OBJECTIVES:To compare HIV testing coverage, prevalence and care cascade engagement between fisherfolk and the general population, and to assess the relevance of individual and community-level definitions of fisherfolk in understanding variation in HIV status and testing. DESIGN:Primary data collection and cross-sectional analysis in 1 year of the SchistoTrack community-based cohort. SETTING:52 shoreline villages in Pakwach, Buliisa and Mayuge districts in rural Uganda. PARTICIPANTS:A total of 3197 individuals aged 5-92 years were tested for HIV in 2024. A subset of 124 HIV-positive participants had viral load measured in 2025. Statistical analyses focused on 1931 adults aged 15 years and older. PRIMARY AND SECONDARY OUTCOME MEASURES:The primary outcomes were lifetime HIV testing, testing in the past 12 months and current HIV status. Secondary measures included self-reported care cascade outcomes and viral load suppression. RESULTS:Overall, 6.94% (134/1931) of adult participants aged 15 years and older were with HIV (people with HIV (PWH)), of whom 22.39% (30/134) were newly diagnosed. 6% (25/415) of adults reporting fishing activities were HIV-positive. Of those, 80% (20/25) were status-aware, 76% (19/25) were on antiretroviral therapy, and 100% (8/8) of those who knew their viral load reported viral suppression. No significant differences in care cascade engagement were found between PWH reporting fishing activities and the general population. Measured viral suppression was 70.59% (72/102) among PWH with no significant differences by fishing activities. Fishing activities were significantly associated with higher odds of ever testing for HIV (OR 1.76 (95% CI 1.22 to 2.54)), but not with testing in the past 12 months or HIV status. No consistent district-level differences were observed. CONCLUSIONS:Individuals reporting fishing activities had higher lifetime testing and comparable HIV prevalence and care cascade engagement to the general population. Gaps remain in recent testing, status awareness and viral suppression for fisherfolk.

Archaeological sediments can be used to retrieve evidence for parasites that infected past populations, giving evidence for disease, diet, sanitation, and migration in the past. To increase our understanding of parasite infections in Roman Britain and determine which parasites may have infected people living at Vindolanda, sediment samples were collected from a drain connected to a latrine at the bath complex of Vindolanda. These samples were used to look for preserved parasite eggs and cysts deposited in the drain with the faeces of people who used the latrine. Microscopic analysis was used to identify eggs of helminths, and enzyme-linked immunosorbent assay (ELISA) was used to look for protozoan parasites that can cause severe diarrhoea. Eggs of Ascaris sp. (roundworm) and Trichuris sp. (whipworm) were found by microscopy and Giardia duodenalis was detected using ELISA. All of these parasites are transmitted by the faecal-oral route, usually through contaminated food and water. This is the first evidence for G. duodenalis in Roman Britain. A range of zoonotic and faecal-oral parasites have been found at other sites in Roman Britain, yet the drain studied from Vindolanda only contained faecal-oral parasites that can be transmitted directly between humans. This predominance of faecal-oral parasites is similar to a pattern found in large urban sites in the Roman Mediterranean and other military sites in the empire. In contrast, sites from larger urban cities in Roman Britain, such as London and York, appear to have a more diverse range of parasites.

TCRγδ+ T cells are a major lymphocyte population of chickens, but their response or contribution to immunity against avian influenza virus (AIV) remains unknown. Here, we report an increase in the proportion and activation state of TCRγδ+CD8α+ T cells in the PBMCs of 3 chicken lines (MHC homozygous H-B2 and H-B21 lines and outbred G-WL line) with the strongest responses observed in the more resistant H-B2 chickens. H9N2 AIV infection induced mRNA upregulation of interferon (IFN)-γ and cytotoxicity-associated molecules, including, Granzyme A, Granzyme K, and perforin in sorted TCRγδ+CD8α+ T cells. Moreover, in ex vivo cultured TCRγδ+CD8α+ T cells in response to H9N2 AIV infected splenocytes, strongly indicates the activation of these cells' cytolytic potential via detection of transcription levels of cytotoxic genes with quantitative reverse transcription polymerase chain reaction (qRT-PCR), and IFN-γ protein level with ELISPOT and an intracellular cytokine staining assays. Most importantly, in vivo depletion of γδ T cells led to reduced H9N2 AIV control, which was particularly evident in the early phase of infection. Taken together, these results indicate that strong TCRγδ+CD8α+T cell response plays a critical role in protecting chicken against H9N2 AIV infection.

