novel computational method named HopPER (Host-prediction-based Probability Estimation of Reassortment), that sturdily estimates reassortment probabilities through host tropism prediction using 147 new features generated from seven physicochemical properties of amino acids. We conducted the experiments on a range of real and synthetic datasets and compared HopPER with several state-of-the-art methods. Results It is shown that 280 out of 318 candidate reassortants have been successfully identified. Additionally, not only can HopPER be applied to complete genomes but its effectiveness on incomplete genomes is also demonstrated. The analysis of evolutionary success of avian, human and swine viruses generated through reassortment across different years using HopPER further revealed the reassortment history of the influenza viruses. Conclusions Our study presents a novel method for the prediction of influenza reassortment. We hope this method could facilitate rapid reassortment detection and provide novel insights into the evolutionary patterns of influenza viruses.
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Affiliation(s)
- Rui Yin
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore.
| | - Xinrui Zhou
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Shamima Rashid
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Chee Keong Kwoh
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
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28
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Domingo E. Virus population dynamics examined with experimental model systems. VIRUS AS POPULATIONS 2020. [PMCID: PMC7153323 DOI: 10.1016/b978-0-12-816331-3.00006-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Experimental evolution permits exploring the effect of controlled environmental variables in virus evolution. Several designs in cell culture and in vivo have established basic concepts that can assist in the interpretation of evolutionary events in the field. Important information has come from cytolytic and persistent infections in cell culture that have unveiled the power of virus-cell coevolution in virus and cell diversification. Equally informative are comparisons of the response of viral populations when subjected to different passage régimens. In particular, plaque-to-plaque transfers in cell culture have revealed unusual genotypes and phenotypes that populate minority layers of viral quasispecies. Some of these viruses display properties that contradict features established in virology textbooks. Several hypotheses and principles of population genetics have found experimental confirmation in experimental designs with viruses. The possibilities of using experimental evolution to understand virus behavior are still largely unexploited.
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LeMessurier KS, Iverson AR, Chang TC, Palipane M, Vogel P, Rosch JW, Samarasinghe AE. Allergic inflammation alters the lung microbiome and hinders synergistic co-infection with H1N1 influenza virus and Streptococcus pneumoniae in C57BL/6 mice. Sci Rep 2019; 9:19360. [PMID: 31852944 PMCID: PMC6920369 DOI: 10.1038/s41598-019-55712-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 11/28/2019] [Indexed: 12/12/2022] Open
Abstract
Asthma is a chronic airways condition that can be exacerbated during respiratory infections. Our previous work, together with epidemiologic findings that asthmatics were less likely to suffer from severe influenza during the 2009 pandemic, suggest that additional complications of influenza such as increased susceptibility to bacterial superinfection, may be mitigated in allergic hosts. To test this hypothesis, we developed a murine model of 'triple-disease' in which mice rendered allergic to Aspergillus fumigatus were co-infected with influenza A virus and Streptococcus pneumoniae seven days apart. Significant alterations to known synergistic effects of co-infection were noted in the allergic mice including reduced morbidity and mortality, bacterial burden, maintenance of alveolar macrophages, and reduced lung inflammation and damage. The lung microbiome of allergic mice differed from that of non-allergic mice during co-infection and antibiotic-induced perturbation to the microbiome rendered allergic animals susceptible to severe morbidity. Our data suggest that responses to co-infection in allergic hosts likely depends on the immune and microbiome states and that antibiotics should be used with caution in individuals with underlying chronic lung disease.
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Affiliation(s)
- Kim S LeMessurier
- Department of Paediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, 38103, USA
- Children's Foundation Research Institute, Memphis, TN, 38103, USA
| | - Amy R Iverson
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Maneesha Palipane
- Department of Paediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, 38103, USA
- Children's Foundation Research Institute, Memphis, TN, 38103, USA
| | - Peter Vogel
- Department of Veterinary Pathology at St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jason W Rosch
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Amali E Samarasinghe
- Department of Paediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, 38103, USA.
- Children's Foundation Research Institute, Memphis, TN, 38103, USA.
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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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Misra RS, Nayak JL. The Importance of Vaccinating Children and Pregnant Women against Influenza Virus Infection. Pathogens 2019; 8:pathogens8040265. [PMID: 31779153 PMCID: PMC6963306 DOI: 10.3390/pathogens8040265] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/20/2019] [Accepted: 11/22/2019] [Indexed: 12/21/2022] Open
Abstract
Influenza virus infection is responsible for significant morbidity and mortality in the pediatric and pregnant women populations, with deaths frequently caused by severe influenza-associated lower respiratory tract infection and acute respiratory distress syndrome (ARDS). An appropriate immune response requires controlling the viral infection through activation of antiviral defenses, which involves cells of the lung and immune system. High levels of viral infection or high levels of inflammation in the lower airways can contribute to ARDS. Pregnant women and young children, especially those born prematurely, may develop serious complications if infected with influenza virus. Vaccination against influenza will lead to lower infection rates and fewer complications, even if the vaccine is poorly matched to circulating viral strains, with maternal vaccination offering infants protection via antibody transmission through the placenta and breast milk. Despite the health benefits of the influenza vaccine, vaccination rates around the world remain well below targets. Trust in the use of vaccines among the public must be restored in order to increase vaccination rates and decrease the public health burden of influenza.
