A comparative exploratory data analysis (EDA) of infectious disease outbreak: A case study of COVID-19, SARS, and EBOLA

1.0 Introduction
The World Health Organization (WHO) defined Coronavirus disease (COVID-19) as an infectious disease that is caused by a newly discovered coronavirus. It is a large family of zoonotic viruses that cause illness ranging from the common cold to severe respiratory diseases. Common symptoms of COVID-19 infection are similar to the common cold and respiratory symptoms and these include dry cough, fever, shortness of breath, and breathing difficulties. In more severe cases, the infection can cause pneumonia, severe acute respiratory syndrome and kidney failure which often result in death.
The COVID-19 infection is spread from one person to another through droplets produced from the respiratory system of infected people, often during coughing or sneezing. According to current data, time from exposure to onset of symptoms is usually between 2 to 14 days, with an average of 5 days for symptomatic and asymptomatic individuals.
To monitor the exponential growth of COVID-19 and other infectious disease outbreak in the past, Data Science Nigeria (DSN) developed a series of dynamic trackers showing a comparative Pan African analysis of COVID-19 spread patterns and previous epidemics such as Ebola and SARS that have ravaged the world. This we showed in real-time. We also provided information about the numbers of deaths, recovered patients, and countries affected in Africa.

1.1 About Data Science Nigeria (DSN)
Data Science Nigeria is a registered non-profit organization with a vision to build a world-class Artificial Intelligence knowledge, research and innovation ecosystem that delivers high impact & transformational research, business use applications, AI-first start-ups, employability and social good use cases; such that in 10 years, Nigeria will become one of the top 10 AI talent/knowledge destinations with 20% GDP multiplier impact. Data Science Nigeria’s tried and true system of training and AI community building has been validated by world-class institutions. In 2019, we won 2 highest Artificial Intelligence awards on the continent space at the Deep Learning Indaba, Kenya: Maathai Impact Award and 2nd Best Research Poster. In addition, we were recognized at the world’s largest Artificial Intelligence Hackathon, Tunisia 2019. Beyond the community and groundbreaking research activities, Data Science Nigeria is a consulting and solution development Organization at the cutting edge of using Artificial Intelligence to solve pressing social and business problems. Data Science Nigeria provides solutions and capacity building for governments, multinationals, local and international humanitarian agencies and local businesses. Please click Data Science Nigeria for more information about DSN.

2.0 COVID-19 Cases in the World
A novel coronavirus (COVID-19) outbreak was first discovered in Wuhan, Hubei Province, China in December 2019. The World Health Organization declared the outbreak to be a Public Health Emergency of International Concern (PHEIC) on January 30, 2020 and recognised it as a pandemic on March 11, 2020.

As of April 23, 2020, data from John Hopkin University showed that there are 2,672,221 confirmed cases, 186,929 deaths, 731,788 recovered and 1,753,504 active cases of COVID-19 globally and by region classifications, Europe has the highest confirmed cases of 1,189,331 while Africa and Oceania have 26,932 and 8,213 confirmed cases respectively.

The interactive map below shows the number of COVID-19 cases in different countries. The United States of America has the highest number of confirmed cases and fatality cases.

2.1 COVID-19 Cases in Africa
On February 15, 2020, the first case of COVID-19 was reported in Africa, a full two months after it was reported in China. Within one month, the virus had spread to over 30 countries in Africa. As of April 28, 2020, the virus had spread to all Africa countries except Comoros, Lesotho, and Saint Helena; over 34,000 confirmed cases with over 1,500 death cases have been reported.
The map below shows the statistics of COVID-19 in Africa in terms of the total number of confirmed cases, recorded deaths, recovered cases, and active cases of each country.

While the chart below shows the daily count of COVID-19 across Africa since its inception.

2.1.2 Population size and testing for COVID-19 in Africa

The rate at which African countries test for COVID-19 is quite low when compared to other continents such as Europe and North America.

As of April 22, 2020:

  • South Africa with a population size of 59,308,690 has tested 126,937 people for COVID-19, out of which only 3,465 have been reported to have coronavirus.
  • Nigeria with a population size of 206,139,589 has tested 8003 people for COVID-19, out of which only 782 have been reported to have coronavirus.
  • Ghana with a population size of 31,072,940 has tested 68, 591 people for COVID-19, out of which only 1,042 have been reported to have coronavirus.
  • Kenya with a population size of 53,771,296 has tested 14,704 people for COVID-19, out of which only 296 have been reported to have coronavirus.
  • To combat the further spread of the virus, the rate of testing needs to be highly increased which means setting up more efficient and accessible testing centers across African countries.

