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Kuryshko M, Landmann M, Luttermann C, Ulrich R, Abdelwhab EM. In turkeys, unlike chickens, the non-structural NS1 protein does not play a significant role in the replication and tissue tropism of the H7N1 avian influenza virus. Virulence 2024; 15:2379371. [PMID: 39014540 PMCID: PMC11259080 DOI: 10.1080/21505594.2024.2379371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 06/28/2024] [Indexed: 07/18/2024] Open
Abstract
The economic losses caused by high pathogenicity (HP) avian influenza viruses (AIV) in the poultry industry worldwide are enormous. Although chickens and turkeys are closely related Galliformes, turkeys are thought to be a bridging host for the adaptation of AIV from wild birds to poultry because of their high susceptibility to AIV infections. HPAIV evolve from low pathogenicity (LP) AIV after circulation in poultry through mutations in different viral proteins, including the non-structural protein (NS1), a major interferon (IFN) antagonist of AIV. At present, it is largely unknown whether the virulence determinants of HPAIV are the same in turkeys and chickens. Previously, we showed that mutations in the NS1 of HPAIV H7N1 significantly reduced viral replication in chickens in vitro and in vivo. Here, we investigated the effect of NS1 on the replication and virulence of HPAIV H7N1 in turkeys after inoculation with recombinant H7N1 carrying a naturally truncated wild-type NS1 (with 224 amino-acid "aa" in length) or an extended NS1 with 230-aa similar to the LP H7N1 ancestor. There were no significant differences in multiple-cycle viral replication or in the efficiency of NS1 in blocking IFN induction in the cell culture. Similarly, all viruses were highly virulent in turkeys and replicated at similar levels in various organs and swabs collected from the inoculated turkeys. These results suggest that NS1 does not play a role in the virulence or replication of HPAIV H7N1 in turkeys and further indicate that the genetic determinants of HPAIV differ in these two closely related galliform species.
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Affiliation(s)
- Maryna Kuryshko
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Maria Landmann
- Institute of Veterinary Pathology, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Christine Luttermann
- Institute of Immunology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Reiner Ulrich
- Institute of Veterinary Pathology, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Elsayed M. Abdelwhab
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
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2
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McMenamy MJ, McKenna R, Bailie VB, Cunningham B, Jeffers A, McCullough K, Forsythe C, Cuartero LG, Flynn O, Byrne C, Connaghan E, Moriarty J, Fanning J, Ronan S, Barrett D, Fusaro A, Monne I, Terregino C, James J, Byrne AMP, Lean FZX, Núñez A, Reid SM, Hansen R, Brown IH, Banyard AC, Lemon K. Evaluating the Impact of Low-Pathogenicity Avian Influenza H6N1 Outbreaks in United Kingdom and Republic of Ireland Poultry Farms during 2020. Viruses 2024; 16:1147. [PMID: 39066308 PMCID: PMC11281592 DOI: 10.3390/v16071147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
In January 2020, increased mortality was reported in a small broiler breeder flock in County Fermanagh, Northern Ireland. Gross pathological findings included coelomitis, oophoritis, salpingitis, visceral gout, splenomegaly, and renomegaly. Clinical presentation included inappetence, pronounced diarrhoea, and increased egg deformation. These signs, in combination with increased mortality, triggered a notifiable avian disease investigation. High pathogenicity avian influenza virus (HPAIV) was not suspected, as mortality levels and clinical signs were not consistent with HPAIV. Laboratory investigation demonstrated the causative agent to be a low-pathogenicity avian influenza virus (LPAIV), subtype H6N1, resulting in an outbreak that affected 15 premises in Northern Ireland. The H6N1 virus was also associated with infection on 13 premises in the Republic of Ireland and six in Great Britain. The close genetic relationship between the viruses in Ireland and Northern Ireland suggested a direct causal link whereas those in Great Britain were associated with exposure to a common ancestral virus. Overall, this rapidly spreading outbreak required the culling of over 2 million birds across the United Kingdom and the Republic of Ireland to stamp out the incursion. This report demonstrates the importance of investigating LPAIV outbreaks promptly, given their substantial economic impacts.
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Affiliation(s)
- Michael J. McMenamy
- Virological Molecular Diagnostics Laboratory, Virology Branch, Agri-Food and Bioscience Institute, Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - Robyn McKenna
- Virological Molecular Diagnostics Laboratory, Virology Branch, Agri-Food and Bioscience Institute, Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - Valerie B. Bailie
- Virological Molecular Diagnostics Laboratory, Virology Branch, Agri-Food and Bioscience Institute, Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - Ben Cunningham
- Virological Molecular Diagnostics Laboratory, Virology Branch, Agri-Food and Bioscience Institute, Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - Adam Jeffers
- Virological Molecular Diagnostics Laboratory, Virology Branch, Agri-Food and Bioscience Institute, Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - Kelly McCullough
- Virological Molecular Diagnostics Laboratory, Virology Branch, Agri-Food and Bioscience Institute, Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - Catherine Forsythe
- Disease Surveillance & Investigation Branch, Agri-Food and Bioscience Institute, Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - Laura Garza Cuartero
- Central Veterinary Research Laboratory, DAFM, Backweston Campus, Stacummy Lane, W23 X3PH Celbridge, Ireland
| | - Orla Flynn
- Central Veterinary Research Laboratory, DAFM, Backweston Campus, Stacummy Lane, W23 X3PH Celbridge, Ireland
| | - Christina Byrne
- Central Veterinary Research Laboratory, DAFM, Backweston Campus, Stacummy Lane, W23 X3PH Celbridge, Ireland
| | - Emily Connaghan
- Central Veterinary Research Laboratory, DAFM, Backweston Campus, Stacummy Lane, W23 X3PH Celbridge, Ireland
| | - John Moriarty
- Central Veterinary Research Laboratory, DAFM, Backweston Campus, Stacummy Lane, W23 X3PH Celbridge, Ireland
| | - June Fanning
- National Disease Control Centre, Department of Agriculture, Food and the Marine, Agriculture House, Kildare Street, D02 WK12 Dublin, Ireland
| | - Stephanie Ronan
- National Disease Control Centre, Department of Agriculture, Food and the Marine, Agriculture House, Kildare Street, D02 WK12 Dublin, Ireland
| | - Damien Barrett
- National Disease Control Centre, Department of Agriculture, Food and the Marine, Agriculture House, Kildare Street, D02 WK12 Dublin, Ireland
| | - Alice Fusaro
- European Union Reference Laboratory (EURL) for Avian Influenza and Newcastle Disease, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padua, Italy
| | - Isabella Monne
- European Union Reference Laboratory (EURL) for Avian Influenza and Newcastle Disease, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padua, Italy
| | - Calogero Terregino
- European Union Reference Laboratory (EURL) for Avian Influenza and Newcastle Disease, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padua, Italy
| | - Joe James
- Department of Virology, Animal and Plant Health Agency—Weybridge, Woodham Lane, New Haw, Addlestone KT15 3NB, UK
| | - Alexander M. P. Byrne
- Department of Virology, Animal and Plant Health Agency—Weybridge, Woodham Lane, New Haw, Addlestone KT15 3NB, UK
| | - Fabian Z. X. Lean
- Pathology and Animal Sciences Department, Animal and Plant Health Agency—Weybridge, Woodham Lane, New Haw, Addlestone KT15 3NB, UK
| | - Alejandro Núñez
- Pathology and Animal Sciences Department, Animal and Plant Health Agency—Weybridge, Woodham Lane, New Haw, Addlestone KT15 3NB, UK
| | - Scott M. Reid
- Department of Virology, Animal and Plant Health Agency—Weybridge, Woodham Lane, New Haw, Addlestone KT15 3NB, UK
| | - Rowena Hansen
- Department of Virology, Animal and Plant Health Agency—Weybridge, Woodham Lane, New Haw, Addlestone KT15 3NB, UK
| | - Ian H. Brown
- Department of Virology, Animal and Plant Health Agency—Weybridge, Woodham Lane, New Haw, Addlestone KT15 3NB, UK
- Now the Pirbright Institute, Ash Road, Woking GU24 0NF, UK
| | - Ashley C. Banyard
- Department of Virology, Animal and Plant Health Agency—Weybridge, Woodham Lane, New Haw, Addlestone KT15 3NB, UK
| | - Ken Lemon
- Virological Molecular Diagnostics Laboratory, Virology Branch, Agri-Food and Bioscience Institute, Stoney Road, Stormont, Belfast BT4 3SD, UK
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3
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Standing JF, Buggiotti L, Guerra-Assuncao JA, Woodall M, Ellis S, Agyeman AA, Miller C, Okechukwu M, Kirkpatrick E, Jacobs AI, Williams CA, Roy S, Martin-Bernal LM, Williams R, Smith CM, Sanderson T, Ashford FB, Emmanuel B, Afzal ZM, Shields A, Richter AG, Dorward J, Gbinigie O, Van Hecke O, Lown M, Francis N, Jani B, Richards DB, Rahman NM, Yu LM, Thomas NPB, Hart ND, Evans P, Andersson M, Hayward G, Hood K, Nguyen-Van-Tam JS, Little P, Hobbs FDR, Khoo S, Butler C, Lowe DM, Breuer J. Randomized controlled trial of molnupiravir SARS-CoV-2 viral and antibody response in at-risk adult outpatients. Nat Commun 2024; 15:1652. [PMID: 38396069 PMCID: PMC10891158 DOI: 10.1038/s41467-024-45641-0] [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: 08/04/2023] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Viral clearance, antibody response and the mutagenic effect of molnupiravir has not been elucidated in at-risk populations. Non-hospitalised participants within 5 days of SARS-CoV-2 symptoms randomised to receive molnupiravir (n = 253) or Usual Care (n = 324) were recruited to study viral and antibody dynamics and the effect of molnupiravir on viral whole genome sequence from 1437 viral genomes. Molnupiravir accelerates viral load decline, but virus is detectable by Day 5 in most cases. At Day 14 (9 days post-treatment), molnupiravir is associated with significantly higher viral persistence and significantly lower anti-SARS-CoV-2 spike antibody titres compared to Usual Care. Serial sequencing reveals increased mutagenesis with molnupiravir treatment. Persistence of detectable viral RNA at Day 14 in the molnupiravir group is associated with higher transition mutations following treatment cessation. Viral viability at Day 14 is similar in both groups with post-molnupiravir treated samples cultured up to 9 days post cessation of treatment. The current 5-day molnupiravir course is too short. Longer courses should be tested to reduce the risk of potentially transmissible molnupiravir-mutated variants being generated. Trial registration: ISRCTN30448031.
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Affiliation(s)
- Joseph F Standing
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK.
- Great Ormond Street Hospital for Children NHS Trust, London, UK.
| | - Laura Buggiotti
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Jose Afonso Guerra-Assuncao
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Maximillian Woodall
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Samuel Ellis
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Akosua A Agyeman
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Charles Miller
- Great Ormond Street Hospital for Children NHS Trust, London, UK
| | - Mercy Okechukwu
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Emily Kirkpatrick
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Amy I Jacobs
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Charlotte A Williams
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Sunando Roy
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Luz M Martin-Bernal
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Rachel Williams
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Claire M Smith
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | | | - Fiona B Ashford
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Beena Emmanuel
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Zaheer M Afzal
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Adrian Shields
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Alex G Richter
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Jienchi Dorward
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Oghenekome Gbinigie
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Oliver Van Hecke
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Mark Lown
- Primary Care Research Centre, University of Southampton, Southampton, UK
| | - Nick Francis
- Primary Care Research Centre, University of Southampton, Southampton, UK
| | - Bhautesh Jani
- School of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Duncan B Richards
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Najib M Rahman
- Respiratory Trials Unit and Oxford NIHR Biomedical Research Centre, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ly-Mee Yu
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | | | - Nigel D Hart
- School of Medicine, Dentistry and Biomedical Sciences. Queen's University Belfast, Belfast, UK
| | - Philip Evans
- APEx (Exeter Collaboration for Academic Primary Care), University of Exeter Medical School, Exeter, UK
- National Institute of Health and Care Research, Clinical Research Network, University of Leeds, Leeds, UK
| | | | - Gail Hayward
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Kerenza Hood
- Centre for Trials Research, Cardiff University, Wales, UK
| | | | - Paul Little
- Primary Care Research Centre, University of Southampton, Southampton, UK
| | - F D Richard Hobbs
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Saye Khoo
- Department of Pharmacology, University of Liverpool and Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Christopher Butler
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - David M Lowe
- Department of Clinical Immunology, Royal Free London NHS Foundation Trust, London, UK
- Institute of Immunity and Transplantation, University College London, London, UK
| | - Judith Breuer
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
- Great Ormond Street Hospital for Children NHS Trust, London, UK
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4
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Liu Y, Kjær LJ, Boklund AE, Hjulsager CK, Larsen LE, Kirkeby CT. Risk factors for avian influenza in Danish poultry and wild birds during the epidemic from June 2020 to May 2021. Front Vet Sci 2024; 11:1358995. [PMID: 38450025 PMCID: PMC10914952 DOI: 10.3389/fvets.2024.1358995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/12/2024] [Indexed: 03/08/2024] Open
Abstract
Exploring the risk factors of avian influenza (AI) occurrence helps us to monitor and control the disease. Since late 2020, the number of avian influenza outbreaks in domestic and wild birds has increased in most European countries, including Denmark. This study was conducted to identify potential risk factors for wild birds and poultry during the epidemic in 2020/2021 in Denmark. Using Danish AI surveillance data of actively surveyed poultry and passively surveyed wild birds from June 2020 to May 2021, we calculated geographical attributes for bird locations and assessed the potential risk factors of AI detections using logistic regression analyses. 4% of actively surveyed poultry and 39% of passively surveyed wild birds were detected with AI circulating or ongoing at the time. Of these, 10 and 99% tested positive for the H5/H7 AI subtypes, respectively. Our analyses did not find any statistically significant risk factors for actively surveyed poultry within the dataset. For passively surveyed wild birds, bird species belonging to the Anseriformes order had a higher risk of being AI virus positive than five other taxonomic bird orders, and Galliformes were of higher risk than two other taxonomic bird orders. Besides, every 1 km increase in the distance to wetlands was associated with a 5.18% decrease in the risk of being AI positive (OR (odds ratio) 0.95, 95% CI 0.91, 0.99), when all other variables were kept constant. Overall, bird orders and distance to wetlands were associated with the occurrence of AI. The findings may provide targets for surveillance strategies using limited resources and assist in risk-based surveillance during epidemics.
