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Mather AE, Gilmour MW, Reid SWJ, French NP. Foodborne bacterial pathogens: genome-based approaches for enduring and emerging threats in a complex and changing world. Nat Rev Microbiol 2024; 22:543-555. [PMID: 38789668 DOI: 10.1038/s41579-024-01051-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2024] [Indexed: 05/26/2024]
Abstract
Foodborne illnesses pose a substantial health and economic burden, presenting challenges in prevention due to the diverse microbial hazards that can enter and spread within food systems. Various factors, including natural, political and commercial drivers, influence food production and distribution. The risks of foodborne illness will continue to evolve in step with these drivers and with changes to food systems. For example, climate impacts on water availability for agriculture, changes in food sustainability targets and evolving customer preferences can all have an impact on the ecology of foodborne pathogens and the agrifood niches that can carry microorganisms. Whole-genome and metagenome sequencing, combined with microbial surveillance schemes and insights from the food system, can provide authorities and businesses with transformative information to address risks and implement new food safety interventions across the food chain. In this Review, we describe how genome-based approaches have advanced our understanding of the evolution and spread of enduring bacterial foodborne hazards as well as their role in identifying emerging foodborne hazards. Furthermore, foodborne hazards exist in complex microbial communities across the entire food chain, and consideration of these co-existing organisms is essential to understanding the entire ecology supporting pathogen persistence and transmission in an evolving food system.
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Affiliation(s)
- Alison E Mather
- Quadram Institute Bioscience, Norwich, UK.
- University of East Anglia, Norwich, UK.
| | - Matthew W Gilmour
- Quadram Institute Bioscience, Norwich, UK
- University of East Anglia, Norwich, UK
| | | | - Nigel P French
- Tāuwharau Ora, School of Veterinary Science, Te Kunenga Ki Pūrehuroa, Massey University, Papaioea, Palmerston North, Aotearoa New Zealand
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2
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Bajerge NM, Khankeh H, Dashtbozorgi A, Farrokhi M. Abstruse Side of Climate Change, Impact on Malaria: A Systematic Evidence Review Comparing Iran versus Globally. IRANIAN JOURNAL OF PUBLIC HEALTH 2024; 53:1047-1057. [PMID: 38912133 PMCID: PMC11188642 DOI: 10.18502/ijph.v53i5.15584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/16/2023] [Indexed: 06/25/2024]
Abstract
Background Infectious outbreaks due to disrupted social and environmental conditions after climate change-induced events complicate disasters. This research aimed to determine the contentions of bioclimatic variables and extreme events on the prevalence of the most common Climate-Sensitive Infectious Disease (CSID); Malaria in Iran. Methods The present narrative systematic review study was conducted on the bioclimatic variable impact on the prevalence of malaria, as a common CSID. The search was conducted in 3 sections: global climate change-related studies, disaster related, and studies that were conducted in Iran. The literature search was focused on papers published in English and Persian from Mar 2000 to Dec 2021, using electronic databases; Scopus, Web of Science, PubMed, Google Scholar, SID, Magiran, and IranDoc. Results Overall, 41 studies met the inclusion criteria. The various types of climatic variables including; Temperature, rainfall, relative humidity, and hydrological events including; flood, drought, and cyclones has been reported as a predictor of malaria. The results of studies, inappropriately and often were inconsistent in both Iran and other parts of the world. Conclusion Identifying malaria outbreak risks is essential to assess vulnerability, and a starting point to identify where the health system is required to reduce the vulnerability and exposure of the population. The finding of most related studies is not congruent to achieve reliable information, more extensive studies in all climates and regions of the country, by climatic models and high accuracy risk map, using the long period of bioclimatic variables and malaria trend is recommended.
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Affiliation(s)
- Nader Majidi Bajerge
- Health in Emergency and Disaster Research Center, Social Health Research Institute, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hamidreza Khankeh
- Health in Emergency and Disaster Research Center, Social Health Research Institute, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Amene Dashtbozorgi
- Center for Remote Sensing and GIS Research, Faculty of Earth Sciences, Shahid Beheshti University, Tehran, Iran
| | - Mehrdad Farrokhi
- Health in Emergency and Disaster Research Center, Social Health Research Institute, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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3
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Cohen M, Laux J, Douagi I. Cytometry in High-Containment Laboratories. Methods Mol Biol 2024; 2779:425-456. [PMID: 38526798 DOI: 10.1007/978-1-0716-3738-8_20] [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] [Indexed: 03/27/2024]
Abstract
The emergence of new pathogens continues to fuel the need for advanced high-containment laboratories across the globe. Here we explore challenges and opportunities for integration of cytometry, a central technology for cell analysis, within high-containment laboratories. We review current applications in infectious disease, vaccine research, and biosafety. Considerations specific to cytometry within high-containment laboratories, such as biosafety requirements, and sample containment strategies are also addressed. We further tour the landscape of emerging technologies, including combination of cytometry with other omics, the application of automation, and artificial intelligence. Finally, we propose a framework to fast track the immersion of advanced technologies into the high-containment research setting to improve global preparedness for new emerging diseases.
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Affiliation(s)
- Melanie Cohen
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Julie Laux
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Iyadh Douagi
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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Zortman I, de Garine-Wichatitsky M, Arsevska E, Dub T, Van Bortel W, Lefrançois E, Vial L, Pollet T, Binot A. A social-ecological systems approach to tick bite and tick-borne disease risk management: Exploring collective action in the Occitanie region in southern France. One Health 2023; 17:100630. [PMID: 38024266 PMCID: PMC10665146 DOI: 10.1016/j.onehlt.2023.100630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/19/2023] [Indexed: 12/01/2023] Open
Abstract
Ticks are amongst the most important zoonotic disease vectors affecting human and animal health worldwide. Tick-borne diseases (TBDs) are rapidly expanding geographically and in incidence, most notably in temperate regions of Europe where ticks are considered the principal zoonotic vector of Public Health relevance, as well as a major health and economic preoccupation in agriculture and equine industries. Tick-borne pathogen (TBP) transmission is contingent on complex, interlinked vector-pathogen-host dynamics, environmental and ecological conditions and human behavior. Tackling TBD therefore requires a better understanding of the interconnected social and ecological variables (i.e., the social-ecological system) that favor disease (re)-emergence. The One Health paradigm recognizes the interdependence of human, animal and environmental health and proposes an integrated approach to manage TBD. However, One Health interventions are limited by significant gaps in our understanding of the complex, systemic nature of TBD risk, in addition to a lack of effective, universally accepted and environmentally conscious tick control measures. Today individual prevention gestures are the most effective strategy to manage TBDs in humans and animals, making local communities important actors in TBD detection, prevention and management. Yet, how they engage and collaborate within a multi-actor TBD network has not yet been explored. Here, we argue that transdisciplinary collaborations that go beyond research, political and medical stakeholders, and extend to local community actors can aid in identifying relevant social-ecological risk indicators key for informing multi-level TBD detection, prevention and management measures. This article proposes a transdisciplinary social-ecological systems framework, based on participatory research approaches, to better understand the necessary conditions for local actor engagement to improve TBD risk. We conclude with perspectives for implementing this methodological framework in a case study in the south of France (Occitanie region), where multi-actor collaborations are mobilized to stimulate multi-actor collective action and identify relevant social-ecological indicators of TBD risk.
