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Sekalala S, Chatikobo T. Colonialism in the new digital health agenda. BMJ Glob Health 2024; 9:e014131. [PMID: 38413105 PMCID: PMC10900325 DOI: 10.1136/bmjgh-2023-014131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/14/2024] [Indexed: 02/29/2024] Open
Abstract
The advancement of digital technologies has stimulated immense excitement about the possibilities of transforming healthcare, especially in resource-constrained contexts. For many, this rapid growth presents a 'digital health revolution'. While this is true, there are also dangers that the proliferation of digital health in the global south reinforces existing colonialities. Underpinned by the rhetoric of modernity, rationality and progress, many countries in the global south are pushing for digital health transformation in ways that ignore robust regulation, increase commercialisation and disregard local contexts, which risks heightened inequalities. We propose a decolonial agenda for digital health which shifts the liner and simplistic understanding of digital innovation as the magic wand for health justice. In our proposed approach, we argue for both conceptual and empirical reimagination of digital health agendas in ways that centre indigenous and intersectional theories. This enables the prioritisation of local contexts and foregrounds digital health regulatory infrastructures as a possible site of both struggle and resistance. Our decolonial digital health agenda critically reflects on who is benefitting from digital health systems, centres communities and those with lived experiences and finally introduces robust regulation to counter the social harms of digitisation.
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Acharya N, Hess S, Kuchler H, Lafontaine J, Malan M, Rai T, van der Westhuizen HM. Negotiating the media's role during pandemics: recommendations for future preparedness. BMJ Glob Health 2023; 8:e014467. [PMID: 38084480 PMCID: PMC10711869 DOI: 10.1136/bmjgh-2023-014467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 11/12/2023] [Indexed: 12/18/2023] Open
Affiliation(s)
- Nina Acharya
- Department of Social Policy and Intervention, University of Oxford, Oxford, UK
| | | | | | - Jesse Lafontaine
- Blavatnik School of Government, University of Oxford, Oxford, UK
| | - Mia Malan
- Bhekisisa Centre for Health Journalism, Johannesburg, South Africa
| | - Tanvi Rai
- Nuffield Department of Primary Care Health Sciences, Oxford University, Oxford, UK
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3
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Tang CY, Li T, Haynes TA, McElroy JA, Ritter D, Hammer RD, Sampson C, Webby R, Hang J, Wan XF. Rural populations facilitated early SARS-CoV-2 evolution and transmission in Missouri, USA. NPJ VIRUSES 2023; 1:7. [PMID: 38186942 PMCID: PMC10769004 DOI: 10.1038/s44298-023-00005-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/20/2023] [Indexed: 01/09/2024]
Abstract
In the United States, rural populations comprise 60 million individuals and suffered from high COVID-19 disease burdens. Despite this, surveillance efforts are biased toward urban centers. Consequently, how rurally circulating SARS-CoV-2 viruses contribute toward emerging variants remains poorly understood. In this study, we aim to investigate the role of rural communities in the evolution and transmission of SARS-CoV-2 during the early pandemic. We collected 544 urban and 435 rural COVID-19-positive respiratory specimens from an overall vaccine-naïve population in Southwest Missouri between July and December 2020. Genomic analyses revealed 53 SARS-CoV-2 Pango lineages in our study samples, with 14 of these lineages identified only in rural samples. Phylodynamic analyses showed that frequent bi-directional diffusions occurred between rural and urban communities in Southwest Missouri, and that four out of seven Missouri rural-origin lineages spread globally. Further analyses revealed that the nucleocapsid protein (N):R203K/G204R paired substitutions, which were detected disproportionately across multiple Pango lineages, were more associated with urban than rural sequences. Positive selection was detected at N:204 among rural samples but was not evident in urban samples, suggesting that viruses may encounter distinct selection pressures in rural versus urban communities. This study demonstrates that rural communities may be a crucial source of SARS-CoV-2 evolution and transmission, highlighting the need to expand surveillance and resources to rural populations for COVID-19 mitigation.
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Affiliation(s)
- Cynthia Y. Tang
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA
- Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
- These authors contributed equally: Cynthia Y. Tang, Tao Li
| | - Tao Li
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- These authors contributed equally: Cynthia Y. Tang, Tao Li
| | - Tricia A. Haynes
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA
- Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Jane A. McElroy
- Family and Community Medicine, University of Missouriś, Columbia, MO, USA
| | - Detlef Ritter
- Anatomic Pathology & Clinical Pathology, University of Missouri, Columbia, MO, USA
| | - Richard D. Hammer
- Anatomic Pathology & Clinical Pathology, University of Missouri, Columbia, MO, USA
| | | | - Richard Webby
- Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Xiu-Feng Wan
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA
- Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA
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4
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Silva DS, Smith MJ. Data Sharing During Pandemics: Reciprocity, Solidarity, and Limits to Obligations. JOURNAL OF BIOETHICAL INQUIRY 2023; 20:667-672. [PMID: 37440154 PMCID: PMC10942926 DOI: 10.1007/s11673-023-10251-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/03/2023] [Indexed: 07/14/2023]
Abstract
South Africa shared with the world the warning of a new strain of SARS-CoV2, Omicron, in November 2021. As a result, many high-income countries (HICs) instituted complete travel bans on persons leaving South Africa and other neighbouring countries. These bans were unnecessary from a scientific standpoint, and they ran counter to the International Health Regulations. In short, South Africa was penalized for sharing data. Data sharing during pandemics is commonly justified by appeals to solidarity. In this paper, we argue that solidarity is, at best, an aspirational ideal to work toward but that it cannot ground an obligation to share data. Instead, low-and-middle income countries (LIMCs) should be guided by the principle of reciprocity, which states that we ought to return good for good received. Reciprocity is necessarily a conditional principle. LMICs, we argue, should only share data during future pandemics on the condition that HICs provide enforceable assurances that the benefits of data sharing will be equitably distributed and that LMICs won't be penalized for sharing information.
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Affiliation(s)
- Diego S Silva
- Sydney Health Ethics, School of Public Health, University of Sydney, Edward Ford Building, A27 Fisher Rd, Camperdown, New South Wales, 2006, Australia.
| | - Maxwell J Smith
- School of Health Studies & Rotman Institute of Philosophy, Western University, 1151 Richmond Street, London, Ontario, N6A 3K7, Canada
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5
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Wang Z, Wu P, Wang L, Li B, Liu Y, Ge Y, Wang R, Wang L, Tan H, Wu CH, Laine M, Salje H, Song H. Marginal effects of public health measures and COVID-19 disease burden in China: A large-scale modelling study. PLoS Comput Biol 2023; 19:e1011492. [PMID: 37721947 PMCID: PMC10538769 DOI: 10.1371/journal.pcbi.1011492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/28/2023] [Accepted: 09/05/2023] [Indexed: 09/20/2023] Open
Abstract
China had conducted some of the most stringent public health measures to control the spread of successive SARS-CoV-2 variants. However, the effectiveness of these measures and their impacts on the associated disease burden have rarely been quantitatively assessed at the national level. To address this gap, we developed a stochastic age-stratified metapopulation model that incorporates testing, contact tracing and isolation, based on 419 million travel movements among 366 Chinese cities. The study period for this model began from September 2022. The COVID-19 disease burden was evaluated, considering 8 types of underlying health conditions in the Chinese population. We identified the marginal effects between the testing speed and reduction in the epidemic duration. The findings suggest that assuming a vaccine coverage of 89%, the Omicron-like wave could be suppressed by 3-day interval population-level testing (PLT), while it would become endemic with 4-day interval PLT, and without testing, it would result in an epidemic. PLT conducted every 3 days would not only eliminate infections but also keep hospital bed occupancy at less than 29.46% (95% CI, 22.73-38.68%) of capacity for respiratory illness and ICU bed occupancy at less than 58.94% (95% CI, 45.70-76.90%) during an outbreak. Furthermore, the underlying health conditions would lead to an extra 2.35 (95% CI, 1.89-2.92) million hospital admissions and 0.16 (95% CI, 0.13-0.2) million ICU admissions. Our study provides insights into health preparedness to balance the disease burden and sustainability for a country with a population of billions.
