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-DjanieEnock 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*, Gordon A. Awandare*

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    21 Citations (SciVal)

    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.
    Original languageEnglish
    Article number2494
    JournalNature Communications
    Volume13
    Issue number1
    DOIs
    Publication statusPublished (VoR) - Dec 2022

    Funding

    The study was facilitated by the Government of Ghana through the Ghana Health Service. ARTIC donated the primers used for the study. All data storage and analyses were performed on Zuputo®, the University of Ghana’s high-performance computing cluster. We acknowledge the Community and Public engagement members; Kyerewaa A. Boateng and Simon Donkor, Andrew M. Nantogmah and the entire WACCBIP and UHAS COVID-19 Teams. The study was funded by a grant from the Rockefeller Foundation (2021 HTH 006), an Institut de Recherche pour le Développement (IRD) grant (ARIACOV), African Research Universities Alliance (ARUA) Vaccine Development Hubs grant with funds from Open Society Foundation, a Wellcome/African Academy of Sciences Developing Excellence in Leadership Training and Science (DELTAS) grant (DEL-15-007 and 107755/Z/15/Z: G.A.A.); National Institute of Health Research (NIHR) (17.63.91) grants using UK aid from the UK Government for a global health research group for Genomic surveillance of malaria in West Africa (Wellcome Sanger Institute, UK) and global research unit for Tackling Infections to Benefit Africa (TIBA partnership, University of Edinburgh); and the World Bank African Centres of Excellence Impact grant (WACCBIP-NCDs: G.A.A.). C.M.M. and D.S.Y.A. are supported by WACCBIP DELTAS PhD fellowships, while P.Q., and Y.B. are supported by a Crick African Network Career Accelerator fellowship. The University of Health and Allied Sciences, COVID-19 Testing and Research Centre was supported by China Novartis Institutes of Biomedical Research (CNIBR-SCD: K.O.D.) and the Grand Challenges Africa programme grant GCA/AMR/rnd2/138: K.O.D.). The views expressed in this publication are those of the author(s) and not necessarily those of the funders. The study was facilitated by the Government of Ghana through the Ghana Health Service. ARTIC donated the primers used for the study. All data storage and analyses were performed on Zuputo®, the University of Ghana’s high-performance computing cluster. We acknowledge the Community and Public engagement members; Kyerewaa A. Boateng and Simon Donkor, Andrew M. Nantogmah and the entire WACCBIP and UHAS COVID-19 Teams. The study was funded by a grant from the Rockefeller Foundation (2021 HTH 006), an Institut de Recherche pour le Développement (IRD) grant (ARIACOV), African Research Universities Alliance (ARUA) Vaccine Development Hubs grant with funds from Open Society Foundation, a Wellcome/African Academy of Sciences Developing Excellence in Leadership Training and Science (DELTAS) grant (DEL-15-007 and 107755/Z/15/Z: G.A.A.); National Institute of Health Research (NIHR) (17.63.91) grants using UK aid from the UK Government for a global health research group for Genomic surveillance of malaria in West Africa (Wellcome Sanger Institute, UK) and global research unit for Tackling Infections to Benefit Africa (TIBA partnership, University of Edinburgh); and the World Bank African Centres of Excellence Impact grant (WACCBIP-NCDs: G.A.A.). C.M.M. and D.S.Y.A. are supported by WACCBIP DELTAS PhD fellowships, while P.Q., and Y.B. are supported by a Crick African Network Career Accelerator fellowship. The University of Health and Allied Sciences, COVID-19 Testing and Research Centre was supported by China Novartis Institutes of Biomedical Research (CNIBR-SCD: K.O.D.) and the Grand Challenges Africa programme grant GCA/AMR/rnd2/138: K.O.D.). The views expressed in this publication are those of the author(s) and not necessarily those of the funders.

    FundersFunder number
    African Research Universities Alliance
    China Novartis Institutes of Biomedical ResearchGCA/AMR/rnd2/138
    DELTASDEL-15-007, 107755/Z/15/Z
    Ghana Health Service
    WACCBIP
    Wellcome Sanger Institute
    Wellcome/African Academy of Sciences Developing Excellence in Leadership Training and Science
    Rockefeller Foundation2021 HTH 006
    Open Society Foundations
    Institut de recherche pour le développement
    Government of the United Kingdom
    National Institute for Health and Care Research17.63.91
    University of Ghana
    University of Health and Allied Sciences

      Keywords

      • *COVID-19/epidemiology Genome, Viral/genetics Ghana/epidemiology Humans Mutation Pandemics Phylogeny *SARS-CoV-2/genetics Spike Glycoprotein, Coronavirus/genetics

      Fingerprint

      Dive into the research topics of 'Genetic diversity of SARS-CoV-2 infections in Ghana from 2020-2021'. Together they form a unique fingerprint.

      Cite this