COVID-19 in Africa: Slow Epidemic or Low Detection?

As the COVID-19 pandemic blazes through North America and Europe, the case counts from Africa remain quite low. The Worldometers website indicates that South Africa leads the tally with 15,515 cases, followed by Egypt (12,229 cases) and Algeria (7,019 cases). Overall, the African continent has reported 86,683 cases, 2,785 deaths. This indicates an Infection Fatality Rate of 3.21% (95% confidence interval: 3.09% to 3.33%). With 33,521 recoveries, the infection recovery rate stands at an impressive 38.67% (95% CI: 38.35% to 39.00%). As far as testing is concerned, South Africa leads the tally with 460,873 tests (7,783 tests per million population), with a testing rate of almost 30 tests per detected case. It is followed by Ghana, where 173,096 tests have been done, (5,586 tests per million population), and a testing rate of a bit over 30 tests per detected case. Mortality tally is led by Egypt, which has reported 630 deaths, representing 22.62% (95% CI: 21.09% to 24.23%) of all deaths reported from Africa due to COVID-19 (n=2,785). Population based infection rate is the highest in Djibouti, which has registered 1,401 cases, and with a population of about 1 million, represents an infection rate of 1,421 cases per million population. 

In comparison, the United States, which has recently emerged as the hotspot driving the global tally of cases, has registered over 1.5 million cases, almost 91,000 deaths, an infection fatality rate of 5.96% (95% CI: 5.92% to 6.0%), infection recovery rate of 22.67% (95% CI: 22.6% to 22.74%); it has conducted almost 12 million tests, at the rate of 35,903 tests per million population, at a testing rate of almost 8 tests per detected case. 

While the numbers from Africa seem really positive, it has also fueled the conjectures that there is an association between temperature and caseloads – a hypothesis which is rapidly losing favor both with the scientific and the general media as the burden of cases continue to rise in tropical countries with improving testing rates. A recent New York Times article highlights the fact that rather than a slow epidemic, massive detection bias is perhaps the reason for the low reporting of cases. Drawing on the examples from Kano, Nigeria and Mogadishu, Somalia, the article states:

“But blazing hot spots are beginning to emerge. Kano is only one of several places in Africa where a relatively low official case count bears no resemblance to what health workers and residents say they are seeing on the ground. In Somalia’s capital, Mogadishu, officials say that burials have tripled. In Tanzania, after cases suddenly rose and the United States Embassy issued a health alert, the Tanzanian government abruptly stopped releasing its data. In Nigeria, some say that with the outbreak in Kano so widespread, the city may already be home to a giant, unintentional experiment in herd immunity.”

Covid-19 Outbreak in Nigeria Is Just One of Africa’s Alarming Hot Spots. New York Times.

Whilst the ongoing responses are getting ramped up, the New York Times piece highlights four concerning aspects of the epidemic, which could perhaps be as dangerous as a falsely low count of cases (bold mine):

  1. Excess Mortality: “One doctor said the department’s death registers for April showed far more patients had died than normal. Most patients were sent home, he said, and the hospital’s staff members often would hear later that they had died.”
  1. Delay in getting test results: “Nigeria, a country of about 200 million people, says it can in theory do 2,500 tests a day, and Kano up to 500. But it has been conducting far fewer tests, typically 1,000 to 1,200 daily. Test results in Kano can take two weeks. Doctors awaiting their test results cannot go to work. People in quarantine cannot leave.”
  1. Lack of PPEs and subsequent infections in healthcare workers: “With no personal protective equipment except surgical masks, the doctors said they knew the risks they were running in treating these patients. They said that they begged the hospital management for N-95 masks, face shields, gloves and aprons, but that none came. They asked for an isolation center at the hospital, scared that patients with other ailments would be infected. They wanted the facilities fumigated. Nothing happened.”
  1. Adverse behavioral patterns discouraging adherence to social/physical distancing norms: “Many in the city think the coronavirus is a hoax, perhaps because public messaging about it is mostly in English, which most Kano residents do not speak, health experts said. Others believe that a Covid-19 diagnosis is a death sentence, the experts said, and do not want their neighbors to think they are infected. So they avoid being tested, and try to behave as if all is normal. They go to burials, and shake fellow mourners’ hands because it would be socially unacceptable not to. They shop, barefaced, in crowded markets. They hold soccer tournaments — a recent one was called the “Coronavirus Cup.””

