1
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Le Sage V, Rockey NC, French AJ, McBride R, McCarthy KR, Rigatti LH, Shephard MJ, Jones JE, Walter SG, Doyle JD, Xu L, Barbeau DJ, Wang S, Frizzell SA, Myerburg MM, Paulson JC, McElroy AK, Anderson TK, Vincent Baker AL, Lakdawala SS. Potential pandemic risk of circulating swine H1N2 influenza viruses. Nat Commun 2024; 15:5025. [PMID: 38871701 PMCID: PMC11176300 DOI: 10.1038/s41467-024-49117-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/17/2024] [Indexed: 06/15/2024] Open
Abstract
Influenza A viruses in swine have considerable genetic diversity and continue to pose a pandemic threat to humans due to a potential lack of population level immunity. Here we describe a pipeline to characterize and triage influenza viruses for their pandemic risk and examine the pandemic potential of two widespread swine origin viruses. Our analysis reveals that a panel of human sera collected from healthy adults in 2020 has no cross-reactive neutralizing antibodies against a α-H1 clade strain (α-swH1N2) but do against a γ-H1 clade strain. The α-swH1N2 virus replicates efficiently in human airway cultures and exhibits phenotypic signatures similar to the human H1N1 pandemic strain from 2009 (H1N1pdm09). Furthermore, α-swH1N2 is capable of efficient airborne transmission to both naïve ferrets and ferrets with prior seasonal influenza immunity. Ferrets with H1N1pdm09 pre-existing immunity show reduced α-swH1N2 viral shedding and less severe disease signs. Despite this, H1N1pdm09-immune ferrets that became infected via the air can still onward transmit α-swH1N2 with an efficiency of 50%. These results indicate that this α-swH1N2 strain has a higher pandemic potential, but a moderate level of impact since there is reduced replication fitness and pathology in animals with prior immunity.
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MESH Headings
- Animals
- Ferrets/virology
- Humans
- Swine
- Influenza, Human/virology
- Influenza, Human/epidemiology
- Influenza, Human/immunology
- Influenza, Human/blood
- Influenza, Human/transmission
- Orthomyxoviridae Infections/virology
- Orthomyxoviridae Infections/immunology
- Orthomyxoviridae Infections/epidemiology
- Orthomyxoviridae Infections/transmission
- Orthomyxoviridae Infections/blood
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Influenza A Virus, H1N2 Subtype/genetics
- Influenza A Virus, H1N2 Subtype/immunology
- Pandemics
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Swine Diseases/virology
- Swine Diseases/epidemiology
- Swine Diseases/immunology
- Swine Diseases/transmission
- Swine Diseases/blood
- Female
- Virus Shedding
- Male
- Adult
- Virus Replication
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Affiliation(s)
- Valerie Le Sage
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Nicole C Rockey
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Civil and Environmental Engineering, Duke University, Durham, NC, USA
| | - Andrea J French
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Ryan McBride
- Departments of Molecular Medicine and Immunology & Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kevin R McCarthy
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lora H Rigatti
- Division of Laboratory Animal Resources, University of Pittsburgh, Pittsburgh, PA, USA
| | - Meredith J Shephard
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Jennifer E Jones
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sydney G Walter
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Joshua D Doyle
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Division of Infectious Diseases, Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lingqing Xu
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Division of Infectious Diseases, Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dominique J Barbeau
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Division of Infectious Diseases, Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shengyang Wang
- Departments of Molecular Medicine and Immunology & Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sheila A Frizzell
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michael M Myerburg
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - James C Paulson
- Departments of Molecular Medicine and Immunology & Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Anita K McElroy
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Division of Infectious Diseases, Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tavis K Anderson
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, USA
| | - Amy L Vincent Baker
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, USA
| | - Seema S Lakdawala
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA.