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Affiliation(s)
- Ravi S Misra
- Department of Pediatrics Division of Neonatology, The University of Rochester Medical Center, Rochester, NY 14623, USA
- Correspondence:
| | - Jennifer L Nayak
- Department of Pediatrics Division of Pediatric Infectious Diseases, The University of Rochester Medical Center, Rochester, NY 14623, USA;
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McGowan DC, Balemans W, Embrechts W, Motte M, Keown JR, Buyck C, Corbera J, Funes M, Moreno L, Cooymans L, Tahri A, Eymard J, Stoops B, Strijbos R, Van den Berg J, Fodor E, Grimes JM, Koul A, Jonckers THM, Raboisson P, Guillemont J. Design, Synthesis, and Biological Evaluation of Novel Indoles Targeting the Influenza PB2 Cap Binding Region. J Med Chem 2019; 62:9680-9690. [PMID: 31647875 DOI: 10.1021/acs.jmedchem.9b01091] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
In the search for novel influenza inhibitors we evaluated 7-fluoro-substituted indoles as bioisosteric replacements for the 7-azaindole scaffold of Pimodivir, a PB2 (polymerase basic protein 2) inhibitor currently in clinical development. Specifically, a 5,7-difluoroindole derivative 11a was identified as a potent and metabolically stable influenza inhibitor. 11a demonstrated a favorable oral pharmacokinetic profile and in vivo efficacy in mice. In addition, it was found that 11a was not at risk of metabolism via aldehyde oxidase, an advantage over previously described inhibitors of this class. The crystal structure of 11a bound to influenza A PB2 cap region is disclosed here and deposited to the PDB.
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Affiliation(s)
- David C McGowan
- Janssen Pharmaceutica, N.V. , Turnhoutseweg 30 , 2340 Beerse , Belgium
| | - Wendy Balemans
- Janssen Pharmaceutica, N.V. , Turnhoutseweg 30 , 2340 Beerse , Belgium
| | - Werner Embrechts
- Janssen Pharmaceutica, N.V. , Turnhoutseweg 30 , 2340 Beerse , Belgium
| | - Magali Motte
- Janssen-Cilag , Campus de Maigremont BP615 , F-27106 Val de Reuil , Cedex , France
| | - Jeremy R Keown
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine , University of Oxford , Oxford OX3 7BN , United Kingdom
| | - Christophe Buyck
- Janssen Pharmaceutica, N.V. , Turnhoutseweg 30 , 2340 Beerse , Belgium
| | - Jordi Corbera
- Eurofins Villapharma Research, S.L., Avda. Isaac Peral , Parque Tecnológico de Fuente Álamo , Ctra. El Estrecho-Lobosillo , 30320 Murcia , Spain
| | - Mario Funes
- Eurofins Villapharma Research, S.L., Avda. Isaac Peral , Parque Tecnológico de Fuente Álamo , Ctra. El Estrecho-Lobosillo , 30320 Murcia , Spain
| | - Laura Moreno
- Eurofins Villapharma Research, S.L., Avda. Isaac Peral , Parque Tecnológico de Fuente Álamo , Ctra. El Estrecho-Lobosillo , 30320 Murcia , Spain
| | - Ludwig Cooymans
- Janssen Pharmaceutica, N.V. , Turnhoutseweg 30 , 2340 Beerse , Belgium
| | - Abdellah Tahri
- Janssen Pharmaceutica, N.V. , Turnhoutseweg 30 , 2340 Beerse , Belgium
| | - Julien Eymard
- Novalix (site Janssen-Cilag) , Campus de Maigremont BP615 , F-27106 Val de Reuil , Cedex , France
| | - Bart Stoops
- Janssen Pharmaceutica, N.V. , Turnhoutseweg 30 , 2340 Beerse , Belgium
| | - Rudy Strijbos
- Charles River Laboratories Beerse , Turnhoutseweg 30 , 2340 Beerse , Belgium
| | - Joke Van den Berg
- Janssen Pharmaceutica, N.V. , Turnhoutseweg 30 , 2340 Beerse , Belgium
| | - Ervin Fodor
- Sir William Dunn School of Pathology , University of Oxford , South Parks Road , Oxford OX1 3RE , United Kingdom
| | - Jonathan M Grimes
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine , University of Oxford , Oxford OX3 7BN , United Kingdom.,Diamond Light Source , Harwell Science and Innovation Campus , Didcot OX11 0DE , United Kingdom
| | - Anil Koul
- Janssen Pharmaceutica, N.V. , Turnhoutseweg 30 , 2340 Beerse , Belgium
| | - Tim H M Jonckers
- Janssen Pharmaceutica, N.V. , Turnhoutseweg 30 , 2340 Beerse , Belgium
| | - Pierre Raboisson
- Janssen Pharmaceutica, N.V. , Turnhoutseweg 30 , 2340 Beerse , Belgium
| | - Jérôme Guillemont
- Janssen-Cilag , Campus de Maigremont BP615 , F-27106 Val de Reuil , Cedex , France
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Muñoz P, Vicent L, Bouza E, Sousa-Casasnovas I, López-Roa P, Juárez M, Eworo A, Devesa C, Bruña V, Catalán P, Fernández-Avilés F, Martínez-Sellés M. Prognostic Implications of Influenza Virus Infection in a Cardiac Intensive Care Unit: Potential Impact of a Screening Program. Cardiology 2019; 143:85-91. [DOI: 10.1159/000501230] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 05/27/2019] [Indexed: 11/19/2022]
Abstract
Objectives: Our goal was to determine the presentation and prognosis of influenza in an intensive cardiac care unit and to analyze the impact of an active surveillance program in the diagnosis. Methods: We performed a prospective registry during the flu season in a coronary unit. In the first phase, no systematic screening was performed. Systematic influenza A and B detection was performed in a second phase for all patients admitted. Results: From 227 patients, we identified 17 (7.5%) with influenza. Influenza patients were more likely to have a non-ischemic cause of admission (14 patients [82.4%] vs. 48 patients [40.3%], p = 0.002), fever (8 patients [47.1%] vs. 3 patients [2.6%], p < 0.001), and respiratory failure (7 patients [41.2%] vs. 8 patients [7%], p = 0.001). Influenza infection was an independent predictor of mortality (odds ratio 12.0, 95% confidence interval 1.9–13.6, p < 0.001). The incidence of influenza was 6.6% (6 patients) when no active screening was performed and 7.9% (11 patients) when systematic detection was performed (p = 0.005). The time to diagnosis was shorter in the systematic screening phase (0.92 ± 1.6 vs. 5.2 ± 3.8 days, p = 0.01). Conclusions: Influenza affects approximately 8% of patients admitted to an intensive cardiac care unit during the flu season, with a high mortality rate. An active surveillance program improves early detection.
