Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense cause human African trypanosomiasis (HAT), a neglected tropical disease that constitutes an important public health issue in sub-Saharan Africa. In the absence of a vaccine, only chemotherapy and vector control has been used to combat the disease. Environmental factors, such as exposure to infected tsetse files, and genetic factors such as variants in the APOL1 gene have been shown to contribute to the risk of developing HAT. However, the known factors only explain a small part of the risk of developing trypanosomiasis. We have undertaken a genome wide association study (GWAS) using 3813 samples from T. b. gambiense and T.b. rhodesiense HAT foci in Guinea, Côte d’Ivoire, Cameroon, DRC, Malawi and Uganda. 2141 samples were genotyped on the H3Africa SNP chip followed by a genotyping a validation cohort of an additional 1,627 samples at candidate loci. After the primary and validation studies we identified a novel locus near SMOC2 with genome-wide significance. We also identified suggestive associations near NXN, NTNG1 and NCKAP5 that have stronger associations with disease susceptibility than the APOL1 loci that has been previously identified by hypothesis driven approaches. These genes offer new entry points for future studies of the underlying genetic mechanisms of HAT.### Competing Interest StatementThe authors have declared no competing interest.### Funding StatementThis work was supported by Human Heredity and Health in Africa (H3Africa) programme under Wellcome Trust grant number 099310/Z/12/Z and H3Africa grant number H3A-18- 004. H3Africa is managed by the Science for Africa Foundation (SFA Foundation) in partnership with Wellcome, NIH and AfSHG. The views expressed herein are those of the author(s) and not necessarily those of the SFA Foundation and her partners.### Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:The Minister de la Sante Publique (Democratic Republic of Congo) gave ethical approval for this work No 1/2013; Ministere de la Sante et de la Lutte Contre le SIDA of Cote d'Ivoıre gave ethical approval for this work; Uganda Vector Control Division Research Ethics Committee (Ministry of Health), gave ethical approval for this work ; Uganda National Council for Science and Technology HS 1344 gave ethical approval for this work; Comite Consultatif de Deontologie et d'Ethique [CCDE] de l'Institut de Recherche pour le Developpement: gave ethical approval for this work; 1-22/04/2013; Cameroon (Le Comite National d'Ethique de la Recherche pour la Sante Humain: 2013/364/L/CNERSH/ SP), Comite National D'Ethique et de la Recherche 2014/No 38/ MSLS/CNER-dkn) gave ethical approval for this work Malawi National Health Sciences Research Committee, protocol numbers NHSRC15/4/1399 and Malawi 1213 gave ethical approval for this work I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.YesAll data produced in the present study are available upon reasonable request to the authors

BACKGROUND:APOL1 variants G1 and G2 are common in populations with recent African ancestry. They are associated with protection from African sleeping sickness, however homozygosity or compound heterozygosity for these variants is associated with chronic kidney disease (CKD) and related conditions. What is not clear is the extent of associations with non-kidney-related disorders, and whether there are clusters of diseases associated with individual APOL1 genotypes.METHODS:Using a cohort of 7462 UK Biobank participants with recent African ancestry, we conducted a phenome-wide association study investigating associations between individual APOL1 genotypes and conditions identified by the International Classification of Disease phenotypes.FINDINGS:We identified 27 potential associations between individual APOL1 genotypes and a diverse range of conditions. G1/G2 compound heterozygotes were specifically associated with 26 of these conditions (all deleteriously), with an over-representation of infectious diseases (including hospitalisation and death resulting from COVID-19). The analysis also exposed complexities in the relationship between APOL1 and CKD that are not evident when risk variants are grouped together: G1 homozygosity, G2 homozygosity, and G1/G2 compound heterozygosity were each shown to be associated with distinct CKD phenotypes. The multi-locus nature of the G1/G2 genotype means that its associations would go undetected in a standard genome-wide association study.INTERPRETATION:Our findings have implications for understanding health risks and better-targeted detection, intervention, and therapeutic strategies, particularly in populations where APOL1 G1 and G2 are common such as in sub-Saharan Africa and its diaspora.FUNDING:This study was funded by the Wellcome Trust (209511/Z/17/Z) and H3Africa (H3A/18/004).

