Genomic analysis of SARS-CoV-2 reveals local viral evolution in Ghana
| Autor: | Linda Boatemaa, Evangeline Obodai, Gordon A. Awandare, Ivy A. Asante, George B. Kyei, Isaac Darko Otchere, Miriam Eshun, Joyce M. Ngoi, Collins M. Morang’a, Joseph H.K. Bonney, Abraham K. Anang, Nicaise Tuikue Ndam, Dominic S. Y. Amuzu, Augustina K. Arjarquah, Lucas Amenga-Etego, Erasmus N. Kotey, Frederick Tei-Maya, William Ampofo, John Kofi Odoom, Evelyn Y. Bonney, Peter K. Quashie, Bright Adu, Vanessa Magnusen, Yaw Bediako, Selassie Kumordjie, Joe Kimanthi Mutungi |
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| Rok vydání: | 2020 |
| Předmět: |
0301 basic medicine
novel coronavirus Sequence assembly Genomics Genome Viral Biology Ghana Genome General Biochemistry Genetics and Molecular Biology Evolution Molecular 03 medical and health sciences 0302 clinical medicine Phylogenetics evolution genomics Humans 030212 general & internal medicine Clade Phylogeny Original Research Genetics Phylogenetic tree SARS-CoV-2 COVID-19 Amplicon 3. Good health 030104 developmental biology Viral evolution |
| Zdroj: | Experimental Biology and Medicine |
| ISSN: | 1535-3699 1535-3702 |
| DOI: | 10.1177/1535370220975351 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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