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Eren ZB, Vatansever C, Kabadayı B, Haykar B, Kuloğlu ZE, Ay S, Nurlybayeva K, Eyikudamacı G, Barlas T, Palaoğlu E, Beşli Y, Kuşkucu MA, Ergönül Ö, Can F. Surveillance of respiratory viruses by aerosol screening in indoor air as an early warning system for epidemics. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13303. [PMID: 38982659 PMCID: PMC11233404 DOI: 10.1111/1758-2229.13303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 05/15/2024] [Indexed: 07/11/2024]
Abstract
The development of effective methods for the surveillance of seasonal respiratory viruses is required for the timely management of outbreaks. We aimed to survey Influenza-A, Influenza-B, RSV-A, Rhinovirus and SARS-CoV-2 surveillance in a tertiary hospital and a campus over 5 months. The effectiveness of air screening as an early warning system for respiratory viruses was evaluated in correlation with respiratory tract panel test results. The overall viral positivity was higher on the campus than in the hospital (55.0% vs. 38.0%). Influenza A was the most prevalent pathogen in both locations. There were two influenza peaks (42nd and 49th weeks) in the hospital air, and a delayed peak was detected on campus in the 1st-week of January. Panel tests indicated a high rate of Influenza A in late December. RSV-A-positivity was higher on the campus than the hospital (21.6% vs. 7.4%). Moreover, we detected two RSV-A peaks in the campus air (48th and 51st weeks) but only one peak in the hospital and panel tests (week 49). Although rhinovirus was the most common pathogen in panel tests, rhinovirus positivity was low in air samples. The air screening for Influenza-B and SARS-Cov-2 revealed comparable positivity rates with panel tests. Air screening can be integrated into surveillance programs to support infection control programs for potential epidemics of respiratory virus infections except for rhinoviruses.
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Affiliation(s)
| | - Cansel Vatansever
- Koç University İşBank Center for Infectious Diseases (KUISCID)IstanbulTurkey
| | | | | | - Zeynep Ece Kuloğlu
- Koç University İşBank Center for Infectious Diseases (KUISCID)IstanbulTurkey
- Koç UniversityGraduate School of Health SciencesIstanbulTurkey
| | - Sedat Ay
- Koç University School of MedicineIstanbulTurkey
| | | | - Gül Eyikudamacı
- Koç University İşBank Center for Infectious Diseases (KUISCID)IstanbulTurkey
- Koç UniversityGraduate School of Health SciencesIstanbulTurkey
| | - Tayfun Barlas
- Koç University İşBank Center for Infectious Diseases (KUISCID)IstanbulTurkey
| | - Erhan Palaoğlu
- Department of Clinical LaboratoryAmerican HospitalIstanbulTurkey
| | - Yeşim Beşli
- Department of Clinical LaboratoryAmerican HospitalIstanbulTurkey
| | - Mert Ahmet Kuşkucu
- Koç University İşBank Center for Infectious Diseases (KUISCID)IstanbulTurkey
- Department of Medical MicrobiologyKoç University School of MedicineIstanbulTurkey
| | - Önder Ergönül
- Koç University İşBank Center for Infectious Diseases (KUISCID)IstanbulTurkey
- Department of Infectious Disease and Clinical MicrobiologyKoç University School of MedicineIstanbulTurkey
| | - Fusun Can
- Koç University İşBank Center for Infectious Diseases (KUISCID)IstanbulTurkey
- Department of Medical MicrobiologyKoç University School of MedicineIstanbulTurkey
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2
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Hay JA, Zhu H, Jiang CQ, Kwok KO, Shen R, Kucharski A, Yang B, Read JM, Lessler J, Cummings DAT, Riley S. Reconstructed influenza A/H3N2 infection histories reveal variation in incidence and antibody dynamics over the life course. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.18.24304371. [PMID: 38562868 PMCID: PMC10984066 DOI: 10.1101/2024.03.18.24304371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Humans experience many influenza infections over their lives, resulting in complex and varied immunological histories. Although experimental and quantitative analyses have improved our understanding of the immunological processes defining an individual's antibody repertoire, how these within-host processes are linked to population-level influenza epidemiology remains unclear. Here, we used a multi-level mathematical model to jointly infer antibody dynamics and individual-level lifetime influenza A/H3N2 infection histories for 1,130 individuals in Guangzhou, China, using 67,683 haemagglutination inhibition (HI) assay measurements against 20 A/H3N2 strains from repeat serum samples collected between 2009 and 2015. These estimated infection histories allowed us to reconstruct historical seasonal influenza patterns and to investigate how influenza incidence varies over time, space and age in this population. We estimated median annual influenza infection rates to be approximately 18% from 1968 to 2015, but with substantial variation between years. 88% of individuals were estimated to have been infected at least once during the study period (2009-2015), and 20% were estimated to have three or more infections in that time. We inferred decreasing infection rates with increasing age, and found that annual attack rates were highly correlated across all locations, regardless of their distance, suggesting that age has a stronger impact than fine-scale spatial effects in determining an individual's antibody profile. Finally, we reconstructed each individual's expected antibody profile over their lifetime and inferred an age-stratified relationship between probability of infection and HI titre. Our analyses show how multi-strain serological panels provide rich information on long term, epidemiological trends, within-host processes and immunity when analyzed using appropriate inference methods, and adds to our understanding of the life course epidemiology of influenza A/H3N2.
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Affiliation(s)
- James A. Hay
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, Imperial College London
| | - Huachen Zhu
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases/MOE Joint Laboratory for International Collaboration in Virology and Emerging Infectious Diseases, Joint Institute of Virology (Shantou University/The University of Hong Kong), Shantou University, Shantou, China
- State Key Laboratory of Emerging Infectious Diseases / World Health Organization Influenza Reference Laboratory, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- 5EKIH (Gewuzhikang) Pathogen Research Institute, Guangdong, China
| | | | - Kin On Kwok
- The Jockey Club School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- Hong Kong Institute of Asia-Pacific Studies, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Ruiyin Shen
- Guangzhou No.12 Hospital, Guangzhou, Guangdong, China
| | - Adam Kucharski
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, United Kingdom
| | - Bingyi Yang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Jonathan M. Read
- Centre for Health Informatics Computing and Statistics, Lancaster University, Lancaster, United Kingdom
| | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
- Department of Epidemiology, UNC Gillings School of Global Public Health, Chapel Hill, United States
- UNC Carolina Population Center, Chapel Hill, United States
| | - Derek A. T. Cummings
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, Imperial College London
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3
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McCreesh N, Mohlamonyane M, Edwards A, Olivier S, Dikgale K, Dayi N, Gareta D, Wood R, Grant AD, White RG, Middelkoop K. Improving Estimates of Social Contact Patterns for Airborne Transmission of Respiratory Pathogens. Emerg Infect Dis 2022; 28:2016-2026. [PMID: 36048756 PMCID: PMC9514345 DOI: 10.3201/eid2810.212567] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Data on social contact patterns are widely used to parameterize age-mixing matrices in mathematical models of infectious diseases. Most studies focus on close contacts only (i.e., persons spoken with face-to-face). This focus may be appropriate for studies of droplet and short-range aerosol transmission but neglects casual or shared air contacts, who may be at risk from airborne transmission. Using data from 2 provinces in South Africa, we estimated age mixing patterns relevant for droplet transmission, nonsaturating airborne transmission, and Mycobacterium tuberculosis transmission, an airborne infection where saturation of household contacts occurs. Estimated contact patterns by age did not vary greatly between the infection types, indicating that widespread use of close contact data may not be resulting in major inaccuracies. However, contact in persons >50 years of age was lower when we considered casual contacts, and therefore the contribution of older age groups to airborne transmission may be overestimated.
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4
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Correlates of the country differences in the infection and mortality rates during the first wave of the COVID-19 pandemic: evidence from Bayesian model averaging. Sci Rep 2022; 12:7099. [PMID: 35501339 PMCID: PMC9058748 DOI: 10.1038/s41598-022-10894-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 04/07/2022] [Indexed: 11/24/2022] Open
Abstract
The COVID-19 pandemic resulted in great discrepancies in both infection and mortality rates between countries. Besides the biological and epidemiological factors, a multitude of social and economic criteria also influenced the extent to which these discrepancies appeared. Consequently, there is an active debate regarding the critical socio-economic and health factors that correlate with the infection and mortality rates outcome of the pandemic. Here, we leverage Bayesian model averaging techniques and country level data to investigate whether 28 variables, which describe a diverse set of health and socio-economic characteristics, correlate with the final number of infections and deaths during the first wave of the coronavirus pandemic. We show that only a few variables are able to robustly correlate with these outcomes. To understand the relationship between the potential correlates in explaining the infection and death rates, we create a Jointness Space. Using this space, we conclude that the extent to which each variable is able to provide a credible explanation for the COVID-19 infections/mortality outcome varies between countries because of their heterogeneous features.
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5
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Lovell-Read FA, Shen S, Thompson RN. Estimating local outbreak risks and the effects of non-pharmaceutical interventions in age-structured populations: SARS-CoV-2 as a case study. J Theor Biol 2022; 535:110983. [PMID: 34915042 PMCID: PMC8670853 DOI: 10.1016/j.jtbi.2021.110983] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 12/02/2021] [Accepted: 12/07/2021] [Indexed: 12/12/2022]
Abstract
During the COVID-19 pandemic, non-pharmaceutical interventions (NPIs) including school closures, workplace closures and social distancing policies have been employed worldwide to reduce transmission and prevent local outbreaks. However, transmission and the effectiveness of NPIs depend strongly on age-related factors including heterogeneities in contact patterns and pathophysiology. Here, using SARS-CoV-2 as a case study, we develop a branching process model for assessing the risk that an infectious case arriving in a new location will initiate a local outbreak, accounting for the age distribution of the host population. We show that the risk of a local outbreak depends on the age of the index case, and we explore the effects of NPIs targeting individuals of different ages. Social distancing policies that reduce contacts outside of schools and workplaces and target individuals of all ages are predicted to reduce local outbreak risks substantially, whereas school closures have a more limited impact. In the scenarios considered here, when different NPIs are used in combination the risk of local outbreaks can be eliminated. We also show that heightened surveillance of infectious individuals reduces the level of NPIs required to prevent local outbreaks, particularly if enhanced surveillance of symptomatic cases is combined with efforts to find and isolate nonsymptomatic infected individuals. Our results reflect real-world experience of the COVID-19 pandemic, during which combinations of intense NPIs have reduced transmission and the risk of local outbreaks. The general modelling framework that we present can be used to estimate local outbreak risks during future epidemics of a range of pathogens, accounting fully for age-related factors.
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Affiliation(s)
| | - Silvia Shen
- Mathematical Institute, University of Oxford, Oxford, United Kingdom; Pembroke College, University of Oxford, Oxford, United Kingdom
| | - Robin N Thompson
- Mathematics Institute, University of Warwick, Coventry, United Kingdom; The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, United Kingdom
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6
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Kingston R, Routledge I, Bhatt S, Bowman LR. Novel Epidemic Metrics to Communicate Outbreak Risk at the Municipality Level: Dengue and Zika in the Dominican Republic. Viruses 2022; 14:v14010162. [PMID: 35062366 PMCID: PMC8781936 DOI: 10.3390/v14010162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 12/28/2022] Open
Abstract
Arboviruses remain a significant cause of morbidity, mortality and economic cost across the global human population. Epidemics of arboviral disease, such as Zika and dengue, also cause significant disruption to health services at local and national levels. This study examined 2014-2016 Zika and dengue epidemic data at the sub-national level to characterise transmission across the Dominican Republic. For each municipality, spatio-temporal mapping was used to characterise disease burden, while data were age and sex standardised to quantify burden distributions among the population. In separate analyses, time-ordered data were combined with the underlying disease migration interval distribution to produce a network of likely transmission chain events, displayed using transmission chain likelihood matrices. Finally, municipal-specific reproduction numbers (Rm) were established using a Wallinga-Teunis matrix. Dengue and Zika epidemics peaked during weeks 39-52 of 2015 and weeks 14-27 of 2016, respectively. At the provincial level, dengue attack rates were high in Hermanas Mirabal and San José de Ocoa (58.1 and 49.2 cases per 10,000 population, respectively), compared with the Zika burden, which was highest in Independencia and San José de Ocoa (21.2 and 13.4 cases per 10,000 population, respectively). Across municipalities, high disease burden was observed in Cotuí (622 dengue cases per 10,000 population) and Jimani (32 Zika cases per 10,000 population). Municipal infector-infectee transmission likelihood matrices identified seven 0% likelihood transmission events throughout the dengue epidemic and two 0% likelihood transmission events during the Zika epidemic. Municipality reproduction numbers (Rm) were consistently higher, and persisted for a greater duration, during the Zika epidemic (Rm = 1.0) than during the dengue epidemic (Rm < 1.0). This research highlights the importance of disease surveillance in land border municipalities as an early warning for infectious disease transmission. It also demonstrates that a high number of importation events are required to sustain transmission in endemic settings, and vice versa for newly emerged diseases. The inception of a novel epidemiological metric, Rm, reports transmission risk using standardised spatial units, and can be used to identify high transmission risk municipalities to better focus public health interventions for dengue, Zika and other infectious diseases.
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Mandal S, Arinaminpathy N, Bhargava B, Panda S. Responsible travel to and within India during the COVID-19 pandemic. J Travel Med 2021; 28:6369825. [PMID: 34519335 PMCID: PMC8499887 DOI: 10.1093/jtm/taab147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/05/2021] [Accepted: 09/07/2021] [Indexed: 02/04/2023]
Abstract
Following the ‘second wave’ of COVID-19 in India, there has been an upsurge of domestic travel to holiday destinations, particularly Himalayan mountain towns. Modelling suggests that such travel could enhance the peak of a third wave in these states by almost 50%. Principles of ‘responsible travel’ should be adhered to.
