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Nasution YN, Sitorus MY, Sukandar K, Nuraini N, Apri M, Salama N. The epidemic forest reveals the spatial pattern of the spread of acute respiratory infections in Jakarta, Indonesia. Sci Rep 2024; 14:7619. [PMID: 38556584 PMCID: PMC10982301 DOI: 10.1038/s41598-024-58390-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 03/28/2024] [Indexed: 04/02/2024] Open
Abstract
Acute respiratory infection (ARI) is a communicable disease of the respiratory tract that implies impaired breathing. The infection can expand from one to the neighboring areas at a region-scale level through a human mobility network. Specific to this study, we leverage a record of ARI incidences in four periods of outbreaks for 42 regions in Jakarta to study its spatio-temporal spread using the concept of the epidemic forest. This framework generates a forest-like graph representing an explicit spread of disease that takes the onset time, spatio-temporal distance, and case prevalence into account. To support this framework, we use logistic curves to infer the onset time of the outbreak for each region. The result shows that regions with earlier onset dates tend to have a higher burden of cases, leading to the idea that the culprits of the disease spread are those with a high load of cases. To justify this, we generate the epidemic forest for the four periods of ARI outbreaks and identify the implied dominant trees (that with the most children cases). We find that the primary infected city of the dominant tree has a relatively higher burden of cases than other trees. In addition, we can investigate the timely ( R t ) and spatial reproduction number ( R c ) by directly evaluating them from the inferred graphs. We find that R t for dominant trees are significantly higher than non-dominant trees across all periods, with regions in western Jakarta tend to have higher values of R c . Lastly, we provide simulated-implied graphs by suppressing 50% load of cases of the primary infected city in the dominant tree that results in a reduced R c , suggesting a potential target of intervention to depress the overall ARI spread.
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Affiliation(s)
- Yuki Novia Nasution
- Department of Mathematics, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - Marli Yehezkiel Sitorus
- Department of Mathematics, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - Kamal Sukandar
- Department of Mathematics, Imperial College London, London, SW7 2RH, United Kingdom
| | - Nuning Nuraini
- Department of Mathematics, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, 40132, Indonesia.
| | - Mochamad Apri
- Department of Mathematics, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - Ngabila Salama
- DKI Jakarta Provincial Health Office, Jakarta, Indonesia
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2
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Shmueli M, Lendner I, Ben-Shimol S. Effect of the COVID-19 pandemic on the pediatric infectious disease landscape. Eur J Pediatr 2024; 183:1001-1009. [PMID: 37726566 DOI: 10.1007/s00431-023-05210-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/11/2023] [Accepted: 09/15/2023] [Indexed: 09/21/2023]
Abstract
This narrative review aims to present an overview of the COVID-19 pandemic's effects on the landscape of pediatric infectious diseases. While COVID-19 generally results in mild symptoms and a favorable prognosis in children, the pandemic brought forth significant consequences. These included persistent symptoms among infected children ("long COVID"), a profound transformation in healthcare utilization (notably through the widespread adoption of telemedicine), and the implementation of optimization strategies within healthcare settings. Furthermore, the pandemic resulted in alterations in the circulation patterns of respiratory pathogens, including influenza, RSV, and Streptococcus pneumoniae. The possible reasons for those changes are discussed in this review. COVID-19 effect was not limited to respiratory infectious diseases, as other diseases, including urinary tract and gastrointestinal infections, have displayed decreased transmission rates, likely attributable to heightened hygiene measures and shifts in care-seeking behaviors. Finally, the disruption of routine childhood vaccination programs has resulted in reduced immunization coverage and an upsurge in vaccine hesitancy. In addition, the pandemic was associated with issues of antibiotic misuse and over-prescription. Conclusion: In conclusion, the COVID-19 pandemic has left a profound and multifaceted impact on the landscape of pediatric infectious diseases, ranging from the emergence of "long COVID" in children to significant changes in healthcare delivery, altered circulation patterns of various pathogens, and concerning disruptions in vaccination programs and antibiotic usage. What is Known: • COVID-19 usually presents with mild symptoms in children, although severe and late manifestations are possible. • The pandemic resulted in a dramatically increased use of health care services, as well as alterations in the circulation patterns of respiratory pathogens, decreased rates of other, non-respiratory, infections, disruption of routine childhood vaccination programs, and antibiotic misuse. What is New: • Possible strategies to tackle future outbreaks are presented, including changes in health care services utilization, implementation of updated vaccine programs and antibiotic stewardship protocols. • The decline in RSV and influenza circulation during COVID-19 was probably not primarily related to NPI measures, and rather related to other, non-NPI measures implementation, including specific pathogen-host interactions on the level of the biological niche (the nasopharynx).
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Affiliation(s)
- Moshe Shmueli
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Idan Lendner
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- Pediatric Department B, Soroka University Medical Center, Beer-Sheva, Israel
| | - Shalom Ben-Shimol
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.
- Pediatric Infectious Disease Unit, Soroka University Medical Center, Beer Sheva, Israel.
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3
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Bolton KJ, McCaw JM, Dafilis MP, McVernon J, Heffernan JM. Seasonality as a driver of pH1N12009 influenza vaccination campaign impact. Epidemics 2023; 45:100730. [PMID: 38056164 DOI: 10.1016/j.epidem.2023.100730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/18/2023] [Accepted: 11/16/2023] [Indexed: 12/08/2023] Open
Abstract
Although the most recent respiratory virus pandemic was triggered by a Coronavirus, sustained and elevated prevalence of highly pathogenic avian influenza viruses able to infect mammalian hosts highlight the continued threat of pandemics of influenza A virus (IAV) to global health. Retrospective analysis of pandemic outcomes, including comparative investigation of intervention efficacy in different regions, provide important contributions to the evidence base for future pandemic planning. The swine-origin IAV pandemic of 2009 exhibited regional variation in onset, infection dynamics and annual infection attack rates (IARs). For example, the UK experienced three severe peaks of infection over two influenza seasons, whilst Australia experienced a single severe wave. We adopt a seasonally forced 2-subtype model for the transmission of pH1N12009 and seasonal H3N2 to examine the role vaccination campaigns may play in explaining differences in pandemic trajectories in temperate regions. Our model differentiates between the nature of vaccine- and infection-acquired immunity. In particular, we assume that immunity triggered by infection elicits heterologous cross-protection against viral shedding in addition to long-lasting neutralising antibody, whereas vaccination induces imperfect reduction in susceptibility. We employ an Approximate Bayesian Computation (ABC) framework to calibrate the model using data for pH1N12009 seroprevalence, relative subtype dominance, and annual IARs for Australia and the UK. Heterologous cross-protection substantially suppressed the pandemic IAR over the posterior, with the strength of protection against onward transmission inversely correlated with the initial reproduction number. We show that IAV pandemic timing relative to the usual seasonal influenza cycle influenced the size of the initial waves of pH1N12009 in temperate regions and the impact of vaccination campaigns.
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Affiliation(s)
- Kirsty J Bolton
- School of Mathematical Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - James M McCaw
- School of Mathematics and Statistics, The University of Melbourne, Parkville, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Australia
| | - Mathew P Dafilis
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Australia
| | - Jodie McVernon
- Peter Doherty Institute for Infection and Immunity, The Royal Melbourne Hospital and The University of Melbourne, Parkville, Australia
| | - Jane M Heffernan
- Centre for Disease Modelling, Mathematics & Statistics, York University, Canada
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Xiao Y, Zhou J, Cheng Q, Yang J, Chen B, Zhang T, Xu L, Xu B, Ren Z, Liu Z, Shen C, Wang C, Liu H, Li X, Li R, Yu L, Guan D, Zhang W, Wang J, Hou L, Deng K, Bai Y, Xu B, Dou D, Gong P. Global age-structured spatial modeling for emerging infectious diseases like COVID-19. PNAS NEXUS 2023; 2:pgad127. [PMID: 37143866 PMCID: PMC10153731 DOI: 10.1093/pnasnexus/pgad127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/27/2023] [Accepted: 03/30/2023] [Indexed: 05/06/2023]
Abstract
Modeling the global dynamics of emerging infectious diseases (EIDs) like COVID-19 can provide important guidance in the preparation and mitigation of pandemic threats. While age-structured transmission models are widely used to simulate the evolution of EIDs, most of these studies focus on the analysis of specific countries and fail to characterize the spatial spread of EIDs across the world. Here, we developed a global pandemic simulator that integrates age-structured disease transmission models across 3,157 cities and explored its usage under several scenarios. We found that without mitigations, EIDs like COVID-19 are highly likely to cause profound global impacts. For pandemics seeded in most cities, the impacts are equally severe by the end of the first year. The result highlights the urgent need for strengthening global infectious disease monitoring capacity to provide early warnings of future outbreaks. Additionally, we found that the global mitigation efforts could be easily hampered if developed countries or countries near the seed origin take no control. The result indicates that successful pandemic mitigations require collective efforts across countries. The role of developed countries is vitally important as their passive responses may significantly impact other countries.
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Affiliation(s)
- Yixiong Xiao
- Business Intelligence Lab, Baidu Research, Beijing 100193, China
| | - Jingbo Zhou
- Business Intelligence Lab, Baidu Research, Beijing 100193, China
| | - Qu Cheng
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jun Yang
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China
| | - Bin Chen
- Division of Landscape Architecture, The University of Hong Kong, Hong Kong 999007, China
| | - Tao Zhang
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China
| | - Lei Xu
- Vanke School of Public Health, Tsinghua University, Beijing 100084, China
| | - Bo Xu
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China
| | - Zhehao Ren
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China
| | - Zhaoyang Liu
- Center for Statistical Science, Tsinghua University, Beijing 100084, China
- Department of Industrial Engineering, Tsinghua University, Beijing 100084, China
| | - Chong Shen
- Center for Statistical Science, Tsinghua University, Beijing 100084, China
- Department of Industrial Engineering, Tsinghua University, Beijing 100084, China
| | - Che Wang
- Center for Statistical Science, Tsinghua University, Beijing 100084, China
- Department of Industrial Engineering, Tsinghua University, Beijing 100084, China
| | - Han Liu
- Business Intelligence Lab, Baidu Research, Beijing 100193, China
| | - Xiaoting Li
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China
| | - Ruiyun Li
- School of Public Health (SPH), Nanjing Medical University, Nanjing 211166, China
| | - Le Yu
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China
| | - Dabo Guan
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China
| | - Wusheng Zhang
- Department of Computer Science and Technology, Institute of High Performance Computing, Tsinghua University, Beijing 100084, China
| | - Jie Wang
- State Key Laboratory of Remote Sensing Science, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100101, China
- AI for Earth Laboratory, Cross-Strait Institute, Tsinghua University, Beijing 100084, China
| | - Lin Hou
- Center for Statistical Science, Tsinghua University, Beijing 100084, China
- Department of Industrial Engineering, Tsinghua University, Beijing 100084, China
| | - Ke Deng
- Center for Statistical Science, Tsinghua University, Beijing 100084, China
- Department of Industrial Engineering, Tsinghua University, Beijing 100084, China
| | - Yuqi Bai
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China
| | - Bing Xu
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China
| | - Dejing Dou
- Business Intelligence Lab, Baidu Research, Beijing 100193, China
| | - Peng Gong
- To whom correspondence should be addressed:
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5
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Kuo FY, Wen TH. Assessing the impact of local context and priorities regarding domestic disease outbreaks and imported risk on early pandemic response: Cross-continental comparisons. Front Public Health 2023; 11:1147768. [PMID: 37033049 PMCID: PMC10076555 DOI: 10.3389/fpubh.2023.1147768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/02/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction Containment and closure policies are effective measures used in the early stages of a highly transmissible global pandemic such as COVID-19 to mitigate the spread and reduce transmissions. However, these policies can have negative impacts on the economy and personal freedom. Governments must carefully consider the necessity of increasing their stringency. Local contexts and priorities regarding domestic disease outbreaks and the risk of imported cases from other countries may vary among different countries, and could influence the decision to increase containment measures. Thus, this study aimed to differentiate the impacts of these affecting factors on the stringency of governmental containment measures through cross-continental comparisons. Methods This study utilized a zero/one inflated beta (ZOIB) regression model to investigate how domestic epidemic, imported risk, and local context affect government responses to a pandemic. We used a country's weekly confirmed case and death numbers as a measure of its domestic threat. The imported risk was measured using a combination of weekly new cases in each country and the air passenger traffic between countries. Results The findings indicate that domestic case numbers are a primary concern for governments when deciding to increase policy stringency. Countries with higher development levels tend to implement stricter policies as they can better handle the negative impacts. Additionally, there is an interaction between case numbers and development level, with countries at the second or third highest development level focusing more on domestic outbreaks than imported risks, while those at the highest level have similar concerns for both. Conclusions We concluded that most countries adjust policies' stringency majorly based on the variation of domestic case number rather than the other pandemic factors and the countries with a high development level tend to implement strict policies since their socio-economical condition could afford such policies. These insights can aid policymakers in improving containment and closure policies for future pandemics.