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Affiliation(s)
- Iyonna Zortman
- Joint Research Unit Animal, Health, Territories, Risks, Ecosystems (UMR ASTRE), French Agricultural Research Centre for International Development (CIRAD), National Research Institute for Agriculture, Food and Environment (INRAE), Montpellier, France
| | - Michel de Garine-Wichatitsky
- Joint Research Unit Animal, Health, Territories, Risks, Ecosystems (UMR ASTRE), French Agricultural Research Centre for International Development (CIRAD), National Research Institute for Agriculture, Food and Environment (INRAE), Montpellier, France
- Kasetsart University, Faculty of Veterinary Medicine, Bangkok, Thailand
| | - Elena Arsevska
- Joint Research Unit Animal, Health, Territories, Risks, Ecosystems (UMR ASTRE), French Agricultural Research Centre for International Development (CIRAD), National Research Institute for Agriculture, Food and Environment (INRAE), Montpellier, France
| | - Timothée Dub
- Infectious Disease Control and Vaccination Unit, Department of Health Security, Finnish Institute for Health and Welfare (THL), Unit Po Box 30. FI-00271 Helsinki, Finland
| | - Wim Van Bortel
- Unit Entomology and Outbreak Research Team, Department of Biomedical Sciences, Institute of Tropical Medicine, Nationalestraat, 155, Antwerpen, Belgium
| | - Estelle Lefrançois
- LIRDEF, Université de Montpellier and Université Paul Valéry Montpellier, France
| | - Laurence Vial
- Joint Research Unit Animal, Health, Territories, Risks, Ecosystems (UMR ASTRE), French Agricultural Research Centre for International Development (CIRAD), National Research Institute for Agriculture, Food and Environment (INRAE), Montpellier, France
| | - Thomas Pollet
- Joint Research Unit Animal, Health, Territories, Risks, Ecosystems (UMR ASTRE), French Agricultural Research Centre for International Development (CIRAD), National Research Institute for Agriculture, Food and Environment (INRAE), Montpellier, France
| | - Aurélie Binot
- Joint Research Unit Animal, Health, Territories, Risks, Ecosystems (UMR ASTRE), French Agricultural Research Centre for International Development (CIRAD), National Research Institute for Agriculture, Food and Environment (INRAE), Montpellier, France
- Maison des Sciences de l'Homme Sud, Montpellier, France
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Lawrence TJ, Takenaka BP, Garg A, Tao D, Deem SL, Fèvre EM, Gluecks I, Sagan V, Shacham E. A global examination of ecological niche modeling to predict emerging infectious diseases: a systematic review. Front Public Health 2023; 11:1244084. [PMID: 38026359 PMCID: PMC10652780 DOI: 10.3389/fpubh.2023.1244084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction As emerging infectious diseases (EIDs) increase, examining the underlying social and environmental conditions that drive EIDs is urgently needed. Ecological niche modeling (ENM) is increasingly employed to predict disease emergence based on the spatial distribution of biotic conditions and interactions, abiotic conditions, and the mobility or dispersal of vector-host species, as well as social factors that modify the host species' spatial distribution. Still, ENM applied to EIDs is relatively new with varying algorithms and data types. We conducted a systematic review (PROSPERO: CRD42021251968) with the research question: What is the state of the science and practice of estimating ecological niches via ENM to predict the emergence and spread of vector-borne and/or zoonotic diseases? Methods We searched five research databases and eight widely recognized One Health journals between 1995 and 2020. We screened 383 articles at the abstract level (included if study involved vector-borne or zoonotic disease and applied ENM) and 237 articles at the full-text level (included if study described ENM features and modeling processes). Our objectives were to: (1) describe the growth and distribution of studies across the types of infectious diseases, scientific fields, and geographic regions; (2) evaluate the likely effectiveness of the studies to represent ecological niches based on the biotic, abiotic, and mobility framework; (3) explain some potential pitfalls of ENM algorithms and techniques; and (4) provide specific recommendation for future studies on the analysis of ecological niches to predict EIDs. Results We show that 99% of studies included mobility factors, 90% modeled abiotic factors with more than half in tropical climate zones, 54% modeled biotic conditions and interactions. Of the 121 studies, 7% include only biotic and mobility factors, 45% include only abiotic and mobility factors, and 45% fully integrated the biotic, abiotic, and mobility data. Only 13% of studies included modifying social factors such as land use. A majority of studies (77%) used well-recognized ENM algorithms (MaxEnt and GARP) and model selection procedures. Most studies (90%) reported model validation procedures, but only 7% reported uncertainty analysis. Discussion Our findings bolster ENM to predict EIDs that can help inform the prevention of outbreaks and future epidemics. Systematic review registration https://www.crd.york.ac.uk/prospero/, identifier (CRD42021251968).