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2
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Holmes KE, VanInsberghe D, Ferreri LM, Elie B, Ganti K, Lee CY, Lowen AC. Viral expansion after transfer is a primary driver of influenza A virus transmission bottlenecks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.19.567585. [PMID: 38014182 PMCID: PMC10680852 DOI: 10.1101/2023.11.19.567585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
For many viruses, narrow bottlenecks acting during transmission sharply reduce genetic diversity in a recipient host relative to the donor. Since genetic diversity represents adaptive potential, such losses of diversity are though to limit the opportunity for viral populations to undergo antigenic change and other adaptive processes. Thus, a detailed picture of evolutionary dynamics during transmission is critical to understanding the forces driving viral evolution at an epidemiologic scale. To advance this understanding, we used a novel barcoded virus library and a guinea pig model of transmission to decipher where in the transmission process diversity is lost for influenza A viruses. In inoculated guinea pigs, we show that a high level of viral genetic diversity is maintained across time. Continuity in the barcodes detected furthermore indicates that stochastic effects are not pronounced within inoculated hosts. Importantly, in both aerosol-exposed and direct contact-exposed animals, we observed many barcodes at the earliest time point(s) positive for infectious virus, indicating robust transfer of diversity through the environment. This high viral diversity is short-lived, however, with a sharp decline seen 1-2 days after initiation of infection. Although major losses of diversity at transmission are well described for influenza A virus, our data indicate that events that occur following viral transfer and during the earliest stages of natural infection have a predominant role in this process. This finding suggests that immune selection may have greater opportunity to operate during influenza A transmission than previously recognized.
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Affiliation(s)
- Katie E. Holmes
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - David VanInsberghe
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Lucas M. Ferreri
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Baptiste Elie
- MIVEGEC, CNRS, IRD, Université de Montpellier, Montpellier, France
| | - Ketaki Ganti
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Chung-Young Lee
- Department of Microbiology, School of Medicine, Kyungpook National University, Jung-gu, Daegu, Republic of Korea
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Emory Center of Excellence for Influenza Research and Response (CEIRR), Atlanta, GA, USA
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3
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Nuñez IA, Jang H, Huang Y, Kelvin A, Ross TM. Influenza virus immune imprinting dictates the clinical outcomes in ferrets challenged with highly pathogenic avian influenza virus H5N1. Front Vet Sci 2023; 10:1286758. [PMID: 38170075 PMCID: PMC10759238 DOI: 10.3389/fvets.2023.1286758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024] Open
Abstract
Zoonotic transmission of H5N1 highly pathogenic avian influenza virus (HPAIV) into the human population is an increasing global threat. The recent 2022 HPAIV outbreak significantly highlighted this possibility, increasing concern in the general population. The clinical outcomes of H5N1 influenza virus exposure can be determined by an individual's primary influenza virus infection (imprinting) or vaccination status. Immunological imprinting with Group 1 - (H1N1, H2N2, and H2N3) increases survival rates following H5N1 viral infection compared to Group 2 - (H3N2) imprinted individuals. Vaccination against H5N1 influenza viruses can offer protection to at-risk populations; however, stockpiled inactivated H5N1 influenza vaccines are not readily available to the public. We hypothesize that the immunological response to vaccination and subsequent clinical outcome following H5N1 influenza virus infection is correlated with the immunological imprinting status of an individual. To test this hypothesis, our lab established a ferret pre-immune model of disease. Naïve ferrets were intranasally inoculated with seasonal influenza viruses and allowed to recover for 84 days prior to H5N1 virus infection. Ferrets imprinted following H1N1 and H2N3 virus infections were completely protected against lethal H5N1 influenza virus challenge (100% survival), with few to no clinical symptoms. In comparison, H3N2 influenza virus-imprinted ferrets had severe clinical symptoms, delayed disease progression, and a sublethal phenotype (40% mortality). Consecutive infections with H1N1 influenza viruses followed by an H3N2 influenza virus infection did not abrogate the immune protection induced by the original H1N1 influenza virus infection. In addition, ferrets consecutively infected with H1N1 and H2N3 viruses had no clinical symptoms or weight loss. H3N2 pre-immune ferrets were vaccinated with a broadly reactive H5 HA-based or H1 NA-based vaccine (Hu-CO 2). These ferrets were protected against H5N1 influenza virus challenge, whereas ferrets vaccinated with the H1N1 wild-type CA/09 rHA vaccine had similar phenotypes as non-vaccinated H3N2-imprinted ferrets with 40% survival. Overall, Group 2 imprinted ferrets, which were vaccinated with heterologous Group 1 HA vaccines, had redirected immune responses to Group 1 influenza viral antigens and rescued a sublethal phenotype to complete protection.