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The Impact of Urbanization and Human Mobility on Seasonal Influenza in Northern China. Viruses 2022; 14:v14112563. [PMID: 36423173 PMCID: PMC9697484 DOI: 10.3390/v14112563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
The intensity of influenza epidemics varies significantly from year to year among regions with similar climatic conditions and populations. However, the underlying mechanisms of the temporal and spatial variations remain unclear. We investigated the impact of urbanization and public transportation size on influenza activity. We used 6-year weekly provincial-level surveillance data of influenza-like disease incidence (ILI) and viral activity in northern China. We derived the transmission potential of influenza for each epidemic season using the susceptible-exposed-infectious-removed-susceptible (SEIRS) model and estimated the transmissibility in the peak period via the instantaneous reproduction number (Rt). Public transport was found to explain approximately 28% of the variance in the seasonal transmission potential. Urbanization and public transportation size explained approximately 10% and 21% of the variance in maximum Rt in the peak period, respectively. For the mean Rt during the peak period, urbanization and public transportation accounted for 9% and 16% of the variance in Rt, respectively. Our results indicated that the differences in the intensity of influenza epidemics among the northern provinces of China were partially driven by urbanization and public transport size. These findings are beneficial for predicting influenza intensity and developing preparedness strategies for the early stages of epidemics.
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Sominina A, Danilenko D, Komissarov A, Karpova L, Pisareva M, Fadeev A, Konovalova N, Eropkin M, Stolyarov K, Shtro A, Burtseva E, Lioznov D. Resurgence of Influenza Circulation in the Russian Federation during the Delta and Omicron COVID-19 Era. Viruses 2022; 14:1909. [PMID: 36146716 PMCID: PMC9506591 DOI: 10.3390/v14091909] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/25/2022] Open
Abstract
Influenza circulation was substantially reduced after March 2020 in the European region and globally due to the wide introduction of non-pharmaceutical interventions (NPIs) against COVID-19. The virus, however, has been actively circulating in natural reservoirs. In summer 2021, NPIs were loosened in Russia, and influenza activity resumed shortly thereafter. Here, we summarize the epidemiological and virological data on the influenza epidemic in Russia in 2021-2022 obtained by the two National Influenza Centers. We demonstrate that the commonly used baseline for acute respiratory infection (ARI) is no longer sufficiently sensitive and BL for ILI incidence was more specific for early recognition of the epidemic. We also present the results of PCR detection of influenza, SARS-CoV-2 and other respiratory viruses as well as antigenic and genetic analysis of influenza viruses. Influenza A(H3N2) prevailed this season with influenza B being detected at low levels at the end of the epidemic. The majority of A(H3N2) viruses were antigenically and genetically homogenous and belonged to the clade 3C.2a1b.2a.2 of the vaccine strain A/Darwin/9/2021 for the season 2022-2023. All influenza B viruses belonged to the Victoria lineage and were similar to the influenza B/Austria/1359417/2021 virus. No influenza A(H1N1)pdm09 and influenza B/Yamagata lineage was isolated last season.
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Affiliation(s)
- Anna Sominina
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia
| | - Daria Danilenko
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia
| | - Andrey Komissarov
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia
| | - Ludmila Karpova
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia
| | - Maria Pisareva
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia
| | - Artem Fadeev
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia
| | - Nadezhda Konovalova
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia
| | - Mikhail Eropkin
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia
| | - Kirill Stolyarov
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia
| | - Anna Shtro
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia
| | - Elena Burtseva
- National Research Center for Epidemiology and Microbiology Named after N.F. Gamaleya, 123098 Moscow, Russia
| | - Dmitry Lioznov
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia
- Department of Infectious Diseases and Epidemiology, First Pavlov State Medical University, 197022 Saint Petersburg, Russia
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Change in Pediatric Health Care Spending and Drug Utilization during the COVID-19 Pandemic. CHILDREN (BASEL, SWITZERLAND) 2021; 8:children8121183. [PMID: 34943379 PMCID: PMC8699860 DOI: 10.3390/children8121183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 11/26/2021] [Accepted: 12/09/2021] [Indexed: 12/23/2022]
Abstract
Objective: To evaluate how the restrictive measures implemented during the SARS-CoV-2 pandemic have influenced the incidence of the most common children’s diseases and the consumption of medications in 2020 compared to 2019. Methods: We involved all family pediatricians of the local health authority of Latina, from which we requested data of monthly visits in 2019 and 2020 for six common diseases disseminated through droplets and contact, and the territorial and integrative pharmaceutical unit of the area, from which we requested data of the net expenditure regarding the most commonly used drugs at pediatric age. Results: There was significant reduction in the incidence of the evaluated diseases and in the consumption of investigated drugs between 2019 and 2020 in the months when the restrictive measures were in place, with an attenuation of this effect during the months of the gradual loosening of those measures. Conclusion: Nonpharmaceutical intervention measures have caused changes in the diffusion of common pediatric diseases. We believe that the implementation of a reasonable containment strategy, even outside of the pandemic, could positively influence the epidemiology of infectious and allergic diseases in children, and healthcare system spending.
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Toelen J, Ritz N, de Winter JP. Changes in pediatric infections during the COVID-19 pandemic: 'a quarantrend for coronials'? Eur J Pediatr 2021; 180:1965-1967. [PMID: 33649911 PMCID: PMC7920544 DOI: 10.1007/s00431-021-03986-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Jaan Toelen
- Division of Woman and Child, University Hospitals Leuven, Leuven, Belgium
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Nicole Ritz
- Paediatric Infectious Diseases and Vaccinology Unit, University of Basel Children's Hospital, Basel, Switzerland
- Department of Pediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - J Peter de Winter
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium.
- Department of Pediatrics, Spaarne Gasthuis, Haarlem/Hoofddorp, the Netherlands.
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Adlhoch C, Pebody R. What to expect for the influenza season 2020/21 with the ongoing COVID-19 pandemic in the World Health Organization European Region. Euro Surveill 2020; 25:2001816. [PMID: 33094719 PMCID: PMC7651872 DOI: 10.2807/1560-7917.es.2020.25.42.2001816] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 11/20/2022] Open
Affiliation(s)
- Cornelia Adlhoch
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Richard Pebody
- World Health Organization Regional Office for Europe, Copenhagen, Denmark
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11
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Chernov AA, Kelbert MY, Shemendyuk AA. Optimal vaccine allocation during the mumps outbreak in two SIR centres. MATHEMATICAL MEDICINE AND BIOLOGY-A JOURNAL OF THE IMA 2020; 37:303-312. [PMID: 31271214 DOI: 10.1093/imammb/dqz012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 04/29/2019] [Accepted: 05/12/2019] [Indexed: 11/14/2022]
Abstract
The aim of this work is to investigate the optimal vaccine sharing between two susceptible, infected, removed (SIR) centres in the presence of migration fluxes of susceptibles and infected individuals during the mumps outbreak. Optimality of the vaccine allocation means the minimization of the total number of lost working days during the whole period of epidemic outbreak $[0,t_f]$, which can be described by the functional $Q=\int _0^{t_f}I(t)\,{\textrm{d}}t$, where $I(t)$ stands for the number of infectives at time $t$. We explain the behaviour of the optimal allocation, which depends on the model parameters and the amount of vaccine available $V$.
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Affiliation(s)
- Alexey A Chernov
- National Research University Higher School of Economics, Moscow, Russian Federation
| | - Mark Y Kelbert
- National Research University Higher School of Economics, Moscow, Russian Federation
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Meslé MMI, Hall IM, Christley RM, Leach S, Read JM. The use and reporting of airline passenger data for infectious disease modelling: a systematic review. Euro Surveill 2019; 24:1800216. [PMID: 31387671 PMCID: PMC6685100 DOI: 10.2807/1560-7917.es.2019.24.31.1800216] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 09/18/2018] [Indexed: 01/06/2023] Open
Abstract
BackgroundA variety of airline passenger data sources are used for modelling the international spread of infectious diseases. Questions exist regarding the suitability and validity of these sources.AimWe conducted a systematic review to identify the sources of airline passenger data used for these purposes and to assess validation of the data and reproducibility of the methodology.MethodsArticles matching our search criteria and describing a model of the international spread of human infectious disease, parameterised with airline passenger data, were identified. Information regarding type and source of airline passenger data used was collated and the studies' reproducibility assessed.ResultsWe identified 136 articles. The majority (n = 96) sourced data primarily used by the airline industry. Governmental data sources were used in 30 studies and data published by individual airports in four studies. Validation of passenger data was conducted in only seven studies. No study was found to be fully reproducible, although eight were partially reproducible.LimitationsBy limiting the articles to international spread, articles focussed on within-country transmission even if they used relevant data sources were excluded. Authors were not contacted to clarify their methods. Searches were limited to articles in PubMed, Web of Science and Scopus.ConclusionWe recommend greater efforts to assess validity and biases of airline passenger data used for modelling studies, particularly when model outputs are to inform national and international public health policies. We also recommend improving reporting standards and more detailed studies on biases in commercial and open-access data to assess their reproducibility.
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Affiliation(s)
- Margaux Marie Isabelle Meslé
- National Institute for Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections at University of Liverpool, Liverpool, United Kingdom
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Ian Melvyn Hall
- National Institute for Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections at University of Liverpool, Liverpool, United Kingdom
- School of Mathematics, University of Manchester, Manchester, United Kingdom
- Emergency Response Department, Public Health England, Salisbury, United Kingdom
- National Institute for Health Research, Health Protection Research Unit in Emergency Preparedness and Response at Kings College London, London, United Kingdom
| | - Robert Matthew Christley
- National Institute for Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections at University of Liverpool, Liverpool, United Kingdom
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Steve Leach
- National Institute for Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections at University of Liverpool, Liverpool, United Kingdom
- Emergency Response Department, Public Health England, Salisbury, United Kingdom
- National Institute for Health Research, Health Protection Research Unit in Emergency Preparedness and Response at Kings College London, London, United Kingdom
- National Institute for Health Research, Health Protection Research Unit in Modelling Methodology at Imperial College London, London, United Kingdom
| | - Jonathan Michael Read
- National Institute for Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections at University of Liverpool, Liverpool, United Kingdom
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
- Centre for Health Informatics Computation and Statistics, Lancaster Medical School, Lancaster University, Lancaster, United Kingdom
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Sheldenkar A, Lim F, Yung CF, Lwin MO. Acceptance and uptake of influenza vaccines in Asia: A systematic review. Vaccine 2019; 37:4896-4905. [PMID: 31301918 DOI: 10.1016/j.vaccine.2019.07.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 06/04/2019] [Accepted: 07/02/2019] [Indexed: 12/17/2022]
Abstract
In Asia, the public health burden of influenza is significant despite the existence of efficacious influenza vaccines. Annual seasonal influenza vaccination can reduce the incidence of influenza significantly, yet influenza vaccination coverage remains low in this part of the world. As a densely populated region with varying climatic zones and a larger proportion of developing countries compared to the West, Asia is at increased risk of influenza. To provide a more comprehensive and nuanced understanding of the Asian region, the key objective of this systematic review is to examine the determinants of vaccination uptake in Asia, beyond that of existing studies that have largely been western-centric. We carried out a systematic review of peer-reviewed scientific research, examining the key determinants, acceptance and uptake of influenza vaccinations across Asia. A comprehensive search strategy was defined to capture studies that met the inclusion criteria of articles published in English, from 2008 to 2018, focusing on adult populations within Asia. A total of 83 relevant studies were appraised in this review. Analyses of the extant data confirmed that vaccination rates within Asia are low, and that most countries lack scientific research on vaccination behaviours. Studies were categorised into four different population groups: healthcare workers, high risk groups, general population and uniform groups. The motivators and deterrents for vaccine uptake varied according to population groups and characteristics. Both general populations and healthcare workers were concerned with vaccine safety and efficacy, and recommendations from health authorities were influential in vaccine uptake within the other populations. The findings suggest that further research is needed within a broader range of Asian countries to garner greater in-depth knowledge of vaccination behaviours in the region. In particular, influenza vaccination programs within Asia should focus on improving engagement more effectively, through greater relatability and transparency of data when educating the public.