2.1.3 Confirmed Cases of COVID-19 per African Country
The bar-race chart below shows the African countries confirmed cases of coronavirus from the date it was first recorded in Egypt and how it spread across Africa. South Africa has recorded the highest cases of coronavirus followed by Egypt. Despite the coronavirus lockdown in each of these countries, we can see that the number is growing exponentially.

2.1.4 Deaths Cases of COVID-19 in Africa
As of April 28, 2020, over 1,000 deaths have been recorded in Africa, with Algeria having the highest number of deaths. The graph below shows the number of deaths across African countries.

2.1.5 Recovered Cases of COVID-19 in Africa
The recovery cases of the COVID-19 have been a bit encouraging. According to the John Hopkin University data, as of April 28, 2020, there have been over 10,000 recovered cases in Africa out of over 34000 confirmed coronavirus cases. The chart below shows the number of recovery cases for each country per day.

2.1.6 Cumulative Growth Rate of COVID-19
COVID-19 keeps increasing per day amidst measures that have been put in place. The chart below shows the trend of confirmed cases, recovered cases, death cases, and total active cases.

2.1.7 Survival Analysis of COVID-19
The fatality rate of COVID-19 is the proportion of death cases from a COVID-19 compared to the total number of people confirmed to have the virus in each country. The line chart of survival analysis of COVID-19 across affected African countries below shows that Burundi, Mauritania, Algeria, and Sudan have fatality rates of 20%, 14.29%, 13.95%, and 11.21%, respectively of the total confirmed cases been resulted to death.

The recovery rate of COVID-19 is the proportion of recovered cases from a COVID-19 compared to the total number of people confirmed to have the virus in each country. The line chart of survival analysis of COVID-19 across affected African countries below shows that Mauritania, Burundi, Mauritius, Central African Republic (CAR) have recovery rates of 85.71%, 80%, 74%, and 71%, respectively of the total confirmed cases of COVID-19 recovered.

2.1.8 COVID-19 Mortality Rate
The mortality rate or death rate is a measure of the number of deaths due to a particular cause in a population. Mortality rate is usually expressed in units of deaths per 1,000, 10,000, and 100,000 or as the case may be per year. It can also be described as percentage death in a specific period. From the line chart below it can be deduced that Algeria, Mauritius, Morocco, Tunisia, and Egypt have mortality rates of 0.89, 0.70, 0.39, 0.32 and 0.26 per 100,000 population respectively.

2.2 COVID-19 in Nigeria
Nigeria recorded the first case of coronavirus on Thursday, February 27, 2020. The Nigeria Centre for Disease Control (NCDC) is working so hard to protect the health of Nigerians and also provides daily updates on COVID-19 occurrence across Nigerian states. As of April 28, 2020, Nigeria has recorded 1532 confirmed cases, 255 recovered cases, and 44 deaths.

2.2.1 COVID-19 Cases in Nigeria
The growth trajectory map below shows detailed cases of COVID-19 in Nigeria. It shows the total cases, active cases, number of deaths, and recovered cases. As of April 28, 2020, Lagos, Abuja and Kano have more confirmed cases than other provinces/states.

The time map below shows daily cases of COVID-19 across Nigerian states since its first occurrence.

The chart below shows the cumulative trend analysis of COVID-19 total cases, active cases, total recovered, and total deaths per day in Nigeria.

The bar race chart below shows the daily confirmed cases of COVID-19 across the state per day of occurrence.

The weekly total confirmed cases of COVID-19 across states in Nigeria is shown below. It can be seen that Lagos has the highest number of cases per week.

2.2.2 Survival Analysis of COVID-19 Across Affected States in Nigeria:
The COVID-19 fatality rate is the proportion of deaths cases compared to the total number of people confirmed to have the virus. As shown in the line chart, Delta, Edo, Akwa Ibom, and Borno have the highest fatality rate of 25%, 13%, 11%, and 11%, respectively.

The proportion of recovered cases from a COVID-19 compared to the total number of people confirmed to have the virus is called the recovery rate. The line chart below shows that Enugu, Osun, Rivers, and Bauchi have the highest recovery rate.

2.2.3 Mortality Analysis of COVID-19 Across Affected States in Nigeria

The mortality rate measures the number of deaths in a particular state with respect to the population. From the line chart below it can be seen that Lagos, Kwara, Abuja, Enugu have the highest mortality rate of 0.02, 0.012, 0.008, and 0.007 respectively per 10,000 population.

2.2.4 COVID-19 State Transmission Risk Analysis in Nigeria

State Transmission Rate measures the risk at which an individual can contract the virus in a state if appropriate precaution is not put into consideration. The table below shows COVID-19 transmission rate across states in Nigeria with Lagos having the highest risk.

