1
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Loes AN, Tarabi RAL, Huddleston J, Touyon L, Wong SS, Cheng SMS, Leung NHL, Hannon WW, Bedford T, Cobey S, Cowling BJ, Bloom JD. High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains. J Virol 2024:e0068924. [PMID: 39315814 DOI: 10.1128/jvi.00689-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 09/01/2024] [Indexed: 09/25/2024] Open
Abstract
The high genetic diversity of influenza viruses means that traditional serological assays have too low throughput to measure serum antibody neutralization titers against all relevant strains. To overcome this challenge, we developed a sequencing-based neutralization assay that simultaneously measures titers against many viral strains using small serum volumes using a workflow similar to traditional neutralization assays. The key innovation is to incorporate unique nucleotide barcodes into the hemagglutinin (HA) genomic segment, and then pool viruses with numerous different barcoded HA variants and quantify the infectivity of all of them simultaneously using next-generation sequencing. With this approach, a single researcher performed the equivalent of 2,880 traditional neutralization assays (80 serum samples against 36 viral strains) in approximately 1 month. We applied the sequencing-based assay to quantify the impact of influenza vaccination on neutralization titers against recent human H1N1 strains for individuals who had or had not also received a vaccine in the previous year. We found that the viral strain specificities of the neutralizing antibodies elicited by vaccination vary among individuals and that vaccination induced a smaller increase in titers for individuals who had also received a vaccine the previous year-although the titers 6 months after vaccination were similar in individuals with and without the previous-year vaccination. We also identified a subset of individuals with low titers to a subclade of recent H1N1 even after vaccination. We provide an experimental protocol (dx.doi.org/10.17504/protocols.io.kqdg3xdmpg25/v1) and computational pipeline (https://github.com/jbloomlab/seqneut-pipeline) for the sequencing-based neutralization assays to facilitate the use of this method by others. IMPORTANCE We describe a new approach that can rapidly measure how the antibodies in human serum inhibit infection by many different influenza strains. This new approach is useful for understanding how viral evolution affects antibody immunity. We apply the approach to study the effect of repeated influenza vaccination.
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Affiliation(s)
- Andrea N Loes
- Howard Hughes Medical Institute, Seattle, Washington, USA
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Rosario Araceli L Tarabi
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - John Huddleston
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Lisa Touyon
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Sook San Wong
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Samuel M S Cheng
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Nancy H L Leung
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - William W Hannon
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, USA
| | - Trevor Bedford
- Howard Hughes Medical Institute, Seattle, Washington, USA
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA
| | - Benjamin J Cowling
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Jesse D Bloom
- Howard Hughes Medical Institute, Seattle, Washington, USA
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
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2
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Chon I, Wagatsuma K, Saito R, Tang JW, Isamu S, Suzuki E, Shirahige Y, Kawashima T, Minato M, Kodo N, Masaki H, Hamabata H, Yoshioka S, Ichikawa Y, Sun Y, Li J, Otoguto T, Watanabe H. Detection of influenza A(H3N2) viruses with polymerase acidic subunit substitutions after and prior to baloxavir marboxil treatment during the 2022-2023 influenza season in Japan. Antiviral Res 2024; 229:105956. [PMID: 38969237 DOI: 10.1016/j.antiviral.2024.105956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 06/29/2024] [Accepted: 07/02/2024] [Indexed: 07/07/2024]
Abstract
Baloxavir marboxil (baloxavir), approved as an anti-influenza drug in Japan in March 2018, can induce reduced therapeutic effectiveness due to PA protein substitutions. We assessed PA substitutions in clinical samples from influenza-infected children and adults pre- and post-baloxavir treatment, examining their impact on fever and symptom duration. During the 2022-2023 influenza season, the predominant circulating influenza subtype detected by cycling-probe RT-PCR was A(H3N2) (n = 234), with a minor circulation of A(H1N1)pdm09 (n = 10). Of the 234 influenza A(H3N2) viruses collected prior to baloxavir treatment, 2 (0.8%) viruses carry PA/I38T substitution. One virus was collected from a toddler and one from an adult, indicating the presence of viruses with reduced susceptibility to baloxavir, without prior exposure to the drug. Of the 54 paired influenza A(H3N2) viruses collected following baloxavir treatment, 8 (14.8%) viruses carried E23 K/G, or I38 M/T substitutions in PA. Variant calling through next-generation sequencing (NGS) showed varying proportions (6-100 %), a polymorphism and a mixture of PA/E23 K/G, and I38 M/T substitutions in the clinical samples. These eight viruses were obtained from children aged 7-14 years, with a median fever duration of 16.7 h and a median symptom duration of 93.7 h, which were similar to those of the wild type. However, the delayed viral clearance associated with the emergence of PA substitutions was observed. No substitutions conferring resistance to neuraminidase inhibitors were detected in 37 paired samples collected before and following oseltamivir treatment. These findings underscore the need for ongoing antiviral surveillance, informing public health strategies and clinical antiviral recommendations for seasonal influenza.
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Affiliation(s)
- Irina Chon
- Division of International Health (Public Health), Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.
| | - Keita Wagatsuma
- Division of International Health (Public Health), Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Reiko Saito
- Division of International Health (Public Health), Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Julian W Tang
- Respiratory Sciences, University of Leicester, Leicester, UK; Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, UK
| | | | | | | | | | | | | | | | | | - Sayaka Yoshioka
- Division of International Health (Public Health), Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Yusuke Ichikawa
- Division of International Health (Public Health), Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Yuyang Sun
- Division of International Health (Public Health), Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Jiaming Li
- Division of International Health (Public Health), Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Teruhime Otoguto
- Division of International Health (Public Health), Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Hisami Watanabe
- Division of International Health (Public Health), Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
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3
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Duwe SC, Milde J, Heider A, Wedde M, Schweiger B, Dürrwald R. Increase of Synergistic Secondary Antiviral Mutations in the Evolution of A(H1N1)pdm09 Influenza Virus Neuraminidases. Viruses 2024; 16:1109. [PMID: 39066271 PMCID: PMC11281601 DOI: 10.3390/v16071109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
The unexpected emergence of oseltamivir-resistant A(H1N1) viruses in 2008 was facilitated in part by the establishment of permissive secondary neuraminidase (NA) substitutions that compensated for the fitness loss due to the NA-H275Y resistance substitution. These viruses were replaced in 2009 by oseltamivir-susceptible A(H1N1)pdm09 influenza viruses. Genetic analysis and screening of A(H1N1)pdm09 viruses circulating in Germany between 2009 and 2024 were conducted to identify any potentially synergistic or resistance-associated NA substitutions. Selected viruses were then subjected to further characterization in vitro. In the NA gene of circulating A(H1N1)pdm09 viruses, two secondary substitutions, NA-V241I and NA-N369K, were identified. These substitutions demonstrated a stable lineage in phylogenetic analysis since the 2010-2011 influenza season. The data indicate a slight increase in viral NA bearing two additional potentially synergistic substitutions, NA-I223V and NA-S247N, in the 2023-2024 season, which both result in a slight reduction in susceptibility to NA inhibitors. The accumulation of secondary synergistic substitutions in the NA of A(H1N1)pdm09 viruses increases the probability of the emergence of antiviral-resistant viruses. Therefore, it is crucial to closely monitor the evolution of circulating influenza viruses and to develop additional antiviral drugs against different target proteins.
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Affiliation(s)
- Susanne C. Duwe
- Unit 17 Influenza and Other Respiratory Viruses, Department 1 Infectious Diseases, Robert Koch-Institute, 13353 Berlin, Germany
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4
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Dupont M, Krischuns T, Gianetto QG, Paisant S, Bonazza S, Brault JB, Douché T, Arragain B, Florez-Prada A, Perez-Perri J, Hentze M, Cusack S, Matondo M, Isel C, Courtney D, Naffakh N. The RBPome of influenza A virus NP-mRNA reveals a role for TDP-43 in viral replication. Nucleic Acids Res 2024; 52:7188-7210. [PMID: 38686810 PMCID: PMC11229366 DOI: 10.1093/nar/gkae291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 03/22/2024] [Accepted: 04/05/2024] [Indexed: 05/02/2024] Open
Abstract
Genome-wide approaches have significantly advanced our knowledge of the repertoire of RNA-binding proteins (RBPs) that associate with cellular polyadenylated mRNAs within eukaryotic cells. Recent studies focusing on the RBP interactomes of viral mRNAs, notably SARS-Cov-2, have revealed both similarities and differences between the RBP profiles of viral and cellular mRNAs. However, the RBPome of influenza virus mRNAs remains unexplored. Herein, we identify RBPs that associate with the viral mRNA encoding the nucleoprotein (NP) of an influenza A virus. Focusing on TDP-43, we show that it binds several influenza mRNAs beyond the NP-mRNA, and that its depletion results in lower levels of viral mRNAs and proteins within infected cells, and a decreased yield of infectious viral particles. We provide evidence that the viral polymerase recruits TDP-43 onto viral mRNAs through a direct interaction with the disordered C-terminal domain of TDP-43. Notably, other RBPs found to be associated with influenza virus mRNAs also interact with the viral polymerase, which points to a role of the polymerase in orchestrating the assembly of viral messenger ribonucleoproteins.
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Affiliation(s)
- Maud Dupont
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - Tim Krischuns
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - Quentin Giai Gianetto
- Institut Pasteur, Université Paris Cité, CNRS UAR2024, Proteomics Platform, Mass Spectrometry for Biology, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HUB, Paris, France
| | - Sylvain Paisant
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - Stefano Bonazza
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, BelfastBT9 7BL, Northern Ireland
| | - Jean-Baptiste Brault
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - Thibaut Douché
- Institut Pasteur, Université Paris Cité, CNRS UAR2024, Proteomics Platform, Mass Spectrometry for Biology, Paris, France
| | - Benoît Arragain
- European Molecular Biology Laboratory, 38042Grenoble, France
| | | | | | | | - Stephen Cusack
- European Molecular Biology Laboratory, 38042Grenoble, France
| | - Mariette Matondo
- Institut Pasteur, Université Paris Cité, CNRS UAR2024, Proteomics Platform, Mass Spectrometry for Biology, Paris, France
| | - Catherine Isel
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - David G Courtney
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, BelfastBT9 7BL, Northern Ireland
| | - Nadia Naffakh
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
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5
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Loes AN, Tarabi RAL, Huddleston J, Touyon L, Wong SS, Cheng SMS, Leung NHL, Hannon WW, Bedford T, Cobey S, Cowling BJ, Bloom JD. High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.584176. [PMID: 38496577 PMCID: PMC10942427 DOI: 10.1101/2024.03.08.584176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The high genetic diversity of influenza viruses means that traditional serological assays have too low throughput to measure serum antibody neutralization titers against all relevant strains. To overcome this challenge, we have developed a sequencing-based neutralization assay that simultaneously measures titers against many viral strains using small serum volumes via a workflow similar to traditional neutralization assays. The key innovation is to incorporate unique nucleotide barcodes into the hemagglutinin (HA) genomic segment, and then pool viruses with numerous different barcoded HA variants and quantify infectivity of all of them simultaneously using next-generation sequencing. With this approach, a single researcher performed the equivalent of 2,880 traditional neutralization assays (80 serum samples against 36 viral strains) in approximately one month. We applied the sequencing-based assay to quantify the impact of influenza vaccination on neutralization titers against recent human H1N1 strains for individuals who had or had not also received a vaccine in the previous year. We found that the viral strain specificities of the neutralizing antibodies elicited by vaccination vary among individuals, and that vaccination induced a smaller increase in titers for individuals who had also received a vaccine the previous year-although the titers six months after vaccination were similar in individuals with and without the previous-year vaccination. We also identified a subset of individuals with low titers to a subclade of recent H1N1 even after vaccination. This study demonstrates the utility of high-throughput sequencing-based neutralization assays that enable titers to be simultaneously measured against many different viral strains. We provide a detailed experimental protocol (DOI: https://dx.doi.org/10.17504/protocols.io.kqdg3xdmpg25/v1) and a computational pipeline (https://github.com/jbloomlab/seqneut-pipeline) for the sequencing-based neutralization assays to facilitate the use of this method by others.
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Affiliation(s)
- Andrea N Loes
- Howard Hughes Medical Institute, Seattle, WA
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Rosario Araceli L Tarabi
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - John Huddleston
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Lisa Touyon
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Sook San Wong
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Samuel M S Cheng
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Nancy H L Leung
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - William W Hannon
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98109, USA
| | - Trevor Bedford
- Howard Hughes Medical Institute, Seattle, WA
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
| | - Benjamin J Cowling
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Jesse D Bloom
- Howard Hughes Medical Institute, Seattle, WA
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
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6
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Fu Y, Wedde M, Smola S, Oh DY, Pfuhl T, Rissland J, Zemlin M, Flockerzi FA, Bohle RM, Thürmer A, Duwe S, Biere B, Reiche J, Schweiger B, Mache C, Wolff T, Herrler G, Dürrwald R. Different populations of A(H1N1)pdm09 viruses in a patient with hemolytic-uremic syndrome. Int J Med Microbiol 2024; 314:151598. [PMID: 38237287 DOI: 10.1016/j.ijmm.2024.151598] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 01/03/2024] [Accepted: 01/09/2024] [Indexed: 03/22/2024] Open
Abstract
Respiratory viral infections may have different impacts ranging from infection without symptoms to severe disease or even death though the reasons are not well characterized. A patient (age group 5-15 years) displaying symptoms of hemolytic uremic syndrome died one day after hospitalization. qPCR, next generation sequencing, virus isolation, antigenic characterization, resistance analysis was performed and virus replication kinetics in well-differentiated airway cells were determined. Autopsy revealed hemorrhagic pneumonia as major pathological manifestation. Lung samples harbored a large population of A(H1N1)pdm09 viruses with the polymorphism H456H/Y in PB1 polymerase. The H456H/Y viruses replicated much faster to high viral titers than upper respiratory tract viruses in vitro. H456H/Y-infected air-liquid interface cultures of differentiated airway epithelial cells did reflect a more pronounced loss of ciliated cells. A different pattern of virus quasispecies was found in the upper airway samples where substitution S263S/F (HA1) was observed. The data support the notion that viral quasispecies had evolved locally in the lung to support high replicative fitness. This change may have initiated further pathogenic processes leading to rapid dissemination of inflammatory mediators followed by development of hemorrhagic lung lesions and fatal outcome.
