Background Plasmodium falciparum ( P. falciparum ) infection remains a significant public health threat in West Africa, where chemoprevention and first-line therapies are key interventions against malaria. However, the development and spread of resistance to commonly used antimalarials poses a growing threat to the efficacy of these strategies. Methods This study characterises the recent landscape of antimalarial resistance in West Africa by analysing targeted amplicon sequences from 17,384 P. falciparum infections, sampled predominantly between 2018 and 2023 across eight countries (The Gambia, Senegal, Sierra Leone, Guinea, Mali, Ghana, Nigeria, Cameroon). Prevalence of resistance-associated alleles within genes mdr1 , dhfr, crt, dhps, kelch13 was estimated by aggregating samples at country and country-year level. Results Across countries, the prevalence of the pyrimethamine resistance–associated dhfr triple mutant allele (51I/59R/108N) exceeded 80%, while its combination with the sulfadoxine resistance–associated dhps 437G exceeded 60% of infections. Unlike the parasite genotypes in East Africa, the prevalence of the dhps 540E mutant was low (1.5%), whereas dhps 436A was common (43.8%). The chloroquine resistance marker crt 76T showed greatest geographic heterogeneity, ranging from low prevalence in Ghana (1.3%) to very common in The Gambia (64.9%). Non-synonymous mutants of kelch13 were uncommon, most with unknown relevance to artemisinin resistance and observed for the first time in Africa. However, mutants that are artemisinin resistance-associated elsewhere were detected in three infection samples from Ghana (574L, 561H, 469Y), and one in Cameroon (538V). Conclusion This large-scale genomic surveillance of P. falciparum infections highlights the need for ongoing monitoring of drug resistance and for data integration throughout the region.

Abstract Where malaria transmission declines, the remaining infections are increasingly low-density and asymptomatic, forming a persistent reservoir that is difficult to track using conventional epidemiological approaches. However, genomic data from such community-level infections remain scarce, limiting the ability to track parasite lineages, detect clonal expansions, and identify persistent chronic infections in pre-elimination settings. Here, 78 single-genotype P. falciparum genome sequences are analysed from community infections within a small area of The Gambia, where malaria transmission has substantially declined over recent decades. Pairwise identity-by-descent (IBD) analysis revealed generally low genetic relatedness among parasites, consistent with ongoing recombination and genetic mixing at the community scale. Nevertheless, eight clusters of near-identical genomes (IBD > 0.9) were identified, enabling the inference of recent de novo mutations that differentiate these genomes. Across these clusters, 43 de novo single-nucleotide polymorphisms and 19 short indels were identified using long-read-derived reference genomes. The observed pattern of mutation in natural infections broadly resembled that previously reported from laboratory mutation-accumulation experiments, including a strong transition bias and enrichment of G:C→A:T substitutions. These results demonstrate that combining IBD analysis with de novo mutation detection enables fine-scale resolution of parasite relatedness and recent transmission history. As malaria transmission continues to decline, such approaches may become increasingly valuable for tracking local transmission, identify parasite lineages, and potentially distinguish persistent infections from reintroduction events.

Understanding evolution of human pathogens requires looking beyond the effects of recent interventions. To study malaria parasites prior to widespread drug selection, Plasmodium falciparum genomes were sequenced from the oldest population-based set of archived research samples yet identified, placental blood collected in the Gambia between 1966 and 1971. High-quality data were obtained from 54 infected samples, showing that genomic complexity within infections was high, most infections were genetically unrelated, and no drug resistance alleles were detected. Strong signatures of positive selection are clearly seen at multiple loci throughout the genome, most of which encode surface proteins that bind erythrocytes and are targets of acquired antibody responses. Comparison of population samples obtained over a following period of almost 50 years revealed major directional allele frequency changes at several loci apart from drug resistance genes. Exceptional changes over this time are seen at gdv1 that regulates the rate of parasite sexual conversion required for transmission, and at the unlinked Pfsa1 and Pfsa3 loci previously associated with infection of individuals with sickle-cell trait. Other affected loci encode surface and transporter proteins warranting targeted functional analyses. This identification of key long-term adaptations is important for understanding and managing future evolution of malaria parasites.

