1
|
Soriano López J, Gómez Gómez JH, Ballesta-Ruiz M, Garcia-Pina R, Sánchez-Rodríguez I, Bonilla-Escobar BA, Salmerón D, Rodríguez BS, Chirlaque MD. COVID-19, social determinants of transmission in the home. A population-based study. Eur J Public Health 2024; 34:427-434. [PMID: 38396184 PMCID: PMC11161145 DOI: 10.1093/eurpub/ckae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Studying transmission within the home is essential to understand the transmission dynamics of numerous infectious diseases. For Coronavirus Disease-2019 (COVID-19), transmission within the home constitutes the majority exposure context. The risk of infection in this setting can be quantified by the household/intra-family secondary attack rate (SAR). In the literature, there are discrepancies in these values and little information about its social determinants. The aim of this study was to investigate transmission in the home by analyzing the influence of occupational social class, country of origin and gender/sex. METHODS This was a retrospective cohort study of a population registry of cohabiting contacts with COVID-19 cases diagnosed from 15 June to 23 December 2020, in the Murcia Region. The household SAR was analyzed considering the characteristics of the primary case (sex, age, symptoms, occupational social class, country of origin and number of people in the household) and contact (age and sex) using a multilevel binary logistic regression model. RESULTS Among the 37 727 contacts included, the intra-family SAR was 39.1%. The contacts of confirmed primary cases in the migrant population (Africa and Latin America) had higher attack rates, even after adjusting for the other variables. Older age and female sex were independent risk factors for contracting Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) within the home. CONCLUSION There was greater intra-domiciliary transmission among immigrants, likely related to the conditions of the home and situation of social vulnerability. Women were more likely to be infected by transmission from a cohabiting infected individual.
Collapse
Affiliation(s)
- Jesús Soriano López
- Murcia Region Health Department, Murcia, Spain
- Teaching Unit of Preventive Medicine and Public Health, Murcia, Spain
| | - Jesús Humberto Gómez Gómez
- Murcia Region Health Department, Murcia, Spain
- Department of Epidemiology, Murcia, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- IMIB Arrixaca, Murcia, Spain
| | - Monica Ballesta-Ruiz
- Murcia Region Health Department, Murcia, Spain
- Department of Epidemiology, Murcia, Spain
- IMIB Arrixaca, Murcia, Spain
- Division of Preventive Medicine and Public Health, Department of Public Health Sciences, University of Murcia, Murcia, Spain
| | - Rocio Garcia-Pina
- Murcia Region Health Department, Murcia, Spain
- Planning and Health Financing Department, Murcia, Spain
| | - Inés Sánchez-Rodríguez
- Murcia Region Health Department, Murcia, Spain
- Department of Epidemiology, Murcia, Spain
- IMIB Arrixaca, Murcia, Spain
| | - Bertha A Bonilla-Escobar
- Government of Spain Ministry of Health, Health Promotion and Equity Area, Deputy Directorate General for Health Promotion and Prevention, Directorate General for Public Madrid, Comunidad de Madrid, Madrid, Spain
- TRAGSATEC, Management of Health, Food Safety and Public Health Madrid, Comunidad de Madrid, Madrid, Spain
| | - Diego Salmerón
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- IMIB Arrixaca, Murcia, Spain
- Department of Health & Social Sciences, University of Murcia, Murcia, Spain
| | - Berta Suárez Rodríguez
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Government of Spain Ministry of Health, Spain Centre for Health Alerts and Emergencies, Directorate General of Public Health, Ministry of Health Madrid, Comunidad de Madrid, Madrid, Spain
| | - Maria-Dolores Chirlaque
- Murcia Region Health Department, Murcia, Spain
- Department of Epidemiology, Murcia, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- IMIB Arrixaca, Murcia, Spain
- Division of Preventive Medicine and Public Health, Department of Public Health Sciences, University of Murcia, Murcia, Spain
| |
Collapse
|
2
|
House T, Riley H, Pellis L, Pouwels KB, Bacon S, Eidukas A, Jahanshahi K, Eggo RM, Sarah Walker A. Inferring risks of coronavirus transmission from community household data. Stat Methods Med Res 2022; 31:1738-1756. [PMID: 36112916 PMCID: PMC9465559 DOI: 10.1177/09622802211055853] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The response of many governments to the COVID-19 pandemic has involved measures to control within- and between-household transmission, providing motivation to improve understanding of the absolute and relative risks in these contexts. Here, we perform exploratory, residual-based, and transmission-dynamic household analysis of the Office for National Statistics COVID-19 Infection Survey data from 26 April 2020 to 15 July 2021 in England. This provides evidence for: (i) temporally varying rates of introduction of infection into households broadly following the trajectory of the overall epidemic and vaccination programme; (ii) susceptible-Infectious transmission probabilities of within-household transmission in the 15-35% range; (iii) the emergence of the Alpha and Delta variants, with the former being around 50% more infectious than wildtype and 35% less infectious than Delta within households; (iv) significantly (in the range of 25-300%) more risk of bringing infection into the household for workers in patient-facing roles pre-vaccine; (v) increased risk for secondary school-age children of bringing the infection into the household when schools are open; (vi) increased risk for primary school-age children of bringing the infection into the household when schools were open since the emergence of new variants.
