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Vos B, Debouverie L, Doggen K, Delvaux N, Aertgeerts B, De Schreye R, Vaes B. Monitoring COVID-19 in Belgian general practice: A tool for syndromic surveillance based on electronic health records. Eur J Gen Pract 2024; 30:2293699. [PMID: 38186340 PMCID: PMC10776082 DOI: 10.1080/13814788.2023.2293699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/04/2023] [Indexed: 01/09/2024] Open
Abstract
BACKGROUND COVID-19 may initially manifest as flu-like symptoms. As such, general practitioners (GPs) will likely to play an important role in monitoring the pandemic through syndromic surveillance. OBJECTIVES To present a COVID-19 syndromic surveillance tool in Belgian general practices. METHODS We performed a nationwide observational prospective study in Belgian general practices. The surveillance tool extracted the daily entries of diagnostic codes for COVID-19 and associated conditions (suspected or confirmed COVID-19, acute respiratory infection and influenza-like illness) from electronic medical records. We calculated the 7-day rolling average for these diagnoses and compared them with data from two other Belgian population-based sources (laboratory-confirmed new COVID-19 cases and hospital admissions for COVID-19), using time series analysis. We also collected data from users and stakeholders about the syndromic surveillance tool and performed a thematic analysis. RESULTS 4773 out of 11,935 practising GPs in Belgium participated in the study. The curve of contacts for suspected COVID-19 followed a similar trend compared with the curves of the official data sources: laboratory-confirmed COVID-19 cases and hospital admissions but with a 10-day delay for the latter. Data were quickly available and useful for decision making, but some technical and methodological components can be improved, such as a greater standardisation between EMR software developers. CONCLUSION The syndromic surveillance tool for COVID-19 in primary care provides rapidly available data useful in all phases of the COVID-19 pandemic to support data-driven decision-making. Potential enhancements were identified for a prospective surveillance tool.
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Affiliation(s)
- Bénédicte Vos
- Health Services Research, Sciensano, Brussels, Belgium
| | | | - Kris Doggen
- Health Services Research, Sciensano, Brussels, Belgium
| | - Nicolas Delvaux
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Bert Aertgeerts
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | | | - Bert Vaes
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
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Perofsky AC, Huddleston J, Hansen CL, Barnes JR, Rowe T, Xu X, Kondor R, Wentworth DE, Lewis N, Whittaker L, Ermetal B, Harvey R, Galiano M, Daniels RS, McCauley JW, Fujisaki S, Nakamura K, Kishida N, Watanabe S, Hasegawa H, Sullivan SG, Barr IG, Subbarao K, Krammer F, Bedford T, Viboud C. Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States. eLife 2024; 13:RP91849. [PMID: 39319780 DOI: 10.7554/elife.91849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2024] Open
Abstract
Influenza viruses continually evolve new antigenic variants, through mutations in epitopes of their major surface proteins, hemagglutinin (HA) and neuraminidase (NA). Antigenic drift potentiates the reinfection of previously infected individuals, but the contribution of this process to variability in annual epidemics is not well understood. Here, we link influenza A(H3N2) virus evolution to regional epidemic dynamics in the United States during 1997-2019. We integrate phenotypic measures of HA antigenic drift and sequence-based measures of HA and NA fitness to infer antigenic and genetic distances between viruses circulating in successive seasons. We estimate the magnitude, severity, timing, transmission rate, age-specific patterns, and subtype dominance of each regional outbreak and find that genetic distance based on broad sets of epitope sites is the strongest evolutionary predictor of A(H3N2) virus epidemiology. Increased HA and NA epitope distance between seasons correlates with larger, more intense epidemics, higher transmission, greater A(H3N2) subtype dominance, and a greater proportion of cases in adults relative to children, consistent with increased population susceptibility. Based on random forest models, A(H1N1) incidence impacts A(H3N2) epidemics to a greater extent than viral evolution, suggesting that subtype interference is a major driver of influenza A virus infection ynamics, presumably via heterosubtypic cross-immunity.
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MESH Headings
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/immunology
- United States/epidemiology
- Influenza, Human/epidemiology
- Influenza, Human/virology
- Influenza, Human/immunology
- Humans
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Epidemics
- Antigenic Drift and Shift/genetics
- Child
- Adult
- Neuraminidase/genetics
- Neuraminidase/immunology
- Adolescent
- Child, Preschool
- Antigens, Viral/immunology
- Antigens, Viral/genetics
- Young Adult
- Evolution, Molecular
- Seasons
- Middle Aged
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Affiliation(s)
- Amanda C Perofsky
- Fogarty International Center, National Institutes of Health, Bethesda, United States
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, United States
| | - John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, United States
| | - Chelsea L Hansen
- Fogarty International Center, National Institutes of Health, Bethesda, United States
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, United States
| | - John R Barnes
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, United States
| | - Thomas Rowe
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, United States
| | - Xiyan Xu
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, United States
| | - Rebecca Kondor
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, United States
| | - David E Wentworth
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, United States
| | - Nicola Lewis
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Lynne Whittaker
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Burcu Ermetal
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Ruth Harvey
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Monica Galiano
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Rodney Stuart Daniels
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - John W McCauley
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Seiichiro Fujisaki
- Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazuya Nakamura
- Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Noriko Kishida
- Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shinji Watanabe
- Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hideki Hasegawa
- Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Sheena G Sullivan
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Ian G Barr
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Kanta Subbarao
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Florian Krammer
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, United States
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Trevor Bedford
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, United States
- Department of Genome Sciences, University of Washington, Seattle, United States
- Howard Hughes Medical Institute, Seattle, United States
| | - Cécile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, United States
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3
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Taouk ML, Taiaroa G, Duchene S, Low SJ, Higgs CK, Lee DYJ, Pasricha S, Higgins N, Ingle DJ, Howden BP, Chen MY, Fairley CK, Chow EPF, Williamson DA. Longitudinal genomic analysis of Neisseria gonorrhoeae transmission dynamics in Australia. Nat Commun 2024; 15:8076. [PMID: 39277590 PMCID: PMC11401900 DOI: 10.1038/s41467-024-52343-0] [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: 04/15/2024] [Accepted: 09/02/2024] [Indexed: 09/17/2024] Open
Abstract
N. gonorrhoeae, which causes the sexually transmissible infection gonorrhoea, remains a significant public health threat globally, with challenges posed by increasing transmission and antimicrobial resistance (AMR). The COVID-19 pandemic introduced exceptional circumstances into communicable disease control, impacting the transmission of gonorrhoea and other infectious diseases. Through phylogenomic and phylodynamic analysis of 5881 N. gonorrhoeae genomes from Australia, we investigated N. gonorrhoeae transmission over five years, including a time period during the COVID-19 pandemic. Using a novel cgMLST-based genetic threshold, we demonstrate persistence of large N. gonorrhoeae genomic clusters over several years, with some persistent clusters associated with heterosexual transmission. We observed a decline in both N. gonorrhoeae transmission and genomic diversity during the COVID-19 pandemic, suggestive of an evolutionary bottleneck. The longitudinal, occult transmission of N. gonorrhoeae over many years further highlights the urgent need for improved diagnostic, treatment, and prevention strategies for gonorrhoea.
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Affiliation(s)
- Mona L Taouk
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - George Taiaroa
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Computational Biology, Institut Pasteur, Paris, France
| | - Soo Jen Low
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Charlie K Higgs
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Darren Y J Lee
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Shivani Pasricha
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Infectious Diseases and Immune Defence Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
| | - Nasra Higgins
- Victorian Department of Health, Melbourne, VIC, Australia
| | - Danielle J Ingle
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Marcus Y Chen
- Melbourne Sexual Health Centre, Alfred Health, Melbourne, VIC, Australia
- School of Translational Medicine, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
| | - Christopher K Fairley
- Melbourne Sexual Health Centre, Alfred Health, Melbourne, VIC, Australia
- School of Translational Medicine, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
| | - Eric P F Chow
- Melbourne Sexual Health Centre, Alfred Health, Melbourne, VIC, Australia
- School of Translational Medicine, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Deborah A Williamson
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Department of Medicine, University of St Andrews, St Andrews, Fife, KY16 9TF, Scotland.
- MRC-University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, Scotland.
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4
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Yang YF, Chen YM, Chen SY, Chiu PH, Chen SC. Burden changes in notifiable infectious diseases in Taiwan during the COVID-19 pandemic. PeerJ 2024; 12:e18048. [PMID: 39267943 PMCID: PMC11391939 DOI: 10.7717/peerj.18048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 08/15/2024] [Indexed: 09/15/2024] Open
Abstract
Background This study aimed to assess the impact of the COVID-19 pandemic on the disease burden of Taiwan's notifiable infectious diseases (NIDs). We compared disease burdens between the pandemic and pre-pandemic year of 2020 (with non-pharmaceutical interventions (NPIs)) and 2010 (without NPIs), respectively, to understand the overall pandemic impact on NIDs in Taiwan. Methods Forty-three national NIDs were analyzed using the Statistics of Communicable Diseases and Surveillance Report by estimating the premature death and disability via different transmission categories, sex, and age groups. The study evaluated the impact of diseases by assessing the years lost due to death (YLLs), the duration of living with disability (YLDs), and the overall disability-adjusted life years (DALYs) by measuring both the severity of the illness and its duration. Results Taiwan recorded 1,577 (2010) and 1,260 (2020) DALYs per million population and lost 43 NIDs, decreasing 317 DALYs per million population. Tuberculosis, HIV/AIDS and acute hepatitis B/D were the leading causes of DALYs, accounting for 89% (2010) and 77% (2020). Conclusion Overall, this study provided the first insight of changes in disease burdens in NIDs between pre- and post-COVID-19 based on a nationwide viewpoint for further preventive measures and interventions to be focused on specific diseases by associated health administrations and policies.
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Affiliation(s)
- Ying-Fei Yang
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei, Taiwan
| | - Yu-Miao Chen
- Department of Public Health, Chung Shan Medical University, Taichung, Taiwan
| | - Si-Yu Chen
- Department of Public Health, Chung Shan Medical University, Taichung, Taiwan
| | - Po-Hao Chiu
- Department of Public Health, Chung Shan Medical University, Taichung, Taiwan
| | - Szu-Chieh Chen
- Department of Public Health, Chung Shan Medical University, Taichung, Taiwan
- Department of Family and Community Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
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5
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Gegin S, ÖZdemir B, ÖZdemir L, Aksu EA, Pazarli AC, YazicioĞlu B. The Effect of Mask Use on Seasonal Virus Diversity in SARS CoV-2 Negative Patients Treated as Inpatients During the 2021-2022 and 2022-2023 Seasonal Flu Period. Pol J Microbiol 2024; 73:377-382. [PMID: 39268955 PMCID: PMC11395415 DOI: 10.33073/pjm-2024-033] [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: 05/18/2024] [Accepted: 07/26/2024] [Indexed: 09/15/2024] Open
Abstract
The study aimed to explore the protective effect of mask use against respiratory tract viral agents during the pandemic. The study included patients with a COVID-19 negative test who were hospitalized in the pulmonary disease clinic with the diagnoses of asthma attack, chronic obstructive pulmonary disease (COPD) exacerbation, and pneumonia in two periods: during mandatory mask use (October 2021 - May 2022) and after the mask mandate was lifted (October 2022 - May 2023). Combined nose and throat swab samples taken from the patients were evaluated for viral agents by using the PCR test method. Viral agents isolated from the patients in the two periods were compared based on hospitalization diagnoses and periods. The study enrolled 1,335 patients, 483 female and 852 male. It was found that viral agents significantly increased during the period without a mask mandate compared to the period when the mask mandate was in effect (41.6% vs. 23.4%) (p < 0.001). During the period without mask mandate, influenza A, H1N1, and RSV/AB viruses significantly increased (p = 0.019, p = 0.003, p < 0.001, respectively). Our results indicated that mask use during the pandemic is protective against the transmission of respiratory tract viruses. Thus, it can be concluded that mask use is important not only in the coronavirus pandemic but also especially in influenza and RSV epidemics.
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Affiliation(s)
- SavaŞ Gegin
- 1Samsun Training and Research Hospital, Pulmonology Clinic, Samsun, Türkiye
| | - Burcu ÖZdemir
- 1Samsun Training and Research Hospital, Pulmonology Clinic, Samsun, Türkiye
| | - Levent ÖZdemir
- 1Samsun Training and Research Hospital, Pulmonology Clinic, Samsun, Türkiye
| | - Esra Arslan Aksu
- 2Samsun University Faculty of Medicine, Pulmonology Department, Samsun, Türkiye
| | - Ahmet Cemal Pazarli
- 3Tokat Gaziosmanpaşa University Faculty of Medicine, Pulmonology Department, Tokat, Türkiye
| | - Bahadir YazicioĞlu
- 4Samsun Training and Research Hospital, Family Medicine, Samsun, Türkiye
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6
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de Jong SP, Conlan A, Han AX, Russell CA. Commuting-driven competition between transmission chains shapes seasonal influenza virus epidemics in the United States. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.09.24311720. [PMID: 39148829 PMCID: PMC11326338 DOI: 10.1101/2024.08.09.24311720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Despite intensive study, much remains unknown about the dynamics of seasonal influenza virus epidemic establishment and spread in the United States (US) each season. By reconstructing transmission lineages from seasonal influenza virus genomes collected in the US from 2014 to 2023, we show that most epidemics consisted of multiple distinct transmission lineages. Spread of these lineages exhibited strong spatiotemporal hierarchies and lineage size was correlated with timing of lineage establishment in the US. Mechanistic epidemic simulations suggest that mobility-driven competition between lineages determined the extent of individual lineages' geographical spread. Based on phylogeographic analyses and epidemic simulations, lineage-specific movement patterns were dominated by human commuting behavior. These results suggest that given the locations of early-season epidemic sparks, the topology of inter-state human mobility yields repeatable patterns of which influenza viruses will circulate where, but the importance of short-term processes limits predictability of regional and national epidemics.
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Affiliation(s)
- Simon P.J. de Jong
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam; Amsterdam, The Netherlands
| | - Andrew Conlan
- Department of Veterinary Medicine, University of Cambridge; Cambridge, United Kingdom
| | - Alvin X. Han
- 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
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7
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Langsted A, Edwards NC, Pasley T, Stewart RA. Acute idiopathic pericarditis during a national lockdown to prevent transmission of SARS-COVID-19. IJC HEART & VASCULATURE 2024; 53:101398. [PMID: 39228974 PMCID: PMC11368592 DOI: 10.1016/j.ijcha.2024.101398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/28/2024] [Accepted: 03/28/2024] [Indexed: 09/05/2024]
Abstract
Background Idiopathic acute pericarditis is often presumed to have a viral cause. We hypothesized that if acute viral infection was the cause, the incidence of acute 'idiopathic' pericarditis would decrease during a public health lockdown introduced to prevent the spread of SARS-COVID-19 in New Zealand when acute viral infections decreased by 75% to 99%. Methods Hospitalization for acute 'idiopathic' pericarditis during 5 months of the national public health lockdown were compared to 54 months before the COVID-19 pandemic from administrative data. Results The hospitalization rate for acute pericarditis was similar before (n = 1364, 24.8 cases/30 days) compared to during the public health lockdown (n = 132, 25.8 cases/30 days), +4% 95 % confidence interval -25 % to +30 % (P = 0.67). Conclusion These observations do not support the hypothesis that acute viral infection is the cause for most cases of acute idiopathic pericarditis.
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Affiliation(s)
- Anne Langsted
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
| | - Nicola C. Edwards
- Greenlane Cardiovascular Service, Auckland City Hospital, Te Whatu Ora – Health New Zealand, Te Toka Tumai, Auckland, New Zealand
- Department of Medicine. University of Auckland, Auckland, New Zealand
| | - Tom Pasley
- Greenlane Cardiovascular Service, Auckland City Hospital, Te Whatu Ora – Health New Zealand, Te Toka Tumai, Auckland, New Zealand
| | - Ralph A.H. Stewart
- Greenlane Cardiovascular Service, Auckland City Hospital, Te Whatu Ora – Health New Zealand, Te Toka Tumai, Auckland, New Zealand
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8
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Noble J, Hatter L, Eathorne A, Hills T, Bean O, Bruce P, Weatherall M, Beasley R. Patterns of asthma medication use and hospital discharges in New Zealand. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. GLOBAL 2024; 3:100258. [PMID: 38745868 PMCID: PMC11090902 DOI: 10.1016/j.jacig.2024.100258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/13/2023] [Accepted: 02/08/2024] [Indexed: 05/16/2024]
Abstract
Background In New Zealand a progressive increase in budesonide/formoterol dispensing, accompanied by a reduction in dispensing of short-acting β2-agonists (SABAs), inhaled corticosteroids (ICSs), and other ICS/long-acting β2-agonists (ICSs/LABAs), occurred in the 18-month period following publication of the 2020 New Zealand asthma guidelines, which recommended budesonide/formoterol anti-inflammatory reliever therapy. Objective Our aim was to investigate more recent trends in asthma medication use and asthma hospital discharges in New Zealand. Methods New Zealand national dispensing data for inhalers for the period from January 2010 to December 2022 were reviewed for patients aged 12 years and older. Monthly rates of dispensing of budesonide/formoterol, ICSs, other ICS/LABAs, and SABAs were displayed graphically by locally weighted scatterplot smoother plots. The rates of dispensing and hospital discharge for asthma were compared between the past 6 months for which dispensing data were available (July-December 2022) and the corresponding period from July to December 2019. Results There has been a progressive increase in dispensing of budesonide/formoterol since 2019, with a 108% increase between the period from July to December 2019 and the period from July to December 2022 in adolescents and adults. In contrast, there was a reduction in rates of dispensing of other ICS/LABAs, ICSs, and SABAs by 3%, 18%, and 5%, respectively. During this period, there was a 17% reduction in hospital discharges for asthma. Conclusion There has been a further widespread uptake of ICS/formoterol reliever and/or maintenance therapy in adolescents and adults with asthma in New Zealand. The changes in prescribing practice have been temporally associated with a reduction in hospital admissions for asthma.