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Affiliation(s)
- Sandip Mandal
- Indian Council of Medical Research, New Delhi 110029, India
| | - Nimalan Arinaminpathy
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
| | | | - Samiran Panda
- Indian Council of Medical Research, New Delhi 110029, India
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8
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Vinh DN, Nhat NTD, de Bruin E, Vy NHT, Thao TTN, Phuong HT, Anh PH, Todd S, Quan TM, Thanh NTL, Lien NTN, Ha NTH, Hong TTK, Thai PQ, Choisy M, Nguyen TD, Simmons CP, Thwaites GE, Clapham HE, Chau NVV, Koopmans M, Boni MF. Age-seroprevalence curves for the multi-strain structure of influenza A virus. Nat Commun 2021; 12:6680. [PMID: 34795239 PMCID: PMC8602397 DOI: 10.1038/s41467-021-26948-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/27/2021] [Indexed: 11/21/2022] Open
Abstract
The relationship between age and seroprevalence can be used to estimate the annual attack rate of an infectious disease. For pathogens with multiple serologically distinct strains, there is a need to describe composite exposure to an antigenically variable group of pathogens. In this study, we assay 24,402 general-population serum samples, collected in Vietnam between 2009 to 2015, for antibodies to eleven human influenza A strains. We report that a principal components decomposition of antibody titer data gives the first principal component as an appropriate surrogate for seroprevalence; this results in annual attack rate estimates of 25.6% (95% CI: 24.1% - 27.1%) for subtype H3 and 16.0% (95% CI: 14.7% - 17.3%) for subtype H1. The remaining principal components separate the strains by serological similarity and associate birth cohorts with their particular influenza histories. Our work shows that dimensionality reduction can be used on human antibody profiles to construct an age-seroprevalence relationship for antigenically variable pathogens.
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MESH Headings
- Algorithms
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Geography
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Humans
- Immunoglobulin G/blood
- Immunoglobulin G/immunology
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H1N1 Subtype/physiology
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza A Virus, H3N2 Subtype/physiology
- Influenza A virus/classification
- Influenza A virus/immunology
- Influenza A virus/physiology
- Influenza, Human/epidemiology
- Influenza, Human/immunology
- Influenza, Human/virology
- Models, Theoretical
- Seroepidemiologic Studies
- Time Factors
- Vietnam/epidemiology
- Virus Replication/immunology
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Affiliation(s)
- Dao Nguyen Vinh
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Duy Nhat
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Erwin de Bruin
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Nguyen Ha Thao Vy
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Tran Thi Nhu Thao
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Huynh Thi Phuong
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Pham Hong Anh
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Stacy Todd
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Liverpool School of Tropical Medicine, Liverpool, UK
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, England
| | - Tran Minh Quan
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Le Thanh
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | | | | | | | - Pham Quang Thai
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Marc Choisy
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tran Dang Nguyen
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Cameron P Simmons
- Institute of Vector Borne Disease, Monash University, Melbourne, VIC, Australia
| | - Guy E Thwaites
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Hannah E Clapham
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | | | - Marion Koopmans
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Maciej F Boni
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA.
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9
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Liu CY, Berlin J, Kiti MC, Del Fava E, Grow A, Zagheni E, Melegaro A, Jenness SM, Omer SB, Lopman B, Nelson K. Rapid Review of Social Contact Patterns During the COVID-19 Pandemic. Epidemiology 2021; 32:781-791. [PMID: 34392254 PMCID: PMC8478104 DOI: 10.1097/ede.0000000000001412] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/02/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Physical distancing measures aim to reduce person-to-person contact, a key driver of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission. In response to unprecedented restrictions on human contact during the coronavirus disease 2019 (COVID-19) pandemic, studies measured social contact patterns under the implementation of physical distancing measures. This rapid review synthesizes empirical data on the changing social contact patterns during the COVID-19 pandemic. METHOD We conducted a systematic review using PubMed, Medline, Embase, and Google Scholar following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We descriptively compared the distribution of contacts observed during the pandemic to pre-COVID data across countries to explore changes in contact patterns during physical distancing measures. RESULTS We identified 12 studies reporting social contact patterns during the COVID-19 pandemic. Eight studies were conducted in European countries and eleven collected data during the initial mitigation period in the spring of 2020 marked by government-declared lockdowns. Some studies collected additional data after relaxation of initial mitigation. Most study settings reported a mean of between 2 and 5 contacts per person per day, a substantial reduction compared to pre-COVID rates, which ranged from 7 to 26 contacts per day. This reduction was pronounced for contacts outside of the home. Consequently, levels of assortative mixing by age substantially declined. After relaxation of initial mitigation, mean contact rates increased but did not return to pre-COVID levels. Increases in contacts post-relaxation were driven by working-age adults. CONCLUSION Information on changes in contact patterns during physical distancing measures can guide more realistic representations of contact patterns in mathematical models for SARS-CoV-2 transmission.
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Affiliation(s)
- Carol Y. Liu
- From the Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA
| | - Juliette Berlin
- From the Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA
| | - Moses C. Kiti
- From the Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA
| | - Emanuele Del Fava
- Laboratory of Digital and Computational Demography, Max Planck Institute for Demographic Research, Rostock, Germany
| | - André Grow
- Laboratory of Digital and Computational Demography, Max Planck Institute for Demographic Research, Rostock, Germany
| | - Emilio Zagheni
- Laboratory of Digital and Computational Demography, Max Planck Institute for Demographic Research, Rostock, Germany
| | - Alessia Melegaro
- Department of Social and Political Sciences, Centre for Research on Social Dynamics and Public Policy and Covid Crisis Lab, Bocconi University, Milan, Italy
| | - Samuel M. Jenness
- From the Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA
| | - Saad B. Omer
- Department of Epidemiology of Microbial Diseases, Yale Institute of Global Health, Yale University, CT
| | - Benjamin Lopman
- From the Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA
| | - Kristin Nelson
- From the Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA
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10
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Sharif O, Islam MR, Hasan MZ, Kabir MA, Hasan ME, AlQahtani SA, Xu G. Analyzing the Impact of Demographic Variables on Spreading and Forecasting COVID-19. JOURNAL OF HEALTHCARE INFORMATICS RESEARCH 2021; 6:72-90. [PMID: 34549163 PMCID: PMC8444526 DOI: 10.1007/s41666-021-00105-8] [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: 11/10/2020] [Revised: 07/13/2021] [Accepted: 08/26/2021] [Indexed: 12/24/2022]
Abstract
The aim of this study is to analyse the coronavirus disease 2019 (COVID-19) outbreak in Bangladesh. This study investigates the impact of demographic variables on the spread of COVID-19 as well as tries to forecast the COVID-19 infected numbers. First of all, this study uses Fisher's Exact test to investigate the association between the infected groups of COVID-19 and demographical variables. Second, it exploits the ANOVA test to examine significant difference in the mean infected number of COVID-19 cases across the population density, literacy rate, and regions/divisions in Bangladesh. Third, this research predicts the number of infected cases in the epidemic peak region of Bangladesh for the year 2021. As a result, from the Fisher's Exact test, we find a very strong significant association between the population density groups and infected groups of COVID-19. And, from the ANOVA test, we observe a significant difference in the mean infected number of COVID-19 cases across the five different population density groups. Besides, the prediction model shows that the cumulative number of infected cases would be raised to around 500,000 in the most densely region of Bangladesh, Dhaka division.
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Affiliation(s)
- Omar Sharif
- Daffodil International University, Dhaka, Bangladesh
| | - Md Rafiqul Islam
- Advanced Analytics Institute (AAi), University of Technology Sydney (UTS), Ultimo, Australia
| | - Md Zobaer Hasan
- School of Science, Monash University Malaysia, Subang Jaya, Selangor D. E. Malaysia
| | - Muhammad Ashad Kabir
- School of Computing and Mathematics, Charles Sturt University, Bathurst, NSW Australia
| | | | - Salman A AlQahtani
- College of Computer and Information Sciences, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Guandong Xu
- Advanced Analytics Institute (AAi), University of Technology Sydney (UTS), Ultimo, Australia
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11
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Gugole F, Coffeng LE, Edeling W, Sanderse B, de Vlas SJ, Crommelin D. Uncertainty quantification and sensitivity analysis of COVID-19 exit strategies in an individual-based transmission model. PLoS Comput Biol 2021; 17:e1009355. [PMID: 34534205 PMCID: PMC8480746 DOI: 10.1371/journal.pcbi.1009355] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 09/29/2021] [Accepted: 08/17/2021] [Indexed: 11/18/2022] Open
Abstract
Many countries are currently dealing with the COVID-19 epidemic and are searching for an exit strategy such that life in society can return to normal. To support this search, computational models are used to predict the spread of the virus and to assess the efficacy of policy measures before actual implementation. The model output has to be interpreted carefully though, as computational models are subject to uncertainties. These can stem from, e.g., limited knowledge about input parameters values or from the intrinsic stochastic nature of some computational models. They lead to uncertainties in the model predictions, raising the question what distribution of values the model produces for key indicators of the severity of the epidemic. Here we show how to tackle this question using techniques for uncertainty quantification and sensitivity analysis. We assess the uncertainties and sensitivities of four exit strategies implemented in an agent-based transmission model with geographical stratification. The exit strategies are termed Flattening the Curve, Contact Tracing, Intermittent Lockdown and Phased Opening. We consider two key indicators of the ability of exit strategies to avoid catastrophic health care overload: the maximum number of prevalent cases in intensive care (IC), and the total number of IC patient-days in excess of IC bed capacity. Our results show that uncertainties not directly related to the exit strategies are secondary, although they should still be considered in comprehensive analysis intended to inform policy makers. The sensitivity analysis discloses the crucial role of the intervention uptake by the population and of the capability to trace infected individuals. Finally, we explore the existence of a safe operating space. For Intermittent Lockdown we find only a small region in the model parameter space where the key indicators of the model stay within safe bounds, whereas this region is larger for the other exit strategies.
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Affiliation(s)
| | - Luc E. Coffeng
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Wouter Edeling
- Centrum Wiskunde & Informatica, Amsterdam, The Netherlands
| | | | - Sake J. de Vlas
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Daan Crommelin
- Centrum Wiskunde & Informatica, Amsterdam, The Netherlands
- Korteweg-de Vries Institute for Mathematics, University of Amsterdam, Amsterdam, The Netherlands
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12
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Conceição GMDS, Barbosa GL, Lorenz C, Bocewicz ACD, Santana LMR, Marques CCDA, Chiaravalloti-Neto F. Effect of social isolation in dengue cases in the state of Sao Paulo, Brazil: An analysis during the COVID-19 pandemic. Travel Med Infect Dis 2021; 44:102149. [PMID: 34455075 DOI: 10.1016/j.tmaid.2021.102149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND Studies have shown that human mobility is an important factor in dengue epidemiology. Changes in mobility resulting from COVID-19 pandemic set up a real-life situation to test this hypothesis. Our objective was to evaluate the effect of reduced mobility due to this pandemic in the occurrence of dengue in the state of São Paulo, Brazil. METHOD It is an ecological study of time series, developed between January and August 2020. We use the number of confirmed dengue cases and residential mobility, on a daily basis, from secondary information sources. Mobility was represented by the daily percentage variation of residential population isolation, obtained from the Google database. We modeled the relationship between dengue occurrence and social distancing by negative binomial regression, adjusted for seasonality. We represent the social distancing dichotomously (isolation versus no isolation) and consider lag for isolation from the dates of occurrence of dengue. RESULTS The risk of dengue decreased around 9.1% (95% CI: 14.2 to 3.7) in the presence of isolation, considering a delay of 20 days between the degree of isolation and the dengue first symptoms. CONCLUSIONS We have shown that mobility can play an important role in the epidemiology of dengue and should be considered in surveillance and control activities.
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Affiliation(s)
| | - Gerson Laurindo Barbosa
- Endemics Control Superintendence (SUCEN), Sao Paulo State Department of Health, Sao Paulo, Brazil
| | - Camila Lorenz
- Department of Epidemiology, School of Public Health, University of Sao Paulo, Sao Paulo, Brazil.
| | | | - Lidia Maria Reis Santana
- Epidemiological Surveillance Center "Professor Alexandre Vranjac" - Sao Paulo State Department of Health (CVE/SES-SP), Sao Paulo, Brazil; Federal University of São Paulo (UNIFESP), Sao Paulo, Brazil
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13
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Lee H, Lee H, Song KH, Kim ES, Park JS, Jung J, Ahn S, Jeong EK, Park H, Kim HB. Impact of Public Health Interventions on Seasonal Influenza Activity During the COVID-19 Outbreak in Korea. Clin Infect Dis 2021; 73:e132-e140. [PMID: 32472687 PMCID: PMC7314207 DOI: 10.1093/cid/ciaa672] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 05/28/2020] [Indexed: 12/12/2022] Open
Abstract
Background COVID-19 was introduced in Korea early and experienced a large outbreak in mid-February. We aimed to review the public health interventions used during the COVID-19 outbreak and describe the impact on seasonal influenza activity in Korea. Methods National response strategies and public health interventions, along with daily COVID-19 confirmed cases in Korea were reviewed during the pandemic. National influenza surveillance data were compared between seven sequential seasons. Characteristics of each season, including the rate of influenza-like illness (ILI), duration of epidemic, date of termination of epidemic, distribution of influenza virus strain and hospitalization were analyzed. Results After various public health interventions including enforced public education on hand hygiene, cough etiquette and staying at home with respiratory symptoms, universal mask use in public places, refrain from non-essential social activities and school closure, the duration of the influenza epidemic in 2019/2020 decreased by 6-12 weeks and the influenza activity peak rated 49.8 ILI/1,000 visits compared to 71.9-86.2 ILI/1,000 visits of previous seasons. During the period of enforced social distancing from week 9 to 17 of 2020, influenza hospitalization cases were 11.9-26.9-fold lower compared with previous seasons. During the 2019/2020 season, influenza B accounted for only 4%, in contrast with previous seasons in which influenza B accounted for 26.6% to 54.9% of all cases. Conclusions Efforts to activate high level national response not only led to a decrease in COVID-19, but also substantial decrease in seasonal influenza activity. Interventions applied to control COVID-19 may serve as useful strategies for prevention and control of influenza in upcoming seasons.
