Genomic analysis of SARS-CoV-2 reveals local viral evolution in Ghana

Ngoi, Joyce M.; Quashie, Peter K.; Morang’a, Collins M.; Bonney, Joseph Humphrey Kofi; Amuzu, Dominic S. Y.; Kumordjie, Selassie; Asante, Ivy A.; Bonney, Evelyn Yayra; Eshun, Miriam; Boatemaa, Linda; Magnusen, Vanessa; Kotey, Erasmus Nikoi; Ndam, Nicaise Tuikue; Tei-Maya, Frederick; Arjarquah, Augustina; Obodai, Evangeline; Otchere, Isaac Darko; Bediako, Yaw; Mutungi, Joe Kimanthi; Amenga-Etego, Lucas; Odoom, John Kofi; Anang, Abraham K.; Kyei, George B.; Adu, Bright; Ampofo, William; Awandare, Gordon A.

doi:10.1177/1535370220975351

Cited by 23 publications

(23 citation statements)

References 41 publications

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“…Our previous genomic study showed evidence of undetected community spread likely caused by asymptomatic individuals 28 . Of note, nearly 80% of people who were seropositive did not report significant COVID-19 symptoms (Figure 3), confirming that SARS-CoV-2 infections in Ghana are predominantly asymptomatic, consistent with reported global trends 8 .…”

Section: Discussionmentioning

confidence: 95%

“…As such, it was not surprising that the socioeconomic divide in prevalence observed in Phase I had mostly disappeared and even appeared reversed by Phase IV. Importantly, Phase IV was the first time the modal surveyed age group (21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38)(39)(40) also demonstrated model seropositivity (24.9%). This trend mimicked hospitalisation and test positivity records since December 2020 3 .…”

Section: Discussionmentioning

confidence: 99%

“…Individuals were recruited from public places in Accra (National capital, where >50% of reported cases occur), Kasoa (a densely-populated town in the Central Region, and a COVID-19 transmission hotspot 28 , which shares a border with Accra), Cape Coast (Central Regional capital), Akropong (a small town in the Eastern Region, a 15-minute drive away from Accra), Navrongo (a small town in the Upper East Region, which hosts a public university and a government Health Research Centre) and Bolgatanga (the Upper East Regional capital) (Figure 1). Medical and research Staff were also screened at facilities across Accra and one in Cape Coast.…”

Section: Study Sitesmentioning

confidence: 99%

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Trends of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody prevalence in selected regions across Ghana

Quashie¹,

Mutungi²,

Dzabeng³

et al. 2021

Wellcome Open Res

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Background: We set out to estimate the community-level exposure to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Ghana. Methods: Phased seroprevalence studies of 2729 participants at selected locations across Ghana were conducted. Phase I (August 2020) sampled 1305 individuals at major markets/lorry stations, shopping malls, hospitals and research institutions involved in coronavirus disease 2019 (COVID-19) work. The study utilized a lateral flow rapid diagnostic test (RDT) which detected IgM and IgG antibodies against SARS-CoV-2 nucleocapsid protein. Results: During Phase I, 252/1305 (19%) tested positive for IgM or IgG or both. Exposure was significantly higher at markets/lorry stations (26.9%) compared to malls (9.4%), with 41–60-year group demonstrating highest seropositivity (27.2%). Exposure was higher in participants with no formal education (26.2%) than those with tertiary education (13.1%); and higher in informally employed workers (24.0%) than those in the formal sector (15.0%). Results from phases II and III, in October and December 2020 respectively, implied either reduced transmissions or loss of antibody expression in some participants. The Upper East region showed the lowest seropositivity (2%). Phase IV, in February 2021, showed doubled seropositivity in the upper income bracket (26.2%) since August 2020, reflective of Ghana’s second wave of symptomatic COVID-19 cases. This suggested that high transmission rates had overcome the initial socioeconomic stratification of exposure risk. Reflective of second wave hospitalisation trends, the 21-40 age group demonstrated modal seropositivity (24.9) in Phase IV whilst 40-60 years and 60+ previously demonstrated highest prevalence. Conclusions: Overall, the data indicates higher COVID-19 seroprevalence than officially acknowledged, likely implying a considerably lower-case fatality rate than the current national figure of 0.84%. The data also suggests that COVID-19 is predominantly asymptomatic COVID-19 in Ghana. The observed trends mimic clinical trends of infection and imply that the methodology used was appropriate.

