Co-Circulation of 2 Oropouche Virus Lineages, Amazon Basin, Colombia, 2024.

In early 2024, explosive outbreaks of Oropouche virus (OROV) linked to a novel lineage were documented in the Amazon Region of Brazil. We report the introduction of this lineage into Colombia and its co-circulation with another OROV lineage. Continued surveillance is needed to prevent further spread of OROV in the Americas.

International survey of people living with chronic conditions (PaRIS survey): effects of general practitioner non-participation on the representativeness of the Norwegian patient data.

BACKGROUND: The International Survey of People living with Chronic Conditions (OECD-PaRIS survey), aims to systematically gather patient-reported experiences (PREMs) and - outcomes (PROMs) and potential predictors for these outcomes for persons with chronic conditions as well as information from professionals about health care provided. In such patient surveys, the advantages of a multilevel (nested) approach in which patients are sampled 'within providers' need to be balanced against the potential for bias if patient populations from participating GPs significantly differ from those of non-participating GPs. The objective was to assess the effects of general practitioner (GP) non-participation on the representativeness of the Norwegian patient data of the International Survey of People living with Chronic Conditions (OECD-PaRIS survey). METHODS: To test all aspects of the first main PaRIS survey, it was preceded by a field trial which this paper reports on the Norwegian part of. For the Norwegian part of the field trial in 2022, we randomly sampled and surveyed 75 GPs and 125 patients 45 years and older for each GP, regardless of whether their GP were also participating in the study. GPs were sampled from a national register that included all GPs. The surveys were primarily digital, but we sent postal questionnaires to non-digital patients and non-responding digital patients. We compared GP and patient characteristics as well as patient-reported experiences and outcomes according to GP participation status in bivariate analysis, supplemented with multiple linear regressions with PREMs/PROMs as dependent variables and participation status as independent adjusting for significant patient factors. RESULTS: 17 of 75 sampled GPs participated (22.7%), of which 993 of 2,015 patients responded (49.3%). 3,347 of 7,080 patients of non-responding GPs answered (47.3%). Persons with chronic conditions from participating GPs reported significantly better patient-centred coordinated care (p = 0.017), overall experiences with the GP office the last 12 months (p = 0.004), mental well-being (p = 0.039) and mental health (p = 0.013) than patients from non-participating GPs. The raw differences between participating and non-participating GPs on patient-reported experiences and - outcomes varied from 1.5 to 2.9 points on a 0-100 scale, and from 2.2 to 3.0 after adjustment for case-mix. CONCLUSIONS: The Norwegian field trial indicates that estimates based on participants in the PaRIS survey may modestly overestimate patient-reported experiences and -outcomes at the aggregated level and the need for more research within and across countries to identify and address this potential bias.

Tear Film Hyperosmolarity is Associated with Increased Variation of Light Scatter Following Cataract Surgery.

Purpose: To study the association between tear film hyperosmolarity and ocular light scatter in a cataract surgery population. Patients and Methods: Contiguous, 20-second objective scatter index (OSI) scans were recorded in hyperosmolar (≥320 mOsm/L) and normal subjects (<308 mOsm/L) with cataract nuclear opacity ≥3. OSI was measured at screening, baseline and 90 days following surgery. Along with symptoms of ocular surface disease, slit-lamp examination included corneal staining (0-3), tear film breakup time (TBUT) and evaluation of meibomian gland disease (MGD). An additional cohort of hyperosmolar subjects were measured for OSI at screening, baseline, and 5, 10, 15 and 30 minutes following instillation of 0.18% sodium hyaluronate (HA). Results: Thirty-one eyes of 31 patients were included. There was a significant difference in post-operative OSI variation when comparing hyperosmolar (0.65±0.30, N=11) to normal subjects (0.33±0.11, N=10, p=0.005). Of note, there were no significant differences in OSI variation when subjects were sorted by staining (p=0.9), TBUT (p=0.7), symptoms (p=0.7), or MGD status (p=0.9). Instillation of 0.18% HA (N=10) did not alter OSI at 5 minutes, but significant reductions in OSI of 28.8%, 38.5% and 36.7% (all p < 0.001) were observed at 10, 15 and 30 minutes. Conclusion: Hyperosmolar patients exhibited significantly increased variation in light scatter following cataract surgery that was undifferentiated by staining or TBUT. Elevated osmolarity may be indicative of light scatter equivalent to that of a grade 2-3 cataract.