Background Human African trypanosomiasis (HAT) is an important disease of sub-Saharan Africa that is approaching elimination in many regions. However, the disease has previously returned from similarly low case numbers in the past, making it important to identify issues that hinder elimination efforts. One important factor is likely to be the recent characterization of individuals with latent HAT infections that are able to tolerate HAT with few symptoms and to control blood parasitaemia to levels that are undetectable by microscopy. Although animal trypanotolerance has been examined in detail, it is unclear how the latent phenotype is maintained in humans.Methods To identify immune components involved in latent HAT, we used targeted RNASeq to examine the expression of 495 immune-related transcripts in blood collected from 287 individuals at active disease foci in Guinea. These samples included latent infections, HAT clinical cases, and uninfected controls. The in vivo effects of IL21 functional blockade was investigated using a murine model of trypanosomiasis.Results Differential expression analysis revealed transcripts involved in T cell activation and B cell development that associated with trypanosome infection, including PD1 , CD70 , and CD80 . In particular, IL21 was found to be elevated in infected individuals, although it was significantly higher in clinical cases relative to latent infections. This pattern was replicated at the protein level when patient sera were examined by ELISA. Reducing IL21 pathway activity in mice infected with Trypanosoma brucei led to increased survivorship and reduced parasitaemia in the model animals.Conclusion Our data show that IL21 is a potential biomarker of Human African Trypanosomiasis and is a cause rather than a consequence of symptoms severity. Further investigation of IL21 will contribute to understanding the factors involved in developing latent HAT, improving control efforts to identify and predict such infections. In the future, the factors identified in this study may also serve as intervention targets to control the symptoms of trypanosomiasis.### Competing Interest StatementThe authors have declared no competing interest.### Funding StatementPC, AC, AML were funded by a Wellcome Senior Fellowship to AML (209511/Z/17/Z). BB was funded by IRD. WJK, HN and HI, were supported through the Human Hereditary and Health in Africa (H3Africa) [H3A/18/004]. The second phase of the Wellcome component of H3Africais being implemented by the African Academy of Sciences (AAS) and the NEPAD Agency's Alliance for Accelerating Excellence in Science in Africa (AESA) in partnership with Wellcome.### Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:All investigations on humans were conducted in accordance with the Declaration of Helsinki. Participants were identified through healthcare providers, community engagement and active surveillance campaigns led by the national contral program, Ministry of Health Guinea. Written informed consents for sample collection, analysis and publication of anonymised data was obtained from all participants by trained local healthcare workers. Subjects or their legal guardian gave consent as a signature or a thumbprint after receiving standardized information in French or their local langage as preferred. Ethical approvals for the study was obtained from within the TrypanoGEN Project following H3Africa Consortium guidelines for informed consent and from Comite Consultatif de Deontologie et ethique (CCDE) at the Institut de recherche pour le Developpent (IRD; 10/06/2013). Research procedures were also approved by the University of Glasgow MVLS Ethics Committee for Non-Clinical Research Involving Human Subjects (Reference no. 200120043). All animal experiments were approved by the University of Glasgow Ethical Review Committee and performed in accordance with the UK Home Office guidelines, UK Animals (Scientific Procedures) Act, 1986 and EU directive 2010/63/EU. All experiments were conducted under SAPO regulations and UK Home Office project licence number PC8C3B25C to Dr. Jean Rodgers. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.YesAll data produced in the present study are available upon reasonable request to the authors and the TrypanoGEN network (H3Africa)

In the search for alternatives for the treatment of parasitic neglected tropical diseases (NTD), an approach combining metal-based drug design and nanotechnology has been developed. On one hand, a potential metal-based drug of the formula [PdCl(L1)], where L1 is a coumarin-thiosemicarbazone hybrid ligand, had been previously reported. This compound demonstrated activity in vitro and in vivo against Trypanosoma cruzi, the etiological agent of Chagas disease. On the other hand, conjugation of gold nanoparticles (AuNPs) to biologically active compounds has shown to enhance drug delivery and efficacy. In this work, these approaches were combined to successfully conjugate [PdCl(L1)] with AuNPs containing a Raman reporter for intracellular tracking. The aim of this conjugation was to exploit the potential of the nanoparticles as carriers and the metal complex as an antiparasitic agent. Conjugated nanotags were fully characterized and both the free palladium complex and the conjugates were tested against Trypanosoma brucei brucei (T. b. b.), the causative agent of a related NTD, African Trypanosomiasis. The results showed that the conjugated nanotags [Pd(L1)-AuNPs] (IC50 = 3.22 mu M) demonstrated almost a 5-fold increase in the anti-T. b. b. activity in comparison with [PdCl(L1)] alone (IC50 = 15.32 mu M) and twice the activity of the unconjugated nanoparticles (IC50 = 6.14 mu M). In addition, the preliminary imaging using Raman microscopy and surface-enhanced Raman scattering (SERS) experiments revealed the successful uptake of [Pd(L1)-AuNPs] by parasites. Although the in vitro selectivity was not improved postconjugation, the promising antitrypanosomatid activity of these conjugates warrant evaluation for performance and selectivity through future in vivo studies. This research paves the way for further exploration of the developed strategy in the fight against parasitic infections.

