1
|
Lu J, Meyer S. A zero-inflated endemic-epidemic model with an application to measles time series in Germany. Biom J 2023; 65:e2100408. [PMID: 37439440 DOI: 10.1002/bimj.202100408] [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: 12/27/2021] [Revised: 04/24/2023] [Accepted: 06/15/2023] [Indexed: 07/14/2023]
Abstract
Count data with an excess of zeros are often encountered when modeling infectious disease occurrence. The degree of zero inflation can vary over time due to nonepidemic periods as well as by age group or region. A well-established approach to analyze multivariate incidence time series is the endemic-epidemic modeling framework, also known as the HHH approach. However, it assumes Poisson or negative binomial distributions and is thus not tailored to surveillance data with excess zeros. Here, we propose a multivariate zero-inflated endemic-epidemic model with random effects that extends HHH. Parameters of both the zero-inflation probability and the HHH part of this mixture model can be estimated jointly and efficiently via (penalized) maximum likelihood inference using analytical derivatives. We found proper convergence and good coverage of confidence intervals in simulation studies. An application to measles counts in the 16 German states, 2005-2018, showed that zero inflation is more pronounced in the Eastern states characterized by a higher vaccination coverage. Probabilistic forecasts of measles cases improved when accounting for zero inflation. We anticipate zero-inflated HHH models to be a useful extension also for other applications and provide an implementation in an R package.
Collapse
Affiliation(s)
- Junyi Lu
- Institute of Medical Informatics, Biometry, and Epidemiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sebastian Meyer
- Institute of Medical Informatics, Biometry, and Epidemiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| |
Collapse
|
2
|
Wilkinson T, Beaver S, Macartney M, McArthur E, Yadav V, Lied‐Lied A. Burden of respiratory syncytial virus in adults in the United Kingdom: A systematic literature review and gap analysis. Influenza Other Respir Viruses 2023; 17:e13188. [PMID: 37744994 PMCID: PMC10511839 DOI: 10.1111/irv.13188] [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: 04/28/2023] [Revised: 07/31/2023] [Accepted: 08/09/2023] [Indexed: 09/26/2023] Open
Abstract
Despite the growing recognition of a potentially significant respiratory syncytial virus (RSV) disease burden in adults, relevant evidence in the United Kingdom (UK) is limited. This systematic literature review (SLR) aimed to identify the disease burden of RSV in UK adults, including certain high-risk subgroups and existing evidence gaps. Published studies (2011 onwards) reporting epidemiological, economic and clinical burden outcomes in UK adults (≥15 years) with RSV were identified from indexed databases, including MEDLINE, Embase and the Cochrane library. High-risk groups included elderly (≥65 years), immunocompromised, co-morbid and co-infected patients. Outcomes included RSV incidence/prevalence, mortality, clinical presentation and direct/indirect resource use/costs. Twenty-eight publications on 28 unique studies were identified, mostly in general/respiratory indicator (n = 17), elderly (n = 10) and immunocompromised (n = 6) cohorts. Main outcomes reported in the general/respiratory indicator cohort were RSV infection incidence (seasonal/annual: 0.09-17.9%/6.6-15.1%), mortality (8,482 deaths/season) and direct resource use (including mean general practitioner [GP] episodes/season: 487,247). Seasonal/annual incidence was 14.6-26.5%/0.7-16% in high-risk cohorts. Attributed to RSV in the elderly were 7,915 deaths/season and 175,070 mean GP episodes/season. Only two studies reported on co-morbid cohorts. Clinical burden outcomes were only reported in general and immunocompromised patients, and no evidence was found in any cohort on indirect economic burden or RSV complications. Evidence captured suggests that RSV may have a substantial burden in UK adults. However, available data were limited and highly heterogenous, with further studies needed to characterise the burden of RSV in adults and to validate our findings.