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Affiliation(s)
- Zengmiao Wang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Peiyi Wu
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Lin Wang
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Bingying Li
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Yonghong Liu
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Yuxi Ge
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Ruixue Wang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Ligui Wang
- Center of Disease Control and Prevention, PLA, Beijing, China
| | - Hua Tan
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chieh-Hsi Wu
- Mathematical Sciences, University of Southampton, Southampton, United Kingdom
| | - Marko Laine
- Finnish Meteorological Institute, Meteorological Research Unit, Helsinki, Finland
| | - Henrik Salje
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Hongbin Song
- Center of Disease Control and Prevention, PLA, Beijing, China
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6
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Yang L, Wang Z, Wang L, Vrancken B, Wang R, Wei Y, Rader B, Wu CH, Chen Y, Wu P, Li B, Lin Q, Dong L, Cui Y, Shi M, Brownstein JS, Stenseth NC, Yang R, Tian H. Association of vaccination, international travel, public health and social measures with lineage dynamics of SARS-CoV-2. Proc Natl Acad Sci U S A 2023; 120:e2305403120. [PMID: 37549270 PMCID: PMC10434302 DOI: 10.1073/pnas.2305403120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/07/2023] [Indexed: 08/09/2023] Open
Abstract
Continually emerging SARS-CoV-2 variants of concern that can evade immune defenses are driving recurrent epidemic waves of COVID-19 globally. However, the impact of measures to contain the virus and their effect on lineage diversity dynamics are poorly understood. Here, we jointly analyzed international travel, public health and social measures (PHSM), COVID-19 vaccine rollout, SARS-CoV-2 lineage diversity, and the case growth rate (GR) from March 2020 to September 2022 across 63 countries. We showed that despite worldwide vaccine rollout, PHSM are effective in mitigating epidemic waves and lineage diversity. An increase of 10,000 monthly travelers in a single country-to-country route between endemic countries corresponds to a 5.5% (95% CI: 2.9 to 8.2%) rise in local lineage diversity. After accounting for PHSM, natural immunity from previous infections, and waning immunity, we discovered a negative association between the GR of cases and adjusted vaccine coverage (AVC). We also observed a complex relationship between lineage diversity and vaccine rollout. Specifically, we found a significant negative association between lineage diversity and AVC at both low and high levels but not significant at the medium level. Our study deepens the understanding of population immunity and lineage dynamics for future pandemic preparedness and responsiveness.
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Affiliation(s)
- Lingyue Yang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing100875, China
| | - Zengmiao Wang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing100875, China
| | - Lin Wang
- Department of Genetics, University of Cambridge, CambridgeCB2 3EH, United Kingdom
| | - Bram Vrancken
- Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, KU Leuven, Leuven3000, Belgium
- Spatial Epidemiology Lab, Université Libre de Bruxelles, 1050Bruxelles, Belgium
| | - Ruixue Wang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing100875, China
| | - Yuanlong Wei
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing100875, China
| | - Benjamin Rader
- Computational Epidemiology Lab, Boston Children’s Hospital, Boston, MA02215
- Department of Epidemiology, Boston University School of Public Health, Boston, MA02118
| | - Chieh-Hsi Wu
- Mathematical Sciences, University of Southampton, SouthamptonSO17 1BJ, United Kingdom
| | - Yuyang Chen
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing100875, China
| | - Peiyi Wu
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing100875, China
| | - Bingying Li
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing100875, China
| | - Qiushi Lin
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing100875, China
| | - Lu Dong
- College of Life Sciences, Beijing Normal University, Beijing100875, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing100071, China
| | - Mang Shi
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen518107, China
| | - John S. Brownstein
- Spatial Epidemiology Lab, Université Libre de Bruxelles, 1050Bruxelles, Belgium
- Harvard Medical School, Harvard University, Boston, MA02115
| | - Nils Chr. Stenseth
- The Centre for Pandemics and One-Health Research, Sustainable Health Unit, Faculty of Medicine, University of Oslo, Oslo0316, Norway
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo0316, Norway
- Vanke School of Public Health, Tsinghua University, Beijing100084, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing100071, China
| | - Huaiyu Tian
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing100875, China
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7
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Tegally H, Wilkinson E, Tsui JLH, Moir M, Martin D, Brito AF, Giovanetti M, Khan K, Huber C, Bogoch II, San JE, Poongavanan J, Xavier JS, Candido DDS, Romero F, Baxter C, Pybus OG, Lessells RJ, Faria NR, Kraemer MUG, de Oliveira T. Dispersal patterns and influence of air travel during the global expansion of SARS-CoV-2 variants of concern. Cell 2023; 186:3277-3290.e16. [PMID: 37413988 PMCID: PMC10247138 DOI: 10.1016/j.cell.2023.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 07/08/2023]
Abstract
The Alpha, Beta, and Gamma SARS-CoV-2 variants of concern (VOCs) co-circulated globally during 2020 and 2021, fueling waves of infections. They were displaced by Delta during a third wave worldwide in 2021, which, in turn, was displaced by Omicron in late 2021. In this study, we use phylogenetic and phylogeographic methods to reconstruct the dispersal patterns of VOCs worldwide. We find that source-sink dynamics varied substantially by VOC and identify countries that acted as global and regional hubs of dissemination. We demonstrate the declining role of presumed origin countries of VOCs in their global dispersal, estimating that India contributed <15% of Delta exports and South Africa <1%-2% of Omicron dispersal. We estimate that >80 countries had received introductions of Omicron within 100 days of its emergence, associated with accelerated passenger air travel and higher transmissibility. Our study highlights the rapid dispersal of highly transmissible variants, with implications for genomic surveillance along the hierarchical airline network.
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Affiliation(s)
- Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | | | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Darren Martin
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Marta Giovanetti
- Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil; Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy
| | - Kamran Khan
- BlueDot, Toronto, ON, Canada; Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, ON, Canada
| | | | - Isaac I Bogoch
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, ON, Canada
| | - James Emmanuel San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jenicca Poongavanan
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Joicymara S Xavier
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Institute of Agricultural Sciences, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brazil
| | - Darlan da S Candido
- MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Filipe Romero
- MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, UK; Pandemic Sciences Institute, University of Oxford, Oxford, UK; Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK
| | - Richard J Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno R Faria
- Department of Biology, University of Oxford, Oxford, UK; MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Jameel Institute, School of Public Health, Imperial College London, London, UK; Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Moritz U G Kraemer
- Department of Biology, University of Oxford, Oxford, UK; Pandemic Sciences Institute, University of Oxford, Oxford, UK.
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa; Department of Global Health, University of Washington, Seattle, WA, USA.
