TY - JOUR
T1 - Genomic analysis of SARS-CoV-2 reveals local viral evolution in Ghana
AU - Ngoi, Joyce M.
AU - Quashie, Peter K.
AU - Morang'a, Collins M.
AU - Bonney, Joseph H.K.
AU - Amuzu, Dominic S.Y.
AU - Kumordjie, Selassie
AU - Asante, Ivy A.
AU - Bonney, Evelyn Y.
AU - Eshun, Miriam
AU - Boatemaa, Linda
AU - Magnusen, Vanessa
AU - Kotey, Erasmus N.
AU - Ndam, Nicaise T.
AU - Tei-Maya, Frederick
AU - Arjarquah, Augustina K.
AU - Obodai, Evangeline
AU - Otchere, Isaac D.
AU - Bediako, Yaw
AU - Mutungi, Joe K.
AU - Amenga-Etego, Lucas N.
AU - Odoom, John K.
AU - Anang, Abraham K.
AU - Kyei, George B.
AU - Adu, Bright
AU - Ampofo, William K.
AU - Awandare, Gordon A.
N1 - Funding Information:
The study was funded by a Wellcome/African Academy of Sciences Developing Excellence in Leadership Training and Science (DELTAS) grant (DEL-15–007 and 107755/Z/15/Z: Awandare); National Institute of Health Research (NIHR) (17.63.91) grants using UK aid from the UK Government for a global health research group for Genomic surveillance of malaria in West Africa (Wellcome Sanger Institute, UK) and global research unit for Tackling Infections to Benefit Africa (TIBA partnership, University of Edinburgh); and the World Bank African Centres of Excellent grant (WACCBIP-NCDs: Awandare). CMM and DSYA are supported by WACCBIP DELTAS PhD fellowships, while PQ, YB, and IOD are supported by a Crick African Network Career Accelerator fellowships. The views expressed in this publication are those of the author(s) and not necessarily those of the funders.
Funding Information:
The study was funded by a Wellcome/African Academy of Sciences Developing Excellence in Leadership Training and Science (DELTAS) grant (DEL-15?007 and 107755/Z/15/Z: Awandare); National Institute of Health Research (NIHR) (17.63.91) grants using UK aid from the UK Government for a global health research group for Genomic surveillance of malaria in West Africa (Wellcome Sanger Institute, UK) and global research unit for Tackling Infections to Benefit Africa (TIBA partnership, University of Edinburgh); and the World Bank African Centres of Excellent grant (WACCBIP-NCDs: Awandare). CMM and DSYA are supported by WACCBIP DELTAS PhD fellowships, while PQ, YB, and IOD are supported by a Crick African Network Career Accelerator fellowships. The views expressed in this publication are those of the author(s) and not necessarily those of the funders.
Publisher Copyright:
© 2020 by the Society for Experimental Biology and Medicine.
PY - 2021/4
Y1 - 2021/4
N2 - 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.
AB - 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.
KW - COVID-19
KW - SARS-CoV-2
KW - evolution
KW - genomics
KW - novel coronavirus
UR - http://www.scopus.com/inward/record.url?scp=85097680956&partnerID=8YFLogxK
U2 - 10.1177/1535370220975351
DO - 10.1177/1535370220975351
M3 - Article
C2 - 33325750
AN - SCOPUS:85097680956
SN - 1535-3702
VL - 246
SP - 960
EP - 970
JO - Experimental Biology and Medicine
JF - Experimental Biology and Medicine
IS - 8
ER -