1
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Russell CA, Fouchier RAM, Ghaswalla P, Park Y, Vicic N, Ananworanich J, Nachbagauer R, Rudin D. Seasonal influenza vaccine performance and the potential benefits of mRNA vaccines. Hum Vaccin Immunother 2024; 20:2336357. [PMID: 38619079 PMCID: PMC11020595 DOI: 10.1080/21645515.2024.2336357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/26/2024] [Indexed: 04/16/2024] Open
Abstract
Influenza remains a public health threat, partly due to suboptimal effectiveness of vaccines. One factor impacting vaccine effectiveness is strain mismatch, occurring when vaccines no longer match circulating strains due to antigenic drift or the incorporation of inadvertent (eg, egg-adaptive) mutations during vaccine manufacturing. In this review, we summarize the evidence for antigenic drift of circulating viruses and/or egg-adaptive mutations occurring in vaccine strains during the 2011-2020 influenza seasons. Evidence suggests that antigenic drift led to vaccine mismatch during four seasons and that egg-adaptive mutations caused vaccine mismatch during six seasons. These findings highlight the need for alternative vaccine development platforms. Recently, vaccines based on mRNA technology have demonstrated efficacy against SARS-CoV-2 and respiratory syncytial virus and are under clinical evaluation for seasonal influenza. We discuss the potential for mRNA vaccines to address strain mismatch, as well as new multi-component strategies using the mRNA platform to improve vaccine effectiveness.
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Affiliation(s)
- Colin A. Russell
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Ron A. M. Fouchier
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
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2
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Fatly ZA, Betjes MGH, Dik WA, Fouchier RAM, Reinders MEJ, de Weerd AE. Mycophenolate mofetil hampers antibody responses to a broad range of vaccinations in kidney transplant recipients: Results from a randomized controlled study. J Infect 2024; 88:106133. [PMID: 38432583 DOI: 10.1016/j.jinf.2024.106133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/10/2024] [Accepted: 02/24/2024] [Indexed: 03/05/2024]
Abstract
OBJECTIVES To study the effect of mycophenolate mofetil (MMF) on various vaccination responses in kidney transplant recipients. METHODS In a randomized controlled trial (EudraCT nr.: 2014-001372-66), low immunologically risk kidney transplant recipients were randomized to TAC/MMF or TAC-monotherapy (TACmono), six months post-transplantation. One year after transplantation, in a pre-specified sub-study, recipients were vaccinated against pneumococcus, tetanus and influenza. Blood was sampled before and 21 days after vaccination. Adequate vaccination responses were defined by international criteria. A post-hoc analysis was conducted on SARS-CoV-2 vaccination responses within the same cohort. RESULTS Seventy-one recipients received pneumococcal and tetanus vaccines (TAC/MMF: n = 37, TACmono: n = 34), with 29 also vaccinated against influenza. When vaccinated, recipients were 60 (54-66) years old, with median eGFR of 54 (44-67) ml/min, tacrolimus trough levels 6.1 (5.4-7.0) ug/L in both groups and TAC/MMF daily MMF dose of 1000 (500-2000) mg. Adequate vaccination responses were: pneumococcal (TAC/MMF 43%, TACmono 74%, p = 0.016), tetanus (TAC/MMF 35%, TACmono 82%, p < 0.0001) and influenza (TAC/MMF 20%, TACmono 71%, p = 0.0092). Only 7% of TAC/MMF responded adequately to all three compared to 36% of TACmono (p = 0.080). Additionally, 40% of TAC/MMF responded inadequately to all three, whereas all TACmono patients responded adequately to at least one vaccination (p = 0.041). Lower SARS-CoV-2 vaccination antibody responses correlated with lower pneumococcal antibody vaccination responses (correlation coefficient: 0.41, p = 0.040). CONCLUSIONS MMF on top of tacrolimus severely hampers antibody responses to a broad range of vaccinations.
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Affiliation(s)
- Z Al Fatly
- Erasmus MC Transplant Institute, Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands.
| | - M G H Betjes
- Erasmus MC Transplant Institute, Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - W A Dik
- Laboratory Medical Immunology, Department of Immunology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - R A M Fouchier
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - M E J Reinders
- Erasmus MC Transplant Institute, Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - A E de Weerd
- Erasmus MC Transplant Institute, Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
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3
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Ribó-Molina P, van Nieuwkoop S, Mykytyn AZ, van Run P, Lamers MM, Haagmans BL, Fouchier RAM, van den Hoogen BG. Human metapneumovirus infection of organoid-derived human bronchial epithelium represents cell tropism and cytopathology as observed in in vivo models. mSphere 2024; 9:e0074323. [PMID: 38265200 PMCID: PMC10900881 DOI: 10.1128/msphere.00743-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024] Open
Abstract
Human metapneumovirus (HMPV), a member of the Pneumoviridae family, causes upper and lower respiratory tract infections in humans. In vitro studies with HMPV have mostly been performed in monolayers of undifferentiated epithelial cells. In vivo studies in cynomolgus macaques and cotton rats have shown that ciliated epithelial cells are the main target of HMPV infection, but these observations cannot be studied in monolayer systems. Here, we established an organoid-derived bronchial culture model that allows physiologically relevant studies on HMPV. Inoculation with multiple prototype HMPV viruses and recent clinical virus isolates led to differences in replication among HMPV isolates. Prolific HMPV replication in this model caused damage to the ciliary layer, including cilia loss at advanced stages post-infection. These cytopathic effects correlated with those observed in previous in vivo studies with cynomolgus macaques. The assessment of the innate immune responses in three donors upon HMPV and RSV inoculation highlighted the importance of incorporating multiple donors to account for donor-dependent variation. In conclusion, these data indicate that the organoid-derived bronchial cell culture model resembles in vivo findings and is therefore a suitable and robust model for future HMPV studies. IMPORTANCE Human metapneumovirus (HMPV) is one of the leading causative agents of respiratory disease in humans, with no treatment or vaccine available yet. The use of primary epithelial cultures that recapitulate the tissue morphology and biochemistry of the human airways could aid in defining more relevant targets to prevent HMPV infection. For this purpose, this study established the first primary organoid-derived bronchial culture model suitable for a broad range of HMPV isolates. These bronchial cultures were assessed for HMPV replication, cellular tropism, cytopathology, and innate immune responses, where the observations were linked to previous in vivo studies with HMPV. This study exposed an important gap in the HMPV field since extensively cell-passaged prototype HMPV B viruses did not replicate in the bronchial cultures, underpinning the need to use recently isolated viruses with a controlled passage history. These results were reproducible in three different donors, supporting this model to be suitable to study HMPV infection.
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Affiliation(s)
- Pau Ribó-Molina
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Anna Z. Mykytyn
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Peter van Run
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Mart M. Lamers
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Bart L. Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Ron A. M. Fouchier
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
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4
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Ma S, Liu L, Eggink D, Herfst S, Fouchier RAM, de Vries RP, Boons GJ. Asymmetrical Biantennary Glycans Prepared by a Stop-and-Go Strategy Reveal Receptor Binding Evolution of Human Influenza A Viruses. JACS Au 2024; 4:607-618. [PMID: 38425896 PMCID: PMC10900492 DOI: 10.1021/jacsau.3c00695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 03/02/2024]
Abstract
Glycan binding properties of respiratory viruses have been difficult to probe due to a lack of biologically relevant glycans for binding studies. Here, a stop-and-go chemoenzymatic methodology is presented that gave access to a panel of 32 asymmetrical biantennary N-glycans having various numbers of N-acetyl lactosamine (LacNAc) repeating units capped by α2,3- or α2,6-sialosides resembling structures found in airway tissues. It exploits that the branching enzymes MGAT1 and MGAT2 can utilize unnatural UDP-2-deoxy-2-trifluoro-N-acetamido-glucose (UDP-GlcNTFA) as donor. The TFA moiety of the resulting glycans can be hydrolyzed to give GlcNH2 at one of the antennae, which temporarily blocks extension by glycosyl transferases. The N-glycans were printed as a microarray that was probed for receptor binding specificities of the evolutionary distinct human A(H3N2) and A(H1N1)pdm09 viruses. It was found that not only the sialoside type but also the length of the LacNAc chain and presentation at the α1,3-antenna of N-glycans are critical for binding. Early A(H3N2) viruses bound to 2,6-sialosides at a single LacNAc moiety at the α1,3-antenna whereas later viruses required the sialoside to be presented at a tri-LacNAc moiety. Surprisingly, most of the A(H3N2) viruses that appeared after 2021 regained binding capacity to sialosides presented at a di-LacNAc moiety. As a result, these viruses again agglutinate erythrocytes, commonly employed for antigenic characterization of influenza viruses. Human A(H1N1)pdm09 viruses have similar receptor binding properties as recent A(H3N2) viruses. The data indicate that an asymmetric N-glycan having 2,6-sialoside at a di-LacNAc moiety is a commonly employed receptor by human influenza A viruses.
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Affiliation(s)
- Shengzhou Ma
- Complex
Carbohydrate Research Center, University
of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Lin Liu
- Complex
Carbohydrate Research Center, University
of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Dirk Eggink
- Amsterdam
UMC Location University of Amsterdam, Department
of Medical Microbiology and Infection prevention, Laboratory of Applied
Evolutionary Biology, 1105
AZ Amsterdam, The
Netherlands
- Center
for Infectious Disease Control, National
Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, The Netherlands
| | - Sander Herfst
- Department
of Viroscience, Erasmus University Medical
Center, 3015 CD Rotterdam, The Netherlands
| | - Ron A. M. Fouchier
- Department
of Viroscience, Erasmus University Medical
Center, 3015 CD Rotterdam, The Netherlands
| | - Robert P. de Vries
- Department
of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Geert-Jan Boons
- Complex
Carbohydrate Research Center, University
of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
- Department
of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
- Department
of Chemistry, University of Georgia, Athens, Georgia 30602, United States
- Bijvoet
Center for Biomolecular Research, Utrecht
University, Padualaan
8, 3584 CH Utrecht, The Netherlands
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5
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de Bruin ACM, Spronken MI, Kok A, Rosu ME, de Meulder D, van Nieuwkoop S, Lexmond P, Funk M, Leijten LM, Bestebroer TM, Herfst S, van Riel D, Fouchier RAM, Richard M. Species-specific emergence of H7 highly pathogenic avian influenza virus is driven by intrahost selection differences between chickens and ducks. PLoS Pathog 2024; 20:e1011942. [PMID: 38408092 PMCID: PMC10919841 DOI: 10.1371/journal.ppat.1011942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 03/07/2024] [Accepted: 01/03/2024] [Indexed: 02/28/2024] Open
Abstract
Highly pathogenic avian influenza viruses (HPAIVs) cause severe hemorrhagic disease in terrestrial poultry and are a threat to the poultry industry, wild life, and human health. HPAIVs arise from low pathogenic avian influenza viruses (LPAIVs), which circulate in wild aquatic birds. HPAIV emergence is thought to occur in poultry and not wild aquatic birds, but the reason for this species-restriction is not known. We hypothesized that, due to species-specific tropism and replication, intrahost HPAIV selection is favored in poultry and disfavored in wild aquatic birds. We tested this hypothesis by co-inoculating chickens, representative of poultry, and ducks, representative of wild aquatic birds, with a mixture of H7N7 HPAIV and LPAIV, mimicking HPAIV emergence in an experimental setting. Virus selection was monitored in swabs and tissues by RT-qPCR and immunostaining of differential N-terminal epitope tags that were added to the hemagglutinin protein. HPAIV was selected in four of six co-inoculated chickens, whereas LPAIV remained the major population in co-inoculated ducks on the long-term, despite detection of infectious HPAIV in tissues at early time points. Collectively, our data support the hypothesis that HPAIVs are more likely to be selected at the intrahost level in poultry than in wild aquatic birds and point towards species-specific differences in HPAIV and LPAIV tropism and replication levels as possible explanations.
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Affiliation(s)
- Anja C. M. de Bruin
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Monique I. Spronken
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Adinda Kok
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Miruna E. Rosu
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Dennis de Meulder
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Pascal Lexmond
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Mathis Funk
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lonneke M. Leijten
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Theo M. Bestebroer
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Sander Herfst
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Debby van Riel
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ron A. M. Fouchier
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Mathilde Richard
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
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6
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Caliendo V, Kleyheeg E, Beerens N, Camphuysen KCJ, Cazemier R, Elbers ARW, Fouchier RAM, Kelder L, Kuiken T, Leopold M, Slaterus R, Spierenburg MAH, van der Jeugd H, Verdaat H, Rijks JM. Effect of 2020-21 and 2021-22 Highly Pathogenic Avian Influenza H5 Epidemics on Wild Birds, the Netherlands. Emerg Infect Dis 2024; 30:50-57. [PMID: 38040665 PMCID: PMC10756359 DOI: 10.3201/eid3001.230970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2023] Open
Abstract
The number of highly pathogenic avian influenza (HPAI) H5-related infections and deaths of wild birds in Europe was high during October 1, 2020-September 30, 2022. To quantify deaths among wild species groups with known susceptibility for HPAI H5 during those epidemics, we collected and recorded mortality data of wild birds in the Netherlands. HPAI virus infection was reported in 51 bird species. The species with the highest numbers of reported dead and infected birds varied per epidemic year; in 2020-21, they were within the Anatidae family, in particular barnacle geese (Branta leucopsis) and in 2021-22, they were within the sea bird group, particularly Sandwich terns (Thalasseus sandvicensis) and northern gannet (Morus bassanus). Because of the difficulty of anticipating and modeling the future trends of HPAI among wild birds, we recommend monitoring live and dead wild birds as a tool for surveillance of the changing dynamics of HPAI.
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7
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Ma S, Liu L, Eggink D, Herfst S, Fouchier RAM, de Vries RP, Boons GJ. Asymmetrical Bi-antennary Glycans Prepared by a Stop-and-Go Strategy Reveal Receptor Binding Evolution of Human Influenza A Viruses. bioRxiv 2023:2023.11.08.566285. [PMID: 37986780 PMCID: PMC10659364 DOI: 10.1101/2023.11.08.566285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Glycan binding properties of respiratory viruses have been difficult to probe due to a lack of biological relevant glycans for binding studies. Here, a stop-and-go chemoenzymatic methodology is presented that gave access to a panel of 32 asymmetrical bi-antennary N-glycans having various numbers of N-acetyl lactosamine (LacNAc) repeating units capped by α2,3- or α2,6-sialosides resembling structures found in airway tissues. It exploits that the branching enzymes MGAT1 and MGAT2 can utilize unnatural UDP-2-deoxy-2-trifluoro-N-acetamido-glucose (UDP-GlcNTFA) as donor. The TFA moiety of the resulting glycans can be hydrolyzed to give GlcNH2 at one of the antennae that temporarily blocks extension by glycosyl transferases. The N-glycans were printed as a microarray that was probed for receptor binding specificities of evolutionary distinct human A(H3N2) and A(H1N1)pdm09 viruses. It was found that not only the sialoside type but also the length of the LacNAc chain and presentation at the α1,3-antenna of N-glycans is critical for binding. Early A(H3N2) viruses bound to 2,6-sialosides at a single LacNAc moiety at the α1,3-antenna whereas later viruses required the sialoside to be presented at a tri-LacNAc moiety. Surprisingly, most of the A(H3N2) viruses that appeared after 2021 regained binding capacity to sialosides presented at a di-LacNAc moiety. As a result, these viruses agglutinate erythrocytes again, commonly employed for antigenic characterization of influenza viruses. Human A(H1N1)pdm09 viruses have similar receptor binding properties as recent A(H3N2) viruses. The data indicates that an asymmetric N-glycan having 2,6-sialoside at a di-LacNAc moiety is a commonly employed receptor by human influenza A viruses.