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Affiliation(s)
- Ivette A. Nuñez
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States
| | - Hyesun Jang
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | - Ying Huang
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | - Alyson Kelvin
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
| | - Ted M. Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States
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4
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Le Sage V, Lowen AC, Lakdawala SS. Block the Spread: Barriers to Transmission of Influenza Viruses. Annu Rev Virol 2023; 10:347-370. [PMID: 37308086 DOI: 10.1146/annurev-virology-111821-115447] [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] [Indexed: 06/14/2023]
Abstract
Respiratory viruses, such as influenza viruses, cause significant morbidity and mortality worldwide through seasonal epidemics and sporadic pandemics. Influenza viruses transmit through multiple modes including contact (either direct or through a contaminated surface) and inhalation of expelled aerosols. Successful human to human transmission requires an infected donor who expels virus into the environment, a susceptible recipient, and persistence of the expelled virus within the environment. The relative efficiency of each mode can be altered by viral features, environmental parameters, donor and recipient host characteristics, and viral persistence. Interventions to mitigate transmission of influenza viruses can target any of these factors. In this review, we discuss many aspects of influenza virus transmission, including the systems to study it, as well as the impact of natural barriers and various nonpharmaceutical and pharmaceutical interventions.
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Affiliation(s)
- Valerie Le Sage
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Anice C Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA;
| | - Seema S Lakdawala
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA;
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5
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Zhang B, Huang W, Pei S, Zeng J, Shen W, Wang D, Wang G, Chen T, Yang L, Cheng P, Wang D, Shu Y, Du X. Mechanisms for the circulation of influenza A(H3N2) in China: A spatiotemporal modelling study. PLoS Pathog 2022; 18:e1011046. [PMID: 36525468 PMCID: PMC9803318 DOI: 10.1371/journal.ppat.1011046] [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: 04/16/2022] [Revised: 12/30/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
Circulation of seasonal influenza is the product of complex interplay among multiple drivers, yet characterizing the underlying mechanism remains challenging. Leveraging the diverse seasonality of A(H3N2) virus and abundant climatic space across regions in China, we quantitatively investigated the relative importance of population susceptibility, climatic factors, and antigenic change on the dynamics of influenza A(H3N2) through an integrative modelling framework. Specifically, an absolute humidity driven multiscale transmission model was constructed for the 2013/2014, 2014/2015 and 2016/2017 influenza seasons that were dominated by influenza A(H3N2). We revealed the variable impact of absolute humidity on influenza transmission and differences in the occurring timing and magnitude of antigenic change for those three seasons. Overall, the initial population susceptibility, climatic factors, and antigenic change explained nearly 55% of variations in the dynamics of influenza A(H3N2). Specifically, the additional variation explained by the initial population susceptibility, climatic factors, and antigenic change were at 33%, 26%, and 48%, respectively. The vaccination program alone failed to fully eliminate the summer epidemics of influenza A(H3N2) and non-pharmacological interventions were needed to suppress the summer circulation. The quantitative understanding of the interplay among driving factors on the circulation of influenza A(H3N2) highlights the importance of simultaneous monitoring of fluctuations for related factors, which is crucial for precise and targeted prevention and control of seasonal influenza.