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Affiliation(s)
- Hyunju Lee
- Department of Pediatrics, Seoul National University Bundang Hospital, Seongnam, Republic of Korea.,Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Heeyoung Lee
- Seoul National University College of Medicine, Seoul, Republic of Korea.,Center for Public Health, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Kyoung-Ho Song
- Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Eu Suk Kim
- Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Jeong Su Park
- Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Jongtak Jung
- Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Soyeon Ahn
- Department of Medical Research Collaborating Center, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Eun Kyeong Jeong
- Korea Centers for Disease Control and Prevention, Cheongju, Republic of Korea
| | - Hyekyung Park
- Korea Centers for Disease Control and Prevention, Cheongju, Republic of Korea
| | - Hong Bin Kim
- Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
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14
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Singh A, Chattopadhyay A. COVID-19 recovery rate and its association with development. INDIAN JOURNAL OF MEDICAL SCIENCES 2021; 73:8-14. [PMCID: PMC8219012 DOI: 10.25259/ijms_229_2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 09/25/2020] [Indexed: 05/31/2023]
Abstract
Objectives: The recovery rate is important to determine a country’s development towards controlling coronavirus. It is a function of myriad factors – death rate, cases requiring hospitalization, quality of care, and discharge policies, among others. India’s recovery rate is growing steadily from an earlier low of 10% to 11%. It is imperative to understand the determinants of recovery rate in a country to enable improvements in the same. Material and Methods: COVID-19 data have been compiled from several sources, including the Ministry of Health and Family Welfare, National Disaster Management Authority, and Indian Council of Medical Research and demographic and health data from Census of India, 2011, National Health Profile, 2019, and were used. The study uses linear regression to understand the relationship between recovery rate and development indicators in India. Results: Our analysis emphasizes the beneficial impacts of the health system and better economy on the recovery rate. Investment in health, urban stay, non-slum and non-poor population, and effective governance is instrumental in improving recovery rate. Conclusion: Scaling up health facilities and medical infrastructure, slum decongestion, focus on economically weaker sections, capacity building of health workers and ameliorating long-term investments in health, health research, and better quality of living are also essential to address recovery of COVID-19.
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Affiliation(s)
- Akancha Singh
- Department of Research Scholar, International Institute for Population Sciences, Mumbai, Maharashtra, India
| | - Aparajita Chattopadhyay
- Department of Development Studies International Institute for Population Sciences, Mumbai, Maharashtra, India
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15
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Paris M, Ying F. Toward a new normality in Via Paolo Sarpi (Milan, Italy)? Social behaviors and spatial transitions during and after the lockdown. JOURNAL OF HUMAN BEHAVIOR IN THE SOCIAL ENVIRONMENT 2021; 31:305-324. [DOI: 10.1080/10911359.2020.1823295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Affiliation(s)
- Mario Paris
- Dipartimento di Architettura e Studi Urbani, Politecnico di Milano, Milano, Italy
| | - Fang Ying
- College of Architecture and Urban Planning, Tongji University, Shanghai, China
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16
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Grantz KH, Cummings DAT, Zimmer S, Vukotich Jr. C, Galloway D, Schweizer ML, Guclu H, Cousins J, Lingle C, Yearwood GMH, Li K, Calderone P, Noble E, Gao H, Rainey J, Uzicanin A, Read JM. Age-specific social mixing of school-aged children in a US setting using proximity detecting sensors and contact surveys. Sci Rep 2021; 11:2319. [PMID: 33504823 PMCID: PMC7840989 DOI: 10.1038/s41598-021-81673-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 12/23/2020] [Indexed: 01/30/2023] Open
Abstract
Comparisons of the utility and accuracy of methods for measuring social interactions relevant to disease transmission are rare. To increase the evidence base supporting specific methods to measure social interaction, we compared data from self-reported contact surveys and wearable proximity sensors from a cohort of schoolchildren in the Pittsburgh metropolitan area. Although the number and type of contacts recorded by each participant differed between the two methods, we found good correspondence between the two methods in aggregate measures of age-specific interactions. Fewer, but longer, contacts were reported in surveys, relative to the generally short proximal interactions captured by wearable sensors. When adjusted for expectations of proportionate mixing, though, the two methods produced highly similar, assortative age-mixing matrices. These aggregate mixing matrices, when used in simulation, resulted in similar estimates of risk of infection by age. While proximity sensors and survey methods may not be interchangeable for capturing individual contacts, they can generate highly correlated data on age-specific mixing patterns relevant to the dynamics of respiratory virus transmission.
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Affiliation(s)
- Kyra H. Grantz
- grid.15276.370000 0004 1936 8091Department of Biology, University of Florida, Gainesville, FL 32611 USA ,grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611 USA ,grid.21107.350000 0001 2171 9311Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | - Derek A. T. Cummings
- grid.15276.370000 0004 1936 8091Department of Biology, University of Florida, Gainesville, FL 32611 USA ,grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611 USA ,grid.21107.350000 0001 2171 9311Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | - Shanta Zimmer
- grid.21925.3d0000 0004 1936 9000Division of General Internal Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA ,grid.241116.10000000107903411Department of Medicine, University of Colorado School of Medicine, Denver, CO 80045 USA
| | - Charles Vukotich Jr.
- grid.21925.3d0000 0004 1936 9000Division of General Internal Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA
| | - David Galloway
- grid.21925.3d0000 0004 1936 9000Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15213 USA
| | - Mary Lou Schweizer
- grid.21925.3d0000 0004 1936 9000Division of General Internal Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA
| | - Hasan Guclu
- grid.21925.3d0000 0004 1936 9000Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15213 USA ,grid.411776.20000 0004 0454 921XPresent Address: Department of Biostatistics and Medical Informatics, School of Medicine, Istanbul Medeniyet University, Istanbul, Turkey
| | - Jennifer Cousins
- grid.21925.3d0000 0004 1936 9000Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15213 USA ,grid.21925.3d0000 0004 1936 9000Present Address: Department of Psychology, University of Pittsburgh, Pittsburgh, PA USA
| | - Carrie Lingle
- grid.21925.3d0000 0004 1936 9000Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15213 USA ,Present Address: Toledo Lucas County Health Department, Toledo, OH USA
| | - Gabby M. H. Yearwood
- grid.21925.3d0000 0004 1936 9000Department of Anthropology, University of Pittsburgh, Pittsburgh, PA 15213 USA
| | - Kan Li
- grid.21925.3d0000 0004 1936 9000Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15213 USA ,Present Address: Merck Pharmaceuticals, Philadelphia, PA USA
| | - Patti Calderone
- grid.21925.3d0000 0004 1936 9000Division of General Internal Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA
| | - Eva Noble
- grid.21107.350000 0001 2171 9311Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | - Hongjiang Gao
- grid.416738.f0000 0001 2163 0069Division of Global Migration and Quarantine, US Centers for Disease Control and Prevention, Atlanta, GA 30033 USA
| | - Jeanette Rainey
- grid.416738.f0000 0001 2163 0069Division of Global Migration and Quarantine, US Centers for Disease Control and Prevention, Atlanta, GA 30033 USA ,grid.416738.f0000 0001 2163 0069Present Address: Division of Global Health Protection, US Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Amra Uzicanin
- grid.416738.f0000 0001 2163 0069Division of Global Migration and Quarantine, US Centers for Disease Control and Prevention, Atlanta, GA 30033 USA
| | - Jonathan M. Read
- grid.9835.70000 0000 8190 6402Centre for Health Informatics Computing and Statistics, Lancaster Medical School, Lancaster University, Lancaster, LA1 4YW UK ,grid.10025.360000 0004 1936 8470Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
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17
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Zhang J, Peng Q, Zhao W, Sun W, Yang J, Liu N. Proteomics in Influenza Research: The Emerging Role of Posttranslational Modifications. J Proteome Res 2020; 20:110-121. [PMID: 33348980 DOI: 10.1021/acs.jproteome.0c00778] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Influenza viruses continue evolving and have the ability to cause a global pandemic, so it is very important to elucidate its pathogenesis and find new treatment methods. In recent years, proteomics has made important contributions to describing the dynamic interaction between influenza viruses and their hosts, especially in posttranslational regulation of a variety of key biological processes. Protein posttranslational modifications (PTMs) increase the diversity of functionality of the organismal proteome and affect almost all aspects of pathogen biology, primarily by regulating the structure, function, and localization of the modified proteins. Considerable technical achievements in mass spectrometry-based proteomics have been made in a large number of proteome-wide surveys of PTMs in many different organisms. Herein we specifically focus on the proteomic studies regarding a variety of PTMs that occur in both the influenza viruses, mainly influenza A viruses (IAVs), and their hosts, including phosphorylation, ubiquitination and ubiquitin-like modification, glycosylation, methylation, acetylation, and some types of acylation. Integration of these data sets provides a unique scenery of the global regulation and interplay of different PTMs during the interaction between IAVs and their hosts. Various techniques used to globally profiling these PTMs, mostly MS-based approaches, are discussed regarding their increasing roles in mechanical regulation of interaction between influenza viruses and their hosts.
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Affiliation(s)
- Jinming Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
| | - Qisheng Peng
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
| | - Weizheng Zhao
- Clinical Medical College, Jilin University, Changchun 130021, PR China
| | - Wanchun Sun
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
| | - Jingbo Yang
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
| | - Ning Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
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18
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Friston K, Costello A, Pillay D. 'Dark matter', second waves and epidemiological modelling. BMJ Glob Health 2020; 5:e003978. [PMID: 33328201 PMCID: PMC7745338 DOI: 10.1136/bmjgh-2020-003978] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 11/14/2020] [Accepted: 11/17/2020] [Indexed: 12/23/2022] Open
Abstract
Recent reports using conventional Susceptible, Exposed, Infected and Removed models suggest that the next wave of the COVID-19 pandemic in the UK could overwhelm health services, with fatalities exceeding the first wave. We used Bayesian model comparison to revisit these conclusions, allowing for heterogeneity of exposure, susceptibility and transmission. We used dynamic causal modelling to estimate the evidence for alternative models of daily cases and deaths from the USA, the UK, Brazil, Italy, France, Spain, Mexico, Belgium, Germany and Canada over the period 25 January 2020 to 15 June 2020. These data were used to estimate the proportions of people (i) not exposed to the virus, (ii) not susceptible to infection when exposed and (iii) not infectious when susceptible to infection. Bayesian model comparison furnished overwhelming evidence for heterogeneity of exposure, susceptibility and transmission. Furthermore, both lockdown and the build-up of population immunity contributed to viral transmission in all but one country. Small variations in heterogeneity were sufficient to explain large differences in mortality rates. The best model of UK data predicts a second surge of fatalities will be much less than the first peak. The size of the second wave depends sensitively on the loss of immunity and the efficacy of Find-Test-Trace-Isolate-Support programmes. In summary, accounting for heterogeneity of exposure, susceptibility and transmission suggests that the next wave of the SARS-CoV-2 pandemic will be much smaller than conventional models predict, with less economic and health disruption. This heterogeneity means that seroprevalence underestimates effective herd immunity and, crucially, the potential of public health programmes.
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Affiliation(s)
- Karl Friston
- Queen Square Institute of Neurology, University College London, London, UK
| | - Anthony Costello
- Institute of Global Health, University College London, London, UK
| | - Deenan Pillay
- University College London Faculty of Medical Sciences, London, UK
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19
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Kucharski AJ, Klepac P, Conlan AJK, Kissler SM, Tang ML, Fry H, Gog JR, Edmunds WJ. Effectiveness of isolation, testing, contact tracing, and physical distancing on reducing transmission of SARS-CoV-2 in different settings: a mathematical modelling study. THE LANCET. INFECTIOUS DISEASES 2020. [PMID: 32559451 DOI: 10.1101/2020.02.16.20023754] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
BACKGROUND The isolation of symptomatic cases and tracing of contacts has been used as an early COVID-19 containment measure in many countries, with additional physical distancing measures also introduced as outbreaks have grown. To maintain control of infection while also reducing disruption to populations, there is a need to understand what combination of measures-including novel digital tracing approaches and less intensive physical distancing-might be required to reduce transmission. We aimed to estimate the reduction in transmission under different control measures across settings and how many contacts would be quarantined per day in different strategies for a given level of symptomatic case incidence. METHODS For this mathematical modelling study, we used a model of individual-level transmission stratified by setting (household, work, school, or other) based on BBC Pandemic data from 40 162 UK participants. We simulated the effect of a range of different testing, isolation, tracing, and physical distancing scenarios. Under optimistic but plausible assumptions, we estimated reduction in the effective reproduction number and the number of contacts that would be newly quarantined each day under different strategies. RESULTS We estimated that combined isolation and tracing strategies would reduce transmission more than mass testing or self-isolation alone: mean transmission reduction of 2% for mass random testing of 5% of the population each week, 29% for self-isolation alone of symptomatic cases within the household, 35% for self-isolation alone outside the household, 37% for self-isolation plus household quarantine, 64% for self-isolation and household quarantine with the addition of manual contact tracing of all contacts, 57% with the addition of manual tracing of acquaintances only, and 47% with the addition of app-based tracing only. If limits were placed on gatherings outside of home, school, or work, then manual contact tracing of acquaintances alone could have an effect on transmission reduction similar to that of detailed contact tracing. In a scenario where 1000 new symptomatic cases that met the definition to trigger contact tracing occurred per day, we estimated that, in most contact tracing strategies, 15 000-41 000 contacts would be newly quarantined each day. INTERPRETATION Consistent with previous modelling studies and country-specific COVID-19 responses to date, our analysis estimated that a high proportion of cases would need to self-isolate and a high proportion of their contacts to be successfully traced to ensure an effective reproduction number lower than 1 in the absence of other measures. If combined with moderate physical distancing measures, self-isolation and contact tracing would be more likely to achieve control of severe acute respiratory syndrome coronavirus 2 transmission. FUNDING Wellcome Trust, UK Engineering and Physical Sciences Research Council, European Commission, Royal Society, Medical Research Council.
