1
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Mahmud AS, Bhattacharjee J, Baker RE, Martinez PP. Alarming Trends in Dengue Incidence and Mortality in Bangladesh. J Infect Dis 2024; 229:4-6. [PMID: 38000901 PMCID: PMC10786241 DOI: 10.1093/infdis/jiad529] [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: 10/02/2023] [Revised: 11/30/2023] [Accepted: 11/22/2023] [Indexed: 11/26/2023] Open
Abstract
Bangladesh is currently experiencing the country's largest and deadliest dengue outbreak on record. This year's outbreak has been characterized by an early seasonal surge in cases, rapid geographic spread, and a high fatality rate. The alarming trends in dengue incidence and mortality this year is an urgent wake-up call for public health policymakers and researchers to pay closer attention to dengue dynamics in South Asia, to strengthen the surveillance system and diagnostic capabilities, and to develop tools and methods for guiding strategic resource allocation and control efforts.
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Affiliation(s)
- Ayesha S Mahmud
- Department of Demography, University of California, Berkeley, Berkeley, California, USA
| | - Joyita Bhattacharjee
- Division of Epidemiology, University of California, Berkeley, Berkeley, California, USA
| | - Rachel E Baker
- Department of Epidemiology, School of Public Health, Brown University, Providence, Rhode Island, USA
- Institute for Environment and Society, Brown University, Providence, Rhode Island, USA
| | - Pamela P Martinez
- Department of Microbiology, University of Illinois Urbana-Champaign, Champaign, Illinois, USA
- Department of Statistics, University of Illinois Urbana-Champaign, Champaign, Illinois, USA
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2
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Kaur U, Jethwani P, Mishra S, Dehade A, Yadav AK, Chakrabarti S, Chakrabarti SS. Did COVID-19 or COVID-19 Vaccines Influence the Patterns of Dengue in 2021? An Exploratory Analysis of Two Observational Studies from North India. Am J Trop Med Hyg 2023; 109:1290-1297. [PMID: 37903443 DOI: 10.4269/ajtmh.23-0418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 09/08/2023] [Indexed: 11/01/2023] Open
Abstract
Dengue experienced a rise in disease burden in 2021 in specific regions of India. We aimed to explore the risk factors of dengue occurrence and severity in the post-COVID-19 and post-COVID-19 vaccination era and performed an exploratory analysis involving participants from two prior observational studies conducted from February 2021 to April 2022 in a tertiary hospital in North India. Health care workers constituted the majority of the study participants. Individuals were stratified into five groups based on COVID-19 infection and timing of vaccination: COVID-No Vaccine, Vaccine-No COVID (VNC), COVID After Vaccine (CAV), Vaccine After COVID (VAC), and No Vaccine-No COVID (NVNC) groups. The occurrence of laboratory-confirmed dengue and severe forms of dengue were the main outcomes of interest. A total of 1,701 participants (1,520 vaccinated, 181 unvaccinated) were included. Of these, symptomatic dengue occurred in 133 (7.8%) and was "severe" in 42 (31.6%) cases. Individuals with a history of COVID-19 in 2020 had a 2-times-higher odds of developing symptomatic dengue (P = 0.002). The VAC group had 3.6 (P = 0.019)-, 2 (P = 0.002)-, and 1.9 (P = 0.01)-times-higher odds of developing symptomatic dengue than the NVNC, VNC, and CAV groups, respectively. The severity of dengue was not affected by COVID-19 vaccination but with marginal statistical significance, a 2-times-higher risk of severe dengue was observed with any COVID-19 of the past (P = 0.08). We conclude that COVID-19 may enhance the risk of developing symptomatic dengue. Future research should explore the predisposition of COVID-19-recovered patients toward other viral illnesses. Individuals receiving COVID-19 vaccines after recovering from COVID-19 particularly seem to be at greater risk of symptomatic dengue and need long-term watchfulness. Possible mechanisms, such as antibody-dependent enhancement or T-cell dysfunction, should be investigated in COVID-19-recovered and vaccinated individuals.
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Affiliation(s)
- Upinder Kaur
- Department of Pharmacology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Parth Jethwani
- Department of Endocrinology and Metabolism, All India Institute of Medical Sciences, Jodhpur, India
| | - Shraddha Mishra
- Department of Pharmacology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Amol Dehade
- Department of Pharmacology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Ashish Kumar Yadav
- Center for Biostatistics, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Sasanka Chakrabarti
- Department of Biochemistry, Maharishi Markandeshwar (deemed to be University), Mullana, India
- Central Research Cell, Maharishi Markandeshwar (deemed to be University), Mullana, India
| | - Sankha Shubhra Chakrabarti
- Department of Geriatric Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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3
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Aogo RA, Zambrana JV, Sanchez N, Ojeda S, Kuan G, Balmaseda A, Gordon A, Harris E, Katzelnick LC. Effects of boosting and waning in highly exposed populations on dengue epidemic dynamics. Sci Transl Med 2023; 15:eadi1734. [PMID: 37967199 PMCID: PMC11001200 DOI: 10.1126/scitranslmed.adi1734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/13/2023] [Indexed: 11/17/2023]
Abstract
Sequential infection with multiple dengue virus (DENV) serotypes is thought to induce enduring protection against dengue disease. However, long-term antibody waning has been observed after repeated DENV infection. Here, we provide evidence that highly immune Nicaraguan children and adults (n = 4478) experience boosting and waning of antibodies during and after major Zika and dengue epidemics. We develop a susceptible-infected-recovered-susceptible (SIRS-type) model that tracks immunity by titer rather than number of infections to show that boosts in highly immune individuals can contribute to herd immunity, delaying their susceptibility to transmissible infection. In contrast, our model of lifelong immunity in highly immune individuals, as previously assumed, results in complete disease eradication after introduction. Periodic epidemics under this scenario can only be sustained with a constant influx of infected individuals into the population or a high basic reproductive number. We also find that Zika virus infection can boost DENV immunity and produce delays and then surges in dengue epidemics, as observed with real epidemiological data. This work provides insight into factors shaping periodicity in dengue incidence and may inform vaccine efforts to maintain population immunity.
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Affiliation(s)
- Rosemary A. Aogo
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-3203, USA
| | - Jose Victor Zambrana
- Sustainable Sciences Institute, Managua, 14007, Nicaragua
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109-2029, USA
| | - Nery Sanchez
- Sustainable Sciences Institute, Managua, 14007, Nicaragua
| | - Sergio Ojeda
- Sustainable Sciences Institute, Managua, 14007, Nicaragua
| | - Guillermina Kuan
- Sustainable Sciences Institute, Managua, 14007, Nicaragua
- Centro de Salud Sócrates Flores Vivas, Ministry of Health, Managua, 12014, Nicaragua
| | - Angel Balmaseda
- Sustainable Sciences Institute, Managua, 14007, Nicaragua
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, 16064, Nicaragua
| | - Aubree Gordon
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109-2029, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720-3370, USA
| | - Leah C. Katzelnick
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-3203, USA
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4
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Fung T, Clapham HE, Chisholm RA. Temporary Cross-Immunity as a Plausible Driver of Asynchronous Cycles of Dengue Serotypes. Bull Math Biol 2023; 85:124. [PMID: 37962713 DOI: 10.1007/s11538-023-01226-4] [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: 01/27/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023]
Abstract
Many infectious diseases exist as multiple variants, with interactions between variants potentially driving epidemiological dynamics. These diseases include dengue, which infects hundreds of millions of people every year and exhibits complex multi-serotype dynamics. Antibodies produced in response to primary infection by one of the four dengue serotypes can produce a period of temporary cross-immunity (TCI) to infection by other serotypes. After this period, the remaining antibodies can facilitate the entry of heterologous serotypes into target cells, thus enhancing severity of secondary infection by a heterologous serotype. This represents antibody-dependent enhancement (ADE). In this study, we analyze an epidemiological model to provide novel insights into the importance of TCI and ADE in producing cyclic outbreaks of dengue serotypes. Our analyses reveal that without TCI, such cyclic outbreaks are synchronous across serotypes and only occur when ADE produces high transmission rates. In contrast, the presence of TCI allows asynchronous cycles of serotypes by inducing a time lag between recovery from primary infection by one serotype and secondary infection by another, with such cycles able to occur without ADE. Our results suggest that TCI is a fundamental driver of asynchronous cycles of dengue serotypes and possibly other multi-variant diseases.
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Affiliation(s)
- Tak Fung
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore.
| | - Hannah E Clapham
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, 12 Science Drive 2, Singapore, 117549, Singapore
| | - Ryan A Chisholm
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
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5
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Gutierrez B, da Silva Candido D, Bajaj S, Rodriguez Maldonado AP, Ayala FG, Rodriguez MDLLT, Rodriguez AA, Arámbula CW, González ER, Martínez IL, Díaz-Quiñónez JA, Pichardo MV, Hill SC, Thézé J, Faria NR, Pybus OG, Preciado-Llanes L, Reyes-Sandoval A, Kraemer MUG, Escalera-Zamudio M. Convergent trends and spatiotemporal patterns of Aedes-borne arboviruses in Mexico and Central America. PLoS Negl Trop Dis 2023; 17:e0011169. [PMID: 37672514 PMCID: PMC10506721 DOI: 10.1371/journal.pntd.0011169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 09/18/2023] [Accepted: 08/21/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND Aedes-borne arboviruses cause both seasonal epidemics and emerging outbreaks with a significant impact on global health. These viruses share mosquito vector species, often infecting the same host population within overlapping geographic regions. Thus, comparative analyses of the virus evolutionary and epidemiological dynamics across spatial and temporal scales could reveal convergent trends. METHODOLOGY/PRINCIPAL FINDINGS Focusing on Mexico as a case study, we generated novel chikungunya and dengue (CHIKV, DENV-1 and DENV-2) virus genomes from an epidemiological surveillance-derived historical sample collection, and analysed them together with longitudinally-collected genome and epidemiological data from the Americas. Aedes-borne arboviruses endemically circulating within the country were found to be introduced multiple times from lineages predominantly sampled from the Caribbean and Central America. For CHIKV, at least thirteen introductions were inferred over a year, with six of these leading to persistent transmission chains. For both DENV-1 and DENV-2, at least seven introductions were inferred over a decade. CONCLUSIONS/SIGNIFICANCE Our results suggest that CHIKV, DENV-1 and DENV-2 in Mexico share evolutionary and epidemiological trajectories. The southwest region of the country was determined to be the most likely location for viral introductions from abroad, with a subsequent spread into the Pacific coast towards the north of Mexico. Virus diffusion patterns observed across the country are likely driven by multiple factors, including mobility linked to human migration from Central towards North America. Considering Mexico's geographic positioning displaying a high human mobility across borders, our results prompt the need to better understand the role of anthropogenic factors in the transmission dynamics of Aedes-borne arboviruses, particularly linked to land-based human migration.
