1
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Han AX, de Jong SPJ, Russell CA. Co-evolution of immunity and seasonal influenza viruses. Nat Rev Microbiol 2023; 21:805-817. [PMID: 37532870 DOI: 10.1038/s41579-023-00945-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2023] [Indexed: 08/04/2023]
Abstract
Seasonal influenza viruses cause recurring global epidemics by continually evolving to escape host immunity. The viral constraints and host immune responses that limit and drive the evolution of these viruses are increasingly well understood. However, it remains unclear how most of these advances improve the capacity to reduce the impact of seasonal influenza viruses on human health. In this Review, we synthesize recent progress made in understanding the interplay between the evolution of immunity induced by previous infections or vaccination and the evolution of seasonal influenza viruses driven by the heterogeneous accumulation of antibody-mediated immunity in humans. We discuss the functional constraints that limit the evolution of the viruses, the within-host evolutionary processes that drive the emergence of new virus variants, as well as current and prospective options for influenza virus control, including the viral and immunological barriers that must be overcome to improve the effectiveness of vaccines and antiviral drugs.
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Affiliation(s)
- Alvin X Han
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Simon P J de Jong
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Colin A Russell
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
- Department of Global Health, School of Public Health, Boston University, Boston, MA, USA.
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2
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Francis ME, Jansen EB, Yourkowski A, Selim A, Swan CL, MacPhee BK, Thivierge B, Buchanan R, Lavender KJ, Darbellay J, Rogers MB, Lew J, Gerdts V, Falzarano D, Skowronski DM, Sjaarda C, Kelvin AA. Previous infection with seasonal coronaviruses does not protect male Syrian hamsters from challenge with SARS-CoV-2. Nat Commun 2023; 14:5990. [PMID: 37752151 PMCID: PMC10522707 DOI: 10.1038/s41467-023-41761-1] [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: 02/22/2023] [Accepted: 09/12/2023] [Indexed: 09/28/2023] Open
Abstract
SARS-CoV-2 variants and seasonal coronaviruses continue to cause disease and coronaviruses in the animal reservoir pose a constant spillover threat. Importantly, understanding of how previous infection may influence future exposures, especially in the context of seasonal coronaviruses and SARS-CoV-2 variants, is still limited. Here we adopted a step-wise experimental approach to examine the primary immune response and subsequent immune recall toward antigenically distinct coronaviruses using male Syrian hamsters. Hamsters were initially inoculated with seasonal coronaviruses (HCoV-NL63, HCoV-229E, or HCoV-OC43), or SARS-CoV-2 pango B lineage virus, then challenged with SARS-CoV-2 pango B lineage virus, or SARS-CoV-2 variants Beta or Omicron. Although infection with seasonal coronaviruses offered little protection against SARS-CoV-2 challenge, HCoV-NL63-infected animals had an increase of the previously elicited HCoV-NL63-specific neutralizing antibodies during challenge with SARS-CoV-2. On the other hand, primary infection with HCoV-OC43 induced distinct T cell gene signatures. Gene expression profiling indicated interferon responses and germinal center reactions to be induced during more similar primary infection-challenge combinations while signatures of increased inflammation as well as suppression of the antiviral response were observed following antigenically distant viral challenges. This work characterizes and analyzes seasonal coronaviruses effect on SARS-CoV-2 secondary infection and the findings are important for pan-coronavirus vaccine design.
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Affiliation(s)
- Magen E Francis
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Ethan B Jansen
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Anthony Yourkowski
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Alaa Selim
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Cynthia L Swan
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
| | - Brian K MacPhee
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Brittany Thivierge
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
| | - Rachelle Buchanan
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kerry J Lavender
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Joseph Darbellay
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
| | - Matthew B Rogers
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jocelyne Lew
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
| | - Volker Gerdts
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
| | - Darryl Falzarano
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
| | - Danuta M Skowronski
- BC Centre for Disease Control, Immunization Programs and Vaccine Preventable Diseases Service, Vancouver, BC, Canada
- University of British Columbia, School of Population and Public Health, Vancouver, BC, Canada
| | - Calvin Sjaarda
- Department of Psychiatry, Queen's University, Kingston, ON, Canada
- Queen's Genomics Lab at Ongwanada (Q-GLO), Ongwanada Resource Centre, Kingston, ON, Canada
| | - Alyson A Kelvin
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada.