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Affiliation(s)
- Adam J Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK.
| | - Petra Klepac
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK; Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
| | - Andrew J K Conlan
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Stephen M Kissler
- Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health, Boston, MA, USA
| | - Maria L Tang
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
| | - Hannah Fry
- Centre for Advanced Spatial Analysis, University College London, London, UK
| | - Julia R Gog
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
| | - W John Edmunds
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
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20
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Sangiorgio V, Parisi F. A multicriteria approach for risk assessment of Covid-19 in urban district lockdown. SAFETY SCIENCE 2020; 130:104862. [PMID: 32536749 PMCID: PMC7275161 DOI: 10.1016/j.ssci.2020.104862] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 05/27/2020] [Indexed: 05/04/2023]
Abstract
At the beginning of 2020, the spread of a new strand of Coronavirus named SARS-CoV-2 (COVID-19) raised the interest of the scientific community about the risk assessment related to the viral infection. The contagion became pandemic in few months forcing many Countries to declare lockdown status. In this context of quarantine, all commercial and productive activities are suspended, and many Countries are experiencing a serious crisis. To this aim, the understanding of risk of contagion in every urban district is fundamental for governments and administrations to establish reopening strategies. This paper proposes the calibration of an index able to predict the risk of contagion in urban districts in order to support the administrations in identifying the best strategies to reduce or restart the local activities during lockdown conditions. The objective regards the achievement of a useful tool to predict the risk of contagion by considering socio-economic data such as the presence of activities, companies, institutions and number of infections in urban districts. The proposed index is based on a factorial formula, simple and easy to be applied by practitioners, calibrated by using an optimization-based procedure and exploiting data of 257 urban districts of Apulian region (Italy). Moreover, a comparison with a more refined analysis, based on the training of Artificial Neural Networks, is performed in order to take into account the non-linearity of the phenomenon. The investigation quantifies the influence of each considered parameter in the risk of contagion useful to obtain risk analysis and forecast scenarios.
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Affiliation(s)
- Valentino Sangiorgio
- Department of Civil, Environmental, Land, Building Engineering and Chemistry (DICATECh), Polytechnic of Bari, Bari, Italy
| | - Fabio Parisi
- Department of Electrical and Information Engineering (DEI), Polytechnic of Bari, Bari, Italy
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21
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Latsuzbaia A, Herold M, Bertemes JP, Mossong J. Evolving social contact patterns during the COVID-19 crisis in Luxembourg. PLoS One 2020; 15:e0237128. [PMID: 32760114 PMCID: PMC7410209 DOI: 10.1371/journal.pone.0237128] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 07/20/2020] [Indexed: 11/19/2022] Open
Abstract
We conducted an internet survey using Survey Monkey over six weeks to evaluate the impact of the government interventions on social contact patterns in Luxembourg. Participants were recruited via the science.lu website on March 25, April 2, April 16, May 1 during lockdown, and June 12 and June 25 after the lockdown to provide an estimate of their number of contacts within the previous 24 hours. During the lockdown, a total of 5,644 survey participants with a mean age of 44.2 years reported 18,118 contacts (mean = 3.2, IQR 1-4). The average number of contacts per day increased by 24% from 2.9 to 3.6 over the lockdown period. The average number of contacts decreased with age: 4.2 (IQR 2-5) for participants below 25 years and 1.7 (IQR 1-2) for participants above 64 years. Residents of Portuguese nationality reported a higher number of contacts (mean = 4.3, IQR 2-5) than Luxembourgish (mean = 3.5, IQR 2-4) or other foreign residents, respectively. After lockdown, 1,119 participants reported 7,974 contacts with 7.1 (IQR 3-9) contacts per day on average, of which 61.7% (4,917/7,974) occurred without a facemask (mean = 4.9, IQR 2-6). While the number of social contacts was substantially lower during the lockdown by more than 80% compared to the pre-pandemic period, we observed a more recent 121% increase during the post lockdown period showing an increased potential for COVID-19 spread. Monitoring social contacts is an important indicator to estimate the possible impact of government interventions on social contacts and the COVID-19 spread in the coming months.
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Affiliation(s)
- Ardashel Latsuzbaia
- Epidemiology and Microbial Genomics Unit, Laboratoire National de Santé, Dudelange, Luxembourg
| | - Malte Herold
- Epidemiology and Microbial Genomics Unit, Laboratoire National de Santé, Dudelange, Luxembourg
| | | | - Joël Mossong
- Epidemiology and Microbial Genomics Unit, Laboratoire National de Santé, Dudelange, Luxembourg
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Grantz KH, Cummings DAT, Zimmer S, Vukotich C, Galloway D, Schweizer ML, Guclu H, Cousins J, Lingle C, Yearwood GMH, Li K, Calderone PA, Noble E, Gao H, Rainey J, Uzicanin A, Read JM. Age-specific social mixing of school-aged children in a US setting using proximity detecting sensors and contact surveys. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.07.12.20151696. [PMID: 32699859 PMCID: PMC7373148 DOI: 10.1101/2020.07.12.20151696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Comparisons of the utility and accuracy of methods for measuring social interactions relevant to disease transmission are rare. To increase the evidence base supporting specific methods to measure social interaction, we compared data from self-reported contact surveys and wearable proximity sensors from a cohort of schoolchildren in the Pittsburgh metropolitan area. Although the number and type of contacts recorded by each participant differed between the two methods, we found good correspondence between the two methods in aggregate measures of age-specific interactions. Fewer, but longer, contacts were reported in surveys, relative to the generally short proximal interactions captured by wearable sensors. When adjusted for expectations of proportionate mixing, though, the two methods produced highly similar, assortative age-mixing matrices. These aggregate mixing matrices, when used in simulation, resulted in similar estimates of risk of infection by age. While proximity sensors and survey methods may not be interchangeable for capturing individual contacts, they can generate highly correlated data on age-specific mixing patterns relevant to the dynamics of respiratory virus transmission.
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23
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Davies NG, Kucharski AJ, Eggo RM, Gimma A, Edmunds WJ. Effects of non-pharmaceutical interventions on COVID-19 cases, deaths, and demand for hospital services in the UK: a modelling study. Lancet Public Health 2020; 5:e375-e385. [PMID: 32502389 PMCID: PMC7266572 DOI: 10.1016/s2468-2667(20)30133-x] [Citation(s) in RCA: 511] [Impact Index Per Article: 127.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/11/2020] [Accepted: 05/18/2020] [Indexed: 12/29/2022]
Abstract
BACKGROUND Non-pharmaceutical interventions have been implemented to reduce transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the UK. Projecting the size of an unmitigated epidemic and the potential effect of different control measures has been crucial to support evidence-based policy making during the early stages of the epidemic. This study assesses the potential impact of different control measures for mitigating the burden of COVID-19 in the UK. METHODS We used a stochastic age-structured transmission model to explore a range of intervention scenarios, tracking 66·4 million people aggregated to 186 county-level administrative units in England, Wales, Scotland, and Northern Ireland. The four base interventions modelled were school closures, physical distancing, shielding of people aged 70 years or older, and self-isolation of symptomatic cases. We also modelled the combination of these interventions, as well as a programme of intensive interventions with phased lockdown-type restrictions that substantially limited contacts outside of the home for repeated periods. We simulated different triggers for the introduction of interventions, and estimated the impact of varying adherence to interventions across counties. For each scenario, we projected estimated new cases over time, patients requiring inpatient and critical care (ie, admission to the intensive care units [ICU]) treatment, and deaths, and compared the effect of each intervention on the basic reproduction number, R0. FINDINGS We projected a median unmitigated burden of 23 million (95% prediction interval 13-30) clinical cases and 350 000 deaths (170 000-480 000) due to COVID-19 in the UK by December, 2021. We found that the four base interventions were each likely to decrease R0, but not sufficiently to prevent ICU demand from exceeding health service capacity. The combined intervention was more effective at reducing R0, but only lockdown periods were sufficient to bring R0 near or below 1; the most stringent lockdown scenario resulted in a projected 120 000 cases (46 000-700 000) and 50 000 deaths (9300-160 000). Intensive interventions with lockdown periods would need to be in place for a large proportion of the coming year to prevent health-care demand exceeding availability. INTERPRETATION The characteristics of SARS-CoV-2 mean that extreme measures are probably required to bring the epidemic under control and to prevent very large numbers of deaths and an excess of demand on hospital beds, especially those in ICUs. FUNDING Medical Research Council.
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Affiliation(s)
- Nicholas G Davies
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK.
| | - Adam J Kucharski
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Rosalind M Eggo
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Amy Gimma
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - W John Edmunds
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
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24
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Upadhyay RK, Chatterjee S, Saha S, Azad RK. Age-group-targeted testing for COVID-19 as a new prevention strategy. NONLINEAR DYNAMICS 2020; 101:1921-1932. [PMID: 32904917 PMCID: PMC7462111 DOI: 10.1007/s11071-020-05879-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 08/03/2020] [Indexed: 05/04/2023]
Abstract
Robust testing and tracing are key to fighting the menace of coronavirus disease 2019 (COVID-19). This outbreak has progressed with tremendous impact on human life, society and economy. In this paper, we propose an age-structured SIQR model to track the progression of the pandemic in India, Italy and USA, taking into account the different age structures of these countries. We have made predictions about the disease dynamics, identified the most infected age groups and analysed the effectiveness of social distancing measures taken in the early stages of infection. The basic reproductive ratio R 0 has been numerically calculated for each country. We propose a strategy of age-targeted testing, with increased testing in the most proportionally infected age groups. We observe a marked flattening of the infection curve upon simulating increased testing in the 15-40 year age groups in India. Thus, we conclude that social distancing and widespread testing are effective methods of control, with emphasis on testing and identifying the hot spots of highly infected populations. It has also been suggested that a complete lockdown, followed by lockdowns in selected regions, is more effective than the reverse.
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Affiliation(s)
- Ranjit Kumar Upadhyay
- Department of Mathematics and Computing, Indian Institute of Technology (Indian School of Mines) Dhanbad, Jharkhand, 826004 India
| | - Sourin Chatterjee
- Indian Institute of Science Education and Research, Kolkata, West Bengal 741246 India
| | - Satvik Saha
- Indian Institute of Science Education and Research, Kolkata, West Bengal 741246 India
| | - Rajeev K. Azad
- Department of Biological Sciences, College of Science, University of North Texas, Denton, TX 76203 USA
- Department of Mathematics, College of Science, University of North Texas, Denton, TX 76203 USA
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25
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Kishore N, Mitchell R, Lash TL, Reed C, Danon L, Sigmundsdóttir G, Vigfusson Y. Flying, phones and flu: Anonymized call records suggest that Keflavik International Airport introduced pandemic H1N1 into Iceland in 2009. Influenza Other Respir Viruses 2019; 14:37-45. [PMID: 31705633 PMCID: PMC6928030 DOI: 10.1111/irv.12690] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 01/29/2023] Open
Abstract
Background Data collected by mobile devices can augment surveillance of epidemics in real time. However, methods and evidence for the integration of these data into modern surveillance systems are sparse. We linked call detail records (CDR) with an influenza‐like illness (ILI) registry and evaluated the role that Icelandic international travellers played in the introduction and propagation of influenza A/H1N1pdm09 virus in Iceland through the course of the 2009 pandemic. Methods This nested case‐control study compared odds of exposure to Keflavik International Airport among cases and matched controls producing longitudinal two‐week matched odds ratios (mORs) from August to December 2009. We further evaluated rates of ILI among 1st‐ and 2nd‐degree phone connections of cases compared to their matched controls. Results The mOR was elevated in the initial stages of the epidemic from 7 August until 21 August (mOR = 2.53; 95% confidence interval (CI) = 1.35, 4.78). During the two‐week period from 17 August through 31 August, we calculated the two‐week incidence density ratio of ILI among 1st‐degree connections to be 2.96 (95% CI: 1.43, 5.84). Conclusions Exposure to Keflavik International Airport increased the risk of incident ILI diagnoses during the initial stages of the epidemic. Using these methods for other regions of Iceland, we evaluated the geographic spread of ILI over the course of the epidemic. Our methods were validated through similar evaluation of a domestic airport. The techniques described in this study can be used for hypothesis‐driven evaluations of locations and behaviours during an epidemic and their associations with health outcomes.
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Affiliation(s)
- Nishant Kishore
- Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Rebecca Mitchell
- Department of Computer Science, Emory University, Atlanta, GA, USA.,Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA, USA
| | - Timothy L Lash
- Department of Epidemiology, Rollins School of Public Health, Atlanta, GA, USA
| | - Carrie Reed
- Epidemiology and Prevention Branch, Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Leon Danon
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, UK.,Alan Turing Institute, British Library, London, UK
| | - Guðrún Sigmundsdóttir
- Centre for Health Security and Communicable Disease Center Control, Directorate of Health of Iceland, Reykjavík, Iceland
| | - Ymir Vigfusson
- Department of Computer Science, Emory University, Atlanta, GA, USA.,School of Computer Science, Reykjavík University, Reykjavík, Iceland
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26
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Zhang J, Klepac P, Read JM, Rosello A, Wang X, Lai S, Li M, Song Y, Wei Q, Jiang H, Yang J, Lynn H, Flasche S, Jit M, Yu H. Patterns of human social contact and contact with animals in Shanghai, China. Sci Rep 2019; 9:15141. [PMID: 31641189 PMCID: PMC6805924 DOI: 10.1038/s41598-019-51609-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 09/29/2019] [Indexed: 12/17/2022] Open
Abstract
East Asia is as a principal hotspot for emerging zoonotic infections. Understanding the likely pathways for their emergence and spread requires knowledge on human-human and human-animal contacts, but such studies are rare. We used self-completed and interviewer-completed contact diaries to quantify patterns of these contacts for 965 individuals in 2017/2018 in a high-income densely-populated area of China, Shanghai City. Interviewer-completed diaries recorded more social contacts (19.3 vs. 18.0) and longer social contact duration (35.0 vs. 29.1 hours) than self-reporting. Strong age-assortativity was observed in all age groups especially among young participants (aged 7-20) and middle aged participants (25-55 years). 17.7% of participants reported touching animals (15.3% (pets), 0.0% (poultry) and 0.1% (livestock)). Human-human contact was very frequent but contact with animals (especially poultry) was rare although associated with frequent human-human contact. Hence, this densely populated area is more likely to act as an accelerator for human-human spread but less likely to be at the source of a zoonosis outbreak. We also propose that telephone interview at the end of reporting day is a potential improvement of the design of future contact surveys.
