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Zhu W, Gu L. Clinical, epidemiological, and genomic characteristics of a seasonal influenza A virus outbreak in Beijing: A descriptive study. J Med Virol 2023; 95:e29106. [PMID: 37712255 DOI: 10.1002/jmv.29106] [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: 08/28/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023]
Abstract
China experienced a severe influenza season that began at the end of February 2023. The aim of this post hoc analysis was to investigate the clinical, epidemiological, and genomic features of this outbreak in Beijing. The number of cases increased rapidly from the end of February and reached its peak in March, with 7262 confirmed cases included in this study. The median age was 33 years, and 50.3% of them were male. The average daily positive rate reached 69% during the peak period. The instantaneous reproduction number (Rt) showed a median of 2.1, exceeded 2.5 initially, and remaining above 1 for the following month. The most common symptoms were fever (75.0%), cough (51.0%), and expectoration (42.9%), with a median body temperature of 38.5°C (interquartile range 38-39). Eight clinical symptoms were more likely to be observed in cases with fever, with odds ratio greater than 1. Viral shedding time ranged from 3 to 25 days, with median of 7.5 days. The circulating viruses in Beijing mainly included H1N1pdm09 (clades 5a.2a and 5a.2a.1), following with H3N2 (clade 2a.2a.3a.1). The descriptive study suggests that influenza viruses in this influenza season had a higher transmissibility and longer shedding duration, with fever being the most common symptom.
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Affiliation(s)
- Wentao Zhu
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Li Gu
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
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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: 0] [Impact Index Per Article: 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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3
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Souquette A, Allen EK, Oshansky CM, Tang L, Wong SS, Jeevan T, Shi L, Pounds S, Elias G, Kuan G, Balmaseda A, Zapata R, Shaw-Saliba K, Damme PV, Tendeloo VV, Dib JC, Ogunjimi B, Webby R, Schultz-Cherry S, Pekosz A, Rothman R, Gordon A, Thomas PG. Integrated Drivers of Basal and Acute Immunity in Diverse Human Populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.25.534227. [PMID: 36993205 PMCID: PMC10055315 DOI: 10.1101/2023.03.25.534227] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Prior studies have identified genetic, infectious, and biological associations with immune competence and disease severity; however, there have been few integrative analyses of these factors and study populations are often limited in demographic diversity. Utilizing samples from 1,705 individuals in 5 countries, we examined putative determinants of immunity, including: single nucleotide polymorphisms, ancestry informative markers, herpesvirus status, age, and sex. In healthy subjects, we found significant differences in cytokine levels, leukocyte phenotypes, and gene expression. Transcriptional responses also varied by cohort, and the most significant determinant was ancestry. In influenza infected subjects, we found two disease severity immunophenotypes, largely driven by age. Additionally, cytokine regression models show each determinant differentially contributes to acute immune variation, with unique and interactive, location-specific herpesvirus effects. These results provide novel insight into the scope of immune heterogeneity across diverse populations, the integrative effects of factors which drive it, and the consequences for illness outcomes.