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Affiliation(s)
- Anita Sheldenkar
- Wee Kim Wee School of Communication and Information, Nanyang Technological University (NTU), Singapore.
| | - Fann Lim
- Wee Kim Wee School of Communication and Information, Nanyang Technological University (NTU), Singapore
| | - Chee Fu Yung
- KK Women's and Children's Hospital (KKH), Singapore; Duke-NUS Graduate Medical School, Singapore
| | - May O Lwin
- Wee Kim Wee School of Communication and Information, Nanyang Technological University (NTU), Singapore
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14
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Zlojutro A, Rey D, Gardner L. A decision-support framework to optimize border control for global outbreak mitigation. Sci Rep 2019; 9:2216. [PMID: 30778107 PMCID: PMC6379393 DOI: 10.1038/s41598-019-38665-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/28/2018] [Indexed: 01/15/2023] Open
Abstract
The introduction and spread of emerging infectious diseases is increasing in both prevalence and scale. Whether naturally, accidentally or maliciously introduced, the substantial uncertainty surrounding the emergence of novel viruses, specifically where they may come from and how they will spread, demands robust and quantifiably validated outbreak control policies that can be implemented in real time. This work presents a novel mathematical modeling framework that integrates both outbreak dynamics and outbreak control into a decision support tool for mitigating infectious disease pandemics that spread through passenger air travel. An ensemble of border control strategies that exploit properties of the air traffic network structure and expected outbreak behavior are proposed. A stochastic metapopulation epidemic model is developed to evaluate and rank the control strategies based on their effectiveness in reducing the spread of outbreaks. Sensitivity analyses are conducted to illustrate the robustness of the proposed control strategies across a range of outbreak scenarios, and a case study is presented for the 2009 H1N1 influenza pandemic. This study highlights the importance of strategically allocating outbreak control resources, and the results can be used to identify the most robust border control policy that can be implemented in the early stages of an outbreak.
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Affiliation(s)
- Aleksa Zlojutro
- School of Civil and Environmental Engineering, University of New South Wales (UNSW) Sydney, Sydney, NSW, 2052, Australia
| | - David Rey
- School of Civil and Environmental Engineering, University of New South Wales (UNSW) Sydney, Sydney, NSW, 2052, Australia
| | - Lauren Gardner
- School of Civil and Environmental Engineering, University of New South Wales (UNSW) Sydney, Sydney, NSW, 2052, Australia.
- Department of Civil Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
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15
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Cai J, Xu B, Chan KKY, Zhang X, Zhang B, Chen Z, Xu B. Roles of Different Transport Modes in the Spatial Spread of the 2009 Influenza A(H1N1) Pandemic in Mainland China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:E222. [PMID: 30646629 PMCID: PMC6352022 DOI: 10.3390/ijerph16020222] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/04/2019] [Accepted: 01/09/2019] [Indexed: 11/16/2022]
Abstract
There is increasing concern about another influenza pandemic in China. However, the understanding of the roles of transport modes in the 2009 influenza A(H1N1) pandemic spread across mainland China is limited. Herein, we collected 127,797 laboratory-confirmed cases of influenza A(H1N1)pdm09 in mainland China from May 2009 to April 2010. Arrival days and peak days were calculated for all 340 prefectures to characterize the dissemination patterns of the pandemic. We first evaluated the effects of airports and railway stations on arrival days and peak days, and then we applied quantile regressions to quantify the relationships between arrival days and air, rail, and road travel. Our results showed that early arrival of the virus was not associated with an early incidence peak. Airports and railway stations in prefectures significantly advanced arrival days but had no significant impact on peak days. The pandemic spread across mainland China from the southeast to the northwest in two phases that were split at approximately 1 August 2009. Both air and road travel played a significant role in accelerating the spread during phases I and II, but rail travel was only significant during phase II. In conclusion, in addition to air and road travel, rail travel also played a significant role in accelerating influenza A(H1N1)pdm09 spread between prefectures. Establishing a multiscale mobility network that considers the competitive advantage of rail travel for mid to long distances is essential for understanding the influenza pandemic transmission in China.
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Affiliation(s)
- Jun Cai
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China.
- Joint Center for Global Change Studies, Beijing 100875, China.
| | - Bo Xu
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China.
- Joint Center for Global Change Studies, Beijing 100875, China.
| | - Karen Kie Yan Chan
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China.
- Joint Center for Global Change Studies, Beijing 100875, China.
| | - Xueying Zhang
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Bing Zhang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China.
| | - Ziyue Chen
- State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing 100875, China.
| | - Bing Xu
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China.
- Joint Center for Global Change Studies, Beijing 100875, China.
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16
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Hirsch A, Katz MA, Laufer Peretz A, Greenberg D, Wendlandt R, Shemer Avni Y, Newes-Adeyi G, Gofer I, Leventer-Roberts M, Davidovitch N, Rosenthal A, Gur-Arie R, Hertz T, Glatman-Freedman A, Monto AS, Azziz-Baumgartner E, Ferdinands JM, Martin ET, Malosh RE, Neyra Quijandría JM, Levine M, Campbell W, Balicer R, Thompson MG. Study of Healthcare Personnel with Influenza and other Respiratory Viruses in Israel (SHIRI): study protocol. BMC Infect Dis 2018; 18:550. [PMID: 30400834 PMCID: PMC6220521 DOI: 10.1186/s12879-018-3444-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 10/16/2018] [Indexed: 01/04/2023] Open
Abstract
Background The Study of Healthcare Personnel with Influenza and other Respiratory Viruses in Israel (SHIRI) prospectively follows a cohort of healthcare personnel (HCP) in two hospitals in Israel. SHIRI will describe the frequency of influenza virus infections among HCP, identify predictors of vaccine acceptance, examine how repeated influenza vaccination may modify immunogenicity, and evaluate influenza vaccine effectiveness in preventing influenza illness and missed work. Methods Cohort enrollment began in October, 2016; a second year of the study and a second wave of cohort enrollment began in June 2017. The study will run for at least 3 years and will follow approximately 2000 HCP (who are both employees and members of Clalit Health Services [CHS]) with routine direct patient contact. Eligible HCP are recruited using a stratified sampling strategy. After informed consent, participants complete a brief enrollment survey with questions about occupational responsibilities and knowledge, attitudes, and practices about influenza vaccines. Blood samples are collected at enrollment and at the end of influenza season; HCP who choose to be vaccinated contribute additional blood one month after vaccination. During the influenza season, participants receive twice-weekly short message service (SMS) messages asking them if they have acute respiratory illness or febrile illness (ARFI) symptoms. Ill participants receive follow-up SMS messages to confirm illness symptoms and duration and are asked to self-collect a nasal swab. Information on socio-economic characteristics, current and past medical conditions, medical care utilization and vaccination history is extracted from the CHS database. Information about missed work due to illness is obtained by self-report and from employee records. Respiratory specimens from self-collected nasal swabs are tested for influenza A and B viruses, respiratory syncytial virus, human metapneumovirus, and coronaviruses using validated multiplex quantitative real-time reverse transcription polymerase chain reaction assays. The hemagglutination inhibition assay will be used to detect the presence of neutralizing influenza antibodies in serum. Discussion SHIRI will expand our knowledge of the burden of respiratory viral infections among HCP and the effectiveness of current and repeated annual influenza vaccination in preventing influenza illness, medical utilization, and missed workdays among HCP who are in direct contact with patients. Trial registration NCT03331991. Registered on November 6, 2017. Electronic supplementary material The online version of this article (10.1186/s12879-018-3444-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Avital Hirsch
- Chief Physician's Office, Clalit Health Services, Clalit Research Institute, Tel Aviv, Israel.
| | - Mark A Katz
- Chief Physician's Office, Clalit Health Services, Clalit Research Institute, Tel Aviv, Israel.,School of Public Health, Medical School for International Health, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel.,Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Alon Laufer Peretz
- Rabin Medical Center, Occupational Medicine Department, Petah Tikva, Israel
| | - David Greenberg
- Pediatric Infectious Disease Unit, Soroka University Medical Center, Beer Sheva, Israel
| | | | - Yonat Shemer Avni
- Clinical Virology, Soroka University Medical Center, Ben Gurion University of the Negev, Beer Sheva, Israel
| | | | - Ilan Gofer
- Chief Physician's Office, Clalit Health Services, Clalit Research Institute, Tel Aviv, Israel
| | - Maya Leventer-Roberts
- Chief Physician's Office, Clalit Health Services, Clalit Research Institute, Tel Aviv, Israel
| | - Nadav Davidovitch
- Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Anat Rosenthal
- Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Rachel Gur-Arie
- Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Tomer Hertz
- Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel.,Vaccine and Infectious Disease Division, Fred Hutch Cancer Research Center, Seattle, WA, USA
| | - Aharona Glatman-Freedman
- Israel Center for Disease Control, Ministry of Health, Tel Hashomer, Ramat Gan, Israel.,Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Arnold S Monto
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | | | | | - Emily Toth Martin
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Ryan E Malosh
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | | | - Min Levine
- Influenza Division, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | | | - Ran Balicer
- Chief Physician's Office, Clalit Health Services, Clalit Research Institute, Tel Aviv, Israel
| | - Mark G Thompson
- Influenza Division, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
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17
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Caini S, Alonso WJ, Séblain CEG, Schellevis F, Paget J. The spatiotemporal characteristics of influenza A and B in the WHO European Region: can one define influenza transmission zones in Europe? ACTA ACUST UNITED AC 2018; 22:30606. [PMID: 28877844 PMCID: PMC5587899 DOI: 10.2807/1560-7917.es.2017.22.35.30606] [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: 11/24/2016] [Accepted: 03/15/2017] [Indexed: 12/24/2022]
Abstract
We aimed to assess the epidemiology and spatiotemporal patterns of influenza in the World Health Organization (WHO) European Region and evaluate the validity of partitioning the Region into five influenza transmission zones (ITZs) as proposed by the WHO. We used the FluNet database and included over 650,000 influenza cases from 2000 to 2015. We analysed the data by country and season (from July to the following June). We calculated the median proportion of cases caused by each virus type in a season, compared the timing of the primary peak between countries and used a range of cluster analysis methods to assess the degree of overlap between the WHO-defined and data-driven ITZs. Influenza A and B caused, respectively, a median of 83% and 17% cases in a season. There was a significant west-to-east and non-significant (p = 0.10) south-to-north gradient in the timing of influenza activity. Typically, influenza peaked in February and March; influenza A earlier than influenza B. Most countries in the WHO European Region would fit into two ITZs: ‘Western Europe’ and ‘Eastern Europe’; countries bordering Asia may be better placed into extra-European ITZs. Our findings have implications for the presentation of surveillance data and prevention and control measures in this large WHO Region.