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Xiong J, Zhao P, Yang P, Yan Q, Jiang L. Evolutionary dynamics of the H7N9 avian influenza virus based on large-scale sequence analysis. PLoS One 2019; 14:e0220249. [PMID: 31404069 PMCID: PMC6690514 DOI: 10.1371/journal.pone.0220249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/11/2019] [Indexed: 11/30/2022] Open
Abstract
Since 2013, epidemics caused by novel H7N9 avian influenza A viruses (AIVs) have become a considerable public health issue. This study investigated the evolution of these viruses at the population level. Compared to H7 and N9 before 2013, there were 18 and 24 substitutions in the majority of novel H7N9 AIVs, respectively. Nine of these in HA and six in NA were rare before 2013, and four of these in HA and two in NA displayed host tropism. S136(128)N and A143(135)V are located on the receptor binding sites of the HA1 subunit and might be important factors in determining the host species of novel H7N9 AIV. On an overall scale, the evolution of H7 and N9, both in terms of time distribution and host species, is under negative selection. However, both in HA and NA, several sites were under positive selection. In both the overall epidemics and the human-derived H7N9 AIVs, eight positive selection sites were identified in HA1, with some located within the known antigen epitopes or the receptor binding site(RBS) domain. This may induce variations in H7N9 AIV with positive selection. It is necessary to strengthen the surveillance of novel H7N9 AIVs, both in human and bird population to determine whether a new virus has emerged through selection pressure and to prevent future epidemics from occurring.
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Affiliation(s)
- Jiasheng Xiong
- College of Marine Science, Shandong University (Weihai), Weihai, People’s Republic of China
| | - Ping Zhao
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People’s Republic of China
| | - Pengfei Yang
- Huai’an Center for Disease Control and Prevention, Huai’an, People’s Republic of China
| | - Qingli Yan
- Huai’an Center for Disease Control and Prevention, Huai’an, People’s Republic of China
| | - Lufang Jiang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People’s Republic of China
- * E-mail:
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35
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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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Abstract
BACKGROUND Avian influenza virus can directly cross species barriers and infect humans with high fatality. As antigen novelty for human host, the public health is being challenged seriously. The pandemic risk of avian influenza viruses should be analyzed and a prediction model should be constructed for virology applications. RESULTS The 178 signature positions in 11 viral proteins were firstly screened as features by the scores of five amino acid factors and their random forest rankings. The Supporting Vector Machine algorithm achieved well performance. The most important amino acid factor (Factor 5) and the minimal range of signature positions (63 amino acid residues) were also explored. Moreover, human-origin avian influenza viruses with three or four genome segments from human virus had pandemic risk with high probability. CONCLUSION Using machine learning methods, the present paper scores the amino acid mutations and predicts pandemic risk with well performance. Although long evolution distances between avian and human viruses suggest that avian influenza virus in nature still need time to fix among human host, it should be notable that there are high pandemic risks for H7N9 and H9N2 avian viruses.
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Affiliation(s)
- Xiaoli Qiang
- Institute of Computing Science and Technology, Guangzhou University, 230 Wai Huan Xi Road, Guangzhou Higher Education Mega Center, Guangzhou, 510006 People’s Republic of China
| | - Zheng Kou
- Institute of Computing Science and Technology, Guangzhou University, 230 Wai Huan Xi Road, Guangzhou Higher Education Mega Center, Guangzhou, 510006 People’s Republic of China
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37
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Viral Factors Important for Efficient Replication of Influenza A Viruses in Cells of the Central Nervous System. J Virol 2019; 93:JVI.02273-18. [PMID: 30867311 PMCID: PMC6532103 DOI: 10.1128/jvi.02273-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/05/2019] [Indexed: 11/20/2022] Open
Abstract
Central nervous system (CNS) disease is one of the most common extrarespiratory tract complications of influenza A virus infections, and the frequency and severity differ between seasonal, pandemic, and zoonotic influenza viruses. However, little is known about the interaction of these viruses with cells of the CNS. Differences among seasonal, pandemic, and zoonotic influenza viruses in replication efficacy in CNS cells, in vitro, suggest that the presence of an alternative HA cleavage mechanism and ability to attach are important viral factors. Identifying these viral factors and detailed knowledge of the interaction between influenza virus and CNS cells are important to prevent and treat this potentially lethal CNS disease. Central nervous system (CNS) disease is one of the most common extrarespiratory tract complications of influenza A virus infections. Remarkably, zoonotic H5N1 virus infections are more frequently associated with CNS disease than seasonal or pandemic influenza viruses. Little is known about the interaction between influenza A viruses and cells of the CNS; therefore, it is currently unknown which viral factors are important for efficient replication. Here, we determined the replication kinetics of a seasonal, pandemic, zoonotic, and lab-adapted influenza A virus in human neuron-like (SK-N-SH) and astrocyte-like (U87-MG) cells and primary mouse cortex neurons. In general, highly pathogenic avian influenza (HPAI) H5N1 virus replicated most efficiently in all cells, which was associated with efficient attachment and infection. Seasonal H3N2 and to a lesser extent pandemic H1N1 virus replicated in a trypsin-dependent manner in SK-N-SH but not in U87-MG cells. In the absence of trypsin, only HPAI H5N1 and WSN viruses replicated. Removal of the multibasic cleavage site (MBCS) from HPAI H5N1 virus attenuated, but did not abrogate, replication. Taken together, our results showed that the MBCS and, to a lesser extent, the ability to attach are important determinants for efficient replication of HPAI H5N1 virus in cells of the CNS. This suggests that both an alternative hemagglutinin (HA) cleavage mechanism and preference for α-2,3-linked sialic acids allowing efficient attachment contribute to the ability of influenza A viruses to replicate efficiently in cells of the CNS. This study further improves our knowledge on potential viral factors important for the neurotropic potential of influenza A viruses. IMPORTANCE Central nervous system (CNS) disease is one of the most common extrarespiratory tract complications of influenza A virus infections, and the frequency and severity differ between seasonal, pandemic, and zoonotic influenza viruses. However, little is known about the interaction of these viruses with cells of the CNS. Differences among seasonal, pandemic, and zoonotic influenza viruses in replication efficacy in CNS cells, in vitro, suggest that the presence of an alternative HA cleavage mechanism and ability to attach are important viral factors. Identifying these viral factors and detailed knowledge of the interaction between influenza virus and CNS cells are important to prevent and treat this potentially lethal CNS disease.