Collapse
Affiliation(s)
- Tom Wilkinson
- Clinical and Experimental SciencesUniversity of Southampton Faculty of MedicineSouthamptonUK
- National Institute for Health and Care Research Southampton Biomedical Research CentreSouthamptonUK
| | | | | | | | | | | |
Collapse
|
3
|
Bennett JC, Emanuels A, Heimonen J, O'Hanlon J, Hughes JP, Han PD, Chow EJ, Ogokeh CE, Rolfes MA, Lockwood CM, Pfau B, Uyeki TM, Shendure J, Hoag S, Fay K, Lee J, Sibley TR, Rogers JH, Starita LM, Englund JA, Chu HY. Streptococcus pneumoniae nasal carriage patterns with and without common respiratory virus detections in households in Seattle, WA, USA before and during the COVID-19 pandemic. Front Pediatr 2023; 11:1198278. [PMID: 37484765 PMCID: PMC10361771 DOI: 10.3389/fped.2023.1198278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/23/2023] [Indexed: 07/25/2023] Open
Abstract
Background Respiratory viruses might influence Streptococcus pneumoniae nasal carriage and subsequent disease risk. We estimated the association between common respiratory viruses and semiquantitative S. pneumoniae nasal carriage density in a household setting before and during the COVID-19 pandemic. Methods From November 2019-June 2021, we enrolled participants in a remote household surveillance study of respiratory pathogens. Participants submitted weekly reports of acute respiratory illness (ARI) symptoms. Mid-turbinate or anterior nasal swabs were self-collected at enrollment, when ARI occurred, and, in the second year of the study only, from household contacts after SARS-CoV-2 was detected in a household member. Specimens were tested using multiplex reverse-transcription PCR for respiratory pathogens, including S. pneumoniae, rhinovirus, adenovirus, common human coronavirus, influenza A/B virus, respiratory syncytial virus (RSV) A/B, human metapneumovirus, enterovirus, and human parainfluenza virus. We estimated differences in semiquantitative S. pneumoniae nasal carriage density, estimated by the inverse of S. pneumoniae relative cycle threshold (Crt) values, with and without viral detection for any virus and for specific respiratory viruses using linear generalized estimating equations of S. pneumoniae Crt values on virus detection adjusted for age and swab type and accounting for clustering of swabs within households. Results We collected 346 swabs from 239 individuals in 151 households that tested positive for S. pneumoniae (n = 157 with and 189 without ≥1 viruses co-detected). Difficulty breathing, cough, and runny nose were more commonly reported among individuals with specimens with viral co-detection compared to without (15%, 80% and 93% vs. 8%, 57%, and 51%, respectively) and ear pain and headache were less commonly reported (3% and 26% vs. 16% and 41%, respectively). For specific viruses among all ages, semiquantitative S. pneumoniae nasal carriage density was greater with viral co-detection for enterovirus, RSV A/B, adenovirus, rhinovirus, and common human coronavirus (P < 0.01 for each). When stratified by age, semiquantitative S. pneumoniae nasal carriage density was significantly greater with viral co-detection among children aged <5 (P = 0.002) and 5-17 years (P = 0.005), but not among adults aged 18-64 years (P = 0.29). Conclusion Detection of common respiratory viruses was associated with greater concurrent S. pneumoniae semiquantitative nasal carriage density in a household setting among children, but not adults.