Collapse
Affiliation(s)
- Thomas House
- Department of Mathematics, 5292University of Manchester, Manchester UK
- IBM Research, Hartree Centre, Daresbury UK
- The Alan Turing Institute for Data Science and Artificial Intelligence, London UK
| | - Heather Riley
- Department of Mathematics, 5292University of Manchester, Manchester UK
| | - Lorenzo Pellis
- Department of Mathematics, 5292University of Manchester, Manchester UK
- The Alan Turing Institute for Data Science and Artificial Intelligence, London UK
| | - Koen B Pouwels
- 105596Nuffield Department of Medicine, University of Oxford, Oxford UK
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford UK
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, , Oxford UK
| | - Sebastian Bacon
- The DataLab, 12205Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford UK
| | | | | | - Rosalind M Eggo
- Centre for Mathematical Modelling of Infectious Diseases, 4906London School of Hygiene and Tropical Medicine, London UK
| | - A Sarah Walker
- 105596Nuffield Department of Medicine, University of Oxford, Oxford UK
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford UK
- The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford UK
- MRC Clinical Trials Unit at UCL, UCL, London UK
| |
Collapse
|
3
|
Ahsan I, Menon I, Gupta R, Arora V, Das D, Ashraf A. Impact of general hygiene behaviors on oral hygiene among adolescents of Ghaziabad - A cross-sectional study. JOURNAL OF INDIAN ASSOCIATION OF PUBLIC HEALTH DENTISTRY 2022. [DOI: 10.4103/jiaphd.jiaphd_163_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
|
4
|
Dahlgren FS, Foppa IM, Stockwell MS, Vargas CY, LaRussa P, Reed C. Household transmission of influenza A and B within a prospective cohort during the 2013-2014 and 2014-2015 seasons. Stat Med 2021; 40:6260-6276. [PMID: 34580901 PMCID: PMC9293304 DOI: 10.1002/sim.9181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/22/2021] [Accepted: 08/15/2021] [Indexed: 01/01/2023]
Abstract
People living within the same household as someone ill with influenza are at increased risk of infection. Here, we use Markov chain Monte Carlo methods to partition the hazard of influenza illness within a cohort into the hazard from the community and the hazard from the household. During the 2013‐2014 influenza season, 49 (4.7%) of the 1044 people enrolled in a community surveillance cohort had an acute respiratory illness (ARI) attributable to influenza. During the 2014‐2015 influenza season, 50 (4.7%) of the 1063 people in the cohort had an ARI attributable to influenza. The secondary attack rate from a household member was 2.3% for influenza A (H1) during 2013‐2014, 5.3% for influenza B during 2013‐2014, and 7.6% for influenza A (H3) during 2014‐2015. Living in a household with a person ill with influenza increased the risk of an ARI attributable to influenza up to 350%, depending on the season and the influenza virus circulating within the household.
Collapse
Affiliation(s)
- F Scott Dahlgren
- Influenza Division, Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ivo M Foppa
- Influenza Division, Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,Battelle Memorial Institute, Atlanta, Georgia, USA
| | - Melissa S Stockwell
- Division of Child and Adolescent Health, Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, New York, USA.,Department of Population and Family Health, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Celibell Y Vargas
- Division of Child and Adolescent Health, Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Philip LaRussa
- Division of Pediatric Infectious Diseases, Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Carrie Reed
- Influenza Division, Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| |
Collapse
|
5
|
Pellis L, Cauchemez S, Ferguson NM, Fraser C. Systematic selection between age and household structure for models aimed at emerging epidemic predictions. Nat Commun 2020; 11:906. [PMID: 32060265 PMCID: PMC7021781 DOI: 10.1038/s41467-019-14229-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 12/20/2019] [Indexed: 01/13/2023] Open
Abstract
Numerous epidemic models have been developed to capture aspects of human contact patterns, making model selection challenging when they fit (often-scarce) early epidemic data equally well but differ in predictions. Here we consider the invasion of a novel directly transmissible infection and perform an extensive, systematic and transparent comparison of models with explicit age and/or household structure, to determine the accuracy loss in predictions in the absence of interventions when ignoring either or both social components. We conclude that, with heterogeneous and assortative contact patterns relevant to respiratory infections, the model’s age stratification is crucial for accurate predictions. Conversely, the household structure is only needed if transmission is highly concentrated in households, as suggested by an empirical but robust rule of thumb based on household secondary attack rate. This work serves as a template to guide the simplicity/accuracy trade-off in designing models aimed at initial, rapid assessment of potential epidemic severity. Models of emerging epidemics can be exceedingly helpful in planning the response, but early on model selection is a difficult task. Here, the authors explore the joint contribution of age stratification and household structure on epidemic spread, and provides a rule of thumb to guide model choice.
Collapse
Affiliation(s)
- Lorenzo Pellis
- Department of Mathematics, University of Manchester, Manchester, UK. .,Zeeman Institute and Warwick Mathematics Institute, University of Warwick, Warwick, UK. .,MRC Centre for Global Infectious Disease Analysis, J-IDEA, School of Public Health, Imperial College, London, UK.
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, 75015, Paris, France
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, School of Public Health, Imperial College, London, UK
| | - Christophe Fraser
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| |
Collapse
|
6
|
Cohen C, Tshangela A, Valley-Omar Z, Iyengar P, Von Mollendorf C, Walaza S, Hellferscee O, Venter M, Martinson N, Mahlase G, McMorrow M, Cowling BJ, Treurnicht FK, Cohen AL, Tempia S. Household Transmission of Seasonal Influenza From HIV-Infected and HIV-Uninfected Individuals in South Africa, 2013-2014. J Infect Dis 2020; 219:1605-1615. [PMID: 30541140 DOI: 10.1093/infdis/jiy702] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/10/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND We estimated the household secondary infection risk (SIR) and serial interval (SI) for influenza transmission from HIV-infected and HIV-uninfected index cases. METHODS Index cases were the first symptomatic person in a household with influenza-like illness, testing influenza positive on real-time reverse transcription polymerase chain reaction (rRT-PCR). Nasopharyngeal swabs collected from household contacts every 4 days were tested by rRT-PCR. Factors associated with SIR were evaluated using logistic regression. RESULTS We enrolled 28 HIV-infected and 57 HIV-uninfected index cases. On multivariable analysis, HIV-infected index cases were less likely to transmit influenza to household contacts (odds ratio [OR] 0.2; 95% confidence interval [CI], 0.1-0.6; SIR 16%, 18/113 vs 27%, 59/220). Factors associated with increased SIR included index age group 1-4 years (OR 3.6; 95% CI, 1.2-11.3) and 25-44 years (OR 8.0; 95% CI, 1.8-36.7), and contact age group 1-4 years (OR 3.5; 95% CI, 1.2-10.3) compared to 5-14 years, and sleeping with index case (OR 2.7; 95% CI, 1.3-5.5). HIV infection of index case was not associated with SI. CONCLUSIONS HIV-infection was not associated with SI. Increased infectiousness of HIV-infected individuals is likely not an important driver of community influenza transmission.