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Andrés C, Peremiquel-Trillas P, Gimferrer L, Piñana M, Codina MG, Rodrigo-Pendás JÁ, Campins-Martí M, Carmen Martín M, Fuentes F, Rubio S, Pumarola T, Antón A. Molecular influenza surveillance at a tertiary university hospital during four consecutive seasons (2012-2016) in Catalonia, Spain. Vaccine 2019; 37:2470-2476. [PMID: 30926297 PMCID: PMC7173002 DOI: 10.1016/j.vaccine.2019.03.046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 03/19/2019] [Accepted: 03/21/2019] [Indexed: 01/14/2023]
Abstract
BACKGROUND Influenza viruses (FLUV) are continuously evolving, which explain the occurrence of seasonal influenza epidemics and the need to review the vaccine strain composition annually. The aim is to describe the genetic diversity and clinical outcomes of FLUV detected at a tertiary university hospital in Barcelona (Spain) during the 2012-2016 seasons. METHODS The detection of FLUV from patients attended at the Emergency Department or admitted to the hospital was performed by either immunofluorescence or PCR-based assays. A specific real-time one-step multiplex RT-PCR was performed for influenza A (FLUAV) subtyping. The complete coding haemagglutinin domain 1 (HA1) and neuraminidase (NA) (2015-2016) protein sequences from a representative sampling were molecular characterised. RESULTS A total 1774 (66.1%) FLUAV and 910 (33.9%) influenza B (FLUBV) cases were laboratory-confirmed. The hospitalisation rate was different between seasons, being the highest (81.4%) during the 2014-2015 season. FLUV were genetically close to vaccine strains except to the 2014-2015, in which most characterised A(H3N2) viruses belonged to a genetic group different from the vaccine strain. During the 2015-2016 season, B/Victoria-like viruses were the most predominant, but this component was not included in the trivalent vaccine used. Mutations D222G or D222N in HA1-domain were found in 3 A(H1N1)pdm09 strains from ICU-admitted cases. Three A(H1N1)pdm09 strains carried the NA H275Y (2) and S247N (1) mutations, respectively related to resistance or decreased susceptibility to oseltamivir. CONCLUSIONS The circulation of drifted A(H3N2) strains during the 2014-2015 season was related to the high hospitalisation rate due to the mismatch with the vaccine strains. The predominance of a FLUBV lineage not included in the trivalent influenza vaccine during the 2015-2016 season highlights the need to use a tetravalent influenza vaccine. Virological surveillance of viral variants carrying protein changes that alter tropism and susceptibility to antivirals features should be strengthened in hospital settings.
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Affiliation(s)
- Cristina Andrés
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Paula Peremiquel-Trillas
- Preventive Medicine and Epidemiology Department, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Vall Hebron Research Institute, Barcelona, Spain
| | - Laura Gimferrer
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria Piñana
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria Gema Codina
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - José Ángel Rodrigo-Pendás
- Preventive Medicine and Epidemiology Department, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Vall Hebron Research Institute, Barcelona, Spain
| | - Magda Campins-Martí
- Preventive Medicine and Epidemiology Department, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Vall Hebron Research Institute, Barcelona, Spain
| | - María Carmen Martín
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Francisco Fuentes
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Susana Rubio
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Tomàs Pumarola
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Andrés Antón
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
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Liu S, Liu L, Xu G, Cao Z, Wang Q, Li S, Peng N, Yin J, Yu H, Li M, Xia Z, Zhou L, Lin Y, Wang X, Li Q, Zhu C, Yang X, Wang J, She Y, Lu M, Zhu Y. Epigenetic Modification Is Regulated by the Interaction of Influenza A Virus Nonstructural Protein 1 with the De Novo DNA Methyltransferase DNMT3B and Subsequent Transport to the Cytoplasm for K48-Linked Polyubiquitination. J Virol 2019; 93:e01587-18. [PMID: 30651365 PMCID: PMC6430541 DOI: 10.1128/jvi.01587-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 01/04/2019] [Indexed: 12/13/2022] Open
Abstract
The influenza virus nonstructural protein 1 (NS1) is a nonstructural protein that plays a major role in antagonizing host interferon responses during infection. However, a clear role for the NS1 protein in epigenetic modification has not been established. In this study, NS1 was found to regulate the expression of some key regulators of JAK-STAT signaling by inhibiting the DNA methylation of their promoters. Furthermore, DNA methyltransferase 3B (DNMT3B) is responsible for this process. Upon investigating the mechanisms underlying this event, NS1 was found to interact with DNMT3B but not DNMT3A, leading to the dissociation of DNMT3B from the promoters of the corresponding genes. In addition, the interaction between NS1 and DNMT3B changed the localization of DNMT3B from the nucleus to the cytosol, resulting in K48-linked ubiquitination and degradation of DNMT3B in the cytosol. We conclude that NS1 interacts with DNMT3B and changes its localization to mediate K48-linked polyubiquitination, subsequently contributing to the modulation of the expression of JAK-STAT signaling suppressors.IMPORTANCE The nonstructural protein 1 (NS1) of the influenza A virus (IAV) is a multifunctional protein that counters cellular antiviral activities and is a virulence factor. However, the involvement of NS1 in DNA methylation during IAV infection has not been established. Here, we reveal that the NS1 protein binds the cellular DNMT3B DNA methyltransferase, thereby inhibiting the methylation of the promoters of genes encoding suppressors of JAK-STAT signaling. As a result, these suppressor genes are induced, and JAK-STAT signaling is inhibited. Furthermore, we demonstrate that the NS1 protein transports DNMT3B to the cytoplasm for ubiquitination and degradation. Thus, we identify the NS1 protein as a potential trigger of the epigenetic deregulation of JAK-STAT signaling suppressors and illustrate a novel mechanism underlying the regulation of host immunity during IAV infection.