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Affiliation(s)
- Saverio Caini
- Netherlands Institute for Health Services Research (NIVEL), Utrecht, The Netherlands
| | | | | | - François Schellevis
- Netherlands Institute for Health Services Research (NIVEL), Utrecht, The Netherlands.,Department of General Practice and Elderly Care Medicine, EMGO Institute for Health and Care research, VU University Medical Center, Amsterdam, The Netherlands
| | - John Paget
- Netherlands Institute for Health Services Research (NIVEL), Utrecht, The Netherlands
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18
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Fox SJ, Miller JC, Meyers LA. Seasonality in risk of pandemic influenza emergence. PLoS Comput Biol 2017; 13:e1005749. [PMID: 29049288 PMCID: PMC5654262 DOI: 10.1371/journal.pcbi.1005749] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 08/30/2017] [Indexed: 11/18/2022] Open
Abstract
Influenza pandemics can emerge unexpectedly and wreak global devastation. However, each of the six pandemics since 1889 emerged in the Northern Hemisphere just after the flu season, suggesting that pandemic timing may be predictable. Using a stochastic model fit to seasonal flu surveillance data from the United States, we find that seasonal flu leaves a transient wake of heterosubtypic immunity that impedes the emergence of novel flu viruses. This refractory period provides a simple explanation for not only the spring-summer timing of historical pandemics, but also early increases in pandemic severity and multiple waves of transmission. Thus, pandemic risk may be seasonal and predictable, with the accuracy of pre-pandemic and real-time risk assessments hinging on reliable seasonal influenza surveillance and precise estimates of the breadth and duration of heterosubtypic immunity.
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Affiliation(s)
- Spencer J. Fox
- Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
| | - Joel C. Miller
- Mathematical Sciences, Monash University, Frankston, Victoria, Australia
- The Institute for Disease Modeling, Bellevue, Washington, United States of America
| | - Lauren Ancel Meyers
- Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
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19
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Liu S, Poccia S, Candan KS, Chowell G, Sapino ML. epiDMS: Data Management and Analytics for Decision-Making From Epidemic Spread Simulation Ensembles. J Infect Dis 2017; 214:S427-S432. [PMID: 28830107 PMCID: PMC7107328 DOI: 10.1093/infdis/jiw305] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Carefully calibrated large-scale computational models of epidemic spread represent a powerful tool to support the decision-making process during epidemic emergencies. Epidemic models are being increasingly used for generating forecasts of the spatial-temporal progression of epidemics at different spatial scales and for assessing the likely impact of different intervention strategies. However, the management and analysis of simulation ensembles stemming from large-scale computational models pose challenges, particularly when dealing with multiple interdependent parameters, spanning multiple layers and geospatial frames, affected by complex dynamic processes operating at different resolutions. Methods We describe and illustrate with examples a novel epidemic simulation data management system, epiDMS, that was developed to address the challenges that arise from the need to generate, search, visualize, and analyze, in a scalable manner, large volumes of epidemic simulation ensembles and observations during the progression of an epidemic. Results and conclusions epiDMS is a publicly available system that facilitates management and analysis of large epidemic simulation ensembles. epiDMS aims to fill an important hole in decision-making during healthcare emergencies by enabling critical services with significant economic and health impact.
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Affiliation(s)
- Sicong Liu
- School of Informatics, and Decision Systems Engineering, Arizona State University, Tempe
| | | | - K Selçuk Candan
- School of Informatics, and Decision Systems Engineering, Arizona State University, Tempe
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20
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Charu V, Zeger S, Gog J, Bjørnstad ON, Kissler S, Simonsen L, Grenfell BT, Viboud C. Human mobility and the spatial transmission of influenza in the United States. PLoS Comput Biol 2017; 13:e1005382. [PMID: 28187123 PMCID: PMC5349690 DOI: 10.1371/journal.pcbi.1005382] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 03/14/2017] [Accepted: 01/26/2017] [Indexed: 11/18/2022] Open
Abstract
Seasonal influenza epidemics offer unique opportunities to study the invasion and re-invasion waves of a pathogen in a partially immune population. Detailed patterns of spread remain elusive, however, due to lack of granular disease data. Here we model high-volume city-level medical claims data and human mobility proxies to explore the drivers of influenza spread in the US during 2002–2010. Although the speed and pathways of spread varied across seasons, seven of eight epidemics likely originated in the Southern US. Each epidemic was associated with 1–5 early long-range transmission events, half of which sparked onward transmission. Gravity model estimates indicate a sharp decay in influenza transmission with the distance between infectious and susceptible cities, consistent with spread dominated by work commutes rather than air traffic. Two early-onset seasons associated with antigenic novelty had particularly localized modes of spread, suggesting that novel strains may spread in a more localized fashion than previously anticipated. The underlying mechanisms dictating the spatial spread of seasonal influenza remain poorly understood, in part because of the lack of spatially resolved disease data to quantify patterns of spread. In this paper, we address this issue by analyzing fine-grain insurance claims data on influenza-like-illnesses over eight seasons in ~300 locations throughout the United States. Using statistical methods, we found that seven of eight epidemics likely originated in the Southern US, that influenza spatial transmission is dominated by local traffic between cities, and that seasons marked by novel influenza virus circulation had a particularly radial, localized spatial structure. These findings are in stark contrast to prevailing theories of influenza spatial transmission that suggest that transmission is favored in low humidity environments and that spread is a dominated by air traffic between populous hubs.
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Affiliation(s)
- Vivek Charu
- Fogarty International Center, National Institutes of Health, Bethesda, MD, United States of America
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
- * E-mail:
| | - Scott Zeger
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Julia Gog
- Fogarty International Center, National Institutes of Health, Bethesda, MD, United States of America
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom
| | - Ottar N. Bjørnstad
- Fogarty International Center, National Institutes of Health, Bethesda, MD, United States of America
- Department of Entomology, Pennsylvania State University, State College, Pennsylvania, United States of America
| | - Stephen Kissler
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom
| | - Lone Simonsen
- Fogarty International Center, National Institutes of Health, Bethesda, MD, United States of America
- Department of Public Health, Copenhagen University, Copenhagen, Denmark
| | - Bryan T. Grenfell
- Fogarty International Center, National Institutes of Health, Bethesda, MD, United States of America
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, United States of America
| | - Cécile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, MD, United States of America
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21
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Her Z, Kam YW, Gan VC, Lee B, Thein TL, Tan JJL, Lee LK, Fink K, Lye DC, Rénia L, Leo YS, Ng LFP. Severity of Plasma Leakage Is Associated With High Levels of Interferon γ-Inducible Protein 10, Hepatocyte Growth Factor, Matrix Metalloproteinase 2 (MMP-2), and MMP-9 During Dengue Virus Infection. J Infect Dis 2016; 215:42-51. [PMID: 28077582 DOI: 10.1093/infdis/jiw494] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 10/12/2016] [Indexed: 12/07/2022] Open
Abstract
BACKGROUND Dengue virus infection typically causes mild dengue fever, but, in severe cases, life-threatening dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS) occur. The pathophysiological hallmark of DHF and DSS is plasma leakage that leads to enhanced vascular permeability, likely due to a cytokine storm. METHODS Ninety patients with dengue during 2010-2012 in Singapore were prospectively recruited and stratified according to their disease phase, primary and secondary infection status, and disease severity, measured by plasma leakage. Clinical parameters were recorded throughout the disease progression. The levels of various immune mediators were quantified using comprehensive multiplex microbead-based immunoassays for 46 immune mediators. RESULTS Associations between clinical parameters and immune mediators were analyzed using various statistical methods. Potential immune markers, including interleukin 1 receptor antagonist, interferon γ-inducible protein 10, hepatocyte growth factor, soluble p75 tumor necrosis factor α receptor, vascular cell adhesion molecule 1, and matrix metalloproteinase 2, were significantly associated with significant plasma leakage. Secondary dengue virus infections were also shown to influence disease outcome in terms of disease severity. CONCLUSIONS This study identified several key markers for exacerbated dengue pathogenesis, notably plasma leakage. This will allow a better understanding of the molecular mechanisms of DHF and DSS in patients with dengue.
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Affiliation(s)
- Zhisheng Her
- Singapore Immunology Network, Agency for Science, Technology, and Research
| | - Yiu-Wing Kam
- Singapore Immunology Network, Agency for Science, Technology, and Research
| | - Victor C Gan
- Communicable Disease Centre, Institute of Infectious Disease and Epidemiology, Tan Tock Seng Hospital
| | - Bernett Lee
- Singapore Immunology Network, Agency for Science, Technology, and Research
| | - Tun-Linn Thein
- Communicable Disease Centre, Institute of Infectious Disease and Epidemiology, Tan Tock Seng Hospital
| | - Jeslin J L Tan
- Singapore Immunology Network, Agency for Science, Technology, and Research
| | | | - Linda K Lee
- Communicable Disease Centre, Institute of Infectious Disease and Epidemiology, Tan Tock Seng Hospital
| | - Katja Fink
- Singapore Immunology Network, Agency for Science, Technology, and Research
| | - David C Lye
- Communicable Disease Centre, Institute of Infectious Disease and Epidemiology, Tan Tock Seng Hospital
| | - Laurent Rénia
- Singapore Immunology Network, Agency for Science, Technology, and Research
| | - Yee-Sin Leo
- Communicable Disease Centre, Institute of Infectious Disease and Epidemiology, Tan Tock Seng Hospital.,Saw Swee Hock School of Public Health, National University of Singapore
| | - Lisa F P Ng
- Singapore Immunology Network, Agency for Science, Technology, and Research.,Institute of Infection and Global Health, University of Liverpool, United Kingdom
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22
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Jnawali K, Morsky B, Poore K, Bauch CT. Emergence and spread of drug resistant influenza: A two-population game theoretical model. Infect Dis Model 2016; 1:40-51. [PMID: 29928720 PMCID: PMC5963319 DOI: 10.1016/j.idm.2016.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 07/08/2016] [Indexed: 12/01/2022] Open
Abstract
Background The potential for emergence of antiviral drug resistance during influenza pandemics has raised great concern for public health. Widespread use of antiviral drugs is a significant factor in producing resistant strains. Recent studies show that some influenza viruses may gain antiviral drug resistance without a fitness penalty. This creates the possibility of strategic interaction between populations considering antiviral drug use strategies. Methods To explain why, we develop and analyze a classical 2-player game theoretical model where each player chooses from a range of possible rates of antiviral drug use, and payoffs are derived as a function of final size of epidemic with the regular and mutant strain. Final sizes are derived from a stochastic compartmental epidemic model that captures transmission within each population and between populations, and the stochastic emergence of antiviral drug resistance. High treatment levels not only increase the spread of the resistant strain in the subject population but also affect the other population by increasing the density of the resistant strain infectious individuals due to travel between populations. Results We found two Nash equilibria where both populations treat at a high rate, or both treat at a low rate. Hence the game theoretical analysis predicts that populations will not choose different treatment strategies than other populations, under these assumptions. The populations may choose to cooperate by maintaining a low treatment rate that does not increase the incidence of mutant strain infections or cause case importations to the other population. Alternatively, if one population is treating at a high rate, this will generate a large number of mutant infections that spread to the other population, in turn incentivizing that population to also treat at a high rate. The prediction of two separate Nash equilibria is robust to the mutation rate and the effectiveness of the drug in preventing transmission, but it is sensitive to the volume of travel between the two populations. Conclusions Model-based evaluations of antiviral influenza drug use during a pandemic usually consider populations in isolation from one another, but our results show that strategic interactions could strongly influence a population's choice of antiviral drug use policy. Furthermore, the high treatment rate Nash equilibrium has the potential to become socially suboptimal (i.e. non-Pareto optimal) under model assumptions that might apply under other conditions. Because of the need for players to coordinate their actions, we conclude that communication and coordination between jurisdictions during influenza pandemics is a priority, especially for influenza strains that do not evolve a fitness penalty under antiviral drug resistance.
