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

• DOI: 10.1038/s41467-022-30219-5
• Publication Date: 2022-05-06T10:13:14Z
• Authors: 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’cor...; 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-...; Sylvester Dassah; Victor Asoala; Kwaku P. Asante; Richard O. Phillips; Mike Y. Osei-Atwe...; John O. Gyapong; Patrick Kuma-Aboagye; William K. Ampofo; Kwabena O. Duedu; Nicaise T. Ndam; Yaw Bediako; Peter K. Quashie; Lucas N. Amenga-E...; Gordon A. Awandare
• Keywords: 0301 basic medicine; Diversity (politics); Evolutionary biology; Plant Science; Infectious disease (medical specialty); FOS: Health sciences; Ghana; Gene; Genetic diversity; Agricultural and Biological Sciences; Engineering; Sociology; Pathology; Disease; Phylogeny; 0303 health sciences; Genome; Evolutionary Dynamics of Genetic Adaptation and Mutation; Q; Life Sciences; FOS: Sociology; 3. Good health; Phylogenetics; Infectious Diseases; Spike Glycoprotein, Coronavirus; Medicine; 570; Science; Population; 610; Infectious Disease; Genome, Viral; Coronavirus Disease 2019 Research; Article; 03 medical and health sciences; Biochemistry, Genetics and Molecular Biology; Virology; Health Sciences; Genetics; Humans; Viral evolution; Pandemics; Biology; Demography; Lineage (genetic); Pandemic; SARS-CoV-2; Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); COVID-19; Outbreak; Transmission (telecommunications); Coronavirus disease 2019 (COVID-19); FOS: Biological sciences; Anthropology; Electrical engineering; Mutation; Viral RNA Silencing and Plant Immunity; Viral Transmission; 2019-20 coronavirus outbreak

AbstractThe 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.