Collapse
Affiliation(s)
- Julia C. Bennett
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - Anne Emanuels
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Jessica Heimonen
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Jessica O'Hanlon
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - James P. Hughes
- Department of Biostatistics, University of Washington, Seattle, WA, United States
| | - Peter D. Han
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, United States
- Military and Health Research Foundation, Laurel, MD, United States
| | - Eric J. Chow
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Epidemiology, University of Washington, Seattle, WA, United States
- Communicable Disease Epidemiology and Immunizations Section, Prevention Division, Public Health – Seattle & King County, Seattle, WA, United States
| | - Constance E. Ogokeh
- Military and Health Research Foundation, Laurel, MD, United States
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Melissa A. Rolfes
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Christine M. Lockwood
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, United States
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Brian Pfau
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, United States
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Timothy M. Uyeki
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, United States
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Samara Hoag
- Student Health Services, Seattle Public Schools, Seattle, WA, United States
| | - Kairsten Fay
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Jover Lee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Thomas R. Sibley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Julia H. Rogers
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - Lea M. Starita
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, United States
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Janet A. Englund
- Seattle Children’s Research Institute, Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - Helen Y. Chu
- Department of Medicine, University of Washington, Seattle, WA, United States
| |
Collapse
|
4
|
Dagan R, van der Beek BA, Ben-Shimol S, Greenberg D, Shemer-Avni Y, Weinberger DM, Danino D. The COVID-19 pandemic as an opportunity for unravelling the causative association between respiratory viruses and pneumococcus-associated disease in young children: a prospective study. EBioMedicine 2023; 90:104493. [PMID: 36857965 PMCID: PMC9970381 DOI: 10.1016/j.ebiom.2023.104493] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND In young children, rates of lower respiratory infections (LRI) and invasive pneumococcal disease (IPD) have been associated with respiratory syncytial virus (RSV), human metapneumovirus (hMPV), influenza (flu), and parainfluenza (PIV) (collectively termed here as pneumonia and pneumococcal disease-associated viruses [PDA-viruses]). However, their contribution to the pathogenesis of these disease endpoints has not yet been elucidated. The COVID-19 pandemic provided a unique opportunity to examine the question. METHODS This prospective study comprised all children <5 years, living in southern Israel, during 2016 through 2021. The data were previously collected in multiple ongoing prospective surveillance programs and include: hospital visits for community-acquired alveolar pneumonia (CAAP), non-CAAP LRI; nasopharyngeal pneumococcal carriage (<3 years of age); respiratory virus activity; and nationwide, all-ages COVID-19 episodes and IPD in children <5 years. A hierarchical statistical model was developed to estimate the proportion of the different clinical endpoints attributable to each virus from monthly time series data, stratified by age and ethnicity. A separate model was fit for each endpoint, with covariates that included a linear time trend, 12-month harmonic variables to capture unexplained seasonal variations, and the proportion of tests positive for each virus in that month. FINDINGS During 2016 through 2021, 3,204, 26,695, 257, and 619 episodes of CAAP, non-CAAP LRI, pneumococcal bacteremic pneumonia and non-pneumonia IPD, respectively, were reported. Compared to 2016-2019, broad declines in the disease endpoints were observed shortly after the pandemic surge, coincident with a complete disappearance of all PDA-viruses and continued circulation of rhinovirus (RhV) and adenovirus (AdV). From April 2021, off-season and abrupt surges of all disease endpoints occurred, associated with similar dynamics among the PDA-viruses, which re-emerged sequentially. Using our model fit to the entire 2016-2021 period, 82% (95% CI, 75-88%) of CAAP episodes in 2021 were attributable to the common respiratory viruses, as were 22%-31% of the other disease endpoints. Virus-specific contributions to CAAP were: RSV, 49% (95% CI, 43-55%); hMPV, 13% (10-17%); PIV, 11% (7-15%); flu, 7% (1-13%). RhV and AdV did not contribute. RSV was the main contributor in all endpoints, especially in infants. Pneumococcal carriage prevalence remained largely stable throughout the study. INTERPRETATION RSV and hMPV play a critical role in the burden of CAAP and pneumococcal disease in children. Interventions targeting these viruses could have a secondary effect on the burden of disease typically attributed to bacteria. FUNDING There was no funding for this study.