Background APOL1 variants G1 and G2 are common in populations with recent sub-Saharan African ancestry. They are known to influence health conditions: most notably being associated with protection from human African trypanosomiasis and increased risk of susceptibility to chronic kidney disease. Association studies have often considered G1 and G2 as equivalent, however we recently presented evidence of substantial phenotypic differences between carriers of the two variants. An additional APOL1 variant, N264K, has previously been shown to modify the damaging effect of G2 on the kidney. Here, we examine the influence of these variants on APOL1 protein concentration. Methods Using a cohort of 1,050 UK Biobank participants with recent African ancestry, we compared APOL1 protein concentration in carriers of variants G1, G2, and N264K and performed a genome-wide association study to identify additional modifiers of APOL1 concentration. We also compared APOL1 concentration across self-reported ethnicities for all 43,330 UK Biobank participants for whom APOL1 concentration data was available. Findings APOL1 G1 and G2 are both associated with increased APOL1 protein concentration, however the effect of G2 is more marked, and it was the only locus that reached genome-wide significance in terms of association with APOL1 concentration (p = 3×10−155). In a G2 background, the presence of N264K is associated with a reduction in APOL1 concentration (p = 6 × 10−5). People with self-reported Black or Black British ethnicity have higher APOL1 concentrations all other self-reported ethnicities in the UK Biobank. Interpretation These findings demonstrate the influence of APOL1 variants and APOL1 protein concentration and identify additional phenotypic differences between the G1 and G2, highlighting the value in considering them as distinct in molecular and association studies. This work also provides further detail on the relationship between the G2 and N264K variants, which has significant implications for diagnosis and therapy in kidney disease. ### Competing Interest Statement Parekh has received research funding and consulting fees from Vertex Pharmaceuticals. MacLeod has received research funding from Astra Zeneca. ### Funding Statement This study was funded by the Wellcome Trust (209511/Z/17/Z) and H3Africa (H3A/18/004). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Access to the UK Biobank data was granted for this work under UK Biobank application number 66821. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes This research has been conducted using data from the UK Biobank, a major biomedical database.

The African trypanosome, Trypanosoma brucei, disseminates systemically in tissues of the infected host resulting in complex immunopathology. The kidneys which are important in the response to the anaemia characteristic of African trypanosomiasis, are prone to acute kidney injury (AKI) from multiple noxious stimuli. Little is known about the transcriptional responses of the kidney to trypanosome infection. To assess the tissue-specific response to infection with Trypanosoma brucei , we profiled the clinicopathologic and transcriptional responses of the kidney in BALB/C (susceptible) and C57BL/6 (tolerant) murine models, at early (7 dpi) and late (21 dpi) time points of infection. Trypanosomes in the renal interstitium, tubular necrosis and inflammation characterised early infection in both mouse strains. By late infection, we observed extensive tubular necrosis in the susceptible BALB/C but reparative tubular regeneration in the tolerant C57BL/6 mice. T.b. brucei infection resulted in significant increases in serum creatinine in both strains. Consistent with the clinicopathologic findings, RNA-seq detected both mouse strain- and time-dependent transcriptional responses in the kidney. These included perturbations in genes associated with solute/ion transport, upregulation of markers of tubular injury, hypoxia, glycolysis, and a profound inflammatory and immune response, mirroring the responses observed in other models of AKI. Differential tissue pathology at late time point is preceded by expansion of CD8+ T cells, profound expression of transcription factors and upregulation of anti-inflammatory pathways in C57BL/6 mice. Our findings demonstrate that experimental T. brucei infection-induced kidney injury (TIKI) is a model of AKI and may have clinical implications for Human African Trypanosomiasis cases, who currently are not routinely screened for markers of kidney function.### Competing Interest StatementThe authors have declared no competing interest.

