Sentinel Surveillance of COVID-19 in 2024–2025 Showed the Persistence of Omicron Circulation and the Introduction of the XFJ Recombinant in the Republic of Guinea
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Introduction: In Guinea, several studies have shown the evolution of SARS-CoV-2 between 2020 and 2023. This study provides updated information on the circulation dynamics of SARS-CoV-2 from 2024 to 2025 and the variants circulating in Guinea. Material and Methods: As part of the integrated Influenza/COVID-19 sentinel surveillance, 2423 nasopharyngeal samples were analysed using RT-PCR, and those positive for SARS-CoV-2 were sequenced using the Illumina COVIDSeq Assay protocol. Results: All age groups, from < 2 years to > 64 years, were affected by COVID-19, with an average SARS-CoV-2 positivity rate of 2.3%. The virus showed sporadic activity throughout the 2024-2025 period, with a higher level of activity during epidemiological week 42 (October) of 2024. Genomic analysis showed that only the Omicron variant circulated, along with its subvariants JN.1 and LF.7 in 2024. The subvariant LF.7 and recombinant XFJ also circulated in 2025. Conclusion: SARS-CoV-2 subvariants continue to circulate sporadically in Guinea, with the detection of the XFJ recombinant in humans. Therefore, it is imperative to strengthen sentinel, genomic, and environmental surveillance for the early detection of any new COVID-19 outbreak and the potential emergence of new variants.