COVID-19 in Sub-Saharan Africa

To facilitate data linkage, in all of our data resources each country is individually identified by the three letter ISO-3 international code (ISO3), and by our own numerical code (CODE) which orders countries alphabetically.

1. Daily updates on core epidemiological indicators (by country and region)

2. Daily updates on trajectories (by country)

3. Weekly updates on weekly numbers of cases and deaths (by country and region)

4. WHO transmission classification (by country)

5. Country-specific testing data

6. Country-level contextual data (by country)

7. Physical distancing measures (by country)

1. Daily updates on core epidemiological indicators (by country and region)

Each day we compile data on number of new COVID-19 cases and deaths, for each country, and use these to calculate attack rates and case fatality risks. Our main source is the European Centre for Disease Control. The data come in two forms. Wide form has one line for each country with one set of six columns (one for each indicator) for each of the days of the outbreak. ‘Long form’ has one line of data for each country on each day of the outbreak, and just six columns (one for each of the indicators). Long form is suitable for time series analyses. These data are updated daily usually in the afternoon, London time (GMT+1).

2. Daily updates on trajectories (by country)

Each day, on completion of the daily updates of epidemiological indicators, we generate a series of graphical displays (time series) for each of the 46 countries to facilitate appreciation of trends. These cover three core indicators

1. a) the cumulative number of cases,
2. b) the cumulative number of deaths among confirmed COVID-19 cases, and
3. c) the case fatality risk (the proportion of confirmed cases that have died, to date, expressed as a percentage).

The x-axis is the number of days since the start of the outbreak in that country, and the y-axis is the value of the indicator. Each graph is scaled to best display the trajectory in that country. Please read the explanatory notes on the opening page of each downloadable file.

2.1. UPDATE ON TRAJECTORIES OF CONFIRMED CASES (CUMULATIVE NUMBERS) IN 46 SUB-SAHARAN AFRICAN COUNTRIES

2.3. UPDATE ON CASE FATALITY RISK IN 45 SUB-SAHARAN AFRICAN COUNTRIES

3. Weekly updates on weekly numbers of cases and deaths (by country and region)

Trends in daily numbers of new cases, deaths and testing activity are difficult to follow – they fluctuate widely given irregular intervals of testing and reporting, and periodic effects (e.g. weekends).

For new cases and deaths, we provide data in our daily updates, at regional level, using 3-day moving averages. At country level the problem is more marked, and trends are better appreciated by observing weekly numbers of reported cases and deaths. In an excel file, we collate these data for each country and region from Week 0 of the outbreak in the region (Monday 24^th February) to  the current week. For each country, we highlight the week with the highest reported number of cases/ deaths, and the number reported in that week. For countries that are currently reporting below that peak, we calculate the % reduction in cases/ deaths since the peak, and the average weekly rate of reduction. For countries/ regions for which weekly cases are still rising, we estimate the doubling time in days. Cells are colour coded to indicate, for that week, whether the country was experiencing sporadic, rising, linear or ‘peaked’ (declining) growth in cases.

The excel file includes worksheets marked ‘tests’ and ‘testpos’. These contain data on weekly numbers of tests, and test positive proportions (%) for each of the countries (currently 18) which report this information daily. Weekly tests and cases, mean daily tests and cases, and tests per million population are also provided in long form (SPSS and Stata format) suitable for time series analysis

4. WHO transmission classification (by country)

Since the beginning of the pandemic, the WHO has been releasing daily worldwide situation reports, which can be viewed and downloaded from their website.

For individual countries these include a judgment of their current status regarding COVID-19 transmission. This is an important characterization, reflecting on the control or otherwise achieved

Up to the 8^th April 2020, WHO used the following classification

– Imported cases only indicates locations where all cases have been acquired outside the location of reporting.

– Local transmission indicates locations where the source of infection is within the reporting location.

– Community transmission is evidenced by the inability to relate confirmed cases through chains of transmission for a large number of cases, or by increasing positive tests through sentinel samples (routine systematic testing of respiratory samples from established laboratories).

Up to the 8^th April, no sub-Saharan African country was classified as experiencing community transmission

From the 9^th April, the WHO applied a revised classification

– No cases: Countries/territories/areas with no confirmed cases (not shown in table)

– Sporadic cases: Countries/territories/areas with one or more cases, imported or locally detected

– Clusters of cases: Countries/territories/areas experiencing cases, clustered in time, geographic location and/or by common exposures

– Community transmission: Countries/area/territories experiencing larger outbreaks of local transmission defined through an assessment of factors including, but not limited to: – Large numbers of cases not linkable to transmission chains – Large numbers of cases from sentinel lab surveillance – Multiple unrelated clusters in several areas of the country/territory/area

Our downloadable transmission status data is available as time series data (one row for each country, for each reporting date, and one column for each indicator variable) in SPSS and Stata formats. The file can be merged with our other time series data using the country code variable (CODE). Data has been extracted from 89 consecutive WHO situation reports to date (27^th May 2020), and we aim to update this daily.