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Affiliation(s)
- Yangfan Liu
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Lene Jung Kjær
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Anette Ella Boklund
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Lars Erik Larsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Carsten Thure Kirkeby
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
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5
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Rzymski P. Avian influenza outbreaks in domestic cats: another reason to consider slaughter-free cell-cultured poultry? Front Microbiol 2023; 14:1283361. [PMID: 38163084 PMCID: PMC10754994 DOI: 10.3389/fmicb.2023.1283361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/24/2023] [Indexed: 01/03/2024] Open
Abstract
Avian influenza causes substantial economic loss in the poultry industry and potentially threatens human health. Over recent years, the highly pathogenic avian influenza A/H5N1 virus has led to devastating losses in poultry flocks and wild birds. At the same time, the number of mammalian species identified to be infected with A/H5N1 is increasing, with recent outbreaks in domestic cats, including household individuals, evidenced in July 2023 in Poland, ultimately creating opportunities for the virus to adapt better to mammalian hosts, including humans. Overall, between 2003 and 2023, over 10 outbreaks in felids have been documented globally, and in six of them, feed based on raw chicken was suspected as a potential source of A/H5N1, fuelling a debate on threats posed by A/H5N1 and methods to decrease the associated risks. This article debates that technology allowing the production of slaughter-free meat, including poultry, from cell and tissue cultures could be considered as a part of a mitigation strategy to decrease the overall burden and threat of adaptation of avian influenza viruses to human hosts. By shifting poultry production to the cultured meat industry, the frequency of A/H5N1 outbreaks in farmed birds may be decreased, leading to a reduced risk of virus acquisition by wild and domesticated mammals that have direct contact with birds or eat raw poultry and have close contact with human (including domestic cats), ultimately minimizing the potential of A/H5N1 to adapt better to mammalian host, including humans. This adds to the list of other benefits of cultured meat that are also reviewed in this paper, including decreased antibiotic use, risk of microbial contamination and parasite transmission, and environmental and ethical advantages over conventional slaughtered meat. In conclusion, further development and implementation of this technology, also in the context of poultry production, is strongly advocated. Although cultured poultry is unlikely to replace the conventional process in the near future due to challenges with scaling up the production and meeting the continuously increased demand for poultry meat, it may still decrease the pressures and threats related to the transmission of highly pathogenic avian influenza in selected world regions.
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Affiliation(s)
- Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, Poznan, Poland
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6
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Carnegie L, Raghwani J, Fournié G, Hill SC. Phylodynamic approaches to studying avian influenza virus. Avian Pathol 2023; 52:289-308. [PMID: 37565466 DOI: 10.1080/03079457.2023.2236568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 08/12/2023]
Abstract
Avian influenza viruses can cause severe disease in domestic and wild birds and are a pandemic threat. Phylodynamics is the study of how epidemiological, evolutionary, and immunological processes can interact to shape viral phylogenies. This review summarizes how phylodynamic methods have and could contribute to the study of avian influenza viruses. Specifically, we assess how phylodynamics can be used to examine viral spread within and between wild or domestic bird populations at various geographical scales, identify factors associated with virus dispersal, and determine the order and timing of virus lineage movement between geographic regions or poultry production systems. We discuss factors that can complicate the interpretation of phylodynamic results and identify how future methodological developments could contribute to improved control of the virus.
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Affiliation(s)
- L Carnegie
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| | - J Raghwani
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| | - G Fournié
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, Marcy l'Etoile, France
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint Genes Champanelle, France
| | - S C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
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7
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Jung Kjær L, Ward MP, Boklund AE, Larsen LE, Hjulsager CK, Kirkeby CT. Using surveillance data for early warning modelling of highly pathogenic avian influenza in Europe reveals a seasonal shift in transmission, 2016-2022. Sci Rep 2023; 13:15396. [PMID: 37717056 PMCID: PMC10505205 DOI: 10.1038/s41598-023-42660-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/13/2023] [Indexed: 09/18/2023] Open
Abstract
Avian influenza in wild birds and poultry flocks constitutes a problem for animal welfare, food security and public health. In recent years there have been increasing numbers of outbreaks in Europe, with many poultry flocks culled after being infected with highly pathogenic avian influenza (HPAI). Continuous monitoring is crucial to enable timely implementation of control to prevent HPAI spread from wild birds to poultry and between poultry flocks within a country. We here utilize readily available public surveillance data and time-series models to predict HPAI detections within European countries and show a seasonal shift that happened during 2021-2022. The output is models capable of monitoring the weekly risk of HPAI outbreaks, to support decision making.
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Affiliation(s)
- Lene Jung Kjær
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Michael P Ward
- Faculty of Science, Sydney School of Veterinary Science, University of Sydney, Camden, NSW, Australia
| | - Anette Ella Boklund
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars Erik Larsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Carsten Thure Kirkeby
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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8
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Wang Q, Zeng X, Tang S, Lan L, Wang X, Lai Z, Liu Z, Hou X, Gao L, Yun C, Zhang Z, Leng J, Fan X. Pathogenicity and anti-infection immunity of animal H3N2 and H6N6 subtype influenza virus cross-species infection with tree shrews. Virus Res 2023; 324:199027. [PMID: 36543317 DOI: 10.1016/j.virusres.2022.199027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 12/11/2022] [Accepted: 12/17/2022] [Indexed: 12/23/2022]
Abstract
Animal influenza viruses can spread across species and pose a fatal threat to human health due to the high pathogenicity and mortality. Animal models are crucial for studying cross-species infection and the pathogenesis of influenza viruses. Tupaia belangeri (tree shrew) has been emerging as an animal model for multiple human virus infections recently because of the close genetic relationship and phylogeny with humans. So far, tree shrew has been reported to be susceptible to human influenza virus subtype H1N1, avian influenza viruses subtype H9N2, subtype H5N1, and subtype H7N9. However, the pathogenicity, infection, and immunity of swine and land avian influenza viruses with low pathogenicity and the potential to jump to humans remain largely unexplored in the tree shrew model. Previously, our team has successfully isolated the newly emerging swine influenza virus subtype H3N2 (A/Swine/GX/NS2783/2010, SW2783) and avian influenza virus subtype H6N6 (A/CK/ZZ/346/2014, ZZ346). In this study, we observed the pathogenicity, immune characteristics, and cross-species infection potential ability of SW2783 and ZZ346 strains in tree shrew model with 50% tissue culture infective dose (TCID50), hematoxylin and eosin (HE) staining, immunohistochemistry (IHC), real-time quantitative PCR (qRT-PCR) and other experimental methods. Both animal-borne influenza viruses had a strong ability on tissue infection in the turbinate and the trachea of tree shrews in vitro, in which SW2783 showed stronger replication ability than in ZZ346. SW2783 and ZZ346 both showed pathogenic ability with infected tree shrews model in vivo without prior adaptive culture, which mainly happened in the upper respiratory tract. However, the infection ability was weak, the clinical symptoms were mild, and the histopathological changes in the respiratory tract were relatively light. Furthermore, innate immune responses and adaptive immunity were observed in the tree shrew model after the infection of SW2783 and ZZ346 strains. We observed that the unadapted SW2783 and ZZ346 virus could transmit among tree shrews by direct contact. We also observed that SW2783 virus could transmit from tree shrews to guinea pigs. These results indicated that both animal-borne influenza viruses could induce similar pathogenicity and immune response to those caused by human-common influenza viruses. Tree shrews may be an excellent animal model for studying the interaction between the influenza virus and the host and the cross-species infection mechanism of the animal influenza virus.
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Affiliation(s)
- Qihui Wang
- Department of Immunology, Guangxi Medical University, Nanning 530021, China; Guangxi Colleges and Universities Key Laboratory of Preclinical Medicine, Guangxi Medical University, Nanning 530021, China
| | - Xia Zeng
- Department of Immunology, Guangxi Medical University, Nanning 530021, China; Guangxi Colleges and Universities Key Laboratory of Preclinical Medicine, Guangxi Medical University, Nanning 530021, China
| | - Shen Tang
- Department of Immunology, Guangxi Medical University, Nanning 530021, China; Guangxi Colleges and Universities Key Laboratory of Preclinical Medicine, Guangxi Medical University, Nanning 530021, China
| | - Li Lan
- Department of Immunology, Guangxi Medical University, Nanning 530021, China
| | - Xinhang Wang
- Department of Immunology, Guangxi Medical University, Nanning 530021, China
| | - Zhenping Lai
- Department of Microbiology, Guangxi Medical University, Nanning 530021, China
| | - Zihe Liu
- Department of Immunology, Guangxi Medical University, Nanning 530021, China
| | - Xiaoqiong Hou
- Department of Immunology, Guangxi Medical University, Nanning 530021, China
| | - Lingxi Gao
- Department of Microbiology, Guangxi Medical University, Nanning 530021, China
| | - Chenxia Yun
- Guangxi Key Laboratory of Translational Medicine for Treating High-Incidence Infectious Diseases with Integrative Medicine, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Zengfeng Zhang
- Guangxi Colleges and Universities Key Laboratory of Preclinical Medicine, Guangxi Medical University, Nanning 530021, China; Department of Microbiology, Guangxi Medical University, Nanning 530021, China.
| | - Jing Leng
- Department of Immunology, Guangxi Medical University, Nanning 530021, China; Guangxi Key Laboratory of Translational Medicine for Treating High-Incidence Infectious Diseases with Integrative Medicine, Guangxi University of Chinese Medicine, Nanning 530200, China.
| | - Xiaohui Fan
- Guangxi Colleges and Universities Key Laboratory of Preclinical Medicine, Guangxi Medical University, Nanning 530021, China; Department of Microbiology, Guangxi Medical University, Nanning 530021, China.
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9
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Kang YM, Cho HK, An SJ, Kim HJ, Lee YJ, Kang HM. Updating the National Antigen Bank in Korea: Protective Efficacy of Synthetic Vaccine Candidates against H5Nx Highly Pathogenic Avian Influenza Viruses Belonging to Clades 2.3.2.1 and 2.3.4.4. Vaccines (Basel) 2022; 10:vaccines10111860. [PMID: 36366368 PMCID: PMC9697692 DOI: 10.3390/vaccines10111860] [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: 10/16/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022] Open
Abstract
Since 2018, Korea has been building an avian influenza (AI) national antigen bank for emergency preparedness; this antigen bank is updated every 2 years. To update the vaccine strains in the antigen bank, we used reverse genetics technology to develop two vaccine candidates against avian influenza strains belonging to clades 2.3.2.1d and 2.3.4.4h, and then evaluated their immunogenicity and protective efficacy in SPF chickens challenged with H5 viruses. The two vaccine candidates, named rgCA2/2.3.2.1d and rgES3/2.3.4.4h, were highly immunogenic, with hemagglutination inhibition (HI) titers of 8.2−9.3 log2 against the vaccine strain, and 7.1−7.3 log2 against the lethal challenge viruses (in which the HA genes shared 97% and 95.4% homology with that of rgCA2/2.3.2.1d and rgES3/2.3.4.4h, respectively). A full dose of each vaccine candidate provided 100% protection against the challenge viruses, with a reduction in clinical symptoms and virus shedding. A 1/10 dose provided similar levels of protection, whereas a 1/100 dose resulted in mortality and virus shedding by 7 dpi. Moreover, immunity induced by the two vaccines was long lasting, with HI titers of >7 log2 against the vaccine strain remaining after 6 months. Thus, the two vaccine candidates show protective efficacy and can be used to update the AI national antigen bank.
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Affiliation(s)
| | | | | | | | | | - Hyun-Mi Kang
- Correspondence: ; Tel.: +82-549120972; Fax: +82-549120977
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10
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Dolinski AC, Homola JJ, Jankowski MD, Robinson JD, Owen JC. Host gene expression is associated with viral shedding magnitude in blue-winged teals (Spatula discors) infected with low-path avian influenza virus. Comp Immunol Microbiol Infect Dis 2022; 90-91:101909. [PMID: 36410069 PMCID: PMC10500253 DOI: 10.1016/j.cimid.2022.101909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022]
Abstract
Intraspecific variation in host infectiousness affects disease transmission dynamics in human, domestic animal, and many wildlife host-pathogen systems including avian influenza virus (AIV); therefore, identifying host factors related to host infectiousness is important for understanding, controlling, and preventing future outbreaks. Toward this goal, we used RNA-seq data collected from low pathogenicity avian influenza virus (LPAIV)-infected blue-winged teal (Spatula discors) to determine the association between host gene expression and intraspecific variation in cloacal viral shedding magnitude, the transmissible fraction of virus. We found that host genes were differentially expressed between LPAIV-infected and uninfected birds early in the infection, host genes were differentially expressed between shed level groups at one-, three-, and five-days post-infection, host gene expression was associated with LPAIV infection patterns over time, and genes of the innate immune system had a positive linear relationship with cloacal viral shedding. This study provides important insights into host gene expression patterns associated with intraspecific LPAIV shedding variation and can serve as a foundation for future studies focused on the identification of host factors that drive or permit the emergence of high viral shedding individuals.
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Affiliation(s)
- Amanda C Dolinski
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA
| | - Jared J Homola
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA
| | - Mark D Jankowski
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA; US Environmental Protection Agency, Region 10, Seattle, WA 98101, USA
| | - John D Robinson
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA
| | - Jennifer C Owen
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA; Michigan State University, Department of Large Animal Clinical Sciences, 736 Wilson Road, East Lansing, MI 48824, USA.
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11
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Aligne CA. Lost Lessons of the 1918 Influenza: The 1920s Working Hypothesis, the Public Health Paradigm, and the Prevention of Deadly Pandemics. Am J Public Health 2022; 112:1454-1464. [PMID: 36007204 PMCID: PMC9480479 DOI: 10.2105/ajph.2022.306976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2022] [Indexed: 11/04/2022]
Abstract
In standard historical accounts, the hyperlethal 1918 flu pandemic was inevitable once a novel influenza virus appeared. However, in the years following the pandemic, it was obvious to distinguished flu experts from around the world that social and environmental conditions interacted with infectious agents and could enhance the virulence of flu germs. On the basis of the timing and geographic pattern of the pandemic, they hypothesized that an "essential cause" of the pandemic's extraordinary lethality was the extreme, prolonged, and industrial-scale overcrowding of US soldiers in World War I, particularly on troopships. This literature synthesis considers research from history, public health, military medicine, veterinary science, molecular genetics, virology, immunology, and epidemiology. Arguments against the hypothesis do not provide disconfirming evidence. Overall, the findings are consistent with an immunologically similar virus varying in virulence in response to war-related conditions. The enhancement-of-virulence hypothesis deserves to be included in the history of the pandemic and the war. These lost lessons of 1918 point to possibilities for blocking the transformation of innocuous infections into deadly disasters and are relevant beyond influenza for diseases like COVID-19. (Am J Public Health. 2022;112(10):1454-1464. https://doi.org/10.2105/AJPH.2022.306976).
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Affiliation(s)
- C Andrew Aligne
- C. Andrew Aligne is with the Hoekelman Center, Department of Pediatrics, Golisano Children's Hospital, University of Rochester School of Medicine & Dentistry, Rochester, NY
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12
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Azeem S, Guo B, Sun D, Killian ML, Baroch JA, Yoon KJ. Evaluation of PCR-based hemagglutinin subtyping as a tool to aid in surveillance of avian influenza viruses in migratory wild birds. J Virol Methods 2022; 308:114594. [PMID: 35931229 DOI: 10.1016/j.jviromet.2022.114594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/28/2022] [Accepted: 07/31/2022] [Indexed: 11/16/2022]
Abstract
The surveillance of migratory wild birds (MWBs) for avian influenza virus (AIV) allows detecting the emergence of highly pathogenic AIV that can infect domestic poultry and mammals, new subtypes, and antigenic/genetic variants. The current AIV surveillance system for MWBs in the United States is based on virus isolation (VI) followed by sequencing isolates. This system primarily focuses on the early detection of H5 and H7 AIVs. However, it is suboptimal in assessing diverse AIV subtypes at any given time because of the low VI success rate. To improve such a shortfall, a SYBR® Green-based real-time reverse transcription-polymerase chain reaction (rtRT-PCR) panel was developed for direct HA subtyping of AIVs in oropharyngeal-cloacal (OPC) swabs from MWBs. Under optimal conditions, the PCR panel detected AIVs of all 16 different HA subtypes with an average limit of detection of 102.6 copies/reaction (2 μl of extract). In testing 90 OPC swabs from 13 MWB species, the PCR provided a significantly faster turnaround of results and demonstrated the presence of more subtypes and concurrent infection among MWBs compared to what the current surveillance testing algorithm showed. In conclusion, newly developed SYBR® Green rtRT-PCR panel can be a useful tool for monitoring MWBs for AIVs.