The 2023 South Sudanese outbreak of Hepatitis E emphasizes ongoing circulation of genotype 1 in North, Central, and East Africa.

In April 2023, an outbreak of acute hepatitis was reported amongst internally displaced persons in the Nazareth community of South Sudan. IgM serology-based screening suggested the likely etiologic agent to be Hepatitis E virus (HEV). In this study, plasma specimens collected from anti-HEV IgM-positive cases were subjected to additional RT-qPCR testing and sequencing of extracted nucleic acids, resulting in the recovery of five full and eight partial HEV genomes. Maximum likelihood phylogenetic reconstruction confirmed the genomes belong to HEV genotype 1. Using distance-based methods, we show that genotype 1 is best split into three sub-genotypes instead of the previously proposed seven, and that these sub-genotypes are geographically restricted. The South Sudanese sequences confidently cluster within sub-genotype 1e, endemic to northeast, central, and east Africa. Bayesian Inference of phylogeny incorporating sampling dates shows that this new outbreak is not directly descended from other recent local outbreaks for which sequence data is available. However, the analysis suggests that sub-genotype 1e has been consistently and cryptically circulating locally for at least the past half century and that the known outbreaks are often not directly descended from one another. The ongoing presence of HEV, combined with poor sanitation and hygiene in the conflict-affected areas in the region, place vulnerable populations at risk for infection and its more serious effects, including progression to fulminant hepatitis.

Dengue Virus Serotype 3 Origins and Genetic Dynamics, Jamaica.

We identified 3 clades of dengue virus serotype 3 belonging to genotype III isolated during 2019-2020 in Jamaica by using whole-genome sequencing and phylogenomic and phylogeographic analyses. The viruses likely originated from Asia in 2014. Newly expanded molecular surveillance efforts in Jamaica will guide appropriate public health responses.

Ecological Changes Exacerbating the Spread of Invasive Ticks has Driven the Dispersal of Severe Fever with Thrombocytopenia Syndrome Virus Throughout Southeast Asia.

Severe fever with thrombocytopenia syndrome virus (SFTSV) is a tick-borne virus recognized by the World Health Organization as an emerging infectious disease of growing concern. Utilizing phylodynamic and phylogeographic methods, we have reconstructed the origin and transmission patterns of SFTSV lineages and the roles demographic, ecological, and climatic factors have played in shaping its emergence and spread throughout Asia. Environmental changes and fluctuations in tick populations, exacerbated by the widespread use of pesticides, have contributed significantly to its geographic expansion. The increased adaptability of Lineage L2 strains to the Haemaphysalis longicornis vector has facilitated the dispersal of SFTSV through Southeast Asia. Increased surveillance and proactive measures are needed to prevent further spread to Australia, Indonesia, and North America.

Development of the Patient-Reported Indicator Surveys (PaRIS) conceptual framework to monitor and improve the performance of primary care for people living with chronic conditions.

BackgroundThe Organisation for Economic Co-operation and Development (OECD) Patient-Reported Indicator Surveys (PaRIS) initiative aims to support countries in improving care for people living with chronic conditions by collecting information on how people experience the quality and performance of primary and (generalist) ambulatory care services. This paper presents the development of the conceptual framework that underpins the rationale for and the instrumentation of the PaRIS survey. METHODS: The guidance of an international expert taskforce and the OECD Health Care Quality Indicators framework (2015) provided initial specifications for the framework. Relevant conceptual models and frameworks were then identified from searches in bibliographic databases (Medline, EMBASE and the Health Management Information Consortium). A draft framework was developed through narrative review. The final version was codeveloped following the participation of an international Patient advisory Panel, an international Technical Advisory Community and online international workshops with patient representatives. RESULTS: 85 conceptual models and frameworks were identified through searches. The final framework maps relationships between the following domains (and subdomains): patient-reported outcomes (symptoms, functioning, self-reported health status, health-related quality of life); patient-reported experiences of care (access, comprehensiveness, continuity, coordination, patient safety, person centeredness, self-management support, trust, overall perceived quality of care); health and care capabilities; health behaviours (physical activity, diet, tobacco and alcohol consumption), sociodemographic characteristics and self-reported chronic conditions; delivery system characteristics (clinic, main healthcare professional); health system, policy and context. DISCUSSION: The PaRIS conceptual framework has been developed through a systematic, accountable and inclusive process. It serves as the basis for the development of the indicators and survey instruments as well as for the generation of specific hypotheses to guide the analysis and interpretation of the findings.

