As of September 5, 2020, over 705 million people in the world live in extreme poverty compared to about 651 million people in 2019 [5]. In 2020, 102,125,917 people are reported to be living in extreme poverty from a total population of 205,323,504 people in Nigeria, the most populous African nation compared to 200,369,248 people, among whom 92,441,550 people lived in extreme poverty in 2019 [5]. The COVID-19 has significantly ravaged economies and posed serious threat to public health and social interaction, spreading across the globe within 3 months of its outbreak [3]. It was hypothesized that low- and middle-income countries, especially African nations, would be seriously hit by the pandemic due to her vulnerability to infectious diseases and inadequate health structure. Surprisingly, there have been very low mortality rate due to COVID-19 in African nations when compared to developed nations in the Americas and Europe where the pandemic has had its highest toll of infection and fatality [7]. This study assessed the possible factors that could have accounted for the low mortality rate due to COVID-19 in Africa.
The dataset from infected patients helps to understand the COVID-19 infection rate, risks, epidemiology, and spread of the disease. The WHO suggested 10–30 tests per confirmed case as an indicator of adequate testing [7]. South Africa has the highest test rate of 3,918,478 people in Africa, representing about 7% of its 59,461,240 population, which is still a way long off from the adequate testing indicator and also when compared with countries with highest prevalence of COVID-19 in other regions: USA (37%), Russia (36%), and Australia (32%) [4]. In same vein, Nigeria, the most populous Black African nation, has only tested 440,248 people representing 0.21% of its over 207 million population. This trend holds true for many other African countries. Hence, caution should be taken while interpreting these data as the true number of COVID-19 cases in Africa might still remain undetected. However, with the current data available, though with daily increasing incidence, the mortality rate due to COVID-19 in Africa has been minimal. Other factor such as late incidence of the disease [10, 18], which gives an advantage for early preparation before the outbreak by enforcing regulatory guidelines (active surveillance, isolation, quarantine, contact tracing, and social distancing among others) in line with the WHO guidelines could have played a key role in managing the pandemic in Africa [7, 8]. The American Public Media (APM) Research laboratory in August 2020 reported 88.4 deaths per 100,000 Black Americans due to COVID-19 compared to 54.4 deaths per 100,000 Latino Americans and 36.4 deaths per 100,000 Asian Americans. The APM findings suggests higher mortality due to COVID-19 in Black Americans in the USA [19]. This raises a concern to understand why Blacks are dying more due to COVID-19 overseas than in Africa.
The present study also looked into the mutational landscape of SARS-CoV-2 genome in Africa. Highly recurrent mutation (D614G) was observed in the S1 domain of S glycoprotein which facilitates viral entry into host by binding to the human angiotensin-converting enzyme 2 (ACE2) receptor. The S2 domain of the S glycoprotein which plays a crucial role in viral-host cell membrane fusion was well conserved; this could serve as an important target for antiviral drug design. The T265I mutation that is prevalent in the USA which aids SARS-CoV-2 survival in the host cell [20] was only observed in 26 viral sequences, predominantly in Senegal (69.23%). P4715L mutation hotspot present in the RNA-dependent RNA polymerase (RdRp) region was first observed in Italy during the sporadic increase in incidence and fatality of COVID-19 in Europe [15]. This supports the evidence that most of Africa’s index case originates from European and American travelers [3, 18], which could have resulted to the vast distribution of these mutations across the infected patients.
The concurrent R203K and G204R mutation are present in the N phosphoprotein region, which plays an important role in viral interaction with the M protein during virion assemblage [21]. Gene variants in the nucleocapsid region alter miRNAs binding, which might contribute to the pathogenesis and progression of infection in the patient [22]. The viral ORF3a and ORF10 proteins can synergistically attack heme on the host’s hemoglobin 1-β chain, thereby disintegrating iron to form porphyrin. This results to reduced hemoglobin-carrying oxygen and carbon dioxide causing extreme poisoning and inflammation of the hepatocytes [23]. Q57H mutation in the ORF3a region was observed to coincide with D614G and P4715L variants. The RdRp P4715L mutation coincides with S protein D614G mutation alongside the concurrent N protein R203K and G204R variants, and in their absence ORF3a Q57H variant. The SARS-CoV-2 membrane, envelope, ORF6, ORF7, and ORF10 proteins were well conserved. These mutational hotspots and conserved domains must be well-considered during drug or vaccine design to avoid vaccine evasion and drug resistance.
Lastly, this study looked at the age distribution of the infected patients as a contributory factor to the low fatality rate. The average life expectancy in Nigeria is 54 years, a reflection of Sub-Saharan Africa (61 years) compared to European union (81 years), China (77 years), and USA (79 years) [24]. Earlier report [3] suggests that COVID-19 has high mortality and severity in older people (> 65 years) than the younger population, which have high chances of recovery from the infection. Only 5.1% of the 924 infected Africans in this present study are over 65 years. This could have played a major role in the relatively high recovery rate (81.21%) and low mortality (2.4%) due to COVID-19 observed in the African population.