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Affiliation(s)
- Bernardo Gutierrez
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Darlan da Silva Candido
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Sumali Bajaj
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | | | - Fabiola Garces Ayala
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, México
| | - María de la Luz Torre Rodriguez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, México
| | - Adnan Araiza Rodriguez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, México
| | - Claudia Wong Arámbula
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, México
| | - Ernesto Ramírez González
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, México
| | - Irma López Martínez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, México
| | - José Alberto Díaz-Quiñónez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, México
- Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Pachuca de Soto, Mexico
| | - Mauricio Vázquez Pichardo
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, México
| | - Sarah C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
| | - Julien Thézé
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint-Genès-Champanelle, France
| | - Nuno R Faria
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, United Kingdom
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
| | - Lorena Preciado-Llanes
- Nuffield Department of Medicine/Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Arturo Reyes-Sandoval
- Nuffield Department of Medicine/Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Instituto Politécnico Nacional (IPN), Av. Luis Enrique Erro s/n., Unidad Adolfo López Mateos, Mexico City, Mexico
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6
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Saad-Roy CM, Levin SA, Grenfell BT, Boots M. Epidemiological impacts of post-infection mortality. Proc Biol Sci 2023; 290:20230343. [PMID: 37434526 PMCID: PMC10336371 DOI: 10.1098/rspb.2023.0343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/16/2023] [Indexed: 07/13/2023] Open
Abstract
Infectious diseases may cause some long-term damage to their host, leading to elevated mortality even after recovery. Mortality due to complications from so-called 'long COVID' is a stark illustration of this potential, but the impacts of such post-infection mortality (PIM) on epidemic dynamics are not known. Using an epidemiological model that incorporates PIM, we examine the importance of this effect. We find that in contrast to mortality during infection, PIM can induce epidemic cycling. The effect is due to interference between elevated mortality and reinfection through the previously infected susceptible pool. In particular, robust immunity (via decreased susceptibility to reinfection) reduces the likelihood of cycling; on the other hand, disease-induced mortality can interact with weak PIM to generate periodicity. In the absence of PIM, we prove that the unique endemic equilibrium is stable and therefore our key result is that PIM is an overlooked phenomenon that is likely to be destabilizing. Overall, given potentially widespread effects, our findings highlight the importance of characterizing heterogeneity in susceptibility (via both PIM and robustness of host immunity) for accurate epidemiological predictions. In particular, for diseases without robust immunity, such as SARS-CoV-2, PIM may underlie complex epidemiological dynamics especially in the context of seasonal forcing.
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Affiliation(s)
- Chadi M. Saad-Roy
- Miller Institute for Basic Research in Science, University of California, Berkeley, CA, USA
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Simon A. Levin
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Bryan T. Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- School of Public and International Affairs, Princeton University, Princeton, NJ, USA
| | - Mike Boots
- Department of Integrative Biology, University of California, Berkeley, CA, USA
- Department of Biosciences, University of Exeter, Penryn, UK
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7
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de Araújo RGS, Jorge DCP, Dorn RC, Cruz-Pacheco G, Esteva MLM, Pinho STR. Applying a multi-strain dengue model to epidemics data. Math Biosci 2023; 360:109013. [PMID: 37127090 DOI: 10.1016/j.mbs.2023.109013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/17/2023] [Accepted: 04/24/2023] [Indexed: 05/03/2023]
Abstract
Dengue disease transmission is a complex vector-borne disease, mainly due to the co-circulation of four serotypes of the virus. Mathematical models have proved to be a useful tool to understand the complexity of this disease. In this work, we extend the model studied by Esteva et al., 2003, originally proposed for two serotypes, to four circulating serotypes. Using epidemic data of dengue fever in Iquitos (Peru) and San Juan (Puerto Rico), we estimate numerically the co-circulation parameter values for selected outbreaks using a bootstrap method, and we also obtained the Basic Reproduction Number, R0, for each serotype, using both analytical calculations and numerical simulations. Our results indicate that the impact of co-circulation of serotypes in population dynamics of dengue infection is such that there is a reduced effect from DENV-3 to DENV-4 in comparison to no-cross effect for epidemics in Iquitos. Concerning San Juan epidemics, also comparing to no-cross effect, we also observed a reduced effect from the predominant serotype DENV-3 to both DENV-2 and DENV-1 epidemics neglecting the very small number of cases of DENV-4.
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Affiliation(s)
| | - Daniel C P Jorge
- Instituto de Física, Universidade Federal da Bahia, Salvador, Brazil; Instituto de Física Teórica, Universidade Estadual Paulista, São Paulo, Brazil.
| | - Rejane C Dorn
- Instituto de Física, Universidade Federal da Bahia, Salvador, Brazil.
| | - Gustavo Cruz-Pacheco
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Autónoma de México, Cuidad de México, Mexico.
| | - M Lourdes M Esteva
- Facultad de Ciências, Universidad Autónoma de México, Cuidad de México, Mexico.
| | - Suani T R Pinho
- Instituto de Física, Universidade Federal da Bahia, Salvador, Brazil; Instituto Nacional de Ciência e Tecnologia - Sistemas Complexos, Brazil.
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8
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Data-rich modeling helps answer increasingly complex questions on variant and disease interactions: Comment on "Mathematical models for dengue fever epidemiology: A 10-year systematic review" by Aguiar et al. Phys Life Rev 2023; 44:197-200. [PMID: 36773393 PMCID: PMC9893800 DOI: 10.1016/j.plrev.2023.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023]
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9
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Zhou W, Tang B, Bai Y, Shao Y, Xiao Y, Tang S. The resurgence risk of COVID-19 in China in the presence of immunity waning and ADE: A mathematical modelling study. Vaccine 2022; 40:7141-7150. [PMID: 36328883 PMCID: PMC9597525 DOI: 10.1016/j.vaccine.2022.10.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/24/2022] [Accepted: 10/19/2022] [Indexed: 01/27/2023]
Abstract
The mass vaccination program has been actively promoted since the end of 2020. However, waning immunity, antibody-dependent enhancement (ADE), and increased transmissibility of variants make the herd immunity untenable and the implementation of dynamic zero-COVID policy challenging in China. To explore how long the vaccination program can prevent China at low resurgence risk, and how these factors affect the long-term trajectory of the COVID-19 epidemics, we developed a dynamic transmission model of COVID-19 incorporating vaccination and waning immunity, calibrated using the data of accumulative vaccine doses administered and the COVID-19 epidemic in 2020 in mainland China. The prediction suggests that the vaccination coverage with at least one dose reach 95.87%, and two doses reach 77.92% on 31 August 2021. However, despite the mass vaccination, randomly introducing infected cases in the post-vaccination period causes large outbreaks quickly with waning immunity, particularly for SARS-CoV-2 variants with higher transmissibility. The results showed that with the current vaccination program and 50% of the population wearing masks, mainland China can be protected at low resurgence risk until 8 January 2023. However, ADE and higher transmissibility for variants would significantly shorten the low-risk period by over 1 year. Furthermore, intermittent outbreaks can occur while the peak values of the subsequent outbreaks decrease, indicating that subsequent outbreaks boosted immunity in the population level, further indicating that follow-up vaccination programs can help mitigate or avoid the possible outbreaks. The findings revealed that the integrated effects of multiple factors: waning immunity, ADE, relaxed interventions, and higher variant transmissibility, make controlling COVID-19 challenging. We should prepare for a long struggle with COVID-19, and not entirely rely on the COVID-19 vaccine.
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Affiliation(s)
- Weike Zhou
- School of Mathematics and Statistics, Shaanxi Normal University, Xi’an 710119, PR China
| | - Biao Tang
- School of Mathematics and Statistics, Xi’an Jiaotong University, Xi’an 710049, PR China
| | - Yao Bai
- Department of Infection Disease Control and Prevention, Xi’an Center for Disease Prevention and Control, Xi’an, 710043, PR China
| | - Yiming Shao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yanni Xiao
- School of Mathematics and Statistics, Xi’an Jiaotong University, Xi’an 710049, PR China,Corresponding author
| | - Sanyi Tang
- School of Mathematics and Statistics, Shaanxi Normal University, Xi’an 710119, PR China,Corresponding author
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10
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Sieben AJ, Mihaljevic JR, Shoemaker LG. Quantifying mechanisms of coexistence in disease ecology. Ecology 2022; 103:e3819. [PMID: 35855596 DOI: 10.1002/ecy.3819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/22/2022] [Accepted: 04/20/2022] [Indexed: 11/06/2022]
Abstract
Pathogen coexistence depends on ecological processes operating at both within and between-host scales, making it difficult to quantify which processes may promote or prevent coexistence. Here, we propose that adapting modern coexistence theory-traditionally applied in plant communities-to pathogen systems provides an exciting approach for examining mechanisms of coexistence operating across different spatial scales. We first overview modern coexistence theory and its mechanistic decomposition; we subsequently adapt the framework to quantify how spatial variation in pathogen density, host resources and immunity, and their interaction may promote pathogen coexistence. We apply this derivation to an example two pathogen, multi-scale model comparing two scenarios with generalist and strain-specific immunity: one with demographic equivalency among pathogens and one with demographic trade-offs among pathogens. We then show how host-pathogen feedbacks generate spatial heterogeneity that promote pathogen coexistence and decompose those mechanisms to quantify how each spatial heterogeneity contributes to that coexistence. Specifically, coexistence of demographically equivalent pathogens occurs due to spatial variation in host resources, immune responses, and pathogen aggregation. With a competition-colonization trade-off, the superior colonizer requires spatial heterogeneity to coexist, whereas the superior competitor does not. Finally, we suggest ways forward for linking theory and empirical tests of coexistence in disease systems.
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Affiliation(s)
- Andrew J Sieben
- Department of Botany, University of Wyoming, Laramie, WY.,School of Medicine, Emory University, Atlanta, GA
| | - Joseph R Mihaljevic
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ
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11
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Cross-reactive immunity potentially drives global oscillation and opposed alternation patterns of seasonal influenza A viruses. Sci Rep 2022; 12:8883. [PMID: 35614123 PMCID: PMC9131982 DOI: 10.1038/s41598-022-08233-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 03/02/2022] [Indexed: 11/08/2022] Open
Abstract
Several human pathogens exhibit distinct patterns of seasonality and circulate as pairs. For instance, influenza A virus subtypes oscillate and peak during winter seasons of the world’s temperate climate zones. Alternation of dominant strains in successive influenza seasons makes epidemic forecasting a major challenge. From the start of the 2009 influenza pandemic we enrolled influenza A virus infected patients (n = 2980) in a global prospective clinical study. Complete hemagglutinin sequences were obtained from 1078 A/H1N1 and 1033 A/H3N2 viruses. We used phylodynamics to construct high resolution spatio-temporal phylogenetic hemagglutinin trees and estimated global influenza A effective reproductive numbers (R) over time (2009–2013). We demonstrate that R oscillates around R = 1 with a clear opposed alternation pattern between phases of the A/H1N1 and A/H3N2 subtypes. Moreover, we find a similar alternation pattern for the number of global viral spread between the sampled geographical locations. Both observations suggest a between-strain competition for susceptible hosts on a global level. Extrinsic factors that affect person-to-person transmission are a major driver of influenza seasonality. The data presented here indicate that cross-reactive host immunity is also a key intrinsic driver of influenza seasonality, which determines the influenza A virus strain at the onset of each epidemic season.
