1
|
Ashraf MA, Raza MA, Amjad MN. Extinction of influenza B Yamagata: Its impact on public health and vaccine implications. J Biomed Res 2024; 38:1-4. [PMID: 39164195 DOI: 10.7555/jbr.38.20240158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2024] Open
Affiliation(s)
- Muhammad Awais Ashraf
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Muhammad Asif Raza
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Muhammad Nabeel Amjad
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| |
Collapse
|
2
|
Bendall EE, Zhu Y, Fitzsimmons WJ, Rolfes M, Mellis A, Halasa N, Martin ET, Grijalva CG, Talbot HK, Lauring AS. Influenza A virus within-host evolution and positive selection in a densely sampled household cohort over three seasons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.15.608152. [PMID: 39229225 PMCID: PMC11370358 DOI: 10.1101/2024.08.15.608152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
While influenza A virus (IAV) antigenic drift has been documented globally, in experimental animal infections, and in immunocompromised hosts, positive selection has generally not been detected in acute infections. This is likely due to challenges in distinguishing selected rare mutations from sequencing error, a reliance on cross-sectional sampling, and/or the lack of formal tests of selection for individual sites. Here, we sequenced IAV populations from 346 serial, daily nasal swabs from 143 individuals collected over three influenza seasons in a household cohort. Viruses were sequenced in duplicate, and intrahost single nucleotide variants (iSNV) were identified at a 0.5% frequency threshold. Within-host populations were subject to purifying selection with >75% mutations present at <2% frequency. Children (0-5 years) had marginally higher within-host evolutionary rates than adolescents (6-18 years) and adults (>18 years, 4.4x10 -6 vs. 9.42x10 -7 and 3.45x10 -6 , p <0.001). Forty-five iSNV had evidence of parallel evolution, but were not overrepresented in HA and NA. Several increased from minority to consensus level, with strong linkage among iSNV across segments. A Wright Fisher Approximate Bayesian Computational model identified positive selection at 23/256 loci (9%) in A(H3N2) specimens and 19/176 loci (11%) in A(H1N1)pdm09 specimens, and these were infrequently found in circulation. Overall, we found that within-host IAV populations were subject to purifying selection and genetic drift, with only subtle differences across seasons, subtypes, and age strata. Positive selection was rare and inconsistently detected.
Collapse
|
3
|
Zeng Z, Liu Y, Jin W, Liang J, Chen J, Chen R, Li Q, Guan W, Liang L, Wu Q, Lai Y, Deng X, Lin Z, Hon C, Yang Z. Molecular epidemiology and phylogenetic analysis of influenza viruses A (H3N2) and B/Victoria during the COVID-19 pandemic in Guangdong, China. Infect Dis Poverty 2024; 13:56. [PMID: 39090685 PMCID: PMC11295596 DOI: 10.1186/s40249-024-01218-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: 01/17/2024] [Accepted: 06/21/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Non-pharmaceutical measures and travel restrictions have halted the spread of coronavirus disease 2019 (COVID-19) and influenza. Nonetheless, with COVID-19 restrictions lifted, an unanticipated outbreak of the influenza B/Victoria virus in late 2021 and another influenza H3N2 outbreak in mid-2022 occurred in Guangdong, southern China. The mechanism underlying this phenomenon remains unknown. To better prepare for potential influenza outbreaks during COVID-19 pandemic, we studied the molecular epidemiology and phylogenetics of influenza A(H3N2) and B/Victoria that circulated during the COVID-19 pandemic in this region. METHODS From January 1, 2018 to December 31, 2022, we collected throat swabs from 173,401 patients in Guangdong who had acute respiratory tract infections. Influenza viruses in the samples were tested using reverse transcription-polymerase chain reaction, followed by subtype identification and sequencing of hemagglutinin (HA) and neuraminidase (NA) genes. Phylogenetic and genetic diversity analyses were performed on both genes from 403 samples. A rigorous molecular clock was aligned with the phylogenetic tree to measure the rate of viral evolution and the root-to-tip distance within strains in different years was assessed using regression curve models to determine the correlation. RESULTS During the early period of COVID-19 control, various influenza viruses were nearly undetectable in respiratory specimens. When control measures were relaxed in January 2020, the influenza infection rate peaked at 4.94% (39/789) in December 2021, with the influenza B/Victoria accounting for 87.18% (34/39) of the total influenza cases. Six months later, the influenza infection rate again increased and peaked at 11.34% (255/2248) in June 2022; influenza A/H3N2 accounted for 94.51% (241/255) of the total influenza cases in autumn 2022. The diverse geographic distribution of HA genes of B/Victoria and A/H3N2 had drastically reduced, and most strains originated from China. The rate of B/Victoria HA evolution (3.11 × 10-3, P < 0.05) was 1.7 times faster than before the COVID-19 outbreak (1.80 × 10-3, P < 0.05). Likewise, the H3N2 HA gene's evolution rate was 7.96 × 10-3 (P < 0.05), which is 2.1 times faster than the strains' pre-COVID-19 evolution rate (3.81 × 10-3, P < 0.05). CONCLUSIONS Despite the extraordinarily low detection rate of influenza infection, concealed influenza transmission may occur between individuals during strict COVID-19 control. This ultimately leads to the accumulation of viral mutations and accelerated evolution of H3N2 and B/Victoria viruses. Monitoring the evolution of influenza may provide insights and alerts regarding potential epidemics in the future.
Collapse
Affiliation(s)
- Zhiqi Zeng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510180, P.R. China
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, People's Republic of China
- Respiratory Disease AI Laboratory on Epidemic Intelligence and Medical Big Data Instrument Applications, Faculty of Innovative Engineering, Macau University of Science and Technology, Macau SAR, China
| | - Yong Liu
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, People's Republic of China
- Kingmed Virology Diagnostic and Translational Center, Guangzhou Kingmed Center for Clinical Laboratory Co., Ltd., Guangzhou, China
| | - Wenxiang Jin
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, People's Republic of China
- Kingmed Virology Diagnostic and Translational Center, Guangzhou Kingmed Center for Clinical Laboratory Co., Ltd., Guangzhou, China
| | - Jingyi Liang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510180, P.R. China
- Department of Engineering Science, Faculty of Innovation Engineering, Macau University of Science and Technology, Taipa, Macau, China
| | - Jinbin Chen
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Ruihan Chen
- Department of Engineering Science, Faculty of Innovation Engineering, Macau University of Science and Technology, Taipa, Macau, China
| | - Qianying Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510180, P.R. China
| | - Wenda Guan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510180, P.R. China
| | - Lixi Liang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510180, P.R. China
| | - Qiubao Wu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510180, P.R. China
| | - Yuanfang Lai
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Xiaoyan Deng
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, People's Republic of China.
| | - Zhengshi Lin
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510180, P.R. China.
- Respiratory Disease AI Laboratory on Epidemic Intelligence and Medical Big Data Instrument Applications, Faculty of Innovative Engineering, Macau University of Science and Technology, Macau SAR, China.
| | - Chitin Hon
- Department of Engineering Science, Faculty of Innovation Engineering, Macau University of Science and Technology, Taipa, Macau, China.
- Guangzhou Laboratory, Guangzhou, China.
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510180, P.R. China.
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, People's Republic of China.
- Guangzhou Laboratory, Guangzhou, China.
- Respiratory Disease AI Laboratory on Epidemic Intelligence and Medical Big Data Instrument Applications, Faculty of Innovative Engineering, Macau University of Science and Technology, Macau SAR, China.
| |
Collapse
|
4
|
Wodniak N, Vilivong K, Khamphaphongphane B, Sengkeopraseuth B, Somoulay V, Chiew M, Ketmayoon P, Jiao M, Phimmasine S, Co KC, Leuangvilay P, Otsu S, Khanthamaly V, Keopaseuth P, Davis WW, Montgomery MP, Xangsayyarath P. Epidemiologic and Virologic Characteristics of Influenza in Lao PDR, 2016-2023. Influenza Other Respir Viruses 2024; 18:e13353. [PMID: 39104091 DOI: 10.1111/irv.13353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/24/2024] [Accepted: 07/01/2024] [Indexed: 08/07/2024] Open
Abstract
BACKGROUND Influenza sentinel surveillance in Lao PDR is used to inform seasonal vaccination programs. This analysis reviews epidemiologic and virologic characteristics of influenza virus infection over 8 years, before and after emergence of SARS-CoV-2. METHODS Data collected for ILI and SARI surveillance during January 2016 through December 2023 were analyzed from nine hospitals. Respiratory specimens from ILI and SARI cases were tested by reverse transcriptase polymerase chain reaction to determine influenza positivity and subtype and lineage. Aggregate counts of outpatient visits and hospitalizations were collected from hospital logbooks. Epidemiologic trends of influenza activity were described, and the proportional contribution of influenza-associated ILI and SARI to outpatient and inpatient loads was estimated. RESULTS Influenza was detected year-round with positivity peaking during September through January and occurring in most years approximately 1 month earlier in the south than the north. After decreasing in 2 years following the emergence of SARS-CoV-2, influenza positivity increased in 2022 and resumed its typical temporal trend. Influenza-associated ILI contribution to outpatient visits was highest among children ages 5-14 years (3.0% of all outpatient visits in 2023), and influenza-associated SARI contribution to inpatient hospitalizations was highest among children ages 2-4 years (2.2% of all hospitalizations in 2023). CONCLUSIONS Influenza surveillance in Lao PDR provides clinicians and public health authorities with information on geographic and temporal patterns of influenza transmission. Influenza surveillance data support current vaccination timing and recommendations to vaccinate certain populations, especially young children.
Collapse
Affiliation(s)
- Natalie Wodniak
- Thailand Ministry of Public Health-U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - KeoOudomphone Vilivong
- National Center for Laboratory and Epidemiology, Vientiane, Lao People's Democratic Republic
| | | | | | - Virasack Somoulay
- National Center for Laboratory and Epidemiology, Vientiane, Lao People's Democratic Republic
| | - May Chiew
- WHO Health Emergencies Programme, World Health Organization, Vientiane, Lao People's Democratic Republic
| | - Pakapak Ketmayoon
- WHO Health Emergencies Programme, World Health Organization, Vientiane, Lao People's Democratic Republic
| | - Melissa Jiao
- WHO Health Emergencies Programme, World Health Organization, Vientiane, Lao People's Democratic Republic
| | - Sonesavanh Phimmasine
- WHO Health Emergencies Programme, World Health Organization, Vientiane, Lao People's Democratic Republic
| | - Kim Carmela Co
- WHO Health Emergencies Programme, World Health Organization, Vientiane, Lao People's Democratic Republic
| | - Phetdavanh Leuangvilay
- WHO Health Emergencies Programme, World Health Organization, Vientiane, Lao People's Democratic Republic
| | - Satoko Otsu
- WHO Health Emergencies Programme, World Health Organization, Vientiane, Lao People's Democratic Republic
| | - Viengphone Khanthamaly
- U.S. Centers for Disease Control and Prevention Collaboration-Laos, Vientiane, Lao People's Democratic Republic
- Influenza Division, National Center for Immunization and Respiratory Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - William W Davis
- Thailand Ministry of Public Health-U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
- Influenza Division, National Center for Immunization and Respiratory Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Martha P Montgomery
- Thailand Ministry of Public Health-U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
- Influenza Division, National Center for Immunization and Respiratory Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | |
Collapse
|
5
|
Caini S, Meijer A, Nunes MC, Henaff L, Zounon M, Boudewijns B, Del Riccio M, Paget J. Probable extinction of influenza B/Yamagata and its public health implications: a systematic literature review and assessment of global surveillance databases. THE LANCET. MICROBE 2024; 5:100851. [PMID: 38729197 DOI: 10.1016/s2666-5247(24)00066-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 05/12/2024]
Abstract
Early after the start of the COVID-19 pandemic, the detection of influenza B/Yamagata cases decreased globally. Given the potential public health implications of this decline, in this Review, we systematically analysed data on influenza B/Yamagata virus circulation (for 2020-23) from multiple complementary sources of information. We identified relevant articles published in PubMed and Embase, and data from the FluNet, Global Initiative on Sharing All Influenza Data, and GenBank databases, webpages of respiratory virus surveillance systems from countries worldwide, and the Global Influenza Hospital Surveillance Network. A progressive decline of influenza B/Yamagata detections was reported across all sources, in absolute terms (total number of cases), as positivity rate, and as a proportion of influenza B detections. Sporadically reported influenza B/Yamagata cases since March, 2020 were mostly vaccine-derived, attributed to data entry errors, or have yet to be definitively confirmed. The likelihood of extinction necessitates a rapid response in terms of reassessing the composition of influenza vaccines, enhanced surveillance for B/Yamagata, and a possible change in the biosafety level when handling B/Yamagata viruses in laboratories.
Collapse
Affiliation(s)
- Saverio Caini
- Netherlands Institute for Health Services Research (NIVEL), Utrecht, Netherlands.
| | - Adam Meijer
- National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Marta C Nunes
- Center of Excellence in Respiratory Pathogens (CERP), Hospices Civils de Lyon, Lyon, France; Centre International de Recherche en Infectiologie, Team Public Health, Epidemiology and Evolutionary Ecology of Infectious Diseases, Université Claude Bernard 1, Inserm U1111, CNRS UMR5308, ENS de Lyon, Lyon, France; South African Medical Research Council, Vaccines & Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Laetitia Henaff
- Centre International de Recherche en Infectiologie, Team Public Health, Epidemiology and Evolutionary Ecology of Infectious Diseases, Université Claude Bernard 1, Inserm U1111, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - Malaika Zounon
- Center of Excellence in Respiratory Pathogens (CERP), Hospices Civils de Lyon, Lyon, France; Centre International de Recherche en Infectiologie, Team Public Health, Epidemiology and Evolutionary Ecology of Infectious Diseases, Université Claude Bernard 1, Inserm U1111, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - Bronke Boudewijns
- Netherlands Institute for Health Services Research (NIVEL), Utrecht, Netherlands
| | - Marco Del Riccio
- Netherlands Institute for Health Services Research (NIVEL), Utrecht, Netherlands; Department of Health Sciences, University of Florence, Florence, Italy
| | - John Paget
- Netherlands Institute for Health Services Research (NIVEL), Utrecht, Netherlands
| |
Collapse
|
6
|
Edler P, Schwab LSU, Aban M, Wille M, Spirason N, Deng YM, Carlock MA, Ross TM, Juno JA, Rockman S, Wheatley AK, Kent SJ, Barr IG, Price DJ, Koutsakos M. Immune imprinting in early life shapes cross-reactivity to influenza B virus haemagglutinin. Nat Microbiol 2024; 9:2073-2083. [PMID: 38890491 DOI: 10.1038/s41564-024-01732-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 05/15/2024] [Indexed: 06/20/2024]
Abstract
Influenza exposures early in life are believed to shape future susceptibility to influenza infections by imprinting immunological biases that affect cross-reactivity to future influenza viruses. However, direct serological evidence linked to susceptibility is limited. Here we analysed haemagglutination-inhibition titres in 1,451 cross-sectional samples collected between 1992 and 2020, from individuals born between 1917 and 2008, against influenza B virus (IBV) isolates from 1940 to 2021. We included testing of 'future' isolates that circulated after sample collection. We show that immunological biases are conferred by early life IBV infection and result in lineage-specific cross-reactivity of a birth cohort towards future IBV isolates. This translates into differential estimates of susceptibility between birth cohorts towards the B/Yamagata and B/Victoria lineages, predicting lineage-specific birth-cohort distributions of observed medically attended IBV infections. Our data suggest that immunological measurements of imprinting could be important in modelling and predicting virus epidemiology.
