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BackgroundCOVID-19, caused by SARS-CoV-2, is one of the deadliest pandemics over the last 100 years. Sequencing is playing an important role in monitoring the evolution of the virus, including the detection of new viral variants. This study describes the genomic epidemiology of SARS-CoV-2 infections in The Gambia.MethodsNasopharyngeal and/or oropharyngeal swabs collected from suspected cases and travellers were tested for SARS-CoV-2 using standard RT-PCR methods. SARS-CoV-2 positive samples were sequenced following standard library preparation and sequencing protocols. Bioinformatic analysis was done using ARTIC pipelines and lineages assigned using Pangolin.FindingsBetween March 2020 to January 2022, there were almost 12,000 SARS-CoV-2 confirmed cases distributed into four waves, each of them lasting between 4 weeks and 4 months, with more cases during the rainy seasons (July-October). As shown by the 1643 sequenced samples, each wave occurred after new viral variants and/or lineages were introduced in The Gambia, generally those already established in Europe and/or in other African countries. Local transmission was higher during the first and third wave, with mostly B.1.416/Senegal/Gambian lineage and AY.34.1/Delta subtype, respectively. The second wave was driven by two variants, namely Alpha and Eta and B.1.1.420 lineage. The Omicron/fourth wave was the shortest.InterpretationEfficient surveillance, including strengthening entry points and screening asymptomatic individuals especially during the rainy seasons would be important to promptly detect and control future waves in The Gambia and the subregion.FundingMedical Research Unit The Gambia at LSHTM, UK Research and Innovation funding (grant reference MC_PC_19084), MRC/UKRI MC_PC_19084 and World Health Organisation.

Background: Strongyloidiasis is a parasitic disease that mainly affects humans and is caused by a roundworm called Strongyloides stercoralis. It is endemic in humid tropical regions that include Africa, Latin America and Southern Asia. Among the public health important soil-transmitted helminths (STHs) classified as neglected tropical diseases, S. stercoralis is the most neglected. A study of schistosomiasis and STHs mapping was conducted and S. stercoralis larvae were detected using the utilized diagnostic method; thus, this current study described the prevalence and risk factors of S. stercoralis infection in districts of Sabach Sanjal and Upper Badibou in The Gambia. Methods: The cross-sectional study enrolled 851 schoolchildren, ages 7 to 14 years old. The participants were enrolled from 17 schools in Sabach Sanjal and Upper Badibou Districts. The WHO random sampling technique n/50 (25 boys and 25 girls) was used. Stool samples were collected from each participant and Kato-Katz smear method was used to screen for S. stercoralis infection. Results: Out of the total 851 pupils, 76 pupils (8.9%) were positive for S. stercoralis infection. The mean age of infected persons was 10.1 years (±2.2). The prevalence of infection was higher among females (9.2%) than males (8.7%). Rates of infection for age categories 7–10 years and 11–14 years were 12.4% and 4.2%, respectively. Rates of infection by districts were 12.3% for Sabach Sanjal and 7.1% for Upper Badibou. Schoolchildren from Sabach Sanjal were 1.6 times more likely to have strongyloidiasis compared to those from Upper Badibou (aOR = 1.64, p-value = 0.058). Schoolchildren aged 7–10 years were 3.2 times more likely to have strongyloidiasis infection compared to the 11–14-year-olds (aOR = 3.20, p-value

Background A national mapping survey of schistosomiasis (SCH) and soil-transmitted helminthiases (STH) was conducted in The Gambia in May, 2015. The survey aimed at establishing endemicity of schistosomiasis and soil-transmitted helminthiases to inform decisions on program planning and implementation of mass drug administration (MDA). Methodology/Principal findings A cross-section of 10,434 eligible school aged children (SAC), aged 7 to 14 years old were enrolled in the survey. The participants were randomly sampled from 209 schools countrywide using N/50, where N = total eligible children per school. Stool, and urine samples were provided