Collapse
Affiliation(s)
- Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Akhona Tshangela
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Ziyaad Valley-Omar
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa
| | | | - Claire Von Mollendorf
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Orienka Hellferscee
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marietjie Venter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria
| | - Neil Martinson
- Perinatal HIV Research Unit, Klerksdorp-Tshepong Hospital, North West Province, South Africa
| | | | - Meredith McMorrow
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia.,Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - 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
| | - Florette K Treurnicht
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Adam L Cohen
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia.,Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa.,Expanded Programme on Immunization, Department of Immunizations, Vaccines, and Biologicals, World Health Organization, Geneva, Switzerland
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia.,Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa
| |
Collapse
|
7
|
Fine-scale family structure shapes influenza transmission risk in households: Insights from primary schools in Matsumoto city, 2014/15. PLoS Comput Biol 2019; 15:e1007589. [PMID: 31877122 PMCID: PMC6959609 DOI: 10.1371/journal.pcbi.1007589] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 01/14/2020] [Accepted: 12/08/2019] [Indexed: 12/19/2022] Open
Abstract
Households are important settings for the transmission of seasonal influenza. Previous studies found that the per-person risk of within-household transmission decreases with household size. However, more detailed heterogeneities driven by household composition and contact patterns have not been studied. We employed a mathematical model that accounts for infections both from outside and within the household. The model was applied to citywide primary school seasonal influenza surveillance and household surveys from 10,486 students during the 2014/15 season in Matsumoto city, Japan. We compared a range of models to estimate the structure of household transmission and found that familial relationship and household composition strongly influenced the transmission patterns of seasonal influenza in households. Children had a substantially high risk of infection from outside the household (up to 20%) compared with adults (1–3%). Intense transmission was observed within-generation (between children/parents/grandparents) and also between mother and child, with transmission risks typically ranging from 5–20% depending on the transmission route and household composition. Children were identified as the largest source of secondary transmission, with family structure influencing infection risk. We characterised detailed heterogeneity in household transmission patterns of influenza by applying a mathematical model to citywide primary school influenza survey data from 10,486 students in Matsumoto city, Japan, one of the largest-scale household surveys on seasonal influenza. Children were identified as the largest source of secondary transmission, with family structure influencing infection risk. This suggests that vaccinating children would have stronger secondary effects on transmission than would be assumed without taking into account transmission patterns within the household.
Collapse
|
8
|
Buchwald AG, Tamboura B, Haidara FC, Coulibaly F, Doumbia M, Diallo F, Boudova S, Keita AM, Sow SO, Kotloff K, Levine M, Tapia MD. Maternal Influenza Vaccination and the Risk of Laboratory-Confirmed Influenza Among Household Contacts Under the Age of Five in Mali. Am J Trop Med Hyg 2019; 100:159-164. [PMID: 30526742 PMCID: PMC6335916 DOI: 10.4269/ajtmh.18-0450] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Influenza transmission is increased among household contacts. Vaccination decreases transmission; however it is unclear how vaccinating a single individual alters disease risk among household contacts, particularly in regions with low vaccination coverage. Pregnant women were randomized to influenza or control vaccination. Households were visited weekly until infants born to enrolled women reached 6 months. Household contacts younger than 5 years were tested for laboratory-confirmed influenza (LCI). Incidence of LCI and rate ratios (RtR) comparing incidence between vaccine groups were calculated. The secondary infection rate (SIR) was calculated for households where LCI was detected. The H1N1 strain in the vaccine was a match for circulating H1N1 during the study, thus, all analyses were performed for H1N1-LCI and any LCI. A total of 5,345 household contacts younger than 5 years followed for a mean of 228 days (standard deviation [SD] = 45 days) experienced 2,957 influenza-like illness episodes. Incidence of any LCI and H1N1-LCI was 23 (N = 276) and 7.3 per 100,000 days (N = 89), respectively. Household contacts of women who received influenza vaccine had fewer LCI (RtR = 0.90; 95% CI: 0.71, 1.14) and fewer H1N1-LCI (RtR = 0.73; 95% CI: 0.48, 1.11) episodes than contacts in control households. Incidence of LCI and household SIR were low in households of women enrolled in an influenza vaccine trial in Mali. Although low incidence made statistical significance difficult to detect, there was a trend for decreased rates of H1N1-LCI in households where a pregnant mother received influenza vaccination.
Collapse
Affiliation(s)
- Andrea G Buchwald
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland
| | | | | | | | - Moussa Doumbia
- Centre pour le Développement des Vaccins-Mali, Bamako, Mali
| | | | - Sarah Boudova
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland
| | - Adama M Keita
- Centre pour le Développement des Vaccins-Mali, Bamako, Mali
| | - Samba O Sow
- Centre pour le Développement des Vaccins-Mali, Bamako, Mali
| | - Karen Kotloff
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland
| | - Myron Levine
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland
| | - Milagritos D Tapia
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland
| |
Collapse
|
9
|
Kombe IK, Munywoki PK, Baguelin M, Nokes DJ, Medley GF. Model-based estimates of transmission of respiratory syncytial virus within households. Epidemics 2019; 27:1-11. [PMID: 30591267 PMCID: PMC6543068 DOI: 10.1016/j.epidem.2018.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 12/14/2018] [Accepted: 12/14/2018] [Indexed: 12/16/2022] Open
Abstract
INTRODUCTION Respiratory syncytial virus (RSV) causes a significant respiratory disease burden in the under 5 population. The transmission pathway to young children is not fully quantified in low-income settings, and this information is required to design interventions. METHODS We used an individual level transmission model to infer transmission parameters using data collected from 493 individuals distributed across 47 households over a period of 6 months spanning the 2009/2010 RSV season. A total of 208 episodes of RSV were observed from 179 individuals. We model competing transmission risk from within household exposure and community exposure while making a distinction between RSV groups A and B. RESULTS We find that 32-53% of all RSV transmissions are between members of the same household; the rate of pair-wise transmission is 58% (95% CrI: 30-74%) lower in larger households (≥8 occupants) than smaller households; symptomatic individuals are 2-7 times more infectious than asymptomatic individuals i.e. 2.48 (95% CrI: 1.22-5.57) among symptomatic individuals with low viral load and 6.7(95% CrI: 2.56-16) among symptomatic individuals with high viral load; previous infection reduces susceptibility to re-infection within the same epidemic by 47% (95% CrI: 17%-68%) for homologous RSV group and 39% (95%CrI: -8%-69%) for heterologous group; RSV B is more frequently introduced into the household, and RSV A is more rapidly transmitted once in the household. DISCUSSION Our analysis presents the first transmission modelling of cohort data for RSV and we find that it is important to consider the household social structuring and household size when modelling transmission. The increased infectiousness of symptomatic individuals implies that a vaccine against RSV related disease would also have an impact on infection transmission. Together, the weak cross immunity between RSV groups and the possibility of different transmission niches could form part of the explanation for the group co-existence.