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Affiliation(s)
- Jonathan Noble
- Medical Research Institute of New Zealand, Wellington, New Zealand
- Victoria University of Wellington, Wellington, New Zealand
| | - Lee Hatter
- Medical Research Institute of New Zealand, Wellington, New Zealand
- Victoria University of Wellington, Wellington, New Zealand
| | - Allie Eathorne
- Medical Research Institute of New Zealand, Wellington, New Zealand
| | - Thomas Hills
- Medical Research Institute of New Zealand, Wellington, New Zealand
| | - Orlagh Bean
- Medical Research Institute of New Zealand, Wellington, New Zealand
| | - Pepa Bruce
- Medical Research Institute of New Zealand, Wellington, New Zealand
| | | | - Richard Beasley
- Medical Research Institute of New Zealand, Wellington, New Zealand
- Victoria University of Wellington, Wellington, New Zealand
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9
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Eren ZB, Vatansever C, Kabadayı B, Haykar B, Kuloğlu ZE, Ay S, Nurlybayeva K, Eyikudamacı G, Barlas T, Palaoğlu E, Beşli Y, Kuşkucu MA, Ergönül Ö, Can F. Surveillance of respiratory viruses by aerosol screening in indoor air as an early warning system for epidemics. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13303. [PMID: 38982659 PMCID: PMC11233404 DOI: 10.1111/1758-2229.13303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 05/15/2024] [Indexed: 07/11/2024]
Abstract
The development of effective methods for the surveillance of seasonal respiratory viruses is required for the timely management of outbreaks. We aimed to survey Influenza-A, Influenza-B, RSV-A, Rhinovirus and SARS-CoV-2 surveillance in a tertiary hospital and a campus over 5 months. The effectiveness of air screening as an early warning system for respiratory viruses was evaluated in correlation with respiratory tract panel test results. The overall viral positivity was higher on the campus than in the hospital (55.0% vs. 38.0%). Influenza A was the most prevalent pathogen in both locations. There were two influenza peaks (42nd and 49th weeks) in the hospital air, and a delayed peak was detected on campus in the 1st-week of January. Panel tests indicated a high rate of Influenza A in late December. RSV-A-positivity was higher on the campus than the hospital (21.6% vs. 7.4%). Moreover, we detected two RSV-A peaks in the campus air (48th and 51st weeks) but only one peak in the hospital and panel tests (week 49). Although rhinovirus was the most common pathogen in panel tests, rhinovirus positivity was low in air samples. The air screening for Influenza-B and SARS-Cov-2 revealed comparable positivity rates with panel tests. Air screening can be integrated into surveillance programs to support infection control programs for potential epidemics of respiratory virus infections except for rhinoviruses.
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Affiliation(s)
| | - Cansel Vatansever
- Koç University İşBank Center for Infectious Diseases (KUISCID)IstanbulTurkey
| | | | | | - Zeynep Ece Kuloğlu
- Koç University İşBank Center for Infectious Diseases (KUISCID)IstanbulTurkey
- Koç UniversityGraduate School of Health SciencesIstanbulTurkey
| | - Sedat Ay
- Koç University School of MedicineIstanbulTurkey
| | | | - Gül Eyikudamacı
- Koç University İşBank Center for Infectious Diseases (KUISCID)IstanbulTurkey
- Koç UniversityGraduate School of Health SciencesIstanbulTurkey
| | - Tayfun Barlas
- Koç University İşBank Center for Infectious Diseases (KUISCID)IstanbulTurkey
| | - Erhan Palaoğlu
- Department of Clinical LaboratoryAmerican HospitalIstanbulTurkey
| | - Yeşim Beşli
- Department of Clinical LaboratoryAmerican HospitalIstanbulTurkey
| | - Mert Ahmet Kuşkucu
- Koç University İşBank Center for Infectious Diseases (KUISCID)IstanbulTurkey
- Department of Medical MicrobiologyKoç University School of MedicineIstanbulTurkey
| | - Önder Ergönül
- Koç University İşBank Center for Infectious Diseases (KUISCID)IstanbulTurkey
- Department of Infectious Disease and Clinical MicrobiologyKoç University School of MedicineIstanbulTurkey
| | - Fusun Can
- Koç University İşBank Center for Infectious Diseases (KUISCID)IstanbulTurkey
- Department of Medical MicrobiologyKoç University School of MedicineIstanbulTurkey
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10
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Townley B, Akin D, Dimaguila GL, Sawires R, Sepulveda Kattan G, King S, Bines J, Wood N, Lambert S, Buttery J. Exploring the Infectious Contribution to Intussusception Causality Using the Effects of COVID-19 Lockdowns in Australia: An Ecological Study. Clin Infect Dis 2024; 79:255-262. [PMID: 38376945 DOI: 10.1093/cid/ciae084] [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: 10/11/2023] [Revised: 02/06/2024] [Accepted: 02/13/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Intussusception is the primary cause of acute bowel obstruction in infants. The majority of cases <2 years of age are classed as idiopathic, with viral infection implicated as one of the causes. Coronavirus disease 2019 (COVID-19) public health measures led to significant decreases in communicable disease prevalence. During these times, reductions in intussusception frequency were greater than would be expected with our previous understanding of its infectious etiology. METHODS We conducted a retrospective, multistate, ecological study over a 12-year period. Monthly case numbers of "intussusception"-coded admissions (code K56.1; International Classification of Diseases and Related Health Problems, Tenth Revision, Australian Modification) were acquired from state-wide admissions data sets from New South Wales, Victoria, and Queensland, representing 77.62% of the eligible Australian population. These counts within differing jurisdictional lockdowns were compared with non-lockdown periods in order to investigate a correlation between intussusception frequency and lockdown periods. RESULTS We found a negative association between intussusception frequency and lockdown periods in both eligible states. The largest reductions were seen in the <2-year age groups, with Victoria experiencing a 62.7% reduction (rate ratio, 0.37; P < .001) and New South Wales a 40.1% reduction (0.599; P = .006) during lockdown times. Controls for variations in lockdown restrictions between both regional and metropolitan areas also showed expected decreases. CONCLUSIONS Our ecological study demonstrates significant decreases in the frequency of pediatric intussusception admissions during the COVID-19 lockdown periods. The unexpected magnitude of the reductions suggests that the true proportion of infectious disease-caused idiopathic intussusception is greatly underestimated.
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Affiliation(s)
- Benjamin Townley
- Child Health Analytics and Informatics Research, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- School of Medicine, Monash University, Clayton, Victoria, Australia
| | - Deniz Akin
- Child Health Analytics and Informatics Research, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Gerardo Luis Dimaguila
- Child Health Analytics and Informatics Research, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Rana Sawires
- Child Health Analytics and Informatics Research, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- School of Medicine, Monash University, Clayton, Victoria, Australia
| | - Gonzalo Sepulveda Kattan
- Child Health Analytics and Informatics Research, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Sebastian King
- Department of Paediatrics, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Pediatric Surgery, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Julie Bines
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- Department of Gastroenterology and Clinical Nutrition, Royal Children's Hospital, Parkville, Victoria, Australia
- Enteric Diseases, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Nicholas Wood
- National Centre for Immunisation Research and Surveillance, Sydney Children's Hospital Network, Sydney, New South Wales, Australia
| | - Stephen Lambert
- National Centre for Immunisation Research and Surveillance, Sydney Children's Hospital Network, Sydney, New South Wales, Australia
- Communicable Diseases Branch, Queensland Health, Brisbane, Queensland, Australia
| | - Jim Buttery
- Child Health Analytics and Informatics Research, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- Infectious Diseases Unit, Royal Children's Hospital, Parkville, Victoria, Australia
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11
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Watson LM, Plank MJ, Armstrong BA, Chapman JR, Hewitt J, Morris H, Orsi A, Bunce M, Donnelly CA, Steyn N. Jointly estimating epidemiological dynamics of Covid-19 from case and wastewater data in Aotearoa New Zealand. COMMUNICATIONS MEDICINE 2024; 4:143. [PMID: 39009723 PMCID: PMC11250817 DOI: 10.1038/s43856-024-00570-3] [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: 08/22/2023] [Accepted: 07/04/2024] [Indexed: 07/17/2024] Open
Abstract
BACKGROUND Timely and informed public health responses to infectious diseases such as COVID-19 necessitate reliable information about infection dynamics. The case ascertainment rate (CAR), the proportion of infections that are reported as cases, is typically much less than one and varies with testing practices and behaviours, making reported cases unreliable as the sole source of data. The concentration of viral RNA in wastewater samples provides an alternate measure of infection prevalence that is not affected by clinical testing, healthcare-seeking behaviour or access to care. METHODS We construct a state-space model with observed data of levels of SARS-CoV-2 in wastewater and reported case incidence and estimate the hidden states of the effective reproduction number, R, and CAR using sequential Monte Carlo methods. RESULTS We analyse data from 1 January 2022 to 31 March 2023 from Aotearoa New Zealand. Our model estimates that R peaks at 2.76 (95% CrI 2.20, 3.83) around 18 February 2022 and the CAR peaks around 12 March 2022. We calculate that New Zealand's second Omicron wave in July 2022 is similar in size to the first, despite fewer reported cases. We estimate that the CAR in the BA.5 Omicron wave in July 2022 is approximately 50% lower than in the BA.1/BA.2 Omicron wave in March 2022. CONCLUSIONS Estimating R, CAR, and cumulative number of infections provides useful information for planning public health responses and understanding the state of immunity in the population. This model is a useful disease surveillance tool, improving situational awareness of infectious disease dynamics in real-time.
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Affiliation(s)
- Leighton M Watson
- School of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand.
| | - Michael J Plank
- School of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand
| | | | - Joanne R Chapman
- Institute of Environmental Science and Research Ltd, Porirua, New Zealand
| | - Joanne Hewitt
- Institute of Environmental Science and Research Ltd, Porirua, New Zealand
| | - Helen Morris
- Institute of Environmental Science and Research Ltd, Porirua, New Zealand
| | - Alvaro Orsi
- Institute of Environmental Science and Research Ltd, Porirua, New Zealand
| | - Michael Bunce
- Institute of Environmental Science and Research Ltd, Porirua, New Zealand
| | - Christl A Donnelly
- Department of Statistics, University of Oxford, Oxford, United Kingdom
- Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
| | - Nicholas Steyn
- Department of Statistics, University of Oxford, Oxford, United Kingdom
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12
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Baumgart SWL, McLachlan A, Kenny H, McKew G, Maddocks S, Chen SCA, Kok J. Deisolation in the Healthcare Setting Following Recent COVID-19 Infection. Viruses 2024; 16:1131. [PMID: 39066294 PMCID: PMC11281359 DOI: 10.3390/v16071131] [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: 05/22/2024] [Revised: 07/06/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND Deisolation of persons infected with SARS-CoV-2, the virus that causes COVID-19, presented a substantial challenge for healthcare workers and policy makers, particularly during the early phases of the pandemic. Data to guide deisolation of SARS-CoV-2-infected patients remain limited, and the risk of transmitting and acquiring infection has changed with the evolution of SARS-CoV-2 variants and population immunity from previous vaccination or infection, or both. AIMS This review examines the evidence to guide the deisolation of SARS-CoV-2-infected inpatients within the hospital setting when clinically improving and also of healthcare workers with COVID-19 prior to returning to work. METHODS A review was performed using relevant search terms in Medline, EMBASE, Google Scholar, and PubMed. RESULTS AND DISCUSSION The evidence is reviewed with regards to the nature of SARS-CoV-2 transmission, the role of testing to guide deisolation, and the impact of SARS-CoV-2-specific immunity. A paradigm and recommendations are proposed to guide deisolation for inpatients and return to work for healthcare workers.
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Affiliation(s)
- Samuel W. L. Baumgart
- Department of Infectious Diseases and Microbiology, Concord Hospital, Concord, NSW 2137, Australia
| | - Aidan McLachlan
- Department of Infectious Diseases and Microbiology, Concord Hospital, Concord, NSW 2137, Australia
| | - Hayden Kenny
- Department of Infectious Diseases and Microbiology, Concord Hospital, Concord, NSW 2137, Australia
| | - Genevieve McKew
- Department of Infectious Diseases and Microbiology, Concord Hospital, Concord, NSW 2137, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Susan Maddocks
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, NSW 2145, Australia;
| | - Sharon C.-A. Chen
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, NSW 2145, Australia;
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia
- Centre for Infectious Diseases and Microbiology—Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, NSW 2145, Australia;
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia
- Centre for Infectious Diseases and Microbiology—Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
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Fang Z, Ma C, Xu W, Shi X, Liu S. Epidemiological Characteristics and Trends of Scarlet Fever in Zhejiang Province of China: Population-Based Surveillance during 2004-2022. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2024; 2024:6257499. [PMID: 39036471 PMCID: PMC11260510 DOI: 10.1155/2024/6257499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 05/29/2024] [Accepted: 06/21/2024] [Indexed: 07/23/2024]
Abstract
Background Over the past two decades, scarlet fever has resurged in some countries or areas. Nationwide nonpharmaceutical interventions changed the patterns of other infectious diseases, but its effects on the spread of scarlet fever were rarely studied. This study aimed to evaluate the changes in scarlet fever incidence in Zhejiang Province, China, before and during the COVID-19 pandemic periods and to provide references for scarlet fever prevention and control. Methods Scarlet fever surveillance data in Zhejiang, China (2004-2022), were analyzed in three stages. Two-sample z test, ANOVA, and Tukey's test were used to compare and analyze the characteristics of disease spread at different stages. The ARIMA model was used to predict the overall trend. The data were obtained from the National Infectious Disease Reporting Information System. Results A total of 28,652 cases of scarlet fever were reported across Zhejiang Province during the study period, with the lowest average monthly incidences in 2020 (0.111/100,000). The predominant areas affected were the northern and central regions of Zhejiang, and all regions of Zhejiang experienced a decrease in incidence in 2020. The steepest decline in incidence in 2020 was found in children aged 0-4 years (67.3% decrease from 23.8/100,000 to 7.8/100,000). The seasonal pattern changed, with peak occurrences in April to June and November to January during 2004-2019 and 2021 and a peak in January in 2020. The median duration from diagnosis to confirmation was highest before COVID-19 (4 days); however, it decreased to 1 day in 2020-2022, matching the other two medians. Conclusions In 2020, Zhejiang experienced an unprecedented decrease in scarlet fever, with the lowest incidence in nearly 18 years, but it rebounded in 2021 and 2022. The seasonal epidemiologic characteristics of scarlet fever also changed with the COVID-19 outbreaks. This suggested that nationwide nonpharmaceutical interventions greatly depressed the spread of scarlet fever. With the relaxation of non-pharmaceutical intervention restrictions, scarlet fever may reappear. Government policymakers should prioritize the control of future scarlet fever outbreaks for public health.
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Affiliation(s)
- Zhen Fang
- Center for Applied StatisticsSchool of StatisticsRenmin University of China, Beijing 100872, China
| | - Chenjin Ma
- College of Statistics and Data ScienceFaculty of ScienceBeijing University of Technology, Beijing 100124, China
| | - Wangli Xu
- Center for Applied StatisticsSchool of StatisticsRenmin University of China, Beijing 100872, China
| | - Xiuxiu Shi
- The Fourth Medical Center of PLA General Hospital, Beijing 100048, China
| | - Shelan Liu
- Department of Infectious DiseasesZhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang 310051, China
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Friedrich F, Lumertz MS, Petry LM, Pieta MP, Bittencourt LB, Nunes BB, Garcia LDCE, Antunes MOB, Scotta MC, Stein RT, Jones MH, Comaru T, Pinto LA. Seasonality of the incidence of bronchiolitis in infants - Brazil, 2016-2022: An interrupted time-series analysis. REVISTA PAULISTA DE PEDIATRIA : ORGAO OFICIAL DA SOCIEDADE DE PEDIATRIA DE SAO PAULO 2024; 43:e2023203. [PMID: 38985050 PMCID: PMC11251454 DOI: 10.1590/1984-0462/2025/43/2023203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/03/2024] [Indexed: 07/11/2024]
Abstract
OBJECTIVE To evaluate the seasonality of acute bronchiolitis in Brazil during the 2020-2022 season and compare it with the previous seasons. METHODS Data from the incidence of hospitalizations due to acute bronchiolitis in infants <1 year of age were obtained from the Department of Informatics of the Brazilian Public Health database for the period between 2016 and 2022. These data were also analyzed by macro-regions of Brazil (North, Northeast, Southeast, South, and Midwest). To describe seasonal and trend characteristics over time, we used the Seasonal Autoregressive Integrated Moving Averages Model. RESULTS Compared to the pre-COVID-19 period, the incidence of hospitalizations related to acute bronchiolitis decreased by 97% during non-pharmacological interventions (March 2020 - August 2021) but increased by 95% after non-pharmacological interventions relaxation (September 2021 - December 2022), resulting in a 16% overall increase. During the pre-COVID-19 period, hospitalizations for acute bronchiolitis followed a seasonal pattern, which was disrupted in 2020-2021 but recovered in 2022, with a peak occurring in May, approximately 4% higher than the pre-COVID-19 peak. CONCLUSIONS This study underscores the significant influence of COVID-19 interventions on acute bronchiolitis hospitalizations in Brazil. The restoration of a seasonal pattern in 2022 highlights the interplay between public health measures and respiratory illness dynamics in young children.
