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Human papillomavirus (HPV) infection is a primary cause of preventable deaths from cervical cancer, a condition of profound inequality with approximately 90% of deaths occurring in low- and middle-income countries, particularly in sub-Saharan Africa. In May 2018, the WHO Director-General declared a Joint Global Commitment to Cervical Cancer Elimination, highlighting the critical role of HPV vaccines in achieving this goal. However, there is a lack of systemically collected data on HPV prevalence in The Gambia, and impact data from high-income countries may not be reliably extrapolated to West African settings due to geographical variation in HPV types and distinct behavioural, biological, and sociodemographic exposures. The Gambia introduced a two-dose HPV vaccination schedule in 2019, but coverage has been very low, interrupted mainly by the COVID-19 pandemic. This presents a key opportunity to generate vital baseline data on HPV prevalence in the population before potential scale-up of vaccination efforts. The PHASE survey, a multi-stage cluster survey, aims to establish the baseline, population prevalence estimates of high-risk and low-risk, vaccine-type and non-vaccine-type HPV infection in 15- to 49-year-old females in The Gambia by measuring urinary HPV-DNA. The survey will also quantify the effects of various exposures on HPV prevalence, including sexual behaviour, the presence of other sexually-transmitted infections (STIs) - Neisseria gonorrhoea (NG), Chlamydia trachomatis (CT), Trichomonas vaginalis (TV), Mycoplasma genitalium (MG), syphilis, as well as blood borne viruses, human immunodeficiency virus (HIV), hepatitis B and hepatitis C; obstetric history, socio-demographic characteristics, and cervical cancer screening and/or treatment. Additionally, the study will provide important antimicrobial resistance (AMR) data for NG and MG in sub-Saharan Africa, a region poorly represented in global surveillance programs. This data is needed to guide regional treatment guidelines and advocate for new solutions, including gonococcal vaccines. The AMR data are expected to immediately influence recommendations regarding the appropriate choice of antibiotics for syndromic STI management in West Africa and hence to address an important driver of AMR in the sub-region. Leveraging on the Medical Research Council Unit The Gambia funded Health Demographic Surveillance system (HDSS) as its sampling frame, the survey will utilize validated diagnostic assays and culturally sensitive data collection methods, to ensure both scientific rigor and local relevance. Tools such as Audio Computer-Assisted Self-Interviewing (ACASI) technology, developed in consultation with local community advisory boards, are included to reduce social desirability bias in reporting sexual behaviour. This approach aims to maximize both the reliability and cultural appropriateness of the findings. This study directly addresses the critical need for baseline epidemiological data on HPV in a West African setting to accelerate vaccine impact and drive new interventions towards cervical cancer elimination. By understanding other factors that influence HPV (like other STIs, sexual behaviour, etc.), the study aims to ensure that, when the vaccine’s impact is measured later, changes in other confounding factors that may impact on HPV prevalence can be accounted for. The study will also establish the population prevalence of the measured STIs and their relationship to common symptoms and other adverse health outcomes related to STIs.