The louse flies in the genus Ornithomya Latreille are avian ectoparasites. The patterns of alar microtrichia on the wings of the Ornithomyae are commonly used to help distinguish the various species, with the patterns in most species found to be constant between individuals. The Finch Louse Fly Ornithomya fringillina (Curtis) in the United Kingdom, Ireland and the Isle of Man, is unusual in that the several patterns have been described. Consequently it has a complicated taxonomic history and there is some confusion about species identification. Louse flies were collected by licensed bird ringers and an analysis of the simple morphological features, phenology and geographical distribution of these traits was performed. No significant differences were found between the three main types, and it was concluded that the differences were not due to sexual dimorphism and did not provide evidence that the different forms were separate species. Analysis of COX1 DNA sequences confirmed this result and proved that these are indeed morphotypes and not distinct species. There was no geographical separation between COX1 sequences from the United Kingdom and those from flies sampled in other parts of the world. The molecular analysis also suggested that Ornithomya bequaerti (Maa) and Ornithomya candida (Maa) may not be valid species, but represent morphotypes of O. fringillina. The three patterns of alar microtrichia are morphotypes of a single species, Ornithomya fringillina. Further research is necessary to determine the status of some other species in the genus Ornithomya.

Polyglucosan bodies are accumulations of insoluble glucose polymers and proteins that form intracytoplasmic inclusions in the brain, large numbers of which can be indicative of neurodegenerative diseases such as Lafora disease. Montserrat orioles ( Icterus oberi) are an icterid passerine endemic to Montserrat with conservation populations maintained in captivity abroad. We demonstrate that polyglucosan bodies are unusually abundant in the cerebellar molecular and Purkinje cell layers and cerebellar peduncles of captive-bred and wild-caught Montserrat orioles. The bodies are periodic acid-Schiff positive and diastase resistant and label with concanavalin A and for ubiquitin, consistent with those seen in humans. We found no association of the polyglucosan bodies with concurrent neurological lesions or clinical signs, nor with EPM2A and EPM2B gene mutations associated with Lafora disease. We conclude that an abundance of cerebellar polyglucosan bodies may be a normal finding in aged Montserrat orioles and not a threat to the captive breeding population.

Knowledge management (KM) involves collecting, organizing, storing, and disseminating information to improve decision-making, innovation, and performance. Implementing KM at scale has become essential for organizations to effectively leverage vast accessible data. This paper is a compilation of concepts that emerged from KM workshops hosted by EMBL-EBI, attended by SMEs and industry. We provide guidance on envisioning, executing, evaluating, and evolving knowledge management platforms. We emphasize essential considerations such as setting knowledge domain boundaries and measuring success, as well as the importance of making knowledge accessible for downstream applications and non-computational users and highlights necessary personal and organizational skills for success. We stress the importance of collaboration and the need for convergence on shared principles and commitment to provide or seek resources to advance KM. The community is invited to join the journey of KM and contribute to the advancement of the field by applying and improving on the guidelines described.