Engaging primary care professionals in OECD's international PaRIS survey: a documentary analysis.

Healthcare professionals have first-hand experience with patients in clinical practice and the dynamics in the healthcare system, which can be of great value in the design, implementation, data analysis and dissemination of research study results. Primary care professionals are particularly important as they provide first contact, accessible, coordinated, comprehensive and continuous people-focused care. However, in-depth examination of the engagement of health professionals in health system research and planning activities-how professionals are engaged and how this varies across national contexts- is limited, particularly in international initiatives. There is a need to identify gaps in the planning of engagement activities to inform the design and successful implementation of future international efforts to improve the responsiveness of health systems to the changing needs of patients and professionals. The aim of this study was to explore how primary care professionals were engaged in the design and implementation plans of an international health policy study led by the Organisation for Economic Co-operation and Development (OECD). The OECD's international PaRIS survey measures and disseminates information on patient-reported outcome and experience measures (PROMs and PREMs) of people living with chronic conditions who are managed in primary care. A documentary analysis of 17 written national implementation plans (country roadmaps) was conducted between January and June 2023. Two reviewers independently performed the screening and data abstraction and resolved disagreements by discussion. We reported the intended target primary care professionals, phase of the study, channel of engagement, level of engagement, and purpose of engagement. All 17 countries aimed to engage primary care professionals in the execution plans for the international PaRIS survey. While organisations of primary care professionals, particularly of family doctors, were the most commonly targeted group, variation was found in the timing of engagement activities during the different phases of the study and in the level of engagement, ranging from co-development (half of the countries co-developed the survey together with primary care professionals) to one-off consultations with whom. International guidance facilitated the participation of primary care professionals. Continuous collaborative efforts at the international and national levels can foster a culture of engagement with primary care organisations and individual professionals and enhance meaningful engagement of primary care professionals.

Mayaro Virus as the cause of Acute Febrile Illness in the Colombian Amazon Basin.

Introduction: Mayaro Fever (MF) is a tropical disease caused by the Mayaro virus (MAYV), with outbreaks documented in Latin America. Methods: A hospital-based fever surveillance in Leticia, Colombian Amazon, collected sera from 1,460 patients aged 5-89 between December 2020 and April 2023. Results: Dengue and malaria were the main diagnoses (19.4 and 5.8%, respectively), leaving 71.4% of cases unidentified after testing. Metagenomic sequencing and real-time RT-qPCR testing identified MAYV in two patients (25-year-old male and an 80-year-old female) exhibiting typical symptoms, of MF including rash, joint pain, and fever. Phylogenetics analysis of these two viruses revealed a close relationship to Peruvian strains within the MAYV D genotype. Discussion: The study of AFI in Leticia, Colombia, identified dengue as prevalent, with malaria, COVID-19, Influenza, and Zika viruses also detected. Despite extensive testing, most cases remained unexplained until metagenomic sequencing revealed MAYV, previously unseen in Colombia but known in neighboring countries. Conclusion: This study presents the first near full-length genomes of MAYV in Colombia, highlighting the need for further seroprevalence studies and enhanced surveillance to understand and control the spread of the virus in the region.

Geochemical insights of arsenic mobilization into the aquifers of Punjab, Pakistan.

It is well known that groundwater arsenic (As) contamination affects million(s) of people throughout the Indus flood plain, Pakistan. In this study, groundwater (n = 96) and drilled borehole samples (n = 87 sediments of 12 boreholes) were collected to investigate geochemical proxy-indicators for As release into groundwater across floodplains of the Indus Basin. The mean dissolved (µg/L) and sedimentary As concentrations (mg/kg) showed significant association in all studied areas viz.; lower reaches of Indus flood plain area (71 and 12.7), upper flood plain areas (33.7 and 7.2), and Thal desert areas (5.3 and 4.7) and are indicative of Basin-scale geogenic As contamination. As contamination in aquifer sediments is dependent on various geochemical factors including particle size (3-4-fold higher As levels in fine clay particles than in fine-coarse sand), sediment types (3-fold higher As in Holocene sediments of floodplain areas vs Pleistocene/Quaternary sediments in the Thal desert) with varying proportion of Al-Fe-Mn oxides/hydroxides. The total organic carbon (TOC) of cored aquifer sediments yielded low TOC content (mean = 0.13 %), which indicates that organic carbon is not a major driver (with a few exceptions) of As mobilization in the Indus Basin. Alkaline pH, high dissolved sulfate and other water quality parameters indicate pH-induced As leaching and the dominance of oxidizing conditions in the aquifers of upper flood plain areas of Punjab, Pakistan while at the lower reaches of the Indus flood plain and alluvial pockets along the rivers with elevated flood-driven dissolved organic carbon (exhibiting high dissolved Mn and Fe and a wide range of redox conditions). Furthermore, we also identified that paired dissolved AsMn values (instead of AsFe) may serve as a geochemical marker of a range of redox conditions throughout Indus flood plains.