Collapse
Affiliation(s)
- Ivy K Kombe
- KEMRI-Wellcome Trust Research Programme, KEMRI Center for Geographical Medical Research-Coast, P.O. Box 230-80108, Kilifi, Kenya; Centre for Mathematical Modelling of Infectious Disease and Department of Global Health and Development, London School of Hygiene and Tropical Medicine, London, WC1H 9SH, UK.
| | - Patrick K Munywoki
- KEMRI-Wellcome Trust Research Programme, KEMRI Center for Geographical Medical Research-Coast, P.O. Box 230-80108, Kilifi, Kenya
| | - Marc Baguelin
- Centre for Mathematical Modelling of Infectious Disease and Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1H 9SH, UK
| | - D James Nokes
- KEMRI-Wellcome Trust Research Programme, KEMRI Center for Geographical Medical Research-Coast, P.O. Box 230-80108, Kilifi, Kenya; School of Life Sciences and Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, University of Warwick, Coventry, CV4 7AL, UK
| | - Graham F Medley
- Centre for Mathematical Modelling of Infectious Disease and Department of Global Health and Development, London School of Hygiene and Tropical Medicine, London, WC1H 9SH, UK
| |
Collapse
|
10
|
Cope RC, Ross JV, Chilver M, Stocks NP, Mitchell L. Characterising seasonal influenza epidemiology using primary care surveillance data. PLoS Comput Biol 2018; 14:e1006377. [PMID: 30114215 PMCID: PMC6112683 DOI: 10.1371/journal.pcbi.1006377] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 08/28/2018] [Accepted: 07/18/2018] [Indexed: 11/19/2022] Open
Abstract
Understanding the epidemiology of seasonal influenza is critical for healthcare resource allocation and early detection of anomalous seasons. It can be challenging to obtain high-quality data of influenza cases specifically, as clinical presentations with influenza-like symptoms may instead be cases of one of a number of alternate respiratory viruses. We use a new dataset of confirmed influenza virological data from 2011-2016, along with high-quality denominators informing a hierarchical observation process, to model seasonal influenza dynamics in New South Wales, Australia. We use approximate Bayesian computation to estimate parameters in a climate-driven stochastic epidemic model, including the basic reproduction number R0, the proportion of the population susceptible to the circulating strain at the beginning of the season, and the probability an infected individual seeks treatment. We conclude that R0 and initial population susceptibility were strongly related, emphasising the challenges of identifying these parameters. Relatively high R0 values alongside low initial population susceptibility were among the results most consistent with these data. Our results reinforce the importance of distinguishing between R0 and the effective reproduction number (Re) in modelling studies. When patients present to their doctor with influenza-like symptoms, they may have influenza, or some other respiratory virus. The only way to discriminate between these viruses is with an expensive test, which is not performed in many cases. Additionally, results other than influenza may not be reported. This means that it can be difficult to determine how much influenza is circulating in the population each season. We used a unique dataset of confirmed influenza with denominators to fit models for seasonal influenza in New South Wales, Australia. Knowing the denominators allowed us to estimate population level trends. We found that the relationship between influenza transmission rates and immunity due to previous infections was critical, with relatively high transmission corresponding to substantial preexisting immunity likely. This existing immunity is critical to understanding and effectively modeling influenza dynamics.
Collapse
Affiliation(s)
- Robert C. Cope
- School of Mathematical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- * E-mail:
| | - Joshua V. Ross
- School of Mathematical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Monique Chilver
- Discipline of General Practice, The University of Adelaide, Adelaide, South Australia, Australia
| | - Nigel P. Stocks
- Discipline of General Practice, The University of Adelaide, Adelaide, South Australia, Australia
| | - Lewis Mitchell
- School of Mathematical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Stream Lead, Data to Decisions CRC, Adelaide, South Australia, Australia
| |
Collapse
|
11
|
le Polain de Waroux O, Cohuet S, Ndazima D, Kucharski AJ, Juan-Giner A, Flasche S, Tumwesigye E, Arinaitwe R, Mwanga-Amumpaire J, Boum Y, Nackers F, Checchi F, Grais RF, Edmunds WJ. Characteristics of human encounters and social mixing patterns relevant to infectious diseases spread by close contact: a survey in Southwest Uganda. BMC Infect Dis 2018; 18:172. [PMID: 29642869 PMCID: PMC5896105 DOI: 10.1186/s12879-018-3073-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 03/27/2018] [Indexed: 11/24/2022] Open
Abstract
Background Quantification of human interactions relevant to infectious disease transmission through social contact is central to predict disease dynamics, yet data from low-resource settings remain scarce. Methods We undertook a social contact survey in rural Uganda, whereby participants were asked to recall details about the frequency, type, and socio-demographic characteristics of any conversational encounter that lasted for ≥5 min (henceforth defined as ‘contacts’) during the previous day. An estimate of the number of ‘casual contacts’ (i.e. < 5 min) was also obtained. Results In total, 566 individuals were included in the study. On average participants reported having routine contact with 7.2 individuals (range 1-25). Children aged 5-14 years had the highest frequency of contacts and the elderly (≥65 years) the fewest (P < 0.001). A strong age-assortative pattern was seen, particularly outside the household and increasingly so for contacts occurring further away from home. Adults aged 25-64 years tended to travel more often and further than others, and males travelled more frequently than females. Conclusion Our study provides detailed information on contact patterns and their spatial characteristics in an African setting. It therefore fills an important knowledge gap that will help more accurately predict transmission dynamics and the impact of control strategies in such areas. Electronic supplementary material The online version of this article (10.1186/s12879-018-3073-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- O le Polain de Waroux
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.