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Affiliation(s)
| | - Bryce P. Takenaka
- College for Public Health and Social Justice, Saint Louis University, St. Louis, MO, United States
| | - Aastha Garg
- College for Public Health and Social Justice, Saint Louis University, St. Louis, MO, United States
| | - Donghua Tao
- Medical Center Library, Saint Louis University, St. Louis, MO, United States
| | - Sharon L. Deem
- Institute for Conservation Medicine, Saint Louis Zoo, St. Louis, MO, United States
| | - Eric M. Fèvre
- International Livestock Research Institute, Nairobi, Kenya
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Ilona Gluecks
- International Livestock Research Institute, Nairobi, Kenya
| | - Vasit Sagan
- Taylor Geospatial Institute, St. Louis, MO, United States
- Department of Earth and Atmospheric Sciences, Saint Louis University, St. Louis, MO, United States
| | - Enbal Shacham
- Taylor Geospatial Institute, St. Louis, MO, United States
- College for Public Health and Social Justice, Saint Louis University, St. Louis, MO, United States
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Khandelwal V, Sharma T, Gupta S, Singh S, Sharma MK, Parashar D, Kashyap VK. Stem cell therapy: a novel approach against emerging and re-emerging viral infections with special reference to SARS-CoV-2. Mol Biol Rep 2023; 50:2663-2683. [PMID: 36536185 PMCID: PMC9762873 DOI: 10.1007/s11033-022-07957-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 09/17/2022] [Indexed: 12/23/2022]
Abstract
The past several decades have witnessed the emergence and re-emergence of many infectious viral agents, flaviviruses, influenza, filoviruses, alphaviruses, and coronaviruses since the advent of human deficiency virus (HIV). Some of them even become serious threats to public health and have raised major global health concerns. Several different medicinal compounds such as anti-viral, anti-malarial, and anti-inflammatory agents, are under investigation for the treatment of these viral diseases. These therapies are effective improving recovery rates and overall survival of patients but are unable to heal lung damage caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Therefore, there is a critical need to identify effective treatments to combat this unmet clinical need. Due to its antioxidant and immunomodulatory properties, stem cell therapy is considered a novel approach to regenerate damaged lungs and reduce inflammation. Stem cell therapy uses a heterogeneous subset of regenerative cells that can be harvested from various adult tissue types and is gaining popularity due to its prodigious regenerative potential as well as immunomodulatory and anti-inflammatory properties. These cells retain expression of cluster of differentiation markers (CD markers), interferon-stimulated gene (ISG), reduce expression of pro-inflammatory cytokines and, show a rapid proliferation rate, which makes them an attractive tool for cellular therapies and to treat various inflammatory and viral-induced injuries. By examining various clinical studies, this review demonstrates positive considerations for the implications of stem cell therapy and presents a necessary approach for treating virally induced infections in patients.
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Affiliation(s)
- Vishal Khandelwal
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, 281406, India
| | - Tarubala Sharma
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, 281406, India
| | - Saurabh Gupta
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, 281406, India
| | - Shoorvir Singh
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, 281406, India
| | - Manish Kumar Sharma
- Department of Microbiology, Dr. Ram Manohar Lohia Avadh University, Faizabad, Uttar Pradesh, 224001, India
| | - Deepak Parashar
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
| | - Vivek K Kashyap
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX, 78504, USA. .,South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX, 78504, USA.
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Devnath P, Karah N, Graham JP, Rose ES, Asaduzzaman M. Evidence of Antimicrobial Resistance in Bats and Its Planetary Health Impact for Surveillance of Zoonotic Spillover Events: A Scoping Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 20:243. [PMID: 36612565 PMCID: PMC9819402 DOI: 10.3390/ijerph20010243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 06/16/2023]
Abstract
As a result of the COVID-19 pandemic, as well as other outbreaks, such as SARS and Ebola, bats are recognized as a critical species for mediating zoonotic infectious disease spillover events. While there is a growing concern of increased antimicrobial resistance (AMR) globally during this pandemic, knowledge of AMR circulating between bats and humans is limited. In this paper, we have reviewed the evidence of AMR in bats and discussed the planetary health aspect of AMR to elucidate how this is associated with the emergence, spread, and persistence of AMR at the human-animal interface. The presence of clinically significant resistant bacteria in bats and wildlife has important implications for zoonotic pandemic surveillance, disease transmission, and treatment modalities. We searched MEDLINE through PubMed and Google Scholar to retrieve relevant studies (n = 38) that provided data on resistant bacteria in bats prior to 30 September 2022. There is substantial variability in the results from studies measuring the prevalence of AMR based on geographic location, bat types, and time. We found all major groups of Gram-positive and Gram-negative bacteria in bats, which are resistant to commonly used antibiotics. The most alarming issue is that recent studies have increasingly identified clinically significant multi-drug resistant bacteria such as Methicillin Resistant Staphylococcus aureus (MRSA), ESBL producing, and Colistin resistant Enterobacterales in samples from bats. This evidence of superbugs abundant in both humans and wild mammals, such as bats, could facilitate a greater understanding of which specific pathways of exposure should be targeted. We believe that these data will also facilitate future pandemic preparedness as well as global AMR containment during pandemic events and beyond.
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Affiliation(s)
- Popy Devnath
- College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
- Department of Microbiology, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Nabil Karah
- Department of Molecular Biology and Umeå Centre for Microbial Research, Umeå University, SE-901 87 Umeå, Sweden
| | - Jay P. Graham
- School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Elizabeth S. Rose
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Muhammad Asaduzzaman
- Department of Community Medicine and Global Health, Institute of Health and Society, Faculty of Medicine, University of Oslo, 450 Oslo, Norway
- Planetary Health Alliance, Boston, MA 02115, USA
- Planetary Health Working Group, Be-Cause Health, Institute of Tropical Medicine, Nationalestraat 155, 2000 Antwerp, Belgium
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Jagadesh S, Combe M, Gozlan RE. Human-Altered Landscapes and Climate to Predict Human Infectious Disease Hotspots. Trop Med Infect Dis 2022; 7:tropicalmed7070124. [PMID: 35878136 PMCID: PMC9325272 DOI: 10.3390/tropicalmed7070124] [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: 06/01/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 02/05/2023] Open
Abstract
Background: Zoonotic diseases account for more than 70% of emerging infectious diseases (EIDs). Due to their increasing incidence and impact on global health and the economy, the emergence of zoonoses is a major public health challenge. Here, we use a biogeographic approach to predict future hotspots and determine the factors influencing disease emergence. We have focused on the following three viral disease groups of concern: Filoviridae, Coronaviridae, and Henipaviruses. Methods: We modelled presence–absence data in spatially explicit binomial and zero-inflation binomial logistic regressions with and without autoregression. Presence data were extracted from published studies for the three EID groups. Various environmental and demographical rasters were used to explain the distribution of the EIDs. True Skill Statistic and deviance parameters were used to compare the accuracy of the different models. Results: For each group of viruses, we were able to identify and map areas at high risk of disease emergence based on the spatial distribution of the disease reservoirs and hosts of the three viral groups. Common influencing factors of disease emergence were climatic covariates (minimum temperature and rainfall) and human-induced land modifications. Conclusions: Using topographical, climatic, and previous disease outbreak reports, we can identify and predict future high-risk areas for disease emergence and their specific underlying human and environmental drivers. We suggest that such a predictive approach to EIDs should be carefully considered in the development of active surveillance systems for pathogen emergence and epidemics at local and global scales.