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Affiliation(s)
- Yuguang Fu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Hannover 30559, Germany
| | - Marianne Wedde
- Influenza and other Respiratory Viruses, Department of Infectious Diseases, Unit 17, Influenza and other Respratory Viruses, Robert Koch Institute, Berlin 13353, Germany
| | - Sigrun Smola
- Institute of Virology, Saarland University Medical Center, Homburg, Saar 66421, Germany
| | - Djin-Ye Oh
- Influenza and other Respiratory Viruses, Department of Infectious Diseases, Unit 17, Influenza and other Respratory Viruses, Robert Koch Institute, Berlin 13353, Germany
| | - Thorsten Pfuhl
- Institute of Virology, Saarland University Medical Center, Homburg, Saar 66421, Germany
| | - Jürgen Rissland
- Institute of Virology, Saarland University Medical Center, Homburg, Saar 66421, Germany
| | - Michael Zemlin
- Department for General Pediatrics and Neonatology, Saarland University Medical Center, Homburg, Saar 66421, Germany
| | - Fidelis A Flockerzi
- Institute of Pathology, Saarland University Medical Center, Homburg, Saar 66421, Germany
| | - Rainer M Bohle
- Institute of Pathology, Saarland University Medical Center, Homburg, Saar 66421, Germany
| | - Andrea Thürmer
- Department Methods Development and Research Infrastructure, Robert Koch Institute, Berlin 13353, Germany
| | - Susanne Duwe
- Influenza and other Respiratory Viruses, Department of Infectious Diseases, Unit 17, Influenza and other Respratory Viruses, Robert Koch Institute, Berlin 13353, Germany
| | - Barbara Biere
- Influenza and other Respiratory Viruses, Department of Infectious Diseases, Unit 17, Influenza and other Respratory Viruses, Robert Koch Institute, Berlin 13353, Germany
| | - Janine Reiche
- Influenza and other Respiratory Viruses, Department of Infectious Diseases, Unit 17, Influenza and other Respratory Viruses, Robert Koch Institute, Berlin 13353, Germany
| | - Brunhilde Schweiger
- Influenza and other Respiratory Viruses, Department of Infectious Diseases, Unit 17, Influenza and other Respratory Viruses, Robert Koch Institute, Berlin 13353, Germany
| | - Christin Mache
- Influenza and other Respiratory Viruses, Department of Infectious Diseases, Unit 17, Influenza and other Respratory Viruses, Robert Koch Institute, Berlin 13353, Germany
| | - Thorsten Wolff
- Influenza and other Respiratory Viruses, Department of Infectious Diseases, Unit 17, Influenza and other Respratory Viruses, Robert Koch Institute, Berlin 13353, Germany
| | - Georg Herrler
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Hannover 30559, Germany
| | - Ralf Dürrwald
- Influenza and other Respiratory Viruses, Department of Infectious Diseases, Unit 17, Influenza and other Respratory Viruses, Robert Koch Institute, Berlin 13353, Germany.
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7
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Rowe T, Davis W, Wentworth DE, Ross T. Differential interferon responses to influenza A and B viruses in primary ferret respiratory epithelial cells. J Virol 2024; 98:e0149423. [PMID: 38294251 PMCID: PMC10878268 DOI: 10.1128/jvi.01494-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/02/2023] [Indexed: 02/01/2024] Open
Abstract
Influenza B viruses (IBV) cocirculate with influenza A viruses (IAV) and cause periodic epidemics of disease, yet antibody and cellular responses following IBV infection are less well understood. Using the ferret model for antisera generation for influenza surveillance purposes, IAV resulted in robust antibody responses following infection, whereas IBV required an additional booster dose, over 85% of the time, to generate equivalent antibody titers. In this study, we utilized primary differentiated ferret nasal epithelial cells (FNECs) which were inoculated with IAV and IBV to study differences in innate immune responses which may result in differences in adaptive immune responses in the host. FNECs were inoculated with IAV (H1N1pdm09 and H3N2 subtypes) or IBV (B/Victoria and B/Yamagata lineages) and assessed for 72 h. Cells were analyzed for gene expression by quantitative real-time PCR, and apical and basolateral supernatants were assessed for virus kinetics and interferon (IFN), respectively. Similar virus kinetics were observed with IAV and IBV in FNECs. A comparison of gene expression and protein secretion profiles demonstrated that IBV-inoculated FNEC expressed delayed type-I/II IFN responses and reduced type-III IFN secretion compared to IAV-inoculated cells. Concurrently, gene expression of Thymic Stromal Lymphopoietin (TSLP), a type-III IFN-induced gene that enhances adaptive immune responses, was significantly downregulated in IBV-inoculated FNECs. Significant differences in other proinflammatory and adaptive genes were suppressed and delayed following IBV inoculation. Following IBV infection, ex vivo cell cultures derived from the ferret upper respiratory tract exhibited reduced and delayed innate responses which may contribute to reduced antibody responses in vivo.IMPORTANCEInfluenza B viruses (IBV) represent nearly one-quarter of all human influenza cases and are responsible for significant clinical and socioeconomic impacts but do not pose the same pandemic risks as influenza A viruses (IAV) and have thus received much less attention. IBV accounts for greater severity and deaths in children, and vaccine efficacy remains low. The ferret can be readily infected with human clinical isolates and demonstrates a similar course of disease and immune responses. IBV, however, generates lower antibodies in ferrets than IAV following the challenge. To determine whether differences in initial innate responses following infection may affect the development of robust adaptive immune responses, ferret respiratory tract cells were isolated, infected with IAV/IBV, and compared. Understanding the differences in the initial innate immune responses to IAV and IBV may be important in the development of more effective vaccines and interventions to generate more robust protective immune responses.
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Affiliation(s)
- Thomas Rowe
- Centers for Disease Control and Prevention, Influenza Division, Atlanta, Georgia, USA
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, USA
| | - William Davis
- Centers for Disease Control and Prevention, Influenza Division, Atlanta, Georgia, USA
| | - David E. Wentworth
- Centers for Disease Control and Prevention, Influenza Division, Atlanta, Georgia, USA
| | - Ted Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, USA
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8
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Thompson AJ, Wu NC, Canales A, Kikuchi C, Zhu X, de Toro BF, Cañada FJ, Worth C, Wang S, McBride R, Peng W, Nycholat CM, Jiménez-Barbero J, Wilson IA, Paulson JC. Evolution of human H3N2 influenza virus receptor specificity has substantially expanded the receptor-binding domain site. Cell Host Microbe 2024; 32:261-275.e4. [PMID: 38307019 PMCID: PMC11057904 DOI: 10.1016/j.chom.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 11/14/2023] [Accepted: 01/09/2024] [Indexed: 02/04/2024]
Abstract
Hemagglutinins (HAs) from human influenza viruses descend from avian progenitors that bind α2-3-linked sialosides and must adapt to glycans with α2-6-linked sialic acids on human airway cells to transmit within the human population. Since their introduction during the 1968 pandemic, H3N2 viruses have evolved over the past five decades to preferentially recognize human α2-6-sialoside receptors that are elongated through addition of poly-LacNAc. We show that more recent H3N2 viruses now make increasingly complex interactions with elongated receptors while continuously selecting for strains maintaining this phenotype. This change in receptor engagement is accompanied by an extension of the traditional receptor-binding site to include residues in key antigenic sites on the surface of HA trimers. These results help explain the propensity for selection of antigenic variants, leading to vaccine mismatching, when H3N2 viruses are propagated in chicken eggs or cells that do not contain such receptors.
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Affiliation(s)
- Andrew J Thompson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicholas C Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Angeles Canales
- Department of Organic Chemistry, Faculty of Chemistry, Universidad Complutense de Madrid, Avd. Complutense s/n, 28040 Madrid, Spain
| | - Chika Kikuchi
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Beatriz Fernández de Toro
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, C/Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Francisco J Cañada
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, C/Ramiro de Maeztu 9, 28040 Madrid, Spain; CIBERES, ISCIII, 28029 Madrid, Spain
| | - Charli Worth
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Shengyang Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ryan McBride
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wenjie Peng
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Corwin M Nycholat
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jesús Jiménez-Barbero
- CIBERES, ISCIII, 28029 Madrid, Spain; CIC bioGUNE Bizkaia Science and Technology Park, 48160 Bilbao, Spain; IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Spain
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - James C Paulson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology & Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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9
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Hu X, Wang S, Fu S, Qin M, Lyu C, Ding Z, Wang Y, Wang Y, Wang D, Zhu L, Jiang T, Sun J, Ding H, Wu J, Chang L, Cui Y, Pang X, Wang Y, Huang W, Yang P, Wang L, Ma G, Wei W. Intranasal mask for protecting the respiratory tract against viral aerosols. Nat Commun 2023; 14:8398. [PMID: 38110357 PMCID: PMC10728126 DOI: 10.1038/s41467-023-44134-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/01/2023] [Indexed: 12/20/2023] Open
Abstract
The spread of many infectious diseases relies on aerosol transmission to the respiratory tract. Here we design an intranasal mask comprising a positively-charged thermosensitive hydrogel and cell-derived micro-sized vesicles with a specific viral receptor. We show that the positively charged hydrogel intercepts negatively charged viral aerosols, while the viral receptor on vesicles mediates the entrapment of viruses for inactivation. We demonstrate that when displaying matched viral receptors, the intranasal masks protect the nasal cavity and lung of mice from either severe acute respiratory syndrome coronavirus 2 or influenza A virus. With computerized tomography images of human nasal cavity, we further conduct computational fluid dynamics simulation and three-dimensional printing of an anatomically accurate human nasal cavity, which is connected to human lung organoids to generate a human respiratory tract model. Both simulative and experimental results support the suitability of intranasal masks in humans, as the likelihood of viral respiratory infections induced by different variant strains is dramatically reduced.
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Affiliation(s)
- Xiaoming Hu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 100190, Beijing, China
- School of Chemical Engineering, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Shuang Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 100190, Beijing, China
- School of Chemical Engineering, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Shaotong Fu
- School of Chemical Engineering, University of Chinese Academy of Sciences, 100049, Beijing, China
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, 100190, Beijing, China
| | - Meng Qin
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, 100029, Beijing, China
| | - Chengliang Lyu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 100190, Beijing, China
| | - Zhaowen Ding
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 100190, Beijing, China
| | - Yan Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 100190, Beijing, China
- School of Chemical Engineering, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yishu Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 100190, Beijing, China
- School of Chemical Engineering, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Dongshu Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, 100071, Beijing, China
| | - Li Zhu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, 100071, Beijing, China
| | - Tao Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 100071, Beijing, China
| | - Jing Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100029, Beijing, China
| | - Hui Ding
- Shenzhen Key Laboratory of Nanozymes and Translational Cancer Research, Department of Otolaryngology, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, 518035, Shenzhen, China
| | - Jie Wu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 100190, Beijing, China
- School of Chemical Engineering, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Lingqian Chang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering School of Biological Science and Medical Engineering, Beihang University, 100083, Beijing, China
| | - Yimin Cui
- Department of Pharmacy, Peking University First Hospital, 100034, Beijing, China
- Institute of Clinical Pharmacology, Peking University, 100191, Beijing, China
| | - Xiaocong Pang
- Department of Pharmacy, Peking University First Hospital, 100034, Beijing, China
- Institute of Clinical Pharmacology, Peking University, 100191, Beijing, China
| | - Youchun Wang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, 102629, Beijing, China
| | - Weijin Huang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, 102629, Beijing, China
| | - Peidong Yang
- Department of Breast Surgery, Affiliated Quanzhou First Hospital of Fujian Medical University, 362000, Quanzhou, China
| | - Limin Wang
- School of Chemical Engineering, University of Chinese Academy of Sciences, 100049, Beijing, China.
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, 100190, Beijing, China.
| | - Guanghui Ma
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 100190, Beijing, China.
- School of Chemical Engineering, University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Wei Wei
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 100190, Beijing, China.
- School of Chemical Engineering, University of Chinese Academy of Sciences, 100049, Beijing, China.
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10
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Wallace LE, de Vries E, van Kuppeveld FJM, de Haan CAM. Neuraminidase-dependent entry of influenza A virus is determined by hemagglutinin receptor-binding specificity. J Virol 2023; 97:e0060223. [PMID: 37754760 PMCID: PMC10617504 DOI: 10.1128/jvi.00602-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/09/2023] [Indexed: 09/28/2023] Open
Abstract
IMPORTANCE Influenza A viruses (IAVs) contain hemagglutinin (HA) proteins involved in sialoglycan receptor binding and neuraminidase (NA) proteins that cleave sialic acids. While the importance of the NA protein in virion egress is well established, its role in virus entry remains to be fully elucidated. NA activity is needed for the release of virions from mucus decoy receptors, but conflicting results have been reported on the importance of NA activity in virus entry in the absence of decoy receptors. We now show that inhibition of NA activity affects virus entry depending on the receptor-binding properties of HA and the receptor repertoire present on cells. Inhibition of entry by the presence of mucus correlated with the importance of NA activity for virus entry, with the strongest inhibition being observed when mucus and OsC were combined. These results shed light on the importance in virus entry of the NA protein, an important antiviral drug target.
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Affiliation(s)
- Louisa E. Wallace
- Section of Virology, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Erik de Vries
- Section of Virology, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Frank J. M. van Kuppeveld
- Section of Virology, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Cornelis A. M. de Haan
- Section of Virology, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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11
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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: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [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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12
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Potdar V, Vijay N, Mukhopadhyay L, Aggarwal N, Bhardwaj SD, Choudhary ML, Gupta N, Kaur H, Narayan J, Kumar P, Singh H, Abdulkader RS, Murhekar M, Mishra M, Thangavel S, Nagamani K, Dhodapkar R, Fomda BA, Varshney U, Majumdar A, Dutta S, Vijayachari P, Turuk J, Majumdar T, Sahoo GC, Pandey K, Bhargava A, Negi SS, Khatri PK, Kalawat U, Biswas D, Khandelwal N, Borkakoty B, Manjushree S, Singh MP, Iravane J, Kaveri K, Shantala GB, Brijwal M, Choudhary A, Dar L, Malhotra B, Jain A. Pan-India influenza-like illness (ILI) and Severe acute respiratory infection (SARI) surveillance: epidemiological, clinical and genomic analysis. Front Public Health 2023; 11:1218292. [PMID: 37927860 PMCID: PMC10624221 DOI: 10.3389/fpubh.2023.1218292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 09/18/2023] [Indexed: 11/07/2023] Open
Abstract
Background Over time, COVID-19 testing has significantly declined across the world. However, it is critical to monitor the virus through surveillance. In late 2020, WHO released interim guidance advising the use of the existing Global Influenza Surveillance and Response System (GISRS) for the integrated surveillance of influenza and SARS-CoV-2. Methods In July 2021, we initiated a pan-India integrated surveillance for influenza and SARS-CoV-2 through the geographically representative network of Virus Research and Diagnostic Laboratories (VRDLs) across 26 hospital and laboratory sites and 70 community sites. A total of 34,260 cases of influenza-like illness (ILI) and Severe acute respiratory infection (SARI) were enrolled from 4 July 2021 to 31 October 2022. Findings Influenza A(H3) and B/Victoria dominated during 2021 monsoon season while A(H1N1)pdm09 dominated during 2022 monsoon season. The SARS-CoV-2 "variants of concern" (VoC) Delta and Omicron predominated in 2021 and 2022, respectively. Increased proportion of SARI was seen in extremes of age: 90% cases in < 1 year; 68% in 1 to 5 years and 61% in ≥ 8 years age group. Approximately 40.7% of enrolled cases only partially fulfilled WHO ILI and SARI case definitions. Influenza- and SARS-CoV-2-infected comorbid patients had higher risks of hospitalization, ICU admission, and oxygen requirement. Interpretation The results depicted the varying strains and transmission dynamics of influenza and SARS-CoV-2 viruses over time, thus emphasizing the need to continue and expand surveillance across countries for improved decision making. The study also describes important information related to clinical outcomes of ILI and SARI patients and highlights the need to review existing WHO ILI and SARI case definitions.