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Affiliation(s)
- Shahan Azeem
- Veterinary Mirobiology and Preventive Medicine, Iowa State University, Ames, IA, United States.
| | - Baoqing Guo
- Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, United States.
| | - Dong Sun
- Veterinary Mirobiology and Preventive Medicine, Iowa State University, Ames, IA, United States.
| | - Mary L Killian
- Diagnostic Virology Laboratory, National Veterinary Services Laboratories, USDA, Ames, IA, United States.
| | - John A Baroch
- National Wildlife Research Center, Fort Collins, CO, United States.
| | - Kyoung-Jin Yoon
- Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, United States.
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13
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Evidence for Different Virulence Determinants and Host Response after Infection of Turkeys and Chickens with Highly Pathogenic H7N1 Avian Influenza Virus. J Virol 2022; 96:e0099422. [PMID: 35993736 PMCID: PMC9472639 DOI: 10.1128/jvi.00994-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Wild birds are the reservoir for all avian influenza viruses (AIV). In poultry, the transition from low pathogenic (LP) AIV of H5 and H7 subtypes to highly pathogenic (HP) AIV is accompanied mainly by changing the hemagglutinin (HA) monobasic cleavage site (CS) to a polybasic motif (pCS). Galliformes, including turkeys and chickens, succumb with high morbidity and mortality to HPAIV infections, although turkeys appear more vulnerable than chickens. Surprisingly, the genetic determinants for virulence and pathogenesis of HPAIV in turkeys are largely unknown. Here, we determined the genetic markers for virulence and transmission of HPAIV H7N1 in turkeys, and we explored the host responses in this species compared to those of chickens. We found that recombinant LPAIV H7N1 carrying pCS was avirulent in chickens but exhibited high virulence in turkeys, indicating that virulence determinants vary in these two galliform species. A transcriptome analysis indicated that turkeys mount a different host response than do chickens, particularly from genes involved in RNA metabolism and the immune response. Furthermore, we found that the HA glycosylation at residue 123, acquired by LP viruses shortly after transmission from wild birds and preceding the transition from LP to HP, had a role in virus fitness and virulence in chickens, though it was not a prerequisite for high virulence in turkeys. Together, these findings indicate variable virulence determinants and host responses in two closely related galliformes, turkeys and chickens, after infection with HPAIV H7N1. These results could explain the higher vulnerability to HPAIV of turkeys compared to chickens. IMPORTANCE Infection with HPAIV in chickens and turkeys, two closely related galliform species, results in severe disease and death. Although the presence of a polybasic cleavage site (pCS) in the hemagglutinin of AIV is a major virulence determinant for the transition of LPAIV to HPAIV, there are knowledge gaps on the genetic determinants (including pCS) and the host responses in turkeys compared to chickens. Here, we found that the pCS alone was sufficient for the transformation of a LP H7N1 into a HPAIV in turkeys but not in chickens. We also noticed that turkeys exhibited a different host response to an HPAIV infection, namely, a widespread downregulation of host gene expression associated with protein synthesis and the immune response. These results are important for a better understanding of the evolution of HPAIV from LPAIV and of the different outcomes and the pathomechanisms of HPAIV infections in chickens and turkeys.
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14
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McDuie F, Matchett EL, Prosser DJ, Takekawa JY, Pitesky ME, Lorenz AA, McCuen MM, T OC, Ackerman JT, De La Cruz SEW, Casazza ML. Pathways for avian influenza virus spread: GPS reveals wild waterfowl in commercial livestock facilities and connectivity with the natural wetland landscape. Transbound Emerg Dis 2022; 69:2898-2912. [PMID: 34974641 PMCID: PMC9788224 DOI: 10.1111/tbed.14445] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/16/2021] [Accepted: 12/18/2021] [Indexed: 12/30/2022]
Abstract
Zoonotic diseases are of considerable concern to the human population and viruses such as avian influenza (AIV) threaten food security, wildlife conservation and human health. Wild waterfowl and the natural wetlands they use are known AIV reservoirs, with birds capable of virus transmission to domestic poultry populations. While infection risk models have linked migration routes and AIV outbreaks, there is a limited understanding of wild waterfowl presence on commercial livestock facilities, and movement patterns linked to natural wetlands. We documented 11 wild waterfowl (three Anatidae species) in or near eight commercial livestock facilities in Washington and California with GPS telemetry data. Wild ducks used dairy and beef cattle feed lots and facility retention ponds during both day and night suggesting use for roosting and foraging. Two individuals (single locations) were observed inside poultry facility boundaries while using nearby wetlands. Ducks demonstrated high site fidelity, returning to the same areas of habitats (at livestock facilities and nearby wetlands), across months or years, showed strong connectivity with surrounding wetlands, and arrived from wetlands up to 1251 km away in the week prior. Telemetry data provides substantial advantages over observational data, allowing assessment of individual movement behaviour and wetland connectivity that has significant implications for outbreak management. Telemetry improves our understanding of risk factors for waterfowl-livestock virus transmission and helps identify factors associated with coincident space use at the wild waterfowl-domestic livestock interface. Our research suggests that even relatively small or isolated natural and artificial water or food sources in/near facilities increases the likelihood of attracting waterfowl, which has important consequences for managers attempting to minimize or prevent AIV outbreaks. Use and interpretation of telemetry data, especially in near-real-time, could provide key information for reducing virus transmission risk between waterfowl and livestock, improving protective barriers between wild and domestic species, and abating outbreaks.
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Affiliation(s)
- Fiona McDuie
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field StationSuite D DixonCaliforniaUSA,San Jose State University Research FoundationMoss Landing Marine LaboratoriesCaliforniaUSA
| | - Elliott L Matchett
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field StationSuite D DixonCaliforniaUSA
| | - Diann J Prosser
- U.S. Geological Survey, Eastern Ecological Science Center at the Patuxent Research Refuge (formerly USGS Patuxent Wildlife Research Center)LaurelMarylandUSA
| | - John Y Takekawa
- Suisun Resource Conservation District, Suisun Marsh ProgramWest SacramentoCaliforniaUSA
| | - Maurice E Pitesky
- University of California Davis, School of Veterinary Medicine, Poultry Health and Food Safety Epidemiology, One Shields AvenueDavisCaliforniaUSA
| | - Austen A Lorenz
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field StationSuite D DixonCaliforniaUSA
| | - Madeline M McCuen
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field StationSuite D DixonCaliforniaUSA
| | - Overton Cory T
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field StationSuite D DixonCaliforniaUSA
| | - Joshua T Ackerman
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field StationSuite D DixonCaliforniaUSA
| | - Susan E. W. De La Cruz
- U.S. Geological Survey Western Ecological Research Center, San Francisco Bay Estuary Field StationMoffett FieldCaliforniaUSA
| | - Michael L Casazza
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field StationSuite D DixonCaliforniaUSA
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15
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de Bruin ACM, Funk M, Spronken MI, Gultyaev AP, Fouchier RAM, Richard M. Hemagglutinin Subtype Specificity and Mechanisms of Highly Pathogenic Avian Influenza Virus Genesis. Viruses 2022; 14:1566. [PMID: 35891546 PMCID: PMC9321182 DOI: 10.3390/v14071566] [Citation(s) in RCA: 16] [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: 05/22/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 02/04/2023] Open
Abstract
Highly Pathogenic Avian Influenza Viruses (HPAIVs) arise from low pathogenic precursors following spillover from wild waterfowl into poultry populations. The main virulence determinant of HPAIVs is the presence of a multi-basic cleavage site (MBCS) in the hemagglutinin (HA) glycoprotein. The MBCS allows for HA cleavage and, consequently, activation by ubiquitous proteases, which results in systemic dissemination in terrestrial poultry. Since 1959, 51 independent MBCS acquisition events have been documented, virtually all in HA from the H5 and H7 subtypes. In the present article, data from natural LPAIV to HPAIV conversions and experimental in vitro and in vivo studies were reviewed in order to compile recent advances in understanding HA cleavage efficiency, protease usage, and MBCS acquisition mechanisms. Finally, recent hypotheses that might explain the unique predisposition of the H5 and H7 HA sequences to obtain an MBCS in nature are discussed.
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Affiliation(s)
- Anja C. M. de Bruin
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (A.C.M.d.B.); (M.F.); (M.I.S.); (A.P.G.); (R.A.M.F.)
| | - Mathis Funk
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (A.C.M.d.B.); (M.F.); (M.I.S.); (A.P.G.); (R.A.M.F.)
| | - Monique I. Spronken
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (A.C.M.d.B.); (M.F.); (M.I.S.); (A.P.G.); (R.A.M.F.)
| | - Alexander P. Gultyaev
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (A.C.M.d.B.); (M.F.); (M.I.S.); (A.P.G.); (R.A.M.F.)
- Group Imaging and Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, 2300 RA Leiden, The Netherlands
| | - Ron A. M. Fouchier
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (A.C.M.d.B.); (M.F.); (M.I.S.); (A.P.G.); (R.A.M.F.)
| | - Mathilde Richard
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (A.C.M.d.B.); (M.F.); (M.I.S.); (A.P.G.); (R.A.M.F.)
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16
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Genomic determinants of Furin cleavage in diverse European SARS-related bat coronaviruses. Commun Biol 2022; 5:491. [PMID: 35637279 PMCID: PMC9151638 DOI: 10.1038/s42003-022-03421-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 04/27/2022] [Indexed: 12/11/2022] Open
Abstract
The furin cleavage site (FCS) in SARS-CoV-2 is unique within the Severe acute respiratory syndrome–related coronavirus (SrC) species. We re-assessed diverse SrC from European horseshoe bats and analyzed the spike-encoding genomic region harboring the FCS in SARS-CoV-2. We reveal molecular features in SrC such as purine richness and RNA secondary structures that resemble those required for FCS acquisition in avian influenza viruses. We discuss the potential acquisition of FCS through molecular mechanisms such as nucleotide substitution, insertion, or recombination, and show that a single nucleotide exchange in two European bat-associated SrC may suffice to enable furin cleavage. Furthermore, we show that FCS occurrence is variable in bat- and rodent-borne counterparts of human coronaviruses. Our results suggest that furin cleavage sites can be acquired in SrC via conserved molecular mechanisms known in other reservoir-bound RNA viruses and thus support a natural origin of SARS-CoV-2. Genomic analyses of spike glycoprotein genes of European bat SARS-related coronaviruses suggest that furin cleavage sites can be acquired in the bat reservoir via conserved molecular mechanisms, supporting a natural origin of SARS-CoV-2.
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17
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Xu W, Navarro-López R, Solis-Hernandez M, Liljehult-Fuentes F, Molina-Montiel M, Lagunas-Ayala M, Rocha-Martinez M, Ferrara-Tijera E, Pérez de la Rosa J, Berhane Y. Evolutionary Dynamics of Mexican Lineage H5N2 Avian Influenza Viruses. Viruses 2022; 14:v14050958. [PMID: 35632700 PMCID: PMC9146523 DOI: 10.3390/v14050958] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 11/17/2022] Open
Abstract
We have demonstrated for the first time a comprehensive evolutionary analysis of the Mexican lineage H5N2 avian influenza virus (AIV) using complete genome sequences (n = 189), from its first isolation in 1993 until 2019. Our study showed that the Mexican lineage H5N2 AIV originated from the North American wild bird gene pool viruses around 1990 and is currently circulating in poultry populations of Mexico, the Dominican Republic, and Taiwan. Since the implementation of vaccination in 1995, the highly pathogenic AIV (HPAIV) H5N2 virus was eradicated from Mexican poultry in mid-1995. However, the low pathogenic AIV (LPAIV) H5N2 virus has continued to circulate in domestic poultry populations in Mexico, eventually evolving into five distinct clades. In the current study, we demonstrate that the evolution of Mexican lineage H5N2 AIVs involves gene reassortments and mutations gained over time. The current circulating Mexican lineage H5N2 AIVs are classified as LPAIV based on the amino acid sequences of the hemagglutinin (HA) protein cleavage site motif as well as the results of the intravenous pathogenicity index (IVPI). The immune pressure from vaccinations most likely has played a significant role in the positive selection of antigenic drift mutants within the Mexican H5N2 AIVs. Most of the identified substitutions in these viruses are located on the critical antigenic residues of the HA protein and as a result, might have contributed to vaccine failures. This study highlights and stresses the need for vaccine updates while emphasizing the importance of continued molecular monitoring of the HA protein for its antigenic changes compared to the vaccines used.
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Affiliation(s)
- Wanhong Xu
- National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3M4, Canada;
| | - Roberto Navarro-López
- Animal Health General Directorate, Animal and Plant Health, Food Inspection and Food Safety National Services (SENASICA), Secretariat of Agriculture, Livestock, Rural Development, Fisheries and Food (SAGARPA), Mexico City 06470, Mexico; (R.N.-L.); (M.M.-M.); (M.L.-A.); (M.R.-M.); (E.F.-T.); (J.P.d.l.R.)
| | - Mario Solis-Hernandez
- United States-Mexico Commission for the Prevention of Foot-and-Mouth Disease and Other Exotic Diseases of Animals, Mexico City 64590, Mexico; (M.S.-H.); (F.L.-F.)
| | - Francisco Liljehult-Fuentes
- United States-Mexico Commission for the Prevention of Foot-and-Mouth Disease and Other Exotic Diseases of Animals, Mexico City 64590, Mexico; (M.S.-H.); (F.L.-F.)
| | - Miguel Molina-Montiel
- Animal Health General Directorate, Animal and Plant Health, Food Inspection and Food Safety National Services (SENASICA), Secretariat of Agriculture, Livestock, Rural Development, Fisheries and Food (SAGARPA), Mexico City 06470, Mexico; (R.N.-L.); (M.M.-M.); (M.L.-A.); (M.R.-M.); (E.F.-T.); (J.P.d.l.R.)
| | - María Lagunas-Ayala
- Animal Health General Directorate, Animal and Plant Health, Food Inspection and Food Safety National Services (SENASICA), Secretariat of Agriculture, Livestock, Rural Development, Fisheries and Food (SAGARPA), Mexico City 06470, Mexico; (R.N.-L.); (M.M.-M.); (M.L.-A.); (M.R.-M.); (E.F.-T.); (J.P.d.l.R.)
| | - Marisol Rocha-Martinez
- Animal Health General Directorate, Animal and Plant Health, Food Inspection and Food Safety National Services (SENASICA), Secretariat of Agriculture, Livestock, Rural Development, Fisheries and Food (SAGARPA), Mexico City 06470, Mexico; (R.N.-L.); (M.M.-M.); (M.L.-A.); (M.R.-M.); (E.F.-T.); (J.P.d.l.R.)
| | - Eduardo Ferrara-Tijera
- Animal Health General Directorate, Animal and Plant Health, Food Inspection and Food Safety National Services (SENASICA), Secretariat of Agriculture, Livestock, Rural Development, Fisheries and Food (SAGARPA), Mexico City 06470, Mexico; (R.N.-L.); (M.M.-M.); (M.L.-A.); (M.R.-M.); (E.F.-T.); (J.P.d.l.R.)
| | - Juan Pérez de la Rosa
- Animal Health General Directorate, Animal and Plant Health, Food Inspection and Food Safety National Services (SENASICA), Secretariat of Agriculture, Livestock, Rural Development, Fisheries and Food (SAGARPA), Mexico City 06470, Mexico; (R.N.-L.); (M.M.-M.); (M.L.-A.); (M.R.-M.); (E.F.-T.); (J.P.d.l.R.)
