In Guinea, genomic surveillance has been established to generate sequences of and to identify locally circulating SARS-CoV-2 variants. This study aims to describe the distributions, genetic diversity, and origins of SARS-CoV-2 lineages circulating in Guinea during the COVID-19 pandemic. A migration analysis was performed by selecting all sequences generated in Guinea for variants of concern and interest. From March 2020 to December 2023, 1038 sequences were generated in Guinea and submitted to the Global Initiative on Sharing All Influenza Data (GISAID) database. Of these, 73.1% corresponded to SARS-CoV-2 variants of concern, which were further grouped into Omicron (69.4%), Delta (21.9%), Alpha (6.6%), and Eta (2.1%). Other variants accounted for 26.9% of the total. Among the total variants analyzed, 75 importations into Guinea from various countries worldwide were identified. Most of the importations (40%) originated from African countries, followed in significance by those from European countries (25.3%) and Asia (18.6%). A significant migratory flow was observed within Guinea. The genomic surveillance reported in this study revealed the diversity of SARS-CoV-2 variants circulating in Guinea, emphasizing the importance of large-scale sequencing analyses in understanding the dynamics of the pandemic.

Background: In December 2019, the world experienced one of the significant health crises of the 21st century with the emergence and rapid spread of the potentially fatal 2019 coronavirus (COVID-19). In this context, sentinel surveillance of SARS-CoV-2 variants was conducted in Conakry. Here we report the first data on reproduction numbers and risk factors during the Omicron post-epidemic period in Guinea.Methods: A sentinel syndromic and genomic surveillance study was conducted on suspected patients from October 2022 to July 2024 at healthcare facilities in Conakry. Individual data and nasopharyngeal swabs were collected and sent to the Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG) laboratory for screening and sequencing by next-generation sequencing (NGS). The effective reproduction number (Rt) were estimated using EpiEstim to assess the transmission potential of the Omicron variant. Generalized linear models based on the binomial distribution were employed to analyze factors associated with SARS-CoV-2 positivity, following the identification of primary risk factors using Bayesian model averaging and the Data balancing algorithm using propensity score matching.Results: Data from 1174 patients with suspected cases with a median age of 31 years (IQR: 20–51), were analyzed. The overall COVID-19 positivity rate was 11.8%. The global effective reproduction number (Rt) was 2.08 [95% CI: 0.35–5.81]. Only ageusia [AOR = 2.0; 95% CI (1.1–3.6)] was independently associated with SARS-CoV-2 test positivity.Conclusion: SARS-CoV-2 is still circulating in Guinea, with a high positivity rate and a high number of effective reproductions in this post-epidemic period in our country. The associated factors and the circulation of variants with a diversity of circulating strains suggest the need to strengthen genomic and epidemiological surveillance, with the support of all those involved in the response to COVID-19, to ensure continuity of alerts and decision-making for public health.

Background: Although arboviruses constitute a growing global public health threat, data on their circulation in Guinea remain limited. This study aimed to estimate the seroprevalence, spatial distribution, and associated factors of arboviruses in Guinea. Methods: We conducted a population-based cross-sectional survey between May and July 2023 among individuals aged ≥5 years in households across Guinea. Household, environmental, and socio-demographic data were collected by using a questionnaire. IgG antibodies against eight arboviruses were detected using Luminex MagPix assays: dengue (DENV), Zika (ZIKV), West Nile (WNV), Usutu (USUV), chikungunya (CHIKV), O’nyong’nyong (ONNV), Rift Valley fever (RVFV), and Crimean–Congo haemorrhagic fever (CCHFV). Seroprevalence and associated factors were analysed by using descriptive statistics and multilevel logistic regression with spatial components. Results: A total of 1098 participants from 367 households were included. Overall seroprevalence of arboviruses was 25.0% [95% confidence interval (CI): 22.0–28.0]. The highest seroprevalences were observed for ZIKV (12.0%; 95% CI 9.8–15.0) and WNV (11.6%; 95% CI 9.5–14.0). Boké and Kindia showed higher seroprevalence for ZIKV (33.0% and 22.9%, respectively), WNV (15.0% and 46.6%, respectively), and USUV (19.0% and 23.7%, respectively). In multilevel logistic regression, age [adjusted odds ratio (aOR) = 1.51; 95% CI 1.32–1.77], female sex (aOR = 1.59; 95% CI 1.17–2.16), and people from rich households (aOR = 1.67; 95% CI 1.11–2.43) were associated with seropositivity, with regional heterogeneity (intercept variance = 1.22; 1.10 SD). Conclusion: This nationwide survey confirmed widespread arbovirus circulation in Guinea, highlighting a largely underestimated burden. Strengthening epidemiological surveillance and vector control are essential to mitigate future outbreaks.

In Guinea, genomic surveillance has been established to generate sequences and identify locally circulating SARS-CoV-2 variants. This study aims to describe the distribution, genetic diversity, evolution, and origin of SARS-CoV-2 lineages circulating in Guinea during the COVID-19 pandemic. We performed a migration analysis by selecting all sequences generated in Guinea for variants of concern and interest. From March 2020 to December 2023, a total of 1 038 sequences were generated in Guinea and submitted to the GISAID database. Of the total, 73.1% corresponded to SARS-CoV-2 variants of concern, including (omicron 69, 4%, delta 21,9%, alpha 6,6%, and eta 2,1%). Other variants, accounting for 26,9%. Of the total number of variants analyzed, 75 importations into Guinea from various countries around the world were identified. The majority of introductions (40%) were from African countries, followed by 25,3% from European countries, and Asia (18,6%). A significant migratory flow has been observed within Guinea. Genomic surveillance has revealed the diversity of SARS-CoV-2 variants circulating in Guinea, highlighting the importance of sequence generation for advanced analysis to understand the dynamics of the pandemic.

Since May 2023, COVID-19 is no longer a Public Health Emergency of International Concern. However, it remains an infection that requires monitoring, especi