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Genomic analysis of SARS-CoV-2 reveals local viral evolution in Ghana.
Ngoi, Joyce M; Quashie, Peter K; Morang'a, Collins M; Bonney, Joseph Hk; Amuzu, Dominic Sy; Kumordjie, Selassie; Asante, Ivy A; Bonney, Evelyn Y; Eshun, Miriam; Boatemaa, Linda; Magnusen, Vanessa; Kotey, Erasmus N; Ndam, Nicaise T; Tei-Maya, Frederick; Arjarquah, Augustina K; Obodai, Evangeline; Otchere, Isaac D; Bediako, Yaw; Mutungi, Joe K; Amenga-Etego, Lucas N; Odoom, John K; Anang, Abraham K; Kyei, George B; Adu, Bright; Ampofo, William K; Awandare, Gordon A.
  • Ngoi JM; West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, GH 0233, Ghana.
  • Quashie PK; Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, GH 0233, Ghana.
  • Morang'a CM; West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, GH 0233, Ghana.
  • Bonney JH; Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, GH 0233, Ghana.
  • Amuzu DS; Department of Biochemistry, Cell and Molecular Biology, School of Biological Sciences, University of Ghana, Accra, GH 0233, Ghana.
  • Kumordjie S; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
  • Asante IA; West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, GH 0233, Ghana.
  • Bonney EY; Department of Biochemistry, Cell and Molecular Biology, School of Biological Sciences, University of Ghana, Accra, GH 0233, Ghana.
  • Eshun M; Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, GH 0233, Ghana.
  • Boatemaa L; West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, GH 0233, Ghana.
  • Magnusen V; Department of Biochemistry, Cell and Molecular Biology, School of Biological Sciences, University of Ghana, Accra, GH 0233, Ghana.
  • Kotey EN; Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, GH 0233, Ghana.
  • Ndam NT; Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, GH 0233, Ghana.
  • Tei-Maya F; Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, GH 0233, Ghana.
  • Arjarquah AK; Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, GH 0233, Ghana.
  • Obodai E; Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, GH 0233, Ghana.
  • Otchere ID; Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, GH 0233, Ghana.
  • Bediako Y; West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, GH 0233, Ghana.
  • Mutungi JK; Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, GH 0233, Ghana.
  • Amenga-Etego LN; Department of Biochemistry, Cell and Molecular Biology, School of Biological Sciences, University of Ghana, Accra, GH 0233, Ghana.
  • Odoom JK; Mère et Enfant en Milieu Tropical, Institut de Recherche pour le Développement, Université de Paris, Paris F-75006, France.
  • Anang AK; West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, GH 0233, Ghana.
  • Kyei GB; Department of Biochemistry, Cell and Molecular Biology, School of Biological Sciences, University of Ghana, Accra, GH 0233, Ghana.
  • Adu B; West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, GH 0233, Ghana.
  • Ampofo WK; Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, GH 0233, Ghana.
  • Awandare GA; Department of Biochemistry, Cell and Molecular Biology, School of Biological Sciences, University of Ghana, Accra, GH 0233, Ghana.
Exp Biol Med (Maywood) ; 246(8): 960-970, 2021 04.
Article in English | MEDLINE | ID: covidwho-978882
Semantic information from SemMedBD (by NLM)
1. COVID-19 COEXISTS_WITH Hydranencephaly with Renal Aplasia-Dysplasia
Subject
COVID-19
Predicate
COEXISTS_WITH
Object
Hydranencephaly with Renal Aplasia-Dysplasia
2. Infected PROCESS_OF Persons
Subject
Infected
Predicate
PROCESS_OF
Object
Persons
3. COVID-19 COEXISTS_WITH Hydranencephaly with Renal Aplasia-Dysplasia
Subject
COVID-19
Predicate
COEXISTS_WITH
Object
Hydranencephaly with Renal Aplasia-Dysplasia
4. Infected PROCESS_OF Persons
Subject
Infected
Predicate
PROCESS_OF
Object
Persons
ABSTRACT
The confirmed case fatality rate for the coronavirus disease 2019 (COVID-19) in Ghana has dropped from a peak of 2% in March to be consistently below 1% since May 2020. Globally, case fatality rates have been linked to the strains/clades of circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within a specific country. Here we present 46 whole genomes of SARS-CoV-2 circulating in Ghana, from two separate sequencing batches 15 isolates from the early epidemic (March 12-April 1 2020) and 31 from later time-points ( 25-27 May 2020). Sequencing was carried out on an Illumina MiSeq system following an amplicon-based enrichment for SARS-CoV-2 cDNA. After genome assembly and quality control processes, phylogenetic analysis showed that the first batch of 15 genomes clustered into five clades 19A, 19B, 20A, 20B, and 20C, whereas the second batch of 31 genomes clustered to only three clades 19B, 20A, and 20B. The imported cases (6/46) mapped to circulating viruses in their countries of origin, namely, India, Hungary, Norway, the United Kingdom, and the United States of America. All genomes mapped to the original Wuhan strain with high similarity (99.5-99.8%). All imported strains mapped to the European superclade A, whereas 5/9 locally infected individuals harbored the B4 clade, from the East Asian superclade B. Ghana appears to have 19B and 20B as the two largest circulating clades based on our sequence analyses. In line with global reports, the D614G linked viruses seem to be predominating. Comparison of Ghanaian SARS-CoV-2 genomes with global genomes indicates that Ghanaian strains have not diverged significantly from circulating strains commonly imported into Africa. The low level of diversity in our genomes may indicate lower levels of transmission, even for D614G viruses, which is consistent with the relatively low levels of infection reported in Ghana.
Subject(s)
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Phylogeny / Genome, Viral / Evolution, Molecular / SARS-CoV-2 Type of study: Observational study / Randomized controlled trials Limits: Humans Country/Region as subject: Africa Language: English Journal: Exp Biol Med (Maywood) Journal subject: Biology / Physiology / Medicine Year: 2021 Document Type: Article Affiliation country: 1535370220975351

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Phylogeny / Genome, Viral / Evolution, Molecular / SARS-CoV-2 Type of study: Observational study / Randomized controlled trials Limits: Humans Country/Region as subject: Africa Language: English Journal: Exp Biol Med (Maywood) Journal subject: Biology / Physiology / Medicine Year: 2021 Document Type: Article Affiliation country: 1535370220975351