Collapse
Affiliation(s)
- Ron Dagan
- The Shraga Segal Deptartment of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Bart Adriaan van der Beek
- The Shraga Segal Deptartment of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Shalom Ben-Shimol
- Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel; The Pediatric Infectious Disease Unit, Soroka University Medical Center, Beer Sheva, Israel
| | - David Greenberg
- Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel; The Pediatric Infectious Disease Unit, Soroka University Medical Center, Beer Sheva, Israel
| | - Yonat Shemer-Avni
- Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel; Clinical Virology Laboratory, Soroka University Medical Center, Beer-Sheva, Israel
| | - Daniel M Weinberger
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Dana Danino
- Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel; The Pediatric Infectious Disease Unit, Soroka University Medical Center, Beer Sheva, Israel
| |
Collapse
|
5
|
Ouldali N, Deceuninck G, Lefebvre B, Gilca R, Quach C, Brousseau N, Tapiero B, De Wals P. Increase of invasive pneumococcal disease in children temporally associated with RSV outbreak in Quebec: a time-series analysis. LANCET REGIONAL HEALTH. AMERICAS 2023; 19:100448. [PMID: 36852331 PMCID: PMC9958468 DOI: 10.1016/j.lana.2023.100448] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/29/2022] [Accepted: 01/31/2023] [Indexed: 02/17/2023]
Abstract
Background Respiratory viruses have been previously suspected to trigger invasive pneumococcal disease (IPD). After progressive non-pharmaceutical interventions (NPI) lifting, an unusual RSV outbreak has been observed in the Fall 2021, raising concerns about the possible consequences on IPD. We aimed to analyse the evolution of IPD incidence across age-groups since NPI lifting, and its temporal association with respiratory viral infections. Methods We conducted a time-series analysis using 1) population-based IPD surveillance data and 2) statistics from the laboratory surveillance network of respiratory viruses in the province of Quebec, Canada, from January 2013 to January 2022. The monthly IPD incidence was analysed by quasi-Poisson regression models across age-groups. The fraction of IPD incidence change potentially attributable to different viruses in 2021-2022 was estimated. Findings A total of 7712 IPD cases were included. After a major decrease in IPD incidence from April 2020, IPD rate started to increase in <5-year-old children in October 2021, exceeding the pre-NPI trend (+62%). This was temporally associated with an unusual surge in RSV cases (+53% versus pre-NPI trend). During this 2021-22 surge, the fraction of IPD attributable to RSV dynamics in children was 77% (95% CI [33-100]). By contrast, the IPD incidence in older age-groups remained low, and was temporally associated with influenza dynamics. Interpretation These results provide new evidence on the role of respiratory viruses in driving IPD dynamics, with possible differences between children and adults. In the coming future, the potential benefit of interventions targeting RSV, such as vaccines, for IPD prevention should be considered. Funding The study was supported by a grant from the Quebec Ministry of Health and Social Services ('ministère de la Santé et des Services sociaux du Québec'). Publication was supported by a grant from "Fondation de l'Assistance Publique - Hôpitaux de Paris et de l'Alliance « Tous Unis contre le Virus » (Fondation de France/Institut Pasteur/APHP)". N.O. was supported by the ESPID (European Society of Pediatric Infectious Diseases) 2021-2023 Fellowship Award and the 2022 ISPPD (International Symposium on Pneumococci and Pneumococcal Diseases) Robert Austrian Research award.
Collapse
Affiliation(s)
- Naïm Ouldali
- Division of Infectious Diseases, Department of Pediatric Infectious Diseases, Sainte Justine University Hospital, University of Montreal, Quebec, Canada,Infection, Antimicrobials, Modelling, Evolution, Inserm UMR 1137, Paris University, Paris, France,Association Clinique et Thérapeutique Infantile du Val-de-Marne, St Maur-des-Fossés, France,Corresponding author. Department of Pediatric Infectious Diseases, Sainte Justine University Hospital, Montreal University, QC H3T 1C5, Montreal, Quebec, Canada.