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Affiliation(s)
- Frederico Friedrich
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Magali Santos Lumertz
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Lucas Montiel Petry
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Marina Puerari Pieta
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | | | - Bruno Brocker Nunes
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | | | | | | | - Renato Tetelbom Stein
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Marcus Herbert Jones
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Talitha Comaru
- Instituto Federal de Education, Ciência e Tecnologia de Farroupilha, Santo Ângelo, RS, Brazil
| | - Leonardo Araújo Pinto
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
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15
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Lau YC, Shan S, Wang D, Chen D, Du Z, Lau EHY, He D, Tian L, Wu P, Cowling BJ, Ali ST. Forecasting of influenza activity and associated hospital admission burden and estimating the impact of COVID-19 pandemic on 2019/20 winter season in Hong Kong. PLoS Comput Biol 2024; 20:e1012311. [PMID: 39083536 PMCID: PMC11318919 DOI: 10.1371/journal.pcbi.1012311] [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: 12/20/2023] [Revised: 08/12/2024] [Accepted: 07/10/2024] [Indexed: 08/02/2024] Open
Abstract
Like other tropical and subtropical regions, influenza viruses can circulate year-round in Hong Kong. However, during the COVID-19 pandemic, there was a significant decrease in influenza activity. The objective of this study was to retrospectively forecast influenza activity during the year 2020 and assess the impact of COVID-19 public health social measures (PHSMs) on influenza activity and hospital admissions in Hong Kong. Using weekly surveillance data on influenza virus activity in Hong Kong from 2010 to 2019, we developed a statistical modeling framework to forecast influenza virus activity and associated hospital admissions. We conducted short-term forecasts (1-4 weeks ahead) and medium-term forecasts (1-13 weeks ahead) for the year 2020, assuming no PHSMs were implemented against COVID-19. We estimated the reduction in transmissibility, peak magnitude, attack rates, and influenza-associated hospitalization rate resulting from these PHSMs. For short-term forecasts, mean ambient ozone concentration and school holidays were found to contribute to better prediction performance, while absolute humidity and ozone concentration improved the accuracy of medium-term forecasts. We observed a maximum reduction of 44.6% (95% CI: 38.6% - 51.9%) in transmissibility, 75.5% (95% CI: 73.0% - 77.6%) in attack rate, 41.5% (95% CI: 13.9% - 55.7%) in peak magnitude, and 63.1% (95% CI: 59.3% - 66.3%) in cumulative influenza-associated hospitalizations during the winter-spring period of the 2019/2020 season in Hong Kong. The implementation of PHSMs to control COVID-19 had a substantial impact on influenza transmission and associated burden in Hong Kong. Incorporating information on factors influencing influenza transmission improved the accuracy of our predictions.
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Affiliation(s)
- Yiu-Chung Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| | - Songwei Shan
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| | - Dong Wang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| | - Dongxuan Chen
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| | - Zhanwei Du
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| | - Eric H. Y. Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
- Institute for Health Transformation, School of Health and Social Development, Deakin University, Burwood, Australia
| | - Daihai He
- Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Linwei Tian
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Peng Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| | - Benjamin J. Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| | - Sheikh Taslim Ali
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
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Turner N, Aminisani N, Huang S, O'Donnell J, Trenholme A, Broderick D, Paynter J, Castelino L, Grant C, McIntyre P. Comparison of the Burden and Temporal Pattern of Hospitalisations Associated With Respiratory Syncytial Virus (RSV) Before and After COVID-19 in New Zealand. Influenza Other Respir Viruses 2024; 18:e13346. [PMID: 38980967 PMCID: PMC11232889 DOI: 10.1111/irv.13346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND Changes in the epidemiology of illnesses caused by respiratory syncytial virus (RSV) infection following the COVID-19 pandemic are reported. The New Zealand (NZ) COVID-19 situation was unique; RSV community transmission was eliminated with the 2020 border closure, with a rapid and large increase in hospitalizations following the relaxation of social isolation measures and the opening of an exclusive border with Australia. METHODS This active population-based surveillance compared the age-specific incidence and seasonality of RSV-associated hospitalizations in Auckland, NZ, for 2 years before and after the 2020 border closures. Hospitalisation rates between years were compared by age, ethnicity (European/other, Māori, Pacific and Asian) and socioeconomic group (1 = least, 5 = most deprived). RESULTS There was no RSV transmission in 2020. In all other years, hospitalisation rates were highest for people of Pacific versus other ethnic groups and for people living in the most deprived quintile of households. RSV hospitalisation rates were higher in 2021 and 2022 than in 2018-19. The epidemic peak was higher in 2021, but not 2022, and the duration was shorter than in 2018-19. In 2021, the increase in RSV hospitalisation rates was significant across all age, sex, ethnic and socioeconomic groups. In 2022, the increase in hospitalisation rates was only significant in one age (1- < 3 years), one ethnic (Asian) and one socioeconomic group (quintile 2). CONCLUSIONS COVID pandemic responses altered RSV-related hospitalisation seasonal patterns. Atypical features of RSV hospitalisation epidemiology were the increase in rates in older children and young adults, which lessened in 2022. Despite these variations, RSV hospitalisations in NZ continue to disproportionately affect individuals of Pacific ethnicity and those living in more socioeconomically deprived households. Whilst future public health strategies focused on RSV disease mitigation need to consider the potential shifts in epidemiological patterns when the transmission is disrupted, these variances must be considered in the context of longer-standing patterns of unequal disease distribution.
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Affiliation(s)
- Nikki Turner
- Department of General Practice and Primary Healthcare, University of Auckland, Auckland, New Zealand
- Institute of Environmental Science and Research, ESR, Wellington, New Zealand
| | - Nayyereh Aminisani
- Institute of Environmental Science and Research, ESR, Wellington, New Zealand
| | - Sue Huang
- Institute of Environmental Science and Research, ESR, Wellington, New Zealand
| | - Jane O'Donnell
- Department of Anaesthesiology, University of Auckland, Auckland, New Zealand
| | - Adrian Trenholme
- Kidz First Childrens Hopsital, Te Whatu Ora - Health New Zealand Counties Manukau, Auckland, New Zealand
- Department of Paediatrics: Child & Youth Health, University of Auckland, Auckland, New Zealand
| | - David Broderick
- Department of General Practice and Primary Healthcare, University of Auckland, Auckland, New Zealand
| | - Janine Paynter
- Department of General Practice and Primary Healthcare, University of Auckland, Auckland, New Zealand
| | - Lorraine Castelino
- Department of General Practice and Primary Healthcare, University of Auckland, Auckland, New Zealand
| | - Cameron Grant
- Department of Paediatrics: Child & Youth Health, University of Auckland, Auckland, New Zealand
- Starship Children's Hospital, Te Whatu Ora - Health New Zealand Te Toka Tumai Auckland, Auckland, New Zealand
| | - Peter McIntyre
- Department of Women's and Children's Health, University of Otago, Dunedin, New Zealand
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17
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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.
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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.
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Trifonova I, Korsun N, Madzharova I, Alexiev I, Ivanov I, Levterova V, Grigorova L, Stoikov I, Donchev D, Christova I. Epidemiological and Genetic Characteristics of Respiratory Viral Coinfections with Different Variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Viruses 2024; 16:958. [PMID: 38932250 PMCID: PMC11209099 DOI: 10.3390/v16060958] [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: 05/21/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
This study aimed to determine the incidence and etiological, seasonal, and genetic characteristics of respiratory viral coinfections involving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Between October 2020 and January 2024, nasopharyngeal samples were collected from 2277 SARS-CoV-2-positive patients. Two multiplex approaches were used to detect and sequence SARS-CoV-2, influenza A/B viruses, and other seasonal respiratory viruses: multiplex real-time polymerase chain reaction (PCR) and multiplex next-generation sequencing. Coinfections of SARS-CoV-2 with other respiratory viruses were detected in 164 (7.2%) patients. The most common co-infecting virus was respiratory syncytial virus (RSV) (38 cases, 1.7%), followed by bocavirus (BoV) (1.2%) and rhinovirus (RV) (1.1%). Patients ≤ 16 years of age had the highest rate (15%) of mixed infections. Whole-genome sequencing produced 19 complete genomes of seasonal respiratory viral co-pathogens, which were subjected to phylogenetic and amino acid analyses. The detected influenza viruses were classified into the genetic groups 6B.1A.5a.2a and 6B.1A.5a.2a.1 for A(H1N1)pdm09, 3C.2a1b.2a.2a.1 and 3C.2a.2b for A(H3N2), and V1A.3a.2 for the B/Victoria lineage. The RSV-B sequences belonged to the genetic group GB5.0.5a, with HAdV-C belonging to type 1, BoV to genotype VP1, and PIV3 to lineage 1a(i). Multiple amino acid substitutions were identified, including at the antibody-binding sites. This study provides insights into respiratory viral coinfections involving SARS-CoV-2 and reinforces the importance of genetic characterization of co-pathogens in the development of therapeutic and preventive strategies.
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Affiliation(s)
- Ivelina Trifonova
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (N.K.); (I.M.); (I.A.); (L.G.); (I.C.)
| | - Neli Korsun
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (N.K.); (I.M.); (I.A.); (L.G.); (I.C.)
| | - Iveta Madzharova
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (N.K.); (I.M.); (I.A.); (L.G.); (I.C.)
| | - Ivailo Alexiev
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (N.K.); (I.M.); (I.A.); (L.G.); (I.C.)
| | - Ivan Ivanov
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (V.L.); (I.S.); (D.D.)
| | - Viktoria Levterova
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (V.L.); (I.S.); (D.D.)
| | - Lyubomira Grigorova
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (N.K.); (I.M.); (I.A.); (L.G.); (I.C.)
| | - Ivan Stoikov
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (V.L.); (I.S.); (D.D.)
| | - Dean Donchev
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (V.L.); (I.S.); (D.D.)
| | - Iva Christova
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (N.K.); (I.M.); (I.A.); (L.G.); (I.C.)
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (V.L.); (I.S.); (D.D.)
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Qiu W, Ding J, Zhang H, Huang S, Huang Z, Lin M, Zhang Y, Chen Z. Mycoplasma pneumoniae detections in children with lower respiratory infection before and during the COVID-19 pandemic: a large sample study in China from 2019 to 2022. BMC Infect Dis 2024; 24:549. [PMID: 38824572 PMCID: PMC11143586 DOI: 10.1186/s12879-024-09438-2] [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: 11/17/2023] [Accepted: 05/27/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND Nonpharmaceutical interventions (NPIs) implemented to reduce the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have suppressed the spread of other respiratory viruses during the coronavirus disease 2019 (COVID-19) pandemic. This study aimed to explore the epidemiological trends and clinical characteristics of Mycoplasma pneumoniae (MP) infection among inpatient children with lower respiratory tract infection (LRTI) before and during the COVID-19 pandemic, and investigate the long-term effects of China's NPIs against COVID-19 on the epidemiology of MP among inpatient children with LRTI. METHODS Children hospitalised for LRTI at the Department of Pulmonology, The Children's Hospital, Zhejiang University School of Medicine (Hangzhou, China) between January 2019 and December 2022 were tested for common respiratory pathogens, including Mycoplasma pneumoniae (MP), Chlamydia trachomatis (CT) and other bacteria. Clinical data on age, sex, season of onset, disease spectrum, and combined infection in children with MP-induced LRTI in the past 4 years were collected and analysed. RESULTS Overall, 15909 patients were enrolled, and MP-positive cases were 1971 (34.0%), 73 (2.4%), 176 (5.8%), and 952 (20.6%) in 2019, 2020, 2021, and 2022, respectively, with a significant statistical difference in the MP-positive rate over the 4 years (p <0.001). The median age of these children was preschool age (3-6 years), except for 2022, when they were school age (7-12 years), with statistical differences. Comparing the positive rates of different age groups, the school-age children (7-12 years) had the highest positive rate, followed by the preschoolers (3-6 years) in each of the 4 years. Compared among different seasons, the positive rate of MP in children with LRTI was higher in summer and autumn, whereas in 2020, it was highest in spring. The monthly positive rate peaked in July 2019, remained low from 2020 to 2021, and rebounded until 2022. Regarding the disease spectrum, severe pneumonia accounted for the highest proportion (46.3%) pre-pandemic and lowest (0%) in 2020. CONCLUSION Trends in MP detection in children with LRTIs suggest a possible correlation between COVID-19 NPIs and significantly reduced detection rates. The positivity rate of MP gradually rose after 2 years. The epidemic season showed some differences, but school-age children were more susceptible to MP before and during the COVID-19 pandemic.
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Affiliation(s)
- Weiling Qiu
- Department of Pulmonology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, No.3333 Binsheng Road, Zhejiang, Hangzhou, People's Republic of China
| | - Jiaying Ding
- Department of Pulmonology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, No.3333 Binsheng Road, Zhejiang, Hangzhou, People's Republic of China
| | - Hongmei Zhang
- Department of Pulmonology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, No.3333 Binsheng Road, Zhejiang, Hangzhou, People's Republic of China
| | - Shumin Huang
- Department of Pulmonology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, No.3333 Binsheng Road, Zhejiang, Hangzhou, People's Republic of China
| | - Zuowei Huang
- Department of Pulmonology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, No.3333 Binsheng Road, Zhejiang, Hangzhou, People's Republic of China
| | - Ming Lin
- Department of Pulmonology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, No.3333 Binsheng Road, Zhejiang, Hangzhou, People's Republic of China
| | - Yuanyuan Zhang
- Department of Pulmonology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, No.3333 Binsheng Road, Zhejiang, Hangzhou, People's Republic of China.
| | - Zhimin Chen
- Department of Pulmonology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, No.3333 Binsheng Road, Zhejiang, Hangzhou, People's Republic of China.
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Xiao M, Banu A, Jia Y, Chang M, Wang G, An J, Huang Y, Hu X, Tang C, Li Z, Niu Y, Tian X, Deng W, Tang C, Du J, Cui X, Chan JFW, Peng R, Yin F. Circulation pattern and genetic variation of rhinovirus infection among hospitalized children on Hainan Island, before and after the dynamic zero-COVID policy, from 2021 to 2023. J Med Virol 2024; 96:e29755. [PMID: 38922896 DOI: 10.1002/jmv.29755] [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: 04/03/2024] [Revised: 05/17/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024]
Abstract
Throughout the COVID-19 pandemic, rhinovirus (RV) remained notable persistence, maintaining its presence while other seasonal respiratory viruses were largely suppressed by pandemic restrictions during national lockdowns. This research explores the epidemiological dynamics of RV infections among pediatric populations on Hainan Island, China, specifically focusing on the impact before and after the zero-COVID policy was lifted. From January 2021 to December 2023, 19 680 samples were collected from pediatric patients hospitalized with acute lower respiratory tract infections (ARTIs) at the Hainan Maternal and Child Health Hospital. The infection of RV was detected by tNGS. RV species and subtypes were identified in 32 RV-positive samples representing diverse time points by analyzing the VP4/VP2 partial regions. Among the 19 680 pediatric inpatients with ARTIs analyzed, 21.55% were found to be positive for RV infection, with notable peaks observed in April 2021 and November 2022. A gradual annual decline in RV infections was observed, alongside a seasonal pattern of higher prevalence during the colder months. The highest proportion of RV infections was observed in the 0-1-year age group. Phylogenetic analysis on 32 samples indicated a trend from RV-A to RV-C in 2022. This observation suggests potential evolving dynamics within the RV species although further studies are needed due to the limited sample size. The research emphasizes the necessity for ongoing surveillance and targeted management, particularly for populations highly susceptible to severe illnesses caused by RV infections.
