Tracking genetic diversity of SARS-CoV-2 infections in Ghana after one year of surveillance

Morang’a, Collins M.; Ngoi, Joyce M.; Gyamfi, Jones; Amuzu, Dominic S. Y.; Nuertey, Benjamin; Soglo, Philip; Appiah, Vincent; Asante, Ivy A.; Owusu-Oduro, Paul; Armoo, Samuel; Adu-Gyasi, Dennis; Amoako, Nicholas; Oliver‐Commey, Joseph; Owusu, Michael; Sylverken, Augustina Angelina; Fenteng, Edward; M'cormack, Violette; Tei-Maya, Frederick; Quansah, Evelyn; Ayivor-Djanie, Reuben; Amoako, Enock; Ogbe, Isaac; Yemi, Bright; Osei-Wusu, Israel; Mettle, Deborah; Saiid, Samirah; Tapela, Kesego; Dzabeng, Francis; Magnussen, Vanessa; Quaye, Jerry; Opurum, Precious; Carr, Rosina A. A.; Ababio, Patrick Tetteh; Abass, Abdul-Karim; Akoriyea, Samuel; Amoako, Emmanuella; Kumi-Ansah, Frederick; Boakye, Oliver; Mibut, Dam; Odoom, Theophilus; Ofori-Boadu, Lawrence; Allegye-Cudjoe, Emmanuel; Dassah, Sylvester; Asoala, Victor; Asante, Kwaku Poku; Phillips, Richard Odame; Osei-Atweneboana, Mike Y.; Gyapong, John; Kuma-Aboagye, Patrick; Ampofo, William; Duedu, Kwabena Obeng; Ndam, Nicaise Tuikue; Bediako, Yaw; Quashie, Peter K.; Amenga-Etego, Lucas; Awandare, Gordon A.

doi:10.21203/rs.3.rs-1088719/v1

Cited by 2 publications

(1 citation statement)

References 6 publications

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“…Among the mutations shared between the different lineages, the fitness substitutions D614G and P681R/H had the highest frequency. 42 …”

Section: Resultsmentioning

confidence: 99%

COVID-19 in 16 West African Countries: An Assessment of the Epidemiology and Genetic Diversity of SARS-CoV-2 after Four Epidemic Waves

Ndiaye,

Beye,

Sow

et al. 2023

The American Journal of Tropical Medicine and Hygiene

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ABSTRACT. West Africa faced the COVID-19 pandemic in early March 2020 and, as of March 31, 2022, had more than 900,000 confirmed cases and more than 12,000 deaths. During this period, SARS-CoV-2 genomes evolved genetically, resulting in the emergence of distinct lineages. This review was conducted to provide the epidemiological profile of COVID-19, the mutational profile of SARS-CoV-2, and the dynamics of its lineages in the 16 west African countries by analyzing data from 33 studies and seven situation reports. For a more complete representation of the epidemiology and genetic diversity of SARS-CoV-2, we used reliable public data in addition to eligible studies. As of March 31, 2022, the 16 west African countries experienced four epidemic waves with variable intensities. Higher mortality was noted during the third wave with a case fatality rate (CFR) of 1.9%. After these four epidemic waves, Liberia recorded the highest CFR (4.0%), whereas Benin had the lowest CFR (0.6%). Through mutational analysis, a high genetic heterogeneity of the genomes was observed, with a predominance of mutations in the spike protein. From this high mutational rate, different lineages emerged. Our analysis of the evolutionary diversity allowed us to count 205 lineages circulating in west Africa. This study has provided a good representation of the mutational profile and the prevalence of SARS CoV-2 lineages beyond the knowledge of the global epidemiology of the 16 African countries.

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“…Among the mutations shared between the different lineages, the fitness substitutions D614G and P681R/H had the highest frequency. 42 …”

Section: Resultsmentioning

confidence: 99%

COVID-19 in 16 West African Countries: An Assessment of the Epidemiology and Genetic Diversity of SARS-CoV-2 after Four Epidemic Waves

Ndiaye,

Beye,

Sow

et al. 2023

The American Journal of Tropical Medicine and Hygiene

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The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

Tegally

San

Cotten

et al. 2022

Preprint

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Investment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massive increase in the number of sequences, exceeding 100,000 genomes generated to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence within their own borders, coupled with a decrease in sequencing turnaround time. Findings from this genomic surveillance underscores the heterogeneous nature of the pandemic but we observe repeated dissemination of SARS-CoV-2 variants within the continent. Sustained investment for genomic surveillance in Africa is needed as the virus continues to evolve, particularly in the low vaccination landscape. These investments are very crucial for preparedness and response for future pathogen outbreaks.One-Sentence SummaryExpanding Africa SARS-CoV-2 sequencing capacity in a fast evolving pandemic.

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Tracking genetic diversity of SARS-CoV-2 infections in Ghana after one year of surveillance

Cited by 2 publications

References 6 publications

COVID-19 in 16 West African Countries: An Assessment of the Epidemiology and Genetic Diversity of SARS-CoV-2 after Four Epidemic Waves

COVID-19 in 16 West African Countries: An Assessment of the Epidemiology and Genetic Diversity of SARS-CoV-2 after Four Epidemic Waves

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

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