In this data set we provide the original WHO classifications in two variables for the periods to which they apply, and then have attempted a synthesis of the classifications via a third working variable into a fourth variable with a single combined classification covering the entire period.

5. Country-specific testing data

We have been compiling data on COVID-19 testing from direct sources (usually Ministry of Health, or an allied organisation), focusing on countries that are providing daily reports of numbers of tests reported on that day, or cumulative numbers to that day, or both, and the numbers of those tests that reported a positive result. None of these sources covers the entire period of the outbreak. These data allow us to calculate daily and cumulative test positive proportions. Daily tests, cases and test positive proportions are also calculated as 3 day moving averages. Where available, we also collate material on a) sub-regional distribution of cases, b) outcomes (recoveries/ deaths/ active cases), transmission (imported/ contact/ community), and surveillance (e.g. contact tracing).

We are currently covering 21 countries (Burkina Faso, Central African Republic, Chad, Cote d’Ivoire, Democratic Republic of Congo, Djibouti, Ethiopia, Guinea, Kenya, Madagascar, Mali, Mozambique, Niger, Nigeria, Rwanda, Senegal, South Africa, Togo, Uganda, Zambia and Zimbabwe). Links are provided to the data sources, and data completeness and quality issues highlighted. We also provide links to government announcements, news media and social media, that provide context on policies, plans and strategies for testing, including resource and infrastructure limitations, and how these are being addressed.

6. Country-level contextual data (by country)

We have provided a rich contextual data set with country level indicators in three main domains, a) demographic data, b) epidemiological data, and c) health system data. This ‘context’ data set has one line of data for each country. Data sets can be merged for analysis using the ‘CODE’ variable, which provides a consistent numerical code for each of the 46 countries sorted in alphabetical order. These data files are updated occasionally.

7. Physical distancing measures (by country)

The World Health Organization has adopted the term ‘physical distancing’ to refer to a set of behaviours and practices that reduce opportunities for COVID-19 transmission by reducing the number of in person encounters that people have, and by increasing the physical distance between themselves and others when these occur. Advice to ‘keep your distance’ (two metres or more) and ‘stay at home where possible’ are now universal. We have focused on gathering information on the measures that governments introduce and enforce to achieve these objectives. Specifically, we have categorised these as

1. Closing schools and colleges
2. Banning mass gatherings of more than a defined number of people.
3. Closing bars, restaurants, night clubs, and other places of entertainment
4. Night-time curfews (whether applied nationally or locally)
5. Cordon sanitaire (sometimes incorrectly referred to as ‘lockdown’). Typically, a cordon sanitaire is applied to a localised hot-spot of COVID-19 infection, and all travel into or out of the area is banned, other than for specific reasons. This can protect other parts of the country, and allow authorities to focus their control efforts on the affected region. However, within the cordon sanitaire, there are no, or limited further controls on movement or activity.
6. Lockdown, which we have defined as a specific and enforced instruction to remain at home, other than for defined and limited purposes. These usually include obtaining food, medical care, and exercise, and travelling to do essential work. We sub-classified lockdown into ‘partial’ (applied to certain regions only) and ‘full’ (applied to the whole country.

For all 46 sub-Saharan African countries, we have tried to ascertain which of these restrictions has been applied and when. All sources of information (119 to date) are indexed, and dated with links.

We are now focused upon collating information about the COVID-19 pandemic across sub-Saharan Africa, the epidemiological data, the government and health system responses, and the experiences and viewpoints of citizens, healthcare workers and other stakeholders.

We are updating, daily, data on newly confirmed cases and deaths among confirmed cases, released by the World Health Organization COVID-19 Outbreak Situation Dashboard. From these data we derive six indicators for each of the 46 countries in the region

1. Daily confirmed cases
2. Cumulative count of confirmed cases
3. Attack rate (the cumulative count of confirmed cases, per 100,000 population)
4. Daily deaths among confirmed cases
5. Cumulative count of deaths among confirmed cases
6. Case Fatality Rate (the proportion of cumulative confirmed cases who have died)

We tabulate these for the day of the report, and provide graphic summaries of trends. These are aggregated for the whole region, and stratified by sub-region (Western, Central, Eastern and Southern SSA). Raw data for each country, on each day can be downloaded in Excel and Stata format, in long form, and as time series data suitable for modelling. As trends for individual countries become clearer and more interpretable, we will highlight these in country-specific summaries and comparisons.