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3
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Tsang TK, Gostic KM, Chen S, Wang Y, Arevalo P, Lau EHY, Cobey S, Cowling BJ. Investigation of the Impact of Childhood Immune Imprinting on Birth Year-Specific Risk of Clinical Infection During Influenza A Virus Epidemics in Hong Kong. J Infect Dis 2023; 228:169-172. [PMID: 36637115 PMCID: PMC10345470 DOI: 10.1093/infdis/jiad009] [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: 10/17/2022] [Revised: 01/04/2023] [Accepted: 01/11/2023] [Indexed: 01/14/2023] Open
Abstract
Influenza imprinting reduces risks of influenza A virus clinical infection by 40%-90%, estimated from surveillance data in western countries. We analyzed surveillance data from 2010 to 2019 in Hong Kong. Based on the best model, which included hemagglutinin group-level imprinting, we estimated that individuals imprinted to H1N1 or H2N2 had a 17% (95% confidence interval [CI], 3%-28%) lower risk of H1N1 clinical infection, and individuals imprinted to H3N2 would have 12% (95% CI, -3% to 26%) lower risk of H3N2 clinical infection. These estimated imprinting protections were weaker than estimates in western countries. Identifying factors affecting imprinting protections is important for control policies and disease modeling.
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Affiliation(s)
- Tim K Tsang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory of Data Discovery for Health, Hong Kong Special Administrative Region, China
| | - Katelyn M Gostic
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA
| | - Sijie Chen
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Yifan Wang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Philip Arevalo
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA
| | - Eric H Y Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory of Data Discovery for Health, Hong Kong Special Administrative Region, China
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory of Data Discovery for Health, Hong Kong Special Administrative Region, China
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Warmath CR, Ortega-Sanchez IR, Duca LM, Porter RM, Usher MG, Bresee JS, Lafond KE, Davis WW. Comparisons in the Health and Economic Assessments of Using Quadrivalent Versus Trivalent Influenza Vaccines: A Systematic Literature Review. VALUE IN HEALTH : THE JOURNAL OF THE INTERNATIONAL SOCIETY FOR PHARMACOECONOMICS AND OUTCOMES RESEARCH 2023; 26:768-779. [PMID: 36436790 DOI: 10.1016/j.jval.2022.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 10/05/2022] [Accepted: 11/16/2022] [Indexed: 05/03/2023]
Abstract
OBJECTIVES Seasonal influenza vaccines protect against 3 (trivalent influenza vaccine [IIV3]) or 4 (quadrivalent influenza vaccine [IIV4]) viruses. IIV4 costs more than IIV3, and there is a trade-off between incremental cost and protection. This is especially the case in low- and middle-income countries (LMICs) with limited budgets; previous reviews have not identified studies of IIV4-IIV3 comparisons in LMICs. We summarized the literature that compared health and economic outcomes of IIV4 and IIV3, focused on LMICs. METHODS We systematically searched 5 databases for articles published before October 6, 2021, that modeled health or economic effects of IIV4 versus IIV3. We abstracted data and compared findings among countries and models. RESULTS Thirty-eight studies fit our selection criteria; 10 included LMICs. Most studies (N = 31) reported that IIV4 was cost-saving or cost-effective compared with IIV3; we observed no difference in health or economic outcomes between LMICs and other countries. Based on cost differences of influenza vaccines, only one study compared coverage of IIV3 with IIV4 and reported that the maximum IIV4 price that would still yield greater public health impact than IIV3 was 13% to 22% higher than IIV3. CONCLUSIONS When vaccination coverage with IIV4 and IIV3 is the same, IIV4 tends to be not only more effective but more cost-effective than IIV3, even with relatively high price differences between vaccine types. Alternatively, where funding is limited as in most LMICs, higher vaccine coverage can be achieved with IIV3 than IIV4, which could result in more favorable health and economic outcomes.