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12
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García-Carreras B, Yang B, Grabowski MK, Sheppard LW, Huang AT, Salje H, Clapham HE, Iamsirithaworn S, Doung-Ngern P, Lessler J, Cummings DAT. Periodic synchronisation of dengue epidemics in Thailand over the last 5 decades driven by temperature and immunity. PLoS Biol 2022; 20:e3001160. [PMID: 35302985 PMCID: PMC8967062 DOI: 10.1371/journal.pbio.3001160] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/30/2022] [Accepted: 02/24/2022] [Indexed: 01/15/2023] Open
Abstract
The spatial distribution of dengue and its vectors (spp. Aedes) may be the widest it has ever been, and projections suggest that climate change may allow the expansion to continue. However, less work has been done to understand how climate variability and change affects dengue in regions where the pathogen is already endemic. In these areas, the waxing and waning of immunity has a large impact on temporal dynamics of cases of dengue haemorrhagic fever. Here, we use 51 years of data across 72 provinces and characterise spatiotemporal patterns of dengue in Thailand, where dengue has caused almost 1.5 million cases over the last 30 years, and examine the roles played by temperature and dynamics of immunity in giving rise to those patterns. We find that timescales of multiannual oscillations in dengue vary in space and time and uncover an interesting spatial phenomenon: Thailand has experienced multiple, periodic synchronisation events. We show that although patterns in synchrony of dengue are similar to those observed in temperature, the relationship between the two is most consistent during synchronous periods, while during asynchronous periods, temperature plays a less prominent role. With simulations from temperature-driven models, we explore how dynamics of immunity interact with temperature to produce the observed patterns in synchrony. The simulations produced patterns in synchrony that were similar to observations, supporting an important role of immunity. We demonstrate that multiannual oscillations produced by immunity can lead to asynchronous dynamics and that synchrony in temperature can then synchronise these dengue dynamics. At higher mean temperatures, immune dynamics can be more predominant, and dengue dynamics more insensitive to multiannual fluctuations in temperature, suggesting that with rising mean temperatures, dengue dynamics may become increasingly asynchronous. These findings can help underpin predictions of disease patterns as global temperatures rise. This study shows that spatially large-scale shifts in temperature can synchronize dengue dynamics across Thailand; however, as average temperatures rise, dengue dynamics may increasingly be dictated by dynamics of immunity, which may in turn mean fewer synchronous outbreaks in the future.
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Affiliation(s)
- Bernardo García-Carreras
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
| | - Bingyi Yang
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Mary K. Grabowski
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Lawrence W. Sheppard
- Department of Ecology and Evolutionary Biology and Kansas Biological Survey, University of Kansas, Lawrence, Kansas, United States of America
- The Marine Biological Association, Plymouth, United Kingdom
| | - Angkana T. Huang
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Henrik Salje
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Hannah Eleanor Clapham
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | | | - Pawinee Doung-Ngern
- Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Derek A. T. Cummings
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
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13
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Aguiar M, Anam V, Blyuss KB, Estadilla CDS, Guerrero BV, Knopoff D, Kooi BW, Srivastav AK, Steindorf V, Stollenwerk N. Mathematical models for dengue fever epidemiology: A 10-year systematic review. Phys Life Rev 2022; 40:65-92. [PMID: 35219611 PMCID: PMC8845267 DOI: 10.1016/j.plrev.2022.02.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/08/2022] [Indexed: 01/11/2023]
Abstract
Mathematical models have a long history in epidemiological research, and as the COVID-19 pandemic progressed, research on mathematical modeling became imperative and very influential to understand the epidemiological dynamics of disease spreading. Mathematical models describing dengue fever epidemiological dynamics are found back from 1970. Dengue fever is a viral mosquito-borne infection caused by four antigenically related but distinct serotypes (DENV-1 to DENV-4). With 2.5 billion people at risk of acquiring the infection, it is a major international public health concern. Although most of the cases are asymptomatic or mild, the disease immunological response is complex, with severe disease linked to the antibody-dependent enhancement (ADE) - a disease augmentation phenomenon where pre-existing antibodies to previous dengue infection do not neutralize but rather enhance the new infection. Here, we present a 10-year systematic review on mathematical models for dengue fever epidemiology. Specifically, we review multi-strain frameworks describing host-to-host and vector-host transmission models and within-host models describing viral replication and the respective immune response. Following a detailed literature search in standard scientific databases, different mathematical models in terms of their scope, analytical approach and structural form, including model validation and parameter estimation using empirical data, are described and analyzed. Aiming to identify a consensus on infectious diseases modeling aspects that can contribute to public health authorities for disease control, we revise the current understanding of epidemiological and immunological factors influencing the transmission dynamics of dengue. This review provide insights on general features to be considered to model aspects of real-world public health problems, such as the current epidemiological scenario we are living in.
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Affiliation(s)
- Maíra Aguiar
- Basque Center for Applied Mathematics, Alameda de Mazarredo 14, Bilbao, E-48009, Basque Country, Spain; Dipartimento di Matematica, Università degli Studi di Trento, Via Sommarive 14, Povo, Trento, 38123, Italy; Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
| | - Vizda Anam
- Basque Center for Applied Mathematics, Alameda de Mazarredo 14, Bilbao, E-48009, Basque Country, Spain
| | - Konstantin B Blyuss
- VU University, Faculty of Science, De Boelelaan 1085, NL 1081, HV Amsterdam, the Netherlands
| | - Carlo Delfin S Estadilla
- Basque Center for Applied Mathematics, Alameda de Mazarredo 14, Bilbao, E-48009, Basque Country, Spain
| | - Bruno V Guerrero
- Basque Center for Applied Mathematics, Alameda de Mazarredo 14, Bilbao, E-48009, Basque Country, Spain
| | - Damián Knopoff
- Basque Center for Applied Mathematics, Alameda de Mazarredo 14, Bilbao, E-48009, Basque Country, Spain; Centro de Investigaciones y Estudios de Matemática CIEM, CONICET, Medina Allende s/n, Córdoba, 5000, Argentina
| | - Bob W Kooi
- University of Sussex, Department of Mathematics, Falmer, Brighton, UK
| | - Akhil Kumar Srivastav
- Basque Center for Applied Mathematics, Alameda de Mazarredo 14, Bilbao, E-48009, Basque Country, Spain
| | - Vanessa Steindorf
- Basque Center for Applied Mathematics, Alameda de Mazarredo 14, Bilbao, E-48009, Basque Country, Spain
| | - Nico Stollenwerk
- Basque Center for Applied Mathematics, Alameda de Mazarredo 14, Bilbao, E-48009, Basque Country, Spain; Dipartimento di Matematica, Università degli Studi di Trento, Via Sommarive 14, Povo, Trento, 38123, Italy
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14
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Steindorf V, Oliva S, Wu J. Cross immunity protection and antibody-dependent enhancement in a distributed delay dynamic model. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:2950-2984. [PMID: 35240815 DOI: 10.3934/mbe.2022136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Dengue fever is endemic in tropical and subtropical countries, and certain important features of the spread of dengue fever continue to pose challenges for mathematical modelling. Here we propose a system of integro-differential equations (IDE) to study the disease transmission dynamics that involve multi-serotypes and cross immunity. Our main objective is to incorporate and analyze the effect of a general time delay term describing acquired cross immunity protection and the effect of antibody-dependent enhancement (ADE), both characteristics of Dengue fever. We perform qualitative analysis of the model and obtain results to show the stability of the epidemiologically important steady solutions that are completely determined by the basic reproduction number and the invasion reproduction number. We establish the global dynamics by constructing a suitable Lyapunov functional. We also conduct some numerical experiments to illustrate bifurcation structures, indicating the occurrence of periodic oscillations for a specific range of values of a key parameter representing ADE.
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Affiliation(s)
- Vanessa Steindorf
- Mathematical and Theoretical Biology Group, Basque Center for Applied Mathematics, BCAM, Bilbao, Spain
| | - Sergio Oliva
- Applied Mathematics Department, Institute of Mathematics and Statistics, University of São Paulo, São Paulo, SP, Brazil
| | - Jianhong Wu
- Laboratory for Industrial and Applied Mathematics, Department of Mathematics and Statistics, Faculty of Science and Engineering, York University, Toronto, Canada
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15
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Rashkov P, Kooi BW. Complexity of host-vector dynamics in a two-strain dengue model. JOURNAL OF BIOLOGICAL DYNAMICS 2021; 15:35-72. [PMID: 33357025 DOI: 10.1080/17513758.2020.1864038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
We introduce a compartmental host-vector model for dengue with two viral strains, temporary cross-immunity for the hosts, and possible secondary infections. We study the conditions on existence of endemic equilibria where one strain displaces the other or the two virus strains co-exist. Since the host and vector epidemiology follow different time scales, the model is described as a slow-fast system. We use the geometric singular perturbation technique to reduce the model dimension. We compare the behaviour of the full model with that of the model with a quasi-steady approximation for the vector dynamics. We also perform numerical bifurcation analysis with parameter values from the literature and compare the bifurcation structure to that of previous two-strain host-only models.
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Affiliation(s)
- Peter Rashkov
- Institute of Mathematics and Informatics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Bob W Kooi
- Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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16
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Katzelnick LC, Escoto AC, Huang AT, Garcia-Carreras B, Chowdhury N, Berry IM, Chavez C, Buchy P, Duong V, Dussart P, Gromowski G, Macareo L, Thaisomboonsuk B, Fernandez S, Smith DJ, Jarman R, Whitehead SS, Salje H, Cummings DA. Antigenic evolution of dengue viruses over 20 years. Science 2021; 374:999-1004. [PMID: 34793238 PMCID: PMC8693836 DOI: 10.1126/science.abk0058] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Infection with one of dengue viruses 1 to 4 (DENV1-4) induces protective antibodies against homotypic infection. However, a notable feature of dengue viruses is the ability to use preexisting heterotypic antibodies to infect Fcγ receptor–bearing immune cells, leading to higher viral load and immunopathological events that augment disease. We tracked the antigenic dynamics of each DENV serotype by using 1944 sequenced isolates from Bangkok, Thailand, between 1994 and 2014 (348 strains), in comparison with regional and global DENV antigenic diversity (64 strains). Over the course of 20 years, the Thailand DENV serotypes gradually evolved away from one another. However, for brief periods, the serotypes increased in similarity, with corresponding changes in epidemic magnitude. Antigenic evolution within a genotype involved a trade-off between two types of antigenic change (within-serotype and between-serotype), whereas genotype replacement resulted in antigenic change away from all serotypes. These findings provide insights into theorized dynamics in antigenic evolution.