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Affiliation(s)
| | - Neetu Vijay
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Labanya Mukhopadhyay
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Neeraj Aggarwal
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | | | | | - Nivedita Gupta
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Harmanmeet Kaur
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Jitendra Narayan
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Prabhat Kumar
- Biomedical Informatics (BMI) Division, Indian Council of Medical Research, New Delhi, India
| | - Harpreet Singh
- Biomedical Informatics (BMI) Division, Indian Council of Medical Research, New Delhi, India
| | | | | | - Meena Mishra
- VRDL, All India Institute of Medical Sciences, Nagpur, India
| | | | - K. Nagamani
- VRDL, Gandhi Medical College, Secunderabad, India
| | - Rahul Dhodapkar
- VRDL, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | | | | | - Agniva Majumdar
- ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - P. Vijayachari
- ICMR-Regional Medical Research Centre, Port Blair, India
| | | | | | | | - Krishna Pandey
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | | | | | | | - Usha Kalawat
- VRDL, Sri Venkateswara Institute of Medical Sciences, Tirupati, India
| | - Debasis Biswas
- VRDL, All India Institute of Medical Sciences, Bhopal, India
| | | | | | | | - Mini P. Singh
- VRDL, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | | | - K. Kaveri
- VRDL, King Institute of Preventive Medicine and Research, Chennai, India
| | - G. B. Shantala
- VRDL, Bangalore Medical College and Research Institute, Bangalore, India
| | - Megha Brijwal
- VRDL, All India Institute of Medical Sciences, New Delhi, India
| | | | - Lalit Dar
- VRDL, All India Institute of Medical Sciences, New Delhi, India
| | | | - Amita Jain
- VRDL, King George’s Medical University, Lucknow, India
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13
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Kikuchi C, Antonopoulos A, Wang S, Maemura T, Karamanska R, Lee C, Thompson AJ, Dell A, Kawaoka Y, Haslam SM, Paulson JC. Glyco-engineered MDCK cells display preferred receptors of H3N2 influenza absent in eggs used for vaccines. Nat Commun 2023; 14:6178. [PMID: 37794004 PMCID: PMC10551000 DOI: 10.1038/s41467-023-41908-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 09/15/2023] [Indexed: 10/06/2023] Open
Abstract
Evolution of human H3N2 influenza viruses driven by immune selection has narrowed the receptor specificity of the hemagglutinin (HA) to a restricted subset of human-type (Neu5Acα2-6 Gal) glycan receptors that have extended poly-LacNAc (Galβ1-4GlcNAc) repeats. This altered specificity has presented challenges for hemagglutination assays, growth in laboratory hosts, and vaccine production in eggs. To assess the impact of extended glycan receptors on virus binding, infection, and growth, we have engineered N-glycan extended (NExt) cell lines by overexpressing β3-Ν-acetylglucosaminyltransferase 2 in MDCK, SIAT, and hCK cell lines. Of these, SIAT-NExt cells exhibit markedly increased binding of H3 HAs and susceptibility to infection by recent H3N2 virus strains, but without impacting final virus titers. Glycome analysis of these cell lines and allantoic and amniotic egg membranes provide insights into the importance of extended glycan receptors for growth of recent H3N2 viruses and relevance to their production for cell- and egg-based vaccines.
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Affiliation(s)
- Chika Kikuchi
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Shengyang Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Tadashi Maemura
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Rositsa Karamanska
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Chiara Lee
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Andrew J Thompson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Anne Dell
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The 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, The University of Tokyo, Tokyo, Japan
| | - Stuart M Haslam
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
| | - James C Paulson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
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14
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Pendrey CG, Strachan J, Peck H, Aziz A, Moselen J, Moss R, Rahaman MR, Barr IG, Subbarao K, Sullivan SG. The re-emergence of influenza following the COVID-19 pandemic in Victoria, Australia, 2021 to 2022. Euro Surveill 2023; 28:2300118. [PMID: 37707981 PMCID: PMC10687983 DOI: 10.2807/1560-7917.es.2023.28.37.2300118] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 06/28/2023] [Indexed: 09/16/2023] Open
Abstract
BackgroundCOVID-19 pandemic mitigation measures, including travel restrictions, limited global circulation of influenza viruses. In Australia, travel bans for non-residents and quarantine requirements for returned travellers were eased in November 2021, providing pathways for influenza viruses to be re-introduced.AimWe aimed to describe the epidemiological and virological characteristics of the re-emergence of influenza in Victoria, Australia to inform public health interventions.MethodsFrom 1 November 2021 to 30 April 2022, we conducted an epidemiological study analysing case notification data from the Victorian Department of Health to describe case demographics, interviewed the first 200 cases to establish probable routes of virus reintroduction and examined phylogenetic and antigenic data to understand virus diversity and susceptibility to current vaccines.ResultsOverall, 1,598 notifications and 1,064 positive specimens were analysed. The majority of cases (61.4%) occurred in the 15-34 years age group. Interviews revealed a higher incidence of international travel exposure during the first month of case detections, and high levels of transmission in university residential colleges were associated with return to campus. Influenza A(H3N2) was the predominant subtype, with a single lineage predominating despite multiple importations.ConclusionEnhanced testing for respiratory viruses during the COVID-19 pandemic provided a more complete picture of influenza virus transmission compared with previous seasons. Returned international travellers were important drivers of influenza reemergence, as were young adults, a group whose role has previously been under-recognised in the establishment of seasonal influenza epidemics. Targeting interventions, including vaccination, to these groups could reduce future influenza transmission.
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Affiliation(s)
- Catherine Ga Pendrey
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- National Centre for Epidemiology and Population Health, Australian National University, Canberra, Australia
- Communicable Diseases, Health Protection Branch, Public Health Division, Department of Health, Victoria, Melbourne, Australia
| | - Janet Strachan
- Communicable Diseases, Health Protection Branch, Public Health Division, Department of Health, Victoria, Melbourne, Australia
| | - Heidi Peck
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Ammar Aziz
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Jean Moselen
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Rob Moss
- School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Md Rezanur Rahaman
- National Centre for Epidemiology and Population Health, Australian National University, Canberra, Australia
| | - Ian G Barr
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Immunology and Microbiology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Kanta Subbarao
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Immunology and Microbiology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Sheena G Sullivan
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Communicable Diseases, Health Protection Branch, Public Health Division, Department of Health, Victoria, Melbourne, Australia
- Department of Infectious Diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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15
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Mettelman RC, Souquette A, Van de Velde LA, Vegesana K, Allen EK, Kackos CM, Trifkovic S, DeBeauchamp J, Wilson TL, St James DG, Menon SS, Wood T, Jelley L, Webby RJ, Huang QS, Thomas PG. Baseline innate and T cell populations are correlates of protection against symptomatic influenza virus infection independent of serology. Nat Immunol 2023; 24:1511-1526. [PMID: 37592015 PMCID: PMC10566627 DOI: 10.1038/s41590-023-01590-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 07/13/2023] [Indexed: 08/19/2023]
Abstract
Evidence suggests that innate and adaptive cellular responses mediate resistance to the influenza virus and confer protection after vaccination. However, few studies have resolved the contribution of cellular responses within the context of preexisting antibody titers. Here, we measured the peripheral immune profiles of 206 vaccinated or unvaccinated adults to determine how baseline variations in the cellular and humoral immune compartments contribute independently or synergistically to the risk of developing symptomatic influenza. Protection correlated with diverse and polyfunctional CD4+ and CD8+ T, circulating T follicular helper, T helper type 17, myeloid dendritic and CD16+ natural killer (NK) cell subsets. Conversely, increased susceptibility was predominantly attributed to nonspecific inflammatory populations, including γδ T cells and activated CD16- NK cells, as well as TNFα+ single-cytokine-producing CD8+ T cells. Multivariate and predictive modeling indicated that cellular subsets (1) work synergistically with humoral immunity to confer protection, (2) improve model performance over demographic and serologic factors alone and (3) comprise the most important predictive covariates. Together, these results demonstrate that preinfection peripheral cell composition improves the prediction of symptomatic influenza susceptibility over vaccination, demographics or serology alone.
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Affiliation(s)
- Robert C Mettelman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Aisha Souquette
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lee-Ann Van de Velde
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kasi Vegesana
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Christina M Kackos
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sanja Trifkovic
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jennifer DeBeauchamp
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Taylor L Wilson
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Microbiology, Immunology and Biochemistry, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Deryn G St James
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Microbiology, Immunology and Biochemistry, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Smrithi S Menon
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Timothy Wood
- Institute of Environmental Science and Research Limited (ESR), Wallaceville Science Centre, Upper Hutt, New Zealand
| | - Lauren Jelley
- Institute of Environmental Science and Research Limited (ESR), Wallaceville Science Centre, Upper Hutt, New Zealand
| | - Richard J Webby
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Q Sue Huang
- Institute of Environmental Science and Research Limited (ESR), Wallaceville Science Centre, Upper Hutt, New Zealand.
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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16
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Sominina A, Danilenko D, Komissarov AB, Pisareva M, Fadeev A, Konovalova N, Eropkin M, Petrova P, Zheltukhina A, Musaeva T, Eder V, Ivanova A, Komissarova K, Stolyarov K, Karpova L, Smorodintseva E, Dorosh A, Krivitskaya V, Kuznetzova E, Majorova V, Petrova E, Boyarintseva A, Ksenafontov A, Shtro A, Nikolaeva J, Bakaev M, Burtseva E, Lioznov D. Assessing the Intense Influenza A(H1N1)pdm09 Epidemic and Vaccine Effectiveness in the Post-COVID Season in the Russian Federation. Viruses 2023; 15:1780. [PMID: 37632122 PMCID: PMC10458445 DOI: 10.3390/v15081780] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/31/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
The COVID-19 pandemic had a profound impact on influenza activity worldwide. However, as the pandemic progressed, influenza activity resumed. Here, we describe the influenza epidemic of high intensity of the 2022-2023 season. The epidemic had an early start and peaked in week 51.2022. The extremely high intensity of the epidemic may have been due to a significant decrease in herd immunity. The results of PCR-testing of 220,067 clinical samples revealed that the influenza A(H1N1)pdm09 virus dominated, causing 56.4% of positive cases, while A(H3N2) influenza subtype accounted for only 0.6%, and influenza B of Victoria lineage-for 34.3%. The influenza vaccine was found to be highly effective, with an estimated effectiveness of 92.7% in preventing admission with laboratory-confirmed influenza severe acute respiratory illness (SARI) cases and 54.7% in preventing influenza-like illness/acute respiratory illness (ILI/ARI) cases due to antigenic matching of circulated viruses with influenza vaccine strains for the season. Full genome next-generation sequencing of 1723 influenza A(H1N1)pdm09 viruses showed that all of them fell within clade 6B.1A.5.a2; nine of them possessed H275Y substitution in the NA gene, a genetic marker of oseltamivir resistance. Influenza A(H3N2) viruses belonged to subclade 3C.2a1b.2a.2 with the genetic group 2b being dominant. All 433 influenza B viruses belonged to subclade V1A.3a.2 encoding HA1 substitutions A127T, P144L, and K203R, which could be further divided into two subgroups. None of the influenza A(H3N2) and B viruses sequenced had markers of resistance to NA inhibitors. Thus, despite the continuing circulation of Omicron descendant lineages, influenza activity has resumed in full force, raising concerns about the intensity of fore coming seasonal epidemics.
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Affiliation(s)
- Anna Sominina
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Daria Danilenko
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Andrey B. Komissarov
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Maria Pisareva
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Artem Fadeev
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Nadezhda Konovalova
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Mikhail Eropkin
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Polina Petrova
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Alyona Zheltukhina
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Tamila Musaeva
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Veronika Eder
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Anna Ivanova
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Kseniya Komissarova
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Kirill Stolyarov
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Ludmila Karpova
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Elizaveta Smorodintseva
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Anna Dorosh
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Vera Krivitskaya
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Elena Kuznetzova
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Victoria Majorova
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Ekaterina Petrova
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Anastassia Boyarintseva
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Andrey Ksenafontov
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Anna Shtro
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Julia Nikolaeva
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Mikhail Bakaev
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Elena Burtseva
- National Research Center for Epidemiology and Microbiology Named after N.F. Gamaleya, 123098 Moscow, Russia
| | - Dmitry Lioznov
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
- Department of Infectious Diseases, First Pavlov State Medical University, 197022 Saint Petersburg, Russia
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17
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Hickerson BT, Petrovskaya SN, Dickensheets H, Donnelly RP, Ince WL, Ilyushina NA. Impact of Baloxavir Resistance-Associated Substitutions on Influenza Virus Growth and Drug Susceptibility. J Virol 2023; 97:e0015423. [PMID: 37404185 PMCID: PMC10373543 DOI: 10.1128/jvi.00154-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 06/10/2023] [Indexed: 07/06/2023] Open
Abstract
Baloxavir marboxil (baloxavir) is a recently FDA-approved influenza virus polymerase acidic (PA) endonuclease inhibitor. Several PA substitutions have been demonstrated to confer reduced susceptibility to baloxavir; however, their impacts on measurements of antiviral drug susceptibility and replication capacity when present as a fraction of the viral population have not been established. We generated recombinant A/California/04/09 (H1N1)-like viruses (IAV) with PA I38L, I38T, or E199D substitutions and B/Victoria/504/2000-like virus (IBV) with PA I38T. These substitutions reduced baloxavir susceptibility by 15.3-, 72.3-, 5.4-, and 54.5-fold, respectively, when tested in normal human bronchial epithelial (NHBE) cells. We then assessed the replication kinetics, polymerase activity, and baloxavir susceptibility of the wild-type:mutant (WT:MUT) virus mixtures in NHBE cells. The percentage of MUT relative to WT virus necessary to detect reduced baloxavir susceptibility in phenotypic assays ranged from 10% (IBV I38T) to 92% (IAV E199D). While I38T did not alter IAV replication kinetics or polymerase activity, IAV PA I38L and E199D MUTs and the IBV PA I38T MUT exhibited reduced replication levels and significantly altered polymerase activity. Differences in replication were detectable when the MUTs comprised ≥90%, ≥90%, or ≥75% of the population, respectively. Droplet digital PCR (ddPCR) and next-generation sequencing (NGS) analyses showed that WT viruses generally outcompeted the respective MUTs after multiple replication cycles and serial passaging in NHBE cells when initial mixtures contained ≥50% of the WT viruses; however, we also identified potential compensatory substitutions (IAV PA D394N and IBV PA E329G) that emerged and appeared to improve the replication capacity of baloxavir-resistant virus in cell culture. IMPORTANCE Baloxavir marboxil, an influenza virus polymerase acidic endonuclease inhibitor, represents a recently approved new class of influenza antivirals. Treatment-emergent resistance to baloxavir has been observed in clinical trials, and the potential spread of resistant variants could diminish baloxavir effectiveness. Here, we report the impact of the proportion of drug-resistant subpopulations on the ability to detect resistance in clinical isolates and the impact of substitutions on viral replication of mixtures containing both drug-sensitive and drug-resistant variants. We also show that ddPCR and NGS methods can be successfully used for detection of resistant subpopulations in clinical isolates and to quantify their relative abundance. Taken together, our data shed light on the potential impact of baloxavir-resistant I38T/L and E199D substitutions on baloxavir susceptibility and other biological properties of influenza virus and the ability to detect resistance in phenotypic and genotypic assays.
