A SARS-CoV-2 Surveillance System in Sub-Saharan Africa: Modeling Study for Persistence and Transmission to Inform Policy Open Access (recommended)
Descriptions
- Resource type(s)
- Article
- Keyword
- global COVID-19 surveillance
African public health surveillance
sub-Saharan African COVID-19
African surveillance metrics
dynamic panel data
generalized method of the moments
African econometrics
African SARS-CoV-2
African COVID-19 surveillance system
African COVID-19 transmission speed
African COVID-19 transmission acceleration
COVID-19 transmission deceleration
COVID-19 transmission jerk
COVID-19 7-day persistence
Sao Tome and Principe
Senegal
Seychelles
Sierra Leone
Somalia
South Africa
South Sudan
Sudan
Suriname
Swaziland
Tanzania
Togo
Uganda
Zambia
Zimbabwe
Gambia
Ghana
Guinea
Guinea-Bissau
Kenya
Lesotho
Liberia
Madagascar
Malawi
Mali
Mauritania
Mauritius
Mozambique
Namibia
Niger
Nigeria
Rwanda
Angola
Benin
Botswana
Burkina Faso
Burundi
Cameroon
Central African Republic
Chad
Comoros
Congo
Cote d'Ivoire
Democratic Republic of Congo
Equatorial Guinea
Eritrea
Ethiopia
Gabon
- Rights
- Attribution 4.0 International
- Creator
-
Post, Lori Ann
Argaw, Salem Tibebe
Jones, Cameron Spencer
Moss, Charles B.
Resnick, Danielle
Singh, Lauren Nadya
Murphy, Robert Leo
Achenbach, Chad J
White, Janine Inui
Issa, Tariq Ziad
Boctor, Michael Jacob
Oehmke, James Francis
- Abstract
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Background: Since the novel coronavirus emerged in late 2019, the scientific and public health community around the world have sought to better understand, surveil, treat, and prevent the disease, COVID-19. In sub-Saharan Africa (SSA), many countries responded aggressively and decisively with lockdown measures and border closures. Such actions may have helped prevent large outbreaks throughout much of the region, though there is substantial variation in caseloads and mortality between nations. Additionally, the health system infrastructure remains a concern throughout much of SSA, and the lockdown measures threaten to increase poverty and food insecurity for the subcontinent's poorest residents. The lack of sufficient testing, asymptomatic infections, and poor reporting practices in many countries limit our understanding of the virus's impact, creating a need for better and more accurate surveillance metrics that account for under-reporting and data contamination. Objective: The goal of this study is to improve infectious disease surveillance by complementing standardized metrics with new and decomposable surveillance metrics of COVID-19 that overcome data limitations and contamination inherent in public health surveillance systems. In addition to prevalence of observed daily and cumulative testing, testing positivity rates, morbidity, and mortality, we derived COVID-19 transmission in terms of speed, acceleration or deceleration, change in acceleration or deceleration (jerk), and 7-day transmission rate persistence, which explains where and how rapidly COVID-19 is transmitting and quantifies shifts in the rate of acceleration or deceleration to inform policies to mitigate and prevent COVID-19 and food insecurity in SSA. Methods: We extracted 60 days of COVID-19 data from public health registries and employed an empirical difference equation to measure daily case numbers in 47 sub-Saharan countries as a function of the prior number of cases, the level of testing, and weekly shift variables based on a dynamic panel model that was estimated using the generalized method of moments approach by implementing the Arellano-Bond estimator in R. Results: Kenya, Ghana, Nigeria, Ethiopia, and South Africa have the most observed cases of COVID-19, and the Seychelles, Eritrea, Mauritius, Comoros, and Burundi have the fewest. In contrast, the speed, acceleration, jerk, and 7-day persistence indicate rates of COVID-19 transmissions differ from observed cases. In September 2020, Cape Verde, Namibia, Eswatini, and South Africa had the highest speed of COVID-19 transmissions at 13.1, 7.1, 3.6, and 3 infections per 100,0000, respectively; Zimbabwe had an acceleration rate of transmission, while Zambia had the largest rate of deceleration this week compared to last week, referred to as ajerk. Finally, the 7-day persistence rate indicates the number of cases on September 15, 2020, which are a function of new infections from September 8, 2020, decreased in South Africa from 216.7 to 173.2 and Ethiopia from 136.7 to 106.3 per 100,000. The statistical approach was validated based on the regression results; they determined recent changes in the pattern of infection, and during the weeks of September 1-8 and September 9-15, there were substantial country differences in the evolution of the SSA pandemic. This change represents a decrease in the transmission model R value for that week and is consistent with a de-escalation in the pandemic for the sub-Saharan African continent in general. Conclusions: Standard surveillance metrics such as daily observed new COVID-19 cases or deaths are necessary but insufficient to mitigate and prevent COVID-19 transmission. Public health leaders also need to know where COVID-19 transmission rates are accelerating or decelerating, whether those rates increase or decrease over short time frames because the pandemic can quickly escalate, and how many cases today are a function of new infections 7 days ago. Even though SSA is home to some of the poorest countries in the world, development and population size are not necessarily predictive of COVID-19 transmission, meaning higher income countries like the United States can learn from African countries on how best to implement mitigation and prevention efforts.
- Original Bibliographic Citation
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Post LA, Argaw ST, Jones C, Moss CB, Resnick D, Singh LN, Murphy RL, Achenbach CJ, White J, Issa TZ, Boctor MJ, Oehmke JF. A SARS-CoV-2 Surveillance System in Sub-Saharan Africa: Modeling Study for Persistence and Transmission to Inform Policy. Journal of Medical Internet Research. 2020;22(11):18.
- Related URL
- Publisher
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JMIR PUBLICATIONS, INC
- Date Created
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2020-11-19
- Original Identifier
- (PMID) 33211026
- Language
- English
- Subject: MESH
-
SARS-CoV-2
Public Health Surveillance
Disease Transmission, Infectious
COVID-19
- Subject: LCSH
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COVID-19 (Disease)
Public health surveillance
Virus diseases--Transmission
- Subject: Geographic Name
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Africa, Sub-Saharan
- Grants and funding
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Feed the Future through the US Agency for International DevelopmentUnited States Agency for International Development (USAID) [7200LA1800003]
- DOI
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10.2196/24248
File Details
- File Properties
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