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Affiliation(s)
- Soushieta Jagadesh
- Heath Geography and Policy, ETH Zurich, Sonneggstrasse 33, 8092 Zurich, Switzerland
- Correspondence:
| | - Marine Combe
- ISEM, Université de Montpellier, CNRS, IRD, 34090 Montpellier, France; (M.C.); (R.E.G.)
| | - Rodolphe Elie Gozlan
- ISEM, Université de Montpellier, CNRS, IRD, 34090 Montpellier, France; (M.C.); (R.E.G.)
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Bwire G, Ario AR, Eyu P, Ocom F, Wamala JF, Kusi KA, Ndeketa L, Jambo KC, Wanyenze RK, Talisuna AO. The COVID-19 pandemic in the African continent. BMC Med 2022; 20:167. [PMID: 35501853 PMCID: PMC9059455 DOI: 10.1186/s12916-022-02367-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/05/2022] [Indexed: 01/13/2023] Open
Abstract
In December 2019, a new coronavirus, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and associated disease, coronavirus disease 2019 (COVID-19), was identified in China. This virus spread quickly and in March, 2020, it was declared a pandemic. Scientists predicted the worst scenario to occur in Africa since it was the least developed of the continents in terms of human development index, lagged behind others in achievement of the United Nations sustainable development goals (SDGs), has inadequate resources for provision of social services, and has many fragile states. In addition, there were relatively few research reporting findings on COVID-19 in Africa. On the contrary, the more developed countries reported higher disease incidences and mortality rates. However, for Africa, the earlier predictions and modelling into COVID-19 incidence and mortality did not fit into the reality. Therefore, the main objective of this forum is to bring together infectious diseases and public health experts to give an overview of COVID-19 in Africa and share their thoughts and opinions on why Africa behaved the way it did. Furthermore, the experts highlight what needs to be done to support Africa to consolidate the status quo and overcome the negative effects of COVID-19 so as to accelerate attainment of the SDGs.
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Affiliation(s)
- Godfrey Bwire
- Department of Integrated Epidemiology Surveillance and Public Health Emergencies, Ministry of Health, P.O Box 7272, Kampala, Uganda
- School of Public Health, Makerere University, P.O. Box 7072, Kampala, Uganda
| | | | - Patricia Eyu
- Uganda National Institute of Public Health, Kampala, Uganda
| | - Felix Ocom
- Uganda National Institute of Public Health, Kampala, Uganda
| | | | - Kwadwo A. Kusi
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Latif Ndeketa
- Malawi-Liverpool-Wellcome Programme (MLW), Blantyre, Malawi
| | - Kondwani C. Jambo
- Malawi-Liverpool-Wellcome Programme (MLW), Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - Rhoda K. Wanyenze
- School of Public Health, Makerere University, P.O. Box 7072, Kampala, Uganda
| | - Ambrose O. Talisuna
- Epidemic Preparedness and Response Cluster, World Health Organization, Regional Office for Africa, Brazzaville, Congo
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Kontowicz E, Brown G, Torner J, Carrel M, Baker KK, Petersen CA. Inclusion of environmentally themed search terms improves Elastic net regression nowcasts of regional Lyme disease rates. PLoS One 2022; 17:e0251165. [PMID: 35271589 PMCID: PMC8912246 DOI: 10.1371/journal.pone.0251165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 02/01/2022] [Indexed: 11/19/2022] Open
Abstract
Lyme disease is the most widely reported vector-borne disease in the United States. 95% of confirmed human cases are reported in the Northeast and upper Midwest (25,778 total confirmed cases from Northeast and upper Midwest / 27,203 total US confirmed cases). Human cases typically occur in the spring and summer months when an infected nymph Ixodid tick takes a blood meal. Current federal surveillance strategies report data on an annual basis, leading to nearly a year lag in national data reporting. These lags in reporting make it difficult for public health agencies to assess and plan for the current burden of Lyme disease. Implementation of a nowcasting model, using historical data to predict current trends, provides a means for public health agencies to evaluate current Lyme disease burden and make timely priority-based budgeting decisions. The objective of the study was to develop and compare the performance of nowcasting models using free data from Google Trends and Centers of Disease Control and Prevention surveillance reports. We developed two sets of elastic net models for five regions of the United States: 1. Using only monthly proportional hit data from the 21 disease symptoms and tick related terms, and 2. Using monthly proportional hit data from terms identified via Google correlate and the disease symptom and vector terms. Elastic net models using the full-term list were highly accurate (Root Mean Square Error: 0.74, Mean Absolute Error: 0.52, R2: 0.97) for four of the five regions of the United States and improved accuracy 1.33-fold while reducing error 0.5-fold compared to predictions from models using disease symptom and vector terms alone. Many of the terms included and found to be important for model performance were environmentally related. These models can be implemented to help local and state public health agencies accurately monitor Lyme disease burden during times of reporting lag from federal public health reporting agencies.
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Affiliation(s)
- Eric Kontowicz
- Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa, United States of America
- Center for Emerging Infectious Diseases, University of Iowa Research Park, Coralville, Iowa, United States of America
| | - Grant Brown
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, Iowa, United States of America
| | - James Torner
- Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa, United States of America
| | - Margaret Carrel
- Department of Geographical and Sustainability Sciences, College of Liberal Arts & Sciences, University of Iowa, Iowa City, Iowa, United States of America
| | - Kelly K. Baker
- Department of Occupational and Environmental Health, College of Public Health, University of Iowa, Iowa City, United States of America
| | - Christine A. Petersen
- Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa, United States of America
- Center for Emerging Infectious Diseases, University of Iowa Research Park, Coralville, Iowa, United States of America
- Immunology Program, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
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Hanna GS, Choo YM, Harbit R, Paeth H, Wilde S, Mackle J, Verga JU, Wolf BJ, Thomas OP, Croot P, Cray J, Thomas C, Li LZ, Hardiman G, Hu JF, Wang X, Patel D, Schinazi RF, O’Keefe BR, Hamann MT. Contemporary Approaches to the Discovery and Development of Broad-Spectrum Natural Product Prototypes for the Control of Coronaviruses. JOURNAL OF NATURAL PRODUCTS 2021; 84:3001-3007. [PMID: 34677966 PMCID: PMC8547502 DOI: 10.1021/acs.jnatprod.1c00625] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Indexed: 05/25/2023]
Abstract
The pressing need for SARS-CoV-2 controls has led to a reassessment of strategies to identify and develop natural product inhibitors of zoonotic, highly virulent, and rapidly emerging viruses. This review article addresses how contemporary approaches involving computational chemistry, natural product (NP) and protein databases, and mass spectrometry (MS) derived target-ligand interaction analysis can be utilized to expedite the interrogation of NP structures while minimizing the time and expense of extraction, purification, and screening in BioSafety Laboratories (BSL)3 laboratories. The unparalleled structural diversity and complexity of NPs is an extraordinary resource for the discovery and development of broad-spectrum inhibitors of viral genera, including Betacoronavirus, which contains MERS, SARS, SARS-CoV-2, and the common cold. There are two key technological advances that have created unique opportunities for the identification of NP prototypes with greater efficiency: (1) the application of structural databases for NPs and target proteins and (2) the application of modern MS techniques to assess protein-ligand interactions directly from NP extracts. These approaches, developed over years, now allow for the identification and isolation of unique antiviral ligands without the immediate need for BSL3 facilities. Overall, the goal is to improve the success rate of NP-based screening by focusing resources on source materials with a higher likelihood of success, while simultaneously providing opportunities for the discovery of novel ligands to selectively target proteins involved in viral infection.