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8
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Oladejo SO, Watson LR, Watson BW, Rajaratnam K, Kotze MJ, Kell DB, Pretorius E. Data sharing: A Long COVID perspective, challenges, and road map for the future. S AFR J SCI 2023; 119:73-80. [PMID: 39324014 PMCID: PMC11423650 DOI: 10.17159/sajs.2023/14719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 03/27/2023] [Indexed: 09/27/2024] Open
Abstract
'Long COVID' is the term used to describe the phenomenon in which patients who have survived a COVID-19 infection continue to experience prolonged SARS-CoV-2 symptoms. Millions of people across the globe are affected by Long COVID. Solving the Long COVID conundrum will require drawing upon the lessons of the COVID-19 pandemic, during which thousands of experts across diverse disciplines such as epidemiology, genomics, medicine, data science, and computer science collaborated, sharing data and pooling resources to attack the problem from multiple angles. Thus far, there has been no global consensus on the definition, diagnosis, and most effective treatment of Long COVID. In this work, we examine the possible applications of data sharing and data science in general with a view to, ultimately, understand Long COVID in greater detail and hasten relief for the millions of people experiencing it. We examine the literature and investigate the current state, challenges, and opportunities of data sharing in Long COVID research.
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Affiliation(s)
- Sunday O Oladejo
- School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Liam R Watson
- School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada
| | - Bruce W Watson
- School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Kanshukan Rajaratnam
- School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Maritha J Kotze
- Division of Chemical Pathology, Department of Pathology, National Health Laboratory Service, Tygerberg Hospital & Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Douglas B Kell
- Department of Biochemistry and Systems Biology, Faculty of Health and Life Sciences, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, South Africa
| | - Etheresia Pretorius
- Department of Biochemistry and Systems Biology, Faculty of Health and Life Sciences, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, South Africa
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9
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Hakim AJ, Victory KR, Summers A, Jalloh MF, Richter P, Bennett SD, Henao OL, Marston B. Toward a Continuum of Measures to Mitigate Primary and Secondary Impacts of COVID-19 and Other Public Health Emergencies. Popul Health Manag 2023; 26:107-112. [PMID: 36940310 DOI: 10.1089/pop.2022.0263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2023] Open
Abstract
The global COVID-19 response focused heavily on nonpharmaceutical interventions (NPIs) until vaccines became available. Even where vaccination coverage is low, over time governments have become increasingly reluctant to use NPIs. Inequities in vaccine and treatment accessibility and coverage, differences in vaccine effectiveness, waning immunity, and immune-escape variants of concern of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reinforce the long-term need for mitigation. Initially, the concept of NPIs, and mitigation more broadly, was focused on prevention of SARS-CoV-2 transmission; however, mitigation can and has done more than prevent transmission. It has been used to address the clinical dimensions of the pandemic as well. The authors propose an expanded conceptualization of mitigation that encompasses a continuum of community and clinical mitigation measures that can help reduce infection, illness, and death from COVID-19. It can further help governments balance these efforts and address the disruptions in essential health services, increased violence, adverse mental health outcomes, and orphanhood precipitated by the pandemic and by NPIs themselves. The COVID-19 pandemic response revealed the benefits of a holistic and layered mitigation approach to public health emergencies from the outset. Lessons learned can inform the next phases of the current pandemic response and planning for future public health emergencies.
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Affiliation(s)
- Avi J Hakim
- CDC COVID-19 Response International Task Force, Atlanta, Georgia, USA
| | - Kerton R Victory
- CDC COVID-19 Response International Task Force, Atlanta, Georgia, USA
| | - Aimee Summers
- CDC COVID-19 Response International Task Force, Atlanta, Georgia, USA
| | | | - Patricia Richter
- CDC COVID-19 Response International Task Force, Atlanta, Georgia, USA
| | - Sarah D Bennett
- CDC COVID-19 Response International Task Force, Atlanta, Georgia, USA
| | - Olga L Henao
- CDC COVID-19 Response International Task Force, Atlanta, Georgia, USA
| | - Barbara Marston
- CDC COVID-19 Response International Task Force, Atlanta, Georgia, USA
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10
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Tegally H, Khan K, Huber C, de Oliveira T, Kraemer MUG. Shifts in global mobility dictate the synchrony of SARS-CoV-2 epidemic waves. J Travel Med 2022; 29:taac134. [PMID: 36367200 PMCID: PMC9793401 DOI: 10.1093/jtm/taac134] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND Human mobility changed in unprecedented ways during the SARS-CoV-2 pandemic. In March and April 2020, when lockdowns and large travel restrictions began in most countries, global air-travel almost entirely halted (92% decrease in commercial global air travel in the months between February and April 2020). Initial recovery in global air travel started around July 2020 and subsequently nearly tripled between May and July 2021. Here, we aim to establish a preliminary link between global mobility patterns and the synchrony of SARS-CoV-2 epidemic waves across the world. METHODS We compare epidemic peaks and human global mobility in two time periods: November 2020 to February 2021 (when just over 70 million passengers travelled) and November 2021 to February 2022 (when more than 200 million passengers travelled). We calculate the time interval during which continental epidemic peaks occurred for both of these time periods, and we calculate the pairwise correlations of epidemic waves between all pairs of countries for the same time periods. RESULTS We find that as air travel increases at the end of 2021, epidemic peaks around the world are more synchronous with one another, both globally and regionally. Continental epidemic peaks occur globally within a 20 day interval at the end of 2021 compared with 73 days at the end of 2020, and epidemic waves globally are more correlated with one another at the end of 2021. CONCLUSIONS This suggests that the rebound in human mobility dictates the synchrony of global and regional epidemic waves. In line with theoretical work, we show that in a more connected world, epidemic dynamics are more synchronized.
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Affiliation(s)
- Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Kamran Khan
- BlueDot, Toronto, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Canada
| | | | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Moritz U G Kraemer
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
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11
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Fischer C, Maponga TG, Yadouleton A, Abílio N, Aboce E, Adewumi P, Afonso P, Akorli J, Andriamandimby SF, Anga L, Ashong Y, Beloufa MA, Bensalem A, Birtles R, Boumba ALM, Bwanga F, Chaponda M, Chibukira P, Chico RM, Chileshe J, Chongwe G, Cissé A, D'Alessandro U, de Lamballerie XN, de Morais JFM, Derrar F, Dia N, Diarra Y, Doumbia L, Drosten C, Dussart P, Echodu R, Eggers Y, Eloualid A, Faye O, Feldt T, Frühauf A, Halatoko A, Ilouga PV, Ismael N, Jambou R, Jarju S, Kamprad A, Katowa B, Kayiwa J, King'wara L, Koita O, Lacoste V, Lagare A, Landt O, Lekana-Douki SE, Lekana-Douki JB, Iipumbu E, Loemba H, Lutwama J, Mamadou S, Maman I, Manyisa B, Martinez PA, Matoba J, Mhuulu L, Moreira-Soto A, Mwangi J, N Dilimabaka N, Nassuna CA, Ndiath MO, Nepolo E, Njouom R, Nourlil J, Nyanjom SG, Odari EO, Okeng A, Ouoba JB, Owusu M, Owusu Donkor I, Phadu KK, Phillips RO, Preiser W, Ruhanya V, Salah F, Salifou S, Sall AA, Sylverken AA, Tagnouokam-Ngoupo PA, Tarnagda Z, Tchikaya FO, Tufa TB, Drexler JF. RETRACTED: Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa. Science 2022; 378:eadd8737. [PMID: 36454863 DOI: 10.1126/science.add8737] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The geographic and evolutionary origins of the SARS-CoV-2 Omicron variant (BA.1), which was first detected mid-November 2021 in Southern Africa, remain unknown. We tested 13,097 COVID-19 patients sampled between mid-2021 to early 2022 from 22 African countries for BA.1 by real-time RT-PCR. By November-December 2021, BA.1 had replaced the Delta variant in all African sub-regions following a South-North gradient, with a peak Rt of 4.1. Polymerase chain reaction and near-full genome sequencing data revealed genetically diverse Omicron ancestors already existed across Africa by August 2021. Mutations, altering viral tropism, replication and immune escape, gradually accumulated in the spike gene. Omicron ancestors were therefore present in several African countries months before Omicron dominated transmission. These data also indicate that travel bans are ineffective in the face of undetected and widespread infection.
