COVID-19 in Africa: outbreak despite interventions?
TL;DR: In this article, the authors investigated the impact of interventions on the COVID-19 outbreak dynamics, focusing on South Africa before and after the national lockdown enacted on March 27, 2020.
Abstract: In Africa, while most countries report some COVID-19 cases, the fraction of reported patients is low, with about 20 000 cases compared to the more than 2.3 million cases reported globally as of April 18, 2020. Few African countries have reported case numbers above one thousand, with South Africa reporting 3 034 cases being hit hardest in Sub-Saharan Africa. Several African countries, especially South Africa, have already taken strong non-pharmaceutical interventions that include physical distancing, restricted economic, educational and leisure activities and reduced human mobility options. The required strengths and overall effectiveness of such interventions, however, are debated because of simultaneous but opposing interests in most African countries: strongly limited health care capacities and testing capabilities largely conflict with pressured national economies and socio-economic hardships on the individual level, limiting compliance to intervention targets. Here we investigate implications of interventions on the COVID-19 outbreak dynamics, focusing on South Africa before and after the national lockdown enacted on March 27, 2020. Our analysis shows that initial exponential growth of existing case numbers is consistent with doubling times of about 2.5 days. After lockdown, the growth remains exponential, now with doubling times of 18 days, but still in contrast to subexponential growth reported for Hubei/China after lockdown. Moreover, a scenario analysis of a computational data-driven agent based mobility model for the Nelson Mandela Bay Municipality (with 1.14 million inhabitants) hints that keeping current levels of intervention measures and compliance until the end of April is of insufficient length and still too weak, too unspecific or too inconsistently complied with to not overload local intensive care capacity. Yet, enduring, slightly stronger, more specific interventions combined with sufficient compliance may constitute a viable option for interventions for regions in South Africa and potentially for large parts of the African continent. EXECUTIVE SUMMARY Evidence before this study Several studies have analyzed the ongoing outbreak of the Corona Virus Disease 2019 (COVID-19) in China and several European countries. However, conditions in African countries are vastly different and often fragile, with conflicting limitations of both the health care system and socio-economic conditions, posing difficult challenges for decisions about enacting and lifting interventions. These countries are currently in the early stages of the outbreak and have been reporting a small but rapidly increasing number of patients diagnosed with COVID-19. Several countries have taken different intervention measures to counter a large-scale COVID-19 outbreak. In particular, in South Africa, with the largest number of cases in Sub-Saharan Africa, case numbers are known to less rapidly increase after national lockdown on March 27, 2020. Added value of this study This study reports a quantitative analysis of the case number dynamics reported by the World Health Organization and Johns Hopkins University until including April 18, 2020, both for Africa overall and South Africa specifically, before and after national lockdown. It also reports and analyzes results of an agent-based mobility simulation for the Nelson Mandela Bay Municipality, South Africa (1.14 million inhabitants). This case study relies on detailed large-scale mobility survey data of about 10% of the population and on estimates of the fractions by which interventions decrease specific activities. The simulational data on outbreak dynamics thus provide qualitative order of magnitude estimates of trends consistent with past data. Combined, both analyses may help to better understand the implications of interventions on and estimate the dynamics of the number of (critically) infected patients. Implications of all the available evidence The results suggest that current interventions are not yet sufficient to contain a larger-scale outbreak. Interventions slightly stronger than those implemented today or a higher degree of compliance to the enacted lockdown, in combination with longer-lasting measures than currently announced for South Africa may help bound the case numbers such that the number of critical patients remains at or below (and does not massively overburden) the local capacity of intensive care units. Strategies for strengthening or lifting interventions should be advised by advanced data analytics and predictive modeling estimates, for instance for evaluating necessary time intervals and required levels of interventions. Overall, the study points to a potentially viable chance for effective non-pharmaceutical countermeasures against COVID-19 epidemics in South Africa, with suggestions for Health Policy for large parts of the African continent and, generally, disadvantaged countries and regions.
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Lagos State University1, University of Pretoria2, Healthcare Improvement Scotland3, University of Glasgow4, University of Belgrade5, University of Botswana6, University of Adelaide7, University of Bamenda8, Memorial Hospital of South Bend9, University of Ghana10, University of Health and Allied Sciences11, University of Nairobi12, University of KwaZulu-Natal13, University of Malawi14, University of Namibia15, Ekiti State University16, University of Pittsburgh17, Sefako Makgatho Health Sciences University18, Qassim University19, University of Khartoum20, Egerton University21, University of Zambia22, College of Health Sciences, Bahrain23, University of London24, University of Zimbabwe25, University of Liverpool26, University of Verona27, Jagiellonian University Medical College28, Strathclyde Institute of Pharmacy and Biomedical Sciences29, Hawler Medical University30, University of Manchester31, RMIT University32, Hanoi University33
TL;DR: There are multiple activities across Africa to reduce the spread of COVID-19 and address misinformation, which can have catastrophic consequences, assisted by the WHO and others, which appear to be working in a number of countries.