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Affiliation(s)
- Brady T. Hickerson
- Division of Biotechnology Review and Research II, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Svetlana N. Petrovskaya
- Division of Biotechnology Review and Research III, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Harold Dickensheets
- Division of Biotechnology Review and Research II, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Raymond P. Donnelly
- Division of Biotechnology Review and Research II, Food and Drug Administration, Silver Spring, Maryland, USA
| | - William L. Ince
- Division of Antivirals, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Natalia A. Ilyushina
- Division of Biotechnology Review and Research II, Food and Drug Administration, Silver Spring, Maryland, USA
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18
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Swanson NJ, Marinho P, Dziedzic A, Jedlicka A, Liu H, Fenstermacher K, Rothman R, Pekosz A. 2019-2020 H1N1 clade A5a.1 viruses have better in vitro fitness compared with the co-circulating A5a.2 clade. Sci Rep 2023; 13:10223. [PMID: 37353648 PMCID: PMC10290074 DOI: 10.1038/s41598-023-37122-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/15/2023] [Indexed: 06/25/2023] Open
Abstract
Surveillance for emerging human influenza virus clades is important for identifying changes in viral fitness and assessing antigenic similarity to vaccine strains. While fitness and antigenic structure are both important aspects of virus success, they are distinct characteristics and do not always change in a complementary manner. The 2019-2020 Northern Hemisphere influenza season saw the emergence of two H1N1 clades: A5a.1 and A5a.2. While several studies indicated that A5a.2 showed similar or even increased antigenic drift compared with A5a.1, the A5a.1 clade was still the predominant circulating clade that season. Clinical isolates of representative viruses from these clades were collected in Baltimore, Maryland during the 2019-2020 season and multiple assays were performed to compare both antigenic drift and viral fitness between clades. Neutralization assays performed on serum from healthcare workers pre- and post-vaccination during the 2019-2020 season show a comparable drop in neutralizing titers against both A5a.1 and A5a.2 viruses compared with the vaccine strain, indicating that A5a.1 did not have antigenic advantages over A5a.2 that would explain its predominance in this population. Plaque assays were performed to investigate fitness differences, and the A5a.2 virus produced significantly smaller plaques compared with viruses from A5a.1 or the parental A5a clade. To assess viral replication, low MOI growth curves were performed on both MDCK-SIAT and primary differentiated human nasal epithelial cell cultures. In both cell cultures, A5a.2 yielded significantly reduced viral titers at multiple timepoints post-infection compared with A5a.1 or A5a. Receptor binding was then investigated through glycan array experiments which showed a reduction in receptor binding diversity for A5a.2, with fewer glycans bound and a higher percentage of total binding attributable to the top three highest bound glycans. Together these data indicate that the A5a.2 clade had a reduction in viral fitness, including reductions in receptor binding, that may have contributed to the limited prevalence observed after emergence.
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Affiliation(s)
- Nicholas J Swanson
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, rm W2116, Baltimore, MD, 21205, USA
| | - Paula Marinho
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, rm W2116, Baltimore, MD, 21205, USA
| | - Amanda Dziedzic
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, rm W2116, Baltimore, MD, 21205, USA
| | - Anne Jedlicka
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, rm W2116, Baltimore, MD, 21205, USA
| | - Hsuan Liu
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, rm W2116, Baltimore, MD, 21205, USA
| | - Katherine Fenstermacher
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Richard Rothman
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, rm W2116, Baltimore, MD, 21205, USA.
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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19
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Yehia N, Rabie N, Adel A, Mossad Z, Nagshabandi MK, Alharbi MT, El-Saadony MT, El-Tarabily KA, Erfan A. Differential replication characteristic of reassortant avian influenza A viruses H5N8 clade 2.3.4.4b in Madin Darby Canine kidney cell. Poult Sci 2023. [DOI: 10.1016/j.psj.2023.102685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
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20
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Swanson NJ, Marinho P, Dziedzic A, Jedlicka A, Liu H, Fenstermacher K, Rothman R, Pekosz A. 2019-20 H1N1 clade A5a.1 viruses have better in vitro replication compared with the co-circulating A5a.2 clade. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.26.530085. [PMID: 36865250 PMCID: PMC9980287 DOI: 10.1101/2023.02.26.530085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Surveillance for emerging human influenza virus clades is important for identifying changes in viral fitness and assessing antigenic similarity to vaccine strains. While fitness and antigenic structure are both important aspects of virus success, they are distinct characteristics and do not always change in a complementary manner. The 2019-20 Northern Hemisphere influenza season saw the emergence of two H1N1 clades: A5a.1 and A5a.2. While several studies indicated that A5a.2 showed similar or even increased antigenic drift compared with A5a.1, the A5a.1 clade was still the predominant circulating clade that season. Clinical isolates of representative viruses from these clades were collected in Baltimore, Maryland during the 2019-20 season and multiple assays were performed to compare both antigenic drift and viral fitness between clades. Neutralization assays performed on serum from healthcare workers pre- and post-vaccination during the 2019-20 season show a comparable drop in neutralizing titers against both A5a.1 and A5a.2 viruses compared with the vaccine strain, indicating that A5a.1 did not have antigenic advantages over A5a.2 that would explain its predominance in this population. Plaque assays were performed to investigate fitness differences, and the A5a.2 virus produced significantly smaller plaques compared with viruses from A5a.1 or the parental A5a clade. To assess viral replication, low MOI growth curves were performed on both MDCK-SIAT and primary differentiated human nasal epithelial cell cultures. In both cell cultures, A5a.2 yielded significantly reduced viral titers at multiple timepoints post-infection compared with A5a.1 or A5a. Receptor binding was then investigated through glycan array experiments which showed a reduction in receptor binding diversity for A5a.2, with fewer glycans bound and a higher percentage of total binding attributable to the top three highest bound glycans. Together these data indicate that the A5a.2 clade had a reduction in viral fitness, including reductions in receptor binding, that may have contributed to the limited prevalence observed after emergence.
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Affiliation(s)
- Nicholas J Swanson
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Paula Marinho
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Amanda Dziedzic
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Anne Jedlicka
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Hsuan Liu
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Katherine Fenstermacher
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Richard Rothman
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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21
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Oh DY, Milde J, Ham Y, Ramos Calderón JP, Wedde M, Dürrwald R, Duwe SC. Preparing for the Next Influenza Season: Monitoring the Emergence and Spread of Antiviral Resistance. Infect Drug Resist 2023; 16:949-959. [PMID: 36814825 PMCID: PMC9939793 DOI: 10.2147/idr.s389263] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/16/2023] [Indexed: 02/17/2023] Open
Abstract
Purpose The relaxation of pandemic restrictions in 2022 has led to a reemergence of respiratory virus circulation worldwide and anticipation of substantial influenza waves for the 2022/2023 Northern Hemisphere winter. Therefore, the antiviral susceptibility profiles of human influenza viruses circulating in Germany were characterized. Methods Between October 2019 (week 40/2019) and March 2022 (week 12/2022), nasal swabs from untreated patients with acute respiratory symptoms were collected in the national German influenza surveillance system. A total of 598 influenza viruses were isolated and analyzed for susceptibility to oseltamivir, zanamivir and peramivir, using a neuraminidase (NA) inhibition assay. In addition, next-generation sequencing was applied to assess molecular markers of resistance to NA, cap-dependent endonuclease (PA) and M2 ion channel inhibitors (NAI, PAI, M2I) in 367 primary clinical samples. Furthermore, a genotyping assay based on RT-PCR and pyrosequencing to rapidly assess the molecular resistance marker PA-I38X in PA genes was designed and established. Results While NAI resistance in the strict sense, defined by a ≥ 10-fold (influenza A) or ≥5-fold (influenza B) increase of NAI IC50, was not detected, a subtype A(H1N1)pdm09 isolate displayed 2.3- to 7.5-fold IC50 increase for all three NAI. This isolate carried the NA-S247N substitution, which is known to enhance NAI resistance induced by NA-H275Y. All sequenced influenza A viruses carried the M2-S31N substitution, which confers resistance to M2I. Of note, one A(H3N2) virus displayed the PA-I38M substitution, which is associated with reduced susceptibility to the PAI baloxavir marboxil. Pyrosequencing analysis confirmed these findings in the original clinical specimen and in cultured virus isolate, suggesting sufficient replicative fitness of this virus mutant. Conclusion Over the last three influenza seasons, the vast majority of influenza viruses in this national-level sentinel were susceptible to NAIs and PAIs. These findings support the use of antivirals in the upcoming influenza season.
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Affiliation(s)
- Djin-Ye Oh
- Robert Koch Institute, Department 1: Infectious Diseases, Unit 17: Influenza and Other Respiratory Viruses, National Influenza Center, Berlin, Germany
| | - Jeanette Milde
- Robert Koch Institute, Department 1: Infectious Diseases, Unit 17: Influenza and Other Respiratory Viruses, National Influenza Center, Berlin, Germany
| | - Youngsun Ham
- Robert Koch Institute, Department 1: Infectious Diseases, Unit 17: Influenza and Other Respiratory Viruses, National Influenza Center, Berlin, Germany
| | - Julia Patricia Ramos Calderón
- Robert Koch Institute, Department 1: Infectious Diseases, Unit 17: Influenza and Other Respiratory Viruses, National Influenza Center, Berlin, Germany
| | - Marianne Wedde
- Robert Koch Institute, Department 1: Infectious Diseases, Unit 17: Influenza and Other Respiratory Viruses, National Influenza Center, Berlin, Germany
| | - Ralf Dürrwald
- Robert Koch Institute, Department 1: Infectious Diseases, Unit 17: Influenza and Other Respiratory Viruses, National Influenza Center, Berlin, Germany
| | - Susanne C Duwe
- Robert Koch Institute, Department 1: Infectious Diseases, Unit 17: Influenza and Other Respiratory Viruses, National Influenza Center, Berlin, Germany
- Correspondence: Susanne C Duwe, Robert Koch Institute, Department 1: Infectious Diseases, Unit 17: Influenza Viruses and Other Respiratory Viruses | National Influenza Center, Seestr. 10, Berlin, 13353, Germany, Tel +49 30 18754 2283, Fax +49 30 18754 2699, Email
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22
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High-throughput droplet-based analysis of influenza A virus genetic reassortment by single-virus RNA sequencing. Proc Natl Acad Sci U S A 2023; 120:e2211098120. [PMID: 36730204 PMCID: PMC9963642 DOI: 10.1073/pnas.2211098120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The segmented RNA genome of influenza A viruses (IAVs) enables viral evolution through genetic reassortment after multiple IAVs coinfect the same cell, leading to viruses harboring combinations of eight genomic segments from distinct parental viruses. Existing data indicate that reassortant genotypes are not equiprobable; however, the low throughput of available virology techniques does not allow quantitative analysis. Here, we have developed a high-throughput single-cell droplet microfluidic system allowing encapsulation of IAV-infected cells, each cell being infected by a single progeny virion resulting from a coinfection process. Customized barcoded primers for targeted viral RNA sequencing enabled the analysis of 18,422 viral genotypes resulting from coinfection with two circulating human H1N1pdm09 and H3N2 IAVs. Results were highly reproducible, confirmed that genetic reassortment is far from random, and allowed accurate quantification of reassortants including rare events. In total, 159 out of the 254 possible reassortant genotypes were observed but with widely varied prevalence (from 0.038 to 8.45%). In cells where eight segments were detected, all 112 possible pairwise combinations of segments were observed. The inclusion of data from single cells where less than eight segments were detected allowed analysis of pairwise cosegregation between segments with very high confidence. Direct coupling analysis accurately predicted the fraction of pairwise segments and full genotypes. Overall, our results indicate that a large proportion of reassortant genotypes can emerge upon coinfection and be detected over a wide range of frequencies, highlighting the power of our tool for systematic and exhaustive monitoring of the reassortment potential of IAVs.
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23
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Scheibner D, Salaheldin AH, Bagato O, Zaeck LM, Mostafa A, Blohm U, Müller C, Eweas AF, Franzke K, Karger A, Schäfer A, Gischke M, Hoffmann D, Lerolle S, Li X, Abd El-Hamid HS, Veits J, Breithaupt A, Boons GJ, Matrosovich M, Finke S, Pleschka S, Mettenleiter TC, de Vries RP, Abdelwhab EM. Phenotypic effects of mutations observed in the neuraminidase of human origin H5N1 influenza A viruses. PLoS Pathog 2023; 19:e1011135. [PMID: 36745654 PMCID: PMC9934401 DOI: 10.1371/journal.ppat.1011135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/16/2023] [Accepted: 01/18/2023] [Indexed: 02/07/2023] Open
Abstract
Global spread and regional endemicity of H5Nx Goose/Guangdong avian influenza viruses (AIV) pose a continuous threat for poultry production and zoonotic, potentially pre-pandemic, transmission to humans. Little is known about the role of mutations in the viral neuraminidase (NA) that accompanied bird-to-human transmission to support AIV infection of mammals. Here, after detailed analysis of the NA sequence of human H5N1 viruses, we studied the role of A46D, L204M, S319F and S430G mutations in virus fitness in vitro and in vivo. Although H5N1 AIV carrying avian- or human-like NAs had similar replication efficiency in avian cells, human-like NA enhanced virus replication in human airway epithelia. The L204M substitution consistently reduced NA activity of H5N1 and nine other influenza viruses carrying NA of groups 1 and 2, indicating a universal effect. Compared to the avian ancestor, human-like H5N1 virus has less NA incorporated in the virion, reduced levels of viral NA RNA replication and NA expression. We also demonstrate increased accumulation of NA at the plasma membrane, reduced virus release and enhanced cell-to-cell spread. Furthermore, NA mutations increased virus binding to human-type receptors. While not affecting high virulence of H5N1 in chickens, the studied NA mutations modulated virulence and replication of H5N1 AIV in mice and to a lesser extent in ferrets. Together, mutations in the NA of human H5N1 viruses play different roles in infection of mammals without affecting virulence or transmission in chickens. These results are important to understand the genetic determinants for replication of AIV in mammals and should assist in the prediction of AIV with zoonotic potential.
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Affiliation(s)
- David Scheibner
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Ahmed H. Salaheldin
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Alexandria University, El-Beheira, Egypt
| | - Ola Bagato
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Water Pollution Research Department, Dokki, Giza, Egypt
| | - Luca M. Zaeck
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Water Pollution Research Department, Dokki, Giza, Egypt
| | - Ulrike Blohm
- Institute of Immunology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Christin Müller
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - Ahmed F. Eweas
- Department of Medicinal Chemistry, National Research Center, Dokki, Giza, Egypt; Department of Science, University of Technology and Applied Sciences-Rustaq, Rustaq, Sultanate of Oman
| | - Kati Franzke
- Institute of Infectology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Axel Karger
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Alexander Schäfer
- Institute of Immunology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Marcel Gischke
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Donata Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Solène Lerolle
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Xuguang Li
- Centre for Biologics Evaluation, Biologics and Genetic Therapies Directorate, HPFB, Health Canada, Ottawa, ON, Canada; Department of Biochemistry, Microbiology and Immunology and Emerging Pathogens Research Centre, University of Ottawa, Ottawa, Ontario, Canada
| | - Hatem S. Abd El-Hamid
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Damanhur University, Al-Buheira, Egypt
| | - Jutta Veits
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Angele Breithaupt
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Geert-Jan Boons
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Science, the Netherlands
| | | | - Stefan Finke
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Stephan Pleschka
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF) partner site Giessen-Marburg-Langen, Germany
| | - Thomas C. Mettenleiter
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Robert P. de Vries
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Science, the Netherlands
| | - Elsayed M. Abdelwhab
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
- * E-mail:
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Korsun N, Trifonova I, Dobrinov V, Madzharova I, Grigorova I, Christova I. Low prevalence of influenza viruses and predominance of A(H3N2) virus with respect to SARS-CoV-2 during the 2021-2022 season in Bulgaria. J Med Virol 2023; 95:e28489. [PMID: 36832544 PMCID: PMC10107854 DOI: 10.1002/jmv.28489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 01/24/2023]
Abstract
Social distancing, mask-wearing, and travel restrictions during the COVID-19 pandemic have significantly impacted the spread of influenza viruses. The objectives of this study were to analyze the pattern of influenza virus circulation with respect to that of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Bulgaria during the 2021-2022 season and to perform a phylogenetic/molecular analysis of the hemagglutinin (HA) and neuraminidase (NA) sequences of representative influenza strains. Influenza infection was confirmed using real-time reverse transcription polymerase chain reaction in 93 (4.2%) of the 2193 patients with acute respiratory illness tested wherein all detected viruses were subtyped as A(H3N2). SARS-CoV-2 was identified in 377 (24.3%) of the 1552 patients tested. Significant differences in the incidence of influenza viruses and SARS-CoV-2 were found between individual age groups, outpatients/inpatients, and in the seasonal distribution of cases. Two cases of coinfections were identified. In hospitalized patients, the Ct values of influenza viruses at admission were lower in adults aged ≥65 years (indicating higher viral load) than in children aged 0-14 years (p < 0.05). In SARS-CoV-2-positive inpatients, this association was not statistically significant. HA genes of all A(H3N2) viruses analyzed belonged to subclade 3C.2a1b.2a. The sequenced viruses carried 11 substitutions in HA and 5 in NA, in comparison to the vaccine virus A/Cambodia/e0826360/2020, including several substitutions in the HA antigenic sites B and C. This study revealed extensive changes in the typical epidemiology of influenza infection, including a dramatic reduction in the number of cases, diminished genetic diversity of circulating viruses, changes in age, and seasonal distribution of cases.