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Affiliation(s)
- Carlo Fischer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Tongai Gibson Maponga
- Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa
| | - Anges Yadouleton
- Laboratoire dés fievres hemorragiques virales de Cotonou, Akpakpa, Benin
| | - Nuro Abílio
- Instituto Nacional de Saúde, Maputo, Mozambique
| | | | - Praise Adewumi
- Laboratoire dés fievres hemorragiques virales de Cotonou, Akpakpa, Benin
| | - Pedro Afonso
- Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola
| | - Jewelna Akorli
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - Latifa Anga
- Institut Pasteur du Maroc, Casablanca, Morocco
| | - Yvonne Ashong
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - Aicha Bensalem
- Institut Pasteur of Algeria, National Influenza Centre, Sidi-Fredj, Algeria
| | - Richard Birtles
- Gulu University Multifunctional Research Laboratories, Gulu, Uganda.,School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Anicet Luc Magloire Boumba
- Faculty of Health Sciences, Marien Ngouabi University, Pointe-Noire, Congo.,Molecular Diagnostic Laboratory HDL, Pointe-Noire, Congo
| | - Freddie Bwanga
- MBN Clinical Laboratories, Kampala, Uganda.,Makerere University College of Health Sciences, Kampala, Uganda
| | - Mike Chaponda
- Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia
| | - Paradzai Chibukira
- National Virology Laboratory, Faculty of Medicine and Health Sciences, University of Zimbabwe, Avondale, Zimbabwe
| | | | - Justin Chileshe
- Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia
| | - Gershom Chongwe
- Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia
| | - Assana Cissé
- Laboratoire National de Référence-Grippes, Ouagadougou, Burkina Faso
| | - Umberto D'Alessandro
- Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | | | | | - Fawzi Derrar
- Institut Pasteur of Algeria, National Influenza Centre, Sidi-Fredj, Algeria
| | - Ndongo Dia
- Institut Pasteur de Dakar (IPD), Dakar, Senegal
| | - Youssouf Diarra
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Lassina Doumbia
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Christian Drosten
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany.,German Centre for Infection Research (DZIF), associated Partner Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Richard Echodu
- Gulu University Multifunctional Research Laboratories, Gulu, Uganda
| | - Yannik Eggers
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia.,Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | | | - Torsten Feldt
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia.,Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Anna Frühauf
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | | | | | | | - Ronan Jambou
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | - Sheikh Jarju
- Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - Antje Kamprad
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Ben Katowa
- Macha Research Trust, Choma, Zambia.,School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - John Kayiwa
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Leonard King'wara
- National Public Health Reference Laboratory, Ministry of Health, Nairobi, Kenya
| | - Ousmane Koita
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | | | - Adamou Lagare
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | | | | | | | - Etuhole Iipumbu
- School of Medicine, University of Namibia, Windhoek, Namibia
| | - Hugues Loemba
- Molecular Diagnostic Laboratory HDL, Pointe-Noire, Congo.,Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Santou Mamadou
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | | | - Brendon Manyisa
- National Virology Laboratory, Faculty of Medicine and Health Sciences, University of Zimbabwe, Avondale, Zimbabwe
| | - Pedro A Martinez
- Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola
| | - Japhet Matoba
- Macha Research Trust, Choma, Zambia.,School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Lusia Mhuulu
- School of Medicine, University of Namibia, Windhoek, Namibia
| | - Andres Moreira-Soto
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Judy Mwangi
- Gulu University Multifunctional Research Laboratories, Gulu, Uganda.,School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Nadine N Dilimabaka
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | | | - Mamadou Ousmane Ndiath
- Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - Emmanuel Nepolo
- School of Medicine, University of Namibia, Windhoek, Namibia
| | | | | | - Steven Ger Nyanjom
- School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Eddy Okoth Odari
- School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | | | | | - Michael Owusu
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Irene Owusu Donkor
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Karabo Kristen Phadu
- Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa
| | - Richard Odame Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Wolfgang Preiser
- Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa.,National Health Laboratory Service Tygerberg Business Unit, Cape Town, South Africa
| | - Vurayai Ruhanya
- National Virology Laboratory, Faculty of Medicine and Health Sciences, University of Zimbabwe, Avondale, Zimbabwe
| | | | | | | | - Augustina Angelina Sylverken
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana.,Department of Theoretical and Applied Biology, KNUST, Kumasi, Ghana
| | | | - Zekiba Tarnagda
- Laboratoire National de Référence-Grippes, Ouagadougou, Burkina Faso
| | | | - Tafese Beyene Tufa
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia.,Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jan Felix Drexler
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany.,German Centre for Infection Research (DZIF), associated Partner Charité-Universitätsmedizin Berlin, Berlin, Germany
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12
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Nsanzimana S, Rawat A, Wilson LA, Forrest JI, Reis G, Ramagopalan S, Muyembe-Tamfum JJ, Ntoumi F, Zumla A, Sow PS, Nachega JB, Binagwaho A, Dybul M, Mills EJ. Toward a New Paradigm of North-South and South-South Partnerships for Pandemic Preparedness: Lessons Learned from COVID-19 and Other Outbreaks. Am J Trop Med Hyg 2022; 107:1162-1165. [PMID: 36375450 PMCID: PMC9768281 DOI: 10.4269/ajtmh.22-0466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
COVID-19 underscores the need to reimagine North-South partnerships and redefine best practices for building public health and research capacity to address emergent health threats and pandemic preparedness in low- and-middle income countries (LMICs). Historically, outbreak and emergency responses have failed to ensure that the Global South has the autonomy and capacity to respond to public health threats in a timely and equitable manner. The COVID-19 response, however, has demonstrated that innovations and solutions in the Global South can not only fill resource and capacity gaps in LMICs but can also provide solutions to challenges globally. These innovations offer valuable lessons about strengthening local manufacturing capacity to produce essential diagnostic, treatment, and prevention tools; implementing high-quality research studies; expanding laboratory and research capacity; and promoting effective cooperation and governance. We discuss specific examples of capacity-building from Rwanda, South Africa, and Senegal. To fulfill promises made to the Global South during the COVID-19 pandemic, restore and resume health service delivery, and effectively prevent and respond to the next health threat, we need to prioritize equitable access to local manufacturing of basic health tools while building health systems capacities in the Global South.