| | | | - D Ndazima
- Epicentre, Uganda Research Centre, Mbarara, Uganda
| | - A J Kucharski
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | | | - S Flasche
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - E Tumwesigye
- Kabwohe Medical Research Centre, Kabwohe, Uganda
| | - R Arinaitwe
- Epicentre, Uganda Research Centre, Mbarara, Uganda
| | - J Mwanga-Amumpaire
- Epicentre, Uganda Research Centre, Mbarara, Uganda.,Mbarara University Of Science and Technology (MUST), Mbarara, Uganda
| | - Y Boum
- Epicentre, Uganda Research Centre, Mbarara, Uganda
| | | | - F Checchi
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | | | - W J Edmunds
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| |
Collapse
|
12
|
Dyson L, Marks M, Crook OM, Sokana O, Solomon AW, Bishop A, Mabey DCW, Hollingsworth TD. Targeted Treatment of Yaws With Household Contact Tracing: How Much Do We Miss? Am J Epidemiol 2018; 187:837-844. [PMID: 29140407 PMCID: PMC5888927 DOI: 10.1093/aje/kwx305] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 08/22/2017] [Indexed: 11/13/2022] Open
Abstract
Yaws is a disabling bacterial infection found primarily in warm and humid tropical areas. The World Health Organization strategy mandates an initial round of total community treatment (TCT) with single-dose azithromycin followed either by further TCT or active case-finding and treatment of cases and their contacts (the Morges strategy). We sought to investigate the effectiveness of the Morges strategy. We employed a stochastic household model to study the transmission of infection using data collected from a pre-TCT survey conducted in the Solomon Islands. We used this model to assess the proportion of asymptomatic infections that occurred in households without active cases. This analysis indicated that targeted treatment of cases and their household contacts would miss a large fraction of asymptomatic infections (65%–100%). This fraction was actually higher at lower prevalences. Even assuming that all active cases and their households were successfully treated, our analysis demonstrated that at all prevalences present in the data set, up to 90% of (active and asymptomatic) infections would not be treated under household-based contact tracing. Mapping was undertaken as part of the study “Epidemiology of Yaws in the Solomon Islands and the Impact of a Trachoma Control Programme,” in September–October 2013.
Collapse
Affiliation(s)
- Louise Dyson
- Mathematics Institute, University of Warwick, Coventry, United Kingdom
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Michael Marks
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Hospital for Tropical Diseases, University College London Hospitals NHS Trust, London, United Kingdom
| | - Oliver M Crook
- Mathematics Institute, University of Warwick, Coventry, United Kingdom
| | - Oliver Sokana
- Ministry of Health and Medical Services, Honiara, Solomon Islands
| | - Anthony W Solomon
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Hospital for Tropical Diseases, University College London Hospitals NHS Trust, London, United Kingdom
| | - Alex Bishop
- Mathematics Institute, University of Warwick, Coventry, United Kingdom
| | - David C W Mabey
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Hospital for Tropical Diseases, University College London Hospitals NHS Trust, London, United Kingdom
| | - T Déirdre Hollingsworth
- Mathematics Institute, University of Warwick, Coventry, United Kingdom
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| |
Collapse
|
13
|
The Determinants of Reported Personal and Household Hygiene Behaviour: A Multi-Country Study. PLoS One 2016; 11:e0159551. [PMID: 27541259 PMCID: PMC4991820 DOI: 10.1371/journal.pone.0159551] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 07/04/2016] [Indexed: 11/19/2022] Open
Abstract
A substantial proportion of the total infectious disease burden world-wide is due to person-to-person spread of pathogens within households. A questionnaire-based survey on the determinants of hand-washing with soap and cleaning of household surfaces was conducted in at least 1000 households in each of twelve countries across the world (N = 12,239). A structural equation model of hygiene behaviour and its consequences derived from theory was then estimated on this dataset for both behaviours, using a maximum likelihood procedure. The analysis showed that the frequency of handwashing with soap is significantly related to how automatically it is performed, and whether or not someone is busy, or tired. Surface cleaning was strongly linked to possessing a cleaning routine, the perception that one is living in a dirty environment and that others are doing the behaviour, whether one has a strong sense of contamination, as well as a felt need to keep one's surroundings tidy. Being concerned with good manners is also linked to the performance of both behaviours. This study is the first to identify the role of manners, orderliness and routine on hygiene behaviours globally. Such findings should prove helpful in designing programs to improve domestic hygiene practices.
Collapse
|
14
|
Information content of household-stratified epidemics. Epidemics 2016; 16:17-26. [PMID: 27663787 DOI: 10.1016/j.epidem.2016.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 02/15/2016] [Accepted: 03/25/2016] [Indexed: 11/23/2022] Open
Abstract
Household structure is a key driver of many infectious diseases, as well as a natural target for interventions such as vaccination programs. Many theoretical and conceptual advances on household-stratified epidemic models are relatively recent, but have successfully managed to increase the applicability of such models to practical problems. To be of maximum realism and hence benefit, they require parameterisation from epidemiological data, and while household-stratified final size data has been the traditional source, increasingly time-series infection data from households are becoming available. This paper is concerned with the design of studies aimed at collecting time-series epidemic data in order to maximize the amount of information available to calibrate household models. A design decision involves a trade-off between the number of households to enrol and the sampling frequency. Two commonly used epidemiological study designs are considered: cross-sectional, where different households are sampled at every time point, and cohort, where the same households are followed over the course of the study period. The search for an optimal design uses Bayesian computationally intensive methods to explore the joint parameter-design space combined with the Shannon entropy of the posteriors to estimate the amount of information in each design. For the cross-sectional design, the amount of information increases with the sampling intensity, i.e., the designs with the highest number of time points have the most information. On the other hand, the cohort design often exhibits a trade-off between the number of households sampled and the intensity of follow-up. Our results broadly support the choices made in existing epidemiological data collection studies. Prospective problem-specific use of our computational methods can bring significant benefits in guiding future study designs.
Collapse
|
15
|
Lydeamore M, Bean N, Black AJ, Ross JV. Choice of Antiviral Allocation Scheme for Pandemic Influenza Depends on Strain Transmissibility, Delivery Delay and Stockpile Size. Bull Math Biol 2016; 78:293-321. [PMID: 26846916 DOI: 10.1007/s11538-016-0144-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 01/20/2016] [Indexed: 02/01/2023]
Abstract
Recently, pandemic response has involved the use of antivirals. These antivirals are often allocated to households dynamically throughout the pandemic with the aim being to retard the spread of infection. A drawback of this is that there is a delay until infection is confirmed and antivirals are delivered. Here an alternative allocation scheme is considered, where antivirals are instead preallocated to households at the start of a pandemic, thus reducing this delay. To compare these two schemes, a deterministic approximation to a novel stochastic household model is derived, which allows efficient computation of key quantities such as the expected epidemic final size, expected early growth rate, expected peak size and expected peak time of the epidemic. It is found that the theoretical best choice of allocation scheme depends on strain transmissibility, the delay in delivering antivirals under a dynamic allocation scheme and the stockpile size. A broad summary is that for realistic stockpile sizes, a dynamic allocation scheme is superior with the important exception of the epidemic final size under a severe pandemic scenario. Our results, viewed in conjunction with the practical considerations of implementing a preallocation scheme, support a focus on attempting to reduce the delay in delivering antivirals under a dynamic allocation scheme during a future pandemic.