The microbiome is a key factor in the health, well-being, and success of vertebrates, contributing to the adaptive capacity of the host. However, the impact of geographic and biotic factors that may affect the microbiome of wild birds in polar environments is not well defined. To address this, we determined the bacterial 16S rRNA gene sequence profiles in faecal samples from pygoscelid penguin populations in the Scotia Arc, focusing on gentoo penguins. This mesopredatory group breeds in defined colonies across a wide geographic range. Since diet could influence microbiome structure, we extracted dietary profiles from a eukaryotic 18S rRNA gene sequence profile. The bacterial microbiome profiles were considered in the context of a diverse set of environmental and ecological measures. Integrating wide geographic sampling with bacterial 16S and eukaryotic 18S rRNA gene sequencing of over 350 faecal samples identified associations between the microbiome profile and a suite of geographic and ecological factors. Microbiome profiles differed according to host species, colony identity, distance between colonies, and diet. Interestingly there was also a relationship between the proportion of host DNA (in relation to total 18S rRNA gene signal) and the microbiome, which may reflect gut passage time. Colony identity provided the strongest association with differences in microbiome profiles indicating that local factors play a key role in the microbiome structure of these polar seabirds. This may reflect the influence of local transfer of microbes either via faecal-oral routes, during chick feeding or other close contact events. Other factors including diet and host species also associate with variation in microbiome profile, and in at least some locations, the microbiome composition varies considerably between individuals. Given the variation in penguin microbiomes associated with diverse factors there is potential for disruption of microbiome associations at a local scale that could influence host health, productivity, and immunological competence. The microbiome represents a sensitive indicator of changing conditions, and the implications of any changes need to be considered in the wider context of environmental change and other stressors.

Colombia is among the countries with the most robust financial protection against personal health spending in the world, with out-of-pocket spending ranking lowest across OECD countries. We investigate the evolution, distribution, and persistence of health spending by age group, sex, health care setting, health condition and geographic region for over 19 million users of Colombia’s health system between 2013 and 2021 (contributory scheme). We use average patient-level expenditure data from the Health-Promoting Entities of the Ministry of Health and Social Protection. We applied multivariate statistical techniques such as multiple correspondence analysis, factor maps and correlations. For both sexes, average health expenditure increases gradually with age until 60 years, accelerating thereafter abruptly. Health conditions with the highest percentage of expenditure were those related to neoplasms, blood diseases, circulatory system, pregnancy, puerperium and perinatal period. We found that home-based care in Amazonía-Orinoquía is almost non-existent, and that outpatient care represents a high proportion in all age groups (over 65

ABSTRACTBackgroundEvidence on the distribution of pre-treatment HIV-1 drug resistance (HIVDR) by risk groups is limited in Africa. We assessed prevalence, trends, and transmission dynamics of pre-treatment HIVDR within-and-between men who have sex with men (MSM), people who inject drugs (PWID), female sex workers (FSW), heterosexuals (HET), and children infected perinatally in Kenya.MethodsHIV-1 partialpolsequences from antiretroviral-naïve samples collected between 1986-2020 were used. Pre-treatment RTI, PI and INSTI mutations were assessed using the Stanford HIVDR database. Phylogenetics methods were used to determine and date transmission clusters.ResultsOf 3567 sequences analysed, 550 (15.4%, 95% CI: 14.2-16.6) had at least one pre-treatment HIVDR mutation, which was most prevalent amongst children (41.3%), followed by PWID (31.0%), MSM (19.9%), FSW (15.1%) and HET (13.9%). No INSTI resistance mutations were detected. Among HET, pre-treatment HIVDR increased from 6.6% in 1986-2005 to 20.2% in 2011-2015 but dropped to 6.5% in 2016-2020. Overall, 22 clusters with shared pre-treatment HIVDR mutations were identified. The largest was a K103N mutation cluster involving 16 MSM sequences sampled between 2010-2017, with an estimated tMRCA of 2005 (HPD, 2000-2008). This lineage had a growth rate=0.1/year and R0=1.1, indicating propagation over 12 years among ART-naïve MSM in Kenya.ConclusionsCompared to HET, children and key populations had higher levels of pre-treatment HIVDR. Introduction of INSTIs after 2016 may have reversed the increase in pre-treatment RTI mutations in Kenya. Continued surveillance of HIVDR, with a particular focus on children and key populations, is warranted to inform treatment strategies in Kenya.SummaryCompared to the heterosexual population, key populations had higher levels of pre-treatment HIV-1 drug resistance (HIVDR). Propagation of HIVDR was risk-group exclusive. Introduction of integrase inhibitors abrogated propagation of reverse transcriptase inhibitors mutations among the heterosexual, but not key populations.