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Affiliation(s)
- Shi Liu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Li Liu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Gang Xu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhongying Cao
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qing Wang
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Shun Li
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Nanfang Peng
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jingchuan Yin
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Haisheng Yu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Mengqi Li
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhangchuan Xia
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Li Zhou
- Animal Biosafety Level III Laboratory, Center for Animal Experiment, School of Medicine, Wuhan University, Wuhan, China
| | - Yong Lin
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Xueyu Wang
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Qian Li
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Chengliang Zhu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xuecheng Yang
- Department of Infectious Diseases, Union Hospital, Wuhan, China
| | - Jun Wang
- Center of Clinical Laboratory, The Fifth People's Hospital of Wuxi, Affiliated with Jiangnan University, Wuxi, Jiangsu, China
| | - Yinglong She
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Mengji Lu
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Ying Zhu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
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40
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Croft DP, Zhang W, Lin S, Thurston SW, Hopke PK, Masiol M, Squizzato S, van Wijngaarden E, Utell MJ, Rich DQ. The Association between Respiratory Infection and Air Pollution in the Setting of Air Quality Policy and Economic Change. Ann Am Thorac Soc 2019; 16:321-330. [PMID: 30398895 PMCID: PMC6394122 DOI: 10.1513/annalsats.201810-691oc] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 11/02/2018] [Indexed: 12/18/2022] Open
Abstract
RATIONALE Fine particulate matter air pollution of 2.5 μm or less in diameter (PM2.5) has been associated with an increased risk of respiratory disease, but assessments of specific respiratory infections in adults are lacking. OBJECTIVES To estimate the rate of respiratory infection healthcare encounters in adults associated with acute increases in PM2.5 concentrations. METHODS Using case-crossover methods, we studied 498,118 adult New York State residents with a primary diagnosis of influenza, bacterial pneumonia, or culture-negative pneumonia upon hospitalization or emergency department (ED) visit (2005-2016). We estimated the relative rate of healthcare encounters associated with increases in PM2.5 in the previous 1-7 days and explored differences before (2005-2007), during (2008-2013), and after (2014-2016) implementation of air quality policies and economic changes. RESULTS Interquartile range increases in PM2.5 over the previous 7 days were associated with increased excess rates (ERs) of culture-negative pneumonia hospitalizations (2.5%; 95% confidence interval [CI], 1.7-3.2%) and ED visits (2.5%; 95% CI, 1.4-3.6%), and increased ERs of influenza ED visits (3.9%; 95% CI, 2.1-5.6%). Bacterial pneumonia hospitalizations, but not ED visits, were associated with increases in PM2.5 and, though imprecise, were of a similar magnitude to culture-negative pneumonia (Lag Day 6 ER, 2.3%; 95% CI, 0.3-4.3). Increased relative rates of influenza ED visits and culture-negative pneumonia hospitalizations were generally larger in the "after" period (P < 0.025 for both outcomes), compared with the "during" period, despite reductions in overall PM2.5 concentrations. CONCLUSIONS Increased rates of culture-negative pneumonia and influenza were associated with increased PM2.5 concentrations during the previous week, which persisted despite reductions in PM2.5 from air quality policies and economic changes. Though unexplained, this temporal variation may reflect altered toxicity of different PM2.5 mixtures or increased pathogen virulence.
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Affiliation(s)
| | - Wangjian Zhang
- Department of Environmental Health Sciences, University at Albany, State University of New York, Albany, New York; and
| | - Shao Lin
- Department of Environmental Health Sciences, University at Albany, State University of New York, Albany, New York; and
| | | | - Philip K. Hopke
- Department of Public Health Sciences, and
- Institute for a Sustainable Environment, and Center for Air Resources Engineering and Science, Clarkson University, Potsdam, New York
| | - Mauro Masiol
- Department of Public Health Sciences, and
- Institute for a Sustainable Environment, and Center for Air Resources Engineering and Science, Clarkson University, Potsdam, New York
| | - Stefania Squizzato
- Department of Public Health Sciences, and
- Institute for a Sustainable Environment, and Center for Air Resources Engineering and Science, Clarkson University, Potsdam, New York
| | - Edwin van Wijngaarden
- Department of Public Health Sciences, and
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York
| | - Mark J. Utell
- Division of Pulmonary and Critical Care Medicine
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York
| | - David Q. Rich
- Division of Pulmonary and Critical Care Medicine
- Department of Public Health Sciences, and
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York
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41
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Wang Q, Liu R, Li Q, Wang F, Zhu B, Zheng M, Cui H, Wen J, Zhao G. Host cell interactome of PB1 N40 protein of H5N1 influenza A virus in chicken cells. J Proteomics 2019; 197:34-41. [PMID: 30790688 DOI: 10.1016/j.jprot.2019.02.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/15/2019] [Accepted: 02/15/2019] [Indexed: 01/06/2023]
Abstract
H5N1 influenza A virus (IAV) causes seasonal epidemics that represent a worldwide threat to public health. IAV relies on host factors for viral replication. PB1 N40 is translated from the fifth starting code (AUG) of PB1 mRNA, which is the product of the ribosomal scan omission. Here, we report the interactome landscape of H5N1 IAV PB1 N40 protein in chicken cells. The interacting complexes were captured by co-immunoprecipitation and analyzed by mass spectrometry. We identified 135 proteins as PB1 N40-interacting proteins. GO and Pathway analysis showed that proteins with biological functions such as protein localization and viral transcription and proteins related to signaling pathways of DNA replication and cell cycle were significantly enriched in virus-host interactions, suggesting the potential roles of them in infection with H5N1 IAV. Comparative analysis among H1N1 and H5N1 revealed conservation of the virus-host protein interaction between different subtypes or strains of influenza virus. ARCN1 was identified as a host interacting factor of H5N1 IAV PB1 N40 protein, which is the component of the coatomer. Knockdown of ARCN1 significantly decreased the titer of H5N1 IAV in chicken cells. BIOLOGICAL SIGNIFICANCE: Influenza A virus (IAV) is a great threat to public health and avian production. However, the manner in which avian IAV recruits the host cellular machinery for replication and how the host antagonizes the IAV infection was previously poorly understood. Here we present the viral-host interactome of the H5N1 IAV PB1 N40 protein and reveal its involvement with dozens of important host genes during the course of IAV infection.
