The COVID-19 Pandemic and Explaining Outcomes in Africa: Could Genomic Variation Add to the Debate?

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of COVID-19, emanated from the Wuhan Province in China and rapidly spread across the globe causing extensive morbidity and mortality rate, and affecting the global economy and livelihoods. Contrary to early predictions of "body bags" across Africa, the African COVID-19 pandemic was marked by apparent low case numbers and an overall mortality rate when compared with the other geographical regions. Factors used to describe this unexpected pattern included a younger population, a swifter and more effective national health policy, limited testing capacities, and the possibility of inadequate reporting of the cases, among others. However, despite genomics contributing to interindividual variations in many diseases across the world, there are inadequate genomic and multiomics data on COVID-19 in Africa that prevent richer transdisciplinary discussions on the contribution of genomics to the spread of COVID-19 pandemic. To invite future debates on comparative studies of COVID-19 genomics and the pandemic spread around the world regions, this expert review evaluates the reported frequency distribution of genetic variants in candidate genes that are likely to affect COVID-19 infection dynamics/disease outcomes. We propose here that genomic variation should be considered among the many factors determining the COVID-19 infection and its outcomes in African populations and across the world.

Keywords: Africa; COVID-19; SARS-CoV-2; epidemiology; genomics; public health.

FIG. 1.

Cumulative global COVID-19 confirmed cases by WHO regions as of June 30, 2022 (adapted from WHO, 2022a).

FIG. 2.

Cumulative global COVID-19 confirmed deaths by WHO regions as of June 30, 2022 (adapted from WHO, 2022a).

FIG. 3.

Distribution of HLA-B alleles implicated in COVID-19 response in select populations (allele frequencies obtained from the AFND) (Gonzalez-Galarza et al, 2020). This figure shows a higher frequency of protective allele HLA-B*40:01 in individuals of Asian descent than the other global populations. HLA-B*40:01 seems absent in African populations. HLA-*46:01 is associated with increased risk of COVID-19 infection. HLA-B*46:01 is absent in African populations and is predominantly European.

FIG. 4.

Distribution of HLA-A alleles implicated in COVID-19 response in select populations (allele frequencies obtained from the AFND) (Gonzalez-Galarza et al, 2020). This figure shows a higher frequency of HLA-A*23:01 in individuals of African descent than the other global populations. HLA-*23:01 is reported to have a protective effect on COVID-19 infection. While HLA-A*02:01 (predominantly European) has been associated with low risk of mortality rate in COVID-19 patients. HLA-A*23:01 (predominantly East Asian) is also associated with a protective role against COVID-19 infection. This infers that protective roles may be driven by very different variants among global populations. Interestingly, HLA-A alleles associated with increased risk of infection do not vary much among global populations. AFND, allele frequency net database; HLA, human leukocyte antigen system.

FIG. 5.

Distribution of various HLA alleles implicated in COVID-19 response in select populations (allele frequencies obtained from the AFND) (Gonzalez-Galarza et al, 2020). This figure shows a higher frequency of allele HLA-DQB1*06:021 in individuals of African descent than the other global populations. HLA-DQB1*06:021 has been associated with an extremely severe course (Iyer et al, 2020) of COVID-19 infection. HLA-C*01 seems absent in African populations, but is present in Japanese and Korean populations; this allele is also associated with a high COVID-19 mortality rate (Iyer et al, 2020).