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Affiliation(s)
- George S. Hanna
- Departments of Drug Discovery and Biomedical Sciences and Public Health, Colleges of Pharmacy and Medicine, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Yeun-Mun Choo
- Department of Chemistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Ryan Harbit
- College of Charleston, Charleston, South Carolina 29425, United States
| | - Heather Paeth
- Departments of Drug Discovery and Biomedical Sciences and Public Health, Colleges of Pharmacy and Medicine, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Sarah Wilde
- Department of Biology, Clemson University, Clemson, South Carolina 29631, United States
| | - James Mackle
- School of Biological Sciences & Institute for Global Food Security, Queens University, Belfast, Northern Ireland, United Kingdom
| | - Jacopo-Umberto Verga
- School of Biological Sciences & Institute for Global Food Security, Queens University, Belfast, Northern Ireland, United Kingdom
| | - Bethany J. Wolf
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Olivier P. Thomas
- Marine Biodiscovery, School of Chemistry and Ryan Institute, National University of Ireland Galway, Galway H91Tk33, Ireland
| | - Peter Croot
- Irish Centre for Research in Applied Geoscience, Earth and Ocean Sciences and Ryan Institute, School of Natural Sciences, National University of Ireland, Galway, Galway, Ireland
| | - James Cray
- Department of Biomedical Education and Anatomy, College of Medicine and Division of Biosciences, College of Dentistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Courtney Thomas
- Department of Chemistry, South Carolina State University, Orangeburg, South Carolina, United States
| | - Ling-Zhi Li
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University/SPU, Shenyang, China
| | - Gary Hardiman
- School of Biological Sciences & Institute for Global Food Security, Queens University, Belfast, Northern Ireland, United Kingdom
| | - Jin-Feng Hu
- School of Advanced Study, Zhejiang Provincial Key Laboratory of Plant Ecology and Conservation, Taizhou University, Zhejiang 318000, China
| | - Xiaojuan Wang
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Dharmeshkhumar Patel
- Department of Pediatrics, Laboratory of Biochemical Pharmacology, Emory University School of Medicine, and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Raymond F. Schinazi
- Department of Pediatrics, Laboratory of Biochemical Pharmacology, Emory University School of Medicine, and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Barry R. O’Keefe
- Molecular Targets Program, Center for Cancer Research, Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Mark T. Hamann
- Departments of Drug Discovery and Biomedical Sciences and Public Health, Colleges of Pharmacy and Medicine, Medical University of South Carolina, Charleston, South Carolina 29425, United States
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12
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The Global Emergence of Human Babesiosis. Pathogens 2021; 10:pathogens10111447. [PMID: 34832603 PMCID: PMC8623124 DOI: 10.3390/pathogens10111447] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/28/2021] [Accepted: 10/30/2021] [Indexed: 12/05/2022] Open
Abstract
Babesiosis is an emerging tick-borne disease caused by intraerythrocytic protozoa that are primarily transmitted by hard-bodied (ixodid) ticks and rarely through blood transfusion, perinatally, and organ transplantation. More than 100 Babesia species infect a wide spectrum of wild and domestic animals worldwide and six have been identified as human pathogens. Babesia microti is the predominant species that infects humans, is found throughout the world, and causes endemic disease in the United States and China. Babesia venatorum and Babesia crassa-like agent also cause endemic disease in China. Babesia divergens is the predominant species in Europe where fulminant cases have been reported sporadically. The number of B. microti infections has been increasing globally in recent decades. In the United States, more than 2000 cases are reported each year, although the actual number is thought to be much higher. In this review of the epidemiology of human babesiosis, we discuss epidemiologic tools used to monitor disease location and frequency; demographics and modes of transmission; the location of human babesiosis; the causative Babesia species in the Americas, Europe, Asia, Africa, and Australia; the primary clinical characteristics associated with each of these infections; and the increasing global health burden of this disease.
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13
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Wu Q, Li Q, Lu J. A One Health strategy for emerging infectious diseases based on the COVID-19 outbreak. JOURNAL OF BIOSAFETY AND BIOSECURITY 2021; 4:5-11. [PMID: 34729464 PMCID: PMC8552662 DOI: 10.1016/j.jobb.2021.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 11/13/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is as an emerging infectious disease (EID) that has caused the worst public health catastrophe of the 21st century thus far. In terms of impact, the COVID-19 pandemic is second only to the Spanish Flu pandemic of 1918 in modern world history. As of 7 September 2021, there have been 220 million confirmed cases of COVID-19 and more than 4.5 million deaths. EIDs pose serious public health and socio-economic risks, and 70% of EIDs originate from wildlife. Preventing development of EIDs such as COVID-19 is a pressing concern. Here, taking the COVID-19 pandemic as an example, we illustrate the disastrous effects of EIDs and assess their emergence and evolution from a One Health perspective. We propose a One Health strategy, centered on ‘moving the gates forward’, for EID prevention and control at the human–animal–environment interface. This strategy may be instructive and provide early warnings of EIDs in the future.