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Affiliation(s)
- Qiao Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ranran Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; State Key Laboratory of Animal Nutrition, Beijing, China
| | - Qinghe Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fei Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; State Key Laboratory of Animal Nutrition, Beijing, China
| | - Bo Zhu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; State Key Laboratory of Animal Nutrition, Beijing, China
| | - Maiqing Zheng
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; State Key Laboratory of Animal Nutrition, Beijing, China
| | - Huanxian Cui
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; State Key Laboratory of Animal Nutrition, Beijing, China
| | - Jie Wen
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; State Key Laboratory of Animal Nutrition, Beijing, China
| | - Guiping Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; School of Life Science and Engineering, Foshan University, Foshan, China.
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42
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Fay EJ, Aron SL, Stone IA, Waring BM, Plemper RK, Langlois RA. Engineered Small-Molecule Control of Influenza A Virus Replication. J Virol 2019; 93:e01677-18. [PMID: 30282710 PMCID: PMC6288343 DOI: 10.1128/jvi.01677-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 09/26/2018] [Indexed: 01/01/2023] Open
Abstract
Influenza A virus (IAV) remains a global health concern despite the availability of a seasonal vaccine. It is difficult to predict which strains will circulate during influenza season, and therefore, it is extremely challenging to test novel vaccines in the human population. To overcome this obstacle, new vaccines must be tested in challenge studies. This approach poses significant safety problems, since current pharmacological interventions for IAV are poorly efficacious. New methods are needed to enhance the safety of these challenge studies. In this study, we have generated a virus expressing a small-molecule-assisted shutoff (SMASh) tag as a safety switch for IAV replication. The addition of the SMASh tag to an essential IAV protein allows for small-molecule-mediated inhibition of replication. Treatment with this drug controls the replication of a SMASh-tagged virus in vitro and in vivo This model for restriction of viral replication has potential for broad applications in vaccine studies, virotherapy, and basic virus research.IMPORTANCE Influenza A virus (IAV) causes significant morbidity and mortality annually worldwide, despite the availability of new formulations of the vaccine each season. There is a critical need to develop more-efficacious vaccines. However, testing novel vaccines in the human population in controlled studies is difficult due to the limited availability and efficacy of intervention strategies should the vaccine fail. There are also significant safety concerns for work with highly pathogenic IAV strains in the laboratory. Therefore, novel strategies are needed to improve the safety of vaccine studies and of research on highly pathogenic IAV. In this study, we developed an IAV strain engineered to contain a small-molecule-mediated safety switch. This tag, when attached to an essential viral protein, allows for the regulation of IAV replication in vitro and in vivo This strategy provides a platform for the regulation of virus replication without targeting viral proteins directly.
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Affiliation(s)
- Elizabeth J Fay
- Biochemistry, Molecular Biology, and Biophysics Graduate Program, University of Minnesota, Minneapolis, Minnesota, USA
- Center for Immunology, University of Minnesota Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Stephanie L Aron
- Center for Immunology, University of Minnesota Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ian A Stone
- Center for Immunology, University of Minnesota Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Barbara M Waring
- Center for Immunology, University of Minnesota Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Richard K Plemper
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, USA
| | - Ryan A Langlois
- Biochemistry, Molecular Biology, and Biophysics Graduate Program, University of Minnesota, Minneapolis, Minnesota, USA
- Center for Immunology, University of Minnesota Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
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Abstract
Pneumonia is a type of acute lower respiratory infection that is common and severe. The outcome of lower respiratory infection is determined by the degrees to which immunity is protective and inflammation is damaging. Intercellular and interorgan signaling networks coordinate these actions to fight infection and protect the tissue. Cells residing in the lung initiate and steer these responses, with additional immunity effectors recruited from the bloodstream. Responses of extrapulmonary tissues, including the liver, bone marrow, and others, are essential to resistance and resilience. Responses in the lung and extrapulmonary organs can also be counterproductive and drive acute and chronic comorbidities after respiratory infection. This review discusses cell-specific and organ-specific roles in the integrated physiological response to acute lung infection, and the mechanisms by which intercellular and interorgan signaling contribute to host defense and healthy respiratory physiology or to acute lung injury, chronic pulmonary disease, and adverse extrapulmonary sequelae. Pneumonia should no longer be perceived as simply an acute infection of the lung. Pneumonia susceptibility reflects ongoing and poorly understood chronic conditions, and pneumonia results in diverse and often persistent deleterious consequences for multiple physiological systems.
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Affiliation(s)
- Lee J Quinton
- Pulmonary Center, Boston University School of Medicine , Boston, Massachusetts
| | - Allan J Walkey
- Pulmonary Center, Boston University School of Medicine , Boston, Massachusetts
| | - Joseph P Mizgerd
- Pulmonary Center, Boston University School of Medicine , Boston, Massachusetts
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44
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Abstract
Pneumonia is an important cause of morbidity and mortality. However, pneumonia is an unusual outcome of respiratory infection. Most of the time, microbes in the lung can be controlled by a combination of constitutive and recruited defense mechanisms. Inflammation is a key component of recruited defenses. Variations in inflammation that influence pneumonia susceptibility and severity are considered here.
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Affiliation(s)
- Joseph P Mizgerd
- Pulmonary Center, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02115, USA.
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45
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Scoring Amino Acid Mutations to Predict Avian-to-Human Transmission of Avian Influenza Viruses. Molecules 2018; 23:molecules23071584. [PMID: 29966263 PMCID: PMC6100476 DOI: 10.3390/molecules23071584] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/13/2018] [Accepted: 06/19/2018] [Indexed: 11/17/2022] Open
Abstract
Avian influenza virus (AIV) can directly cross species barriers and infect humans with high fatality. Using machine learning methods, the present paper scores the amino acid mutations and predicts interspecies transmission. Initially, 183 signature positions in 11 viral proteins were screened by the scores of five amino acid factors and their random forest rankings. The most important amino acid factor (Factor 3) and the minimal range of signature positions (50 amino acid residues) were explored by a supporting vector machine (the highest-performing classifier among four tested classifiers). Based on these results, the avian-to-human transmission of AIVs was analyzed and a prediction model was constructed for virology applications. The distributions of human-origin AIVs suggested that three molecular patterns of interspecies transmission emerge in nature. The novel findings of this paper provide important clues for future epidemic surveillance.
