The basic reproduction number of COVID-19 across Africa
TL;DR: In this paper, the authors used a simple SEIR model and a Bayesian inference framework to estimate the basic reproduction number of COVID-19 across Africa, with a median of 3.67 (90% CrI: 3.31 - 4.12).
Abstract: The pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) took the world by surprise. Following the first outbreak of COVID-19 in December 2019, several models have been developed to study and understand its transmission dynamics.
Although the spread of COVID-19 is being slowed down by vaccination and other interventions, there is still a need to have a clear understanding of the evolution of the pandemic across countries, states and communities.
To this end, there is a need to have a clearer picture of the initial spread of the disease in different regions.
In this project, we used a simple SEIR model and a Bayesian inference framework to estimate the basic reproduction number of COVID-19 across Africa.
Our estimates vary between 1.98 (Sudan) and 9.66 (Mauritius), with a median of 3.67 (90% CrI: 3.31 - 4.12). The estimates provided in this paper will help to inform COVID-19 modeling in the respective countries/regions.
Citations
More filters
TL;DR: 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 as mentioned in this paper .
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. Description
6 citations
TL;DR: In this article , the authors consider the COVID-19 pandemic and find that the appropriate policy response depends on the relative time-horizon of the pandemic (i.e., the time it takes to develop effective vaccines and treatments) and the relative cost of social distancing.
Abstract: Abstract The COVID-19 pandemic has called for swift action from local governments, which have instated non-pharmaceutical interventions (NPIs) to curb the spread of the disease. The swift implementation of social distancing policies has raised questions about the costs and benefits of strategies that either aim to keep cases as low as possible (suppression) or aim to reach herd immunity quickly (mitigation) to tackle the COVID-19 pandemic. While curbing COVID-19 required blunt instruments, it is unclear whether a less-transmissible and less-deadly emerging pathogen would justify the same response. This paper illuminates this question using a parsimonious transmission model by formulating the social distancing lives vs. livelihoods dilemma as a boundary value problem using calculus of variations. In this setup, society balances the costs and benefits of social distancing contingent on the costs of reducing transmission relative to the burden imposed by the disease. We consider both single-objective and multi-objective formulations of the problem. To the best of our knowledge, our approach is distinct in the sense that strategies emerge from the problem structure rather than being imposed a priori. We find that the relative time-horizon of the pandemic (i.e., the time it takes to develop effective vaccines and treatments) and the relative cost of social distancing influence the choice of the optimal policy. Unsurprisingly, we find that the appropriate policy response depends on these two factors. We discuss the conditions under which each policy archetype (suppression vs. mitigation) appears to be the most appropriate.
1 citations
TL;DR: In this paper , mobile phone calling data was used to provide a spatially refined analysis of sub-national human mobility patterns during the COVID-19 pandemic from March 2020-July 2021 in Zambia.
Abstract: The COVID-19 pandemic has impacted many facets of human behavior, including human mobility partially driven by the implementation of non-pharmaceutical interventions (NPIs) such as stay at home orders, travel restrictions, and workplace and school closures. Given the importance of human mobility in the transmission of SARS-CoV-2, there have been an increase in analyses of mobility data to understand the COVID-19 pandemic to date. However, despite an abundance of these analyses, few have focused on Sub-Saharan Africa (SSA). Here, we use mobile phone calling data to provide a spatially refined analysis of sub-national human mobility patterns during the COVID-19 pandemic from March 2020-July 2021 in Zambia. Overall, among highly trafficked intra-province routes, mobility decreased up to 52% from March-May 2020 compared to baseline, which was also the time period of the strictest NPIs. However, despite dips in mobility during the first wave of COVID-19 cases, mobility returned to baseline levels and did not drop again suggesting COVID-19 cases did not influence mobility in subsequent waves.
1 citations
TL;DR: In this article , the authors used a SARS-CoV-2 transmission model to estimate the level of immunity accrued before the launch of vaccination in the Southwest Shewa Zone (SWSZ) and to evaluate the impact of alternative age priority vaccination targets in a context of limited vaccine supply.
Abstract: Abstract The worldwide inequitable access to vaccination claims for a re-assessment of policies that could minimize the COVID-19 burden in low-income countries. Nine months after the launch of the national vaccination program in March 2021, only 3.4% of the Ethiopian population received two doses of COVID-19 vaccine. We used a SARS-CoV-2 transmission model to estimate the level of immunity accrued before the launch of vaccination in the Southwest Shewa Zone (SWSZ) and to evaluate the impact of alternative age priority vaccination targets in a context of limited vaccine supply. The model was informed with available epidemiological evidence and detailed contact data collected across different geographical settings (urban, rural, or remote). We found that, during the first year of the pandemic, the mean proportion of critical cases occurred in SWSZ attributable to infectors under 30 years of age would range between 24.9 and 48.0%, depending on the geographical setting. During the Delta wave, the contribution of this age group in causing critical cases was estimated to increase on average to 66.7–70.6%. Our findings suggest that, when considering the vaccine product available at the time (ChAdOx1 nCoV-19; 65% efficacy against infection after 2 doses), prioritizing the elderly for vaccination remained the best strategy to minimize the disease burden caused by Delta, irrespectively of the number of available doses. Vaccination of all individuals aged ≥ 50 years would have averted 40 (95%PI: 18–60), 90 (95%PI: 61–111), and 62 (95%PI: 21–108) critical cases per 100,000 residents in urban, rural, and remote areas, respectively. Vaccination of all individuals aged ≥ 30 years would have averted an average of 86–152 critical cases per 100,000 individuals, depending on the setting considered. Despite infections among children and young adults likely caused 70% of critical cases during the Delta wave in SWSZ, most vulnerable ages should remain a key priority target for vaccination against COVID-19.