| | - Yohannes Berhane
- National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3M4, Canada;
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2S2, Canada
- Correspondence: ; Tel.: +1-204-789-7062
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18
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Wille M, Grillo V, Ban de Gouvea Pedroso S, Burgess GW, Crawley A, Dickason C, Hansbro PM, Hoque MA, Horwood PF, Kirkland PD, Kung NYH, Lynch SE, Martin S, McArthur M, O’Riley K, Read AJ, Warner S, Hoye BJ, Lisovski S, Leen T, Hurt AC, Butler J, Broz I, Davies KR, Mileto P, Neave MJ, Stevens V, Breed AC, Lam TTY, Holmes EC, Klaassen M, Wong FYK. Australia as a global sink for the genetic diversity of avian influenza A virus. PLoS Pathog 2022; 18:e1010150. [PMID: 35536868 PMCID: PMC9089890 DOI: 10.1371/journal.ppat.1010150] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/13/2022] [Indexed: 12/03/2022] Open
Abstract
Most of our understanding of the ecology and evolution of avian influenza A virus (AIV) in wild birds is derived from studies conducted in the northern hemisphere on waterfowl, with a substantial bias towards dabbling ducks. However, relevant environmental conditions and patterns of avian migration and reproduction are substantially different in the southern hemisphere. Through the sequencing and analysis of 333 unique AIV genomes collected from wild birds collected over 15 years we show that Australia is a global sink for AIV diversity and not integrally linked with the Eurasian gene pool. Rather, AIV are infrequently introduced to Australia, followed by decades of isolated circulation and eventual extinction. The number of co-circulating viral lineages varies per subtype. AIV haemagglutinin (HA) subtypes that are rarely identified at duck-centric study sites (H8-12) had more detected introductions and contemporary co-circulating lineages in Australia. Combined with a lack of duck migration beyond the Australian-Papuan region, these findings suggest introductions by long-distance migratory shorebirds. In addition, on the available data we found no evidence of directional or consistent patterns in virus movement across the Australian continent. This feature corresponds to patterns of bird movement, whereby waterfowl have nomadic and erratic rainfall-dependant distributions rather than consistent intra-continental migratory routes. Finally, we detected high levels of virus gene segment reassortment, with a high diversity of AIV genome constellations across years and locations. These data, in addition to those from other studies in Africa and South America, clearly show that patterns of AIV dynamics in the Southern Hemisphere are distinct from those in the temperate north.
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Affiliation(s)
- Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
- Department of Microbiology and Immunology, at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | | | | | - Graham W. Burgess
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia
| | | | | | - Philip M. Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, Australia
| | - Md. Ahasanul Hoque
- Chattogram (previously Chittagong) Veterinary and Animal Sciences University, Khulshi, Bangladesh
| | - Paul F. Horwood
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia
| | - Peter D. Kirkland
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, Australia
| | - Nina Yu-Hsin Kung
- Animal Biosecurity & Welfare, Biosecurity Queensland, Department of Agriculture and Fisheries, Health Food Science Precinct, Coopers Plains, Australia
| | - Stacey E. Lynch
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Australia
| | - Sue Martin
- Department of Primary Industries, Parks, Water and Environment, Hobart, Australia
| | - Michaela McArthur
- Department of Primary Industries and Regional Development, Kensington, Australia
| | - Kim O’Riley
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Australia
| | - Andrew J. Read
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, Australia
| | - Simone Warner
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Australia
| | - Bethany J. Hoye
- Centre for Integrative Ecology, Deakin University, Geelong, Australia
| | - Simeon Lisovski
- Centre for Integrative Ecology, Deakin University, Geelong, Australia
| | - Trent Leen
- Geelong Field & Game, Geelong, Australia
- Wetlands Environmental Taskforce, Field & Game Australia, Seymour, Australia
| | - Aeron C. Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Jeff Butler
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
| | - Ivano Broz
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
| | - Kelly R. Davies
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
| | - Patrick Mileto
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
| | - Matthew J. Neave
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
| | - Vicky Stevens
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
| | - Andrew C. Breed
- Department of Agriculture, Water and the Environment, Canberra, Australia
- University of Queensland, St. Lucia, Australia
| | - Tommy T. Y. Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, PR China
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Marcel Klaassen
- Centre for Integrative Ecology, Deakin University, Geelong, Australia
| | - Frank Y. K. Wong
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
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19
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Zamperin G, Bianco A, Smith J, Bortolami A, Vervelde L, Schivo A, Fortin A, Marciano S, Panzarin V, Mazzetto E, Milani A, Berhane Y, Digard P, Bonfante F, Monne I. Heterogeneity of Early Host Response to Infection with Four Low-Pathogenic H7 Viruses with a Different Evolutionary History in the Field. Viruses 2021; 13:2323. [PMID: 34835129 PMCID: PMC8620788 DOI: 10.3390/v13112323] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022] Open
Abstract
Once low-pathogenic avian influenza viruses (LPAIVs) of the H5 and H7 subtypes from wild birds enter into poultry species, there is the possibility of them mutating into highly pathogenic avian influenza viruses (HPAIVs), resulting in severe epizootics with up to 100% mortality. This mutation from a LPAIV to HPAIV strain is the main cause of an AIV's major economic impact on poultry production. Although AIVs are inextricably linked to their hosts in their evolutionary history, the contribution of host-related factors in the emergence of HPAI viruses has only been marginally explored so far. In this study, transcriptomic sequencing of tracheal tissue from chickens infected with four distinct LP H7 viruses, characterized by a different history of pathogenicity evolution in the field, was implemented. Despite the inoculation of a normalized infectious dose of viruses belonging to the same subtype (H7) and pathotype (LPAI), the use of animals of the same age, sex and species as well as the identification of a comparable viral load in the target samples, the analyses revealed a heterogeneity in the gene expression profile in response to infection with each of the H7 viruses administered.
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Affiliation(s)
- Gianpiero Zamperin
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, 35020 Padua, Italy; (A.B.); (A.B.); (A.S.); (A.F.); (S.M.); (V.P.); (E.M.); (A.M.); (F.B.); (I.M.)
| | - Alice Bianco
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, 35020 Padua, Italy; (A.B.); (A.B.); (A.S.); (A.F.); (S.M.); (V.P.); (E.M.); (A.M.); (F.B.); (I.M.)
| | - Jacqueline Smith
- Easter Bush Campus, The University of Edinburgh, Roslin EH25 9RG, UK; (J.S.); (L.V.); (P.D.)
| | - Alessio Bortolami
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, 35020 Padua, Italy; (A.B.); (A.B.); (A.S.); (A.F.); (S.M.); (V.P.); (E.M.); (A.M.); (F.B.); (I.M.)
| | - Lonneke Vervelde
- Easter Bush Campus, The University of Edinburgh, Roslin EH25 9RG, UK; (J.S.); (L.V.); (P.D.)
| | - Alessia Schivo
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, 35020 Padua, Italy; (A.B.); (A.B.); (A.S.); (A.F.); (S.M.); (V.P.); (E.M.); (A.M.); (F.B.); (I.M.)
| | - Andrea Fortin
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, 35020 Padua, Italy; (A.B.); (A.B.); (A.S.); (A.F.); (S.M.); (V.P.); (E.M.); (A.M.); (F.B.); (I.M.)
| | - Sabrina Marciano
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, 35020 Padua, Italy; (A.B.); (A.B.); (A.S.); (A.F.); (S.M.); (V.P.); (E.M.); (A.M.); (F.B.); (I.M.)
| | - Valentina Panzarin
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, 35020 Padua, Italy; (A.B.); (A.B.); (A.S.); (A.F.); (S.M.); (V.P.); (E.M.); (A.M.); (F.B.); (I.M.)
| | - Eva Mazzetto
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, 35020 Padua, Italy; (A.B.); (A.B.); (A.S.); (A.F.); (S.M.); (V.P.); (E.M.); (A.M.); (F.B.); (I.M.)
| | - Adelaide Milani
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, 35020 Padua, Italy; (A.B.); (A.B.); (A.S.); (A.F.); (S.M.); (V.P.); (E.M.); (A.M.); (F.B.); (I.M.)
| | - Yohannes Berhane
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, 1015 Arlington, Winnipeg, MB R3E 3M4, Canada;
| | - Paul Digard
- Easter Bush Campus, The University of Edinburgh, Roslin EH25 9RG, UK; (J.S.); (L.V.); (P.D.)
| | - Francesco Bonfante
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, 35020 Padua, Italy; (A.B.); (A.B.); (A.S.); (A.F.); (S.M.); (V.P.); (E.M.); (A.M.); (F.B.); (I.M.)
| | - Isabella Monne
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, 35020 Padua, Italy; (A.B.); (A.B.); (A.S.); (A.F.); (S.M.); (V.P.); (E.M.); (A.M.); (F.B.); (I.M.)
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20
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Dupré G, Hoede C, Figueroa T, Bessière P, Bertagnoli S, Ducatez M, Gaspin C, Volmer R. Phylodynamic Study of the Conserved RNA Structure Encompassing the Hemagglutinin Cleavage Site Encoding Region of H5 and H7 Low Pathogenic Avian Influenza Viruses. Virus Evol 2021; 7:veab093. [PMID: 35299790 PMCID: PMC8923263 DOI: 10.1093/ve/veab093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/07/2021] [Accepted: 10/29/2021] [Indexed: 11/14/2022] Open
Abstract
Abstract
Highly Pathogenic Avian Influenza Viruses (HPAIV) evolve from Low Pathogenic Avian Influenza Viruses (LPAIV) of the H5 and H7 subtypes. This evolution is characterized by the acquisition of a multi-basic cleavage site (MBCS) motif in the hemagglutinin (HA) that leads to an extended viral tropism and severe disease in poultry. One key unanswered question is whether the risk of transition to HPAIV is similar for all LPAIV H5 or H7 strains, or whether specific determinants in the HA sequence of some H5 or H7 LPAIV strains correlate with a higher risk of transition to HPAIV. Here we determined if specific features of the conserved RNA stem loop located at the hemagglutinin cleavage site-encoding region could be detected along the LPAIV to HPAIV evolutionary pathway. Analysis of the thermodynamic stability of the predicted RNA structures showed no specific patterns common to HA sequences leading to HPAIV and distinct from those remaining LPAIV. However, RNA structure clustering analysis revealed that most of the American lineage ancestors leading to H7 emergences via recombination shared the same vRNA structure topology at the HA1/HA2 boundary region. Our study thus identified predicted secondary RNA structures present in the HA of H7 viruses, which could promote genetic recombination and acquisition of a MBCS.
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Affiliation(s)
- Gabriel Dupré
- Ecole nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, UMR 1225, Toulouse, France
| | - Claire Hoede
- INRAE, UR875 Mathématiques et Informatique Appliquées Toulouse, Plateforme GenoToul BioInfo, F-31326 Castanet-Tolosan, France
| | - Thomas Figueroa
- Ecole nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, UMR 1225, Toulouse, France
| | - Pierre Bessière
- Ecole nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, UMR 1225, Toulouse, France
| | - Stéphane Bertagnoli
- Ecole nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, UMR 1225, Toulouse, France
| | - Mariette Ducatez
- Ecole nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, UMR 1225, Toulouse, France
| | - Christine Gaspin
- INRAE, UR875 Mathématiques et Informatique Appliquées Toulouse, Plateforme GenoToul BioInfo, F-31326 Castanet-Tolosan, France
| | - Romain Volmer
- Ecole nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, UMR 1225, Toulouse, France
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21
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Goldhill DH, Barclay WS. 2020 Hindsight: Should evolutionary virologists have expected the unexpected during a pandemic? Evolution 2021; 75:2311-2316. [PMID: 34342897 PMCID: PMC8444725 DOI: 10.1111/evo.14317] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/21/2021] [Accepted: 07/12/2021] [Indexed: 12/11/2022]
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22
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Virus Adaptation Following Experimental Infection of Chickens with a Domestic Duck Low Pathogenic Avian Influenza Isolate from the 2017 USA H7N9 Outbreak Identifies Polymorphic Mutations in Multiple Gene Segments. Viruses 2021; 13:v13061166. [PMID: 34207098 PMCID: PMC8234733 DOI: 10.3390/v13061166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/09/2021] [Accepted: 06/15/2021] [Indexed: 11/17/2022] Open
Abstract
In March 2017, highly pathogenic (HP) and low pathogenic (LP) avian influenza virus (AIV) subtype H7N9 were detected from poultry farms and backyard birds in several states in the southeast United States. Because interspecies transmission is a known mechanism for evolution of AIVs, we sought to characterize infection and transmission of a domestic duck-origin H7N9 LPAIV in chickens and genetically compare the viruses replicating in the chickens to the original H7N9 clinical field samples used as inoculum. The results of the experimental infection demonstrated virus replication and transmission in chickens, with overt clinical signs of disease and shedding through both oral and cloacal routes. Unexpectedly, higher levels of virus shedding were observed in some cloacal swabs. Next generation sequencing (NGS) analysis identified numerous non-synonymous mutations at the consensus level in the polymerase genes (i.e., PA, PB1, and PB2) and the hemagglutinin (HA) receptor binding site in viruses recovered from chickens, indicating possible virus adaptation in the new host. For comparison, NGS analysis of clinical samples obtained from duck specimen collected during the outbreak indicated three polymorphic sides in the M1 segment and a minor population of viruses carrying the D139N (21.4%) substitution in the NS1 segment. Interestingly, at consensus level, A/duck/Alabama (H7N9) had isoleucine at position 105 in NP protein, similar to HPAIV (H7N9) but not to LPAIV (H7N9) isolated from the same 2017 influenza outbreak in the US. Taken together, this work demonstrates that the H7N9 viruses could readily jump between avian species, which may have contributed to the evolution of the virus and its spread in the region.
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23
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Telwatte S, Kumar N, Vallejo-Gracia A, Kumar GR, Lu CM, Ott M, Wong JK, Yukl SA. Novel RT-ddPCR assays for simultaneous quantification of multiple noncoding and coding regions of SARS-CoV-2 RNA. J Virol Methods 2021; 292:114115. [PMID: 33667568 PMCID: PMC7923865 DOI: 10.1016/j.jviromet.2021.114115] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/02/2021] [Accepted: 02/25/2021] [Indexed: 12/19/2022]
Abstract
A hallmark of coronavirus transcription is the generation of negative-sense RNA intermediates that serve as the templates for the synthesis of positive-sense genomic RNA (gRNA) and an array of subgenomic mRNAs (sgRNAs) encompassing sequences arising from discontinuous transcription. Existing PCR-based diagnostic assays for SAR-CoV-2 are qualitative or semi-quantitative and do not provide the resolution needed to assess the complex transcription dynamics of SARS-CoV-2 over the course of infection. We developed and validated a novel panel of sensitive, quantitative RT-ddPCR assays designed to target regions spanning the genome of SARS-CoV-2. Our assays target untranslated regions (5', 3') as well as different coding regions, including non-structural genes that are only found in full length (genomic) RNA and structural genes that are found in genomic as well as different subgenomic RNAs. Application of these assays to clinically relevant samples will enhance our understanding of SARS-CoV-2 gene expression and may also inform the development of improved diagnostic tools and therapeutics.