In the skin, Trypanosoma brucei colonises the subcutaneous white adipose tissue, and is proposed to be competent for forward transmission. The interaction between parasites, adipose tissue, and the local immune system is likely to drive the adipose tissue wasting and weight loss observed in cattle and humans infected with T. brucei. However, mechanistically, events leading to subcutaneous white adipose tissue wasting are not fully understood. Here, using several complementary approaches, including mass cytometry by time of flight, bulk and single cell transcriptomics, and in vivo genetic models, we show that T. brucei infection drives local expansion of several IL-17A-producing cells in the murine WAT, including TH17 and Vγ6+ cells. We also show that global IL-17 deficiency, or deletion of the adipocyte IL-17 receptor protect from infection-induced WAT wasting and weight loss. Unexpectedly, we find that abrogation of adipocyte IL-17 signalling results in a significant accumulation of Dpp4+ Pi16+ interstitial preadipocytes and increased extravascular parasites in the WAT, highlighting a critical role for IL-17 signalling in controlling preadipocyte fate, subcutaneous WAT dynamics, and local parasite burden. Taken together, our study highlights the central role of adipocyte IL-17 signalling in controlling WAT responses to infection, suggesting that adipocytes are critical coordinators of tissue dynamics and immune responses to T. brucei infection.

AbstractBackgroundInfectious diseases are a major driving force of natural selection. One human gene associated with strong evolutionary selection isAPOL1. TwoAPOL1variants, G1 and G2, emerged in sub-Saharan Africa in the last 10,000 years, possibly due to protection from the fatal African sleeping sickness, analogous toPlasmodium-driven selection of the sickle-cell trait. As homozygosity for the HbS allele causes sickle cell anaemia, homozygosity for theAPOL1G1 and G2 variants has also been associated with chronic kidney disease (CKD) and other kidney-related conditions. What is not known is the extend of non-kidney-related disorders and if there are clusters of diseases associated with individual APOL1 genotypes.MethodsUsing principal component analysis, we identified a cohort of 10,179 UK Biobank participants with recent African ancestry. We conducted a phenome-wide association test between all combinations ofAPOL1G1 and G2 genotypes and conditions identified with International Classification of Disease phenotypes using Firth’s bias-reduced logistic regression and a false discovery rate to correct for multiple testing. We further examined associations with chronic kidney disease indicators: estimated glomerular filtration rate (eGFR) and urinary albumin:creatinine (uACR).ResultsThe phenome-wide screen revealed 74 (mostly deleterious) potential associations with hospitalisation for a range of conditions. G1/G2 compound heterozygotes were specifically associated with hospitalisation in 64 (86.5%) of these conditions, with an over-representation of infectious diseases (including COVID-19) and endocrine, nutritional, and metabolic diseases. The analysis also revealed complexities in the relationship betweenAPOL1and CKD that are not evident when the risk variants are grouped together: high uACR was associated specifically with G1 homozygosity; low eGFR with G2 homozygosity and G1/G2 compound heterozygosity; progression to end stage kidney disease was associated with G1/G2 compound heterozygosity.ConclusionsAmong 9,594 participants, stratifying individualAPOL1risk variant genotypes had a differential effect on associations with both kidney and non-kidney phenotypes. The compound heterozygous G1/G2 genotype was distinguished as uniquely deleterious in its association with a range of ICD-10 phenotypes. The epistatic nature of the G1/G2 interaction means that such associations may go undetected in a standard genome-wide association study. These observations have the potential to significantly impact the way that health risks are understood, particularly in populations whereAPOL1G1 and G2 are common such as in sub-Saharan Africa and its diaspora.