by each child and examined for schistosomiasis and soil-transmitted helminthic infections using double Kato-Katz, urine filtration, dipstick techniques and CCA rapid test kits. Data were managed using online LINKS system enabling real-time data availability and access. Epi Info version 3.5.3 and health mapper version 4.3.2 were used to generate outputs of endemicity and distribution. Descriptions of mapped districts for MDA eligibility and frequency were done with reference to WHO PC strategy recommendations. Mapping results indicated that nationally, the prevalence of schistosomiasis (SCH) and soil-transmitted helminthiases (STH) was 4.3% and 2.5% respectively. In terms of distribution STH are more common in Western Region One (WR1) at 4.1% prevalence, then Lower River Region (LRR) 3.6%, and Western Region Two (WR2) 3.0%. In contrast, SCH indicated much higher prevalence in Central River Region (CRR) at a rate of 14.2%. This is within medium prevalence range, and is followed by Upper River Region (URR) at 9.4%, which is within low prevalence range. At the district level, schistosomiasis prevalence seems to be highest in Niani district (22%) in CRR. Banjul island, the capital city, seems to have the highest prevalence of STH (up to 55%), followed by Kombo South with 22% prevalence. Schistosoma haematobium characterised by haematuria, was the most dominant infection of schistosomiasis discovered followed by Schistosoma mansoni which reported in 0.1% of infections. Out of 42 districts mapped 14, or 38%, of them are co-endemic for soil-transmitted helminthiases (ascariasis, trichuriasis, and hook-worm infections) and schistosomiasis (S. haematobium and S. mansoni). Conclusions We identified that 24/42(57%) districts mapped in The Gambia are endemic for schistosomiasis expressing the need for preventive chemotherapy. Twenty (47%) of the districts mapped are endemic for STH. However, only two STH endemic districts namely Banjul (55%) and Kombo South (22%) were within rates eligible for mass drug administration., Author summary The Gambia joined the international community in the fight against neglected tropical diseases (NTDs), in order to enable control and eventual elimination by year 2020. This goal is in line with Africa regional targets for NTDs control and elimination. This decision was the driving force for a tabletop analysis of the existing NTD situation in the country, culminating in the development of a comprehensive five-year NTD Master plan 2015–2020, and an Annual Work Plan 2016. The World Health Organisation regional office for Africa’s Regional Program Review Group (WHO/AFRO RPRG) supported this work by granting approval for the mapping of schistosomiasis (SCH) and soil-transmitted helminthiases (STHs) across the country in May 2015. In this publication, we describe the purpose of the survey, how the survey was conducted, and how data and specimens were collected, handled, analyzed and interpreted. We have discovered that schistosomiasis exists in twenty-four districts in the country. Most of these districts are located in the eastern half of the country in Upper and Central River Regions. This means that communities in the affected districts require treatment to reduce the burden of disease. Treatment for schistosomiasis is unlike soil-transmitted helminthiases because all districts with schistosomiasis are eligible for treatment irrespective of the level of prevalence and endemicity according to the guidelines of the World Health Organisation (WHO). In comparison to STH, mass drug administration is not required for low STH endemic communities where the prevalence was less than 20%. Instead such communities will benefit from case by case treatment STH. Mass treatment will be required in district where STH prevalence was at least moderate or 20% and above. Soil-transmitted helminthiases were found in twenty districts. However, it is important to highlight that only two of these districts, with prevalence of 22% and 55%, respectively were eligible for mass drug administration in accordance with WHO guidelines. The guidelines recommend that districts with a prevalence of soil-transmitted helminthiases of less than 20% do not require mass community treatment in order to achieve disease elimination.