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Affiliation(s)
- Sushama Telwatte
- Department of Medicine, University of California, San Francisco, CA, USA; Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, USA
| | - Nitasha Kumar
- Department of Medicine, University of California, San Francisco, CA, USA; Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, USA
| | | | - G Renuka Kumar
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
| | - Chuanyi M Lu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA; Department of Laboratory Medicine, San Francisco VA Health Care System, San Francisco, CA, USA
| | - Melanie Ott
- Department of Medicine, University of California, San Francisco, CA, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
| | - Joseph K Wong
- Department of Medicine, University of California, San Francisco, CA, USA; Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, USA
| | - Steven A Yukl
- Department of Medicine, University of California, San Francisco, CA, USA; Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, USA.
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24
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Greening SS, Rawdon TG, Mulqueen K, French NP, Gates MC. Using multiple data sources to explore disease transmission risk between commercial poultry, backyard poultry, and wild birds in New Zealand. Prev Vet Med 2021; 190:105327. [PMID: 33740595 DOI: 10.1016/j.prevetmed.2021.105327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 03/07/2021] [Accepted: 03/09/2021] [Indexed: 11/30/2022]
Abstract
The movements of backyard poultry and wild bird populations are known to pose a disease risk to the commercial poultry industry. However, it is often difficult to estimate this risk due to the lack of accurate data on the numbers, locations, and movement patterns of these populations. The main aim of this study was to evaluate the use of three different data sources when investigating disease transmission risk between poultry populations in New Zealand including (1) cross-sectional survey data looking at the movement of goods and services within the commercial poultry industry, (2) backyard poultry sales data from the online auction site TradeMe®, and (3) citizen science data from the wild bird monitoring project eBird. The cross-sectional survey data and backyard poultry sales data were transformed into network graphs showing the connectivity of commercial and backyard poultry producers across different geographical regions. The backyard poultry network was also used to parameterise a Susceptible-Infectious (SI) simulation model to explore the behaviour of potential disease outbreaks. The citizen science data was used to create an additional map showing the spatial distribution of wild bird observations across New Zealand. To explore the potential for diseases to spread between each population, maps were combined into bivariate choropleth maps showing the overlap between movements within the commercial poultry industry, backyard poultry trades and, wild bird observations. Network analysis revealed that the commercial poultry network was highly connected with geographical clustering around the urban centres of Auckland, New Plymouth and Christchurch. The backyard poultry network was also a highly active trade network and displayed similar geographic clustering to the commercial network. In the disease simulation models, the high connectivity resulted in all suburbs becoming infected in 96.4 % of the SI simulations. Analysis of the eBird data included reports of over 80 species; the majority of which were identified as coastal seabirds or wading birds that showed little overlap with either backyard or commercial poultry. Overall, our study findings highlight how the spatial patterns of trading activity within the commercial poultry industry, alongside the movement of backyard poultry and wild birds, have the potential to contribute significantly to the spread of diseases between these populations. However, it is clear that in order to fully understand this risk landscape, further data integration is needed; including the use of additional datasets that have further information on critical variables such as environmental factors.
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Affiliation(s)
- Sabrina S Greening
- Massey University School of Veterinary Science, Palmerston North, 4442, New Zealand.
| | - Thomas G Rawdon
- Diagnostic and Surveillance Services Directorate, Ministry for Primary Industries, Wellington, 6140, New Zealand
| | - Kerry Mulqueen
- Poultry Industry Association of New Zealand (PIANZ), Auckland, 1023, New Zealand
| | - Nigel P French
- Infectious Disease Research Centre, Massey University School of Veterinary Science, Palmerston North, 4442, New Zealand; New Zealand Food Safety Science and Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, 4442, New Zealand
| | - M Carolyn Gates
- Massey University School of Veterinary Science, Palmerston North, 4442, New Zealand
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25
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Kjaer LJ, Hjulsager CK, Larsen LE, Boklund AE, Halasa T, Ward MP, Kirkeby CT. Landscape effects and spatial patterns of avian influenza virus in Danish wild birds, 2006-2020. Transbound Emerg Dis 2021; 69:706-719. [PMID: 33600073 PMCID: PMC9291307 DOI: 10.1111/tbed.14040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/22/2021] [Accepted: 02/16/2021] [Indexed: 11/28/2022]
Abstract
Avian influenza (AI) is a contagious disease of birds with zoonotic potential. AI virus (AIV) can infect most bird species, but clinical signs and mortality vary. Assessing the distribution and factors affecting AI presence can direct targeted surveillance to areas at risk of disease outbreaks, or help identify disease hotspots or areas with inadequate surveillance. Using virus surveillance data from passive and active AIV wild bird surveillance, 2006−2020, we investigated the association between the presence of AIV and a range of landscape factors and game bird release. Furthermore, we assessed potential bias in the passive AIV surveillance data submitted by the public, via factors related to public accessibility. Lastly, we tested the AIV data for possible hot‐ and cold spots within Denmark. The passive surveillance data was biased regarding accessibility to areas (distance to roads, cities and coast) compared to random locations within Denmark. For both the passive and active AIV surveillance data, we found significant (p < .01) associations with variables related to coast, wetlands and cities, but not game bird release. We used these variables to predict the risk of AIV presence throughout Denmark, and found high‐risk areas concentrated along the coast and fjords. For both passive and active surveillance data, low‐risk clusters were mainly seen in Jutland and northern Zealand, whereas high‐risk clusters were found in Jutland, Zealand, Funen and the southern Isles such as Lolland and Falster. Our results suggest that landscape affects AIV presence, as coastal areas and wetlands attract waterfowl and migrating birds and therefore might increase the potential for AIV transmission. Our findings have enabled us to create risk maps of AIV presence in wild birds and pinpoint high‐risk clusters within Denmark. This will aid targeted surveillance efforts within Denmark and potentially aid in planning the location of future poultry farms.
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Affiliation(s)
- Lene Jung Kjaer
- Faculty of Health and Medical Sciences, Section for Animal Welfare and Disease Control, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Lars Erik Larsen
- Faculty of Health and Medical Sciences, Section for Animal Welfare and Disease Control, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Anette Ella Boklund
- Faculty of Health and Medical Sciences, Section for Animal Welfare and Disease Control, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Tariq Halasa
- Faculty of Health and Medical Sciences, Section for Animal Welfare and Disease Control, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Michael P Ward
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Camden NSW, Australia
| | - Carsten Thure Kirkeby
- Faculty of Health and Medical Sciences, Section for Animal Welfare and Disease Control, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
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26
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Gultyaev AP, Spronken MI, Funk M, Fouchier RAM, Richard M. Insertions of codons encoding basic amino acids in H7 hemagglutinins of influenza A viruses occur by recombination with RNA at hotspots near snoRNA binding sites. RNA (NEW YORK, N.Y.) 2021; 27:123-132. [PMID: 33188057 PMCID: PMC7812872 DOI: 10.1261/rna.077495.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/06/2020] [Indexed: 06/11/2023]
Abstract
The presence of multiple basic amino acids in the protease cleavage site of the hemagglutinin (HA) protein is the main molecular determinant of virulence of highly pathogenic avian influenza (HPAI) viruses. Recombination of HA RNA with other RNA molecules of host or virus origin is a dominant mechanism of multibasic cleavage site (MBCS) acquisition for H7 subtype HA. Using alignments of HA RNA sequences from documented cases of MBCS insertion due to recombination, we show that such recombination with host RNAs is most likely to occur at particular hotspots in ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), and viral RNAs. The locations of these hotspots in highly abundant RNAs indicate that RNA recombination is facilitated by the binding of small nucleolar RNA (snoRNA) near the recombination points.
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MESH Headings
- Amino Acids, Basic/genetics
- Amino Acids, Basic/metabolism
- Animals
- Base Pairing
- Base Sequence
- Chickens/virology
- Codon
- Gene Expression Regulation
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/metabolism
- Host-Pathogen Interactions/genetics
- Humans
- Influenza A virus/genetics
- Influenza A virus/metabolism
- Influenza A virus/pathogenicity
- Influenza in Birds/virology
- Influenza, Human/virology
- Mutagenesis, Insertional
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Recombination, Genetic
- Sequence Alignment
- Virulence
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Affiliation(s)
- Alexander P Gultyaev
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, the Netherlands
- Group Imaging and Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, 2300 RA Leiden, the Netherlands
| | - Monique I Spronken
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, the Netherlands
| | - Mathis Funk
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, the Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, the Netherlands
| | - Mathilde Richard
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, the Netherlands
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27
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Telwatte S, Kumar N, Vallejo-Gracia A, Kumar GR, Lu CM, Ott M, Wong JK, Yukl SA. Novel RT-ddPCR Assays for determining the transcriptional profile of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.12.425991. [PMID: 33469579 PMCID: PMC7814816 DOI: 10.1101/2021.01.12.425991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The exact mechanism of coronavirus replication and transcription is not fully understood; however, a hallmark of coronavirus transcription is the generation of negative-sense RNA intermediates that serve as the templates for the synthesis of positive-sense genomic RNA (gRNA) and an array of subgenomic mRNAs (sgRNAs) encompassing sequences arising from discontinuous transcription. Existing PCR-based diagnostic assays for SAR-CoV-2 are qualitative or semi-quantitative and do not provide the resolution needed to assess the complex transcription dynamics of SARS-CoV-2 over the course of infection. We developed and validated a novel panel of specially designed SARS-CoV-2 ddPCR-based assays to map the viral transcription profile. Application of these assays to clinically relevant samples will enhance our understanding of SARS-CoV-2 replication and transcription and may also inform the development of improved diagnostic tools and therapeutics.
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Affiliation(s)
- Sushama Telwatte
- Department of Medicine, University of California, San Francisco, CA, USA
- Department of Infectious Diseases, San Francisco VA Health Care System, San Francisco, CA, USA
| | - Nitasha Kumar
- Department of Medicine, University of California, San Francisco, CA, USA
- Department of Infectious Diseases, San Francisco VA Health Care System, San Francisco, CA, USA
| | | | - G. Renuka Kumar
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
| | - Chuanyi M. Lu
- Department of Medicine, University of California, San Francisco, CA, USA
- Department of Infectious Diseases, San Francisco VA Health Care System, San Francisco, CA, USA
| | - Melanie Ott
- Department of Medicine, University of California, San Francisco, CA, USA
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
| | - Joseph K. Wong
- Department of Medicine, University of California, San Francisco, CA, USA
- Department of Infectious Diseases, San Francisco VA Health Care System, San Francisco, CA, USA
| | - Steven A. Yukl
- Department of Medicine, University of California, San Francisco, CA, USA
- Department of Infectious Diseases, San Francisco VA Health Care System, San Francisco, CA, USA
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Sánchez-González R, Ramis A, Nofrarías M, Wali N, Valle R, Pérez M, Perlas A, Majó N. Experimental infection of domestic geese ( Anser anser var. domesticus) with H5N8 Gs/GD and H7N1 highly pathogenic avian influenza viruses. Avian Pathol 2020; 49:642-657. [PMID: 32795171 DOI: 10.1080/03079457.2020.1809635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Prior to the emergence of the Asian-origin H5 Goose/Guangdong/1/96 (Gs/GD) lineage, highly pathogenic avian influenza viruses (HPAIV) had rarely caused high mortalities in domestic geese. In 2016/2017 European epidemics, H5N8 Gs/GD clade 2.3.4.4 Group B produced an unprecedented number of outbreaks in waterfowl holdings. In this study, the pathogenesis of H5N8 HPAIV in comparison with H7N1 HPAIV, and the role of domestic geese in the epidemiology of these viruses, were evaluated. Local and commercial geese (Anser anser var. domesticus) were intranasally inoculated with 105 ELD50 of A/goose/Spain/IA17CR02699/2017 (H5N8) or A/Chicken/Italy/5093/1999 (H7N1) and monitored daily during 15 days. H5N8 was highly virulent to domestic geese, reaching 100% mortality by 10 days post-infection. Systemic microscopic necrotizing lesions associated with widespread AIV-antigen were detected by IHC techniques, the central nervous system being the most severely affected. High viral loads, measured by qRT-PCR, were present in all samples collected: oral and cloacal swabs, plasma tissues, and moderate levels in pool water. Domestic geese were also susceptible to H7N1 infection, as demonstrated by seroconversion and detection of viral RNA in tissues and plasma in some geese, but all lacked clinical signs. Viral shedding was confirmed in only some geese and was restricted to the oral route, but levels were high and still detected at the end of the study. Overall, H7N1 presents a lower lethality and shedding than H5N8 in geese; however, the viral shedding indicates that these species could play a role in the epidemiology of Gs/GD and other lineages of HPAIVs. RESEARCH HIGHLIGHTS H5N8 Gs/GD clade 2.3.4.4 Group B is highly virulent to domestic geese. The severity of H5N8 is associated with multisystemic replication. H7N1 can infect domestic geese but is avirulent to this species. Domestic geese could play a role in the epidemiology of Gs/GD HPAIVs.
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Affiliation(s)
- R Sánchez-González
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, España.,Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, España
| | - A Ramis
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, España.,Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, España
| | - M Nofrarías
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, España
| | - N Wali
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, España
| | - R Valle
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, España
| | - M Pérez
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, España
| | - A Perlas
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, España
| | - N Majó
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, España.,Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, España
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29
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Escalera-Zamudio M, Golden M, Gutiérrez B, Thézé J, Keown JR, Carrique L, Bowden TA, Pybus OG. Parallel evolution in the emergence of highly pathogenic avian influenza A viruses. Nat Commun 2020; 11:5511. [PMID: 33139731 PMCID: PMC7608645 DOI: 10.1038/s41467-020-19364-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/12/2020] [Indexed: 01/30/2023] Open
Abstract
Parallel molecular evolution and adaptation are important phenomena commonly observed in viruses. Here, we exploit parallel molecular evolution to understand virulence evolution in avian influenza viruses (AIV). Highly-pathogenic AIVs evolve independently from low-pathogenic ancestors via acquisition of polybasic cleavage sites. Why some AIV lineages but not others evolve in this way is unknown. We hypothesise that the parallel emergence of highly-pathogenic AIV may be facilitated by permissive or compensatory mutations occurring across the viral genome. We combine phylogenetic, statistical and structural approaches to discover parallel mutations in AIV genomes associated with the highly-pathogenic phenotype. Parallel mutations were screened using a statistical test of mutation-phenotype association and further evaluated in the contexts of positive selection and protein structure. Our resulting mutational panel may help to reveal new links between virulence evolution and other traits, and raises the possibility of predicting aspects of AIV evolution.
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Affiliation(s)
| | - Michael Golden
- Department of Zoology, Oxford University, Parks Rd, Oxford, OX1 3PS, UK
| | | | - Julien Thézé
- Department of Zoology, Oxford University, Parks Rd, Oxford, OX1 3PS, UK
| | - Jeremy Russell Keown
- Division of Structural Biology, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Loic Carrique
- Division of Structural Biology, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Oliver G Pybus
- Department of Zoology, Oxford University, Parks Rd, Oxford, OX1 3PS, UK.
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK.
