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Zhang P, Swaminathan A, Uddin AA. Pulmonary disease detection and classification in patient respiratory audio files using long short-term memory neural networks. Front Med (Lausanne) 2023; 10:1269784. [PMID: 38020156 PMCID: PMC10656606 DOI: 10.3389/fmed.2023.1269784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction In order to improve the diagnostic accuracy of respiratory illnesses, our research introduces a novel methodology to precisely diagnose a subset of lung diseases using patient respiratory audio recordings. These lung diseases include Chronic Obstructive Pulmonary Disease (COPD), Upper Respiratory Tract Infections (URTI), Bronchiectasis, Pneumonia, and Bronchiolitis. Methods Our proposed methodology trains four deep learning algorithms on an input dataset consisting of 920 patient respiratory audio files. These audio files were recorded using digital stethoscopes and comprise the Respiratory Sound Database. The four deployed models are Convolutional Neural Networks (CNN), Long Short-Term Memory (LSTM), CNN ensembled with unidirectional LSTM (CNN-LSTM), and CNN ensembled with bidirectional LSTM (CNN-BLSTM). Results The aforementioned models are evaluated using metrics such as accuracy, precision, recall, and F1-score. The best performing algorithm, LSTM, has an overall accuracy of 98.82% and F1-score of 0.97. Discussion The LSTM algorithm's extremely high predictive accuracy can be attributed to its penchant for capturing sequential patterns in time series based audio data. In summary, this algorithm is able to ingest patient audio recordings and make precise lung disease predictions in real-time.
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Affiliation(s)
- Pinzhi Zhang
- College of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | | | - Ahmed Abrar Uddin
- College of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, GA, United States
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2
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Spencer JA, Shutt DP, Moser SK, Clegg H, Wearing HJ, Mukundan H, Manore CA. Distinguishing viruses responsible for influenza-like illness. J Theor Biol 2022; 545:111145. [PMID: 35490763 DOI: 10.1016/j.jtbi.2022.111145] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 10/18/2022]
Abstract
The many respiratory viruses that cause influenza-like illness (ILI) are reported and tracked as one entity, defined by the CDC as a group of symptoms that include a fever of 100 degrees Fahrenheit, a cough, and/or a sore throat. In the United States alone, ILI impacts 9-49 million people every year. While tracking ILI as a single clinical syndrome is informative in many respects, the underlying viruses differ in parameters and outbreak properties. Most existing models treat either a single respiratory virus or ILI as a whole. However, there is a need for models capable of comparing several individual viruses that cause respiratory illness, including ILI. To address this need, here we present a flexible model and simulations of epidemics for influenza, RSV, rhinovirus, seasonal coronavirus, adenovirus, and SARS/MERS, parameterized by a systematic literature review and accompanied by a global sensitivity analysis. We find that for these biological causes of ILI, their parameter values, timing, prevalence, and proportional contributions differ substantially. These results demonstrate that distinguishing the viruses that cause ILI will be an important aspect of future work on diagnostics, mitigation, modeling, and preparation for future pandemics.
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Affiliation(s)
- Julie A Spencer
- A-1 Information Systems and Modeling, Los Alamos National Laboratory, NM87545, USA.
| | - Deborah P Shutt
- A-1 Information Systems and Modeling, Los Alamos National Laboratory, NM87545, USA
| | - S Kane Moser
- B-10 Biosecurity and Public Health, Los Alamos National Laboratory, NM87545, USA
| | - Hannah Clegg
- A-1 Information Systems and Modeling, Los Alamos National Laboratory, NM87545, USA
| | - Helen J Wearing
- Department of Biology, University of New Mexico, NM87131, USA; Department of Mathematics and Statistics, University of New Mexico, NM87102, USA
| | - Harshini Mukundan
- C-PCS Physical Chemistry and Applied Spectroscopy, Los Alamos National Laboratory, NM87545, USA
| | - Carrie A Manore
- T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM87545, USA
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3
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Rhinoviruses: molecular diversity and clinical characteristics. Int J Infect Dis 2022; 118:144-149. [PMID: 35248716 DOI: 10.1016/j.ijid.2022.02.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/19/2022] [Accepted: 02/26/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Rhinoviruses are commonly considered simple "common cold" agents. The link between their molecular epidemiology and patient clinical presentation and outcomes remains unclear in adult populations. MATERIALS/METHODS All nasopharyngeal or bronchoalveolar lavages were screened using multiplex PCR in three Parisian hospitals from January to September 2018. For all detected rhinoviruses, the VP2/VP4 region was subtyped by sequencing. RESULTS The study included 178 human rhinovirus (HRV) positive unique patients. They were primarily male (56%), with a median age of 62.2 [IQR: 46.8-71.4], frequently presenting chronic respiratory diseases (56%) and/or immunosuppression (46%). Of these, 63% were admitted for respiratory distress, including pneumonia for 25%; 95 (53%), 27 (15%), and 56 (32%) were positive for HRV-A, -B, and -C, respectively. HRV-B appeared more associated with immunosuppressive treatments (58% vs. 30% and 36% of patients for HRV-A and -C, respectively, p = 0.038), higher coinfection rates (54% vs. 34% and 23%, p = 0.03), and higher ICU admission rates (35% vs. 17% and 13%, p = 0.048). Conversely, HRV-A was more frequently associated with pneumonia (54% vs. 31% and 11% for HRV-B and -C, respectively, p = 0.01). CONCLUSIONS This study highlights the high proportion of chronic respiratory diseases or immunosuppression among hospitalized patients infected with a rhinovirus.
