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de Abreu Góes Pereira VM, Gularte JS, Demoliner M, da Silva MS, Girardi V, Filippi M, Frohlich J, Fink P, Hansen AW, Ferreira HL, Afrough B, Kritz-Wilson A, Spilki FR. Influenza outbreak during the surge of SARS-CoV-2 omicron in a metropolitan area from southern Brazil: genomic surveillance. J Med Virol 2024; 96:e29944. [PMID: 39360646 DOI: 10.1002/jmv.29944] [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: 03/18/2024] [Revised: 08/08/2024] [Accepted: 09/16/2024] [Indexed: 10/04/2024]
Abstract
Influenza circulation was significantly affected in 2020-21 by the COVID-19 pandemic. During this time, few influenza cases were recorded. However, in the summer of 2021-22, an increase in atypical influenza cases was observed, leading to the resurgence of influenza in the southernmost state of Brazil, Rio Grande do Sul (RS). The present study aimed to identify the circulation of FLUAV, FLUBV and SARS-CoV-2 and characterize the influenza genomes in respiratory samples using high-throughput sequencing technology (HTS). Respiratory samples (n = 694) from patients in RS were selected between July 2021 and August 2022. The samples were typed using reverse transcriptase real-time PCR (RT-qPCR) and showed 32% (223/694) of the samples to be positive for SARS-CoV-2, 7% for FLUAV (H3) (49/694). FLUBV was not detected. RT-qPCR data also resulted in FLUAV and SARS-CoV-2 co-infections in 1.7% (4/223) of samples tested. Whole genome sequencing of FLUAV produced 15 complete genomes of the H3N2 subtype, phylogenetically classified in the 3C.2a1b.2a.2a.3 subclade and revealing the dominance of viruses in the southern region of Brazil. Mutation analysis identified 72 amino acid substitutions in all genes, highlighting ongoing genetic evolution with potential implications for vaccine effectiveness, viral fitness, and pathogenicity. This study underscores limitations in current surveillance systems, advocating for comprehensive data inclusion to enhance understanding of influenza epidemiology in southern Brazil. These findings contribute valuable insights to inform more effective public health responses and underscore the critical need for continuous genomic surveillance.
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Affiliation(s)
| | - Juliana Schons Gularte
- Departamento de Virologia, Laboratório de Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Meriane Demoliner
- Departamento de Virologia, Laboratório de Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Mariana Soares da Silva
- Departamento de Virologia, Laboratório de Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Viviane Girardi
- Departamento de Virologia, Laboratório de Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Micheli Filippi
- Departamento de Virologia, Laboratório de Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Julia Frohlich
- Departamento de Virologia, Laboratório de Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Pietra Fink
- Departamento de Virologia, Laboratório de Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Alana Witt Hansen
- Departamento de Virologia, Laboratório de Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Helena Lage Ferreira
- Department of Veterinary Medicine, FZEA- USP, University of Sao Paulo, Pirassununga, São Paulo, Brazil
| | - Babak Afrough
- Health Security Agency, New Variant Assessment Platform (NVAP), UK
| | | | - Fernando Rosado Spilki
- Departamento de Virologia, Laboratório de Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
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Arragain B, Krischuns T, Pelosse M, Drncova P, Blackledge M, Naffakh N, Cusack S. Structures of influenza A and B replication complexes give insight into avian to human host adaptation and reveal a role of ANP32 as an electrostatic chaperone for the apo-polymerase. Nat Commun 2024; 15:6910. [PMID: 39160148 PMCID: PMC11333492 DOI: 10.1038/s41467-024-51007-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 07/16/2024] [Indexed: 08/21/2024] Open
Abstract
Replication of influenza viral RNA depends on at least two viral polymerases, a parental replicase and an encapsidase, and cellular factor ANP32. ANP32 comprises an LRR domain and a long C-terminal low complexity acidic region (LCAR). Here we present evidence suggesting that ANP32 is recruited to the replication complex as an electrostatic chaperone that stabilises the encapsidase moiety within apo-polymerase symmetric dimers that are distinct for influenza A and B polymerases. The ANP32 bound encapsidase, then forms the asymmetric replication complex with the replicase, which is embedded in a parental ribonucleoprotein particle (RNP). Cryo-EM structures reveal the architecture of the influenza A and B replication complexes and the likely trajectory of the nascent RNA product into the encapsidase. The cryo-EM map of the FluB replication complex shows extra density attributable to the ANP32 LCAR wrapping around and stabilising the apo-encapsidase conformation. These structures give new insight into the various mutations that adapt avian strain polymerases to use the distinct ANP32 in mammalian cells.
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Affiliation(s)
- Benoît Arragain
- European Molecular Biology Laboratory, Grenoble, Cedex 9, France
| | - Tim Krischuns
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology of Influenza Virus, Paris, France
- Heidelberg University, Department of Infectious Diseases, Virology, Schaller Research Group, Heidelberg, Germany
| | - Martin Pelosse
- European Molecular Biology Laboratory, Grenoble, Cedex 9, France
| | - Petra Drncova
- European Molecular Biology Laboratory, Grenoble, Cedex 9, France
| | - Martin Blackledge
- Institut de Biologie Structurale, Université Grenoble-Alpes-CEA-CNRS UMR5075, Grenoble, France
| | - Nadia Naffakh
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology of Influenza Virus, Paris, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble, Cedex 9, France.
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3
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Robertson D, Heriot G, Jamrozik E. Herd immunity to endemic diseases: Historical concepts and implications for public health policy. J Eval Clin Pract 2024; 30:625-631. [PMID: 38562003 DOI: 10.1111/jep.13983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 04/04/2024]
Abstract
BACKGROUND "Herd immunity" became a contested term during the COVID-19 pandemic. Although the term "herd immunity" is often used to refer to thresholds at which some diseases can be eliminated (e.g., due to mass vaccination), the term has multiple referents. Different concepts of herd immunity have been relevant throughout the history of immunology and infectious disease epidemiology. For some diseases, herd immunity plays a role in the development of an endemic equilibrium, rather than elimination via threshold effects. METHODS We reviewed academic literature from 1920 to 2022, using historical and philosophical analysis to identify and develop relevant concepts of herd immunity. RESULTS This paper analyses the ambiguity surrounding the concept of herd immunity during the pandemic. We argue for the need to recapture a long-standing interpretation of this concept as one of the factors that leads to a dynamic endemic equilibrium between a host population and a mutating respiratory pathogen. CONCLUSIONS Informed by the history of infectious disease epidemiology, we argue that understanding the concept in this way will help us manage both SARS-CoV-2 and hundreds of other seasonal respiratory pathogens with which we live but which have been disrupted due to sustained public health measures/non-pharmaceutical interventions targeting SARS-CoV-2.
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Affiliation(s)
- David Robertson
- Swiss National Science Foundation; Faculty of History, Oxford Centre for the History of Science, Medicine, and Technology, University of Oxford, Oxford, UK
| | - George Heriot
- Department of Infectious Diseases, Melbourne Medical School, University of Melbourne, Melbourne, Australia
| | - Euzebiusz Jamrozik
- Nuffield Department of Population Health, The Ethox Centre & Wellcome Centre for Ethics and Humanities, University of Oxford, Oxford, UK
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4
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Khalil AM, Martinez-Sobrido L, Mostafa A. Zoonosis and zooanthroponosis of emerging respiratory viruses. Front Cell Infect Microbiol 2024; 13:1232772. [PMID: 38249300 PMCID: PMC10796657 DOI: 10.3389/fcimb.2023.1232772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Lung infections in Influenza-Like Illness (ILI) are triggered by a variety of respiratory viruses. All human pandemics have been caused by the members of two major virus families, namely Orthomyxoviridae (influenza A viruses (IAVs); subtypes H1N1, H2N2, and H3N2) and Coronaviridae (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2). These viruses acquired some adaptive changes in a known intermediate host including domestic birds (IAVs) or unknown intermediate host (SARS-CoV-2) following transmission from their natural reservoirs (e.g. migratory birds or bats, respectively). Verily, these acquired adaptive substitutions facilitated crossing species barriers by these viruses to infect humans in a phenomenon that is known as zoonosis. Besides, these adaptive substitutions aided the variant strain to transmit horizontally to other contact non-human animal species including pets and wild animals (zooanthroponosis). Herein we discuss the main zoonotic and reverse-zoonosis events that occurred during the last two pandemics of influenza A/H1N1 and SARS-CoV-2. We also highlight the impact of interspecies transmission of these pandemic viruses on virus evolution and possible prophylactic and therapeutic interventions. Based on information available and presented in this review article, it is important to close monitoring viral zoonosis and viral reverse zoonosis of pandemic strains within a One-Health and One-World approach to mitigate their unforeseen risks, such as virus evolution and resistance to limited prophylactic and therapeutic interventions.
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Affiliation(s)
- Ahmed Magdy Khalil
- Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
- Department of Zoonotic Diseases, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Luis Martinez-Sobrido
- Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Ahmed Mostafa
- Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
- Center of Scientific Excellence for Influenza Viruses, Water Pollution Research Department, Environment and Climate Change Research Institute, National Research Centre, Giza, Egypt
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Rigby CV, Sabsay KR, Bisht K, Eggink D, Jalal H, te Velthuis AJW. Evolution of transient RNA structure-RNA polymerase interactions in respiratory RNA virus genomes. Virus Evol 2023; 9:vead056. [PMID: 37692892 PMCID: PMC10492445 DOI: 10.1093/ve/vead056] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/02/2023] [Accepted: 08/24/2023] [Indexed: 09/12/2023] Open
Abstract
RNA viruses are important human pathogens that cause seasonal epidemics and occasional pandemics. Examples are influenza A viruses (IAV) and coronaviruses (CoV). When emerging IAV and CoV spill over to humans, they adapt to evade immune responses and optimize their replication and spread in human cells. In IAV, adaptation occurs in all viral proteins, including the viral ribonucleoprotein (RNP) complex. RNPs consist of a copy of the viral RNA polymerase, a double-helical coil of nucleoprotein, and one of the eight segments of the IAV RNA genome. The RNA segments and their transcripts are partially structured to coordinate the packaging of the viral genome and modulate viral mRNA translation. In addition, RNA structures can affect the efficiency of viral RNA synthesis and the activation of host innate immune response. Here, we investigated if RNA structures that modulate IAV replication processivity, so-called template loops (t-loops), vary during the adaptation of pandemic and emerging IAV to humans. Using cell culture-based replication assays and in silico sequence analyses, we find that the sensitivity of the IAV H3N2 RNA polymerase to t-loops increased between isolates from 1968 and 2017, whereas the total free energy of t-loops in the IAV H3N2 genome was reduced. This reduction is particularly prominent in the PB1 gene. In H1N1 IAV, we find two separate reductions in t-loop free energy, one following the 1918 pandemic and one following the 2009 pandemic. No destabilization of t-loops is observed in the influenza B virus genome, whereas analysis of SARS-CoV-2 isolates reveals destabilization of viral RNA structures. Overall, we propose that a loss of free energy in the RNA genome of emerging respiratory RNA viruses may contribute to the adaption of these viruses to the human population.
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Affiliation(s)
- Charlotte V Rigby
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Department of Pathology, Addenbrooke’s Hospital, University of Cambridge, Hills Road, Cambridge CB2 2QQ, UK
- Addenbrooke’s Hospital, Public Health England, Hills Road, Cambridge CB2 2QQ, UK
| | - Kimberly R Sabsay
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Carl Icahn Laboratory, Lewis-Sigler Institute, Princeton University, South Drive, Princeton, NJ 08544, USA
| | - Karishma Bisht
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Dirk Eggink
- Department of Medical Microbiology, Amsterdam UMC, Meibergdreef 9, Amsterdam 1105 AZ, The Netherlands
| | - Hamid Jalal
- Addenbrooke’s Hospital, Public Health England, Hills Road, Cambridge CB2 2QQ, UK
| | - Aartjan J W te Velthuis
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, the Netherlands
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6
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Wasik BR, Rothschild E, Voorhees IEH, Reedy SE, Murcia PR, Pusterla N, Chambers TM, Goodman LB, Holmes EC, Kile JC, Parrish CR. Understanding the divergent evolution and epidemiology of H3N8 influenza viruses in dogs and horses. Virus Evol 2023; 9:vead052. [PMID: 37692894 PMCID: PMC10484056 DOI: 10.1093/ve/vead052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/12/2023] [Accepted: 08/16/2023] [Indexed: 09/12/2023] Open
Abstract
Cross-species virus transmission events can lead to dire public health emergencies in the form of epidemics and pandemics. One example in animals is the emergence of the H3N8 equine influenza virus (EIV), first isolated in 1963 in Miami, FL, USA, after emerging among horses in South America. In the early 21st century, the American lineage of EIV diverged into two 'Florida' clades that persist today, while an EIV transferred to dogs around 1999 and gave rise to the H3N8 canine influenza virus (CIV), first reported in 2004. Here, we compare CIV in dogs and EIV in horses to reveal their host-specific evolution, to determine the sources and connections between significant outbreaks, and to gain insight into the factors controlling their different evolutionary fates. H3N8 CIV only circulated in North America, was geographically restricted after the first few years, and went extinct in 2016. Of the two EIV Florida clades, clade 1 circulates widely and shows frequent transfers between the USA and South America, Europe and elsewhere, while clade 2 was globally distributed early after it emerged, but since about 2018 has only been detected in Central Asia. Any potential zoonotic threat of these viruses to humans can only be determined with an understanding of its natural history and evolution. Our comparative analysis of these three viral lineages reveals distinct patterns and rates of sequence variation yet with similar overall evolution between clades, suggesting epidemiological intervention strategies for possible eradication of H3N8 EIV.
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Affiliation(s)
- Brian R Wasik
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Evin Rothschild
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Ian E H Voorhees
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Stephanie E Reedy
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, Scotland
| | - Nicola Pusterla
- Department of Medicine & Epidemiology, School Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Thomas M Chambers
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA
| | - Laura B Goodman
- Baker Institute for Animal Health, Department of Public and Ecosystems Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - James C Kile
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Colin R Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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7
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Rigby C, Sabsay K, Bisht K, Eggink D, Jalal H, te Velthuis AJ. Evolution of transient RNA structure-RNA polymerase interactions in respiratory RNA virus genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542331. [PMID: 37292879 PMCID: PMC10245964 DOI: 10.1101/2023.05.25.542331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
RNA viruses are important human pathogens that cause seasonal epidemics and occasional pandemics. Examples are influenza A viruses (IAV) and coronaviruses (CoV). When emerging IAV and CoV spill over to humans, they adapt to evade immune responses and optimize their replication and spread in human cells. In IAV, adaptation occurs in all viral proteins, including the viral ribonucleoprotein (RNP) complex. RNPs consists of a copy of the viral RNA polymerase, a double-helical coil of nucleoprotein, and one of the eight segments of the IAV RNA genome. The RNA segments and their transcripts are partially structured to coordinate the packaging of the viral genome and modulate viral mRNA translation. In addition, RNA structures can affect the efficiency of viral RNA synthesis and the activation of host innate immune response. Here, we investigated if RNA structures that modulate IAV replication processivity, so called template loops (t-loops), vary during the adaptation of pandemic and emerging IAV to humans. Using cell culture-based replication assays and in silico sequence analyses, we find that the sensitivity of the IAV H3N2 RNA polymerase to t-loops increased between isolates from 1968 and 2017, whereas the total free energy of t-loops in the IAV H3N2 genome was reduced. This reduction is particularly prominent in the PB1 gene. In H1N1 IAV, we find two separate reductions in t-loop free energy, one following the 1918 pandemic and one following the 2009 pandemic. No destabilization of t-loops is observed in the IBV genome, whereas analysis of SARS-CoV-2 isolates reveals destabilization of viral RNA structures. Overall, we propose that a loss of free energy in the RNA genome of emerging respiratory RNA viruses may contribute to the adaption of these viruses to the human population.
