Estimates of the COVID-19 Infection Fatality Rate for 48 African Countries: A Model-Based Analysis

(1) Background: Examine global data from 48 African countries to estimate the SARS-CoV-2 infection fatality rate; (2) Methods: We analyzed time series data on the 135,126 confirmed cases and 3922 deaths from COVID-19 disease outbreak in Africa through 30 May 2020. In a Bayesian prediction model based on the Monte Carlo approach, we adjusted for demographic, economic, biological, and societal variables to account for the untested people; (3) Results: We calculated a total of 1,686,879 COVID-19 infections after correcting for possible risk variables in the Bayesian model, equal to 13 infections per confirmed case. In Africa, the IFR is projected to be 0.23% (95% CI: 0.14–0.33%). The percentages varied by country, ranging from 0.004% in Botswana and the Central African Republic to 1.53% in Nigeria. The projected IFR is twelvefold greater than the WHO’s 2009 H1N1 influenza pandemic estimate (0.02%). In four countries: Morocco, Nigeria, Cameroon, and South Africa, the inverse distance weighted interpolation map shows high IFR variability; (4) Conclusions: COVID-19 infection mortality rates can vary significantly between regions, and this might be due to changes in demography, underlying health conditions in the community, healthcare system capacity, positive health seeking behavior, and other variables.</jats:p

Estimates of the COVID-19 Infection Fatality Rate for 48 African Countries: A Model-Based Analysis

(1) Background: Examine global data from 48 African countries to estimate the SARS-CoV-2 infection fatality rate; (2) Methods: We analyzed time series data on the 135,126 confirmed cases and 3922 deaths from COVID-19 disease outbreak in Africa through 30 May 2020. In a Bayesian prediction model based on the Monte Carlo approach, we adjusted for demographic, economic, biological, and societal variables to account for the untested people; (3) Results: We calculated a total of 1,686,879 COVID-19 infections after correcting for possible risk variables in the Bayesian model, equal to 13 infections per confirmed case. In Africa, the IFR is projected to be 0.23% (95% CI: 0.14–0.33%). The percentages varied by country, ranging from 0.004% in Botswana and the Central African Republic to 1.53% in Nigeria. The projected IFR is twelvefold greater than the WHO’s 2009 H1N1 influenza pandemic estimate (0.02%). In four countries: Morocco, Nigeria, Cameroon, and South Africa, the inverse distance weighted interpolation map shows high IFR variability; (4) Conclusions: COVID-19 infection mortality rates can vary significantly between regions, and this might be due to changes in demography, underlying health conditions in the community, healthcare system capacity, positive health seeking behavior, and other variables

Using Supervised Machine Learning and Empirical Bayesian Kriging to reveal Correlates and Patterns of COVID-19 Disease outbreak in sub-Saharan Africa: Exploratory Data Analysis

AbstractIntroductionCoronavirus disease 2019 (COVID-19) is an emerging infectious disease that was first reported in Wuhan1,2, China, and has subsequently spread worldwide. Knowledge of coronavirus-related risk factors can help countries build more systematic and successful responses to COVID-19 disease outbreak. Here we used Supervised Machine Learning and Empirical Bayesian Kriging (EBK) techniques to reveal correlates and patterns of COVID-19 Disease outbreak in sub-Saharan Africa (SSA).MethodsWe analyzed time series aggregate data compiled by Johns Hopkins University on the outbreak of COVID-19 disease across SSA. COVID-19 data was merged with additional data on socio-demographic and health indicator survey data for 39 of SSA’s 48 countries that reported confirmed cases and deaths from coronavirus between February 28, 2020 through March 26, 2020. We used supervised machine learning algorithm, Lasso for variable selection and statistical inference. EBK was used to also create a raster estimating the spatial distribution of COVID-19 disease outbreak.ResultsThe lasso Cross-fit partialing out predictive model ascertained seven variables significantly associated with the risk of coronavirus infection (i.e. new HIV infections among pediatric, adolescent, and middle-aged adult PLHIV, time (days), pneumococcal conjugate-based vaccine, incidence of malaria and diarrhea treatment). Our study indicates, the doubling time in new coronavirus cases was 3 days. The steady three-day decrease in coronavirus outbreak rate of change (ROC) from 37% on March 23, 2020 to 23% on March 26, 2020 indicates the positive impact of countries’ steps to stymie the outbreak. The interpolated maps show that coronavirus is rising every day and appears to be severely confined in South Africa. In the West African region (i.e. Burkina Faso, Ghana, Senegal, Cote d’Iviore, Cameroon, and Nigeria), we predict that new cases and deaths from the virus are most likely to increase.InterpretationIntegrated and efficiently delivered interventions to reduce HIV, pneumonia, malaria and diarrhea, are essential to accelerating global health efforts. Scaling up screening and increasing COVID-19 testing capacity across SSA countries can help provide better understanding on how the pandemic is progressing and possibly ensure a sustained decline in the ROC of coronavirus outbreak.FundingAuthors were wholly responsible for the costs of data collation and analysis.</jats:sec

Tuberculosis care quality in urban Nigeria: A cross-sectional study of adherence to screening and treatment initiation guidelines in multi-cadre networks of private health service providers.