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In pursuit of the right tail for the COVID-19 incubation period. Public Health 2021; 194:149-155. [PMID: 33915459 PMCID: PMC7997403 DOI: 10.1016/j.puhe.2021.03.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/24/2021] [Accepted: 03/09/2021] [Indexed: 01/08/2023]
Abstract
Definition of the incubation period for COVID-19 is critical for implementing quarantine and thus infection control. Whereas the classical definition relies on the time from exposure to time of first symptoms, a more practical working definition is the time from exposure to time of first live virus excretion. For COVID-19, average incubation period times commonly span 5–7 days which are generally longer than for most typical other respiratory viruses. There is considerable variability reported however for the late right-hand statistical distribution. A small but yet epidemiologically important subset of patients may have the late end of the incubation period extend beyond the 14 days that is frequently assumed. Conservative assumptions of the right tail end distribution favor safety, but pragmatic working modifications may be required to accommodate high rates of infection and/or healthcare worker exposures. Despite the advent of effective vaccines, further attention and study in these regards are warranted. It is predictable that vaccine application will be associated with continued confusion over protection and its longevity. Measures for the application of infectivity will continue to be extremely relevant.
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Dai M, Wu Y, Tan H, Deng J, Hou M, Peng W, Chen G, Li Y, Li H, Pan P, Lu J. Cross-infection of adenovirus among medical staff: A warning from the intensive care unit in a tertiary care teaching hospital in China. Int J Infect Dis 2020; 98:390-397. [PMID: 32623086 PMCID: PMC7330577 DOI: 10.1016/j.ijid.2020.06.103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 12/28/2022] Open
Abstract
Human adenovirus-55 in a single patient had strong transmission potential in ICU. This infectious event involved more than 20 medical staff members in adult ICU. Contact with patient, lack of hand hygiene or gloving adherence, were risk factors.
Rationale In 2019, a small HAdV55-associated outbreak of adenovirus infection occurred among the intensive care unit (ICU) staff in Xiangya Hospital of Central South University in Hunan Province, China, during the treatment of a patient. Objective To investigate the characteristics of a nosocomial adenovirus outbreak in an ICU. Methods We evaluated all the patients treated and the medical staff working in the ICU from August 1 to September 4, 2019. We further performed an epidemiological and molecular analysis for this outbreak from patient to healthcare workers and between healthcare workers. After the outbreak, we adopted exposure prevention and droplet prevention measures based on standard precautions. Measurements and main results Between August 1 and August 27, 2019, 27 cases of human adenovirus cross-infection were reported in our institution. Among the cases, eleven were doctors (41%), eleven were nurses (41%), three were respiratory therapists (11%), and two were caregivers (7%). The attack rate was 28.4%, and the fatality rate was 0. The results showed that contact with the index case, lack of hand hygiene or gloving adherence were risk factors for infection after adenovirus exposure. After taking specific precautions, no new cases of infection have appeared since August 27. Conclusions Our results show that HAdV55 in a single patient had strong transmission potential in an intensive care unit with adequate facilities and standardized operation. We provide convincing evidence indicating that attention could be highlighted on the role of standard and specific precautions for controlling the spread of adenovirus in ICUs.