Background Infectious diseases are a major driving force of natural selection. One human gene associated with strong evolutionary selection is APOL1 . Two APOL1 variants, G1 and G2, emerged in sub-Saharan Africa in the last 10,000 years, possibly due to protection from the fatal African sleeping sickness, analogous to Plasmodium -driven selection of the sickle-cell trait. As homozygosity for the HbS allele causes sickle cell anaemia, homozygosity for the APOL1 G1 and G2 variants has also been associated with chronic kidney disease (CKD) and other kidney-related conditions. What is not known is the extend of non-kidney-related disorders and if there are clusters of diseases associated with individual APOL1 genotypes. Methods Using principal component analysis, we identified a cohort of 10,179 UK Biobank participants with recent African ancestry. We conducted a phenome-wide association test between all combinations of APOL1 G1 and G2 genotypes and conditions identified with International Classification of Disease phenotypes using Firth’s bias-reduced logistic regression and a false discovery rate to correct for multiple testing. We further examined associations with chronic kidney disease indicators: estimated glomerular filtration rate (eGFR) and urinary albumin:creatinine (uACR). Results The phenome-wide screen revealed 74 (mostly deleterious) potential associations with hospitalisation for a range of conditions. G1/G2 compound heterozygotes were specifically associated with hospitalisation in 64 (86.5%) of these conditions, with an over-representation of infectious diseases (including COVID-19) and endocrine, nutritional, and metabolic diseases. The analysis also revealed complexities in the relationship between APOL1 and CKD that are not evident when the risk variants are grouped together: high uACR was associated specifically with G1 homozygosity; low eGFR with G2 homozygosity and G1/G2 compound heterozygosity; progression to end stage kidney disease was associated with G1/G2 compound heterozygosity. Conclusions Among 9,594 participants, stratifying individual APOL1 risk variant genotypes had a differential effect on associations with both kidney and non-kidney phenotypes. The compound heterozygous G1/G2 genotype was distinguished as uniquely deleterious in its association with a range of ICD-10 phenotypes. The epistatic nature of the G1/G2 interaction means that such associations may go undetected in a standard genome-wide association study. These observations have the potential to significantly impact the way that health risks are understood, particularly in populations where APOL1 G1 and G2 are common such as in sub-Saharan Africa and its diaspora. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This study was funded by the Wellcome Trust (209511/Z/17/Z) and H3Africa (H3A/18/004). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Access to the UK Biobank data was granted for this work under UK Biobank application number 66821. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes This research has been conducted using the UK Biobank Resource under application number 66821. All bona fide researchers can apply to use the UK Biobank resource for health related research that is in the public interest. <https://www.ukbiobank.ac.uk>

In the mammalian host, the biology of tissue-dwelling Trypanosoma brucei parasites is not completely understood, especially the mechanisms involved in their extravascular colonization. The trypanosome flagellum is an essential organelle in multiple aspects of the parasites' development. The flagellar protein termed FLAgellar Member 8 (FLAM8) acts as a docking platform for a pool of cyclic AMP response protein 3 (CARP3) that is involved in signaling. FLAM8 exhibits a stage-specific distribution suggesting specific functions in the mammalian and vector stages of the parasite. Analyses of knockdown and knockout trypanosomes in their mammalian forms demonstrated that FLAM8 is not essential in vitro for survival, growth, motility and stumpy differentiation. Functional investigations in experimental infections showed that FLAM8-deprived trypanosomes can establish and maintain an infection in the blood circulation and differentiate into insect transmissible forms. However, quantitative bioluminescence imaging and gene expression analysis revealed that FLAM8-null parasites exhibit a significantly impaired dissemination in the extravascular compartment, that is restored by the addition of a single rescue copy of FLAM8. In vitro trans-endothelial migration assays revealed significant defects in trypanosomes lacking FLAM8. FLAM8 is the first flagellar component shown to modulate T. brucei distribution in the host tissues, possibly through sensing functions, contributing to the maintenance of extravascular parasite populations in mammalian anatomical niches, especially in the skin.

African trypanosomes colonise the skin to ensure parasite transmission. However, how the skin responds to trypanosome infection remains unresolved. Here, we investigate the local immune response of the skin in a murine model of infection using spatial and single cell transcriptomics. We detect expansion of dermal IL-17A-producing Vγ6 + cells during infection, which occurs in the subcutaneous adipose tissue. In silico cell-cell communication analysis suggests that subcutaneous interstitial preadipocytes trigger T cell activation via Cd40 and Tnfsf18 signalling, amongst others. In vivo, we observe that female mice deficient for IL-17A-producing Vγ6 + cells show extensive inflammation and limit subcutaneous adipose tissue wasting, independently of parasite burden. Based on these observations, we propose that subcutaneous adipocytes and Vγ6 + cells act in concert to limit skin inflammation and adipose tissue wasting. These studies provide new insights into the role of γδ T cell and subcutaneous adipocytes as homeostatic regulators of skin immunity during chronic infection.