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Affiliation(s)
- Bing Zhang
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
- Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, People’s Republic of China
| | - Weijuan Huang
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Sen Pei
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, United States of America
| | - Jinfeng Zeng
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
| | - Wei Shen
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
- Department of Rheumatology and Immunology, Drum Tower Clinic Medical College of Nanjing Medical University, Nanjing, People’s Republic of China
| | - Daoze Wang
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
| | - Gang Wang
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
| | - Tao Chen
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Lei Yang
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Peiwen Cheng
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- * E-mail: (DW); (YS); (XD)
| | - Yuelong Shu
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Institute of Pathogen Biology of Chinese Academy of Medical Science (CAMS)/ Peking Union Medical College (PUMC), Beijing, People’s Republic of China
- * E-mail: (DW); (YS); (XD)
| | - Xiangjun Du
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, People’s Republic of China
- * E-mail: (DW); (YS); (XD)
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6
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Bivalent H1 and H3 COBRA Recombinant Hemagglutinin Vaccines Elicit Seroprotective Antibodies against H1N1 and H3N2 Influenza Viruses from 2009 to 2019. J Virol 2022; 96:e0165221. [PMID: 35289635 DOI: 10.1128/jvi.01652-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Commercial influenza virus vaccines often elicit strain-specific immune responses and have difficulties preventing illness caused by antigenically drifted viral variants. In the last 20 years, the H3N2 component of the annual vaccine has been updated nearly twice as often as the H1N1 component, and in 2019, a mismatch between the wild-type (WT) H3N2 vaccine strain and circulating H3N2 influenza strains led to a vaccine efficacy of ∼9%. Modern methods of developing computationally optimized broadly reactive antigens (COBRAs) for H3N2 influenza viruses utilize current viral surveillance information to design more broadly reactive vaccine antigens. Here, 7 new recombinant hemagglutinin (rHA) H3 COBRA hemagglutinin (HA) antigens were evaluated in mice. Subsequently, two candidates, J4 and NG2, were selected for further testing in influenza-preimmune animals based on their ability to elicit broadly reactive antibodies against antigenically drifted H3N2 viral isolates. In the preimmune model, monovalent formulations of J4 and NG2 elicited broadly reactive antibodies against recently circulating H3N2 influenza viruses from 2019. Bivalent mixtures of COBRA H1 and H3 rHA, Y2 + J4, and Y2 + NG2 outperformed multiple WT H1+H3 bivalent rHA mixtures by eliciting seroprotective antibodies against H1N1 and H3N2 isolates from 2009 to 2019. Overall, the newly generated COBRA HA antigens, namely, Y2, J4, and NG2, had the ability to induce broadly reactive antibodies in influenza-naive and preimmune animals in both monovalent and bivalent formulations, and these antigens outperformed H1 and H3 WT rHA vaccine antigens by eliciting seroprotective antibodies against panels of antigenically drifted historical H1N1 and H3N2 vaccine strains from 2009 to 2019. IMPORTANCE Standard-of-care influenza virus vaccines are composed of a mixture of antigens from different influenza viral subtypes. For the first time, lead COBRA H1 and H3 HA antigens, formulated as a bivalent vaccine, have been investigated in animals with preexisting immunity to influenza viruses. The cocktail of COBRA HA antigens elicited more broadly reactive anti-HA antibodies than those elicited by a comparator bivalent wild-type HA vaccine against H1 and H3 influenza viruses isolated between 2009 and 2019.
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7
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Foote SL, Jones S, Lockmuller J, Brown L, Breen J, Gururaj A. Parsing Immune Correlates of Protection Against SARS-CoV-2 from Biomedical Literature. AMIA ... ANNUAL SYMPOSIUM PROCEEDINGS. AMIA SYMPOSIUM 2022; 2021:466-475. [PMID: 35308924 PMCID: PMC8861695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
After the emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in 2019, identification of immune correlates of protection (CoPs) have become increasingly important to understand the immune response to SARS-CoV-2. The vast amount of preprint and published literature related to COVID-19 makes it challenging for researchers to stay up to date on research results regarding CoPs against SARS-CoV-2. To address this problem, we developed a machine learning classifier to identify papers relevant to CoPs and a customized named entity recognition (NER) model to extract terms of interest, including CoPs, vaccines, assays, and animal models. A user-friendly visualization tool was populated with the extracted and normalized NER results and associated publication information including links to full-text articles and clinical trial information where available. The goal of this pilot project is to provide a basis for developing real-time informatics platforms that can inform researchers with scientific insights from emerging research.