Cell cultures are models in biological and medical research to understand physiological and pathological processes. Cell lines are not always available depending on cell type and required species. In addition, the immortalization process often affects cell biology. Primary cells generally maintain a greater degree of similarity in short-term culture to the cells in tissue. Goal of this study was to verify the suitability of chicken primary epithelial caecal cells (PECCs) for in vitro investigations of host-pathogen interactions. Epithelial nature of PECCs was confirmed by detection of tight and adherens junctions and cobblestone-like cell morphology. Sialic acids distribution was similar to that in caecal cyrosections. To understand the capacity of PECCs to respond to microbial challenges, the Toll-like receptors (TLRs) repertoire was determined. Exposure of PECCs to polyinosinic-polycytidylic acid (poly(I:C)) or lipopolysaccharide (LPS) led to upregulation of type I and III interferon (IFN) as well as interleukin (IL-) 1 beta, IL-6 and IL-8 mRNA expression. Overall, the PECCs showed properties of polarized epithelial cells. The presence of TLRs, their differential expression, as well as pattern recognition receptor dependent immune responses enable PECCs to act as suitable in vitro model for host-pathogen interaction studies, which are difficult to conduct under in vivo conditions.

Avian influenza viruses (AIVs) are a major economic burden to the poultry industry and pose serious zoonotic risks, with human infections being reported every year. To date, the vaccination of birds remains the most important method for the prevention and control of AIV outbreaks. Most national vaccination strategies against AIV infection use whole virus-inactivated vaccines, which predominantly trigger a systemic antibody-mediated immune response. There are currently no studies that have examined the antibody repertoire of birds that were infected with and/or vaccinated against AIV. To this end, we evaluate the changes in the H9N2-specific IgM and IgY repertoires in chickens subjected to vaccination(s) and/or infectious challenge. We show that a large proportion of the IgM and IgY clones were shared across multiple individuals, and these public clonal responses are dependent on both the immunisation status of the birds and the specific tissue that was examined. Furthermore, the analysis revealed specific clonal expansions that are restricted to particular H9N2 immunisation regimes. These results indicate that both the nature and number of immunisations are important drivers of the antibody responses and repertoire profiles in chickens following H9N2 antigenic stimulation. We discuss how the repertoire biology of avian B-cell responses may affect the success of AIV vaccination in chickens, in particular the implications of public versus private clonal selection.

Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.

The pronounced growth in livestock populations since the 1950s has altered the epidemiological and evolutionary trajectory of their associated pathogens. For example, Marek's disease virus (MDV), which causes lymphoid tumors in chickens, has experienced a marked increase in virulence over the past century. Today, MDV infections kill >90% of unvaccinated birds, and controlling it costs more than US$1 billion annually. By sequencing MDV genomes derived from archeological chickens, we demonstrate that it has been circulating for at least 1000 years. We functionally tested the Meq oncogene, one of 49 viral genes positively selected in modern strains, demonstrating that ancient MDV was likely incapable of driving tumor formation. Our results demonstrate the power of ancient DNA approaches to trace the molecular basis of virulence in economically relevant pathogens.