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Affiliation(s)
- Leah C. Katzelnick
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, United States
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Ana Coello Escoto
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, United States
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Angkana T. Huang
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, United States
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Bernardo Garcia-Carreras
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, United States
| | - Nayeem Chowdhury
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, United States
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, United States
| | - Chris Chavez
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, United States
| | - Philippe Buchy
- GlaxoSmithKline (GSK) Vaccines, 637421 Singapore, Singapore
| | - Veasna Duong
- Institut Pasteur in Cambodia, Réseau International des Instituts Pasteur, Phnom Penh 12201, Cambodia
| | - Philippe Dussart
- Institut Pasteur in Cambodia, Réseau International des Instituts Pasteur, Phnom Penh 12201, Cambodia
| | - Gregory Gromowski
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, United States
| | - Louis Macareo
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Butsaya Thaisomboonsuk
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Derek J. Smith
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom
| | - Richard Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, United States
| | - Stephen S. Whitehead
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Henrik Salje
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, United States
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom
| | - Derek A.T. Cummings
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, United States
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17
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Alexander LW, Ben-Shachar R, Katzelnick LC, Kuan G, Balmaseda A, Harris E, Boots M. Boosting can explain patterns of fluctuations of ratios of inapparent to symptomatic dengue virus infections. Proc Natl Acad Sci U S A 2021; 118:e2013941118. [PMID: 33811138 PMCID: PMC8040803 DOI: 10.1073/pnas.2013941118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dengue is the most prevalent arboviral disease worldwide, and the four dengue virus (DENV) serotypes circulate endemically in many tropical and subtropical regions. Numerous studies have shown that the majority of DENV infections are inapparent, and that the ratio of inapparent to symptomatic infections (I/S) fluctuates substantially year-to-year. For example, in the ongoing Pediatric Dengue Cohort Study (PDCS) in Nicaragua, which was established in 2004, the I/S ratio has varied from 16.5:1 in 2006-2007 to 1.2:1 in 2009-2010. However, the mechanisms explaining these large fluctuations are not well understood. We hypothesized that in dengue-endemic areas, frequent boosting (i.e., exposures to DENV that do not lead to extensive viremia and result in a less than fourfold rise in antibody titers) of the immune response can be protective against symptomatic disease, and this can explain fluctuating I/S ratios. We formulate mechanistic epidemiologic models to examine the epidemiologic effects of protective homologous and heterologous boosting of the antibody response in preventing subsequent symptomatic DENV infection. We show that models that include frequent boosts that protect against symptomatic disease can recover the fluctuations in the I/S ratio that we observe, whereas a classic model without boosting cannot. Furthermore, we show that a boosting model can recover the inverse relationship between the number of symptomatic cases and the I/S ratio observed in the PDCS. These results highlight the importance of robust dengue control efforts, as intermediate dengue control may have the potential to decrease the protective effects of boosting.
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Affiliation(s)
| | - Rotem Ben-Shachar
- Integrative Biology, University of California, Berkeley, CA 94720
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720
| | - Leah C Katzelnick
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720
| | - Guillermina Kuan
- Centro de Salud Sócrates Flores Vivas, Ministry of Health, 12014 Managua, Nicaragua
- Sustainable Sciences Institute, 14007 Managua, Nicaragua
| | - Angel Balmaseda
- Sustainable Sciences Institute, 14007 Managua, Nicaragua
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, 16064 Managua, Nicaragua
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720
| | - Mike Boots
- Integrative Biology, University of California, Berkeley, CA 94720;
- Biosciences, University of Exeter, Penryn TR10 9EZ, United Kingdom
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18
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Immune memory in convalescent patients with asymptomatic or mild COVID-19. Cell Discov 2021; 7:18. [PMID: 33767156 PMCID: PMC7993859 DOI: 10.1038/s41421-021-00250-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 02/09/2021] [Indexed: 12/29/2022] Open
Abstract
It is important to evaluate the durability of the protective immune response elicited by primary infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we systematically evaluated the SARS-CoV-2-specific memory B cell and T cell responses in healthy controls and individuals recovered from asymptomatic or symptomatic infection approximately 6 months prior. Comparatively low frequencies of memory B cells specific for the receptor-binding domain (RBD) of spike glycoprotein (S) persisted in the peripheral blood of individuals who recovered from infection (median 0.62%, interquartile range 0.48-0.69). The SARS-CoV-2 RBD-specific memory B cell response was detected in 2 of 13 individuals who recovered from asymptomatic infection and 10 of 20 individuals who recovered from symptomatic infection. T cell responses induced by S, membrane (M), and nucleocapsid (N) peptide libraries from SARS-CoV-2 were observed in individuals recovered from coronavirus disease 2019 (COVID-19), and cross-reactive T cell responses to SARS-CoV-2 were also detected in healthy controls.
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19
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Xue L, Ren X, Magpantay F, Sun W, Zhu H. Optimal Control of Mitigation Strategies for Dengue Virus Transmission. Bull Math Biol 2021; 83:8. [PMID: 33404917 DOI: 10.1007/s11538-020-00839-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/21/2020] [Indexed: 11/30/2022]
Abstract
Dengue virus is transmitted by Aedes mosquitoes, posing threat to people's health and leading to great economic cost in many tropical and subtropical regions. We develop an ordinary differential equation model taking into account multiple strains of dengue virus. Using the model, we assess the effectiveness of human vaccination considering its waning and failure. We derive the lower bound and upper bound for the final size of the epidemic. Sensitivity analysis quantifies the impact of parameters on the basic reproduction number. Different scenarios of vaccinating humans show that it is better to vaccinate humans at early stages. We find that the cumulative number of infected humans is small when the vaccination rate is high or the waning rate is low for previously infected humans. We analyze the necessary conditions for implementing optimal control and derive the corresponding optimal solutions for mitigation dengue virus transmission by applying Pontryagin's Maximum Principle. Our findings may provide guidance for the public health authorities to implement human vaccination and other mitigation strategies.
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Affiliation(s)
- Ling Xue
- College of Automation, Harbin Engineering University, Harbin, 150001, China.,College of Mathematical Sciences, Harbin Engineering University, Harbin, 150001, China
| | - Xue Ren
- College of Automation, Harbin Engineering University, Harbin, 150001, China.,College of Mathematical Sciences, Harbin Engineering University, Harbin, 150001, China
| | - Felicia Magpantay
- Department of Mathematics and Statistics, Queen's University, Kingston, K7L 3N6, Canada
| | - Wei Sun
- College of Mathematical Sciences, Harbin Engineering University, Harbin, 150001, China.
| | - Huaiping Zhu
- Department of Mathematics and Statistics, York University, Toronto, M3J 1P3, Canada
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20
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Saad-Roy CM, Wagner CE, Baker RE, Morris SE, Farrar J, Graham AL, Levin SA, Mina MJ, Metcalf CJE, Grenfell BT. Immune life history, vaccination, and the dynamics of SARS-CoV-2 over the next 5 years. Science 2020; 370:811-818. [PMID: 32958581 PMCID: PMC7857410 DOI: 10.1126/science.abd7343] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/16/2020] [Indexed: 01/08/2023]
Abstract
The future trajectory of the coronavirus disease 2019 (COVID-19) pandemic hinges on the dynamics of adaptive immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); however, salient features of the immune response elicited by natural infection or vaccination are still uncertain. We use simple epidemiological models to explore estimates for the magnitude and timing of future COVID-19 cases, given different assumptions regarding the protective efficacy and duration of the adaptive immune response to SARS-CoV-2, as well as its interaction with vaccines and nonpharmaceutical interventions. We find that variations in the immune response to primary SARS-CoV-2 infections and a potential vaccine can lead to markedly different immune landscapes and burdens of critically severe cases, ranging from sustained epidemics to near elimination. Our findings illustrate likely complexities in future COVID-19 dynamics and highlight the importance of immunological characterization beyond the measurement of active infections for adequately projecting the immune landscape generated by SARS-CoV-2 infections.
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Affiliation(s)
- Chadi M Saad-Roy
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | - Caroline E Wagner
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
- Princeton Environmental Institute, Princeton University, Princeton, NJ 08544, USA
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0C3, Canada
| | - Rachel E Baker
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
- Princeton Environmental Institute, Princeton University, Princeton, NJ 08544, USA
| | - Sinead E Morris
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | | | - Andrea L Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Simon A Levin
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Michael J Mina
- Departments of Epidemiology and Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - C Jessica E Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
- Princeton School of Public and International Affairs, Princeton University, Princeton, NJ 08544, USA
| | - Bryan T Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
- Princeton School of Public and International Affairs, Princeton University, Princeton, NJ 08544, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
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21
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Madec S, Gjini E. Predicting N-Strain Coexistence from Co-colonization Interactions: Epidemiology Meets Ecology and the Replicator Equation. Bull Math Biol 2020; 82:142. [PMID: 33119836 PMCID: PMC7595998 DOI: 10.1007/s11538-020-00816-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/30/2020] [Indexed: 01/02/2023]
Abstract
Multi-type infection processes are ubiquitous in ecology, epidemiology and social systems, but remain hard to analyze and to understand on a fundamental level. Here, we study a multi-strain susceptible-infected-susceptible model with coinfection. A host already colonized by one strain can become more or less vulnerable to co-colonization by a second strain, as a result of facilitating or competitive interactions between the two. Fitness differences between N strains are mediated through \documentclass[12pt]{minimal}
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\begin{document}$$N^2$$\end{document}N2 altered susceptibilities to secondary infection that depend on colonizer-cocolonizer identities (\documentclass[12pt]{minimal}
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\begin{document}$$K_{ij}$$\end{document}Kij). By assuming strain similarity in such pairwise traits, we derive a model reduction for the endemic system using separation of timescales. This ‘quasi-neutrality’ in trait space sets a fast timescale where all strains interact neutrally, and a slow timescale where selective dynamics unfold. We find that these slow dynamics are governed by the replicator equation for N strains. Our framework allows to build the community dynamics bottom-up from only pairwise invasion fitnesses between members. We highlight that mean fitness of the multi-strain network, changes with their individual dynamics, acts equally upon each type, and is a key indicator of system resistance to invasion. By uncovering the link between N-strain epidemiological coexistence and the replicator equation, we show that the ecology of co-colonization relates to Fisher’s fundamental theorem and to Lotka-Volterra systems. Besides efficient computation and complexity reduction for any system size, these results open new perspectives into high-dimensional community ecology, detection of species interactions, and evolution of biodiversity.
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Affiliation(s)
- Sten Madec
- Institut Denis Poisson, University of Tours, Tours, France
| | - Erida Gjini
- Instituto Gulbenkian de Ciência, Oeiras, Portugal. .,Center for Computational and Stochastic Mathematics, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal.
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22
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Affiliation(s)
- Jeffrey Shaman
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY 10032, USA.
| | - Marta Galanti
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
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23
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The age distribution of mortality from novel coronavirus disease (COVID-19) suggests no large difference of susceptibility by age. Sci Rep 2020; 10:16642. [PMID: 33024235 PMCID: PMC7538918 DOI: 10.1038/s41598-020-73777-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/18/2020] [Indexed: 01/08/2023] Open
Abstract
Among Italy, Spain, and Japan, the age distributions of COVID-19 mortality show only small variation even though the number of deaths per country shows large variation. To understand the determinant for this situation, we constructed a mathematical model describing the transmission dynamics and natural history of COVID-19 and analyzed the dataset of mortality in Italy, Spain, and Japan. We estimated the parameter which describes the age-dependency of susceptibility by fitting the model to reported data, including the effect of change in contact patterns during the epidemics of COVID-19, and the fraction of symptomatic infections. Our study revealed that if the mortality rate or the fraction of symptomatic infections among all COVID-19 cases does not depend on age, then unrealistically different age-dependencies of susceptibilities against COVID-19 infections between Italy, Japan, and Spain are required to explain the similar age distribution of mortality but different basic reproduction numbers (R0). Variation of susceptibility by age itself cannot explain the robust age distribution in mortality by COVID-19 infections in those three countries, however it does suggest that the age-dependencies of (i) the mortality rate and (ii) the fraction of symptomatic infections among all COVID-19 cases determine the age distribution of mortality by COVID-19.