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Affiliation(s)
- Qin Wu
- School of Public Health, Sun Yat-sen University, Guangzhou, China.,Key Laboratory for Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China.,One Health Center of Excellence for Research and Training, Guangzhou, China.,State Key Laboratory for Surveillance and Evaluation of Vaccines and Biological Products, Guangzhou, China
| | - Qianlin Li
- School of Public Health, Sun Yat-sen University, Guangzhou, China.,Key Laboratory for Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China.,One Health Center of Excellence for Research and Training, Guangzhou, China.,State Key Laboratory for Surveillance and Evaluation of Vaccines and Biological Products, Guangzhou, China
| | - Jiahai Lu
- School of Public Health, Sun Yat-sen University, Guangzhou, China.,Key Laboratory for Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China.,One Health Center of Excellence for Research and Training, Guangzhou, China.,State Key Laboratory for Surveillance and Evaluation of Vaccines and Biological Products, Guangzhou, China
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14
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Wan MM, Doan Q, Kissoon N. The knowledge needs for Canadian paediatric emergency physicians in the diagnosis and management of tropical diseases: A national physician survey. Paediatr Child Health 2021; 26:e138-e144. [PMID: 33936343 PMCID: PMC8077208 DOI: 10.1093/pch/pxaa022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 01/07/2020] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To assess the knowledge gaps and need for continuing medical education (CME) resources for Canadian paediatric emergency department (PED) physician management of common tropical diseases. METHODS A cross-sectional survey study of Canadian PED was performed from May to July 2017 using the Pediatric Emergency Research Canada (PERC) database. RESULTS The response rate was 56.4% (133/236). The mean performance on the case-based vignettes identifying clinical presentation of tropical illnesses ranged from 59.9% to 76.0%, with only 15.8% (n=21) to 31.1% (n=42) of participants scoring maximum points. Those who 'always' asked about fever performed better than those who only 'sometimes' asked (40.4% versus 23.8%). For management cases, the majority of the participants (59.4% to 89.5%) were able to interpret investigations; however, many were unsure of subsequent actions relating to initial treatment, discharge instructions, and reporting requirements. Many would consult infectious diseases (87.8% to 99.3%). Fifty-three per cent of the participants reported a low comfort level in diagnosing or managing these patients. They rated the importance of CME materials with a median of 50/100, via various modalities such as case studies (71.9%), emphasizing a need for PED-specific content. CONCLUSION This study identified a knowledge gap in the recognition and management of pediatric tropical diseases by Canadian PED physicians. There is a need for formal CME materials to supplement physician practice.
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Affiliation(s)
- Melissa Mengyan Wan
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia
| | - Quynh Doan
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia
- Division of Emergency Medicine, BC Children’s Hospital, Vancouver, British Columbia
- BC Children’s Hospital Research Institute, Vancouver, British Columbia
| | - Niranjan Kissoon
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia
- BC Children’s Hospital Research Institute, Vancouver, British Columbia
- Division of Critical Care, BC Children’s Hospital, Vancouver, British Columbia
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15
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Bistolas K, Vega Thurber R. Viral discovery in the 'realm' of COVID-19. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:62-67. [PMID: 33258558 PMCID: PMC7753244 DOI: 10.1111/1758-2229.12912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 11/26/2020] [Indexed: 06/12/2023]
Affiliation(s)
- Kalia Bistolas
- Department of MicrobiologyOregon State University, Nash HallCorvallisOR97331USA
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16
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Kojom LP, Singh V. A Review on Emerging Infectious Diseases Prioritized Under the 2018 WHO Research and Development Blueprint: Lessons from the Indian Context. Vector Borne Zoonotic Dis 2020; 21:149-159. [PMID: 33316200 DOI: 10.1089/vbz.2020.2661] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Objective: This review describes the current scenario of a priority group of emerging infectious diseases (EIDs) listed by World Health Organization (WHO), and their main determinants and drivers for the emergence/spread of the diseases. The gaps and strategies developed by India to meet the WHO guidelines on the effective control of epidemic-prone diseases and outbreaks are also presented in the review. Methods: Epidemiologic information of EIDs, namely Crimean-Congo hemorrhagic fever (CCHF), Ebola and Marburg viruses (EboV and MarV), Zika virus (ZIKAV), Rift Valley fever (RVF), Middle East respiratory syndrome, severe acute respiratory syndrome (SARS), Nipah and Hendra virus (NiV and HeV), and Lassa fever virus (LASV), was drawn from international and national electronic databases to assess the situation. A brief view on the novel coronavirus disease 2019 (COVID-19) in India is also included. Results: There are no reports for human infection of EboV, MarV, RVF, and LASV in India. CCHF, SARS, ZIKAV, and NiV have been involved in outbreaks in eight states of India, while COVID-19 is currently reported from majority of states. India has deeply strengthened its surveillance and response system of outbreaks and epidemic-prone diseases. Conclusions: Despite its enormous improvements made in the anticipation of such threats, still more efforts are needed in sensitization of populations as well as hospital management in the context to EIDs, as addressed in the review. Furthermore, there is still a need for more research and development activities to efficiently control EIDs.
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Affiliation(s)
- Loick Pradel Kojom
- Cell Biology Laboratory and Malaria Parasite Bank, ICMR-National Institute of Malaria Research, New-Delhi, India
| | - Vineeta Singh
- Cell Biology Laboratory and Malaria Parasite Bank, ICMR-National Institute of Malaria Research, New-Delhi, India
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17
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Oh IH, Ock M, Jang SY, Go DS, Kim YE, Jung YS, Kim KB, Park H, Jo MW, Yoon SJ. Years of Life Lost Attributable to COVID-19 in High-incidence Countries. J Korean Med Sci 2020; 35:e300. [PMID: 32808515 PMCID: PMC7431288 DOI: 10.3346/jkms.2020.35.e300] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/05/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) pandemic is a major public health problem of international concern. It is important to estimate its impact of COVID-19 for health policy decision-making. We estimated the years of life lost (YLLs) due to COVID-19 in high-incidence countries. METHODS We collected the YLLs due to COVID-19 in 30 high-incidence countries as of April 13, 2020 and followed up as of July 14, 2020. Incidence and mortality were collected using each country's formal reports, articles, and other electronic sources. The life expectancy of Japanese females by age and the UN population data were used to calculate YLLs in total and per 100,000. RESULTS As of April 22, 2020, there were 1,699,574 YLLs due to COVID-19 in 30 high-incidence countries. On July 14, 2020, this increased to 4,072,325. Both on April 22 and July 14, the total YLLs due to COVID-19 was highest in the USA (April 22, 534,481 YLLs; July 14, 1,199,510 YLLs), and the YLLs per 100,000 population was highest in Belgium (April 22, 868.12 YLLs/100,000; July 14, 1,593.72 YLLs/100,000). YLLs due to COVID-19 were higher among males than among females and higher in those aged ≥ 60 years than in younger individuals. Belgium had the highest proportion of YLLs attributable to COVID-19 as a proportion of the total YLLs and the highest disability-adjusted life years per 100,000 population. CONCLUSION This study estimated YLLs due to COVID-19 in 30 countries. COVID-19 is a high burden in the USA and Belgium, among males and the elderly. The YLLs are very closely related with the incidence as well as the mortality. This highlights the importance of the early detection of incident case that minimizes severe acute respiratory syndrome coronavirus-2 fatality.