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Affiliation(s)
- Meifang Xiao
- Department of Clinical Laboratory, Center for Laboratory Medicine, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, Hainan, China
- Department of Microbiology, Faculty of Medicine, Lincoln University College, Petaling Jaya, Malaysia
| | - Afreen Banu
- Department of Microbiology, Faculty of Medicine, Lincoln University College, Petaling Jaya, Malaysia
| | - Yibo Jia
- Medical Administration Division, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
- Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, Hainan, China
- International School of Public Health and One Health, Hainan Medical College, Haikou, Hainan, China
| | - Meng Chang
- Department of Clinical Laboratory, Center for Laboratory Medicine, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, Hainan, China
- Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, Hainan, China
| | - Gaoyu Wang
- Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, Hainan, China
| | - Jing An
- Department of Clinical Laboratory, Center for Laboratory Medicine, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, Hainan, China
| | - Yi Huang
- Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, Hainan, China
| | - Xiaoyuan Hu
- Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, Hainan, China
| | - Chuanning Tang
- Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, Hainan, China
| | - Zihan Li
- Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, Hainan, China
| | - Yi Niu
- Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, Hainan, China
| | - Xiuying Tian
- Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, Hainan, China
| | - Wanxin Deng
- Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, Hainan, China
| | - Cheng Tang
- Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, Hainan, China
| | - Jiang Du
- Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, Hainan, China
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiuji Cui
- Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, Hainan, China
- Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, China
| | - Jasper Fuk-Woo Chan
- Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, Hainan, China
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Infectious Diseases and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Ruoyan Peng
- Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, Hainan, China
| | - Feifei Yin
- Department of Clinical Laboratory, Center for Laboratory Medicine, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, Hainan, China
- Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, Hainan, China
- Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, China
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21
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Armero G, Guitart C, Soler-Garcia A, Melé M, Esteva C, Brotons P, Muñoz-Almagro C, Jordan I, Launes C. Non-Pharmacological Interventions During SARS-CoV-2 Pandemic: Effects on Pediatric Viral Respiratory Infections. Arch Bronconeumol 2024:S0300-2896(24)00183-2. [PMID: 38853117 DOI: 10.1016/j.arbres.2024.05.019] [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: 02/19/2024] [Revised: 05/08/2024] [Accepted: 05/15/2024] [Indexed: 06/11/2024]
Abstract
INTRODUCTION Viral lower respiratory tract infections frequently cause morbidity and mortality in children. The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic led to isolation and hygiene measures, resulting in decreased respiratory virus transmission and pediatric admissions. This study aimed to assess the impact of these measures and their uplifting on respiratory virus circulation in children before and during the SARS-CoV-2 pandemic (January 2017-December 2022). METHODS We conducted a weekly time series analysis of multiple virus molecular assays in children. This included those admitted to a university reference hospital's Pediatric Intensive Care Unit (PICU) and those with risk pathologies exhibiting fever and/or respiratory symptoms. We included patients aged 0-18 years residing in Catalonia and adjusted the positive results to account for diagnostic effort. RESULTS We performed a total of 2991 respiratory virus tests during the period. Confinement significantly decreased the detection of all viruses, especially Rhinovirus (RV). After the deconfinement of children, the viral detection trend remained stable for all viruses, with no short-term impact on virus transmission. The mandatory implementation of facemasks in those aged ≥6 years led to decreased viral circulation, but we observed an influenza virus rebound after facemask removal. At that time, we also noticed an interrupted drop in the detection rates of RV and respiratory syncytial virus (RSV). The reopening of schools led to a progressive increase in viral detections, especially of Rhinovirus. CONCLUSION Non-pharmacological interventions significantly impact the circulation of respiratory viruses among children. We observed these effects even when some measures did not specifically target preschool-aged children.
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Affiliation(s)
- Georgina Armero
- Pediatrics Department, Hospital Sant Joan de Déu, Barcelona, Spain; Infectious Diseases and Microbiome Research Group. Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain
| | - Carmina Guitart
- Infectious Diseases and Microbiome Research Group. Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain; Pediatrics Intensive Care Unit, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Aleix Soler-Garcia
- Pediatrics Department, Hospital Sant Joan de Déu, Barcelona, Spain; Infectious Diseases and Microbiome Research Group. Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain; Department of Surgery and Medical-Surgical Specialties, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Maria Melé
- Pediatrics Department, Hospital Sant Joan de Déu, Barcelona, Spain; Infectious Diseases and Microbiome Research Group. Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain
| | - Cristina Esteva
- Infectious Diseases and Microbiome Research Group. Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain; Microbiology Department, Hospital Sant Joan de Déu, Barcelona, Spain; CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Pedro Brotons
- Infectious Diseases and Microbiome Research Group. Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain; CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain; Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Carmen Muñoz-Almagro
- Infectious Diseases and Microbiome Research Group. Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain; Microbiology Department, Hospital Sant Joan de Déu, Barcelona, Spain; CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain; Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Iolanda Jordan
- Infectious Diseases and Microbiome Research Group. Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain; Pediatrics Intensive Care Unit, Hospital Sant Joan de Déu, Barcelona, Spain; Department of Surgery and Medical-Surgical Specialties, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain; CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Cristian Launes
- Pediatrics Department, Hospital Sant Joan de Déu, Barcelona, Spain; Infectious Diseases and Microbiome Research Group. Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain; Department of Surgery and Medical-Surgical Specialties, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain; CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.
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Perofsky AC, Huddleston J, Hansen C, Barnes JR, Rowe T, Xu X, Kondor R, Wentworth DE, Lewis N, Whittaker L, Ermetal B, Harvey R, Galiano M, Daniels RS, McCauley JW, Fujisaki S, Nakamura K, Kishida N, Watanabe S, Hasegawa H, Sullivan SG, Barr IG, Subbarao K, Krammer F, Bedford T, Viboud C. Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.10.02.23296453. [PMID: 37873362 PMCID: PMC10593063 DOI: 10.1101/2023.10.02.23296453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Influenza viruses continually evolve new antigenic variants, through mutations in epitopes of their major surface proteins, hemagglutinin (HA) and neuraminidase (NA). Antigenic drift potentiates the reinfection of previously infected individuals, but the contribution of this process to variability in annual epidemics is not well understood. Here we link influenza A(H3N2) virus evolution to regional epidemic dynamics in the United States during 1997-2019. We integrate phenotypic measures of HA antigenic drift and sequence-based measures of HA and NA fitness to infer antigenic and genetic distances between viruses circulating in successive seasons. We estimate the magnitude, severity, timing, transmission rate, age-specific patterns, and subtype dominance of each regional outbreak and find that genetic distance based on broad sets of epitope sites is the strongest evolutionary predictor of A(H3N2) virus epidemiology. Increased HA and NA epitope distance between seasons correlates with larger, more intense epidemics, higher transmission, greater A(H3N2) subtype dominance, and a greater proportion of cases in adults relative to children, consistent with increased population susceptibility. Based on random forest models, A(H1N1) incidence impacts A(H3N2) epidemics to a greater extent than viral evolution, suggesting that subtype interference is a major driver of influenza A virus infection dynamics, presumably via heterosubtypic cross-immunity.
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Affiliation(s)
- Amanda C Perofsky
- Fogarty International Center, National Institutes of Health, United States
- Brotman Baty Institute for Precision Medicine, University of Washington, United States
| | - John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, United States
| | - Chelsea Hansen
- Fogarty International Center, National Institutes of Health, United States
- Brotman Baty Institute for Precision Medicine, University of Washington, United States
| | - John R Barnes
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), United States
| | - Thomas Rowe
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), United States
| | - Xiyan Xu
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), United States
| | - Rebecca Kondor
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), United States
| | - David E Wentworth
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), United States
| | - Nicola Lewis
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, United Kingdom
| | - Lynne Whittaker
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, United Kingdom
| | - Burcu Ermetal
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, United Kingdom
| | - Ruth Harvey
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, United Kingdom
| | - Monica Galiano
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, United Kingdom
| | - Rodney Stuart Daniels
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, United Kingdom
| | - John W McCauley
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, United Kingdom
| | - Seiichiro Fujisaki
- Influenza Virus Research Center, National Institute of Infectious Diseases, Japan
| | - Kazuya Nakamura
- Influenza Virus Research Center, National Institute of Infectious Diseases, Japan
| | - Noriko Kishida
- Influenza Virus Research Center, National Institute of Infectious Diseases, Japan
| | - Shinji Watanabe
- Influenza Virus Research Center, National Institute of Infectious Diseases, Japan
| | - Hideki Hasegawa
- Influenza Virus Research Center, National Institute of Infectious Diseases, Japan
| | - Sheena G Sullivan
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Australia
| | - Ian G Barr
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Australia
| | - Kanta Subbarao
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Australia
| | - Florian Krammer
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, United States
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, United States
| | - Trevor Bedford
- Brotman Baty Institute for Precision Medicine, University of Washington, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, United States
- Department of Genome Sciences, University of Washington, United States
- Howard Hughes Medical Institute, Seattle, United States
| | - Cécile Viboud
- Fogarty International Center, National Institutes of Health, United States
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23
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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.
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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
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24
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Li K, Rui J, Song W, Luo L, Zhao Y, Qu H, Liu H, Wei H, Zhang R, Abudunaibi B, Wang Y, Zhou Z, Xiang T, Chen T. Temporal shifts in 24 notifiable infectious diseases in China before and during the COVID-19 pandemic. Nat Commun 2024; 15:3891. [PMID: 38719858 PMCID: PMC11079007 DOI: 10.1038/s41467-024-48201-8] [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: 11/19/2023] [Accepted: 04/24/2024] [Indexed: 05/12/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, along with the implementation of public health and social measures (PHSMs), have markedly reshaped infectious disease transmission dynamics. We analysed the impact of PHSMs on 24 notifiable infectious diseases (NIDs) in the Chinese mainland, using time series models to forecast transmission trends without PHSMs or pandemic. Our findings revealed distinct seasonal patterns in NID incidence, with respiratory diseases showing the greatest response to PHSMs, while bloodborne and sexually transmitted diseases responded more moderately. 8 NIDs were identified as susceptible to PHSMs, including hand, foot, and mouth disease, dengue fever, rubella, scarlet fever, pertussis, mumps, malaria, and Japanese encephalitis. The termination of PHSMs did not cause NIDs resurgence immediately, except for pertussis, which experienced its highest peak in December 2023 since January 2008. Our findings highlight the varied impact of PHSMs on different NIDs and the importance of sustainable, long-term strategies, like vaccine development.
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Affiliation(s)
- Kangguo Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, Xiamen, China
| | - Jia Rui
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, Xiamen, China
| | - Wentao Song
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, Xiamen, China
| | - Li Luo
- Health Care Departmen, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Yunkang Zhao
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, Xiamen, China
| | - Huimin Qu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, Xiamen, China
| | - Hong Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, Xiamen, China
| | - Hongjie Wei
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, Xiamen, China
| | - Ruixin Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, Xiamen, China
| | - Buasiyamu Abudunaibi
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, Xiamen, China
| | - Yao Wang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, Xiamen, China
| | - Zecheng Zhou
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, Xiamen, China
| | - Tianxin Xiang
- Jiangxi Medical Center for Critical Public Health Events, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China.
- Jiangxi Hospital of China-Japan Friendship Hospital, Nanchang, China.
| | - Tianmu Chen
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, Xiamen, China.
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25
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Kim SJ, Kim T, Choi H, Shin TR, Kim HI, Jang SH, Hong JY, Lee CY, Chung S, Choi JH, Sim YS. Respiratory pathogen and clinical features of hospitalized patients in acute exacerbation of chronic obstructive pulmonary disease after COVID 19 pandemic. Sci Rep 2024; 14:10462. [PMID: 38714885 PMCID: PMC11076476 DOI: 10.1038/s41598-024-61360-4] [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: 02/18/2024] [Accepted: 05/06/2024] [Indexed: 05/12/2024] Open
Abstract
Respiratory infections are common causes of acute exacerbation of chronic obstructive lung disease (AECOPD). We explored whether the pathogens causing AECOPD and clinical features changed from before to after the coronavirus disease 2019 (COVID-19) outbreak. We reviewed the medical records of patients hospitalized with AECOPD at four university hospitals between January 2017 and December 2018 and between January 2021 and December. We evaluated 1180 patients with AECOPD for whom medication histories were available. After the outbreak, the number of patients hospitalized with AECOPD was almost 44% lower compared with before the outbreak. Patients hospitalized with AECOPD after the outbreak were younger (75 vs. 77 years, p = 0.003) and more often stayed at home (96.6% vs. 88.6%, p < 0.001) than patients of AECOPD before the outbreak. Hospital stay was longer after the outbreak than before the outbreak (10 vs. 8 days. p < 0.001). After the COVID-19 outbreak, the identification rates of S. pneumoniae (15.3 vs. 6.2%, p < 0.001) and Hemophilus influenzae (6.4 vs. 2.4%, p = 0.002) decreased, whereas the identification rates of P. aeruginosa (9.4 vs. 13.7%, p = 0.023), Klebsiella pneumoniae (5.3 vs. 9.8%, p = 0.004), and methicillin-resistant Staphylococcus aureus (1.0 vs. 2.8%, p = 0.023) increased. After the outbreak, the identification rate of influenza A decreased (10.4 vs. 1.0%, p = 0.023). After the outbreak, the number of patients hospitalized with AECOPD was lower and the identification rates of community-transmitted pathogens tended to decrease, whereas the rates of pathogens capable of chronic colonization tended to increase. During the period of large-scale viral outbreaks that require quarantine, patients with AECOPD might be given more consideration for treatment against strains that can colonize chronic respiratory disease rather than community acquired pathogens.
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Affiliation(s)
- Soo Jung Kim
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Hallym University Kangnam Sacred Heart Hospital, Seoul, Korea
- Lung Research Institute, Hallym University College of Medicine, Chuncheon, Korea
| | - Taehee Kim
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Hallym University Kangnam Sacred Heart Hospital, Seoul, Korea
- Lung Research Institute, Hallym University College of Medicine, Chuncheon, Korea
| | - Hayoung Choi
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Hallym University Kangnam Sacred Heart Hospital, Seoul, Korea
- Lung Research Institute, Hallym University College of Medicine, Chuncheon, Korea
| | - Tae Rim Shin
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Hallym University Kangnam Sacred Heart Hospital, Seoul, Korea
- Lung Research Institute, Hallym University College of Medicine, Chuncheon, Korea
| | - Hwan Il Kim
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Hallym University Sacred Heart Hospital, Anyang-si, Korea
- Lung Research Institute, Hallym University College of Medicine, Chuncheon, Korea
| | - Seung Hun Jang
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Hallym University Sacred Heart Hospital, Anyang-si, Korea
- Lung Research Institute, Hallym University College of Medicine, Chuncheon, Korea
| | - Ji Young Hong
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Hallym University Chuncheon Sacred Heart Hospital, Chuncheon-si, Korea
- Lung Research Institute, Hallym University College of Medicine, Chuncheon, Korea
| | - Chang Youl Lee
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Hallym University Chuncheon Sacred Heart Hospital, Chuncheon-si, Korea
- Lung Research Institute, Hallym University College of Medicine, Chuncheon, Korea
| | - Soojie Chung
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Hallym University Dongtan Sacred Heart Hospital, Dongtan-si, Korea
- Lung Research Institute, Hallym University College of Medicine, Chuncheon, Korea
| | - Jeong-Hee Choi
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Hallym University Dongtan Sacred Heart Hospital, Dongtan-si, Korea
- Lung Research Institute, Hallym University College of Medicine, Chuncheon, Korea
| | - Yun Su Sim
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Hallym University Kangnam Sacred Heart Hospital, Seoul, Korea.
- Lung Research Institute, Hallym University College of Medicine, Chuncheon, Korea.
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26
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Altawalah H, Alfouzan W, Al-Fadalah T, Zalzala MA, Ezzikouri S. Viral etiology of severe lower respiratory tract infections in SARS-CoV-2 negative hospitalized patients during the COVID-19 pandemic in Kuwait. Heliyon 2024; 10:e29855. [PMID: 38681623 PMCID: PMC11046192 DOI: 10.1016/j.heliyon.2024.e29855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
Background The prevalence of respiratory infections is largely underexplored in Kuwait. The aim of our study is to determine the etiology of infections from patients who are SARS-CoV-2 negative hospitalized with severe lower respiratory tract infections (LRTIs) in Kuwait during the coronavirus disease 2019 (COVID-19) pandemic. Methods We conducted an observational cross-sectional study among severe LRTI patients between September 2021 and March 2022. Respiratory samples from 545 non-COVID-19 severe LRTIs patients were prospectively evaluated with FTD Respiratory 21 Plus® real-time PCR, targeting 20 different viruses and 1 atypical bacterial pathogen. Results Among all 545 hospitalized cases, 411 (75.4 %) tested positive for at least one respiratory pathogen. The most common were rhinovirus (HRV) (32.7 %), respiratory syncytial virus (RSV) (20.9 %), metapneumovirus (HMPV) (14.1 %), bocavirus (13.2 %), and influenza A (12.7 %). The proportion of pathogens detected was highest in the under-5 age group, while HKU1 (44.4 %) predominated in the elderly (>50 years). Conclusion Our study reveals a high prevalence of respiratory viruses in severe acute lower respiratory tract infections among non-COVID-19 hospitalized patients in Kuwait. HRV remains the main etiology affecting the country, particularly in infants. These results underscore the necessity of employing multiplex PCR for accurate diagnosis and describing the epidemiology of infections among severe lower respiratory tract infections. This will facilitate the use of specific antiviral therapy and help avoid excessive or inappropriate antibiotic therapy.