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Affiliation(s)
- Clara R Warmath
- Department of Epidemiology, School of Public Health, Brown University, Providence, RI, USA
| | - Ismael R Ortega-Sanchez
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lindsey M Duca
- Influenza Division, National Center for Immunization and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Rachael M Porter
- Influenza Division, National Center for Immunization and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Molly G Usher
- Department of Epidemiology, School of Public Health, Brown University, Providence, RI, USA
| | - Joseph S Bresee
- Partnership for Influenza Vaccine Introduction, The Task Force for Global Health, Decatur, GA, USA
| | - Kathryn E Lafond
- Influenza Division, National Center for Immunization and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, GA, USA
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5
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Jurkowicz M, Nemet I, Atari N, Fratty IS, Kliker L, Sherbany H, Keller N, Leibovitz E, Mendelson E, Mandelboim M, Stein M. Cocirculation of A(H3N2) and B/Victoria increased morbidity in hospitalized patients in the 2019-2020 A(H1N1)pdm09 predominant influenza season in Israel. J Med Virol 2023; 95:e28498. [PMID: 36653733 PMCID: PMC10107483 DOI: 10.1002/jmv.28498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/03/2023] [Accepted: 01/14/2023] [Indexed: 01/20/2023]
Abstract
Community surveillance found the 2019-2020 A(H1N1)pdm09 predominant influenza season in Israel to be a high-intensity season with an early and steep morbidity peak. To further characterize disease severity in the 2019-2020 season, we analyzed a cohort of hospitalized patients with laboratory-confirmed influenza from this season (n = 636). Quantitative polymerase chain reaction was performed on clinical samples to detect the presence of influenza. Demographic, clinical, and laboratory data were retrieved via electronic health records and MDClone. Electronic health records were accessed to obtain data on intensive care unit patients, missing data and for data verification purposes. Univariate analysis was performed to compare demographic, comorbidity, and clinical characteristics across the three influenza strains. The A(H1N1)pdm09 predominant 2019-2020 influenza season in Israel was characterized by an early and steep morbidity peak, vaccine delays and shortages, and with the A(H3N2) and B/Victoria strains disproportionately targeting children and young adults, most probably due to reduced immunity to these strains. A greater proportion of children <5 years infected with A(H3N2) and B/Victoria developed severe influenza compared with those infected with A(H1N1)pdm09. Our study emphasizes the vulnerability of infants and young children in the face of rapidly evolving influenza strains and underscores the importance of influenza prevention measures in this population.
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Affiliation(s)
- Menucha Jurkowicz
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Infectious Disease Unit, The Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Centre, Ramat Gan, Israel
| | - Ital Nemet
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Nofar Atari
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Ilana S Fratty
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel.,The Israel Center for Disease Control, Ministry of Health, Tel Hashomer, Israel
| | - Limor Kliker
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Hilda Sherbany
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | | | - Eugene Leibovitz
- Pediatric Infectious Disease Unit, The Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Centre, Ramat Gan, Israel
| | - Ella Mendelson
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Michal Mandelboim
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Michal Stein
- Pediatric Infectious Disease Unit, The Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Centre, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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6
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Yang B, García-Carreras B, Lessler J, Read JM, Zhu H, Metcalf CJE, Hay JA, Kwok KO, Shen R, Jiang CQ, Guan Y, Riley S, Cummings DA. Long term intrinsic cycling in human life course antibody responses to influenza A(H3N2): an observational and modeling study. eLife 2022; 11:81457. [PMID: 36458815 PMCID: PMC9757834 DOI: 10.7554/elife.81457] [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: 06/28/2022] [Accepted: 12/01/2022] [Indexed: 12/05/2022] Open
Abstract
