RESUMEN
In the last two years, Cameroon has faced five waves of COVID-19, with its fourth wave of the B.1.1.529 Omicron variant in December 2021 and subsequently hosted the African Cup of Nation of Football Men's competition that gathered thousands of people from across the world in January 2022 with no increase in the number of cases/deaths. A fifth wave of BA.4, and BA.5 Omicron variants was seen in August 2022. The country as claimed 123 785 cases, 121 633 recovered and 1960 death by 30th September 2022. Despite a low vaccination coverage of 8.7% the country has seen a limited impact of COVID-19 as compared to the international prediction. The response of Cameroon focused in limiting the spread of the SARS-CoV-2 in the population, reducing the morbidity and mortality due to COVID-19 and limiting the socio economic impact of the COVID-19 in Cameroon. The contextualized Cameroonian response was based on an important epidemiologic surveillance relying on mass testing strategy and adaptative measure that ensure the continuity of the of planned mass gathering activities including hosting the African Cup of Nations of Football in the COVID-19 context and the continuity of education. While the COVID-19 has shown some weakness in the health system it has been an opportunity to show its resilience and the opportunity for strengthening the health system including the implementation of a genomic surveillance platform. The lessons learnt from COVID-19 including the importance of coordination through the Public Health Emergency Operating Centre will help the country to address the future public health emergencies and move toward cholera elimination by 2030.
RESUMEN
Background: At the global level, the dynamics of the COVID-19 pandemic have been driven by several epidemiological waves, determined by the emergence of new SARS-CoV-2 variants from the original viral lineage from Wuhan, China. While the SARS-CoV-2 dynamic has been described globally, there is a lack of data from Sub-Saharan African. Method(s): A laboratory-based survey was conducted in Cameroon, from March 1, 2020 to March 30, 2022, through an assessment of the evolutionary patterns of SARS-CoV-2 lineages across the four COVID-19 waves in the country. Data on full-length sequencing from all four sequencing laboratories were consecutively entered into the GISAID platform. These data were downloaded, and the molecular phylogeny of the SARS-CoV-2 sequences was performed using Nexstrain. The Mann-Whitney U test was used to calculate the correlation between the duration of each outbreak and the number of confirmed cases and between hospitalised cases and CFR, with a p value < 0.05 considered statistically significant. Result(s): A total of 3,881 samples were successfully processed, of which 38.9% (n=1,509) using PCR mutation assay, 41.5% (n=1,612) using targeted sequencing, and 19.6% (n=760) using whole-genome sequencing. The mean age of the study population was 36 years (min-max: 2-86), and 45% were within the age range 26-45. Regarding gender distribution, 50.9% were male, and 49.1% were female. Phylogenetic analysis of the 760 whole-genome sequences generated from March 2020 to March 2022 revealed that the greater proportion of SARS-CoV-2 circulating in Cameroon belonged to the viral sub-lineages of the original strain from Wuhan (74%), 15% Delta variant, 6% Omicron variant, 3% Alpha variant and 2% Beta variant.The pandemic was driven by SARS-CoV-2 lineages of origin in Wave 1 (16 weeks, 2.3% CFR), the Alpha and Beta variants in Wave 2 (21 weeks, 1.6% CFR), Delta variants in Wave 3 (11 weeks, 2.0% CFR), and Omicron variants in Wave 4 (8 weeks, 0.73% CFR), with a declining trend over time (p=0.01208). Conclusion(s): In a nutshell, the SARS-CoV-2 epidemic in Cameroon appears to have been driven by the SARS-CoV-2 lineage of origin in Wave 1, the cointroduction of the Alpha and Beta variants in Wave 2, the Delta variant in Wave 3, and the Omicron variant in Wave 4, with an overall declining trend in the wave duration, confirmed cases and hospitalisations over time.The SARS-CoV-2 lineage of origin and the Delta variant appeared to be the drivers of COVID-19 severity in Cameroon.