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Affiliation(s)
- Shengzhou Ma
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Lin Liu
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Dirk Eggink
- Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Applied Evolutionary Biology, Amsterdam, The Netherlands
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, The Netherlands
| | - Sander Herfst
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robert P de Vries
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
- Department of Chemistry, University of Georgia, Athens, GA, USA
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8
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Ribó-Molina P, Weiss HJ, Susma B, van Nieuwkoop S, Persoons L, Zheng Y, Ruzek M, Daelemans D, Fouchier RAM, O'Neill LAJ, van den Hoogen BG. 4-Octyl itaconate reduces influenza A replication by targeting the nuclear export protein CRM1. J Virol 2023; 97:e0132523. [PMID: 37823646 PMCID: PMC10617539 DOI: 10.1128/jvi.01325-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Itaconate derivates, as well as the naturally produced metabolite, have been proposed as antivirals against influenza virus. Here, the mechanism behind the antiviral effects of exogenous 4-octyl itaconate (4-OI), a derivative of itaconate, against the influenza A virus replication is demonstrated. The data indicate that 4-OI targets the cysteine at position 528 of the CRM1 protein, resulting in inhibition of the nuclear export of viral ribonucleoprotein complexes in a similar manner as previously described for other selective inhibitors of nuclear export. These results postulate a mechanism not observed before for this immuno-metabolite derivative. This knowledge is helpful for the development of derivatives of 4-OI as potential antiviral and anti-inflammatory therapeutics.
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Affiliation(s)
- Pau Ribó-Molina
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Hauke J. Weiss
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | | | | | - Leentje Persoons
- Laboratory of Virology and Chemotherapy, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Yunan Zheng
- AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - Melanie Ruzek
- AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - Dirk Daelemans
- Laboratory of Virology and Chemotherapy, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Ron A. M. Fouchier
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Luke A. J. O'Neill
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
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9
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Kok A, Scheuer R, Bestebroer TM, Burke DF, Wilks SH, Spronken MI, de Meulder D, Lexmond P, Pronk M, Smith DJ, Herfst S, Fouchier RAM, Richard M. Characterization of A/H7 influenza virus global antigenic diversity and key determinants in the hemagglutinin globular head mediating A/H7N9 antigenic evolution. mBio 2023; 14:e0048823. [PMID: 37565755 PMCID: PMC10655666 DOI: 10.1128/mbio.00488-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/26/2023] [Indexed: 08/12/2023] Open
Abstract
IMPORTANCE A/H7 avian influenza viruses cause outbreaks in poultry globally, resulting in outbreaks with significant socio-economical impact and zoonotic risks. Occasionally, poultry vaccination programs have been implemented to reduce the burden of these viruses, which might result in an increased immune pressure accelerating antigenic evolution. In fact, evidence for antigenic diversification of A/H7 influenza viruses exists, posing challenges to pandemic preparedness and the design of vaccination strategies efficacious against drifted variants. Here, we performed a comprehensive analysis of the global antigenic diversity of A/H7 influenza viruses and identified the main substitutions in the hemagglutinin responsible for antigenic evolution in A/H7N9 viruses isolated between 2013 and 2019. The A/H7 antigenic map and knowledge of the molecular determinants of their antigenic evolution add value to A/H7 influenza virus surveillance programs, the design of vaccines and vaccination strategies, and pandemic preparedness.
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Affiliation(s)
- Adinda Kok
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Rachel Scheuer
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Theo M. Bestebroer
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - David F. Burke
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Samuel H. Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Monique I. Spronken
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Dennis de Meulder
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Pascal Lexmond
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Mark Pronk
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Derek J. Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Sander Herfst
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ron A. M. Fouchier
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Mathilde Richard
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
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10
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Spruit CM, Sweet IR, Maliepaard JCL, Bestebroer T, Lexmond P, Qiu B, Damen MJA, Fouchier RAM, Reiding KR, Snijder J, Herfst S, Boons GJ, de Vries RP. Contemporary human H3N2 influenza A viruses require a low threshold of suitable glycan receptors for efficient infection. Glycobiology 2023; 33:784-800. [PMID: 37471650 PMCID: PMC10629718 DOI: 10.1093/glycob/cwad060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 07/03/2023] [Accepted: 07/16/2023] [Indexed: 07/22/2023] Open
Abstract
Recent human H3N2 influenza A viruses have evolved to employ elongated glycans terminating in α2,6-linked sialic acid as their receptors. These glycans are displayed in low abundancies by (humanized) Madin-Darby Canine Kidney cells, which are commonly employed to propagate influenza A virus, resulting in low or no viral propagation. Here, we examined whether the overexpression of the glycosyltransferases β-1,3-N-acetylglucosaminyltransferase and β-1,4-galactosyltransferase 1, which are responsible for the elongation of poly-N-acetyllactosamines (LacNAcs), would result in improved A/H3N2 propagation. Stable overexpression of β-1,3-N-acetylglucosaminyltransferase and β-1,4-galactosyltransferase 1 in Madin-Darby Canine Kidney and "humanized" Madin-Darby Canine Kidney cells was achieved by lentiviral integration and subsequent antibiotic selection and confirmed by qPCR and protein mass spectrometry experiments. Flow cytometry and glycan mass spectrometry experiments using the β-1,3-N-acetylglucosaminyltransferase and/or β-1,4-galactosyltransferase 1 knock-in cells demonstrated increased binding of viral hemagglutinins and the presence of a larger number of LacNAc repeating units, especially on "humanized" Madin-Darby Canine Kidney-β-1,3-N-acetylglucosaminyltransferase cells. An increase in the number of glycan receptors did, however, not result in a greater infection efficiency of recent human H3N2 viruses. Based on these results, we propose that H3N2 influenza A viruses require a low number of suitable glycan receptors to infect cells and that an increase in the glycan receptor display above this threshold does not result in improved infection efficiency.
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Affiliation(s)
- Cindy M Spruit
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584CG Utrecht, The Netherlands
| | - Igor R Sweet
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584CG Utrecht, The Netherlands
| | - Joshua C L Maliepaard
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Theo Bestebroer
- Department of Viroscience, Erasmus University Medical Center, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
| | - Pascal Lexmond
- Department of Viroscience, Erasmus University Medical Center, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
| | - Boning Qiu
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584CG Utrecht, The Netherlands
| | - Mirjam J A Damen
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus University Medical Center, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
| | - Karli R Reiding
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Sander Herfst
- Department of Viroscience, Erasmus University Medical Center, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands
| | - Geert-Jan Boons
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584CG Utrecht, The Netherlands
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, United States
| | - Robert P de Vries
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584CG Utrecht, The Netherlands
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11
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Wilks SH, Mühlemann B, Shen X, Türeli S, LeGresley EB, Netzl A, Caniza MA, Chacaltana-Huarcaya JN, Corman VM, Daniell X, Datto MB, Dawood FS, Denny TN, Drosten C, Fouchier RAM, Garcia PJ, Halfmann PJ, Jassem A, Jeworowski LM, Jones TC, Kawaoka Y, Krammer F, McDanal C, Pajon R, Simon V, Stockwell MS, Tang H, van Bakel H, Veguilla V, Webby R, Montefiori DC, Smith DJ. Mapping SARS-CoV-2 antigenic relationships and serological responses. Science 2023; 382:eadj0070. [PMID: 37797027 DOI: 10.1126/science.adj0070] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/23/2023] [Indexed: 10/07/2023]
Abstract
During the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, multiple variants escaping preexisting immunity emerged, causing reinfections of previously exposed individuals. Here, we used antigenic cartography to analyze patterns of cross-reactivity among 21 variants and 15 groups of human sera obtained after primary infection with 10 different variants or after messenger RNA (mRNA)-1273 or mRNA-1273.351 vaccination. We found antigenic differences among pre-Omicron variants caused by substitutions at spike-protein positions 417, 452, 484, and 501. Quantifying changes in response breadth over time and with additional vaccine doses, our results show the largest increase between 4 weeks and >3 months after a second dose. We found changes in immunodominance of different spike regions, depending on the variant an individual was first exposed to, with implications for variant risk assessment and vaccine-strain selection.
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Affiliation(s)
- Samuel H Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Barbara Mühlemann
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Xiaoying Shen
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Sina Türeli
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Eric B LeGresley
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Antonia Netzl
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Miguela A Caniza
- Department of Global Pediatric Medicine, Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Victor M Corman
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Xiaoju Daniell
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Michael B Datto
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | | | - Thomas N Denny
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Christian Drosten
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | | | - Patricia J Garcia
- School of Public Health, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Science, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Agatha Jassem
- BC Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Lara M Jeworowski
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Terry C Jones
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Science, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo, Japan
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Cellular and Molecular Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Charlene McDanal
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | | | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Cellular and Molecular Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa S Stockwell
- Division of Child and Adolescent Health, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, and Department of Population and Family Health, Mailman School of Public Health, New York, NY, USA
| | - Haili Tang
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vic Veguilla
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Richard Webby
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David C Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Derek J Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
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12
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Mühlemann B, Wilks SH, Baracco L, Bekliz M, Carreño JM, Corman VM, Davis-Gardner ME, Dejnirattisai W, Diamond MS, Douek DC, Drosten C, Eckerle I, Edara VV, Ellis M, Fouchier RAM, Frieman M, Godbole S, Haagmans B, Halfmann PJ, Henry AR, Jones TC, Katzelnick LC, Kawaoka Y, Kimpel J, Krammer F, Lai L, Liu C, Lusvarghi S, Meyer B, Mongkolsapaya J, Montefiori DC, Mykytyn A, Netzl A, Pollett S, Rössler A, Screaton GR, Shen X, Sigal A, Simon V, Subramanian R, Supasa P, Suthar M, Türeli S, Wang W, Weiss CD, Smith DJ. Comparative Analysis of SARS-CoV-2 Antigenicity across Assays and in Human and Animal Model Sera. bioRxiv 2023:2023.09.27.559689. [PMID: 37808679 PMCID: PMC10557678 DOI: 10.1101/2023.09.27.559689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The antigenic evolution of SARS-CoV-2 requires ongoing monitoring to judge the immune escape of newly arising variants. A surveillance system necessitates an understanding of differences in neutralization titers measured in different assays and using human and animal sera. We compared 18 datasets generated using human, hamster, and mouse sera, and six different neutralization assays. Titer magnitude was lowest in human, intermediate in hamster, and highest in mouse sera. Fold change, immunodominance patterns and antigenic maps were similar among sera. Most assays yielded similar results, except for differences in fold change in cytopathic effect assays. Not enough data was available for conclusively judging mouse sera, but hamster sera were a consistent surrogate for human first-infection sera.
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Affiliation(s)
- Barbara Mühlemann
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Samuel H Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Lauren Baracco
- Center for Pathogen Research, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Meriem Bekliz
- Department of Medicine, Faculty of Medicine, University of Geneva, Switzerland
- Centre for Emerging Viral Diseases, University Hospitals of Geneva and University of Geneva, Switzerland
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Victor M Corman
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Meredith E Davis-Gardner
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Wanwisa Dejnirattisai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Division of Emerging Infectious Disease, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi, Bangkok 10700, Thailand
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Andrew M. and Jane M. Bursky the Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Christian Drosten
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Isabella Eckerle
- Department of Medicine, Faculty of Medicine, University of Geneva, Switzerland
- Centre for Emerging Viral Diseases, University Hospitals of Geneva and University of Geneva, Switzerland
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Venkata-Viswanadh Edara
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Madison Ellis
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Ron A M Fouchier
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Matthew Frieman
- Center for Pathogen Research, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Sucheta Godbole
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Bart Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Amy R Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Terry C Jones
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Leah C Katzelnick
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo 162-8655, Japan
| | - Janine Kimpel
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Cellular and Molecular Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lilin Lai
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Sabrina Lusvarghi
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA
| | - Benjamin Meyer
- Centre of Vaccinology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - David C Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Anna Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Antonia Netzl
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Simon Pollett
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Annika Rössler
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Xiaoying Shen
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Cellular and Molecular Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rahul Subramanian
- Office of Data Science and Emerging Technologies, Office of Science Management and Operations, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Mehul Suthar
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Sina Türeli
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Wei Wang
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA
| | - Carol D Weiss
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA
| | - Derek J Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
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13
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Herfst S, Begeman L, Spronken MI, Poen MJ, Eggink D, de Meulder D, Lexmond P, Bestebroer TM, Koopmans MPG, Kuiken T, Richard M, Fouchier RAM. A Dutch highly pathogenic H5N6 avian influenza virus showed remarkable tropism for extra-respiratory organs and caused severe disease but was not transmissible via air in the ferret model. mSphere 2023; 8:e0020023. [PMID: 37428085 PMCID: PMC10449504 DOI: 10.1128/msphere.00200-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/01/2023] [Indexed: 07/11/2023] Open
Abstract
Continued circulation of A/H5N1 influenza viruses of the A/goose/Guangdong/1/96 lineage in poultry has resulted in the diversification in multiple genetic and antigenic clades. Since 2009, clade 2.3.4.4 hemagglutinin (HA) containing viruses harboring the internal and neuraminidase (NA) genes of other avian influenza A viruses have been detected. As a result, various HA-NA combinations, such as A/H5N1, A/H5N2, A/H5N3, A/H5N5, A/H5N6, and A/H5N8 have been identified. As of January 2023, 83 humans have been infected with A/H5N6 viruses, thereby posing an apparent risk for public health. Here, as part of a risk assessment, the in vitro and in vivo characterization of A/H5N6 A/black-headed gull/Netherlands/29/2017 is described. This A/H5N6 virus was not transmitted between ferrets via the air but was of unexpectedly high pathogenicity compared to other described A/H5N6 viruses. The virus replicated and caused severe lesions not only in respiratory tissues but also in multiple extra-respiratory tissues, including brain, liver, pancreas, spleen, lymph nodes, and adrenal gland. Sequence analyses demonstrated that the well-known mammalian adaptation substitution D701N was positively selected in almost all ferrets. In the in vitro experiments, no other known viral phenotypic properties associated with mammalian adaptation or increased pathogenicity were identified. The lack of transmission via the air and the absence of mammalian adaptation markers suggest that the public health risk of this virus is low. The high pathogenicity of this virus in ferrets could not be explained by the known mammalian pathogenicity factors and should be further studied. IMPORTANCE Avian influenza A/H5 viruses can cross the species barrier and infect humans. These infections can have a fatal outcome, but fortunately these influenza A/H5 viruses do not spread between humans. However, the extensive circulation and reassortment of A/H5N6 viruses in poultry and wild birds warrant risk assessments of circulating strains. Here an in-depth characterization of the properties of an avian A/H5N6 influenza virus isolated from a black-headed gull in the Netherlands was performed in vitro and in vivo, in ferrets. The virus was not transmissible via the air but caused severe disease and spread to extra-respiratory organs. Apart from the detection in ferrets of a mutation that increased virus replication, no other mammalian adaptation phenotypes were identified. Our results suggest that the risk of this avian A/H5N6 virus for public health is low. The underlying reasons for the high pathogenicity of this virus are unexplained and should be further studied.
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Affiliation(s)
- Sander Herfst
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Lineke Begeman
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Monique I. Spronken
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marjolein J. Poen
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Dirk Eggink
- Academic Medical Center Amsterdam, Laboratory of Experimental Virology, Amsterdam, the Netherlands
| | - Dennis de Meulder
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Pascal Lexmond
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Theo M. Bestebroer
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marion P. G. Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Thijs Kuiken
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Mathilde Richard
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Ron A. M. Fouchier
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
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14
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Kutter JS, Linster M, de Meulder D, Bestebroer TM, Lexmond P, Rosu ME, Richard M, de Vries RP, Fouchier RAM, Herfst S. Continued adaptation of A/H2N2 viruses during pandemic circulation in humans. J Gen Virol 2023; 104:001881. [PMID: 37650875 PMCID: PMC10721047 DOI: 10.1099/jgv.0.001881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/27/2023] [Indexed: 09/01/2023] Open
Abstract
Influenza A viruses of the H2N2 subtype sparked a pandemic in 1957 and circulated in humans until 1968. Because A/H2N2 viruses still circulate in wild birds worldwide and human population immunity is low, the transmissibility of six avian A/H2N2 viruses was investigated in the ferret model. None of the avian A/H2N2 viruses was transmitted between ferrets, suggesting that their pandemic risk may be low. The transmissibility, receptor binding preference and haemagglutinin (HA) stability of human A/H2N2 viruses were also investigated. Human A/H2N2 viruses from 1957 and 1958 bound to human-type α2,6-linked sialic acid receptors, but the 1958 virus had a more stable HA, indicating adaptation to replication and spread in the new host. This increased stability was caused by a previously unknown stability substitution G205S in the 1958 H2N2 HA, which became fixed in A/H2N2 viruses after 1958. Although individual substitutions were identified that affected the HA receptor binding and stability properties, they were not found to have a substantial effect on transmissibility of A/H2N2 viruses via the air in the ferret model. Our data demonstrate that A/H2N2 viruses continued to adapt during the first year of pandemic circulation in humans, similar to what was previously shown for the A/H1N1pdm09 virus.