Objective: We carried out a study to estimate the vaccine effectiveness (VE) of homologous vaccination schedules against COVID-19, using data from mandatory information systems from Bogota, Colombia.Methods: A test-negative case-control study in adults from Bogota (Colombia), between March 1st of 2021 and February 25th of 2022. We assess VE among symptomatic COVID-19 cases during the Mul, Delta, and Omicron predominance periods in Bogota, with controls matched by sex, age (+/- 5 years), and date of testing (+/- 7 days), using a case:control ratio of 1:1. We selected homologous vaccination schedules with ChAdOx1, CoronaVac, BNT162b2, mRNA-1273, and Ad26.COV2.S. VE was reported as one minus the odds ratio in adjusted conditional logistic regressions, with their 95% confidence intervals (CI). A p-value < 0.05 was considered statistically significant.Results: 52,913 cases were matched to controls, 16,722 for Mu, 14,094 for Delta, and 22,097 for Omicron. VE was high against COVID-19 during Mu weeks with full vaccination using the monovalent BNT162b2 (VE: 69; 95% CI, 65 to 72) vaccine and ChAdOx1 (VE: 64; 95% CI, 31 to 81) and significantly lower with CoronaVac (P < 0.001) and Ad26.COV2.S (P = 0.005). During Delta, VE against COVID-19 was higher with BNT162b2 (VE: 55; 95% CI, 51 to 58). The VE for COVID-19 cases during Omicron was higher with a booster dose of monovalent BNT162b2 (VE: 45; 95% CI, 34 to 54). The VE of primary series and booster for ChAdOx1, Ad26.COV2.S, and CoronaVac did not show protection for Omicron.Conclusion: Our study provides further evidence on the protective effect of mRNA vaccines for Omicron, and warrant that the duration of protection against symptomatic infection may last for only a few months.

Advice from avian influenza experts suggests that there is a high risk that highly pathogenic avian influenza will arrive in the Southern Ocean during the austral summers.

Background: We aim to estimate the magnitude of the reduction in pneumococcal pneumonia and meningitis mortality after the mass introduction of pneumococcal conjugate vaccine (PCV)7 and PCV13 in children in the United States. Methods: We assessed the trends in mortality rates from pneumococcal pneumonia and meningitis, in the United States between 1994 and 2017. We fitted an interrupted time-series negative binomial regression model (adjusted by trend, seasonality, PCV7/PCV13 coverage, and H. influenzae type b vaccine coverage) to estimate the counterfactual rates without vaccination. We reported a percent reduction in mortality estimates relative to the projected no-vaccination scenario, using the formula 1 minus the incidence risk ratio, with 95% confidence intervals (CIs). Results: Between 1994 and 1999 (the prevaccination period), the all-cause pneumonia mortality rate for 0–1-month-old children was 2.55 per 100,00 pop., whereas for 2–11 months-old children, this rate was 0.82 deaths per 100,000 pop. During the PCV7-period in 0–59-month-old children in the United States, the adjusted reduction of all-cause pneumonia was 13% (95% CI: 4–21) and 19% (95% CI: 0–33) of all-cause meningitis For PCV13, the reductions in this age group were 21% (95% CI: 4–35) for all-cause pneumonia mortality and 22% (95% CI: −19 to 48) for all-cause meningitis mortality. PCV13 had greater reductions of all-cause pneumonia than PCV13 in 6–11-month-old infants. Conclusions: The universal introduction of PCV7, and later PCV13, for children 0–59 months old in the United States was associated with decreases in mortality due to all-cause pneumonia.

Microbial colonisation is paramount to the normal development of the immune system, particularly at mucosal sites. However, the relationships between the microbiome and the adaptive immune repertoire have mostly been explored in rodents and humans. Here, we report a high-throughput sequencing analysis of the chicken TCRβ repertoire and the influences of microbial colonisation on tissue-resident TCRβ+ cells. The results reveal that the microbiome is an important driver of TCRβ diversity in both intestinal tissues and the bursa of Fabricius, but not in the spleen. Of note, public TCRβ sequences (shared across individuals) make a substantial contribution to the repertoire. Additionally, different tissues exhibit biases in terms of their V family and J gene usage, and these effects were influenced by the gut-associated microbiome. TCRβ clonal expansions were identified in both colonised and germ-free birds, but differences between the groups were indicative of an influence of the microbiota. Together, these findings provide an insight into the avian adaptive immune system and the influence of the microbiota on the TCRβ repertoire.