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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.
RESUMEN
Background: The Omicron variant B.1.1.529 has led to a new dynamic in the COVID-19 pan-demic, with an increase in cases worldwide. Its rapid propagation favors the emergence of novel sub-lineages, including BA.4 and BA.5. The latter has shown increased transmissibility compared to other Omicron sub-lineages. In Senegal, the emergence of the Omicron variant in December 2021 characterized the triggering of a short and dense epidemiological wave that peaked at the end of February. This wave was followed by a period with a significant drop in the number of COVID-19 cases, but an upsurge in SARS-CoV-2 infection has been noted since mid-June. Objective(s): The purpose of this brief report is to give an update regarding the genomic situation of SARS-CoV-2 in Dakar during this phase of recrudescence of cases. Method(s): We performed amplicon-based SARS-CoV-2 sequencing on nasopharyngeal swab samples from declared COVID-19 patients and outbound travelers that tested positive. Result(s): Ongoing genomic surveillance activities showed that more than half of recent COVID-19 cases were due to the BA.4 and BA.5 sub-lineages that share two critical mutations associated with increased transmissibility and immune response escape. The circulation of recombinants between Omicron sub-lineages was also noted. Conclusion(s): Despite the lack of proven severity of BA.4 and BA.5 sub-lineages, their increased transmis-sibility causes a rapid spread of the virus, hence a surge in the number of cases. This rapid spread consti-tutes a greater risk of exposure for vulnerable patients. To tackle this issue, any increase in the number of cases must be monitored to support public health stakeholders. Therefore, genomic surveillance is an ever-essential element in managing this pandemic.Copyright © 2022 Bentham Science Publishers.
RESUMEN
The SARS-CoV-2 genetic variants emergence doesn't spare the West African continent which has to face vaccination implementation delay. Beside classical qRT-PCR diagnostic testing, strengthening of sequencing capacity is the cornerstone for tracking and fighting the emergence of SARS-CoV-2 variants in real time. From March 12th, 2020 to July 16th, 2021, a panel of 136 full length genomes of SARS-CoV-2 mutants/variants present in human nasopharyngeal swab samples conserved in the Biobank of the Institut Pasteur De Guinée were sequenced using Illumina methodology. The Guinean sequences, originating from the general population, expatriates, and travelers, were distributed into 7 clades. During March- August 2020, the sequences were exclusively distributed into 2 clades, 20A and 20B, most originating from Europe. The 20D and 20C clades were furtively observed in October 2020 and February 2021 respectively. The SARS-CoV-2 variant of concern (VOC) 20I/B.1.1.7/Alpha was first identified in January 2021, increased in incidence up to March 2021, and then decreased from April to June 2021, corresponding to the dynamic described in Africa. The variant of interest (VOI) 21D/B.1.525/Eta originating from Nigeria circulated in February-May 2021. The 21A/B.1.617.2/Delta VOC was detected from May 2021 in Guinea, became dominant in July and persisted behind the present sampling over August and September 2021. A similar dynamic was globally observed in Africa resulting in a clear increase of lethality in the population. In contrast, other variants previously found in Africa, such as the 20H/B.1.351/Beta VOC and variants from the sublineage A (A.23.1 lineage from East Africa and the A.27 lineage), were not detected in this study. This overview of SARS-CoV-2 over 1.5 years in Guinea demonstrates that virus clades, VOC and VOI were progressively introduced, mostly by travelers through the Conakry Airport, before spreading through the country. The tracking of viral evolution by sequencing is a continuous task. Since November 2021, a new wave is related to the emergence of the VOC Omicron. Making countries autonomous in sequencing is a challenge in Africa, not only to fight Covid-19, but also to face the numerous other emerging zoonoses which circulate across the continent.