Collecting reliable sexual behaviour data remains a major challenge in conservative, low-literacy contexts such as The Gambia, where stigma, privacy concerns, and social desirability bias influence responses. The Prevalence of Human Papillomavirus, Antimicrobial resistance, and Sexually transmitted infection Estimation (PHASE) survey sought to address this challenge by introducing Audio Computer-Assisted Self-Interviewing (ACASI) for the first time in The Gambia. This paper documents the design, development, and piloting of the ACASI tool, highlighting key lessons for similar settings in sub-Saharan Africa. A Community Advisory Board (CAB) was central to the tool’s development, ensuring cultural sensitivity, acceptability, and linguistic accuracy. CAB members guided the drafting and adaptation of sexual behaviour questions, advised on culturally relevant response categories, and reviewed translations into four local languages (Mandinka, Serahule, Fula, Wolof). They also oversaw the design of non-threatening, familiar images to accompany response options and ensured accurate, context-appropriate audio recordings. Technical implementation was achieved using the SurveyCTO platform, allowing offline use, encryption, and integration of multilingual audio and images. Privacy safeguards were embedded, including screen codes replacing text to prevent disclosure in shared settings and restricted staff access to individual responses. Pilot testing revealed critical operational considerations. Many women lacked prior experience with digital tools and required extra support during the introductory phase. Adjustments included re-recording unclear questions, reordering items to reduce priming effects, and randomising response lists to enhance validity. Additional measures, such as repeating select questions at different points, improved internal consistency checks. Despite these challenges, participants demonstrated increasing confidence with the tool, and CAB feedback confirmed that ACASI was more acceptable for sensitive questions than face-to-face interviewing. Our experience demonstrates that ACASI is a feasible and culturally appropriate method to collect sexual behaviour data in The Gambia, even within low-literacy, conservative populations. The use of familiar images, validated translations, and community engagement enhanced usability, while technical refinements addressed privacy and confidentiality concerns. Key challenges related to computer literacy and dialect variation were addressed through training, piloting, and iterative refinement. This process illustrates that by prioritizing community involvement, technical adaptation, and cultural sensitivity, ACASI offers a promising framework to enhance the acceptability and potentially the accuracy of sexual behaviour reporting in large-scale epidemiological surveys. These lessons can be applied to similar sub-Saharan African contexts seeking to generate high-quality data to inform HPV (human papillomavirus), STI (sexually transmitted infection), and sexual health research.

Background Human metapneumovirus (HMPV) is a causal agent of acute respiratory infection, especially in primarily children. At the clinical level, HMPV is associated to several diseases including bronchitis, croup, pneumonia, bronchiolitis, reactive airway disease, chronic obstructive pulmonary disease and asthma exacerbations, specifically in children less than 5 years. Here, we carried out a retrospective pilot study, based on the processing of nasopharyngeal swabs, with a focus on the epidemiology and molecular characteristics of HMPV in Senegal. Methods This retrospective study was conducted from January 2012 to December 2016. Briefly, all outpatients presenting to healthcare sentinel sites were screened for surveillance enrollment and included if they met criteria for ILI. Naso-oropharyngeal swabs were collected from eligible participants. For viral respiratory pathogens detection, including HMPV, the Anyplex™ II RV16 Detection kit was used. A fragment of the hMPV F gene was targeted for sequencing. Results In total, 8209 patients with ILI were enrolled. Half of them (49.7%) were children under 5 years. Fever was the most common symptom followed by cough, and rhinitis. Three hundred eight patients were positive for HMPV (3.75%). 89 (28.9%) were detected as single infection. In co-infection cases, the most common co-infecting viruses were influenza, adenovirus and rhinovirus. HMPV detection rates in the different age groups varied significantly with the children under 5 years group accounting for 71.7% of positive patients. The temporal distribution pattern for HMPV infection showed a clear seasonal pattern with a higher activity during the rainy period (July–September). Phylogenetic analyses revealed that HMPV specimens circulating in Senegal were distributed into the two main genetic lineages, A and B. We also noted a co-circulation of both genetic lineages during the whole study period except in 2014. Conclusion In summary, the present study characterized the recent prevalence, seasonality and genetic diversity of HMPV in a large outpatient population presented with ILI in Senegal between 2012 and 2016. Globally our results show a clear seasonal circulation pattern of HMPV in Senegal. Our findings identified children less than 5 years as more susceptible group to HMPV infection. Molecular studies identified A2, B1 and B2 as the major genotypes circulating.