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Laleye AT, Abolnik C. Emergence of highly pathogenic H5N2 and H7N1 influenza A viruses from low pathogenic precursors by serial passage in ovo. PLoS One 2020; 15:e0240290. [PMID: 33031421 PMCID: PMC7544131 DOI: 10.1371/journal.pone.0240290] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/24/2020] [Indexed: 02/01/2023] Open
Abstract
Highly pathogenic (HPAI) strains emerge from their low pathogenic (LPAI) precursors and cause severe disease in poultry with enormous economic losses, and zoonotic potential. Understanding the mechanisms involved in HPAI emergence is thus an important goal for risk assessments. In this study ostrich-origin H5N2 and H7N1 LPAI progenitor viruses were serially passaged seventeen times in 14-day old embryonated chicken eggs and Ion Torrent ultra-deep sequencing was used to monitor the incremental changes in the consensus genome sequences. Both virus strains increased in virulence with successive passages, but the H7N1 virus attained a virulent phenotype sooner. Mutations V63M, E228V and D272G in the HA protein, Q357K in the nucleoprotein (NP) and H155P in the neuraminidase protein correlated with the increased pathogenicity of the H5N2 virus; whereas R584H and L589I substitutions in the polymerase B2 protein, A146T and Q220E in HA plus D231N in the matrix 1 protein correlated with increased pathogenicity of the H7N1 virus in embryos. Enzymatic cleavage of HA protein is the critical virulence determinant, and HA cleavage site motifs containing multibasic amino acids were detected at the sub-consensus level. The motifs PQERRR/GLF and PQRERR/GLF were first detected in passages 11 and 15 respectively of the H5N2 virus, and in the H7N1 virus the motifs PELPKGKK/GLF and PELPKRR/GLF were detected as early as passage 7. Most significantly, a 13 nucleotide insert of unknown origin was identified at passage 6 of the H5N2 virus, and at passage 17 a 42 nucleotide insert derived from the influenza NP gene was identified. This is the first report of non-homologous recombination at the HA cleavage site in an H5 subtype virus. This study provides insights into how HPAI viruses emerge from low pathogenic precursors and demonstrated the pathogenic potential of H5N2 and H7N1 strains that have not yet been implicated in HPAI outbreaks.
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Affiliation(s)
- Agnes Tinuke Laleye
- National Veterinary Research Institute, Vom, Nigeria
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Celia Abolnik
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
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31
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Sriwilaijaroen N, Suzuki Y. Host Receptors of Influenza Viruses and Coronaviruses-Molecular Mechanisms of Recognition. Vaccines (Basel) 2020; 8:E587. [PMID: 33036202 PMCID: PMC7712180 DOI: 10.3390/vaccines8040587] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 12/19/2022] Open
Abstract
Among the four genera of influenza viruses (IVs) and the four genera of coronaviruses (CoVs), zoonotic αIV and βCoV have occasionally caused airborne epidemic outbreaks in humans, who are immunologically naïve, and the outbreaks have resulted in high fatality rates as well as social and economic disruption and losses. The most devasting influenza A virus (IAV) in αIV, pandemic H1N1 in 1918, which caused at least 40 million deaths from about 500 million cases of infection, was the first recorded emergence of IAVs in humans. Usually, a novel human-adapted virus replaces the preexisting human-adapted virus. Interestingly, two IAV subtypes, A/H3N2/1968 and A/H1N1/2009 variants, and two lineages of influenza B viruses (IBV) in βIV, B/Yamagata and B/Victoria lineage-like viruses, remain seasonally detectable in humans. Both influenza C viruses (ICVs) in γIV and four human CoVs, HCoV-229E and HCoV-NL63 in αCoV and HCoV-OC43 and HCoV-HKU1 in βCoV, usually cause mild respiratory infections. Much attention has been given to CoVs since the global epidemic outbreaks of βSARS-CoV in 2002-2004 and βMERS-CoV from 2012 to present. βSARS-CoV-2, which is causing the ongoing COVID-19 pandemic that has resulted in 890,392 deaths from about 27 million cases of infection as of 8 September 2020, has provoked worldwide investigations of CoVs. With the aim of developing efficient strategies for controlling virus outbreaks and recurrences of seasonal virus variants, here we overview the structures, diversities, host ranges and host receptors of all IVs and CoVs and critically review current knowledge of receptor binding specificity of spike glycoproteins, which mediates infection, of IVs and of zoonotic, pandemic and seasonal CoVs.
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Affiliation(s)
- Nongluk Sriwilaijaroen
- Department of Preclinical Sciences, Faculty of Medicine, Thammasat University, Pathumthani 12120, Thailand
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Shizuoka 422-8526, Japan
| | - Yasuo Suzuki
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Shizuoka 422-8526, Japan
- College of Life and Health Sciences, Chubu University, Kasugai, Aichi 487-8501, Japan
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Flores-Alanis A, Sandner-Miranda L, Delgado G, Cravioto A, Morales-Espinosa R. The receptor binding domain of SARS-CoV-2 spike protein is the result of an ancestral recombination between the bat-CoV RaTG13 and the pangolin-CoV MP789. BMC Res Notes 2020; 13:398. [PMID: 32854762 PMCID: PMC7450963 DOI: 10.1186/s13104-020-05242-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/19/2020] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE In December 2019 a novel coronavirus (SARS-CoV-2) that is causing the current COVID-19 pandemic was identified in Wuhan, China. Many questions have been raised about its origin and adaptation to humans. In the present work we performed a genetic analysis of the Spike glycoprotein (S) of SARS-CoV-2 and other related coronaviruses (CoVs) isolated from different hosts in order to trace the evolutionary history of this protein and the adaptation of SARS-CoV-2 to humans. RESULTS Based on the sequence analysis of the S gene, we suggest that the origin of SARS-CoV-2 is the result of recombination events between bat and pangolin CoVs. The hybrid SARS-CoV-2 ancestor jumped to humans and has been maintained by natural selection. Although the S protein of RaTG13 bat CoV has a high nucleotide identity with the S protein of SARS-CoV-2, the phylogenetic tree and the haplotype network suggest a non-direct parental relationship between these CoVs. Moreover, it is likely that the basic function of the receptor-binding domain (RBD) of S protein was acquired by the SARS-CoV-2 from the MP789 pangolin CoV by recombination and it has been highly conserved.
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Affiliation(s)
- Alejandro Flores-Alanis
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luisa Sandner-Miranda
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Gabriela Delgado
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Alejandro Cravioto
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rosario Morales-Espinosa
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Seekings AH, Howard WA, Nuñéz A, Slomka MJ, Banyard AC, Hicks D, Ellis RJ, Nuñéz-García J, Hartgroves LC, Barclay WS, Banks J, Brown IH. The Emergence of H7N7 Highly Pathogenic Avian Influenza Virus from Low Pathogenicity Avian Influenza Virus Using an in ovo Embryo Culture Model. Viruses 2020; 12:v12090920. [PMID: 32839404 PMCID: PMC7552004 DOI: 10.3390/v12090920] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/15/2020] [Accepted: 08/18/2020] [Indexed: 01/19/2023] Open
Abstract
Outbreaks of highly pathogenic avian influenza virus (HPAIV) often result in the infection of millions of poultry, causing up to 100% mortality. HPAIV has been shown to emerge from low pathogenicity avian influenza virus (LPAIV) in field outbreaks. Direct evidence for the emergence of H7N7 HPAIV from a LPAIV precursor with a rare di-basic cleavage site (DBCS) was identified in the UK in 2008. The DBCS contained an additional basic amino acid compared to commonly circulating LPAIVs that harbor a single-basic amino acid at the cleavage site (SBCS). Using reverse genetics, outbreak HPAIVs were rescued with a DBCS (H7N7DB), as seen in the LPAIV precursor or an SBCS representative of common H7 LPAIVs (H7N7SB). Passage of H7N7DB in chicken embryo tissues showed spontaneous evolution to a HPAIV. In contrast, deep sequencing of extracts from embryo tissues in which H7N7SB was serially passaged showed retention of the LPAIV genotype. Thus, in chicken embryos, an H7N7 virus containing a DBCS appears naturally unstable, enabling rapid evolution to HPAIV. Evaluation in embryo tissue presents a useful approach to study AIV evolution and allows a laboratory-based dissection of molecular mechanisms behind the emergence of HPAIV.
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Affiliation(s)
- Amanda H. Seekings
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, UK; (W.A.H.); (M.J.S.); (A.C.B.); (J.B.); (I.H.B.)
- Correspondence:
| | - Wendy A. Howard
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, UK; (W.A.H.); (M.J.S.); (A.C.B.); (J.B.); (I.H.B.)
| | - Alejandro Nuñéz
- Pathology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, UK; (A.N.); (D.H.)
| | - Marek J. Slomka
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, UK; (W.A.H.); (M.J.S.); (A.C.B.); (J.B.); (I.H.B.)
| | - Ashley C. Banyard
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, UK; (W.A.H.); (M.J.S.); (A.C.B.); (J.B.); (I.H.B.)
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
- Institute for Infection and Immunity, St. George’s Hospital Medical School, University of London, London SW17 0RE, UK
| | - Daniel Hicks
- Pathology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, UK; (A.N.); (D.H.)
| | - Richard J. Ellis
- Surveillance and Laboratory Services Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, UK; (R.J.E.); (J.N.-G.)
| | - Javier Nuñéz-García
- Surveillance and Laboratory Services Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, UK; (R.J.E.); (J.N.-G.)
| | | | - Wendy S. Barclay
- Virology Department, Imperial College, London W2 1NY, UK; (L.C.H.); (W.S.B.)
| | - Jill Banks
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, UK; (W.A.H.); (M.J.S.); (A.C.B.); (J.B.); (I.H.B.)
| | - Ian H. Brown
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, UK; (W.A.H.); (M.J.S.); (A.C.B.); (J.B.); (I.H.B.)
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Genetic characteristics and pathogenesis of H5 low pathogenic avian influenza viruses from wild birds and domestic ducks in South Korea. Sci Rep 2020; 10:12151. [PMID: 32699272 PMCID: PMC7376034 DOI: 10.1038/s41598-020-68720-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/09/2020] [Indexed: 02/07/2023] Open
Abstract
H5 and H7 subtypes of low pathogenic avian influenza viruses (LPAIVs) can mutate to highly pathogenic forms and are therefore subject to stringent controls. We characterized H5 LPAIVs isolated from wild-bird habitats and duck farms in South Korea from 2010 to 2017. Through nationwide active surveillance for AIVs, 59 H5 LPAIVs were isolated from wild-bird habitats (a mean annual rate of 5.3% of AIV isolations). In 2015, one LPAI H5N3 strain was isolated on a duck farm. Phylogenetic analysis revealed that the hemagglutinin (HA) gene of H5 isolates belonged to the Eurasian lineage, classified into three subgroups (HA-II, HA-III, and HA-IV). The H5 LPAIVs of the HA-III and HA-IV subgroups appeared in 2015 and 2017 in unusually high proportions (13.1% and 14.4%, respectively). In gene-constellation analysis, H5 LPAIVs isolated from 2015 to 2017 constituted ≥ 35 distinct genotypes, representing high levels of genetic diversity. Representative strains of three HA subgroups replicated restrictively in specific-pathogen-free chickens. Among the 11 isolates that were tested, 10 infected and replicated in mice without prior adaptation. The frequency of recent H5 LPAIV isolates with high genetic diversity indicates the importance of continued surveillance in both wild birds and poultry to monitor genetic and pathobiological changes.
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Zhou H, Chen X, Hu T, Li J, Song H, Liu Y, Wang P, Liu D, Yang J, Holmes EC, Hughes AC, Bi Y, Shi W. A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein. Curr Biol 2020; 30:2196-2203.e3. [PMID: 32416074 PMCID: PMC7211627 DOI: 10.1016/j.cub.2020.05.023] [Citation(s) in RCA: 374] [Impact Index Per Article: 93.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/01/2020] [Accepted: 05/06/2020] [Indexed: 01/10/2023]
Abstract
The unprecedented pandemic of pneumonia caused by a novel coronavirus, SARS-CoV-2, in China and beyond has had major public health impacts on a global scale [1, 2]. Although bats are regarded as the most likely natural hosts for SARS-CoV-2 [3], the origins of the virus remain unclear. Here, we report a novel bat-derived coronavirus, denoted RmYN02, identified from a metagenomic analysis of samples from 227 bats collected from Yunnan Province in China between May and October 2019. Notably, RmYN02 shares 93.3% nucleotide identity with SARS-CoV-2 at the scale of the complete virus genome and 97.2% identity in the 1ab gene, in which it is the closest relative of SARS-CoV-2 reported to date. In contrast, RmYN02 showed low sequence identity (61.3%) to SARS-CoV-2 in the receptor-binding domain (RBD) and might not bind to angiotensin-converting enzyme 2 (ACE2). Critically, and in a similar manner to SARS-CoV-2, RmYN02 was characterized by the insertion of multiple amino acids at the junction site of the S1 and S2 subunits of the spike (S) protein. This provides strong evidence that such insertion events can occur naturally in animal betacoronaviruses.
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Affiliation(s)
- Hong Zhou
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University, and Shandong Academy of Medical Sciences, Taian 271000, China
| | - Xing Chen
- Landscape Ecology Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Tao Hu
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University, and Shandong Academy of Medical Sciences, Taian 271000, China
| | - Juan Li
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University, and Shandong Academy of Medical Sciences, Taian 271000, China
| | - Hao Song
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanran Liu
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University, and Shandong Academy of Medical Sciences, Taian 271000, China
| | - Peihan Wang
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University, and Shandong Academy of Medical Sciences, Taian 271000, China
| | - Di Liu
- Computational Virology Group, Center for Bacteria and Virus Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jing Yang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS Center for Influenza Research and Early-Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Alice C Hughes
- Landscape Ecology Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China.
| | - Yuhai Bi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS Center for Influenza Research and Early-Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China.
| | - Weifeng Shi
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University, and Shandong Academy of Medical Sciences, Taian 271000, China; The First Affiliated Hospital of Shandong First Medical University (Shandong Provincial Qianfoshan Hospital), Ji'nan 250014, China.
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Gonzales JL, Pritz-Verschuren S, Bouwstra R, Wiegel J, Elbers ARW, Beerens N. Seasonal risk of low pathogenic avian influenza virus introductions into free-range layer farms in the Netherlands. Transbound Emerg Dis 2020; 68:127-136. [PMID: 32506770 PMCID: PMC8048991 DOI: 10.1111/tbed.13649] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 05/06/2020] [Accepted: 05/20/2020] [Indexed: 01/30/2023]
Abstract
Poultry can become infected with avian influenza viruses (AIV) via (in) direct contact with infected wild birds. Free‐range chicken farms in the Netherlands were shown to have a higher risk for introduction of low pathogenic avian influenza (LPAI) virus than indoor chicken farms. Therefore, during outbreaks of highly pathogenic avian influenza (HPAI), free‐range layers are confined indoors as a risk mitigation measure. In this study, we characterized the seasonal patterns of AIV introductions into free‐range layer farms, to determine the high‐risk period. Data from the LPAI serological surveillance programme for the period 2013–2016 were used to first estimate the time of virus introduction into affected farms and then assess seasonal patterns in the risk of introduction. Time of introduction was estimated by fitting a mathematical model to seroprevalence data collected longitudinally from infected farms. For the period 2015–2016, longitudinal follow‐up included monthly collections of eggs for serological testing from a cohort of 261 farms. Information on the time of introduction was then used to estimate the monthly incidence and seasonality by fitting harmonic and Poisson regression models. A significant yearly seasonal risk of introduction that lasted around 4 months (November to February) was identified with the highest risk observed in January. The risk for introduction of LPAI viruses in this period was on average four times significantly higher than the period of low risk around the summer months. Although the data for HPAI infections were limited in the period 2014–2018, a similar risk period for introduction of HPAI viruses was observed. The results of this study can be used to optimize risk‐based surveillance and inform decisions on timing and duration of indoor confinement when HPAI viruses are known to circulate in the wild bird population.