As more accurate tests, which are cheaper to deploy, have better sensitivity and specificity, and are less technically demanding become available, it is hoped that public pressure and demand for testing for COVID-19 will lead to ramping up of the testing in African countries. If this does indeed happen, it will be interesting to see whether newer patterns emerge. Many African nations are perhaps not testing as much as they could, but of those which are (South Africa, for example), their infection detection rate, fatality and other indicators are broadly in line with the situation seen in countries with slower, smoldering spread of the epidemic of COVID-19. As case counts continue to mount in tropical countries with similar socioeconomic profiles and infectious disease burden, it remains to be seen if improved testing rates will lead to a change in the trajectory of the epidemic curve in Africa. 

Epidemic Curves of 5 African Countries with Highest Case Counts Reported

COVID-19 and Testing Times

Disclaimer: This post represents my personal opinion. This does not represent the opinion or policy position of my employer or any organization or agency or group that I am affiliated with.


The global spread of the COVID-19 pandemic has brought us face to face with new realities and unanticipated challenges. Globally, health systems have needed to adapt and change strategies as the changing epidemiology and emerging data has provided us with more intelligence about this viral contagion. The basic strategy to combat COVID-19 is simple: prevent the occurrence of new cases; detect new cases early and effectively, as soon as they appear; treat the cases to prevent occurrence of complications and death; and manage them through social distancing strategies to prevent the spread. One of the key components of this strategy is testing to identify the new cases. Given the novel nature of the pathogen, and the limited capacity to produce quality assured testing kits, this was a major challenge globally. In a country of 1.3 billion people, strategic optimization of the limited testing resources is essential to ensure equitable access. There has been accelerated scaling up of testing capacity in India, with a 70-fold increase in daily tests done in the last 40 days. Along with this exponential increment in testing in India, there has been a gradual widening of the ambit of testing beyond the high-risk groups, consistently conducting around 25 tests for every positive case detected over the same period.

Testing Status: May 3, 2020

India has entered a select group of countries, which have conducted over 1 million tests for COVID-19. When compared to the other nine countries, India has the lowest number of cases (39,980 as of 3rd May, 2020) and lowest population-based mortality (0.9 per million) from COVID-19. These numbers in themselves are remarkable, but given the complexities of scaling up a real time PCR based diagnostic test over a vast terrain such as India, it stands as a testimony to the political will, foreplanning and broad-based support required to achieve this.

Total cases, deaths per million and total tests of COVID-19 in countries with 1 million or more total tests done

The testing strategy has kept pace with the changing transmission dynamics of COVID-19. In the early stages of the epidemic in India, when transmission was limited to travelers coming from countries where there was already ongoing transmission of COVID-19, testing was limited to high risk travelers and was augmented with screening at ports of entry, in tandem with travel and visa restrictions for select high burden countries. As the infection began to spread, testing was also ramped up. Iterative calibration of the testing strategy, keeping pace with the evolving epidemiology of COVID-19, has enabled access to diagnostic testing for groups that need it most, ensured the prevention of wasteful or unnecessary testing and encouraged optimal scaling up of the testing infrastructure while other preventive public health interventions were being put in place.

COVID-19 Burden in India (May 3, 2020)

Although testing is an important window into the evolution of COVID-19 in India, it is not a single-point panacea to help survive the pandemic. It is part of a larger package of interventions, and as such, needs to be recursively supportive of the other strategies. Multi-pronged approaches like physical distancing, bolstering health services infrastructure, and public health measures informed by optimal testing in sync with epidemic progression are necessary to beat COVID-19.