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Kumar YN, Jeyakodi G, Kumar NP, Gunasekaran K, Jambulingam P. Molecular modelling analysis of T219A mutant envelope protein revealed novel virulence enhancing factors in Dengue virus isolated from Kerala state, India. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2020; 195:105481. [PMID: 32497770 DOI: 10.1016/j.cmpb.2020.105481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/11/2020] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
Dengue virus (DENV) is an emerging health threat and its envelope glycoprotein E, is involved in the anchoring and fusion mechanisms. Anchoring followed by conformational changes of E-protein are responsible for the fusion and entry of DENV into host. The variation in the conformation of the E-protein due to mutations, results in its altered binding with antibodies (Abs) and also its receptors. This leads to failure of neutralization of DENV and enhance the infection. In our earlier studies we have identified T219A mutation in the E-protein of DENV and the present study is focused on the impact of this mutation on the conformation of E-protein and also its binding variation with Abs and Fc-γ receptor. A comparative molecular modelling studies of wild type and T219A mutant E-proteins revealed that, the mutation induced several conformational variations in the E-protein and resulted in the variable binding orientation with altered affinities. Further, the mutation was also observed to enhance the fusion mechanism by Fc-γ receptors that mediate the efficient entry of DENV into host cell through altered membrane fusion mechanism. Such conformational variations of E-protein could be the responsible factors for enhanced virulence of DENV infections.
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Affiliation(s)
- Y Nanda Kumar
- Biomedical Informatics Centre, Vector Control Research Center, Indian Council of Medical Research, Pondicherry, India, 605006; Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - G Jeyakodi
- Biomedical Informatics Centre, Vector Control Research Center, Indian Council of Medical Research, Pondicherry, India, 605006
| | - N Pradeep Kumar
- Biomedical Informatics Centre, Vector Control Research Center, Indian Council of Medical Research, Pondicherry, India, 605006
| | - K Gunasekaran
- Biomedical Informatics Centre, Vector Control Research Center, Indian Council of Medical Research, Pondicherry, India, 605006
| | - P Jambulingam
- Biomedical Informatics Centre, Vector Control Research Center, Indian Council of Medical Research, Pondicherry, India, 605006
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25
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Kabir KMA, Tanimoto J. Cost-efficiency analysis of voluntary vaccination against n-serovar diseases using antibody-dependent enhancement: A game approach. J Theor Biol 2020; 503:110379. [PMID: 32622789 PMCID: PMC7331570 DOI: 10.1016/j.jtbi.2020.110379] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/16/2020] [Accepted: 06/15/2020] [Indexed: 02/08/2023]
Abstract
Records of epidemics acknowledge immunological multi-serotype illnesses as an important aspect of the occurrence and control of contagious diseases. These patterns occur due to antibody-dependent-enhancement (ADE) among serotype diseases, which leads to infection of secondary infectious classes. One example of this is dengue hemorrhagic fever and dengue shock syndrome, which comprises the following four serotypes: DEN-1, DEN-2, DEN-3, and DEN-4. The evolutionary vaccination game approach is able to shed light on this long-standing issue in a bid to evaluate the success of various control programs. Although immunization is regarded as one of the most accepted approaches for minimizing the risk of infection, cost and efficiency are important factors that must also be considered. To analyze the n-serovar aspect alongside ADE consequence in voluntary vaccination, this study establishes a new mathematical epidemiological model that is dovetailed with evolutionary game theory, an approach through which we explored two vaccine programs: primary and secondary. Our findings illuminate that the 'cost-efficiency' effect for vaccination decision exhibits an impact on controlling n-serovar infectious diseases and should be designed in such a manner as to avoid adverse effects. Furthermore, our numerical result justifies the fact that adopting ADE significantly boosted emerging disease incidence, it also suggest that the joint vaccine policy works even better when the complex cyclical epidemic outbreak takes place among multi serotypes interactions. Research also exposes that the primary vaccine is a better controlling tool than the secondary; however, introducing a highly-efficiency secondary vaccine against secondary infection plays a key role to control the disease prevalence.
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Affiliation(s)
- K M Ariful Kabir
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga-koen, Kasuga-shi, Fukuoka 816-8580, Japan; Department of Mathematics, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Jun Tanimoto
- Faculty of Engineering Sciences, Kyushu University, Kasuga-koen, Kasuga-shi, Fukuoka 816-8580, Japan; Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga-koen, Kasuga-shi, Fukuoka 816-8580, Japan
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26
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Katz DL, Rollston R, Galea S, Frates EP, Rifai T, McNaughton CD. Knowing Well, Being Well: well-being born of understanding. Am J Health Promot 2020; 34:686-694. [DOI: 10.1177/0890117120930536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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27
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Subramanian R, Romeo-Aznar V, Ionides E, Codeço CT, Pascual M. Predicting re-emergence times of dengue epidemics at low reproductive numbers: DENV1 in Rio de Janeiro, 1986-1990. J R Soc Interface 2020; 17:20200273. [PMID: 32574544 PMCID: PMC7328382 DOI: 10.1098/rsif.2020.0273] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Predicting arbovirus re-emergence remains challenging in regions with limited off-season transmission and intermittent epidemics. Current mathematical models treat the depletion and replenishment of susceptible (non-immune) hosts as the principal drivers of re-emergence, based on established understanding of highly transmissible childhood diseases with frequent epidemics. We extend an analytical approach to determine the number of ‘skip’ years preceding re-emergence for diseases with continuous seasonal transmission, population growth and under-reporting. Re-emergence times are shown to be highly sensitive to small changes in low R0 (secondary cases produced from a primary infection in a fully susceptible population). We then fit a stochastic Susceptible–Infected–Recovered (SIR) model to observed case data for the emergence of dengue serotype DENV1 in Rio de Janeiro. This aggregated city-level model substantially over-estimates observed re-emergence times either in terms of skips or outbreak probability under forward simulation. The inability of susceptible depletion and replenishment to explain re-emergence under ‘well-mixed’ conditions at a city-wide scale demonstrates a key limitation of SIR aggregated models, including those applied to other arboviruses. The predictive uncertainty and high skip sensitivity to epidemiological parameters suggest a need to investigate the relevant spatial scales of susceptible depletion and the scaling of microscale transmission dynamics to formulate simpler models that apply at coarse resolutions.
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Affiliation(s)
- Rahul Subramanian
- Division of Biological Sciences, University of Chicago, Chicago, IL, USA
| | - Victoria Romeo-Aznar
- Department of Ecology and Evolution, and, University of Chicago, Chicago, IL, USA.,Manseuto Institute for Urban Innovation, University of Chicago, Chicago, IL, USA
| | - Edward Ionides
- Department of Statistics, University of Michigan, Ann Arbor, MI, USA
| | - Claudia T Codeço
- Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Mercedes Pascual
- Department of Ecology and Evolution, and, University of Chicago, Chicago, IL, USA.,Santa Fe Institute, Santa Fe, NM, USA
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28
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McNaughton CD. Herd Immunity: Knowns, Unknowns, Challenges, and Strategies. Am J Health Promot 2020; 34:692-694. [PMID: 32551934 DOI: 10.1177/0890117120930536d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Candace D McNaughton
- Department of Emergency Medicine, Vanderbilt University Medical Center, Tennessee Valley Healthcare System, VA, USA
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29
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Wagner CE, Hooshyar M, Baker RE, Yang W, Arinaminpathy N, Vecchi G, Metcalf CJE, Porporato A, Grenfell BT. Climatological, virological and sociological drivers of current and projected dengue fever outbreak dynamics in Sri Lanka. J R Soc Interface 2020; 17:20200075. [PMID: 32486949 PMCID: PMC7328388 DOI: 10.1098/rsif.2020.0075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/11/2020] [Indexed: 01/16/2023] Open
Abstract
The largest ever Sri Lankan dengue outbreak of 2017 provides an opportunity for investigating the relative contributions of climatological, epidemiological and sociological drivers on the epidemic patterns of this clinically important vector-borne disease. To do so, we develop a climatologically driven disease transmission framework for dengue virus using spatially resolved temperature and precipitation data as well as the time-series susceptible-infected-recovered (SIR) model. From this framework, we first demonstrate that the distinct climatological patterns encountered across the island play an important role in establishing the typical yearly temporal dynamics of dengue, but alone are unable to account for the epidemic case numbers observed in Sri Lanka during 2017. Using a simplified two-strain SIR model, we demonstrate that the re-introduction of a dengue virus serotype that had been largely absent from the island in previous years may have played an important role in driving the epidemic, and provide a discussion of the possible roles for extreme weather events and human mobility patterns on the outbreak dynamics. Lastly, we provide estimates for the future burden of dengue across Sri Lanka using the Coupled Model Intercomparison Phase 5 climate projections. Critically, we demonstrate that climatological and serological factors can act synergistically to yield greater projected case numbers than would be expected from the presence of a single driver alone. Altogether, this work provides a holistic framework for teasing apart and analysing the various complex drivers of vector-borne disease outbreak dynamics.
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Affiliation(s)
- Caroline E. Wagner
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
- Princeton Environmental Institute, Princeton University, Princeton, NJ 08544, USA
| | - Milad Hooshyar
- Princeton Environmental Institute, Princeton University, Princeton, NJ 08544, USA
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Rachel E. Baker
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
- Princeton Environmental Institute, Princeton University, Princeton, NJ 08544, USA
| | - Wenchang Yang
- Princeton Environmental Institute, Princeton University, Princeton, NJ 08544, USA
- Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
| | - Nimalan Arinaminpathy
- Department of Infectious Disease Epidemiology, Imperial College School of Medicine, London, UK
| | - Gabriel Vecchi
- Princeton Environmental Institute, Princeton University, Princeton, NJ 08544, USA
- Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
| | - C. Jessica E. Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Amilcare Porporato
- Princeton Environmental Institute, Princeton University, Princeton, NJ 08544, USA
- Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
| | - Bryan T. Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
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30
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Thompson RN, Thompson CP, Pelerman O, Gupta S, Obolski U. Increased frequency of travel in the presence of cross-immunity may act to decrease the chance of a global pandemic. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180274. [PMID: 31056047 DOI: 10.1098/rstb.2018.0274] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The high frequency of modern travel has led to concerns about a devastating pandemic since a lethal pathogen strain could spread worldwide quickly. Many historical pandemics have arisen following pathogen evolution to a more virulent form. However, some pathogen strains invoke immune responses that provide partial cross-immunity against infection with related strains. Here, we consider a mathematical model of successive outbreaks of two strains-a low virulence (LV) strain outbreak followed by a high virulence (HV) strain outbreak. Under these circumstances, we investigate the impacts of varying travel rates and cross-immunity on the probability that a major epidemic of the HV strain occurs, and the size of that outbreak. Frequent travel between subpopulations can lead to widespread immunity to the HV strain, driven by exposure to the LV strain. As a result, major epidemics of the HV strain are less likely, and can potentially be smaller, with more connected subpopulations. Cross-immunity may be a factor contributing to the absence of a global pandemic as severe as the 1918 influenza pandemic in the century since. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'. This issue is linked with the subsequent theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'.
