In December 2019, the world faced one of the most significant health crises of the 21st century with the emergence and rapid spread of the potentially fatal coronavirus 2019 (COVID-19). The infection, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first reported in Wuhan, Hubei province, China (1). At the onset of the disease, in China the basic reproduction number (R₀) was estimated to range between 2.24 (95% CI: 1.96–2.55) and 3.58 (95% CI: 2.89–4.39) (2, 3) with the mean incubation period of 6.4 days (range: 2.1–11.1 days) and evidence of potential asymptomatic transmission (2, 4). In Africa, an analysis of data from 2020 estimated a reproduction rate of 2.02 ± 0.7, ranging from 1.12 to 3.64 (5). By late 2021, following the emergence of the Omicron variant, multiple studies estimated the basic (R0) and effective (Rt) reproduction rates for this variant and its early sub-variants. An analysis of 15 studies covering Europe, America, Asia, and three studies from South Africa (the only African country included), reported mean numbers of basic (R0) and effective (Rt) reproduction values for the Omicron variant at 9.5 (range: 5.5–24) and 3.4 (range: 0.88–9.4) respectively (6). Since the start of the pandemic, the attack rate of COVID-19 has increased, with regional variations observed in African countries (7). In addition, as the pandemic evolves, the SARS-CoV-2 virus, like any pathogen, mutates over time (8). These mutations are manifested by the increased transmissibility of the virus, disease severity, and escape of neutralizing antibodies, and are classified as variants of concern (VOC) (9). These variants typically result in a moderate clinical presentation of the disease, with symptoms resolving within 2–6 weeks, except for the Delta variant (10). Common symptoms of COVID-19 include myalgia, nasal symptoms, headache, fever, asthenia, dry cough, difficulty breathing, sore throat, chest pain, runny nose, and diarrhea, loss of taste or smell (11–14). Several studies have also reported factors associated with COVID-19 positivity. Studies in Europe (15) and Africa (16, 17) have identified numerous factors associated with SARS-CoV-2 positivity, including contact with a confirmed case, the presence of one or more household members, typical SARS-CoV-2 symptoms, male gender, fatigue, fever, cough, headache and respiratory problems. The variation in reproduction numbers, symptoms, and associated factors across different geographical areas highlights the similarities in symptoms found in most infectious diseases and the multiplicity of presumed associated factors. This suggests the need for systematic screening for this disease in healthcare settings. Understanding the factors associated with positivity is essential for improving surveillance and thus, effectively reduce transmission of COVID-19, reviewing screening strategies, strengthening community communication, and enhancing management efforts.

Following the global outbreak of COVID-19, particularly in Africa, the surveillance of respiratory diseases has gained increasing attention in several Sub-Saharan African countries (18, 19). Consequently, international public health institutions have recognized the necessity for joint coordination in the surveillance of these severe acute respiratory diseases (18, 19).

In Guinea, since the official declaration of the first cases in March 2020 by the Ministry of Health and Public Hygiene, Conakry has remained the epicenter of the COVID-19 pandemic, accounting for over 80% of cases and low vaccination coverage of 28% in February 2023 according to the Agence Nationale de Sécurité Sanitaire (ANSS) (20). Several public health institutions are involved in the epidemiological surveillance of severe acute respiratory infections (ARIs) in the country, including the Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG).

With this in mind, CERFIG has established surveillance of COVID-19 variants in sentinel sites. We report here the first data on reproduction numbers and risk factors in the post-epidemic period.

In a context where the number of screening sites in the country has been reduced by more than 90%, and as part of the support for surveillance of COVID-19, including its variants, we analyzed transmission rates and factors associated with SARS-CoV-2 infection among suspected cases in health facilities in Conakry.

The positive rate for SARS-CoV-2 infection found in suspected cases exceeded 10% in Conakry. For comparison, rate were reported at 6.4% in four sub-Saharan African countries (Côte d'Ivoire, Burkina Faso, Central African Republic and Madagascar), ranging from 4.0% to 16.6% (32).