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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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Liao Y, Xue S, Xie Y, Zhang Y, Wang D, Zhao T, Du W, Chen T, Miao H, Qin Y, Zheng J, Yang X, Peng Z, Yu J. Characterization of influenza seasonality in China, 2010-2018: Implications for seasonal influenza vaccination timing. Influenza Other Respir Viruses 2022; 16:1161-1171. [PMID: 36062624 PMCID: PMC9530570 DOI: 10.1111/irv.13047] [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] [Received: 06/24/2022] [Revised: 08/10/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022] Open
Abstract
Background Optimizing the timing of influenza vaccination based on regional temporal seasonal influenza illness patterns may make seasonal influenza vaccination more effective in China. Methods We obtained provincial weekly influenza surveillance data for 30 of 31 provinces in mainland China from the Chinese Center for Disease Control and Prevention for the years 2010–2018. Influenza epidemiological regions were constructed by clustering analysis. For each region, we calculated onset date, end date, and duration of seasonal influenza epidemics by the modified mean threshold method. To help identify initial vaccination target populations, we acquired weekly influenza surveillance data for four age groups (0–4, 5–18, 19–59, and ≥60 years) in each region and in 171 cities of wide‐ranging size. We used linear regression analyses to explore the association of epidemic onset dates by age group, city, and epidemiological region and provide evidence for initial target populations for seasonal influenza vaccination. Results We determined that northern, mid, southwestern, southeast regions of mainland China have distinct seasonal influenza epidemic patterns. We found significant regional, temporal, and spatial heterogeneity of seasonal influenza epidemics. There were significant differences by age group and city size in the interval between epidemic onset in the city or age group and regional spread (epidemic lead time), with longer epidemic lead times for 5‐ to 18‐year‐old children and larger cities. Conclusions Knowledge of influenza epidemic characteristics may help optimize local influenza vaccination timing and identify initial target groups for seasonal influenza vaccination in mainland China. Similar analyses may help inform seasonal influenza vaccination strategies in other regions and countries.
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Affiliation(s)
- Yilan Liao
- State Key Laboratory of Resources and Environmental Information System, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Shan Xue
- State Key Laboratory of Resources and Environmental Information System, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yiran Xie
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yanping Zhang
- Division of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dayan Wang
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Tong Zhao
- State Key Laboratory of Resources and Environmental Information System, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Wei Du
- School of Public Health, Southeast University, Nanjing, China
| | - Tao Chen
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hui Miao
- College of Art and Science, Ohio State University, Columbus, Ohio, USA
| | - Ying Qin
- Division of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jiandong Zheng
- Division of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaokun Yang
- Division of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhibin Peng
- Division of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jianxing Yu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Canaday LM, Resnick JD, Liu H, Powell H, McCoy AM, Nguyen D, Pekosz A. HA and M2 sequences alter the replication of 2013-16 H1 live attenuated influenza vaccine infection in human nasal epithelial cell cultures. Vaccine 2022; 40:4544-4553. [PMID: 35718589 DOI: 10.1016/j.vaccine.2022.05.088] [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: 11/12/2021] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 10/18/2022]
Abstract
From 2013 to 2016, the H1N1 component of live, attenuated influenza vaccine (LAIV) performed very poorly in contrast to the inactivated influenza vaccine. We utilized a primary, differentiated human nasal epithelial cell (hNEC) culture system to assess the replication differences between isogenic LAIVs containing the HA segment from either A/Bolivia/559/2013 (rBol), which showed poor vaccine efficacy, and A/Slovenia/2903/2015 (rSlov), which had reasonable vaccine efficacy. There were minimal differences in infectious virus production in Madin-Darby Canine Kidney (MDCK) cells, but the rSlov LAIV showed markedly improved replication in hNEC cultures at both 32 °C and 37 °C, demonstrating that the HA segment alone could impact LAIV replication in physiologically relevant systems. The rSlov-infected hNEC cultures showed stronger production of interferon and proinflammatory chemokines which might also be contributing to the increased overall vaccine effectiveness through enhanced recruitment and activation of immune cells. An M2-S86A mutation had no positive effects on H1 LAIV replication in hNEC cultures, in contrast to the increased infectious virus production seen in an H3 LAIV. No obvious defects in viral RNA packaging were detected, suggesting that HA function, rather than defective particle production, may be driving the differential infectious virus production in hNEC cultures. Overall, we have shown that not all H1 HA segments can be successfully used in LAIV, and this phenotype cannot be fully explained by segment incompatibilities. Physiologically relevant temperatures and primary cell cultures should be used to demonstrate that candidate LAIVs can replicate efficiently, which is a necessary property for effective vaccines.
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Affiliation(s)
- Laura M Canaday
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jessica D Resnick
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hsuan Liu
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Harrison Powell
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Alyssa M McCoy
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Dat Nguyen
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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