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Section: Discussionmentioning

confidence: 95%

Section: Discussionmentioning

confidence: 99%

Section: Study Sitesmentioning

confidence: 99%

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Trends of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody prevalence in selected regions across Ghana

Quashie¹,

Mutungi²,

Dzabeng³

et al. 2021

Wellcome Open Res

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“…By April 4 th , positive cases who had neither travel history nor known contact with confirmed cases, were detected, implying local transmission. To estimate COVID-19 community spread in Ghana, over a 7-month period, we randomly screened for IgM and IgG antibodies against SARS-CoV-2 in people at various public places in Accra (National capital, where >50% of reported cases occur), Kasoa (a densely-populated town in the Central Region, and a COVID-19 transmission hotspot [27] and which shares a border with Accra), Cape Coast (Central Regional capital), Akropong (a small town in the Eastern Region, a 15-minute drive away from Accra), Navrongo (a small town in the Upper East Region, which hosts a public university and a government Health Research Centre) and Bolgatanga (the Upper East Regional capital) (Figure 1). A questionnaire administered during the study collected demographic data as well and evaluated the COVID-19 knowledge, attitudes and perceptions (KAP) of study participants.…”

Section: Introductionmentioning

confidence: 99%

Trends of SARS-CoV-2 antibody prevalence in selected regions across Ghana

Quashie

Mutungi

Dzabeng

et al. 2021

Preprint

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To estimate the level of community exposure to SARS–CoV–2 in Ghana, we conducted phased seroprevalence studies of 2729 participants in selected locations across Ghana. Phase I screening (August 2020) covered a total of 1305 individuals screened at major markets/lorry stations, major shopping malls, hospitals and research institutions involved in COVID–19 work. The screening was performed using a strip–in–cassette lateral flow type Rapid Diagnostic Test (RDT) kit that simultaneously and separately detected IgM and IgG antibodies against SARS–CoV–2 nucleocapsid protein. In Phase I, 252/1305 (19%) tested positive for IgM or IgG or both. Exposure rate was significantly higher among individuals tested at markets/lorry stations (26.9%) compared to those at Shopping Malls (9.4%). The 41—60–years age group had the highest exposure rate (27.2%). People with only a basic level or no formal education had a higher exposure rate (26.2%) than those with tertiary level education (13.1%); and higher in informally employed workers (24.0%) than those in the formal sector (15.0%). Phases II and III screening activities in October and December 2020, respectively, showed no evidence of increased seroprevalence, indicating either a reduced transmission rate or loss of antibody expression in a subset of the participants. The Upper East region has the lowest exposure rate, with only 4 of 200 participants (2%) seropositivity. Phase IV screening in February 2021 showed that exposure rates in the upper income earners (26.2%) had almost doubled since August 2020, reflective of Ghana′s second wave of symptomatic COVID–19 cases, which began in December 2020. The Phase IV results suggest that seroprevalence levels have become so high that the initial socioeconomic stratification of exposure has been lost. Overall, the data indicates a much higher COVID–19 seroprevalence in the Greater Accra Region than was officially acknowledged, likely implying a considerably lower case fatality rate than the current national figure of 0.84%. Additionally, the high exposure levels seen in the communities suggest that COVID–19 in Ghana still predominantly presents with none–to–mild symptoms. Our results lay the foundation for more extensive SARS–CoV–2 surveillance in Ghana and the West African sub–region, including deploying rapid antigen test kits in concert to determine the actual infection burden since antibody development lags infection.

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“…However, specific allocation of funds to institutions to conduct research and generate the local evidence to guide the national response was not obvious and scientists used internal resources to support the response. The limited activities included the modelling of the spread of the epidemic coordinated by the Science Section of the Ghana Academy of Arts and Sciences, the sequencing of the virus circulating in Ghana 4 by Noguchi Memorial Institute for Medical Research and the West African Centre for Cell Biology of Infectious Pathogens of the University of Ghana and their collaborators.…”

mentioning

confidence: 99%