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Affiliation(s)
- Sydney L Foote
- Office of Data Science and Emerging Technologies, NIAID, NIH, Rockville, MD, USA
- Both authors contributed to the work equally
| | - Sara Jones
- Office of Data Science and Emerging Technologies, NIAID, NIH, Rockville, MD, USA
- Both authors contributed to the work equally
| | - Jane Lockmuller
- Office of Data Science and Emerging Technologies, NIAID, NIH, Rockville, MD, USA
| | - Liliana Brown
- Division of Microbiology and Infectious Diseases, NIAID, NIH, Rockville, MD, USA
| | - Joseph Breen
- Division of Allergy, Immunology, and Transplantation, NIAID, NIH, Rockville, MD, USA
| | - Anupama Gururaj
- Division of Allergy, Immunology, and Transplantation, NIAID, NIH, Rockville, MD, USA
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8
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Soda K, Yamane M, Hidaka C, Miura K, Ung TTH, Nguyen HLK, Ito H, LE MQ, Ito T. Prior infection with antigenically heterologous low pathogenic avian influenza viruses interferes with the lethality of the H5 highly pathogenic strain in domestic ducks. J Vet Med Sci 2021; 83:1899-1906. [PMID: 34732612 PMCID: PMC8762415 DOI: 10.1292/jvms.21-0515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Low and highly pathogenic avian influenza viruses (LPAIVs and HPAIVs, respectively) have been co-circulating in poultry populations in Asian, Middle Eastern, and African countries. In our avian-flu surveillance in Vietnamese domestic ducks, viral genes of LPAIV and HPAIV have been frequently detected in the same individual. To assess the influence of LPAIV on the pathogenicity of H5 HPAIV in domestic ducks, an experimental co-infection study was performed. One-week-old domestic ducks were inoculated intranasally and orally with PBS (control) or 106 EID50 of LPAIVs (A/duck/Vietnam/LBM678/2014 (H6N6) or A/Muscovy duck/Vietnam/LBM694/2014 (H9N2)). Seven days later, these ducks were inoculated with HPAIV (A/Muscovy duck/Vietnam/LBM808/2015 (H5N6)) in the same manner. The respective survival rates were 100% and 50% in ducks pre-infected with LBM694 or LBM678 strains and both higher than the survival of the control group (25%). The virus titers in oral/cloacal swabs of each LPAIV pre-inoculation group were significantly lower at 3-5 days post-HPAIV inoculation. Notably, almost no virus was detected in swabs from surviving individuals of the LBM678 pre-inoculation group. Antigenic cross-reactivity among the viruses was not observed in the neutralization test. These results suggest that pre-infection with LPAIV attenuates the pathogenicity of HPAIV in domestic ducks, which might be explained by innate and/or cell-mediated immunity induced by the initial infection with LPAIV.
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Affiliation(s)
- Kosuke Soda
- Department of Joint Veterinary Medicine, Faculty of Agriculture, Tottori University.,Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University
| | - Maya Yamane
- Department of Joint Veterinary Medicine, Faculty of Agriculture, Tottori University
| | - Chiharu Hidaka
- The United Graduate School of Veterinary Science, Yamaguchi University
| | - Kozue Miura
- Vietnam Research Station, Nagasaki University, c/o National Institute of Hygiene and Epidemiology.,Present address: Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Trang T H Ung
- Department of Virology, National Institute of Hygiene and Epidemiology
| | - Hang L K Nguyen
- Department of Virology, National Institute of Hygiene and Epidemiology
| | - Hiroshi Ito
- Department of Joint Veterinary Medicine, Faculty of Agriculture, Tottori University.,Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University
| | - Mai Q LE
- Department of Virology, National Institute of Hygiene and Epidemiology
| | - Toshihiro Ito
- Department of Joint Veterinary Medicine, Faculty of Agriculture, Tottori University.,Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University
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9
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Allen JD, Ross TM. Evaluation of Next-Generation H3 Influenza Vaccines in Ferrets Pre-Immune to Historical H3N2 Viruses. Front Immunol 2021; 12:707339. [PMID: 34475872 PMCID: PMC8406686 DOI: 10.3389/fimmu.2021.707339] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/21/2021] [Indexed: 11/13/2022] Open
Abstract
Each person has a unique immune history to past influenza virus infections. Exposure to influenza viruses early in life establishes memory B cell populations that influence future immune responses to influenza vaccination. Current influenza vaccines elicit antibodies that are typically strain specific and do not offer broad protection against antigenically drifted influenza strains in all age groups of people. This is particularly true for vaccine antigens of the A(H3N2) influenza virus subtype, where continual antigenic drift necessitates frequent vaccine reformulation. Broadly-reactive influenza virus vaccine antigens offer a solution to combat antigenic drift, but they also need to be equally effective in all populations, regardless of prior influenza virus exposure history. This study examined the role that pre-existing immunity plays on influenza virus vaccination. Ferrets were infected with historical A(H3N2) influenza viruses isolated from either the 1970’s, 1980’s, or 1990’s and then vaccinated with computationally optimized broadly reactive antigens (COBRA) or wild-type (WT) influenza virus like particles (VLPs) expressing hemagglutinin (HA) vaccine antigens to examine the expansion of immune breadth. Vaccines with the H3 COBRA HA antigens had more cross-reactive antibodies following a single vaccination in all three pre-immune regimens than vaccines with WT H3 HA antigens against historical, contemporary, and future drifted A(H3N2) influenza viruses. The H3 COBRA HA vaccines also induced antibodies capable of neutralizing live virus infections against modern drifted A(H3N2) strains at higher titers than the WT H3 HA vaccine comparators.