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Affiliation(s)
- R N Thompson
- 1 Mathematical Institute, University of Oxford , Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG , UK.,2 Department of Zoology, University of Oxford , South Parks Road, Oxford OX1 3PS , UK.,3 Christ Church, University of Oxford , St Aldate's, Oxford OX1 1DP , UK
| | - C P Thompson
- 2 Department of Zoology, University of Oxford , South Parks Road, Oxford OX1 3PS , UK
| | - O Pelerman
- 4 The Chaim Rosenberg School of Jewish Studies, Tel Aviv University , Tel Aviv 69978 , Israel
| | - S Gupta
- 2 Department of Zoology, University of Oxford , South Parks Road, Oxford OX1 3PS , UK
| | - U Obolski
- 2 Department of Zoology, University of Oxford , South Parks Road, Oxford OX1 3PS , UK.,5 School of Public Health , Tel Aviv University, Tel Aviv , Israel.,6 Porter School of the Environment and Earth Sciences, Tel Aviv University , Israel
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31
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McLure A, Glass K. Some simple rules for estimating reproduction numbers in the presence of reservoir exposure or imported cases. Theor Popul Biol 2020; 134:182-194. [PMID: 32304644 PMCID: PMC7159883 DOI: 10.1016/j.tpb.2020.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 03/29/2020] [Accepted: 04/10/2020] [Indexed: 02/04/2023]
Abstract
For many diseases, the basic reproduction number (R0) is a threshold parameter for disease extinction or survival in isolated populations. However no human population is fully isolated from other human or animal populations. We use compartmental models to derive simple rules for the basic reproduction number in populations where an endemic disease is sustained by a combination of local transmission within the population and exposure from some other source: either a reservoir exposure or imported cases. We introduce the idea of a reservoir-driven or importation-driven disease: diseases that would become extinct in the population of interest without reservoir exposure or imported cases (since R0<1), but nevertheless may be sufficiently transmissible that many or most infections are acquired from humans in that population. We show that in the simplest case, R0<1 if and only if the proportion of infections acquired from the external source exceeds the disease prevalence and explore how population heterogeneity and the interactions of multiple strains affect this rule. We apply these rules in two case studies of Clostridium difficile infection and colonisation: C. difficile in the hospital setting accounting for imported cases, and C. difficile in the general human population accounting for exposure to animal reservoirs. We demonstrate that even the hospital-adapted, highly-transmissible NAP1/RT027 strain of C. difficile had a reproduction number <1 in a landmark study of hospitalised patients and therefore was sustained by colonised and infected admissions to the study hospital. We argue that C. difficile should be considered reservoir-driven if as little as 13.0% of transmission can be attributed to animal reservoirs.
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Affiliation(s)
- Angus McLure
- Research School of Population Health, Australian National University, 62 Mills Rd, Acton, 0200, ACT, Australia.
| | - Kathryn Glass
- Research School of Population Health, Australian National University, 62 Mills Rd, Acton, 0200, ACT, Australia
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32
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Tang B, Xiao Y, Sander B, Kulkarni MA, RADAM-LAC Research Team, Wu J. Modelling the impact of antibody-dependent enhancement on disease severity of Zika virus and dengue virus sequential and co-infection. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191749. [PMID: 32431874 PMCID: PMC7211844 DOI: 10.1098/rsos.191749] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/12/2020] [Indexed: 05/22/2023]
Abstract
Human infections with viruses of the genus Flavivirus, including dengue virus (DENV) and Zika virus (ZIKV), are of increasing global importance. Owing to antibody-dependent enhancement (ADE), secondary infection with one Flavivirus following primary infection with another Flavivirus can result in a significantly larger peak viral load with a much higher risk of severe disease. Although several mathematical models have been developed to quantify the virus dynamics in the primary and secondary infections of DENV, little progress has been made regarding secondary infection of DENV after a primary infection of ZIKV, or DENV-ZIKV co-infection. Here, we address this critical gap by developing compartmental models of virus dynamics. We first fitted the models to published data on dengue viral loads of the primary and secondary infections with the observation that the primary infection reaches its peak much more gradually than the secondary infection. We then quantitatively show that ADE is the key factor determining a sharp increase/decrease of viral load near the peak time in the secondary infection. In comparison, our simulations of DENV and ZIKV co-infection (simultaneous rather than sequential) show that ADE has very limited influence on the peak DENV viral load. This indicates pre-existing immunity to ZIKV is the determinant of a high level of ADE effect. Our numerical simulations show that (i) in the absence of ADE effect, a subsequent co-infection is beneficial to the second virus; and (ii) if ADE is feasible, then a subsequent co-infection can induce greater damage to the host with a higher peak viral load and a much earlier peak time for the second virus, and for the second peak for the first virus.
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Affiliation(s)
- Biao Tang
- Laboratory for Industrial and Applied Mathematics (LIAM), York University, Toronto, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Canada
- Toronto Health Economics and Technology Assessment, Toronto, Ontario, Canada
| | - Yanni Xiao
- School of Mathematics and Statistics, Xi’an Jiaotong University, Xi’an, 710049, People’s Republic of China
| | - Beate Sander
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Canada
- Toronto Health Economics and Technology Assessment, Toronto, Ontario, Canada
| | - Manisha A. Kulkarni
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Canada
| | | | - Jianhong Wu
- Laboratory for Industrial and Applied Mathematics (LIAM), York University, Toronto, Canada
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Gulbudak H, Browne CJ. Infection severity across scales in multi-strain immuno-epidemiological Dengue model structured by host antibody level. J Math Biol 2020; 80:1803-1843. [PMID: 32157381 DOI: 10.1007/s00285-020-01480-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 01/19/2020] [Indexed: 01/08/2023]
Abstract
Infection by distinct Dengue virus serotypes and host immunity are intricately linked. In particular, certain levels of cross-reactive antibodies in the host may actually enhance infection severity leading to Dengue hemorrhagic fever (DHF). The coupled immunological and epidemiological dynamics of Dengue calls for a multi-scale modeling approach. In this work, we formulate a within-host model which mechanistically recapitulates characteristics of antibody dependent enhancement in Dengue infection. The within-host scale is then linked to epidemiological spread by a vector-host partial differential equation model structured by host antibody level. The coupling allows for dynamic population-wide antibody levels to be tracked through primary and secondary infections by distinct Dengue strains, along with waning of cross-protective immunity after primary infection. Analysis of both the within-host and between-host systems are conducted. Stability results in the epidemic model are formulated via basic and invasion reproduction numbers as a function of immunological variables. Additionally, we develop numerical methods in order to simulate the multi-scale model and assess the influence of parameters on disease spread and DHF prevalence in the population.
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Affiliation(s)
- Hayriye Gulbudak
- Mathematics Department, University of Louisiana at Lafayette, Lafayette, LA, USA.
| | - Cameron J Browne
- Mathematics Department, University of Louisiana at Lafayette, Lafayette, LA, USA
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34
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Virus-virus interactions impact the population dynamics of influenza and the common cold. Proc Natl Acad Sci U S A 2019; 116:27142-27150. [PMID: 31843887 PMCID: PMC6936719 DOI: 10.1073/pnas.1911083116] [Citation(s) in RCA: 267] [Impact Index Per Article: 53.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
When multiple pathogens cocirculate this can lead to competitive or cooperative forms of pathogen–pathogen interactions. It is believed that such interactions occur among cold and flu viruses, perhaps through broad-acting immunity, resulting in interlinked epidemiological patterns of infection. However, to date, quantitative evidence has been limited. We analyzed a large collection of diagnostic reports collected over multiple years for 11 respiratory viruses. Our analyses provide strong statistical support for the existence of interactions among respiratory viruses. Using computer simulations, we found that very short-lived interferences may explain why common cold infections are less frequent during flu seasons. Improved understanding of how the epidemiology of viral infections is interlinked can help improve disease forecasting and evaluation of disease control interventions. The human respiratory tract hosts a diverse community of cocirculating viruses that are responsible for acute respiratory infections. This shared niche provides the opportunity for virus–virus interactions which have the potential to affect individual infection risks and in turn influence dynamics of infection at population scales. However, quantitative evidence for interactions has lacked suitable data and appropriate analytical tools. Here, we expose and quantify interactions among respiratory viruses using bespoke analyses of infection time series at the population scale and coinfections at the individual host scale. We analyzed diagnostic data from 44,230 cases of respiratory illness that were tested for 11 taxonomically broad groups of respiratory viruses over 9 y. Key to our analyses was accounting for alternative drivers of correlated infection frequency, such as age and seasonal dependencies in infection risk, allowing us to obtain strong support for the existence of negative interactions between influenza and noninfluenza viruses and positive interactions among noninfluenza viruses. In mathematical simulations that mimic 2-pathogen dynamics, we show that transient immune-mediated interference can cause a relatively ubiquitous common cold-like virus to diminish during peak activity of a seasonal virus, supporting the potential role of innate immunity in driving the asynchronous circulation of influenza A and rhinovirus. These findings have important implications for understanding the linked epidemiological dynamics of viral respiratory infections, an important step towards improved accuracy of disease forecasting models and evaluation of disease control interventions.
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Impacts of Zika emergence in Latin America on endemic dengue transmission. Nat Commun 2019; 10:5730. [PMID: 31844054 PMCID: PMC6915707 DOI: 10.1038/s41467-019-13628-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 11/14/2019] [Indexed: 02/07/2023] Open
Abstract
In 2015 and 2016, Zika virus (ZIKV) swept through dengue virus (DENV) endemic areas of Latin America. These viruses are of the same family, share a vector and may interact competitively or synergistically through human immune responses. We examine dengue incidence from Brazil and Colombia before, during, and after the Zika epidemic. We find evidence that dengue incidence was atypically low in 2017 in both countries. We investigate whether subnational Zika incidence is associated with changes in dengue incidence and find mixed results. Using simulations with multiple assumptions of interactions between DENV and ZIKV, we find cross-protection suppresses incidence of dengue following Zika outbreaks and low periods of dengue incidence are followed by resurgence. Our simulations suggest correlations in DENV and ZIKV reproduction numbers could complicate associations between ZIKV incidence and post-ZIKV DENV incidence and that periods of low dengue incidence are followed by large increases in dengue incidence. Dengue and Zika virus are related flaviviruses, and introduction of Zika in the Americas may have impacted dengue epidemiology. Here, Borchering et al. show that dengue incidence was unusually low in 2017 in Brazil and Colombia, and simulations incorporating immune-mediated interactions predict reductions in dengue following Zika outbreaks with subsequent rebounds.
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36
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Gutiérrez-Barbosa H, Castañeda NY, Castellanos JE. Differential replicative fitness of the four dengue virus serotypes circulating in Colombia in human liver Huh7 cells. Braz J Infect Dis 2019; 24:13-24. [PMID: 31843340 PMCID: PMC9392035 DOI: 10.1016/j.bjid.2019.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 11/12/2019] [Accepted: 11/24/2019] [Indexed: 12/20/2022] Open
Abstract
Dengue has been a significant public health problem in Colombia since the simultaneous circulation of the four dengue virus serotypes. The replicative fitness of dengue is a biological feature important for virus evolution and contributes to elucidating the behavior of virus populations and viral pathogenesis. However, it has not yet been studied in Colombian isolates. This study aimed to compare the replicative fitness of the four dengue virus serotypes and understand the association between the serotypes, their in vitro infection ability, and their replication in target cells. We used three isolates of each DENV serotype to infect Huh-7 cells at an MOI of 0.5. The percentage of infected cells was evaluated by flow cytometry, cell viability was evaluated by MTT assay, and the pathogenicity index was calculated as a ratio of both parameters. The replicative fitness was measured by the number of viral genome copies produced using quantitative PCR and the production of infectious viral progeny was measured by plaque assay. We showed that Huh-7 cells were susceptible to infection with all the different strain isolates. Nevertheless, the biological characteristics, such as infectious ability and cell viability, were strain-dependent. We also found different degrees of pathogenicity between strains of the four serotypes, representative of the heterogeneity displayed in the circulating population. When we analyzed the replicative fitness using the mean values obtained from RT-qPCR and plaque assay for the different strains, we found serotype-dependent behavior. The highest mean values of replicative fitness were obtained for DENV-1 (log 4.9 PFU/ml) and DENV-4 (log 5.28 PFU/ml), followed by DENV-2 (log 3.9 PFU/ml) and DENV-3 (log 4.31 PFU/ml). The internal heterogeneity of the replicative fitness within each serotype could explain the simultaneous circulation of the four DENV serotypes in Colombia.