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Affiliation(s)
- In Hwan Oh
- Department of Preventive Medicine, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Minsu Ock
- Department of Preventive Medicine, University of Ulsan College of Medicine, Seoul, Korea
- Department of Preventive Medicine, Ulsan University Hospital, Ulsan, Korea
| | - Su Yeon Jang
- Department of Preventive Medicine, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Dun Sol Go
- Department of Health Care Policy Research, Korea Institute for Health and Social Affairs, Sejong, Korea
| | - Young Eun Kim
- Big Data Department, National Health Insurance Service, Wonju, Korea
| | - Yoon Sun Jung
- Department of Public Health, Graduate School, Korea University, Seoul, Korea
| | - Ki Beom Kim
- Department of Public Health, Graduate School, Korea University, Seoul, Korea
| | - Hyesook Park
- Department of Preventive Medicine, Ewha Womans University School of Medicine, Seoul, Korea
| | - Min Woo Jo
- Department of Preventive Medicine, University of Ulsan College of Medicine, Seoul, Korea.
| | - Seok Jun Yoon
- Department of Preventive Medicine, Korea University College of Medicine, Seoul, Korea.
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Artika IM, Wiyatno A, Ma'roef CN. Pathogenic viruses: Molecular detection and characterization. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 81:104215. [PMID: 32006706 PMCID: PMC7106233 DOI: 10.1016/j.meegid.2020.104215] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 01/23/2020] [Accepted: 01/28/2020] [Indexed: 12/14/2022]
Abstract
Pathogenic viruses are viruses that can infect and replicate within human cells and cause diseases. The continuous emergence and re-emergence of pathogenic viruses has become a major threat to public health. Whenever pathogenic viruses emerge, their rapid detection is critical to enable implementation of specific control measures and the limitation of virus spread. Further molecular characterization to better understand these viruses is required for the development of diagnostic tests and countermeasures. Advances in molecular biology techniques have revolutionized the procedures for detection and characterization of pathogenic viruses. The development of PCR-based techniques together with DNA sequencing technology, have provided highly sensitive and specific methods to determine virus circulation. Pathogenic viruses potentially having global catastrophic consequences may emerge in regions where capacity for their detection and characterization is limited. Development of a local capacity to rapidly identify new viruses is therefore critical. This article reviews the molecular biology of pathogenic viruses and the basic principles of molecular techniques commonly used for their detection and characterization. The principles of good laboratory practices for handling pathogenic viruses are also discussed. This review aims at providing researchers and laboratory personnel with an overview of the molecular biology of pathogenic viruses and the principles of molecular techniques and good laboratory practices commonly implemented for their detection and characterization.
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Affiliation(s)
- I Made Artika
- Biosafety Level 3 Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia; Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Darmaga Campus, Bogor 16680, Indonesia.
| | - Ageng Wiyatno
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia
| | - Chairin Nisa Ma'roef
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia
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19
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Malvy D, Gaüzère BA, Migliani R. [Epidemic and emerging prone-infectious diseases: Lessons learned and ways forward]. Presse Med 2019; 48:1536-1550. [PMID: 31784255 PMCID: PMC7127531 DOI: 10.1016/j.lpm.2019.09.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 09/26/2019] [Indexed: 01/20/2023] Open
Abstract
Africa along side with south-east Asia are the epicentres of emerging and epidemic prone-infectious diseases and megacity biosecurity threat scenarios. Massive mobility and reluctance in the populations exposed to epidemic and emerging prone-infectious diseases coupled by a weak health system made disease alert and control measures difficult to implement. The investigation of virus detection and persistence in semen across a range of emerging viruses is useful for clinical and public health reasons, in particular for viruses that lead to high mortality or morbidity rates or to epidemics. Innovating built facility to safely treat patients with highly pathogenic infectious diseases is urgently need, not only to prevent the spread of infection from patients to healthcare workers but also to offer provision of relatively invasive organ support, whenever considered appropriate, without posing additional risk to staff. Despite multiple challenges, the need to conduct research during epidemics is inevitable, and candidate products must continue undergoing rigorous trials. Preparedness including management of complex humanitarian crises with community distrust is a cornerstone in response to high consequence emerging infectious disease outbreaks and imposes strengthening of the public health response infrastructure and emergency outbreak systems in high-risk regions.
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Affiliation(s)
- Denis Malvy
- Université de Bordeaux, centre René Labusquière, département universitaire de médecine tropicale et santé internationale clinique, 33000Bordeaux, France; Université de Bordeaux, Inserm 1219, 33000Bordeaux, France; CHU de Bordeaux, établissement de santé de référence risque épidémique et biologique Sud-Ouest, service des maladies infectieuses et tropicales, 33000Bordeaux, France.
| | - Bernard-Alex Gaüzère
- Université de Bordeaux, centre René Labusquière, département universitaire de médecine tropicale et santé internationale clinique, 33000Bordeaux, France
| | - René Migliani
- Université de Bordeaux, centre René Labusquière, département universitaire de médecine tropicale et santé internationale clinique, 33000Bordeaux, France.
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20
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Ghosh S, Voigt J, Wynne T, Nelson T. Developing an In-House Biological Safety Cabinet Certification Program at the University of North Dakota. APPLIED BIOSAFETY 2019; 24:153-160. [PMID: 36032333 PMCID: PMC9134467 DOI: 10.1177/1535676019859787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/17/2023]
Abstract
INTRODUCTION Biological safety cabinets (BSCs) are the primary means of containment used in laboratories worldwide. To ensure the proper functioning of BSCs, they need to be certified annually, at a minimum, per National Sanitation Foundation (NSF)/American National Standards Institute Standard 49. OBJECTIVES A common problem most organizations face is that in many instances, the technicians who certify the cabinets are not accredited by the NSF. Additionally, in states or regions that do not have local NSF accredited field certifiers, it takes weeks to get a service request completed, thereby delaying the research work of the laboratory. Moreover, in such instances, the cost associated with cabinet certification and repair can be very high. MATERIALS AND METHODS This led the Office of Safety at the University of North Dakota to do a thorough cost-benefit analysis of developing an in-house BSC certification program. After completing the training and testing requirements for the NSF's advanced accreditation program, the BSC certification program was initiated on campus. RESULTS The identified benefits led to the initiation of a program in both local and regional capacity for repair, maintenance, and certification of BSCs, and the university's experiences were shared with other universities. CONCLUSIONS By developing an in-house BSC certification program, the University of North Dakota was able to reduce wait times associated with service repairs, reduce costs, and generate revenue for the department. Furthermore, this led to improved hands-on training programs related to BSC use in laboratories working with biohazardous agents.