Abstract: Background The COVID-19 pandemic has already claimed considerable lives. There are major concerns in Africa due to existing high prevalence rates for both infectious and non-infectious diseases and limited resources in terms of personnel, beds and equipment. Alongside this, concerns that lockdown and other measures will have on prevention and management of other infectious diseases and non-communicable diseases (NCDs). NCDs are an increasing issue with rising morbidity and mortality rates. The World Health Organization (WHO) warns that a lack of nets and treatment could result in up to 18 million additional cases of malaria and up to 30,000 additional deaths in sub-Saharan Africa. Objective Document current prevalence and mortality rates from COVID-19 alongside economic and other measures to reduce its spread and impact across Africa. In addition, suggested ways forward among all key stakeholder groups. Our approach Contextualise the findings from a wide range of publications including internet-based publications coupled with input from senior-level personnel. Ongoing activities Prevalence and mortality rates are currently lower in Africa than among several Western countries and the USA. This could be due to a number of factors including early instigation of lockdown and border closures, the younger age of the population, lack of robust reporting systems and as yet unidentified genetic and other factors. Innovation is accelerating to address concerns with available equipment. There are ongoing steps to address the level of misinformation and its consequences including fines. There are also ongoing initiatives across Africa to start addressing the unintended consequences of COVID-19 activities including lockdown measures and their impact on NCDs including the likely rise in mental health disorders, exacerbated by increasing stigma associated with COVID-19. Strategies include extending prescription lengths, telemedicine and encouraging vaccination. However, these need to be accelerated to prevent increased morbidity and mortality. Conclusion There are multiple activities across Africa to reduce the spread of COVID-19 and address misinformation, which can have catastrophic consequences, assisted by the WHO and others, which appear to be working in a number of countries. Research is ongoing to clarify the unintended consequences given ongoing concerns to guide future activities. Countries are learning from each other.
137 citations
TL;DR: The results imply that automated DRT systems are applicable to reduce the economic and environmental costs of transportation when applied in the interplay of rural and urban areas.
Abstract: Disruptive developments in automated driving systems, new powertrain concepts and digital mobility are shaping changes in the way people move in rural and urban areas. In combination with these technical potentials, novel mobility concepts as for instance demand responsive transportation (DRT) can improve the everyday mobility of people in terms of both cost-efficiency and sustainability. Moreover, challenges related to demographic transitions and urbanisation can be addressed and negative developments mitigated. One potential application of DRT might be the connection of rural areas with the urban core. The following paper aims to evaluate the viability and feasibility of DRT systems in the interplay of rural and urban areas. The city of Bremerhaven and the immediate surrounding are selected as area of investigation and the agent-based modelling framework MATSim is used to simulate the inhabitant mobility behaviour. On this basis, the global operational costs are calculated for different scenarios, e.g. fully automated vehicles and various powertrain types. The results imply that automated DRT systems are applicable to reduce the economic and environmental costs of transportation when applied in the interplay of rural and urban areas.
12 citations
TL;DR: The major impact of the pandemic is likely to be on welfare, rather than on trip substitution, and there is a need to focus policy on the mitigation of these impacts and ways of measuring changes in transport disadvantage and exclusion so that reliable data are available to inform mitigation strategies.
Abstract: Background: After coronavirus disease 2019 (COVID-19) was declared a pandemic, movement restrictions were implemented across sub-Saharan Africa. There has been much speculation on what the long-term impacts on urban transport might be. Objectives: The aim of this paper is to identify the revealed and future travel impacts of the pandemic. Method: To pursue this aim, evidence was compiled from two sources: secondary big data;and a ( n = 15) two-wave Delphi panel survey of experts in the region. Results: It is predicted that longer-term impacts will take the form of: reduced travel by, and accessibility for, low-income households residing in peripheral locations because of decreased welfare;reduced transport service availability;operator reduction (particularly amongst unsubsidised formal operators);increased remote activity participation for a minority of better resourced households with white-collar workers;and disrupted trip distributions as the mix of city-centre land use changes in response to business attrition in economic recession rather than to disrupted bid rents. Conclusion: The major impact of the pandemic is likely to be on welfare, rather than on trip substitution. There is a need, therefore, to focus policy on the mitigation of these impacts and, more particularly, on ways of measuring changes in transport disadvantage and exclusion so that reliable data are available to inform mitigation strategies. The mitigation strategies considered should include investment in affordable ‘digital connectivity’ as a means of complementing accessibility from physical proximity and mobility. The pandemic also highlights the need to develop more robust transport planning practices to deal with uncertainty.
5 citations
TL;DR: In this paper , the authors applied system dynamics modelling to investigate the impacts of COVID-19 on coastal tourism in NMB to provide decision-support and inform tourism recovery strategies through model analysis, a suite of management interventions was tested under two 'what-if' scenarios, with reference to the business-as-usual governance response scenario.