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Georgieva M, Buckee CO, Lipsitch M. Models of immune selection for multi-locus antigenic diversity of pathogens. Nat Rev Immunol 2019; 19:55-62. [PMID: 30479379 DOI: 10.1038/s41577-018-0092-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
It is well accepted that pathogens can evade recognition and elimination by the host immune system by varying their antigenic targets. Thus, it has become a truism that host immunity is a major driver and determinant of the antigenic diversity of pathogens. However, it remains puzzling how host immunity selects for antigenic diversity at the level of the pathogen population, given that hosts have acquired immune responses to multiple antigens of most pathogens - sometimes through multiple effectors of both humoral and cellular immunity. In this Opinion article, we address this puzzle and the related question of why pathogens often have diversity at multiple antigenic loci. Here, we describe five hypotheses to explain the polymorphism of multiple antigens in a single pathogen species and highlight research relevant to our current models of thinking about multi-locus antigenic diversity.
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Affiliation(s)
- Maria Georgieva
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA. .,Department of Physiology, University of Lausanne, Lausanne, Switzerland.
| | - Caroline O Buckee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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38
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Abstract
A wide range of research has promised new tools for forecasting infectious disease dynamics, but little of that research is currently being applied in practice, because tools do not address key public health needs, do not produce probabilistic forecasts, have not been evaluated on external data, or do not provide sufficient forecast skill to be useful. We developed an open collaborative forecasting challenge to assess probabilistic forecasts for seasonal epidemics of dengue, a major global public health problem. Sixteen teams used a variety of methods and data to generate forecasts for 3 epidemiological targets (peak incidence, the week of the peak, and total incidence) over 8 dengue seasons in Iquitos, Peru and San Juan, Puerto Rico. Forecast skill was highly variable across teams and targets. While numerous forecasts showed high skill for midseason situational awareness, early season skill was low, and skill was generally lowest for high incidence seasons, those for which forecasts would be most valuable. A comparison of modeling approaches revealed that average forecast skill was lower for models including biologically meaningful data and mechanisms and that both multimodel and multiteam ensemble forecasts consistently outperformed individual model forecasts. Leveraging these insights, data, and the forecasting framework will be critical to improve forecast skill and the application of forecasts in real time for epidemic preparedness and response. Moreover, key components of this project-integration with public health needs, a common forecasting framework, shared and standardized data, and open participation-can help advance infectious disease forecasting beyond dengue.
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39
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A Population Dynamics Model of Mosquito-Borne Disease Transmission, Focusing on Mosquitoes' Biased Distribution and Mosquito Repellent Use. Bull Math Biol 2019; 81:4977-5008. [PMID: 31595380 DOI: 10.1007/s11538-019-00666-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 09/24/2019] [Indexed: 01/03/2023]
Abstract
We present an improved mathematical model of population dynamics of mosquito-borne disease transmission. Our model considers the effect of mosquito repellent use and the mosquito's behavior or attraction to the infected human, which cause mosquitoes' biased distribution around the human population. Our analysis of the model clearly shows the existence of thresholds for mosquito repellent efficacy and its utilization rate in the human population with respect to the elimination of mosquito-borne diseases. Further, the results imply that the suppression of mosquito-borne diseases becomes more difficult when the mosquitoes' distribution is biased to a greater extent around the human population.
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40
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Wang W, Liu QH, Liang J, Hu Y, Zhou T. Coevolution spreading in complex networks. PHYSICS REPORTS 2019; 820:1-51. [PMID: 32308252 PMCID: PMC7154519 DOI: 10.1016/j.physrep.2019.07.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 06/27/2019] [Accepted: 07/18/2019] [Indexed: 05/03/2023]
Abstract
The propagations of diseases, behaviors and information in real systems are rarely independent of each other, but they are coevolving with strong interactions. To uncover the dynamical mechanisms, the evolving spatiotemporal patterns and critical phenomena of networked coevolution spreading are extremely important, which provide theoretical foundations for us to control epidemic spreading, predict collective behaviors in social systems, and so on. The coevolution spreading dynamics in complex networks has thus attracted much attention in many disciplines. In this review, we introduce recent progress in the study of coevolution spreading dynamics, emphasizing the contributions from the perspectives of statistical mechanics and network science. The theoretical methods, critical phenomena, phase transitions, interacting mechanisms, and effects of network topology for four representative types of coevolution spreading mechanisms, including the coevolution of biological contagions, social contagions, epidemic-awareness, and epidemic-resources, are presented in detail, and the challenges in this field as well as open issues for future studies are also discussed.
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Affiliation(s)
- Wei Wang
- Cybersecurity Research Institute, Sichuan University, Chengdu 610065, China
- Big Data Research Center, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Quan-Hui Liu
- Big Data Research Center, University of Electronic Science and Technology of China, Chengdu 610054, China
- Compleχ Lab, University of Electronic Science and Technology of China, Chengdu 610054, China
- College of Computer Science, Sichuan University, Chengdu 610065, China
| | - Junhao Liang
- School of Mathematics, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yanqing Hu
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou 510006, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, 519082, China
| | - Tao Zhou
- Big Data Research Center, University of Electronic Science and Technology of China, Chengdu 610054, China
- Compleχ Lab, University of Electronic Science and Technology of China, Chengdu 610054, China
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41
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Marchi J, Lässig M, Mora T, Walczak AM. Multi-Lineage Evolution in Viral Populations Driven by Host Immune Systems. Pathogens 2019; 8:E115. [PMID: 31362404 PMCID: PMC6789611 DOI: 10.3390/pathogens8030115] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 12/20/2022] Open
Abstract
Viruses evolve in the background of host immune systems that exert selective pressure and drive viral evolutionary trajectories. This interaction leads to different evolutionary patterns in antigenic space. Examples observed in nature include the effectively one-dimensional escape characteristic of influenza A and the prolonged coexistence of lineages in influenza B. Here, we use an evolutionary model for viruses in the presence of immune host systems with finite memory to obtain a phase diagram of evolutionary patterns in a two-dimensional antigenic space. We find that, for small effective mutation rates and mutation jump ranges, a single lineage is the only stable solution. Large effective mutation rates combined with large mutational jumps in antigenic space lead to multiple stably co-existing lineages over prolonged evolutionary periods. These results combined with observations from data constrain the parameter regimes for the adaptation of viruses, including influenza.
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Affiliation(s)
- Jacopo Marchi
- Laboratoire de physique de l'École normale supérieure (PSL University), CNRS, Sorbonne Université, and Université de Paris, 75005 Paris, France
| | - Michael Lässig
- Institute of Theoretical Physics, University of Cologne, 50937 Cologne, Germany
| | - Thierry Mora
- Laboratoire de physique de l'École normale supérieure (PSL University), CNRS, Sorbonne Université, and Université de Paris, 75005 Paris, France.
| | - Aleksandra M Walczak
- Laboratoire de physique de l'École normale supérieure (PSL University), CNRS, Sorbonne Université, and Université de Paris, 75005 Paris, France.
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42
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Champagne C, Paul R, Ly S, Duong V, Leang R, Cazelles B. Dengue modeling in rural Cambodia: Statistical performance versus epidemiological relevance. Epidemics 2019; 26:43-57. [DOI: 10.1016/j.epidem.2018.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 07/19/2018] [Accepted: 08/27/2018] [Indexed: 02/07/2023] Open
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43
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Champagne C, Cazelles B. Comparison of stochastic and deterministic frameworks in dengue modelling. Math Biosci 2019; 310:1-12. [PMID: 30735695 DOI: 10.1016/j.mbs.2019.01.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 01/28/2019] [Accepted: 01/30/2019] [Indexed: 11/16/2022]
Abstract
We perform estimations of compartment models for dengue transmission in rural Cambodia with increasing complexity regarding both model structure and the account for stochasticity. On the one hand, we successively account for three embedded sources of stochasticity: observation noise, demographic variability and environmental hazard. On the other hand, complexity in the model structure is increased by introducing vector-borne transmission, explicit asymptomatic infections and interacting virus serotypes. Using two sources of case data from dengue epidemics in Kampong Cham (Cambodia), models are estimated in the bayesian framework, with Markov Chain Monte Carlo and Particle Markov Chain Monte Carlo. We highlight the advantages and drawbacks of the different formulations in a practical setting. Although in this case the deterministic models provide a good approximation of the mean trajectory for a low computational cost, the stochastic frameworks better reflect and account for parameter and simulation uncertainty.
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Affiliation(s)
- Clara Champagne
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS UMR 8197,46 rue d'Ulm, Paris 75005, France; CREST, ENSAE, Université Paris Saclay, 5, avenue Henry Le Chatelier, Palaiseau cedex 91764, France.
| | - Bernard Cazelles
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS UMR 8197,46 rue d'Ulm, Paris 75005, France; International Center for Mathematical and Computational Modeling of Complex Systems (UMMISCO), UMI 209 Sorbonne Université - IRD, Bondy cedex, France
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44
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Zhang XS, Zhao H, Vynnycky E, Chalker V. Positively interacting strains that co-circulate within a network structured population induce cycling epidemics of Mycoplasma pneumoniae. Sci Rep 2019; 9:541. [PMID: 30679460 PMCID: PMC6345813 DOI: 10.1038/s41598-018-36325-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 11/13/2018] [Indexed: 02/01/2023] Open
Abstract
Mycoplasma pneumoniae (MP) is considered a common cause of pneumonia, causing about 15–20% of adult community-acquired pneumonia (CAP) and up to 40% of cases in children. It has often been observed that MP epidemics last approximately 1–2 years and occur every 3–7 years, with the dominant strains alternating between epidemics. However, the underlying mechanism by which these cycles and changes in the dominant strains occur remains unclear. The traditional models for the periodicity of MP epidemics neglected two phenomena: structured contact patterns among people and co-circulating strains of MP. We also believe that the two distinctive aspects of MP epidemics: prevalent serotype shifts among epidemics and incidence cycling of MP, are interconnected. We propose a network transmission model that assumes two strains of MP are transmitted within a network structured population and they can interact as secondary infections with primary infections. Our studies show that multiple strains that co-circulate within a network structured population and interact positively generate the observed patterns of recurrent epidemics of MP. Hence our study provides a possible mechanism for the cycling epidemics of MP, and could provide useful information for future vaccine design and vaccine evaluation/monitoring processes.