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Affiliation(s)
- Charlotte Rigby
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, 08544 New Jersey, United States
- University of Cambridge, Department of Pathology, Addenbrooke’s Hospital, Cambridge CB2 2QQ, United Kingdom
- Public Health England, Addenbrooke’s Hospital, Cambridge CB2 2QQ, United Kingdom
| | - Kimberly Sabsay
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, 08544 New Jersey, United States
- Sigler Institute, Princeton University, Princeton, NJ 08544, United States
| | - Karishma Bisht
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, 08544 New Jersey, United States
| | - Dirk Eggink
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam, The Netherlands
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Hamid Jalal
- Public Health England, Addenbrooke’s Hospital, Cambridge CB2 2QQ, United Kingdom
| | - Aartjan J.W. te Velthuis
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, 08544 New Jersey, United States
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8
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Peacock TP, Sheppard CM, Lister MG, Staller E, Frise R, Swann OC, Goldhill DH, Long JS, Barclay WS. Mammalian ANP32A and ANP32B Proteins Drive Differential Polymerase Adaptations in Avian Influenza Virus. J Virol 2023; 97:e0021323. [PMID: 37074204 PMCID: PMC10231198 DOI: 10.1128/jvi.00213-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/14/2023] [Indexed: 04/20/2023] Open
Abstract
ANP32 proteins, which act as influenza polymerase cofactors, vary between birds and mammals. In mammals, ANP32A and ANP32B have been reported to serve essential but redundant roles to support influenza polymerase activity. The well-known mammalian adaptation PB2-E627K enables influenza polymerase to use mammalian ANP32 proteins. However, some mammalian-adapted influenza viruses do not harbor this substitution. Here, we show that alternative PB2 adaptations, Q591R and D701N, also allow influenza polymerase to use mammalian ANP32 proteins, whereas other PB2 mutations, G158E, T271A, and D740N, increase polymerase activity in the presence of avian ANP32 proteins as well. Furthermore, PB2-E627K strongly favors use of mammalian ANP32B proteins, whereas D701N shows no such bias. Accordingly, PB2-E627K adaptation emerges in species with strong pro-viral ANP32B proteins, such as humans and mice, while D701N is more commonly seen in isolates from swine, dogs, and horses, where ANP32A proteins are the preferred cofactor. Using an experimental evolution approach, we show that the passage of viruses containing avian polymerases in human cells drove acquisition of PB2-E627K, but not in the absence of ANP32B. Finally, we show that the strong pro-viral support of ANP32B for PB2-E627K maps to the low-complexity acidic region (LCAR) tail of ANP32B. IMPORTANCE Influenza viruses naturally reside in wild aquatic birds. However, the high mutation rate of influenza viruses allows them to rapidly and frequently adapt to new hosts, including mammals. Viruses that succeed in these zoonotic jumps pose a pandemic threat whereby the virus adapts sufficiently to efficiently transmit human-to-human. The influenza virus polymerase is central to viral replication and restriction of polymerase activity is a major barrier to species jumps. ANP32 proteins are essential for influenza polymerase activity. In this study, we describe how avian influenza viruses can adapt in several different ways to use mammalian ANP32 proteins. We further show that differences between mammalian ANP32 proteins can select different adaptive changes and are responsible for some of the typical mutations that arise in mammalian-adapted influenza polymerases. These different adaptive mutations may determine the relative zoonotic potential of influenza viruses and thus help assess their pandemic risk.
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Affiliation(s)
- Thomas P. Peacock
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Carol M. Sheppard
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Margaret G. Lister
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Ecco Staller
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Rebecca Frise
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Olivia C. Swann
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Daniel H. Goldhill
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Jason S. Long
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Wendy S. Barclay
- Department of Infectious Disease, Imperial College London, London, United Kingdom
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9
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Yehia N, Rabie N, Adel A, Mossad Z, Nagshabandi MK, Alharbi MT, El-Saadony MT, El-Tarabily KA, Erfan A. Differential replication characteristic of reassortant avian influenza A viruses H5N8 clade 2.3.4.4b in Madin Darby Canine kidney cell. Poult Sci 2023. [DOI: 10.1016/j.psj.2023.102685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
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10
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Avian Influenza A Virus Polymerase Can Utilize Human ANP32 Proteins To Support cRNA but Not vRNA Synthesis. mBio 2023; 14:e0339922. [PMID: 36645303 PMCID: PMC9973007 DOI: 10.1128/mbio.03399-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Host restriction limits the emergence of novel pandemic strains from the influenza A virus avian reservoir. For efficient replication in mammalian cells, the avian influenza RNA-dependent RNA polymerase must adapt to use human orthologues of the host factor ANP32, which lack a 33-amino-acid insertion relative to avian ANP32A. Here, we find that influenza polymerase requires ANP32 proteins to support both steps of genome replication: cRNA and vRNA synthesis. However, avian strains are only restricted in vRNA synthesis in human cells. Therefore, avian influenza polymerase can use human ANP32 orthologues to support cRNA synthesis, without acquiring mammalian adaptations. This implies a fundamental difference in the mechanism by which ANP32 proteins support cRNA versus vRNA synthesis. IMPORTANCE To infect humans and cause a pandemic, avian influenza must first adapt to use human versions of the proteins the virus hijacks for replication, instead of the avian orthologues found in bird cells. One critical host protein is ANP32. Understanding the details of how host proteins such as ANP32 support viral activity may allow the design of new antiviral strategies that disrupt these interactions. Here, we use cells that lack ANP32 to unambiguously demonstrate ANP32 is needed for both steps of influenza genome replication. Unexpectedly, however, we found that avian influenza can use human ANP32 proteins for the first step of replication, to copy a complementary strand, without adaptation but can only utilize avian ANP32 for the second step of replication that generates new genomes. This suggests ANP32 may have a distinct role in supporting the second step of replication, and it is this activity that is specifically blocked when avian influenza infects human cells.
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11
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Chu JT, Gu H, Sun W, Fan RL, Nicholls JM, Valkenburg SA, Poon LL. Heterosubtypic immune pressure accelerates emergence of influenza A virus escape phenotypes in mice. Virus Res 2023; 323:198991. [PMID: 36302472 PMCID: PMC10194115 DOI: 10.1016/j.virusres.2022.198991] [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: 09/29/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 11/07/2022]
Abstract
Rapid antigenic evolution of the influenza A virus surface antigen hemagglutinin undermines protection conferred by seasonal vaccines. Protective correlates targeted by universal vaccines such as cytotoxic T cells or HA stem directed broadly neutralizing antibodies have been shown to select for immune escape mutants during infection. We developed an in vivo serial passage mouse model for viral adaptation and used next generation sequencing to evaluate full genome viral evolution in the context of broadly protective immunity. Heterosubtypic immune pressure increased the incidence of genome-wide single nucleotide variants, though mutations found in early adapted populations were predominantly stochastic in nature. Prolonged adaptation under heterosubtypic immune selection resulted in the manifestation of highly virulent phenotypes that ablated vaccine mediated protection from mortality. High frequency mutations unique to escape phenotypes were identified within the polymerase encoding segments. These findings suggest that a suboptimial usage of population-wide universal influenza vaccine may drive formation of escape variants attributed to polygenic changes.
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Affiliation(s)
- Julie Ts Chu
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Haogao Gu
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Wanying Sun
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Rebecca Ly Fan
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - John M Nicholls
- Department of Pathology, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Sophie A Valkenburg
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Leo Lm Poon
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; HKU-Pasteur Research Pole, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Centre for Immunology & Infection, Hong Kong Science Park, Hong Kong Special Administrative Region, China.
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12
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Qurashi MA, Rashid S, Alshehri AM, Jarad F, Safdar F. New numerical dynamics of the fractional monkeypox virus model transmission pertaining to nonsingular kernels. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:402-436. [PMID: 36650772 DOI: 10.3934/mbe.2023019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Monkeypox (MPX) is a zoonotic illness that is analogous to smallpox. Monkeypox infections have moved across the forests of Central Africa, where they were first discovered, to other parts of the world. It is transmitted by the monkeypox virus, which is a member of the Poxviridae species and belongs to the Orthopoxvirus genus. In this article, the monkeypox virus is investigated using a deterministic mathematical framework within the Atangana-Baleanu fractional derivative that depends on the generalized Mittag-Leffler (GML) kernel. The system's equilibrium conditions are investigated and examined for robustness. The global stability of the endemic equilibrium is addressed using Jacobian matrix techniques and the Routh-Hurwitz threshold. Furthermore, we also identify a criterion wherein the system's disease-free equilibrium is globally asymptotically stable. Also, we employ a new approach by combining the two-step Lagrange polynomial and the fundamental concept of fractional calculus. The numerical simulations for multiple fractional orders reveal that as the fractional order reduces from 1, the virus's transmission declines. The analysis results show that the proposed strategy is successful at reducing the number of occurrences in multiple groups. It is evident that the findings suggest that isolating affected people from the general community can assist in limiting the transmission of pathogens.
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Affiliation(s)
- Maysaa Al Qurashi
- Department of Mathematics, King Saud University, P. O. Box 22452, Riyadh 11495, Saudi Arabia
- Department of Mathematics, Saudi Electronic University, Riyadh, Saudi Arabia
| | - Saima Rashid
- Department of Mathematics, Government College University, Faisalabad 38000, Pakistan
| | - Ahmed M Alshehri
- Department of Mathematics, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fahd Jarad
- Department of Mathematics, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Mathematics, Cankaya University, Ankara, Turkey
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Farhat Safdar
- Department of Mathematics, SBK for Women University, Quetta, Pakistan
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13
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Jacquet S, Culbertson M, Zhang C, El Filali A, De La Myre Mory C, Pons JB, Filippi-Codaccioni O, Lauterbur ME, Ngoubangoye B, Duhayer J, Verez C, Park C, Dahoui C, Carey CM, Brennan G, Enard D, Cimarelli A, Rothenburg S, Elde NC, Pontier D, Etienne L. Adaptive duplication and genetic diversification of protein kinase R contribute to the specificity of bat-virus interactions. SCIENCE ADVANCES 2022; 8:eadd7540. [PMID: 36417524 PMCID: PMC9683710 DOI: 10.1126/sciadv.add7540] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/05/2022] [Indexed: 05/29/2023]
Abstract
Several bat species act as asymptomatic reservoirs for many viruses that are highly pathogenic in other mammals. Here, we have characterized the functional diversification of the protein kinase R (PKR), a major antiviral innate defense system. Our data indicate that PKR has evolved under positive selection and has undergone repeated genomic duplications in bats in contrast to all studied mammals that have a single copy of the gene. Functional testing of the relationship between PKR and poxvirus antagonists revealed how an evolutionary conflict with ancient pathogenic poxviruses has shaped a specific bat host-virus interface. We determined that duplicated PKRs of the Myotis species have undergone genetic diversification, allowing them to collectively escape from and enhance the control of DNA and RNA viruses. These findings suggest that viral-driven adaptations in PKR contribute to modern virus-bat interactions and may account for bat-specific immunity.
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Affiliation(s)
- Stéphanie Jacquet
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, UCBL1, CNRS, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Michelle Culbertson
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Chi Zhang
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, USA
| | - Adil El Filali
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, UCBL1, CNRS, Lyon, France
| | - Clément De La Myre Mory
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Jean-Baptiste Pons
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, UCBL1, CNRS, Lyon, France
| | | | - M. Elise Lauterbur
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Barthélémy Ngoubangoye
- International Centre of Medical Research of Franceville, Primatology Centre, Franceville, Gabon
| | - Jeanne Duhayer
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, UCBL1, CNRS, Lyon, France
| | - Clément Verez
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Chorong Park
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, USA
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Clara Dahoui
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Clayton M. Carey
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Greg Brennan
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, USA
| | - David Enard
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Andrea Cimarelli
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Stefan Rothenburg
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, USA
| | - Nels C. Elde
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA
| | - Dominique Pontier
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, UCBL1, CNRS, Lyon, France
| | - Lucie Etienne
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
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14
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Lutz M, Schmierer J, Takimoto T. Host adaptive mutations in the 2009 H1N1 pandemic influenza A virus PA gene regulate translation efficiency of viral mRNAs via GRSF1. Commun Biol 2022; 5:1102. [PMID: 36253464 PMCID: PMC9576711 DOI: 10.1038/s42003-022-04082-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/06/2022] [Indexed: 11/08/2022] Open
Abstract
Avian species are the major natural reservoir from which pandemic influenza A viruses can be introduced to humans. Avian influenza A virus genes, including the three viral polymerase genes, PA, PB1 and PB2, require host-adaptive mutations to allow for viral replication and transmission in humans. Previously, PA from the 2009 pH1N1 viral polymerase was found to harbor host-adaptive mutations leading to enhanced viral polymerase activity. By quantifying translation and mRNA transcription, we found that the 2009 pH1N1 PA, and the associated host-adaptive mutations, led to greater translation efficiency. This was due to enhanced cytosolic accumulation of viral mRNA, which was dependent on the host RNA binding protein GRSF1. Mutations to the GRSF1 binding site in viral mRNA, as well as GRSF1 knockdown, reduced cytosolic accumulation and translation efficiency of viral mRNAs. This study identifies a previously unrecognized mechanism by which host-adaptive mutations in PA regulate viral replication and host adaptation. Importantly, these results provide greater insight into the host adaptation process of IAVs and reveal the importance of GRSF1 in the lifecycle of IAV.
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Affiliation(s)
- Michael Lutz
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Jordana Schmierer
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Toru Takimoto
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA.
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15
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Drews SJ, O’Brien SF. Lessons Learned from the COVID-19 Pandemic and How Blood Operators Can Prepare for the Next Pandemic. Viruses 2022; 14:2126. [PMID: 36298680 PMCID: PMC9608827 DOI: 10.3390/v14102126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/08/2022] [Accepted: 09/22/2022] [Indexed: 11/17/2022] Open
Abstract
Humans interact with virus-infected animal hosts, travel globally, and maintain social networks that allow for novel viruses to emerge and develop pandemic potential. There are key lessons-learned from the coronavirus diseases 2019 (COVID-19) pandemic that blood operators can apply to the next pandemic. Warning signals to the COVID-19 pandemic included outbreaks of Severe acute respiratory syndrome-related coronavirus-1 (SARS-CoV-1) and Middle East respiratory syndrome-related coronavirus (MERS-CoV) in the prior two decades. It will be critical to quickly determine whether there is a risk of blood-borne transmission of a new pandemic virus. Prior to the next pandemic blood operators should be prepared for changes in activities, policies, and procedures at all levels of the organization. Blood operators can utilize "Plan-Do-Study-Act" cycles spanning from: vigilance for emerging viruses, surveillance activities and studies, operational continuity, donor engagement and trust, and laboratory testing if required. Occupational health and donor safety issues will be key areas of focus even if the next pandemic virus is not transfusion transmitted. Blood operators may also be requested to engage in new activities such as the development of therapeutics or supporting public health surveillance activities. Activities such as scenario development, tabletop exercises, and drills will allow blood operators to prepare for the unknowns of the next pandemic.