International cross-cultural development and field testing of the primary care practice questionnaire for the PaRIS survey (PaRIS-PCPQ).

BACKGROUND: The PaRIS survey, an initiative of the Organisation for Economic Co-operation and Development (OECD), aims to assess health systems performance in delivering primary care by measuring the care experiences and outcomes of people over 45 who used primary care services in the past six months. In addition, linked data from primary care practices are collected to analyse how the organisation of primary care practices and their care processes impact care experiences and outcomes. This article describes the development and validation of the primary care practice questionnaire for the PaRIS survey, the PaRIS-PCPQ. METHOD: The PaRIS-PCPQ was developed based on domains of primary care practice and professional characteristics included in the PaRIS conceptual framework. Questionnaire development was conducted in four phases: (1) a multi-step consensus-based development of the source questionnaire, (2) translation of the English source questionnaire into 17 languages, (3) cross-national cognitive testing with primary care professionals in participating countries, and (4) cross-national field-testing. RESULTS: 70 items were selected from 7 existing questionnaires on primary care characteristics, of which 49 were included in a first draft. Feedback from stakeholders resulted in a modified 34-item version (practice profile, care coordination, chronic care management, patient follow-up, and respondent characteristics) designed to be completed online by medical or non-medical staff working in a primary care practice. Cognitive testing led to changes in the source questionnaire as well as to country specific localisations. The resulting 32-item questionnaire was piloted in an online survey and field test. Data from 540 primary care practices from 17 countries were collected and analysed. Final revision resulted in a 34-item questionnaire. CONCLUSIONS: The cross-national development of a primary care practice questionnaire is challenging due to the differences in care delivery systems. Rigorous translation and cognitive testing as well as stakeholder engagement helped to overcome most challenges. The PaRIS-PCPQ will be used to assess how key characteristics of primary care practices relate to the care experiences and outcomes of people living with chronic conditions. As such, policymakers and care providers will be informed about the performance of primary care from the patient's perspective.

Next-generation sequencing survey of acute febrile illness in Senegal (2020-2022).

Introduction: Acute febrile illnesses (AFI) in developing tropical and sub-tropical nations are challenging to diagnose due to the numerous causes and non-specific symptoms. The proliferation of rapid diagnostic testing and successful control campaigns against malaria have revealed that non-Plasmodium pathogens still contribute significantly to AFI burden. Thus, a more complete understanding of local trends and potential causes is important for selecting the correct treatment course, which in turn will reduce morbidity and mortality. Next-generation sequencing (NGS) in a laboratory setting can be used to identify known and novel pathogens in individuals with AFI. Methods: In this study, plasma was collected from 228 febrile patients tested negative for malaria at clinics across Senegal from 2020-2022. Total nucleic acids were extracted and converted to metagenomic NGS libraries. To identify viral pathogens, especially those present at low concentration, an aliquot of each library was processed with a viral enrichment panel and sequenced. Corresponding metagenomic libraries were also sequenced to identify non-viral pathogens. Results and Discussion: Sequencing reads for pathogens with a possible link to febrile illness were identified in 51/228 specimens, including (but not limited to): Borrelia crocidurae (N = 7), West Nile virus (N = 3), Rickettsia felis (N = 2), Bartonella quintana (N = 1), human herpesvirus 8 (N = 1), and Saffold virus (N = 1). Reads corresponding to Plasmodium falciparum were detected in 19 specimens, though their presence in the cohort was likely due to user error of rapid diagnostic testing or incorrect specimen segregation at the clinics. Mosquito-borne pathogens were typically detected just after the conclusion of the rainy season, while tick-borne pathogens were mostly detected before the rainy season. The three West Nile virus strains were phylogenetically characterized and shown to be related to both European and North American clades. Surveys such as this will increase the understanding of the potential causes of non-malarial AFI, which may help inform diagnostic and treatment options for clinicians who provide care to patients in Senegal.