Background Over a life course, human adaptive immunity to antigenically mutable pathogens exhibits competitive and facilitative interactions. We hypothesize that such interactions may lead to cyclic dynamics in immune responses over a lifetime. Methods To investigate the cyclic behavior, we analyzed hemagglutination inhibition titers against 21 historical influenza A(H3N2) strains spanning 47 years from a cohort in Guangzhou, China, and applied Fourier spectrum analysis. To investigate possible biological mechanisms, we simulated individual antibody profiles encompassing known feedbacks and interactions due to generally recognized immunological mechanisms. Results We demonstrated a long-term periodicity (about 24 years) in individual antibody responses. The reported cycles were robust to analytic and sampling approaches. Simulations suggested that individual-level cross-reaction between antigenically similar strains likely explains the reported cycle. We showed that the reported cycles are predictable at both individual and birth cohort level and that cohorts show a diversity of phases of these cycles. Phase of cycle was associated with the risk of seroconversion to circulating strains, after accounting for age and pre-existing titers of the circulating strains. Conclusions Our findings reveal the existence of long-term periodicities in individual antibody responses to A(H3N2). We hypothesize that these cycles are driven by preexisting antibody responses blunting responses to antigenically similar pathogens (by preventing infection and/or robust antibody responses upon infection), leading to reductions in antigen-specific responses over time until individual's increasing risk leads to an infection with an antigenically distant enough virus to generate a robust immune response. These findings could help disentangle cohort effects from individual-level exposure histories, improve our understanding of observed heterogeneous antibody responses to immunizations, and inform targeted vaccine strategy. Funding This study was supported by grants from the NIH R56AG048075 (DATC, JL), NIH R01AI114703 (DATC, BY), the Wellcome Trust 200861/Z/16/Z (SR), and 200187/Z/15/Z (SR). This work was also supported by research grants from Guangdong Government HZQB-KCZYZ-2021014 and 2019B121205009 (YG and HZ). DATC, JMR and SR acknowledge support from the National Institutes of Health Fogarty Institute (R01TW0008246). JMR acknowledges support from the Medical Research Council (MR/S004793/1) and the Engineering and Physical Sciences Research Council (EP/N014499/1). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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Affiliation(s)
- Bingyi Yang
- Department of Biology, University of FloridaGainesvilleUnited States
- Emerging Pathogens Institute, University of FloridaGainesvilleUnited States
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong KongHong KongChina
| | - Bernardo García-Carreras
- Department of Biology, University of FloridaGainesvilleUnited States
- Emerging Pathogens Institute, University of FloridaGainesvilleUnited States
| | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
- Department of Epidemiology, UNC Gillings School of Global Public HealthChapel HillUnited States
- UNC Carolina Population CenterChapel HillUnited States
| | - Jonathan M Read
- Centre for Health Informatics Computing and Statistics, Lancaster UniversityLancasterUnited Kingdom
| | - Huachen Zhu
- Guangdong‐Hong Kong Joint Laboratory of Emerging Infectious Diseases/MOE Joint Laboratory for International Collaboration in Virology and Emerging Infectious Diseases, Joint Institute of Virology (Shantou University/The University of Hong Kong), Shantou UniversityShantouChina
- State Key Laboratory of Emerging Infectious Diseases / World Health Organization Influenza Reference Laboratory, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong KongHong KongChina
- EKIH (Gewuzhikang) Pathogen Research InstituteGuangdongChina
| | - C Jessica E Metcalf
- Department of Ecology and Evolutionary Biology, Princeton UniversityPrincetonUnited States
| | - James A Hay
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College LondonLondonUnited Kingdom
- Center for Communicable Disease Dynamics, Harvard TH Chan School of Public HealthBostonUnited States
| | - Kin O Kwok
- The Jockey Club School of Public Health and Primary Care, Chinese University of Hong KongHong KongChina
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong KongHong KongChina
- Shenzhen Research Institute of The Chinese University of Hong KongGuangdongChina
| | - Ruiyun Shen
- Guangzhou No.12 Hospital, GuangzhouGuangdongChina
| | - Chao Q Jiang
- Guangzhou No.12 Hospital, GuangzhouGuangdongChina
| | - Yi Guan
- Guangdong‐Hong Kong Joint Laboratory of Emerging Infectious Diseases/MOE Joint Laboratory for International Collaboration in Virology and Emerging Infectious Diseases, Joint Institute of Virology (Shantou University/The University of Hong Kong), Shantou UniversityShantouChina