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Affiliation(s)
- Steven J. Drews
- Canadian Blood Services, Microbiology, Donation and Policy Studies, Canadian Blood Services, Edmonton, AB T6G 2R8, Canada
- Division of Applied and Diagnostic Microbiology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Sheila F. O’Brien
- Epidemiology and Surveillance, Donation Policy and Studies, Canadian Blood Services, Ottawa, ON K1G 4J5, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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16
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Rattanaburi S, Sawaswong V, Nimsamer P, Mayuramart O, Sivapornnukul P, Khamwut A, Chanchaem P, Kongnomnan K, Suntronwong N, Poovorawan Y, Payungporn S. Genome characterization and mutation analysis of human influenza A virus in Thailand. Genomics Inform 2022; 20:e21. [PMID: 35794701 PMCID: PMC9299564 DOI: 10.5808/gi.21077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/05/2022] [Indexed: 11/20/2022] Open
Abstract
The influenza A viruses have high mutation rates and cause a serious health problem worldwide. Therefore, this study focused on genome characterization of the viruses isolated from Thai patients based on the next-generation sequencing technology. The nasal swabs were collected from patients with influenza-like illness in Thailand during 2017-2018. Then, the influenza A viruses were detected by reverse transcription-quantitative polymerase chain reaction and isolated by MDCK cells. The viral genomes were amplified and sequenced by Illumina MiSeq platform. Whole genome sequences were used for characterization, phylogenetic construction, mutation analysis and nucleotide diversity of the viruses. The result revealed that 90 samples were positive for the viruses including 44 of A/H1N1 and 46 of A/H3N2. Among these, 43 samples were successfully isolated and then the viral genomes of 25 samples were completely amplified. Finally, 17 whole genomes of the viruses (A/H1N1, n=12 and A/H3N2, n=5) were successfully sequenced with an average of 232,578 mapped reads and 1,720 genome coverage per sample. Phylogenetic analysis demonstrated that the A/H1N1 viruses were distinguishable from the recommended vaccine strains. However, the A/H3N2 viruses from this study were closely related to the recommended vaccine strains. The nonsynonymous mutations were found in all genes of both viruses, especially in HA and NA genes. The nucleotide diversity analysis revealed negative selection in the PB1, PA, hemagglutinin (HA) and neuraminidase (NA) genes of the A/H1N1 viruses. High-throughput data in this study allow for genetic characterization of circulating influenza viruses which would be crucial for preparation against pandemic and epidemic outbreaks in the future.
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Affiliation(s)
- Somruthai Rattanaburi
- Interdisciplinary Program of Biomedical Sciences, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand.,Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Vorthon Sawaswong
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pattaraporn Nimsamer
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Oraphan Mayuramart
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pavaret Sivapornnukul
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Ariya Khamwut
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Prangwalai Chanchaem
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kritsada Kongnomnan
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nungruthai Suntronwong
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
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17
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Decker CH, Rapier-Sharman N, Pickett BE. Mutation in Hemagglutinin Antigenic Sites in Influenza A pH1N1 Viruses from 2015-2019 in the United States Mountain West, Europe, and the Northern Hemisphere. Genes (Basel) 2022; 13:909. [PMID: 35627294 PMCID: PMC9141826 DOI: 10.3390/genes13050909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/17/2022] [Accepted: 05/17/2022] [Indexed: 11/17/2022] Open
Abstract
H1N1 influenza A virus is a respiratory pathogen that undergoes antigenic shift and antigenic drift to improve viral fitness. Tracking the evolutionary trends of H1N1 aids with the current detection and the future response to new viral strains as they emerge. Here, we characterize antigenic drift events observed in the hemagglutinin (HA) sequence of the pandemic H1N1 lineage from 2015-2019. We observed the substitutions S200P, K147N, and P154S, together with other mutations in structural, functional, and/or epitope regions in 2015-2019 HA protein sequences from the Mountain West region of the United States, the larger United States, Europe, and other Northern Hemisphere countries. We reconstructed multiple phylogenetic trees to track the relationships and spread of these mutations and tested for evidence of selection pressure on HA. We found that the prevalence of amino acid substitutions at positions 147, 154, 159, 200, and 233 significantly changed throughout the studied geographical regions between 2015 and 2019. We also found evidence of coevolution among a subset of these amino acid substitutions. The results from this study could be relevant for future epidemiological tracking and vaccine prediction efforts. Similar analyses in the future could identify additional sequence changes that could affect the pathogenicity and/or infectivity of this virus in its human host.
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Affiliation(s)
| | | | - Brett E. Pickett
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA; (C.H.D.); (N.R.-S.)
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18
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Ullah S, Ross TM. Next generation live-attenuated influenza vaccine platforms. Expert Rev Vaccines 2022; 21:1097-1110. [PMID: 35502639 DOI: 10.1080/14760584.2022.2072301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Influenza virus is a major cause of seasonal epidemics and intermittent pandemics. Despite the current molecular biology and vaccine development, influenza virus infection is a significant burden. Vaccines are considered an essential countermeasure for effective control and prevention of influenza virus infection. Even though current influenza virus vaccines provide efficient protection against seasonal influenza outbreaks, the efficacy of these vaccines is not suitable due to antigenic changes of the viruses. AREAS COVERED This review focuses on different live-attenuated platforms for influenza virus vaccine development and proposes essential considerations for a rational universal influenza virus vaccine design. EXPERT OPINION Despite the recent efforts for universal influenza virus vaccines, there is a lack of broadly reactive antibodies' induction that can confer broad and long-lasting protection. Various strategies using live-attenuated influenza virus vaccines (LAIVs) are investigated to induce broadly reactive, durable, and cross-protective immune responses. LAIVs based on NS segment truncation prevent influenza virus infection and have shown to be effective vaccine candidates among other vaccine platforms. Although many approaches have been used for LAIVs generation, there is still a need to focus on the LAIVs development platforms to generate a universal influenza virus vaccine candidate.
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Affiliation(s)
- Subhan Ullah
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, USA
| | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, USA.,Department of Infectious Diseases, University of Georgia, Athens, Georgia, USA
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19
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Nguyen ATV, Hoang VT, Sung HW, Yeo SJ, Park H. Genetic Characterization and Pathogenesis of Three Novel Reassortant H5N2 Viruses in South Korea, 2018. Viruses 2021; 13:v13112192. [PMID: 34834997 PMCID: PMC8619638 DOI: 10.3390/v13112192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 12/03/2022] Open
Abstract
The outbreaks of H5N2 avian influenza viruses have occasionally caused the death of thousands of birds in poultry farms. Surveillance during the 2018 winter season in South Korea revealed three H5N2 isolates in feces samples collected from wild birds (KNU18-28: A/Wild duck/South Korea/KNU18-28/2018, KNU18-86: A/Bean Goose/South Korea/KNU18-86/2018, and KNU18-93: A/Wild duck/South Korea/KNU18-93/2018). Phylogenetic tree analysis revealed that these viruses arose from reassortment events among various virus subtypes circulating in South Korea and other countries in the East Asia–Australasian Flyway. The NS gene of the KNU18-28 and KNU18-86 isolates was closely related to that of China’s H10N3 strain, whereas the KNU18-93 strain originated from the H12N2 strain in Japan, showing two different reassortment events and different from a low pathogenic H5N3 (KNU18-91) virus which was isolated at the same day and same place with KNU18-86 and KNU18-93. These H5N2 isolates were characterized as low pathogenic avian influenza viruses. However, many amino acid changes in eight gene segments were identified to enhance polymerase activity and increase adaptation and virulence in mice and mammals. Experiments reveal that viral replication in MDCK cells was quite high after 12 hpi, showing the ability to replicate in mouse lungs. The hematoxylin and eosin-stained (H&E) lung sections indicated different degrees of pathogenicity of the three H5N2 isolates in mice compared with that of the control H1N1 strain. The continuing circulation of these H5N2 viruses may represent a potential threat to mammals and humans. Our findings highlight the need for intensive surveillance of avian influenza virus circulation in South Korea to prevent the risks posed by these reassortment viruses to animal and public health.
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Affiliation(s)
- Anh Thi Viet Nguyen
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 54538, Korea; (A.T.V.N.); (V.T.H.)
| | - Vui Thi Hoang
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 54538, Korea; (A.T.V.N.); (V.T.H.)
| | - Haan Woo Sung
- College of Veterinary Medicine, Kangwon National University, Chuncheon 24341, Korea;
| | - Seon-Ju Yeo
- Department of Tropical Medicine and Parasitology, College of Medicine, Seoul National University, Seoul 03080, Korea
- Correspondence: (S.-J.Y.); (H.P.)
| | - Hyun Park
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 54538, Korea; (A.T.V.N.); (V.T.H.)
- Correspondence: (S.-J.Y.); (H.P.)
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20
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Zolotarova O, Fesenko A, Holubka O, Radchenko L, Bortz E, Budzanivska I, Mironenko A. Genotypic Variants of Pandemic H1N1 Influenza A Viruses Isolated from Severe Acute Respiratory Infections in Ukraine during the 2015/16 Influenza Season. Viruses 2021; 13:2125. [PMID: 34834932 PMCID: PMC8619959 DOI: 10.3390/v13112125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/05/2021] [Accepted: 10/15/2021] [Indexed: 01/15/2023] Open
Abstract
Human type A influenza viruses A(H1N1)pdm09 have caused seasonal epidemics of influenza since the 2009-2010 pandemic. A(H1N1)pdm09 viruses had a leading role in the severe epidemic season of 2015/16 in the Northern Hemisphere and caused a high incidence of acute respiratory infection (ARI) in Ukraine. Serious complications of influenza-associated severe ARI (SARI) were observed in the very young and individuals at increased risk, and 391 fatal cases occurred in the 2015/16 epidemic season. We analyzed the genetic changes in the genomes of A(H1N1)pdm09 influenza viruses isolated from SARI cases in Ukraine during the 2015/16 season. The viral hemagglutinin (HA) fell in H1 group 6B.1 for all but four isolates, with known mutations affecting glycosylation, the Sa antigenic site (S162N in all 6B.1 isolates), or virulence (D222G/N in two isolates). Other mutations occurred in antigenic site Ca (A141P and S236P), and a subgroup of four strains were in group 6B.2, with potential alterations to antigenicity in A(H1N1)pdm09 viruses circulating in 2015/16 in Ukraine. A cluster of Ukrainian isolates exhibited novel D2E and N48S mutations in the RNA binding domain, and E125D in the effector domain, of immune evasion nonstructural protein 1 (NS1). The diverse spectrum of amino-acid substitutions in HA, NS1, and other viral proteins including nucleoprotein (NP) and the polymerase complex suggested the concurrent circulation of multiple lineages of A(H1N1)pdm09 influenza viruses in the human population in Ukraine, a country with low vaccination coverage, complicating public health measures against influenza.
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Affiliation(s)
- Oksana Zolotarova
- Educational Scientific Centre “Institute of Biology and Medicine”, Taras Shevchenko National University of Kyiv, 01601 Kyiv, Ukraine;
| | - Anna Fesenko
- Gromashevsky L.V. Institute of Epidemiology and Infectious Diseases, National Academy of Medical Sciences of Ukraine, 03680 Kyiv, Ukraine; (A.F.); (O.H.); (L.R.); (A.M.)
| | - Olga Holubka
- Gromashevsky L.V. Institute of Epidemiology and Infectious Diseases, National Academy of Medical Sciences of Ukraine, 03680 Kyiv, Ukraine; (A.F.); (O.H.); (L.R.); (A.M.)
| | - Larysa Radchenko
- Gromashevsky L.V. Institute of Epidemiology and Infectious Diseases, National Academy of Medical Sciences of Ukraine, 03680 Kyiv, Ukraine; (A.F.); (O.H.); (L.R.); (A.M.)
| | - Eric Bortz
- Department of Biological Sciences, University of Alaska, 3211 Providence Dr., Anchorage, AK 99508, USA;
| | - Iryna Budzanivska
- Educational Scientific Centre “Institute of Biology and Medicine”, Taras Shevchenko National University of Kyiv, 01601 Kyiv, Ukraine;
| | - Alla Mironenko
- Gromashevsky L.V. Institute of Epidemiology and Infectious Diseases, National Academy of Medical Sciences of Ukraine, 03680 Kyiv, Ukraine; (A.F.); (O.H.); (L.R.); (A.M.)
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21
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Todorović-Raković N, Whitfield JR. Between immunomodulation and immunotolerance: The role of IFNγ in SARS-CoV-2 disease. Cytokine 2021; 146:155637. [PMID: 34242899 PMCID: PMC8253693 DOI: 10.1016/j.cyto.2021.155637] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 12/21/2022]
Abstract
Interferons have prominent roles in various pathophysiological conditions, mostly related to inflammation. Interferon-gamma (IFNγ) was, initially discovered as a potent antiviral agent, over 50 years ago, and has recently garnered renewed interest as a promising factor involved in both innate and adaptive immunity. When new disease epidemics appear such as SARS-CoV (severe acute respiratory syndrome coronavirus), MERS-CoV (Middle East respiratory syndrome coronavirus), IAV (Influenza A virus), and in particular the current SARS-CoV-2 pandemic, it is especially timely to review the complexity of immune system responses to viral infections. Here we consider the controversial roles of effectors like IFNγ, discussing its actions in immunomodulation and immunotolerance. We explore the possibility that modulation of IFNγ could be used to influence the course of such infections. Importantly, not only could endogenous expression of IFNγ influence the outcome, there are existing IFNγ therapeutics that can readily be applied in the clinic. However, our understanding of the molecular mechanisms controlled by IFNγ suggests that the exact timing for application of IFNγ-based therapeutics could be crucial: it should be earlier to significantly reduce the viral load and thus decrease the overall severity of the disease.
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Affiliation(s)
- Nataša Todorović-Raković
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Belgrade, Serbia.
| | - Jonathan R Whitfield
- Vall d'Hebron Institute of Oncology (VHIO), Carrer Natzaret 115, Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
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22
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Genetic Characterization of Highly Pathogenic Avian Influenza A(H5N8) Virus in Pakistani Live Bird Markets Reveals Rapid Diversification of Clade 2.3.4.4b Viruses. Viruses 2021; 13:v13081633. [PMID: 34452498 PMCID: PMC8402709 DOI: 10.3390/v13081633] [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: 07/08/2021] [Revised: 08/06/2021] [Accepted: 08/16/2021] [Indexed: 11/17/2022] Open
Abstract
The highly pathogenic (HPAI) avian influenza A(H5N1) viruses have undergone reassortment with multiple non-N1-subtype neuraminidase genes since 2008, leading to the emergence of H5Nx viruses. H5Nx viruses established themselves quickly in birds and disseminated from China to Africa, the Middle East, Europe and North America. Multiple genetic clades have successively evolved through frequent mutations and reassortment, posing a continuous threat to domestic poultry and causing substantial economic losses. Live bird markets are recognized as major sources of avian-to-human infection and for the emergence of zoonotic influenza. In Pakistan, the A(H5N1) virus was first reported in domestic birds in 2007; however, avian influenza surveillance is limited and there is a lack of knowledge on the evolution and transmission of the A(H5) virus in the country. We collected oropharyngeal swabs from domestic poultry and environmental samples from six different live bird markets during 2018–2019. We detected and sequenced HPAI A(H5N8) viruses from two chickens, one quail and one environmental sample in two markets. Temporal phylogenetics indicated that all novel HPAI A(H5N8) viruses belonged to clade 2.3.4.4b, with all eight genes of Pakistan A(H5N8) viruses most closely related to 2017 Saudi Arabia A(H5N8) viruses, which were likely introduced via cross-border transmission from neighboring regions approximately three months prior to virus detection into domestic poultry. Our data further revealed that clade 2.3.4.4b viruses underwent rapid lineage expansion in 2017 and acquired significant amino acid mutations, including mutations associated with increased haemagglutinin affinity to human α-2,6 receptors, prior to the first human A(H5N8) infection in Russian poultry workers in 2020. These results highlight the need for systematic avian influenza surveillance in live bird markets in Pakistan to monitor for potential A(H5Nx) variants that may arise from poultry populations.
