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Chiara M, D’Erchia AM, Gissi C, Manzari C, Parisi A, Resta N, Zambelli F, Picardi E, Pavesi G, Horner DS, Pesole G. Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities. Brief Bioinform 2021; 22:616-630. [PMID: 33279989 PMCID: PMC7799330 DOI: 10.1093/bib/bbaa297] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/27/2020] [Accepted: 10/07/2020] [Indexed: 12/31/2022] Open
Abstract
Various next generation sequencing (NGS) based strategies have been successfully used in the recent past for tracing origins and understanding the evolution of infectious agents, investigating the spread and transmission chains of outbreaks, as well as facilitating the development of effective and rapid molecular diagnostic tests and contributing to the hunt for treatments and vaccines. The ongoing COVID-19 pandemic poses one of the greatest global threats in modern history and has already caused severe social and economic costs. The development of efficient and rapid sequencing methods to reconstruct the genomic sequence of SARS-CoV-2, the etiological agent of COVID-19, has been fundamental for the design of diagnostic molecular tests and to devise effective measures and strategies to mitigate the diffusion of the pandemic. Diverse approaches and sequencing methods can, as testified by the number of available sequences, be applied to SARS-CoV-2 genomes. However, each technology and sequencing approach has its own advantages and limitations. In the current review, we will provide a brief, but hopefully comprehensive, account of currently available platforms and methodological approaches for the sequencing of SARS-CoV-2 genomes. We also present an outline of current repositories and databases that provide access to SARS-CoV-2 genomic data and associated metadata. Finally, we offer general advice and guidelines for the appropriate sharing and deposition of SARS-CoV-2 data and metadata, and suggest that more efficient and standardized integration of current and future SARS-CoV-2-related data would greatly facilitate the struggle against this new pathogen. We hope that our 'vademecum' for the production and handling of SARS-CoV-2-related sequencing data, will contribute to this objective.
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Affiliation(s)
- Matteo Chiara
- molecular biology and bioinformatics at the University of Milan
| | - Anna Maria D’Erchia
- molecular biology at the University of Bari and research associate at the Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari
| | - Carmela Gissi
- molecular biology at the University of Bari and research associate at the Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari
| | - Caterina Manzari
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari
| | - Antonio Parisi
- Genetic and Molecular Epidemiology Laboratory at the Experimental Zooprophylactic Institute of Apulia and Basilicata
| | - Nicoletta Resta
- Medical Genetics at the University of Bari. She heads the Laboratory Unit of Medical Genetics and the School of Specialization in Medical Genetics
| | | | - Ernesto Picardi
- molecular biology and bioinformatics at the University of Bari and research associate at the Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari
| | - Giulio Pavesi
- Associate Professor of bioinformatics at the University of Milan (Italy)
| | - David S Horner
- molecular biology and bioinformatics at the University of Milan
| | - Graziano Pesole
- molecular biology at the University of Bari and Research Associate at the Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari
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Shi Z, Li G, Zhang L, Ma M, Jia W. Klebsiella pneumoniae infection inhibits autophagy by alveolar type II epithelial cells. Exp Ther Med 2020; 20:3703-3708. [PMID: 32905119 PMCID: PMC7465052 DOI: 10.3892/etm.2020.9123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 07/21/2020] [Indexed: 12/20/2022] Open
Abstract
To investigate the molecular mechanism underlying the interaction between autophagosomes of alveolar type II epithelial (A549) cells and Klebsiella pneumoniae, an in vitro model of K. pneumoniae-infected A549 cells was established. Western blot analysis and immunofluorescence staining were used to detect the distribution of microtubule-associated protein 1A/1B-light chain 3 (LC3) and the expression of the LC3-phosphatidylethanolamine conjugate (LC3-II). K. pneumoniae-infected A549 cells were treated with different concentrations of an autophagy inhibitor or promoter for different time periods to assess the level of autophagy. Western blot analysis and immunofluorescence staining showed that K. pneumoniae could induce autophagy by A549 cells. With an increase in bacterial concentration and time of infection, autophagy gradually increased. The autophagy inhibitor significantly downregulated, while the promoter upregulated, expression of the autophagy-related protein LC3-II. Autophagy plays an important role in the resistance of alveolar type II epithelial (A549) cells to K. pneumoniae infection.