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Affiliation(s)
- Juanjuan Zhang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Petra Klepac
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Jonathan M Read
- Centre for Health Informatics, Computation and Statistics, Lancaster Medical School, Lancaster University, Lancashire, UK
| | - Alicia Rosello
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Xiling Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Shengjie Lai
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
- WorldPop, School of Geography and Environmental Science, University of Southampton, Southampton, UK
- Flowminder Foundation, Stockholm, Sweden
| | - Meng Li
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Yujian Song
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Qingzhen Wei
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Hao Jiang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Juan Yang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Henry Lynn
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Stefan Flasche
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Mark Jit
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, UK
- Modelling and Economics Unit, Public Health England, London, UK
- School of Public Health, University of Hong Kong, Hong Kong, China
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China.
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27
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Park JE, Son WS, Ryu Y, Choi SB, Kwon O, Ahn I. Effects of temperature, humidity, and diurnal temperature range on influenza incidence in a temperate region. Influenza Other Respir Viruses 2019; 14:11-18. [PMID: 31631558 PMCID: PMC6928031 DOI: 10.1111/irv.12682] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 09/13/2019] [Accepted: 09/13/2019] [Indexed: 01/13/2023] Open
Abstract
Background The effect of temperature and humidity on the incidence of influenza may differ by climate region. In addition, the effect of diurnal temperature range on influenza incidence is unclear, according to previous study findings. Objectives The aim of this study was to analyze the effects of temperature, humidity, and diurnal temperature range on the incidence of influenza in Seoul, Republic of Korea, which is located in a temperate region. Methods We used Korean National Health insurance data to assess the weekly influenza incidence between 2010 and 2016, and used meteorological data from Seoul. To investigate the effect of temperature, relative humidity, and diurnal temperature range levels on influenza incidence, we used a distributed lag non‐linear model. Results The risk of influenza incidence was significantly increased with low daily temperatures of 0‐5°C and low (30%–40%) or high (70%) relative humidity. We found a positive significant association between diurnal temperature range and influenza incidence in this study. Conclusions Influenza incidence increased with low temperature and low/high humidity in a temperate region. Influenza incidence also increased with high diurnal temperature range, after considering temperature and humidity.
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Affiliation(s)
- Ji-Eun Park
- Korea Institute of Oriental Medicine, Daejeon, Korea.,Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, Korea
| | - Woo-Sik Son
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, Korea.,National Institute for Mathematical Science, Daejeon, Korea
| | - Yeonhee Ryu
- Korea Institute of Oriental Medicine, Daejeon, Korea
| | - Soo Beom Choi
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, Korea.,Biomedical Prediction Technology Laboratory, Korea Institute of Science and Technology Information, Daejeon, Korea
| | - Okyu Kwon
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, Korea.,National Institute for Mathematical Science, Daejeon, Korea
| | - Insung Ahn
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, Korea.,Biomedical Prediction Technology Laboratory, Korea Institute of Science and Technology Information, Daejeon, Korea.,Department of Data-centric Problem Solving Research, Korea Institute of Science and Technology Information, Daejeon, Korea
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28
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Schaber KL, Paz-Soldan VA, Morrison AC, Elson WHD, Rothman AL, Mores CN, Astete-Vega H, Scott TW, Waller LA, Kitron U, Elder JP, Barker CM, Perkins TA, Vazquez-Prokopec GM. Dengue illness impacts daily human mobility patterns in Iquitos, Peru. PLoS Negl Trop Dis 2019; 13:e0007756. [PMID: 31545804 PMCID: PMC6776364 DOI: 10.1371/journal.pntd.0007756] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 10/03/2019] [Accepted: 09/05/2019] [Indexed: 11/25/2022] Open
Abstract
Background Human mobility plays a central role in shaping pathogen transmission by generating spatial and/or individual variability in potential pathogen-transmitting contacts. Recent research has shown that symptomatic infection can influence human mobility and pathogen transmission dynamics. Better understanding the complex relationship between symptom severity, infectiousness, and human mobility requires quantification of movement patterns throughout infectiousness. For dengue virus (DENV), human infectiousness peaks 0–2 days after symptom onset, making it paramount to understand human movement patterns from the beginning of illness. Methodology and principal findings Through community-based febrile surveillance and RT-PCR assays, we identified a cohort of DENV+ residents of the city of Iquitos, Peru (n = 63). Using retrospective interviews, we measured the movements of these individuals when healthy and during each day of symptomatic illness. The most dramatic changes in mobility occurred during the first three days after symptom onset; individuals visited significantly fewer locations (Wilcoxon test, p = 0.017) and spent significantly more time at home (Wilcoxon test, p = 0.005), compared to when healthy. By 7–9 days after symptom onset, mobility measures had returned to healthy levels. Throughout an individual’s symptomatic period, the day of illness and their subjective sense of well-being were the most significant predictors for the number of locations and houses they visited. Conclusions/Significance Our study is one of the first to collect and analyze human mobility data at a daily scale during symptomatic infection. Accounting for the observed changes in human mobility throughout illness will improve understanding of the impact of disease on DENV transmission dynamics and the interpretation of public health-based surveillance data. Dengue is the most important mosquito-borne viral disease of humans worldwide. Due to the limited mobility of the mosquitoes that transmit dengue virus, human mobility can be a key to both understanding an individual’s exposure to the virus and explaining the spread of dengue throughout a population. Accurate disease models should include human mobility; however, changes in human movement patterns due to the presence of symptoms need to be taken into account. We quantified the impact of symptom presence on human mobility throughout the infectious period by analyzing a dataset on the daily movements of dengue virus infected individuals. Accounting for these changing patterns of mobility will improve understanding of the complex relationship between symptom severity, human movement, and dengue virus transmission. Furthermore, dengue transmission models that incorporate symptom-driven mobility changes can be used to evaluate scenarios and strategies for disease prevention.
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Affiliation(s)
- Kathryn L. Schaber
- Program of Population Biology, Ecology and Evolution, Emory University, Atlanta, Georgia, United States of America
| | - Valerie A. Paz-Soldan
- Department of Global Community Health and Behavioral Sciences, Tulane School of Public Health and Tropical Medicine, New Orleans, Louisiana, United States of America
| | - Amy C. Morrison
- Department of Entomology and Nematology, University of California Davis, Davis, California, United States of America
| | - William H. D. Elson
- Department of Entomology and Nematology, University of California Davis, Davis, California, United States of America
| | - Alan L. Rothman
- Institute for Immunology and Informatics and Department of Cell and Molecular Biology, University of Rhode Island, Providence, Rhode Island, United States of America
| | - Christopher N. Mores
- Department of Virology and Emerging Infections, U.S. Naval Medical Research Unit No. 6, Lima and Iquitos, Peru
| | - Helvio Astete-Vega
- Department of Virology and Emerging Infections, U.S. Naval Medical Research Unit No. 6, Lima and Iquitos, Peru
| | - Thomas W. Scott
- Department of Entomology and Nematology, University of California Davis, Davis, California, United States of America
| | - Lance A. Waller
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Uriel Kitron
- Department of Environmental Sciences, Emory University, Atlanta, Georgia, United States of America
| | - John P. Elder
- Graduate School of Public Health, San Diego State University, San Diego, California, United States of America
| | - Christopher M. Barker
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - T. Alex Perkins
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Gonzalo M. Vazquez-Prokopec
- Program of Population Biology, Ecology and Evolution, Emory University, Atlanta, Georgia, United States of America
- Department of Environmental Sciences, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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29
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Yang JR, Kuo CY, Huang HY, Hsu SZ, Wu FT, Wu FT, Li CH, Liu MT. Seasonal dynamics of influenza viruses and age distribution of infected individuals across nine seasons covering 2009-2018 in Taiwan. J Formos Med Assoc 2019; 119:850-860. [PMID: 31521467 DOI: 10.1016/j.jfma.2019.08.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/23/2019] [Accepted: 08/29/2019] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND/PURPOSE A swine-origin influenza A/H1N1 virus (termed A/H1N1pdm) caused a pandemic in 2009 and has continuously circulated in the human population. To investigate its possible ecological effects on circulating influenza strains, the seasonal patterns of influenza viruses and the respective age distribution of infected patients were studies. METHODS The data obtained from national influenza surveillance systems in Taiwan from July 2009 to June 2018 were analyzed. RESULTS The A/H1N1pdm and A/H3N2 strains usually caused a higher ratio of severe to mild cases than influenza B. New variants of A/H1N1pdm and A/H3N2 emerged accompanied by a large epidemic peak. However, the new influenza B variants intended to circulate for several seasons before causing a large epidemic. The major group of outpatients affected by A/H1N1pdm were aged 13-23 years in the pandemic wave, and the age range of infected individuals gradually shifted to 24-49 and 0-6 years across seasons; A/H1N1pdm-infected inpatients were aged 24-49 years in 2009-2011, and the age range gradually switched to older groups aged 50-65 and >65 years. Individuals aged 0-6 or 24-49 years accounted for the majority of A/H3N2-infected outpatients across seasons, whereas most of the inpatients affected by A/H3N2 were aged >65 years. CONCLUSION Understanding the effects of new variants and changes in dominant circulating viral strains on the age distribution of the affected human population, disease severity and epidemic levels is useful for the establishment of fine-tuned strategies for further improvement of influenza control.
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Affiliation(s)
- Ji-Rong Yang
- Centers for Disease Control, Taipei, Taiwan, ROC
| | - Chuan-Yi Kuo
- Centers for Disease Control, Taipei, Taiwan, ROC
| | | | - Shu-Zhen Hsu
- Centers for Disease Control, Taipei, Taiwan, ROC
| | - Fu-Ting Wu
- Centers for Disease Control, Taipei, Taiwan, ROC
| | - Fang-Tzy Wu
- Centers for Disease Control, Taipei, Taiwan, ROC
| | - Chung-Hao Li
- Centers for Disease Control, Taipei, Taiwan, ROC
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30
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Kiti MC, Melegaro A, Cattuto C, Nokes DJ. Study design and protocol for investigating social network patterns in rural and urban schools and households in a coastal setting in Kenya using wearable proximity sensors. Wellcome Open Res 2019; 4:84. [PMID: 31489381 PMCID: PMC6719676 DOI: 10.12688/wellcomeopenres.15268.2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2019] [Indexed: 11/28/2022] Open
Abstract
Background: Social contact patterns shape the transmission of respiratory infections spread via close interactions. There is a paucity of observational data from schools and households, particularly in developing countries. Portable wireless sensors can record unbiased proximity events between individuals facing each other, shedding light on pathways of infection transmission. Design and methods: The aim is to characterize face-to-face contact patterns that may shape the transmission of respiratory infections in schools and households in Kilifi, Kenya. Two schools, one each from a rural and urban area, will be purposively selected. From each school, 350 students will be randomly selected proportional to class size and gender to participate. Nine index students from each school will be randomly selected and followed-up to their households. All index household residents will be recruited into the study. A further 3-5 neighbouring households will also be recruited to give a maximum of 350 participants per household setting. The sample size per site is limited by the number of sensors available for data collection. Each participant will wear a wireless proximity sensor lying on their chest area for 7 consecutive days. Data on proximal dyadic interactions will be collected automatically by the sensors only for participants who are face-to-face. Key characteristics of interest include the distribution of degree and the frequency and duration of contacts and their variation in rural and urban areas. These will be stratified by age, gender, role, and day of the week. Expected results: Resultant data will inform on social contact patterns in rural and urban areas of a previously unstudied population. Ensuing data will be used to parameterize mathematical simulation models of transmission of a range of respiratory viruses, including respiratory syncytial virus, and used to explore the impact of intervention measures such as vaccination and social distancing.
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Affiliation(s)
- Moses Chapa Kiti
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | - Alessia Melegaro
- Department of Social and Political Sciences, Bocconi University, Milan, Italy
| | - Ciro Cattuto
- Data Science Laboratory, Institute for Scientific Interchange Foundation, Turin, Italy
| | - David James Nokes
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya.,Zeeman Institute of Systems Biology and Infectious Disease Research, University of Warwick, Coventry, UK.,School of Life Sciences, University of Warwick, Coventry, UK
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31
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Kiti MC, Melegaro A, Cattuto C, Nokes DJ. Study design and protocol for investigating social network patterns in rural and urban schools and households in a coastal setting in Kenya using wearable proximity sensors. Wellcome Open Res 2019; 4:84. [DOI: 10.12688/wellcomeopenres.15268.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2019] [Indexed: 11/20/2022] Open
Abstract
Background: Social contact patterns shape the transmission of respiratory infections spread via close interactions. There is a paucity of observational data from schools and households, particularly in developing countries. Portable wireless sensors can record unbiased proximity events between individuals facing each other, shedding light on pathways of infection transmission. Design and methods: The aim is to characterize face-to-face contact patterns that may shape the transmission of respiratory infections in schools and households in Kilifi, Kenya. Two schools, one each from a rural and urban area, will be purposively selected. From each school, 350 students will be randomly selected proportional to class size and gender to participate. Nine index students from each school will be randomly selected and followed-up to their households. All index household residents will be recruited into the study. A further 3-5 neighbouring households will also be recruited to give a maximum of 350 participants per household setting. The sample size per site is limited by the number of sensors available for data collection. Each participant will wear a wireless proximity sensor lying on their chest area for 7 consecutive days. Data on proximal dyadic interactions will be collected automatically by the sensors only for participants who are face-to-face. Key characteristics of interest include the distribution of degree and the frequency and duration of contacts and their variation in rural and urban areas. These will be stratified by age, gender, role, and day of the week. Expected results: Resultant data will inform on social contact patterns in rural and urban areas of a previously unstudied population. Ensuing data will be used to parameterize mathematical simulation models of transmission of a range of respiratory viruses, including respiratory syncytial virus, and used to explore the impact of intervention measures such as vaccination and social distancing.