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Affiliation(s)
- Kamal Jnawali
- Department of Mathematics and Statistics, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| | - Bryce Morsky
- Department of Mathematics and Statistics, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| | - Keith Poore
- Department of Mathematics and Statistics, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| | - Chris T Bauch
- Department of Applied Mathematics, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
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23
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Chowell G, Sattenspiel L, Bansal S, Viboud C. Mathematical models to characterize early epidemic growth: A review. Phys Life Rev 2016; 18:66-97. [PMID: 27451336 PMCID: PMC5348083 DOI: 10.1016/j.plrev.2016.07.005] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 07/01/2016] [Accepted: 07/02/2016] [Indexed: 10/21/2022]
Abstract
There is a long tradition of using mathematical models to generate insights into the transmission dynamics of infectious diseases and assess the potential impact of different intervention strategies. The increasing use of mathematical models for epidemic forecasting has highlighted the importance of designing reliable models that capture the baseline transmission characteristics of specific pathogens and social contexts. More refined models are needed however, in particular to account for variation in the early growth dynamics of real epidemics and to gain a better understanding of the mechanisms at play. Here, we review recent progress on modeling and characterizing early epidemic growth patterns from infectious disease outbreak data, and survey the types of mathematical formulations that are most useful for capturing a diversity of early epidemic growth profiles, ranging from sub-exponential to exponential growth dynamics. Specifically, we review mathematical models that incorporate spatial details or realistic population mixing structures, including meta-population models, individual-based network models, and simple SIR-type models that incorporate the effects of reactive behavior changes or inhomogeneous mixing. In this process, we also analyze simulation data stemming from detailed large-scale agent-based models previously designed and calibrated to study how realistic social networks and disease transmission characteristics shape early epidemic growth patterns, general transmission dynamics, and control of international disease emergencies such as the 2009 A/H1N1 influenza pandemic and the 2014-2015 Ebola epidemic in West Africa.
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Affiliation(s)
- Gerardo Chowell
- School of Public Health, Georgia State University, Atlanta, GA, USA; Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA.
| | - Lisa Sattenspiel
- Department of Anthropology, University of Missouri, Columbia, MO, USA
| | - Shweta Bansal
- Department of Biology, Georgetown University, Washington DC, USA; Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Cécile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
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Allen LJS. Power law incidence rate in epidemic models: Comment on: "Mathematical models to characterize early epidemic growth: A review" by Gerardo Chowell et al. Phys Life Rev 2016; 18:98-99. [PMID: 27562084 DOI: 10.1016/j.plrev.2016.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 08/16/2016] [Indexed: 11/16/2022]
Affiliation(s)
- Linda J S Allen
- Department of Mathematics and Statistics, Texas Tech University, Lubbock, TX 79409-1042, United States.
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Arunorat J, Charoenvisal N, Woonwong Y, Kedkovid R, Thanawongnuwech R. Determination of current reference viruses for serological study of swine influenza viruses after the introduction of pandemic 2009 H1N1 (pdmH1N1) in Thailand. J Virol Methods 2016; 236:5-9. [PMID: 27355862 DOI: 10.1016/j.jviromet.2016.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/17/2016] [Accepted: 06/25/2016] [Indexed: 11/19/2022]
Abstract
Since the introduction of pandemic H1N1 2009 virus (pdmH1N1) in pigs, the status of Thai swine influenza virus (SIV) has changed. The pdmH1N1 and its reassortant viruses have become the predominant strain circulating in the Thai swine population based on the surveillance data from 2012 to 2014. For this reason, the reference viruses for serological assays using the hemagglutination inhibition (HI) test needed to be updated. Six anti-sera against reference viruses from 2006 to 2009 (enH1N1-06, enH1N1-09, enH1N2-09, pdmH1N1-09, enH3N2-07 and enH3N2-09) were used for the HI test with four contemporary viruses (enH1N1-10, pdmH1N1-10, rH1N2 and rH3N2) and the selected reference viruses were tested with sera collected from the field to determine the current SIV status. The results showed that anti-sera of swH1N1-06 had the highest titers against enH1N1-10. Anti-sera of pdmH1N1-09 had the highest titers against pdmH1N1-10 and rH1N2, whereas, anti-sera of enH3N2-09 had the highest titers against rH3N2. The results demonstrated that enH1N1-06, pdmH1N1-09 and enH3N2-09 should be selected as reference viruses for contemporary serological studies and HI tests. The seroprevalence results from 410 samples revealed enH1N1 (37.79%), pdmH1N1 (37.32%) and H3N2 (35.86%), respectively. The present study indicated that pdmH1N1 was widespread and commonly found in the Thai pig population increasing the risk of novel reassortant viruses and should be added as a reference virus for HI test. SIV surveillance program and serological studies should be conducted for the benefits of SIV control and prevention as well as monitoring for zoonotic potential.
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Affiliation(s)
- Jirapat Arunorat
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Henri-Dunant Rd., Bangkok 10330, Thailand
| | - Nataya Charoenvisal
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Henri-Dunant Rd., Bangkok 10330, Thailand
| | - Yonlayong Woonwong
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Henri-Dunant Rd., Bangkok 10330, Thailand
| | - Roongtham Kedkovid
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Henri-Dunant Rd., Bangkok 10330, Thailand
| | - Roongroje Thanawongnuwech
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Henri-Dunant Rd., Bangkok 10330, Thailand; Center of Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Henri-Dunant Rd., Bangkok 10330, Thailand.
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Reynolds JJH, Hirsch BT, Gehrt SD, Craft ME. Raccoon contact networks predict seasonal susceptibility to rabies outbreaks and limitations of vaccination. J Anim Ecol 2015; 84:1720-31. [PMID: 26172427 DOI: 10.1111/1365-2656.12422] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 06/25/2015] [Indexed: 12/24/2022]
Abstract
Infectious disease transmission often depends on the contact structure of host populations. Although it is often challenging to capture the contact structure in wild animals, new technology has enabled biologists to obtain detailed temporal information on wildlife social contacts. In this study, we investigated the effects of raccoon contact patterns on rabies spread using network modelling. Raccoons (Procyon lotor) play an important role in the maintenance of rabies in the United States. It is crucial to understand how contact patterns influence the spread of rabies in raccoon populations in order to design effective control measures and to prevent transmission to human populations and other animals. We constructed a dynamic system of contact networks based on empirical data from proximity logging collars on a wild suburban raccoon population and then simulated rabies spread across these networks. Our contact networks incorporated the number and duration of raccoon interactions. We included differences in contacts according to sex and season, and both short-term acquaintances and long-term associations. Raccoons may display different behaviours when infectious, including aggression (furious behaviour) and impaired mobility (dumb behaviour); the network model was used to assess the impact of potential behavioural changes in rabid raccoons. We also tested the effectiveness of different vaccination coverage levels. Our results demonstrate that when rabies enters a suburban raccoon population, the likelihood of a disease outbreak affecting the majority of the population is high. Both the magnitude of rabies outbreaks and the speed of rabies spread depend strongly on the time of year that rabies is introduced into the population. When there is a combination of dumb and furious behaviours in the rabid raccoon population, there are similar outbreak sizes and speed of spread to when there are no behavioural changes due to rabies infection. By incorporating detailed data describing the variation in raccoon contact rates into a network modelling approach, we were able to show that suburban raccoon populations are highly susceptible to rabies outbreaks, that the risk of large outbreaks varies seasonally and that current vaccination target levels may be inadequate to prevent the spread of rabies within these populations. Our findings provide new insights into rabies dynamics in raccoon populations and have important implications for disease control.
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Affiliation(s)
- Jennifer J H Reynolds
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, USA
| | - Ben T Hirsch
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA.,Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Panamá, República de, Panamá
| | - Stanley D Gehrt
- School of Environment and Natural Resources, The Ohio State University, Columbus, OH, USA
| | - Meggan E Craft
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, USA
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Shao Q, Jia M. Influences on influenza transmission within terminal based on hierarchical structure of personal contact network. BMC Public Health 2015; 15:257. [PMID: 25849344 PMCID: PMC4376360 DOI: 10.1186/s12889-015-1536-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Accepted: 02/13/2015] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Since the outbreak of pandemics, influenza has caused extensive attention in the field of public health. It is actually hard to distinguish what is the most effective method to control the influenza transmission within airport terminal. The purpose of this study was to quantitatively evaluate the influences of passenger source, immunity difference and social relation structure on the influenza transmission in terminal. METHODS A method combining hierarchical structure of personal contact network with agent-based SEIR model was proposed to analyze the characteristics of influenza diffusion within terminal. Based on the spatial distance between individuals, the hierarchical structure of personal contact network was defined to construct a complex relationship of passengers in the real world. Moreover, the agent-based SEIR model was improved by considering the individual level of influenza spread characteristics. To evaluate the method, this process was fused in simulation based on the constructed personal contact network. RESULTS In the terminal we investigated, personal contact network was defined by following four layers: social relation structure, procedure partition, procedure area, and the whole terminal. With the growing of layer, the degree distribution curves move right. The value of degree distribution p(k) reached a peak at a specific value, and then back down. Besides, with the increase of layer α, the clustering coefficients presented a tendency to exponential decay. Based on the influenza transmission experiments, the main infected areas were concluded when considering different factors. Moreover, partition of passenger sources was found to impact a lot in departure, while social relation structure imposed a great influence in arrival. Besides, immunity difference exerted no obvious effect on the spread of influenza in the transmission process both in departure and arrival. CONCLUSIONS The proposed method is efficient to reproduce the evolution process of influenza transmission, and exhibits various roles of each factor in different processes, also better reflects the effect of passenger topological character on influenza spread. It contributes to proposing effective influenza measures by airport relevant department and improving the efficiency and ability of epidemic prevention on the public health.
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Affiliation(s)
- Quan Shao
- College of Civil Aviation, Nanjing University of Aeronautics and Astronautics, 29 Jiangjun St., Nanjing, 211106 China
| | - Meng Jia
- College of Civil Aviation, Nanjing University of Aeronautics and Astronautics, 29 Jiangjun St., Nanjing, 211106 China
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Davidson MW, Haim DA, Radin JM. Using networks to combine "big data" and traditional surveillance to improve influenza predictions. Sci Rep 2015; 5:8154. [PMID: 25634021 PMCID: PMC5389136 DOI: 10.1038/srep08154] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 12/24/2014] [Indexed: 11/09/2022] Open
Abstract
Seasonal influenza infects approximately 5-20% of the U.S. population every year, resulting in over 200,000 hospitalizations. The ability to more accurately assess infection levels and predict which regions have higher infection risk in future time periods can instruct targeted prevention and treatment efforts, especially during epidemics. Google Flu Trends (GFT) has generated significant hope that "big data" can be an effective tool for estimating disease burden and spread. The estimates generated by GFT come in real-time--two weeks earlier than traditional surveillance data collected by the U.S. Centers for Disease Control and Prevention (CDC). However, GFT had some infamous errors and is significantly less accurate at tracking laboratory-confirmed cases than syndromic influenza-like illness (ILI) cases. We construct an empirical network using CDC data and combine this with GFT to substantially improve its performance. This improved model predicts infections one week into the future as well as GFT predicts the present and does particularly well in regions that are most likely to facilitate influenza spread and during epidemics.