Collapse
Affiliation(s)
- Peta Edler
- Department of Infectious Diseases, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Lara S U Schwab
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Malet Aban
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
| | - Natalie Spirason
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Yi-Mo Deng
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Michael A Carlock
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA
- Florida Research and Innovation Centre, Cleveland Clinic, Port Saint Lucie, FL, USA
| | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA
- Florida Research and Innovation Centre, Cleveland Clinic, Port Saint Lucie, FL, USA
- Department of Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jennifer A Juno
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Steve Rockman
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Vaccine Product Development, CSL Seqirus Ltd, Parkville, Victoria, Australia
| | - Adam K Wheatley
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Health, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Ian G Barr
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - David J Price
- Department of Infectious Diseases, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia.
| |
Collapse
|
7
|
Del Riccio M, Caini S, Bonaccorsi G, Lorini C, Paget J, van der Velden K, Meijer A, Haag M, McGovern I, Zanobini P. Global analysis of respiratory viral circulation and timing of epidemics in the pre-COVID-19 and COVID-19 pandemic eras, based on data from the Global Influenza Surveillance and Response System (GISRS). Int J Infect Dis 2024; 144:107052. [PMID: 38636684 DOI: 10.1016/j.ijid.2024.107052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/30/2024] [Accepted: 04/09/2024] [Indexed: 04/20/2024] Open
Abstract
OBJECTIVES The COVID-19 pandemic significantly changed respiratory viruses' epidemiology due to non-pharmaceutical interventions and possible viral interactions. This study investigates whether the circulation patterns of respiratory viruses have returned to pre-pandemic norms by comparing their peak timing and duration during the first three SARS-CoV-2 seasons to pre-pandemic times. METHODS Global Influenza Surveillance and Response System data from 194 countries (2014-2023) was analyzed for epidemic peak timing and duration, focusing on pre-pandemic and pandemic periods across both hemispheres and the intertropical belt. The analysis was restricted to countries meeting specific data thresholds to ensure robustness. RESULTS In 2022/2023, the northern hemisphere experienced earlier influenza and respiratory syncytial virus (RSV) peaks by 1.9 months (P <0.001). The duration of influenza epidemics increased by 2.2 weeks (P <0.001), with RSV showing a similar trend. The southern hemisphere's influenza peak shift was not significant (P = 0.437). Intertropical regions presented no substantial change in peak timing but experienced a significant reduction in the duration for human metapneumovirus and adenovirus (7.2 and 6.5 weeks shorter, respectively, P <0.001). CONCLUSIONS The pandemic altered the typical patterns of influenza and RSV, with earlier peaks in 2022 in temperate areas. These findings highlight the importance of robust surveillance data to inform public health strategies on evolving viral dynamics in the years to come.
Collapse
Affiliation(s)
- Marco Del Riccio
- Department of Health Sciences, University of Florence, Florence, Italy; Department of Primary and Community Care, Radboud University Medical Centre, HB Nijmegen, The Netherlands
| | - Saverio Caini
- Netherlands Institute for Health Services Research, CR Utrecht, The Netherlands.
| | | | - Chiara Lorini
- Department of Health Sciences, University of Florence, Florence, Italy
| | - John Paget
- Netherlands Institute for Health Services Research, CR Utrecht, The Netherlands
| | - Koos van der Velden
- Department of Primary and Community Care, Radboud University Medical Centre, HB Nijmegen, The Netherlands
| | - Adam Meijer
- National Institute for Public Health and the Environment, BA Bilthoven, The Netherlands
| | | | - Ian McGovern
- Center for Outcomes Research and Epidemiology, Seqirus Inc, Cambridge, USA
| | - Patrizio Zanobini
- Department of Health Sciences, University of Florence, Florence, Italy
| |
Collapse
|
8
|
Alshiban NM, Aleyiydi MS, Nassar MS, Alhumaid NK, Almangour TA, Tawfik YM, Damiati LA, Almutairi AS, Tawfik EA. Epidemiologic and clinical updates on viral infections in Saudi Arabia. Saudi Pharm J 2024; 32:102126. [PMID: 38966679 PMCID: PMC11223122 DOI: 10.1016/j.jsps.2024.102126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024] Open
Abstract
In the past two decades, the world has witnessed devastating pandemics affecting the global healthcare infrastructure and disrupting society and the economy worldwide. Among all pathogens, viruses play a critical role that is associated with outbreaks due to their wide range of species, involvement of animal hosts, easily transmitted to humans, and increased rates of infectivity. Viral disease outbreaks threaten public health globally due to the challenges associated with controlling and eradicating them. Implementing effective viral disease control programs starts with ongoing surveillance data collection and analyses to detect infectious disease trends and patterns, which is critical for maintaining public health. Viral disease control strategies include improved hygiene and sanitation facilities, eliminating arthropod vectors, vaccinations, and quarantine. The Saudi Ministry of Health (MOH) and the Public Health Authority (also known as Weqayah) in Saudi Arabia are responsible for public health surveillance to control and prevent infectious diseases. The notifiable viral diseases based on the Saudi MOH include hepatitis diseases, viral hemorrhagic fevers, respiratory viral diseases, exanthematous viral diseases, neurological viral diseases, and conjunctivitis. Monitoring trends and detecting changes in these viral diseases is essential to provide proper interventions, evaluate the established prevention programs, and develop better prevention strategies. Therefore, this review aims to highlight the epidemiological updates of the recently reported viral infections in Saudi Arabia and to provide insights into the recent clinical treatment and prevention strategies.
Collapse
Affiliation(s)
- Noura M. Alshiban
- Advanced Diagnostics and Therapeutics Institute, Health Sector, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| | - Munirah S. Aleyiydi
- Advanced Diagnostics and Therapeutics Institute, Health Sector, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| | - Majed S. Nassar
- Advanced Diagnostics and Therapeutics Institute, Health Sector, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| | - Nada K. Alhumaid
- Advanced Diagnostics and Therapeutics Institute, Health Sector, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| | - Thamer A. Almangour
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Yahya M.K. Tawfik
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Laila A. Damiati
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah 23218, Saudi Arabia
| | | | - Essam A. Tawfik
- Advanced Diagnostics and Therapeutics Institute, Health Sector, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| |
Collapse
|
9
|
Korsun N, Trifonova I, Madzharova I, Christova I. Resurgence of influenza with increased genetic diversity of circulating viruses during the 2022-2023 season. J Med Microbiol 2024; 73. [PMID: 39073070 DOI: 10.1099/jmm.0.001864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024] Open
Abstract
Introduction. After two seasons of absence and low circulation, influenza activity increased significantly in the winter of 2022-2023. This study aims to characterize virological and epidemiological aspects of influenza infection in Bulgaria during the 2022-2023 season and perform a phylogenetic/molecular analysis of the hemagglutinin (HA) and neuraminidase (NA) sequences of representative influenza strains.Hypothesis/Gap Statement. Influenza A and B viruses generate new genetic groups/clades each season, replacing previously circulating variants. This results in increased antigenic distances from current vaccine strains. Strengthening existing influenza surveillance is essential to meet the challenges posed by the co-circulation of influenza and SARS-CoV-2.Methodology. We tested 2713 clinical samples from patients with acute respiratory illnesses using a multiplex real-time RT-PCR kit (FluSC2) to detect influenza A/B and Severe acute respiratory syndrome coronavirus-2(SARS-CoV-2) simultaneously. Representative Bulgarian influenza strains were sequenced at the WHO Collaborating Centres in London, UK, and Atlanta, USA.Results. Influenza virus was detected in 694 (25.6 %) patients. Of these, 364 (52.4 %), 213 (30.7 %) and 117 (16.9 %) were positive for influenza A(H1N1)pdm09, A(H3N2) and B/Victoria lineage virus, respectively. HA genes of the 47 influenza A(H1N1)pdm09 viruses fell into clades 5a.2. and 5a.2a.1 within the 6B.5A.1A.5a.2 group. Twenty-seven A(H3N2) viruses belonging to subclades 2b, 2a.1, 2a.1b and 2a.3a.1 within the 3C.2a1b.2a.2 group were analysed. All 23 sequenced B/Victoria lineage viruses were classified into the V1A.3a.2 group. We identified amino acid substitutions in HA and NA compared with the vaccine strains, including several substitutions in the HA antigenic sites.Conclusion. The study's findings showed genetic diversity among the influenza A viruses and, to a lesser extent, among B viruses, circulating in the first season after the lifting of anti-COVID-19 measures.
Collapse
MESH Headings
- Humans
- Influenza, Human/virology
- Influenza, Human/epidemiology
- Genetic Variation
- Phylogeny
- Influenza B virus/genetics
- Influenza B virus/classification
- Influenza B virus/isolation & purification
- SARS-CoV-2/genetics
- SARS-CoV-2/classification
- Neuraminidase/genetics
- Adult
- Male
- Middle Aged
- Female
- Bulgaria/epidemiology
- Young Adult
- Aged
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Child, Preschool
- Child
- Adolescent
- COVID-19/epidemiology
- COVID-19/virology
- Infant
- Seasons
- Influenza A virus/genetics
- Influenza A virus/classification
- Influenza A virus/isolation & purification
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/classification
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/classification
- Influenza A Virus, H3N2 Subtype/isolation & purification
Collapse
Affiliation(s)
- Neli Korsun
- National Laboratory "Influenza and ARI", Department of Virology, National Center of Infectious and Parasitic Diseases, 44A Stoletov Blvd, 1233 Sofia, Bulgaria
| | - Ivelina Trifonova
- National Laboratory "Influenza and ARI", Department of Virology, National Center of Infectious and Parasitic Diseases, 44A Stoletov Blvd, 1233 Sofia, Bulgaria
| | - Iveta Madzharova
- National Laboratory "Influenza and ARI", Department of Virology, National Center of Infectious and Parasitic Diseases, 44A Stoletov Blvd, 1233 Sofia, Bulgaria
| | - Iva Christova
- National Laboratory "Influenza and ARI", Department of Virology, National Center of Infectious and Parasitic Diseases, 44A Stoletov Blvd, 1233 Sofia, Bulgaria
| |
Collapse
|
10
|
Fung T, Goh J, Chisholm RA. Long-term effects of non-pharmaceutical interventions on total disease burden in parsimonious epidemiological models. J Theor Biol 2024; 587:111817. [PMID: 38599566 DOI: 10.1016/j.jtbi.2024.111817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/12/2024]
Abstract
The recent global COVID-19 pandemic resulted in governments enacting non-pharmaceutical interventions (NPIs) targeted at reducing transmission of SARS-CoV-2. But the NPIs also affected the transmission of viruses causing non-target seasonal respiratory diseases, including influenza and respiratory syncytial virus (RSV). In many countries, the NPIs were found to reduce cases of such seasonal respiratory diseases, but there is also evidence that subsequent relaxation of NPIs led to outbreaks of these diseases that were larger than pre-pandemic ones, due to the accumulation of susceptible individuals prior to relaxation. Therefore, the net long-term effects of NPIs on the total disease burden of non-target diseases remain unclear. Knowledge of this is important for infectious disease management and maintenance of public health. In this study, we shed light on this issue for the simplified scenario of a set of NPIs that prevent or reduce transmission of a seasonal respiratory disease for about a year and are then removed, using mathematical analyses and numerical simulations of a suite of four epidemiological models with varying complexity and generality. The model parameters were estimated using empirical data pertaining to seasonal respiratory diseases and covered a wide range. Our results showed that NPIs reduced the total disease burden of a non-target seasonal respiratory disease in the long-term. Expressed as a percentage of population size, the reduction was greater for larger values of the basic reproduction number and the immunity loss rate, reflecting larger outbreaks and hence more infections averted by imposition of NPIs. Our study provides a foundation for exploring the effects of NPIs on total disease burden in more-complex scenarios.
Collapse
Affiliation(s)
- Tak Fung
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore 117558, Singapore.
| | - Jonah Goh
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore 117558, Singapore.
| | - Ryan A Chisholm
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore 117558, Singapore.
| |
Collapse
|
11
|
Velasco JM, Valderama MT, Diones PC, Leonardia S, Alcantara S, Joonlasak K, Chinnawirotpisan P, Manasatienkij W, Klungthong C, Arellano ER, Osia CM, Magistrado-Payot J, Fajardo P, Navarro FC, Wuertz KM, Farmer A. Outbreak of influenza and SARS-CoV-2 at the Armed Forces of the Philippines Health Service Education and Training Center, September 25-October 10, 2023. MSMR 2024; 31:9-15. [PMID: 38847656 PMCID: PMC11189823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
In the last week of September 2023, a surge of influenza-like illness was observed among students of the Armed Forces of the Philippines (AFP) Health Service Education and Training Center, where 48 (27 males and 21 females; age in years: mean 33, range 27-41) of 247 military students at the Center presented with respiratory symptoms. Between September 25 and October 10, 2023, all 48 symptomatic students were evaluated with real-time reverse transcription polymerase chain reaction and sequencing for both influenza and SARS-CoV-2. Thirteen (27%) students were found positive for influenza A/H3 only, 6 (13%) for SARS-CoV-2 only, and 4 (8%) were co-infected with influenza A/H3 and SARS-CoV-2. Seventeen influenza A/ H3N2 viruses belonged to the same clade, 3C.2a1b.2a.2a.3a, and 4 SARSCoV-2 sequences belonged to the JE1.1 lineage, indicating a common source outbreak for both. The influenza A/H3N2 circulating virus belonged to a different clade than the vaccine strain for 2023 (3C.2a1b.2a.2a). Only 4 students had received the influenza vaccine for 2023. In response, the AFP Surgeon General issued a memorandum to all military health institutions on October 19, 2023 that mandated influenza vaccination as a prerequisite for enrollment of students at all education and training centers, along with implementation of non-pharmaceutical interventions and early notification and testing of students exhibiting influenza-like-illness.
Collapse
Affiliation(s)
- John Mark Velasco
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- University of the Philippines Manila, Ermita
| | - Maria Theresa Valderama
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Paula Corazon Diones
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Susie Leonardia
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Simon Alcantara
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Khajohn Joonlasak
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Piyawan Chinnawirotpisan
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Wudtichai Manasatienkij
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Chonticha Klungthong
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Errol Roy Arellano
- V. Luna Medical Center, AFP Health Service Command, Quezon City, Philippines
| | - Carrol Mae Osia
- Public Health Service Center, Armed Forces of the Philippines Health Service Command, Quezon City, Philippines
| | - Joy Magistrado-Payot
- Office of the Surgeon General, Camp General Emilio Aguinaldo, Quezon City, Philippines
| | - Paul Fajardo
- Public Health Service Center, Armed Forces of the Philippines Health Service Command, Quezon City, Philippines
| | - Fatima Claire Navarro
- Office of the Surgeon General, Camp General Emilio Aguinaldo, Quezon City, Philippines
| | - Kathryn McGuckin Wuertz
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Aaron Farmer
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| |
Collapse
|
12
|
Wu F, Cai D, Shi X, Li P, Ma L. Multiplexed detection of eight respiratory viruses based on nanozyme colorimetric microfluidic immunoassay. Front Bioeng Biotechnol 2024; 12:1402831. [PMID: 38817925 PMCID: PMC11137192 DOI: 10.3389/fbioe.2024.1402831] [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: 03/18/2024] [Accepted: 04/15/2024] [Indexed: 06/01/2024] Open
Abstract
Pandemics caused by respiratory viruses, such as the SARS-CoV-1/2, influenza virus, and respiratory syncytial virus, have resulted in serious consequences to humans and a large number of deaths. The detection of such respiratory viruses in the early stages of infection can help control diseases by preventing the spread of viruses. However, the diversity of respiratory virus species and subtypes, their rapid antigenic mutations, and the limited viral release during the early stages of infection pose challenges to their detection. This work reports a multiplexed microfluidic immunoassay chip for simultaneous detection of eight respiratory viruses with noticeable infection population, namely, influenza A virus, influenza B virus, respiratory syncytial virus, SARS-CoV-2, human bocavirus, human metapneumovirus, adenovirus, and human parainfluenza viruses. The nanomaterial of the nanozyme (Au@Pt nanoparticles) was optimized to improve labeling efficiency and enhance the detection sensitivity significantly. Nanozyme-binding antibodies were used to detect viral proteins with a limit of detection of 0.1 pg/mL with the naked eye and a microplate reader within 40 min. Furthermore, specific antibodies were screened against the conserved proteins of each virus in the immunoassay, and the clinical sample detection showed high specificity without cross reactivity among the eight pathogens. In addition, the microfluidic chip immunoassay showed high accuracy, as compared with the RT-PCR assay for clinical sample detection, with 97.2%/94.3% positive/negative coincidence rates. This proposed approach thus provides a convenient, rapid, and sensitive method for simultaneous detection of eight respiratory viruses, which is meaningful for the early diagnosis of viral infections. Significantly, it can be widely used to detect pathogens and biomarkers by replacing only the antigen-specific antibodies.