A sentinel syndromic surveillance study in Malawi from July 2020 to April 2022 revealed a SARS-CoV-2 positivity rate of 11.5% (33). In Madagascar, a higher positivity rate of 24.5% was recorded between March 2020 and May 2022 (34). In Ethiopia, authors reported a 9.2% positivity rate at national sentinel surveillance sites for severe acute respiratory infections (SARI) and influenza-like illness (ILI) over an 18-month period (January 2021 to June 2022) (35). Similarly, a study in Kenya conducted across eight sentinel sites between April 2020 and March 2022 reported a positivity rate of 10.7% (36). In Uganda, a study from January to December 2022 found a positivity rate of 7.7% (37).

Our results indicated a slightly higher positivity rate during the surveillance period, occurring against the backdrop of the May 2023 declaration of the end of the international emergency (38). This led to reduced screening and barrier measures across the country, including during national and international travel. Variations in positivity rates can be attributed to differences in sample sizes, surveillance durations, study populations, and local sample collection strategies.

Additionally, our study identified the first case of the Omicron variant in Guinea. All sequences obtained were of the Omicron variant, with a high frequency of the XBB.1.5 sub-lineage. This sub-variant, first identified in August 2022, had been predominant globally since February 2024 and was noted for being more transmissible than its XBB.1 counterpart (39). The sub-variants found in our study align with those identified elsewhere during the pandemic, including their emergence periods (40, 41). In addition, the variations of effective reproduction number (Rt) revealed a complex epidemic dynamic, characterized by periods of intense transmission and phases of stabilization or decline. This would suggest that several epidemic waves followed one another during these periods, but also that the virus was circulating actively, probably encouraged by factors such as social behavior, environmental conditions or insufficient collective immunity. The persistence of a high Rt (Rt = 2.08) in July 2024 gives cause for concern. This suggests that the epidemic was not yet under control at that date, with the potential for transmission still significant. This figure indicates that each infectious case generated an average of two others, which could have led to a new wave if additional measures were not taken. This situation could be explained by the emergence of new variants, a drop in adherence to health measures, or insufficient vaccination coverage. In addition, although progress was made during the warm periods of the pandemic, the introduction of this surveillance system alerted public health players to the probable emergence of new strains and the need for ongoing surveillance to prevent future epidemic waves and protect public health. Similar data were reported in Mali and Senegal, with reproduction rates of 3.98 (90% CI: 3.61–4.43) and 3.78 (90% CI: 3.16–4.10), respectively (42). A study analyzing data for the period March to May 2020, generated by the COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at the Johns Hopkins University, revealed that an estimated basic reproduction number of 1.61 (1.46, 1.77) for Guinea (43).

These results highlight the rapid circulation of COVID-19 in Conakry and other African cities during this period, despite vaccination campaigns and a global decline in cases. A seroprevalence survey conducted in June 2022 in Conakry indicated an overall seroprevalence of IgG against the spike and core proteins of SARS-CoV-2 at 71.57% (44). This survey suggested that nearly the entire population of Conakry had been in contact with the virus, which may support the Rt values observed during the surveillance period. Furthermore, it suggests poor screening and underreporting of cases at the national level, abandonment of preventive measures (such as social distancing and participation in mass gatherings), and potential waning of vaccine immunity. The WHO reported in its latest COVID-19 global risk assessment in June 2024 that positivity rates for SARS-CoV-2 infection in sentinel sites and wastewater surveillance indicate high circulation worldwide (45), corroborating the results from our surveillance.