Collapse
Affiliation(s)
- Michael Lydeamore
- School of Mathematical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.,School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Nigel Bean
- School of Mathematical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.,ARC Centre of Excellence for Mathematical and Statistical Frontiers, Parkville, VIC, Australia
| | - Andrew J Black
- School of Mathematical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Joshua V Ross
- School of Mathematical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
| |
Collapse
|
16
|
Tsang TK, Lau LLH, Cauchemez S, Cowling BJ. Household Transmission of Influenza Virus. Trends Microbiol 2015; 24:123-133. [PMID: 26612500 PMCID: PMC4733423 DOI: 10.1016/j.tim.2015.10.012] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 10/05/2015] [Accepted: 10/28/2015] [Indexed: 12/13/2022]
Abstract
Human influenza viruses cause regular epidemics and occasional pandemics with a substantial public health burden. Household transmission studies have provided valuable information on the dynamics of influenza transmission. We reviewed published studies and found that once one household member is infected with influenza, the risk of infection in a household contact can be up to 38%, and the delay between onset in index and secondary cases is around 3 days. Younger age was associated with higher susceptibility. In the future, household transmission studies will provide information on transmission dynamics, including the correlation of virus shedding and symptoms with transmission, and the correlation of new measures of immunity with protection against infection. Historically, household cohort studies have provided valuable information on the incidence of respiratory infections and risk factors for infection. However, these studies require substantial resources and can provide limited information on transmission dynamics. Household transmission studies provide an efficient approach to describing the risk of influenza transmission and factors affecting transmission. In these studies, households with at least one member infected by influenza are eligible and are followed intensively for 1–2 weeks to observe secondary transmission within the household. Transmission studies also provide a model for evaluation of interventions in randomized controlled trials, and have been used to determine the efficacy of antiviral drugs for treatment and prophylaxis, and nonpharmaceutical interventions such as face masks and hand hygiene.
Collapse
Affiliation(s)
- Tim K Tsang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Lincoln L H Lau
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Paris, France
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China.
| |
Collapse
|
17
|
Abstract
Model parameter inference has become increasingly popular in recent years in the field of computational epidemiology, especially for models with a large number of parameters. Techniques such as Approximate Bayesian Computation (ABC) or maximum/partial likelihoods are commonly used to infer parameters in phenomenological models that best describe some set of data. These techniques rely on efficient exploration of the underlying parameter space, which is difficult in high dimensions, especially if there are correlations between the parameters in the model that may not be known a priori. The aim of this article is to demonstrate the use of the recently invented Adaptive Metropolis algorithm for exploring parameter space in a practical way through the use of a simple epidemiological model.
Collapse
Affiliation(s)
- Anthony O'Hare
- Computing Science and Mathematics, School of Natural Sciences, University of Stirling , Stirling, United Kingdom
| |
Collapse
|
18
|
Optimal prophylactic vaccination in segregated populations: When can we improve on the equalising strategy? Epidemics 2015; 11:7-13. [DOI: 10.1016/j.epidem.2015.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 01/13/2015] [Accepted: 01/14/2015] [Indexed: 11/17/2022] Open
|
19
|
Ball F, Shaw L. Estimating the within-household infection rate in emerging SIR epidemics among a community of households. J Math Biol 2015; 71:1705-35. [PMID: 25820343 DOI: 10.1007/s00285-015-0872-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 03/06/2015] [Indexed: 11/26/2022]
Abstract
This paper is concerned with estimation of the within-household infection rate γL for a susceptible --> infective --> recovered epidemic among a population of households, from observation of the early, exponentially growing phase of an epidemic. Specifically, it is assumed that an estimate of the exponential growth rate is available from general data on an emerging epidemic and more-detailed, household-level data are available in a sample of households. Estimates of γL obtained using the final size distribution of single-household epidemics are usually biased owing to the emerging nature of the epidemic. A new method, which accounts correctly for the emerging nature of the epidemic, is developed by exploiting the asymptotic theory of supercritical branching processes and proved to yield a strongly consistent estimator of γL as the population and sampled households both tend to infinity in an appropriate fashion. The theory is illustrated by simulations which demonstrate that the new method is feasible for finite populations and numerical studies are used to explore how changes to the parameters governing the spread of an epidemic affect the bias of estimates based on single-household final size distributions.
Collapse
Affiliation(s)
- Frank Ball
- School of Mathematical Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - Laurence Shaw
- School of Mathematical Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| |
Collapse
|
20
|
Social deprivation and burden of influenza: Testing hypotheses and gaining insights from a simulation model for the spread of influenza. Epidemics 2015; 11:71-9. [PMID: 25979284 DOI: 10.1016/j.epidem.2015.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 09/03/2014] [Accepted: 03/15/2015] [Indexed: 11/21/2022] Open
Abstract
Factors associated with the burden of influenza among vulnerable populations have mainly been identified using statistical methodologies. Complex simulation models provide mechanistic explanations, in terms of spatial heterogeneity and contact rates, while controlling other factors and may be used to better understand statistical patterns and, ultimately, design optimal population-level interventions. We extended a sophisticated simulation model, which was applied to forecast epidemics and validated for predictive ability, to identify mechanisms for the empirical relationship between social deprivation and the burden of influenza. Our modeled scenarios and associated epidemic metrics systematically assessed whether neighborhood composition and/or spatial arrangement could qualitatively replicate this empirical relationship. We further used the model to determine consequences of local-scale heterogeneities on larger scale disease spread. Our findings indicated that both neighborhood composition and spatial arrangement were critical to qualitatively match the empirical relationship of interest. Also, when social deprivation was fully included in the model, we observed lower age-based attack rates and greater delay in epidemic peak week in the most socially deprived neighborhoods. Insights from simulation models complement current understandings from statistical-based association studies. Additional insights from our study are: (1) heterogeneous spatial arrangement of neighborhoods is a necessary condition for simulating observed disparities in the burden of influenza and (2) unmeasured factors may lead to a better quantitative match between simulated and observed rate ratio in the burden of influenza between the most and least socially deprived populations.