Plasmodium falciparum merozoites invade erythrocytes using various ligand-receptor interactions. Important ligands encoded by the eba and Rh gene families have varying expression levels in different parasite isolates, affecting their vaccine candidacy. Analyses of clinical isolates from endemic areas in Africa have indicated that most variation in these expression profiles exists within each local area, and only minor differences are seen between areas, although comparisons with non-African populations have not previously been performed. To enable this, relative transcript levels of three eba genes and five Rh genes have been analysed in new population samples, Malaysian isolates sampled from Sabah State in Borneo prior to endemic malaria elimination, and Gambian isolates, cultured under the same conditions to harvest schizonts for reverse transcription quantitative PCR assays. Significant differences between these populations were seen for three of the ligand genes, levels of eba175 being higher in Malaysia, while levels of eba181 and Rh2b were lower in Malaysia. The variation in gene transcript profiles was not associated with having single or multiple genotypes within each isolate. The distinctness of the Malaysian population expression profile was also supported by comparing previous data on clinical isolates from Ghana. In tests for correlation with previously determined parasite multiplication rates, eba181 transcript levels correlated positively among Malaysian isolates but not among Gambian isolates. These findings suggest that expression of three P. falciparum merozoite ligands involved in invasion may be regionally differentiated, and further analysis of Asian parasite populations would be important if vaccines based on these candidates are to be considered for future use.

Background Most tuberculosis (TB) cases in The Gambia are notified in the Greater Banjul Area (GBA). We conducted an Enhanced-Case-Finding (ECF) intervention in the GBA and determined its effect on TB case notifications and ongoing TB transmission. Methods This was a cluster randomized trial in which randomly assigned intervention areas of grouped settlements received three rounds of an ECF strategy consisting of sensitization followed by auramine microscopy, whereas people with TB in control areas continued to be identified through passive case finding. People with TB were recruited at the TB diagnostic and treatment centers serving both the intervention- and control areas. The primary outcome was TB case notification rate. To exclude that an increase in notified cases, followed by a decrease in notified cases, would hide the future impact of the intervention, we tested for changes in transmission dynamics using both genetic clustering and phylodynamic methods. Results 3,047 people living with TB were recruited in the study, evenly split between intervention and control regions. No significant difference in TB case notification rates, transmission clustering or effective reproductive number was detected between intervention and control areas using either a case notification rate or phylodynamic approach. Conclusion Although we did not find evidence for decreased TB case notification nor TB transmission through the ECF strategy used, this approach is an examplar of how both classical epidemiology and genomic phylodynamics approaches can be integrated to better assess public health intervention outcomes.

Abstract The Plasmodium falciparum PIMMS43 gene encodes an ookinete protein that is important for mosquito infection. Here, large indel variants within the coding sequence are identified, and frequencies in natural infections of humans and mosquitoes investigated. Comparing long-read genome sequences in a small panel of P. falciparum strains and related species revealed a 150 bp deletion in the central part of the gene in several strains including the standard 3D7 reference genome. Mapping of short-read genome sequence data from 524 P. falciparum infections from nine different countries to full-length PIMMS43 showed the 150 bp deletion and an alternative 90 bp deletion to be common structural variants. Across African populations, the 150 bp deletion had a mean allele frequency of 32%, and the 90 bp deletion a mean frequency of 12%, with significant geographical variation. Targeted genotyping of 30 oocysts from naturally infected mosquitoes in Tanzania by nested PCR showed overall deletion variant frequencies similar to those seen in human infections in the same country. Although sample size was limited, a difference in the variant frequencies in oocysts from Anopheles gambiae and Anopheles funestus suggests potential vector-specific selection. The findings highlight the importance of surveying structural genomic variation and its potential role in parasite adaptation. Data summary The long-read genome sequence data sources are listed in the Supplementary Information (Supplementary Table 1). The short-read genome sequence data from human infections were extracted as a selected subset of those in the Pf7 release of global data from the MalariaGEN Consortium as described in the Methods. The SNP and indel genotypes derived from each sample of parasites cultured in the laboratory and from natural mosquito infections are given in the Supplementary Information (Supplementary Tables 1 and 3, Supplementary Figure 1). Impact statement This study identifies large indel polymorphisms in the malaria parasite transmission-stage gene PIMMS43 , reflecting substantial structural variation previously overlooked by genome-wide SNP-focused analyses. Using long- and short-read genomic data across diverse samples followed by targeted genotyping, we show that deletion variants are frequent and geographically structured, with initial evidence consistent with potential vector-specific selection. This highlights the importance of incorporating structural variation into population genomic surveillance and studies of parasite adaptation.