Nigeria has a high burden of tuberculosis (TB) and low case detection rates. Nigerias large private health sector footprint represents an untapped resource for combating the disease. To examine the quality of private sector contributions to TB, the USAID-funded Sustaining Health Outcomes through the Private Sector (SHOPS) Plus program evaluated adherence to national standards for management of presumptive and confirmed TB among the clinical facilities, laboratories, pharmacies, and drug shops it trained to deliver TB services. The study used a standardized patient (SP) survey methodology to measure case management protocol adherence among 837 private and 206 public providers in urban Lagos and Kano. It examined two different scenarios: a textbook case of presumptive TB and a treatment initiation case where SPs presented as referred patients with confirmed TB diagnoses. Private sector results were benchmarked against public sector results. A bottleneck analysis examined protocol adherence departures at key points along the case management sequence that providers were trained to follow. Except for laboratories, few providers met the criteria for fully correct management of presumptive TB, though more than 70% of providers correctly engaged in TB screening. In the treatment initiation case 18% of clinical providers demonstrated fully correct case management. Private and public providers adherence was not significantly different. Bottleneck analysis revealed that the most common deviations from correct management were failure to initiate sputum collection for presumptive patients and failure to conduct sufficiently thorough treatment initiation counseling for confirmed patients. This study found the quality of private providers TB case management to be comparable to public providers in Nigeria, as well as to providers in other high burden countries. Findings support continued efforts to include private providers in Nigerias national TB program. Though most providers fell short of desired quality, the bottleneck analysis points to specific issues that TB stakeholders can feasibly address with system- and provider-level interventions

Tuberculosis care quality in urban Nigeria: A cross-sectional study of adherence to screening and treatment initiation guidelines in multi-cadre networks of private health service providers

Nigeria has a high burden of tuberculosis (TB) and low case detection rates. Nigeria’s large private health sector footprint represents an untapped resource for combating the disease. To examine the quality of private sector contributions to TB, the USAID-funded Sustaining Health Outcomes through the Private Sector (SHOPS) Plus program evaluated adherence to national standards for management of presumptive and confirmed TB among the clinical facilities, laboratories, pharmacies, and drug shops it trained to deliver TB services. The study used a standardized patient (SP) survey methodology to measure case management protocol adherence among 837 private and 206 public providers in urban Lagos and Kano. It examined two different scenarios: a “textbook” case of presumptive TB and a treatment initiation case where SPs presented as referred patients with confirmed TB diagnoses. Private sector results were benchmarked against public sector results. A bottleneck analysis examined protocol adherence departures at key points along the case management sequence that providers were trained to follow. Except for laboratories, few providers met the criteria for fully correct management of presumptive TB, though more than 70% of providers correctly engaged in TB screening. In the treatment initiation case 18% of clinical providers demonstrated fully correct case management. Private and public providers’ adherence was not significantly different. Bottleneck analysis revealed that the most common deviations from correct management were failure to initiate sputum collection for presumptive patients and failure to conduct sufficiently thorough treatment initiation counseling for confirmed patients. This study found the quality of private providers’ TB case management to be comparable to public providers in Nigeria, as well as to providers in other high burden countries. Findings support continued efforts to include private providers in Nigeria’s national TB program. Though most providers fell short of desired quality, the bottleneck analysis points to specific issues that TB stakeholders can feasibly address with system- and provider-level interventions.</jats:p

Tuberculosis care quality in urban Nigeria: A cross-sectional study of adherence to screening and treatment initiation guidelines in multi-cadre networks of private health service providers.

Nigeria has a high burden of tuberculosis (TB) and low case detection rates. Nigeria's large private health sector footprint represents an untapped resource for combating the disease. To examine the quality of private sector contributions to TB, the USAID-funded Sustaining Health Outcomes through the Private Sector (SHOPS) Plus program evaluated adherence to national standards for management of presumptive and confirmed TB among the clinical facilities, laboratories, pharmacies, and drug shops it trained to deliver TB services. The study used a standardized patient (SP) survey methodology to measure case management protocol adherence among 837 private and 206 public providers in urban Lagos and Kano. It examined two different scenarios: a "textbook" case of presumptive TB and a treatment initiation case where SPs presented as referred patients with confirmed TB diagnoses. Private sector results were benchmarked against public sector results. A bottleneck analysis examined protocol adherence departures at key points along the case management sequence that providers were trained to follow. Except for laboratories, few providers met the criteria for fully correct management of presumptive TB, though more than 70% of providers correctly engaged in TB screening. In the treatment initiation case 18% of clinical providers demonstrated fully correct case management. Private and public providers' adherence was not significantly different. Bottleneck analysis revealed that the most common deviations from correct management were failure to initiate sputum collection for presumptive patients and failure to conduct sufficiently thorough treatment initiation counseling for confirmed patients. This study found the quality of private providers' TB case management to be comparable to public providers in Nigeria, as well as to providers in other high burden countries. Findings support continued efforts to include private providers in Nigeria's national TB program. Though most providers fell short of desired quality, the bottleneck analysis points to specific issues that TB stakeholders can feasibly address with system- and provider-level interventions