Collapse
|
21
|
Hsu CY, Yen AMF, Chen LS, Chen HH. Analysis of household data on influenza epidemic with Bayesian hierarchical model. Math Biosci 2015; 261:13-26. [PMID: 25484132 PMCID: PMC7094348 DOI: 10.1016/j.mbs.2014.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 11/14/2014] [Accepted: 11/22/2014] [Indexed: 11/25/2022]
Abstract
Data used for modelling the household transmission of infectious diseases, such as influenza, have inherent multilevel structures and correlated property, which make the widely used conventional infectious disease transmission models (including the Greenwood model and the Reed-Frost model) not directly applicable within the context of a household (due to the crowded domestic condition or socioeconomic status of the household). Thus, at the household level, the effects resulting from individual-level factors, such as vaccination, may be confounded or modified in some way. We proposed the Bayesian hierarchical random-effects (random intercepts and random slopes) model under the context of generalised linear model to capture heterogeneity and variation on the individual, generation, and household levels. It was applied to empirical surveillance data on the influenza epidemic in Taiwan. The parameters of interest were estimated by using the Markov chain Monte Carlo method in conjunction with the Bayesian directed acyclic graphical models. Comparisons between models were made using the deviance information criterion. Based on the result of the random-slope Bayesian hierarchical method under the context of the Reed-Frost transmission model, the regression coefficient regarding the protective effect of vaccination varied statistically significantly from household to household. The result of such a heterogeneity was robust to the use of different prior distributions (including non-informative, sceptical, and enthusiastic ones). By integrating out the uncertainty of the parameters of the posterior distribution, the predictive distribution was computed to forecast the number of influenza cases allowing for random-household effect.
Collapse
Affiliation(s)
- C Y Hsu
- Department of Emergency Medicine, Taipei City Hospital, Zhongxing Branch, Taipei, Taiwan ; Division of Biostatistics, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - A M F Yen
- School of Oral Hygiene, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
| | - L S Chen
- School of Oral Hygiene, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
| | - H H Chen
- Division of Biostatistics, College of Public Health, National Taiwan University, Taipei, Taiwan.
| |
Collapse
|
22
|
Black AJ, Ross JV. Computation of epidemic final size distributions. J Theor Biol 2014; 367:159-165. [PMID: 25497476 DOI: 10.1016/j.jtbi.2014.11.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 11/24/2014] [Accepted: 11/27/2014] [Indexed: 11/17/2022]
Abstract
We develop a new methodology for the efficient computation of epidemic final size distributions for a broad class of Markovian models. We exploit a particular representation of the stochastic epidemic process to derive a method which is both computationally efficient and numerically stable. The algorithms we present are also physically transparent and so allow us to extend this method from the basic SIR model to a model with a phase-type infectious period and another with waning immunity. The underlying theory is applicable to many Markovian models where we wish to efficiently calculate hitting probabilities.
Collapse
Affiliation(s)
- Andrew J Black
- School of Mathematical Sciences, The University of Adelaide, Adelaide SA 5005, Australia.
| | - J V Ross
- School of Mathematical Sciences, The University of Adelaide, Adelaide SA 5005, Australia
| |
Collapse
|
23
|
Chowell G, Nishiura H. Transmission dynamics and control of Ebola virus disease (EVD): a review. BMC Med 2014; 12:196. [PMID: 25300956 PMCID: PMC4207625 DOI: 10.1186/s12916-014-0196-0] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 09/30/2014] [Indexed: 11/22/2022] Open
Abstract
The complex and unprecedented Ebola epidemic ongoing in West Africa has highlighted the need to review the epidemiological characteristics of Ebola Virus Disease (EVD) as well as our current understanding of the transmission dynamics and the effect of control interventions against Ebola transmission. Here we review key epidemiological data from past Ebola outbreaks and carry out a comparative review of mathematical models of the spread and control of Ebola in the context of past outbreaks and the ongoing epidemic in West Africa. We show that mathematical modeling offers useful insights into the risk of a major epidemic of EVD and the assessment of the impact of basic public health measures on disease spread. We also discuss the critical need to collect detailed epidemiological data in real-time during the course of an ongoing epidemic, carry out further studies to estimate the effectiveness of interventions during past outbreaks and the ongoing epidemic, and develop large-scale modeling studies to study the spread and control of viral hemorrhagic fevers in the context of the highly heterogeneous economic reality of African countries.
Collapse
Affiliation(s)
- Gerardo Chowell
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA. .,Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, 31 Center Drive, MSC 2220, Bethesda, MD, 20892-2220, USA.
| | - Hiroshi Nishiura
- Department of Global Health Policy, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 110-0033, Japan.
| |
Collapse
|
24
|
Ball F, Britton T, House T, Isham V, Mollison D, Pellis L, Scalia Tomba G. Seven challenges for metapopulation models of epidemics, including households models. Epidemics 2014; 10:63-7. [PMID: 25843386 DOI: 10.1016/j.epidem.2014.08.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 08/05/2014] [Accepted: 08/08/2014] [Indexed: 10/24/2022] Open
Abstract
This paper considers metapopulation models in the general sense, i.e. where the population is partitioned into sub-populations (groups, patches,...), irrespective of the biological interpretation they have, e.g. spatially segregated large sub-populations, small households or hosts themselves modelled as populations of pathogens. This framework has traditionally provided an attractive approach to incorporating more realistic contact structure into epidemic models, since it often preserves analytic tractability (in stochastic as well as deterministic models) but also captures the most salient structural inhomogeneity in contact patterns in many applied contexts. Despite the progress that has been made in both the theory and application of such metapopulation models, we present here several major challenges that remain for future work, focusing on models that, in contrast to agent-based ones, are amenable to mathematical analysis. The challenges range from clarifying the usefulness of systems of weakly-coupled large sub-populations in modelling the spread of specific diseases to developing a theory for endemic models with household structure. They include also developing inferential methods for data on the emerging phase of epidemics, extending metapopulation models to more complex forms of human social structure, developing metapopulation models to reflect spatial population structure, developing computationally efficient methods for calculating key epidemiological model quantities, and integrating within- and between-host dynamics in models.