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Affiliation(s)
- Minhui Dai
- Respiratory Department, Xiangya Hospital, Central South University, China
| | - Yanhao Wu
- Respiratory Department, Xiangya Hospital, Central South University, China
| | - Hongyi Tan
- Central Hospital, Changsha, Hunan Province, China
| | - Jing Deng
- Central South University Xiangya School of Public Health, China
| | - Maodan Hou
- Respiratory Department, Xiangya Hospital, Central South University, China
| | - Wenzhong Peng
- Respiratory Department, Xiangya Hospital, Central South University, China
| | - Guo Chen
- Respiratory Department, Xiangya Hospital, Central South University, China
| | - Yi Li
- Respiratory Department, Xiangya Hospital, Central South University, China
| | - Haitao Li
- Cancer Hospital of Hunan Province, China
| | - Pinhua Pan
- State Key Laboratory of Anti-Infective Drug Development, Dongguan 523871, China; Respiratory Department, Xiangya Hospital, Central South University, China.
| | - Jingmei Lu
- Respiratory Department, Xiangya Hospital, Central South University, China.
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Alahmadi A, Belet S, Black A, Cromer D, Flegg JA, House T, Jayasundara P, Keith JM, McCaw JM, Moss R, Ross JV, Shearer FM, Tun STT, Walker J, White L, Whyte JM, Yan AWC, Zarebski AE. Influencing public health policy with data-informed mathematical models of infectious diseases: Recent developments and new challenges. Epidemics 2020; 32:100393. [PMID: 32674025 DOI: 10.1016/j.epidem.2020.100393] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 04/25/2020] [Indexed: 12/16/2022] Open
Abstract
Modern data and computational resources, coupled with algorithmic and theoretical advances to exploit these, allow disease dynamic models to be parameterised with increasing detail and accuracy. While this enhances models' usefulness in prediction and policy, major challenges remain. In particular, lack of identifiability of a model's parameters may limit the usefulness of the model. While lack of parameter identifiability may be resolved through incorporation into an inference procedure of prior knowledge, formulating such knowledge is often difficult. Furthermore, there are practical challenges associated with acquiring data of sufficient quantity and quality. Here, we discuss recent progress on these issues.
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Affiliation(s)
- Amani Alahmadi
- School of Mathematics, Faculty of Science, Monash University, Melbourne, Australia
| | - Sarah Belet
- School of Mathematics, Faculty of Science, Monash University, Melbourne, Australia; Australian Research Council Centre of Excellence for Mathematical and Statistical Frontiers (ACEMS)
| | - Andrew Black
- School of Mathematical Sciences, University of Adelaide, Adelaide, Australia; Australian Research Council Centre of Excellence for Mathematical and Statistical Frontiers (ACEMS)
| | - Deborah Cromer
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, Australia and School of Mathematics and Statistics, UNSW Sydney, Sydney, Australia
| | - Jennifer A Flegg
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia.
| | - Thomas House
- Department of Mathematics, University of Manchester, Manchester, UK; IBM Research, Hartree Centre, Sci-Tech Daresbury, Warrington, UK.
| | | | - Jonathan M Keith
- School of Mathematics, Faculty of Science, Monash University, Melbourne, Australia; Australian Research Council Centre of Excellence for Mathematical and Statistical Frontiers (ACEMS)
| | - James M McCaw
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia.
| | - Robert Moss
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Joshua V Ross
- School of Mathematical Sciences, University of Adelaide, Adelaide, Australia; Australian Research Council Centre of Excellence for Mathematical and Statistical Frontiers (ACEMS).
| | - Freya M Shearer
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Sai Thein Than Tun
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, UK
| | - James Walker
- School of Mathematical Sciences, University of Adelaide, Adelaide, Australia
| | - Lisa White
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, UK
| | - Jason M Whyte
- Centre of Excellence for Biosecurity Risk Analysis (CEBRA), School of BioSciences, University of Melbourne, Melbourne, Australia; Australian Research Council Centre of Excellence for Mathematical and Statistical Frontiers (ACEMS)
| | - Ada W C Yan
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
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Lessler J, Ott CT, Carcelen AC, Konikoff JM, Williamson J, Bi Q, Kucirka LM, Cummings DA, Reich NG, Chaisson LH. Times to key events in Zika virus infection and implications for blood donation: a systematic review. Bull World Health Organ 2018; 94:841-849. [PMID: 27821887 PMCID: PMC5096355 DOI: 10.2471/blt.16.174540] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/20/2016] [Accepted: 06/22/2016] [Indexed: 11/27/2022] Open
Abstract
Objective To estimate the timing of key events in the natural history of Zika virus infection. Methods In February 2016, we searched PubMed, Scopus and the Web of Science for publications containing the term Zika. By pooling data, we estimated the incubation period, the time to seroconversion and the duration of viral shedding. We estimated the risk of Zika virus contaminated blood donations. Findings We identified 20 articles on 25 patients with Zika virus infection. The median incubation period for the infection was estimated to be 5.9 days (95% credible interval, CrI: 4.4–7.6), with 95% of people who developed symptoms doing so within 11.2 days (95% CrI: 7.6–18.0) after infection. On average, seroconversion occurred 9.1 days (95% CrI: 7.0–11.6) after infection. The virus was detectable in blood for 9.9 days (95% CrI: 6.9–21.4) on average. Without screening, the estimated risk that a blood donation would come from an infected individual increased by approximately 1 in 10 000 for every 1 per 100 000 person–days increase in the incidence of Zika virus infection. Symptom-based screening may reduce this rate by 7% (relative risk, RR: 0.93; 95% CrI: 0.89–0.99) and antibody screening, by 29% (RR: 0.71; 95% CrI: 0.28–0.88). Conclusion Neither symptom- nor antibody-based screening for Zika virus infection substantially reduced the risk that blood donations would be contaminated by the virus. Polymerase chain reaction testing should be considered for identifying blood safe for use in pregnant women in high-incidence areas.