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Affiliation(s)
- Zhiyun Shi
- Medical Experimental Center, General Hospital of Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China.,Key Laboratory of Ningxia Clinical Pathogenic Microorganisms, Institute of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Gang Li
- Medical Experimental Center, General Hospital of Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China.,Key Laboratory of Ningxia Clinical Pathogenic Microorganisms, Institute of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Lin Zhang
- Department of Laboratory, Institute of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Miao Ma
- Department of Laboratory, Institute of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Wei Jia
- Medical Experimental Center, General Hospital of Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China.,Key Laboratory of Ningxia Clinical Pathogenic Microorganisms, Institute of Clinical Medicine, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
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Ha BTT, Pham Van T, Mirzoev T. <p>Implementation of Health Policy on Establishment of Provincial Center of Diseases Control (CDC) in Vietnam</p>. Healthc Policy 2020; 13:915-926. [PMID: 32801966 PMCID: PMC7406358 DOI: 10.2147/rmhp.s250748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 07/14/2020] [Indexed: 01/17/2023] Open
Abstract
Purpose Methods Results Conclusion
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Affiliation(s)
- Bui Thi Thu Ha
- Hanoi University of Public Health, Hanoi, Vietnam
- Correspondence: Bui Thi Thu Ha Hanoi University of Public Health, No. 1A Duc Thang Road, Duc Thang Ward, North Tu Liem District, Hanoi, VietnamTel +84-0913363603 Email
| | - Tac Pham Van
- Department of Manpower, Ministry of Health, Hanoi, Vietnam
| | - Tolib Mirzoev
- Nuffield Centre for International Health and Development, University of Leeds, Leeds, UK
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Tappero JW, Cassell CH, Bunnell RE, Angulo FJ, Craig A, Pesik N, Dahl BA, Ijaz K, Jafari H, Martin R. US Centers for Disease Control and Prevention and Its Partners' Contributions to Global Health Security. Emerg Infect Dis 2018; 23. [PMID: 29155656 PMCID: PMC5711315 DOI: 10.3201/eid2313.170946] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
To achieve compliance with the revised World Health Organization International Health Regulations (IHR 2005), countries must be able to rapidly prevent, detect, and respond to public health threats. Most nations, however, remain unprepared to manage and control complex health emergencies, whether due to natural disasters, emerging infectious disease outbreaks, or the inadvertent or intentional release of highly pathogenic organisms. The US Centers for Disease Control and Prevention (CDC) works with countries and partners to build and strengthen global health security preparedness so they can quickly respond to public health crises. This report highlights selected CDC global health protection platform accomplishments that help mitigate global health threats and build core, cross-cutting capacity to identify and contain disease outbreaks at their source. CDC contributions support country efforts to achieve IHR 2005 compliance, contribute to the international framework for countering infectious disease crises, and enhance health security for Americans and populations around the world.
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Fitzmaurice AG, Mahar M, Moriarty LF, Bartee M, Hirai M, Li W, Gerber AR, Tappero JW, Bunnell R. Contributions of the US Centers for Disease Control and Prevention in Implementing the Global Health Security Agenda in 17 Partner Countries. Emerg Infect Dis 2018; 23. [PMID: 29155676 PMCID: PMC5711326 DOI: 10.3201/eid2313.170898] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The Global Health Security Agenda (GHSA), a partnership of nations, international organizations, and civil society, was launched in 2014 with a mission to build countries’ capacities to respond to infectious disease threats and to foster global compliance with the International Health Regulations (IHR 2005). The US Centers for Disease Control and Prevention (CDC) assists partner nations to improve IHR 2005 capacities and achieve GHSA targets. To assess progress through these CDC-supported efforts, we analyzed country activity reports dating from April 2015 through March 2017. Our analysis shows that CDC helped 17 Phase I countries achieve 675 major GHSA accomplishments, particularly in the cross-cutting areas of public health surveillance, laboratory systems, workforce development, and emergency response management. CDC’s engagement has been critical to these accomplishments, but sustained support is needed until countries attain IHR 2005 capacities, thereby fostering national and regional health protection and ensuring a world safer and more secure from global health threats.
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Abstract
In the U.S., migration has been documented to affect the prevalence of infectious disease. As a mitigation entity, border security has been recorded by numerous scholarly works as being essential to the support of the health of the U.S. population. Consequently, the lack of current health care monitoring of the permeable U.S. border places the U.S. population at risk in the broad sectors of infectious disease and interpersonal violence. Visualizing border security in the context of public health mitigation has significant potential to protect migrant health as well as that of all populations on both sides of the border. Examples of how commonly this philosophy is held can be found in the expansive use of security-focused terms regarding public health. Using tools such as GIS to screen for disease in people before their entrance into a nation would be more efficient and ethical than treating patients once they have entered a population and increased the impact on the healthcare system. (Disaster Med Public Health Preparedness. 2018;12:554-562).