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Affiliation(s)
- Michael W Davidson
- University of California, San Diego, Department of Political Science, La Jolla, CA, 92093, USA
| | - Dotan A Haim
- University of California, San Diego, Department of Political Science, La Jolla, CA, 92093, USA
| | - Jennifer M Radin
- University of California, San Diego/San Diego State University Joint Doctoral Program in Public Health (Epidemiology), La Jolla, CA 92093, USA
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Responding to vaccine safety signals during pandemic influenza: a modeling study. PLoS One 2014; 9:e115553. [PMID: 25536228 PMCID: PMC4275236 DOI: 10.1371/journal.pone.0115553] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 11/25/2014] [Indexed: 01/04/2023] Open
Abstract
Background Managing emerging vaccine safety signals during an influenza pandemic is challenging. Federal regulators must balance vaccine risks against benefits while maintaining public confidence in the public health system. Methods We developed a multi-criteria decision analysis model to explore regulatory decision-making in the context of emerging vaccine safety signals during a pandemic. We simulated vaccine safety surveillance system capabilities and used an age-structured compartmental model to develop potential pandemic scenarios. We used an expert-derived multi-attribute utility function to evaluate potential regulatory responses by combining four outcome measures into a single measure of interest: 1) expected vaccination benefit from averted influenza; 2) expected vaccination risk from vaccine-associated febrile seizures; 3) expected vaccination risk from vaccine-associated Guillain-Barre Syndrome; and 4) expected change in vaccine-seeking behavior in future influenza seasons. Results Over multiple scenarios, risk communication, with or without suspension of vaccination of high-risk persons, were the consistently preferred regulatory responses over no action or general suspension when safety signals were detected during a pandemic influenza. On average, the expert panel valued near-term vaccine-related outcomes relative to long-term projected outcomes by 3∶1. However, when decision-makers had minimal ability to influence near-term outcomes, the response was selected primarily by projected impacts on future vaccine-seeking behavior. Conclusions The selected regulatory response depends on how quickly a vaccine safety signal is identified relative to the peak of the pandemic and the initiation of vaccination. Our analysis suggested two areas for future investment: efforts to improve the size and timeliness of the surveillance system and behavioral research to understand changes in vaccine-seeking behavior.
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Wu J, Zou L, Ni H, Pei L, Zeng X, Liang L, Zhong H, He J, Song Y, Kang M, Zhang X, Lin J, Ke C. Serologic screenings for H7N9 from three sources among high-risk groups in the early stage of H7N9 circulation in Guangdong Province, China. Virol J 2014; 11:184. [PMID: 25342002 PMCID: PMC4283156 DOI: 10.1186/1743-422x-11-184] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/07/2014] [Indexed: 11/25/2022] Open
Abstract
Background The aim of this study was to assess the prevalence of the novel avian influenza A virus (H7N9) in three high risk groups. The groups were divided into those exposed through infected individuals, those exposed through poultry and those individuals exposed through the external environment, in the early stage of the epidemic in Guangdong Province, which is located in the southern region of China. Methods Serologic studies were conducted among samples collected from individuals who had close contact with the first H7N9 infected patient reported in Guangdong Province, those who were most likely exposed to the first group of H7N9 infected poultry, and those who might have been exposed to H7N9 in the environmental settings, namely hemagglutinin inhibition (HI) and microneutralizaiton(MN) assays using three viruses as antigens. Results The alignment results of the viral sequences indicated the similarity of the HA gene sequence among viruses from exposure to infected poultry, infected humans and contaminated environments were highly conserved. Seven samples of individuals exposed to contaminated environments were positive in the HI assay and one sample among them was positive in the MN assay using poultry H7N9 virus as the antigen. One sample was positive against human H7N9 virus and 3 samples were positive against environmental H7N9 among those that were in contact with infected patients in HI assay. None of these were positive in MN assay. All HI titers of the 240 samples from those individuals in contact with infected poultry were less than 40 aganist the antigens from three viruses. Conclusions The results suggest that when the H7N9 virus was in the early stages of circulation in Guangdong Province, the antigenic sites of the HA proteins of the H7N9 strain isolated from different hosts were highly conserved. The risk of new infection is low in individuals who have contact with the infected patients, poultry or a contaminated environment in the early stages of the circulation of the H7N9 virus.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Changwen Ke
- Center for Disease Control and Prevention of Guangdong Province, Guangzhou 511430, China.
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Marmara V, Cook A, Kleczkowski A. Estimation of force of infection based on different epidemiological proxies: 2009/2010 Influenza epidemic in Malta. Epidemics 2014; 9:52-61. [PMID: 25480134 DOI: 10.1016/j.epidem.2014.09.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 09/02/2014] [Accepted: 09/29/2014] [Indexed: 11/25/2022] Open
Abstract
Information about infectious disease outbreaks is often gathered indirectly, from doctor's reports and health board records. It also typically underestimates the actual number of cases, but the relationship between the observed proxies and the numbers that drive the diseases is complicated, nonlinear and potentially time- and state-dependent. We use a combination of data collection from the 2009-2010 H1N1 outbreak in Malta, compartmental modelling and Bayesian inference to explore the effect of using various sources of information (consultations, doctor's diagnose, swabbing and molecular testing) on estimation of the effective basic reproduction ratio, R(t). Different proxies and different sampling rates (daily and weekly) lead to similar behaviour of R(t) as the epidemic unfolds, although individual parameters (force of infection, length of latent and infectious period) vary. We also demonstrate that the relationship between different proxies varies as epidemic progresses, with the first period characterised by high ratio of consultations and influenza diagnoses to actual confirmed cases of H1N1. This has important consequences for modelling that is based on reconstructing influenza cases from doctor's reports.
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Affiliation(s)
- V Marmara
- University of Stirling, Stirling FK9 4LA, United Kingdom.
| | - A Cook
- National University of Singapore, Singapore 119246, Singapore
| | - A Kleczkowski
- University of Stirling, Stirling FK9 4LA, United Kingdom
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Eichner M, Schwehm M, Hain J, Uphoff H, Salzberger B, Knuf M, Schmidt-Ott R. 4Flu - an individual based simulation tool to study the effects of quadrivalent vaccination on seasonal influenza in Germany. BMC Infect Dis 2014; 14:365. [PMID: 24993051 PMCID: PMC4099094 DOI: 10.1186/1471-2334-14-365] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 06/03/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Influenza vaccines contain Influenza A and B antigens and are adjusted annually to match the characteristics of circulating viruses. In Germany, Influenza B viruses belonged to the B/Yamagata lineage, but since 2001, the antigenically distinct B/Victoria lineage has been co-circulating. Trivalent influenza vaccines (TIV) contain antigens of the two A subtypes A(H3N2) and A(H1N1), yet of only one B lineage, resulting in frequent vaccine mismatches. Since 2012, the WHO has been recommending vaccine strains from both B lineages, paving the way for quadrivalent influenza vaccines (QIV). METHODS Using an individual-based simulation tool, we simulate the concomitant transmission of four influenza strains, and compare the effects of TIV and QIV on the infection incidence. Individuals are connected in a dynamically evolving age-dependent contact network based on the POLYMOD matrix; their age-distribution reproduces German demographic data and predictions. The model considers maternal protection, boosting of existing immunity, loss of immunity, and cross-immunizing events between the B lineages. Calibration to the observed annual infection incidence of 10.6% among young adults yielded a basic reproduction number of 1.575. Vaccinations are performed annually in October and November, whereby coverage depends on the vaccinees' age, their risk status and previous vaccination status. New drift variants are introduced at random time points, leading to a sudden loss of protective immunity for part of the population and occasionally to reduced vaccine efficacy. Simulations run for 50 years, the first 30 of which are used for initialization. During the final 20 years, individuals receive TIV or QIV, using a mirrored simulation approach. RESULTS Using QIV, the mean annual infection incidence can be reduced from 8,943,000 to 8,548,000, i.e. by 395,000 infections, preventing 11.2% of all Influenza B infections which still occur with TIV (95% CI: 10.7-11.8%). Using a lower B lineage cross protection than the baseline 60%, the number of Influenza B infections increases and the number additionally prevented by QIV can be 5.5 times as high. CONCLUSIONS Vaccination with TIV substantially reduces the Influenza incidence compared to no vaccination. Depending on the assumed degree of B lineage cross protection, QIV further reduces Influenza B incidence by 11-33%.
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Affiliation(s)
- Martin Eichner
- Department for Clinical Epidemiology and Applied Biometry, University of Tübingen, Silcherstr. 5, 72076 Tübingen, Germany
- Epimos GmbH, Uhlandstr. 3, 72144 Dusslingen, Germany
| | - Markus Schwehm
- ExploSYS GmbH, Otto-Hahn-Weg 6, 70771 Leinfelden-Echterdingen, Germany
| | - Johannes Hain
- GlaxoSmithKline GmbH & Co. KG, Prinzregentenplatz 9, 81675 München, Germany
| | - Helmut Uphoff
- Hessisches Landesprüfungs- und Untersuchungsamt im Gesundheitswesen, Zentrum für Gesundheitsschutz, Wolframstr. 33, 35683 Dillenburg, Germany
| | - Bernd Salzberger
- Klinik f. Innere Medizin, Universitätsklinikum Regensburg, 93042 Regensburg, Germany
| | - Markus Knuf
- Dr. Horst Schmidt Klinik, Klinik für Kinder und Jugendliche, Ludwig-Erhard-Str. 100, 65199 Wiesbaden, Germany
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Prieto D, Das TK. An operational epidemiological model for calibrating agent-based simulations of pandemic influenza outbreaks. Health Care Manag Sci 2014; 19:1-19. [PMID: 24710651 DOI: 10.1007/s10729-014-9273-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Accepted: 02/12/2014] [Indexed: 12/20/2022]
Abstract
Uncertainty of pandemic influenza viruses continue to cause major preparedness challenges for public health policymakers. Decisions to mitigate influenza outbreaks often involve tradeoff between the social costs of interventions (e.g., school closure) and the cost of uncontrolled spread of the virus. To achieve a balance, policymakers must assess the impact of mitigation strategies once an outbreak begins and the virus characteristics are known. Agent-based (AB) simulation is a useful tool for building highly granular disease spread models incorporating the epidemiological features of the virus as well as the demographic and social behavioral attributes of tens of millions of affected people. Such disease spread models provide excellent basis on which various mitigation strategies can be tested, before they are adopted and implemented by the policymakers. However, to serve as a testbed for the mitigation strategies, the AB simulation models must be operational. A critical requirement for operational AB models is that they are amenable for quick and simple calibration. The calibration process works as follows: the AB model accepts information available from the field and uses those to update its parameters such that some of its outputs in turn replicate the field data. In this paper, we present our epidemiological model based calibration methodology that has a low computational complexity and is easy to interpret. Our model accepts a field estimate of the basic reproduction number, and then uses it to update (calibrate) the infection probabilities in a way that its effect combined with the effects of the given virus epidemiology, demographics, and social behavior results in an infection pattern yielding a similar value of the basic reproduction number. We evaluate the accuracy of the calibration methodology by applying it for an AB simulation model mimicking a regional outbreak in the US. The calibrated model is shown to yield infection patterns closely replicating the input estimates of the basic reproduction number. The calibration method is also tested to replicate an initial infection incidence trend for a H1N1 outbreak like that of 2009.