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Affiliation(s)
- Sabin Nsanzimana
- University Teaching Hospital, Butare, Rwanda;,University of Global Health Equity, Rwanda
| | - Angeli Rawat
- Department of Health Research Methods, Evidence and Impact, Faculty of Health Sciences, McMaster University, Hamilton, Canada;,University of British Columbia, Vancouver, Canada
| | - Lindsay A. Wilson
- University of British Columbia, Vancouver, Canada;,Platform Life Sciences, Vancouver, Canada
| | - Jamie I. Forrest
- University of British Columbia, Vancouver, Canada;,Platform Life Sciences, Vancouver, Canada;,Department of Real World and Advanced Analytics, Vancouver, Cytel, Vancouver, Canada
| | - Gilmar Reis
- Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Francine Ntoumi
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of Congo;,Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Alimuddin Zumla
- Division of Infection and Immunity, Centre for Clinical Microbiology, University College London;,NIHR Biomedical Research Centre, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Papa Salif Sow
- Faculte de Medecine Service des Maladies Infectieuses, Universite Cheikh Anta Diop Dakar, Senegal
| | - Jean B. Nachega
- Department of Medicine, Division of Infectious Diseases, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa;,Departments of Epidemiology and International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland;,Departments of Epidemiology, Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania
| | | | - Mark Dybul
- Center for Global Health Practice and Impact, Georgetown University, Washington, DC
| | - Edward J. Mills
- Department of Health Research Methods, Evidence and Impact, Faculty of Health Sciences, McMaster University, Hamilton, Canada;,Platform Life Sciences, Vancouver, Canada;,Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, Brazil;,Address correspondence to Edward J. Mills, Department of Health Research Methods, Evidence, and Impact, Faculty of Health Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4L8, Canada. E-mail:
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13
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Moodley K, Cengiz N, Domingo A, Nair G, Obasa AE, Lessells RJ, de Oliveira T. Ethics and governance challenges related to genomic data sharing in southern Africa: the case of SARS-CoV-2. Lancet Glob Health 2022; 10:e1855-e1859. [PMID: 36309034 PMCID: PMC9826954 DOI: 10.1016/s2214-109x(22)00417-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 11/17/2022]
Abstract
Data sharing in research is fraught with controversy. Academic success is premised on competitive advantage, with research teams protecting their research findings until publication. Research funders, by contrast, often require data sharing. Beyond traditional research and funding requirements, surveillance data have become contentious. Public health emergencies involving pathogens require intense genomic surveillance efforts and call for the rapid sharing of data on the basis of public interest. Under these circumstances, timely sharing of data becomes a matter of scientific integrity. During the COVID-19 pandemic, the transformative potential of genomic pathogen data sharing became obvious and advanced the debate on data sharing. However, when the genomic sequencing data of the omicron (B.1.1.529) variant was shared and announced by scientists in southern Africa, various challenges arose, including travel bans. The scientific, economic, and moral impact was catastrophic. Yet, travel restrictions failed to mitigate the spread of the variant already present in countries outside Africa. Public perceptions of the negative effect of data sharing are detrimental to the willingness of research participants to consent to sharing data in postpandemic research and future pandemics. Global health governance organisations have an important role in developing guidance on responsible sharing of genomic pathogen data in public health emergencies.
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Affiliation(s)
- Keymanthri Moodley
- Centre for Medical Ethics and Law, Faculty of Medicine and Health Sciences Parow, Stellenbosch University, Cape Town, South Africa
| | - Nezerith Cengiz
- Centre for Medical Ethics and Law, Faculty of Medicine and Health Sciences Parow, Stellenbosch University, Cape Town, South Africa
| | - Aneeka Domingo
- Centre for Medical Ethics and Law, Faculty of Medicine and Health Sciences Parow, Stellenbosch University, Cape Town, South Africa
| | - Gonasagrie Nair
- Centre for Medical Ethics and Law, Faculty of Medicine and Health Sciences Parow, Stellenbosch University, Cape Town, South Africa
| | - Adetayo Emmanuel Obasa
- Centre for Medical Ethics and Law, Faculty of Medicine and Health Sciences Parow, Stellenbosch University, Cape Town, South Africa
| | - Richard John Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban, South Africa,London School of Hygiene and Tropical Medicine, University of London, London, UK
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban, South Africa,School for Data Science and Computational Thinking, Faculty of Science, Stellenbosch University, Stellenbosch, South Africa
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14
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Tegally H, Wilkinson E, Martin D, Moir M, Brito A, Giovanetti M, Khan K, Huber C, Bogoch II, San JE, Tsui JLH, Poongavanan J, Xavier JS, Candido DDS, Romero F, Baxter C, Pybus OG, Lessells R, Faria NR, Kraemer MUG, de Oliveira T. Global Expansion of SARS-CoV-2 Variants of Concern: Dispersal Patterns and Influence of Air Travel. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.11.22.22282629. [PMID: 36451885 PMCID: PMC9709793 DOI: 10.1101/2022.11.22.22282629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
In many regions of the world, the Alpha, Beta and Gamma SARS-CoV-2 Variants of Concern (VOCs) co-circulated during 2020-21 and fueled waves of infections. During 2021, these variants were almost completely displaced by the Delta variant, causing a third wave of infections worldwide. This phenomenon of global viral lineage displacement was observed again in late 2021, when the Omicron variant disseminated globally. In this study, we use phylogenetic and phylogeographic methods to reconstruct the dispersal patterns of SARS-CoV-2 VOCs worldwide. We find that the source-sink dynamics of SARS-CoV-2 varied substantially by VOC, and identify countries that acted as global hubs of variant dissemination, while other countries became regional contributors to the export of specific variants. We demonstrate a declining role of presumed origin countries of VOCs to their global dispersal: we estimate that India contributed <15% of all global exports of Delta to other countries and South Africa <1-2% of all global Omicron exports globally. We further estimate that >80 countries had received introductions of Omicron BA.1 100 days after its inferred date of emergence, compared to just over 25 countries for the Alpha variant. This increased speed of global dissemination was associated with a rebound in air travel volume prior to Omicron emergence in addition to the higher transmissibility of Omicron relative to Alpha. Our study highlights the importance of global and regional hubs in VOC dispersal, and the speed at which highly transmissible variants disseminate through these hubs, even before their detection and characterization through genomic surveillance. Highlights Global phylogenetic analysis reveals relationship between air travel and speed of dispersal of SARS-CoV-2 variants of concern (VOCs)Omicron VOC spread to 5x more countries within 100 days of its emergence compared to all other VOCsOnward transmission and dissemination of VOCs Delta and Omicron was primarily from secondary hubs rather than initial country of detection during a time of increased global air travelAnalysis highlights highly connected countries identified as major global and regional exporters of VOCs.
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Affiliation(s)
- Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Darren Martin
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Anderson Brito
- Instituto Todos pela Saúde, São Paulo, São Paulo, Brazil
| | - Marta Giovanetti
- Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy
| | - Kamran Khan
- BlueDot, Toronto, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Canada
| | | | - Isaac I Bogoch
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Canada
| | - James Emmanuel San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | - Jenicca Poongavanan
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Joicymara S Xavier
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Institute of Agricultural Sciences, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brazil
| | - Darlan da S Candido
- MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Filipe Romero
- MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, UK
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Jameel Institute, School of Public Health, Imperial College London, London, UK
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
- Department of Biology, University of Oxford, Oxford, UK
| | - Moritz U G Kraemer
- Department of Biology, University of Oxford, Oxford, UK
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
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15
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Sachs JD, Karim SSA, Aknin L, Allen J, Brosbøl K, Colombo F, Barron GC, Espinosa MF, Gaspar V, Gaviria A, Haines A, Hotez PJ, Koundouri P, Bascuñán FL, Lee JK, Pate MA, Ramos G, Reddy KS, Serageldin I, Thwaites J, Vike-Freiberga V, Wang C, Were MK, Xue L, Bahadur C, Bottazzi ME, Bullen C, Laryea-Adjei G, Ben Amor Y, Karadag O, Lafortune G, Torres E, Barredo L, Bartels JGE, Joshi N, Hellard M, Huynh UK, Khandelwal S, Lazarus JV, Michie S. The Lancet Commission on lessons for the future from the COVID-19 pandemic. Lancet 2022; 400:1224-1280. [PMID: 36115368 PMCID: PMC9539542 DOI: 10.1016/s0140-6736(22)01585-9] [Citation(s) in RCA: 262] [Impact Index Per Article: 131.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/01/2022] [Accepted: 08/11/2022] [Indexed: 02/03/2023]
Affiliation(s)
- Jeffrey D Sachs
- Center for Sustainable Development, Columbia University, New York, NY, United States.