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Affiliation(s)
- Jasmin S. Kutter
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Martin Linster
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
- Present address: Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Dennis de Meulder
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Theo M. Bestebroer
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Pascal Lexmond
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Miruna E. Rosu
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Mathilde Richard
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Robert P. de Vries
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | - Ron A. M. Fouchier
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Sander Herfst
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
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15
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Wilks SH, Mühlemann B, Shen X, Türeli S, LeGresley EB, Netzl A, Caniza MA, Chacaltana-Huarcaya JN, Corman VM, Daniell X, Datto MB, Dawood FS, Denny TN, Drosten C, Fouchier RAM, Garcia PJ, Halfmann PJ, Jassem A, Jeworowski LM, Jones TC, Kawaoka Y, Krammer F, McDanal C, Pajon R, Simon V, Stockwell MS, Tang H, van Bakel H, Veguilla V, Webby R, Montefiori DC, Smith DJ. Mapping SARS-CoV-2 antigenic relationships and serological responses. bioRxiv 2023:2022.01.28.477987. [PMID: 35860221 PMCID: PMC9298128 DOI: 10.1101/2022.01.28.477987] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
During the SARS-CoV-2 pandemic, multiple variants escaping pre-existing immunity emerged, causing concerns about continued protection. Here, we use antigenic cartography to analyze patterns of cross-reactivity among a panel of 21 variants and 15 groups of human sera obtained following primary infection with 10 different variants or after mRNA-1273 or mRNA-1273.351 vaccination. We find antigenic differences among pre-Omicron variants caused by substitutions at spike protein positions 417, 452, 484, and 501. Quantifying changes in response breadth over time and with additional vaccine doses, our results show the largest increase between 4 weeks and >3 months post-2nd dose. We find changes in immunodominance of different spike regions depending on the variant an individual was first exposed to, with implications for variant risk assessment and vaccine strain selection.
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Affiliation(s)
- Samuel H Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Barbara Mühlemann
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Xiaoying Shen
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Sina Türeli
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Eric B LeGresley
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Antonia Netzl
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Miguela A Caniza
- Department of Global Pediatric Medicine, Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Victor M Corman
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Xiaoju Daniell
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Michael B Datto
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | | | - Thomas N Denny
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Christian Drosten
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | | | - Patricia J Garcia
- School of Public Health, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Science, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Agatha Jassem
- BC Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Lara M Jeworowski
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Terry C Jones
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Science, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo, Japan
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Cellular and Molecular Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Charlene McDanal
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | | | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Cellular and Molecular Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa S Stockwell
- Division of Child and Adolescent Health, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, and Department of Population and Family Health, Mailman School of Public Health, New York, NY, USA
| | - Haili Tang
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vic Veguilla
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Richard Webby
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David C Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Derek J Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
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16
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Runstadler JA, Lowen AC, Kayali G, Tompkins SM, Albrecht RA, Fouchier RAM, Stallknecht DE, Lakdawala SS, Goodrum FD, Casadevall A, Enquist LW, Alwine JC, Imperiale MJ, Schultz-Cherry S, Webby RJ. Field Research Is Essential to Counter Virological Threats. J Virol 2023; 97:e0054423. [PMID: 37166327 DOI: 10.1128/jvi.00544-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
The interface between humans and wildlife is changing and, with it, the potential for pathogen introduction into humans has increased. Avian influenza is a prominent example, with an ongoing outbreak showing the unprecedented expansion of both geographic and host ranges. Research in the field is essential to understand this and other zoonotic threats. Only by monitoring dynamic viral populations and defining their biology in situ can we gather the information needed to ensure effective pandemic preparation.
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Affiliation(s)
- Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, Boston, Massachusetts, USA
- Center for Research on Influenza Pathogenesis and Transmission (CRIPT) CEIRR, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Anice C Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR), Atlanta, Georgia, USA
| | - Ghazi Kayali
- Human-Link DMCC, Dubai, UAE
- University of Texas School of Public Health, Houston, Texas, USA
- St Jude Center of Excellence for Influenza Research and Response (SJ-CEIRR), Memphis, Tennessee, USA
| | - S Mark Tompkins
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, USA
- Center for Influenza Disease and Emergence Research (CIDER) CEIRR, Athens, Georgia, USA
| | - Randy A Albrecht
- Center for Research on Influenza Pathogenesis and Transmission (CRIPT) CEIRR, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ron A M Fouchier
- Center for Research on Influenza Pathogenesis and Transmission (CRIPT) CEIRR, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - David E Stallknecht
- St Jude Center of Excellence for Influenza Research and Response (SJ-CEIRR), Memphis, Tennessee, USA
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Seema S Lakdawala
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
- Penn Center of Excellence for Influenza Research and Response (Penn-CEIRR), Philadelphia, Pennsylvania, USA
| | - Felicia D Goodrum
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, Baltimore, Maryland, USA
| | - Lynn W Enquist
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - James C Alwine
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael J Imperiale
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Stacey Schultz-Cherry
- St Jude Center of Excellence for Influenza Research and Response (SJ-CEIRR), Memphis, Tennessee, USA
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Richard J Webby
- St Jude Center of Excellence for Influenza Research and Response (SJ-CEIRR), Memphis, Tennessee, USA
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
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17
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Turner S, Alisoltani A, Bratt D, Cohen-Lavi L, Dearlove BL, Drosten C, Fischer WM, Fouchier RAM, Gonzalez-Reiche AS, Jaroszewski L, Khalil Z, LeGresley E, Johnson M, Jones TC, Mühlemann B, O'Connor D, Sedova M, Shukla M, Theiler J, Wallace ZS, Yoon H, Zhang Y, van Bakel H, Degrace MM, Ghedin E, Godzik A, Hertz T, Korber B, Lemieux J, Niewiadomska AM, Post DJ, Rolland M, Scheuermann R, Smith DJ. US National Institutes of Health Prioritization of SARS-CoV-2 Variants. Emerg Infect Dis 2023; 29:e221646. [PMID: 37054986 PMCID: PMC10124642 DOI: 10.3201/eid2905.221646] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023] Open
Abstract
Since late 2020, SARS-CoV-2 variants have regularly emerged with competitive and phenotypic differences from previously circulating strains, sometimes with the potential to escape from immunity produced by prior exposure and infection. The Early Detection group is one of the constituent groups of the US National Institutes of Health National Institute of Allergy and Infectious Diseases SARS-CoV-2 Assessment of Viral Evolution program. The group uses bioinformatic methods to monitor the emergence, spread, and potential phenotypic properties of emerging and circulating strains to identify the most relevant variants for experimental groups within the program to phenotypically characterize. Since April 2021, the group has prioritized variants monthly. Prioritization successes include rapidly identifying most major variants of SARS-CoV-2 and providing experimental groups within the National Institutes of Health program easy access to regularly updated information on the recent evolution and epidemiology of SARS-CoV-2 that can be used to guide phenotypic investigations.
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18
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Mykytyn AZ, Rosu ME, Kok A, Rissmann M, van Amerongen G, Geurtsvankessel C, de Vries RD, Munnink BBO, Smith DJ, Koopmans MPG, Lamers MM, Fouchier RAM, Haagmans BL. Antigenic mapping of emerging SARS-CoV-2 omicron variants BM.1.1.1, BQ.1.1, and XBB.1. Lancet Microbe 2023; 4:e294-e295. [PMID: 36657480 PMCID: PMC9842387 DOI: 10.1016/s2666-5247(22)00384-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 01/19/2023]
Affiliation(s)
- Anna Z Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | - Miruna E Rosu
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | - Adinda Kok
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | - Melanie Rissmann
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | | | | | - Rory D de Vries
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | - Bas B Oude Munnink
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | - Derek J Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Marion P G Koopmans
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | - Mart M Lamers
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | - Ron A M Fouchier
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands
| | - Bart L Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam 3015CN, Netherlands.
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19
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Kuiken T, Fouchier RAM, Koopmans MPG. Being ready for the next influenza pandemic? Lancet Infect Dis 2023; 23:398-399. [PMID: 36898404 DOI: 10.1016/s1473-3099(23)00117-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 03/09/2023]
Affiliation(s)
- Thijs Kuiken
- Viroscience Department, Erasmus University Medical Centre, Rotterdam 3015 GD, Netherlands
| | - Ron A M Fouchier
- Viroscience Department, Erasmus University Medical Centre, Rotterdam 3015 GD, Netherlands
| | - Marion P G Koopmans
- Viroscience Department, Erasmus University Medical Centre, Rotterdam 3015 GD, Netherlands.
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20
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de Bruin ACM, Spronken MI, Bestebroer TM, Fouchier RAM, Richard M. Conserved Expression and Functionality of Furin between Chickens and Ducks as an Activating Protease of Highly Pathogenic Avian Influenza Virus Hemagglutinins. Microbiol Spectr 2023; 11:e0460222. [PMID: 36916982 PMCID: PMC10100678 DOI: 10.1128/spectrum.04602-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/23/2023] [Indexed: 03/15/2023] Open
Abstract
Highly pathogenic avian influenza viruses (HPAIVs) typically emerge from low-pathogenic avian influenza viruses (LPAIVs) of the H5 and H7 subtypes upon spillover from wild aquatic birds into poultry. The conversion from LPAIV to HPAIV is characterized by the acquisition of a multibasic cleavage site (MBCS) at the proteolytic cleavage site in the viral binding and fusion protein, hemagglutinin (HA), resulting in cleavage and activation of HA by ubiquitously expressed furin-like proteases. The ensuing HPAIVs disseminate systemically in gallinaceous poultry, are endotheliotropic, and cause hemorrhagic disease with high mortality. HPAIV infections in wild aquatic birds are generally milder, often asymptomatic, and generally not associated with systemic dissemination nor endotheliotropic. As MBCS cleavage by host proteases is the main virulence determinant of HPAIVs in poultry, we set out to determine whether cleavage of HPAIV HA by host proteases might influence the observed species-specific pathogenesis and tropism. Here, we sequenced, cloned, and characterized the expression and functionality of duck furin. The furin sequence was strongly conserved between chickens and ducks, and duck furin cleaved HPAIV and tetrabasic HA in an overexpression system, confirming its functionality. Furin was expressed ubiquitously and to similar extents in duck and chicken tissues, including in primary duck endothelial cells, which sustained multicycle replication of H5N1 HPAIV but not LPAIVs. In conclusion, differences in furin-like protease biology between wild aquatic birds and gallinaceous poultry are unlikely to largely determine the stark differences observed in species-specific pathogenesis of HPAIVs. IMPORTANCE HPAIV outbreaks are a global concern due to the health risks for poultry, wildlife, and humans and their major economic impact. The number of LPAIV-to-HPAIV conversions, which is associated with spillover from wild birds to poultry, has been increasing over recent decades. Furthermore, H5 HPAIVs from the A/goose/Guangdong/1/96 lineage have been circulating in migratory birds, causing increasingly frequent epizootics in poultry and wild birds. Milder symptoms in migratory birds allow for dispersion of HPAIVs over long distances, justifying the importance of understanding the pathogenesis of HPAIVs in wild birds. Here, we examined whether host proteases are a likely candidate to explain some differences in the degree of HPAIV systemic dissemination between avian species. This is the first report to show that furin function and expression is comparable between chickens and ducks, which renders the hypothesis unlikely that furin-like protease differences influence the HPAIV species-specific pathogenesis and tropism.
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Affiliation(s)
- Anja C. M. de Bruin
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Monique I. Spronken
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Theo M. Bestebroer
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Ron A. M. Fouchier
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Mathilde Richard
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
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21
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Wille M, Lisovski S, Roshier D, Ferenczi M, Hoye BJ, Leen T, Warner S, Fouchier RAM, Hurt AC, Holmes EC, Klaassen M. Strong host phylogenetic and ecological effects on host competency for avian influenza in Australian wild birds. Proc Biol Sci 2023; 290:20222237. [PMID: 36651046 PMCID: PMC9845974 DOI: 10.1098/rspb.2022.2237] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Host susceptibility to parasites is mediated by intrinsic and external factors such as genetics, ecology, age and season. While waterfowl are considered central to the reservoir community for low pathogenic avian influenza A viruses (LPAIV), the role of host phylogeny has received limited formal attention. Herein, we analysed 12 339 oropharyngeal and cloacal swabs and 10 826 serum samples collected over 11 years from wild birds in Australia. As well as describing age and species-level differences in prevalence and seroprevalence, we reveal that host phylogeny is a key driver in host range. Seasonality effects appear less pronounced than in the Northern Hemisphere, while annual variations are potentially linked to El Niño-Southern Oscillation. Our study provides a uniquely detailed insight into the evolutionary ecology of LPAIV in its avian reservoir community, defining distinctive processes on the continent of Australia and expanding our understanding of LPAIV globally.
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Affiliation(s)
- Michelle Wille
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia,WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia,Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Simeon Lisovski
- Centre for Integrative Ecology, Deakin University, Geelong, VIC 3217, Australia
| | - David Roshier
- Centre for Integrative Ecology, Deakin University, Geelong, VIC 3217, Australia
| | - Marta Ferenczi
- Centre for Integrative Ecology, Deakin University, Geelong, VIC 3217, Australia
| | - Bethany J. Hoye
- Centre for Integrative Ecology, Deakin University, Geelong, VIC 3217, Australia
| | - Trent Leen
- Geelong Field and Game, Geelong, VIC 3340, Australia,Wetlands Environmental Taskforce, Field and Game Australia, Seymour, VIC 3660, Australia
| | - Simone Warner
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - Ron A. M. Fouchier
- Department of Viroscience, Erasmus Medical Centre, Rotterdam 3015GE, The Netherlands
| | - Aeron C. Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Marcel Klaassen
- Centre for Integrative Ecology, Deakin University, Geelong, VIC 3217, Australia,Victorian Wader Study Group, Thornbury, Victoria 3071, Australia,Australasian Wader Studies Group, Curtin, ACT 2605, Australia
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22
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Jesse ST, Ribó-Molina P, Jo WK, Rautenschlein S, Vuong O, Fouchier RAM, Ludlow M, Osterhaus ADME. Molecular characterization of avian metapneumovirus subtype C detected in wild mallards (Anas platyrhynchos) in The Netherlands. Transbound Emerg Dis 2022; 69:3360-3370. [PMID: 36029486 DOI: 10.1111/tbed.14688] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 07/21/2022] [Accepted: 08/10/2022] [Indexed: 02/07/2023]
Abstract
Avian metapneumovirus (AMPV) represents a long-term threat to the poultry industry due to its etiological role in the induction of acute respiratory disease and/or egg drop syndrome in domestic turkeys, chickens, and ducks. Although this disease is commonly referred to as turkey rhinotracheitis, the host range of AMPV encompasses many avian species. We have screened 1323 oropharyngeal- and cloacal swab samples obtained from wild mallards in the Netherlands from 2017 to 2019 by RT-PCR using a degenerate primer pair to detect all members of the Paramyxoviridae and Pneumoviridae or an avian metapneumovirus subtype C (AMPV-C)-specific RT-qPCR assay. We identified a total of seven cases of AMPV-C infections in wild, healthy mallards (Anas platyrhynchos), of which two AMPV-C positive samples were further processed using next-generation sequencing. Phylogenetic analysis of the two complete genomes showed that the newly identified AMPV-C strains share closest sequence identity (97%) with Eurasian lineage AMPV-C strains identified in Muscovy ducks in China that presented with severe respiratory disease and egg production loss in 2011. Further analysis of G protein amino acid sequences showed a high degree of variability between the newly identified AMPV-C variants. PONDR scoring of the G protein has revealed the ectodomain of AMPV-C to be partitioned into a long intrinsically disordered and short ordered region, giving insights into AMPV G protein structural biology. In summary, we provide the first report of full-length AMPV-C genome sequences derived from wild birds in Europe. This emphasizes the need for further surveillance efforts to better characterize the host range, epidemiologic distribution, and pathogenicity of AMPV-C to determine the risk posed by cross-species jumps from wildfowl to domesticated avian species.