Following the 2014 outbreak, active surveillance of the EV-D68 has been implemented in many countries worldwide. Despite subsequent EV-D68 outbreaks (2014 and 2016) reported in many areas, EV-D68 circulation remains largely unexplored in Africa except in Senegal, where low levels of EV-D68 circulation were first noted during the 2014 outbreak. Here we investigate subsequent epidemiology of EV-D68 in Senegal from June to September 2016 by screening respiratory specimens from ILI and stool from AFP surveillance. EV-D68 was detected in 7.4% (44/596) of patients; 40 with ILI and 4 with AFP. EV-D68 detection was significantly more common in children under 5 years (56.8%, p = 0.016). All EV-D68 strains detected belonged to the newly defined subclade B3. This study provides the first evidence of EV-D68 B3 subclade circulation in Africa from patients with ILI and AFP during a 2016 outbreak in Senegal. Enhanced surveillance of EV-D68 is needed to better understand the epidemiology of EV-D68 in Africa.

is a major human pathogen. Panton-Valentine leukocidin (PVL) is a virulence factor produced by some strains that causes leukocyte lysis and tissue necrosis. PVL-associated (PVL-SA) predominantly causes skin and soft-tissue infections (SSTIs) but can also cause invasive infections such as necrotizing pneumonia. It is carried by both community-associated methicillin susceptible (CA-MSSA) and methicillin resistant (CA-MRSA). This study aims to determine the prevalence of PVL-SA among patients seen at an urban Gambian hospital and associated antibiotic resistance. Archived clinical (70 invasive bacteraemia and 223 non-invasive SSTIs) from 293 patients were retrieved as well as relevant data from clinical records where available. Antibiotic susceptibility was assessed using disc diffusion according to Clinical Laboratory Standards Institute (CLSI) guidelines. Genomic DNA was extracted and the presence of lukF and lukS PVL genes was detected by conventional gel-based PCR. PVL-SA strains accounted for 61.4% (180/293) of isolates. PVL prevalence was high in both Gambian bacteraemia and SSTIs strains. Antimicrobial resistance was low and included chloramphenicol (4.8%), cefoxitin (2.4%), ciprofloxacin (3.8%), erythromycin (8.9%), gentamicin (5.5%) penicillin (92.5%), tetracycline (41.0%), and sulfamethoxazole-trimethoprim (24.2%). There was no association of PVL with antimicrobial resistance. PVL expression is high among clinical strains among Gambian patients. Reporting of PVL-SA clinical infections is necessary to enable the monitoring of the clinical impact of these strains in the population and guide prevention of the spread of virulent PVL-positive CA-MRSA strains.   ( ) is a major human pathogen with several virulence factors. We performed a retrospective analysis to investigate the prevalence of one such virulence factor (PVL) amongst clinical samples. We found a high prevalence in our setting but antimicrobial resistance including methicillin resistance was low.

In 2022, many regions around the world experienced a severe respiratory syncytial virus ( RSV) epidemic with an earlier-than-usual start and increased numbers of paediatric patients in emergency departments. Here we carried out this study to describe the epidemiology and genetic characteristics of RSV infection in patients hospitalized with severe acute respiratory infections in 2022. Samples were tested for RSV by multiplex real time reverse transcription polymerase chain reaction. Subsequently, a subset of RSV positive samples was selected for NGS sequencing. RSV was detected in 16.04%, among which RSV-A was confirmed in 7.5% and RSV-B in 76.7%. RSV infection were more identified in infants aged ≤ 11 months (83.3%) and a shift in the circulation pattern was observed, with highest incidences between September–November. Phylogenetic analyses revealed that all RSV-A strains belonged to GA2.3.5 genotype and all RSV-B strains to GB5.0.5a genotype. Three putative N-glycosylation sites at amino acid positions 103, 135, 237 were predicted among RSV-A strains, while four N-linked glycosylation sites at positions 81, 86, 231 and 294 were identified in RSV-B strains. Globally, our findings reveal an exclusive co-circulation of two genetic lineages of RSV within the pediatric population in Senegal, especially in infants aged ≤ 11 months.

In December 2023, we observed through hospital-based surveillance a severe outbreak of enterovirus D68 infection in pediatric inpatients in Dakar, Senegal. Molecular characterization revealed that subclade B3, the dominant lineage in outbreaks worldwide, was responsible for the outbreak. Enhanced surveillance in inpatient settings, including among patients with neurologic illnesses, is needed.