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46
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Maginnis MS. Virus-Receptor Interactions: The Key to Cellular Invasion. J Mol Biol 2018; 430:2590-2611. [PMID: 29924965 PMCID: PMC6083867 DOI: 10.1016/j.jmb.2018.06.024] [Citation(s) in RCA: 196] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 06/04/2018] [Accepted: 06/08/2018] [Indexed: 11/05/2022]
Abstract
Virus–receptor interactions play a key regulatory role in viral host range, tissue tropism, and viral pathogenesis. Viruses utilize elegant strategies to attach to one or multiple receptors, overcome the plasma membrane barrier, enter, and access the necessary host cell machinery. The viral attachment protein can be viewed as the “key” that unlocks host cells by interacting with the “lock”—the receptor—on the cell surface, and these lock-and-key interactions are critical for viruses to successfully invade host cells. Many common themes have emerged in virus–receptor utilization within and across virus families demonstrating that viruses often target particular classes of molecules in order to mediate these events. Common viral receptors include sialylated glycans, cell adhesion molecules such as immunoglobulin superfamily members and integrins, and phosphatidylserine receptors. The redundancy in receptor usage suggests that viruses target particular receptors or “common locks” to take advantage of their cellular function and also suggests evolutionary conservation. Due to the importance of initial virus interactions with host cells in viral pathogenesis and the redundancy in viral receptor usage, exploitation of these strategies would be an attractive target for new antiviral therapeutics. Viral receptors are key regulators of host range, tissue tropism, and viral pathogenesis. Many viruses utilize common viral receptors including sialic acid, cell adhesion molecules such as immunoglobulin superfamily members and integrins, and phosphatidylserine receptors. Detailed molecular interactions between viruses and receptors have been defined through elegant biochemical analyses including glycan array screens, structural–functional analyses, and cell-based approaches providing tremendous insights into these initial events in viral infection. Commonalities in virus–receptor interactions present promising targets for the development of broad-spectrum antiviral therapies.
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Affiliation(s)
- Melissa S Maginnis
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, ME 04469-5735, USA.
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47
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Wang Q, Li Q, Liu T, Chang G, Sun Z, Gao Z, Wang F, Zhou H, Liu R, Zheng M, Cui H, Chen G, Li H, Yuan X, Wen J, Peng D, Zhao G. Host Interaction Analysis of PA-N155 and PA-N182 in Chicken Cells Reveals an Essential Role of UBA52 for Replication of H5N1 Avian Influenza Virus. Front Microbiol 2018; 9:936. [PMID: 29867845 PMCID: PMC5963055 DOI: 10.3389/fmicb.2018.00936] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 04/23/2018] [Indexed: 01/17/2023] Open
Abstract
PA-N155 and PA-N182 proteins were translated from the 11th and 13th start codon AUG of the RNA polymerase acidic protein (PA) mRNA of H5N1 influenza A virus (IAV), which plays an important role in viral replication. Little is known about the interactions between PA-N155 and PA-N182 and the host proteins. This study investigated the interaction landscape of PA-N155 and PA-N182 of H5N1 IAV in chicken cells while their interacting complexes were captured by immunoprecipitation and analyzed by mass spectrometry. A total of 491 (PA-N155) and 302 (PA-N182) interacting proteins were identified. Gene ontology and pathway enrichment analyses showed that proteins of the two interactomes were enriched in RNA processing, viral processing and protein transport, and proteins related to signaling pathways of proteasome, ribosome, and aminoacy1-tRNA biosynthesis were significantly enriched, suggesting their potential roles in H5N1 IAV infection. Comparative analysis of the interactome of PA, PA-N155, and PA-N182 identified UBA52 as a conserved host factor that interacted with all three viral proteins. UBA52 is a fusion protein consisting of ubiquitin at the N terminus and ribosomal protein L40 at the C terminus. Knockdown of UBA52 significantly decreased the titer of H5N1 IAV in chicken cells and was accompanied with attenuated production of proinflammatory cytokines. Our analyses of the influenza–host protein interactomes identified UBA52 as a PA interaction protein for virus replication.
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Affiliation(s)
- Qiao Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,State Key Laboratory of Animal Nutrition, Beijing, China
| | - Qinghe Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,State Key Laboratory of Animal Nutrition, Beijing, China
| | - Tao Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guobin Chang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhihao Sun
- School of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Zhao Gao
- School of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Fei Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,State Key Laboratory of Animal Nutrition, Beijing, China
| | - Huaijun Zhou
- Department of Animal Sciences, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States
| | - Ranran Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,State Key Laboratory of Animal Nutrition, Beijing, China
| | - Maiqing Zheng
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,State Key Laboratory of Animal Nutrition, Beijing, China
| | - Huanxian Cui
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,State Key Laboratory of Animal Nutrition, Beijing, China
| | - Guohong Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Hua Li
- School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Xiaoya Yuan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jie Wen
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,State Key Laboratory of Animal Nutrition, Beijing, China
| | - Daxin Peng
- School of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Guiping Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,State Key Laboratory of Animal Nutrition, Beijing, China.,School of Life Sciences and Engineering, Foshan University, Foshan, China
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48
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Pearce DC, McCaw JM, McVernon J, Mathews JD. Influenza as a trigger for cardiovascular disease: An investigation of serotype, subtype and geographic location. ENVIRONMENTAL RESEARCH 2017; 156:688-696. [PMID: 28477579 DOI: 10.1016/j.envres.2017.04.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 04/20/2017] [Accepted: 04/20/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Seasonal peaks of influenza and cardiovascular disease tend to coincide. Many excess deaths may be triggered by influenza, and the severity of this effect may vary with the virulence of the circulating influenza strain and host susceptibility. We aimed to explore the association between hospital admissions for influenza and/or pneumonia (IP) and acute myocardial infarction (AMI) or ischaemic heart disease (IHD) in Queensland, Australia, taking into account temporal and spatial variation of influenza virus type and subtype in 2007, 2008 and 2009. METHODS This ecological study at Statistical Subdivision level (SSD, n=38) used linked patient-level data. For each study year, Standardized Morbidity Ratios (SMRs) were calculated for hospital admissions with diagnoses of IP, AMI and IHD. We investigated the associations between IP and AMI or IHD using spatial autoregressive modelling, adjusting for socio-demographic factors. RESULTS Spatial autocorrelation was detected in SMRs, possibly reflecting underlying social and behavioural risk factors, but consistent with infectious disease spread. SMRs for IP were consistently predictive of SMRs for AMI and IHD when adjusted for socioeconomic status, population density and per cent Indigenous population (coefficient: 0.707, 95% confidence interval (CI): 0.318 - 1.096; 0.553, 0.222 - 0.884; 0.598, 0.307 - 0.888 and 1.017, 0.711 - 1.323; 0.650, 0.342 - 0.958; 1.031, 0.827 - 1.236) in 2007, 2008 and 2009, respectively. CONCLUSIONS This ecological study provides further evidence that severe respiratory infections may trigger the onset of cardiovascular events, implicating the influenza virus as a contributing factor.