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Affiliation(s)
- Neli Korsun
- National Laboratory "Influenza and ARI", Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivelina Trifonova
- National Laboratory "Influenza and ARI", Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Veselin Dobrinov
- National Laboratory "Influenza and ARI", Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Iveta Madzharova
- National Laboratory "Influenza and ARI", Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Iliyana Grigorova
- National Laboratory "Influenza and ARI", Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Iva Christova
- National Laboratory "Influenza and ARI", Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
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25
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Antigenic Characterization of Human Monoclonal Antibodies for Therapeutic Use against H7N9 Avian Influenza Virus. J Virol 2023; 97:e0143122. [PMID: 36541801 PMCID: PMC9888198 DOI: 10.1128/jvi.01431-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Since 2013, H7N9 avian influenza viruses (AIVs) have caused more than 1,500 human infections and the culling of millions of poultry. Despite large-scale poultry vaccination, H7N9 AIVs continue to circulate among poultry in China and pose a threat to human health. Previously, we isolated and generated four monoclonal antibodies (mAbs) derived from humans naturally infected with H7N9 AIV. Here, we investigated the hemagglutinin (HA) epitopes of H7N9 AIV targeted by these mAbs (L3A-44, K9B-122, L4A-14, and L4B-18) using immune escape studies. Our results revealed four key antigenic epitopes at HA amino acid positions 125, 133, 149, and 217. The mutant H7N9 viruses representing escape mutations containing an alanine-to-threonine substitution at residue 125 (A125T), a glycine-to-glutamic acid substitution at residue 133 (G133E), an asparagine-to-aspartic acid substitution at residue 149 (N149D), or a leucine-to-glutamine substitution at residue 217 (L217Q) showed reduced or completely abolished cross-reactivity with the mAbs, as measured by a hemagglutination inhibition (HI) assay. We further assessed the potential risk of these mutants to humans should they emerge following mAb treatment by measuring the impact of these HA mutations on virus fitness and evasion of host adaptive immunity. Here, we showed that the L4A-14 mAb had broad neutralizing capabilities, and its escape mutant N149D had reduced viral stability and human receptor binding and could be neutralized by both postinfection and antigen-induced sera. Therefore, the L4A-14 mAb could be a therapeutic candidate for H7N9 AIV infection in humans and warrants further investigation for therapeutic applications. IMPORTANCE Avian influenza virus (AIV) H7N9 continues to circulate and evolve in birds, posing a credible threat to humans. Antiviral drugs have proven useful for the treatment of severe influenza infections in humans; however, concerns have been raised as antiviral-resistant mutants have emerged. Monoclonal antibodies (mAbs) have been studied for both prophylactic and therapeutic applications in infectious disease control and have demonstrated great potential. For example, mAb treatment has significantly reduced the risk of people developing severe disease with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. In addition to the protection efficiency, we should also consider the potential risk of the escape mutants generated by mAb treatment to public health by assessing their viral fitness and potential to compromise host adaptive immunity. Considering these parameters, we assessed four human mAbs derived from humans naturally infected with H7N9 AIV and showed that the mAb L4A-14 displayed potential as a therapeutic candidate.
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26
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Patel MC, Flanigan D, Feng C, Chesnokov A, Nguyen HT, Elal AA, Steel J, Kondor RJ, Wentworth DE, Gubareva LV, Mishin VP. An optimized cell-based assay to assess influenza virus replication by measuring neuraminidase activity and its applications for virological surveillance. Antiviral Res 2022; 208:105457. [PMID: 36332755 PMCID: PMC10149149 DOI: 10.1016/j.antiviral.2022.105457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/12/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
Abstract
Year-round virological characterization of circulating epidemic influenza viruses is conducted worldwide to detect the emergence of viruses that may escape pre-existing immunity or acquire resistance to antivirals. High throughput phenotypic assays are needed to complement the sequence-based analysis of circulating viruses and improve pandemic preparedness. The recent entry of a polymerase inhibitor, baloxavir, into the global market further highlighted this need. Here, we optimized a cell-based assay that considerably streamlines antiviral and antigenic testing by replacing lengthy immunostaining and imaging procedures used in current assay with measuring the enzymatic activity of nascent neuraminidase (NA) molecules expressed on the surface of virus-infected cells. For convenience, this new assay was named IRINA (Influenza Replication Inhibition Neuraminidase-based Assay). IRINA was successfully validated to assess inhibitory activity of baloxavir on virus replication by testing a large set (>150) of influenza A and B viruses, including drug resistant strains and viruses collected during 2017-2022. To test its versatility, IRINA was utilized to evaluate neutralization activity of a broadly reactive human anti-HA monoclonal antibody, FI6, and post-infection ferret antisera, as well as the inhibition of NA enzyme activity by NA inhibitors. Performance of IRINA was tested in parallel using respective conventional assays. IRINA offers an attractive alternative to current phenotypic assays, while maintaining reproducibility and high throughput capacity. Additionally, the improved turnaround time may prove to be advantageous when conducting time sensitive studies, such as investigating a new virus outbreak. This assay can meet the needs of surveillance laboratories by providing a streamlined and cost-effective approach for virus characterization.
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Affiliation(s)
- Mira C Patel
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Daniel Flanigan
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA; General Dynamics Information Technology, Atlanta, GA, USA
| | - Chenchen Feng
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA; Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Anton Chesnokov
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ha T Nguyen
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Anwar Abd Elal
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA; Cherokee Nation Integrated Health, L.L.C., Atlanta, GA, USA
| | - John Steel
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Rebecca J Kondor
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - David E Wentworth
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Larisa V Gubareva
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Vasiliy P Mishin
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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27
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Schorderet Weber S, Bulliard X, Bonfante R, Xiang Y, Biselli S, Steiner S, Constant S, Pugin R, Laurent A, Majeed S, Lebrun S, Palmieri M, Hogg A, Kuczaj A, Peitsch MC, Hoeng J, Stan A. In vitro testing of salt coating of fabrics as a potential antiviral agent in reusable face masks. Sci Rep 2022; 12:17041. [PMID: 36220878 PMCID: PMC9552714 DOI: 10.1038/s41598-022-21442-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 09/27/2022] [Indexed: 12/29/2022] Open
Abstract
During the coronavirus disease (COVID-19) pandemic, wearing face masks in public spaces became mandatory in most countries. The risk of self-contamination when handling face masks, which was one of the earliest concerns, can be mitigated by adding antiviral coatings to the masks. In the present study, we evaluated the antiviral effectiveness of sodium chloride deposited on a fabric suitable for the manufacturing of reusable cloth masks using techniques adapted to the home environment. We tested eight coating conditions, involving both spraying and dipping methods and three salt dilutions. Influenza A H3N2 virus particles were incubated directly on the salt-coated materials, collected, and added to human 3D airway epithelial cultures. Live virus replication in the epithelia was quantified over time in collected apical washes. Relative to the non-coated material, salt deposits at or above 4.3 mg/cm2 markedly reduced viral replication. However, even for larger quantities of salt, the effectiveness of the coating remained dependent on the crystal size and distribution, which in turn depended on the coating technique. These findings confirm the suitability of salt coating as antiviral protection on cloth masks, but also emphasize that particular attention should be paid to the coating protocol when developing consumer solutions.
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Affiliation(s)
| | - Xavier Bulliard
- Centre Suisse d'Electronique et de Microtechnique SA (CSEM), Rue Jaquet-Droz 1, 2002, Neuchâtel, Switzerland
| | - Rosy Bonfante
- Epithelix Sàrl, Chemin des Aulx 18, 1228, Plan-les-Ouates, Geneva, Switzerland
| | - Yang Xiang
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Silvia Biselli
- Centre Suisse d'Electronique et de Microtechnique SA (CSEM), Rue Jaquet-Droz 1, 2002, Neuchâtel, Switzerland
| | - Sandro Steiner
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Samuel Constant
- Epithelix Sàrl, Chemin des Aulx 18, 1228, Plan-les-Ouates, Geneva, Switzerland
| | - Raphael Pugin
- Centre Suisse d'Electronique et de Microtechnique SA (CSEM), Rue Jaquet-Droz 1, 2002, Neuchâtel, Switzerland
| | - Alexandra Laurent
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Shoaib Majeed
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Stefan Lebrun
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Michele Palmieri
- Centre Suisse d'Electronique et de Microtechnique SA (CSEM), Rue Jaquet-Droz 1, 2002, Neuchâtel, Switzerland
| | - Andreas Hogg
- Coat-X SA, Eplatures-Grise 17, 2300, La Chaux-de-Fonds, Switzerland
| | - Arkadiusz Kuczaj
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Manuel C Peitsch
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Adrian Stan
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
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28
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Sominina A, Danilenko D, Komissarov A, Karpova L, Pisareva M, Fadeev A, Konovalova N, Eropkin M, Stolyarov K, Shtro A, Burtseva E, Lioznov D. Resurgence of Influenza Circulation in the Russian Federation during the Delta and Omicron COVID-19 Era. Viruses 2022; 14:1909. [PMID: 36146716 PMCID: PMC9506591 DOI: 10.3390/v14091909] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/25/2022] Open
Abstract
Influenza circulation was substantially reduced after March 2020 in the European region and globally due to the wide introduction of non-pharmaceutical interventions (NPIs) against COVID-19. The virus, however, has been actively circulating in natural reservoirs. In summer 2021, NPIs were loosened in Russia, and influenza activity resumed shortly thereafter. Here, we summarize the epidemiological and virological data on the influenza epidemic in Russia in 2021-2022 obtained by the two National Influenza Centers. We demonstrate that the commonly used baseline for acute respiratory infection (ARI) is no longer sufficiently sensitive and BL for ILI incidence was more specific for early recognition of the epidemic. We also present the results of PCR detection of influenza, SARS-CoV-2 and other respiratory viruses as well as antigenic and genetic analysis of influenza viruses. Influenza A(H3N2) prevailed this season with influenza B being detected at low levels at the end of the epidemic. The majority of A(H3N2) viruses were antigenically and genetically homogenous and belonged to the clade 3C.2a1b.2a.2 of the vaccine strain A/Darwin/9/2021 for the season 2022-2023. All influenza B viruses belonged to the Victoria lineage and were similar to the influenza B/Austria/1359417/2021 virus. No influenza A(H1N1)pdm09 and influenza B/Yamagata lineage was isolated last season.
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Affiliation(s)
- Anna Sominina
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia
| | - Daria Danilenko
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia
| | - Andrey Komissarov
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia
| | - Ludmila Karpova
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia
| | - Maria Pisareva
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia
| | - Artem Fadeev
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia
| | - Nadezhda Konovalova
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia
| | - Mikhail Eropkin
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia
| | - Kirill Stolyarov
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia
| | - Anna Shtro
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia
| | - Elena Burtseva
- National Research Center for Epidemiology and Microbiology Named after N.F. Gamaleya, 123098 Moscow, Russia
| | - Dmitry Lioznov
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia
- Department of Infectious Diseases and Epidemiology, First Pavlov State Medical University, 197022 Saint Petersburg, Russia
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29
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Byrd-Leotis L, Jia N, Matsumoto Y, Lu D, Kawaoka Y, Steinhauer DA, Cummings RD. Sialylated and sulfated N-Glycans in MDCK and engineered MDCK cells for influenza virus studies. Sci Rep 2022; 12:12757. [PMID: 35882911 PMCID: PMC9325728 DOI: 10.1038/s41598-022-16605-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/12/2022] [Indexed: 11/08/2022] Open
Abstract
The Madin-Darby canine kidney (MDCK) cell line is an in vitro model for influenza A virus (IAV) infection and propagation. MDCK-SIAT1 (SIAT1) and humanized MDCK (hCK) cell lines are engineered MDCK cells that express N-glycans with elevated levels of sialic acid (Sia) in α2,6-linkage (α2,6-Sia) that are recognized by many human IAVs. To characterize the N-glycan structures in these cells and the potential changes compared to the parental MDCK cell line resulting from engineering, we analyzed the N-glycans from these cells at different passages, using both mass spectrometry and specific lectin and antibody binding. We observed significant differences between the three cell lines in overall complex N-glycans and terminal galactose modifications. MDCK cells express core fucosylated, bisected complex-type N-glycans at all passage stages, in addition to expressing α2,6-Sia on short N-glycans and α2,3-Sia on larger N-glycans. By contrast, SIAT1 cells predominantly express α2,6-Sia glycans and greatly reduced level of α2,3-Sia glycans. Additionally, they express bisected, sialylated N-glycans that are scant in MDCK cells. The hCK cells exclusively express α2,6-Sia glycans. Unexpectedly, hCK glycoproteins bound robustly to the plant lectin MAL-1, indicating α2,3-Sia glycans, but such binding was not Sia-dependent and closely mirrored that of an antibody that recognizes glycans with terminal 3-O-sulfate galactose (3-O-SGal). The 3-O-SGal epitope is highly expressed in N-glycans on multiple hCK glycoproteins. These results indicate vastly different N-glycomes between MDCK cells and the engineered clones that could relate to IAV infectivity.
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Affiliation(s)
- Lauren Byrd-Leotis
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Surgery and Harvard Medical School Center for Glycoscience, Beth Israel Deaconess Medical Center, Harvard Medical School, CLS 11087 - 3 Blackfan Circle, Boston, MA, 02115, USA
- Centers for Excellence in Influenza Research and Surveillance, Emory-UGA CEIRS, Atlanta, GA, USA
| | - Nan Jia
- Department of Surgery and Harvard Medical School Center for Glycoscience, Beth Israel Deaconess Medical Center, Harvard Medical School, CLS 11087 - 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Yasuyuki Matsumoto
- Department of Surgery and Harvard Medical School Center for Glycoscience, Beth Israel Deaconess Medical Center, Harvard Medical School, CLS 11087 - 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Dongli Lu
- Department of Surgery and Harvard Medical School Center for Glycoscience, Beth Israel Deaconess Medical Center, Harvard Medical School, CLS 11087 - 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - David A Steinhauer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Centers for Excellence in Influenza Research and Surveillance, Emory-UGA CEIRS, Atlanta, GA, USA
| | - Richard D Cummings
- Department of Surgery and Harvard Medical School Center for Glycoscience, Beth Israel Deaconess Medical Center, Harvard Medical School, CLS 11087 - 3 Blackfan Circle, Boston, MA, 02115, USA.