1 ‘Confirmed cases’ are confirmed by DNA analysis of throat and nasal swabs that identify current infection with COVID-19. The number of cases confirmed will under-estimate considerably the true number of cases in the country. The extent of the under-estimate will depend upon
a) the capacity of the country’s system to perform tests (the availability of test kits, and laboratories to perform the test)
b) help-seeking
c) the country’s policy regarding testing – are they focusing on frontline healthcare workers, severely ill people in hospital only, suspected cases in the community, or people in the community in general. Are they able to cover all regions, or urban areas only?

2 Deaths are only reported in confirmed cases. There may well be other deaths from COVID-19 in people who have not had their status confirmed through testing. Conversely, deaths among people who are confirmed to have COVID-19 infection may not have been caused by that infection.

3 The ‘Attack Rate’ gives a better sense of the density of the infection in the population than the crude number of cases. A relatively small number of cases, in a small country, may still be highly significant. But interpretation of the Attack Rate is complicated by the same issues as for ‘confirmed cases’. It will tend to be under-estimated.

4 The Case Fatality Rate will be influenced by the vulnerability of the population, and the effectiveness of the healthcare responses, particularly for severely and critically ill patients. It is therefore a critically important indicator for SSA countries. It will be influenced by issues relating to detection and reporting of both confirmed cases and deaths.

Measures implemented to control transmission. In the light of the very limited healthcare services for severely and critically ill patients with COVID-19, it is essential that governments in the region act effectively to control transmission, limiting the total number of infections and the demand upon scarce healthcare resources. These include:

1. Controlling the influx of infection from other countries

• checking the health of visitors
• quarantining visitors from some or all countries with COVID-19 outbreaks
• prohibiting flights/ entry to visitors from some or all countries with COVID-19 outbreaks
• closing airports and ports to all but cargo traffic
• closing borders

2. Controlling in country transmission, once community transmission is established

• effective contact tracing and testing
• quarantining and self-isolation advice for those with symptoms and those in contact with those with symptoms
• social distancing advice, and working from home policies
• banning public gatherings
• closing public entertainment and sports venues
• closing non-essential shops and businesses
• closing public transport
• ‘cordon sanitaire’ effectively isolating whole cities or regions from other parts of the country with few or no reported cases
• national lockdown, with strictly enforced advice to remain at home

These measures are likely to have a beneficial impact on the localization of the initial spread of the infection, and the rate and extent of the increase in cases and deaths once community transmission is established.

We are collecting, documenting and collating information from all available sources on exactly which control measures were introduced, when, for each of the 46 SSA countries. These can then be related to the development of the outbreak within and across countries, to assess their implementation and effectivenes.

3. Testing capacity and policy

The number of tests conducted places an absolute ceiling on the potential number of confirmed cases. Constraints include the number of tests kits available (negligible in March 2020, although 1.1 million kits were delivered last week), the availability of reagents, laboratories equipped and trained to conduct the test procedures.

The critical indicators here are

• the number of tests conducted daily (ideally the number of individuals tested, as some may be tested repeatedly)
• the proportion testing positive
• the policy or policies under which the tests were conducted.

Rationales for testing will include

• to confirm the status of severely ill patients in hospitals (high test +ve rate, high case fatality rate);
• to confirm the status of suspected cases in the community (moderate test +ve rate, low case fatality rate);
• to establish the status of healthcare workers, for their protection and that of patients (low to moderate test +ve rate, low case fatality rate)
• to establish the attack rate in the general community (low test +ve rate, low case fatality rate)

Policies and priorities will change over time as the outbreak unfolds, as will the numbers of tests conducted. Although these indicators are not currently being reported routinely, we shall attempt to monitor and document this to the extent possible for the 46 SSA countries.

We wish to support the policies and actions of the governments of the 46 sub-Saharan African countries, and the intergovernmental agencies who collectively provide technical advice and support for the COVID-19 response (the World Health Organization, the WHO AFRO regional office, AFRICA CDC). We use data on the outbreak collected by governments, and reported to the WHO. To inform yourself and understand the risk to the public we recommend that you should rely on your government agencies, and the World Health Organization.

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Some useful links follow below

https://www.ecdc.europa.eu/en/geographical-distribution-2019-ncov-cases

https://www.who.int/emergencies/diseases/novel-coronavirus-2019

https://www.afro.who.int/health-topics/coronavirus-covid-19

https://africacdc.org/

https://au.int/en/covid19

Other relevant and useful sources of data and information

https://coronavirus.jhu.edu/map.html

https://ourworldindata.org/coronavirus

https://www.globaldashboard.org/tag/covid-19/