Background. The diagnosis of gambiense human African trypanosomiasis (gHAT) typically involves 2 steps: a serological screen, followed by the detection of living trypanosome parasites in the blood or lymph node aspirate. Live parasites can, however, remain undetected in some seropositive individuals, who, we hypothesize, are infected with Trypanosoma brucei gambiense parasites in their extravascular dermis. Methods. To test this hypothesis, we conducted a prospective observational cohort study in the gHAT focus of Forecariah, Republic of Guinea. Of the 5417 subjects serologically screened for gHAT, 66 were enrolled into our study and underwent a dermatological examination. At enrollment, 11 seronegative, 8 unconfirmed seropositive, and 18 confirmed seropositive individuals had blood samples and skin biopsies taken and examined for trypanosomes by molecular and immunohistological methods. Results. In seropositive individuals, dermatological symptoms were significantly more frequent, relative to seronegative controls. T.b. gambiense parasites were present in the blood of all confirmed cases (n = 18) but not in unconfirmed seropositive individuals (n = 8). However, T. brucei parasites were detected in the extravascular dermis of all unconfirmed seropositive individuals and all confirmed cases. Skin biopsies of all treated cases and most seropositive untreated individuals progressively became negative for trypanosomes 6 and 20 months later. Conclusions. Our results highlight the skin as a potential reservoir for African trypanosomes, with implications for our understanding of this disease's epidemiology in the context of its planned elimination and underlining the skin as a novel target for gHAT diagnostics.

Human African Trypanosomiasis (HAT) has been responsible for several deadly epidemics throughout the 20th century, but a renewed commitment to disease control has significantly reduced new cases and motivated a target for the elimination of Trypanosoma brucei gambiense-HAT by 2030. However, the recent identification of latent human infections, and the detection of trypanosomes in extravascular tissues hidden from current diagnostic tools, such as the skin, has added new complexity to identifying infected individuals. New and improved diagnostic tests to detect Trypanosoma brucei infection by interrogating the skin are therefore needed. Recent advances have improved the cost, sensitivity and portability of Raman spectroscopy technology for non-invasive medical diagnostics, making it an attractive tool for gambiense-HAT detection. The aim of this work was to assess and develop a new non-invasive diagnostic method for T. brucei through Raman spectroscopy of the skin. Infections were performed in an established murine disease model using the animal-infective Trypanosoma brucei brucei subspecies. The skin of infected and matched control mice was scrutinized ex vivo using a confocal Raman microscope with 532 nm excitation and in situ at 785 nm excitation with a portable field-compatible instrument. Spectral evaluation and Principal Component Analysis confirmed discrimination of T. brucei-infected from uninfected tissue, and a characterisation of biochemical changes in lipids and proteins in parasite-infected skin indicated by prominent Raman peak intensities was performed. This study is the first to demonstrate the application of Raman spectroscopy for the detection of T. brucei by targeting the skin of the host. The technique has significant potential to discriminate between infected and non-infected tissue and could represent a unique, non-invasive diagnostic tool in the goal for elimination of gambiense-HAT as well as for Animal African Trypanosomiasis (AAT).

Risk of hospitalisation or death from COVID-19 in the UK is disproportionately high in people of African ancestry. Two APOL1 haplotypes (G1 and G2) found at high frequency only in populations of African descent are associated with increased risk of non-communicable and infectious diseases. Here, we test the hypothesis that adverse COVID-19 outcomes are also associated with these APOL1 high-risk variants. Within 9,433 individuals with African ancestry in the UK Biobank, there were 172 hospitalisations and 47 deaths attributed to COVID-19 as of December 2021. We examined APOL1 genotypes for association with hospitalisation and death while controlling for risk factors previously associated with poor COVID-19 outcomes. We identified an association between carriage of two APOL1 high-risk variants and death from COVID-19 (OR=2.7, 95% CI: 1.2-6.4). Stratified by genotype, those with G1/G2 had a higher odds of COVID-19 hospitalisation (OR=2.1, 95% CI: 1.1-3.8) and death (OR=5.9, 95% CI: 2.2-15.3) than G0/G0. There was no significant association detected in carriers of G1/G1 and G2/G2. These data suggest that the APOL1 G1/G2 genotype contributes to the increased rates of hospitalisation and mortality from COVID-19 in people of African ancestry, and could help to identify those at higher risk of severe COVID-19. This is especially relevant to geographical regions where APOL1 G1 and G2 high-risk variants are common, such as West and Central Africa and their diaspora.