Abstract: Globally, the COVID-19 pandemic bought devastating impacts to multiple economic sectors, with a major downfall observed in the tourism sector owing to explicit travel bans on foreign and domestic tourism. In Nelson Mandela Bay (NMB), South Africa, tourism plays an important role; however, negative effects from the pandemic and resulting restrictions has left the sector dwindling and in need of a path to recovery. Working together with local government and stakeholders, this study applied system dynamics modelling to investigate the impacts of COVID-19 on coastal tourism in NMB to provide decision-support and inform tourism recovery strategies. Through model analysis, a suite of management interventions was tested under two ‘what-if’ scenarios, with reference to the business-as-usual governance response scenario. Scenario one specifically aimed to investigate a desirable tourism recovery strategy assuming governance control, whereas scenario two investigated a scenario where the effects of governance responses were impeded on by the exogenous effects from the virus. Results suggest that uncertainty remained prevalent in the trajectory of the infection rate as well as in associated trends in tourism; however, through the lifting of travel restrictions and the continual administration of vaccines, a path to recovery was shown to be evident.
5 citations
TL;DR: A first comprehensive genomic analysis of SARS-CoV-2 variants circulating in North African countries, including Algeria, Egypt, Libya, Morocco, Sudan and Tunisia, with respect to genomic clades and mutational patterns is reported, leading to a better guiding of public health intervention measures.
Abstract: Here, we report a first comprehensive genomic analysis of SARS-CoV-2 variants circulating in North African countries, including Algeria, Egypt, Libya, Morocco, Sudan and Tunisia, with respect to genomic clades and mutational patterns. As of December 2021, a total of 1669 high-coverage whole-genome sequences submitted to EpiCoV GISAID database were analyzed to infer clades and mutation annotation compared with the wild-type variant Wuhan-Hu-1. Phylogenetic analysis of SARS-CoV-2 genomes revealed the existence of eleven GISAID clades with GR (variant of the spike protein S-D614G and nucleocapsid protein N-G204R), GH (variant of the ORF3a coding protein ORF3a-Q57H) and GK (variant S-T478K) being the most common with 25.9%, 19.9%, and 19.6%, respectively, followed by their parent clade G (variant S-D614G) (10.3%). Lower prevalence was noted for GRY (variant S-N501Y) (5.1%), S (variant ORF8-L84S) (3.1%) and GV (variant of the ORF3a coding protein NS3-G251V) (2.0%). Interestingly, 1.5% of total genomes were assigned as GRA (Omicron), the newly emerged clade. Across the North African countries, 108 SARS-CoV-2 lineages using the Pangolin assignment were identified, whereby most genomes fell within six major lineages and variants of concern (VOC) including B.1, the Delta variants (AY.X, B.1.617.2), C.36, B.1.1.7 and B.1.1. The effect of mutations in SAR-CoV-2 genomes highlighted similar profiles with D614G spike (S) and ORF1b-P314L variants as the most changes found in 95.3% and 87.9% of total sequences, respectively. In addition, mutations affecting other viral proteins appeared frequently including; N:RG203KR, N:G212V, NSP3:T428I, ORF3a:Q57H, S:N501Y, M:I82T and E:V5F. These findings highlight the importance of genomic surveillance for understanding the SARS-CoV-2 genetic diversity and its spread patterns, leading to a better guiding of public health intervention measures. The know-how analysis of the present work could be implemented worldwide in order to overcome this health crisis through harmonized approaches.
4 citations
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TL;DR: The current outbreak of the novel coronavirus Covid-19 (coronavirus disease 2019; previously 2019-nCoV), epi-centered in Hubei Province of the People's Republic of China, has spread to many other countries and the incidence in other Asian countries, in Europe and North America remains low so far.
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TL;DR: A parsimonious model is introduced that captures both quarantine of symptomatic infected individuals, as well as population-wide isolation practices in response to containment policies or behavioral changes, and shows that the model captures the observed growth behavior accurately.
Abstract: The recent outbreak of coronavirus disease 2019 (COVID-19) in mainland China was characterized by a distinctive subexponential increase of confirmed cases during the early phase of the epidemic, contrasting with an initial exponential growth expected for an unconstrained outbreak. We show that this effect can be explained as a direct consequence of containment policies that effectively deplete the susceptible population. To this end, we introduce a parsimonious model that captures both quarantine of symptomatic infected individuals, as well as population-wide isolation practices in response to containment policies or behavioral changes, and show that the model captures the observed growth behavior accurately. The insights provided here may aid the careful implementation of containment strategies for ongoing secondary outbreaks of COVID-19 or similar future outbreaks of other emergent infectious diseases.
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TL;DR: The association of mortality with health care resources should provide guidance for resource-limited regions on how and when to prepare for possible local outbreaks.
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412 citations
TL;DR: Each African country’s risk of importation of COVID-19 from China is identified, using data on the volume of air travel from three airports in provinces in China to African countries, and the capacity of countries to detect and respond to cases is determined, using the WHO Infectious Disease Vulnerability Index.
274 citations