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Affiliation(s)
- D Prieto
- Department of Industrial and Manufacturing Engineering, Western Michigan University, 1903 W. Michigan Ave., Kalamazoo, MI, 49008-5336, USA.
| | - T K Das
- Department of Industrial and Management Systems Engineering, University of South Florida, Tampa, FL, 33620, USA
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Lee B, Haidari L, Lee M. Modelling during an emergency: the 2009 H1N1 influenza pandemic. Clin Microbiol Infect 2013; 19:1014-22. [DOI: 10.1111/1469-0691.12284] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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How human location-specific contact patterns impact spatial transmission between populations? Sci Rep 2013; 3:1468. [PMID: 23511929 PMCID: PMC3601479 DOI: 10.1038/srep01468] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 03/01/2013] [Indexed: 11/16/2022] Open
Abstract
The structured-population model has been widely used to study the spatial transmission of epidemics in human society. Many seminal works have demonstrated the impact of human mobility on the epidemic threshold, assuming that the contact pattern of individuals is mixing homogeneously. Inspired by the recent evidence of location-related factors in reality, we introduce two categories of location-specific heterogeneous human contact patterns into a phenomenological model based on the commuting and contagion processes, which significantly decrease the epidemic threshold and thus favor the outbreak of diseases. In more detail, we find that a monotonic mode presents for the variance of disease prevalence in dependence on the contact rates under the destination-driven contact scenario; while under the origin-driven scenario, enhancing the contact rate counterintuitively weakens the disease prevalence in some parametric regimes. The inclusion of heterogeneity of human contacts is expected to provide valuable support to public health implications.
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A universal model for predicting dynamics of the epidemics caused by special pathogens. BIOMED RESEARCH INTERNATIONAL 2013; 2013:467078. [PMID: 23998125 PMCID: PMC3741903 DOI: 10.1155/2013/467078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 06/24/2013] [Accepted: 07/07/2013] [Indexed: 11/18/2022]
Abstract
A universal model intended primarily for predicting dynamics of the mass epidemics (outbreaks) caused by special pathogens is being developed at the State Research Center of Virology and Biotechnology Vector. The model includes the range of major countermeasures: preventive and emergency mass vaccination, vaccination of risk groups as well as search for and isolation/observation of infected cases, contacts, and suspects, and quarantine. The intensity of interventions depends on the availability of the relevant resources. The effect of resource limitations on the development of a putative epidemic of Ebola hemorrhagic fever is demonstrated. The modeling results allow for estimation of the material and human resources necessary for eradication of an epidemic.
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Chao DL. Modeling the global transmission of antiviral-resistant influenza viruses. Influenza Other Respir Viruses 2013; 7 Suppl 1:58-62. [PMID: 23279898 DOI: 10.1111/irv.12043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
BACKGROUND The mutations that confer resistance to antiviral agents are thought to be detrimental, or at best neutral, to influenza virus fitness. The fact that resistant influenza strains can circulate and sometimes replace sensitive strains is of great public health concern. OBJECTIVES We used mathematical modeling to test various hypotheses about the transmission of antiviral-resistant influenza viruses by comparing the model's output with the observed rise in antiviral resistance of seasonal A(H1N1) influenza viruses between 2006 and 2009. METHODS We developed a mathematical model of the transmission of influenza among 321 cities around the globe. In the model, influenza strains resistant to antiviral agents competed with sensitive strains. RESULTS AND CONCLUSIONS We found that a resistant strain of influenza could not displace the sensitive strain as rapidly as has been observed unless it was more transmissible than the sensitive strain in the general population. We believe that an antiviral-resistant strain displaced the antiviral-sensitive seasonal A(H1N1) virus by hitchhiking on an escape mutation. Because of the complex global patterns of influenza circulation, tracking the emergence and spread of antiviral resistance must be a coordinated global effort.
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Affiliation(s)
- Dennis L Chao
- Center for Statistics and Quantitative Infectious Diseases, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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Perminov V. On evaluation of infection probabilities for different age groups. Biosystems 2013; 112:305-8. [DOI: 10.1016/j.biosystems.2013.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 03/04/2013] [Accepted: 03/19/2013] [Indexed: 11/28/2022]
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Huang Z, Wu X, Garcia AJ, Fik TJ, Tatem AJ. An open-access modeled passenger flow matrix for the global air network in 2010. PLoS One 2013; 8:e64317. [PMID: 23691194 PMCID: PMC3655160 DOI: 10.1371/journal.pone.0064317] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 04/10/2013] [Indexed: 11/24/2022] Open
Abstract
The expanding global air network provides rapid and wide-reaching connections accelerating both domestic and international travel. To understand human movement patterns on the network and their socioeconomic, environmental and epidemiological implications, information on passenger flow is required. However, comprehensive data on global passenger flow remain difficult and expensive to obtain, prompting researchers to rely on scheduled flight seat capacity data or simple models of flow. This study describes the construction of an open-access modeled passenger flow matrix for all airports with a host city-population of more than 100,000 and within two transfers of air travel from various publicly available air travel datasets. Data on network characteristics, city population, and local area GDP amongst others are utilized as covariates in a spatial interaction framework to predict the air transportation flows between airports. Training datasets based on information from various transportation organizations in the United States, Canada and the European Union were assembled. A log-linear model controlling the random effects on origin, destination and the airport hierarchy was then built to predict passenger flows on the network, and compared to the results produced using previously published models. Validation analyses showed that the model presented here produced improved predictive power and accuracy compared to previously published models, yielding the highest successful prediction rate at the global scale. Based on this model, passenger flows between 1,491 airports on 644,406 unique routes were estimated in the prediction dataset. The airport node characteristics and estimated passenger flows are freely available as part of the Vector-Borne Disease Airline Importation Risk (VBD-Air) project at: www.vbd-air.com/data.
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Affiliation(s)
- Zhuojie Huang
- Department of Geography, University of Florida, Gainesville, Florida, United States of America.
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Okomo-Adhiambo M, Sleeman K, Lysén C, Nguyen HT, Xu X, Li Y, Klimov AI, Gubareva LV. Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Influenza Other Respir Viruses 2013; 7:645-58. [PMID: 23575174 PMCID: PMC5781198 DOI: 10.1111/irv.12113] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2013] [Indexed: 12/12/2022] Open
Abstract
Background Neuraminidase (NA) inhibitors (NAIs) are currently the only antivirals effective against influenza infections due to widespread resistance to M2 inhibitors. Methods Influenza A and B viruses (n = 1079) collected worldwide between April 01, 2011, and September 30, 2011, were assessed for susceptibility to FDA‐approved NAIs, oseltamivir and zanamivir, and investigational peramivir, using the fluorescent‐based NA‐Fluor™ Influenza Neuraminidase Assay Kit. A subset of viruses (n = 98) were tested for susceptibility to the investigational NAI, laninamivir. Results Influenza A(H1N1)pdm09 viruses (n = 326) were sensitive to all NAIs, except for two (0·6%) with H275Y (N1 numbering; H274Y in N2 numbering) substitution, which exhibited elevated IC50s for oseltamivir and peramivir, and a third with previously unreported N325K substitution, exhibiting reduced susceptibility to oseltamivir. Influenza A(H3N2) viruses (n = 407) were sensitive to all NAIs. Influenza B viruses (n = 346) were sensitive to all NAIs, except two (0·6%) with H273Y (N1 numbering; H274Y in N2 numbering) substitution, exhibiting reduced susceptibility to oseltamivir and peramivir, and one with previously unreported G140R and N144K substitutions, exhibiting reduced susceptibility to oseltamivir, zanamivir, and peramivir. All influenza A and B viruses were sensitive to laninamivir. It is unknown whether substitutions N325K, G140R, and N144K were present in the virus prior to culturing because clinical specimens were unavailable for testing. Conclusions This study summarizes NAI susceptibility of influenza viruses circulating worldwide during the 2011 Southern Hemisphere (SH) season, assessed using the NA‐Fluor™ Kit. Despite low resistance to NAIs among tested influenza viruses, constant surveillance of influenza virus susceptibility to NAIs should be emphasized.
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Affiliation(s)
- Margaret Okomo-Adhiambo
- Virus Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases, WHO Collaborating Center for Surveillance, Epidemiology and Control of Influenza, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Matrajt L, Halloran ME, Longini IM. Optimal vaccine allocation for the early mitigation of pandemic influenza. PLoS Comput Biol 2013; 9:e1002964. [PMID: 23555207 PMCID: PMC3605056 DOI: 10.1371/journal.pcbi.1002964] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 01/16/2013] [Indexed: 01/18/2023] Open
Abstract
With new cases of avian influenza H5N1 (H5N1AV) arising frequently, the threat of a new influenza pandemic remains a challenge for public health. Several vaccines have been developed specifically targeting H5N1AV, but their production is limited and only a few million doses are readily available. Because there is an important time lag between the emergence of new pandemic strain and the development and distribution of a vaccine, shortage of vaccine is very likely at the beginning of a pandemic. We coupled a mathematical model with a genetic algorithm to optimally and dynamically distribute vaccine in a network of cities, connected by the airline transportation network. By minimizing the illness attack rate (i.e., the percentage of people in the population who become infected and ill), we focus on optimizing vaccine allocation in a network of 16 cities in Southeast Asia when only a few million doses are available. In our base case, we assume the vaccine is well-matched and vaccination occurs 5 to 10 days after the beginning of the epidemic. The effectiveness of all the vaccination strategies drops off as the timing is delayed or the vaccine is less well-matched. Under the best assumptions, optimal vaccination strategies substantially reduced the illness attack rate, with a maximal reduction in the attack rate of 85%. Furthermore, our results suggest that cooperative strategies where the resources are optimally distributed among the cities perform much better than the strategies where the vaccine is equally distributed among the network, yielding an illness attack rate 17% lower. We show that it is possible to significantly mitigate a more global epidemic with limited quantities of vaccine, provided that the vaccination campaign is extremely fast and it occurs within the first weeks of transmission.
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Affiliation(s)
- Laura Matrajt
- Department of Applied Mathematics, University of Washington, Seattle, Washington, United States of America.
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Environmental predictors of seasonal influenza epidemics across temperate and tropical climates. PLoS Pathog 2013; 9:e1003194. [PMID: 23505366 PMCID: PMC3591336 DOI: 10.1371/journal.ppat.1003194] [Citation(s) in RCA: 321] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 12/26/2012] [Indexed: 11/19/2022] Open
Abstract
Human influenza infections exhibit a strong seasonal cycle in temperate regions. Recent laboratory and epidemiological evidence suggests that low specific humidity conditions facilitate the airborne survival and transmission of the influenza virus in temperate regions, resulting in annual winter epidemics. However, this relationship is unlikely to account for the epidemiology of influenza in tropical and subtropical regions where epidemics often occur during the rainy season or transmit year-round without a well-defined season. We assessed the role of specific humidity and other local climatic variables on influenza virus seasonality by modeling epidemiological and climatic information from 78 study sites sampled globally. We substantiated that there are two types of environmental conditions associated with seasonal influenza epidemics: "cold-dry" and "humid-rainy". For sites where monthly average specific humidity or temperature decreases below thresholds of approximately 11-12 g/kg and 18-21°C during the year, influenza activity peaks during the cold-dry season (i.e., winter) when specific humidity and temperature are at minimal levels. For sites where specific humidity and temperature do not decrease below these thresholds, seasonal influenza activity is more likely to peak in months when average precipitation totals are maximal and greater than 150 mm per month. These findings provide a simple climate-based model rooted in empirical data that accounts for the diversity of seasonal influenza patterns observed across temperate, subtropical and tropical climates.
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Viboud C, Nelson MI, Tan Y, Holmes EC. Contrasting the epidemiological and evolutionary dynamics of influenza spatial transmission. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120199. [PMID: 23382422 DOI: 10.1098/rstb.2012.0199] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In the past decade, rapid increases in the availability of high-resolution molecular and epidemiological data, combined with developments in statistical and computational methods to simulate and infer migration patterns, have provided key insights into the spatial dynamics of influenza A viruses in humans. In this review, we contrast findings from epidemiological and molecular studies of influenza virus transmission at different spatial scales. We show that findings are broadly consistent in large-scale studies of inter-regional or inter-hemispheric spread in temperate regions, revealing intense epidemics associated with multiple viral introductions, followed by deep troughs driven by seasonal bottlenecks. However, aspects of the global transmission dynamics of influenza viruses are still debated, especially with respect to the existence of tropical source populations experiencing high levels of genetic diversity and the extent of prolonged viral persistence between epidemics. At the scale of a country or community, epidemiological studies have revealed spatially structured diffusion patterns in seasonal and pandemic outbreaks, which were not identified in molecular studies. We discuss the role of sampling issues in generating these conflicting results, and suggest strategies for future research that may help to fully integrate the epidemiological and evolutionary dynamics of influenza virus over space and time.