Collapse
Affiliation(s)
- Feng Wu
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- Shenzhen Institute for Drug Control, Shenzhen, China
| | - Defeng Cai
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- Department of Clinical Laboratory (Pathology) Centre, South China Hospital of Shenzhen University, Shenzhen, China
| | - Xueying Shi
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Ping Li
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Lan Ma
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, China
| |
Collapse
|
13
|
Perofsky AC, Hansen CL, Burstein R, Boyle S, Prentice R, Marshall C, Reinhart D, Capodanno B, Truong M, Schwabe-Fry K, Kuchta K, Pfau B, Acker Z, Lee J, Sibley TR, McDermot E, Rodriguez-Salas L, Stone J, Gamboa L, Han PD, Adler A, Waghmare A, Jackson ML, Famulare M, Shendure J, Bedford T, Chu HY, Englund JA, Starita LM, Viboud C. Impacts of human mobility on the citywide transmission dynamics of 18 respiratory viruses in pre- and post-COVID-19 pandemic years. Nat Commun 2024; 15:4164. [PMID: 38755171 PMCID: PMC11098821 DOI: 10.1038/s41467-024-48528-2] [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: 12/11/2023] [Accepted: 05/02/2024] [Indexed: 05/18/2024] Open
Abstract
Many studies have used mobile device location data to model SARS-CoV-2 dynamics, yet relationships between mobility behavior and endemic respiratory pathogens are less understood. We studied the effects of population mobility on the transmission of 17 endemic viruses and SARS-CoV-2 in Seattle over a 4-year period, 2018-2022. Before 2020, visits to schools and daycares, within-city mixing, and visitor inflow preceded or coincided with seasonal outbreaks of endemic viruses. Pathogen circulation dropped substantially after the initiation of COVID-19 stay-at-home orders in March 2020. During this period, mobility was a positive, leading indicator of transmission of all endemic viruses and lagging and negatively correlated with SARS-CoV-2 activity. Mobility was briefly predictive of SARS-CoV-2 transmission when restrictions relaxed but associations weakened in subsequent waves. The rebound of endemic viruses was heterogeneously timed but exhibited stronger, longer-lasting relationships with mobility than SARS-CoV-2. Overall, mobility is most predictive of respiratory virus transmission during periods of dramatic behavioral change and at the beginning of epidemic waves.
Collapse
Affiliation(s)
- Amanda C Perofsky
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA.
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA.
| | - Chelsea L Hansen
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
- PandemiX Center, Department of Science & Environment, Roskilde University, Roskilde, Denmark
| | - Roy Burstein
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Shanda Boyle
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | - Robin Prentice
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | - Cooper Marshall
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | - David Reinhart
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | - Ben Capodanno
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | - Melissa Truong
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | - Kristen Schwabe-Fry
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | - Kayla Kuchta
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | - Brian Pfau
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | - Zack Acker
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | - Jover Lee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Thomas R Sibley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Evan McDermot
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | - Leslie Rodriguez-Salas
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | - Jeremy Stone
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | - Luis Gamboa
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | - Peter D Han
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Amanda Adler
- Seattle Children's Research Institute, Seattle, WA, USA
| | - Alpana Waghmare
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | | | - Michael Famulare
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Trevor Bedford
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Helen Y Chu
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Janet A Englund
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
- Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Lea M Starita
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Cécile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
14
|
Nagasawa M, Shimoyama T, Hashimoto S, Nakagawa R, Yokoyama H, Okada M, Udagawa T, Oshiba A. Impact of the Omicron Strain on Febrile Convulsions Requiring Hospitalization in Children: A Single-Center Observational Study. Pediatr Rep 2024; 16:399-409. [PMID: 38804377 PMCID: PMC11130907 DOI: 10.3390/pediatric16020034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND The emergence of the Omicron strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the end of December 2021 has drastically increased the number of infected children in Japan, along with the number of children with febrile convulsions, but its clinical impact is unclear. MATERIALS AND METHODS We compared the frequency of SARS-CoV-2 infection in children hospitalized with febrile convulsions with the frequency of SARS-CoV-2 infection in children with fever and respiratory symptoms without convulsions. RESULTS In 2021 and 2022, 49 and 58 children required emergency hospitalization for febrile convulsions (FC group) with status epilepticus or cluster spasms, in which 24 and 38 children underwent a Filmarray® respiratory panel test (FA test), respectively, and others received a quantitative antigen test for SARS-CoV-2. In 2022, only six patients tested positive for SARS-CoV-2 (10.3%, 6/58). As a reference group, 655 children aged <10 years who underwent the FA test for fever and respiratory symptoms during the same period were investigated, and 4 (1.8%, 4/223) and 42 (9.7%, 42/432) tested positive for SARS-CoV-2 in 2021 and 2022, respectively. Rhinovirus/enterovirus (RV/EV) was the most frequently detected virus (40.3%, 264/655), followed by respiratory syncytial virus (RSV) (18.9%, 124/655) and parainfluenza virus 3 (PIV3) (7.8%, 51/655). There was no significant difference in the trend of detected viruses between the two groups. CONCLUSIONS The frequency and severity of febrile convulsions requiring hospitalization associated with SARS-CoV-2 infection of the Omicron strain may be similar to that of other respiratory viruses in children.
Collapse
Affiliation(s)
- Masayuki Nagasawa
- Department of Pediatrics, Musashino Red Cross Hospital, 1-26-1, Kyonan-cho, Musashino 180-8610, Tokyo, Japan; (T.S.); (S.H.); (T.U.); (A.O.)
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Gao X, Xu Y. Markovian Approach for Exploring Competitive Diseases with Heterogeneity-Evidence from COVID-19 and Influenza in China. Bull Math Biol 2024; 86:71. [PMID: 38719993 DOI: 10.1007/s11538-024-01300-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/19/2024] [Indexed: 05/23/2024]
Abstract
Due to the complex interactions between multiple infectious diseases, the spreading of diseases in human bodies can vary when people are exposed to multiple sources of infection at the same time. Typically, there is heterogeneity in individuals' responses to diseases, and the transmission routes of different diseases also vary. Therefore, this paper proposes an SIS disease spreading model with individual heterogeneity and transmission route heterogeneity under the simultaneous action of two competitive infectious diseases. We derive the theoretical epidemic spreading threshold using quenched mean-field theory and perform numerical analysis under the Markovian method. Numerical results confirm the reliability of the theoretical threshold and show the inhibitory effect of the proportion of fully competitive individuals on epidemic spreading. The results also show that the diversity of disease transmission routes promotes disease spreading, and this effect gradually weakens when the epidemic spreading rate is high enough. Finally, we find a negative correlation between the theoretical spreading threshold and the average degree of the network. We demonstrate the practical application of the model by comparing simulation outputs to temporal trends of two competitive infectious diseases, COVID-19 and seasonal influenza in China.
Collapse
Affiliation(s)
- Xingyu Gao
- School of Mathematics and Statistics, Changshu Institute of Technology, Changshu, 215500, China.
| | - Yuchao Xu
- GE HealthCare Technologies Inc, No. 1 Huatuo Road, Shanghai, 201210, China
| |
Collapse
|
16
|
Nguyen THO, Rowntree LC, Chua BY, Thwaites RS, Kedzierska K. Defining the balance between optimal immunity and immunopathology in influenza virus infection. Nat Rev Immunol 2024:10.1038/s41577-024-01029-1. [PMID: 38698083 DOI: 10.1038/s41577-024-01029-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2024] [Indexed: 05/05/2024]
Abstract
Influenza A viruses remain a global threat to human health, with continued pandemic potential. In this Review, we discuss our current understanding of the optimal immune responses that drive recovery from influenza virus infection, highlighting the fine balance between protective immune mechanisms and detrimental immunopathology. We describe the contribution of innate and adaptive immune cells, inflammatory modulators and antibodies to influenza virus-specific immunity, inflammation and immunopathology. We highlight recent human influenza virus challenge studies that advance our understanding of susceptibility to influenza and determinants of symptomatic disease. We also describe studies of influenza virus-specific immunity in high-risk groups following infection and vaccination that inform the design of future vaccines to promote optimal antiviral immunity, particularly in vulnerable populations. Finally, we draw on lessons from the COVID-19 pandemic to refocus our attention to the ever-changing, highly mutable influenza A virus, predicted to cause future global pandemics.
Collapse
Affiliation(s)
- Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Louise C Rowntree
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Brendon Y Chua
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ryan S Thwaites
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
| |
Collapse
|
17
|
Menon T, Illing PT, Chaurasia P, McQuilten HA, Shepherd C, Rowntree LC, Petersen J, Littler DR, Khuu G, Huang Z, Allen LF, Rockman S, Crowe J, Flanagan KL, Wakim LM, Nguyen THO, Mifsud NA, Rossjohn J, Purcell AW, van de Sandt CE, Kedzierska K. CD8 + T-cell responses towards conserved influenza B virus epitopes across anatomical sites and age. Nat Commun 2024; 15:3387. [PMID: 38684663 PMCID: PMC11059233 DOI: 10.1038/s41467-024-47576-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 04/03/2024] [Indexed: 05/02/2024] Open
Abstract
Influenza B viruses (IBVs) cause substantive morbidity and mortality, and yet immunity towards IBVs remains understudied. CD8+ T-cells provide broadly cross-reactive immunity and alleviate disease severity by recognizing conserved epitopes. Despite the IBV burden, only 18 IBV-specific T-cell epitopes restricted by 5 HLAs have been identified currently. A broader array of conserved IBV T-cell epitopes is needed to develop effective cross-reactive T-cell based IBV vaccines. Here we identify 9 highly conserved IBV CD8+ T-cell epitopes restricted to HLA-B*07:02, HLA-B*08:01 and HLA-B*35:01. Memory IBV-specific tetramer+CD8+ T-cells are present within blood and tissues. Frequencies of IBV-specific CD8+ T-cells decline with age, but maintain a central memory phenotype. HLA-B*07:02 and HLA-B*08:01-restricted NP30-38 epitope-specific T-cells have distinct T-cell receptor repertoires. We provide structural basis for the IBV HLA-B*07:02-restricted NS1196-206 (11-mer) and HLA-B*07:02-restricted NP30-38 epitope presentation. Our study increases the number of IBV CD8+ T-cell epitopes, and defines IBV-specific CD8+ T-cells at cellular and molecular levels, across tissues and age.
Collapse
Affiliation(s)
- Tejas Menon
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Patricia T Illing
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Priyanka Chaurasia
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Hayley A McQuilten
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Chloe Shepherd
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Louise C Rowntree
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Jan Petersen
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Dene R Littler
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Grace Khuu
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Ziyi Huang
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Lilith F Allen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Steve Rockman
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
- CSL Seqirus Ltd, Parkville, VIC, Australia
| | - Jane Crowe
- Deepdene Surgery, Deepdene, VIC, Australia
| | - Katie L Flanagan
- Tasmanian Vaccine Trial Centre, Launceston General Hospital, Launceston, TAS, Australia
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, TAS, Australia
- School of Health and Biomedical Science, RMIT University, Melbourne, VIC, Australia
| | - Linda M Wakim
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Nicole A Mifsud
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Anthony W Purcell
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Carolien E van de Sandt
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia.
| |
Collapse
|
18
|
Ni CQ, Xie WQ. Quantifying sodium hypochlorite content in hypochlorite-based disinfectants via phase-conversion headspace technique. J Chromatogr A 2024; 1721:464812. [PMID: 38569297 DOI: 10.1016/j.chroma.2024.464812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 02/23/2024] [Accepted: 03/10/2024] [Indexed: 04/05/2024]
Abstract
In this work, a novel and efficient approach for sodium hypochlorite analysis is proposed via phase-conversion headspace technique, which is based on the gas chromatography (GC) detection of generated carbon dioxide (CO2) from the redox reaction of sodium hypochlorite with sodium oxalate. The data obtained by the proposed method suggest the high detecting precision and accuracy. In addition, the method has low detection limits (limit of quantification (LOQ) = 0.24 μg/mL), and the recoveries of added standard ranged from 98.33 to 101.27 %. The proposed phase-conversion headspace technique is efficient and automated, thereby offering an efficient strategy for highly efficient analysis of sodium hypochlorite and related products.
Collapse
Affiliation(s)
- Chen-Quan Ni
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Wei-Qi Xie
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China.
| |
Collapse
|
19
|
Lee K, Park K, Sung H, Kim MN. Phylogenetic lineage dynamics of global parainfluenza virus type 3 post-COVID-19 pandemic. mSphere 2024; 9:e0062423. [PMID: 38501829 PMCID: PMC11036794 DOI: 10.1128/msphere.00624-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
During the coronavirus disease 2019 (COVID-19) pandemic, outbreaks of parainfluenza virus type 3 (PIV-3) decreased due to infection control measures. However, a post-pandemic resurgence of PIV-3 has recently been observed. Nonetheless, the role of viral genetic epidemiology, possibly influenced by a genetic bottleneck effect, remains unexplored. We investigated the phylogenetic structure of the publicly available PIV-3 whole-genome and hemagglutinin-neuraminidase (HN) gene sequences spanning the last 65 years, including the COVID-19 pandemic. Sequences were retrieved from the nucleotide database of the National Center for Biotechnology Information using the search term "Human respirovirus 3." Sequence subsets covering all six genes of PIV-3 or the HN gene were designated as the whole-genome and HN surveillance data sets, respectively. Using these data sets, we constructed maximum-likelihood phylogenetic trees and performed a time-scaled analysis using a Bayesian SkyGrid coalescent prior. A total of 455 whole-genome and 1,139 HN gene sequences were extracted, revealing 10 and 11 distinct lineages, respectively, with >98% concurrence in lineage assignments. During the 2020 COVID-19 pandemic, only three single-lineage clusters were identified in Japan, Korea, and the USA. The inferred year of origin for PIV-3 was 1938 (1903-1963) for the whole-genome data set and 1955 (1930-1963) for the HN gene data set. Our study suggests that PIV-3 epidemics in the post-COVID era are likely influenced by a pandemic-driven bottleneck phenomenon and supports previous hypotheses suggesting s that PIV-3 originated during the early half of the 20th century.IMPORTANCEUsing publicly available parainfluenza virus type 3 (PIV-3) whole-genome sequences, we estimated that PIV-3 originated during the 1930s, consistent with previous hypotheses. Lineage typing and time-scaled phylogenetic analysis revealed that PIV-3 experienced a bottleneck phenomenon in Korea and the USA during the coronavirus disease 2019 pandemic. We identified the conservative hemagglutinin-neuraminidase gene as a viable alternative marker in long-term epidemiological studies of PIV-3 when whole-genome analysis is limited.