- State Key Laboratory of Emerging Infectious Diseases / World Health Organization Influenza Reference Laboratory, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong KongHong KongChina
- EKIH (Gewuzhikang) Pathogen Research InstituteGuangdongChina
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College LondonLondonUnited Kingdom
| | - Derek A Cummings
- Department of Biology, University of FloridaGainesvilleUnited States
- Emerging Pathogens Institute, University of FloridaGainesvilleUnited States
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7
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Xie R, Adam DC, Edwards KM, Gurung S, Wei X, Cowling BJ, Dhanasekaran V. Genomic Epidemiology of Seasonal Influenza Circulation in China During Prolonged Border Closure from 2020 to 2021. Virus Evol 2022; 8:veac062. [PMID: 35919872 PMCID: PMC9338706 DOI: 10.1093/ve/veac062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 12/04/2022] Open
Abstract
China experienced a resurgence of seasonal influenza activity throughout 2021 despite intermittent control measures and prolonged international border closure. We show genomic evidence for multiple A(H3N2), A(H1N1), and B/Victoria transmission lineages circulating over 3 years, with the 2021 resurgence mainly driven by two B/Victoria clades. Phylodynamic analysis revealed unsampled ancestry prior to widespread outbreaks in December 2020, showing that influenza lineages can circulate cryptically under non-pharmaceutical interventions enacted against COVID-19. Novel haemagglutinin gene mutations and altered age profiles of infected individuals were observed, and Jiangxi province was identified as a major source for nationwide outbreaks. Following major holiday periods, fluctuations in the effective reproduction number were observed, underscoring the importance of influenza vaccination prior to holiday periods or travel. Extensive heterogeneity in seasonal influenza circulation patterns in China determined by historical strain circulation indicates that a better understanding of demographic patterns is needed for improving effective controls.
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Affiliation(s)
- 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
| | - Dillon C Adam
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong , Hong Kong, China
| | - Kimberly M Edwards
- 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
| | - Shreya Gurung
- 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
| | - Xiaoman Wei
- 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
| | - Benjamin J Cowling
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong , Hong Kong, China
| | - 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
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8
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Vaccine Mismatches, Viral Circulation, and Clinical Severity Patterns of Influenza B Victoria and Yamagata Infections in Brazil over the Decade 2010-2020: A Statistical and Phylogeny-Trait Analyses. Viruses 2022; 14:v14071477. [PMID: 35891457 PMCID: PMC9321334 DOI: 10.3390/v14071477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/25/2022] [Accepted: 07/01/2022] [Indexed: 12/15/2022] Open
Abstract
Worldwide, infections by influenza viruses are considered a major public health challenge. In this study, influenza B vaccine mismatches and clinical aspects of Victoria and Yamagata infections in Brazil were assessed. Clinical samples were collected from patients suspected of influenza infection. In addition, sociodemographic, clinical, and epidemiological information were collected by the epidemiological surveillance teams. Influenza B lineages were determined by real-time RT-PCR and/or Sanger sequencing. In addition, putative phylogeny−trait associations were assessed by using the BaTS program after phylogenetic reconstruction by a Bayesian Markov Chain Monte Carlo method (BEAST software package). Over 2010−2020, B/Victoria and B/Yamagata-like lineages co-circulated in almost all seasonal epidemics, with B/Victoria predominance in most years. Vaccine mismatches between circulating viruses and the trivalent vaccine strains occurred in five of the eleven seasons (45.5%). No significant differences were identified in clinical presentation or disease severity caused by both strains, but subjects infected by B/Victoria-like viruses were significantly younger than their B/Yamagata-like counterparts (16.7 vs. 31.4 years, p < 0.001). This study contributes to a better understanding of the circulation patterns and clinical outcomes of B/Victoria- and B/Yamagata-like lineages in Brazil and advocate for the inclusion of a quadrivalent vaccine in the scope of the Brazilian National Immunization Program.