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Souty C, Amoros P, Falchi A, Capai L, Bonmarin I, van der Werf S, Masse S, Turbelin C, Rossignol L, Vilcu A, Lévy‐Bruhl D, Lina B, Minodier L, Dorléans Y, Guerrisi C, Hanslik T, Blanchon T. Influenza epidemics observed in primary care from 1984 to 2017 in France: A decrease in epidemic size over time. Influenza Other Respir Viruses 2019; 13:148-157. [PMID: 30428158 PMCID: PMC6379635 DOI: 10.1111/irv.12620] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 09/07/2018] [Accepted: 11/06/2018] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Epidemiological analysis of past influenza epidemics remains essential to understand the evolution of the disease and optimize control and prevention strategies. Here, we aimed to use data collected by a primary care surveillance system over the last three decades to study trends in influenza epidemics and describe epidemic profiles according to circulating influenza viruses. METHODS Influenza-like illness (ILI) weekly incidences were estimated using cases reported by general practitioners participating in the French Sentinelles network, between 1984 and 2017. Influenza epidemics were detected by applying a periodic regression to this time series. Epidemic (co-)dominant influenza virus (sub)types were determined using French virology data. RESULTS During the study period, 297 607 ILI cases were reported allowing the detection of 33 influenza epidemics. On average, seasonal epidemics lasted 9 weeks and affected 4.1% of the population (95% CI 3.5; 4.7). Mean age of cases was 29 years. Epidemic size decreased over time by -66 cases per 100 000 population per season on average (95% CI -132; -0.2, P value = 0.049) and epidemic height decreased by -15 cases per 100 000 (95% CI -28; -2, P value = 0.022). Epidemic duration appeared stable over time. Epidemics were mostly dominated by A(H3N2) (n = 17, 52%), associated with larger epidemic size, higher epidemic peak and older age of cases. CONCLUSIONS The declining trend in influenza epidemic size and height over the last 33 years might be related to several factors like increased vaccine coverage, hygiene improvements or changing in influenza viruses. However, further researches are needed to assess the impact of potential contributing factors to adapt influenza plans.
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Affiliation(s)
- Cécile Souty
- Sorbonne UniversitéINSERMInstitut Pierre Louis d’Épidémiologie et de Santé Publique (IPLESP)ParisFrance
| | - Philippe Amoros
- Sorbonne UniversitéINSERMInstitut Pierre Louis d’Épidémiologie et de Santé Publique (IPLESP)ParisFrance
| | - Alessandra Falchi
- EA7310, Laboratoire de VirologieUniversité de Corse‐InsermCorteFrance
| | - Lisandru Capai
- Sorbonne UniversitéINSERMInstitut Pierre Louis d’Épidémiologie et de Santé Publique (IPLESP)ParisFrance
- EA7310, Laboratoire de VirologieUniversité de Corse‐InsermCorteFrance
| | - Isabelle Bonmarin
- Department of Infectious DiseasesSanté publique FranceSaint‐MauriceFrance
| | - Sylvie van der Werf
- Institut PasteurUnité de Génétique Moléculaire des Virus à ARNParisFrance
- Institut PasteurCentre Coordonnateur du Centre National de Référence des virus des infections respiratoires (dont la grippe)ParisFrance
- UMR CNRS 3569ParisFrance
- Université Paris DiderotSorbonne Paris CitéUnité de Génétique Moléculaire des Virus à ARNParisFrance
| | - Shirley Masse
- Sorbonne UniversitéINSERMInstitut Pierre Louis d’Épidémiologie et de Santé Publique (IPLESP)ParisFrance
- EA7310, Laboratoire de VirologieUniversité de Corse‐InsermCorteFrance
| | - Clément Turbelin
- Sorbonne UniversitéINSERMInstitut Pierre Louis d’Épidémiologie et de Santé Publique (IPLESP)ParisFrance
| | - Louise Rossignol
- Sorbonne UniversitéINSERMInstitut Pierre Louis d’Épidémiologie et de Santé Publique (IPLESP)ParisFrance
| | - Ana‐Maria Vilcu
- Sorbonne UniversitéINSERMInstitut Pierre Louis d’Épidémiologie et de Santé Publique (IPLESP)ParisFrance
| | - Daniel Lévy‐Bruhl
- Department of Infectious DiseasesSanté publique FranceSaint‐MauriceFrance
| | - Bruno Lina
- Laboratoire de VirologieHospices Civils de LyonInstitut des Agents Infectieux (IAI)Centre National de Référence des virus respiratoires (dont la grippe)Centre de Biologie et de Pathologie NordGroupement Hospitalier NordLyonFrance
- Université de LyonVirpath, CIRI, INSERM U1111CNRS UMR5308ENS Lyon, Université Claude Bernard Lyon 1LyonFrance
| | - Laëtitia Minodier
- EA7310, Laboratoire de VirologieUniversité de Corse‐InsermCorteFrance
| | - Yves Dorléans
- Sorbonne UniversitéINSERMInstitut Pierre Louis d’Épidémiologie et de Santé Publique (IPLESP)ParisFrance
| | - Caroline Guerrisi
- Sorbonne UniversitéINSERMInstitut Pierre Louis d’Épidémiologie et de Santé Publique (IPLESP)ParisFrance
| | - Thomas Hanslik
- Sorbonne UniversitéINSERMInstitut Pierre Louis d’Épidémiologie et de Santé Publique (IPLESP)ParisFrance
- Université de Versailles Saint‐Quentin‐en‐YvelinesUVSQUFR de MédecineVersaillesFrance
- Service de Médecine InterneHôpital Ambroise ParéAssistance Publique – Hôpitaux de ParisAPHPBoulogne BillancourtFrance
| | - Thierry Blanchon
- Sorbonne UniversitéINSERMInstitut Pierre Louis d’Épidémiologie et de Santé Publique (IPLESP)ParisFrance
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le Polain de Waroux O, Flasche S, Kucharski AJ, Langendorf C, Ndazima D, Mwanga-Amumpaire J, Grais RF, Cohuet S, Edmunds WJ. Identifying human encounters that shape the transmission of Streptococcus pneumoniae and other acute respiratory infections. Epidemics 2018; 25:72-79. [PMID: 30054196 PMCID: PMC6227246 DOI: 10.1016/j.epidem.2018.05.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/17/2018] [Accepted: 05/17/2018] [Indexed: 01/23/2023] Open
Abstract
Although patterns of social contacts are believed to be an important determinant of infectious disease transmission, it remains unclear how the frequency and nature of human interactions shape an individual's risk of infection. We analysed data on daily social encounters individually matched to data on S. pneumoniae carriage and acute respiratory symptoms (ARS), from 566 individuals who took part in a survey in South-West Uganda. We found that the frequency of physical (i.e. skin-to-skin), long (≥1 h) and household contacts - which capture some measure of close (i.e. relatively intimate) contact - was higher among pneumococcal carriers than non-carriers, and among people with ARS compared to those without, irrespective of their age. With each additional physical encounter the age-adjusted risk of carriage and ARS increased by 6% (95%CI 2-9%) and 7% (2-13%) respectively. In contrast, the number of casual contacts (<5 min long) was not associated with either pneumococcal carriage or ARS. A detailed analysis by age of contacts showed that the number of close contacts with young children (<5 years) was particularly higher among older children and adult carriers than non-carriers, while the higher number of contacts among people suffering from ARS was more homogeneous across contacts of all ages. Our findings provide key evidence that the frequency of close interpersonal contact is important for transmission of respiratory infections, but not that of casual contacts. Those results are essential for both improving disease prevention and control efforts as well as informing research on infectious disease dynamics and transmission models, and more studies should be undertaken to further validate our results.
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Affiliation(s)
- Olivier le Polain de Waroux
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, WC1E 7HT, London, United Kingdom.
| | - Stefan Flasche
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, WC1E 7HT, London, United Kingdom
| | - Adam J Kucharski
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, WC1E 7HT, London, United Kingdom
| | - Celine Langendorf
- Department of Research, Epicentre, 8 Rue Saint-Sabin, 75011, Paris, France
| | - Donny Ndazima
- Epicentre Mbarara Research Centre, PO Box 1956, Mbarara, Uganda
| | - Juliet Mwanga-Amumpaire
- Epicentre Mbarara Research Centre, PO Box 1956, Mbarara, Uganda; Mbarara Universityof Science and Technology, Mbarara University, PO Box 1410, Mbarara, Uganda
| | - Rebecca F Grais
- Department of Research, Epicentre, 8 Rue Saint-Sabin, 75011, Paris, France
| | - Sandra Cohuet
- Department of Field Epidemiology, Epicentre, 8 Rue Saint-Sabin, 75011, Paris, France
| | - W John Edmunds
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, WC1E 7HT, London, United Kingdom
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Cazelles B, Champagne C, Dureau J. Accounting for non-stationarity in epidemiology by embedding time-varying parameters in stochastic models. PLoS Comput Biol 2018; 14:e1006211. [PMID: 30110322 PMCID: PMC6110518 DOI: 10.1371/journal.pcbi.1006211] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 08/27/2018] [Accepted: 05/18/2018] [Indexed: 11/19/2022] Open
Abstract
The spread of disease through human populations is complex. The characteristics of disease propagation evolve with time, as a result of a multitude of environmental and anthropic factors, this non-stationarity is a key factor in this huge complexity. In the absence of appropriate external data sources, to correctly describe the disease propagation, we explore a flexible approach, based on stochastic models for the disease dynamics, and on diffusion processes for the parameter dynamics. Using such a diffusion process has the advantage of not requiring a specific mathematical function for the parameter dynamics. Coupled with particle MCMC, this approach allows us to reconstruct the time evolution of some key parameters (average transmission rate for instance). Thus, by capturing the time-varying nature of the different mechanisms involved in disease propagation, the epidemic can be described. Firstly we demonstrate the efficiency of this methodology on a toy model, where the parameters and the observation process are known. Applied then to real datasets, our methodology is able, based solely on simple stochastic models, to reconstruct complex epidemics, such as flu or dengue, over long time periods. Hence we demonstrate that time-varying parameters can improve the accuracy of model performances, and we suggest that our methodology can be used as a first step towards a better understanding of a complex epidemic, in situation where data is limited and/or uncertain.
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Affiliation(s)
- Bernard Cazelles
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS UMR 8197, Paris, France
- International Center for Mathematical and Computational Modeling of Complex Systems (UMMISCO), UMI 209, UPMC/IRD, France
- Hosts, Vectors and Infectious Agents, CNRS URA 3012, Institut Pasteur, Paris, France
| | - Clara Champagne
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS UMR 8197, Paris, France
- CREST, ENSAE, Université Paris Saclay, Palaiseau, France
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Kucharski AJ, Wenham C, Brownlee P, Racon L, Widmer N, Eames KTD, Conlan AJK. Structure and consistency of self-reported social contact networks in British secondary schools. PLoS One 2018; 13:e0200090. [PMID: 30044816 PMCID: PMC6059423 DOI: 10.1371/journal.pone.0200090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/19/2018] [Indexed: 12/02/2022] Open
Abstract
Self-reported social mixing patterns are commonly used in mathematical models of infectious diseases. It is particularly important to quantify patterns for school-age children given their disproportionate role in transmission, but it remains unclear how the structure of such social interactions changes over time. By integrating data collection into a public engagement programme, we examined self-reported contact networks in year 7 groups in four UK secondary schools. We collected data from 460 unique participants across four rounds of data collection conducted between January and June 2015, with 7,315 identifiable contacts reported in total. Although individual-level contacts varied over the study period, we were able to obtain out-of-sample accuracies of more than 90% and F-scores of 0.49-0.84 when predicting the presence or absence of social contacts between specific individuals across rounds of data collection. Network properties such as clustering and number of communities were broadly consistent within schools between survey rounds, but varied significantly between schools. Networks were assortative according to gender, and to a lesser extent school class, with the estimated clustering coefficient larger among males in all surveyed co-educational schools. Our results demonstrate that it is feasible to collect longitudinal self-reported social contact data from school children and that key properties of these data are consistent between rounds of data collection.
