Genomic epidemiology of SARS-CoV-2 infections in The Gambia: an analysis of routinely collected surveillance data between March, 2020, and January, 2022.

BACKGROUND: COVID-19, caused by SARS-CoV-2, is one of the deadliest pandemics of the past 100 years. Genomic sequencing has an important role in monitoring of the evolution of the virus, including the detection of new viral variants. We aimed to describe the genomic epidemiology of SARS-CoV-2 infections in The Gambia. METHODS: Nasopharyngeal or oropharyngeal swabs collected from people with suspected cases of COVID-19 and international travellers were tested for SARS-CoV-2 with standard RT-PCR methods. SARS-CoV-2-positive samples were sequenced according to standard library preparation and sequencing protocols. Bioinformatic analysis was done using ARTIC pipelines and Pangolin was used to assign lineages. To construct phylogenetic trees, sequences were first stratified into different COVID-19 waves (waves 1-4) and aligned. Clustering analysis was done and phylogenetic trees constructed. FINDINGS: Between March, 2020, and January, 2022, 11 911 confirmed cases of COVID-19 were recorded in The Gambia, and 1638 SARS-CoV-2 genomes were sequenced. Cases were broadly distributed into four waves, with more cases during the waves that coincided with the rainy season (July-October). Each wave occurred after the introduction of new viral variants or lineages, or both, generally those already established in Europe or in other African countries. Local transmission was higher during the first and third waves (ie, those that corresponded with the rainy season), in which the B.1.416 lineage and delta (AY.34.1) were dominant, respectively. The second wave was driven by the alpha and eta variants and the B.1.1.420 lineage. The fourth wave was driven by the omicron variant and was predominantly associated with the BA.1.1 lineage. INTERPRETATION: More cases of SARS-CoV-2 infection were recorded in The Gambia during peaks of the pandemic that coincided with the rainy season, in line with transmission patterns for other respiratory viruses. The introduction of new lineages or variants preceded epidemic waves, highlighting the importance of implementing well structured genomic surveillance at a national level to detect and monitor emerging and circulating variants. FUNDING: Medical Research Unit The Gambia at London School of Hygiene & Tropical Medicine, UK Research and Innovation, WHO.

Mapping survey of schistosomiasis and soil-transmitted helminthiases towards mass drug administration in The Gambia.

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.

Prevalence and risk factors of schistosomiasis among primary school children in four selected regions of The Gambia.

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.

Prevalence and risk factors of strongyloidiasis among schoolchildren in Sabach Sanjal and Upper Badibou districts in the North Bank East Region of The Gambia.

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 <0.001). Schoolchildren who 'sometimes' have water or tissue after defaecation have more infection rate compared to those who 'always' have water or tissue after defaecation. However, this difference was not statistically significant (aOR = 1.36, p-value = 0.308). CONCLUSION: The study revealed the prevalence of strongyloidiasis in Sabach Sanjal and Upper Badibou districts of The Gambia. Kato-Katz technique might be inadequate for detecting S. stercoralis; thus, more studies are needed to determine the true prevalence of the disease in these two districts through the combined use of highly sensitive techniques such as Baermann, Koga Agar Culture and polymerase chain reaction.

Field evaluation of a schistosome circulating cathodic antigen rapid test kit at point-of-care for mapping of schistosomiasis endemic districts in The Gambia.

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.