| | | | - Brigitte Lefebvre
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Rodica Gilca
- Centre de recherche du CHU de Québec-Université Laval, Québec, Canada,Department of Social and Preventive Medicine, Faculty of Medicine, Laval University, Quebec City, Canada,Direction des risques biologiques, Institut national de santé publique du Québec, Québec, Canada
| | - Caroline Quach
- Division of Infectious Diseases, Department of Pediatric Infectious Diseases, Sainte Justine University Hospital, University of Montreal, Quebec, Canada,Department of Microbiology, Infectious Diseases and Immunology, University of Montreal, Quebec, Canada
| | - Nicholas Brousseau
- Centre de recherche du CHU de Québec-Université Laval, Québec, Canada,Department of Social and Preventive Medicine, Faculty of Medicine, Laval University, Quebec City, Canada,Direction des risques biologiques, Institut national de santé publique du Québec, Québec, Canada
| | - Bruce Tapiero
- Division of Infectious Diseases, Department of Pediatric Infectious Diseases, Sainte Justine University Hospital, University of Montreal, Quebec, Canada
| | - Philippe De Wals
- Centre de recherche du CHU de Québec-Université Laval, Québec, Canada,Department of Social and Preventive Medicine, Faculty of Medicine, Laval University, Quebec City, Canada,Direction des risques biologiques, Institut national de santé publique du Québec, Québec, Canada
| |
Collapse
|
6
|
Campling J, Vyse A, Liu HH, Wright H, Slack M, Reinert RR, Drayson M, Richter A, Singh D, Barlow G, Kassianos G, Ellsbury G. A review of evidence for pneumococcal vaccination in adults at increased risk of pneumococcal disease: risk group definitions and optimization of vaccination coverage in the United Kingdom. Expert Rev Vaccines 2023; 22:785-800. [PMID: 37694398 DOI: 10.1080/14760584.2023.2256394] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/02/2023] [Accepted: 09/04/2023] [Indexed: 09/12/2023]
Abstract
INTRODUCTION Pneumococcal disease (PD) significantly contributes to morbidity and mortality, carrying substantial economic and public health burden. This article is a targeted review of evidence for pneumococcal vaccination in the UK, the definitions of groups at particular risk of PD and vaccine effectiveness. AREAS COVERED Relevant evidence focusing on UK data from surveillance systems, randomized controlled trials, observational studies and publicly available government documents is collated and reviewed. Selected global data are included where appropriate. EXPERT OPINION National vaccination programs have reduced the incidence of vaccine-type PD, despite the rising prominence of non-vaccine serotypes in the UK. The introduction of higher-valency conjugate vaccines provides an opportunity to improve protection against PD for adults in risk groups. Several incentives are in place to encourage general practitioners to vaccinate risk groups, but uptake is low-suboptimal particularly among at-risk individuals. Wider awareness and understanding among the public and healthcare professionals may increase vaccination uptake and coverage. National strategies targeting organizational factors are urgently needed to achieve optimal access to vaccines. Finally, identifying new risk factors and approaches to risk assessment for PD are crucial to ensure those at risk of PD can benefit from pneumococcal vaccination.
Collapse
Affiliation(s)
| | - Andrew Vyse
- Medical Affairs, Pfizer Ltd, Walton Oaks, UK
| | | | | | - Mary Slack
- School of Medicine & Dentistry, Griffith University, Southport, Queensland, Australia
| | | | - Mark Drayson
- Institute of Immunology and Immunotherapy, Medical School, University of Birmingham, Edgbaston, Birmingham, UK
| | - Alex Richter
- Institute of Immunology and Immunotherapy, Medical School, University of Birmingham, Edgbaston, Birmingham, UK
| | - Dave Singh
- Division of Immunology, Immunity to Infection and Respiratory Medicine, University of Manchester, Manchester, UK
| | - Gavin Barlow
- Hull York Medical School, University of York, York, UK
| | - George Kassianos
- Royal College of General Practitioners, London, UK
- British Global & Travel Health Association, Bath, UK
| | | |
Collapse
|
7
|
Spatiotemporal dynamics and potential ecological drivers of acute respiratory infectious diseases: an example of scarlet fever in Sichuan Province. BMC Public Health 2022; 22:2139. [PMID: 36411416 PMCID: PMC9680133 DOI: 10.1186/s12889-022-14469-y] [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: 05/05/2022] [Accepted: 10/17/2022] [Indexed: 11/23/2022] Open