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Tappero JW, Cassell CH, Bunnell RE, Angulo FJ, Craig A, Pesik N, Dahl BA, Ijaz K, Jafari H, Martin R. US Centers for Disease Control and Prevention and Its Partners’ Contributions to Global Health Security. Emerg Infect Dis 2017. [DOI: 10.3201/eid23s1.170946] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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Heymann DL, Chen L, Takemi K, Fidler DP, Tappero JW, Thomas MJ, Kenyon TA, Frieden TR, Yach D, Nishtar S, Kalache A, Olliaro PL, Horby P, Torreele E, Gostin LO, Ndomondo-Sigonda M, Carpenter D, Rushton S, Lillywhite L, Devkota B, Koser K, Yates R, Dhillon RS, Rannan-Eliya RP. Global health security: the wider lessons from the west African Ebola virus disease epidemic. Lancet 2015; 385:1884-901. [PMID: 25987157 PMCID: PMC5856330 DOI: 10.1016/s0140-6736(15)60858-3] [Citation(s) in RCA: 264] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The Ebola virus disease outbreak in West Africa was unprecedented in both its scale and impact. Out of this human calamity has come renewed attention to global health security--its definition, meaning, and the practical implications for programmes and policy. For example, how does a government begin to strengthen its core public health capacities, as demanded by the International Health Regulations? What counts as a global health security concern? In the context of the governance of global health, including WHO reform, it will be important to distil lessons learned from the Ebola outbreak. The Lancet invited a group of respected global health practitioners to reflect on these lessons, to explore the idea of global health security, and to offer suggestions for next steps. Their contributions describe some of the major threats to individual and collective human health, as well as the values and recommendations that should be considered to counteract such threats in the future. Many different perspectives are proposed. Their common goal is a more sustainable and resilient society for human health and wellbeing.
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Affiliation(s)
- David L Heymann
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK; Centre on Global Health Security, London, UK.
| | | | | | - David P Fidler
- Indiana University Maurer School of Law, Bloomington, IN, USA
| | | | | | | | | | - Derek Yach
- Vitality Institute, New York, NY, USA; World Economic Forum Global Agenda Council on Ageing, Geneva, Switzerland
| | | | - Alex Kalache
- International Longevity Centre (ILC) Global Alliance and ILC-Brazil, Rio de Janeiro, Brazil; New York Academy of Medicine, NY, USA; HelpAge International, London, UK
| | - Piero L Olliaro
- UNICEF/UNDP/World Bank/WHO Special Programme on Research and Training in Tropical Diseases (TDR), World Health Organization, Geneva, Switzerland; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Els Torreele
- Public Health Program, Open Society Foundations, New York, NY, USA
| | - Lawrence O Gostin
- O'Neill Institute for National and Global Health Law, Georgetown University Law Center, Washington, DC, USA
| | | | - Daniel Carpenter
- Department of Government, Harvard University, Cambridge, MA, USA
| | - Simon Rushton
- Chatham House, Royal Institute of International Affairs, London, UK; Department of Politics, University of Sheffield, Sheffield, UK
| | - Louis Lillywhite
- Chatham House, Royal Institute of International Affairs, London, UK
| | - Bhimsen Devkota
- Chatham House, Royal Institute of International Affairs, London, UK; Tribhuvan University, Kathmandu, Nepal
| | | | - Rob Yates
- Chatham House, Royal Institute of International Affairs, London, UK
| | - Ranu S Dhillon
- Division of Global Health Equity, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Cambridge, MA, USA; Earth Institute, Columbia University, New York, NY, USA
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Hanefeld J. The US Centers for Disease Control: a crucial actor in global health. Lancet 2014; 384:953. [PMID: 25220968 DOI: 10.1016/s0140-6736(14)61624-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Johanna Hanefeld
- London School of Hygiene and Tropical Medicine, London WC1H 9SH, UK.
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Pandemic preparedness and the Influenza Risk Assessment Tool (IRAT). Curr Top Microbiol Immunol 2014; 385:119-36. [PMID: 25085014 DOI: 10.1007/82_2014_419] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Influenza infections have resulted in millions of deaths and untold millions of illnesses throughout history. Influenza vaccines are the cornerstone of influenza prevention and control. Recommendations are made by the World Health Organization (WHO) 6-9 months in advance of the influenza season regarding what changes, if any, should be made in the formulation of seasonal influenza vaccines. This allows time to manufacture, test, distribute, and administer vaccine prior to the beginning of the influenza season. At the same time experts also consider which viruses not currently circulating in the human population, but with pandemic potential, pose the greatest risk to public health. Experts may conclude that one or more of these viruses are of enough concern to warrant development of a high-growth reassortant candidate vaccine virus. Subsequently, national authorities may determine that a vaccine should be manufactured, tested in clinical trials, and even stockpiled in some circumstances. The Influenza Risk Assessment Tool (IRAT) was created in an effort to develop a standardized set of elements that could be applied for decision making when evaluating pre-pandemic viruses. The tool is a simple, additive model, based on multi-attribute decision analysis . The ultimate goal is to identify an appropriate candidate vaccine virus and prepare a human vaccine before the virus adapts to infect and efficiently transmit in susceptible human populations. This pre-pandemic preparation allows production of vaccine-a strategy that could save lives and mitigate illness during a pandemic.
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