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Affiliation(s)
- Haya Altawalah
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, 24923, Kuwait
- Virology Unit, Yacoub Behbehani Center, Sabah Hospital, Ministry of Health, Kuwait, Kuwait
| | - Wadha Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, 24923, Kuwait
- Laboratory Medicine, Farwania Hospital, Ministry of Health, Farwania, Kuwait
| | - Talal Al-Fadalah
- Qualities and Accreditation Directorate, Ministry of Health, Kuwait, Kuwait
| | - Mariam Ali Zalzala
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, 24923, Kuwait
| | - Sayeh Ezzikouri
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
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27
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Chen M, Zhou Y, Jin S, Bai S, Tang X, Liu Q, Wang L, Ji R, Liu H, Zhong W, Chen Y, Fang D, Zhang J, Hua L. Changing clinical characteristics of pediatric inpatients with pneumonia during COVID-19 pandamic: a retrospective study. Ital J Pediatr 2024; 50:84. [PMID: 38650007 PMCID: PMC11036576 DOI: 10.1186/s13052-024-01651-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 04/07/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND The COVID-19 pandemic have impacts on the prevalence of other pathogens and people's social lifestyle. This study aimed to compare the pathogen, allergen and micronutrient characteristics of pediatric inpatients with pneumonia prior to and during the COVID-19 pandemic in a large tertiary hospital in Shanghai, China. METHODS Patients with pneumonia admitted to the Department of Pediatric Pulmonology of Xinhua Hospital between March-August 2019 and March-August 2020 were recruited. And clinical characteristics of the patients in 2019 were compared with those in 2020. RESULTS Hospitalizations for pneumonia decreased by 74% after the COVID-19 pandemic. For pathogens, virus, mycoplasma pneumoniae (MP) and mixed infection rates were all much lower in 2020 than those in 2019 (P < 0.01). Regarding allergens, compared with 2019, the positive rates of house dust mite, shrimp and crab were significantly higher in 2020 (P < 0.01). And for micronutrients, the levels of vitamin B2, B6, C and 25-hydroxyvitamin D (25(OH)D) in 2020 were observed to be significantly lower than those in 2019 (P < 0.05). For all the study participants, longer hospital stay (OR = 1.521, P = 0.000), milk allergy (OR = 6.552, P = 0.033) and calcium (Ca) insufficiency (OR = 12.048, P = 0.019) were identified as high-risk factors for severe pneumonia by multivariate analysis. CONCLUSIONS The number of children hospitalized with pneumonia and incidence of common pathogen infections were both reduced, and that allergy and micronutrient status in children were also changed after the outbreak of the COVID-19 pandemic.
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Affiliation(s)
- Mengxue Chen
- Department of Pediatric Pulmonology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, 200092, Shanghai, China
| | - Yabing Zhou
- Department of Traditional Chinese Medicine, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shengjie Jin
- Department of Mathematics, Statistics and Insurance, Hang Seng University of Hong Kong, Hong Kong, China
| | - Shasha Bai
- Department of Pediatric Pulmonology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, 200092, Shanghai, China
| | - Xiaoyu Tang
- Department of Pediatric Pulmonology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, 200092, Shanghai, China
| | - Quanhua Liu
- Department of Pediatric Pulmonology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, 200092, Shanghai, China
| | - Liwei Wang
- Department of Pediatric Pulmonology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, 200092, Shanghai, China
| | - Ruoxu Ji
- Department of Pediatric Pulmonology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, 200092, Shanghai, China
| | - Haipei Liu
- Department of Pediatric Pulmonology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, 200092, Shanghai, China
| | - Wenwei Zhong
- Department of Pediatric Pulmonology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, 200092, Shanghai, China
| | - Yi Chen
- Department of Pediatric Pulmonology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, 200092, Shanghai, China
| | - Dingzhu Fang
- Department of Pediatric Pulmonology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, 200092, Shanghai, China
| | - Jianhua Zhang
- Department of Pediatric Pulmonology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, 200092, Shanghai, China.
| | - Li Hua
- Department of Pediatric Pulmonology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, 200092, Shanghai, China.
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28
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Raya S, Malla B, Shrestha S, Sthapit N, Kattel H, Sharma ST, Tuladhar R, Maharjan R, Takeda T, Kitajima M, Tandukar S, Haramoto E. Quantification of multiple respiratory viruses in wastewater in the Kathmandu Valley, Nepal: Potential implications of wastewater-based epidemiology for community disease surveillance in developing countries. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:170845. [PMID: 38340866 DOI: 10.1016/j.scitotenv.2024.170845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/04/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
Despite being the major cause of death, clinical surveillance of respiratory viruses at the community level is very passive, especially in developing countries. This study focused on the surveillance of three respiratory viruses [severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A virus (IFV-A), and respiratory syncytial virus (RSV)] in the Kathmandu Valley, Nepal, by implication of wastewater-based epidemiology (WBE). Fifty-one untreated wastewater samples were from two wastewater treatment plants (WWTPs) between April and October 2022. Among eight combinations of the pre-evaluated methods, the combination of concentration by simple centrifugation, pretreatment by DNA/RNA Shield (Zymo Research), and extraction by the QIAamp Viral RNA Mini Kit (QIAGEN) showed the best performance for detecting respiratory viruses. Using this method with a one-step reverse transcription-quantitative polymerase chain reaction (RT-qPCR), SARS-CoV-2 RNA was successfully detected from both WWTPs (positive ratio, 100 % and 81 %) at concentrations of 5.6 ± 0.6 log10 copies/L from each WWTP. Forty-six SARS-CoV-2 RNA-positive samples were further tested for three mutation site-specific one-step RT-qPCR (L452R, T478K, and E484A/G339D), where G339D/E484A mutations were frequently detected in both WWTPs (96 %). IFV-A RNA was more frequently detected in WWTP A (84 %) compared to WWTP B (38 %). RSV RNA was also detected in both WWTPs (28 % and 8 %, respectively). This is the first study on detecting IFV-A and RSV in wastewater in Nepal, showing the applicability and importance of WBE for respiratory viruses in developing countries where clinical data are lacking.
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Affiliation(s)
- Sunayana Raya
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Bikash Malla
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Sadhana Shrestha
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Niva Sthapit
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Hari Kattel
- Department of Microbiology, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Sangita Tara Sharma
- Department of Microbiology, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Reshma Tuladhar
- Department of Microbiology, Tribhuvan University, Kathmandu, Nepal
| | - Rabin Maharjan
- Department of Civil Engineering, Institute of Engineering, Tribhuvan University, Lalitpur, Nepal
| | - Tomoko Takeda
- Department of Earth and Planetary Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Masaaki Kitajima
- Division of Environmental Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan.
| | | | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
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29
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Jia W, Zhang X, Sun R, Li P, Song C. Impact of the COVID-19 outbreak and interventions on hand, foot and mouth disease in Zhengzhou, China, 2014-2022: a retrospective study. BMC Infect Dis 2024; 24:386. [PMID: 38594638 PMCID: PMC11005130 DOI: 10.1186/s12879-024-09244-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/21/2024] [Indexed: 04/11/2024] Open
Abstract
BACKGROUND Since December 2019, COVID-19 has spread rapidly around the world, and studies have shown that measures to prevent COVID-19 can largely reduce the spread of other infectious diseases. This study explored the impact of the COVID-19 outbreak and interventions on the incidence of HFMD. METHODS We gathered data on the prevalence of HFMD from the Children's Hospital Affiliated to Zhengzhou University. An autoregressive integrated moving average model was constructed using HFMD incidence data from 2014 to 2019, the number of cases predicted from 2020 to 2022 was predicted, and the predicted values were compared with the actual measurements. RESULTS From January 2014 to October 2022, the Children's Hospital of Zhengzhou University admitted 103,995 children with HFMD. The average number of cases of HFMD from 2020 to 2022 was 4,946, a significant decrease from 14,859 cases from 2014 to 2019. We confirmed the best ARIMA (2,0,0) (1,1,0)12 model. From 2020 to 2022, the yearly number of cases decreased by 46.58%, 75.54%, and 66.16%, respectively, compared with the forecasted incidence. Trends in incidence across sexes and ages displayed patterns similar to those overall. CONCLUSIONS The COVID-19 outbreak and interventions reduced the incidence of HFMD compared to that before the outbreak. Strengthening public health interventions remains a priority in the prevention of HFMD.
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Affiliation(s)
- Wanyu Jia
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, No. 1, South University Road, Erqi District, 450018, Zhengzhou, China
| | - Xue Zhang
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, No. 1, South University Road, Erqi District, 450018, Zhengzhou, China
| | - Ruiyang Sun
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, No. 1, South University Road, Erqi District, 450018, Zhengzhou, China
| | - Peng Li
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, No. 1, South University Road, Erqi District, 450018, Zhengzhou, China
| | - Chunlan Song
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, No. 1, South University Road, Erqi District, 450018, Zhengzhou, China.
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Li M, Cong B, Wei X, Wang Y, Kang L, Gong C, Huang Q, Wang X, Li Y, Huang F. Characterising the changes in RSV epidemiology in Beijing, China during 2015-2023: results from a prospective, multi-centre, hospital-based surveillance and serology study. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2024; 45:101050. [PMID: 38699290 PMCID: PMC11064721 DOI: 10.1016/j.lanwpc.2024.101050] [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: 12/22/2023] [Revised: 02/01/2024] [Accepted: 03/11/2024] [Indexed: 05/05/2024]
Abstract
Background Respiratory syncytial virus (RSV) has posed substantial morbidity and mortality burden to young children and older adults globally. The coronavirus disease 2019 (COVID-19) pandemic was reported to have altered RSV epidemiology and could have important implications for RSV prevention and control strategies. We aimed to compare RSV epidemiology in different phases of the COVID-19 pandemic with the pre-pandemic period by leveraging epidemiological, molecular, and serological data collected from a prospective respiratory pathogen surveillance and serology study. Methods This study was based on the data during July 1, 2015 to November 30, 2023 from the Respiratory Pathogen Surveillance System (RPSS), a sentinel-hospital based surveillance system of acute respiratory infections consisting of 35 hospitals that represent residents of all ages from all 16 districts in Beijing, China. RSV infection status was tested by RT-PCR and gene sequencing and phylogenetic analysis was conducted among the identified RSV strains. We further supplemented RPSS data with three serology surveys conducted during 2017-2023 that tested RSV IgG levels from serum specimens. RSV detection rate was calculated by calendar month and compared across RSV seasons (defined as the July 1 through June 30 of the following year). RSV IgG positivity proportion was calculated by quarter of the year and was correlated with quarterly aggregated RSV detection rate for understanding the relationship between infection and immunity at the population level. Findings Overall, a total of 52,931 respiratory specimens were collected and tested over the study period. RSV detection rates ranged from 1.24% (94/7594) in the 2017-2018 season to 2.80% (219/7824) in the 2018-2019 season, and from 1.06% (55/5165) in the 2022-2023 season to 2.98% (147/4938) in the 2021-2022 season during the pre-pandemic and pandemic period, respectively. ON1 and BA9 remained the predominant genotypes during the pandemic period; no novel RSV strains were identified. RSV circulation followed a winter-months seasonal pattern in most seasons. One exception was the 2020-2021 season when an extensive year-round circulation was observed, possibly associated with partial relaxation of non-pharmaceutical interventions (NPIs). The other exception was the 2022-2023 season when very low RSV activity was observed during the usual winter months (possibly due to the concurrent local COVID-19 epidemic), and followed by an out-of-season resurgence in the spring, with RSV detection persisting to the end of the study period (November 2023). During the two seasons above, we noted an age-group related asynchrony in the RSV detection rate; the RSV detection rate in young children remained similar (or even increased with borderline significance; 43/594, 7.24%, and 42/556, 7.55% vs 292/5293, 5.52%; P = 0.10 and P = 0.06, respectively) compared with the pre-pandemic seasons whereas the detection rate in older adults decreased significantly (8/1779, 0.45%, and 3/2021, 0.15% vs 160/10,348, 1.55%; P < 0.001 in two comparisons). Results from serology surveys showed significantly declined RSV IgG positivity in the 2022-2023 season compared to the pre-pandemic seasons (9.32%, 29/311 vs 20.16%, 100/496; P < 0.001); older adults had significantly higher RSV IgG positivity than young children in both pre-pandemic and pandemic periods (P values < 0.001). Interpretation Our study documented the trajectory of RSV detection along with the changes in the stringency of NPIs, measured IgG positivity, and local COVID-19 epidemics. The findings suggest the interplay between contact patterns, immunity dynamics, and SARS-CoV-2 infection in shaping the RSV epidemics of population of different ages. These findings provide novel insights into the potential drivers of RSV circulating patterns and have important implications for RSV prevention and control strategies. Funding The High-qualified Public Health Professionals Development Project, Capital's Funds for Health Improvement and Research, and the Public Health Personnel Training Support Program.
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Affiliation(s)
- Maozhong Li
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing, 100013, People's Republic of China
- Beijing Research Center for Respiratory Infectious Diseases, Beijing, 100013, People's Republic of China
| | - Bingbing Cong
- Department of Epidemiology, National Vaccine Innovation Platform, School of Public Health, Nanjing Medical University, Nanjing, 211166, People's Republic of China
| | - Xiaofeng Wei
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing, 100013, People's Republic of China
- School of Public Health, Capital Medical University, Beijing, 100069, People's Republic of China
| | - Yiting Wang
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing, 100013, People's Republic of China
- Beijing Research Center for Respiratory Infectious Diseases, Beijing, 100013, People's Republic of China
| | - Lu Kang
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing, 100013, People's Republic of China
- Beijing Research Center for Respiratory Infectious Diseases, Beijing, 100013, People's Republic of China
| | - Cheng Gong
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing, 100013, People's Republic of China
- Beijing Research Center for Respiratory Infectious Diseases, Beijing, 100013, People's Republic of China
| | - Qi Huang
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing, 100013, People's Republic of China
- School of Public Health, Capital Medical University, Beijing, 100069, People's Republic of China
| | - Xin Wang
- Department of Biostatistics, National Vaccine Innovation Platform, School of Public Health, Nanjing Medical University, Nanjing, 211166, People's Republic of China
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG, United Kingdom
| | - You Li
- Department of Epidemiology, National Vaccine Innovation Platform, School of Public Health, Nanjing Medical University, Nanjing, 211166, People's Republic of China
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG, United Kingdom
- Changzhou Third People's Hospital, Changzhou Medical Centre, Nanjing Medical University, Changzhou, 213000, People's Republic of China
| | - Fang Huang
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing, 100013, People's Republic of China
- Beijing Research Center for Respiratory Infectious Diseases, Beijing, 100013, People's Republic of China
- School of Public Health, Capital Medical University, Beijing, 100069, People's Republic of China
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Xie LY, Wang T, Yu T, Hu X, Yang L, Zhong LL, Zhang B, Zeng SZ. Seasonality of respiratory syncytial virus infection in children hospitalized with acute lower respiratory tract infections in Hunan, China, 2013-2022. Virol J 2024; 21:62. [PMID: 38454522 PMCID: PMC10921640 DOI: 10.1186/s12985-024-02336-8] [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: 01/07/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND In China, respiratory syncytial virus (RSV) infections traditionally occur during the spring and winter seasons. However, a shift in the seasonal trend was noted in 2020-2022, during the coronavirus disease 2019 (COVID-19) pandemic. METHODS This study investigated the seasonal characteristics of RSV infection in children hospitalized with acute lower respiratory tract infections (ALRTIs). The RSV epidemic season was defined as RSV positivity in > 10% of the hospitalized ALRTI cases each week. Nine RSV seasons were identified between 2013 and 2022, and nonlinear ordinary least squares regression models were used to assess the differences in year-to-year epidemic seasonality trends. RESULTS We enrolled 49,658 hospitalized children diagnosed with ALRTIs over a 9-year period, and the RSV antigen-positive rate was 15.2% (n = 7,566/49,658). Between 2013 and 2022, the average onset and end of the RSV season occurred in week 44 (late October) and week 17 of the following year, respectively, with a typical duration of 27 weeks. However, at the onset of the COVID-19 pandemic, the usual spring RSV peak did not occur. Instead, the 2020 epidemic started in week 32, and RSV seasonality persisted into 2021, lasting for an unprecedented 87 weeks before concluding in March 2022. CONCLUSIONS RSV seasonality was disrupted during the COVID-19 pandemic, and the season exhibited an unusually prolonged duration. These findings may provide valuable insights for clinical practice and public health considerations.
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Affiliation(s)
- Le-Yun Xie
- Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), 410005, Changsha, China
| | - Tao Wang
- Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), 410005, Changsha, China
| | - Tian Yu
- Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), 410005, Changsha, China.
| | - Xian Hu
- Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), 410005, Changsha, China
| | - Le Yang
- Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), 410005, Changsha, China
| | - Li-Li Zhong
- Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), 410005, Changsha, China
| | - Bing Zhang
- Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), 410005, Changsha, China
| | - Sai-Zhen Zeng
- Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), 410005, Changsha, China.
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Wang G, Yao W. An application of small-world network on predicting the behavior of infectious disease on campus. Infect Dis Model 2024; 9:177-184. [PMID: 38261962 PMCID: PMC10797140 DOI: 10.1016/j.idm.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/14/2023] [Accepted: 12/25/2023] [Indexed: 01/25/2024] Open
Abstract
Networks haven been widely used to understand the spread of infectious disease. This study examines the properties of small-world networks in modeling infectious disease on campus. Two different small-world models are developed and the behaviors of infectious disease in the models are observed through numerical simulations. The results show that the behavior pattern of infectious disease in a small-world network is different from those in a regular network or a random network. The spread of the infectious disease increases as the proportion of long-distance connections p increasing, which indicates that reducing the contact among people is an effective measure to control the spread of infectious disease. The probability of node position exchange in a network (p2) had no significant effect on the spreading speed, which suggests that reducing human mobility in closed environments does not help control infectious disease. However, the spreading speed is proportional to the number of shared nodes (s), which means reducing connections between different groups and dividing students into separate sections will help to control infectious disease. In the end, the simulating speed of the small-world network is tested and the quadratic relationship between simulation time and the number of nodes may limit the application of the SW network in areas with large populations.