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Affiliation(s)
- Sonja T Jesse
- Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany
| | - Pau Ribó-Molina
- Department Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Wendy K Jo
- Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany
| | - Silke Rautenschlein
- Clinic for Poultry, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Oanh Vuong
- Department Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ron A M Fouchier
- Clinic for Poultry, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Martin Ludlow
- Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany
| | - Albert D M E Osterhaus
- Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany
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23
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Rosu ME, Lexmond P, Bestebroer TM, Hauser BM, Smith DJ, Herfst S, Fouchier RAM. Substitutions near the HA receptor binding site explain the origin and major antigenic change of the B/Victoria and B/Yamagata lineages. Proc Natl Acad Sci U S A 2022; 119:e2211616119. [PMID: 36215486 PMCID: PMC9586307 DOI: 10.1073/pnas.2211616119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/13/2022] [Indexed: 11/18/2022] Open
Abstract
Influenza B virus primarily infects humans, causing seasonal epidemics globally. Two antigenic variants-Victoria-like and Yamagata-like-were detected in the 1980s, of which the molecular basis of emergence is still incompletely understood. Here, the antigenic properties of a unique collection of historical virus isolates, sampled from 1962 to 2000 and passaged exclusively in mammalian cells to preserve antigenic properties, were determined with the hemagglutination inhibition assay and an antigenic map was built to quantify and visualize the divergence of the lineages. The antigenic map revealed only three distinct antigenic clusters-Early, Victoria, and Yamagata-with relatively little antigenic diversity in each cluster until 2000. Viruses with Victoria-like antigenic properties emerged around 1972 and diversified subsequently into two genetic lineages. Viruses with Yamagata-like antigenic properties evolved from one lineage and became clearly antigenically distinct from the Victoria-like viruses around 1988. Recombinant mutant viruses were tested to show that insertions and deletions (indels), as observed frequently in influenza B virus hemagglutinin, had little effect on antigenic properties. In contrast, amino-acid substitutions at positions 148, 149, 150, and 203, adjacent to the hemagglutinin receptor binding site, determined the main antigenic differences between the Early, Victoria-like, and Yamagata-like viruses. Surprisingly, substitutions at two of the four positions reverted in recent viruses of the Victoria lineage, resulting in antigenic properties similar to viruses circulating ∼50 y earlier. These data shed light on the antigenic diversification of influenza viruses and suggest there may be limits to the antigenic evolution of influenza B virus.
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Affiliation(s)
- Miruna E. Rosu
- Department of Viroscience, Erasmus Medical Centre, Rotterdam 3015 CE, The Netherlands
| | - Pascal Lexmond
- Department of Viroscience, Erasmus Medical Centre, Rotterdam 3015 CE, The Netherlands
| | - Theo M. Bestebroer
- Department of Viroscience, Erasmus Medical Centre, Rotterdam 3015 CE, The Netherlands
| | - Blake M. Hauser
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Derek J. Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Sander Herfst
- Department of Viroscience, Erasmus Medical Centre, Rotterdam 3015 CE, The Netherlands
| | - Ron A. M. Fouchier
- Department of Viroscience, Erasmus Medical Centre, Rotterdam 3015 CE, The Netherlands
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24
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Wille M, Tolf C, Latorre-Margalef N, Fouchier RAM, Halpin RA, Wentworth DE, Ragwani J, Pybus OG, Olsen B, Waldenström J. Evolutionary features of a prolific subtype of avian influenza A virus in European waterfowl. Virus Evol 2022; 8:veac074. [PMID: 36128050 PMCID: PMC9477075 DOI: 10.1093/ve/veac074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 06/12/2022] [Accepted: 08/25/2022] [Indexed: 11/26/2022] Open
Abstract
Avian influenza A virus (AIV) is ubiquitous in waterfowl and is detected annually at high prevalence in waterfowl during the Northern Hemisphere autumn. Some AIV subtypes are globally common in waterfowl, such as H3N8, H4N6, and H6N2, and are detected in the same populations at a high frequency, annually. In order to investigate genetic features associated to the long-term maintenance of common subtypes in migratory ducks, we sequenced 248 H4 viruses isolated across 8 years (2002–9) from mallards (Anas platyrhynchos) sampled in southeast Sweden. Phylogenetic analyses showed that both H4 and N6 sequences fell into three distinct lineages, structured by year of isolation. Specifically, across the 8 years of the study, we observed lineage replacement, whereby a different HA lineage circulated in the population each year. Analysis of deduced amino acid sequences of the HA lineages illustrated key differences in regions of the globular head of hemagglutinin that overlap with established antigenic sites in homologous hemagglutinin H3, suggesting the possibility of antigenic differences among these HA lineages. Beyond HA, lineage replacement was common to all segments, such that novel genome constellations were detected across years. A dominant genome constellation would rapidly amplify in the duck population, followed by unlinking of gene segments as a result of reassortment within 2–3 weeks following introduction. These data help reveal the evolutionary dynamics exhibited by AIV on both annual and decadal scales in an important reservoir host.
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Affiliation(s)
- Michelle Wille
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Universitetsplatsen 1, Kalmar SE-39231, Sweden
| | - Conny Tolf
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Universitetsplatsen 1, Kalmar SE-39231, Sweden
| | - Neus Latorre-Margalef
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Universitetsplatsen 1, Kalmar SE-39231, Sweden
| | - Ron A M Fouchier
- Department of Virology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | | | - Jayna Ragwani
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK.,Department of Pathobiology and Population Sciences, The Royal Veterinary College, London AL9 7TA, UK
| | - Björn Olsen
- Section of Infectious Diseases, Department of Medical Sciences, Uppsala University, Uppsala SE751 85, Sweden
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Universitetsplatsen 1, Kalmar SE-39231, Sweden
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25
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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:v14071566. [PMID: 35891546 PMCID: PMC9321182 DOI: 10.3390/v14071566] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [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.)
- Correspondence:
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26
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Rissmann M, Noack D, van Riel D, Schmitz KS, de Vries RD, van Run P, Lamers MM, GeurtsvanKessel CH, Koopmans MPG, Fouchier RAM, Kuiken T, Haagmans BL, Rockx B. Pulmonary lesions following inoculation with the SARS-CoV-2 Omicron BA.1 (B.1.1.529) variant in Syrian golden hamsters. Emerg Microbes Infect 2022; 11:1778-1786. [PMID: 35787236 PMCID: PMC9295819 DOI: 10.1080/22221751.2022.2095932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
AbstractThe Omicron BA.1 (B.1.1.529) SARS-CoV-2 variant is characterized by a high number of mutations in the viral genome, associated with immune-escape and increased viral spread. It remains unclear whether milder COVID-19 disease progression observed after infection with Omicron BA.1 in humans is due to reduced pathogenicity of the virus or due to pre-existing immunity from vaccination or previous infection. Here, we inoculated hamsters with Omicron BA.1 to evaluate pathogenicity and kinetics of viral shedding, compared to Delta (B.1.617.2) and to animals re-challenged with Omicron BA.1 after previous SARS-CoV-2 614G infection. Omicron BA.1 infected animals showed reduced clinical signs, pathological changes, and viral shedding, compared to Delta-infected animals, but still showed gross- and histopathological evidence of pneumonia. Pre-existing immunity reduced viral shedding and protected against pneumonia. Our data indicate that the observed decrease of disease severity is in part due to intrinsic properties of the Omicron BA.1 variant.
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Affiliation(s)
- Melanie Rissmann
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Danny Noack
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Debby van Riel
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Katharina S Schmitz
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Rory D de Vries
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Peter van Run
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Mart M Lamers
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Marion P G Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Thijs Kuiken
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Barry Rockx
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
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27
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de Graaf JF, Huberts M, Groeneveld D, van Nieuwkoop S, van Eijck CHJ, Fouchier RAM, van den Hoogen BG. Comparison between intratumoral and intravenously administered oncolytic virus therapy with Newcastle disease virus in a xenograft murine model for pancreatic adenocarcinoma. Heliyon 2022; 8:e09915. [PMID: 35874055 PMCID: PMC9304737 DOI: 10.1016/j.heliyon.2022.e09915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/29/2022] [Accepted: 07/05/2022] [Indexed: 11/24/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by a poor clinical prognosis and is usually a metastatic disease. In the last decades, oncolytic viro-immunotherapy has shown a promise as treatment strategy with encouraging results for a variety of tumors. Newcastle Disease Virus (NDV) is an oncolytic virus which selectively infects and damages tumors either by directly killing tumor cells or by promoting an anti-tumor immune response. Several studies have demonstrated that NDV strains with a multi-basic cleavage site (MBCS) in the fusion protein (F) have increased anti-tumor efficacy upon intratumoral injection in murine tumor models. However, intravenous injections, in which the oncolytic virus spreads systemically, could be more beneficial to treat metastasized PDAC in addition to the primary tumor. In this study, we compared the oncolytic efficacy and safety of intratumoral and intravenous injections with NDV containing an MBCS in F (NDV F3aa) in an immune deficient murine xenograft (BxPC3) model for PDAC. In this model, both intratumoral and intravenous injections with NDV F3aa induced anti-tumor efficacy as measured at 10 days after the first injection. Upon intravenous injection virus was detected in some of the tumors, indicating the systemic spread of the virus. Upon both treatments, mice did not display weight loss or abnormalities and treated mice did not secrete virus to the environment. These data demonstrate that intravenous injections of NDV F3aa can be applicable to treat metastasized cancers in immune deficient hosts without inflicting adverse effects.
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Affiliation(s)
| | - Marco Huberts
- Viroscience Department, Erasmus Medical Centrum, Rotterdam, the Netherlands
| | - Daphne Groeneveld
- Viroscience Department, Erasmus Medical Centrum, Rotterdam, the Netherlands
| | | | | | - Ron A M Fouchier
- Viroscience Department, Erasmus Medical Centrum, Rotterdam, the Netherlands
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28
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DeGrace MM, Ghedin E, Frieman MB, Krammer F, Grifoni A, Alisoltani A, Alter G, Amara RR, Baric RS, Barouch DH, Bloom JD, Bloyet LM, Bonenfant G, Boon ACM, Boritz EA, Bratt DL, Bricker TL, Brown L, Buchser WJ, Carreño JM, Cohen-Lavi L, Darling TL, Davis-Gardner ME, Dearlove BL, Di H, Dittmann M, Doria-Rose NA, Douek DC, Drosten C, Edara VV, Ellebedy A, Fabrizio TP, Ferrari G, Fischer WM, Florence WC, Fouchier RAM, Franks J, García-Sastre A, Godzik A, Gonzalez-Reiche AS, Gordon A, Haagmans BL, Halfmann PJ, Ho DD, Holbrook MR, Huang Y, James SL, Jaroszewski L, Jeevan T, Johnson RM, Jones TC, Joshi A, Kawaoka Y, Kercher L, Koopmans MPG, Korber B, Koren E, Koup RA, LeGresley EB, Lemieux JE, Liebeskind MJ, Liu Z, Livingston B, Logue JP, Luo Y, McDermott AB, McElrath MJ, Meliopoulos VA, Menachery VD, Montefiori DC, Mühlemann B, Munster VJ, Munt JE, Nair MS, Netzl A, Niewiadomska AM, O'Dell S, Pekosz A, Perlman S, Pontelli MC, Rockx B, Rolland M, Rothlauf PW, Sacharen S, Scheuermann RH, Schmidt SD, Schotsaert M, Schultz-Cherry S, Seder RA, Sedova M, Sette A, Shabman RS, Shen X, Shi PY, Shukla M, Simon V, Stumpf S, Sullivan NJ, Thackray LB, Theiler J, Thomas PG, Trifkovic S, Türeli S, Turner SA, Vakaki MA, van Bakel H, VanBlargan LA, Vincent LR, Wallace ZS, Wang L, Wang M, Wang P, Wang W, Weaver SC, Webby RJ, Weiss CD, Wentworth DE, Weston SM, Whelan SPJ, Whitener BM, Wilks SH, Xie X, Ying B, Yoon H, Zhou B, Hertz T, Smith DJ, Diamond MS, Post DJ, Suthar MS. Defining the risk of SARS-CoV-2 variants on immune protection. Nature 2022; 605:640-652. [PMID: 35361968 PMCID: PMC9345323 DOI: 10.1038/s41586-022-04690-5] [Citation(s) in RCA: 93] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/24/2022] [Indexed: 11/09/2022]
Abstract
The global emergence of many severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants jeopardizes the protective antiviral immunity induced after infection or vaccination. To address the public health threat caused by the increasing SARS-CoV-2 genomic diversity, the National Institute of Allergy and Infectious Diseases within the National Institutes of Health established the SARS-CoV-2 Assessment of Viral Evolution (SAVE) programme. This effort was designed to provide a real-time risk assessment of SARS-CoV-2 variants that could potentially affect the transmission, virulence, and resistance to infection- and vaccine-induced immunity. The SAVE programme is a critical data-generating component of the US Government SARS-CoV-2 Interagency Group to assess implications of SARS-CoV-2 variants on diagnostics, vaccines and therapeutics, and for communicating public health risk. Here we describe the coordinated approach used to identify and curate data about emerging variants, their impact on immunity and effects on vaccine protection using animal models. We report the development of reagents, methodologies, models and notable findings facilitated by this collaborative approach and identify future challenges. This programme is a template for the response to rapidly evolving pathogens with pandemic potential by monitoring viral evolution in the human population to identify variants that could reduce the effectiveness of countermeasures.
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Affiliation(s)
- Marciela M DeGrace
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Elodie Ghedin
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institutes of Health, Rockville, MD, USA
| | - Matthew B Frieman
- Center for Pathogen Research, Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, MD, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Boston, MA, USA
| | - Rama R Amara
- Department of Microbiology and Immunology, Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jesse D Bloom
- Fred Hutch Cancer Center, Howard Hughes Medical Institute, Seattle, WA, USA
| | - Louis-Marie Bloyet
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Gaston Bonenfant
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Adrianus C M Boon
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Eli A Boritz
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Debbie L Bratt
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- CAMRIS, Contractor for NIAID, Bethesda, MD, USA
| | - Traci L Bricker
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Liliana Brown
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - William J Buchser
- High Throughput Screening Center, Washington University School of Medicine, St Louis, MO, USA
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Liel Cohen-Lavi
- National Institute for Biotechnology in the Negev, Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
| | - Tamarand L Darling
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Meredith E Davis-Gardner
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Bethany L Dearlove
- US Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Han Di
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Meike Dittmann
- Microbiology Department, New York University Grossman School of Medicine, New York, NY, USA
| | - Nicole A Doria-Rose
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Daniel C Douek
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin and German Center for Infection Research (DZIF), Berlin, Germany
| | - Venkata-Viswanadh Edara
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Ali Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Thomas P Fabrizio
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Guido Ferrari
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Will M Fischer
- Los Alamos National Laboratory, New Mexico Consortium, Los Alamos, NM, USA
| | - William C Florence
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | | | - John Franks
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adam Godzik
- University of California Riverside School of Medicine, Riverside, CA, USA
| | - Ana Silvia Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aubree Gordon
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Bart L Haagmans
- Department Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Michael R Holbrook
- National Institute of Allergy and Infectious Diseases Integrated Research Facility, Frederick, MD, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Sarah L James
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Lukasz Jaroszewski
- University of California Riverside School of Medicine, Riverside, CA, USA
| | - Trushar Jeevan
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert M Johnson
- Center for Pathogen Research, Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, MD, USA
| | - Terry C Jones
- Institute of Virology, Charité-Universitätsmedizin and German Center for Infection Research (DZIF), Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Astha Joshi
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, Tokyo, Japan
| | - Lisa Kercher
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Bette Korber
- Los Alamos National Laboratory, New Mexico Consortium, Los Alamos, NM, USA
| | - Eilay Koren
- National Institute for Biotechnology in the Negev, Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
- The Shraga Segal Department of Microbiology and Immunology, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Richard A Koup
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Eric B LeGresley
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - Mariel J Liebeskind
- High Throughput Screening Center, Washington University School of Medicine, St Louis, MO, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Brandi Livingston
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - James P Logue
- Center for Pathogen Research, Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yang Luo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Adrian B McDermott
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | | | - Victoria A Meliopoulos
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Vineet D Menachery
- Department of Microbiology and Immunology, Institute for Human Infection and Immunity, World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | | | - Barbara Mühlemann
- Institute of Virology, Charité-Universitätsmedizin and German Center for Infection Research (DZIF), Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Vincent J Munster
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Jenny E Munt
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Manoj S Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Antonia Netzl
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - Sijy O'Dell
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Andrew Pekosz
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Marjorie C Pontelli
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Barry Rockx
- Department Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Morgane Rolland
- US Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Paul W Rothlauf
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Sinai Sacharen
- National Institute for Biotechnology in the Negev, Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
- The Shraga Segal Department of Microbiology and Immunology, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | | | - Stephen D Schmidt
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert A Seder
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Mayya Sedova
- University of California Riverside School of Medicine, Riverside, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Reed S Shabman
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Xiaoying Shen
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Maulik Shukla
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Data Science and Learning Division, Argonne National Laboratory, Argonne, IL, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Spencer Stumpf
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Nancy J Sullivan
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Larissa B Thackray
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - James Theiler
- Los Alamos National Laboratory, New Mexico Consortium, Los Alamos, NM, USA
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Sanja Trifkovic
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Sina Türeli
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Samuel A Turner
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Maria A Vakaki
- High Throughput Screening Center, Washington University School of Medicine, St Louis, MO, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura A VanBlargan
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Leah R Vincent
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Zachary S Wallace
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Li Wang
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Maple Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Wei Wang
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Scott C Weaver
- Department of Microbiology and Immunology, Institute for Human Infection and Immunity, World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Richard J Webby
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Carol D Weiss
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - David E Wentworth
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stuart M Weston
- Center for Pathogen Research, Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Bradley M Whitener
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Samuel H Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Baoling Ying
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Hyejin Yoon
- Los Alamos National Laboratory, New Mexico Consortium, Los Alamos, NM, USA
| | - Bin Zhou
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Tomer Hertz
- Department of Microbiology, Immunology and Genetics Faculty of Health Sciences Ben-Gurion University of the Negev, Be'er Sheva, Israel.
| | - Derek J Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK.
| | - Michael S Diamond
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA.