Objectives To synthesise evidence on oral and dental side-effects experienced by head and neck cancer (HNC) patients, assess the strength and quality of existing systematic reviews, evaluate the evidence for prevention and management interventions and identify key gaps to inform future research. Data Systematic reviews (with/without meta-analysis) published from 2015 onwards involving adults with HNC reporting oral/dental complications and/or interventions were included. Sources MEDLINE (OVID), Embase, Cochrane Database of Systematic Reviews and Scopus were searched (19 June 2025). Two reviewers screened and extracted data independently. Study Selection An umbrella review (PROSPERO CRD420251063188) was conducted following JBI/Cochrane guidance and reported in line with PRISMA 2020. Methodological quality was assessed using AMSTAR-2 and primary-study overlap quantified using corrected-covered-area (CCA). Owing to heterogeneity, findings were synthesised narratively by domain. Conclusions A total of 131 systematic reviews were included, with most rated as low or critically low confidence. Oral mucositis was the most frequently reported complication, followed by xerostomia, dysphagia, trismus, dental caries, and dysgeusia; osteoradionecrosis was less common. Preventive and therapeutic interventions are widely studied but largely supported by low-quality evidence. Photobiomodulation was associated with reduced oral mucositis, while intensity-modulated radiotherapy was associated with reduced xerostomia and mandibular osteoradionecrosis. Overall, the evidence base is fragmented and of low confidence. Standardised outcome measures and high-quality prospective studies are needed to strengthen the evidence base and improve survivorship care. Clinical Significance Head and neck cancer patients experience a high burden of oral complications, yet dental management strategies are supported by limited high-quality evidence. This review highlights key areas of uncertainty and reinforces the need for multidisciplinary, evidence-based care, while identifying priorities for research to improve long-term oral health and quality of life.

Importance Cigarette smoking is a strong risk factor for mortality in patients diagnosed with head and neck squamous cell carcinoma (HNSCC). However, little evidence supports which smoking metric best models the association between smoking and survival in HNSCC. Objective To determine which smoking metric best models a linear association between smoking exposure and overall survival (OS) in patients with HNSCC. Design, Setting, and Participants A retrospective multicenter cohort study of 6 clinical epidemiological studies was performed. Five were part of the Human Papillomavirus, Oral and Oropharyngeal Cancer Genomic Research (VOYAGER) consortium. Participants included patients 18 years and older with pathologically confirmed HNSCC. Data were collected from January 2002 to December 2019, and data were analyzed between January 2022 to November 2024. Main Outcomes and Measures The primary outcome was OS. The performance of 8 smoking metrics, including pack-years, duration, and log cig-years (calculated as log 10 [cigarettes smoked per day + 1] × number of years smoked) for modeling OS were compared. Metric performance was measured by the strength of association in Cox proportional hazard models, linearity based on P for linear trend, Akaike information criterion (AIC; lower value indicates better model fit), and visual assessment of spline curves. Secondary outcomes included modeling OS in clinicodemographic subgroups and HNSCC anatomic subsites. Exploratory outcomes included cancer-specific survival and noncancer survival. Results In total, 8875 patients with HNSCC (2114 [24%] female; median [IQR] age, 61 [54-69] years) were included. Of 8 smoking metrics evaluated, smoking duration (adjusted hazard ratio [aHR], 1.11 [95% CI, 1.03-1.19]) and log cig-years (aHR, 1.11 [95% CI, 1.04-1.18]) had the highest aHRs; both had a statistically significant linear association with OS. Log cig-years had the lowest AIC linear value and the most visually linear spline curve when modeling OS. Duration and log cig-years outperformed pack-years for modeling OS regardless of age, smoking status, and cancer stage. Both performed well in lip and oral cavity, laryngeal (only duration was significant), and human papillomavirus–negative oropharyngeal subsites. In an exploratory analysis, duration had the highest aHR (1.15 [95% CI, 1.02-1.29]), and log cig-years had the lowest AIC linear value when modeling noncancer survival. Conclusions and Relevance In this cohort study, smoking duration and log cig-years best modeled a linear relationship with OS for patients with HNSCC. Both metrics maintained robust performance within specific clinicodemographic subgroups and anatomic subsites. Although most HNSCC survival models control for smoking exposure using smoking status or pack-years, duration and log cig-years may be superior metrics to account for the effects of smoking on survival.