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Affiliation(s)
- Guojin Wang
- School of Management, Fudan University, 220 Handan Road, Shanghai, 200433, China
| | - Wei Yao
- Shanghai Key Laboratory of Acupuncture Mechanism and Acupoint Function, Fudan University, 220 Handan Road, Shanghai, 200433, China
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Jain A, Mahesh S, Prakash O, Khan DN, Verma AK, Rastogi Y. Effect of COVID-19 pandemic on influenza; observation of a tertiary level virology laboratory. Virusdisease 2024; 35:27-33. [PMID: 38817401 PMCID: PMC11133273 DOI: 10.1007/s13337-024-00860-3] [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: 10/26/2023] [Accepted: 03/02/2024] [Indexed: 06/01/2024] Open
Abstract
The lockdown enforced amid the COVID-19 pandemic has affected the occurrence and trends of various respiratory virus infections, with a particular focus on influenza. Our study seeks to analyze the repercussions of the COVID-19 pandemic on the positivity of the influenza virus throughout a 4-year span, encompassing both the pre-COVID-19 era (2018 and 2019) and the COVID-19 period (2020 and 2021). Data collected from patients clinically diagnosed with Influenza-like Illness and Severe Acute Respiratory Illness (SARI) from January 2018 to December 2021 for influenza virus detection were acquired and analyzed through multiplex RT-qPCR. The statistical analysis was conducted using SPSS (Statistical Package for Social Sciences) Version 21.0 Software. A total of 4464 samples were tested over 4 years (2018-2021), with 3201 samples from the pre-COVID era and 1263 samples from the COVID era. Influenza A positivity dropped from 17.7 to 9.57% and Influenza B positivity decreased from 3.74 to 2.61%. Subtyping revealed changes in prevalence for both viruses. Seasonal variations showed more pronounced peaks in the pre-COVID-19 era with reduced activity during lockdown. Influenza A saw a resurgence in August 2021. Throughout the COVID-19 pandemic (2020-2021) SARI cases did not decrease. The positivity rate for Influenza A slightly rose to 7.79% from 4.23% in the COVID period (2020-2021). This increase correlates with heightened hospitalization rates during the pandemic, sparking concerns of potential coinfection with coronavirus and Influenza A. The notable drop in influenza cases in 2020-2021 is likely due to stringent precautions, lockdowns, drug repurposing, and prioritized testing, indicating no reduction in influenza transmission. Increased influenza positivity in SARI patients during COVID-19 highlights a heightened risk of coinfection. Emphasizing solely on COVID-19 may lead to underreporting of other respiratory pathogens, including influenza viruses.
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Affiliation(s)
- Amita Jain
- Department of Microbiology, King George’s Medical University, Lucknow, India
| | - Shreya Mahesh
- Department of Microbiology, King George’s Medical University, Lucknow, India
| | - Om Prakash
- Department of Microbiology, King George’s Medical University, Lucknow, India
| | - Danish N. Khan
- Department of Microbiology, King George’s Medical University, Lucknow, India
| | - Anil Kumar Verma
- Department of Microbiology, King George’s Medical University, Lucknow, India
| | - Yashasvi Rastogi
- Department of Microbiology, King George’s Medical University, Lucknow, India
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Yan H, Zhai B, Yang F, Wang P, Zhou Y. The Impact of Non-pharmacological Interventions Measures Against COVID-19 on Respiratory Virus in Preschool Children in Henan, China. J Epidemiol Glob Health 2024; 14:54-62. [PMID: 38048027 PMCID: PMC11043251 DOI: 10.1007/s44197-023-00168-3] [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: 05/15/2023] [Accepted: 11/09/2023] [Indexed: 12/05/2023] Open
Abstract
OBJECTIVES To investigate the long-term effects of non-pharmacological interventions (NPIs) measures on the epidemiological characteristics of common respiratory viruses in preschool children in Henan, China. METHODS This was a retrospective observational study containing data from 17 prefecture-level cities in Henan, China. We analyzed and compared laboratory results and clinical data of preschool children presenting to outpatient clinics for acute respiratory infections (ARTI) after COVID-19 (January 2020-October 2022) and before COVID-19 (December 2017-December 2019). Each year was divided into quarters. The ratio of the odds ratios (ORs) of testing positive for eight respiratory viruses in each year after the pandemic to the prepandemic period was estimated applying a generalized linear model (GLM), using the mean of the positive detection rates in 2018-2019 as a reference. RESULTS A total of 11,400 children were enrolled from December 2017 to October 2022. The number of positive detections for all respiratory viruses decreased in 2020-2022 compared to the average of 2018-2019. Human respiratory syncytial virus (hRSV), human rhinovirus (hRV), and influenza virus (IFV) accounted for a larger proportion of all detected viruses before COVID-19 pandemic, whereas hRV, human bocavirus (hBoV), and human adenovirus (hAdV) accounted for a significantly larger proportion after COVID-19 pandemic. The positive detection rates of enveloped viruses [IFV, human parainfluenza virus (hPIV), hRSV, human metapneumovirus (hMPV), and human coronavirus (hCoV)] decreased sharply and the seasonal activity of these viruses was weakened, while the positive detection rates of non-enveloped viruses (hRV, hBoV, and hAdV) increased, especially hRV. The conditions described above tended to occur more frequently in boys and children older than 1 year, and they were also more sensitive to the NPIs. CONCLUSIONS NPIs transformed the epidemiological profile of common respiratory viruses among preschool children during the COVID-19 pandemic. To improve the overall public health response to all respiratory viruses, interventions targeting non-enveloped viruses need to be strengthened to mitigate their continued transmission.
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Affiliation(s)
- Hui Yan
- Henan Provincial Clinical Research Center for Pediatric Diseases, Henan Key Laboratory of Pediatric Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Bo Zhai
- Henan Provincial Clinical Research Center for Pediatric Diseases, Henan Key Laboratory of Pediatric Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Fang Yang
- Henan Provincial Clinical Research Center for Pediatric Diseases, Henan Key Laboratory of Pediatric Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Penggao Wang
- Henan Provincial Clinical Research Center for Pediatric Diseases, Henan Key Laboratory of Pediatric Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Yang Zhou
- Henan Provincial Clinical Research Center for Pediatric Diseases, Henan Key Laboratory of Pediatric Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China.
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Rathored J, Soni R, Patel KK, Shende S, Samal D. Influenza A (H1N1) Virus Outbreak in the Districts of Chhattisgarh: A Cross-Sectional Study. Cureus 2024; 16:e55365. [PMID: 38562351 PMCID: PMC10982610 DOI: 10.7759/cureus.55365] [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] [Received: 01/30/2024] [Accepted: 03/01/2024] [Indexed: 04/04/2024] Open
Abstract
Background The H1N1 flu is a subtype of the influenza A virus, also known as the swine flu. An entirely new strain of the H1N1 virus started sickening people in the 2009-2010 flu season. It was a novel influenza virus combination that can infect humans, pigs, and birds. It was frequently referred to as the "swine flu." The virus may be able to spread for a little while longer in children and individuals with compromised immune systems. Objective The objective is to investigate the outbreaks of H1N1 among young adults in the Bastar District of Chhattisgarh. Methods Collection of the blood samples of 342 individuals between December 2015 and November 2017 was done. Thirty-one cases of Influenza A (H1N1) PDM09 virus infection were identified and confirmed. The molecular relationship between viruses is identified by the real-time polymerase chain reaction (RT-PCR) method. Result The majority of samples (n=13) were sourced from Raipur Medical College, followed by contributions from Durg District Hospital (n=5), Raigarh Medical College (n=4), Rajnandgaon District Hospital (n=3), Jagdalpur Medical College (n=2), Bilaspur Medical College (n=2), and smaller contributions from Dhamtari District Hospital and Gariyabandh Primary Health Care. Among these, 31 samples tested positive for Influenza A (H1N1) PDM 2009 virus, with a slightly higher prevalence among 19 female patients. Age-wise distribution revealed higher proportions of positive cases in the age groups of 0-10 years, 31-40 years, and 21-30 years. In the molecular analysis, 154 samples showed no target amplification, while 125 samples exhibited amplification of only Influenza A without subtype (H1) amplification. Remarkably, 31 patients who tested positive for Influenza A (H1N1) died from the virus; most of the deaths were in children under five and middle-aged adults. Conclusion The detection of Influenza A (H1N1) PDM 2009 virus, especially among females, indicates its persistent circulation. Positive cases were prevalent among younger and middle-aged individuals. Molecular analysis showed subtype variations, with significant fatalities observed in children under five and middle-aged adults, emphasizing the severity of the virus across different age groups. It is advised that in order to keep Indian influenza surveillance up to date and robust, more epidemiological data should be gathered, along with information on risk factors like immunization status, hospitalization, and mortality rates should be estimated, and influenza case subtyping should be improved.
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Affiliation(s)
- Jaishriram Rathored
- School of Allied Health Sciences, Central Research Laboratory and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Rani Soni
- Department of Microbiology, Late Baliram Kashyap Memorial Government Medical College, Jagdalpur, IND
| | - Krishna K Patel
- Department of Microbiology, Government TCL Postgraduate College, Janjgir, IND
| | - Sandesh Shende
- School of Allied Health Sciences, Central Research Laboratory and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Debashish Samal
- Department of Microbiology, Late Baliram Kashyap Memorial Government Medical College, Jagdalpur, IND
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Pan L, Yuan Y, Cui Q, Zhang X, Huo Y, Liu Q, Zou W, Zhao B, Hao L. Impact of the COVID-19 pandemic on the prevalence of respiratory viral pathogens in patients with acute respiratory infection in Shanghai, China. Front Public Health 2024; 12:1230139. [PMID: 38384888 PMCID: PMC10880446 DOI: 10.3389/fpubh.2024.1230139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024] Open
Abstract
Objective This study aimed to evaluate the impact of nonpharmaceutical interventions (NPIs) taken to combat COVID-19 on the prevalence of respiratory viruses (RVs) of acute respiratory infections (ARIs) in Shanghai. Methods Samples from ARI patients were collected and screened for 17 respiratory viral pathogens using TagMan low density microfluidic chip technology in Shanghai from January 2019 to December 2020. Pathogen data were analyzed to assess changes in acute respiratory infections between 2019 and 2020. Results A total of 2,744 patients were enrolled, including 1,710 and 1,034 in 2019 and 2020, respectively. The total detection rate of RVs decreased by 149.74% in 2020. However, detection rates for human respiratory syncytial virus B (RSVB), human coronavirus 229E (HCoV229E), human coronavirus NL63 (HCoVNL63), and human parainfluenza virus 3 (HPIV3) increased by 91.89, 58.33, 44.68 and 24.29%, in 2020. The increased positive rates of RSVB, HPIV3, resulted in more outpatients in 2020 than in 2019. IFV detection rates declined dramatically across gender, age groups, and seasons in 2020. Conclusion NPIs taken to eliminate COVID-19 had an impact on the prevalence of respiratory viral pathogens, especially the IFVs in the early phases of the pandemic. Partial respiratory viruses resurged with the lifting of NPIs, leading to an increase in ARIs infection.
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Affiliation(s)
- Lifeng Pan
- Shanghai Pudong New Area Center for Disease Control and Prevention, Shanghai, China
- Research Base of Key Laboratory of Surveillance and Early-warning on Infectious Disease in China CDC, Shanghai, China
| | - Yang Yuan
- Shanghai Pudong New Area Center for Disease Control and Prevention, Shanghai, China
| | - Qiqi Cui
- Shanghai Pudong New Area Center for Disease Control and Prevention, Shanghai, China
- Research Base of Key Laboratory of Surveillance and Early-warning on Infectious Disease in China CDC, Shanghai, China
| | - Xuechun Zhang
- Shanghai Pudong New Area Center for Disease Control and Prevention, Shanghai, China
| | - Yujia Huo
- Shanghai Pudong New Area Center for Disease Control and Prevention, Shanghai, China
| | - Qing Liu
- Shanghai Pudong New Area Center for Disease Control and Prevention, Shanghai, China
| | - Wenwei Zou
- Shanghai Pudong New Area Center for Disease Control and Prevention, Shanghai, China
| | - Bing Zhao
- Shanghai Pudong New Area Center for Disease Control and Prevention, Shanghai, China
- Research Base of Key Laboratory of Surveillance and Early-warning on Infectious Disease in China CDC, Shanghai, China
| | - Lipeng Hao
- Shanghai Pudong New Area Center for Disease Control and Prevention, Shanghai, China
- Research Base of Key Laboratory of Surveillance and Early-warning on Infectious Disease in China CDC, Shanghai, China
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Ruiz J, Aldewereld Z, Elgarten C. Chemotherapy Delays Due to SARS-CoV-2 Infection in Children With Leukemia or Lymphoma. JAMA Netw Open 2024; 7:e2355679. [PMID: 38363574 DOI: 10.1001/jamanetworkopen.2023.55679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/17/2024] Open
Affiliation(s)
- Jenny Ruiz
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Zachary Aldewereld
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Caitlin Elgarten
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
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Huang QS, Turner N, Wood T, Anglemyer A, McIntyre P, Aminisani N, Dowell T, Trenholme A, Byrnes C, Balm M, McIntosh C, Jefferies S, Grant CC, Nesdale A, Dobinson HC, Campbell‐Stokes P, Daniells K, Geoghegan J, de Ligt J, Jelley L, Seeds R, Jennings T, Rensburg M, Cueto J, Caballero E, John J, Penghulan E, Tan CE, Ren X, Berquist K, O'Neill M, Marull M, Yu C, McNeill A, Kiedrzynski T, Roberts S, McArthur C, Stanley A, Taylor S, Wong C, Lawrence S, Baker MG, Kvalsvig A, Van Der Werff K, McAuliffe G, Antoszewska H, Dilcher M, Fahey J, Werno A, Elvy J, Grant J, Addidle M, Zacchi N, Mansell C, Widdowson M, Thomas PG, Webby RJ. Impact of the COVID-19 related border restrictions on influenza and other common respiratory viral infections in New Zealand. Influenza Other Respir Viruses 2024; 18:e13247. [PMID: 38350715 PMCID: PMC10864123 DOI: 10.1111/irv.13247] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND New Zealand's (NZ) complete absence of community transmission of influenza and respiratory syncytial virus (RSV) after May 2020, likely due to COVID-19 elimination measures, provided a rare opportunity to assess the impact of border restrictions on common respiratory viral infections over the ensuing 2 years. METHODS We collected the data from multiple surveillance systems, including hospital-based severe acute respiratory infection surveillance, SHIVERS-II, -III and -IV community cohorts for acute respiratory infection (ARI) surveillance, HealthStat sentinel general practice (GP) based influenza-like illness surveillance and SHIVERS-V sentinel GP-based ARI surveillance, SHIVERS-V traveller ARI surveillance and laboratory-based surveillance. We described the data on influenza, RSV and other respiratory viral infections in NZ before, during and after various stages of the COVID related border restrictions. RESULTS We observed that border closure to most people, and mandatory government-managed isolation and quarantine on arrival for those allowed to enter, appeared to be effective in keeping influenza and RSV infections out of the NZ community. Border restrictions did not affect community transmission of other respiratory viruses such as rhinovirus and parainfluenza virus type-1. Partial border relaxations through quarantine-free travel with Australia and other countries were quickly followed by importation of RSV in 2021 and influenza in 2022. CONCLUSION Our findings inform future pandemic preparedness and strategies to model and manage the impact of influenza and other respiratory viral threats.