Collapse
Affiliation(s)
- Frank Ball
- School of Mathematical Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Tom Britton
- Department of Mathematics, Stockholm University, Stockholm 106 91, Sweden
| | - Thomas House
- Warwick Infectious Disease Epidemiology Research Centre (WIDER) and Warwick Mathematics Institute, University of Warwick, Coventry CV4 7AL, UK
| | - Valerie Isham
- Department of Statistical Science, University College London, London WC1E 6BT, UK
| | - Denis Mollison
- Department of Actuarial Mathematics and Statistics, Heriot-Watt University, Edinburgh EH14 4AS, Scotland, UK
| | - Lorenzo Pellis
- Warwick Infectious Disease Epidemiology Research Centre (WIDER) and Warwick Mathematics Institute, University of Warwick, Coventry CV4 7AL, UK
| | | |
Collapse
|
25
|
Malik R, Deardon R, Kwong GP, Cowling BJ. Individual-level modeling of the spread of influenza within households. J Appl Stat 2014. [DOI: 10.1080/02664763.2014.881787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
26
|
Lee B, Haidari L, Lee M. Modelling during an emergency: the 2009 H1N1 influenza pandemic. Clin Microbiol Infect 2013; 19:1014-22. [DOI: 10.1111/1469-0691.12284] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
27
|
Black AJ, House T, Keeling MJ, Ross JV. Epidemiological consequences of household-based antiviral prophylaxis for pandemic influenza. J R Soc Interface 2013; 10:20121019. [PMID: 23389899 PMCID: PMC3627116 DOI: 10.1098/rsif.2012.1019] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Antiviral treatment offers a fast acting alternative to vaccination; as such it is viewed as a first-line of defence against pandemic influenza in protecting families and households once infection has been detected. In clinical trials, antiviral treatments have been shown to be efficacious in preventing infection, limiting disease and reducing transmission, yet their impact at containing the 2009 influenza A(H1N1)pdm outbreak was limited. To understand this seeming discrepancy, we develop a general and computationally efficient model for studying household-based interventions. This allows us to account for uncertainty in quantities relevant to the 2009 pandemic in a principled way, accounting for the heterogeneity and variability in each epidemiological process modelled. We find that the population-level effects of delayed antiviral treatment and prophylaxis mean that their limited overall impact is quantitatively consistent (at current levels of precision) with their reported clinical efficacy under ideal conditions. Hence, effective control of pandemic influenza with antivirals is critically dependent on early detection and delivery ideally within 24 h.
Collapse
Affiliation(s)
- Andrew J Black
- Stochastic Modelling Group, School of Mathematical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | | | | | | |
Collapse
|
28
|
Mizumoto K, Nishiura H, Yamamoto T. Effectiveness of antiviral prophylaxis coupled with contact tracing in reducing the transmission of the influenza A (H1N1-2009): a systematic review. Theor Biol Med Model 2013; 10:4. [PMID: 23324555 PMCID: PMC3563494 DOI: 10.1186/1742-4682-10-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 01/14/2013] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND During the very early stage of the 2009 pandemic, mass chemoprophylaxis was implemented as part of containment measure. The purposes of the present study were to systematically review the retrospective studies that investigated the effectiveness of antiviral prophylaxis during the 2009 pandemic, and to explicitly estimate the effectiveness by employing a mathematical model. METHODS A systematic review identified 17 articles that clearly defined the cases and identified exposed individuals based on contact tracing. Analysing a specific school-driven outbreak, we estimated the effectiveness of antiviral prophylaxis using a renewal equation model. Other parameters, including the reproduction number and the effectiveness of antiviral treatment and school closure, were jointly estimated. RESULTS Based on the systematic review, median secondary infection risks (SIRs) among exposed individuals with and without prophylaxis were estimated at 2.1% (quartile: 0, 12.2) and 16.6% (quartile: 8.4, 32.4), respectively. A very high heterogeneity in the SIR was identified with an estimated I2 statistic at 71.8%. From the outbreak data in Madagascar, the effectiveness of mass chemoprophylaxis in reducing secondary transmissions was estimated to range from 92.8% to 95.4% according to different model assumptions and likelihood functions, not varying substantially as compared to other parameters. CONCLUSIONS Only based on the meta-analysis of retrospective studies with different study designs and exposure settings, it was not feasible to estimate the effectiveness of antiviral prophylaxis in reducing transmission. However, modelling analysis of a single outbreak successfully yielded an estimate of the effectiveness that appeared to be robust to model assumptions. Future studies should fill the data gap that has existed in observational studies and allow mathematical models to be used for the analysis of meta-data.
Collapse
Affiliation(s)
- Kenji Mizumoto
- School of Public Health, The University of Hong Kong, 100 Cyberport Road, Pokfulam, Hong Kong, China
| | | | | |
Collapse
|
29
|
Toward unbiased assessment of treatment and prevention: modeling household transmission of pandemic influenza. BMC Med 2012; 10:118. [PMID: 23046539 PMCID: PMC3520753 DOI: 10.1186/1741-7015-10-118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 10/09/2012] [Indexed: 11/23/2022] Open
Abstract
Providing valid and reliable estimates of the transmissibility and severity of pandemic influenza in real time is key to guide public health policymaking. In particular, early estimates of the transmissibility are indispensable for determining the type and intensity of interventions. A recent study by House and colleagues in BMC Medicine devised a stochastic transmission model to estimate the unbiased risk of transmission within households, applying the method to datasets of the 2009 A/H1N1 influenza pandemic. Here, we discuss future challenges in household transmission studies and underscore the need to systematically collect epidemiological data to decipher the household transmission dynamics. We emphasize the need to consider three critical issues for future improvements: (i) capturing age-dependent heterogeneity within households calls for intensive modeling efforts, (ii) the timeline of observation during the course of an epidemic and the length of follow-up should be aligned with study objectives, and (iii) the use of laboratory methods, especially molecular techniques, is encouraged to distinguish household transmissions from those arising in the community.See related article: http://www.biomedcentral.com/1741-7015/10/117.
Collapse
|