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23
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Han AX, Felix Garza ZC, Welkers MRA, Vigeveno RM, Tran ND, Le TQM, Pham Quang T, Dang DT, Tran TNA, Ha MT, Nguyen TH, Le QT, Le TH, Hoang TBN, Chokephaibulkit K, Puthavathana P, Nguyen VVC, Nghiem MN, Nguyen VK, Dao TT, Tran TH, Wertheim HFL, Horby PW, Fox A, van Doorn HR, Eggink D, de Jong MD, Russell CA. Within-host evolutionary dynamics of seasonal and pandemic human influenza A viruses in young children. eLife 2021; 10:e68917. [PMID: 34342576 PMCID: PMC8382297 DOI: 10.7554/elife.68917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/02/2021] [Indexed: 01/14/2023] Open
Abstract
The evolution of influenza viruses is fundamentally shaped by within-host processes. However, the within-host evolutionary dynamics of influenza viruses remain incompletely understood, in part because most studies have focused on infections in healthy adults based on single timepoint data. Here, we analyzed the within-host evolution of 82 longitudinally sampled individuals, mostly young children, infected with A/H1N1pdm09 or A/H3N2 viruses between 2007 and 2009. For A/H1N1pdm09 infections during the 2009 pandemic, nonsynonymous minority variants were more prevalent than synonymous ones. For A/H3N2 viruses in young children, early infection was dominated by purifying selection. As these infections progressed, nonsynonymous variants typically increased in frequency even when within-host virus titers decreased. Unlike the short-lived infections of adults where de novo within-host variants are rare, longer infections in young children allow for the maintenance of virus diversity via mutation-selection balance creating potentially important opportunities for within-host virus evolution.
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Affiliation(s)
- Alvin X Han
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical CenterAmsterdamNetherlands
| | - Zandra C Felix Garza
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical CenterAmsterdamNetherlands
| | - Matthijs RA Welkers
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical CenterAmsterdamNetherlands
| | - René M Vigeveno
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical CenterAmsterdamNetherlands
| | - Nhu Duong Tran
- National Institute of Hygiene and EpidemiologyHanoiViet Nam
| | | | | | | | | | | | | | | | - Thanh Hai Le
- Vietnam National Children's HospitalHanoiViet Nam
| | | | | | | | | | | | | | | | - Tinh Hien Tran
- Siriraj Hospital, Mahidol UniversityBangkokThailand
- Oxford University Clinical Research UnitHo Chi Minh cityViet Nam
| | - Heiman FL Wertheim
- Oxford University Clinical Research UnitHo Chi Minh cityViet Nam
- Radboud Medical Centre, Radboud UniversityNijmegenNetherlands
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Peter W Horby
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Oxford University Clinical Research UnitHanoiViet Nam
| | - Annette Fox
- Oxford University Clinical Research UnitHanoiViet Nam
- Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneAustralia
- WHO Collaborating Centre for Reference and Research on InfluenzaMelbourneAustralia
| | - H Rogier van Doorn
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Oxford University Clinical Research UnitHanoiViet Nam
| | - Dirk Eggink
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical CenterAmsterdamNetherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the EnvironmentBilthovenNetherlands
| | - Menno D de Jong
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical CenterAmsterdamNetherlands
| | - Colin A Russell
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical CenterAmsterdamNetherlands
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Goldhill DH, Yan A, Frise R, Zhou J, Shelley J, Gallego Cortés A, Miah S, Akinbami O, Galiano M, Zambon M, Lackenby A, Barclay WS. Favipiravir-resistant influenza A virus shows potential for transmission. PLoS Pathog 2021; 17:e1008937. [PMID: 34061908 PMCID: PMC8195362 DOI: 10.1371/journal.ppat.1008937] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 06/11/2021] [Accepted: 05/03/2021] [Indexed: 12/11/2022] Open
Abstract
Favipiravir is a nucleoside analogue which has been licensed to treat influenza in the event of a new pandemic. We previously described a favipiravir resistant influenza A virus generated by in vitro passage in presence of drug with two mutations: K229R in PB1, which conferred resistance at a cost to polymerase activity, and P653L in PA, which compensated for the cost of polymerase activity. However, the clinical relevance of these mutations is unclear as the mutations have not been found in natural isolates and it is unknown whether viruses harbouring these mutations would replicate or transmit in vivo. Here, we infected ferrets with a mix of wild type p(H1N1) 2009 and corresponding favipiravir-resistant virus and tested for replication and transmission in the absence of drug. Favipiravir-resistant virus successfully infected ferrets and was transmitted by both contact transmission and respiratory droplet routes. However, sequencing revealed the mutation that conferred resistance, K229R, decreased in frequency over time within ferrets. Modelling revealed that due to a fitness advantage for the PA P653L mutant, reassortment with the wild-type virus to gain wild-type PB1 segment in vivo resulted in the loss of the PB1 resistance mutation K229R. We demonstrated that this fitness advantage of PA P653L in the background of our starting virus A/England/195/2009 was due to a maladapted PA in first wave isolates from the 2009 pandemic. We show there is no fitness advantage of P653L in more recent pH1N1 influenza A viruses. Therefore, whilst favipiravir-resistant virus can transmit in vivo, the likelihood that the resistance mutation is retained in the absence of drug pressure may vary depending on the genetic background of the starting viral strain.
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Affiliation(s)
- Daniel H. Goldhill
- Department of Infectious Disease, Imperial College, London, United Kingdom
| | - Ada Yan
- Department of Infectious Disease Epidemiology, Imperial College, London, United Kingdom
| | - Rebecca Frise
- Department of Infectious Disease, Imperial College, London, United Kingdom
| | - Jie Zhou
- Department of Infectious Disease, Imperial College, London, United Kingdom
| | - Jennifer Shelley
- Department of Infectious Disease, Imperial College, London, United Kingdom
| | - Ana Gallego Cortés
- Department of Infectious Disease, Imperial College, London, United Kingdom
| | | | | | | | | | | | - Wendy S. Barclay
- Department of Infectious Disease, Imperial College, London, United Kingdom
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25
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Ben Hamed S, Elargoubi A, Harrabi M, Srihi H, Souiai O, Mastouri M, Almalki MA, Gharbi J, Ben M’hadheb M. Phylogenetic analysis of the neuraminidase segment gene of Influenza A/H1N1 strains isolated from Monastir Region (Tunisia) during the 2017-2018 outbreak. Biologia (Bratisl) 2021; 76:1797-1806. [PMID: 33727729 PMCID: PMC7952816 DOI: 10.1007/s11756-021-00723-y] [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: 07/20/2020] [Accepted: 02/19/2021] [Indexed: 11/25/2022]
Abstract
Influenza A/H1N1 is widely considered to be a very evolutionary virus causing major public health problems. Since the pandemic of 2009, there has been a rapid rise in human Influenza virus characterization. However, little data is available in Tunisia regarding its genetic evolution. In light of this fact, our paper aim is to genetically characterize the Neuraminidase, known as the target of antiviral inhibitors, in Tunisian isolates circulating in Monastir region during 2017-2018. In total of 31 positive Influenza A/H1N1 detected by multiplex real-time PCR, RT-PCR of neuraminidase was performed. Among the 31 positive samples, 7 samples representing fatal and most severe cases were conducted for sequencing and genetic analysis. The results thus obtained showed genetic evolution of the A/H1N1 neuraminidase between 2009 and 2010 and 2018-2019 outbreaks. All Tunisian isolates were genetically related to the recommended vaccine strain with a specific evolution. Moreover, the phylogenetic analysis demonstrated that France and especially Italian strains were the major related strains. Interestingly, our results revealed a specific cluster of Tunisian isolates where two intragroup were evolved in correlation with the severity and the fatalities cases. From the outcome of our investigation, this study confirms the genetic evolution of the Influenza A virus circulating in Tunisia and gives a preliminary analysis for a better comprehension of new emerging Tunisian strain's virulence and thus, a more appropriate monitoring of Influenza virus A/H1N1 during each round of outbreaks. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11756-021-00723-y.
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Affiliation(s)
- Sabrine Ben Hamed
- Unité de Recherche UR17ES30 “Génomique Biotechnologie et Stratégies Antivirales” (ViroBiotech), Institut Supérieur de Biotechnologie, Université de Monastir, BP74, Avenue Tahar Hadded, Monastir, 5000 Tunisia
| | - Aida Elargoubi
- Laboratoire de Recherche LR99ES27 “Maladies Transmissibles & Substances Biologiquement Actives”, Faculté de Pharmacie de Monastir, Avenue Avicenne, Monastir, Tunisia
| | - Myriam Harrabi
- Unité de Recherche UR17ES30 “Génomique Biotechnologie et Stratégies Antivirales” (ViroBiotech), Institut Supérieur de Biotechnologie, Université de Monastir, BP74, Avenue Tahar Hadded, Monastir, 5000 Tunisia
- Laboratoroire de “BioInformatique, bioMathematique & bioStatistique” (BIMS), Institut Pasteur de Tunis, BP 74, 13, place Pasteur Tunis, 1002 Tunis, Tunisia
| | - Haythem Srihi
- Unité de Recherche UR17ES30 “Génomique Biotechnologie et Stratégies Antivirales” (ViroBiotech), Institut Supérieur de Biotechnologie, Université de Monastir, BP74, Avenue Tahar Hadded, Monastir, 5000 Tunisia
| | - Oussema Souiai
- Laboratoroire de “BioInformatique, bioMathematique & bioStatistique” (BIMS), Institut Pasteur de Tunis, BP 74, 13, place Pasteur Tunis, 1002 Tunis, Tunisia
| | - Maha Mastouri
- Laboratoire de Recherche LR99ES27 “Maladies Transmissibles & Substances Biologiquement Actives”, Faculté de Pharmacie de Monastir, Avenue Avicenne, Monastir, Tunisia
| | - Mohammed Awadh Almalki
- Department of Biological Sciences, College of Science, King Faisal University, P.O. Box 380, Al-Ahsa, 31982 Kingdom of Saudi Arabia
| | - Jawhar Gharbi
- Unité de Recherche UR17ES30 “Génomique Biotechnologie et Stratégies Antivirales” (ViroBiotech), Institut Supérieur de Biotechnologie, Université de Monastir, BP74, Avenue Tahar Hadded, Monastir, 5000 Tunisia
- Department of Biological Sciences, College of Science, King Faisal University, P.O. Box 380, Al-Ahsa, 31982 Kingdom of Saudi Arabia
| | - Manel Ben M’hadheb
- Unité de Recherche UR17ES30 “Génomique Biotechnologie et Stratégies Antivirales” (ViroBiotech), Institut Supérieur de Biotechnologie, Université de Monastir, BP74, Avenue Tahar Hadded, Monastir, 5000 Tunisia
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26
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Lau K, Dorigatti I, Miraldo M, Hauck K. SARIMA-modelled greater severity and mortality during the 2010/11 post-pandemic influenza season compared to the 2009 H1N1 pandemic in English hospitals. Int J Infect Dis 2021; 105:161-171. [PMID: 33548552 DOI: 10.1016/j.ijid.2021.01.070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 10/22/2022] Open
Abstract
OBJECTIVE The COVID-19 pandemic demonstrates the need for understanding pathways to healthcare demand, morbidity, and mortality of pandemic patients. We estimate H1N1 (1) hospitalization rates, (2) severity rates (length of stay, ventilation, pneumonia, and death) of those hospitalized, (3) mortality rates, and (4) time lags between infections and hospitalizations during the pandemic (June 2009 to March 2010) and post-pandemic influenza season (November 2010 to February 2011) in England. METHODS Estimates of H1N1 infections from a dynamic transmission model are combined with hospitalizations and severity using time series econometric analyses of administrative patient-level hospital data. RESULTS Hospitalization rates were 34% higher and severity rates of those hospitalized were 20%-90% higher in the post-pandemic period than the pandemic. Adults (45-64-years-old) had the highest ventilation and pneumonia hospitalization rates. Hospitalizations did not lag infection during the pandemic for the young (<24-years-old) but lagged by one or more weeks for all ages in the post-pandemic period. DISCUSSION The post-pandemic flu season exhibited heightened H1N1 severity, long after the pandemic was declared over. Policymakers should remain vigilant even after pandemics seem to have subsided. Analysis of administrative hospital data and epidemiological modelling estimates can provide valuable insights to inform responses to COVID-19 and future influenza and other disease pandemics.
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Affiliation(s)
- Krystal Lau
- Imperial College Business School: Department of Economics & Public Policy; Centre for Health Economics & Policy Innovation, London, United Kingdom SW7 2AZ.
| | - Ilaria Dorigatti
- Imperial College London: MRC Centre for Global Infectious Disease Analysis (MRC GIDA), Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, London, United Kingdom W2 1PG
| | - Marisa Miraldo
- Imperial College Business School: Department of Economics & Public Policy; Centre for Health Economics & Policy Innovation, London, United Kingdom SW7 2AZ
| | - Katharina Hauck
- Imperial College London: MRC Centre for Global Infectious Disease Analysis (MRC GIDA), Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, London, United Kingdom W2 1PG
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27
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Blumenkrantz DR, Mehoke T, Shaw-Saliba K, Powell H, Wohlgemuth N, Liu H, Macias E, Evans J, Lewis M, Medina R, Hardick J, Sauer LM, Dugas A, DuVal A, Lane AP, Gaydos C, Rothman R, Thielen P, Pekosz A. Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. Virus Evol 2021; 7:veab047. [PMID: 34131512 PMCID: PMC8197029 DOI: 10.1093/ve/veab047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The 2014-15 influenza season saw the emergence of an H3N2 antigenic drift variant that formed the 3C.2a HA clade. Whole viral genomes were sequenced from nasopharyngeal swabs of ninety-four patients with confirmed influenza A virus infection and primary human nasal epithelial cell cultures used to efficiently isolate H3N2 viruses. The isolates were classified by HA clade and the presence of a new set of co-selected mutations in NA (a glycosylation site, NAg+) and PB1-F2 (H75P). The NA and PB1-F2 mutations were present in a subset of clade 3C.2a viruses (NAg+F2P), which dominated during the subsequent influenza seasons. In human nasal epithelial cell cultures, a virus with the novel NAg+F2P genotype replicated less well compared with a virus with the parental genotype. Retrospective analyses of clinical data showed that NAg+F2P genotype viruses were associated with increased cough and shortness of breath in infected patients.