BackgroundLaryngeal squamous cell cancer (LSCC) accounts for around one‐third of head and neck cancers, with smoking and alcohol as major risk factors. Despite advances in organ preservation, survival rates have stagnated globally over recent decades. The impact of socioeconomic deprivation on LSCC outcomes in the West of Scotland remains underexplored. We hypothesized that survival outcomes in the West of Scotland are poorer than cohorts from other developed nations.AimTo evaluate characteristics and survival outcomes for LSCC patients in the West of Scotland and identify predictors of survival.MethodsA retrospective cohort study of 867 LSCC patients in the West of Scotland (2014–2020) analyzed demographics, tumor staging, performance status, treatments, and socioeconomic status (Scottish Index of Multiple Deprivation, SIMD). Subgroup differences were assessed using chi‐squared tests. Survival analysis was performed with Kaplan–Meier curves, log‐rank tests, and Cox proportional hazards modeling.ResultsThe cohort had a male‐to‐female ratio of 3.2:1, with a mean age of 65.5 years, with 56% presenting with advanced disease. Most patients (70.7%) lived in the most deprived areas. Supraglottic cancers were the most common subsite (51%). Five‐year overall survival (OS) was 46%, with a median OS of 52 months. Glottic cancers had better outcomes (64% OS) compared to supraglottic cancers (36%). Predictors of survival included age, subsite, performance status, alcohol use, treatment modality, and deprivation.ConclusionLSCC survival in the West of Scotland is lower than in other European nations, influenced by advanced‐stage presentation, deprivation, and frailty. Addressing these factors is vital to improving outcomes.Level of evidence: III Laryngoscope, 2025

Climate change has resulted in an increase in heat exposure globally. There is strong evidence that this increased heat stress is associated with poor maternal and fetal outcomes, especially in vulnerable populations. However, there remains poor understanding of the biological pathways and mechanisms involved in the impact of heat in pregnancy. This observational cohort study of 764 pregnant participants based in sub-Saharan Africa, a geographical region at risk of extreme heat events, aims to evaluate the physiological and biochemical changes that occur in pregnancy due to heat stress. The key objectives of the study are to 1) map exposure to heat stress in the cohort and understand what environmental, social and community factors increase the risk of extreme heat exposure; 2) assess the impact of heat stress on maternal health, e.g. heat strain, subjective psychological well-being, sleep and activity level; 3) evaluate how heat stress impacts placenta structure and function; 4) determine how chronic heat exposure impacts birth outcomes; and 5) explore the epigenetic changes in the placenta and infant by heat stress exposure per trimester. Pregnant women will be recruited from two distinct regions in The Gambia to exploit the naturally occurring heat gradient across the country. Microclimate mapping of the area of recruitment will give detailed exposure measurements. Participants will be asked to wear a watch-style device at 28- and 35-weeks gestational age to evaluate maternal heart rate, activity and sleep. At the end of the week, an ultrasound scan will be performed to evaluate fetal size and placental blood flow. At delivery, birth outcomes will be recorded and maternal, placental and cord samples taken for epigenetic, biochemical and histological evaluation. Evaluation of neuro-behaviour and final infant samples will be taken at 1 month following birth.