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Affiliation(s)
- Adam J. Kucharski
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Clare Wenham
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Department of Health Policy, London School of Economics, London, United Kingdom
| | | | - Lucie Racon
- St Bonaventure’s School, London, United Kingdom
| | - Natasha Widmer
- St Paul’s Catholic College, Burgess Hill, United Kingdom
| | - Ken T. D. Eames
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Andrew J. K. Conlan
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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36
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Brinkhues S, Schram MT, Hoebe CJPA, Kretzschmar MEE, Koster A, Dagnelie PC, Sep SJS, van Kuijk SMJ, Savelkoul PHM, Dukers-Muijrers NHTM. Social networks in relation to self-reported symptomatic infections in individuals aged 40-75 - the Maastricht study. BMC Infect Dis 2018; 18:300. [PMID: 29973154 PMCID: PMC6030801 DOI: 10.1186/s12879-018-3197-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 06/18/2018] [Indexed: 01/28/2023] Open
Abstract
Background Most infections are spread through social networks (detrimental effect). However, social networks may also lower infection acquisition (beneficial effect). This study aimed to examine associations between social network parameters and prevalence of self-reported upper and lower respiratory, gastrointestinal and urinary tract infections in a population aged 40–75. Methods In this population-based cross-sectional cohort study (N = 3004, mean age 60.0 ± 8.2 years, 49% women), infections within the past two months were assessed by self-administered questionnaires. Social network parameters were assessed using a name generator questionnaire. To examine the associated beneficial and detrimental network parameters, univariable and multivariable logistic regression was used. Results Participants reported an average of 10 people (alters) with whom they had 231 contacts per half year. Prevalences were 31.1% for upper respiratory, 11.5% for lower respiratory, 12.5% for gastrointestinal, and 5.7% for urinary tract infections. Larger network size, and a higher percentage of alters that were friends or acquaintances were associated with higher odds of upper respiratory, lower respiratory and/or gastrointestinal infections (detrimental). A higher total number of contacts, higher percentages of alters of the same age, and higher percentages of family members/acquaintances were associated with lower odds of upper respiratory, lower respiratory and/or gastrointestinal infections (beneficial). Conclusion We identified both detrimental and beneficial associations of social network parameters with the prevalence of infections. Our findings can be used to complement mathematical models on infection spread, as well as to optimize current infectious disease control. Electronic supplementary material The online version of this article (10.1186/s12879-018-3197-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stephanie Brinkhues
- Department of Medical Microbiology, Maastricht University Medical Centre (MUMC+); CAPHRI, Care and Public Health Research Institute, Maastricht University, P.O. Box 616, 6200, MD, Maastricht, The Netherlands.,Department of Sexual Health, Infectious Diseases and Environmental Health, Public Health Service South Limburg, Postbus 33, 6400AA, Heerlen, The Netherlands
| | - Miranda T Schram
- Department of Medicine, Maastricht University Medical Centre (MUMC+); CARIM, Cardiovascular Research Institute Maastricht, Maastricht University, P.O. Box 616, 6200, MD, Maastricht, The Netherlands
| | - Christian J P A Hoebe
- Department of Medical Microbiology, Maastricht University Medical Centre (MUMC+); CAPHRI, Care and Public Health Research Institute, Maastricht University, P.O. Box 616, 6200, MD, Maastricht, The Netherlands.,Department of Sexual Health, Infectious Diseases and Environmental Health, Public Health Service South Limburg, Postbus 33, 6400AA, Heerlen, The Netherlands
| | - Mirjam E E Kretzschmar
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, University Medical Centre Utrecht, Julius Centre for Health Sciences and Primary Care, Utrecht, The Netherlands
| | - Annemarie Koster
- Department of Social Medicine; CAPHRI, School for Public Health and Primary Care, Maastricht University, P.O. Box 616, 6200, MD, Maastricht, The Netherlands
| | - Pieter C Dagnelie
- Department of Epidemiology, CARIM, Cardiovascular Research Institute Maastricht; CAPHRI, Care and Public Health Research Institute, Maastricht University, P.O. Box 616, 6200, MD, Maastricht, The Netherlands
| | - Simone J S Sep
- Department of Medicine, Maastricht University Medical Centre (MUMC+); CARIM, Cardiovascular Research Institute Maastricht, Maastricht University, P.O. Box 616, 6200, MD, Maastricht, The Netherlands
| | - Sander M J van Kuijk
- Department of Clinical Epidemiology and Medical Technology Assessment (KEMTA), Maastricht University Medical Centre (MUMC+), P.O. Box 616, 6200, MD, Maastricht, The Netherlands
| | - Paul H M Savelkoul
- Department of Medical Microbiology, Maastricht University Medical Centre (MUMC+); CAPHRI, Care and Public Health Research Institute, Maastricht University, P.O. Box 616, 6200, MD, Maastricht, The Netherlands.,Department of Medical Microbiology & Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - Nicole H T M Dukers-Muijrers
- Department of Medical Microbiology, Maastricht University Medical Centre (MUMC+); CAPHRI, Care and Public Health Research Institute, Maastricht University, P.O. Box 616, 6200, MD, Maastricht, The Netherlands. .,Department of Sexual Health, Infectious Diseases and Environmental Health, Public Health Service South Limburg, Postbus 33, 6400AA, Heerlen, The Netherlands.
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37
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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: 57] [Impact Index Per Article: 9.5] [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.
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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
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Klepac P, Kissler S, Gog J. Contagion! The BBC Four Pandemic - The model behind the documentary. Epidemics 2018; 24:49-59. [PMID: 29576516 DOI: 10.1016/j.epidem.2018.03.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 03/14/2018] [Accepted: 03/14/2018] [Indexed: 11/19/2022] Open
Abstract
To mark the centenary of the 1918 influenza pandemic, the broadcasting network BBC have put together a 75-min documentary called 'Contagion! The BBC Four Pandemic'. Central to the documentary is a nationwide citizen science experiment, during which volunteers in the United Kingdom could download and use a custom mobile phone app called BBC Pandemic, and contribute their movement and contact data for a day. As the 'maths team', we were asked to use the data from the app to build and run a model of how a pandemic would spread in the UK. The headline results are presented in the TV programme. Here, we document in detail how the model works, and how we shaped it according the incredibly rich data coming from the BBC Pandemic app. We have barely scratched the depth of the volunteer data available from the app. The work presented in this article had the sole purpose of generating a single detailed simulation of a pandemic influenza-like outbreak in the UK. When the BBC Pandemic app has completed its collection period, the vast dataset will be made available to the scientific community (expected early 2019). It will take much more time and input from a broad range of researchers to fully exploit all that this dataset has to offer. But here at least we were able to harness some of the power of the BBC Pandemic data to contribute something which we hope will capture the interest and engagement of a broad audience.
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Affiliation(s)
- Petra Klepac
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK; Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, UK.
| | - Stephen Kissler
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
| | - Julia Gog
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK.
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Lee EC, Arab A, Goldlust SM, Viboud C, Grenfell BT, Bansal S. Deploying digital health data to optimize influenza surveillance at national and local scales. PLoS Comput Biol 2018. [PMID: 29513661 PMCID: PMC5858836 DOI: 10.1371/journal.pcbi.1006020] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The surveillance of influenza activity is critical to early detection of epidemics and pandemics and the design of disease control strategies. Case reporting through a voluntary network of sentinel physicians is a commonly used method of passive surveillance for monitoring rates of influenza-like illness (ILI) worldwide. Despite its ubiquity, little attention has been given to the processes underlying the observation, collection, and spatial aggregation of sentinel surveillance data, and its subsequent effects on epidemiological understanding. We harnessed the high specificity of diagnosis codes in medical claims from a database that represented 2.5 billion visits from upwards of 120,000 United States healthcare providers each year. Among influenza seasons from 2002-2009 and the 2009 pandemic, we simulated limitations of sentinel surveillance systems such as low coverage and coarse spatial resolution, and performed Bayesian inference to probe the robustness of ecological inference and spatial prediction of disease burden. Our models suggest that a number of socio-environmental factors, in addition to local population interactions, state-specific health policies, as well as sampling effort may be responsible for the spatial patterns in U.S. sentinel ILI surveillance. In addition, we find that biases related to spatial aggregation were accentuated among areas with more heterogeneous disease risk, and sentinel systems designed with fixed reporting locations across seasons provided robust inference and prediction. With the growing availability of health-associated big data worldwide, our results suggest mechanisms for optimizing digital data streams to complement traditional surveillance in developed settings and enhance surveillance opportunities in developing countries. Influenza contributes substantially to global morbidity and mortality each year, and epidemiological surveillance for influenza is typically conducted by sentinel physicians and health care providers recruited to report cases of influenza-like illness. While population coverage and representativeness, and geographic distribution are considered during sentinel provider recruitment, systems cannot always achieve these standards due to the administrative burdens of data collection. We present spatial estimates of influenza disease burden across United States counties by leveraging the volume and fine spatial resolution of medical claims data, and existing socio-environmental hypotheses about the determinants of influenza disease disease burden. Using medical claims as a testbed, this study adds to literature on the optimization of surveillance system design by considering conditions of limited reporting and spatial aggregation. We highlight the importance of considering sampling biases and reporting locations when interpreting surveillance data, and suggest that local mobility and regional policies may be critical to understanding the spatial distribution of reported influenza-like illness.
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Affiliation(s)
- Elizabeth C. Lee
- Department of Biology, Georgetown University, Washington, DC, United States of America
- * E-mail: (ECL); (SB)
| | - Ali Arab
- Department of Mathematics & Statistics, Georgetown University, Washington, DC, United States of America
| | - Sandra M. Goldlust
- Department of Biology, Georgetown University, Washington, DC, United States of America
| | - Cécile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Bryan T. Grenfell
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Ecology & Evolutionary Biology and Woodrow Wilson School, Princeton University, Princeton, New Jersey, United States of America
| | - Shweta Bansal
- Department of Biology, Georgetown University, Washington, DC, United States of America
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (ECL); (SB)
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40
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Russell K, Chung JR, Monto AS, Martin ET, Belongia EA, McLean HQ, Gaglani M, Murthy K, Zimmerman RK, Nowalk MP, Jackson ML, Jackson LA, Flannery B. Influenza vaccine effectiveness in older adults compared with younger adults over five seasons. Vaccine 2018; 36:1272-1278. [PMID: 29402578 PMCID: PMC5812289 DOI: 10.1016/j.vaccine.2018.01.045] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/12/2018] [Accepted: 01/17/2018] [Indexed: 02/02/2023]
Abstract
BACKGROUND There have been inconsistent reports of decreased vaccine effectiveness (VE) against influenza viruses among older adults (aged ≥ 65 years) compared with younger adults in the United States. A direct comparison of VE over multiple seasons is needed to assess the consistency of these observations. METHODS We performed a pooled analysis of VE over 5 seasons among adults aged ≥ 18 years who were systematically enrolled in the U.S. Flu VE Network. Outpatients with medically-attended acute respiratory illness (cough with illness onset ≤ 7 days prior to enrollment) were tested for influenza by reverse transcription polymerase chain reaction. We compared differences in VE and vaccine failures among older adult age group (65-74, ≥75, and ≥ 65 years) to adults aged 18-49 years by influenza type and subtype using interaction terms to test for statistical significance and stratified by prior season vaccination status. RESULTS Analysis included 20,022 adults aged ≥ 18 years enrolled during the 2011-12 through 2015-16 influenza seasons; 4,785 (24%) tested positive for influenza. VE among patients aged ≥ 65 years was not significantly lower than VE among patients aged 18-49 years against any subtype with no significant interaction of age and vaccination. VE against A(H3N2) viruses was 14% (95% confidence interval [CI] -14% to 36%) for adults ≥ 65 years and 21% (CI 9-32%) for adults 18-49 years. VE against A(H1N1)pdm09 was 49% (95% CI 22-66%) for adults ≥ 65 years and 48% (95% CI 41-54%) for adults 18-49 years and against B viruses was 62% (95% CI 44-74%) for adults ≥ 65 years and 55% (95% CI 45-63%) for adults 18-49 years. There was no significant interaction of age and vaccination for separate strata of prior vaccination status. CONCLUSIONS Over 5 seasons, influenza vaccination provided similar levels of protection among older and younger adults, with lower levels of protection against influenza A(H3N2) in all ages.
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Affiliation(s)
- Kate Russell
- Epidemic Intelligence Service, CDC, United States; Influenza Division, National Center for Immunization and Respiratory Diseases, CDC, United States.
| | - Jessie R Chung
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC, United States
| | - Arnold S Monto
- University of Michigan and Henry Ford Health System, United States
| | - Emily T Martin
- University of Michigan and Henry Ford Health System, United States
| | | | | | - Manjusha Gaglani
- Baylor Scott and White Health, Texas A&M University Health Science Center College of Medicine, United States
| | - Kempapura Murthy
- Baylor Scott and White Health, Texas A&M University Health Science Center College of Medicine, United States
| | - Richard K Zimmerman
- University of Pittsburgh Schools of the Health Sciences and UPMC, United States
| | | | - Michael L Jackson
- Kaiser Permanente Washington Health Research Institute, United States
| | - Lisa A Jackson
- Kaiser Permanente Washington Health Research Institute, United States
| | - Brendan Flannery
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC, United States
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41
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Opatowski L, Baguelin M, Eggo RM. Influenza interaction with cocirculating pathogens and its impact on surveillance, pathogenesis, and epidemic profile: A key role for mathematical modelling. PLoS Pathog 2018; 14:e1006770. [PMID: 29447284 PMCID: PMC5814058 DOI: 10.1371/journal.ppat.1006770] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Evidence is mounting that influenza virus interacts with other pathogens colonising or infecting the human respiratory tract. Taking into account interactions with other pathogens may be critical to determining the real influenza burden and the full impact of public health policies targeting influenza. This is particularly true for mathematical modelling studies, which have become critical in public health decision-making. Yet models usually focus on influenza virus acquisition and infection alone, thereby making broad oversimplifications of pathogen ecology. Herein, we report evidence of influenza virus interactions with bacteria and viruses and systematically review the modelling studies that have incorporated interactions. Despite the many studies examining possible associations between influenza and Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, Neisseria meningitidis, respiratory syncytial virus (RSV), human rhinoviruses, human parainfluenza viruses, etc., very few mathematical models have integrated other pathogens alongside influenza. The notable exception is the pneumococcus-influenza interaction, for which several recent modelling studies demonstrate the power of dynamic modelling as an approach to test biological hypotheses on interaction mechanisms and estimate the strength of those interactions. We explore how different interference mechanisms may lead to unexpected incidence trends and possible misinterpretation, and we illustrate the impact of interactions on public health surveillance using simple transmission models. We demonstrate that the development of multipathogen models is essential to assessing the true public health burden of influenza and that it is needed to help improve planning and evaluation of control measures. Finally, we identify the public health, surveillance, modelling, and biological challenges and propose avenues of research for the coming years.