Collapse
Affiliation(s)
| | - Kuenyoul Park
- Department of Laboratory Medicine, Sanggye Paik Hospital, School of Medicine, Inje University, Seoul, South Korea
| | - Heungsup Sung
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Mi-Na Kim
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| |
Collapse
|
20
|
Moso MA, Taiaroa G, Steinig E, Zhanduisenov M, Butel-Simoes G, Savic I, Taouk ML, Chea S, Moselen J, O'Keefe J, Prestedge J, Pollock GL, Khan M, Soloczynskyj K, Fernando J, Martin GE, Caly L, Barr IG, Tran T, Druce J, Lim CK, Williamson DA. Non-SARS-CoV-2 respiratory viral detection and whole genome sequencing from COVID-19 rapid antigen test devices: a laboratory evaluation study. THE LANCET. MICROBE 2024; 5:e317-e325. [PMID: 38359857 DOI: 10.1016/s2666-5247(23)00375-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 11/01/2023] [Accepted: 11/15/2023] [Indexed: 02/17/2024]
Abstract
BACKGROUND There has been high uptake of rapid antigen test device use for point-of-care COVID-19 diagnosis. Individuals who are symptomatic but test negative on COVID-19 rapid antigen test devices might have a different respiratory viral infection. We aimed to detect and sequence non-SARS-CoV-2 respiratory viruses from rapid antigen test devices, which could assist in the characterisation and surveillance of circulating respiratory viruses in the community. METHODS We applied archival clinical nose and throat swabs collected between Jan 1, 2015, and Dec 31, 2022, that previously tested positive for a common respiratory virus (adenovirus, influenza, metapneumovirus, parainfluenza, rhinovirus, respiratory syncytial virus [RSV], or seasonal coronavirus; 132 swabs and 140 viral targets) on PCR to two commercially available COVID-19 rapid antigen test devices, the Panbio COVID-19 Ag Rapid Test Device and Roche SARS-CoV-2 Antigen Self-Test. In addition, we collected 31 COVID-19 rapid antigen test devices used to test patients who were symptomatic at The Royal Melbourne Hospital emergency department in Melbourne, Australia. We extracted total nucleic acid from the device paper test strips and assessed viral recovery using multiplex real-time PCR (rtPCR) and capture-based whole genome sequencing. Sequence and genome data were analysed through custom computational pipelines, including subtyping. FINDINGS Of the 140 respiratory viral targets from archival samples, 89 (64%) and 88 (63%) were positive on rtPCR for the relevant taxa following extraction from Panbio or Roche rapid antigen test devices, respectively. Recovery was variable across taxa: we detected influenza A in nine of 18 samples from Panbio and seven of 18 from Roche devices; parainfluenza in 11 of 20 samples from Panbio and 12 of 20 from Roche devices; human metapneumovirus in 11 of 16 from Panbio and 14 of 16 from Roche devices; seasonal coronavirus in eight of 19 from Panbio and two of 19 from Roche devices; rhinovirus in 24 of 28 from Panbio and 27 of 28 from Roche devices; influenza B in four of 15 in both devices; and RSV in 16 of 18 in both devices. Of the 31 COVID-19 devices collected from The Royal Melbourne Hospital emergency department, 11 tested positive for a respiratory virus on rtPCR, including one device positive for influenza A virus, one positive for RSV, four positive for rhinovirus, and five positive for SARS-CoV-2. Sequences of target respiratory viruses from archival samples were detected in 55 (98·2%) of 56 samples from Panbio and 48 (85·7%) of 56 from Roche rapid antigen test devices. 98 (87·5%) of 112 viral genomes were completely assembled from these data, enabling subtyping for RSV and influenza viruses. All 11 samples collected from the emergency department had viral sequences detected, with near-complete genomes assembled for influenza A and RSV. INTERPRETATION Non-SARS-CoV-2 respiratory viruses can be detected and sequenced from COVID-19 rapid antigen devices. Recovery of near full-length viral sequences from these devices provides a valuable opportunity to expand genomic surveillance programmes for public health monitoring of circulating respiratory viruses. FUNDING Australian Government Medical Research Future Fund and Australian National Health and Medical Research Council.
Collapse
Affiliation(s)
- Michael A Moso
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - George Taiaroa
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Eike Steinig
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Madiyar Zhanduisenov
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Grace Butel-Simoes
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Ivana Savic
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Mona L Taouk
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Socheata Chea
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jean Moselen
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jacinta O'Keefe
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jacqueline Prestedge
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Georgina L Pollock
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Mohammad Khan
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Katherine Soloczynskyj
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Janath Fernando
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Genevieve E Martin
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Leon Caly
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Ian G Barr
- WHO Collaborating Centre for Reference and Research on Influenza, Melbourne, VIC, Australia
| | - Thomas Tran
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Julian Druce
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Chuan K Lim
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Deborah A Williamson
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.
| |
Collapse
|
21
|
Cilloniz C, Dy-Agra G, Pagcatipunan RS, Torres A. Viral Pneumonia: From Influenza to COVID-19. Semin Respir Crit Care Med 2024; 45:207-224. [PMID: 38228165 DOI: 10.1055/s-0043-1777796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Respiratory viruses are increasingly recognized as a cause of community-acquired pneumonia (CAP). The implementation of new diagnostic technologies has facilitated their identification, especially in vulnerable population such as immunocompromised and elderly patients and those with severe cases of pneumonia. In terms of severity and outcomes, viral pneumonia caused by influenza viruses appears similar to that caused by non-influenza viruses. Although several respiratory viruses may cause CAP, antiviral therapy is available only in cases of CAP caused by influenza virus or respiratory syncytial virus. Currently, evidence-based supportive care is key to managing severe viral pneumonia. We discuss the evidence surrounding epidemiology, diagnosis, management, treatment, and prevention of viral pneumonia.
Collapse
Affiliation(s)
- Catia Cilloniz
- Hospital Clinic of Barcelona, IDIBAPS, CIBERESA, Barcelona, Spain
- Faculty of Health Sciences, Continental University, Huancayo, Peru
| | - Guinevere Dy-Agra
- Institute of Pulmonary Medicine, St Luke's Medical Center-Global City, Taguig, Metro Manila, Philippines
| | - Rodolfo S Pagcatipunan
- Institute of Pulmonary Medicine, St Luke's Medical Center-Global City, Taguig, Metro Manila, Philippines
| | - Antoni Torres
- Hospital Clinic of Barcelona, IDIBAPS, CIBERESA, Barcelona, Spain
- School of Medicine, University of Barcelona, Barcelona, Spain
| |
Collapse
|
22
|
Owusu D, Ndegwa LK, Ayugi J, Kinuthia P, Kalani R, Okeyo M, Otieno NA, Kikwai G, Juma B, Munyua P, Kuria F, Okunga E, Moen AC, Emukule GO. Use of Sentinel Surveillance Platforms for Monitoring SARS-CoV-2 Activity: Evidence From Analysis of Kenya Influenza Sentinel Surveillance Data. JMIR Public Health Surveill 2024; 10:e50799. [PMID: 38526537 PMCID: PMC11002741 DOI: 10.2196/50799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 12/19/2023] [Accepted: 02/02/2024] [Indexed: 03/26/2024] Open
Abstract
BACKGROUND Little is known about the cocirculation of influenza and SARS-CoV-2 viruses during the COVID-19 pandemic and the use of respiratory disease sentinel surveillance platforms for monitoring SARS-CoV-2 activity in sub-Saharan Africa. OBJECTIVE We aimed to describe influenza and SARS-CoV-2 cocirculation in Kenya and how the SARS-CoV-2 data from influenza sentinel surveillance correlated with that of universal national surveillance. METHODS From April 2020 to March 2022, we enrolled 7349 patients with severe acute respiratory illness or influenza-like illness at 8 sentinel influenza surveillance sites in Kenya and collected demographic, clinical, underlying medical condition, vaccination, and exposure information, as well as respiratory specimens, from them. Respiratory specimens were tested for influenza and SARS-CoV-2 by real-time reverse transcription polymerase chain reaction. The universal national-level SARS-CoV-2 data were also obtained from the Kenya Ministry of Health. The universal national-level SARS-CoV-2 data were collected from all health facilities nationally, border entry points, and contact tracing in Kenya. Epidemic curves and Pearson r were used to describe the correlation between SARS-CoV-2 positivity in data from the 8 influenza sentinel sites in Kenya and that of the universal national SARS-CoV-2 surveillance data. A logistic regression model was used to assess the association between influenza and SARS-CoV-2 coinfection with severe clinical illness. We defined severe clinical illness as any of oxygen saturation <90%, in-hospital death, admission to intensive care unit or high dependence unit, mechanical ventilation, or a report of any danger sign (ie, inability to drink or eat, severe vomiting, grunting, stridor, or unconsciousness in children younger than 5 years) among patients with severe acute respiratory illness. RESULTS Of the 7349 patients from the influenza sentinel surveillance sites, 76.3% (n=5606) were younger than 5 years. We detected any influenza (A or B) in 8.7% (629/7224), SARS-CoV-2 in 10.7% (768/7199), and coinfection in 0.9% (63/7165) of samples tested. Although the number of samples tested for SARS-CoV-2 from the sentinel surveillance was only 0.2% (60 per week vs 36,000 per week) of the number tested in the universal national surveillance, SARS-CoV-2 positivity in the sentinel surveillance data significantly correlated with that of the universal national surveillance (Pearson r=0.58; P<.001). The adjusted odds ratios (aOR) of clinical severe illness among participants with coinfection were similar to those of patients with influenza only (aOR 0.91, 95% CI 0.47-1.79) and SARS-CoV-2 only (aOR 0.92, 95% CI 0.47-1.82). CONCLUSIONS Influenza substantially cocirculated with SARS-CoV-2 in Kenya. We found a significant correlation of SARS-CoV-2 positivity in the data from 8 influenza sentinel surveillance sites with that of the universal national SARS-CoV-2 surveillance data. Our findings indicate that the influenza sentinel surveillance system can be used as a sustainable platform for monitoring respiratory pathogens of pandemic potential or public health importance.
Collapse
Affiliation(s)
- Daniel Owusu
- Influenza Division, US Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Linus K Ndegwa
- Global Influenza Branch, Influenza Division, US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Jorim Ayugi
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | | | - Rosalia Kalani
- Disease Surveillance and Response Unit, Ministry of Health, Nairobi, Kenya
| | - Mary Okeyo
- National Influenza Centre Laboratory, National Public Health Laboratories, Ministry of Health, Nairobi, Kenya
| | - Nancy A Otieno
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Gilbert Kikwai
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Bonventure Juma
- Global Influenza Branch, Influenza Division, US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Peninah Munyua
- Global Influenza Branch, Influenza Division, US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Francis Kuria
- Directorate of Public Health, Ministry of Health, Nairobi, Kenya
| | - Emmanuel Okunga
- Disease Surveillance and Response Unit, Ministry of Health, Nairobi, Kenya
| | - Ann C Moen
- Influenza Division, US Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Gideon O Emukule
- Global Influenza Branch, Influenza Division, US Centers for Disease Control and Prevention, Nairobi, Kenya
| |
Collapse
|
23
|
Guo J, Chen X, Guo Y, Liu M, Li P, Tao Y, Liu Z, Yang Z, Zhan S, Sun F. Real-world effectiveness of seasonal influenza vaccination and age as effect modifier: A systematic review, meta-analysis and meta-regression of test-negative design studies. Vaccine 2024; 42:1883-1891. [PMID: 38423813 DOI: 10.1016/j.vaccine.2024.02.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/05/2024] [Accepted: 02/20/2024] [Indexed: 03/02/2024]
Abstract
BACKGROUND Under the global risk of epidemic rebound of influenza after COVID-19 outbreak, the study aimed to provide a comprehensive evaluation of the seasonal influenza vaccine effectiveness (IVE) and to explore the potential effect modifiers. METHODS We searched for test-negative design studies with IVE estimates published between January 1, 2017 and December 31, 2022. We estimated pooled IVE using random-effects meta-analysis, and conducted meta-regression with study site, age, sex and comorbidity as explanatory variables. RESULTS We identified 2429 publications and included 191 in the meta-analysis. The pooled IVE was 41.4 % (95 % CI: 39.2-43.5 %) against any influenza. For specific strains, the IVE was 55.4 % (95 % CI: 52.7-58.1 %) against A/H1N1, 26.8 % (95 % CI: 23.5-29.9 %) against A/H3N2, 47.2 % (95 % CI: 38.1-54.9 %) against B/Yamagata, and 40.6 % (95 % CI: 23.7-53.7 %) against B/Victoria, and the effectiveness against A/H3N2 was significantly lower than A/H1N1 (p < 0.0001) and B/Yamagata (p < 0.0001). The pooled IVE was 39.2 % (95 % CI: 36.5-41.9 %) in preventing influenza-associated outpatient visit and 43.7 % (95 % CI: 39.7-47.4 %) in preventing influenza-related hospitalization. The IVE against any influenza was 48.6 % (95 % CI: 44.7-52.2 %) for children aged < 18 years, 36.7 % (95 % CI: 31.9-41.1 %) for adults aged 18-64 years, and 30.6 % (95 % CI: 26.2-34.8 %) for elderly aged ≥65 years. Meta-regression revealed that the IVE was associated with the average age of study participants, in which both young adults [relative odds ratio (ROR) = 1.225, 95 % confidence interval (CI): 1.099-1.365, p = 0.0002] and elderly (ROR = 1.245, 95 % CI: 1.083-1.431, p = 0.002) manifested a significantly decreased effectiveness compared with children. CONCLUSIONS Influenza vaccines provided moderate protection against laboratory-confirmed influenza and related outpatient visit and hospitalization. However, the effectiveness may vary substantially by virus type and age group, suggesting the necessity to tailor vaccination strategies especially for older individuals and against the A/H3N2 strain, and to promote annual immunization and annual analysis of vaccine effectiveness.
Collapse
Affiliation(s)
- Jinxin Guo
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education/Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Xin Chen
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education/Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Yu Guo
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education/Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Mengze Liu
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education/Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Pei Li
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education/Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Yiming Tao
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education/Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Zhike Liu
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education/Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Zhirong Yang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Siyan Zhan
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education/Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China; Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, China; Center for Intelligent Public Health, Institute for Artificial Intelligence, Peking University, Beijing, China.
| | - Feng Sun
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education/Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China.
| |
Collapse
|
24
|
Parino F, Gustani-Buss E, Bedford T, Suchard MA, Trovão NS, Rambaut A, Colizza V, Poletto C, Lemey P. Integrating dynamical modeling and phylogeographic inference to characterize global influenza circulation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.14.24303719. [PMID: 38559244 PMCID: PMC10980132 DOI: 10.1101/2024.03.14.24303719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Global seasonal influenza circulation involves a complex interplay between local (seasonality, demography, host immunity) and global factors (international mobility) shaping recurrent epidemic patterns. No studies so far have reconciled the two spatial levels, evaluating the coupling between national epidemics, considering heterogeneous coverage of epidemiological and virological data, integrating different data sources. We propose a novel combined approach based on a dynamical model of global influenza spread (GLEAM), integrating high-resolution demographic and mobility data, and a generalized linear model of phylogeographic diffusion that accounts for time-varying migration rates. Seasonal migration fluxes across global macro-regions simulated with GLEAM are tested as phylogeographic predictors to provide model validation and calibration based on genetic data. Seasonal fluxes obtained with a specific transmissibility peak time and recurrent travel outperformed the raw air-transportation predictor, previously considered as optimal indicator of global influenza migration. Influenza A subtypes supported autumn-winter reproductive number as high as 2.25 and an average immunity duration of 2 years. Similar dynamics were preferred by influenza B lineages, with a lower autumn-winter reproductive number. Comparing simulated epidemic profiles against FluNet data offered comparatively limited resolution power. The multiscale approach enables model selection yielding a novel computational framework for describing global influenza dynamics at different scales - local transmission and national epidemics vs. international coupling through mobility and imported cases. Our findings have important implications to improve preparedness against seasonal influenza epidemics. The approach can be generalized to other epidemic contexts, such as emerging disease outbreaks to improve the flexibility and predictive power of modeling.
Collapse
Affiliation(s)
- Francesco Parino
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidemiologie et de Santé Publique (IPLESP), Paris, France
| | - Emanuele Gustani-Buss
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, 3000 Leuven, Belgium
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
- Howard Hughes Medical Institute, Seattle, Washington 98109, USA
| | - Marc A. Suchard
- Departments of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, 90095, USA
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA
| | | | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Vittoria Colizza
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidemiologie et de Santé Publique (IPLESP), Paris, France
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Chiara Poletto
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, 3000 Leuven, Belgium
| |
Collapse
|
25
|
Kim DJ, Cho KH, Kim S, Lee H. Influenza vaccination before and during the COVID-19 pandemic in the elderly in South Korea. J Infect Public Health 2024; 17:503-508. [PMID: 38295673 DOI: 10.1016/j.jiph.2023.11.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 11/06/2023] [Accepted: 11/30/2023] [Indexed: 02/19/2024] Open
Abstract
BACKGROUND Influenza epidemics are a significant cause of mortality and morbidity in older adults; thus, vaccination is recommended. However, the coronavirus disease 2019 (COVID-19) pandemic could affect influenza vaccination. METHODS The influenza vaccination rate was estimated from the Korea Community Health Survey data from 2011 to 2021 using Joinpoint regression. We used multiple logistic regression analysis from each two flu seasons data before (2017-18 and 2018-19 seasons) and during (2019-20 and 2020-21 seasons) the COVID-19 pandemic to identify older adults who were not been vaccinated during the COVID-19 pandemic. Additionally, we stratified changes in influenza vaccination according to the flu season, demographic and socioeconomic characteristics, and health status. RESULTS The annual percentage change in influenza non-vaccination rate from 2010-11 to 2018-19 seasons and from 2019-20 to 2020-21 seasons was -8.31% (confidence interval (CI), -9.60 to -7.00) and 11.41% (CI, -3.22 to 28.25), respectively. Compared to before COVID-19, in the 2019-20 and 2020-21 seasons, the odds ratio (OR) of non-vaccination was 0.87 (CI, 0.83-0.91) and 1.18 (95% CI, 1.13-1.24), respectively. The decrease in influenza vaccination among older individuals with higher education (OR, 1.24; CI, 1.11-1.39) was greater than that among those with lower education (OR, 1.09; CI, 0.98-1.22). Older individuals with the lowest income level or poor self-rated health showed reduced influenza vaccination. CONCLUSIONS We estimated the trends of influenza vaccination and identified subgroups with decreased vaccination rates during the COVID-19 pandemic among older adults in South Korea. Health policy decision-makers, practitioners, and researchers should consider the implications of COVID-19 on changes in influenza vaccination, particularly for older individuals at risk of influenza.