| | - Salim S Abdool Karim
- Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Lara Aknin
- Department of Psychology, Simon Fraser University, Burnaby, BC, Canada
| | - Joseph Allen
- Department of Environmental Health, Harvard T H Chan School of Public Health, Boston, MA, United States
| | | | - Francesca Colombo
- Health Division, Organisation for Economic Co-operation and Development, Paris, France
| | | | | | - Vitor Gaspar
- Fiscal Affairs Department, International Monetary Fund, Washington, DC, United States
| | | | - Andy Haines
- Department of Public Health, Environments and Society, London School of Hygiene and Tropical Medicine, London, UK; Department of Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Peter J Hotez
- National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Phoebe Koundouri
- Department of International and European Economic Studies, Athens University of Economics and Business, Athens, Greece; Department of Technology, Management and Economics, Technical University of Denmark, Kongens Lyngby, Denmark; European Association of Environmental and Resource Economists, Athens, Greece
| | - Felipe Larraín Bascuñán
- Department of Economics and Administration, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jong-Koo Lee
- National Academy of Medicine of Korea, Seoul, Republic of Korea
| | - Muhammad Ali Pate
- Department of Global Health and Population, Harvard T H Chan School of Public Health, Boston, MA, United States
| | | | | | | | - John Thwaites
- Monash Sustainable Development Institute, Monash University, Clayton, VIC, Australia
| | | | - Chen Wang
- National Clinical Research Center for Respiratory Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China; National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | | | - Lan Xue
- Schwarzman College, Tsinghua University, Beijing, China
| | - Chandrika Bahadur
- The Lancet COVID-19 Commission Regional Task Force: India, New Delhi, India
| | - Maria Elena Bottazzi
- National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Chris Bullen
- National Institute for Health Innovation, University of Auckland, Auckland, New Zealand
| | | | - Yanis Ben Amor
- Center for Sustainable Development, Columbia University, New York, NY, United States
| | - Ozge Karadag
- Center for Sustainable Development, Columbia University, New York, NY, United States
| | | | - Emma Torres
- United Nations Sustainable Development Solutions Network, New York, NY, United States
| | - Lauren Barredo
- United Nations Sustainable Development Solutions Network, New York, NY, United States
| | - Juliana G E Bartels
- Center for Sustainable Development, Columbia University, New York, NY, United States
| | - Neena Joshi
- United Nations Sustainable Development Solutions Network, New York, NY, United States
| | | | | | | | - Jeffrey V Lazarus
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Susan Michie
- Centre for Behaviour Change, University College London, London, UK
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16
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Thommana A, Shakya M, Gandhi J, Fung CK, Chain PSG, Maljkovic Berry I, Conte MA. Intrahost SARS-CoV-2 k-mer Identification Method (iSKIM) for Rapid Detection of Mutations of Concern Reveals Emergence of Global Mutation Patterns. Viruses 2022; 14:2128. [PMID: 36298683 PMCID: PMC9609618 DOI: 10.3390/v14102128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/23/2022] [Accepted: 09/24/2022] [Indexed: 11/27/2022] Open
Abstract
Despite unprecedented global sequencing and surveillance of SARS-CoV-2, timely identification of the emergence and spread of novel variants of concern (VoCs) remains a challenge. Several million raw genome sequencing runs are now publicly available. We sought to survey these datasets for intrahost variation to study emerging mutations of concern. We developed iSKIM ("intrahost SARS-CoV-2 k-mer identification method") to relatively quickly and efficiently screen the many SARS-CoV-2 datasets to identify intrahost mutations belonging to lineages of concern. Certain mutations surged in frequency as intrahost minor variants just prior to, or while lineages of concern arose. The Spike N501Y change common to several VoCs was found as a minor variant in 834 samples as early as October 2020. This coincides with the timing of the first detected samples with this mutation in the Alpha/B.1.1.7 and Beta/B.1.351 lineages. Using iSKIM, we also found that Spike L452R was detected as an intrahost minor variant as early as September 2020, prior to the observed rise of the Epsilon/B.1.429/B.1.427 lineages in late 2020. iSKIM rapidly screens for mutations of interest in raw data, prior to genome assembly, and can be used to detect increases in intrahost variants, potentially providing an early indication of novel variant spread.
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Affiliation(s)
- Ashley Thommana
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Montgomery Blair High School, Silver Spring, MD 20901, USA
| | - Migun Shakya
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jaykumar Gandhi
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Christian K. Fung
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Patrick S. G. Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Matthew A. Conte
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
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17
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Pickersgill M, Manda-Taylor L, Niño-Machado N. Pandemic preparedness means policy makers need to work with social scientists. Lancet 2022; 400:547-549. [PMID: 35654080 PMCID: PMC9150864 DOI: 10.1016/s0140-6736(22)00983-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 02/02/2023]
Affiliation(s)
- Martyn Pickersgill
- Usher Institute, Old Medical School, University of Edinburgh, Edinburgh EH8 9AG, UK.
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18
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Thommana A, Shakya M, Gandhi J, Fung CK, Chain PSG, Berry IM, Conte MA. Intrahost SARS-CoV-2 k-mer identification method (iSKIM) for rapid detection of mutations of concern reveals emergence of global mutation patterns. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.08.16.504117. [PMID: 36032969 PMCID: PMC9413717 DOI: 10.1101/2022.08.16.504117] [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] [Indexed: 06/15/2023]
Abstract
Despite unprecedented global sequencing and surveillance of SARS-CoV-2, timely identification of the emergence and spread of novel variants of concern (VoCs) remains a challenge. Several million raw genome sequencing runs are now publicly available. We sought to survey these datasets for intrahost variation to study emerging mutations of concern. We developed iSKIM ("intrahost SARS-CoV-2 k-mer identification method") to relatively quickly and efficiently screen the many SARS-CoV-2 datasets to identify intrahost mutations belonging to lineages of concern. Certain mutations surged in frequency as intrahost minor variants just prior to, or while lineages of concern arose. The Spike N501Y change common to several VoCs was found as a minor variant in 834 samples as early as October 2020. This coincides with the timing of the first detected samples with this mutation in the Alpha/B.1.1.7 and Beta/B.1.351 lineages. Using iSKIM, we also found that Spike L452R was detected as an intrahost minor variant as early as September 2020, prior to the observed rise of the Epsilon/B.1.429/B.1.427 lineages in late 2020. iSKIM rapidly screens for mutations of interest in raw data, prior to genome assembly, and can be used to detect increases in intrahost variants, potentially providing an early indication of novel variant spread.
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Affiliation(s)
- Ashley Thommana
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Montgomery Blair High School, Silver Spring, MD, USA
| | - Migun Shakya
- Los Alamos National Laboratory, Biosecurity and Public Health Group, Bioscience Division, Los Alamos, NM, USA
| | - Jaykumar Gandhi
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Christian K Fung
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Patrick S G Chain
- Los Alamos National Laboratory, Biosecurity and Public Health Group, Bioscience Division, Los Alamos, NM, USA
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Matthew A Conte
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
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19
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Travel in the Time of COVID: A Review of International Travel Health in a Global Pandemic. Curr Infect Dis Rep 2022; 24:129-145. [PMID: 35965881 PMCID: PMC9361911 DOI: 10.1007/s11908-022-00784-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2022] [Indexed: 11/03/2022]
Abstract
Abstract
Purpose of Review
This review critically considers the impact of the COVID-19 pandemic on global travel and the practice of travel medicine, highlights key innovations that have facilitated the resumption of travel, and anticipates how travel medicine providers should prepare for the future of international travel.
Recent Findings
Since asymptomatic transmission of the virus was first recognized in March 2020, extensive efforts have been made to characterize the pattern and dynamics of SARS-CoV-2 transmission aboard commercial aircraft, cruise ships, rail and bus transport, and in mass gatherings and quarantine facilities. Despite the negative impact of further waves of COVID-19 driven by the more transmissible Omicron variant, rapid increases of international tourist arrivals are occurring and modeling anticipates further growth. Mitigation of spread requires an integrated approach that combines masking, physical distancing, improving ventilation, testing, and quarantine. Vaccines and therapeutics have played a significant role in reopening society and accelerating the resumption of travel and further therapeutic innovation is likely.