3.0 COVID-19 and other Pandemics
3.1 Severe Acute Respiratory Syndrome coronavirus (SARS-CoV)

A species of coronavirus known as Severe Acute Respiratory Syndrome (SARS) is capable of infecting humans, bats, and other mammals. The first outbreak was identified in the Guangdong province of southern China in November 2002. It has affected 29 countries, resulting in more than 8000 cases and 774 deaths in 2003. SARS was predominant in Asian countries with China recording the highest cases of 5281 and 349 deaths. No African country was affected by this virus and WHO reported that no areas of the world are currently reporting the transmission of SARS since the end of the global epidemic in July 2003.

3.1.1 COVID-19 Versus SARS-COV
The Radial treemap below compares COVID-19 and SARS-CoV cases from the first month to the fourth month of the countries affected. It can be deduced from the chart that COVID-19 has more than 100% increase in the number of cases recorded when compared to SARS in the respective countries and at different durations except for Hong Kong which recorded more cases of SARS than that of COVID-19 within 3 months duration. This confirms the high infectiousness of COVID-19 as compared to SARS-CoV.

The 100% column chart below also compares the percentage of SARS and COVID-19 recorded in each affected country. We can deduce from the chart that as much as COVID-19 is more predominant in the world, countries like China, Hong Kong, Taiwan, Mongolia, Singapore and Vietnam on average, experience higher outbreak of SARS than COVID-19.

3.2 Ebola Virus Disease (EVD)
Ebola also known as Ebola hemorrhagic fever is a deadly virus that causes severe bleeding, organ failure and can lead to death. The virus is transmitted to people from wild animals and spreads in the human population through human-to-human transmission.

The Ebola outbreak was first recorded in South Sudan in 1976 and the 2014–2016 outbreak in West Africa was the largest Ebola outbreak since 40 Years of Ebola Virus Disease around the World according to the Centers for Disease Control and Prevention (CDC).

3.2.1 COVID-19 and Ebola Pandemics in African Countries
The charts below show the pattern at which Ebola and COVID-19 viruses spread in the first 10 to 85 days across affected African countries. Ebola only affected 6 African countries and its spread was low compared to COVID-19 that has affected more than 50 African countries in the first 10 to 85 days.


We also examined countries that Ebola ravaged to see how they contained the current COVID-19 pandemic. It can be seen from the chart that countries such as Sierra Leone, Guinea, and Liberia did not have COVID-19 until after 50 days of its existence in Africa. Can we say those countries learnt their lesson from the Ebola epidemic? It is important to recall that Sierra Leone, Guinea, and Liberia had 3,704 (54.5%), 1979 (29.1%) and 1107 (16.3%) confirmed Ebola deaths respectively.

3.2.2 Survival Analysis of Ebola in Affected African Countries
The‌ ‌line‌ ‌chart‌ ‌below‌ ‌shows‌ ‌that‌ ‌Liberia, Mali, Guinea, and Sierra Leone‌ ‌have‌ the ‌‌fatality‌ ‌rate‌ ‌of‌ ‌81.73%,‌ ‌71.43%,‌ ‌62.16%,‌ ‌and‌ ‌41.23% ‌respectively‌ ‌of‌ ‌the‌ ‌total‌ ‌confirmed‌ ‌cases‌ ‌that ‌resulted‌ ‌to‌ ‌‌death.‌
Senegal, Nigeria, and Sierra Leone‌ ‌have‌ the ‌recovery ‌rate‌ ‌of‌ 100%,‌ ‌63.16%,‌ ‌and‌ ‌58.77% respectively‌ ‌of‌ ‌the‌ ‌total‌ ‌confirmed‌ ‌Ebola patients that ‌recovered.‌
‌Liberia, Sierra Leone, and Guinea‌ ‌have‌ ‌a mortality‌ ‌rate‌ ‌of‌ ‌62.34,‌ ‌44.99,‌ ‌and‌ ‌15.86‌ ‌per‌ ‌100,000‌ ‌population‌ ‌respectively.‌

4.0 Summary and Conclusion

The unavailability of vaccines to combat the further spread of COVID-19 still poses a huge threat to global public health and the economy. The number of deaths associated with COVID-19 has greatly exceeded the death cases from other viruses that the world has ever experienced.
As of April 30, 2020, the total number of COVID-19 confirmed cases in Africa is reported to be 37,692; 12,630 recovered cases and 1,592 death cases. In Nigeria, this pandemic has claimed not less than 51 lives while only 307 people have recovered out of 1728 confirmed cases.



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