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Affiliation(s)
- Q. Sue Huang
- Institute of Environmental Science and ResearchWellingtonNew Zealand
| | | | - Tim Wood
- Institute of Environmental Science and ResearchWellingtonNew Zealand
| | - Andrew Anglemyer
- Institute of Environmental Science and ResearchWellingtonNew Zealand
- University of OtagoDunedinNew Zealand
| | | | | | | | - Adrian Trenholme
- Te Whatu Ora, Health New Zealand Counties ManukauAucklandNew Zealand
| | - Cass Byrnes
- Te Whatu Ora, Health New Zealand Te Toka Tumai AucklandAucklandNew Zealand
| | - Michelle Balm
- Te Whatu Ora, Health New Zealand Capital, Coast and Hutt ValleyWellingtonNew Zealand
| | | | - Sarah Jefferies
- Institute of Environmental Science and ResearchWellingtonNew Zealand
| | - Cameron C. Grant
- University of AucklandAucklandNew Zealand
- Te Whatu Ora, Health New Zealand Te Toka Tumai AucklandAucklandNew Zealand
| | - Annette Nesdale
- Regional Public HealthTe Whatu Ora, Health New Zealand Capital, Coast and Hutt ValleyWellingtonNew Zealand
| | - Hazel C. Dobinson
- Te Whatu Ora, Health New Zealand Capital, Coast and Hutt ValleyWellingtonNew Zealand
| | - Priscilla Campbell‐Stokes
- Regional Public HealthTe Whatu Ora, Health New Zealand Capital, Coast and Hutt ValleyWellingtonNew Zealand
| | - Karen Daniells
- Institute of Environmental Science and ResearchWellingtonNew Zealand
| | - Jemma Geoghegan
- Institute of Environmental Science and ResearchWellingtonNew Zealand
- University of OtagoDunedinNew Zealand
| | - Joep de Ligt
- Institute of Environmental Science and ResearchWellingtonNew Zealand
| | - Lauren Jelley
- Institute of Environmental Science and ResearchWellingtonNew Zealand
- University of OtagoDunedinNew Zealand
| | - Ruth Seeds
- Institute of Environmental Science and ResearchWellingtonNew Zealand
| | - Tineke Jennings
- Regional Public HealthTe Whatu Ora, Health New Zealand Capital, Coast and Hutt ValleyWellingtonNew Zealand
| | - Megan Rensburg
- Regional Public HealthTe Whatu Ora, Health New Zealand Capital, Coast and Hutt ValleyWellingtonNew Zealand
| | - Jort Cueto
- Regional Public HealthTe Whatu Ora, Health New Zealand Capital, Coast and Hutt ValleyWellingtonNew Zealand
| | - Ernest Caballero
- Regional Public HealthTe Whatu Ora, Health New Zealand Capital, Coast and Hutt ValleyWellingtonNew Zealand
| | - Joshma John
- Regional Public HealthTe Whatu Ora, Health New Zealand Capital, Coast and Hutt ValleyWellingtonNew Zealand
| | - Emmanuel Penghulan
- Regional Public HealthTe Whatu Ora, Health New Zealand Capital, Coast and Hutt ValleyWellingtonNew Zealand
| | - Chor Ee Tan
- Institute of Environmental Science and ResearchWellingtonNew Zealand
| | - Xiaoyun Ren
- Institute of Environmental Science and ResearchWellingtonNew Zealand
| | - Klarysse Berquist
- Institute of Environmental Science and ResearchWellingtonNew Zealand
| | - Meaghan O'Neill
- Institute of Environmental Science and ResearchWellingtonNew Zealand
| | - Maritza Marull
- Institute of Environmental Science and ResearchWellingtonNew Zealand
| | - Chang Yu
- Institute of Environmental Science and ResearchWellingtonNew Zealand
| | - Andrea McNeill
- Institute of Environmental Science and ResearchWellingtonNew Zealand
| | - Tomasz Kiedrzynski
- Te Pou Hauora Tūmatanui, the Public Health AgencyManatū Hauora, Ministry of HealthWellingtonNew Zealand
| | - Sally Roberts
- Te Whatu Ora, Health New Zealand Te Toka Tumai AucklandAucklandNew Zealand
| | - Colin McArthur
- Te Whatu Ora, Health New Zealand Te Toka Tumai AucklandAucklandNew Zealand
| | - Alicia Stanley
- Te Whatu Ora, Health New Zealand Te Toka Tumai AucklandAucklandNew Zealand
| | - Susan Taylor
- Te Whatu Ora, Health New Zealand Counties ManukauAucklandNew Zealand
| | - Conroy Wong
- Te Whatu Ora, Health New Zealand Counties ManukauAucklandNew Zealand
| | - Shirley Lawrence
- Te Whatu Ora, Health New Zealand Counties ManukauAucklandNew Zealand
| | | | | | - Koen Van Der Werff
- Te Whatu Ora, Health New Zealand Capital, Coast and Hutt ValleyWellingtonNew Zealand
| | - Gary McAuliffe
- Te Whatu Ora, Health New Zealand Te Toka Tumai AucklandAucklandNew Zealand
| | - Hanna Antoszewska
- Te Whatu Ora, Health New Zealand Te Toka Tumai AucklandAucklandNew Zealand
| | - Meik Dilcher
- Te Whatu Ora, Health New Zealand Waitaha CanterburyChristchurchNew Zealand
| | - Jennifer Fahey
- Te Whatu Ora, Health New Zealand Waitaha CanterburyChristchurchNew Zealand
| | - Anja Werno
- Te Whatu Ora, Health New Zealand Waitaha CanterburyChristchurchNew Zealand
| | - Juliet Elvy
- Southern Community LaboratoriesDunedinNew Zealand
| | - Jenny Grant
- Southern Community LaboratoriesDunedinNew Zealand
| | - Michael Addidle
- Te Whatu Ora, Health New Zealand Hauora a Toi Bay of PlentyTaurangaNew Zealand
| | - Nicolas Zacchi
- Te Whatu Ora, Health New Zealand Hauora a Toi Bay of PlentyTaurangaNew Zealand
| | - Chris Mansell
- Te Whatu Ora, Health New Zealand WaikatoHamiltonNew Zealand
| | | | - Paul G. Thomas
- WHO Collaborating CentreSt Jude Children's Research HospitalMemphisTennesseeUSA
| | - BorderRestrictionImpactOnFluRSV Consortium
- Institute of Environmental Science and ResearchWellingtonNew Zealand
- Te Whatu Ora, Health New Zealand Counties ManukauAucklandNew Zealand
- Te Whatu Ora, Health New Zealand Te Toka Tumai AucklandAucklandNew Zealand
- Regional Public HealthTe Whatu Ora, Health New Zealand Capital, Coast and Hutt ValleyWellingtonNew Zealand
- Te Whatu Ora, Health New Zealand Waitaha CanterburyChristchurchNew Zealand
| | - Richard J. Webby
- WHO Collaborating CentreSt Jude Children's Research HospitalMemphisTennesseeUSA
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Aizawa Y, Ikuse T, Izumita R, Habuka R, Yamanaka T, Saitoh A. Human Rhinovirus as a Cause of Fever in Neonates and Young Infants During the COVID-19 Pandemic, 2020-2022. Pediatr Infect Dis J 2024; 43:130-135. [PMID: 37851974 DOI: 10.1097/inf.0000000000004139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
BACKGROUND Human rhinovirus (HRV) was predominant and persistent during the coronavirus disease 2019 (COVID-19) pandemic despite nonpharmaceutical interventions. The data whether HRV persistence also occurred in neonates and young infants were very limited. METHODS This prospective observational study was conducted in Niigata, Japan, between January 2020 and September 2022. The participants were hospitalized neonates and infants less than 4 months of age with fever. We excluded patients with evidence of bacterial infection or obvious sick contact with influenza or respiratory syncytial virus infection, as confirmed by rapid antigen detection tests. COVID-19 diagnosed by polymerase chain reaction (PCR) or rapid antigen detection tests were also excluded. Parechovirus and enterovirus were examined by PCR using serum and/or cerebrospinal fluid. FilmArray Respiratory Panel v1.7 was conducted on nasopharyngeal swabs. If HRV was positive, the genotype was identified. RESULTS We included 72 patients (median age, 54 days; interquartile range, 28.5-79 days), and sepsis was diagnosed in 31 (43.1%) patients. In total, 27 (37.5%) patients had had positive multiplex PCR tests. These patients were more likely to have rhinorrhea ( P = 0.004), cough ( P = 0.01), and sick contact ( P < 0.001) than those who with negative multiplex PCR. HRV was the most frequently detected virus (n = 23, 85.2%), and species A (n = 15, 71.4%) and C (n = 6, 28.6%) were genotyped. No seasonality or monthly predominance of the specific HRV types was observed. CONCLUSIONS HRV was an important cause of fever in neonates and young infants during the COVID-19 pandemic, 2020 to 2022.
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Affiliation(s)
- Yuta Aizawa
- From the Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Tatsuki Ikuse
- From the Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ryohei Izumita
- From the Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- Department of Pediatrics, Niigata City General Hospital, Niigata, Japan
| | - Rie Habuka
- From the Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- Department of Pediatrics, Niigata City General Hospital, Niigata, Japan
| | - Takayuki Yamanaka
- Department of Pediatrics, Niigata City General Hospital, Niigata, Japan
| | - Akihiko Saitoh
- From the Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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40
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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.
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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
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41
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Wang Y, Liu Y, Wang Y, Mai H, Chen Y, Zhang Y, Ji Y, Cong X, Gao Y. Clinical characteristics of outpatients with influenza-B-associated pneumonia and molecular evolution of influenza B virus in Beijing, China, during the 2021-2022 influenza season. Arch Virol 2024; 169:30. [PMID: 38233704 PMCID: PMC10794387 DOI: 10.1007/s00705-023-05957-6] [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: 07/03/2023] [Accepted: 11/28/2023] [Indexed: 01/19/2024]
Abstract
We analyzed the clinical characteristics of outpatients with influenza-B-associated pneumonia during the 2021-2022 influenza season and analyzed the molecular epidemiology and evolution of influenza B virus. The presence of influenza B virus was confirmed by reverse transcription polymerase chain reaction (RT-PCR). Electronic medical records were used to collect and analyze data of outpatients. The HA and NA genes were phylogenetically analyzed using ClustalW 2.10 and MEGA 11.0. Out of 1569 outpatients who tested positive for influenza B virus, 11.7% (184/1569) developed pneumonia, and of these, 19.0% (35/184) had underlying diseases. Fever, cough, and sore throat were the most common symptoms. Among the complications, acute respiratory distress syndrome (ARDS), acute kidney injury (AKI), and shock accounted for 2.7% (5/184), 4.9% (9/184), and 1.6% (3/184), respectively. Of the outpatients, 2.7% (5/184) were admitted to the hospital, and 0.5% (1/184) of them died. All of the strains from Beijing were identified as belonging to the B/Victoria lineage. The HA and NA gene sequences of 41 influenza B viruses showed high similarity to each other, and all of them belonged to clade 1A.3. Compared with the vaccine strain B/Washington/02/2019, all of the isolates contained N150K, G181E, and S194D mutations. S194D, E195K, and K200R mutations were detected in the 190 helix of the receptor binding region of HA. Co-mutations of H122Q, A127T, P144L, N150K, G181E, S194D, and K200R in HA and D53N, N59S, and G233E in NA were detected in 78.0% (32/41) of the isolates, and 56.3% (18/32) of these were from outpatients with influenza-B-associated pneumonia. Influenza outpatients with underlying diseases were more likely to develop pneumonia. No significant differences were observed in clinical symptoms or laboratory results between outpatients with and without pneumonia, so testing for influenza virus seems to be a good choice. The observed amino acid variations suggest that current vaccines might not provide effective protection.
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Affiliation(s)
- Yanxin Wang
- Department of Infectious Diseases, Peking University People's Hospital, Beijing, China
| | - Yafen Liu
- Department of Infectious Diseases, Peking University People's Hospital, Beijing, China
| | - Yue Wang
- Department of Infectious Diseases, Peking University People's Hospital, Beijing, China
| | - Huan Mai
- Department of Infectious Diseases, Peking University People's Hospital, Beijing, China
| | - Yuanyuan Chen
- Department of Infectious Diseases, Peking University People's Hospital, Beijing, China
| | - Yifan Zhang
- Department of Infectious Diseases, Peking University People's Hospital, Beijing, China
| | - Ying Ji
- Peking University Hepatology Institute, Peking University People's Hospital, Beijing, China
| | - Xu Cong
- Peking University Hepatology Institute, Peking University People's Hospital, Beijing, China
| | - Yan Gao
- Department of Infectious Diseases, Peking University People's Hospital, Beijing, China.
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42
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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.
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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.
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Treggiari D, Pomari C, Zavarise G, Piubelli C, Formenti F, Perandin F. Characteristics of Respiratory Syncytial Virus Infections in Children in the Post-COVID Seasons: A Northern Italy Hospital Experience. Viruses 2024; 16:126. [PMID: 38257826 PMCID: PMC10820224 DOI: 10.3390/v16010126] [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: 11/21/2023] [Revised: 01/11/2024] [Accepted: 01/14/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Public health measures for COVID-19 mitigation influenced the circulation of Respiratory Syncytial Virus (RSV) during the 2020-2021 winter season. In the following autumn, an unprecedented resurgence of RSV occurred. Our study monitored RSV pediatric infections one and two years after the relaxation of containment measures for the COVID-19 pandemic. METHODS We analyzed diagnostic molecular data for SARS-CoV-2, flu, and RSV infections and clinical data from children with respiratory symptoms referring to our hospital during the 2021-2022 and 2022-2023 seasons. RESULTS In the 2021-2022 season, the number of RSV-affected children was very high, especially for babies <1 year. The outbreak appeared in a shorter interval of time, with a high clinical severity. In the 2022-23 season, a reduced number of infected pediatric patients were detected, with a similar hospitalization rate (46% vs. 40%), and RSV accounted for 12% of the infections. Coinfections were observed in age <2 years. In RSV patients, symptoms were similar across the two seasons. CONCLUSIONS The clinical presentation of RSV in the two post-COVID seasons suggests that the pathophysiology of the virus did not change across these two years. Further studies are needed to continuously monitor RSV to support an effective prevention strategy.
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Affiliation(s)
- Davide Treggiari
- Department of Tropical, Infectious Diseases and Microbiology, IRCCS Sacro Cuore-Don Calabria Hospital, 37024 Negrar di Valpolicella, Verona, Italy; (F.F.); (F.P.)
| | - Chiara Pomari
- Andrus Center, University of Southern California, Los Angeles, CA 90089, USA;
| | - Giorgio Zavarise
- Department of Pediatrics, IRCCS Sacro Cuore-Don Calabria Hospital, 37024 Negrar di Valpolicella, Verona, Italy;
| | - Chiara Piubelli
- Department of Tropical, Infectious Diseases and Microbiology, IRCCS Sacro Cuore-Don Calabria Hospital, 37024 Negrar di Valpolicella, Verona, Italy; (F.F.); (F.P.)
| | - Fabio Formenti
- Department of Tropical, Infectious Diseases and Microbiology, IRCCS Sacro Cuore-Don Calabria Hospital, 37024 Negrar di Valpolicella, Verona, Italy; (F.F.); (F.P.)
| | - Francesca Perandin
- Department of Tropical, Infectious Diseases and Microbiology, IRCCS Sacro Cuore-Don Calabria Hospital, 37024 Negrar di Valpolicella, Verona, Italy; (F.F.); (F.P.)
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44
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Pedroza-Uribe IM, Vega Magaña N, Muñoz-Valle JF, Peña-Rodriguez M, Carranza-Aranda AS, Sánchez-Sánchez R, Venancio-Landeros AA, García-González OP, Zavala-Mejía JJ, Ramos-Solano M, Viera-Segura O, García-Chagollán M. Beyond SARS-CoV-2: epidemiological surveillance of respiratory viruses in Jalisco, Mexico. Front Public Health 2024; 11:1292614. [PMID: 38274524 PMCID: PMC10808461 DOI: 10.3389/fpubh.2023.1292614] [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: 09/11/2023] [Accepted: 12/28/2023] [Indexed: 01/27/2024] Open
Abstract
Introduction Respiratory viral infections represent a significant global health burden. Historically, influenza, rhinovirus, respiratory syncytial virus, and adenovirus have been the prevalent viruses; however, the landscape shifted with the widespread emergence of SARS-CoV-2. The aim of this study is to present a comprehensive epidemiological analysis of viral respiratory infections in Jalisco, Mexico. Methods Data encompassing individuals with flu-like symptoms from July 2021 to February 2023 was scrutinized for viral diagnosis through PCR multiplex. The effect of social mobility on the increase in respiratory viral diagnosis infection was considered to estimate its impact. Additionally, sequences of respiratory viruses stored in public databases were retrieved to ascertain the phylogenetic classification of previously reported viruses in Mexico. Results SARS-CoV-2 was the most detected virus (n = 5,703; 92.2%), followed by influenza (n = 479; 7.78%). These viruses were also found as the most common co-infection (n = 11; 50%), and for those with influenza, a higher incidence of severe disease was reported (n = 122; 90.4%; p < 0.001). Regarding comorbidities and unhealthy habits, smoking was found to be a risk factor for influenza infection but a protective factor for SARS-CoV-2 (OR = 2.62; IC 95%: 1.66-4.13; OR = 0.65; IC 95%: 0.45-0.94), respectively. Furthermore, our findings revealed a direct correlation between mobility and the prevalence of influenza infection (0.214; p < 0.001). Discussion The study presents evidence of respiratory virus reemergence and prevalence during the social reactivation, facilitating future preventive measures.