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Affiliation(s)
- Justin Lessler
- Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland, MD 21205, United States of America (USA)
| | - Cassandra T Ott
- Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland, MD 21205, United States of America (USA)
| | - Andrea C Carcelen
- Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland, MD 21205, United States of America (USA)
| | - Jacob M Konikoff
- Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland, MD 21205, United States of America (USA)
| | - Joe Williamson
- Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland, MD 21205, United States of America (USA)
| | - Qifang Bi
- Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland, MD 21205, United States of America (USA)
| | | | | | - Nicholas G Reich
- School of Public Health and Health Sciences, University of Massachusetts Amherst, Amherst, USA
| | - Lelia H Chaisson
- Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland, MD 21205, United States of America (USA)
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8
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Affiliation(s)
- Adam J. Kucharski
- Centre for the Mathematical Modelling of Infectious Disease, London School of Hygiene and Tropical Medicine, London, United Kingdom
- * E-mail:
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9
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Rodó X, Ballester J, Curcoll R, Boyard-Micheau J, Borràs S, Morguí JA. Revisiting the role of environmental and climate factors on the epidemiology of Kawasaki disease. Ann N Y Acad Sci 2016; 1382:84-98. [PMID: 27603178 DOI: 10.1111/nyas.13201] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/03/2016] [Accepted: 07/14/2016] [Indexed: 12/16/2022]
Abstract
Can environmental factors, such as air-transported preformed toxins, be of key relevance to the health outcomes of poorly understood human ailments (e.g., rheumatic diseases such as vasculitides, some inflammatory diseases, or even severe childhood acquired heart diseases)? Can the physical, chemical, or biological features of air masses be linked to the emergence of diseases such as Kawasaki disease (KD), Henoch-Schönlein purpura, Takayasu's aortitis, and ANCA-associated vasculitis? These diseases surprisingly share some common epidemiological features. For example, they tend to appear as clusters of cases grouped geographically and temporarily progress in nonrandom sequences that repeat every year in a similar way. They also show concurrent trend changes within regions in countries and among different world regions. In this paper, we revisit transdisciplinary research on the role of environmental and climate factors in the epidemiology of KD as a paradigmatic example of this group of diseases. Early-warning systems based on environmental alerts, if successful, could be implemented as a way to better inform patients who are predisposed to, or at risk for, developing KD. Further research on the etiology of KD could facilitate the development of vaccines and specific medical therapies.
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Affiliation(s)
- Xavier Rodó
- Institut Català de Ciències del Clima (IC3).,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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Association of host, agent and environment characteristics and the duration of incubation and symptomatic periods of norovirus gastroenteritis. Epidemiol Infect 2014; 143:2308-14. [PMID: 25483148 DOI: 10.1017/s0950268814003288] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
We analysed the reported duration of incubation and symptomatic periods of norovirus for a dataset of 1022 outbreaks, 64 of which reported data on the average incubation period and 87 on the average symptomatic period. We found the mean and median incubation periods for norovirus to be 32·8 [95% confidence interval (CI) 30·9-34·6] hours and 33·5 (95% CI 32·0-34·0) hours, respectively. For the symptomatic period we found the mean and median to be 44·2 (95% CI 38·9-50·7) hours and 43·0 (95% CI 36·0-48·0) hours, respectively. We further investigated how these average periods were associated with several reported host, agent and environmental characteristics. We did not find any strong, biologically meaningful associations between the duration of incubation or symptomatic periods and the reported host, pathogen and environmental characteristics. Overall, we found that the distributions of incubation and symptomatic periods for norovirus infections are fairly constant and showed little differences with regard to the host, pathogen and environmental characteristics we analysed.