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Affiliation(s)
- James D Allen
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States.,Department of Infectious Diseases, University of Georgia, Athens, GA, United States
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Nguyen TQ, Rollon R, Choi YK. Animal Models for Influenza Research: Strengths and Weaknesses. Viruses 2021; 13:1011. [PMID: 34071367 PMCID: PMC8228315 DOI: 10.3390/v13061011] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 12/16/2022] Open
Abstract
Influenza remains one of the most significant public health threats due to its ability to cause high morbidity and mortality worldwide. Although understanding of influenza viruses has greatly increased in recent years, shortcomings remain. Additionally, the continuous mutation of influenza viruses through genetic reassortment and selection of variants that escape host immune responses can render current influenza vaccines ineffective at controlling seasonal epidemics and potential pandemics. Thus, there is a knowledge gap in the understanding of influenza viruses and a corresponding need to develop novel universal vaccines and therapeutic treatments. Investigation of viral pathogenesis, transmission mechanisms, and efficacy of influenza vaccine candidates requires animal models that can recapitulate the disease. Furthermore, the choice of animal model for each research question is crucial in order for researchers to acquire a better knowledge of influenza viruses. Herein, we reviewed the advantages and limitations of each animal model-including mice, ferrets, guinea pigs, swine, felines, canines, and non-human primates-for elucidating influenza viral pathogenesis and transmission and for evaluating therapeutic agents and vaccine efficacy.
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Affiliation(s)
- Thi-Quyen Nguyen
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Korea; (T.-Q.N.); (R.R.)
| | - Rare Rollon
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Korea; (T.-Q.N.); (R.R.)
| | - Young-Ki Choi
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Korea; (T.-Q.N.); (R.R.)
- Zoonotic Infectious Diseases Research Center, Chungbuk National University, Cheongju 28644, Korea
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Cell-Culture Adaptation of H3N2 Influenza Virus Impacts Acid Stability and Reduces Airborne Transmission in Ferret Model. Viruses 2021; 13:v13050719. [PMID: 33919124 PMCID: PMC8143181 DOI: 10.3390/v13050719] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/11/2021] [Accepted: 04/14/2021] [Indexed: 12/14/2022] Open
Abstract
Airborne transmission of seasonal and pandemic influenza viruses is the reason for their epidemiological success and public health burden in humans. Efficient airborne transmission of the H1N1 influenza virus relies on the receptor specificity and pH of fusion of the surface glycoprotein hemagglutinin (HA). In this study, we examined the role of HA pH of fusion on transmissibility of a cell-culture-adapted H3N2 virus. Mutations in the HA head at positions 78 and 212 of A/Perth/16/2009 (H3N2), which were selected after cell culture adaptation, decreased the acid stability of the virus from pH 5.5 (WT) to pH 5.8 (mutant). In addition, the mutant H3N2 virus replicated to higher titers in cell culture but had reduced airborne transmission in the ferret model. These data demonstrate that, like H1N1 HA, the pH of fusion for H3N2 HA is a determinant of efficient airborne transmission. Surprisingly, noncoding regions of the NA segment can impact the pH of fusion of mutant viruses. Taken together, our data confirm that HA acid stability is an important characteristic of epidemiologically successful human influenza viruses and is influenced by HA/NA balance.
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