Collapse
Affiliation(s)
- Dong Jun Kim
- Department of Preventive Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Department of Public Health, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea
| | - Kyoung Hee Cho
- Department of Health Policy and Management, Sangji University, Wonju, Gangwon-do, Republic of Korea
| | - Seongju Kim
- Department of Preventive Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Department of Public Health and healthcare management, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hooyeon Lee
- Department of Preventive Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Department of Public Health, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea; Department of Public Health and healthcare management, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea.
| |
Collapse
|
26
|
Wang Y, Liu Y, Liu G, Sun X, Zhang Z, Shen J. Analysis of data from two influenza surveillance hospitals in Zhejiang province, China, for the period 2018-2022. PLoS One 2024; 19:e0299488. [PMID: 38416761 PMCID: PMC10901301 DOI: 10.1371/journal.pone.0299488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/11/2024] [Indexed: 03/01/2024] Open
Abstract
PURPOSE To assess the epidemiology of seasonal influenza in Huzhou City, Zhejiang Province, China, during 2018-2022 and provide insights for influenza prevention. METHODS Following the National Influenza Surveillance Program, we conducted pathogen surveillance by randomly sampling throat swabs from cases with influenza-like illness (ILI) at two sentinel hospitals. RESULTS From 2018 to 2022, a total of 3,813,471 cases were treated at two hospitals in Huzhou, China. Among them, there were 112,385 cases of Influenza-Like Illness (ILI), accounting for 2.95% of the total number of cases. A total of 11,686 ILI throat swab samples were tested for influenza viruses, with 1,602 cases testing positive for influenza virus nucleic acid, resulting in a positivity rate of 13.71%. Among the positive strains, there were 677 strains of A(H3N2) virus, 301 strains of A(H1N1) virus, 570 strains of B/Victoria virus, and 54 strains of B/Yamagata virus. The ILI percentage (ILI%) and influenza nucleic acid positivity rate showed winter-spring peaks in the years 2018, 2019, 2021, and 2022, with the peaks concentrated in January and February. Additionally, a small peak was observed in August 2022 during the summer season. No peak was observed during the winter-spring season of 2020. The highest proportion of ILI cases was observed in children aged 0-4 years, followed by school-age children aged 5-14 years. There was a positive correlation between ILI% and influenza virus nucleic acid positivity rate (r = 0.60, p < 0.05). CONCLUSIONS The influenza outbreak in Huzhou from 2020 to 2022 was to some extent influenced by the COVID-19 pandemic and public health measures. After the conclusion of the COVID-19 pandemic, the influenza outbreak in Huzhou may become more severe. Therefore, it is crucial to promptly assess the influenza outbreak trends based on the ILI% and the positivity rate of influenza virus nucleic acid tests.
Collapse
Affiliation(s)
- Yuda Wang
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang, China
| | - Yan Liu
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang, China
| | - Guangtao Liu
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang, China
| | - Xiuxiu Sun
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang, China
| | - Zizhe Zhang
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang, China
| | - Jianyong Shen
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang, China
| |
Collapse
|
27
|
Handabile C, Ohno M, Sekiya T, Nomura N, Kawakita T, Kawahara M, Endo M, Nishimura T, Okumura M, Toba S, Sasaki M, Orba Y, Chua BY, Rowntree LC, Nguyen THO, Shingai M, Sato A, Sawa H, Ogasawara K, Kedzierska K, Kida H. Immunogenicity and protective efficacy of a co-formulated two-in-one inactivated whole virus particle COVID-19/influenza vaccine. Sci Rep 2024; 14:4204. [PMID: 38378856 PMCID: PMC10879490 DOI: 10.1038/s41598-024-54421-1] [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: 11/02/2023] [Accepted: 02/13/2024] [Indexed: 02/22/2024] Open
Abstract
Due to the synchronous circulation of seasonal influenza viruses and severe acute respiratory coronavirus 2 (SARS-CoV-2) which causes coronavirus disease 2019 (COVID-19), there is need for routine vaccination for both COVID-19 and influenza to reduce disease severity. Here, we prepared individual WPVs composed of formalin-inactivated SARS-CoV-2 WK 521 (Ancestral strain; Co WPV) or influenza virus [A/California/07/2009 (X-179A) (H1N1) pdm; Flu WPV] to produce a two-in-one Co/Flu WPV. Serum analysis from vaccinated mice revealed that a single dose of Co/Flu WPV induced antigen-specific neutralizing antibodies against both viruses, similar to those induced by either type of WPV alone. Following infection with either virus, mice vaccinated with Co/Flu WPV showed no weight loss, reduced pneumonia and viral titers in the lung, and lower gene expression of proinflammatory cytokines, as observed with individual WPV-vaccinated. Furthermore, a pentavalent vaccine (Co/qFlu WPV) comprising of Co WPV and quadrivalent influenza vaccine (qFlu WPV) was immunogenic and protected animals from severe COVID-19. These results suggest that a single dose of the two-in-one WPV provides efficient protection against SARS-CoV-2 and influenza virus infections with no evidence of vaccine interference in mice. We propose that concomitant vaccination with the two-in-one WPV can be useful for controlling both diseases.
Collapse
Affiliation(s)
- Chimuka Handabile
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Marumi Ohno
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Toshiki Sekiya
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Naoki Nomura
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Tomomi Kawakita
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Division of Vaccine Immunology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Mamiko Kawahara
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | | | | | | | - Shinsuke Toba
- Shionogi Pharmaceutical Research Center, Shionogi & Company, Limited, Toyonaka, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Michihito Sasaki
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yasuko Orba
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Brendon Y Chua
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Louise C Rowntree
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Masashi Shingai
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Division of Vaccine Immunology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Akihiko Sato
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Shionogi Pharmaceutical Research Center, Shionogi & Company, Limited, Toyonaka, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hirofumi Sawa
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kazumasa Ogasawara
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Katherine Kedzierska
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Hiroshi Kida
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan.
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
- Division of Vaccine Immunology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
| |
Collapse
|
28
|
Lieber CM, Kang HJ, Aggarwal M, Lieberman NA, Sobolik EB, Yoon JJ, Natchus MG, Cox RM, Greninger AL, Plemper RK. Influenza A virus resistance to 4'-fluorouridine coincides with viral attenuation in vitro and in vivo. PLoS Pathog 2024; 20:e1011993. [PMID: 38300953 PMCID: PMC10863857 DOI: 10.1371/journal.ppat.1011993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/13/2024] [Accepted: 01/22/2024] [Indexed: 02/03/2024] Open
Abstract
Pre-existing or rapidly emerging resistance of influenza viruses to approved antivirals makes the development of novel therapeutics to mitigate seasonal influenza and improve preparedness against future influenza pandemics an urgent priority. We have recently identified the chain-terminating broad-spectrum nucleoside analog clinical candidate 4'-fluorouridine (4'-FlU) and demonstrated oral efficacy against seasonal, pandemic, and highly pathogenic avian influenza viruses in the mouse and ferret model. Here, we have resistance-profiled 4'-FlU against a pandemic A/CA/07/2009 (H1N1) (CA09). In vitro viral adaptation yielded six independently generated escape lineages with distinct mutations that mediated moderate resistance to 4'-FlU in the genetically controlled background of recombinant CA09 (recCA09). Mutations adhered to three distinct structural clusters that are all predicted to affect the geometry of the active site of the viral RNA-dependent RNA polymerase (RdRP) complex for phosphodiester bond formation. Escape could be achieved through an individual causal mutation, a combination of mutations acting additively, or mutations functioning synergistically. Fitness of all resistant variants was impaired in cell culture, and all were attenuated in the mouse model. Oral 4'-FlU administered at lowest-efficacious (2 mg/kg) or elevated (10 mg/kg) dose overcame moderate resistance when mice were inoculated with 10 LD50 units of parental or resistant recCA09, demonstrated by significantly reduced virus load and complete survival. In the ferret model, invasion of the lower respiratory tract by variants representing four adaptation lineages was impaired. Resistant variants were either transmission-incompetent, or spread to untreated sentinels was fully blocked by therapeutic treatment of source animals with 4'-FlU.
Collapse
Affiliation(s)
- Carolin M. Lieber
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, Georgia, United States of America
| | - Hae-Ji Kang
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, Georgia, United States of America
| | - Megha Aggarwal
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, Georgia, United States of America
| | - Nicole A. Lieberman
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington, United States of America
| | - Elizabeth B. Sobolik
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington, United States of America
| | - Jeong-Joong Yoon
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, Georgia, United States of America
| | - Michael G. Natchus
- Emory Institute for Drug Development, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Robert M. Cox
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, Georgia, United States of America
| | - Alexander L. Greninger
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington, United States of America
| | - Richard K. Plemper
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, Georgia, United States of America
| |
Collapse
|
29
|
Vink E, Banda L, Amoah AS, Kasenda S, Read JM, Jewell C, Denis B, Mwale AC, Crampin A, Anscombe C, Menyere M, Ho A. Prevalence of Endemic Respiratory Viruses During the COVID-19 Pandemic in Urban and Rural Malawi. Open Forum Infect Dis 2024; 11:ofad643. [PMID: 38312213 PMCID: PMC10836885 DOI: 10.1093/ofid/ofad643] [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: 11/30/2023] [Accepted: 12/19/2023] [Indexed: 02/06/2024] Open
Abstract
Background We investigated endemic respiratory virus circulation patterns in Malawi, where no lockdown was imposed, during the COVID-19 pandemic. Methods Within a prospective household cohort in urban and rural Malawi, adult participants provided upper respiratory tract (URT) samples at 4 time points between February 2021 and April 2022. Polymerase chain reaction (PCR) was performed for SARS-CoV-2, influenza, and other endemic respiratory viruses. Results 1626 URT samples from 945 participants in 542 households were included. Overall, 7.6% (n = 123) samples were PCR- positive for >1 respiratory virus; SARS-CoV-2 (4.4%) and rhinovirus (2.0%) were most common. No influenza A virus was detected. Influenza B and respiratory syncytial virus (RSV) were rare. Higher virus positivity were detected in the rural setting and at earlier time points. Coinfections were infrequent. Conclusions Endemic respiratory viruses circulated in the community in Malawi during the pandemic, though influenza and RSV were rarely detected. Distinct differences in virus positivity and demographics were observed between urban and rural cohorts.
Collapse
Affiliation(s)
- Elen Vink
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Louis Banda
- Malawi Epidemiology and Intervention Research Unit, Lilongwe and Chilumba, Malawi
| | - Abena S Amoah
- Malawi Epidemiology and Intervention Research Unit, Lilongwe and Chilumba, Malawi
- Department of Population Health, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- Leiden University Medical Center, Leiden, the Netherlands
| | - Stephen Kasenda
- Malawi Epidemiology and Intervention Research Unit, Lilongwe and Chilumba, Malawi
| | - Jonathan M Read
- Centre for Health Information Computation and Statistics, Lancaster Medical School, Lancaster University, Lancaster, UK
| | - Chris Jewell
- Department of Mathematics and Statistics, Lancaster University, Lancaster, UK
| | - Brigitte Denis
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | | | - Amelia Crampin
- Malawi Epidemiology and Intervention Research Unit, Lilongwe and Chilumba, Malawi
- Department of Population Health, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- School of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Catherine Anscombe
- Department of Mathematics and Statistics, Lancaster University, Lancaster, UK
- Liverpool School of Tropical Medicine, University of Liverpool, Liverpool, UK
| | - Mavis Menyere
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| |
Collapse
|
30
|
Petro-Turnquist E, Corder Kampfe B, Gadeken A, Pekarek MJ, Weaver EA. Multivalent Epigraph Hemagglutinin Vaccine Protects against Influenza B Virus in Mice. Pathogens 2024; 13:97. [PMID: 38392835 PMCID: PMC10892733 DOI: 10.3390/pathogens13020097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Influenza B virus is a respiratory pathogen that contributes to seasonal epidemics, accounts for approximately 25% of global influenza infections, and can induce severe disease in young children. While vaccination is the most commonly used method of preventing influenza infections, current vaccines only induce strain-specific responses and have suboptimal efficacy when mismatched from circulating strains. Further, two influenza B virus lineages have been described, B/Yamagata-like and B/Victoria-like, and the limited cross-reactivity between the two lineages provides an additional barrier in developing a universal influenza B virus vaccine. Here, we report a novel multivalent vaccine using computationally designed Epigraph hemagglutinin proteins targeting both the B/Yamagata-like and B/Victoria-like lineages. When compared to the quadrivalent commercial vaccine, the Epigraph vaccine demonstrated increased breadth of neutralizing antibody and T cell responses. After lethal heterologous influenza B virus challenge, mice immunized with the Epigraph vaccine were completely protected against both weight loss and mortality. The superior cross-reactive immunity conferred by the Epigraph vaccine immunogens supports their continued investigation as a universal influenza B virus vaccine.
Collapse
Affiliation(s)
- Erika Petro-Turnquist
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Brigette Corder Kampfe
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
- Science Department, North Arkansas College, Harrison, AR 72601, USA
| | - Amber Gadeken
- College of Agricultural Sciences and Natural Resources, University of Nebraska-Lincoln, Lincoln, NE 68583, USA;
| | - Matthew J. Pekarek
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Eric A. Weaver
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| |
Collapse
|
31
|
de Jong SPJ, Felix Garza ZC, Gibson JC, van Leeuwen S, de Vries RP, Boons GJ, van Hoesel M, de Haan K, van Groeningen LE, Hulme KD, van Willigen HDG, Wynberg E, de Bree GJ, Matser A, Bakker M, van der Hoek L, Prins M, Kootstra NA, Eggink D, Nichols BE, Han AX, de Jong MD, Russell CA. Determinants of epidemic size and the impacts of lulls in seasonal influenza virus circulation. Nat Commun 2024; 15:591. [PMID: 38238318 PMCID: PMC10796432 DOI: 10.1038/s41467-023-44668-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 12/21/2023] [Indexed: 01/22/2024] Open
Abstract
During the COVID-19 pandemic, levels of seasonal influenza virus circulation were unprecedentedly low, leading to concerns that a lack of exposure to influenza viruses, combined with waning antibody titres, could result in larger and/or more severe post-pandemic seasonal influenza epidemics. However, in most countries the first post-pandemic influenza season was not unusually large and/or severe. Here, based on an analysis of historical influenza virus epidemic patterns from 2002 to 2019, we show that historic lulls in influenza virus circulation had relatively minor impacts on subsequent epidemic size and that epidemic size was more substantially impacted by season-specific effects unrelated to the magnitude of circulation in prior seasons. From measurements of antibody levels from serum samples collected each year from 2017 to 2021, we show that the rate of waning of antibody titres against influenza virus during the pandemic was smaller than assumed in predictive models. Taken together, these results partially explain why the re-emergence of seasonal influenza virus epidemics was less dramatic than anticipated and suggest that influenza virus epidemic dynamics are not currently amenable to multi-season prediction.