1 citations
TL;DR: A year-structured susceptible, infected, mild severs, critical severe, and recover (SIMCR) compartmental model is presented of COVID-19 disease transmission with incidence rate during the pandemic period and SIMCR model is used to describe the transmission of CO VID-19 among five high-burden African countries.
Abstract: Background Today, coronavirus disease-19 has left a permanent dark mark on the history of human beings. The ongoing global pandemic outbreak of COVID-19 has spread to 58 African countries, with over 6.07 million confirmed cases and over 151,412 deaths. The five high burden African countries are South Africa, Morocco, Tunisia, Ethiopia, and Libya, with case fatality rates (CFR) of nearly 0.15%, 0.042%, 0.22%, 0.006%, and 0.086%, respectively. This is why the research aims to adequately understand the transmission dynamics of the virus and its variants in five high-burden African countries. Methods Our study is a deterministic model, where the population is partitioned into five components on the epidemiological state of the individuals. We presented a year-structured susceptible, infected, mild severs, critical severe, and recover (SIMCR) compartmental model of COVID-19 disease transmission with incidence rate during the pandemic period. Results The number of susceptible individuals increased by 30,711,930 in South Africa, 5,919,837 in Morocco, 3,485,020 in Tunisia, 7,833,642 in Ethiopia, and 2,145,404 in Libya in the next 3 decades with compare to the unvaccinated population and the number of infected individuals decreased by 30,479,271 in South Africa, 19,809,751 in Morocco, 3,456,406 in Tunisia, 7,761,993 in Ethiopia, and 2,125,038 in Libya. Conclusion SIMCR model is used to describe the transmission of COVID-19 among five high-burden African countries. For the next 30 years, we will have around 86 million infected individuals and millions of death only in those five African countries. To reduce those problems, vaccination is the best and most effective mechanism. So vaccinating half of the populations in those countries helps to control and reduce the transmission rate of COVID-19 in Africa for the next 30 years. This leads to preventing 17,212,405 people from becoming infected and millions of deaths being reduced in those five high-burden African countries.
1 citations
References
More filters
TL;DR: There is evidence that human-to-human transmission has occurred among close contacts since the middle of December 2019 and considerable efforts to reduce transmission will be required to control outbreaks if similar dynamics apply elsewhere.
Abstract: Background The initial cases of novel coronavirus (2019-nCoV)–infected pneumonia (NCIP) occurred in Wuhan, Hubei Province, China, in December 2019 and January 2020. We analyzed data on the...
13,101 citations
TL;DR: A precise definition of the basic reproduction number, R0, is presented for a general compartmental disease transmission model based on a system of ordinary differential equations and it is shown that, if R0<1, then the disease free equilibrium is locally asymptotically stable; whereas if R 0>1,Then it is unstable.
Abstract: A precise definition of the basic reproduction number, Ro, is presented for a general compartmental disease transmission model based on a system of ordinary dierential equations. It is shown that, if Ro 1, then it is unstable. Thus,Ro is a threshold parameter for the model. An analysis of the local centre manifold yields a simple criterion for the existence and stability of super- and sub-threshold endemic equilibria for Ro near one. This criterion, together with the definition of Ro, is illustrated by treatment, multigroup, staged progression, multistrain and vectorhost models and can be applied to more complex models. The results are significant for disease control.
7,106 citations
TL;DR: Results of an analysis of nasal and throat swabs from 17 patients in Zhuhai, China, who had received a diagnosis of Covid-19 and found SARS-CoV-2 Viral Load in Upper Respiratory Specimens positive.
Abstract: SARS-CoV-2 Viral Load in Upper Respiratory Specimens The authors report results of an analysis of nasal and throat swabs from 17 patients in Zhuhai, China, who had received a diagnosis of Covid-19....
4,236 citations
TL;DR: It is shown that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus, and scenarios by which they could have arisen are discussed.
Abstract: SARS-CoV-2 is the seventh coronavirus known to infect humans; SARSCoV, MERS-CoV and SARS-CoV-2 can cause severe disease, whereas HKU1, NL63, OC43 and 229E are associated with mild symptoms6. Here we review what can be deduced about the origin of SARS-CoV-2 from comparative analysis of genomic data. We offer a perspective on the notable features of the SARS-CoV-2 genome and discuss scenarios by which they could have arisen. Our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus.
3,893 citations
TL;DR: It is shown that in certain special cases one can easily compute or estimate the expected number of secondary cases produced by a typical infected individual during its entire period of infectiousness in a completely susceptible population.
Abstract: The expected number of secondary cases produced by a typical infected individual during its entire period of infectiousness in a completely susceptible population is mathematically defined as the dominant eigenvalue of a positive linear operator. It is shown that in certain special cases one can easily compute or estimate this eigenvalue. Several examples involving various structuring variables like age, sexual disposition and activity are presented.
3,885 citations