Abstract
OBJECT Scarlet fever is an acute respiratory infectious disease that endangers public health and imposes a huge economic burden. In this paper, we systematically studied its spatial and temporal evolution and explore its potential ecological drivers. The goal of this research is to provide a reference for analysis based on surveillance data of scarlet fever and other acute respiratory infectious illnesses, and offer suggestions for prevention and control. METHOD This research is based on a spatiotemporal multivariate model (Endemic-Epidemic model). Firstly, we described the epidemiology status of the scarlet fever epidemic in Sichuan Province from 2016 to 2019. Secondly, we used spatial autocorrelation analysis to understand the spatial pattern. Thirdly, we applied the endemic-epidemic model to analyze the spatiotemporal dynamics by quantitatively decomposing cases into endemic, autoregressive, and spatiotemporal components. Finally, we explored potential ecological drivers that could influence the spread of scarlet fever. RESULTS From 2016 to 2019, the incidence of scarlet fever in Sichuan Province varied much among cities. In terms of temporal distribution, there were 1-2 epidemic peaks per year, and they were mainly concentrated from April to June and October to December. In terms of transmission, the endemic and temporal spread were predominant. Our findings imply that the school holiday could help to reduce the spread of scarlet fever, and a standard increase in Gross Domestic Product (GDP) was associated with 2.6 folds contributions to the epidemic among cities. CONCLUSION Scarlet fever outbreaks are more susceptible to previous cases, as temporal spread accounted for major transmission in many areas in Sichuan Province. The school holidays and GDP can influence the spread of infectious diseases. Given that covariates could not fully explain heterogeneity, adding random effects was essential to improve accuracy. Paying attention to critical populations and hotspots, as well as understanding potential drivers, is recommended for acute respiratory infections such as scarlet fever. For example, our study reveals GDP is positively associated with spatial spread, indicating we should consider GDP as an important factor when analyzing the potential drivers of acute infectious disease.
Collapse
|
8
|
Plumb ID, Harris R, Green HK, Ellis J, Baisley K, Pebody RG. Changes in characteristics and case-severity in patients hospitalised with influenza A (H1N1) pdm09 infection between two epidemic waves-England, 2009-2010. Influenza Other Respir Viruses 2021; 15:599-607. [PMID: 33942500 PMCID: PMC8404053 DOI: 10.1111/irv.12863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/28/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND During 2009-2010, pandemic influenza A (H1N1) pdm09 virus (pH1N1) infections in England occurred in two epidemic waves. Reasons for a reported increase in case-severity during the second wave are unclear. METHODS We analysed hospital-based surveillance for patients with pH1N1 infections in England during 2009-2010 and linked national data sets to estimate ethnicity, socio-economic status and death within 28 days of admission. We used multivariable logistic regression to assess whether changes in demographic, clinical and management characteristics of patients could explain an increase in ICU admission or death, and accounted for missing values using multiple imputation. RESULTS During the first wave, 54/960 (6%) hospitalised patients required intensive care and 21/960 (2%) died; during the second wave 143/1420 (10%) required intensive care and 55/1420 (4%) died. In a multivariable model, during the second wave patients were less likely to be from an ethnic minority (OR 0.33, 95% CI 0.26-0.42), have an elevated deprivation score (OR 0.75, 95% CI 0.68-0.83), have known comorbidity (OR 0.78, 95% CI 0.63-0.97) or receive antiviral therapy ≤2 days before onset (OR 0.72, 95% CI 0.56-0.92). Increased case-severity during the second wave was not explained by changes in demographic, clinical or management characteristics. CONCLUSIONS Monitoring changes in patient characteristics could help target interventions during multiple waves of COVID-19 or a future influenza pandemic. To understand and respond to changes in case-severity, surveillance is needed that includes additional factors such as admission thresholds and seasonal coinfections.