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Affiliation(s)
- Deena R Blumenkrantz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health,Laurel, MD, USA
| | - Thomas Mehoke
- Research and Exploratory Development Department, Johns Hopkins Applied Physics Laboratory, Laurel, MD, USA
| | - Kathryn Shaw-Saliba
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health,Laurel, MD, USA
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Harrison Powell
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health,Laurel, MD, USA
| | - Nicholas Wohlgemuth
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health,Laurel, MD, USA
| | - Hsuan Liu
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health,Laurel, MD, USA
| | - Elizabeth Macias
- Epidemiology Laboratory Service, United States Air Force School of Aerospace Medicine, Wright-Patterson Air Force Base, OH, USA
| | - Jared Evans
- Research and Exploratory Development Department, Johns Hopkins Applied Physics Laboratory, Laurel, MD, USA
| | - Mitra Lewis
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rebecca Medina
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Justin Hardick
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lauren M Sauer
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrea Dugas
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anna DuVal
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew P Lane
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Charlotte Gaydos
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Richard Rothman
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter Thielen
- Research and Exploratory Development Department, Johns Hopkins Applied Physics Laboratory, Laurel, MD, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health,Laurel, MD, USA
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28
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Trinh TTT, Duong BT, Nguyen ATV, Tuong HT, Hoang VT, Than DD, Nam S, Sung HW, Yun KJ, Yeo SJ, Park H. Emergence of Novel Reassortant H1N1 Avian Influenza Viruses in Korean Wild Ducks in 2018 and 2019. Viruses 2020; 13:v13010030. [PMID: 33375376 PMCID: PMC7823676 DOI: 10.3390/v13010030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 12/19/2020] [Accepted: 12/24/2020] [Indexed: 02/08/2023] Open
Abstract
Influenza A virus subtype H1N1 has caused global pandemics like the “Spanish flu” in 1918 and the 2009 H1N1 pandemic several times. H1N1 remains in circulation and survives in multiple animal sources, including wild birds. Surveillance during the winter of 2018–2019 in Korea revealed two H1N1 isolates in samples collected from wild bird feces: KNU18-64 (A/Greater white-fronted goose/South Korea/KNU18-64/2018(H1N1)) and WKU19-4 (A/wild bird/South Korea/WKU19-4/2019(H1N1)). Phylogenetic analysis indicated that M gene of KNU18-64(H1N1) isolate resembles that of the Alaskan avian influenza virus, whereas WKU19-4(H1N1) appears to be closer to the Mongolian virus. Molecular characterization revealed that they harbor the amino acid sequence PSIQRS↓GLF and are low-pathogenicity influenza viruses. In particular, the two isolates harbored three different mutation sites, indicating that they have different virulence characteristics. The mutations in the PB1-F2 and PA protein of WKU19-4(H1N1) indicate increasing polymerase activity. These results corroborate the kinetic growth data for WKU19-4 in MDCK cells: a dramatic increase in the viral titer after 12 h post-inoculation compared with that in the control group H1N1 (CA/04/09(pdm09)). The KNU18-64(H1N1) isolate carries mutations indicating an increase in mammal adaptation; this characterization was confirmed by the animal study in mice. The KNU18-64(H1N1) group showed the presence of viruses in the lungs at days 3 and 6 post-infection, with titers of 2.71 ± 0.16 and 3.71 ± 0.25 log10(TCID50/mL), respectively, whereas the virus was only detected in the WKU19-4(H1N1) group at day 6 post-infection, with a lower titer of 2.75 ± 0.51 log10(TCID50/mL). The present study supports the theory that there is a relationship between Korea and America with regard to reassortment to produce novel viral strains. Therefore, there is a need for increased surveillance of influenza virus circulation in free-flying and wild land-based birds in Korea, particularly with regard to Alaskan and Asian strains.
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Affiliation(s)
- Thuy-Tien Thi Trinh
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 570-749, Korea; (T.-T.T.T.); (B.T.D.); (A.T.V.N.); (H.T.T.); (V.T.H.); (D.D.T.)
| | - Bao Tuan Duong
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 570-749, Korea; (T.-T.T.T.); (B.T.D.); (A.T.V.N.); (H.T.T.); (V.T.H.); (D.D.T.)
| | - Anh Thi Viet Nguyen
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 570-749, Korea; (T.-T.T.T.); (B.T.D.); (A.T.V.N.); (H.T.T.); (V.T.H.); (D.D.T.)
| | - Hien Thi Tuong
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 570-749, Korea; (T.-T.T.T.); (B.T.D.); (A.T.V.N.); (H.T.T.); (V.T.H.); (D.D.T.)
| | - Vui Thi Hoang
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 570-749, Korea; (T.-T.T.T.); (B.T.D.); (A.T.V.N.); (H.T.T.); (V.T.H.); (D.D.T.)
| | - Duong Duc Than
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 570-749, Korea; (T.-T.T.T.); (B.T.D.); (A.T.V.N.); (H.T.T.); (V.T.H.); (D.D.T.)
| | - SunJeong Nam
- Division of EcoScience, Ewha University, Seoul 03760, Korea;
| | - Haan Woo Sung
- College of Veterinary Medicine, Kangwon National University, Chuncheon 200-701, Korea;
| | - Ki-Jung Yun
- Department of Pathology, School of Medicine, Wonkwang University, Iksan 570-749, Korea;
| | - Seon-Ju Yeo
- Department of Tropical Medicine and Parasitology, College of Medicine, Seoul National University, Seoul 03080, Korea
- Correspondence: (S.-J.Y.); (H.P.)
| | - Hyun Park
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 570-749, Korea; (T.-T.T.T.); (B.T.D.); (A.T.V.N.); (H.T.T.); (V.T.H.); (D.D.T.)
- Correspondence: (S.-J.Y.); (H.P.)
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29
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Soliman MS, Kamel MM, Alorabi JA, Mohamed NM, El-Kholy AA, Abdel-Moneim AS. Characterization and mutational analysis of haemagglutinin and neuraminidase of H3N2 and H1N1pdm09 human influenza A viruses in Egypt. Virusdisease 2020; 31:262-269. [PMID: 32837970 PMCID: PMC7268970 DOI: 10.1007/s13337-020-00609-8] [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: 04/23/2020] [Accepted: 05/26/2020] [Indexed: 11/17/2022] Open
Abstract
Seasonal influenza viruses constitute a major global concern. Currently, H3N2 and H1N1pdm09 are the commonly circulating influenza A viruses. The haemagglutin and neuraminidase genes of influenza A(H3N2) and A(H1N1)pdm09 viruses from Egyptian paediatric patients with respiratory distress were sequenced. Mutational analysis of all published sequences from Egypt was evolutionary tracked for both HA and NA genes. Phylogenetic analysis of H3N2 HA showed that the Egyptian strains belong to 3C2 subclade while Egyptian A(H1N1)pdm09 strains belong to 6B1 subclade. Some Egyptian A(H1N1)pdm09, 2013-2014, strains form a new subclade; 6B3. High score of mutations were recorded in HA of H1N1pdm09 but higher was recorded in H3N2 strains. These findings confirmed a high mutation rate of influenza A subtypes specially H3N2 strains.
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Affiliation(s)
- May S. Soliman
- Clinical Pathology Department, Faculty of Medicine, Cairo University, Giza, Egypt
| | - Mahmoud M. Kamel
- Clinical Pathology Department, National Cancer Institute, Cairo University, Giza, Egypt
| | - Jamal A. Alorabi
- Biology Department, College of Science, Taif University, Al-Taif, 21944 Saudi Arabia
| | - Nader M. Mohamed
- Department of Paediatrics and Neonatology, Al Ahrar Hospital, Zagazig, Egypt
- Department of Paediatrics and Neonatology, College of Medicine, Taif University, Al-Taif, 21944 Saudi Arabia
| | - Amani A. El-Kholy
- Clinical Pathology Department, Faculty of Medicine, Cairo University, Giza, Egypt
| | - Ahmed S. Abdel-Moneim
- Microbiology Department, College of Medicine, Taif University, Al-Taif, 21944 Saudi Arabia
- Virology Department, Faculty of Veterinary Medicine, Beni-Suef University, Beni Suef, 62511 Egypt
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30
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Kovacevic P, Matijasevic J, Dragic S, Zlojutro B, Gavrilovic S, Jandric M, Andrijevic A, Kovacevic T, Carapic V, Travar M, Preradovic L, Momcicevic D. Characteristics and outcomes of critically ill patients with influenza A (H1N1) in the Western Balkans during the 2019 post-pandemic season. Indian J Med Microbiol 2020; 38:415-420. [PMID: 33154256 DOI: 10.4103/ijmm.ijmm_20_169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Background This study looked at the characteristics and outcomes of critically ill patients with confirmed influenza A (H1N1) pdm09 infection in the Western Balkans in the post-pandemic period. Materials and Methods This retrospective observational study of medical records and associated data collected during the post-pandemic period included all mechanically ventilated adult patients of two university-affiliated hospitals of the Western Balkans between 1 January and 31 March 2019 who had influenza A (H1N1) pdm09 infection confirmed by real-time reverse transcriptase-polymerase chain reaction from nasopharyngeal swab specimens and respiratory secretions. Results The study included 89 patients, 49 males (55.1%), aged 56.09 ± 12.64 years. The median time from shift from hospital time to intensive care unit was 1 day (range: 1-2). In the post-pandemic period, cases observed in this study were found to have the following comorbidities: cardiovascular diseases in 44 (49.4%) patients and diabetes in 21 (23.6%) patients. Thirty-one patients (34.8%) in this study were obese. All 89 patients (100%) experienced some degree of acute respiratory distress syndrome, and 39 (44%) had multiorgan failure. Eighty-three patients (93%) were intubated and mechanically ventilated, 6 (7%) received non-invasive mechanical ventilation, 12 (13%) were treated with vvECMO and 36 (40%) received renal replacement therapy. Vasoactive support was needed by 56 (63%) patients. The median duration of mechanical ventilation was 9 (6-15.5) days. The hospital mortality rate was 44%. Conclusion Critically ill patients with confirmed influenza A (H1N1) pdm09 infection in the post-pandemic season were older, required vasoactive drugs more often, and there was a trend of higher survival compared to H1N1 infection patients in the previous pandemic seasons.
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Affiliation(s)
- Pedja Kovacevic
- Medical Intensive Care Unit, University Clinical Center of Republika Srpska; Faculty of Medicine, University of Banja Luka, Bosnia and Herzegovina, Novi Sad, Serbia
| | - Jovan Matijasevic
- Institute for Pulmonary Diseases, Medical School University of Novi Sad, Novi Sad, Serbia
| | - Sasa Dragic
- Medical Intensive Care Unit, University Clinical Center of Republika Srpska, Novi Sad, Serbia
| | - Biljana Zlojutro
- Medical Intensive Care Unit, University Clinical Center of Republika Srpska, Novi Sad, Serbia
| | - Srdjan Gavrilovic
- Institute for Pulmonary Diseases, Medical School University of Novi Sad, Novi Sad, Serbia
| | - Milka Jandric
- Medical Intensive Care Unit, University Clinical Center of Republika Srpska, Novi Sad, Serbia
| | - Ana Andrijevic
- Institute for Pulmonary Diseases, Medical School University of Novi Sad, Novi Sad, Serbia
| | - Tijana Kovacevic
- Faculty of Medicine, University of Banja Luka, Bosnia and Herzegovina; Department of Pharmacy, University Clinical Center of Republika Srpska, Novi Sad, Serbia
| | - Vladimir Carapic
- Institute for Pulmonary Diseases, Medical School University of Novi Sad, Novi Sad, Serbia
| | - Maja Travar
- Faculty of Medicine, University of Banja Luka, Bosnia and Herzegovina; Department of Microbiology, University Clinical Center of Republika Srpska, Novi Sad, Serbia
| | - Ljubisa Preradovic
- Faculty of Medicine, University of Banja Luka, Bosnia and Herzegovina, Novi Sad, Serbia
| | - Danica Momcicevic
- Medical Intensive Care Unit, University Clinical Center of Republika Srpska, Novi Sad, Serbia
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Bankuru SV, Kossol S, Hou W, Mahmoudi P, Rychtář J, Taylor D. A game-theoretic model of Monkeypox to assess vaccination strategies. PeerJ 2020; 8:e9272. [PMID: 32607280 PMCID: PMC7316080 DOI: 10.7717/peerj.9272] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/11/2020] [Indexed: 01/05/2023] Open
Abstract
Monkeypox (MPX) is a zoonotic disease similar to smallpox. Its fatality rate is about 11% and it is endemic to the Central and West African countries. In this paper, we analyze a compartmental model of MPX dynamics. Our goal is to see whether MPX can be controlled and eradicated by voluntary vaccinations. We show that there are three equilibria—disease free, fully endemic and previously neglected semi-endemic (with disease existing only among humans). The existence of semi-endemic equilibrium has severe implications should the MPX virus mutate to increased viral fitness in humans. We find that MPX is controllable and can be eradicated in a semi-endemic equilibrium by vaccination. However, in a fully endemic equilibrium, MPX cannot be eradicated by vaccination alone.
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Affiliation(s)
- Sri Vibhaav Bankuru
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Samuel Kossol
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, VA, United States of America
| | - William Hou
- Department of Kinesiology and Health Sciences, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Parsa Mahmoudi
- Department of Biology, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Jan Rychtář
- Department of Mathematics and Applied Mathematics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Dewey Taylor
- Department of Mathematics and Applied Mathematics, Virginia Commonwealth University, Richmond, VA, United States of America
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Swine ANP32A Supports Avian Influenza Virus Polymerase. J Virol 2020; 94:JVI.00132-20. [PMID: 32269123 PMCID: PMC7307101 DOI: 10.1128/jvi.00132-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 03/23/2020] [Indexed: 12/15/2022] Open
Abstract
Avian influenza viruses can jump from wild birds and poultry into mammalian species such as humans or swine, but they only continue to transmit if they accumulate mammalian adapting mutations. Pigs appear uniquely susceptible to both avian and human strains of influenza and are often described as virus “mixing vessels.” In this study, we describe how a host factor responsible for regulating virus replication, ANP32A, is different between swine and humans. Swine ANP32A allows a greater range of influenza viruses, specifically those from birds, to replicate. It does this by binding the virus polymerase more tightly than the human version of the protein. This work helps to explain the unique properties of swine as mixing vessels. Avian influenza viruses occasionally infect and adapt to mammals, including humans. Swine are often described as “mixing vessels,” being susceptible to both avian- and human-origin viruses, which allows the emergence of novel reassortants, such as the precursor to the 2009 H1N1 pandemic. ANP32 proteins are host factors that act as influenza virus polymerase cofactors. In this study, we describe how swine ANP32A, uniquely among the mammalian ANP32 proteins tested, supports the activity of avian-origin influenza virus polymerases and avian influenza virus replication. We further show that after the swine-origin influenza virus emerged in humans and caused the 2009 pandemic, it evolved polymerase gene mutations that enabled it to more efficiently use human ANP32 proteins. We map the enhanced proviral activity of swine ANP32A to a pair of amino acids, 106 and 156, in the leucine-rich repeat and central domains and show these mutations enhance binding to influenza virus trimeric polymerase. These findings help elucidate the molecular basis for the mixing vessel trait of swine and further our understanding of the evolution and ecology of viruses in this host. IMPORTANCE Avian influenza viruses can jump from wild birds and poultry into mammalian species such as humans or swine, but they only continue to transmit if they accumulate mammalian adapting mutations. Pigs appear uniquely susceptible to both avian and human strains of influenza and are often described as virus “mixing vessels.” In this study, we describe how a host factor responsible for regulating virus replication, ANP32A, is different between swine and humans. Swine ANP32A allows a greater range of influenza viruses, specifically those from birds, to replicate. It does this by binding the virus polymerase more tightly than the human version of the protein. This work helps to explain the unique properties of swine as mixing vessels.