Summary
COVID-19 is likely to persist as an endemic infection, and surveillance will assume an even more important role. The pandemic has provided an impetus to advance technology for telemedicine, to adopt mobile devices and GPS in contact tracing, and to apply digital applications in research. The future of travel medicine should continue to harness these novel platforms in the clinical, research, and educational arenas.
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20
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Rahimi F, Talebi Bezmin Abadi A, Kamali N. Immediate countermeasures against the monkeypox outbreak. Int J Surg 2022; 104:106733. [PMID: 35760342 PMCID: PMC9533842 DOI: 10.1016/j.ijsu.2022.106733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 06/22/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Farid Rahimi
- Research School of Biology, The Australian National University, Ngunnawal and Ngambri Country, Canberra, Australia
| | - Amin Talebi Bezmin Abadi
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Negin Kamali
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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21
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de Oliveira T. Infectious diseases science in Africa takes a leading place in the world. Lancet 2022; 399:2249-2250. [PMID: 35644165 PMCID: PMC9135374 DOI: 10.1016/s0140-6736(22)00977-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 05/20/2022] [Indexed: 12/19/2022]
Affiliation(s)
- Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, Stellenbosch, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, 4001 Durban, South Africa.
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22
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Moodley K. The ethics behind mandatory COVID-19 vaccination post-Omicron: The South African context. S AFR J SCI 2022. [DOI: 10.17159/sajs.2022/13239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The legitimacy of mandatory vaccine policies is underscored by a public health ethics framework based on the principles of limited autonomy, social justice and the common good. Ideally, vaccine uptake ought to occur on a voluntary basis as an act of solidarity to ensure that everyone is protected. Given that the altruistic approach has failed and vaccine uptake remains sub-optimal in South Africa, in this paper, I argue for vaccine mandates, in a post-Omicron context. This viewpoint is substantiated by several considerations. Healthcare workers are fatigued after 2 years of treating COVID-19 and many are still treating patients with post-viral syndromes, mental health conditions and cardiovascular complications. Health systems remain under pressure as people with non-COVID diseases, neglected during the pandemic, are also now presenting to medical practices and hospitals. Although South Africa has emerged from a relatively less severe fourth wave of COVID-19, there have been many deaths. Vaccine and natural immunity in a relatively young general population has been advantageous. However, the country has a high prevalence of HIV and those who are untreated may not be able to clear the coronavirus easily. Similarly chronic illnesses place many at risk for severe disease from COVID variants, especially if unvaccinated. The future is shrouded in uncertainty. The next variant could be similar to or less severe than Omicron, yet still impact negatively on health systems, education and the economy. Physical distancing is not ideal in many low socio-economic settings, making vaccines an important component of our prevention toolbox. Our safest option now is to ensure that as many South Africans as possible are vaccinated and receive boosters. Vaccine mandates work to achieve this end.
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Affiliation(s)
- Keymanthri Moodley
- Centre for Medical Ethics and Law, Department of Medicine, Stellenbosch University, Cape Town, South Africa
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23
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d'Almeida S. Impact of Vaccine and Immunity Passports in the Context of COVID-19: A Time Series Analysis in Overseas France. Vaccines (Basel) 2022; 10:vaccines10060852. [PMID: 35746459 PMCID: PMC9229335 DOI: 10.3390/vaccines10060852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 12/04/2022] Open
Abstract
(1) Background: By summer 2021, overseas France turned COVID-19 vaccine and immunity certificates into passports to open travel bubbles. Subsequently, its territories set French records for both COVID-19 and 6-month excess all-cause mortality. (2) Methods: Official time series were collected to compare time correlations between air traffic and COVID-19 transmission and mortality in overseas France, before and after the implementation of immunity passports. (3) Results: Air traffic initially had a reversed relationship with COVID-19, which transitioned into a leader–follower relationship with the introduction of immunity passports. Essentially, air traffic increased 16 days before COVID-19 cases increased (r = 0.61) and 26 days before deaths increased (r = 0.31) in Martinique, 26 days (r = 0.72) and 40 days (r = 0.82) before in Guadeloupe, and 29 days (r = 0.60) and 31 days (r = 0.41) before in Réunion upon introduction of immunity passports. Moreover, air traffic became as correlated as community transmission to COVID-19 mortality in Guadeloupe. (4) Conclusions: Since the introduction of immunity passports, air traffic has been pacesetting COVID-19 within one month for transmission, and within an additional two weeks for mortality in overseas France. Responding to WHO’s call for real-world evidence, this study suggests that COVID-19 passports are not commensurate with health system goals.
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24
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Kahn K, Pettifor A, Mataboge P, Kelly NK, Mashinini DP, Nair H, Campbell H, Cohen C, Gómez-Olivé FX, Tollman S. COVID-19 vaccine hesitancy in rural South Africa: Deepening understanding to increase uptake and access. J Glob Health 2022; 12:05013. [PMID: 35567586 PMCID: PMC9107307 DOI: 10.7189/jogh.12.05013] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background To date, COVID-19 vaccine coverage in the African region falls far too short of global goals. Increasing vaccination rates requires understanding barriers to vaccination so that effective interventions that sensitively and effectively address barriers to vaccination can be implemented. Methods To assess COVID-19 vaccination levels and identify major barriers to vaccine uptake we conducted a population-based, cross-sectional survey among 1662 adults 18 and older from August 25 to October 29 2021 in the Agincourt Health and Socio-Demographic Surveillance System (AHDSS) area, Mpumalanga, South Africa. Results Half of participants reported receiving a COVID-19 vaccine (50.4%) with 41.1% being fully vaccinated and 9.3% being partially vaccinated; 49.6% were unvaccinated. More women than men were vaccinated (55.5% vs 42.8%, P < 0.001), and older age groups were more likely to be vaccinated than younger age groups (P < 0.001). Among the unvaccinated, 69.0% planned to get vaccinated as soon as possible, while 14.7% reported definitely not wanting the vaccine. Major barriers to vaccination included lacking information on eligibility (12.3%) or where to get vaccinated (13.0%), concerns about side effects (12.5%), and inconvenient hours and locations for vaccination (11.0%). Confidence in the safety and efficacy of COVID-19 vaccines was higher among those vaccinated than unvaccinated (75.3% vs 51.2%, 75.8% vs 51.0%, both P < 0.001, respectively). Conclusions Increasing vaccination in South Africa beyond current levels will require a concerted effort to address concerns around vaccine safety and increase confidence in vaccine efficacy. Clarifying eligibility and ensuring access to vaccines at times and places that are convenient to younger populations, men, and other vulnerable groups is necessary.