Collapse
Affiliation(s)
- Ian D. Plumb
- Public Health EnglandLondonUK
- London School of Hygiene and Tropical MedicineLondonUK
| | | | | | | | - Kathy Baisley
- London School of Hygiene and Tropical MedicineLondonUK
| | | |
Collapse
|
9
|
Lu J, Meyer S. An endemic–epidemic beta model for time series of infectious disease proportions. J Appl Stat 2021; 49:3769-3783. [DOI: 10.1080/02664763.2021.1962264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Junyi Lu
- Institute of Medical Informatics, Biometry, and Epidemiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sebastian Meyer
- Institute of Medical Informatics, Biometry, and Epidemiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| |
Collapse
|
10
|
Fitzpatrick T, Malcolm W, McMenamin J, Reynolds A, Guttmann A, Hardelid P. Community-Based Antibiotic Prescribing Attributable to Respiratory Syncytial Virus and Other Common Respiratory Viruses in Young Children: A Population-Based Time-series Study of Scottish Children. Clin Infect Dis 2021; 72:2144-2153. [PMID: 32270199 DOI: 10.1093/cid/ciaa403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 04/07/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Inappropriate antibiotic prescribing, such as for viral illness, remains common in primary care. The objective of this study was to estimate the proportion of community-prescribed antibiotics to children aged less than 5 years attributable to common respiratory viruses. METHODS We fitted time-series negative binomial models to predict weekly antibiotic prescribing rates from positive viral pathogen tests for the period 1 April 2009 through 27 December 2017 using comprehensive, population-based administrative data for all children (<5 years) living in Scotland. Multiple respiratory viral pathogens were considered, including respiratory syncytial virus (RSV), influenza, human metapneumovirus (HMPV), rhinovirus, and human parainfluenza (HPIV) types 1-4. We estimated the proportion of antibiotic prescriptions explained by virus circulation according to type of virus, by age group, presence of high-risk chronic conditions, and antibiotic class. RESULTS We included data on 6 066 492 antibiotic prescriptions among 452 877 children. The antibiotic-prescribing rate among all Scottish children (<5 years) was 609.7 per 1000 child-years. Our final model included RSV, influenza, HMPV, HPIV-1, and HPIV-3. An estimated 6.9% (95% confidence interval, 5.6-8.3%), 2.4% (1.7-3.1%), and 2.3% (.8-3.9%) of antibiotics were attributable to RSV, influenza, and HMPV, respectively. RSV was consistently associated with the highest proportion of prescribed antibiotics, particularly among children without chronic conditions and for amoxicillin and macrolide prescriptions. CONCLUSIONS Nearly 14% of antibiotics prescribed to children in this study were estimated to be attributable to common viruses for which antibiotics are not recommended. A future RSV vaccine could substantially reduce unnecessary antibiotic prescribing among children.
Collapse
Affiliation(s)
- Tiffany Fitzpatrick
- UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom.,SickKids Research Institute, The Hospital for Sick Children, Toronto, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - William Malcolm
- Health Protection Scotland, NHS National Services Scotland Meridian Court, Glasgow, United Kingdom
| | - Jim McMenamin
- Health Protection Scotland, NHS National Services Scotland Meridian Court, Glasgow, United Kingdom
| | - Arlene Reynolds
- Health Protection Scotland, NHS National Services Scotland Meridian Court, Glasgow, United Kingdom
| | - Astrid Guttmann
- SickKids Research Institute, The Hospital for Sick Children, Toronto, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Canada.,ICES, Toronto, Canada
| | - Pia Hardelid
- UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| |
Collapse
|
11
|
Gessner BD, Isturiz R, Snow V, Grant LR, Theilacker C, Jodar L. The rationale for use of clinically defined outcomes in assessing the impact of pneumococcal conjugate vaccines against pneumonia. Expert Rev Vaccines 2021; 20:269-280. [PMID: 33602035 DOI: 10.1080/14760584.2021.1889376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Introduction: When evaluating the public health value of adult pneumococcal conjugate vaccine (PCV) for pneumonia, regulatory agencies and vaccine technical committees (VTCs) emphasize vaccine serotype (VT), radiologically confirmed community-acquired pneumonia (CAP) to the exclusion of clinically defined pneumonia and thus may underestimate PCV's public health value.Areas covered: We review the critiques that have been raised to using clinically defined pneumonia as a complement to VT-CAP in evaluating the public health value of adult PCVs.Expert opinion: PCV13 efficacies for preventing hospitalized CAP ranged from 6% to 11% and for a combination of primary and secondary care from 4% to 12%, with relatively high associated rate reductions. These efficacy values are larger than estimated from multiplying PCV13 efficacy against vaccine-type CAP by the proportion of CAP identified as vaccine-type through tests, such as a serotype-specific urinary antigen detection assay. Current understanding of pneumococcal epidemiology and limitations of diagnostic tests suggest the efficacy values for clinically defined outcomes are plausible and potentially generalizable. Regulatory agencies and VTCs have accepted clinically defined outcomes for assessing pediatric vaccines and - while additional studies assessing adult clinical CAP VE are needed - they might consider existing data when evaluating adult PCV use.