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Affiliation(s)
- Cécile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA.
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Tizzoni M, Bajardi P, Poletto C, Ramasco JJ, Balcan D, Gonçalves B, Perra N, Colizza V, Vespignani A. Real-time numerical forecast of global epidemic spreading: case study of 2009 A/H1N1pdm. BMC Med 2012; 10:165. [PMID: 23237460 PMCID: PMC3585792 DOI: 10.1186/1741-7015-10-165] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 12/13/2012] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Mathematical and computational models for infectious diseases are increasingly used to support public-health decisions; however, their reliability is currently under debate. Real-time forecasts of epidemic spread using data-driven models have been hindered by the technical challenges posed by parameter estimation and validation. Data gathered for the 2009 H1N1 influenza crisis represent an unprecedented opportunity to validate real-time model predictions and define the main success criteria for different approaches. METHODS We used the Global Epidemic and Mobility Model to generate stochastic simulations of epidemic spread worldwide, yielding (among other measures) the incidence and seeding events at a daily resolution for 3,362 subpopulations in 220 countries. Using a Monte Carlo Maximum Likelihood analysis, the model provided an estimate of the seasonal transmission potential during the early phase of the H1N1 pandemic and generated ensemble forecasts for the activity peaks in the northern hemisphere in the fall/winter wave. These results were validated against the real-life surveillance data collected in 48 countries, and their robustness assessed by focusing on 1) the peak timing of the pandemic; 2) the level of spatial resolution allowed by the model; and 3) the clinical attack rate and the effectiveness of the vaccine. In addition, we studied the effect of data incompleteness on the prediction reliability. RESULTS Real-time predictions of the peak timing are found to be in good agreement with the empirical data, showing strong robustness to data that may not be accessible in real time (such as pre-exposure immunity and adherence to vaccination campaigns), but that affect the predictions for the attack rates. The timing and spatial unfolding of the pandemic are critically sensitive to the level of mobility data integrated into the model. CONCLUSIONS Our results show that large-scale models can be used to provide valuable real-time forecasts of influenza spreading, but they require high-performance computing. The quality of the forecast depends on the level of data integration, thus stressing the need for high-quality data in population-based models, and of progressive updates of validated available empirical knowledge to inform these models.
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Affiliation(s)
- Michele Tizzoni
- Computational Epidemiology Laboratory, Institute for Scientific Interchange, ISI, Torino, Italy
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Chowell G, Nishiura H, Viboud C. Modeling rapidly disseminating infectious disease during mass gatherings. BMC Med 2012; 10:159. [PMID: 23217051 PMCID: PMC3532170 DOI: 10.1186/1741-7015-10-159] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 12/07/2012] [Indexed: 11/25/2022] Open
Abstract
We discuss models for rapidly disseminating infectious diseases during mass gatherings (MGs), using influenza as a case study. Recent innovations in modeling and forecasting influenza transmission dynamics at local, regional, and global scales have made influenza a particularly attractive model scenario for MG. We discuss the behavioral, medical, and population factors for modeling MG disease transmission, review existing model formulations, and highlight key data and modeling gaps related to modeling MG disease transmission. We argue that the proposed improvements will help integrate infectious-disease models in MG health contingency plans in the near future, echoing modeling efforts that have helped shape influenza pandemic preparedness plans in recent years.
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Affiliation(s)
- Gerardo Chowell
- School of Human Evolution and Social Change, Arizona State University, 900 S. Cady Mall, Tempe, AZ 85287-2402, USA.
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Weinberger DM, Krause TG, Mølbak K, Cliff A, Briem H, Viboud C, Gottfredsson M. Influenza epidemics in Iceland over 9 decades: changes in timing and synchrony with the United States and Europe. Am J Epidemiol 2012; 176:649-55. [PMID: 22962250 DOI: 10.1093/aje/kws140] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Influenza epidemics exhibit a strongly seasonal pattern, with winter peaks that occur with similar timing across temperate areas of the Northern Hemisphere. This synchrony could be influenced by population movements, environmental factors, host immunity, and viral characteristics. The historical isolation of Iceland and subsequent increase in international contacts make it an ideal setting to study epidemic timing. The authors evaluated changes in the timing and regional synchrony of influenza epidemics using mortality and morbidity data from Iceland, North America, and Europe during the period from 1915 to 2007. Cross-correlations and wavelet analyses highlighted 2 major changes in influenza epidemic patterns in Iceland: first was a shift from nonseasonal epidemics prior to the 1930s to a regular winter-seasonal pattern, and second was a change in the early 1990s when a 1-month lag between Iceland and the United States and Europe was no longer detectable with monthly data. There was a moderate association between increased synchrony and the number of foreign visitors to Iceland, providing a plausible explanation for the second shift in epidemic timing. This suggests that transportation might have a minor effect on epidemic timing, but efforts to restrict air travel during influenza epidemics would likely have a limited impact, even for island populations.
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Affiliation(s)
- Daniel M Weinberger
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA.
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Inferring the structure of social contacts from demographic data in the analysis of infectious diseases spread. PLoS Comput Biol 2012; 8:e1002673. [PMID: 23028275 PMCID: PMC3441445 DOI: 10.1371/journal.pcbi.1002673] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 07/22/2012] [Indexed: 11/23/2022] Open
Abstract
Social contact patterns among individuals encode the transmission route of infectious diseases and are a key ingredient in the realistic characterization and modeling of epidemics. Unfortunately, the gathering of high quality experimental data on contact patterns in human populations is a very difficult task even at the coarse level of mixing patterns among age groups. Here we propose an alternative route to the estimation of mixing patterns that relies on the construction of virtual populations parametrized with highly detailed census and demographic data. We present the modeling of the population of 26 European countries and the generation of the corresponding synthetic contact matrices among the population age groups. The method is validated by a detailed comparison with the matrices obtained in six European countries by the most extensive survey study on mixing patterns. The methodology presented here allows a large scale comparison of mixing patterns in Europe, highlighting general common features as well as country-specific differences. We find clear relations between epidemiologically relevant quantities (reproduction number and attack rate) and socio-demographic characteristics of the populations, such as the average age of the population and the duration of primary school cycle. This study provides a numerical approach for the generation of human mixing patterns that can be used to improve the accuracy of mathematical models in the absence of specific experimental data. The dynamics of infectious diseases caused by pathogens transmissible from human to human strongly depends on contact patterns between individuals. High quality observational data on contact patterns, usually presented in the form of age-specific contact matrices, are difficult to gather and are currently available only for few countries worldwide. Here we propose a computational approach, based on the simulation of a virtual society of agents, allowing the estimation of contact patterns by age for 26 European countries. We validate the estimated contact matrices against those obtained by the most extensive field study on contact patterns, with data collected in eight European countries. We show that our contact matrices share some common features, e.g. individuals tend to mix preferentially with individuals their own age, and country-specific differences, which can be partly explained by differences in population structures due to different demographic trajectories followed after WWII. Our analysis highlights well defined correlations between epidemiological parameters and socio-demographic features of the populations. This study provides the first estimates of contact matrices for many European countries where specific experimental data are still not available.
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Newall AT, Dehollain JP, Wood JG. Under-explored assumptions in influenza vaccination models: implications for the universal vaccination of children. Vaccine 2012; 30:5776-81. [PMID: 22789505 DOI: 10.1016/j.vaccine.2012.06.067] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2011] [Revised: 06/20/2012] [Accepted: 06/20/2012] [Indexed: 10/28/2022]
Abstract
The aim of this study was to explore several important (but uncertain) assumptions in influenza models which affect the estimated benefits of vaccination programs. We combined consideration of these factors with the seasonal variability of influenza transmissibility to gain a better understanding of how they may influence influenza control efforts. As our case study, we considered the potential impact of universal seasonal childhood vaccination in Australia using a simplified age-stratified Susceptible Exposed Infectious Recovered (SEIR) model to simulate influenza epidemics and the impact of vaccination. We found that the choice of vaccine efficacy model was influential in determining the impact of vaccination. This choice interacted with other model assumption such as those around the infectiousness of asymptomatic cases and the match of the vaccine to the circulating strains. The methodological approach used to estimate influenza hospitalisations was also highly influential. Our study highlights the role that key modelling assumptions play when estimating the impact of vaccination against influenza.
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Affiliation(s)
- Anthony T Newall
- School of Public Health and Community Medicine, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia.
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Delivery of subunit influenza vaccine to skin with microneedles improves immunogenicity and long-lived protection. Sci Rep 2012; 2:357. [PMID: 22500210 PMCID: PMC3324956 DOI: 10.1038/srep00357] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 03/22/2012] [Indexed: 11/23/2022] Open
Abstract
Influenza infection represents a major socio-economic burden worldwide. Novel delivery methods can render influenza vaccination easier and more acceptable by the public, and importantly confer protection equal or superior to that induced by conventional systemic administration. An attractive target for vaccine delivery is the skin. Recent studies have demonstrated improved immune responses after transdermal delivery of inactivated influenza virus with microneedle patches. Here we show that immunization with a licensed influenza subunit vaccine coated on metal microneedles can activate both humoral and cellular arms of the immune response and confer improved long-term protection in the mouse model when compared to the conventional systemic route of delivery. These results demonstrate the promising potential of microneedle delivery of licensed influenza subunit vaccines, that could be beneficial in increasing vaccine coverage and protection and reducing influenza-related mortality worldwide.
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Aplasca-De Los Reyes MR, Dimaano E, Macalalad N, Dbaibo G, Bianco V, Baine Y, Miller J. The investigational meningococcal serogroups A, C, W-135, Y tetanus toxoid conjugate vaccine (ACWY-TT) and the seasonal influenza virus vaccine are immunogenic and well-tolerated when co-administered in adults. Hum Vaccin Immunother 2012; 8:881-7. [PMID: 22485048 PMCID: PMC3495724 DOI: 10.4161/hv.20212] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Co-administration of meningococcal serogroups A, C, W-135 and Y conjugate vaccine (ACWY-TT) with seasonal influenza vaccine was investigated in a subset of adults enrolled in a larger study evaluating lot-to-lot consistency of ACWY-TT and non-inferiority to licensed tetravalent meningococcal polysaccharide vaccine (MenPS). Subjects in this sub-study were randomized (3:1:1) to receive ACWY-TT alone (ACWY-TT group) or with seasonal influenza vaccine (Coad), or licensed MenPS alone. Serum bactericidal antibodies (rSBA) and serum haemagglutination-inhibition (HI) antibody titers were measured pre- and 1 mo post-vaccination. Non-inferiority of the Coad group compared with ACWY-TT group was demonstrated in terms of rSBA geometric mean antibody titers (GMTs) to serogroups A, W-135 and Y. For serogroup C the pre-defined non-inferiority limit was marginally exceeded. Post-vaccination rSBA GMTs were significantly higher (exploratory analysis) in the Coad group compared with the MenPS group for serogroups A, W-135, and Y and were similar to the MenPS group for serogroup C. Overall, > 97% of subjects achieved rSBA titers ≥ 1:128 for all serogroups. The Coad group met all criteria defined by the Committee on Human Medicinal Products (CHMP) for seroprotection, seroconversion and seroconversion factor for HI antibodies for all three influenza strains. Grade 3 solicited local/general symptoms were reported by ≤ 1.9% of subjects in any group. These data support the co-administration of ACWY-TT with seasonal influenza vaccine when protection is needed against both diseases.
This study is registered at clinicaltrials.gov NCT00453986
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