Genetic diversity of SARS-CoV-2 infections in Ghana from 2020-2021

Collins M. Morang’a, Joyce M. Ngoi, Jones Gyamfi, Dominic S. Y. Amuzu, Benjamin D. Nuertey, Philip M. Soglo, Vincent Appiah, Ivy A. Asante, Paul Owusu-Oduro, Samuel Armoo, Dennis Adu-Gyasi, Nicholas Amoako, Joseph Oliver-Commey, Michael Owusu, Augustina Sylverken, Edward D. Fenteng, Violette V. M’cormack, Frederick Tei-Maya, Evelyn B. Quansah, Reuben Ayivor-Djanie, Enock K. Amoako, Isaac T. Ogbe, Bright K. Yemi, Israel Osei-Wusu, Deborah N. A. Mettle, Samirah Saiid, Kesego Tapela, Francis Dzabeng, Vanessa Magnussen, Jerry Quaye, Precious C. Opurum, Rosina A. Carr, Patrick T. Ababio, Abdul-Karim Abass, Samuel K. Akoriyea, Emmanuella Amoako, Frederick Kumi-Ansah, Oliver D. Boakye, Dam K. Mibut, Theophilus Odoom, Lawrence Ofori-Boadu, Emmanuel Allegye-Cudjoe, Sylvester Dassah, Victor Asoala, Kwaku P. Asante, Richard O. Phillips, Mike Y. Osei-Atweneboana, John O. Gyapong, Patrick Kuma-Aboagye, William K. Ampofo, Kwabena O. Duedu, Nicaise T. Ndam, Yaw Bediako, Peter K. Quashie (), Lucas N. Amenga-Etego () and Gordon A. Awandare ()
Additional contact information
Collins M. Morang’a: University of Ghana
Joyce M. Ngoi: University of Ghana
Jones Gyamfi: University of Health and Allied Sciences COVID-19 Testing and Research Centre
Dominic S. Y. Amuzu: University of Ghana
Benjamin D. Nuertey: Tamale Teaching Hospital Intensive Care Unit, Ghana Health Service
Philip M. Soglo: University of Ghana
Vincent Appiah: University of Ghana
Ivy A. Asante: University of Ghana, Legon
Paul Owusu-Oduro: LEDing Medical Laboratory
Samuel Armoo: Biomedical and Public Health Research Unit, Council for Scientific and Industrial Research
Dennis Adu-Gyasi: Kintampo Health Research Centre, Research and Development Division, Ghana Health Service
Nicholas Amoako: University of Ghana
Joseph Oliver-Commey: Ghana Infectious Disease Centre
Michael Owusu: Kwame Nkrumah University of Science and Technology
Augustina Sylverken: Kwame Nkrumah University of Science and Technology
Edward D. Fenteng: Veterinary Services Directorate
Violette V. M’cormack: University of Ghana
Frederick Tei-Maya: University of Ghana
Evelyn B. Quansah: University of Ghana
Reuben Ayivor-Djanie: University of Health and Allied Sciences COVID-19 Testing and Research Centre
Enock K. Amoako: University of Ghana
Isaac T. Ogbe: University of Ghana
Bright K. Yemi: University of Ghana
Israel Osei-Wusu: University of Ghana
Deborah N. A. Mettle: University of Ghana
Samirah Saiid: University of Ghana
Kesego Tapela: University of Ghana
Francis Dzabeng: University of Ghana
Vanessa Magnussen: University of Ghana
Jerry Quaye: University of Ghana
Precious C. Opurum: University of Ghana
Rosina A. Carr: University of Health and Allied Sciences COVID-19 Testing and Research Centre
Patrick T. Ababio: Veterinary Services Directorate
Abdul-Karim Abass: Tamale Public Health and Reference Laboratory, Ghana Health Service
Samuel K. Akoriyea: Institutional Care Division (ICD), Ghana Health Service
Emmanuella Amoako: Cape Coast Teaching Hospital, Ghana Health Service
Frederick Kumi-Ansah: Cape Coast Teaching Hospital, Ghana Health Service
Oliver D. Boakye: Ghana Health Service
Dam K. Mibut: Tamale Teaching Hospital Intensive Care Unit, Ghana Health Service
Theophilus Odoom: Ghana Health Service
Lawrence Ofori-Boadu: Ghana Health Service
Emmanuel Allegye-Cudjoe: Pong-Tamale Central Veterinary Laboratory, National Veterinary Services Directorate
Sylvester Dassah: Navrongo Health Research Centre, Research and Development Division, Ghana Health Service
Victor Asoala: Navrongo Health Research Centre, Research and Development Division, Ghana Health Service
Kwaku P. Asante: Kintampo Health Research Centre, Research and Development Division, Ghana Health Service
Richard O. Phillips: Kwame Nkrumah University of Science and Technology
Mike Y. Osei-Atweneboana: Biomedical and Public Health Research Unit, Council for Scientific and Industrial Research
John O. Gyapong: University of Health and Allied Sciences COVID-19 Testing and Research Centre
Patrick Kuma-Aboagye: Ghana Health Service
William K. Ampofo: University of Ghana, Legon
Kwabena O. Duedu: University of Health and Allied Sciences COVID-19 Testing and Research Centre
Nicaise T. Ndam: Institut de Recherche pour le Développement
Yaw Bediako: University of Ghana
Peter K. Quashie: University of Ghana
Lucas N. Amenga-Etego: University of Ghana
Gordon A. Awandare: University of Ghana

Nature Communications, 2022, vol. 13, issue 1, 1-11

Abstract: Abstract The COVID-19 pandemic is one of the fastest evolving pandemics in recent history. As such, the SARS-CoV-2 viral evolution needs to be continuously tracked. This study sequenced 1123 SARS-CoV-2 genomes from patient isolates (121 from arriving travellers and 1002 from communities) to track the molecular evolution and spatio-temporal dynamics of the SARS-CoV-2 variants in Ghana. The data show that initial local transmission was dominated by B.1.1 lineage, but the second wave was overwhelmingly driven by the Alpha variant. Subsequently, an unheralded variant under monitoring, B.1.1.318, dominated transmission from April to June 2021 before being displaced by Delta variants, which were introduced into community transmission in May 2021. Mutational analysis indicated that variants that took hold in Ghana harboured transmission enhancing and immune escape spike substitutions. The observed rapid viral evolution demonstrates the potential for emergence of novel variants with greater mutational fitness as observed in other parts of the world.

Date: 2022
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DOI: 10.1038/s41467-022-30219-5

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