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Affiliation(s)
- Isaac Murisi Pedroza-Uribe
- Doctorado en Microbiología Médica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Natali Vega Magaña
- Laboratorio de Diagnóstico de Enfermedades Emergentes y Reemergentes (LaDEER), Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - José Francisco Muñoz-Valle
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Marcela Peña-Rodriguez
- Laboratorio de Diagnóstico de Enfermedades Emergentes y Reemergentes (LaDEER), Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Ahtziri Socorro Carranza-Aranda
- Doctorado en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | | | | | | | - Jacob Jecsan Zavala-Mejía
- Licenciatura en Médico Cirujano y Partero, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Moisés Ramos-Solano
- Instituto de Investigación en Cáncer en la Infancia y Adolescencia (INICIA), Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Oliver Viera-Segura
- Laboratorio de Diagnóstico de Enfermedades Emergentes y Reemergentes (LaDEER), Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Mariel García-Chagollán
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
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Chen Z, Liu Y, Yue H, Chen J, Hu X, Zhou L, Liang B, Lin G, Qin P, Feng W, Wang D, Wu D. The role of meteorological factors on influenza incidence among children in Guangzhou China, 2019-2022. Front Public Health 2024; 11:1268073. [PMID: 38259781 PMCID: PMC10800649 DOI: 10.3389/fpubh.2023.1268073] [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: 07/27/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
Objective Analyzing the epidemiological characteristics of influenza cases among children aged 0-17 years in Guangzhou from 2019 to 2022. Assessing the relationships between multiple meteorological factors and influenza, improving the early warning systems for influenza, and providing a scientific basis for influenza prevention and control measures. Methods The influenza data were obtained from the Chinese Center for Disease Control and Prevention. Meteorological data were provided by Guangdong Meteorological Service. Spearman correlation analysis was conducted to examine the relevance between meteorological factors and the number of influenza cases. Distributed lag non-linear models (DLNM) were used to explore the effects of meteorological factors on influenza incidence. Results The relationship between mean temperature, rainfall, sunshine hours, and influenza cases presented a wavy pattern. The correlation between relative humidity and influenza cases was illustrated by a U-shaped curve. When the temperature dropped below 13°C, Relative risk (RR) increased sharply with decreasing temperature, peaking at 5.7°C with an RR of 83.78 (95% CI: 25.52, 275.09). The RR was increased when the relative humidity was below 66% or above 79%, and the highest RR was 7.50 (95% CI: 22.92, 19.25) at 99%. The RR was increased exponentially when the rainfall exceeded 1,625 mm, reaching a maximum value of 2566.29 (95% CI: 21.85, 3558574.07) at the highest rainfall levels. Both low and high sunshine hours were associated with reduced incidence of influenza, and the lowest RR was 0.20 (95% CI: 20.08, 0.49) at 9.4 h. No significant difference of the meteorological factors on influenza was observed between males and females. The impacts of cumulative extreme low temperature and low relative humidity on influenza among children aged 0-3 presented protective effects and the 0-3 years group had the lowest RRs of cumulative extreme high relative humidity and rainfall. The highest RRs of cumulative extreme effect of all meteorological factors (expect sunshine hours) were observed in the 7-12 years group. Conclusion Temperature, relative humidity, rainfall, and sunshine hours can be used as important predictors of influenza in children to improve the early warning system of influenza. Extreme weather reduces the risk of influenza in the age group of 0-3 years, but significantly increases the risk for those aged 7-12 years.
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Affiliation(s)
- Zhitao Chen
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, China
| | - Yanhui Liu
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
- School of Public Health, Institute of Public Health, Guangzhou Medical University and Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Haiyan Yue
- Guangzhou Meteorological Observatory, Guangzhou, 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, Guangdong, China
| | - Xiangzhi Hu
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, China
| | - Lijuan Zhou
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
- School of Public Health, Institute of Public Health, Guangzhou Medical University and Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Boheng Liang
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
- School of Public Health, Institute of Public Health, Guangzhou Medical University and Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Guozhen Lin
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
- School of Public Health, Institute of Public Health, Guangzhou Medical University and Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Pengzhe Qin
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
- School of Public Health, Institute of Public Health, Guangzhou Medical University and Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Wenru Feng
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
- School of Public Health, Institute of Public Health, Guangzhou Medical University and Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Dedong Wang
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
- School of Public Health, Institute of Public Health, Guangzhou Medical University and Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Di Wu
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
- School of Public Health, Institute of Public Health, Guangzhou Medical University and Guangzhou Center for Disease Control and Prevention, Guangzhou, China
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Green MA, McKee M, Massey J, Mackenna B, Mehrkar A, Bacon S, Macleod J, Sheikh A, Shah SA, Katikireddi SV. Trends in inequalities in avoidable hospitalisations across the COVID-19 pandemic: a cohort study of 23.5 million people in England. BMJ Open 2024; 14:e077948. [PMID: 38191251 PMCID: PMC10806625 DOI: 10.1136/bmjopen-2023-077948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/04/2023] [Indexed: 01/10/2024] Open
Abstract
OBJECTIVE To determine whether periods of disruption were associated with increased 'avoidable' hospital admissions and wider social inequalities in England. DESIGN Observational repeated cross-sectional study. SETTING England (January 2019 to March 2022). PARTICIPANTS With the approval of NHS England we used individual-level electronic health records from OpenSAFELY, which covered ~40% of general practices in England (mean monthly population size 23.5 million people). PRIMARY AND SECONDARY OUTCOME MEASURES We estimated crude and directly age-standardised rates for potentially preventable unplanned hospital admissions: ambulatory care sensitive conditions and urgent emergency sensitive conditions. We considered how trends in these outcomes varied by three measures of social and spatial inequality: neighbourhood socioeconomic deprivation, ethnicity and geographical region. RESULTS There were large declines in avoidable hospitalisations during the first national lockdown (March to May 2020). Trends increased post-lockdown but never reached 2019 levels. The exception to these trends was for vaccine-preventable ambulatory care sensitive admissions which remained low throughout 2020-2021. While trends were consistent by each measure of inequality, absolute levels of inequalities narrowed across levels of neighbourhood socioeconomic deprivation, Asian ethnicity (compared with white ethnicity) and geographical region (especially in northern regions). CONCLUSIONS We found no evidence that periods of healthcare disruption from the COVID-19 pandemic resulted in more avoidable hospitalisations. Falling avoidable hospital admissions has coincided with declining inequalities most strongly by level of deprivation, but also for Asian ethnic groups and northern regions of England.
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Affiliation(s)
- Mark Alan Green
- Geography & Planning, University of Liverpool, Liverpool, UK
| | | | - Jon Massey
- Nuffield Department of Primary Care Health Sciences, Oxford University, Oxford, UK
| | - Brian Mackenna
- Medicines and Diagnostics Policy Unit, NHS England, London, UK
| | - Amir Mehrkar
- Nuffield Department of Primary Care Health Sciences, Oxford University, Oxford, UK
| | - Seb Bacon
- Nuffield Department of Primary Care Health Sciences, Oxford University, Oxford, UK
| | | | - Aziz Sheikh
- Division of Community Health Sciences, University of Edinburgh, Edinburgh, UK
| | - Syed Ahmar Shah
- The University of Edinburgh Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
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Lacey JA, Bennett J, James TB, Hines BS, Chen T, Lee D, Sika-Paotonu D, Anderson A, Harwood M, Tong SY, Baker MG, Williamson DA, Moreland NJ. A worldwide population of Streptococcus pyogenes strains circulating among school-aged children in Auckland, New Zealand: a genomic epidemiology analysis. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2024; 42:100964. [PMID: 38035130 PMCID: PMC10684382 DOI: 10.1016/j.lanwpc.2023.100964] [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: 07/23/2023] [Revised: 09/20/2023] [Accepted: 10/29/2023] [Indexed: 12/02/2023]
Abstract
Background Acute rheumatic fever (ARF) is a serious post-infectious sequala of Group A Streptococcus (GAS, Streptococcus pyogenes). In New Zealand (NZ) ARF is a major cause of health inequity. This study describes the genomic analysis of GAS isolates associated with childhood skin and throat infections in Auckland NZ. Methods Isolates (n = 469) collected between March 2018 and October 2019 from the throats and skin of children (5-14 years) underwent whole genomic sequencing. Equal representation across three ethnic groups was ensured through sample quotas with isolates obtained from Indigenous Māori (n = 157, 33%), NZ European/Other (n = 149, 32%) and Pacific Peoples children (n = 163, 35%). Using in silico techniques isolates were classified, assessed for diversity, and examined for distribution differences between groups. Comparisons were also made with GAS strains identified globally. Findings Genomic analysis revealed a diverse population consisting of 65 distinct sequence clusters. These sequence clusters spanned 49 emm-types, with 11 emm-types comprised of several, distinct sequence clusters. There is evidence of multiple global introductions of different lineages into the population, as well as local clonal expansion. The M1UK lineage comprised 35% of all emm1 isolates. Interpretation The GAS population was characterized by a high diversity of strains, resembling patterns observed in low- and middle-income countries. However, strains associated with outbreaks and antimicrobial resistance commonly found in high-income countries were also observed. This unique combination poses challenges for vaccine development, disease management and control. Funding The work was supported by the Health Research Council of New Zealand (HRC), award number 16/005.
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Affiliation(s)
- Jake A. Lacey
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Julie Bennett
- The Department of Public Health, University of Otago, Wellington, New Zealand
- The Maurice Wilkins Centre for Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Taylah B. James
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin S. Hines
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Victoria, Australia
| | - Tiffany Chen
- Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland, Auckland, New Zealand
| | - Darren Lee
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Anneka Anderson
- Te Kupenga Hauora Māori, The University of Auckland, New Zealand
| | - Matire Harwood
- Department of General Practice and Primary Healthcare, The University of Auckland, Auckland, New Zealand
| | - Steven Y.C. Tong
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Infectious Diseases at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Michael G. Baker
- The Department of Public Health, University of Otago, Wellington, New Zealand
- The Maurice Wilkins Centre for Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Deborah A. Williamson
- Department of Infectious Diseases at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Nicole J. Moreland
- The Maurice Wilkins Centre for Biodiscovery, The University of Auckland, Auckland, New Zealand
- Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland, Auckland, New Zealand
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48
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Farquharson KA, Anthony D, Menzies R, Homaira N. Burden of respiratory syncytial virus disease across the lifespan in Australia and New Zealand: a scoping review. Public Health 2024; 226:8-16. [PMID: 37980838 DOI: 10.1016/j.puhe.2023.10.031] [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: 06/25/2023] [Revised: 10/04/2023] [Accepted: 10/13/2023] [Indexed: 11/21/2023]
Abstract
OBJECTIVES Respiratory syncytial virus (RSV) is the leading cause of acute lower respiratory tract infection in young children worldwide. RSV is increasingly associated with severe respiratory disease in people aged >65 years. The heterogeneous landscape of RSV in Australia and New Zealand makes generalisation of results from global studies to local contexts difficult. Given the changing landscape of RSV, we aimed to examine the existing literature on the burden of RSV disease and identify evidence gaps in Australia and New Zealand. STUDY DESIGN Scoping review. METHODS We designed a scoping review protocol and searched the Web of Science and Scopus databases for eligible peer-reviewed publications. Data from eligible studies were charted and summarised in tabular and narrative form. RESULTS Of the 153 eligible publications identified, 123 investigated RSV disease in a hospital setting and six in primary care. Only six studies reported the economic burden of disease, all of which estimated direct healthcare costs associated with treatment and/or hospitalisation; no studies quantified the indirect costs or costs to families. CONCLUSIONS In this scoping review, we describe the effect of RSV disease in several high-risk populations, including children and adults. An improved understanding of the RSV burden of disease, both in primary care settings and economically, within the local context will assist with the implementation of preventative strategies, including vaccination programmes. Future studies to determine the true burden of RSV-associated morbidity, mortality and economic burden across the entire patient journey and among different healthcare settings will help prioritise emerging RSV therapeutics.
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Affiliation(s)
- K A Farquharson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia; Edge Medical Communications, Port Macquarie, NSW, Australia
| | - D Anthony
- Sanofi Vaccines ANZ, Melbourne, VIC, Australia
| | - R Menzies
- Sanofi Vaccines ANZ, Macquarie Park, Sydney, NSW, Australia
| | - N Homaira
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia; Respiratory Department, Sydney Children's Hospital, Randwick, Sydney, NSW, Australia; James P. Grant School of Public Health, BRAC University, Bangladesh.
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49
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Telfar-Barnard L, Baker MG, Wilson N, Howden-Chapman P. The rise and fall of excess winter mortality in New Zealand from 1876 to 2020. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2024; 68:89-100. [PMID: 38010416 PMCID: PMC10752914 DOI: 10.1007/s00484-023-02573-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/25/2023] [Accepted: 10/25/2023] [Indexed: 11/29/2023]
Abstract
Excess winter mortality (EWM) has been used as a measure of how well populations and policy moderate the health effects of cold weather. We aimed to investigate long-term changes in the EWM of Aotearoa New Zealand (NZ), and potential drivers of change, and to test for structural breaks in trends. We calculated NZ EWM indices from 1876 (4,698 deaths) to 2020 (33,310 deaths), total and by age-group and sex, comparing deaths from June to September (the coldest months) to deaths from February to May and October to January. The mean age and sex-standardised EWM Index (EWMI) for the full study period, excluding 1918, was 1.22. However, mean EWMI increased from 1.20 for 1886 to 1917, to 1.34 for the 1920s, then reduced over time to 1.14 in the 2010s, with excess winter deaths averaging 4.5% of annual deaths (1,450 deaths per year) in the 2010s, compared to 7.9% in the 1920s. Children under 5 years transitioned from a summer to winter excess between 1886 and 1911. Otherwise, the EWMI age-distribution was J-shaped in all time periods. Structural break testing showed the 1918 influenza pandemic strain had a significant impact on trends in winter and non-winter mortality and winter excess for subsequent decades. It was not possible to attribute the post-1918 reduction in EWM to any single factor among improved living standards, reduced severe respiratory infections, or climate change.
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Affiliation(s)
| | - Michael G Baker
- Department of Public Health, University of Otago, Wellington, New Zealand
| | - Nick Wilson
- Department of Public Health, University of Otago, Wellington, New Zealand
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50
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Rerkasem A, Thaichana P, Bunsermvicha N, Nopparatkailas R, Arwon S, Orrapin S, Reanpang T, Apichartpiyakul P, Orrapin S, Siribumrungwong B, Lumjuan N, Rerkasem K, Derraik JGB. A COVID-19 Silver Lining-Decline in Antibiotic Resistance in Ischemic Leg Ulcers during the Pandemic: A 6-Year Retrospective Study from a Regional Tertiary Hospital (2017-2022). Antibiotics (Basel) 2023; 13:35. [PMID: 38247594 PMCID: PMC10812686 DOI: 10.3390/antibiotics13010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 12/13/2023] [Accepted: 12/21/2023] [Indexed: 01/23/2024] Open
Abstract
Antibiotic resistance (AR) associated with chronic limb-threatening ischemia (CLTI) poses additional challenges for the management of ischemic leg ulcers, increasing the likelihood of severe outcomes. This study assessed AR prevalence in bacteria isolated from CLTI-associated leg ulcers before (1 January 2017-10 March 2020; n = 69) and during (11 March 2020-31 December 2022; n = 59) the COVID-19 pandemic from patients admitted with positive wound cultures to a regional hospital in Chiang Mai (Thailand). There was a marked reduction in AR rates from 78% pre-pandemic to 42% during the pandemic (p < 0.0001), with rates of polymicrobial infections 22 percentage points lower (from 61% to 39%, respectively; p = 0.014). There were reduced AR rates to amoxicillin/clavulanate (from 42% to 4%; p < 0.0001) and ampicillin (from 16% to 2%; p = 0.017), as well as multidrug resistance (19% to 8%; p = 0.026). Factors associated with increased AR odds were polymicrobial infections (adjusted odds ratio (aOR) 5.6 (95% CI 2.1, 15.0); p = 0.001), gram-negative bacteria (aOR 7.0 (95% CI 2.4, 20.5); p < 0.001), and prior use of antibiotics (aOR 11.9 (95% CI 1.1, 128.2); p = 0.041). Improvements in infection control measures and hygiene practices in the community during the pandemic were likely key factors contributing to lower AR rates. Thus, strategic public health interventions, including community education on hygiene and the informed use of antibiotics, may be crucial in mitigating the challenges posed by AR in CLTI. Further, advocating for more judicious use of empirical antibiotics in clinical settings can balance effective treatment against AR development, thereby improving patient outcomes.
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Affiliation(s)
- Amaraporn Rerkasem
- Environmental-Occupational Health Sciences and Non-Communicable Diseases Research Center, Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (A.R.); (P.T.)
- Research Center for Infectious Disease and Substance Use, Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Pak Thaichana
- Environmental-Occupational Health Sciences and Non-Communicable Diseases Research Center, Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (A.R.); (P.T.)
| | - Nuttida Bunsermvicha
- Clinical Surgical Research Center, Department of Surgery, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (N.B.); (S.A.); (S.O.); (T.R.); (P.A.)
| | - Rawee Nopparatkailas
- Department of Family Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Supapong Arwon
- Clinical Surgical Research Center, Department of Surgery, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (N.B.); (S.A.); (S.O.); (T.R.); (P.A.)
| | - Saranat Orrapin
- Clinical Surgical Research Center, Department of Surgery, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (N.B.); (S.A.); (S.O.); (T.R.); (P.A.)
| | - Termpong Reanpang
- Clinical Surgical Research Center, Department of Surgery, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (N.B.); (S.A.); (S.O.); (T.R.); (P.A.)
| | - Poon Apichartpiyakul
- Clinical Surgical Research Center, Department of Surgery, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (N.B.); (S.A.); (S.O.); (T.R.); (P.A.)
| | - Saritphat Orrapin
- Department of Surgery, Faculty of Medicine, Thammasat University, Rangsit Campus, Pathum Thani 12120, Thailand; (S.O.); (B.S.)
| | - Boonying Siribumrungwong
- Department of Surgery, Faculty of Medicine, Thammasat University, Rangsit Campus, Pathum Thani 12120, Thailand; (S.O.); (B.S.)
| | - Nongkran Lumjuan
- Research Center for Molecular and Cell Biology, Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Kittipan Rerkasem
- Environmental-Occupational Health Sciences and Non-Communicable Diseases Research Center, Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (A.R.); (P.T.)
- Clinical Surgical Research Center, Department of Surgery, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (N.B.); (S.A.); (S.O.); (T.R.); (P.A.)
| | - José G. B. Derraik
- Environmental-Occupational Health Sciences and Non-Communicable Diseases Research Center, Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (A.R.); (P.T.)
- Department of Women’s and Children’s Health, Uppsala University, 75185 Uppsala, Sweden
- Department of Pediatrics: Child and Youth Health, Faculty of Medical and Health Sciences, University of Auckland, Auckland 1142, New Zealand
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