[Encuesta Internacional de Indicadores de Salud Referidos por los Pacientes: el protocolo del Estudio PaRIS en España.] / International Patient-Reported Indicators Surveys: The PaRIS study protocol in Spain.

OBJECTIVE: The PaRIS Survey is an initiative led by the Organization for Economic Cooperation and Development in twenty-one countries, including Spain, to promote people-centred health care. The objective of the study aimed to describe PROMS and PREMS (Patient Reported Outcomes and Experience Measures, respectively) from patients who were in contact with Primary Care Centres, in order to establish a set of reliable, valid and internationally comparable indicators. METHODS: A cross-sectional study with two questionnaires will be carried out: one applied online for professionals from Primary Care Centres and another by telephone or online for patients aged forty-five and older of the same Health Care Centres. The domains covered are: characteristics of the Health Centre and of the professionals; sociodemographic characteristics of the patients; lifestyles; health care capacities; PROMs and PREMs. CONCLUSIONS: The study offers a unique opportunity to evaluate the health outcomes and experiences of the care received in Primary Care from patient's perspective. This information is essential to help policymakers better understand the performance of their health system and how it could be improved, particularly in relation to chronic care in Primary Care.

OBJETIVO: La Encuesta de Indicadores Referidos por los Pacientes (PaRIS, por sus siglas en inglés) es una iniciativa liderada por la Organización para la Cooperación y el Desarrollo Económicos en veintiún países, incluyendo España, para promover una atención sanitaria centrada en las personas. El objetivo del estudio fue describir los resultados en salud y las experiencias referidas por los pacientes (PROMs y PREMs, por sus siglas en inglés Patient Reported Outcomes and Experience Measures, respectivamente) que tuvieron contacto con los Centros de Atención Primaria (CAP), con la finalidad de establecer un conjunto de indicadores confiables, válidos e internacionalmente comparables. METODOS: Se realizará un estudio transversal, con dos cuestionarios: online para profesionales de los Centros de Atención Primaria y telefónico u online para los pacientes de cuarenta y cinco años y más, que acudieron a los CAP. Los dominios abarcados son: características del Centro de Atención Primaria y de los profesionales; características sociodemográficas de los pacientes; estilos de vida; capacidades; PROMs y PREMs. CONCLUSIONES: PaRIS ofrece una oportunidad para medir resultados de salud y las experiencias en Atención Primaria desde la perspectiva del paciente. Esta información es fundamental para ayudar a los gestores a comprender mejor el desempeño del sistema de salud y detectar posibilidades de mejora, particularmente en relación con la atención crónica.

Characterization of Dengue Virus Serotype 2 Cosmopolitan Genotype Circulating in Colombia.

Dengue virus (DENV) is the etiological agent of dengue fever (DF), which is among the most prevalent vector-borne diseases in the tropics. In 2022, the Colombian health surveillance system reported more than 69,000 cases of DF. As part of a hospital-based fever surveillance study, acute-phase sera were collected from 4,545 patients with suspected dengue between 2020 and 2023 in three municipalities of Colombia. Combined reverse transcription-polymerase chain reaction and antigen rapid testing confirmed that 376 patients (8.3%) had DF. The virus was isolated in cell culture from 166 of these patients (44.1%), and genome sequencing was performed successfully on 122 (73.5%). Three DENV serotypes (1, 2, and 3) were identified. Phylogenetic analyses of the DENV-2 sequences revealed that 42 of 50 of the isolates (84%) belonged to the DENV-2 cosmopolitan genotype lineage, clustering with sequences from Asia, Peru, and Brazil. We report the detection, isolation, and whole-genome sequencing (11 Kb) of the DENV-2 cosmopolitan genotype and its recent introduction to Colombia.

Parallel evolution of picobirnaviruses from distinct ancestral origins.

