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

Olayinka Sunday Okoh; Nicholas Israel Nii-Trebi; Abdulrokeeb Jakkari; Tosin Titus Olaniran; Tosin Yetunde Senbadejo; Anna Aba Kafintu-kwashie; Emmanuel Oluwatobi Dairo; Tajudeen Oladunni Ganiyu; Ifiokakaninyene Ekpo Akaninyene; Louis Odinakaose Ezediuno; Idowu Jesulayomi Adeosun; Michael Asebake Ockiya; Esther Moradeyo Jimah; David J. Spiro; Elijah Kolawole Oladipo; Nídia S. Trovão

doi:10.1016/j.isci.2022.103880

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

Olayinka Sunday Okoh, Nicholas Israel Nii-Trebi, Abdulrokeeb Jakkari, Tosin Titus Olaniran, Tosin Yetunde Senbadejo, Anna Aba Kafintu-kwashie, Emmanuel Oluwatobi Dairo, Tajudeen Oladunni Ganiyu, Ifiokakaninyene Ekpo Akaninyene, Louis Odinakaose Ezediuno, Idowu Jesulayomi Adeosun, Michael Asebake Ockiya, Esther Moradeyo Jimah, David J. Spiro, Elijah Kolawole Oladipo, Nídia S. Trovão

Department of Medical Laboratory Sciences

Research output: Contribution to journal › Article › peer-review

6 Citations (Scopus)

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.

Original language	English
Article number	103880
Journal	iScience
Volume	25
Issue number	3
DOIs	https://doi.org/10.1016/j.isci.2022.103880
Publication status	Published - 18 Mar 2022

Keywords

Genomics
Phylogenetics
Virology

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1016/j.isci.2022.103880

Cite this

Okoh, O. S., Nii-Trebi, N. I., Jakkari, A., Olaniran, T. T., Senbadejo, T. Y., Kafintu-kwashie, A. A., Dairo, E. O., Ganiyu, T. O., Akaninyene, I. E., Ezediuno, L. O., Adeosun, I. J., Ockiya, M. A., Jimah, E. M., Spiro, D. J., Oladipo, E. K., & Trovão, N. S. (2022). Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa. iScience, 25(3), Article 103880. https://doi.org/10.1016/j.isci.2022.103880

@article{71e6bb4441ff4c2fa75e920f828fd38c,

title = "Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa",

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",

author = "Okoh, {Olayinka Sunday} and Nii-Trebi, {Nicholas Israel} and Abdulrokeeb Jakkari and Olaniran, {Tosin Titus} and Senbadejo, {Tosin Yetunde} and Kafintu-kwashie, {Anna Aba} and Dairo, {Emmanuel Oluwatobi} and Ganiyu, {Tajudeen Oladunni} and Akaninyene, {Ifiokakaninyene Ekpo} and Ezediuno, {Louis Odinakaose} and Adeosun, {Idowu Jesulayomi} and Ockiya, {Michael Asebake} and Jimah, {Esther Moradeyo} and Spiro, {David J.} and Oladipo, {Elijah Kolawole} and Trov{\~a}o, {N{\'i}dia S.}",

note = "Publisher Copyright: {\textcopyright} 2022",

year = "2022",

month = mar,

day = "18",

doi = "10.1016/j.isci.2022.103880",

language = "English",

volume = "25",

journal = "iScience",

issn = "2589-0042",

publisher = "Elsevier Inc.",

number = "3",

}

Okoh, OS, Nii-Trebi, NI, Jakkari, A, Olaniran, TT, Senbadejo, TY, Kafintu-kwashie, AA, Dairo, EO, Ganiyu, TO, Akaninyene, IE, Ezediuno, LO, Adeosun, IJ, Ockiya, MA, Jimah, EM, Spiro, DJ, Oladipo, EK & Trovão, NS 2022, 'Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa', iScience, vol. 25, no. 3, 103880. https://doi.org/10.1016/j.isci.2022.103880

TY - JOUR

T1 - Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa

AU - Okoh, Olayinka Sunday

AU - Nii-Trebi, Nicholas Israel

AU - Jakkari, Abdulrokeeb

AU - Olaniran, Tosin Titus

AU - Senbadejo, Tosin Yetunde

AU - Kafintu-kwashie, Anna Aba

AU - Dairo, Emmanuel Oluwatobi

AU - Ganiyu, Tajudeen Oladunni

AU - Akaninyene, Ifiokakaninyene Ekpo

AU - Ezediuno, Louis Odinakaose

AU - Adeosun, Idowu Jesulayomi

AU - Ockiya, Michael Asebake

AU - Jimah, Esther Moradeyo

AU - Spiro, David J.

AU - Oladipo, Elijah Kolawole

AU - Trovão, Nídia S.

PY - 2022/3/18

Y1 - 2022/3/18

N2 - 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.

AB - 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.

KW - Genomics

KW - Phylogenetics

KW - Virology

UR - http://www.scopus.com/inward/record.url?scp=85124948880&partnerID=8YFLogxK

U2 - 10.1016/j.isci.2022.103880

DO - 10.1016/j.isci.2022.103880

M3 - Article

AN - SCOPUS:85124948880

SN - 2589-0042

VL - 25

JO - iScience

JF - iScience

IS - 3

M1 - 103880

ER -

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

Abstract

Keywords

UN SDGs

Access to Document

Other files and links

Fingerprint

Cite this