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33
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Singanayagam A, Zhou J, Elderfield RA, Frise R, Ashcroft J, Galiano M, Miah S, Nicolaou L, Barclay WS. Characterising viable virus from air exhaled by H1N1 influenza-infected ferrets reveals the importance of haemagglutinin stability for airborne infectivity. PLoS Pathog 2020; 16:e1008362. [PMID: 32097448 PMCID: PMC7059951 DOI: 10.1371/journal.ppat.1008362] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 03/06/2020] [Accepted: 01/28/2020] [Indexed: 12/18/2022] Open
Abstract
The transmissibility and pandemic potential of influenza viruses depends on their ability to efficiently replicate and be released from an infected host, retain viability as they pass through the environment, and then initiate infection in the next host. There is a significant gap in knowledge about viral properties that enable survival of influenza viruses between hosts, due to a lack of experimental methods to reliably isolate viable virus from the air. Using a novel technique, we isolate and characterise infectious virus from droplets emitted by 2009 pandemic H1N1-infected ferrets. We demonstrate that infectious virus is predominantly released early after infection. A virus containing a mutation destabilising the haemagglutinin (HA) surface protein displayed reduced survival in air. Infectious virus recovered from droplets exhaled by ferrets inoculated with this virus contained mutations that conferred restabilisation of HA, indicating the importance of influenza HA stability for between-host survival. Using this unique approach can improve knowledge about the determinants and mechanisms of influenza transmissibility and ultimately could be applied to studies of airborne virus exhaled from infected people. Influenza viruses can transmit through the air between two hosts. For virus to successfully transmit through the air, it must be exhaled from an infected donor in sufficient quantities and retain infectiousness in the air. These aspects of transmission are poorly understood due to a paucity of methods for quantifying infectious virus from airborne particles. Using a novel technique of virus plaque isolation from depositing airborne droplets, we show that ferrets infected with an airborne transmissible influenza virus exhaled a peak of infectious virus early after infection. We demonstrate the importance of virion stability for the retention of infectivity as virus travels through the air. Our findings highlight the fate of infectious virus outside the respiratory tract as an important parameter for understanding influenza transmission.
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Affiliation(s)
- Anika Singanayagam
- Department of Medicine, St. Marys Campus, Imperial College, London, United Kingdom
| | - Jie Zhou
- Department of Medicine, St. Marys Campus, Imperial College, London, United Kingdom
| | - Ruth A. Elderfield
- Department of Medicine, St. Marys Campus, Imperial College, London, United Kingdom
| | - Rebecca Frise
- Department of Medicine, St. Marys Campus, Imperial College, London, United Kingdom
| | - Jonathan Ashcroft
- Department of Medicine, St. Marys Campus, Imperial College, London, United Kingdom
| | - Monica Galiano
- Virus Reference Department, Public Health England, Colindale, United Kingdom
| | - Shahjahan Miah
- Virus Reference Department, Public Health England, Colindale, United Kingdom
| | - Laura Nicolaou
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Wendy S. Barclay
- Department of Medicine, St. Marys Campus, Imperial College, London, United Kingdom
- * E-mail:
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34
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Co-circulation of influenza A(H1N1), A(H3N2), B(Yamagata) and B(Victoria) during the 2017-2018 influenza season in Zhejiang Province, China. Epidemiol Infect 2020; 148:e296. [PMID: 32054554 PMCID: PMC7770466 DOI: 10.1017/s0950268820000412] [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] [Indexed: 12/19/2022] Open
Abstract
Influenza is a major human respiratory pathogen. Due to the high levels of influenza-like illness (ILI) in Zhejiang, China, the control and prevention of influenza was challenging during the 2017-2018 season. To identify the clinical spectrum of illness related to influenza and characterise the circulating influenza virus strains during this period, the characteristics of ILI were studied. Viral sequencing and phylogenetic analyses were conducted to investigate the virus types, substitutions at the amino acid level and phylogenetic relationships between sequences. This study has shown that the 2017/18 influenza season was characterised by the co-circulation of influenza A (H1N1) pdm09, A (H3N2) and B viruses (both Yamagata and Victoria lineage). From week 36 of 2017 to week 12 of 2018, ILI cases accounted for 5.58% of the total number of outpatient and emergency patient visits at the surveillance sites. Several amino acid substitutions were detected. Vaccination mismatch may be a potential reason for the high percentage of ILI. Furthermore, it is likely that multiple viral introductions played a role in the endemic co-circulation of influenza in Zhejiang, China. More detailed information regarding the molecular epidemiology of influenza should be included in long-term influenza surveillance.
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35
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He WT, Wang L, Zhao Y, Wang N, Li G, Veit M, Bi Y, Gao GF, Su S. Adaption and parallel evolution of human-isolated H5 avian influenza viruses. J Infect 2020; 80:630-638. [PMID: 32007525 DOI: 10.1016/j.jinf.2020.01.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 01/13/2020] [Accepted: 01/18/2020] [Indexed: 12/12/2022]
Abstract
Avian-to-human transmission of highly pathogenic avian influenza viruses (HPAIV) and their subsequent adaptation to humans are of great concern to public health. Surveillance and early warning of AIVs with the potential to infect humans and pandemic potential is crucial. In this study, we determined whether adaptive evolution occurred in human-isolated H5 viruses. We evaluated all available genomes of H5N1 and H5N6 avian influenza A virus. Firstly, we systematically identified several new mutations in H5 AIV that might be associated with human adaptation using a combination of novel comparative phylogenetic methods and structural analysis. Some changes are the result of parallel evolution, further demonstrating their importance. In total, we identified 102 adaptive evolution sites in eight genes. Some residues had been previously identified, such as 227 in HA and 627 in PB2, while others have not been reported so far. Ten sites from four genes evolved in parallel but no obvious positive selection was detected. Our study suggests that during infection of humans, H5 viruses evolved to adapt to their new host environment and that the sites of adaptive/parallel evolution might play a role in crossing the species barrier and are the response to new selection pressure. The results provide insight to implement early detection systems for transitional stages in H5 AIV evolution before its potential adaptation for humans. Author summary line The prerequisite of surveillance and early warning of avian influenza viruses with the potential to infect humans depends on the identification of human-adaptation related mutations. In this study, we used a novel approach combining both phylogenetic and structural analysis to identify possible human-adaptation related mutations in H5 AIVs. Previous studies reported human-adaptation related mutations and some novel mutations exhibiting parallel evolution. Our result provides new insights into how AIVs adapt to humans by point mutations.
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Affiliation(s)
- Wan-Ting He
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Liang Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuhui Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ningning Wang
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Gairu Li
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Michael Veit
- Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Robert-von-OstertagStraβe 7-13, Berlin, Germany
| | - Yuhai Bi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - George F Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuo Su
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.
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Fu Y, Dürrwald R, Meng F, Tong J, Wu NH, Su A, Yin X, Haas L, Schmidtke M, Zell R, Krumbholz A, Herrler G. Infection Studies in Pigs and Porcine Airway Epithelial Cells Reveal an Evolution of A(H1N1)pdm09 Influenza A Viruses Toward Lower Virulence. J Infect Dis 2020; 219:1596-1604. [PMID: 30776304 PMCID: PMC7107423 DOI: 10.1093/infdis/jiy719] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 01/31/2018] [Indexed: 12/15/2022] Open
Abstract
We analyzed the virulence of pandemic H1N1 2009 influenza A viruses in vivo and in vitro. Selected viruses isolated in 2009, 2010, 2014, and 2015 were assessed using an aerosol-mediated high-dose infection model for pigs as well as air-liquid interface cultures of differentiated airway epithelial cells. Using a dyspnea score, rectal temperature, lung lesions, and viral load in the lung as parameters, the strains from 2014–2015 were significantly less virulent than the strains isolated in 2009–2010. In vitro, the viruses from 2009–2010 also differed from the 2014–2015 viruses by increased release of infectious virus, a more pronounced loss of ciliated cells, and a reduced thickness of the epithelial cell layer. Our in vivo and in vitro results reveal an evolution of A(H1N1)pdm09 viruses toward lower virulence. Our in vitro culture system can be used to predict the virulence of influenza viruses.
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Affiliation(s)
- Yuguang Fu
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Germany.,State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences
| | - Ralf Dürrwald
- Division of Experimental Virology, Department for Medical Microbiology, Jena University Hospital, Friedrich Schiller University, Germany
| | - Fandan Meng
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Germany.,State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences
| | - Jie Tong
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Germany
| | - Nai-Huei Wu
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Germany
| | - Ang Su
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Germany
| | - Xiangping Yin
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences
| | - Ludwig Haas
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Germany
| | - Michaela Schmidtke
- Division of Experimental Virology, Department for Medical Microbiology, Jena University Hospital, Friedrich Schiller University, Germany
| | - Roland Zell
- Division of Experimental Virology, Department for Medical Microbiology, Jena University Hospital, Friedrich Schiller University, Germany
| | - Andi Krumbholz
- Institute of Infection Medicine, Kiel University, Germany
| | - Georg Herrler
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Germany
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37
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Jha A, Dunning J, Tunstall T, Thwaites RS, Hoang LT, Kon OM, Zambon MC, Hansel TT, Openshaw PJ. Patterns of systemic and local inflammation in patients with asthma hospitalised with influenza. Eur Respir J 2019; 54:13993003.00949-2019. [PMID: 31391224 DOI: 10.1183/13993003.00949-2019] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/25/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Patients with asthma are at risk of hospitalisation with influenza, but the reasons for this predisposition are unknown. STUDY SETTING A prospective observational study of adults with PCR-confirmed influenza in 11 UK hospitals, measuring nasal, nasopharyngeal and systemic immune mediators and whole-blood gene expression. RESULTS Of 133 admissions, 40 (30%) had previous asthma; these were more often female (70% versus 38.7%, OR 3.69, 95% CI 1.67-8.18; p=0.0012), required less mechanical ventilation (15% versus 37.6%, Chi-squared 6.78; p=0.0338) and had shorter hospital stays (mean 8.3 versus 15.3 days, p=0.0333) than those without. In patients without asthma, severe outcomes were more frequent in those given corticosteroids (OR 2.63, 95% CI 1.02-6.96; p=0.0466) or presenting >4 days after disease onset (OR 5.49, 95% CI 2.28-14.03; p=0.0002). Influenza vaccination in at-risk groups (including asthma) were lower than intended by national policy and the early use of antiviral medications were less than optimal. Mucosal immune responses were equivalent between groups. Those with asthma had higher serum interferon (IFN)-α, but lower serum tumour necrosis factor, interleukin (IL)-5, IL-6, CXCL8, CXCL9, IL-10, IL-17 and CCL2 levels (all p<0.05); both groups had similar serum IL-13, total IgE, periostin and blood eosinophil gene expression levels. Asthma diagnosis was unrelated to viral load, IFN-α, IFN-γ, IL-5 or IL-13 levels. CONCLUSIONS Asthma is common in those hospitalised with influenza, but may not represent classical type 2-driven disease. Those admitted with influenza tend to be female with mild serum inflammatory responses, increased serum IFN-α levels and good clinical outcomes.
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Affiliation(s)
- Akhilesh Jha
- National Heart and Lung Institute, Imperial College London, St Mary's Campus, London, UK.,Dept of Medicine, University of Cambridge, Cambridge, UK
| | - Jake Dunning
- National Heart and Lung Institute, Imperial College London, St Mary's Campus, London, UK.,Public Health England (formerly Health Protection Agency), London, UK
| | - Tanushree Tunstall
- National Heart and Lung Institute, Imperial College London, St Mary's Campus, London, UK
| | - Ryan S Thwaites
- National Heart and Lung Institute, Imperial College London, St Mary's Campus, London, UK
| | - Long T Hoang
- National Heart and Lung Institute, Imperial College London, St Mary's Campus, London, UK
| | | | - Onn Min Kon
- National Heart and Lung Institute, Imperial College London, St Mary's Campus, London, UK
| | - Maria C Zambon
- Public Health England (formerly Health Protection Agency), London, UK
| | - Trevor T Hansel
- National Heart and Lung Institute, Imperial College London, St Mary's Campus, London, UK
| | - Peter J Openshaw
- National Heart and Lung Institute, Imperial College London, St Mary's Campus, London, UK
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Poux C, Dondalska A, Bergenstråhle J, Pålsson S, Contreras V, Arasa C, Järver P, Albert J, Busse DC, LeGrand R, Lundeberg J, Tregoning JS, Spetz AL. A Single-Stranded Oligonucleotide Inhibits Toll-Like Receptor 3 Activation and Reduces Influenza A (H1N1) Infection. Front Immunol 2019; 10:2161. [PMID: 31572376 PMCID: PMC6751283 DOI: 10.3389/fimmu.2019.02161] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/28/2019] [Indexed: 12/18/2022] Open
Abstract
The initiation of an immune response is dependent on the activation and maturation of dendritic cells after sensing pathogen associated molecular patterns by pattern recognition receptors. However, the response needs to be balanced as excessive pro-inflammatory cytokine production in response to viral or stress-induced pattern recognition receptor signaling has been associated with severe influenza A virus (IAV) infection. Here, we use an inhibitor of Toll-like receptor (TLR)3, a single-stranded oligonucleotide (ssON) with the capacity to inhibit certain endocytic routes, or a TLR3 agonist (synthetic double-stranded RNA PolyI:C), to evaluate modulation of innate responses during H1N1 IAV infection. Since IAV utilizes cellular endocytic machinery for viral entry, we also assessed ssON's capacity to affect IAV infection. We first show that IAV infected human monocyte-derived dendritic cells (MoDC) were unable to up-regulate the co-stimulatory molecules CD80 and CD86 required for T cell activation. Exogenous TLR3 stimulation did not overcome the IAV-mediated inhibition of co-stimulatory molecule expression in MoDC. However, TLR3 stimulation using PolyI:C led to an augmented pro-inflammatory cytokine response. We reveal that ssON effectively inhibited PolyI:C-mediated pro-inflammatory cytokine production in MoDC, notably, ssON treatment maintained an interferon response induced by IAV infection. Accordingly, RNAseq analyses revealed robust up-regulation of interferon-stimulated genes in IAV cultures treated with ssON. We next measured reduced IAV production in MoDC treated with ssON and found a length requirement for its anti-viral activity, which overlapped with its capacity to inhibit uptake of PolyI:C. Hence, in cases wherein an overreacting TLR3 activation contributes to IAV pathogenesis, ssON can reduce this signaling pathway. Furthermore, concomitant treatment with ssON and IAV infection in mice resulted in maintained weight and reduced viral load in the lungs. Therefore, extracellular ssON provides a mechanism for immune regulation of TLR3-mediated responses and suppression of IAV infection in vitro and in vivo in mice.