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11
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Tropospheric winds from northeastern China carry the etiologic agent of Kawasaki disease from its source to Japan. Proc Natl Acad Sci U S A 2014; 111:7952-7. [PMID: 24843117 DOI: 10.1073/pnas.1400380111] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Evidence indicates that the densely cultivated region of northeastern China acts as a source for the wind-borne agent of Kawasaki disease (KD). KD is an acute, coronary artery vasculitis of young children, and still a medical mystery after more than 40 y. We used residence times from simulations with the flexible particle dispersion model to pinpoint the source region for KD. Simulations were generated from locations spanning Japan from days with either high or low KD incidence. The postepidemic interval (1987-2010) and the extreme epidemics (1979, 1982, and 1986) pointed to the same source region. Results suggest a very short incubation period (<24 h) from exposure, thus making an infectious agent unlikely. Sampling campaigns over Japan during the KD season detected major differences in the microbiota of the tropospheric aerosols compared with ground aerosols, with the unexpected finding of the Candida species as the dominant fungus from aloft samples (54% of all fungal strains). These results, consistent with the Candida animal model for KD, provide support for the concept and feasibility of a windborne pathogen. A fungal toxin could be pursued as a possible etiologic agent of KD, consistent with an agricultural source, a short incubation time and synchronized outbreaks. Our study suggests that the causative agent of KD is a preformed toxin or environmental agent rather than an organism requiring replication. We propose a new paradigm whereby an idiosyncratic immune response, influenced by host genetics triggered by an environmental exposure carried on winds, results in the clinical syndrome known as acute KD.
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12
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Rudolph KE, Lessler J, Moloney RM, Kmush B, Cummings DAT. Incubation periods of mosquito-borne viral infections: a systematic review. Am J Trop Med Hyg 2014; 90:882-91. [PMID: 24639305 PMCID: PMC4015582 DOI: 10.4269/ajtmh.13-0403] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 11/14/2013] [Indexed: 11/07/2022] Open
Abstract
Mosquito-borne viruses are a major public health threat, but their incubation periods are typically uncited, non-specific, and not based on data. We systematically review the published literature on six mosquito-borne viruses selected for their public health importance: chikungunya, dengue, Japanese encephalitis, Rift Valley fever, West Nile, and yellow fever viruses. For each, we identify the literature's consensus on the incubation period, evaluate the evidence for this consensus, and provide detailed estimates of the incubation period and distribution based on published experimental and observational data. We abstract original data as doubly interval-censored observations. Assuming a log-normal distribution, we estimate the median incubation period, dispersion, 25th and 75th percentiles by maximum likelihood. We include bootstrapped 95% confidence intervals for each estimate. For West Nile and yellow fever viruses, we also estimate the 5th and 95th percentiles of their incubation periods.
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Affiliation(s)
| | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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13
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Lee RM, Lessler J, Lee RA, Rudolph KE, Reich NG, Perl TM, Cummings DAT. Incubation periods of viral gastroenteritis: a systematic review. BMC Infect Dis 2013; 13:446. [PMID: 24066865 PMCID: PMC3849296 DOI: 10.1186/1471-2334-13-446] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 09/12/2013] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Accurate knowledge of incubation period is important to investigate and to control infectious diseases and their transmission, however statements of incubation period in the literature are often uncited, inconsistent, and/or not evidence based. METHODS In a systematic review of the literature on five enteric viruses of public health importance, we found 256 articles with incubation period estimates, including 33 with data for pooled analysis. RESULTS We fit a log-normal distribution to pooled data and found the median incubation period to be 4.5 days (95% CI 3.9-5.2 days) for astrovirus, 1.2 days (95% CI 1.1-1.2 days) for norovirus genogroups I and II, 1.7 days (95% CI 1.5-1.8 days) for sapovirus, and 2.0 days (95% CI 1.4-2.4 days) for rotavirus. CONCLUSIONS Our estimates combine published data and provide sufficient quantitative detail to allow for these estimates to be used in a wide range of clinical and modeling applications. This can translate into improved prevention and control efforts in settings with transmission or the risk of transmission.
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Affiliation(s)
- Rachel M Lee
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - Rose A Lee
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - Kara E Rudolph
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - Nicholas G Reich
- Division of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusettes Amherst, Amherst, USA
| | - Trish M Perl
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Derek AT Cummings
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
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