Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Mar 18;25(3):103880.
doi: 10.1016/j.isci.2022.103880. Epub 2022 Feb 5.

Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa

Olayinka Sunday Okoh  1 , Nicholas Israel Nii-Trebi  2 , Abdulrokeeb Jakkari  3 , Tosin Titus Olaniran  4   5 , Tosin Yetunde Senbadejo  6 , Anna Aba Kafintu-Kwashie  7 , Emmanuel Oluwatobi Dairo  5   8 , Tajudeen Oladunni Ganiyu  6 , Ifiokakaninyene Ekpo Akaninyene  4   5 , Louis Odinakaose Ezediuno  9 , Idowu Jesulayomi Adeosun  10   11 , Michael Asebake Ockiya  12 , Esther Moradeyo Jimah  5   13 , David J Spiro  14 , Elijah Kolawole Oladipo  5   10 , Nídia S Trovão  14
Affiliations

Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa

Olayinka Sunday Okoh et al. iScience. .

Abstract

There is a dearth of information on COVID-19 disease dynamics in Africa. To fill this gap, we investigated the epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in the continent. We retrieved 5229 complete genomes collected in 33 African countries from the GISAID database. We investigated the circulating diversity, reconstructed the viral evolutionary divergence and history, and studied the case and death trends in the continent. Almost a fifth (144/782, 18.4%) of Pango lineages found worldwide circulated in Africa, with five different lineages dominating over time. Phylogenetic analysis revealed that African viruses cluster more closely with those from Europe. We also identified two motifs that could function as integrin-binding sites and N-glycosylation domains. These results shed light on the epidemiological and evolutionary dynamics of the circulating viral diversity in Africa. They also emphasize the need to expand surveillance efforts in Africa to help inform and implement better public health measures.

Keywords: Genomics; Phylogenetics; Virology.

PubMed Disclaimer

Figures

None
Graphical abstract
Figure 1
Figure 1
Number of COVID-19 reported cases and deaths per 100,000 population in the different continents The red line represents the average absolute number of COVID-19 cases worldwide per 100,000 population in the world (i.e., (global COVID-19 cases/world population) x 100,000). The orange points represent the average number of deaths per 100,000 population in the different continents with its scale on the left y axis. The orange line represents the number of deaths globally per 100,000 world population.
Figure 2
Figure 2
COVID-19 cases reported in African countries Absolute number of cases (left). Number of cases per 100,000 population (right).
Figure 3
Figure 3
Reported deaths from COVID-19 in Africa Absolute number of total deaths (left) per country. Number of deaths per 1,000 reported cases (right).
Figure 4
Figure 4
Number of SARS-CoV-2 tests conducted in African countries Absolute number of tests (left). Number of tests per 100,000 population (right).
Figure 5
Figure 5
COVID-19 positivity rate in Africa Number of positive patients out of every 1000 COVID-19 tests. Gray shades represent countries for which data is not available.
Figure 6
Figure 6
Sequences from African countries submitted to GISAID Absolute number of sequences from Africa submitted to GISAID (left). Sequences available in GISAID per 1,000 SARS-CoV-2 cases in Africa (right). Gray shade represents countries for which no sequences were available (n = 27/57 (47.4%) countries).
Figure 7
Figure 7
The incidence of the top five Pango lineages circulating in Africa between March 1, 2020 and January 7, 2021.
Figure 8
Figure 8
Maximum likelihood tree colored by continent Phylogenetic tree inferred for a dataset with genetic sequences from all continents.
Figure 9
Figure 9
Evolutionary divergence of SARS-CoV-2 across continents Violin plots represent the distribution of pairwise genetic distances between all sequences for isolates in each continent. Vertical lines depict the mean pairwise genetic distance between all samples in each continent.
See this image and copyright information in PMC

Update of

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Abena P.M., Decloedt E.H., Bottieau E., Suleman F., Adejumo P., Sam-Agudu N.A., Tamfum J.J.M., Seydi M., Eholie S.P., Mills E.J. Chloroquine and hydroxychloroquine for the prevention or treatment of COVID-19 in Africa: caution for inappropriate off-label use in healthcare settings. Am. J. Trop. Med. Hyg. 2020;102:1184–1188. - PMC - PubMed
    1. Abu-Raddad L.J., Chemaitelly H., Butt A.A. Effectiveness of the BNT162b2 Covid-19 vaccine against the B. 1.1. 7 and B. 1.351 variants. New Engl. J. Med. 2021;385:187–189. - PMC - PubMed
    1. Adler D., Kelly S.T. Vioplot: violin plot. R package version 0.3.7. 2020. https://github.com/TomKellyGenetics/vioplot
    1. African Centres for Disease Control Novel Coronavirus (2019-nCoV) Global Epidemic – 31 March 2020. 2020. https://africacdc.org/disease-outbreak/novel-coronavirus-2019-ncov-globa...
    1. Aiewsakun P., Wongtrakoongate P., Thawornwattana Y., Hongeng S., Thitithanyanont A. SARS-CoV-2 genetic variations associated with COVID-19 severity. MedRxiv. 2020 doi: 10.1101/2020.05.27.20114546. Preprint at. - DOI - PMC - PubMed

LinkOut - more resources