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.
Highlights
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a growing public health nightmare with over 30 million individuals infected as at 20 September 2020 and over 950,000 deaths worldwide (Table 1).[1,2] There is no approved standard treatment, cure, or vaccine against COVID-19 and it is expected that both infections and mortalities will continue to rise globally.[3,4,5] The epicenter of the pandemic has moved from Wuhan, China, through Europe and is in the United States of America where currently the highest number of infections and deaths is being reported
Ghana started screening for SARS-CoV-2 at the ports of entry on 6 February 2020, even before COVID-19 was declared a “Pandemic” on 11 March 2020 by the World Health Organisation.[26,27,28]
Ghana had implemented monitoring controls at all major ports of entry and suspected cases reporting to health facilities were forwarded to the Noguchi Memorial Institute for Medical Research (NMIMR) for testing
Summary
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a growing public health nightmare with over 30 million individuals infected as at 20 September 2020 and over 950,000 deaths worldwide (Table 1).[1,2] There is no approved standard treatment, cure, or vaccine against COVID-19 and it is expected that both infections and mortalities will continue to rise globally.[3,4,5] The epicenter of the pandemic has moved from Wuhan, China, through Europe and is in the United States of America where currently the highest number of infections and deaths is being reported
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