The recent discovery of genetic mutations in Plasmodium falciparum —the most lethal malaria parasite—that enable it to overcome the protective effects of sickle cell trait, raises fundamental questions about the underlying biological and evolutionary interactions. Here we develop a geostatistical model to compare sickle haemoglobin genotype frequencies to the Plasmodium falciparum sickle-associated alleles across global populations, and find a robust association at multiple geographical scales, implying that sickle drives positive selection for these parasite mutations. A model of parasite evolution and an analysis of local haplotype patterns suggest that key features of these mutations – that they are polymorphic in all African populations and are mutually correlated despite lying in different genome regions - are caused by geographical variation in selection pressure, and that the alleles may have been maintained by balancing selection over timescales comparable to the age of the sickle mutation itself. The predicted impact of this host-parasite interaction on disease outcomes varies widely across populations, and functional data are needed to discover the biological mechanisms involved. ### Competing Interest Statement The authors have declared no competing interest. Wellcome Trust, https://ror.org/029chgv08, 304926/Z/23/Z National Natural Science Foundation of China, T2350610281, 82273731 Zhejiang University Education Foundation Global Partnership Fund, 188170-11103

Understanding the genetic diversity and transmission dynamics of Plasmodium falciparum , the causative agent of malaria, is crucial for effective control and elimination efforts. In some endemic regions, malaria is highly seasonal with no or little transmission during up to 8 mo, yet little is known about how seasonality affects the parasite population genetics. Here, we conducted a longitudinal study over 2.5 y on 1516 participants in the Upper River Region of The Gambia. With 425 P. falciparum genetic barcodes genotyped from asymptomatic infections, we developed an identity by descent (IBD) based pipeline and validated its accuracy against 199 parasite genomes sequenced from the same isolates. Genetic relatedness between isolates revealed a very low inbreeding level, suggesting continuous recombination among parasites rather than the dominance of specific strains. However, isolates from the same household were sixfold more likely to be genetically related compared to those from other villages, suggesting close transmission links within households. Seasonal variation also influenced parasite genetics, with most differentiation occurring during the transition from the low transmission season to the subsequent high transmission season. Yet chronic infections presented exceptions, including one individual who had a continuous infection by the same parasite genotype for at least 18 mo. Our findings highlight the burden of asymptomatic chronic malaria carriers and the importance of characterizing the parasite genetic population at the community-level. Most importantly, ‘reactive’ approaches for malaria elimination should not be limited to acute malaria cases but be broadened to households of asymptomatic carriers.

The significance of multiplication rate variation in malaria parasites needs to be determined, particularly for Plasmodium falciparum, the species that causes most virulent infections. To investigate this, parasites from cases presenting to hospital in The Gambia and from local community infections were culture-established and then tested under exponential growth conditions in a standardised six-day multiplication rate assay. The multiplication rate distribution was lower than seen previously in clinical isolates from another area in West Africa where infection is more highly endemic. Multiplication rates were higher in cultured isolates derived from hospital cases (N = 23, mean = 2.9-fold per 48 h) than in those from community infections (N = 11, mean = 1.8-fold)(Mann-Whitney P < 0.001). There was a positive correlation between levels of parasitaemia in peripheral blood of sampled individuals and multiplication rates of the isolates in culture (Spearman’s rho = 0.45, P = 0.017). There was no significant difference between isolates containing single parasite genotypes or multiple genotypes at the time of assay, suggesting that parasites do not modify their multiplication rates in response to the presence of different genotypes. It will be important to uncover the mechanisms of this intrinsic multiplication rate variation, and to also investigate the epidemiological distribution and potential associations with infection phenotypes in other populations.