- Centers for Excellence in Influenza Research and Surveillance, Emory-UGA CEIRS, Atlanta, GA, USA.
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30
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Praena B, Wan XF. Influenza Virus Infections in Polarized Cells. Viruses 2022; 14:1307. [PMID: 35746778 PMCID: PMC9231244 DOI: 10.3390/v14061307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/09/2022] [Accepted: 06/11/2022] [Indexed: 02/05/2023] Open
Abstract
In humans and other mammals, the respiratory tract is represented by a complex network of polarized epithelial cells, forming an apical surface facing the external environment and a basal surface attached to the basement layer. These cells are characterized by differential expression of proteins and glycans, which serve as receptors during influenza virus infection. Attachment between these host receptors and the viral surface glycoprotein hemagglutinin (HA) initiates the influenza virus life cycle. However, the virus receptor binding specificities may not be static. Sialylated N-glycans are the most well-characterized receptors but are not essential for the entry of influenza viruses, and other molecules, such as O-glycans and non-sialylated glycans, may be involved in virus-cell attachment. Furthermore, correct cell polarity and directional trafficking of molecules are essential for the orderly development of the system and affect successful influenza infection; on the other hand, influenza infection can also change cell polarity. Here we review recent advances in our understanding of influenza virus infection in the respiratory tract of humans and other mammals, particularly the attachment between the virus and the surface of the polar cells and the polarity variation of these cells due to virus infection.
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Affiliation(s)
- Beatriz Praena
- MU Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO 65211, USA;
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, 1201 Rollins St., Columbia, MO 65211, USA
- Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, MO 65211, USA
| | - Xiu-Feng Wan
- MU Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO 65211, USA;
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, 1201 Rollins St., Columbia, MO 65211, USA
- Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, MO 65211, USA
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, 1201 Rollins St., Columbia, MO 65211, USA
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31
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Ashtiwi NM, Sarr D, Nagy T, Reneer ZB, Tripp RA, Rada B. The Hypothiocyanite and Amantadine Combination Treatment Prevents Lethal Influenza A Virus Infection in Mice. Front Immunol 2022; 13:859033. [PMID: 35663985 PMCID: PMC9159274 DOI: 10.3389/fimmu.2022.859033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/12/2022] [Indexed: 11/21/2022] Open
Abstract
The influenza virus has a large clinical burden and is associated with significant mortality and morbidity. The development of effective drugs for the treatment or prevention of influenza is important in order to reduce its impact. Adamantanes and neuraminidase inhibitors are two classes of anti-influenza drugs in which resistance has developed; thus, there is an urgent need to explore new therapeutic options. Boosting antiviral innate immune mechanisms in the airways represents an attractive approach. Hypothiocyanite (OSCN-) is produced by the airway epithelium and is effective in reducing the replication of several influenza A virus strains in vitro. It remains, however, largely unexplored whether OSCN- has such an antiviral effect in vivo. Here we determined the therapeutic potential of OSCN-, alone or in combination with amantadine (AMT), in preventing lethal influenza A virus replication in mice and in vitro. Mice intranasally infected with a lethal dose of A/Puerto Rico/8/1934 (H1N1) or A/Hong Kong/8/1968 (H3N2) were cured by the combination treatment of OSCN- and AMT. Monotherapy with OSCN- or AMT alone did not substantially improve survival outcomes. However, AMT+OSCN- treatment significantly inhibited viral replication, and in vitro treatment inhibited viral entry and nuclear transport of different influenza A virus strains (H1N1 and H3N2) including the AMT-resistant strain A/WSN/33 (H1N1). A triple combination treatment consisting of AMT, oseltamivir, and OSCN- was also tested and further inhibited in vitro viral replication of the AMT-resistant A/WSN/33 strain. These results suggest that OSCN- is a promising anti-influenza treatment option when combined with other antiviral drugs.
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Affiliation(s)
- Nuha Milad Ashtiwi
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Demba Sarr
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Tamás Nagy
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Z. Beau Reneer
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Ralph A. Tripp
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Balázs Rada
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
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Pujić I, Perreault H. Recent advancements in glycoproteomic studies: Glycopeptide enrichment and derivatization, characterization of glycosylation in SARS CoV2, and interacting glycoproteins. MASS SPECTROMETRY REVIEWS 2022; 41:488-507. [PMID: 33393161 DOI: 10.1002/mas.21679] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/13/2020] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
Abstract
Proteomics studies allow for the determination of the identity, amount, and interactions of proteins under specific conditions that allow the biological state of an organism to ultimately change. These conditions can be either beneficial or detrimental. Diseases are due to detrimental changes caused by either protein overexpression or underexpression caused by as a result of a mutation or posttranslational modifications (PTM), among other factors. Identification of disease biomarkers through proteomics can be potentially used as clinical information for diagnostics. Common biomarkers to look for include PTM. For example, aberrant glycosylation of proteins is a common marker and will be a focus of interest in this review. A common way to analyze glycoproteins is by glycoproteomics involving mass spectrometry. Due to factors such as micro- and macroheterogeneity which result in a lower abundance of each version of a glycoprotein, it is difficult to obtain meaningful results unless rigorous sample preparation procedures are in place. Microheterogeneity represents the diversity of glycans at a single site, whereas macroheterogeneity depicts glycosylation levels at each site of a protein. Enrichment and derivatization of glycopeptides help to overcome these limitations. Over the time range of 2016 to 2020, several methods have been proposed in the literature and have contributed to drastically improve the outcome of glycosylation analysis, as presented in the sampling surveyed in this review. As a current topic in 2020, glycoproteins carried by pathogens can also cause disease and this is seen with SARS CoV2, causing the COVID-19 pandemic. This review will discuss glycoproteomic studies of the spike glycoprotein and interacting proteins such as the ACE2 receptor.
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Affiliation(s)
- Ivona Pujić
- Chemistry Department, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Hélène Perreault
- Chemistry Department, University of Manitoba, Winnipeg, Manitoba, Canada
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Hickerson BT, Adams SE, Barman S, Miller L, Lugovtsev VY, Webby RJ, Ince WL, Donnelly RP, Ilyushina NA. Pleiotropic Effects of Influenza H1, H3, and B Baloxavir-Resistant Substitutions on Replication, Sensitivity to Baloxavir, and Interferon Expression. Antimicrob Agents Chemother 2022; 66:e0000922. [PMID: 35262375 PMCID: PMC9017380 DOI: 10.1128/aac.00009-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/04/2022] [Indexed: 11/20/2022] Open
Abstract
Baloxavir is an anti-influenza endonuclease inhibitor that targets the polymerase acidic (PA) protein of influenza A and B viruses. Our knowledge regarding the pleiotropic effects of baloxavir resistance-associated substitutions is limited. We generated recombinant A/California/04/09 (H1N1)-, A/Hong Kong/218849/2006 (H3N2)-, and B/Victoria/504/2000-like viruses that contained PA substitutions identified in baloxavir clinical trials and surveillance that could potentially be associated with baloxavir resistance. We characterized their susceptibility to baloxavir, impact on polymerase activity, viral growth, and ability to induce interferon (IFN) and IFN-stimulated genes expression in vitro. Four PA substitutions, H1N1 I38L/T, E199D, and B G199R, significantly reduced the sensitivity of the recombinant viruses to baloxavir (14.1-fold). We confirmed our findings by using the luciferase-based ribonucleoprotein minigenome assay and by using virus yield reduction assay in Calu-3 and normal human bronchial epithelial (NHBE) cells. We observed that I38L and E199D resulted in decreased viral replication of the H1N1 wild-type virus (1.4-fold) but the H1N1 I38T and B G199R substitutions did not significantly alter replication capacity in Calu-3 cells. In addition, H1N1 variants with PA I38L/T and E199D induced significantly higher levels of IFNB1 gene expression compared to the wild-type virus (4.2-fold). In contrast, the B variant, G199R, triggered the lowest levels of IFN genes in Calu-3 cells (1.6-fold). Because baloxavir is a novel anti-influenza therapeutic agent, identifying and characterizing substitutions associated with reduced sensitivity to baloxavir, as well as the impact of these substitutions on viral fitness, is paramount to the strategic implementation of this novel countermeasure.
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Affiliation(s)
- Brady T. Hickerson
- Division of Biotechnology Review and Research II, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Simone E. Adams
- Division of Biotechnology Review and Research II, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Subrata Barman
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Lance Miller
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Vladimir Y. Lugovtsev
- Division of Viral Products, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Richard J. Webby
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - William L. Ince
- Division of Antiviral Products, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Raymond P. Donnelly
- Division of Biotechnology Review and Research II, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Natalia A. Ilyushina
- Division of Biotechnology Review and Research II, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
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Wang Y, Tang CY, Wan XF. Antigenic characterization of influenza and SARS-CoV-2 viruses. Anal Bioanal Chem 2022; 414:2841-2881. [PMID: 34905077 PMCID: PMC8669429 DOI: 10.1007/s00216-021-03806-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/21/2021] [Accepted: 11/24/2021] [Indexed: 12/24/2022]
Abstract
Antigenic characterization of emerging and re-emerging viruses is necessary for the prevention of and response to outbreaks, evaluation of infection mechanisms, understanding of virus evolution, and selection of strains for vaccine development. Primary analytic methods, including enzyme-linked immunosorbent/lectin assays, hemagglutination inhibition, neuraminidase inhibition, micro-neutralization assays, and antigenic cartography, have been widely used in the field of influenza research. These techniques have been improved upon over time for increased analytical capacity, and some have been mobilized for the rapid characterization of the SARS-CoV-2 virus as well as its variants, facilitating the development of highly effective vaccines within 1 year of the initially reported outbreak. While great strides have been made for evaluating the antigenic properties of these viruses, multiple challenges prevent efficient vaccine strain selection and accurate assessment. For influenza, these barriers include the requirement for a large virus quantity to perform the assays, more than what can typically be provided by the clinical samples alone, cell- or egg-adapted mutations that can cause antigenic mismatch between the vaccine strain and circulating viruses, and up to a 6-month duration of vaccine development after vaccine strain selection, which allows viruses to continue evolving with potential for antigenic drift and, thus, antigenic mismatch between the vaccine strain and the emerging epidemic strain. SARS-CoV-2 characterization has faced similar challenges with the additional barrier of the need for facilities with high biosafety levels due to its infectious nature. In this study, we review the primary analytic methods used for antigenic characterization of influenza and SARS-CoV-2 and discuss the barriers of these methods and current developments for addressing these challenges.
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Affiliation(s)
- Yang Wang
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Cynthia Y Tang
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Xiu-Feng Wan
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA.
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA.
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA.
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CRISPR-Cas9 mediated knockout of AnxA6 gene enhances influenza A virus replication in low-permissive HEK293FT cell line. Gene 2022; 809:146024. [PMID: 34673207 DOI: 10.1016/j.gene.2021.146024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 07/26/2021] [Accepted: 10/14/2021] [Indexed: 11/21/2022]
Abstract
Using cell cultures of human origin for the propagation of influenza virus is an attractive way to preserve its glycosylation profile and antigenic properties, which is essential in influenza surveillance and vaccine production. However, only few cell lines are highly permissive to influenza virus, and none of them are of human origin. The barrier might be associated with host restriction factors inhibiting influenza growth, such as AnxA6 protein counteracting the process of influenza virion packaging. In the presented work we explore the CRISPR-Cas9 mediated knockout of ANXA6 gene as a way to overcome the host restriction barrier and increase the susceptibility of human cell line to influenza infection. By CRISPR-Cas9 genome editing we modified HEK293FT cells and obtained several clones defective in the ANXA6 gene. The replication of the influenza A virus in original HEK293FT cells and the HEK293FT-ANXA6-/- mutant cells was compared in growth curve experiments. By combination of methods including TCID assay and flow cytometry we showed that accumulation of influenza A virus in the mutant HEK293FT-ANXA6-/- cells significantly exceeded the virus titer in the original HEK293FT cells.
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Abstract
The neuraminidase (NA) of influenza A and B viruses plays a distinct role in viral replication and has a highly conserved catalytic site. Numerous sialic (neuraminic) acid analogs that competitively bind to the NA active site and potently inhibit enzyme activity have been synthesized and tested. Four NA inhibitors are now licensed in various parts of the world (zanamivir, oseltamivir, peramivir, and laninamivir) to treat influenza A and B infections. NA changes, naturally occurring or acquired under selective pressure, have been shown to reduce drug binding, thereby affecting the effectiveness of NA inhibitors. Drug resistance and other drawbacks have prompted the search for the next-generation NA-targeting therapeutics. One of the promising approaches is the identification of monoclonal antibodies (mAbs) targeting the conserved NA epitopes. Anti-NA mAbs demonstrate Fab-based antiviral activity supplemented with Fc-mediated immune effector functions. Antiviral Fc-conjugates offer another cutting-edge strategy that is based on a multimodal mechanism of action. These novel antiviral agents are composed of a small-molecule NA inhibitor and an Fc-region that simultaneously engages the immune system. The significant advancements made in recent years further support the value of NA as an attractive target for the antiviral development.
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Affiliation(s)
- Larisa Gubareva
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30329-4027, USA
| | - Teena Mohan
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30329-4027, USA
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Matrosovich MN, Gambaryan AS. Characterization of Influenza Virus Binding to Receptors on Isolated Cell Membranes. Methods Mol Biol 2022; 2556:149-168. [PMID: 36175633 DOI: 10.1007/978-1-0716-2635-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
An interplay between receptor-binding properties of influenza viruses (IVs) and spectrum of sialic acid-containing receptors on target cells in birds and mammals determine viral host range, tissue tropism, and pathogenicity. Here, we describe method that allows to characterize binding of IVs to biologically relevant cellular receptors using a conventional solid-phase enzyme-linked assay. In this method, we isolate plasma membranes from respiratory and intestinal epithelial cells of animal origin (Subheading 3.2). We adsorb the membranes in the wells of 96-well ELISA plates, incubate the membrane-coated wells with serially diluted IVs, and determine amounts of IVs attached to the membranes using viral ability to bind peroxidase-labeled sialoglycoprotein fetuin. Based on the concentration dependence of IV binding to the membrane, we estimate binding avidity and number of binding sites. We describe two variants of the assay in Subheadings 3.6 and 3.7 and provide examples.
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Affiliation(s)
| | - Alexandra S Gambaryan
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences, Moscow, Russia
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38
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Imai M, Takada K, Kawaoka Y. Receptor-Binding Specificity of Influenza Viruses. Methods Mol Biol 2022; 2556:79-96. [PMID: 36175629 DOI: 10.1007/978-1-0716-2635-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Influenza A virus infection begins with the attachment of virus particles to sialic acid-containing receptors on the surface of host cells. This attachment is mediated by the viral surface glycoprotein hemagglutinin (HA). Influenza A viruses have a wide host range, meaning they are able to infect many mammal and bird species. Influenza pandemics have been caused by viruses that contain genes from avian influenza viruses. Therefore, the infection of humans with avian influenza viruses, including avian H5Nx and H7Nx viruses, poses a huge threat to public health. These avian influenza viruses can transmit directly to humans from infected poultry, but do not spread easily among people, in part, due to differences in the receptor-binding specificities of human and avian influenza viruses. Therefore, conversion from avian- to human-type receptor-binding specificity is widely believed to be necessary for the efficient transmission of avian influenza viruses among humans. Accordingly, constant monitoring of the receptor-binding specificity of avian influenza viruses is important. In this chapter, we describe the protocol for assessing the receptor-binding specificity of influenza A viruses.