IMPORTANCE: Picobirnaviruses (PBVs) are highly heterogeneous viruses encoding a capsid and RdRp. Detected in a wide variety of animals with and without disease, their association with gastrointestinal and respiratory infections, and consequently their public health importance, has rightly been questioned. Determining the "true" host of Picobirnavirus lies at the center of this debate, as evidence exists for them having both vertebrate and prokaryotic origins. Using integrated and time-stamped phylogenetic approaches, we show they are contemporaneous viruses descending from two different ancestors: avian Reovirus and fungal Partitivirus. The fungal PBV-R2 species emerged with a single segment (RdRp) until it acquired a capsid from vertebrate PBV-R1 and PBV-R3 species. Protein and RNA folding analyses revealed how the former came to resemble the latter over time. Thus, parallel evolution from disparate hosts has driven the adaptation and genetic diversification of the Picobirnaviridae family.

The Principles of SARS-CoV-2 Intervariant Competition Are Exemplified in the Pre-Omicron Era of the Colombian Epidemic.

The first 18 months of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in Colombia were characterized by three epidemic waves. During the third wave, from March through August 2021, intervariant competition resulted in Mu replacing Alpha and Gamma. We employed Bayesian phylodynamic inference and epidemiological modeling to characterize the variants in the country during this period of competition. Phylogeographic analysis indicated that Mu did not emerge in Colombia but acquired increased fitness there through local transmission and diversification, contributing to its export to North America and Europe. Despite not having the highest transmissibility, Mu's genetic composition and ability to evade preexisting immunity facilitated its domination of the Colombian epidemic landscape. Our results support previous modeling studies demonstrating that both intrinsic factors (transmissibility and genetic diversity) and extrinsic factors (time of introduction and acquired immunity) influence the outcome of intervariant competition. This analysis will help set practical expectations about the inevitable emergences of new variants and their trajectories. IMPORTANCE Before the appearance of the Omicron variant in late 2021, numerous SARS-CoV-2 variants emerged, were established, and declined, often with different outcomes in different geographic areas. In this study, we considered the trajectory of the Mu variant, which only successfully dominated the epidemic landscape of a single country: Colombia. We demonstrate that Mu competed successfully there due to its early and opportune introduction time in late 2020, combined with its ability to evade immunity granted by prior infection or the first generation of vaccines. Mu likely did not effectively spread outside of Colombia because other immune-evading variants, such as Delta, had arrived in those locales and established themselves first. On the other hand, Mu's early spread within Colombia may have prevented the successful establishment of Delta there. Our analysis highlights the geographic heterogeneity of early SARS-CoV-2 variant spread and helps to reframe the expectations for the competition behaviors of future variants.

Temporal and coevolutionary analyses reveal the events driving the emergence and circulation of human mamastroviruses.

Characterized by high genetic diversity, broad host range, and resistance to adverse conditions, coupled with recent reports of neurotropic astroviruses circulating in humans, mamastroviruses pose a threat to public health. The current astrovirus classification system based on host source prevents determining whether strains with distinct tropism or virulence are emerging. By using integrated phylogeny, we propose a standardized demarcation of species and genotypes, with reproducible cut-off values that reconcile the pairwise sequence distribution, genetic distances between lineages, and the topological reconstruction of the Mamastrovirus genus. We further define the various links established by co-evolution and resolve the dynamics of transmission chains to identify host-jump events and the sources from which different mamastrovirus species circulating in humans have emerged. We observed that recombination is relatively infrequent and restricted to within genotypes. The well-known "human" astrovirus, defined here as mamastrovirus species 7, has co-speciated with humans, while there have been two additional host-jumps into humans from distinct hosts. Newly defined species 6 genotype 2, linked to severe gastroenteritis in children, resulted from a marmot to human jump taking place ∼200 years ago while species 6 genotype 7 (MastV-Sp6Gt7), linked to neurological disease in immunocompromised patients, jumped from bovines only ∼50 years ago. Through demographic reconstruction, we determined that the latter reached coalescent viral population growth only 20 years ago and is evolving at a much higher evolutionary rate than other genotypes infecting humans. This study constitutes mounting evidence of MastV-Sp6Gt7 active circulation and highlights the need for diagnostics capable of detecting it.

Groundwater salinity in the Horn of Africa: Spatial prediction modeling and estimated people at risk.