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Affiliation(s)
- Jose L Gonzales
- Wageningen Bioveterinary Research (WBVR), Lelystad, the Netherlands
| | | | | | | | - Armin R W Elbers
- Wageningen Bioveterinary Research (WBVR), Lelystad, the Netherlands
| | - Nancy Beerens
- Wageningen Bioveterinary Research (WBVR), Lelystad, the Netherlands
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Abstract
In 1918, a strain of influenza A virus caused a human pandemic resulting in the deaths of 50 million people. A century later, with the advent of sequencing technology and corresponding phylogenetic methods, we know much more about the origins, evolution and epidemiology of influenza epidemics. Here we review the history of avian influenza viruses through the lens of their genetic makeup: from their relationship to human pandemic viruses, starting with the 1918 H1N1 strain, through to the highly pathogenic epidemics in birds and zoonoses up to 2018. We describe the genesis of novel influenza A virus strains by reassortment and evolution in wild and domestic bird populations, as well as the role of wild bird migration in their long-range spread. The emergence of highly pathogenic avian influenza viruses, and the zoonotic incursions of avian H5 and H7 viruses into humans over the last couple of decades are also described. The threat of a new avian influenza virus causing a human pandemic is still present today, although control in domestic avian populations can minimize the risk to human health. This article is part of the theme issue ‘Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes’. This issue is linked with the subsequent theme issue ‘Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control’.
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Affiliation(s)
| | | | - Paul Digard
- The Roslin Institute, University of Edinburgh , Edinburgh , UK
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Xu W, Weese JS, Ojkic D, Lung O, Handel K, Berhane Y. Phylogenetic Inference of H3N2 Canine Influenza A Outbreak in Ontario, Canada in 2018. Sci Rep 2020; 10:6309. [PMID: 32286409 PMCID: PMC7156495 DOI: 10.1038/s41598-020-63278-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/12/2020] [Indexed: 11/09/2022] Open
Abstract
The first Canadian H3N2 canine influenza A outbreak involving an Asian-origin H3N2 canine influenza virus (CIV) began in southwestern Ontario, Canada, in late December 2017. More H3N2 CIV cases were identified in central and eastern Ontario between March and October 2018. Based on epidemiological investigation, 5 clusters were identified (C1, C2, C3a, C3b, and C4); however, the origin of infection has only been revealed for epidemiological cluster C1. Here, we use phylogenetic analyses to unravel the links of virus transmission between the 5 epidemiological clusters and the origin of infection for all epidemiological clusters. Our results demonstrate that the Canadian H3N2 CIV sequences were grouped into four distinct phylogenetic clusters with minimal genetic diversity between these clusters. Large scale phylogenetic analysis of H3N2 CIV from around the globe showed that the Canadian CIVs formed a distinct new clade along with CIVs that have been circulating in the USA since 2017-2018 and in China since 2017. This clade shares a common ancestor of Asian origin. This study concludes that the H3N2 CIV outbreak in Ontario was driven by multiple introductions of South Korean/Chinese-origin H3N2 CIVs over 10 months.
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Affiliation(s)
- Wanhong Xu
- National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3M4, Canada
| | - J Scott Weese
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Davor Ojkic
- Animal Health Laboratory, University of Guelph, Guelph, Ontario, Canada
| | - Oliver Lung
- National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3M4, Canada
| | - Katherine Handel
- National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3M4, Canada
| | - Yohannes Berhane
- National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3M4, Canada. .,Department of Animal Science, University of Manitoba, Winnipeg, Manitoba, Canada.
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Beerens N, Heutink R, Harders F, Bossers A, Koch G, Peeters B. Emergence and Selection of a Highly Pathogenic Avian Influenza H7N3 Virus. J Virol 2020; 94:e01818-19. [PMID: 31969434 PMCID: PMC7108855 DOI: 10.1128/jvi.01818-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/09/2020] [Indexed: 01/21/2023] Open
Abstract
Low-pathogenicity avian influenza (LPAI) viruses of subtypes H5 and H7 have the ability to spontaneously mutate to highly pathogenic (HPAI) virus variants, causing high mortality in poultry. The highly pathogenic phenotype is caused by mutation of the hemagglutinin (HA) cleavage site, but additional mutations may play a role. Evidence from the field for the switch to high pathogenicity remains scarce. This study provides direct evidence for LPAI-to-HPAI virus mutation during H7N3 infection of a turkey farm in the Netherlands. No severe clinical symptoms were reported at the farm, but deep sequencing of isolates from the infected turkeys revealed a minority of HPAI virus sequences (0.06%) in the virus population. The HPAI virus contained a 12-nucleotide insertion in the HA cleavage site that was likely introduced by a single event as no intermediates with shorter inserts were identified. This suggests nonhomologous recombination as the mechanism of insertion. Analysis of different organs of the infected turkeys showed the largest amount of HPAI virus in the lung (4.4%). The HPAI virus was rapidly selected in experimentally infected chickens after both intravenous and intranasal/intratracheal inoculation with a mixed virus preparation. Full-genome sequencing revealed that both pathotypes contained a deletion in the stalk region of the neuraminidase protein. We identified additional mutations in HA and polymerase basic protein 1 (PB1) in the HPAI virus, which were already present as minority variants in the LPAI virus population. Our findings provide more insight into the molecular changes and mechanisms involved in the emergence and selection of HPAI viruses.IMPORTANCE Low-pathogenicity avian influenza (LPAI) viruses circulate in wild birds and can be transmitted to poultry. LPAI viruses can mutate to become highly pathogenic avian influenza (HPAI) viruses causing severe disease and death in poultry. Little is known about this switch to high pathogenicity. We isolated an LPAI H7N3 virus from an infected turkey farm and showed that this contains small amounts of HPAI virus. The HPAI virus rapidly outcompeted the LPAI virus in chickens that were experimentally infected with this mixture of viruses. We analyzed the genome sequences of the LPAI and HPAI viruses and identified several changes that may be important for a virus to become highly pathogenic. This knowledge may be used for timely identification of LPAI viruses that pose a risk of becoming highly pathogenic in the field.
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Affiliation(s)
- Nancy Beerens
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Rene Heutink
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Frank Harders
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Alex Bossers
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Guus Koch
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Ben Peeters
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
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Bhatta TR, Chamings A, Vibin J, Klaassen M, Alexandersen S. Detection of a Reassortant H9N2 Avian Influenza Virus with Intercontinental Gene Segments in a Resident Australian Chestnut Teal. Viruses 2020; 12:E88. [PMID: 31940999 PMCID: PMC7019556 DOI: 10.3390/v12010088] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 12/16/2022] Open
Abstract
The present study reports the genetic characterization of a low-pathogenicity H9N2 avian influenza virus, initially from a pool and subsequently from individual faecal samples collected from Chestnut teals (Anas castanea) in southeastern Australia. Phylogenetic analyses of six full gene segments and two partial gene segments obtained from next-generation sequencing showed that this avian influenza virus, A/Chestnut teal/Australia/CT08.18/12952/2018 (H9N2), was a typical, low-pathogenicity, Eurasian aquatic bird lineage H9N2 virus, albeit containing the North American lineage nucleoprotein (NP) gene segment detected previously in Australian wild birds. This is the first report of a H9N2 avian influenza virus in resident wild birds in Australia, and although not in itself a cause of concern, is a clear indication of spillover and likely reassortment of influenza viruses between migratory and resident birds, and an indication that any lineage could potentially be introduced in this way.
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Affiliation(s)
- Tarka Raj Bhatta
- Geelong Centre for Emerging Infectious Diseases, Geelong, Victoria 3220, Australia
- School of Medicine, Deakin University, Geelong, Victoria 3220, Australia
| | - Anthony Chamings
- Geelong Centre for Emerging Infectious Diseases, Geelong, Victoria 3220, Australia
- School of Medicine, Deakin University, Geelong, Victoria 3220, Australia
| | - Jessy Vibin
- Geelong Centre for Emerging Infectious Diseases, Geelong, Victoria 3220, Australia
- School of Medicine, Deakin University, Geelong, Victoria 3220, Australia
| | - Marcel Klaassen
- Geelong Centre for Emerging Infectious Diseases, Geelong, Victoria 3220, Australia
- Centre for Integrative Ecology, Deakin University, Victoria 3220, Australia
| | - Soren Alexandersen
- Geelong Centre for Emerging Infectious Diseases, Geelong, Victoria 3220, Australia
- School of Medicine, Deakin University, Geelong, Victoria 3220, Australia
- Barwon Health, University Hospital Geelong, Geelong, Victoria 3220, Australia
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41
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Bryson KJ, Garrido D, Esposito M, McLachlan G, Digard P, Schouler C, Guabiraba R, Trapp S, Vervelde L. Precision cut lung slices: a novel versatile tool to examine host-pathogen interaction in the chicken lung. Vet Res 2020; 51:2. [PMID: 31924278 PMCID: PMC6954617 DOI: 10.1186/s13567-019-0733-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/12/2019] [Indexed: 01/12/2023] Open
Abstract
The avian respiratory tract is a common entry route for many pathogens and an important delivery route for vaccination in the poultry industry. Immune responses in the avian lung have mostly been studied in vivo due to the lack of robust, relevant in vitro and ex vivo models mimicking the microenvironment. Precision-cut lung slices (PCLS) have the major advantages of maintaining the 3-dimensional architecture of the lung and includes heterogeneous cell populations. PCLS have been obtained from a number of mammalian species and from chicken embryos. However, as the embryonic lung is physiologically undifferentiated and immunologically immature, it is less suitable to examine complex host-pathogen interactions including antimicrobial responses. Here we prepared PCLS from immunologically mature chicken lungs, tested different culture conditions, and found that serum supplementation has a detrimental effect on the quality of PCLS. Viable cells in PCLS remained present for ≥ 40 days, as determined by viability assays and sustained motility of fluorescent mononuclear phagocytic cells. The PCLS were responsive to lipopolysaccharide stimulation, which induced the release of nitric oxide, IL-1β, type I interferons and IL-10. Mononuclear phagocytes within the tissue maintained phagocytic activity, with live cell imaging capturing interactions with latex beads and an avian pathogenic Escherichia coli strain. Finally, the PCLS were also shown to be permissive to infection with low pathogenic avian influenza viruses. Taken together, immunologically mature chicken PCLS provide a suitable model to simulate live organ responsiveness and cell dynamics, which can be readily exploited to examine host-pathogen interactions and inflammatory responses.
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Affiliation(s)
- Karen Jane Bryson
- Division of Infection and Immunity, The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, Edinburgh, Scotland EH25 9RG UK
| | - Damien Garrido
- INRAE, Université de Tours, UMR ISP, Centre Val de Loire, 37380 Nouzilly, France
| | - Marco Esposito
- Division of Developmental Biology, The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, Edinburgh, Scotland EH25 9RG UK
| | - Gerry McLachlan
- Division of Developmental Biology, The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, Edinburgh, Scotland EH25 9RG UK
| | - Paul Digard
- Division of Infection and Immunity, The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, Edinburgh, Scotland EH25 9RG UK
| | - Catherine Schouler
- INRAE, Université de Tours, UMR ISP, Centre Val de Loire, 37380 Nouzilly, France
| | - Rodrigo Guabiraba
- INRAE, Université de Tours, UMR ISP, Centre Val de Loire, 37380 Nouzilly, France
| | - Sascha Trapp
- INRAE, Université de Tours, UMR ISP, Centre Val de Loire, 37380 Nouzilly, France
| | - Lonneke Vervelde
- Division of Infection and Immunity, The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, Edinburgh, Scotland EH25 9RG UK
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42
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Al-Badry M, Al-Mubarak F. Molecular surveillance of avian influenza A viruses in Basrah and Wasit. BULGARIAN JOURNAL OF VETERINARY MEDICINE 2020. [DOI: 10.15547/bjvm.2019-0016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The aim of this study was to detect influenza A virus in broiler chickens and wild ducks in different geographical regions of Basrah and Wasit provinces, Iraq. This study was authenticated by analysing the viral genome and designing a set of universal primers for the detection of all influenza A subtypes in a single enzymatic reaction through the amplification of a highly conserved region of viral M gene. A total of 157 and 155 oropharyngeal and cloacal swabs from broiler chickens and wild ducks, respectively, were analysed. The study shows that influenza A viruses were prevalent in these birds in all study regions with a significantly higher percentage in wild ducks compared to broiler chickens. The results showed that 92/157 samples (54/75 wild ducks and 38/82 broiler chickens) and 96/155 samples (38/75 wild ducks and 58/80 broiler chickens) in Basrah and Wasit, respectively, were positive for the viral M gene. In addition, there was no significant difference in virus prevalence between Basrah and Wasit provinces.
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43
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Bianchini J, Humblet M, Cargnel M, Van der Stede Y, Koenen F, de Clercq K, Saegerman C. Prioritization of livestock transboundary diseases in Belgium using a multicriteria decision analysis tool based on drivers of emergence. Transbound Emerg Dis 2020; 67:344-376. [PMID: 31520577 PMCID: PMC7168563 DOI: 10.1111/tbed.13356] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 08/27/2019] [Accepted: 09/11/2019] [Indexed: 11/30/2022]
Abstract
During the past decade, livestock diseases have (re-)emerged in areas where they had been previously eradicated or never been recorded before. Drivers (i.e. factors of (re-)emergence) have been identified. Livestock diseases spread irrespective of borders, and therefore, reliable methods are required to help decision-makers to identify potential threats and try stopping their (re-)emergence. Ranking methods and multicriteria approaches are cost-effective tools for such purpose and were applied to prioritize a list of selected diseases (N = 29 including 6 zoonoses) based on the opinion of 62 experts in accordance with 50 drivers-related criteria. Diseases appearing in the upper ranking were porcine epidemic diarrhoea, foot-and-mouth disease, low pathogenic avian influenza, African horse sickness and highly pathogenic avian influenza. The tool proposed uses a multicriteria decision analysis approach to prioritize pathogens according to drivers and can be applied to other countries or diseases.
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Affiliation(s)
- Juana Bianchini
- Faculty of Veterinary MedicineResearch Unit in Epidemiology and Risk Analysis Applied to Veterinary Sciences (UREAR‐ULiege)Fundamental and Applied Research for Animals & Health (FARAH)Centre, Liege UniversityLiegeBelgium
| | - Marie‐France Humblet
- Department of Occupational Safety and HygieneBiosafety and Biosecurity UnitLiege UniversityLiegeBelgium
| | - Mickaël Cargnel
- Faculty of Veterinary MedicineResearch Unit in Epidemiology and Risk Analysis Applied to Veterinary Sciences (UREAR‐ULiege)Fundamental and Applied Research for Animals & Health (FARAH)Centre, Liege UniversityLiegeBelgium
- SciensanoBrusselsBelgium
| | | | | | | | - Claude Saegerman
- Faculty of Veterinary MedicineResearch Unit in Epidemiology and Risk Analysis Applied to Veterinary Sciences (UREAR‐ULiege)Fundamental and Applied Research for Animals & Health (FARAH)Centre, Liege UniversityLiegeBelgium
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44
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Naguib MM, Verhagen JH, Mostafa A, Wille M, Li R, Graaf A, Järhult JD, Ellström P, Zohari S, Lundkvist Å, Olsen B. Global patterns of avian influenza A (H7): virus evolution and zoonotic threats. FEMS Microbiol Rev 2019; 43:608-621. [PMID: 31381759 PMCID: PMC8038931 DOI: 10.1093/femsre/fuz019] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/31/2019] [Indexed: 01/16/2023] Open
Abstract
Avian influenza viruses (AIVs) continue to impose a negative impact on animal and human health worldwide. In particular, the emergence of highly pathogenic AIV H5 and, more recently, the emergence of low pathogenic AIV H7N9 have led to enormous socioeconomical losses in the poultry industry and resulted in fatal human infections. While H5N1 remains infamous, the number of zoonotic infections with H7N9 has far surpassed those attributed to H5. Despite the clear public health concerns posed by AIV H7, it is unclear why specifically this virus subtype became endemic in poultry and emerged in humans. In this review, we bring together data on global patterns of H7 circulation, evolution and emergence in humans. Specifically, we discuss data from the wild bird reservoir, expansion and epidemiology in poultry, significant increase in their zoonotic potential since 2013 and genesis of highly pathogenic H7. In addition, we analysed available sequence data from an evolutionary perspective, demonstrating patterns of introductions into distinct geographic regions and reassortment dynamics. The integration of all aspects is crucial in the optimisation of surveillance efforts in wild birds, poultry and humans, and we emphasise the need for a One Health approach in controlling emerging viruses such as AIV H7.