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Affiliation(s)
- Candice Poux
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Aleksandra Dondalska
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Joseph Bergenstråhle
- Science for Life Laboratory, Department of Gene Technology, Royal Institute of Technology, Stockholm, Sweden
| | - Sandra Pålsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Vanessa Contreras
- CEA, UMR1184, IDMIT Department, Institut de Biologie François Jacob, DRF, Fontenay-aux-Roses, France
| | - Claudia Arasa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Peter Järver
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - David C Busse
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Roger LeGrand
- CEA, UMR1184, IDMIT Department, Institut de Biologie François Jacob, DRF, Fontenay-aux-Roses, France
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, Royal Institute of Technology, Stockholm, Sweden
| | - John S Tregoning
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Anna-Lena Spetz
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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39
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Clohisey S, Baillie JK. Host susceptibility to severe influenza A virus infection. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2019; 23:303. [PMID: 31488196 PMCID: PMC6729070 DOI: 10.1186/s13054-019-2566-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/13/2019] [Indexed: 11/30/2022]
Abstract
Most people exposed to a new flu virus do not notice any symptoms. A small minority develops critical illness. Some of this extremely broad variation in susceptibility is explained by the size of the initial inoculum or the influenza exposure history of the individual; some is explained by generic host factors, such as frailty, that decrease resilience following any systemic insult. Some demographic factors (pregnancy, obesity, and advanced age) appear to confer a more specific susceptibility to severe illness following infection with influenza viruses. As with other infectious diseases, a substantial component of susceptibility is determined by host genetics. Several genetic susceptibility variants have now been reported with varying levels of evidence. Susceptible hosts may have impaired intracellular controls of viral replication (e.g. IFITM3, TMPRS22 variants), defective interferon responses (e.g. GLDC, IRF7/9 variants), or defects in cell-mediated immunity with increased baseline levels of systemic inflammation (obesity, pregnancy, advanced age). These mechanisms may explain the prolonged viral replication reported in critically ill patients with influenza: patients with life-threatening disease are, by definition, abnormal hosts. Understanding these molecular mechanisms of susceptibility may in the future enable the design of host-directed therapies to promote resilience.
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Affiliation(s)
- Sara Clohisey
- Division of Genetics and Genomics, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - John Kenneth Baillie
- Division of Genetics and Genomics, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK. .,Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK.
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40
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Sharma V, Sharma M, Dhull D, Kaushik S, Kaushik S. Phylogenetic analysis of the hemagglutinin gene of influenza A(H1N1)pdm09 and A(H3N2) virus isolates from Haryana, India. Virusdisease 2019; 30:336-343. [DOI: 10.1007/s13337-019-00532-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/03/2019] [Indexed: 10/26/2022] Open
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Influenza Virus with Increased pH of Hemagglutinin Activation Has Improved Replication in Cell Culture but at the Cost of Infectivity in Human Airway Epithelium. J Virol 2019; 93:JVI.00058-19. [PMID: 31189708 PMCID: PMC6694820 DOI: 10.1128/jvi.00058-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/02/2019] [Indexed: 01/09/2023] Open
Abstract
The pH stability of the hemagglutinin surface protein varies between different influenza strains and subtypes and can affect the virus’ ability to replicate and transmit. Here, we demonstrate a delicate balance that the virus strikes within and without the target cell. We show that a pH-stable hemagglutinin enables a human influenza virus to replicate more effectively in human airway cells and mouse lungs by facilitating virus survival in the extracellular environment of the upper respiratory tract. Conversely, after entering target cells, being more pH stable confers a relative disadvantage, resulting in less efficient delivery of the viral genome to the host cell nucleus. Since the balance we describe will be affected differently in different host environments, it may restrict a virus’ ability to cross species. In addition, our findings imply that different influenza viruses may show variation in how well they are controlled by antiviral strategies targeting pH-dependent steps in the virus replication cycle. Pandemic H1N1 (pH1N1) influenza virus emerged from swine in 2009 with an adequate capability to infect and transmit between people. In subsequent years, it has circulated as a seasonal virus and evolved further human-adapting mutations. Mutations in the hemagglutinin (HA) stalk that increase pH stability have been associated with human adaptation and airborne transmission of pH1N1 virus. Yet, our understanding of how pH stability impacts virus-host interactions is incomplete. Here, using recombinant viruses with point mutations that alter the pH stability of pH1N1 HA, we found distinct effects on virus phenotypes in different experimental models. Increased pH sensitivity enabled viruses to uncoat in endosomes more efficiently, manifesting as increased replication rate in typical continuous cell cultures under single-cycle conditions. A more acid-labile HA also conferred a small reduction in sensitivity to antiviral therapeutics that act at the pH-sensitive HA fusion step. Conversely, in primary human airway epithelium cultured at the air-liquid interface, increased pH sensitivity attenuated multicycle viral replication by compromising virus survival in the extracellular microenvironment. In a mouse model of influenza pathogenicity, there was an optimum HA activation pH, and viruses with either more- or less-pH-stable HA were less virulent. Opposing pressures inside and outside the host cell that determine pH stability may influence zoonotic potential. The distinct effects that changes in pH stability exert on viral phenotypes underscore the importance of using the most appropriate systems for assessing virus titer and fitness, which has implications for vaccine manufacture, antiviral drug development, and pandemic risk assessment. IMPORTANCE The pH stability of the hemagglutinin surface protein varies between different influenza strains and subtypes and can affect the virus’ ability to replicate and transmit. Here, we demonstrate a delicate balance that the virus strikes within and without the target cell. We show that a pH-stable hemagglutinin enables a human influenza virus to replicate more effectively in human airway cells and mouse lungs by facilitating virus survival in the extracellular environment of the upper respiratory tract. Conversely, after entering target cells, being more pH stable confers a relative disadvantage, resulting in less efficient delivery of the viral genome to the host cell nucleus. Since the balance we describe will be affected differently in different host environments, it may restrict a virus’ ability to cross species. In addition, our findings imply that different influenza viruses may show variation in how well they are controlled by antiviral strategies targeting pH-dependent steps in the virus replication cycle.
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Hussain S, Turnbull ML, Pinto RM, McCauley JW, Engelhardt OG, Digard P. Segment 2 from influenza A(H1N1) 2009 pandemic viruses confers temperature-sensitive haemagglutinin yield on candidate vaccine virus growth in eggs that can be epistatically complemented by PB2 701D. J Gen Virol 2019; 100:1079-1092. [PMID: 31169484 DOI: 10.1099/jgv.0.001279] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Candidate vaccine viruses (CVVs) for seasonal influenza A virus are made by reassortment of the antigenic virus with an egg-adapted strain, typically A/Puerto Rico/8/34 (PR8). Many 2009 A(H1N1) pandemic (pdm09) high-growth reassortants (HGRs) selected this way contain pdm09 segment 2 in addition to the antigenic genes. To investigate this, we made CVV mimics by reverse genetics (RG) that were either 6 : 2 or 5 : 3 reassortants between PR8 and two pdm09 strains, A/California/7/2009 (Cal7) and A/England/195/2009, differing in the source of segment 2. The 5 : 3 viruses replicated better in MDCK-SIAT1 cells than the 6 : 2 viruses, but the 6 : 2 CVVs gave higher haemagglutinin (HA) antigen yields from eggs. This unexpected phenomenon reflected temperature sensitivity conferred by pdm09 segment 2, as the egg HA yields of the 5 : 3 viruses improved substantially when viruses were grown at 35 °C compared with 37.5 °C, whereas the 6 : 2 virus yields did not. However, the authentic 5 : 3 pdm09 HGRs, X-179A and X-181, were not markedly temperature sensitive despite their PB1 sequences being identical to that of Cal7, suggesting compensatory mutations elsewhere in the genome. Sequence comparisons of the PR8-derived backbone genes identified polymorphisms in PB2, NP, NS1 and NS2. Of these, PB2 N701D affected the temperature dependence of viral transcription and, furthermore, improved and drastically reduced the temperature sensitivity of the HA yield from the 5 : 3 CVV mimic. We conclude that the HA yield of pdm09 CVVs can be affected by an epistatic interaction between PR8 PB2 and pdm09 PB1, but that this can be minimized by ensuring that the backbones used for vaccine manufacture in eggs contain PB2 701D.
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Affiliation(s)
- Saira Hussain
- 1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK.,2 The Francis Crick Institute, London, NW1 1AT, UK
| | - Matthew L Turnbull
- 1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Rute M Pinto
- 1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | | | - Othmar G Engelhardt
- 3 National Institute for Biological Standards and Control, South Mimms, Potters Bar, Hertfordshire, EN6 3QG, UK
| | - Paul Digard
- 1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK
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Klingen TR, Loers J, Stanelle-Bertram S, Gabriel G, McHardy AC. Structures and functions linked to genome-wide adaptation of human influenza A viruses. Sci Rep 2019; 9:6267. [PMID: 31000776 PMCID: PMC6472403 DOI: 10.1038/s41598-019-42614-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/27/2019] [Indexed: 11/12/2022] Open
Abstract
Human influenza A viruses elicit short-term respiratory infections with considerable mortality and morbidity. While H3N2 viruses circulate for more than 50 years, the recent introduction of pH1N1 viruses presents an excellent opportunity for a comparative analysis of the genome-wide evolutionary forces acting on both subtypes. Here, we inferred patches of sites relevant for adaptation, i.e. being under positive selection, on eleven viral protein structures, from all available data since 1968 and correlated these with known functional properties. Overall, pH1N1 have more patches than H3N2 viruses, especially in the viral polymerase complex, while antigenic evolution is more apparent for H3N2 viruses. In both subtypes, NS1 has the highest patch and patch site frequency, indicating that NS1-mediated viral attenuation of host inflammatory responses is a continuously intensifying process, elevated even in the longtime-circulating subtype H3N2. We confirmed the resistance-causing effects of two pH1N1 changes against oseltamivir in NA activity assays, demonstrating the value of the resource for discovering functionally relevant changes. Our results represent an atlas of protein regions and sites with links to host adaptation, antiviral drug resistance and immune evasion for both subtypes for further study.
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MESH Headings
- Drug Resistance, Viral/genetics
- Evolution, Molecular
- Genome, Viral/genetics
- 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, Human/genetics
- Influenza, Human/pathology
- Influenza, Human/virology
- Oseltamivir/therapeutic use
- Respiratory Tract Infections/genetics
- Respiratory Tract Infections/virology
- Viral Nonstructural Proteins/genetics
- Virus Replication/genetics
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Affiliation(s)
- Thorsten R Klingen
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research (HZI), Braunschweig, Germany
| | - Jens Loers
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research (HZI), Braunschweig, Germany
| | | | - Gülsah Gabriel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- University of Veterinary Medicine, Hannover, Germany
| | - Alice C McHardy
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research (HZI), Braunschweig, Germany.
- German Center for Infection Research (DZIF), Braunschweig, Germany.
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44
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Lesch M, Luckner M, Meyer M, Weege F, Gravenstein I, Raftery M, Sieben C, Martin-Sancho L, Imai-Matsushima A, Welke RW, Frise R, Barclay W, Schönrich G, Herrmann A, Meyer TF, Karlas A. RNAi-based small molecule repositioning reveals clinically approved urea-based kinase inhibitors as broadly active antivirals. PLoS Pathog 2019; 15:e1007601. [PMID: 30883607 PMCID: PMC6422253 DOI: 10.1371/journal.ppat.1007601] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 01/29/2019] [Indexed: 12/13/2022] Open
Abstract
Influenza viruses (IVs) tend to rapidly develop resistance to virus-directed vaccines and common antivirals targeting pathogen determinants, but novel host-directed approaches might preclude resistance development. To identify the most promising cellular targets for a host-directed approach against influenza, we performed a comparative small interfering RNA (siRNA) loss-of-function screen of IV replication in A549 cells. Analysis of four different IV strains including a highly pathogenic avian H5N1 strain, an influenza B virus (IBV) and two human influenza A viruses (IAVs) revealed 133 genes required by all four IV strains. According to gene enrichment analyses, these strain-independent host genes were particularly enriched for nucleocytoplasmic trafficking. In addition, 360 strain-specific genes were identified with distinct patterns of usage for IAVs versus IBV and human versus avian IVs. The strain-independent host genes served to define 43 experimental and otherwise clinically approved drugs, targeting reportedly fourteen of the encoded host factors. Amongst the approved drugs, the urea-based kinase inhibitors (UBKIs) regorafenib and sorafenib exhibited a superior therapeutic window of high IV antiviral activity and low cytotoxicity. Both UBKIs appeared to block a cell signaling pathway involved in IV replication after internalization, yet prior to vRNP uncoating. Interestingly, both compounds were active also against unrelated viruses including cowpox virus (CPXV), hantavirus (HTV), herpes simplex virus 1 (HSV1) and vesicular stomatitis virus (VSV) and showed antiviral efficacy in human primary respiratory cells. An in vitro resistance development analysis for regorafenib failed to detect IV resistance development against this drug. Taken together, the otherwise clinically approved UBKIs regorafenib and sorafenib possess high and broad-spectrum antiviral activity along with substantial robustness against resistance development and thus constitute attractive host-directed drug candidates against a range of viral infections including influenza. Conventional medications against influenza infections, including vaccination and antiviral drug therapy, are targeted against viral determinants–an approach collectively referred to as pathogen-directed. However, influenza viruses mutate fast and quickly develop resistance to these pathogen-directed treatments. An alternative, yet not well established, is to block host cellular molecules required by the virus to successfully multiply. Such a host-directed approach is anticipated to be more robust against the development of drug resistance. This notion is founded on the different modes of action of the two principal approaches: Virus-directed therapeutics target the virus itself. Thus, just a single mutation could abrogate sensitivity to a virus-directed therapeutic. In contrast, it is unlikely that viruses can easily circumvent a pharmacological blockage of a cellular factor by means of just a few mutations. Instead, the virus needs to either exploit an immediate parallel cellular pathway or adjust its replication cycle to a different cellular factor–the latter being a process likely to require multiple mutations, if possible at all. To identify the most promising targets for a host-directed therapy, we performed a small interfering RNA (siRNA) screen with four different influenza virus strains using a lung epithelial cell line. Subsequently, we tested a series of drugs, specific for the products of the genes that are required for replication of all four influenza virus strains tested. Regorafenib and sorafenib, two chemically related urea-based kinase inhibitors already clinically approved for cancer treatment, turned out to be effective inhibitors of all influenza viruses and displayed low cytotoxicity. These drugs blocked viral replication at an early stage of the life cycle not only in cell lines but also in human primary respiratory cells. Moreover, these drugs exhibited high efficacy even against unrelated viruses. In addition, no development of resistance was observed against regorafenib, which was used in an in vitro assay representatively of urea-based kinase inhibitors. Our results suggest that regorafenib and sorafenib are promising drug candidates for a host-directed therapy of influenza and other viral infections.