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Affiliation(s)
- Kathleen Kahn
- MRC/Wits Rural Public Health and Health Transitions Research Unit, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Audrey Pettifor
- MRC/Wits Rural Public Health and Health Transitions Research Unit, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Palesa Mataboge
- MRC/Wits Rural Public Health and Health Transitions Research Unit, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole K Kelly
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Duduzile P Mashinini
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Harish Nair
- College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
| | - Harry Campbell
- College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - F Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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25
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Nel J, Venter WDF. Decoding the next SARS-CoV-2 variant. Lancet Glob Health 2022; 10:e928-e929. [PMID: 35597251 PMCID: PMC9116896 DOI: 10.1016/s2214-109x(22)00199-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 11/25/2022]
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26
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Kucharski AJ, Jit M, Logan JG, Cotten M, Clifford S, Quilty BJ, Russell TW, Peeling RW, Antonio M, Heymann DL. Travel measures in the SARS-CoV-2 variant era need clear objectives. Lancet 2022; 399:1367-1369. [PMID: 35247312 PMCID: PMC8890754 DOI: 10.1016/s0140-6736(22)00366-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 02/18/2022] [Indexed: 12/19/2022]
Affiliation(s)
- Adam J Kucharski
- Centre for Epidemic Preparedness and Response, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK.
| | - Mark Jit
- Centre for Epidemic Preparedness and Response, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - James G Logan
- Department of Disease Control, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - Matthew Cotten
- Centre for Epidemic Preparedness and Response, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK; Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda; Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Samuel Clifford
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - Billy J Quilty
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - Timothy W Russell
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - Rosanna W Peeling
- Centre for Epidemic Preparedness and Response, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - Martin Antonio
- Centre for Epidemic Preparedness and Response, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK; Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Serekunda, The Gambia
| | - David L Heymann
- Centre for Epidemic Preparedness and Response, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
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27
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Preiser W, Engelbrecht S, Maponga T. No point in travel bans if countries with poor surveillance are ignored. Lancet 2022; 399:1224. [PMID: 35339220 PMCID: PMC8947807 DOI: 10.1016/s0140-6736(22)00363-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/18/2022] [Indexed: 01/22/2023]
Affiliation(s)
- Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, University of Stellenbosch, National Health Laboratory Service (NHLS) Tygerberg, Cape Town 8000, South Africa.
| | - Susan Engelbrecht
- Division of Medical Virology, Faculty of Medicine and Health Sciences, University of Stellenbosch, National Health Laboratory Service (NHLS) Tygerberg, Cape Town 8000, South Africa
| | - Tongai Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, University of Stellenbosch, National Health Laboratory Service (NHLS) Tygerberg, Cape Town 8000, South Africa
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28
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Mahmud-Al-Rafat A, Hewins B, Mannan A, Kelvin DJ, Billah MM. COVID-19 vaccine inequity, dependency, and production capability in low-income and middle-income countries: the case of Bangladesh. THE LANCET. INFECTIOUS DISEASES 2022; 22:310-312. [PMID: 35101243 PMCID: PMC8798084 DOI: 10.1016/s1473-3099(22)00028-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/20/2021] [Accepted: 01/11/2022] [Indexed: 02/05/2023]
Affiliation(s)
- Abdullah Mahmud-Al-Rafat
- Department of Microbiology and Immunology, Canadian Center for Vaccinology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Benjamin Hewins
- Department of Microbiology and Immunology, Canadian Center for Vaccinology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Adnan Mannan
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - David J Kelvin
- Department of Microbiology and Immunology, Canadian Center for Vaccinology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada; Laboratory of Immunity, Shantou University Medical College, Guangdong, China
| | - Md Morsaline Billah
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh.
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29
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Swartz L. African science and global opinions. S AFR J SCI 2022. [DOI: 10.17159/sajs.2022/13062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Leslie Swartz
- Academy of Science of South Africa, Pretoria, South Africa
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Gupta H. On ascending limb of our learning curve. WHO South East Asia J Public Health 2022; 11:65-66. [PMID: 36308275 DOI: 10.4103/who-seajph.whoseajph_7_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Affiliation(s)
- Harish Gupta
- Department of Medicine, KG's Medical University, Lucknow - 226 003, Uttar Pradesh, India
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Durrance-Bagale A, Marzouk M, Ananthakrishnan A, Nagashima-Hayashi M, Lam ST, Sittimart M, Howard N. 'Science is only half of it': Expert perspectives on operationalising infectious disease control cooperation in the ASEAN region. PLOS GLOBAL PUBLIC HEALTH 2022; 2:e0000424. [PMID: 36962233 PMCID: PMC10021729 DOI: 10.1371/journal.pgph.0000424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/03/2022] [Indexed: 11/19/2022]
Abstract
Governmental awareness of the potential spread of infectious disease, exemplified by the current Covid-19 pandemic, ideally results in collective action, as countries coordinate a response that benefits all, contributing expertise, resources, knowledge and experience to achieve a common public good. However, operationalising regional cooperation is difficult, with barriers including lack of political will, regional heterogeneity, and existing geopolitical issues. We interviewed 23 people with regional expertise focusing on Asia, Africa, the Americas and Europe. All interviewees held senior positions in regional bodies or networks or had significant experience working with them. Operationalisation of a regional infectious disease body is complex but areas interviewees highlighted-organisational factors (e.g. integration and harmonisation; cross-border issues; funding, financing and sustainability; capacity-building; data sharing); governance and diplomacy (e.g. building collaborations and partnerships; communication; role of communities; diplomacy; leadership; ownership; sovereignty; political commitment); and stakeholders and multilateral agreements-will help promote successful operationalisation. The international infectious disease community has learned valuable lessons from the Covid-19 pandemic, not least the necessity of pooling human, financial and technological resources, constructing positive working relationships with neighbours, and sharing data. Without this kind of regional cooperation, infectious diseases will continue to threaten our future, and the next pandemic may have even more far-reaching effects.
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Affiliation(s)
- Anna Durrance-Bagale
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Manar Marzouk
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Aparna Ananthakrishnan
- Health Intervention and Technology Assessment Program, Ministry of Public Health, Nonthaburi, Thailand
| | - Michiko Nagashima-Hayashi
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Sze Tung Lam
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Manit Sittimart
- Health Intervention and Technology Assessment Program, Ministry of Public Health, Nonthaburi, Thailand
| | - Natasha Howard
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- London School of Hygiene and Tropical Medicine, London, United Kingdom
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Banerjee I, Robinson J, Banerjee I, Sathian B. Omicron: The pandemic propagator and lockdown instigator - what can be learnt from South Africa and such discoveries in future. Nepal J Epidemiol 2021; 11:1126-1129. [PMID: 35070471 PMCID: PMC8730344 DOI: 10.3126/nje.v11i4.41569] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 11/18/2022] Open
Abstract
The SARS-CoV-2 virus which causes the disease termed COVID-19 ripped through the globe in the latter part of 2019 and has left a state of fear, death and destruction in its wake. The Omicron variant was officially announced by the South African authorities on the 24th of November 2021, with the first confirmed sample of the infection being collected on the 9th of November 2021. The initial cases were flagged as a possible new variant due to the stark differences in the presentation and clinical features of the patients. At the time of Omicron's discovery, the predominant variant circulating within South Africa was the Delta variant B.1.617.2 which typically presented with more severe and distinct symptoms. Omicron spread rapidly within the Southern Africa and abroad, principally South Africa, Botswana, Hongkong and Israel were among the first countries to record cases of the new variant. The first European case of the Omicron variant was confirmed on the 26th of November 2021 in Belgium. Towards the end of November 2021 cases of the new variant had been confirmed and recorded in France, the United Kingdom, Germany, Portugal and Scotland. Additional cases of the Omicron variant have been confirmed in Canada, Australia, India and United States. At this current point in the development of the Omicron upsurge in cases the international community should aim for further vaccinations among their fellow countrymen, but more so vaccine equality should be ensured. Such equality should be ensured in the developing nations as the virus does not respect any boundaries or territories and thus a higher level of vaccination worldwide will confer greater protection to the global community as a whole.
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Affiliation(s)
| | - Jared Robinson
- Sir Seewoosagur Ramgoolam Medical College, Belle Rive, Mauritius
| | - Indraneel Banerjee
- Consultant Uro oncologist and Robotic Surgeon, Apollo multi speciality Hospitals, Kolkata, West Bengal, India
| | - Brijesh Sathian
- Geriatric and long term care Department, Rumailah Hospital, Hamad Medical Corporation, Doha, Qatar
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