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Affiliation(s)
- Mahmoud M Naguib
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Husargatan 3, Uppsala University, Uppsala SE-75237, Sweden
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, 7 Nadi El-Seid Street, Giza 12618, Egypt
| | - Josanne H Verhagen
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, 44008 Hus Vita, Kalmar SE-391 82 , Sweden
| | - Ahmed Mostafa
- Institute of Medical Virology, Justus Liebig University Giessen, Schubertstrasse 81, Giessen 35392, Germany
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), 33 El-Buhouth street, Giza 12622, Egypt
| | - Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne 3000, Victoria, Australia
| | - Ruiyun Li
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, Praed Street, London W2 1PG, United Kingdom
| | - Annika Graaf
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Josef D Järhult
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Sjukhusvägen 85, Uppsala SE-75185, Sweden
| | - Patrik Ellström
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Sjukhusvägen 85, Uppsala SE-75185, Sweden
| | - Siamak Zohari
- Department of Microbiology, National Veterinary Institute, Ulls väg 2B, Uppsala SE-75189, Sweden
| | - Åke Lundkvist
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Husargatan 3, Uppsala University, Uppsala SE-75237, Sweden
| | - Björn Olsen
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Sjukhusvägen 85, Uppsala SE-75185, Sweden
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45
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Jeyaram RA, Radha CA, Gromiha MM, Veluraja K. Design of fluorinated sialic acid analog inhibitor to H5 hemagglutinin of H5N1 influenza virus through molecular dynamics simulation study. J Biomol Struct Dyn 2019; 38:3504-3513. [PMID: 31594458 DOI: 10.1080/07391102.2019.1677500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Influenza epidemics and pandemics are caused by influenza A virus. The cell surface protein of hemagglutinin and neuraminidase is responsible for viral infection and release of progeny virus on the host cell membrane. Now 18 hemagglutinin and 11 neuraminidase subtypes are identified. The avian influenza virus of H5N1 is an emergent threat to public health issues. To control the influenza viral infection it is necessary to develop antiviral inhibitors and vaccination. In the present investigation we carried out 50 ns Molecular Dynamics simulation on H5 hemagglutinin of Influenza A virus H5N1 complexed with fluorinated sialic acid by substituting fluorine atoms at any two hydroxyls of sialic acid by considering combinatorial combination. The binding affinity between the protein-ligand complex system is investigated by calculating pair interaction energy and MM-PBSA binding free energy. All the complex structures are stabilized by hydrogen bonding interactions between the H5 protein and the ligand fluorinated sialic acid. It is concluded from all the analyses that the fluorinated complexes enhance the inhibiting potency against H5 hemagglutinin and the order of inhibiting potency is SIA-F9 ≫ SIA-F2 ≈ SIA-F7 ≈ SIA-F2F4 ≈ SIA-F2F9 ≈ SIA-F7F9 > SIA-F7F8 ≈ SIA-F2F8 ≈ SIA-F8F9 > SIA-F4 ≈ SIA-F4F7 ≈ SIA-F4F8 ≈ SIA-F8 ≈ SIA-F2F7 ≈ SIA > SIA-F4F9. This study suggests that one can design the inhibitor by using the mono fluorinated models SIA-F9, SIA-F2 and SIA-F7 and difluorinated models SIA-F2F4, SIA-F2F9 and SIA-F7F9 to inhibit H5 of H5N1 to avoid Influenza A viral infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- R A Jeyaram
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - C Anu Radha
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - K Veluraja
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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46
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Youk S, Lee DH, Ferreira HL, Afonso CL, Absalon AE, Swayne DE, Suarez DL, Pantin-Jackwood MJ. Rapid evolution of Mexican H7N3 highly pathogenic avian influenza viruses in poultry. PLoS One 2019; 14:e0222457. [PMID: 31513638 PMCID: PMC6742402 DOI: 10.1371/journal.pone.0222457] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/29/2019] [Indexed: 02/06/2023] Open
Abstract
Highly pathogenic avian influenza (HPAI) virus subtype H7N3 has been circulating in poultry in Mexico since 2012 and vaccination has been used to control the disease. In this study, eight Mexican H7N3 HPAI viruses from 2015–2017 were isolated and fully sequenced. No evidence of reassortment was detected with other avian influenza (AI) viruses, but phylogenetic analyses show divergence of all eight gene segments into three genetic clusters by 2015, with 94.94 to 98.78 percent nucleotide homology of the HA genes when compared to the index virus from 2012. The HA protein of viruses from each cluster showed a different number of basic amino acids (n = 5–7) in the cleavage site, and six different patterns at the predicted N-glycosylation sites. Comparison of the sequences of the Mexican lineage H7N3 HPAI viruses and American ancestral wild bird AI viruses to characterize the virus evolutionary dynamics showed that the nucleotide substitution rates in PB2, PB1, PA, HA, NP, and NS genes greatly increased once the virus was introduced into poultry. The global nonsynonymous and synonymous ratios imply strong purifying selection driving the evolution of the virus. Forty-nine positively selected sites out of 171 nonsynonymous mutations were identified in the Mexican H7N3 HPAI viruses, including 7 amino acid changes observed in higher proportion in North American poultry origin AI viruses isolates than in wild bird-origin viruses. Continuous monitoring and molecular characterization of the H7N3 HPAI virus is important for better understanding of the virus evolutionary dynamics and further improving control measures including vaccination.
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Affiliation(s)
- Sungsu Youk
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, Georgia, United States of America
| | - Dong-Hun Lee
- Department of Pathobiology & Veterinary Science, University of Connecticut, Storrs, Mansfield, Connecticut, United States of America
| | - Helena L Ferreira
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, Georgia, United States of America.,University of Sao Paulo, ZMV- FZEA, Pirassununga, Brazil
| | - Claudio L Afonso
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, Georgia, United States of America
| | - Angel E Absalon
- Instituto Politécnico Nacional, Centro de Investigación en Biotecnología Aplicada, Tlaxcala, México
| | - David E Swayne
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, Georgia, United States of America
| | - David L Suarez
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, Georgia, United States of America
| | - Mary J Pantin-Jackwood
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, Georgia, United States of America
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47
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Variable impact of the hemagglutinin polybasic cleavage site on virulence and pathogenesis of avian influenza H7N7 virus in chickens, turkeys and ducks. Sci Rep 2019; 9:11556. [PMID: 31399610 PMCID: PMC6689016 DOI: 10.1038/s41598-019-47938-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 07/24/2019] [Indexed: 11/09/2022] Open
Abstract
Avian influenza viruses (AIV) are classified into 16 hemagglutinin (HA; H1-H16) and 9 neuraminidase (NA; N1-N9) subtypes. All AIV are low pathogenic (LP) in birds, but subtypes H5 and H7 AIV can evolve into highly pathogenic (HP) forms. In the last two decades evolution of HPAIV H7 from LPAIV has been frequently reported. However, little is known about the pathogenesis and evolution of HP H7 from LP ancestors particularly, in non-chicken hosts. In 2015, both LP and HP H7N7 AIV were isolated from chickens in two neighbouring farms in Germany. Here, the virulence of these isogenic H7N7 LP, HP and LP virus carrying a polybasic HA cleavage site (HACS) from HP (designated LP-Poly) was studied in chickens, turkeys and different duck breeds. The LP precursor was avirulent in all birds. In contrast, all inoculated and contact chickens and turkeys died after infection with HP. HP infected Pekin and Mallard ducks remained clinically healthy, while Muscovy ducks exhibited moderate depression and excreted viruses at significantly higher amounts. The polybasic HACS increased virulence in a species-specific manner with intravenous pathogenicity indices of 3.0, 1.9 and 0.2 in chickens, turkeys and Muscovy ducks, respectively. Infection of endothelial cells was only observed in chickens. In summary, Pekin and Mallard were more resistant to HPAIV H7N7 than chickens, turkeys and Muscovy ducks. The polybasic HACS was the main determinant for virulence and endotheliotropism of HPAIV H7N7 in chickens, whereas other viral and/or host factors play an essential role in virulence and pathogenesis in turkeys and ducks.
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Świętoń E, Olszewska-Tomczyk M, Giza A, Śmietanka K. Evolution of H9N2 low pathogenic avian influenza virus during passages in chickens. INFECTION GENETICS AND EVOLUTION 2019; 75:103979. [PMID: 31351233 DOI: 10.1016/j.meegid.2019.103979] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/19/2019] [Accepted: 07/23/2019] [Indexed: 11/16/2022]
Abstract
The process of avian influenza virus (AIV) evolution in a new host was investigated in the experiment in which ten serial passages of a turkey-derived H9N2 AIV were carried out in specific pathogen free chickens (3 birds/group) inoculated by oculonasal route. Oropharyngeal swabs collected 3 days post infection were used for inoculation of birds in the next passage and subjected to analysis using deep sequencing. In total, eight mutations in the consensus sequence were found in the viral pool derived from the 10th passage: four mutations (2 in PB1 and 2 in HA) were present in the inoculum as minority variants while the other four (2 in NP, 1 in PA and 1 in HA) emerged during the passages in chickens. The detected fluctuations in the genetic heterogeneity of viral pools from consecutive passages were most likely attributed to the selective bottleneck. The genes known for bearing molecular determinants of the AIV host specificity (HA, PB2, PB1, PA) contributed most to the overall virus diversity. In some cases, a fast selection of the novel variant was noticed. For example, the amino-acid substitution N337K in the haemagglutinin (HA) cleavage site region detected in the 6th passage as low frequency variant had undergone rapid selection and became predominant in the 7th passage. Interestingly, detection of identical mutation in the field H9N2 isolates 1-year apart suggests that this substitution might provide the virus with a selective advantage. However, the role of specific mutations and their influence on the virus adaptation or fitness are mostly unknown and require further investigations.
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Affiliation(s)
- Edyta Świętoń
- Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100 Puławy, Poland.
| | - Monika Olszewska-Tomczyk
- Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100 Puławy, Poland
| | - Aleksandra Giza
- Department of Omics Analyses, National Veterinary Research Institute, Al. Partyzantów 57, 24-100 Puławy, Poland
| | - Krzysztof Śmietanka
- Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100 Puławy, Poland
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49
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Kingstad-Bakke BA, Chandrasekar SS, Phanse Y, Ross KA, Hatta M, Suresh M, Kawaoka Y, Osorio JE, Narasimhan B, Talaat AM. Effective mosaic-based nanovaccines against avian influenza in poultry. Vaccine 2019; 37:5051-5058. [PMID: 31300285 DOI: 10.1016/j.vaccine.2019.06.077] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/15/2019] [Accepted: 06/24/2019] [Indexed: 01/09/2023]
Abstract
Avian influenza virus (AIV) is an extraordinarily diverse pathogen that causes significant morbidity in domesticated poultry populations and threatens human life with looming pandemic potential. Controlling avian influenza in susceptible populations requires highly effective, economical and broadly reactive vaccines. Several AIV vaccines have proven insufficient despite their wide use, and better technologies are needed to improve their immunogenicity and broaden effectiveness. Previously, we developed a "mosaic" H5 subtype hemagglutinin (HA) AIV vaccine and demonstrated its broad protection against diverse highly pathogenic H5N1 and seasonal H1N1 virus strains in mouse and non-human primate models. There is a significant interest in developing effective and safe vaccines against AIV that cannot contribute to the emergence of new strains of the virus once circulating in poultry. Here, we report on the development of an H5 mosaic (H5M) vaccine antigen formulated with polyanhydride nanoparticles (PAN) that provide sustained release of encapsulated antigens. H5M vaccine constructs were immunogenic whether delivered by the modified virus Ankara (MVA) strain or encapsulated within PAN. Both humoral and cellular immune responses were generated in both specific-pathogen free (SPF) and commercial chicks. Importantly, chicks vaccinated by H5M constructs were protected in terms of viral shedding from divergent challenge with a low pathogenicity avian influenza (LPAI) strain at 8 weeks post-vaccination. In addition, protective levels of humoral immunity were generated against highly pathogenic avian influenza (HPAI) of the similar H5N1 and genetically dissimilar H5N2 viruses. Overall, the developed platform technologies (MVA vector and PAN encapsulation) were safe and provided high levels of sustained protection against AIV in chickens. Such approaches could be used to design more efficacious vaccines against other important poultry infections.
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Affiliation(s)
- Brock A Kingstad-Bakke
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA; Pan Genome Systems, Madison, WI, USA
| | - Shaswath S Chandrasekar
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | | | - Kathleen A Ross
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
| | - Masato Hatta
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - M Suresh
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Jorge E Osorio
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Balaji Narasimhan
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
| | - Adel M Talaat
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA; Pan Genome Systems, Madison, WI, USA.
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50
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Lu J, Raghwani J, Pryce R, Bowden TA, Thézé J, Huang S, Song Y, Zou L, Liang L, Bai R, Jing Y, Zhou P, Kang M, Yi L, Wu J, Pybus OG, Ke C. Molecular Evolution, Diversity, and Adaptation of Influenza A(H7N9) Viruses in China. Emerg Infect Dis 2019; 24:1795-1805. [PMID: 30226157 PMCID: PMC6154164 DOI: 10.3201/eid2410.171063] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The substantial increase in prevalence and emergence of antigenically divergent or highly pathogenic influenza A(H7N9) viruses during 2016–17 raises concerns about the epizootic potential of these viruses. We investigated the evolution and adaptation of H7N9 viruses by analyzing available data and newly generated virus sequences isolated in Guangdong Province, China, during 2015–2017. Phylogenetic analyses showed that circulating H7N9 viruses belong to distinct lineages with differing spatial distributions. Hemagglutination inhibition assays performed on serum samples from patients infected with these viruses identified 3 antigenic clusters for 16 strains of different virus lineages. We used ancestral sequence reconstruction to identify parallel amino acid changes on multiple separate lineages. We inferred that mutations in hemagglutinin occur primarily at sites involved in receptor recognition or antigenicity. Our results indicate that highly pathogenic strains likely emerged from viruses circulating in eastern Guangdong Province during March 2016 and are associated with a high rate of adaptive molecular evolution.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antigenic Variation
- Birds
- China/epidemiology
- Evolution, Molecular
- Genetic Variation
- Genome, Viral
- Genotype
- Geography, Medical
- History, 21st Century
- Humans
- Influenza A Virus, H7N9 Subtype/classification
- Influenza A Virus, H7N9 Subtype/genetics
- Influenza A Virus, H7N9 Subtype/immunology
- Influenza A Virus, H7N9 Subtype/isolation & purification
- Influenza in Birds/epidemiology
- Influenza in Birds/history
- Influenza in Birds/virology
- Influenza, Human/epidemiology
- Influenza, Human/history
- Influenza, Human/virology
- Phylogeny
- RNA, Viral
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