The results of the multivariate analysis revealed that the presence of ageusia would increase the likelihood of testing positive for SARS-CoV-2 infection. Previous studies have indicated that factors associated with COVID-19 in Africa include fever, cough, headache, respiratory problems, and age ≥60 years are the factors associated with COVID-19 in Africa (16, 46). Given the combination of these factors, it is important to consider other pathologies as well. Data from studies conducted in some European countries show that anosmia, ageusia, fever, breathlessness, and cough were strongly associated with test positivity. The association between symptoms and test status varied based on the duration of illness, timing of testing, broader testing criteria, and context (by country and testing platform) (47). In Serbia, during a period of Omicron circulation, authors found that hospitalized, elderly, unvaccinated, and previously infected patients, as well as smokers, were more likely to test positive for SARS-CoV-2 (48). Other studies have noted associations between SARS-CoV-2 positivity and sensory deficiencies, severe symptoms, loss of smell, loss of taste, cardiovascular disease, neuropsychiatric disease, and endocrine disease (49). Hunter et al. reported that factors such as mask-wearing habits, foreign travel history, household size, employment status, and contact with specific age groups contributed to the risk of SARS-CoV-2 positivity (50). The variations in associated factors across these studies may be attributed to differences in data collection methods, statistical approaches, and sample sizes.

This study has certain limitations. Firstly, symptom and vaccination status data were collected declaratively, and the cross-sectional nature of the study may lead to reporting bias. The sample only included individuals who visited the sentinel sites, limiting the generalizability of the results to the entire population of Conakry. Positivity rate of 11.8% could indicate incomplete case detection, particularly among asymptomatic or minimally symptomatic individuals. Secondly, although the estimated effective reproduction rate (Rt = 2.08) reflects active transmission of the virus, it could be amplified by delays in reporting or changes in screening policies. Furthermore, the results are based on global data, without explicit consideration of contextual or regional disparities that could affect epidemic dynamics.

Nevertheless, this study raises significant issues. It is one of the first to focus on calculating the effective reproduction numbers of the Omicron variant, as well as the risk factors for COVID-19 in the post-epidemic period. Additionally, it underscores the ongoing and likely large-scale circulation of SARS-CoV-2 and its variants in Conakry. Surveillance of epidemic diseases in the Guinean healthcare system dates back to the colonial period, characterized by the intervention of mobile teams to combat endemic diseases and the selective establishment of hospitals in major cities (48). This surveillance system, centered on primary health care (PHC), has evolved over time and has faced a resurgence of epidemic diseases (Ebola, Marburg, Lassa, COVID-19, etc.) since 2014, within a context marked by numerous vertical projects and programs (51).

The sentinel surveillance conducted in this study represents the only syndromic surveillance of COVID-19 currently in effect in Guinea during this post-epidemic period. This aligns with the latest WHO guidelines, which recommend collaborative surveillance of COVID-19 to inform situational awareness, risk assessment, and the detection of significant changes in virus characteristics, transmission, disease severity, and population immunity. It is also essential to continue making COVID-19-related data (including mortality and morbidity statistics, SARS-CoV-2 genetic sequences, and metadata) available through open sources (45).

The data collection strategy employed for this surveillance involved telephone calls and face-to-face interviews during consultation visits over a 22-month period. A notable strength of this work is the use of the Bayesian model-averaging approach for identifying factors associated with SARS-CoV-2 positivity, which provides a more robust estimate of the effects of variables on the event of interest by integrating multiple models into the analysis (28). This method selects only those models that meet a certain probability threshold, aiding optimal model selection without overfitting. Additionally, multivariate logistic regression was applied using a sub-sampling technique to address class imbalance in the datasets (48).

SARS-CoV-2 continues to circulate in Guinea, with high positivity rates and effective reproduction numbers in excess of 1 in the post-epidemic period. The disease remains poorly understood due to the numerous mutations of the virus, which can contribute to increased transmissibility and severity of illness. Factors independently associated with test positive SARS-CoV-2 infection was ageusia. This study underscores the persistence of COVID-19 cases and emphasizes the necessity of ongoing variant monitoring, particularly in light of the observed reduction in COVID-19 cases globally. The diversity of circulating strains highlights the urgent need to enhance genomic and epidemiological surveillance. Implementing effective screening strategies in healthcare facilities, along with preventive measures, is essential. Collaboration among all stakeholders involved in the COVID-19 response is crucial to ensure continuous alertness, informed public health decision-making, and to mitigate the risk of potential epidemic outbreaks.