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9
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Howson-Wells HC, Tsoleridis T, Zainuddin I, Tarr AW, Irving WL, Ball JK, Berry L, Clark G, McClure CP. Enterovirus D68 epidemic, UK, 2018, was caused by subclades B3 and D1, predominantly in children and adults, respectively, with both subclades exhibiting extensive genetic diversity. Microb Genom 2022; 8:mgen000825. [PMID: 35532121 PMCID: PMC9465064 DOI: 10.1099/mgen.0.000825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enterovirus D68 (EV-D68) has recently been identified in biennial epidemics coinciding with diagnoses of non-polio acute flaccid paralysis/myelitis (AFP/AFM). We investigated the prevalence, genetic relatedness and associated clinical features of EV-D68 in 193 EV-positive samples from 193 patients in late 2018, UK. EV-D68 was detected in 83 (58 %) of 143 confirmed EV-positive samples. Sequencing and phylogenetic analysis revealed extensive genetic diversity, split between subclades B3 (n=50) and D1 (n=33), suggesting epidemiologically unrelated infections. B3 predominated in children and younger adults, and D1 in older adults and the elderly (P=0.0009). Clinical presentation indicated causation or exacerbation of respiratory distress in 91.4 % of EV-D68-positive individuals, principally cough (75.3 %), shortness of breath (56.8 %), coryza (48.1 %), wheeze (46.9 %), supplemental oxygen required (46.9 %) and fever (38.9 %). Two cases of AFM were observed, one with EV-D68 detectable in the cerebrospinal fluid, but otherwise neurological symptoms were rarely reported (n=4). Both AFM cases and all additional instances of intensive care unit (ICU) admission (n=5) were seen in patients infected with EV-D68 subclade B3. However, due to the infrequency of severe infection in our cohort, statistical significance could not be assessed.
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Affiliation(s)
| | - Theocharis Tsoleridis
- School of Life Sciences, University of Nottingham, Nottingham, UK.,Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, UK
| | - Izzah Zainuddin
- Clinical Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Alexander W Tarr
- School of Life Sciences, University of Nottingham, Nottingham, UK.,Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, UK
| | - William L Irving
- Clinical Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, UK.,School of Life Sciences, University of Nottingham, Nottingham, UK.,Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, UK
| | - Jonathan K Ball
- School of Life Sciences, University of Nottingham, Nottingham, UK.,Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, UK
| | - Louise Berry
- Clinical Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, UK.,School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Gemma Clark
- Clinical Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - C Patrick McClure
- School of Life Sciences, University of Nottingham, Nottingham, UK.,Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, UK
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10
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Human seasonal influenza under COVID-19 and the potential consequences of influenza lineage elimination. Nat Commun 2022; 13:1721. [PMID: 35361789 PMCID: PMC8971476 DOI: 10.1038/s41467-022-29402-5] [Citation(s) in RCA: 96] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 03/11/2022] [Indexed: 11/24/2022] Open
Abstract
Annual epidemics of seasonal influenza cause hundreds of thousands of deaths, high levels of morbidity, and substantial economic loss. Yet, global influenza circulation has been heavily suppressed by public health measures and travel restrictions since the onset of the COVID-19 pandemic. Notably, the influenza B/Yamagata lineage has not been conclusively detected since April 2020, and A(H3N2), A(H1N1), and B/Victoria viruses have since circulated with considerably less genetic diversity. Travel restrictions have largely confined regional outbreaks of A(H3N2) to South and Southeast Asia, B/Victoria to China, and A(H1N1) to West Africa. Seasonal influenza transmission lineages continue to perish globally, except in these select hotspots, which will likely seed future epidemics. Waning population immunity and sporadic case detection will further challenge influenza vaccine strain selection and epidemic control. We offer a perspective on the potential short- and long-term evolutionary dynamics of seasonal influenza and discuss potential consequences and mitigation strategies as global travel gradually returns to pre-pandemic levels. COVID-19 control measures have suppressed circulation of other infections including influenza. Here, the authors analyse WHO global influenza sequence and case report data and describe changes in the phylogenetic and geographic distribution of influenza lineages during the COVID-19 pandemic.