Background The Gambia initiated a control programme for schistosomiasis in 2015. In light of this, recent and comprehensive data on schistosomiasis is required to effectively guide the control programme. This study aimed to evaluate the prevalence and associated risk factors of schistosomiasis among primary school children in The Gambia. Methods We utilised data from a previous study conducted in 2015 in 4 regions of The Gambia: North Bank Region (NBR), Lower River Region (LRR), Central River Region (CRR) and Upper River Region (URR). In the parent study, ten schools were selected randomly from each region. Urine and stool samples collected from 25 boys and 25 girls (7–14 years) in each school were examined for urinary schistosomiasis (Schistosoma haematobium infection) and intestinal schistosomiasis (Schistosoma mansoni infection) using urine filtration, dipstick and Kato-Katz methods. Principal findings Urinary schistosomiasis had an overall prevalence of 10.2% while intestinal schistosomiasis had a prevalence of 0.3% among the sampled school children. Prevalence of urinary schistosomiasis was significantly different among regions (χ 2 = 279.958, df = 3, p < 0.001), with CRR (27.6%) being the most endemic region, followed by URR (12.0%), then LRR (0.6%), and NBR (0.0%). Prevalence of intestinal schistosomiasis was also significantly variable among regions, with 4 of the 5 positive cases detected in CRR and 1 case in URR. Every school sampled in CRR had at least one student infected with S. haematobium, 50% of schools in URR had S. haematobium infection, and just one school in LRR had S. haematobium infection. While S. haematobium infection was significantly higher in boys (χ 2 = 4.440, df = 1, p = 0.035), no significant difference in infection rate was observed among age groups (χ 2 = 0.882, df = 2, p = 0.643). Two of the 5 students infected with S. mansoni were boys and 3 were girls. Four of these 5 students were in the 10–12 years age group and 1 was in the 7–9 years age group. Macrohaematuria and microhaematuria were found to be statistically associated with presence of S. haematobium eggs in urine. Being a male was a risk factor of S. haematobium infection. Bathing, playing and swimming in water bodies were found to pose less risk for S. haematobium infection, indicating that the true water contact behaviour of children was possibly underrepresented. Conclusion The findings of this study provide invaluable information on the prevalence of schistosomiasis in The Gambia. This was useful for the schistosomiasis control efforts of the country, as it guided mass drug administration campaigns in eligible districts in the study area. More studies on S. mansoni and its intermediate snail hosts are required to establish its true status in The Gambia. As children sometimes tend to provide responses that potentially please the research or their teacher, data collection frameworks and approaches that ensure true responses in studies involving children should be devised and used., Author summary In this study, we utilised data collected from a previous study that investigated schistosomiasis among primary school children in four regions (NBR, LRR, CRR and URR) of The Gambia, to assess the prevalence and risk factors of the disease. Our analysis revealed that urinary schistosomiasis was the most prevalent (10.2%) form of the disease and intestinal schistosomiasis was very rare (0.3%) among the school children. Urinary schistosomiasis was found in all study regions except NBR. CRR had the highest prevalence of urinary schistosomiasis and all the schools sampled in the region had at least on student with the infection. Fifty percent of schools in URR had urinary schistosomiasis infection and just one school in LRR had the infection. Presence of blood in urine was a good indicator of urinary schistosomiasis. While being male increases the chance of getting urinary schistosomiasis, playing, bathing and swimming in water bodies unexpedly turned out to pose less risk for infection, indicating the true water contact activities of the children were probably underrepresented in the data. The study provides vital information for the schistosomiasis control efforts of The Gambia. Further studies are required to know the real status of intestinal schistosomiasis in the country.

Background Studies in Sub Saharan Africa have shown that the Circulating Cathodic Antigen point-of-care-test (POC-CCA) is more accurate in the detections of S. mansoni than the microscopic Kato-Katz technique but less is known about the accuracy of this rapid test in detecting S. haematobium infections. This study was intended to evaluate the field accuracy of POC-CCA as a rapid test kit for schistosomiasis mapping in The Gambia. Methods This prospective study was conducted in 4 regions in the country. Ten schools were randomly selected from each region, and a total of 2018 participants whose ages range from 7 to 14 years were enrolled in the study. Stool and urine samples were collected from each participant from May to June 2015, and tested for S. haematobium and S. mansoni infections in field and laboratory settings. The tests conducted included POC-CCA, double Kato-Katz slides, urine filtration and dipstick for hematuria. Results Of the 1954 participants that had complete data, the mean age of participants was 9.9 years. The prevalence of children infected with S. haematobium, using urine filtration technique was 10.1% (95% CI: 8.87–11.55). Central River Region had the highest level of urinary schistosomiasis with a prevalence of 28.0% (24.13–32.12).The lowest urinary schistosomiasis prevalence of 0.6% (0.12–1.86) was found in Lower River Region and North Bank Region had no cases of schistosomiasis detected. Only 5 participants were infected with S. mansoni. Using urine filtration as reference standard for the detection of S. haematobium, the sensitivity and specificity of POC-CCA was 47.7% and 75.8%. Whilst sensitivity and specificity of POC-CCA for detecting S. mansoni were 60.0% and 71.2% using double Kato-Katz as reference standard. Conclusion This study showed lower sensitivity of POC-CCA in detecting S. haematobium. Therefore POC-CCA is less useful for rapid diagnosis of urinary schistosomiasis.