Collapse
Affiliation(s)
- Simon P J de Jong
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Zandra C Felix Garza
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Joseph C Gibson
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Sarah van Leeuwen
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Robert P de Vries
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Geert-Jan Boons
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
- Department of Chemistry, University of Georgia, Athens, GA, USA
| | - Marliek van Hoesel
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Karen de Haan
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Laura E van Groeningen
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Katina D Hulme
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Hugo D G van Willigen
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Elke Wynberg
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, The Netherlands
| | - Godelieve J de Bree
- Department of Infectious Diseases, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Amy Matser
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, The Netherlands
| | - Margreet Bakker
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Lia van der Hoek
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Maria Prins
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, The Netherlands
- Department of Infectious Diseases, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Neeltje A Kootstra
- Department of Experimental Immunology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Dirk Eggink
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Brooke E Nichols
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Department of Global Health, School of Public Health, Boston University, Boston, MA, USA
| | - Alvin X Han
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Menno D de Jong
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Colin A Russell
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.
- Department of Global Health, School of Public Health, Boston University, Boston, MA, USA.
| |
Collapse
|
32
|
Uno N, Ross TM. Multivalent next generation influenza virus vaccines protect against seasonal and pre-pandemic viruses. Sci Rep 2024; 14:1440. [PMID: 38228649 PMCID: PMC10792005 DOI: 10.1038/s41598-023-51024-0] [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: 03/03/2023] [Accepted: 12/29/2023] [Indexed: 01/18/2024] Open
Abstract
Each year, new influenza virus vaccine formulations are generated to keep up with continuously circulating and mutating viral variants. A next-generation influenza virus vaccine would provide long-lasting, broadly-reactive immune protection against current and future influenza virus strains for both seasonal and pre-pandemic viruses. Next generation immunogens were designed using computationally optimized broadly reactive antigen (COBRA) methodology to protect against a broad range of strains over numerous seasons. Novel HA and NA amino acid sequences were derived from multilayered consensus sequence alignment for multiple subtypes of influenza. This multivalent formulation was hypothesized to elicit broadly protective immune responses against both seasonal and pre-pandemic influenza viruses. Mice were vaccinated with multivalent mixtures of HA and NA (H1, H2, H3, H5, H7, N1, N2) proteins. Multivalent COBRA vaccinations elicited antibodies that recognized a broad panel of strains and vaccinated mice were protected against viruses representing multiple subtypes. This is a promising candidate for a universal influenza vaccine that elicits protective immune responses against seasonal and pre-pandemic strains over multiple seasons.
Collapse
Affiliation(s)
- Naoko Uno
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
- Department of Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA.
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA.
- Florida Research and Innovation Center, Cleveland Clinic Florida, 9801 SW Discovery Way, Port Saint Lucie, FL, 34986, USA.
- Department of Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
| |
Collapse
|
33
|
Kandeel A, Fahim M, Deghedy O, BahaaEldin H, Roshdy WH, Khalifa MK, Kandeil A, El Shesheny R, Naguib A, AbdelFatah M, Afifi S, Abdel Ghaffar K. Comparative analysis of COVID-19 and influenza prevalence among Egyptian pilgrims returning from Hajj and Umrah in 2022: epidemiology, clinical characteristics, and genomic sequencing. Arch Public Health 2024; 82:6. [PMID: 38216978 PMCID: PMC10785524 DOI: 10.1186/s13690-023-01229-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 12/14/2023] [Indexed: 01/14/2024] Open
Abstract
PURPOSE To describe the changes that occurred in the SARS-CoV-2 and influenza Prevalence, epidemiology, clinical picture, and prevalent genotypes among the Egyptian pilgrims returning from Hajj and Umrah 2022 seasons. METHODS Pilgrims were contacted at the airport and invited to participate in the survey. Pilgrims who consented were interviewed using a standardized line list that included participant demographics, respiratory symptoms if any, previous COVID-19 infection, influenza vaccination whereas COVID-19 vaccination information were collected from vaccination cards. Participants were asked to provide throat and nasopharyngeal swabs for SARS-CoV-2 and influenza testing using RT-PCR and a subset of isolates were sequenced. Descriptive data analysis was performed to describe the epidemiology and clinical symptoms of SARS-CoV-2 and influenza. Prevalence rates of SARS-CoV-2 and influenza during Hajj were calculated and compared to Umrah surveys using chi2 and t-test with a significance level < 0.05. RESULTS Overall, 3,862 Egyptian pilgrims enrolled, their mean age was 50.5 ± 47 years, half of them were > 50 years of age and 58.2% were males. Of them, 384 (9.9%) tested positive for SARS-CoV-2 and 51 (1.3%) for influenza viruses. Prevalence of SARS-CoV-2 infections (vaccine breakthrough) increased significantly between the Umrah and Hajj surveys (6.7% vs. 9.9%, p < 0.001), and variants of the virus varied considerably. Whereas no significant difference was found in influenza prevalence, vaccine coverage and vaccine breakthrough infection rates (11.7 vs. 9.2%, 26.9 vs. 26.8%, and 1.4 vs. 1.1% respectively). CONCLUSIONS SARS-CoV-2 prevalence among Egyptian pilgrims returning from Hajj in July increased with reduced vaccine effectiveness compared to Umrah in March 2022 suggesting a possible wave of SARS-CoV-2 in the upcoming winter.
Collapse
Affiliation(s)
- Amr Kandeel
- Preventive Sector, Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt
| | - Manal Fahim
- Department of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt
| | - Ola Deghedy
- Department of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt
| | - Hala BahaaEldin
- Department of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt.
| | - Wael H Roshdy
- Central Public Health Laboratory, Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt
| | - Mohamed Kamal Khalifa
- Central Public Health Laboratory, Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt
| | - Ahmed Kandeil
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, 12622 Dokki, Giza, Egypt
| | - Rabeh El Shesheny
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, 12622 Dokki, Giza, Egypt
| | - Amel Naguib
- Central Public Health Laboratory, Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt
| | - Mohamad AbdelFatah
- Preventive Sector, Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt
| | - Salma Afifi
- Ministry of Health and Population Consultant, Governmental District, New Administrative Capital, Cairo, Egypt
| | - Khaled Abdel Ghaffar
- Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt
| |
Collapse
|
34
|
Zhang Y, Huang X, Zhang J, Tao Z. Risk factors for hospitalization and pneumonia development of pediatric patients with seasonal influenza during February-April 2023. Front Public Health 2024; 11:1300228. [PMID: 38249383 PMCID: PMC10797015 DOI: 10.3389/fpubh.2023.1300228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/15/2023] [Indexed: 01/23/2024] Open
Abstract
Objectives In China influenza remains a low activity for continuous 3 years due to COVID-19 controls. We here sought to study the clinical characteristics and risk factors of the influenza infection among children after the mandatory COVID-19 restrictions were lifted. Methods We included 1,006 pediatric patients with influenza A virus (IAV) infection, enrolled in one tertiary hospital in Zhenjiang, Jiangsu Province, China, during February to April 2023. Patients were divided into the outpatient (n = 798) and inpatient (n = 208) groups, and their baseline characteristics were compared between two groups to conclude the risk factors for pediatric hospitalization. Separately, pediatric inpatients (n = 208) were further divided into the pneumonia and non-pneumonia groups with comparison of their clinical characteristics, including their laboratory test results and representative radiological features, to derive the key determinants for pneumonia development after hospitalization. Results Compared to outpatients, IAV-infected pediatric inpatients exhibited younger age, higher female: male ratio, more co-infection of influenza B virus (IBV) and hematological abnormality. Multivariate regression analysis determined the independent risk factors of hospitalization to be the clinical symptom of abdominal pain (OR = 2.63, [95% CI, 1.05-6.57], p = 0.039), co-infection of IBV (OR = 44.33, [95% CI, 25.10-78.30], p = 0.001), elevated levels of lymphocytes (OR = 2.24, [95% CI,1.65-3.05], p = 0.001) and c-reactive proteins (CRPs) (OR = 1.06, [95% CI, 1.03-1.08], p = 0.001) upon hospital admission. Furthermore, the cough symptom (OR = 17.39, [95% CI, 3.51-86.13], p = 0.001) and hospitalization length (OR = 1.36, [95% CI, 1.12-1.67], p = 0.002) were determined to be risk factors of pneumonia acquirement for pediatric inpatients. Conclusion While the abdominal pain, viral co-infection and some hematological abnormality mainly contribute to hospitalization of pediatric patients with IAV infection, the length of hospital stay and clinical sign of coughing upon hospital admission constitute the key determinants for nosocomial pneumonia development.
Collapse
Affiliation(s)
- Yuqian Zhang
- Department of Emergency Medicine, The Affiliated Hospital, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xing Huang
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jianguo Zhang
- Department of Emergency Medicine, The Affiliated Hospital, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Zhimin Tao
- Department of Emergency Medicine, The Affiliated Hospital, Jiangsu University, Zhenjiang, Jiangsu, China
- Jiangsu Province Key Laboratory of Medical Science and Laboratory Medicine, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| |
Collapse
|
35
|
Nadeau S, Devaux AJ, Bagutti C, Alt M, Ilg Hampe E, Kraus M, Würfel E, Koch KN, Fuchs S, Tschudin-Sutter S, Holschneider A, Ort C, Chen C, Huisman JS, Julian TR, Stadler T. Influenza transmission dynamics quantified from RNA in wastewater in Switzerland. Swiss Med Wkly 2024; 154:3503. [PMID: 38579316 DOI: 10.57187/s.3503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024] Open
Abstract
INTRODUCTION Influenza infections are challenging to monitor at the population level due to many mild and asymptomatic cases and similar symptoms to other common circulating respiratory diseases, including COVID-19. Methods for tracking cases outside of typical reporting infrastructure could improve monitoring of influenza transmission dynamics. Influenza shedding into wastewater represents a promising source of information where quantification is unbiased by testing or treatment-seeking behaviours. METHODS We quantified influenza A and B virus loads from influent at Switzerland's three largest wastewater treatment plants, serving about 14% of the Swiss population (1.2 million individuals). We estimated trends in infection incidence and the effective reproductive number (Re) in these catchments during a 2021/22 epidemic and compared our estimates to typical influenza surveillance data. RESULTS Wastewater data captured the same overall trends in infection incidence as laboratory-confirmed case data at the catchment level. However, the wastewater data were more sensitive in capturing a transient peak in incidence in December 2021 than the case data. The Re estimated from the wastewater data was roughly at or below the epidemic threshold of 1 during work-from-home measures in December 2021 but increased to at or above the epidemic threshold in two of the three catchments after the relaxation of these measures. The third catchment yielded qualitatively the same results but with wider confidence intervals. The confirmed case data at the catchment level yielded comparatively less precise R_e estimates before and during the work-from-home period, with confidence intervals that included one before and during the work-from-home period. DISCUSSION Overall, we show that influenza RNA in wastewater can help monitor nationwide influenza transmission dynamics. Based on this research, we developed an online dashboard for ongoing wastewater-based influenza surveillance in Switzerland.
Collapse
Affiliation(s)
- Sarah Nadeau
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | | | - Monica Alt
- State Laboratory of Basel-Stadt, Basel, Switzerland
| | | | - Melanie Kraus
- Department of Health, Canton of Basel-Stadt, Basel, Switzerland
| | - Eva Würfel
- Department of Health, Canton of Basel-Stadt, Basel, Switzerland
| | - Katrin N Koch
- Cantonal Office of Public Health, Department of Economics and Health, Canton of Basel-Landschaft, Liestal, Switzerland
| | - Simon Fuchs
- Department of Health, Canton of Basel-Stadt, Basel, Switzerland
| | - Sarah Tschudin-Sutter
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel and University of Basel, Basel, Switzerland
| | | | - Christoph Ort
- Department of Environmental Microbiology, EAWAG, Dübendorf, Switzerland
| | - Chaoran Chen
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jana S Huisman
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Timothy R Julian
- Department of Environmental Microbiology, EAWAG, Dübendorf, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| |
Collapse
|
36
|
Sharmila F, Muthamizhkumaran S, Ratchagadasse VR, Ramamurthy N, Sistla S, Dhodapkar R. Influence of COVID-19 over seasonal influenza activity in southern India. Indian J Med Microbiol 2024; 47:100531. [PMID: 38246243 DOI: 10.1016/j.ijmmb.2024.100531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 10/15/2023] [Accepted: 01/15/2024] [Indexed: 01/23/2024]
Abstract
Basic epidemiological data is urgently needed in order to ascertain the changes brought about by COVID-19 pandemic, and help researchers, clinicians, and policy makers in addressing these issues. Data on influenza positivity from 2009 to 2019 was collected from Regional Influenza laboratory, JIPMER. Being COVID testing centre we tested samples (2020-2023) from Tamilnadu and Pondicherry. All SARI samples which were negative for COVID-19 were subjected to Influenza testing as regular surveillance activity was suspended. On comparison we found significant reduction in detection rates of influenza A H1N1, H3N2 and influenza B (p value = <0.01).
Collapse
Affiliation(s)
- Ferdinamarie Sharmila
- Regional Influenza Lab, Department of Microbiology, Jawaharlal Institute of Post-Graduate Medical Education and Research (JIPMER), Puducherry, 605006, India.
| | - S Muthamizhkumaran
- Regional Influenza Lab, Department of Microbiology, Jawaharlal Institute of Post-Graduate Medical Education and Research (JIPMER), Puducherry, 605006, India.
| | - Vimal Raj Ratchagadasse
- Regional Influenza Lab, Department of Microbiology, Jawaharlal Institute of Post-Graduate Medical Education and Research (JIPMER), Puducherry, 605006, India.
| | - Narayan Ramamurthy
- Regional Influenza Lab, Department of Microbiology, Jawaharlal Institute of Post-Graduate Medical Education and Research (JIPMER), Puducherry, 605006, India.
| | - Sujatha Sistla
- Regional Influenza Lab, Department of Microbiology, Jawaharlal Institute of Post-Graduate Medical Education and Research (JIPMER), Puducherry, 605006, India.
| | - Rahul Dhodapkar
- Regional Influenza Lab, Department of Microbiology, Jawaharlal Institute of Post-Graduate Medical Education and Research (JIPMER), Puducherry, 605006, India.