Replication rates and virulence of pathogens are hypothesised to evolve in response to varying intensity of transmission and competition among genotypes. Under exponential growth conditions in culture, clinical isolates of the malaria parasite Plasmodium falciparum have variable intrinsic multiplication rates, but comparisons of samples from different areas are needed. To analyse parasites from an area of low endemicity, Malaysian clinical isolates cryopreserved prior to malaria elimination were studied. The mean and range of P. falciparum multiplication rates in Malaysian isolates were no less than that seen among isolates from more highly endemic populations in Africa, which does not support a hypothesis of adaptation to prevailing levels of infection endemicity. Moreover, the distribution of multiplication rates was similar between isolates with single parasite genotypes and those containing multiple genotypes, which does not support a hypothesis of facultative adjustment to competing parasites. Based solely on clinical isolates, the findings indicate that parasites may not evolve lower multiplication rates under conditions of reduced transmission, and that the virulence potential is likely to be undiminished in pre-elimination settings. This encourages efforts to eliminate endemic infection completely, as has been achieved at the national level in Malaysia.

Diagnosis, positioned between disease prevention and treatment, is essential for head and neck cancer management. Delays in diagnosis contribute to disease upstaging, leading to more complex treatment with poorer survival and functional outcomes. This article focuses on current and future innovative diagnostic approaches, which vary in maturity and implementation, to promote early diagnosis. These include symptom-based triaging, telemedicine, diagnostic hubs, machine learning, and circulating tumor markers. COVID-19 brought about new diagnostic pathways, many of which remained in place, generating encouraging evidence of pathway efficiency. However, nuanced diagnostic tools for early cancer detection remain far from implementation in a real-world setting.

We describe the Pf8 data resource, the latest MalariaGEN release of curated genome variation data on over 33,000 Plasmodium falciparum samples from 99 partner studies and 122 locations over more than 50 years. This release provides open access to raw sequencing data and genotypes at over 12 million genomic positions. For the first time, it includes copy-number variation (CNV) calls in the drug-resistance associated genes gch1 and crt. As in Pf7, CNV calls are provided for mdr1 and plasmepsin2/3, along with calls for deletion in hrp2 and hrp3, genes associated with rapid diagnostic test failures. This data resource additionally features derived datasets, interactive web applications for exploring patterns of drug resistance and variation in over 5,000 genes, an updated Python package providing methods for accessing and analysing the data, and open access analysis notebooks that can be used as starting points for further analyses. In addition, informative example analyses show contrasting profiles of the decline of chloroquine resistance-associated mutations in Africa, and variation in copy number variation across 10 distinct sub-populations. To the best of our knowledge, Pf8 is the largest open data set of genome variation in any eukaryotic species, making it an invaluable foundational resource for understanding evolution, including that of pathogens.

Background: Inequalities in oral health disproportionately affect low and middle income countries and a pattern of increased prevalence of dental caries in children has been reported. Objectives: To determine the burden of disease and behavioural and toothache history of six- and 12-year-old Malawi schoolchildren. Methods: Ethical approval was granted by Malawi's National Health Sciences Research Committee. The survey was undertaken by nine Malawian dental therapists and three UK dentists in 24 schools. Stratified cluster sampling ensured that the children were representative of Malawi's three Regions. Dental caries (into dentine), fluorosis, oral hygiene and PUFA index data were collected via a dental examination. Questionnaires were completed by each child and by the Head Teacher from each school. Results: A total of 1,330 six-year-old and 1,611 12-year-old children were examined, evenly split between the sexes. Dental caries was identified in 47% of six-year-olds and 23% of 12-year-olds. None of the children had filled teeth. The mean dmft/DMFT for children with caries experience was 3.0 for six-year-olds and 1.8 for 12-year-olds. Dental fluorosis was recorded for 7% of 12-year-olds. A history of toothache was reported by 29% of six-year-olds and 42% of 12-year-olds. Conclusions: The prevalence of caries and absence of signs of past clinical care highlight the need to implement activities identified in Malawi's National Oral Health Policy around the provision of appropriate preventive and treatment services for children.