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Affiliation(s)
- D C Pearce
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Level 3, 207 Bouverie Street, The University of Melbourne, Victoria 3010, Australia; Faculty of Science & Technology, Federation University Australia, University Drive, Mt Helen, Victoria 3350, Australia.
| | - J M McCaw
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Level 3, 207 Bouverie Street, The University of Melbourne, Victoria 3010, Australia; Modelling and Simulation, Infection and Immunity Theme, Murdoch Childrens Research Institute, 9th floor, The Royal Children's Hospital, 50 Flemington Road, Parkville, Victoria 3052, Australia; School of Mathematics and Statistics, Level 3, Old Geology South, The University of Melbourne, Victoria 3010, Australia.
| | - J McVernon
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Level 3, 207 Bouverie Street, The University of Melbourne, Victoria 3010, Australia; Modelling and Simulation, Infection and Immunity Theme, Murdoch Childrens Research Institute, 9th floor, The Royal Children's Hospital, 50 Flemington Road, Parkville, Victoria 3052, Australia.
| | - J D Mathews
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Level 3, 207 Bouverie Street, The University of Melbourne, Victoria 3010, Australia.
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Risk factors for avian influenza virus contamination of live poultry markets in Zhejiang, China during the 2015-2016 human influenza season. Sci Rep 2017; 7:42722. [PMID: 28256584 PMCID: PMC5335333 DOI: 10.1038/srep42722] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/12/2017] [Indexed: 11/13/2022] Open
Abstract
Live bird markets (LBMs), being a potential source of avian influenza virus, require effective environmental surveillance management. In our study, a total of 2865 environmental samples were collected from 292 LBMs during the 2015–2016 human influenza season from 10 cities in Zhejiang province, China. The samples were tested by real-time quantitative polymerase chain reaction (RT-PCR). Field investigations were carried out to investigate probable risk factors. Of the environmental samples, 1519 (53.0%) were contaminated by A subtype. The highest prevalence of the H9 subtype was 30.2%, and the frequencies of the H5 and H7 subtype were 9.3% and 17.3%, respectively. Hangzhou and Jinhua cities were contaminated more seriously than the others. The prevalence of H5/H7/H9 in drinking water samples was highest, at 50.9%, and chopping board swabs ranked second, at 49.3%. Duration of sales per day, types of live poultry, LBM location and the number of live poultry were the main risk factors for environmental contamination, according to logistic regression analysis. In conclusion, LBMs in Zhejiang were contaminated by avian influenza. Our study has provided clues for avian influenza prevention and control during the human influenza season, especially in areas where LBMs are not closed.
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Joseph U, Su YCF, Vijaykrishna D, Smith GJD. The ecology and adaptive evolution of influenza A interspecies transmission. Influenza Other Respir Viruses 2017; 11:74-84. [PMID: 27426214 PMCID: PMC5155642 DOI: 10.1111/irv.12412] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2016] [Indexed: 12/16/2022] Open
Abstract
Since 2013, there have been several alarming influenza-related events; the spread of highly pathogenic avian influenza H5 viruses into North America, the detection of H10N8 and H5N6 zoonotic infections, the ongoing H7N9 infections in China and the continued zoonosis of H5N1 viruses in parts of Asia and the Middle East. The risk of a new influenza pandemic increases with the repeated interspecies transmission events that facilitate reassortment between animal influenza strains; thus, it is of utmost importance to understand the factors involved that promote or become a barrier to cross-species transmission of Influenza A viruses (IAVs). Here, we provide an overview of the ecology and evolutionary adaptations of IAVs, with a focus on a review of the molecular factors that enable interspecies transmission of the various virus gene segments.
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MESH Headings
- Animals
- Animals, Wild
- Asia/epidemiology
- China/epidemiology
- Disease Reservoirs/virology
- Ducks/virology
- Evolution, Molecular
- Geese/virology
- Humans
- Influenza A Virus, H5N1 Subtype/genetics
- Influenza A Virus, H5N1 Subtype/pathogenicity
- Influenza A Virus, H5N1 Subtype/physiology
- Influenza A Virus, H7N9 Subtype/genetics
- Influenza A Virus, H7N9 Subtype/pathogenicity
- Influenza A Virus, H7N9 Subtype/physiology
- Influenza A virus/genetics
- Influenza A virus/pathogenicity
- Influenza A virus/physiology
- Influenza in Birds/virology
- Influenza, Human/transmission
- Influenza, Human/virology
- Orthomyxoviridae Infections/transmission
- Orthomyxoviridae Infections/virology
- Phylogeny
- Reassortant Viruses/genetics
- Reassortant Viruses/pathogenicity
- Reassortant Viruses/physiology
- Zoonoses
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Affiliation(s)
| | | | | | - Gavin J. D. Smith
- Duke‐NUS Medical SchoolSingapore
- Duke Global Health InstituteDuke UniversityDurhamNCUSA
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