| |
Collapse
|
37
|
Pontiroli AE, Scovenna F, Carlini V, Tagliabue E, Martin-Delgado J, Sala LL, Tanzi E, Zanoni I. Vaccination against influenza viruses reduces infection, not hospitalization or death, from respiratory COVID-19: A systematic review and meta-analysis. J Med Virol 2024; 96:e29343. [PMID: 38163281 PMCID: PMC10924223 DOI: 10.1002/jmv.29343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/01/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19 and has brought a huge burden in terms of human lives. Strict social distance and influenza vaccination have been recommended to avoid co-infections between influenza viruses and SARS-CoV-2. Scattered reports suggested a protective effect of influenza vaccine on COVID-19 development and severity. We analyzed 51 studies on the capacity of influenza vaccination to affect infection with SARS-CoV-2, hospitalization, admission to Intensive Care Units (ICU), and mortality. All subjects taken into consideration did not receive any anti-SARS-CoV-2 vaccine, although their status with respect to previous infections with SARS-CoV-2 is not known. Comparison between vaccinated and not-vaccinated subjects for each of the four endpoints was expressed as odds ratio (OR), with 95% confidence intervals (CIs); all analyses were performed by DerSimonian and Laird model, and Hartung-Knapp model when studies were less than 10. In a total of 61 029 936 subjects from 33 studies, influenza vaccination reduced frequency of SARS-CoV-2 infection [OR plus 95% CI = 0.70 (0.65-0.77)]. The effect was significant in all studies together, in health care workers and in the general population; distance from influenza vaccination and the type of vaccine were also of importance. In 98 174 subjects from 11 studies, frequency of ICU admission was reduced with influenza vaccination [OR (95% CI) = 0.71 (0.54-0.94)]; the effect was significant in all studies together, in pregnant women and in hospitalized subjects. In contrast, in 4 737 328 subjects from 14 studies hospitalization was not modified [OR (95% CI) = 1.05 (0.82-1.35)], and in 4 139 660 subjects from 19 studies, mortality was not modified [OR (95% CI) = 0.76 (0.26-2.20)]. Our study emphasizes the importance of influenza vaccination in the protection against SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Antonio E. Pontiroli
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, 20142 Milan, Italy
| | - Francesco Scovenna
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, 20142 Milan, Italy
| | - Valentina Carlini
- IRCCS MultiMedica, Laboratory of Cardiovascular and Dysmetabolic Disease, 20138 Milan, Italy
| | - Elena Tagliabue
- IRCCS MultiMedica, Value-Based Healthcare Unit, 20099 Milan, Italy
| | - Jimmy Martin-Delgado
- Hospital Luis Vernaza, Junta de Beneficiencia de Guayaquil 090603, Ecuador
- Instituto de Investigacion e Innovacion en Salud Integral, Universidad Catolica de Santiago de Guayaquil, Guayaquil 090603, Ecuador
| | - Lucia La Sala
- IRCCS MultiMedica, Laboratory of Cardiovascular and Dysmetabolic Disease, 20138 Milan, Italy
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Milan, Italy
| | - Elisabetta Tanzi
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, 20142 Milan, Italy
| | - Ivan Zanoni
- Harvard Medical School, Boston Children’s Hospital, Division of Immunology and Division of Gastroenterology, Boston, MA 02115, USA
| |
Collapse
|
38
|
Do THT, Wheatley AK, Kent SJ, Koutsakos M. Influenza B virus neuraminidase: a potential target for next-generation vaccines? Expert Rev Vaccines 2024; 23:39-48. [PMID: 38037386 DOI: 10.1080/14760584.2023.2290691] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/29/2023] [Indexed: 12/02/2023]
Abstract
INTRODUCTION Influenza B viruses (IBV) cause a significant health and economic burden annually. Due to lower antigenic drift rate, less extensive antigenic diversity, and lack of animal reservoirs, the development of highly effective universal vaccines against IBV might be in reach. Current seasonal influenza vaccines are formulated to induce antibodies against the Hemagglutinin (HA) protein, but their effectiveness is reduced by mismatch between vaccine and circulating strains. AREAS COVERED Given antibodies against the Neuraminidase (NA) have been associated with protection during influenza infection, there is considerable interest in the development of NA-based influenza vaccines. This review summarizes insights into the role of NA-based immunity against IBV and highlights knowledge gaps that should be addressed to inform the design of next-generation influenza B vaccines. We discuss how antibodies recognize broadly cross-reactive epitopes on the NA and the lack of understanding of IBV NA antigenic evolution which would benefit vaccine development in the future. EXPERT OPINION Demonstrating NA antibodies as correlates of protection for IBV in humans would be paramount. Determining the extent of IBV NA antigenic evolution will be informative. Finally, it will be critical to determine optimal strategies for incorporating the appropriate NA antigens in existing clinically approved vaccine formulations.
Collapse
Affiliation(s)
- Thi Hoai Thu Do
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute of Infection and Immunity, Melbourne, Australia
| | - Adam K Wheatley
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute of Infection and Immunity, Melbourne, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute of Infection and Immunity, Melbourne, Australia
- Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute of Infection and Immunity, Melbourne, Australia
| |
Collapse
|
39
|
Forero EL, Knoester M, Gard L, Ott A, Brandenburg AH, McCall MBB, Niesters HGM, Van Leer-Buter C. Changes in enterovirus epidemiology after easing of lockdown measures. J Clin Virol 2023; 169:105617. [PMID: 37977075 DOI: 10.1016/j.jcv.2023.105617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
INTRODUCTION Public health measures aimed at controlling transmission of SARS-CoV-2, otherwise known as "lockdown" measures, had profound effects on circulation of non-SARS viruses, many of which decreased to very low levels. The interrupted transmission of these viruses may have lasting effects. Some of the influenza clades seem to have disappeared during this period, a phenomenon which is described as a "funnel effect". It is currently unknown if the lockdown measures had any effect on the diversity of circulating viruses, other than influenza. Enteroviruses are especially interesting in this context, as the clinical presentation of an infection with a particular enterovirus-type may be clade-dependent. METHODS AND MATERIALS Enteroviruses were detected in clinical materials using a 5'UTR-based detection PCR, and partial VP-1 sequences were obtained, using methods described before. All samples with EV detections from a large part of the Netherlands were included in the study. The samples originated from general practitioners, general hospitals, university hospitals and public health offices. RESULTS Five EV-genotypes circulated in significant numbers before and after the lockdown, EV-D68, E-11, CV-A6, CV-B5 and CV-A2. All five genotypes showed decreased genetic diversity after the lockdown, and four indicate a significant number of sequences clustering together with a very high sequence homology. Moreover, children with E-11 and CV-B5 detections were significantly older after the lockdown than before. CONCLUSIONS The reduced enterovirus transmission in the Netherlands during the pandemic, seems to have led to a decrease in genetic diversity in the five most commonly detected enterovirus serotypes.
Collapse
Affiliation(s)
- Erley Lizarazo Forero
- Department of medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Marjolein Knoester
- Department of medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Lilli Gard
- Department of medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Alewijn Ott
- Certe, department of Medical Microbiology Groningen, The Netherlands
| | - Afke H Brandenburg
- Certe, department of Medical Microbiology Friesland|NOP, The Netherlands
| | - Matthew B B McCall
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hubert G M Niesters
- Department of medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Coretta Van Leer-Buter
- Department of medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, The Netherlands.
| |
Collapse
|
40
|
Varela-Lasheras I, Perfeito L, Mesquita S, Gonçalves-Sá J. The effects of weather and mobility on respiratory viruses dynamics before and during the COVID-19 pandemic in the USA and Canada. PLOS DIGITAL HEALTH 2023; 2:e0000405. [PMID: 38127792 PMCID: PMC10734953 DOI: 10.1371/journal.pdig.0000405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 11/07/2023] [Indexed: 12/23/2023]
Abstract
The flu season is caused by a combination of different pathogens, including influenza viruses (IVS), that cause the flu, and non-influenza respiratory viruses (NIRVs), that cause common colds or influenza-like illness. These viruses exhibit similar dynamics and meteorological conditions have historically been regarded as a principal modulator of their epidemiology, with outbreaks in the winter and almost no circulation during the summer, in temperate regions. However, after the emergence of SARS-CoV2, in late 2019, the dynamics of these respiratory viruses were strongly perturbed worldwide: some infections displayed near-eradication, while others experienced temporal shifts or occurred "off-season". This disruption raised questions regarding the dominant role of weather while also providing an unique opportunity to investigate the roles of different determinants on the epidemiological dynamics of IVs and NIRVs. Here, we employ statistical analysis and modelling to test the effects of weather and mobility in viral dynamics, before and during the COVID-19 pandemic. Leveraging epidemiological surveillance data on several respiratory viruses, from Canada and the USA, from 2016 to 2023, we found that whereas in the pre-COVID-19 pandemic period, weather had a strong effect, in the pandemic period the effect of weather was strongly reduced and mobility played a more relevant role. These results, together with previous studies, indicate that behavioral changes resulting from the non-pharmacological interventions implemented to control SARS-CoV2, interfered with the dynamics of other respiratory viruses, and that the past dynamical equilibrium was disturbed, and perhaps permanently altered, by the COVID-19 pandemic.
Collapse
Affiliation(s)
- Irma Varela-Lasheras
- Nova School of Business and Economics, Universidade Nova de Lisboa, Carcavelos, Portugal
| | - Lilia Perfeito
- LIP, Laboratório de Instrumentação e Física Experimental de Partículas, Lisbon, Portugal
| | - Sara Mesquita
- LIP, Laboratório de Instrumentação e Física Experimental de Partículas, Lisbon, Portugal
- Nova Medical School, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Joana Gonçalves-Sá
- Nova School of Business and Economics, Universidade Nova de Lisboa, Carcavelos, Portugal
- LIP, Laboratório de Instrumentação e Física Experimental de Partículas, Lisbon, Portugal
| |
Collapse
|
41
|
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.
Collapse
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.
| |
Collapse
|
42
|
Bouzid D, Visseaux B, Ferré VM, Peiffer-Smadja N, Le Hingrat Q, Loubet P. Respiratory syncytial virus in adults with comorbidities: an update on epidemiology, vaccines, and treatments. Clin Microbiol Infect 2023; 29:1538-1550. [PMID: 37666450 DOI: 10.1016/j.cmi.2023.08.028] [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: 05/25/2023] [Revised: 08/19/2023] [Accepted: 08/30/2023] [Indexed: 09/06/2023]
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is widely known as a frequent cause of respiratory distress among adults, particularly in older people. Recent years have witnessed several improvements in respiratory virus detection, leading to more questions about therapeutic management strategies. OBJECTIVES This narrative review focuses on the RSV burden in older people and adults with risk factors and provides an update on the main recent developments regarding managing this infection. SOURCES A comprehensive PubMed search was conducted till August 2023 to identify studies on RSV among the adult population. We included observational studies, RCTs on vaccines, and different therapies. CONTENT This review should give clinicians an overview of RSV epidemiology and burden among older people and adults with pre-existing risk factors, the most recent randomized clinical trials on RSV vaccines, and the existing data on the different therapeutics existing and under development. IMPLICATIONS There is a growing body of evidence on RSV burden in adults. The landscape of preventive and curative treatments is quickly evolving.
Collapse
Affiliation(s)
- Donia Bouzid
- Université Paris Cité, INSERM UMR1137, IAME, F-75018, Paris, France; AP-HP Nord, Emergency Department, Bichat-Claude Bernard University Hospital, Paris, France
| | - Benoit Visseaux
- Laboratoire Cerba, Infectious Diseases Department, Saint Ouen l'Aumône, France
| | - Valentine Marie Ferré
- Université Paris Cité, INSERM UMR1137, IAME, F-75018, Paris, France; AP-HP Nord, Infectious Diseases Department, Bichat-Claude Bernard University Hospital, Paris, France
| | - Nathan Peiffer-Smadja
- Université Paris Cité, INSERM UMR1137, IAME, F-75018, Paris, France; AP-HP Nord, Virology Department, Bichat-Claude Bernard University Hospital, Paris, France
| | - Quentin Le Hingrat
- Université Paris Cité, INSERM UMR1137, IAME, F-75018, Paris, France; AP-HP Nord, Infectious Diseases Department, Bichat-Claude Bernard University Hospital, Paris, France
| | - Paul Loubet
- Université de Montpellier, VBMI, Inserm U1047, Nîmes, France; Department of Infectious and Tropical Diseases, CHU Nîmes, Université de Montpellier, Nîmes, France.
| |
Collapse
|
43
|
Chadaga K, Prabhu S, Bhat V, Sampathila N, Umakanth S, Upadya P S. COVID-19 diagnosis using clinical markers and multiple explainable artificial intelligence approaches: A case study from Ecuador. SLAS Technol 2023; 28:393-410. [PMID: 37689365 DOI: 10.1016/j.slast.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 08/16/2023] [Accepted: 09/06/2023] [Indexed: 09/11/2023]
Abstract
The COVID-19 pandemic erupted at the beginning of 2020 and proved fatal, causing many casualties worldwide. Immediate and precise screening of affected patients is critical for disease control. COVID-19 is often confused with various other respiratory disorders since the symptoms are similar. As of today, the reverse transcription-polymerase chain reaction (RT-PCR) test is utilized for diagnosing COVID-19. However, this approach is sometimes prone to producing erroneous and false negative results. Hence, finding a reliable diagnostic method that can validate the RT-PCR test results is crucial. Artificial intelligence (AI) and machine learning (ML) applications in COVID-19 diagnosis has proven to be beneficial. Hence, clinical markers have been utilized for COVID-19 diagnosis with the help of several classifiers in this study. Further, five different explainable artificial intelligence techniques have been utilized to interpret the predictions. Among all the algorithms, the k-nearest neighbor obtained the best performance with an accuracy, precision, recall and f1-score of 84%, 85%, 84% and 84%. According to this study, the combination of clinical markers such as eosinophils, lymphocytes, red blood cells and leukocytes was significant in differentiating COVID-19. The classifiers can be utilized synchronously with the standard RT-PCR procedure making diagnosis more reliable and efficient.
Collapse
Affiliation(s)
- Krishnaraj Chadaga
- Department of Computer Science and Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - Srikanth Prabhu
- Department of Computer Science and Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India.
| | - Vivekananda Bhat
- Department of Computer Science and Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - Niranjana Sampathila
- Department of Biomedical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India.
| | - Shashikiran Umakanth
- Department of Medicine, Dr. TMA Hospital, Manipal Academy of Higher Education, Manipal, India
| | - Sudhakara Upadya P
- Manipal School of Information Sciences, Manipal Academy of Higher Education, Manipal, India
| |
Collapse
|
44
|
Cao L, Lu Y, Xie C, Chen Y, Liang L, Zhou T, Zeng Z, Wen C, Di B, Li B, Li K, Zhang Z. Emerging triple-reassortant influenza C virus with household-associated infection during an influenza A(H3N2) outbreak, China, 2022. Emerg Microbes Infect 2023; 12:2175593. [PMID: 36881645 PMCID: PMC10013421 DOI: 10.1080/22221751.2023.2175593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Recent research have shown that influenza C virus (ICV) has a possible higher clinical impact than previously thought. But knowledge about ICV is limited compared with influenza A and B viruses, due to poor systematic surveillance and inability to propagate. Herein, a case infected with triple reassortant ICV was identified during an influenza A(H3N2) outbreak, which was the first report of ICV infection in mainland China. Phylogenetic analysis showed that this ICV was triple reassortant. Serological evidence revealed that the index case might be related to family-clustering infection. Therefore, it is essential to heighten surveillance for the prevalence and variation of ICV in China, during the COVID-19 pandemic.
Collapse
Affiliation(s)
- Lan Cao
- Institute of Public Health, Guangzhou Medical University and Guangzhou Center for Disease Control and Prevention, Guangzhou, People's Republic of China
| | - Ying Lu
- Institute of Public Health, Guangzhou Medical University and Guangzhou Center for Disease Control and Prevention, Guangzhou, People's Republic of China
| | - Chaojun Xie
- Huadu District Center for Disease Control and Prevention, Guangzhou, People's Republic of China
| | - Yiyun Chen
- Institute of Public Health, Guangzhou Medical University and Guangzhou Center for Disease Control and Prevention, Guangzhou, People's Republic of China
| | - Lijun Liang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, People's Republic of China
| | - Tengfei Zhou
- Institute of Public Health, Guangzhou Medical University and Guangzhou Center for Disease Control and Prevention, Guangzhou, People's Republic of China
| | - Ziyi Zeng
- Huadu District Center for Disease Control and Prevention, Guangzhou, People's Republic of China
| | - Chen Wen
- Huadu District Center for Disease Control and Prevention, Guangzhou, People's Republic of China
| | - Biao Di
- Institute of Public Health, Guangzhou Medical University and Guangzhou Center for Disease Control and Prevention, Guangzhou, People's Republic of China
| | - Baisheng Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, People's Republic of China
| | - Kuibiao Li
- Institute of Public Health, Guangzhou Medical University and Guangzhou Center for Disease Control and Prevention, Guangzhou, People's Republic of China
| | - Zhoubin Zhang
- Institute of Public Health, Guangzhou Medical University and Guangzhou Center for Disease Control and Prevention, Guangzhou, People's Republic of China
| |
Collapse
|
45
|
Zhang R, Lai KY, Liu W, Liu Y, Ma X, Webster C, Luo L, Sarkar C. Associations between Short-Term Exposure to Ambient Air Pollution and Influenza: An Individual-Level Case-Crossover Study in Guangzhou, China. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:127009. [PMID: 38078424 PMCID: PMC10711742 DOI: 10.1289/ehp12145] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/12/2023] [Accepted: 10/27/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND Influenza imposes a heavy burden on public health. Little is known, however, of the associations between detailed measures of exposure to ambient air pollution and influenza at an individual level. OBJECTIVE We examined individual-level associations between six criteria air pollutants and influenza using case-crossover design. METHODS In this individual-level time-stratified case-crossover study, we linked influenza cases collected by the Guangzhou Center for Disease Control and Prevention from 1 January 2013 to 31 December 2019 with individual residence-level exposure to particulate matter (PM 2.5 and PM 10 ), sulfur dioxide (SO 2 ), nitrogen dioxide (NO 2 ), ozone (O 3 ) and carbon monoxide (CO). The exposures were estimated for the day of onset of influenza symptoms (lag 0), 1-7 d before the onset (lags 1-7), as well as an 8-d moving average (lag07), using a random forest model and linked to study participants' home addresses. Conditional logistic regression was developed to investigate the associations between short-term exposure to air pollution and influenza, adjusting for mean temperature, relative humidity, public holidays, population mobility, and community influenza susceptibility. RESULTS N = 108,479 eligible cases were identified in our study. Every 10 - μ g / m 3 increase in exposure to PM 2.5 , PM 10 , NO 2 , and CO and every 5 - μ g / m 3 increase in SO 2 over 8-d moving average (lag07) was associated with higher risk of influenza with a relative risk (RR) of 1.028 (95% CI: 1.018, 1.038), 1.041 (95% CI: 1.032, 1.049), 1.169 (95% CI: 1.151, 1.188), 1.004 (95% CI: 1.003, 1.006), and 1.134 (95% CI: 1.107, 1.163), respectively. There was a negative association between O 3 and influenza with a RR of 0.878 (95% CI: 0.866, 0.890). CONCLUSIONS Our findings suggest that short-term exposure to air pollution, except for O 3 , is associated with greater risk for influenza. Further studies are necessary to decipher underlying mechanisms and design preventive interventions and policies. https://doi.org/10.1289/EHP12145.