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA.
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA.
| | - Diane J Post
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
| | - Mehul S Suthar
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA.
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Caliendo V, Leijten L, van de Bildt M, Germeraad E, Fouchier RAM, Beerens N, Kuiken T. Tropism of Highly Pathogenic Avian Influenza H5 Viruses from the 2020/2021 Epizootic in Wild Ducks and Geese. Viruses 2022; 14:280. [PMID: 35215873 PMCID: PMC8880460 DOI: 10.3390/v14020280] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 01/27/2023] Open
Abstract
Highly pathogenic avian influenza (HPAI) outbreaks have become increasingly frequent in wild bird populations and have caused mass mortality in many wild bird species. The 2020/2021 epizootic was the largest and most deadly ever reported in Europe, and many new bird species tested positive for HPAI virus for the first time. This study investigated the tropism of HPAI virus in wild birds. We tested the pattern of virus attachment of 2020 H5N8 virus to intestinal and respiratory tissues of key bird species; and characterized pathology of naturally infected Eurasian wigeons (Mareca penelope) and barnacle geese (Branta leucopsis). This study determined that 2020 H5N8 virus had a high level of attachment to the intestinal epithelium (enterotropism) of dabbling ducks and geese and retained attachment to airway epithelium (respirotropism). Natural HPAI 2020 H5 virus infection in Eurasian wigeons and barnacle geese also showed a high level of neurotropism, as both species presented with brain lesions that co-localized with virus antigen expression. We concluded that the combination of respirotropism, neurotropism, and possibly enterotropism, contributed to the successful adaptation of 2020/2021 HPAI H5 viruses to wild waterbird populations.
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Affiliation(s)
- Valentina Caliendo
- Department of Viroscience, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (L.L.); (M.v.d.B.); (R.A.M.F.); (T.K.)
| | - Lonneke Leijten
- Department of Viroscience, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (L.L.); (M.v.d.B.); (R.A.M.F.); (T.K.)
| | - Marco van de Bildt
- Department of Viroscience, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (L.L.); (M.v.d.B.); (R.A.M.F.); (T.K.)
| | - Evelien Germeraad
- Department of Virology, Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands; (E.G.); (N.B.)
| | - Ron A. M. Fouchier
- Department of Viroscience, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (L.L.); (M.v.d.B.); (R.A.M.F.); (T.K.)
| | - Nancy Beerens
- Department of Virology, Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands; (E.G.); (N.B.)
| | - Thijs Kuiken
- Department of Viroscience, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (L.L.); (M.v.d.B.); (R.A.M.F.); (T.K.)
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de Bruin ACM, Spronken MI, Bestebroer TM, Fouchier RAM, Richard M. Reduced Replication of Highly Pathogenic Avian Influenza Virus in Duck Endothelial Cells Compared to Chicken Endothelial Cells Is Associated with Stronger Antiviral Responses. Viruses 2022; 14:v14010165. [PMID: 35062369 PMCID: PMC8779112 DOI: 10.3390/v14010165] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 12/11/2022] Open
Abstract
Highly pathogenic avian influenza viruses (HPAIVs) cause fatal systemic infections in chickens, which are associated with endotheliotropism. HPAIV infections in wild birds are generally milder and not endotheliotropic. Here, we aimed to elucidate the species-specific endotheliotropism of HPAIVs using primary chicken and duck aortic endothelial cells (chAEC and dAEC respectively). Viral replication kinetics and host responses were assessed in chAEC and dAEC upon inoculation with HPAIV H5N1 and compared to embryonic fibroblasts. Although dAEC were susceptible to HPAIV upon inoculation at high multiplicity of infection, HPAIV replicated to lower levels in dAEC than chAEC during multi-cycle replication. The susceptibility of duck embryonic endothelial cells to HPAIV was confirmed in embryos. Innate immune responses upon HPAIV inoculation differed between chAEC, dAEC, and embryonic fibroblasts. Expression of the pro-inflammatory cytokine IL8 increased in chicken cells but decreased in dAEC. Contrastingly, the induction of antiviral responses was stronger in dAEC than in chAEC, and chicken and duck fibroblasts. Taken together, these data demonstrate that although duck endothelial cells are permissive to HPAIV infection, they display markedly different innate immune responses than chAEC and embryonic fibroblasts. These differences may contribute to the species-dependent differences in endotheliotropism and consequently HPAIV pathogenesis.
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31
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Kok A, Fouchier RAM, Richard M. Cross-Reactivity Conferred by Homologous and Heterologous Prime-Boost A/H5 Influenza Vaccination Strategies in Humans: A Literature Review. Vaccines (Basel) 2021; 9:vaccines9121465. [PMID: 34960210 PMCID: PMC8708856 DOI: 10.3390/vaccines9121465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022] Open
Abstract
Avian influenza viruses from the A/H5 A/goose/Guangdong/1/1996 (GsGd) lineage pose a continuing threat to animal and human health. Since their emergence in 1997, these viruses have spread across multiple continents and have become enzootic in poultry. Additionally, over 800 cases of human infection with A/H5 GsGd viruses have been reported to date, which raises concerns about the potential for a new influenza virus pandemic. The continuous circulation of A/H5 GsGd viruses for over 20 years has resulted in the genetic and antigenic diversification of their hemagglutinin (HA) surface glycoprotein, which poses a serious challenge to pandemic preparedness and vaccine design. In the present article, clinical studies on A/H5 influenza vaccination strategies were reviewed to evaluate the breadth of antibody responses induced upon homologous and heterologous prime-boost vaccination strategies. Clinical data on immunological endpoints were extracted from studies and compiled into a dataset, which was used for the visualization and analysis of the height and breadth of humoral immune responses. Several aspects leading to high immunogenicity and/or cross-reactivity were identified, although the analysis was limited by the heterogeneity in study design and vaccine type used in the included studies. Consequently, crucial questions remain to be addressed in future studies on A/H5 GsGd vaccination strategies.
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Worp N, Koopmans MPG, Fouchier RAM, Oude Munnink BB. [Mutations in the SARS-CoV-2 genome: the emergence of variants and the impact on vaccines]. Ned Tijdschr Geneeskd 2021; 165:D6496. [PMID: 35138744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Almost two years after the introduction of SARS-CoV-2, it has become clear that the virus is unlikely to disappear any time soon. It is also clear that the virus mutates, resulting in specific variants of SARS-CoV-2. The exact implications of these variants are being investigated but it is likely that they have a selective advantage over previously circulating variants. It is possible that SARS-CoV-2 will mutate in the coming years to such an extent that existing vaccines do not offer sufficient protection against hospitalizations in the general population. At present, the protection of current vaccines against infection is observed to be reduced by the emergence of variants but remains high against hospitalizations and severe disease. Booster vaccinations are currently advised for specific risk groups where the regular vaccination schedule leads to an insufficient immune response, and are being considered for people in old age where the vaccine effectiveness is lower.
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33
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Oude Munnink BB, Worp N, Nieuwenhuijse DF, Sikkema RS, Haagmans B, Fouchier RAM, Koopmans M. Author Correction: The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology. Nat Med 2021; 27:2048. [PMID: 34611328 PMCID: PMC8491748 DOI: 10.1038/s41591-021-01567-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Bas B Oude Munnink
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Nathalie Worp
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - David F Nieuwenhuijse
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Reina S Sikkema
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Bart Haagmans
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands.
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34
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Oude Munnink BB, Worp N, Nieuwenhuijse DF, Sikkema RS, Haagmans B, Fouchier RAM, Koopmans M. The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology. Nat Med 2021; 27:1518-1524. [PMID: 34504335 DOI: 10.1038/s41591-021-01472-w] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/20/2021] [Indexed: 02/08/2023]
Abstract
The current coronavirus disease 2019 (COVID-19) pandemic is the first to apply whole-genome sequencing near to real time, with over 2 million severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequences generated and shared through the GISAID platform. This genomic resource informed public health decision-making throughout the pandemic; it also allowed detection of mutations that might affect virulence, pathogenesis, host range or immune escape as well as the effectiveness of SARS-CoV-2 diagnostics and therapeutics. However, genotype-to-phenotype predictions cannot be performed at the rapid pace of genomic sequencing. To prepare for the next phase of the pandemic, a systematic approach is needed to link global genomic surveillance and timely assessment of the phenotypic characteristics of novel variants, which will support the development and updating of diagnostics, vaccines, therapeutics and nonpharmaceutical interventions. This Review summarizes the current knowledge on key viral mutations and variants and looks to the next phase of surveillance of the evolving pandemic.
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Affiliation(s)
- Bas B Oude Munnink
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Nathalie Worp
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - David F Nieuwenhuijse
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Reina S Sikkema
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Bart Haagmans
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands.
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35
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Lewis NS, Banyard AC, Whittard E, Karibayev T, Al Kafagi T, Chvala I, Byrne A, Meruyert Akberovna S, King J, Harder T, Grund C, Essen S, Reid SM, Brouwer A, Zinyakov NG, Tegzhanov A, Irza V, Pohlmann A, Beer M, Fouchier RAM, Akhmetzhan Akievich S, Brown IH. Emergence and spread of novel H5N8, H5N5 and H5N1 clade 2.3.4.4 highly pathogenic avian influenza in 2020. Emerg Microbes Infect 2021; 10:148-151. [PMID: 33400615 PMCID: PMC7832535 DOI: 10.1080/22221751.2021.1872355] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Analyses of HPAI H5 viruses from poultry outbreaks across a wide Eurasian region since July 2020 including the Russian Federation, Republics of Iraq and Kazakhstan, and recent detections in migratory waterfowl in the Netherlands, revealed undetected maintenance of H5N8, likely in galliform poultry since 2017/18 and both H5N5 and H5N1. All viruses belong to A/H5 clade 2.3.4.4b with closely related HA genes. Heterogeneity in Eurasian H5Nx HPAI emerging variants threatens poultry production, food security and veterinary public health.
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Affiliation(s)
- Nicola S Lewis
- Department of Virology, Animal and Plant Health Agency, OIE/FAO International Reference Laboratory for Avian Influenza, Swine Influenza and Newcastle Disease Virus, Surrey, UK.,Department of Pathobiology and Population Sciences, Royal Veterinary College, Addlestone, UK
| | - Ashley C Banyard
- Department of Virology, Animal and Plant Health Agency, OIE/FAO International Reference Laboratory for Avian Influenza, Swine Influenza and Newcastle Disease Virus, Surrey, UK
| | - Elliot Whittard
- Department of Virology, Animal and Plant Health Agency, OIE/FAO International Reference Laboratory for Avian Influenza, Swine Influenza and Newcastle Disease Virus, Surrey, UK
| | - Talgat Karibayev
- National Veterinary Reference Centre, Infectious Diseases Laboratory, The Committee for Veterinary Control and Supervision, Nur-Sultan City, Republic of Kazakhstan
| | | | - Ilya Chvala
- National Reference Laboratory for Avian Influenza and Newcastle Disease, Federal Centre for Animal Health (FGBI "ARRIAH"), Yur'evets Vladimir, Russia
| | - Alex Byrne
- Department of Virology, Animal and Plant Health Agency, OIE/FAO International Reference Laboratory for Avian Influenza, Swine Influenza and Newcastle Disease Virus, Surrey, UK
| | - Saduakassova Meruyert Akberovna
- Department of Virology, The Kazakh Scientific Research Veterinary Institute (KazSRVI), Non-Commercial JSC "National Agrarian Science and Educational Centre", Almaty, Republic of Kazakhstan
| | - Jacqueline King
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute of Animal Health, Greifswald-Insel Riems, Germany
| | - Timm Harder
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute of Animal Health, Greifswald-Insel Riems, Germany
| | - Christian Grund
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute of Animal Health, Greifswald-Insel Riems, Germany
| | - Steve Essen
- Department of Virology, Animal and Plant Health Agency, OIE/FAO International Reference Laboratory for Avian Influenza, Swine Influenza and Newcastle Disease Virus, Surrey, UK
| | - Scott M Reid
- Department of Virology, Animal and Plant Health Agency, OIE/FAO International Reference Laboratory for Avian Influenza, Swine Influenza and Newcastle Disease Virus, Surrey, UK
| | - Adam Brouwer
- Department of Virology, Animal and Plant Health Agency, OIE/FAO International Reference Laboratory for Avian Influenza, Swine Influenza and Newcastle Disease Virus, Surrey, UK
| | - Nikolay G Zinyakov
- National Reference Laboratory for Avian Influenza and Newcastle Disease, Federal Centre for Animal Health (FGBI "ARRIAH"), Yur'evets Vladimir, Russia
| | - Azimkhan Tegzhanov
- National Veterinary Reference Centre, Infectious Diseases Laboratory, The Committee for Veterinary Control and Supervision, Nur-Sultan City, Republic of Kazakhstan
| | - Victor Irza
- National Reference Laboratory for Avian Influenza and Newcastle Disease, Federal Centre for Animal Health (FGBI "ARRIAH"), Yur'evets Vladimir, Russia
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute of Animal Health, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute of Animal Health, Greifswald-Insel Riems, Germany
| | | | - Sultanov Akhmetzhan Akievich
- Department of Virology, The Kazakh Scientific Research Veterinary Institute (KazSRVI), Non-Commercial JSC "National Agrarian Science and Educational Centre", Almaty, Republic of Kazakhstan
| | - Ian H Brown
- Department of Virology, Animal and Plant Health Agency, OIE/FAO International Reference Laboratory for Avian Influenza, Swine Influenza and Newcastle Disease Virus, Surrey, UK
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36
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Groen K, van Nieuwkoop S, Bestebroer TM, Fraaij PL, Fouchier RAM, van den Hoogen BG. Whole genome sequencing of human metapneumoviruses from clinical specimens using MinION nanopore technology. Virus Res 2021; 302:198490. [PMID: 34146613 DOI: 10.1016/j.virusres.2021.198490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/27/2021] [Accepted: 06/07/2021] [Indexed: 11/16/2022]
Abstract
Human metapneumovirus (HMPV), a member of the Pneumoviridae family, is a causative agent of respiratory illness in young children, the elderly, and immunocompromised individuals. Globally, viruses belonging to two main genetic lineages circulate, A and B, which are further divided into four genetic sublineages (A1, A2, B1, B2). Classical genotyping of HMPV is based on the sequence of the fusion (F) and attachment (G) glycoprotein genes, which are under direct antibody-mediated immune pressure. Whole genome sequencing provides more information than sequencing of subgenomic fragments and is therefore a powerful tool for studying virus evolution and disease epidemiology and for identifying transmission events and nosocomial outbreaks. Here, we report a robust method to obtain whole genome sequences for HMPV using MinION Nanopore technology. This assay is able to generate HMPV whole genome sequences from clinical specimens with good coverage of the highly variable G gene and is equally sensitive for strains of all four genetic HMPV sublineages. This method can be used for studying HMPV genetics, epidemiology, and evolutionary dynamics.