Background The diagnosis of Human African Trypanosomiasis (HAT) typically involves two steps: a serological screen, followed by the detection of living trypanosome parasites in the blood or lymph node aspirate. Live parasites can, however, remain undetected in some seropositive individuals, who we hypothesize are infected with Trypanosoma brucei gambiense parasites in their extravascular dermis. Methods and findings To test this hypothesis, we conducted a prospective observational cohort study in the gambiense HAT (gHAT) focus of Forecariah, in the Republic of Guinea. 5,417 subjects in this disease foci underwent serological screening for gHAT. Of these individuals, 66 were enrolled into our study, of whom 40 were seronegative, 8 were seropositive but unconfirmed, and 18 confirmed gHAT cases. Enrolled individuals underwent a dermatological examination, and had blood samples and skin biopsies taken and examined for trypanosomes by molecular and immuno-histological methods. In confirmed cases, dermatological symptoms were significantly more frequent, relative to seronegative controls. T. b. gambiense parasites were present in the blood of all confirmed cases but not in unconfirmed seropositive individuals. However, trypanosomes were detected in the dermis of all unconfirmed seropositive individuals and confirmed cases. After 6 and 20 months of treatment, dermal trypanosome numbers in skin biopsies of confirmed cases progressively reduced. Conclusions Our results thus highlight the skin as a potential reservoir for trypanosomes, with implications for our understanding of this disease’s epidemiology in the context of its planned elimination and highlighting the skin as a novel target for gHAT diagnostics. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was supported by the Wellcome Trust (209511/Z/17/Z), the Institut de Recherche pour le Développement, the Institut Pasteur, the French Government Investissement d’Avenir programme - Laboratoire d’Excellence “Integrative Biology of Emerging Infectious Diseases” (ANR-10-LABX-62-IBEID) and the French National Agency for Scientific Research (projects ANR-14-CE14-0019-01 EnTrypa and ANR-18-CE15-0012 TrypaDerm). None of these funding sources has a direct scientific or editorial role in the present study. ### Author Declarations All relevant ethical guidelines have been followed; any necessary IRB and/or ethics committee approvals have been obtained and details of the IRB/oversight body are included in the manuscript. Yes All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes Upon request, the original protocol and associated forms, as well as an anonymised dataset, could be obtained from the corresponding author rotureau{at}pasteur.fr.

Myotonic dystrophy type 1 (DM1) is a rare genetic disorder, characterised by muscular dystrophy, myotonia, and other symptoms. DM1 is caused by the expansion of a CTG repeat in the 3’-untranslated region of DMPK . Longer CTG expansions are associated with greater symptom severity and earlier age at onset. The primary mechanism of pathogenesis is thought to be mediated by a gain of function of the CUG-containing RNA, that leads to trans -dysregulation of RNA metabolism of many other genes. Specifically, the alternative splicing (AS) and alternative polyadenylation (APA) of many genes is known to be disrupted. In the context of clinical trials of emerging DM1 treatments, it is important to be able to objectively quantify treatment efficacy at the level of molecular biomarkers. We show how previously described candidate mRNA biomarkers can be used to model an effective reduction in CTG length, using modern high-dimensional statistics (machine learning), and a blood and muscle mRNA microarray dataset. We show how this model could be used to detect treatment effects in the context of a clinical trial.

Antarctic krill inhabit areas of the Southern Ocean that can exceed 4.0°C, yet they preferentially inhabit regions with temperatures of −1.5 to ≤1.5°C. Successful embryonic development and hatching are key to their life cycle, but despite the rapid climatic warming seen across their main spawning areas, the effects of elevated temperatures on embryogenesis, hatching success, and nauplii malformations are unknown. We incubated 24,483 krill embryos in two independent experiments to investigate the hypothesis that temperatures exceeding 1.5°C have a negative impact on hatching success and increase the numbers of malformed nauplii. Field experiments were on krill collected from near the northern, warm limit of their range and embryos incubated soon after capture, while laboratory experiments were on embryos from krill acclimated to laboratory conditions. The hatching success of embryo batches varied enormously, from 0 to 98% (mean 27%). Both field and laboratory experiments showed that hatching success decreased markedly above 3.0°C. Our field experiments also showed an approximate doubling of the percentage of malformed nauplii at elevated temperatures, reaching 50% at 5.0°C. At 3.0°C or below, however, temperature was not the main factor driving the large variation in embryo hatching success. Our observations of highly variable and often low success of hatching to healthy nauplii suggest that indices of reproductive potential of female krill relate poorly to the subsequent production of viable krill larvae and may help to explain spatial discrepancies between the distribution of the spawning stock and larval distribution.