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Affiliation(s)
- Masaki Imai
- 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
| | - Kosuke Takada
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Yoshihiro Kawaoka
- 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.
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.
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Peck H, Laurie KL, Rockman S, Leung V, Lau H, Soppe S, Rynehart C, Baas C, Trusheim H, Barr IG. Enhanced isolation of influenza viruses in qualified cells improves the probability of well-matched vaccines. NPJ Vaccines 2021; 6:149. [PMID: 34887440 PMCID: PMC8660794 DOI: 10.1038/s41541-021-00415-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 11/12/2021] [Indexed: 01/04/2023] Open
Abstract
Influenza vaccines are utilised to combat seasonal and pandemic influenza. The key to influenza vaccination currently is the availability of candidate vaccine viruses (CVVs). Ideally, CVVs reflect the antigenic characteristics of the circulating virus, which may vary depending upon the isolation method. For traditional inactivated egg-based vaccines, CVVs are isolated in embryonated chicken eggs, while for cell-culture production, CVV's are isolated in either embryonated eggs or qualified cell lines. We compared isolation rates, growth characteristics, genetic stability and antigenicity of cell and egg CVV's derived from the same influenza-positive human clinical respiratory samples collected from 2008-2020. Influenza virus isolation rates in MDCK33016PF cells were twice that of eggs and mutations in the HA protein were common in egg CVVs but rare in cell CVVs. These results indicate that fully cell-based influenza vaccines will improve the choice, match and potentially the effectiveness, of seasonal influenza vaccines compared to egg-based vaccines.
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Affiliation(s)
- Heidi Peck
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, The Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia.
| | | | - Steve Rockman
- Seqirus Ltd, Parkville, VIC, Australia.,Department of Immunology and Microbiology, The University of Melbourne, Parkville, VIC, Australia
| | - Vivian Leung
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, The Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Hilda Lau
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, The Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Sally Soppe
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, The Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Cleve Rynehart
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, The Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | | | | | - Ian G Barr
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, The Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia.,Department of Immunology and Microbiology, The University of Melbourne, Parkville, VIC, Australia
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Siegers JY, Dhanasekaran V, Xie R, Deng YM, Patel S, Ieng V, Moselen J, Peck H, Aziz A, Sarr B, Chin S, Heng S, Khalakdina A, Kinzer M, Chau D, Raftery P, Duong V, Sovann L, Barr IG, Karlsson EA. Genetic and Antigenic Characterization of an Influenza A(H3N2) Outbreak in Cambodia and the Greater Mekong Subregion during the COVID-19 Pandemic, 2020. J Virol 2021; 95:e0126721. [PMID: 34586866 PMCID: PMC8610588 DOI: 10.1128/jvi.01267-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/09/2021] [Indexed: 11/20/2022] Open
Abstract
Introduction of non-pharmaceutical interventions to control COVID-19 in early 2020 coincided with a global decrease in active influenza circulation. However, between July and November 2020, an influenza A(H3N2) epidemic occurred in Cambodia and in other neighboring countries in the Greater Mekong Subregion in Southeast Asia. We characterized the genetic and antigenic evolution of A(H3N2) in Cambodia and found that the 2020 epidemic comprised genetically and antigenically similar viruses of Clade3C2a1b/131K/94N, but they were distinct from the WHO recommended influenza A(H3N2) vaccine virus components for 2020-2021 Northern Hemisphere season. Phylogenetic analysis revealed multiple virus migration events between Cambodia and bordering countries, with Laos PDR and Vietnam also reporting similar A(H3N2) epidemics immediately following the Cambodia outbreak: however, there was limited circulation of these viruses elsewhere globally. In February 2021, a virus from the Cambodian outbreak was recommended by WHO as the prototype virus for inclusion in the 2021-2022 Northern Hemisphere influenza vaccine. IMPORTANCE The 2019 coronavirus disease (COVID-19) pandemic has significantly altered the circulation patterns of respiratory diseases worldwide and disrupted continued surveillance in many countries. Introduction of control measures in early 2020 against Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infection has resulted in a remarkable reduction in the circulation of many respiratory diseases. Influenza activity has remained at historically low levels globally since March 2020, even when increased influenza testing was performed in some countries. Maintenance of the influenza surveillance system in Cambodia in 2020 allowed for the detection and response to an influenza A(H3N2) outbreak in late 2020, resulting in the inclusion of this virus in the 2021-2022 Northern Hemisphere influenza vaccine.
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Affiliation(s)
- Jurre Y. Siegers
- National Influenza Center of Cambodia, Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Vijaykrishna Dhanasekaran
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Ruopeng Xie
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yi-Mo Deng
- World Health Organization Collaborating Center, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Sarika Patel
- World Health Organization Country Office, Phnom Penh, Cambodia
| | - Vanra Ieng
- World Health Organization Country Office, Phnom Penh, Cambodia
| | - Jean Moselen
- World Health Organization Collaborating Center, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Heidi Peck
- World Health Organization Collaborating Center, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Ammar Aziz
- World Health Organization Collaborating Center, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Borann Sarr
- U.S. Centers for Disease Control and Prevention, Phnom Penh, Cambodia
| | - Savuth Chin
- National Institute of Public Health, Ministry of Health, Phnom Penh, Cambodia
| | - Seng Heng
- Centers for Disease Control and Prevention, Ministry of Health, Phnom Penh, Cambodia
| | | | - Michael Kinzer
- U.S. Centers for Disease Control and Prevention, Phnom Penh, Cambodia
| | - Darapheak Chau
- National Institute of Public Health, Ministry of Health, Phnom Penh, Cambodia
| | | | - Veasna Duong
- National Influenza Center of Cambodia, Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Ly Sovann
- Centers for Disease Control and Prevention, Ministry of Health, Phnom Penh, Cambodia
| | - Ian G. Barr
- World Health Organization Collaborating Center, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Erik A. Karlsson
- National Influenza Center of Cambodia, Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
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41
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Suderman M, Moniwa M, Alkie TN, Ojkic D, Broes A, Pople N, Berhane Y. Comparative Susceptibility of Madin–Darby Canine Kidney (MDCK) Derived Cell Lines for Isolation of Swine Origin Influenza A Viruses from Different Clinical Specimens. Viruses 2021; 13:v13122346. [PMID: 34960614 PMCID: PMC8704103 DOI: 10.3390/v13122346] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/15/2021] [Accepted: 11/19/2021] [Indexed: 12/19/2022] Open
Abstract
Madin–Darby canine kidney (MDCK) cells are commonly used for the isolation of mammalian influenza A viruses. The goal of this study was to compare the sensitivity and suitability of the original MDCK cell line in comparison with MDCK-derived cell lines, MDCK.2, MDCK SIAT-1 and MDCK-London for isolation of swine-origin influenza A viruses (IAV-S) from clinical specimens. One-hundred thirty clinical specimens collected from pigs in the form of nasal swabs, lung tissue and oral fluids that were positive by PCR for the presence of IAV-S RNA were inoculated in the cell cultures listed above. MDCK-SIAT1 cells yielded the highest proportion of positive IAV-S isolations from all specimen types. For nasal swabs, 58.62% of the specimens were IAV-S positive in MDCK-SIAT1 cells, followed by MDCK-London (36.21%), and conventional MDCK and MDCK.2 cells (27.5%). For lung specimens, 59.38% were IAV-S positive in MDCK-SIAT1 cells, followed by MDCK-London (40.63%), and conventional MDCK and MDCK.2 cells (18.75–31.25%). Oral fluids yielded the lowest number of positive virus isolation results, but MDCK-SIAT1 cells were still had the highest rate (35%) of IAV-S isolation, whereas the isolation rate in other cells ranged from 5–7.5%. Samples with lower IAV-S PCR cycle threshold (Ct) values were more suitable for culturing and isolation. The isolated IAV-S represented H1N1-β, H1N2-α, H1N1pdm and H3N2 cluster IV and cluster IVB viruses. The result of the current study demonstrated the importance of using the most appropriate MDCK cells when isolating IAV-S from clinical samples.
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Affiliation(s)
- Matthew Suderman
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3R2, Canada; (M.S.); (M.M.); (T.N.A.)
| | - Mariko Moniwa
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3R2, Canada; (M.S.); (M.M.); (T.N.A.)
| | - Tamiru N. Alkie
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3R2, Canada; (M.S.); (M.M.); (T.N.A.)
| | - Davor Ojkic
- Animal Health Laboratory, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Andre Broes
- Biovet Inc., Saint-Hyacinthe, QC J2S 8W2, Canada;
| | - Neil Pople
- Veterinary Diagnostic Services, Manitoba Agriculture and Resource Development, 545 University Crescent, Winnipeg, MB R3T 5S6, Canada;
| | - Yohannes Berhane
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3R2, Canada; (M.S.); (M.M.); (T.N.A.)
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
- Correspondence:
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Hansen L, Zhou F, Amdam H, Trieu MC, Cox RJ. Repeated Influenza Vaccination Boosts and Maintains H1N1pdm09 Neuraminidase Antibody Titers. Front Immunol 2021; 12:748264. [PMID: 34721417 PMCID: PMC8551669 DOI: 10.3389/fimmu.2021.748264] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/28/2021] [Indexed: 11/17/2022] Open
Abstract
Antibodies to influenza surface protein neuraminidase (NA) have been found to reduce disease severity and may be an independent correlate of protection. Despite this, current influenza vaccines have no regulatory requirements for the quality or quantity of the NA antigen and are not optimized for induction of NA-specific antibodies. Here we investigate the induction and durability of NA-specific antibody titers after pandemic AS03-adjuvanted monovalent H1N1 vaccination and subsequent annual vaccination in health care workers in a five-year longitudinal study. NA-specific antibodies were measured by endpoint ELISA and functional antibodies measured by enzyme-linked lectin assay (ELLA) and plaque reduction naturalisation assay. We found robust induction of NA inhibition (NAI) titers with a 53% seroconversion rate (>4-fold) after pandemic vaccination in 2009. Furthermore, the endpoint and NAI geometric mean titers persisted above pre-vaccination levels up to five years after vaccination in HCWs that only received the pandemic vaccine, which demonstrates considerable durability. Vaccination with non-adjuvanted trivalent influenza vaccines (TIV) in subsequent influenza seasons 2010/2011 – 2013/2014 further boosted NA-specific antibody responses. We found that each subsequent vaccination increased durable endpoint titers and contributed to maintaining the durability of functional antibody titers. Although the trivalent influenza vaccines boosted NA-specific antibodies, the magnitude of fold-increase at day 21 declined with repeated vaccination, particularly for functional antibody titers. High levels of pre-existing antibodies were associated with lower fold-induction in repeatedly vaccinated HCWs. In summary, our results show that durable NA-specific antibody responses can be induced by an adjuvanted influenza vaccine, which can be maintained and further boosted by TIVs. Although NA-specific antibody responses are boosted by annual influenza vaccines, high pre-existing titers may negatively affect the magnitude of fold-increase in repeatedly vaccinated individuals. Our results support continued development and standardization of the NA antigen to supplement current influenza vaccines and reduce the burden of morbidity and mortality.
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Affiliation(s)
- Lena Hansen
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Fan Zhou
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Håkon Amdam
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Mai-Chi Trieu
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Rebecca Jane Cox
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Microbiology, Haukeland University Hospital, Bergen, Norway
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Hussain S, Daniels RS, Wharton SA, Howell S, Halai C, Kunzelmann S, Whittaker L, McCauley JW. Reduced sialidase activity of influenza A(H3N2) neuraminidase associated with positively charged amino acid substitutions. J Gen Virol 2021; 102. [PMID: 34596510 DOI: 10.1099/jgv.0.001648] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Neuraminidase (NA) inhibitors (NAI), oseltamivir and zanamivir, are the main antiviral medications for influenza and monitoring of susceptibility to these antivirals is routinely done by determining 50 % inhibitory concentrations (IC50) with MUNANA substrate. During 2010-2019, levels of A(H3N2) viruses presenting reduced NAI inhibition (RI) were low (~0.75 %) but varied year-on-year. The highest proportions of viruses showing RI were observed during the 2013-2014, 2016-2017 and 2017-2018 Northern Hemisphere seasons. The majority of RI viruses were found to contain positively charged NA amino acid substitutions of N329K, K/S329R, S331R or S334R, being notably higher during the 2016-2017 season. Sialidase activity kinetics were determined for viruses of RI phenotype and contemporary wild-type (WT) viruses showing close genetic relatedness and displaying normal inhibition (NI). RI phenotypes resulted from reduced sialidase activity compared to relevant WT viruses. Those containing S329R or N329K or S331R showed markedly higher Km for the substrate and Ki values for NAIs, while those with S334R showed smaller effects. Substitutions at N329 and S331 disrupt a glycosylation sequon (NDS), confirmed to be utilised by mass spectrometry. However, gain of positive charge at all three positions was the major factor influencing the kinetic effects, not loss of glycosylation. Because of the altered enzyme characteristics NAs carrying these substitutions cannot be assessed reliably for susceptibility to NAIs using standard MUNANA-based assays due to reductions in the affinity of the enzyme for its substrate and the concentration of the substrate usually used.
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Affiliation(s)
- Saira Hussain
- Worldwide Influenza Centre, The Francis Crick Institute, London, NW1 1AT, UK
| | - Rodney S Daniels
- Worldwide Influenza Centre, The Francis Crick Institute, London, NW1 1AT, UK
| | - Stephen A Wharton
- Worldwide Influenza Centre, The Francis Crick Institute, London, NW1 1AT, UK
| | - Steven Howell
- Protein Analysis and Proteomics Science Technology Platform, The Francis Crick Institute, London, NW1 1AT, UK
| | - Chandrika Halai
- Worldwide Influenza Centre, The Francis Crick Institute, London, NW1 1AT, UK
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, NW1 1AT, UK
| | - Lynne Whittaker
- Worldwide Influenza Centre, The Francis Crick Institute, London, NW1 1AT, UK
| | - John W McCauley
- Worldwide Influenza Centre, The Francis Crick Institute, London, NW1 1AT, UK
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44
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Korsun N, Trifonova I, Voleva S, Grigorova I, Angelova S. Genetic characterisation of the influenza viruses circulating in Bulgaria during the 2019-2020 winter season. Virus Genes 2021; 57:401-412. [PMID: 34156583 PMCID: PMC8217981 DOI: 10.1007/s11262-021-01853-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/04/2021] [Indexed: 11/24/2022]
Abstract
Influenza viruses have a high potential for genetic changes. The objectives of this study were to analyse influenza virus circulation in Bulgaria during the 2019/2020 season, to perform a phylogenetic and molecular analyses of the haemagglutinin (HA) and neuraminidase (NA) sequences of representative influenza strains, and to identify amino acid substitutions compared to the current vaccine strains. Seasonal influenza viruses A(H3N2), A(H1N1)pdm09 and B/Victoria-lineage were detected using a real-time RT-PCR in 323 (23.3%), 149 (10.7%) and 138 (9.9%) out of 1387 patient samples studied, respectively. The HA genes of A(H3N2) viruses analysed belonged to clades 3C.3a (21 strains) and 3C.2a (5 strains): subclades 3C.2a1b + T131K, 3C.2a1b + T135K-B and 3C.2a1b + T135K-A. The clade 3C.3a and subclade 3C.2a1b viruses carried 5 and 14-17 substitutions in HA, as well as 3 and 9 substitutions in NA, respectively, in comparison with the A/Kansas/14/2017 vaccine virus, including some substitutions in the HA antigenic sites A, B, C and E. All 21 A(H1N1)pdm09 viruses sequenced fell into 6B.1A5A subclade. Amino acid sequence analysis revealed the presence of 7-11 substitutions in HA, compared to the A/Brisbane/02/2018 vaccine virus, three of which occurred in antigenic site Sb, along with 6-9 changes at positions in NA. All 10 B/Victoria-lineage viruses sequenced belonged to clade 1A with a triple deletion in HA1 (genetic group 1A(Δ3)B) and carried 7 and 3 substitutions in HA and NA, respectively, with respect to the B/Colorado/06/2017 vaccine virus. The results of this study confirm the rapid evolution of influenza viruses and the need for continuous antigenic and genetic surveillance.