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Affiliation(s)
- Kevin Groen
- Department of Viroscience, Erasmus MC, Wijtemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Stefan van Nieuwkoop
- Department of Viroscience, Erasmus MC, Wijtemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Theo M Bestebroer
- Department of Viroscience, Erasmus MC, Wijtemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Pieter L Fraaij
- Department of Viroscience, Erasmus MC, Wijtemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus MC, Wijtemaweg 80, 3015 CN Rotterdam, The Netherlands
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Postnikova Y, Treshchalina A, Boravleva E, Gambaryan A, Ishmukhametov A, Matrosovich M, Fouchier RAM, Sadykova G, Prilipov A, Lomakina N. Diversity and Reassortment Rate of Influenza A Viruses in Wild Ducks and Gulls. Viruses 2021; 13:v13061010. [PMID: 34072256 PMCID: PMC8230314 DOI: 10.3390/v13061010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 01/18/2023] Open
Abstract
Influenza A viruses (IAVs) evolve via point mutations and reassortment of viral gene segments. The patterns of reassortment in different host species differ considerably. We investigated the genetic diversity of IAVs in wild ducks and compared it with the viral diversity in gulls. The complete genomes of 38 IAVs of H1N1, H1N2, H3N1, H3N2, H3N6, H3N8, H4N6, H5N3, H6N2, H11N6, and H11N9 subtypes isolated from wild mallard ducks and gulls resting in a city pond in Moscow, Russia were sequenced. The analysis of phylogenetic trees showed that stable viral genotypes do not persist from year to year in ducks owing to frequent gene reassortment. For comparison, similar analyses were carried out using sequences of IAVs isolated in the same period from ducks and gulls in The Netherlands. Our results revealed a significant difference in diversity and rates of reassortment of IAVs in ducks and gulls.
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Affiliation(s)
- Yulia Postnikova
- Chumakov Federal Scientific Center for the Research and Development of Immune-and-Biological Products, Village of Institute of Poliomyelitis, Settlement “Moskovskiy”, 108819 Moscow, Russia; (Y.P.); (A.T.); (E.B.); (A.I.)
| | - Anastasia Treshchalina
- Chumakov Federal Scientific Center for the Research and Development of Immune-and-Biological Products, Village of Institute of Poliomyelitis, Settlement “Moskovskiy”, 108819 Moscow, Russia; (Y.P.); (A.T.); (E.B.); (A.I.)
| | - Elizaveta Boravleva
- Chumakov Federal Scientific Center for the Research and Development of Immune-and-Biological Products, Village of Institute of Poliomyelitis, Settlement “Moskovskiy”, 108819 Moscow, Russia; (Y.P.); (A.T.); (E.B.); (A.I.)
| | - Alexandra Gambaryan
- Chumakov Federal Scientific Center for the Research and Development of Immune-and-Biological Products, Village of Institute of Poliomyelitis, Settlement “Moskovskiy”, 108819 Moscow, Russia; (Y.P.); (A.T.); (E.B.); (A.I.)
- Correspondence: ; Tel.: +7-985-136-3586
| | - Aydar Ishmukhametov
- Chumakov Federal Scientific Center for the Research and Development of Immune-and-Biological Products, Village of Institute of Poliomyelitis, Settlement “Moskovskiy”, 108819 Moscow, Russia; (Y.P.); (A.T.); (E.B.); (A.I.)
| | - Mikhail Matrosovich
- Institute of Virology, Philipps University, Hans-Meerwein-Str. 2, D-35043 Marburg, Germany;
| | - Ron A. M. Fouchier
- Department of Virology, Erasmus Medical Centre, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands;
| | - Galina Sadykova
- The Gamaleya National Center of Epidemiology and Microbiology of the Russian Ministry of Health, 123098 Moscow, Russia; (G.S.); (A.P.); (N.L.)
| | - Alexey Prilipov
- The Gamaleya National Center of Epidemiology and Microbiology of the Russian Ministry of Health, 123098 Moscow, Russia; (G.S.); (A.P.); (N.L.)
| | - Natalia Lomakina
- The Gamaleya National Center of Epidemiology and Microbiology of the Russian Ministry of Health, 123098 Moscow, Russia; (G.S.); (A.P.); (N.L.)
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38
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Herfst S, Zhang J, Richard M, McBride R, Lexmond P, Bestebroer TM, Spronken MIJ, de Meulder D, van den Brand JM, Rosu ME, Martin SR, Gamblin SJ, Xiong X, Peng W, Bodewes R, van der Vries E, Osterhaus ADME, Paulson JC, Skehel JJ, Fouchier RAM. Hemagglutinin Traits Determine Transmission of Avian A/H10N7 Influenza Virus between Mammals. Cell Host Microbe 2021; 28:602-613.e7. [PMID: 33031770 DOI: 10.1016/j.chom.2020.08.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 06/04/2020] [Accepted: 08/26/2020] [Indexed: 01/19/2023]
Abstract
In 2014, an outbreak of avian A/H10N7 influenza virus occurred among seals along North-European coastal waters, significantly impacting seal populations. Here, we examine the cross-species transmission and mammalian adaptation of this influenza A virus, revealing changes in the hemagglutinin surface protein that increase stability and receptor binding. The seal A/H10N7 virus was aerosol or respiratory droplet transmissible between ferrets. Compared with avian H10 hemagglutinin, seal H10 hemagglutinin showed stronger binding to the human-type sialic acid receptor, with preferential binding to α2,6-linked sialic acids on long extended branches. In X-ray structures, changes in the 220-loop of the receptor-binding pocket caused similar interactions with human receptor as seen for pandemic strains. Two substitutions made seal H10 hemagglutinin more stable than avian H10 hemagglutinin and similar to human hemagglutinin. Consequently, identification of avian-origin influenza viruses across mammals appears critical to detect influenza A viruses posing a major threat to humans and other mammals.
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Affiliation(s)
- Sander Herfst
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus MC University Medical Center, 3015GE, Rotterdam, the Netherlands
| | - Jie Zhang
- Structural Biology of Disease Processes Laboratory, the Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Mathilde Richard
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus MC University Medical Center, 3015GE, Rotterdam, the Netherlands
| | - Ryan McBride
- Departments of Molecular Medicine, Immunology and Microbiology, the Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pascal Lexmond
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus MC University Medical Center, 3015GE, Rotterdam, the Netherlands
| | - Theo M Bestebroer
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus MC University Medical Center, 3015GE, Rotterdam, the Netherlands
| | - Monique I J Spronken
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus MC University Medical Center, 3015GE, Rotterdam, the Netherlands
| | - Dennis de Meulder
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus MC University Medical Center, 3015GE, Rotterdam, the Netherlands
| | - Judith M van den Brand
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus MC University Medical Center, 3015GE, Rotterdam, the Netherlands
| | - Miruna E Rosu
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus MC University Medical Center, 3015GE, Rotterdam, the Netherlands
| | - Stephen R Martin
- Structural Biology of Disease Processes Laboratory, the Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Steve J Gamblin
- Structural Biology of Disease Processes Laboratory, the Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Xiaoli Xiong
- Structural Biology of Disease Processes Laboratory, the Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Wenjie Peng
- Departments of Molecular Medicine, Immunology and Microbiology, the Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rogier Bodewes
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus MC University Medical Center, 3015GE, Rotterdam, the Netherlands
| | - Erhard van der Vries
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus MC University Medical Center, 3015GE, Rotterdam, the Netherlands
| | - Albert D M E Osterhaus
- Research Centre for Emerging Infections and Zoonoses, University of Veterinary Medicine, 30559, Hannover, Germany
| | - James C Paulson
- Departments of Molecular Medicine, Immunology and Microbiology, the Scripps Research Institute, La Jolla, CA 92037, USA
| | - John J Skehel
- Structural Biology of Disease Processes Laboratory, the Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ron A M Fouchier
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus MC University Medical Center, 3015GE, Rotterdam, the Netherlands.
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39
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Roosenhoff R, Reed V, Kenwright A, Schutten M, Boucher CA, Monto A, Clinch B, Kumar D, Whitley R, Nguyen-Van-Tam JS, Osterhaus ADME, Fouchier RAM, Fraaij PLA. Viral Kinetics and Resistance Development in Children Treated with Neuraminidase Inhibitors: The Influenza Resistance Information Study (IRIS). Clin Infect Dis 2021; 71:1186-1194. [PMID: 31560055 PMCID: PMC7442852 DOI: 10.1093/cid/ciz939] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 09/19/2019] [Indexed: 01/17/2023] Open
Abstract
Background We studied the effect of age, baseline viral load, vaccination status, antiviral therapy, and emergence of drug resistance on viral shedding in children infected with influenza A or B virus. Methods Samples from children (aged ≤13 years) enrolled during the 7 years of the prospective Influenza Resistance Information Study were analyzed using polymerase chain reaction to determine the influenza virus (sub-)type, viral load, and resistance mutations. Disease severity was assessed; clinical symptoms were recorded. The association of age with viral load and viral clearance was examined by determining the area under the curve for viral RNA shedding using logistic regression and Kaplan-Meier analyses. Results A total of 2131 children infected with influenza (683, A/H1N1pdm09; 825, A/H3N2; 623, influenza B) were investigated. Age did not affect the mean baseline viral load. Children aged 1−5 years had prolonged viral RNA shedding (±1–2 days) compared with older children and up to 1.2-fold higher total viral burden. Besides, in older age (odds ratio [OR], 1.08; confidence interval [CI], 1.05–1.12), prior vaccination status (OR, 1.72; CI, 1.22–2.43) and antiviral treatment (OR, 1.74; CI, 1.43–2.12) increased the rate of viral clearance. Resistance mutations were detected in 49 children infected with influenza A virus (34, A/H1N1pdm09; 15, A/H3N2) treated with oseltamivir, most of whom were aged <5 years (n = 39). Conclusions Children aged 1−5 years had a higher total viral burden with prolonged virus shedding and had an increased risk of acquiring resistance mutations following antiviral treatment. Clinical Trials Registration NCT00884117.
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Affiliation(s)
| | | | | | | | - Charles A Boucher
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Arnold Monto
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Barry Clinch
- Roche Products Ltd, Welwyn Garden City, United Kingdom
| | - Deepali Kumar
- Transplant Infectious Diseases and Multi Organ Transplant Program, University Health Network, Toronto, Ontario, Canada
| | - Richard Whitley
- Department of Pediatrics, Microbiology, Medicine, and Neurosurgery, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jonathan S Nguyen-Van-Tam
- School of Medicine, Division of Epidemiology and Public Health, University of Nottingham, Nottingham, United Kingdom
| | - Albert D M E Osterhaus
- Research Institute for Infectious Diseases and Zoonosis, University of Veterinary Medicine, Hannover, Germany.,Artemis One Health Research Institute, Utrecht, The Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Pieter L A Fraaij
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Pediatrics, Subdivision Infectious Diseases and Immunology, Erasmus Medical Center-Sophia, Rotterdam, The Netherlands
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40
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Kutter JS, de Meulder D, Bestebroer TM, Lexmond P, Mulders A, Richard M, Fouchier RAM, Herfst S. SARS-CoV and SARS-CoV-2 are transmitted through the air between ferrets over more than one meter distance. Nat Commun 2021; 12:1653. [PMID: 33712573 PMCID: PMC7955093 DOI: 10.1038/s41467-021-21918-6] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/19/2021] [Indexed: 02/08/2023] Open
Abstract
SARS-CoV-2 emerged in late 2019 and caused a pandemic, whereas the closely related SARS-CoV was contained rapidly in 2003. Here, an experimental set-up is used to study transmission of SARS-CoV and SARS-CoV-2 through the air between ferrets over more than a meter distance. Both viruses cause a robust productive respiratory tract infection resulting in transmission of SARS-CoV-2 to two of four indirect recipient ferrets and SARS-CoV to all four. A control pandemic A/H1N1 influenza virus also transmits efficiently. Serological assays confirm all virus transmission events. Although the experiments do not discriminate between transmission via small aerosols, large droplets and fomites, these results demonstrate that SARS-CoV and SARS-CoV-2 can remain infectious while traveling through the air. Efficient virus transmission between ferrets is in agreement with frequent SARS-CoV-2 outbreaks in mink farms. Although the evidence for virus transmission via the air between humans under natural conditions is absent or weak for SARS-CoV and SARS-CoV-2, ferrets may represent a sensitive model to study interventions aimed at preventing virus transmission.
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Affiliation(s)
- Jasmin S Kutter
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Dennis de Meulder
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Theo M Bestebroer
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Pascal Lexmond
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ard Mulders
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mathilde Richard
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sander Herfst
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands.
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41
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Roosenhoff R, Schutten M, Reed V, Clinch B, van der Linden A, Fouchier RAM, Fraaij PLA. Secondary substitutions in the hemagglutinin and neuraminidase genes associated with neuraminidase inhibitor resistance are rare in the Influenza Resistance Information Study (IRIS). Antiviral Res 2021; 189:105060. [PMID: 33713731 DOI: 10.1016/j.antiviral.2021.105060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/16/2021] [Accepted: 03/05/2021] [Indexed: 10/21/2022]
Abstract
Amino acid substitutions in influenza virus neuraminidase (NA) that cause resistance to neuraminidase inhibitors (NAI) generally result in virus attenuation. However, influenza viruses may acquire secondary substitutions in the NA and hemagglutinin (HA) proteins that can restore viral fitness. To assess to which extent this happens, the emergence of NAI resistance substitutions and secondary - potentially compensatory - substitutions was quantified in influenza viruses of immunocompetent individuals included in the Influenza Resistance Information Study (IRIS; NCT00884117). Known resistance substitutions were detected by mutation specific RT-PCR in viruses of 57 of 1803 (3.2%) oseltamivir-treated individuals, including 39 individuals infected with A/H1N1pdm09 [H275Y] virus and 18 with A/H3N2 [R292K] virus. A total of fifteen and ten other amino acid substitutions were acquired in HA and NA respectively, of A/H1N1pdm09, A/H3N2 and influenza B viruses upon treatment with oseltamivir but none of these was associated with resistance to oseltamivir. All cultured viruses with the known resistance substitutions H275Y or R292K showed reduced susceptibility to oseltamivir in the NA-star assay. Upon next-generation sequencing, the vast majority of NAI resistant A/H1N1pdm09 and A/H3N2 viruses had no resistance-associated secondary substitutions at high frequency. Only in two A/H1N1pdm09 [H275Y] viruses, the potentially compensatory secondary substitutions HA-D52N and NA-R152K were detected. We conclude that the emergence of secondary substitutions that may restore viral fitness upon the emergence of known influenza virus NAI resistance substitutions was a rare event in this immunocompetent population.
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Affiliation(s)
- Rueshandra Roosenhoff
- Department of Viroscience, Erasmus Medical Center, Rotterdam, 3015GE, the Netherlands
| | - Martin Schutten
- Clinical Virology and Diagnostics, 1817HL, Alkmaar, the Netherlands
| | | | - Barry Clinch
- Roche Products Ltd, Welwyn Garden City, AL7 1TW, United Kingdom
| | - Anne van der Linden
- Department of Viroscience, Erasmus Medical Center, Rotterdam, 3015GE, the Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus Medical Center, Rotterdam, 3015GE, the Netherlands
| | - Pieter L A Fraaij
- Department of Viroscience, Erasmus Medical Center, Rotterdam, 3015GE, the Netherlands; Department of Pediatrics, Subdivision Infectious Diseases and Immunology, Erasmus Medical Center - Sophia, Rotterdam, the Netherlands.
