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 indi viduals 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.