Collapse
Affiliation(s)
- Rong Zhang
- Healthy High Density Cities Lab, HKUrbanLab, University of Hong Kong (HKU), Hong Kong, China
- Department of Urban Planning and Design, HKU, Hong Kong, China
| | - Ka Yan Lai
- Healthy High Density Cities Lab, HKUrbanLab, University of Hong Kong (HKU), Hong Kong, China
- Department of Urban Planning and Design, HKU, Hong Kong, China
| | - Wenhui Liu
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Yanhui Liu
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Xiaowei Ma
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Chris Webster
- Healthy High Density Cities Lab, HKUrbanLab, University of Hong Kong (HKU), Hong Kong, China
- Department of Urban Planning and Design, HKU, Hong Kong, China
| | - Lei Luo
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Chinmoy Sarkar
- Healthy High Density Cities Lab, HKUrbanLab, University of Hong Kong (HKU), Hong Kong, China
- Department of Urban Planning and Design, HKU, Hong Kong, China
- Department of Psychiatry, Warneford Hospital, University of Oxford, Oxford, UK
| |
Collapse
|
46
|
Zafeiriadou A, Kaltsis L, Kostakis M, Kapes V, Thomaidis NS, Markou A. Wastewater surveillance of the most common circulating respiratory viruses in Athens: The impact of COVID-19 on their seasonality. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:166136. [PMID: 37567285 DOI: 10.1016/j.scitotenv.2023.166136] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/06/2023] [Accepted: 08/06/2023] [Indexed: 08/13/2023]
Abstract
Due to governments' actions to contain the spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the activity of common circulating respiratory viruses was significantly disrupted after the COVID-19 pandemic and thorough surveillance of respiratory pathogens was considered essential worldwide. Wastewater-based epidemiology has proven to be a valuable tool, that provides complementary information on disease outbreaks and is increasingly used to study the infection dynamics of other viruses, apart from SARS-CoV-2. The aims of the present study were the detection of four commonly circulating respiratory viruses: SARS-CoV-2, influenza A, B and Human Respiratory Syncytial Virus (RSV), the evaluation of the COVID-19 pandemic impact on their seasonality and the determination of the possible common trends in the viral load of these viruses in the wastewater of the Attica region. A standardized and validated concentration and extraction protocol was used, generic for all four viruses, followed by Reverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR) assays. The study proved that there was a prolonged period when all four viruses circulated in the population and an early outbreak of seasonal influenza and RSV in 2022-2023, compared to data from the pre-COVID-19 period. SARS-CoV-2, influenza A and RSV concentrations showed peak levels during December, followed by a slight decline in influenza A concentrations, followed by steady increase of influenza B concentrations in January 2023. SARS-CoV-2 was the dominant virus throughout the whole study period. This is the first study in Greece that investigated the most common circulating viruses simultaneously and in one of the largest timelines, providing crucial information about their infection dynamics during a period when an outbreak of respiratory diseases was declared by the National Public Health Organization. Presented results highlight the establishment of environmental surveillance as a non-invasive and complementary virus outbreak monitoring tool and the importance of influenza A, B and RSV integration into a wastewater-based surveillance system to help in disease management.
Collapse
Affiliation(s)
- Anastasia Zafeiriadou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771, Athens, Greece
| | - Lazaros Kaltsis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771, Athens, Greece
| | - Marios Kostakis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771, Athens, Greece
| | - Vasileios Kapes
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771, Athens, Greece
| | - Nikolaos S Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771, Athens, Greece
| | - Athina Markou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771, Athens, Greece.
| |
Collapse
|
47
|
Sergeeva MV, Romanovskaya-Romanko EA, Krivitskaya VZ, Kudar PA, Petkova NN, Kudria KS, Lioznov DA, Stukova MA, Desheva YA. Longitudinal Analysis of Neuraminidase and Hemagglutinin Antibodies to Influenza A Viruses after Immunization with Seasonal Inactivated Influenza Vaccines. Vaccines (Basel) 2023; 11:1731. [PMID: 38006063 PMCID: PMC10675551 DOI: 10.3390/vaccines11111731] [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: 09/25/2023] [Revised: 11/06/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Neuraminidase (NA)-based immunity could reduce the harmful impact of novel antigenic variants of influenza viruses. The detection of neuraminidase-inhibiting (NI) antibodies in parallel with anti-hemagglutinin (HA) antibodies may enhance research on the immunogenicity and duration of antibody responses to influenza vaccines. To assess anti-NA antibodies after vaccination with seasonal inactivated influenza vaccines, we used the enzyme-linked lectin assay, and anti-HA antibodies were detected in the hemagglutination inhibition assay. The dynamics of the anti-NA antibody response differed depending on the virus subtype: antibodies to A/H3N2 virus neuraminidase increased later than antibodies to A/H1N1pdm09 subtype neuraminidase and persisted longer. In contrast to HA antibodies, the fold increase in antibody titers to NA after vaccination poorly depended on the preexisting level. At the same time, NA antibody levels after vaccination directly correlated with titers before vaccination. A difference was found in response to NA antigen between split and subunit-adjuvanted vaccines and in NA functional activity in the vaccine formulations.
Collapse
Affiliation(s)
- Mariia V. Sergeeva
- Smorodintsev Research Institute of Influenza, Ministry of Health of the Russian Federation, 197022 Saint Petersburg, Russia; (M.V.S.); (E.A.R.-R.); (V.Z.K.); (K.S.K.); (D.A.L.); (M.A.S.)
| | - Ekaterina A. Romanovskaya-Romanko
- Smorodintsev Research Institute of Influenza, Ministry of Health of the Russian Federation, 197022 Saint Petersburg, Russia; (M.V.S.); (E.A.R.-R.); (V.Z.K.); (K.S.K.); (D.A.L.); (M.A.S.)
| | - Vera Z. Krivitskaya
- Smorodintsev Research Institute of Influenza, Ministry of Health of the Russian Federation, 197022 Saint Petersburg, Russia; (M.V.S.); (E.A.R.-R.); (V.Z.K.); (K.S.K.); (D.A.L.); (M.A.S.)
| | - Polina A. Kudar
- ‘Institute of Experimental Medicine’, 197022 Saint Petersburg, Russia; (P.A.K.); (N.N.P.)
| | - Nadezhda N. Petkova
- ‘Institute of Experimental Medicine’, 197022 Saint Petersburg, Russia; (P.A.K.); (N.N.P.)
| | - Kira S. Kudria
- Smorodintsev Research Institute of Influenza, Ministry of Health of the Russian Federation, 197022 Saint Petersburg, Russia; (M.V.S.); (E.A.R.-R.); (V.Z.K.); (K.S.K.); (D.A.L.); (M.A.S.)
| | - Dmitry A. Lioznov
- Smorodintsev Research Institute of Influenza, Ministry of Health of the Russian Federation, 197022 Saint Petersburg, Russia; (M.V.S.); (E.A.R.-R.); (V.Z.K.); (K.S.K.); (D.A.L.); (M.A.S.)
| | - Marina A. Stukova
- Smorodintsev Research Institute of Influenza, Ministry of Health of the Russian Federation, 197022 Saint Petersburg, Russia; (M.V.S.); (E.A.R.-R.); (V.Z.K.); (K.S.K.); (D.A.L.); (M.A.S.)
| | - Yulia A. Desheva
- ‘Institute of Experimental Medicine’, 197022 Saint Petersburg, Russia; (P.A.K.); (N.N.P.)
| |
Collapse
|
48
|
Tokuyama K, Kitamura T, Maruyama K, Toriumi S, Murano Y, Yoneoka D, Nakazawa T, Shimizu T. High number of seizures and unconsciousness in patients with SARS-CoV-2 omicron variants: a retrospective study. Front Pediatr 2023; 11:1273464. [PMID: 38034823 PMCID: PMC10684743 DOI: 10.3389/fped.2023.1273464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) omicron variants are now a pandemic. There are differences in clinical features in SARS-CoV-2 variants and we conducted this study to assess the clinical features of coronavirus disease (COVID-19) in children with SARS-CoV-2 omicron variants. The study included children with COVID-19 arrivedto Tokyo Metropolitan Toshima Hospital between January 2020 and October 2022. The clinical features of 214 children with SARS-CoV-2 non-omicron variants and 557 children with omicron variants were compared. In the SARS-CoV-2 omicron variant group, more patients had fever, sore throat, nausea and/or vomiting, and seizures and/or disorders of consciousness. In SARS-CoV-2 non-omicron variants, there was only one patient with seizure and/or unconsciousness whereas there were 92 children in omicron variants. Among these 92 patients, 46 (49%) were diagnosed with simple febrile seizures; 23 (25%), with complex febrile seizures; 10 (11%) with status epilepticus; and two (2%) with encephalopathy. Their mean age was 4.0 ± 3.0 years-a wider age distribution than that in other febrile seizures but similar to that in febrile seizures in patients with influenza. SARS-CoV-2 omicron variants are likely to cause seizures and unconsciousness in children and their age distribution was wider than other febrile seizures patients but similar to those in influenza patients. In clinical practice in patients with COVID-19 and influenza, clinicians should be aware of these features.
Collapse
Affiliation(s)
- Kishin Tokuyama
- Division of Pediatrics, Tokyo Metropolitan Toshima Hospital, Tokyo, Japan
| | - Tsubasa Kitamura
- Division of Pediatrics, Tokyo Metropolitan Toshima Hospital, Tokyo, Japan
| | - Kazutaka Maruyama
- Division of Pediatrics, Tokyo Metropolitan Toshima Hospital, Tokyo, Japan
- Department of Pediatrics, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Shun Toriumi
- Division of Pediatrics, Tokyo Metropolitan Toshima Hospital, Tokyo, Japan
- Department of Pediatrics, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Yayoi Murano
- Division of Pediatrics, Tokyo Metropolitan Toshima Hospital, Tokyo, Japan
- Department of Pediatrics, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Daisuke Yoneoka
- Center for Surveillance, Immunization, and Epidemiologic Research, National Center of Infectious Disease, Tokyo, Japan
| | - Tomoyuki Nakazawa
- Division of Pediatrics, Tokyo Metropolitan Toshima Hospital, Tokyo, Japan
- Department of Pediatrics, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Toshiaki Shimizu
- Department of Pediatrics, Faculty of Medicine, Juntendo University, Tokyo, Japan
| |
Collapse
|
49
|
Chan AHY, Tomlin A, Chan E, Harrison J, Beyene KA. Effect of the COVID-19 pandemic on asthma exacerbations in New Zealand: An interrupted time series analysis. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. GLOBAL 2023; 2:100157. [PMID: 37781646 PMCID: PMC10509955 DOI: 10.1016/j.jacig.2023.100157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/22/2023] [Accepted: 04/07/2023] [Indexed: 10/03/2023]
Abstract
Background New Zealand (NZ) implemented some of the strictest restrictions during the novel coronavirus pandemic (coronavirus disease 2019 [COVID-19]), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). How this impacted asthma exacerbation rates in NZ is unknown. Objective We sought to explore the effects of the COVID-19 restrictions on asthma exacerbations in NZ during 2020. Methods We used a population-based, interrupted time series to examine the impact of the first COVID-19 lockdown in NZ on asthma exacerbation rate. The primary outcome measure was change in the monthly exacerbation rate, defined as hospitalization and/or course of corticosteroids, before and after the first lockdown. In a secondary analysis, we quantified the number of patients with asthma, the actual asthma exacerbation rate from March to December 2019 versus March to December 2020, and the number of asthma hospitalizations. Results There was a significant drop in the exacerbation rate immediately after lockdown (-3.02; P < .0001) followed by a significant and sustained increasing trend; the rate postlockdown increased relative to that prelockdown (0.27; P < .0001). Similar patterns were observed in all sociodemographic groups. In our secondary analysis, we identified 507,622 people with asthma; this reduced to 458,023 in 2020 postlockdown. The overall asthma exacerbation rate was 33.3% less in 2020 than in 2019 (reduction from 48.6/1000 patients to 32.4/1000 patients). The rate of asthma hospitalizations decreased from 9.5 per 1000 patients in 2019 to 6.2 per 1000 patients in 2020; this decrease was observed across all demographic groups. Conclusions The first COVID-19 lockdown in 2020 in NZ significantly reduced asthma exacerbation rates across all sociodemographic groups. Whether these reductions are sustained requires further investigation.
Collapse
Affiliation(s)
- Amy Hai Yan Chan
- School of Pharmacy, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Andrew Tomlin
- School of Pharmacy, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Eliza Chan
- School of Pharmacy, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Jeff Harrison
- School of Pharmacy, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Kebede A. Beyene
- School of Pharmacy, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
- Department of Pharmaceutical and Administrative Sciences, St Louis College of Pharmacy, University of Health Sciences and Pharmacy, St Louis, Mo
| |
Collapse
|
50
|
Kim HK, Min KD, Cho SI. Analysis of the effectiveness of non-pharmaceutical interventions on influenza during the Coronavirus disease 2019 pandemic by time-series forecasting. BMC Infect Dis 2023; 23:717. [PMID: 37875817 PMCID: PMC10594831 DOI: 10.1186/s12879-023-08640-y] [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: 06/01/2023] [Accepted: 09/25/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) was first identified in South Korea during the 2019-2020 seasonal influenza epidemic. The social distancing measures, as effective non-pharmaceutical interventions (NPIs), adopted to mitigate the spread of COVID-19 might have influenced influenza activity. We evaluated IFV(influenza virus) activity during the COVID-19 pandemic and the effect of NPI intensity on influenza transmission. METHODS IFV activity and epidemic duration during COVID-19 pandemic were predicted under a counterfactual scenario with no NPIs against COVID-19. The Seasonal Autoregressive Integrated Moving Average Model was used to quantify the effects of NPIs on the transmission of influenza virus. Influenza-like illness/1000 outpatients and IFV positivity rate from the 2011-2012 to 2021-2022 seasons were used in this study. RESULTS Comparison of the 2020-2021 and 2021-2022 seasonal influenza activities with those in 2013-2019 showed that COVID-19 outbreaks and associated NPIs such as face mask use, school closures, and travel restrictions reduced the influenza incidence by 91%. Without NPIs against COVID-19, the rates of influenza-like illness and IFV positivity would have been high during the influenza epidemic season, as in previous seasons. NPI intensity decreased the transmission of influenza; the magnitude of the reduction increased as the intensity of social-distancing measures increased (weak social distancing; step-by-step daily recovery: 58.10%, strong social distancing; special quarantine measures: 95.12%). CONCLUSIONS Our results suggest that NPIs and personal hygiene can be used to suppress influenza transmission. NPIs against COVID-19 may be useful strategies for the prevention and control of influenza epidemics.
Collapse
Affiliation(s)
- Hyun Kyung Kim
- Department of Public Health Science, Graduate School of Public Health, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Korea
| | - Kyung-Duk Min
- College of Veterinary Medicine, Chungbuk National University, Cheongju, South Korea
| | - Sung-Il Cho
- Department of Public Health Science, Graduate School of Public Health, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Korea.
- Institute of Health and Environment, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Korea.
| |
Collapse
|