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42
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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 2021; 27:123-132. [PMID: 33188057 PMCID: PMC7812872 DOI: 10.1261/rna.077495.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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43
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Kuhn JH, Adkins S, Alioto D, Alkhovsky SV, Amarasinghe GK, Anthony SJ, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Bartonička T, Basler C, Bavari S, Beer M, Bente DA, Bergeron É, Bird BH, Blair C, Blasdell KR, Bradfute SB, Breyta R, Briese T, Brown PA, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Buzkan N, Calisher CH, Cao M, Casas I, Chamberlain J, Chandran K, Charrel RN, Chen B, Chiumenti M, Choi IR, Clegg JCS, Crozier I, da Graça JV, Dal Bó E, Dávila AMR, de la Torre JC, de Lamballerie X, de Swart RL, Di Bello PL, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Dolja VV, Dolnik O, Drebot MA, Drexler JF, Dürrwald R, Dufkova L, Dundon WG, Duprex WP, Dye JM, Easton AJ, Ebihara H, Elbeaino T, Ergünay K, Fernandes J, Fooks AR, Formenty PBH, Forth LF, Fouchier RAM, Freitas-Astúa J, Gago-Zachert S, Gāo GF, García ML, García-Sastre A, Garrison AR, Gbakima A, Goldstein T, Gonzalez JPJ, Griffiths A, Groschup MH, Günther S, Guterres A, Hall RA, Hammond J, Hassan M, Hepojoki J, Hepojoki S, Hetzel U, Hewson R, Hoffmann B, Hongo S, Höper D, Horie M, Hughes HR, Hyndman TH, Jambai A, Jardim R, Jiāng D, Jin Q, Jonson GB, Junglen S, Karadağ S, Keller KE, Klempa B, Klingström J, Kobinger G, Kondō H, Koonin EV, Krupovic M, Kurath G, Kuzmin IV, Laenen L, Lamb RA, Lambert AJ, Langevin SL, Lee B, Lemos ERS, Leroy EM, Li D, Lǐ J, Liang M, Liú W, Liú Y, Lukashevich IS, Maes P, Marciel de Souza W, Marklewitz M, Marshall SH, Martelli GP, Martin RR, Marzano SYL, Massart S, McCauley JW, Mielke-Ehret N, Minafra A, Minutolo M, Mirazimi A, Mühlbach HP, Mühlberger E, Naidu R, Natsuaki T, Navarro B, Navarro JA, Netesov SV, Neumann G, Nowotny N, Nunes MRT, Nylund A, Økland AL, Oliveira RC, Palacios G, Pallas V, Pályi B, Papa A, Parrish CR, Pauvolid-Corrêa A, Pawęska JT, Payne S, Pérez DR, Pfaff F, Radoshitzky SR, Rahman AU, Ramos-González PL, Resende RO, Reyes CA, Rima BK, Romanowski V, Robles Luna G, Rota P, Rubbenstroth D, Runstadler JA, Ruzek D, Sabanadzovic S, Salát J, Sall AA, Salvato MS, Sarpkaya K, Sasaya T, Schwemmle M, Shabbir MZ, Shí X, Shí Z, Shirako Y, Simmonds P, Širmarová J, Sironi M, Smither S, Smura T, Song JW, Spann KM, Spengler JR, Stenglein MD, Stone DM, Straková P, Takada A, Tesh RB, Thornburg NJ, Tomonaga K, Tordo N, Towner JS, Turina M, Tzanetakis I, Ulrich RG, Vaira AM, van den Hoogen B, Varsani A, Vasilakis N, Verbeek M, Wahl V, Walker PJ, Wang H, Wang J, Wang X, Wang LF, Wèi T, Wells H, Whitfield AE, Williams JV, Wolf YI, Wú Z, Yang X, Yáng X, Yu X, Yutin N, Zerbini FM, Zhang T, Zhang YZ, Zhou G, Zhou X. 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Arch Virol 2020; 165:3023-3072. [PMID: 32888050 PMCID: PMC7606449 DOI: 10.1007/s00705-020-04731-2] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/04/2020] [Indexed: 12/13/2022]
Abstract
In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
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Affiliation(s)
- Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA.
| | - Scott Adkins
- United States Department of Agriculture, Agricultural Research Service, US Horticultural Research Laboratory, Fort Pierce, FL, USA
| | - Daniela Alioto
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Portici, Italy
| | - Sergey V Alkhovsky
- D.I. Ivanovsky Institute of Virology of N.F. Gamaleya National Center on Epidemiology and Microbiology of Ministry of Health of Russian Federation, Moscow, Russia
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Simon J Anthony
- Mailman School of Public Health, Columbia University, New York, NY, USA
- EcoHealth Alliance, New York, NY, USA
| | | | - María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Justin Bahl
- Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Institute of Bioinformatics, Center for Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Anne Balkema-Buschmann
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Matthew J Ballinger
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Tomáš Bartonička
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Christopher Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Sina Bavari
- Edge BioInnovation Consulting and Mgt, Frederick, MD, USA
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Dennis A Bente
- Galveston National Laboratory, The University of Texas, Medical Branch at Galveston, Galveston, TX, USA
| | - Éric Bergeron
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Brian H Bird
- School of Veterinary Medicine, One Health Institute, University of California, Davis, CA, USA
| | - Carol Blair
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Kim R Blasdell
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Steven B Bradfute
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Rachel Breyta
- US Geological Survey, Western Fisheries Research Center, Seattle, WA, USA
| | - Thomas Briese
- Department of Epidemiology, Mailman School of Public Health, Center for Infection and Immunity, Columbia University, New York, NY, USA
| | - Paul A Brown
- Laboratory of Ploufragan-Plouzané-Niort, French Agency for Food, Environmental and Occupational Heath Safety ANSES, Ploufragan, France
| | - Ursula J Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael J Buchmeier
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Alexander Bukreyev
- Galveston National Laboratory, The University of Texas, Medical Branch at Galveston, Galveston, TX, USA
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Felicity Burt
- Division of Virology, National Health Laboratory Service, University of the Free State, Bloemfontein, Republic of South Africa
| | - Nihal Buzkan
- Department of Plant Protection, Faculty of Agriculture, Kahramanmaras Sütçü Imam University, Avsar Campus, 46060, Kahramanmaras, Turkey
| | | | - Mengji Cao
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Inmaculada Casas
- Respiratory Virus and Influenza Unit, National Microbiology Center, Instituto de Salud Carlos III, Madrid, Spain
| | - John Chamberlain
- Virology and Pathogenesis Group, National Infection Service, Public Health England, Porton Down, UK
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rémi N Charrel
- Unité des Virus Emergents (Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), Marseille, France
| | - Biao Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangdong, China
| | - Michela Chiumenti
- Istituto per la Protezione Sostenibile delle Piante-Consiglio Nazionale delle ricerche (Institute for Sustainable Plant Protection-National Research Council), Bari, Italy
| | - Il-Ryong Choi
- Plant Breeding Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | | | - Ian Crozier
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - John V da Graça
- Texas A&M University-Kingsville Citrus Center, Weslaco, TX, USA
| | - Elena Dal Bó
- CIDEFI. Facultad de Ciencias Agrarias y Forestales, Universidad de La Plata, La Plata, Argentina
| | - Alberto M R Dávila
- Laboratório de Biologia Computacional e Sistemas, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology IMM-6, The Scripps Research Institute, La Jolla, CA, USA
| | - Xavier de Lamballerie
- Unité des Virus Emergents (Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), Marseille, France
| | - Rik L de Swart
- Department Viroscience, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Patrick L Di Bello
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Nicholas Di Paola
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante-Consiglio Nazionale delle ricerche (Institute for Sustainable Plant Protection-National Research Council), Bari, Italy
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Michele Digiaro
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, Valenzano, Italy
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Olga Dolnik
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Michael A Drebot
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Jan Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | | | | | - William G Dundon
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - W Paul Duprex
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - John M Dye
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Andrew J Easton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hideki Ebihara
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Koray Ergünay
- Virology Unit, Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Jorlan Fernandes
- Laboratório de Hantaviroses e Rickettsioses, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | | | | | - Leonie F Forth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Ron A M Fouchier
- Department Viroscience, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | | | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - George Fú Gāo
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, CONICET UNLP, La Plata, Argentina
| | | | - Aura R Garrison
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Aiah Gbakima
- Metabiota, Inc. Sierra Leone, Freetown, Sierra Leone
| | - Tracey Goldstein
- One Health Institute, Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Jean-Paul J Gonzalez
- Department of Microbiology and Immunology, Division of Biomedical Graduate Research Organization, School of Medicine, Georgetown University, Washington, DC, 20057, USA
- Centaurus Biotechnologies, CTP, Manassas, VA, USA
| | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Martin H Groschup
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Stephan Günther
- Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arboviruses and Hemorrhagic Fever Reference and Research, Hamburg, Germany
| | - Alexandro Guterres
- Laboratório de Hantaviroses e Rickettsioses, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Roy A Hall
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - John Hammond
- United States Department of Agriculture, Agricultural Research Service, USNA, Floral and Nursery Plants Research Unit, Beltsville, MD, USA
| | - Mohamed Hassan
- Department of Agricultural Botany, Faculty of Agriculture, Fayoum University, Fayoum, Egypt
| | - Jussi Hepojoki
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
- Vetsuisse Faculty, Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - Satu Hepojoki
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
- Mobidiag Ltd, Espoo, Finland
| | - Udo Hetzel
- Institute of Veterinary Pathology, University of Zuerich, Zurich, Switzerland
| | - Roger Hewson
- Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Bernd Hoffmann
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Seiji Hongo
- Department of Infectious Diseases, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Masayuki Horie
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - Holly R Hughes
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Timothy H Hyndman
- School of Veterinary Medicine, Murdoch University, Murdoch, WA, Australia
| | - Amara Jambai
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Rodrigo Jardim
- Laboratório de Biologia Computacional e Sistemas, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Dàohóng Jiāng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qi Jin
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Gilda B Jonson
- Department of Agricultural Biotechnology, Center for Fungal Pathogenesis, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
| | - Serpil Karadağ
- Republic Of Turkey Ministry Of Agriculture And Forestry, Pistachio Research Institute, Gaziantep, Turkey
| | - Karen E Keller
- United States Department of Agriculture, Agricultural Research Service, Horticulture Crops Research Unit, Corvallis, OR, USA
| | - Boris Klempa
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jonas Klingström
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Gary Kobinger
- Department of Microbiology, Immunology and Infectious Diseases, Université Laval, Quebec City, Canada
| | - Hideki Kondō
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Gael Kurath
- US Geological Survey Western Fisheries Research Center, Seattle, WA, USA
| | - Ivan V Kuzmin
- US Department of Agriculture, Animal and Plant Health Inspection, National Veterinary Services Laboratories, Diagnostic Virology Laboratory, Ames, USA
| | - Lies Laenen
- Zoonotic Infectious Diseases Unit, KU Leuven, Rega Institute, Leuven, Belgium
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Robert A Lamb
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Howard Hughes Medical Institute, Northwestern University, Evanston, IL, USA
| | - Amy J Lambert
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | | | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elba R S Lemos
- Laboratório de Hantaviroses e Rickettsioses, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Eric M Leroy
- MIVEGEC (IRD-CNRS-Montpellier university) Unit, French National Research Institute for Sustainable Development (IRD), Montpellier, France
| | - Dexin Li
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jiànróng Lǐ
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Mifang Liang
- Key Laboratory for Medical Virology, NHFPC, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Wénwén Liú
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yàn Liú
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Igor S Lukashevich
- Department of Pharmacology and Toxicology, School of Medicine, The Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Piet Maes
- Department of Agricultural Biotechnology, Center for Fungal Pathogenesis, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | | | - Marco Marklewitz
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
| | - Sergio H Marshall
- Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Giovanni P Martelli
- Department of Plant, Soil and Food Sciences, University "Aldo Moro", Bari, Italy
| | - Robert R Martin
- United States Department of Agriculture, Horticultural Crops Research Unit, Corvallis, OR, USA
| | - Shin-Yi L Marzano
- Department of Biology and Microbiology, Department of Plant Sciences, South Dakota State University, Brookings, SD, USA
| | - Sébastien Massart
- Gembloux Agro-Bio Tech, TERRA, Plant Pathology Laboratory, Liège University, Liège, Belgium
| | - John W McCauley
- Worldwide Influenza Centre, Francis Crick Institute, London, UK
| | | | - Angelantonio Minafra
- Istituto per la Protezione Sostenibile delle Piante-Consiglio Nazionale delle ricerche (Institute for Sustainable Plant Protection-National Research Council), Bari, Italy
| | - Maria Minutolo
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Portici, Italy
| | | | | | - Elke Mühlberger
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Rayapati Naidu
- Department of Plant Pathology, Irrigated Agricultural Research and Extension Center, Washington State University, Prosser, WA, USA
| | - Tomohide Natsuaki
- School of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, Japan
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante-Consiglio Nazionale delle ricerche (Institute for Sustainable Plant Protection-National Research Council), Bari, Italy
| | - José A Navarro
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Sergey V Netesov
- Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia
| | - Gabriele Neumann
- Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, USA
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | - Are Nylund
- Fish Disease Research Group, Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Arnfinn L Økland
- Fish Disease Research Group, Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Renata C Oliveira
- Laboratório de Hantaviroses e Rickettsioses, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Vicente Pallas
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Cientificas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Bernadett Pályi
- National Biosafety Laboratory, National Public Health Center, Budapest, Hungary
| | - Anna Papa
- National Reference Centre for Arboviruses and Haemorrhagic Fever Viruses, Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloníki, Greece
| | - Colin R Parrish
- College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Alex Pauvolid-Corrêa
- Department of Veterinary Integrated Biosciences and Department of Entomology, Texas A&M University, College Station, USA
| | - Janusz T Pawęska
- Center for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham-Johannesburg, Gauteng, South Africa
| | - Susan Payne
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Daniel R Pérez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Sheli R Radoshitzky
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Aziz-Ul Rahman
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | | | - Renato O Resende
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Carina A Reyes
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Bertus K Rima
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, Northern Ireland, UK
| | - Víctor Romanowski
- Instituto de Biotecnología y Biología Molecular, Centro Cientifico Technológico-La Plata, Consejo Nacional de Investigaciones Científico Tecnológico-Universidad Nacional de La Plata, La Plata, Argentina
| | - Gabriel Robles Luna
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Paul Rota
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dennis Rubbenstroth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Tufts University Cummings School of Veterinary Medicine, 200 Westboro Road, North Grafton, MA, 01536, USA
| | - Daniel Ruzek
- Veterinary Research Institute, Brno, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, 37005, Ceske Budejovice, Czech Republic
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | - Jiří Salát
- Veterinary Research Institute, Brno, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, 37005, Ceske Budejovice, Czech Republic
| | | | - Maria S Salvato
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kamil Sarpkaya
- Department of Forestry Engineering, Faculty of Forestry, Karabuk University (UNIKA), Karabük, Turkey
| | - Takahide Sasaya
- Western Region Agricultural Research Center, National Agriculture and Food Research Organization, Fukuyama, Japan
| | - Martin Schwemmle
- Faculty of Medicine, University Medical Center-University Freiburg, Freiburg, Germany
| | - Muhammad Z Shabbir
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Xiǎohóng Shí
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
| | - Zhènglì Shí
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| | - Yukio Shirako
- Asian Center for Bioresources and Environmental Sciences, University of Tokyo, Tokyo, Japan
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Manuela Sironi
- Bioinformatics Unit, Scientific Institute IRCCS "E. Medea", Bosisio Parini, Italy
| | - Sophie Smither
- CBR Division, Dstl, Porton Down, Salisbury, Wiltshire, UK
| | - Teemu Smura
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
| | - Jin-Won Song
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Kirsten M Spann
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Jessica R Spengler
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mark D Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - David M Stone
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | | | - Ayato Takada
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Robert B Tesh
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | | | - Keizō Tomonaga
- Institute for Frontier Life and Medical Sciences (inFront), Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Institut Pasteur, Unité des Stratégies Antivirales, WHO Collaborative Centre for Viral Haemorrhagic Fevers and Arboviruses, OIE Reference Laboratory for RVFV and CCHFV, Paris, France
- Institut Pasteur de Guinée, Conakry, Guinea
| | - Jonathan S Towner
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Ioannis Tzanetakis
- Division of Agriculture, Department of Entomology and Plant Pathology, University of Arkansas System, Fayetteville, AR, 72701, USA
| | - Rainer G Ulrich
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Südufer 10, 17493, Greifswald-Insel Riems, Germany
- German Center of Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Insel Riems, Greifswald-Insel Riems, Germany
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), 73 Strada delle Cacce, 10135, Turin, Italy
| | - Bernadette van den Hoogen
- Department of Viroscience, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Nikos Vasilakis
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Martin Verbeek
- Wageningen University and Research, Biointeractions and Plant Health, Wageningen, The Netherlands
| | - Victoria Wahl
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD, USA
| | - Peter J Walker
- School of Biological Sciences, University of Queensland, St. Lucia, Queensland, Australia
| | - Hui Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB-Fondation Mérieux, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Tàiyún Wèi
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Heather Wells
- Mailman School of Public Health, Center for Infection and Immunity, Columbia University, New York, USA
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - John V Williams
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Zhìqiáng Wú
- MOH Key Laboratory of Systems Biology of Pathogens, IPB, CAMS, Beijing, China
| | - Xin Yang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangdong, China
| | - Xīnglóu Yáng
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| | - Xuejie Yu
- Wuhan University School of Health Sciences, Wuhan, China
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - F Murilo Zerbini
- Departamento de Fitopatologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Tong Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangdong, China
| | - Yong-Zhen Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
- Shanghai Public Health Clinical Center, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Guohui Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangdong, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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de Graaf JF, Huberts M, Fouchier RAM, van den Hoogen BG. Determinants of the efficacy of viro-immunotherapy: A review. Cytokine Growth Factor Rev 2020; 56:124-132. [PMID: 32919831 DOI: 10.1016/j.cytogfr.2020.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 07/02/2020] [Indexed: 10/23/2022]
Abstract
Oncolytic virus immunotherapy is rapidly gaining interest in the field of immunotherapy against cancer. The minimal toxicity upon treatment and the dual activity of direct oncolysis and immune activation make therapy with oncolytic viruses (OVs) an interesting treatment modality. The safety and efficacy of several OVs have been assessed in clinical trials and, so far, the Food and Drug Administration (FDA) has approved one OV. Unfortunately, most treatments with OVs have shown suboptimal responses in clinical trials, while they appeared more promising in preclinical studies, with tumours reducing after immune cell influx. In several clinical trials with OVs, parameters such as virus replication, virus-specific antibodies, systemic immune responses, immune cell influx into tumours and tumour-specific antibodies have been studied as predictors or correlates of therapy efficacy. In this review, these studies are summarized to improve our understanding of the determinants of the efficacy of OV therapies in humans and to provide insights for future developments in the viro-immunotherapy treatment field.