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Affiliation(s)
- Neli Korsun
- Department of Virology, National Laboratory "Influenza and ARI", National Centre of Infectious and Parasitic Diseases, Sofia, Bulgaria.
| | - Ivelina Trifonova
- Department of Virology, National Laboratory "Influenza and ARI", National Centre of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Silvia Voleva
- Department of Virology, National Laboratory "Influenza and ARI", National Centre of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Iliyana Grigorova
- Department of Virology, National Laboratory "Influenza and ARI", National Centre of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Svetla Angelova
- Department of Virology, National Laboratory "Influenza and ARI", National Centre of Infectious and Parasitic Diseases, Sofia, Bulgaria
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45
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Ison MG, Hayden FG, Hay AJ, Gubareva LV, Govorkova EA, Takashita E, McKimm-Breschkin JL. Influenza polymerase inhibitor resistance: Assessment of the current state of the art - A report of the isirv Antiviral group. Antiviral Res 2021; 194:105158. [PMID: 34363859 PMCID: PMC9012257 DOI: 10.1016/j.antiviral.2021.105158] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/31/2022]
Abstract
It is more than 20 years since the neuraminidase inhibitors, oseltamivir and zanamivir were approved for the treatment and prevention of influenza. Guidelines for global surveillance and methods for evaluating resistance were established initially by the Neuraminidase Inhibitor Susceptibility Network (NISN), which merged 10 years ago with the International Society for influenza and other Respiratory Virus Diseases (isirv) to become the isirv-Antiviral Group (isirv-AVG). With the ongoing development of new influenza polymerase inhibitors and recent approval of baloxavir marboxil, the isirv-AVG held a closed meeting in August 2019 to discuss the impact of resistance to these inhibitors. Following this meeting and review of the current literature, this article is intended to summarize current knowledge regarding the clinical impact of resistance to polymerase inhibitors and approaches for surveillance and methods for laboratory evaluation of resistance, both in vitro and in animal models. We highlight limitations and gaps in current knowledge and suggest some strategies for addressing these gaps, including the need for additional clinical studies of influenza antiviral drug combinations. Lessons learned from influenza resistance monitoring may also be helpful for establishing future drug susceptibility surveillance and testing for SARS-CoV-2.
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Affiliation(s)
- Michael G Ison
- Divisions of Infectious Diseases and Organ Transplantation, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
| | - Frederick G Hayden
- Division of Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, VA, USA.
| | - Alan J Hay
- The Francis Crick Institute, London, UK.
| | - Larisa V Gubareva
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Elena A Govorkova
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA.
| | - Emi Takashita
- National Institute of Infectious Diseases, Tokyo, Japan.
| | - Jennifer L McKimm-Breschkin
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria, Australia.
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46
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Cell-Adapted Mutations and Antigenic Diversity of Influenza B Viruses in Missouri, 2019-2020 Season. Viruses 2021; 13:v13101896. [PMID: 34696325 PMCID: PMC8538563 DOI: 10.3390/v13101896] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/12/2021] [Accepted: 09/16/2021] [Indexed: 01/31/2023] Open
Abstract
Influenza B viruses (IBVs) are causing an increasing burden of morbidity and mortality, yet the prevalence of culture-adapted mutations in human seasonal IBVs are unclear. We collected 368 clinical samples from patients with influenza-like illness in Missouri during the 2019–2020 influenza season and recovered 146 influenza isolates including 38 IBV isolates. Of MDCK-CCL34, MDCK-Siat1, and humanized MDCK (hCK), hCK showed the highest virus recovery efficiency. All Missourian IBVs belonged to the Victoria V1A.3 lineage, all of which contained a three-amino acid deletion on the HA protein and were antigenically distant from the Victoria lineage IBV vaccine strain used during that season. By comparing genomic sequences of these IBVs in 31 paired samples, eight cell-adapted nonsynonymous mutations were identified, with the majority in the RNA polymerase. Analyses of IBV clinical sample–isolate pairs from public databases further showed that cell- and egg-adapted mutations occurred more widely in viral proteins, including the receptor and antibody binding sites on HA. Our study suggests that hCK is an effective platform for IBV isolation and that culture-adapted mutations may occur during IBV isolation. As culture-adapted mutations may affect subsequent virus studies and vaccine development, the knowledge from this study may help optimize strategies for influenza surveillance, vaccine strain selection, and vaccine development.
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47
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Broszeit F, van Beek RJ, Unione L, Bestebroer TM, Chapla D, Yang JY, Moremen KW, Herfst S, Fouchier RAM, de Vries RP, Boons GJ. Glycan remodeled erythrocytes facilitate antigenic characterization of recent A/H3N2 influenza viruses. Nat Commun 2021; 12:5449. [PMID: 34521834 PMCID: PMC8440751 DOI: 10.1038/s41467-021-25713-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 08/18/2021] [Indexed: 01/04/2023] Open
Abstract
During circulation in humans and natural selection to escape antibody recognition for decades, A/H3N2 influenza viruses emerged with altered receptor specificities. These viruses lost the ability to agglutinate erythrocytes critical for antigenic characterization and give low yields and acquire adaptive mutations when cultured in eggs and cells, contributing to recent vaccine challenges. Examination of receptor specificities of A/H3N2 viruses reveals that recent viruses compensated for decreased binding of the prototypic human receptor by recognizing α2,6-sialosides on extended LacNAc moieties. Erythrocyte glycomics shows an absence of extended glycans providing a rationale for lack of agglutination by recent A/H3N2 viruses. A glycan remodeling approach installing functional receptors on erythrocytes, allows antigenic characterization of recent A/H3N2 viruses confirming the cocirculation of antigenically different viruses in humans. Computational analysis of HAs in complex with sialosides having extended LacNAc moieties reveals that mutations distal to the RBD reoriented the Y159 side chain resulting in an extended receptor binding site.
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MESH Headings
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/metabolism
- Binding Sites
- Carbohydrate Sequence
- Erythrocytes/metabolism
- Erythrocytes/virology
- Glycomics/methods
- Glycosides/chemistry
- Glycosides/metabolism
- Hemagglutination Inhibition Tests
- Hemagglutinins, Viral/chemistry
- Hemagglutinins, Viral/genetics
- Hemagglutinins, Viral/metabolism
- Host-Pathogen Interactions/genetics
- Humans
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/metabolism
- Influenza, Human/virology
- Microarray Analysis/methods
- Polysaccharides/chemistry
- Polysaccharides/metabolism
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Receptors, Virus/metabolism
- Sialic Acids/chemistry
- Sialic Acids/metabolism
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Affiliation(s)
- Frederik Broszeit
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, 3584 CG, The Netherlands
| | - Rosanne J van Beek
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, 3584 CG, The Netherlands
| | - Luca Unione
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, 3584 CG, The Netherlands
| | - Theo M Bestebroer
- Department of Viroscience, Erasmus MC, P.O. Box 2040, Rotterdam, 3000 CA, The Netherlands
| | - Digantkumar Chapla
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
| | - Sander Herfst
- Department of Viroscience, Erasmus MC, P.O. Box 2040, Rotterdam, 3000 CA, The Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus MC, P.O. Box 2040, Rotterdam, 3000 CA, The Netherlands
| | - Robert P de Vries
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, 3584 CG, The Netherlands.
| | - Geert-Jan Boons
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, 3584 CG, The Netherlands.
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA.
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA.
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48
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Chauveau L, Bridgeman A, Tan TK, Beveridge R, Frost JN, Rijal P, Pedroza‐Pacheco I, Partridge T, Gilbert‐Jaramillo J, Knight ML, Liu X, Russell RA, Borrow P, Drakesmith H, Townsend AR, Rehwinkel J. Inclusion of cGAMP within virus-like particle vaccines enhances their immunogenicity. EMBO Rep 2021; 22:e52447. [PMID: 34142428 PMCID: PMC8339669 DOI: 10.15252/embr.202152447] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/21/2021] [Accepted: 05/26/2021] [Indexed: 01/30/2023] Open
Abstract
Cyclic GMP-AMP (cGAMP) is an immunostimulatory molecule produced by cGAS that activates STING. cGAMP is an adjuvant when administered alongside antigens. cGAMP is also incorporated into enveloped virus particles during budding. Here, we investigate whether inclusion of cGAMP within viral vaccine vectors enhances their immunogenicity. We immunise mice with virus-like particles (VLPs) containing HIV-1 Gag and the vesicular stomatitis virus envelope glycoprotein G (VSV-G). cGAMP loading of VLPs augments CD4 and CD8 T-cell responses. It also increases VLP- and VSV-G-specific antibody titres in a STING-dependent manner and enhances virus neutralisation, accompanied by increased numbers of T follicular helper cells. Vaccination with cGAMP-loaded VLPs containing haemagglutinin induces high titres of influenza A virus neutralising antibodies and confers protection upon virus challenge. This requires cGAMP inclusion within VLPs and is achieved at markedly reduced cGAMP doses. Similarly, cGAMP loading of VLPs containing the SARS-CoV-2 Spike protein enhances Spike-specific antibody titres. cGAMP-loaded VLPs are thus an attractive platform for vaccination.
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Affiliation(s)
- Lise Chauveau
- Medical Research Council Human Immunology UnitRadcliffe Department of MedicineMedical Research Council Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
- Present address:
Institut de recherche en infectiologie de Montpellier (IRIM)CNRS UMR 9004MontpellierFrance
| | - Anne Bridgeman
- Medical Research Council Human Immunology UnitRadcliffe Department of MedicineMedical Research Council Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
| | - Tiong K Tan
- Medical Research Council Human Immunology UnitRadcliffe Department of MedicineMedical Research Council Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
| | - Ryan Beveridge
- MRC Molecular Hematology UnitMRC Weatherall Institute of Molecular MedicineJohn Radcliffe HospitalUniversity of OxfordOxfordUK
- Virus Screening FacilityMRC Weatherall Institute of Molecular MedicineJohn Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Joe N Frost
- Medical Research Council Human Immunology UnitRadcliffe Department of MedicineMedical Research Council Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
| | - Pramila Rijal
- Medical Research Council Human Immunology UnitRadcliffe Department of MedicineMedical Research Council Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
| | | | - Thomas Partridge
- Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUK
| | - Javier Gilbert‐Jaramillo
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Michael L Knight
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| | - Xu Liu
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
- Key Laboratory of Human Disease Comparative MedicineNational Health Commission of China (NHC), Institute of Laboratory Animal SciencePeking Union Medicine CollegeChinese Academy of Medical SciencesBeijingChina
| | | | - Persephone Borrow
- Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUK
| | - Hal Drakesmith
- Medical Research Council Human Immunology UnitRadcliffe Department of MedicineMedical Research Council Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
| | - Alain R Townsend
- Medical Research Council Human Immunology UnitRadcliffe Department of MedicineMedical Research Council Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
| | - Jan Rehwinkel
- Medical Research Council Human Immunology UnitRadcliffe Department of MedicineMedical Research Council Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
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49
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Wang L, Fan X, Bonenfant G, Cui D, Hossain J, Jiang N, Larson G, Currier M, Liddell J, Wilson M, Tamin A, Harcourt J, Ciomperlik-Patton J, Pang H, Dybdahl-Sissoko N, Campagnoli R, Shi PY, Barnes J, Thornburg NJ, Wentworth DE, Zhou B. Susceptibility to SARS-CoV-2 of Cell Lines and Substrates Commonly Used to Diagnose and Isolate Influenza and Other Viruses. Emerg Infect Dis 2021; 27:1380-1392. [PMID: 33900165 PMCID: PMC8084484 DOI: 10.3201/eid2705.210023] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Co-infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other viruses has been reported. We evaluated cell lines commonly used to isolate viruses and diagnose related diseases for their susceptibility to SARS-CoV-2. Although multiple kidney cell lines from monkeys were susceptible to SARS-CoV-2, we found many cell types derived from humans, dogs, minks, cats, mice, and chicken were not. We analyzed MDCK cells, which are most commonly used for surveillance and study of influenza viruses, and found that they were not susceptible to SARS-CoV-2. The low expression level of the angiotensin converting enzyme 2 receptor and lower receptor affinity to SARS-CoV-2 spike, which could be overcome by overexpression of canine angiotensin converting enzyme 2 in trans, strengthened the cellular barrier to productive infection. Moreover, a D614G mutation in the spike protein did not appear to affect SARS-CoV-2 cell tropism. Our findings should help avert inadvertent propagation of SARS-CoV-2 from diagnostic cell lines.
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50
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Barnard KN, Wasik BR, Alford BK, Hayward JJ, Weichert WS, Voorhees IEH, Holmes EC, Parrish CR. Sequence dynamics of three influenza A virus strains grown in different MDCK cell lines, including those expressing different sialic acid receptors. J Evol Biol 2021; 34:1878-1900. [PMID: 34114711 DOI: 10.1111/jeb.13890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 06/02/2021] [Accepted: 06/08/2021] [Indexed: 12/12/2022]
Abstract
Viruses are often cultured in cell lines for research and vaccine development, and those often differ from the natural hosts or tissues. Cell lines can also differ in the presence of virus receptors, such as the sialic acid (Sia) receptors used by influenza A viruses (IAV), which can vary in linkage (α2,3- or α2,6-linkage) and form (N-glycolylneuraminic acid [Neu5Gc] or N-acetylneuraminic acid [Neu5Ac]). The selective pressures resulting from passaging viruses in cell types with host-specific variations in viral receptors are still only partially understood. IAV are commonly cultured in MDCK cells which are both derived from canine kidney tubule epithelium and inherently heterogeneous. MDCK cells naturally present Neu5Ac and α2,3-linked Sia forms. Here, we examine natural MDCK variant lineages, as well as engineered variants that synthesize Neu5Gc and/or α2,6-linkages. We determined how viral genetic variation occurred within human H3N2, H1N1 pandemic and canine H3N2 IAV populations when serially passaged in MDCK cell lines that vary in cell type (MDCK-Type I or MDCK-Type II clones) and in Sia display. Deep sequencing of viral genomes showed small numbers of consensus-level mutations, mostly within the hemagglutinin (HA) gene. Both human IAV showed variants in the HA stem and the HA receptor-binding site of populations passaged in cells displaying Neu5Gc. Canine H3N2 showed variants near the receptor-binding site when passaged in cells displaying Neu5Gc or α2,6-linkages. Viruses replicated to low titres in MDCK-Type II cells, suggesting that not all cell types in heterogeneous MDCK cell populations are equally permissive to infection.
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Affiliation(s)
- Karen N Barnard
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA.,Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Brian R Wasik
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Brynn K Alford
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Jessica J Hayward
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Wendy S Weichert
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Ian E H Voorhees
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Colin R Parrish
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
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