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Affiliation(s)
- Lulla Opatowski
- Université de Versailles Saint Quentin, Institut Pasteur, Inserm, Paris, France
| | - Marc Baguelin
- London School of Hygiene & Tropical Medicine, London, United Kingdom
- Public Health England, London, United Kingdom
| | - Rosalind M. Eggo
- London School of Hygiene & Tropical Medicine, London, United Kingdom
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42
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Kwok KO, Cowling B, Wei V, Riley S, Read JM. Temporal variation of human encounters and the number of locations in which they occur: a longitudinal study of Hong Kong residents. J R Soc Interface 2018; 15:20170838. [PMID: 29367241 PMCID: PMC5805989 DOI: 10.1098/rsif.2017.0838] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 01/02/2018] [Indexed: 01/30/2023] Open
Abstract
Patterns of social contact between individuals are important for the transmission of many pathogens and shaping patterns of immunity at the population scale. To refine our understanding of how human social behaviour may change over time, we conducted a longitudinal study of Hong Kong residents. We recorded the social contact patterns for 1450 individuals, up to four times each between May 2012 and September 2013. We found individuals made contact with an average of 12.5 people within 2.9 geographical locations, and spent an average estimated total duration of 9.1 h in contact with others during a day. Distributions of the number of contacts and locations in which contacts were made were not significantly different between study waves. Encounters were assortative by age, and the age mixing pattern was broadly consistent across study waves. Fitting regression models, we examined the association of contact rates (number of contacts, total duration of contact, number of locations) with covariates and calculated the inter- and intra-participant variation in contact rates. Participant age was significantly associated with the number of contacts made, the total duration of contact and the number of locations in which contact occurred, with children and parental-age adults having the highest rates of contact. The number of contacts and contact duration increased with the number of contact locations. Intra-individual variation in contact rate was consistently greater than inter-individual variation. Despite substantial individual-level variation, remarkable consistency was observed in contact mixing at the population scale. This suggests that aggregate measures of mixing behaviour derived from cross-sectional information may be appropriate for population-scale modelling purposes, and that if more detailed models of social interactions are required for improved public health modelling, further studies are needed to understand the social processes driving intra-individual variation.
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Affiliation(s)
- Kin On Kwok
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
- Shenzhen Research Institute, Chinese University of Hong Kong, Shenzhen, People's Republic of China
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
| | - Ben Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
| | - Vivian Wei
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
| | - Steven Riley
- MRC Centre for Outbreak Analysis and Modelling, Department for Infectious Disease Epidemiology, Imperial College, London, UK
| | - Jonathan M Read
- Centre for Health Informatics, Computation and Statistics, Lancaster Medical School, Faculty of Health and Medicine, Lancaster University, Lancashire, UK
- Institute of Infection and Global Health, The Farr Institute@HeRC, University of Liverpool, Liverpool, UK
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43
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Nainu F, Shiratsuchi A, Nakanishi Y. Induction of Apoptosis and Subsequent Phagocytosis of Virus-Infected Cells As an Antiviral Mechanism. Front Immunol 2017; 8:1220. [PMID: 29033939 PMCID: PMC5624992 DOI: 10.3389/fimmu.2017.01220] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/14/2017] [Indexed: 01/14/2023] Open
Abstract
Viruses are infectious entities that hijack host replication machineries to produce their progeny, resulting, in most cases, in disease and, sometimes, in death in infected host organisms. Hosts are equipped with an array of defense mechanisms that span from innate to adaptive as well as from humoral to cellular immune responses. We previously demonstrated that mouse cells underwent apoptosis in response to influenza virus infection. These apoptotic, virus-infected cells were then targeted for engulfment by macrophages and neutrophils. We more recently reported similar findings in the fruit fly Drosophila melanogaster, which lacks adaptive immunity, after an infection with Drosophila C virus. In these experiments, the inhibition of phagocytosis led to severe influenza pathologies in mice and early death in Drosophila. Therefore, the induction of apoptosis and subsequent phagocytosis of virus-infected cells appear to be an antiviral innate immune mechanism that is conserved among multicellular organisms. We herein discuss the underlying mechanisms and significance of the apoptosis-dependent phagocytosis of virus-infected cells. Investigations on the molecular and cellular features responsible for this underrepresented virus–host interaction may provide a promising avenue for the discovery of novel substances that are targeted in medical treatments against virus-induced intractable diseases.
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Affiliation(s)
- Firzan Nainu
- Laboratory of Pharmacology and Toxicology, Faculty of Pharmacy, Hasanuddin University, Makassar, Indonesia.,Laboratory of Host Defense and Responses, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Akiko Shiratsuchi
- Laboratory of Host Defense and Responses, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Yoshinobu Nakanishi
- Laboratory of Host Defense and Responses, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
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44
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Garattini C, Raffle J, Aisyah DN, Sartain F, Kozlakidis Z. Big Data Analytics, Infectious Diseases and Associated Ethical Impacts. PHILOSOPHY & TECHNOLOGY 2017; 32:69-85. [PMID: 31024785 PMCID: PMC6451937 DOI: 10.1007/s13347-017-0278-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 08/02/2017] [Indexed: 12/16/2022]
Abstract
The exponential accumulation, processing and accrual of big data in healthcare are only possible through an equally rapidly evolving field of big data analytics. The latter offers the capacity to rationalize, understand and use big data to serve many different purposes, from improved services modelling to prediction of treatment outcomes, to greater patient and disease stratification. In the area of infectious diseases, the application of big data analytics has introduced a number of changes in the information accumulation models. These are discussed by comparing the traditional and new models of data accumulation. Big data analytics is fast becoming a crucial component for the modelling of transmission-aiding infection control measures and policies-emergency response analyses required during local or international outbreaks. However, the application of big data analytics in infectious diseases is coupled with a number of ethical impacts. Four key areas are discussed in this paper: (i) automation and algorithmic reliance impacting freedom of choice, (ii) big data analytics complexity impacting informed consent, (iii) reliance on profiling impacting individual and group identities and justice/fair access and (iv) increased surveillance and population intervention capabilities impacting behavioural norms and practices. Furthermore, the extension of big data analytics to include information derived from personal devices, such as mobile phones and wearables as part of infectious disease frameworks in the near future and their potential ethical impacts are discussed. Considered together, the need for a constructive and transparent inclusion of ethical questioning in this rapidly evolving field becomes an increasing necessity in order to provide a moral foundation for the societal acceptance and responsible development of the technological advancement.
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Affiliation(s)
- Chiara Garattini
- Anthropology and UX Research, Health and Life Sciences, Intel, London, UK
| | - Jade Raffle
- Division of Infection and Immunity, University College London, Cruciform Building, Gower Street, London, WC1E 6BT UK
| | - Dewi N Aisyah
- Department of Infectious Disease Informatics, University College London, Farr Institute of Health Informatics Research, 222 Euston Road, London, NW1 2DA UK
| | | | - Zisis Kozlakidis
- Division of Infection and Immunity, University College London, Cruciform Building, Gower Street, London, WC1E 6BT UK
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45
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Leung K, Jit M, Lau EHY, Wu JT. Social contact patterns relevant to the spread of respiratory infectious diseases in Hong Kong. Sci Rep 2017. [PMID: 28801623 DOI: 10.5281/zenodo.3874808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
The spread of many respiratory infections is determined by contact patterns between infectious and susceptible individuals in the population. There are no published data for quantifying social contact patterns relevant to the spread of respiratory infectious diseases in Hong Kong which is a hotspot for emerging infectious diseases due to its high population density and connectivity in the air transportation network. We adopted a commonly used diary-based design to conduct a social contact survey in Hong Kong in 2015/16 using both paper and online questionnaires. Participants using paper questionnaires reported more contacts and longer contact duration than those using online questionnaires. Participants reported 13 person-hours of contact and 8 contacts per day on average, which decreased over age but increased with household size, years of education and income level. Prolonged and frequent contacts, and contacts at home, school and work were more likely to involve physical contacts. Strong age-assortativity was observed in all age groups. We evaluated the characteristics of social contact patterns relevant to the spread of respiratory infectious diseases in Hong Kong. Our findings could help to improve the design of future social contact surveys, parameterize transmission models of respiratory infectious diseases, and inform intervention strategies based on model outputs.
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Affiliation(s)
- Kathy Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Mark Jit
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Modelling and Economics Unit, Public Health England, London, United Kingdom
| | - Eric H Y Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Joseph T Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China.
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46
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Social contact patterns relevant to the spread of respiratory infectious diseases in Hong Kong. Sci Rep 2017; 7:7974. [PMID: 28801623 PMCID: PMC5554254 DOI: 10.1038/s41598-017-08241-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/10/2017] [Indexed: 11/08/2022] Open
Abstract
The spread of many respiratory infections is determined by contact patterns between infectious and susceptible individuals in the population. There are no published data for quantifying social contact patterns relevant to the spread of respiratory infectious diseases in Hong Kong which is a hotspot for emerging infectious diseases due to its high population density and connectivity in the air transportation network. We adopted a commonly used diary-based design to conduct a social contact survey in Hong Kong in 2015/16 using both paper and online questionnaires. Participants using paper questionnaires reported more contacts and longer contact duration than those using online questionnaires. Participants reported 13 person-hours of contact and 8 contacts per day on average, which decreased over age but increased with household size, years of education and income level. Prolonged and frequent contacts, and contacts at home, school and work were more likely to involve physical contacts. Strong age-assortativity was observed in all age groups. We evaluated the characteristics of social contact patterns relevant to the spread of respiratory infectious diseases in Hong Kong. Our findings could help to improve the design of future social contact surveys, parameterize transmission models of respiratory infectious diseases, and inform intervention strategies based on model outputs.
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47
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Affiliation(s)
- Adam J. Kucharski
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Marc Baguelin
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Respiratory Diseases Department, Public Health England, London, United Kingdom
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48
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Kwok KO, Riley S, Perera RAPM, Wei VWI, Wu P, Wei L, Chu DKW, Barr IG, Malik Peiris JS, Cowling BJ. Relative incidence and individual-level severity of seasonal influenza A H3N2 compared with 2009 pandemic H1N1. BMC Infect Dis 2017; 17:337. [PMID: 28494805 PMCID: PMC5425986 DOI: 10.1186/s12879-017-2432-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 04/28/2017] [Indexed: 12/25/2022] Open
Abstract
Background Two subtypes of influenza A currently circulate in humans: seasonal H3N2 (sH3N2, emerged in 1968) and pandemic H1N1 (pH1N1, emerged in 2009). While the epidemiological characteristics of the initial wave of pH1N1 have been studied in detail, less is known about its infection dynamics during subsequent waves or its severity relative to sH3N2. Even prior to 2009, few data was available to estimate the risk of severe outcomes following infection with one circulating influenza strain relative to another. Methods We analyzed antibodies in quadruples of sera from individuals in Hong Kong collected between July 2009 and December 2011, a period that included three distinct influenza virus epidemics. We estimated infection incidence using these assay data and then estimated rates of severe outcomes per infection using population-wide clinical data. Results Cumulative incidence of infection was high among children in the first epidemic of pH1N1. There was a change towards the older age group in the age distribution of infections for pH1N1 from the first to the second epidemic, with the age distribution of the second epidemic of pH1N1 more similar to that of sH3N2. We found no serological evidence that individuals were infected in both waves of pH1N1. The risks of excess mortality conditional on infection were higher for sH3N2 than for pH1N1, with age-standardized risk ratios of 2.6 [95% CI: 1.8, 3.7] for all causes and 1.5 [95% CI: 1.0, 2.1] for respiratory causes throughout the study period. Conclusions Overall increase in clinical incidence of pH1N1 and higher rates of severity in older adults in post pandemic waves were in line with an age-shift in infection towards the older age groups. The absence of repeated infection is good evidence that waning immunity did not cause the second wave. Despite circulating in humans since 1968, sH3N2 is substantially more severe per infection than the pH1N1 strain. Infection-based estimates of individual-level severity have a role in assessing emerging strains; updating seasonal vaccine components; and optimizing of vaccination programs. Electronic supplementary material The online version of this article (doi:10.1186/s12879-017-2432-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kin On Kwok
- JC School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong, Special Administrative Region of China.,Tanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, Hong Kong, Hong Kong, Special Administrative Region of China.,WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong, Special Administrative Region of China
| | - Steven Riley
- MRC Centre for Outbreak Analysis and Modelling, Department for Infectious Disease Epidemiology, Imperial College London, London, UK.
| | - Ranawaka A P M Perera
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong, Special Administrative Region of China
| | - Vivian W I Wei
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong, Special Administrative Region of China
| | - Peng Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong, Special Administrative Region of China
| | - Lan Wei
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong, Special Administrative Region of China
| | - Daniel K W Chu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong, Special Administrative Region of China
| | - Ian G Barr
- WHO Collaborating Centre for Reference and Research, Melbourne, VIC, Australia.,Department of Microbiology and Immunology, University of Melbourne, Melbourne, VIC, Australia
| | - J S Malik Peiris
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong, Special Administrative Region of China
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong, Special Administrative Region of China
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49
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Ewing A, Lee EC, Viboud C, Bansal S. Contact, Travel, and Transmission: The Impact of Winter Holidays on Influenza Dynamics in the United States. J Infect Dis 2017; 215:732-739. [PMID: 28031259 DOI: 10.1093/infdis/jiw642] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 12/27/2016] [Indexed: 11/13/2022] Open
Abstract
Background The seasonality of influenza is thought to vary according to environmental factors and human behavior. During winter holidays, potential disease-causing contact and travel deviate from typical patterns. We aim to understand these changes on age-specific and spatial influenza transmission. Methods We characterized the changes to transmission and epidemic trajectories among children and adults in a spatial context before, during, and after the winter holidays among aggregated physician medical claims in the United States from 2001 to 2009 and among synthetic data simulated from a deterministic, age-specific spatial metapopulation model. Results Winter holidays reduced influenza transmission and delayed the trajectory of influenza season epidemics. The holiday period was marked by a shift in the relative risk of disease from children toward adults. Model results indicated that holidays delayed epidemic peaks and synchronized incidence across locations, and that contact reductions from school closures, rather than age-specific mixing and travel, produced these observed holiday influenza dynamics. Conclusions Winter holidays delay seasonal influenza epidemic peaks and shift disease risk toward adults because of changes in contact patterns. These findings may inform targeted influenza information and vaccination campaigns during holiday periods.
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Affiliation(s)
- Anne Ewing
- Department of Biology, Georgetown University, Washington, D. C. USA
| | - Elizabeth C Lee
- Department of Biology, Georgetown University, Washington, D. C. USA
| | - Cécile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Shweta Bansal
- Department of Biology, Georgetown University, Washington, D. C. USA.,Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
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50
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van de Kassteele J, van Eijkeren J, Wallinga J. Efficient estimation of age-specific social contact rates between men and women. Ann Appl Stat 2017. [DOI: 10.1214/16-aoas1006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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