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Affiliation(s)
- J F de Graaf
- Viroscience Department, Erasmus Medical Centrum, Rotterdam, The Netherlands
| | - M Huberts
- Viroscience Department, Erasmus Medical Centrum, Rotterdam, The Netherlands
| | - R A M Fouchier
- Viroscience Department, Erasmus Medical Centrum, Rotterdam, The Netherlands
| | - B G van den Hoogen
- Viroscience Department, Erasmus Medical Centrum, Rotterdam, The Netherlands.
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Caliendo V, Leijten L, Begeman L, Poen MJ, Fouchier RAM, Beerens N, Kuiken T. Enterotropism of highly pathogenic avian influenza virus H5N8 from the 2016/2017 epidemic in some wild bird species. Vet Res 2020; 51:117. [PMID: 32928280 PMCID: PMC7491185 DOI: 10.1186/s13567-020-00841-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/02/2020] [Indexed: 12/17/2022] Open
Abstract
In 2016/2017, H5N8 highly pathogenic avian influenza (HPAI) virus of the Goose/Guangdong lineage spread from Asia to Europe, causing the biggest and most widespread HPAI epidemic on record in wild and domestic birds in Europe. We hypothesized that the wide dissemination of the 2016 H5N8 virus resulted at least partly from a change in tissue tropism from the respiratory tract, as in older HPAIV viruses, to the intestinal tract, as in low pathogenic avian influenza (LPAI) viruses, allowing more efficient faecal-oral transmission. Therefore, we determined the tissue tropism and associated lesions in wild birds found dead during the 2016 H5N8 epidemic, as well as the pattern of attachment of 2016 H5N8 virus to respiratory and intestinal tissues of four key wild duck species. We found that, out of 39 H5N8-infected wild birds of 12 species, four species expressed virus antigen in both respiratory and intestinal epithelium, one species only in respiratory epithelium, and one species only in intestinal epithelium. Virus antigen expression was association with inflammation and necrosis in multiple tissues. The level of attachment to wild duck intestinal epithelia of 2016 H5N8 virus was comparable to that of LPAI H4N5 virus, and higher than that of 2005 H5N1 virus for two of the four duck species and chicken tested. Overall, these results indicate that 2016 H5N8 may have acquired a similar enterotropism to LPAI viruses, without having lost the respirotropism of older HPAI viruses of the Goose/Guangdong lineage. The increased enterotropism of 2016 H5N8 implies that this virus had an increased chance to persist long term in the wild waterbird reservoir.
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Affiliation(s)
- Valentina Caliendo
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lonneke Leijten
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lineke Begeman
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Marjolein J Poen
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Nancy Beerens
- Department of Virology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Thijs Kuiken
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
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46
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Mühlemann B, Vinner L, Margaryan A, Wilhelmson H, de la Fuente Castro C, Allentoft ME, de Barros Damgaard P, Hansen AJ, Holtsmark Nielsen S, Strand LM, Bill J, Buzhilova A, Pushkina T, Falys C, Khartanovich V, Moiseyev V, Jørkov MLS, Østergaard Sørensen P, Magnusson Y, Gustin I, Schroeder H, Sutter G, Smith GL, Drosten C, Fouchier RAM, Smith DJ, Willerslev E, Jones TC, Sikora M. Diverse variola virus (smallpox) strains were widespread in northern Europe in the Viking Age. Science 2020; 369:369/6502/eaaw8977. [PMID: 32703849 DOI: 10.1126/science.aaw8977] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 02/13/2020] [Accepted: 05/29/2020] [Indexed: 12/14/2022]
Abstract
Smallpox, one of the most devastating human diseases, killed between 300 million and 500 million people in the 20th century alone. We recovered viral sequences from 13 northern European individuals, including 11 dated to ~600-1050 CE, overlapping the Viking Age, and reconstructed near-complete variola virus genomes for four of them. The samples predate the earliest confirmed smallpox cases by ~1000 years, and the sequences reveal a now-extinct sister clade of the modern variola viruses that were in circulation before the eradication of smallpox. We date the most recent common ancestor of variola virus to ~1700 years ago. Distinct patterns of gene inactivation in the four near-complete sequences show that different evolutionary paths of genotypic host adaptation resulted in variola viruses that circulated widely among humans.
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Affiliation(s)
- Barbara Mühlemann
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK.,Institute of Virology, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany.,German Center for Infection Research (DZIF), Associated Partner Site, Berlin, Germany
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Center, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Ashot Margaryan
- Lundbeck Foundation GeoGenetics Center, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark.,Institute of Molecular Biology, National Academy of Sciences of Armenia, 0014 Yerevan, Armenia
| | - Helene Wilhelmson
- Department of Archaeology and Ancient History, Lund University, 221 00 Lund, Sweden.,Sydsvensk Arkeologi AB, 291 22 Kristianstad, Sweden
| | | | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Center, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark.,Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, 6102 Perth, WA, Australia
| | - Peter de Barros Damgaard
- Lundbeck Foundation GeoGenetics Center, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Anders Johannes Hansen
- Lundbeck Foundation GeoGenetics Center, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Sofie Holtsmark Nielsen
- Lundbeck Foundation GeoGenetics Center, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Lisa Mariann Strand
- Department of Archaeology and Cultural History, Norwegian University of Science and Technology University Museum, 7491 Trondheim, Norway
| | - Jan Bill
- Museum of Cultural History, University of Oslo, 0130 Oslo, Norway
| | - Alexandra Buzhilova
- Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow 125009, Russian Federation
| | - Tamara Pushkina
- Department of Archaeology, Faculty of History, Lomonosov Moscow State University, Moscow 119992, Russian Federation
| | - Ceri Falys
- Thames Valley Archaeological Services, Reading RG1 5NR, UK
| | - Valeri Khartanovich
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russian Federation
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russian Federation
| | - Marie Louise Schjellerup Jørkov
- Laboratory of Biological Anthropology, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | | | - Ingrid Gustin
- Department of Archaeology and Ancient History, Lund University, 221 00 Lund, Sweden
| | - Hannes Schroeder
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Gerd Sutter
- Institute for Infectious Diseases and Zoonoses, LMU University of Munich, 80539 Munich, Germany.,German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Geoffrey L Smith
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Christian Drosten
- Institute of Virology, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany.,German Center for Infection Research (DZIF), Associated Partner Site, Berlin, Germany
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus Medical Centre, 3015 CN Rotterdam, Netherlands
| | - Derek J Smith
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Center, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark. .,Lundbeck Foundation GeoGenetics Center, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK.,Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.,Danish Institute for Advanced Study, University of Southern Denmark, 5230 Odense M, Denmark
| | - Terry C Jones
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK. .,Institute of Virology, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany.,German Center for Infection Research (DZIF), Associated Partner Site, Berlin, Germany
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Center, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark.
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Richard M, Kok A, de Meulder D, Bestebroer TM, Lamers MM, Okba NMA, Fentener van Vlissingen M, Rockx B, Haagmans BL, Koopmans MPG, Fouchier RAM, Herfst S. SARS-CoV-2 is transmitted via contact and via the air between ferrets. Nat Commun 2020. [PMID: 32641684 DOI: 10.1101/2020.04.16.044503v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
SARS-CoV-2, a coronavirus that emerged in late 2019, has spread rapidly worldwide, and information about the modes of transmission of SARS-CoV-2 among humans is critical to apply appropriate infection control measures and to slow its spread. Here we show that SARS-CoV-2 is transmitted efficiently via direct contact and via the air (via respiratory droplets and/or aerosols) between ferrets, 1 to 3 days and 3 to 7 days after exposure respectively. The pattern of virus shedding in the direct contact and indirect recipient ferrets is similar to that of the inoculated ferrets and infectious virus is isolated from all positive animals, showing that ferrets are productively infected via either route. This study provides experimental evidence of robust transmission of SARS-CoV-2 via the air, supporting the implementation of community-level social distancing measures currently applied in many countries in the world and informing decisions on infection control measures in healthcare settings.
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Affiliation(s)
- Mathilde Richard
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Adinda Kok
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Dennis de Meulder
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Theo M Bestebroer
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mart M Lamers
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Nisreen M A Okba
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Barry Rockx
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sander Herfst
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands.
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48
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Richard M, Kok A, de Meulder D, Bestebroer TM, Lamers MM, Okba NMA, Fentener van Vlissingen M, Rockx B, Haagmans BL, Koopmans MPG, Fouchier RAM, Herfst S. SARS-CoV-2 is transmitted via contact and via the air between ferrets. Nat Commun 2020; 11:3496. [PMID: 32641684 DOI: 10.1101/2020.04.16.044503] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/25/2020] [Indexed: 05/22/2023] Open
Abstract
SARS-CoV-2, a coronavirus that emerged in late 2019, has spread rapidly worldwide, and information about the modes of transmission of SARS-CoV-2 among humans is critical to apply appropriate infection control measures and to slow its spread. Here we show that SARS-CoV-2 is transmitted efficiently via direct contact and via the air (via respiratory droplets and/or aerosols) between ferrets, 1 to 3 days and 3 to 7 days after exposure respectively. The pattern of virus shedding in the direct contact and indirect recipient ferrets is similar to that of the inoculated ferrets and infectious virus is isolated from all positive animals, showing that ferrets are productively infected via either route. This study provides experimental evidence of robust transmission of SARS-CoV-2 via the air, supporting the implementation of community-level social distancing measures currently applied in many countries in the world and informing decisions on infection control measures in healthcare settings.
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Affiliation(s)
- Mathilde Richard
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Adinda Kok
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Dennis de Meulder
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Theo M Bestebroer
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mart M Lamers
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Nisreen M A Okba
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Barry Rockx
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sander Herfst
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands.
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49
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Richard M, Kok A, de Meulder D, Bestebroer TM, Lamers MM, Okba NMA, Fentener van Vlissingen M, Rockx B, Haagmans BL, Koopmans MPG, Fouchier RAM, Herfst S. SARS-CoV-2 is transmitted via contact and via the air between ferrets. Nat Commun 2020; 11:3496. [PMID: 32641684 PMCID: PMC7343828 DOI: 10.1038/s41467-020-17367-2] [Citation(s) in RCA: 335] [Impact Index Per Article: 83.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/25/2020] [Indexed: 11/08/2022] Open
Abstract
SARS-CoV-2, a coronavirus that emerged in late 2019, has spread rapidly worldwide, and information about the modes of transmission of SARS-CoV-2 among humans is critical to apply appropriate infection control measures and to slow its spread. Here we show that SARS-CoV-2 is transmitted efficiently via direct contact and via the air (via respiratory droplets and/or aerosols) between ferrets, 1 to 3 days and 3 to 7 days after exposure respectively. The pattern of virus shedding in the direct contact and indirect recipient ferrets is similar to that of the inoculated ferrets and infectious virus is isolated from all positive animals, showing that ferrets are productively infected via either route. This study provides experimental evidence of robust transmission of SARS-CoV-2 via the air, supporting the implementation of community-level social distancing measures currently applied in many countries in the world and informing decisions on infection control measures in healthcare settings.
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Affiliation(s)
- Mathilde Richard
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Adinda Kok
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Dennis de Meulder
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Theo M Bestebroer
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mart M Lamers
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Nisreen M A Okba
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Barry Rockx
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sander Herfst
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands.
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50
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Verhagen JH, Poen M, Stallknecht DE, van der Vliet S, Lexmond P, Sreevatsan S, Poulson RL, Fouchier RAM, Lebarbenchon C. Phylogeography and Antigenic Diversity of Low-Pathogenic Avian Influenza H13 and H16 Viruses. J Virol 2020; 94:e00537-20. [PMID: 32321814 PMCID: PMC7307148 DOI: 10.1128/jvi.00537-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/13/2020] [Indexed: 11/20/2022] Open
Abstract
Low-pathogenic avian influenza viruses (LPAIVs) are genetically highly variable and have diversified into multiple evolutionary lineages that are primarily associated with wild-bird reservoirs. Antigenic variation has been described for mammalian influenza viruses and for highly pathogenic avian influenza viruses that circulate in poultry, but much less is known about antigenic variation of LPAIVs. In this study, we focused on H13 and H16 LPAIVs that circulate globally in gulls. We investigated the evolutionary history and intercontinental gene flow based on the hemagglutinin (HA) gene and used representative viruses from genetically distinct lineages to determine their antigenic properties by hemagglutination inhibition assays. For H13, at least three distinct genetic clades were evident, while for H16, at least two distinct genetic clades were evident. Twenty and ten events of intercontinental gene flow were identified for H13 and H16 viruses, respectively. At least two antigenic variants of H13 and at least one antigenic variant of H16 were identified. Amino acid positions in the HA protein that may be involved in the antigenic variation were inferred, and some of the positions were located near the receptor binding site of the HA protein, as they are in the HA protein of mammalian influenza A viruses. These findings suggest independent circulation of H13 and H16 subtypes in gull populations, as antigenic patterns do not overlap, and they contribute to the understanding of the genetic and antigenic variation of LPAIVs naturally circulating in wild birds.IMPORTANCE Wild birds play a major role in the epidemiology of low-pathogenic avian influenza viruses (LPAIVs), which are occasionally transmitted-directly or indirectly-from them to other species, including domestic animals, wild mammals, and humans, where they can cause subclinical to fatal disease. Despite a multitude of genetic studies, the antigenic variation of LPAIVs in wild birds is poorly understood. Here, we investigated the evolutionary history, intercontinental gene flow, and antigenic variation among H13 and H16 LPAIVs. The circulation of subtypes H13 and H16 seems to be maintained by a narrower host range, in particular gulls, than the majority of LPAIV subtypes and may therefore serve as a model for evolution and epidemiology of H1 to H12 LPAIVs in wild birds. The findings suggest that H13 and H16 LPAIVs circulate independently of each other and emphasize the need to investigate within-clade antigenic variation of LPAIVs in wild birds.
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Affiliation(s)
- Josanne H Verhagen
- Erasmus Medical Center, Department of Viroscience, Rotterdam, The Netherlands
- Linnaeus University, Department of Biology and Environmental Science, Kalmar, Sweden
| | - Marjolein Poen
- Erasmus Medical Center, Department of Viroscience, Rotterdam, The Netherlands
| | - David E Stallknecht
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, Department of Population Health, University of Georgia, Athens, Georgia, USA
| | | | - Pascal Lexmond
- Erasmus Medical Center, Department of Viroscience, Rotterdam, The Netherlands
| | - Srinand Sreevatsan
- Michigan State University, College of Veterinary Medicine, Department of Pathobiology and Diagnostic Investigation, East Lansing, Michigan, USA
| | - Rebecca L Poulson
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, Department of Population Health, University of Georgia, Athens, Georgia, USA
| | - Ron A M Fouchier
- Erasmus Medical Center, Department of Viroscience, Rotterdam, The Netherlands
| | - Camille Lebarbenchon
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, Department of Population Health, University of Georgia, Athens, Georgia, USA
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical, INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
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