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11
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Wraith S, Balmaseda A, Carrillo FAB, Kuan G, Huddleston J, Kubale J, Lopez R, Ojeda S, Schiller A, Lopez B, Sanchez N, Webby R, Nelson MI, Harris E, Gordon A. Homotypic protection against influenza in a pediatric cohort in Managua, Nicaragua. Nat Commun 2022; 13:1190. [PMID: 35246548 PMCID: PMC8897407 DOI: 10.1038/s41467-022-28858-9] [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: 09/28/2021] [Accepted: 02/16/2022] [Indexed: 12/02/2022] Open
Abstract
The period of protection from repeat infection following symptomatic influenza is not well established due to limited availability of longitudinal data. Using data from a pediatric cohort in Managua, Nicaragua, we examine the effects of natural influenza virus infection on subsequent infection with the same influenza virus subtype/lineage across multiple seasons, totaling 2,170 RT-PCR-confirmed symptomatic influenza infections. Logistic regression models assessed whether infection in the prior influenza season protected against homologous reinfection. We sequenced viruses from 2011-2019 identifying dominant clades and measuring antigenic distances between hemagglutinin clades. We observe homotypic protection from repeat infection in children infected with influenza A/H1N1pdm (OR 0.12, CI 0.02-0.88), A/H3N2 (OR 0.41, CI 0.24-0.73), and B/Victoria (OR 0.00, CI 0.00-0.14), but not with B/Yamagata viruses (OR 0.60, CI 0.09-2.10). Overall, protection wanes as time or antigenic distance increases. Individuals infected with one subtype or lineage of influenza virus have significantly lower odds of homologous reinfection for the following one to two years; after two years this protection wanes. This protection is demonstrated across multiple seasons, subtypes, and lineages among children.
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Affiliation(s)
- Steph Wraith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Angel Balmaseda
- Sustainable Sciences Institute, Managua, Nicaragua
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Fausto Andres Bustos Carrillo
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Guillermina Kuan
- Sustainable Sciences Institute, Managua, Nicaragua
- Centro de Salud Sócrates Flores Vivas, Ministry of Health, Managua, Nicaragua
| | - John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - John Kubale
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Roger Lopez
- Sustainable Sciences Institute, Managua, Nicaragua
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Sergio Ojeda
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Amy Schiller
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Brenda Lopez
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Nery Sanchez
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Richard Webby
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Aubree Gordon
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA.
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12
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Bull MB, Cohen CA, Leung NH, Valkenburg SA. Universally Immune: How Infection Permissive Next Generation Influenza Vaccines May Affect Population Immunity and Viral Spread. Viruses 2021; 13:1779. [PMID: 34578360 PMCID: PMC8472936 DOI: 10.3390/v13091779] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 12/24/2022] Open
Abstract
Next generation influenza vaccines that target conserved epitopes are becoming a clinical reality but still have challenges to overcome. Universal next generation vaccines are considered a vital tool to combat future pandemic viruses and have the potential to vastly improve long-term protection against seasonal influenza viruses. Key vaccine strategies include HA-stem and T cell activating vaccines; however, they could have unintended effects for virus adaptation as they recognise the virus after cell entry and do not directly block infection. This may lead to immune pressure on residual viruses. The potential for immune escape is already evident, for both the HA stem and T cell epitopes, and mosaic approaches for pre-emptive immune priming may be needed to circumvent key variants. Live attenuated influenza vaccines have not been immunogenic enough to boost T cells in adults with established prior immunity. Therefore, viral vectors or peptide approaches are key to harnessing T cell responses. A plethora of viral vector vaccines and routes of administration may be needed for next generation vaccine strategies that require repeated long-term administration to overcome vector immunity and increase our arsenal against diverse influenza viruses.
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Affiliation(s)
- Maireid B. Bull
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China; (M.B.B.); (C.A.C.)
| | - Carolyn A. Cohen
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China; (M.B.B.); (C.A.C.)
| | - 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, China;
| | - Sophie A. Valkenburg
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China; (M.B.B.); (C.A.C.)
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