Collapse
|
12
|
Yu L, Wang J, Zou Y, Zeng H, Cheng W, Jing X. Qingfei oral liquid inhibited autophagy to alleviate inflammation via mTOR signaling pathway in RSV-infected asthmatic mice. Biomed Pharmacother 2021; 138:111449. [PMID: 33706133 DOI: 10.1016/j.biopha.2021.111449] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/22/2021] [Accepted: 02/26/2021] [Indexed: 12/30/2022] Open
Abstract
Qingfei oral liquid (QF) is a traditional Chinese medicine that has been used to treat patients with viral pneumonia and asthma for decades. Our previous study revealed that QF prevents airway inflammation and reduces airway hyperresponsiveness (AHR) in respiratory syncytial virus (RSV)-infected asthmatic mice. RSV infection can exacerbate asthma in pediatric patients and induce autophagy, which leads to the promotion of inflammatory cytokine production in the pathology of this disease. The effect of QF on regulating autophagy in RSV-infected asthma patients has not been fully elucidated. In this study, we identified compounds of QF by HPLC-DAD-Q-TOF-MS/MS. The RSV infected OVA challenged mice, we evaluated the RSV-infected asthma model. We found that treatment with QF alleviated airway inflammation and mitigated airway AHR in RSV-infected asthmatic mice. In addition, we found that QF inhibited autophagosome formation and the expression of LC3 protein by using electron and laser confocal microscopy, respectively, to assess RSV-infected asthmatic mice lung tissues. Furthermore, QF was found to reduce the quantity of autophagy and its related proteins LC3B (light chain 3B), Beclin-1, p62 and Atg5 (autophagy-related gene 5) and downstream inflammatory cytokines TNF-α, IL-4, IL-6, and IL-13 via an action in mTOR-dependent signaling in vivo and in vitro. These findings suggest that QF can alleviate the inflammation caused by RSV infection in asthmatic mice, and its mechanism may be involved in the regulation of autophagy via the mTOR signaling pathway.
Collapse
Affiliation(s)
- Linlin Yu
- Department of Traditional Chinese Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, China
| | - Jing Wang
- Department of Traditional Chinese Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, China
| | - Ya Zou
- Department of Traditional Chinese Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, China
| | - Hairong Zeng
- Department of Traditional Chinese Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, China
| | - Weiwei Cheng
- Department of Traditional Chinese Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, China
| | - Xiaoping Jing
- Department of Traditional Chinese Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, China.
| |
Collapse
|
13
|
Detection of 20 respiratory viruses and bacteria by influenza-like illness surveillance in Beijing, China, 2016-2018. J Infect 2019; 80:350-371. [PMID: 31778686 PMCID: PMC7126004 DOI: 10.1016/j.jinf.2019.11.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 11/21/2019] [Indexed: 11/30/2022]
|