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Affiliation(s)
- Markus Lesch
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
- Steinbeis Innovation Center for Systems Biomedicine, Falkensee, Germany
| | - Madlen Luckner
- Group of Molecular Biophysics, Department of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Michael Meyer
- Steinbeis Innovation Center for Systems Biomedicine, Falkensee, Germany
| | - Friderike Weege
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | | | - Martin Raftery
- Institute of Virology, Charité University Medicine, Berlin, Germany
| | - Christian Sieben
- Group of Molecular Biophysics, Department of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Laura Martin-Sancho
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Aki Imai-Matsushima
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Robert-William Welke
- Group of Molecular Biophysics, Department of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Rebecca Frise
- Section of Virology, Department of Medicine, Imperial College London, St Mary's Campus, London, United Kingdom
| | - Wendy Barclay
- Section of Virology, Department of Medicine, Imperial College London, St Mary's Campus, London, United Kingdom
| | | | - Andreas Herrmann
- Group of Molecular Biophysics, Department of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Thomas F. Meyer
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
- Steinbeis Innovation Center for Systems Biomedicine, Falkensee, Germany
- * E-mail: (TFM); (AK)
| | - Alexander Karlas
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
- Steinbeis Innovation Center for Systems Biomedicine, Falkensee, Germany
- * E-mail: (TFM); (AK)
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45
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Blanco-Lobo P, Nogales A, Rodríguez L, Martínez-Sobrido L. Novel Approaches for The Development of Live Attenuated Influenza Vaccines. Viruses 2019; 11:E190. [PMID: 30813325 PMCID: PMC6409754 DOI: 10.3390/v11020190] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 02/19/2019] [Accepted: 02/19/2019] [Indexed: 01/04/2023] Open
Abstract
Influenza virus still represents a considerable threat to global public health, despite the advances in the development and wide use of influenza vaccines. Vaccination with traditional inactivate influenza vaccines (IIV) or live-attenuated influenza vaccines (LAIV) remains the main strategy in the control of annual seasonal epidemics, but it does not offer protection against new influenza viruses with pandemic potential, those that have shifted. Moreover, the continual antigenic drift of seasonal circulating influenza viruses, causing an antigenic mismatch that requires yearly reformulation of seasonal influenza vaccines, seriously compromises vaccine efficacy. Therefore, the quick optimization of vaccine production for seasonal influenza and the development of new vaccine approaches for pandemic viruses is still a challenge for the prevention of influenza infections. Moreover, recent reports have questioned the effectiveness of the current LAIV because of limited protection, mainly against the influenza A virus (IAV) component of the vaccine. Although the reasons for the poor protection efficacy of the LAIV have not yet been elucidated, researchers are encouraged to develop new vaccination approaches that overcome the limitations that are associated with the current LAIV. The discovery and implementation of plasmid-based reverse genetics has been a key advance in the rapid generation of recombinant attenuated influenza viruses that can be used for the development of new and most effective LAIV. In this review, we provide an update regarding the progress that has been made during the last five years in the development of new LAIV and the innovative ways that are being explored as alternatives to the currently licensed LAIV. The safety, immunogenicity, and protection efficacy profile of these new LAIVs reveal their possible implementation in combating influenza infections. However, efforts by vaccine companies and government agencies will be needed for controlled testing and approving, respectively, these new vaccine methodologies for the control of influenza infections.
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Affiliation(s)
- Pilar Blanco-Lobo
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, New York, NY 14642, USA.
| | - Aitor Nogales
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, New York, NY 14642, USA.
| | - Laura Rodríguez
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, New York, NY 14642, USA.
| | - Luis Martínez-Sobrido
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, New York, NY 14642, USA.
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46
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Sklenovská N, Van Ranst M. Emergence of Monkeypox as the Most Important Orthopoxvirus Infection in Humans. Front Public Health 2018; 6:241. [PMID: 30234087 PMCID: PMC6131633 DOI: 10.3389/fpubh.2018.00241] [Citation(s) in RCA: 297] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/10/2018] [Indexed: 01/15/2023] Open
Abstract
Monkeypox is an emerging zoonotic disease recognized as the most important orthopoxvirus infection in humans in the smallpox post-eradication era. The clinical presentation of monkeypox is similar to the one of smallpox. The case fatality rate of monkeypox (10%) lies between the case fatality rate of variola major (30%) and variola minor (1%). The disease is endemic in the Democratic Republic of the Congo, but other countries of Central and West Africa either reported cases of monkeypox in humans or circulation in wildlife. The disease was also imported once into the USA. The disease has always been considered rare and self-limiting, however recent sporadic reports suggest otherwise. Unfortunately, the collected data is limited, dispersed and often incomplete. Therefore, the objective of this review is to trace all reported human monkeypox outbreaks and relevant epidemiological information. The frequency and geographical spread of human monkeypox cases have increased in recent years, and there are huge gaps in our understanding of the disease's emergence, epidemiology, and ecology. The monkeypox virus is considered a high threat pathogen causing a disease of public health importance. Therefore, there is an urgent need to focus on building surveillance capacities which will provide valuable information for designing appropriate prevention, preparedness and response activities.
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Affiliation(s)
- Nikola Sklenovská
- Laboratory of Clinical Virology, Department of Microbiology & Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Marc Van Ranst
- Laboratory of Clinical Virology, Department of Microbiology & Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
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47
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Pandey S, Sahu M, Potdar V, Barde P. Molecular analysis of influenza A H1N1pdm09 virus circulating in Madhya Pradesh, India in the year 2017. Virusdisease 2018; 29:380-384. [PMID: 30159375 PMCID: PMC6111952 DOI: 10.1007/s13337-018-0474-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 07/07/2018] [Indexed: 10/28/2022] Open
Abstract
Influenza A (H1N1) pdm09 emerged as a major public health problem in 2009. The virus has evolved since then and has acquired several mutations that are epidemiologically important. Viral hemagglutinin (HA) protein is crucial determinant for virus entry, antigenicity, and virulence. The information regarding amino acid substitutions in HA protein of viruses circulating in India during 2017 is lacking. We sequenced HA gene of Influenza A (H1N1) pdm09 detected in Central India and compared the amino acid sequences with present vaccine component and contemporary Influenza A (H1N1) pdm09 sequences. We observed 7 amino acid changes of which two (T508A and I510T) were novel to Central Indian strain. Further, the substitution of Aspartate by Glycine at 222, which is known to have clinical implications, was detected in sequences from western India. The phylogenetic analysis revealed that the circulating virus belonged to clade 6B.1. The appreciable acquired mutations by the virus are not important antigenically and the present vaccine provides effective protection. On the other hand, the amino acid substitutions may play important role in epidemiology; we suggest rigorous molecular monitoring and documentation for timely interventions.
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Affiliation(s)
- Salonee Pandey
- Division of Virology and Zoonoses, ICMR-National Institute for Research in Tribal Health, Nagpur Road, Jabalpur, MP India
| | - Mahima Sahu
- Division of Virology and Zoonoses, ICMR-National Institute for Research in Tribal Health, Nagpur Road, Jabalpur, MP India
| | - Varsha Potdar
- Influenza Division, ICMR-National Institute of Virology, 20-A Dr. Ambedkar Road Camp, Pune, 411001 India
| | - Pradip Barde
- Division of Virology and Zoonoses, ICMR-National Institute for Research in Tribal Health, Nagpur Road, Jabalpur, MP India
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48
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Dunning J, Blankley S, Hoang LT, Cox M, Graham CM, James PL, Bloom CI, Chaussabel D, Banchereau J, Brett SJ, Moffatt MF, O'Garra A, Openshaw PJM. Progression of whole-blood transcriptional signatures from interferon-induced to neutrophil-associated patterns in severe influenza. Nat Immunol 2018; 19:625-635. [PMID: 29777224 PMCID: PMC5985949 DOI: 10.1038/s41590-018-0111-5] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/13/2018] [Indexed: 12/21/2022]
Abstract
Transcriptional profiles and host-response biomarkers are used increasingly to investigate the severity, subtype and pathogenesis of disease. We now describe whole-blood mRNA signatures and concentrations of local and systemic immunological mediators in 131 adults hospitalized with influenza, from whom extensive clinical and investigational data were obtained by MOSAIC investigators. Signatures reflective of interferon-related antiviral pathways were common up to day 4 of symptoms in patients who did not require mechanical ventilator support; in those who needed mechanical ventilation, an inflammatory, activated-neutrophil and cell-stress or death ('bacterial') pattern was seen, even early in disease. Identifiable bacterial co-infection was not necessary for this 'bacterial' signature but was able to enhance its development while attenuating the early 'viral' signature. Our findings emphasize the importance of timing and severity in the interpretation of host responses to acute viral infection and identify specific patterns of immune-system activation that might enable the development of novel diagnostic and therapeutic tools for severe influenza.
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Affiliation(s)
- Jake Dunning
- Respiratory Infection Section, National Heart and Lung Institute, Imperial College London, London, UK
- National Infection Service, Public Health England, London, UK
| | - Simon Blankley
- Laboratory of Immunoregulation & Infection, The Francis Crick Institute, London, UK
| | - Long T Hoang
- Respiratory Infection Section, National Heart and Lung Institute, Imperial College London, London, UK
| | - Mike Cox
- Genomic Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - Christine M Graham
- Laboratory of Immunoregulation & Infection, The Francis Crick Institute, London, UK
| | - Philip L James
- Genomic Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - Chloe I Bloom
- Laboratory of Immunoregulation & Infection, The Francis Crick Institute, London, UK
| | | | | | - Stephen J Brett
- Surgery and Cancer, National Heart and Lung Institute, Imperial College London, London, UK
| | - Miriam F Moffatt
- Genomic Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - Anne O'Garra
- Laboratory of Immunoregulation & Infection, The Francis Crick Institute, London, UK.
| | - Peter J M Openshaw
- Respiratory Infection Section, National Heart and Lung Institute, Imperial College London, London, UK.
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49
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Groves HT, McDonald JU, Langat P, Kinnear E, Kellam P, McCauley J, Ellis J, Thompson C, Elderfield R, Parker L, Barclay W, Tregoning JS. Mouse Models of Influenza Infection with Circulating Strains to Test Seasonal Vaccine Efficacy. Front Immunol 2018; 9:126. [PMID: 29445377 PMCID: PMC5797846 DOI: 10.3389/fimmu.2018.00126] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/16/2018] [Indexed: 12/29/2022] Open
Abstract
Influenza virus infection is a significant cause of morbidity and mortality worldwide. The surface antigens of influenza virus change over time blunting both naturally acquired and vaccine induced adaptive immune protection. Viral antigenic drift is a major contributing factor to both the spread and disease burden of influenza. The aim of this study was to develop better infection models using clinically relevant, influenza strains to test vaccine induced protection. CB6F1 mice were infected with a range of influenza viruses and disease, inflammation, cell influx, and viral load were characterized after infection. Infection with circulating H1N1 and representative influenza B viruses induced a dose-dependent disease response; however, a recent seasonal H3N2 virus did not cause any disease in mice, even at high titers. Viral infection led to recoverable virus, detectable both by plaque assay and RNA quantification after infection, and increased upper airway inflammation on day 7 after infection comprised largely of CD8 T cells. Having established seasonal infection models, mice were immunized with seasonal inactivated vaccine and responses were compared to matched and mismatched challenge strains. While the H1N1 subtype strain recommended for vaccine use has remained constant in the seven seasons between 2010 and 2016, the circulating strain of H1N1 influenza (2009 pandemic subtype) has drifted both genetically and antigenically since 2009. To investigate the effect of this observed drift on vaccine induced protection, mice were immunized with antigens from A/California/7/2009 (H1N1) and challenged with H1N1 subtype viruses recovered from 2009, 2010, or 2015. Vaccination with A/California/7/2009 antigens protected against infection with either the 2009 or 2010 strains, but was less effective against the 2015 strain. This observed reduction in protection suggests that mouse models of influenza virus vaccination and infection can be used as an additional tool to predict vaccine efficacy against drift strains.
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Affiliation(s)
- Helen T Groves
- Mucosal Infection and Immunity Group, Section of Virology, Department of Medicine, St Mary's Campus, Imperial College London, London, United Kingdom
| | - Jacqueline U McDonald
- Mucosal Infection and Immunity Group, Section of Virology, Department of Medicine, St Mary's Campus, Imperial College London, London, United Kingdom
| | - Pinky Langat
- Mucosal Infection and Immunity Group, Section of Virology, Department of Medicine, St Mary's Campus, Imperial College London, London, United Kingdom
| | - Ekaterina Kinnear
- Mucosal Infection and Immunity Group, Section of Virology, Department of Medicine, St Mary's Campus, Imperial College London, London, United Kingdom
| | - Paul Kellam
- Mucosal Infection and Immunity Group, Section of Virology, Department of Medicine, St Mary's Campus, Imperial College London, London, United Kingdom
| | | | - Joanna Ellis
- Respiratory Virus Unit, Public Health England, London, United Kingdom
| | | | - Ruth Elderfield
- Molecular Virology, Section of Virology, Department of Medicine, St Mary's Campus, Imperial College London, London, United Kingdom
| | - Lauren Parker
- Molecular Virology, Section of Virology, Department of Medicine, St Mary's Campus, Imperial College London, London, United Kingdom
| | - Wendy Barclay
- Molecular Virology, Section of Virology, Department of Medicine, St Mary's Campus, Imperial College London, London, United Kingdom
| | - John S Tregoning
- Mucosal Infection and Immunity Group, Section of Virology, Department of Medicine, St Mary's Campus, Imperial College London, London, United Kingdom
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Klingen TR, Reimering S, Loers J, Mooren K, Klawonn F, Krey T, Gabriel G, McHardy AC. Sweep Dynamics (SD) plots: Computational identification of selective sweeps to monitor the adaptation of influenza A viruses. Sci Rep 2018; 8:373. [PMID: 29321538 PMCID: PMC5762865 DOI: 10.1038/s41598-017-18791-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 12/18/2017] [Indexed: 01/08/2023] Open
Abstract
Monitoring changes in influenza A virus genomes is crucial to understand its rapid evolution and adaptation to changing conditions e.g. establishment within novel host species. Selective sweeps represent a rapid mode of adaptation and are typically observed in human influenza A viruses. We describe Sweep Dynamics (SD) plots, a computational method combining phylogenetic algorithms with statistical techniques to characterize the molecular adaptation of rapidly evolving viruses from longitudinal sequence data. SD plots facilitate the identification of selective sweeps, the time periods in which these occurred and associated changes providing a selective advantage to the virus. We studied the past genome-wide adaptation of the 2009 pandemic H1N1 influenza A (pH1N1) and seasonal H3N2 influenza A (sH3N2) viruses. The pH1N1 influenza virus showed simultaneous amino acid changes in various proteins, particularly in seasons of high pH1N1 activity. Partially, these changes resulted in functional alterations facilitating sustained human-to-human transmission. In the evolution of sH3N2 influenza viruses, we detected changes characterizing vaccine strains, which were occasionally revealed in selective sweeps one season prior to the WHO recommendation. Taken together, SD plots allow monitoring and characterizing the adaptive evolution of influenza A viruses by identifying selective sweeps and their associated signatures.
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MESH Headings
- Algorithms
- Computational Biology/methods
- Evolution, Molecular
- Hemagglutinins, Viral/chemistry
- Hemagglutinins, Viral/genetics
- Hemagglutinins, Viral/immunology
- Humans
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza Vaccines/genetics
- Influenza Vaccines/immunology
- Influenza, Human/immunology
- Influenza, Human/virology
- Models, Molecular
- Phylogeny
- Protein Conformation
- Sequence Analysis, RNA/methods
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Affiliation(s)
- Thorsten R Klingen
- Department for Computational Biology of Infection Research1, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Susanne Reimering
- Department for Computational Biology of Infection Research1, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Jens Loers
- Department for Computational Biology of Infection Research1, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Kyra Mooren
- Department for Computational Biology of Infection Research1, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Frank Klawonn
- Biostatistics Group, Helmholtz Center for Infection Research, Braunschweig, Germany
- Department of Computer Science, Ostfalia University of Applied Sciences, Wolfenbüttel, Germany
| | - Thomas Krey
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Gülsah Gabriel
- Viral Zoonoses and Adaptation, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- University of Lübeck, Lübeck, Germany
| | - Alice C McHardy
- Department for Computational Biology of Infection Research1, Helmholtz Center for Infection Research, Braunschweig, Germany.
- German Center for Infection Research (DZIF), Braunschweig, Germany.
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