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Affiliation(s)
- Xu-Sheng Zhang
- Centre for Infectious Disease Surveillance and Control, Public Health England, London, UK. .,Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College School of Public Health, London, UK.
| | - Hongxin Zhao
- Centre for Infectious Disease Surveillance and Control, Public Health England, London, UK
| | - Emilia Vynnycky
- Centre for Infectious Disease Surveillance and Control, Public Health England, London, UK.,TB Modelling Group, TB Centre, Centre for Mathematical Modelling of Infectious Diseases and Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Vicki Chalker
- Centre for Infectious Disease Surveillance and Control, Public Health England, London, UK
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45
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Tang B, Huo X, Xiao Y, Ruan S, Wu J. A conceptual model for optimizing vaccine coverage to reduce vector-borne infections in the presence of antibody-dependent enhancement. Theor Biol Med Model 2018; 15:13. [PMID: 30173664 PMCID: PMC6120075 DOI: 10.1186/s12976-018-0085-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 07/13/2018] [Indexed: 11/10/2022] Open
Abstract
Background Many vector-borne diseases co-circulate, as the viruses from the same family are also transmitted by the same vector species. For example, Zika and dengue viruses belong to the same Flavivirus family and are primarily transmitted by a common mosquito species Aedes aegypti. Zika outbreaks have also commonly occurred in dengue-endemic areas, and co-circulation and co-infection of both viruses have been reported. As recent immunological cross-reactivity studies have confirmed that convalescent plasma following dengue infection can enhance Zika infection, and as global efforts of developing dengue and Zika vaccines are intensified, it is important to examine whether and how vaccination against one disease in a large population may affect infection dynamics of another disease due to antibody-dependent enhancement. Methods Through a conceptual co-infection dynamics model parametrized by reported dengue and Zika epidemic and immunological cross-reactivity characteristics, we evaluate impact of a hypothetical dengue vaccination program on Zika infection dynamics in a single season when only one particular dengue serotype is involved. Results We show that an appropriately designed and optimized dengue vaccination program can not only help control the dengue spread but also, counter-intuitively, reduce Zika infections. We identify optimal dengue vaccination coverages for controlling dengue and simultaneously reducing Zika infections, as well as the critical coverages exceeding which dengue vaccination will increase Zika infections. Conclusion This study based on a conceptual model shows the promise of an integrative vector-borne disease control strategy involving optimal vaccination programs, in regions where different viruses or different serotypes of the same virus co-circulate, and convalescent plasma following infection from one virus (serotype) can enhance infection against another virus (serotype). The conceptual model provides a first step towards well-designed regional and global vector-borne disease immunization programs.
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Affiliation(s)
- Biao Tang
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China.,Centre for Disease Modelling, Laboratory for Industrial and Applied Mathematics, York University, Toronto, M3J 1P3, Canada
| | - Xi Huo
- Centre for Disease Modelling, Laboratory for Industrial and Applied Mathematics, York University, Toronto, M3J 1P3, Canada.,Department of Mathematics, University of Miami, Coral Gables, 33146, USA
| | - Yanni Xiao
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Shigui Ruan
- Department of Mathematics, University of Miami, Coral Gables, 33146, USA
| | - Jianhong Wu
- Centre for Disease Modelling, Laboratory for Industrial and Applied Mathematics, York University, Toronto, M3J 1P3, Canada.
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46
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Imran M, Usman M, Malik T, Ansari AR. Mathematical analysis of the role of hospitalization/isolation in controlling the spread of Zika fever. Virus Res 2018; 255:95-104. [PMID: 30003923 PMCID: PMC7127007 DOI: 10.1016/j.virusres.2018.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 06/27/2018] [Accepted: 07/03/2018] [Indexed: 11/27/2022]
Abstract
The Zika virus is transmitted to humans primarily through Aedes mosquitoes and through sexual contact. It is documented that the virus can be transmitted to newborn babies from their mothers. We consider a deterministic model for the transmission dynamics of the Zika virus infectious disease that spreads in, both humans and vectors, through horizontal and vertical transmission. The total populations of both humans and mosquitoes are assumed to be constant. Our models consist of a system of eight differential equations describing the human and vector populations during the different stages of the disease. We have included the hospitalization/isolation class in our model to see the effect of the controlling strategy. We determine the expression for the basic reproductive number R0 in terms of horizontal as well as vertical disease transmission rates. An in-depth stability analysis of the model is performed, and it is consequently shown, that the model has a globally asymptotically stable disease-free equilibrium when the basic reproduction number R0 < 1. It is also shown that when R0 > 1, there exists a unique endemic equilibrium. We showed that the endemic equilibrium point is globally asymptotically stable when it exists. We were able to prove this result in a reduced model. Furthermore, we conducted an uncertainty and sensitivity analysis to recognize the impact of crucial model parameters on R0. The uncertainty analysis yields an estimated value of the basic reproductive number R0 = 1.54. Assuming infection prevalence in the population under constant control, optimal control theory is used to devise an optimal hospitalization/isolation control strategy for the model. The impact of isolation on the number of infected individuals and the accumulated cost is assessed and compared with the constant control case.
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Affiliation(s)
- Mudassar Imran
- International Center for Applied Mathematics and Computational Bioengineering, Department of Mathematics and Natural Sciences, Gulf University for Science & Technology, Mishref, Kuwait.
| | - Muhammad Usman
- Department of Mathematics, University of Dayton, Dayton, OH 45469-2316, USA
| | - Tufail Malik
- Department of Science and Mathematics, Arizona State University, Mesa, AZ 85212, USA
| | - Ali R Ansari
- International Center for Applied Mathematics and Computational Bioengineering, Department of Mathematics and Natural Sciences, Gulf University for Science & Technology, Mishref, Kuwait
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47
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Abstract
Coinfecting parasites and pathogens remain a leading challenge for global public health due to their consequences for individual-level infection risk and disease progression. However, a clear understanding of the population-level consequences of coinfection is lacking. Here, we constructed a model that includes three individual-level effects of coinfection: mortality, fecundity, and transmission. We used the model to investigate how these individual-level consequences of coinfection scale up to produce population-level infection patterns. To parameterize this model, we conducted a 4-y cohort study in African buffalo to estimate the individual-level effects of coinfection with two bacterial pathogens, bovine tuberculosis (bTB) and brucellosis, across a range of demographic and environmental contexts. At the individual level, our empirical results identified bTB as a risk factor for acquiring brucellosis, but we found no association between brucellosis and the risk of acquiring bTB. Both infections were associated with reductions in survival and neither infection was associated with reductions in fecundity. The model reproduced coinfection patterns in the data and predicted opposite impacts of coinfection at individual and population scales: Whereas bTB facilitated brucellosis infection at the individual level, our model predicted the presence of brucellosis to have a strong negative impact on bTB at the population level. In modeled populations where brucellosis was present, the endemic prevalence and basic reproduction number ([Formula: see text]) of bTB were lower than in populations without brucellosis. Therefore, these results provide a data-driven example of competition between coinfecting pathogens that occurs when one pathogen facilitates secondary infections at the individual level.
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48
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Lee H, Kim JE, Lee S, Lee CH. Potential effects of climate change on dengue transmission dynamics in Korea. PLoS One 2018; 13:e0199205. [PMID: 29953493 PMCID: PMC6023222 DOI: 10.1371/journal.pone.0199205] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/04/2018] [Indexed: 11/22/2022] Open
Abstract
Dengue fever is a major international public health concern, with more than 55% of the world population at risk of infection. Recent climate changes related to global warming have increased the potential risk of domestic outbreaks of dengue in Korea. In this study, we develop a two-strain dengue model associated with climate-dependent parameters based on Representative Concentration Pathway (RCP) scenarios provided by the Korea Meteorological Administration. We assess the potential risks of dengue outbreaks by means of the vector capacity and intensity under various RCP scenarios. A sensitivity analysis of the temperature-dependent parameters is performed to explore the effects of climate change on dengue transmission dynamics. Our results demonstrate that a higher temperature significantly enhances the potential threat of domestic dengue outbreaks in Korea. Furthermore, we investigate the effects of countermeasures on the cumulative incidence of humans and vectors. The current main control measures (comprising only travel restrictions) for infected humans in Korea are not as effective as combined control measures (travel restrictions and vector control), dramatically reducing the possibilities of dengue outbreaks.
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Affiliation(s)
- Hyojung Lee
- Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Jung Eun Kim
- Department of Mathematical Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Sunmi Lee
- Department of Applied Mathematics, Kyung Hee University, Yongin, Republic of Korea
| | - Chang Hyeong Lee
- Department of Mathematical Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
- * E-mail:
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49
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Lourenço J, Tennant W, Faria NR, Walker A, Gupta S, Recker M. Challenges in dengue research: A computational perspective. Evol Appl 2018; 11:516-533. [PMID: 29636803 PMCID: PMC5891037 DOI: 10.1111/eva.12554] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 09/08/2017] [Indexed: 01/12/2023] Open
Abstract
The dengue virus is now the most widespread arbovirus affecting human populations, causing significant economic and social impact in South America and South-East Asia. Increasing urbanization and globalization, coupled with insufficient resources for control, misguided policies or lack of political will, and expansion of its mosquito vectors are some of the reasons why interventions have so far failed to curb this major public health problem. Computational approaches have elucidated on dengue's population dynamics with the aim to provide not only a better understanding of the evolution and epidemiology of the virus but also robust intervention strategies. It is clear, however, that these have been insufficient to address key aspects of dengue's biology, many of which will play a crucial role for the success of future control programmes, including vaccination. Within a multiscale perspective on this biological system, with the aim of linking evolutionary, ecological and epidemiological thinking, as well as to expand on classic modelling assumptions, we here propose, discuss and exemplify a few major computational avenues-real-time computational analysis of genetic data, phylodynamic modelling frameworks, within-host model frameworks and GPU-accelerated computing. We argue that these emerging approaches should offer valuable research opportunities over the coming years, as previously applied and demonstrated in the context of other pathogens.
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Affiliation(s)
| | - Warren Tennant
- Centre for Mathematics and the EnvironmentUniversity of ExeterPenrynUK
| | | | | | | | - Mario Recker
- Centre for Mathematics and the EnvironmentUniversity of ExeterPenrynUK
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50
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GURAV AMOL, JANA C, UPADHYAY D, DANGI SS, SHARMA AK, GAUTAM S. A retrospective study of disease prevalence in domestic animals of hill region. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2018. [DOI: 10.56093/ijans.v88i3.78256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The present study was aimed at recording the prevalence and types of various disorders in the domestic animals of hill region. The retrospective data of three years (2014–16) was collected from outpatient case record of veterinary dispensary unit, Indian Veterinary Research Institute, Mukteswar. A total of 577 cases were recorded during the period, of which, majority of cases were of cattle followed by goats. The autumn observed highest percentage of cases with lowest % in winter. Ectoparasitic infestation, endoparasitism, diarrhea and weakness were noticed as major clinical problems in cattle. Among infectious diseases, mastitis prevailed most among all other diseases of cattle. Haematuria, injury/wound and repeat breeding were also recorded frequently in cattle. Highest prevalence (70.58%) of haematuria was observed in the age group of 5–10 years. Retrospective epidemiological data on goats revealed that ecto-endoparasitic infestation and stomatitis were major diseases/disorders observed among goats of the region. About 46.92% of goat patients were recorded in autumn while winter observed 10.05% cases only. The retrospective epidemiological data generated during the present study helps in better understanding of the animal disease pattern in temperate climatic conditions, which will further help in implementing control measures against infectious and non-infectious diseases.
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