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Affiliation(s)
- Sumit Ghosh
- The Research Institute at Nationwide Children’s Hospital, Department of Research Safety, Columbus, OH, USA
| | - Jeffrey Voigt
- University of North Dakota, Department of Public Safety, Grand Forks, ND, USA
| | - Terrance Wynne
- University of North Dakota, Department of Public Safety, Grand Forks, ND, USA
| | - Terrance Nelson
- University of North Dakota, School of Medicine and Health Sciences, Grand Forks, ND, USA
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21
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Hecht LS, Jurado-Jimenez A, Hess M, Halas HE, Bochenek G, Mohammed H, Alzahrani F, Asiri MO, Hasan R, Alamri A, Alotaibi S. Verification and diagnostic evaluation of the RealStar ® Middle East respiratory syndrome coronavirus (N gene) reverse transcription-PCR kit 1.0. Future Microbiol 2019; 14:941-948. [PMID: 31271059 PMCID: PMC7079715 DOI: 10.2217/fmb-2019-0067] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/12/2019] [Indexed: 01/08/2023] Open
Abstract
Aim: We report the diagnostic evaluation of a confirmatory reverse transcription-PCR (RT-PCR) kit targeting the Middle East respiratory syndrome coronavirus (MERS-CoV) N gene. Material & methods: 33 patient samples from two collections sites in Riyadh, Saudi Arabia, which were pre-characterized via real-time RT-PCR targeting MERS-CoV orf1a and upE, and were tested using the MERS-CoV N gene, as a confirmatory assay. This diagnostic procedure follows a two-step diagnostics scheme, recommended by the WHO. Results: 18/33 samples tested positive, 11/33 tested negative for MERS-CoV RNA and 2/33 showed uncertain results. Conclusion: The results suggest, that the RealStar® MERS-CoV (N gene) RT-PCR kit 1.0 can be considered a suitable and reliable confirmatory assay in combination with the RealStar MERS-CoV RT-PCR kit 1.0 according to the diagnostic scheme recommended by WHO.
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Affiliation(s)
| | | | | | | | | | - Hala Mohammed
- Ministry of Health, Riyadh Regional Laboratory, Riyadh, Saudi Arabia
| | - Fahd Alzahrani
- Ministry of Health, Riyadh Regional Laboratory, Riyadh, Saudi Arabia
| | - Mohammed O Asiri
- Ministry of Health, Riyadh Regional Laboratory, Riyadh, Saudi Arabia
| | - Rami Hasan
- King Fahad Medical City, Riyadh, Saudi Arabia
| | - Aref Alamri
- Ministry of Health, Riyadh Regional Laboratory, Riyadh, Saudi Arabia
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Abstract
Global climate change, driven by anthropogenic greenhouse gas emissions, is being particularly felt in Canada, with warming generally greater than in the rest of the world. Continued warming will be accompanied by changes in precipitation, which will vary across the country and seasons, and by increasing climate variability and extreme weather events. Climate change will likely drive the emergence of infectious diseases in Canada by northward spread from the United States and introduction from elsewhere in the world via air and sea transport. Diseases endemic to Canada are also likely to re-emerge. This special issue describes key infectious disease risks associated with climate change. These include emergence of tick-borne diseases in addition to Lyme disease, the possible introduction of exotic mosquito-borne diseases such as malaria and dengue, more epidemics of Canada-endemic vector-borne diseases such as West Nile virus, and increased incidence of foodborne illnesses. Risk is likely to be compounded by an aging population affected by chronic diseases, which results in greater sensitivity to infectious diseases. Identifying emerging disease risks is essential to assess our vulnerability, and a starting point to identify where public health effort is required to reduce the vulnerability and exposure of the Canadian population.
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Ogden NH, Wilson JRU, Richardson DM, Hui C, Davies SJ, Kumschick S, Le Roux JJ, Measey J, Saul WC, Pulliam JRC. Emerging infectious diseases and biological invasions: a call for a One Health collaboration in science and management. ROYAL SOCIETY OPEN SCIENCE 2019; 6:181577. [PMID: 31032015 PMCID: PMC6458372 DOI: 10.1098/rsos.181577] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/18/2019] [Indexed: 05/11/2023]
Abstract
The study and management of emerging infectious diseases (EIDs) and of biological invasions both address the ecology of human-associated biological phenomena in a rapidly changing world. However, the two fields work mostly in parallel rather than in concert. This review explores how the general phenomenon of an organism rapidly increasing in range or abundance is caused, highlights the similarities and differences between research on EIDs and invasions, and discusses shared management insights and approaches. EIDs can arise by: (i) crossing geographical barriers due to human-mediated dispersal, (ii) crossing compatibility barriers due to evolution, and (iii) lifting of environmental barriers due to environmental change. All these processes can be implicated in biological invasions, but only the first defines them. Research on EIDs is embedded within the One Health concept-the notion that human, animal and ecosystem health are interrelated and that holistic approaches encompassing all three components are needed to respond to threats to human well-being. We argue that for sustainable development, biological invasions should be explicitly considered within One Health. Management goals for the fields are the same, and direct collaborations between invasion scientists, disease ecologists and epidemiologists on modelling, risk assessment, monitoring and management would be mutually beneficial.
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Affiliation(s)
- Nick H. Ogden
- National Microbiology Laboratory, Public Health Agency of Canada, Canada
- South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, South Africa
| | - John R. U. Wilson
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont, Cape Town, South Africa
| | - David M. Richardson
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, South Africa
| | - Cang Hui
- Centre for Invasion Biology, Department of Mathematical Sciences, Stellenbosch University, Matieland 7602, South Africa
- Mathematical and Physical Biosciences, African Institute for Mathematical Sciences (AIMS), Muizenberg 7945, South Africa
| | - Sarah J. Davies
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, South Africa
| | - Sabrina Kumschick
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont, Cape Town, South Africa
| | - Johannes J. Le Roux
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, South Africa
- Department of Biological Sciences, Macquarie University, Sydney 2109, Australia
| | - John Measey
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, South Africa
| | - Wolf-Christian Saul
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, South Africa
- Centre for Invasion Biology, Department of Mathematical Sciences, Stellenbosch University, Matieland 7602, South Africa
| | - Juliet R. C. Pulliam
- South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, South Africa
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