The spread of severe acute respiratory syndrome coronavirus 2 began later in Africa than in Asia and Europe. Senegal confirmed its first case of coronavirus disease on March 2, 2020. By March 4, a total of 4 cases had been confirmed, all in patients who traveled from Europe.

In this research, alternate random wave sine and cosine for discrete time-varying processes via Autoregressive Integrated Moving Average (ARIMA) in a deterministic manner were developed. The mean and variance of the cosine and sine periodical time-varying wavy functions were derived such that Maclaurin series via full Taylor series expansion was used to rewrite the mean and variance functions. Wavy buoys of sea temperature, significant wave height, and mean wave direction of Belmullet Inner (Berth B) and Belmullet Outer (Berth A) of the Atlantic Ocean based on the west coastal of Ireland were subjected to the random sine and cosine wave functions of ARIMA. Cosine-ARIMA (1, 1, 3) and cosine-ARIMA (0, 1, 1) were the sea temperature inner and outer oceanic climate wave buoys of Berth B and A with time-periods of 8437.5 and 8035.714 respectively. Cosine-ARIMA (5, 1, 0) gave minimum performance for peak direction of inner and outer oceanic climate wave buoys of both Berth B and A, but with different time-periods of 168750 and 56250 respectively. Lastly, cosine-ARIMA (2, 1, 2) and sine-ARIMA (0, 1, 5) put in the ideal generalization for wave height of Berth B and A with the same associated wave time-periods of 56250, that is, it takes 56250 seconds to complete one swaying cycle.

Despite extensive experience with influenza surveillance in humans in Senegal, there is limited knowledge about the actual situation and genetic diversity of avian influenza viruses (AIVs) circulating in the country, hindering control measures and pandemic risk assessment. Therefore, as part of the “One Health” approach to influenza surveillance, we conducted active AIV surveillance in two live bird markets (LBMs) in Dakar to better understand the dynamics and diversity of influenza viruses in Senegal, obtain genetic profiles of circulating AIVs, and assess the risk of emergence of novel strains and their transmission to humans. Cloacal swabs from poultry and environmental samples collected weekly from the two LBMs were screened by RT-qPCR for H5, H7, and H9 AIVs. Subsequently, a subset of H9-positive samples was selected for whole sequencing. From December 2023 to October 2024, 499 samples were tested, and AIV was detected in 58.3% of them. Among these, A/H9N2 was the only subtype detected in both markets, with a detection rate of 47.7% (82/172) in Thiaroye and 35.3% (42/119) in Tilene, resulting in an overall positivity rate of 42.6% (124/291). Genome sequencing of 22 A/H9N2 isolates, including 11 poultry drinking water samples, 7 carcass wash water samples, 3 fecal samples, and 1 cloacal swab, yielded 7 complete and 15 partial genomic sequences. Phylogenetic analyses of the resulting sequences showed that the A/H9N2 isolates obtained in this study formed a monophyletic cluster and were closely related to the Senegalese human strain (A/Senegal/0243/2019) identified through the national influenza sentinel surveillance program. These strains were also closely related to the A/H9N2 viruses of the G1 lineage circulating in neighboring countries, suggesting cross-border transmission. The A/H9N2 strains carried the low pathogenicity RSSR/GLF motif at the HA cleavage site and possessed several key amino acid mutations, including HA-I155T and HA-Q226L, which are associated with human host adaptation, PB2-T105V, PB2-A661T, and PB2-A588V, which are linked to the human-to-human transmission and increased polymerase activity, NS2-T14M, NS2-M100I, NS1-I106M, NS1-V222M, NS1-E223A, NS1-I226V, NS1-E227G, and NS1-P228S, which are known to alter virulence (increased or reduced) in humans or mice, and M2-S31N, which promotes drug resistance. Seven potential N-glycosylation sites were predicted in the HA protein and six in the NA protein. The selection pressure analysis revealed that the A/H9N2 isolates were primarily under neutral evolution or purifying selection pressure. Overall, our findings highlight the potential for cross-species transmission of Senegalese A/H9N2 viruses, emphasizing the need for sustained monitoring of these viruses in both animal and human populations.