BACKGROUND: Changes in climate and anthropogenic activities have made water salinization a significant threat worldwide, affecting biodiversity, crop productivity and contributing to water insecurity. The Horn of Africa, which includes eastern Ethiopia, northeast Kenya, Eritrea, Djibouti, and Somalia, has natural characteristics that favor high groundwater salinity. Excess salinity has been linked to infrastructure and health problems, including increased infant mortality. This region has suffered successive droughts that have limited the availability of safe drinking water resources, leading to a humanitarian crisis for which little spatially explicit information about groundwater salinity is available. METHODS: Machine learning (random forest) is used to make spatial predictions of salinity levels at three electrical conductivity (EC) thresholds using data from 8646 boreholes and wells along with environmental predictor variables. Attention is paid to understanding the input data, balancing classes, performing many iterations, specifying cut-off values, employing spatial cross-validation, and identifying spatial uncertainties. RESULTS: Estimates are made for this transboundary region of the population potentially exposed to hazardous salinity levels. The findings indicate that about 11.6 million people (∼7% of the total population), including 400,000 infants and half a million pregnant women, rely on groundwater for drinking and live in areas of high groundwater salinity (EC > 1500 µS/cm). Somalia is the most affected and has the largest number of people potentially exposed. Around 50% of the Somali population (5 million people) may be exposed to unsafe salinity levels in their drinking water. In only five of Somalia's 18 regions are less than 50% of infants potentially exposed to unsafe salinity levels. The main drivers of high salinity include precipitation, groundwater recharge, evaporation, ocean proximity, and fractured rocks. The combined overall accuracy and area under the curve of multiple runs is âˆ¼ 82%. CONCLUSIONS: The modelled groundwater salinity maps for three different salinity thresholds in the Horn of Africa highlight the uneven spatial distribution of salinity in the studied countries and the large area affected, which is mainly arid flat lowlands. The results of this study provide the first detailed mapping of groundwater salinity in the region, providing essential information for water and health scientists along with decision-makers to identify and prioritize areas and populations in need of assistance.

Metagenomic Detection of Divergent Insect- and Bat-Associated Viruses in Plasma from Two African Individuals Enrolled in Blood-Borne Surveillance.

Metagenomic next-generation sequencing (mNGS) has enabled the high-throughput multiplexed identification of sequences from microbes of potential medical relevance. This approach has become indispensable for viral pathogen discovery and broad-based surveillance of emerging or re-emerging pathogens. From 2015 to 2019, plasma was collected from 9586 individuals in Cameroon and the Democratic Republic of the Congo enrolled in a combined hepatitis virus and retrovirus surveillance program. A subset (n = 726) of the patient specimens was analyzed by mNGS to identify viral co-infections. While co-infections from known blood-borne viruses were detected, divergent sequences from nine poorly characterized or previously uncharacterized viruses were also identified in two individuals. These were assigned to the following groups by genomic and phylogenetic analyses: densovirus, nodavirus, jingmenvirus, bastrovirus, dicistrovirus, picornavirus, and cyclovirus. Although of unclear pathogenicity, these viruses were found circulating at high enough concentrations in plasma for genomes to be assembled and were most closely related to those previously associated with bird or bat excrement. Phylogenetic analyses and in silico host predictions suggested that these are invertebrate viruses likely transmitted through feces containing consumed insects or through contaminated shellfish. This study highlights the power of metagenomics and in silico host prediction in characterizing novel viral infections in susceptible individuals, including those who are immunocompromised from hepatitis viruses and retroviruses, or potentially exposed to zoonotic viruses from animal reservoir species.

Purifying selection decreases the potential for Bangui orthobunyavirus outbreaks in humans.

Pathogens carried by insects, such as bunyaviruses, are frequently transmitted into human populations and cause diseases. Knowing which spillover events represent a public health threat remains a challenge. Metagenomic next-generation sequencing (mNGS) can support infectious disease diagnostics by enabling the detection of any pathogen from clinical specimens. mNGS was performed on blood samples to identify potential viral coinfections in human immunodeficiency virus (HIV)-positive individuals from Kinshasa, the Democratic Republic of the Congo (DRC), participating in an HIV diversity cohort study. Time-resolved phylogenetics and molecular assay development assisted in viral characterization. The nearly complete genome of a novel orthobunyavirus related to Nyangole virus, a virus previously identified in neighboring Uganda, was assembled from a hepatitis B virus-positive patient. A quantitative polymerase chain reaction assay was designed and used to screen >2,500 plasma samples from Cameroon, the DRC, and Uganda, failing to identify any additional cases. The recent sequencing of a US Center for Disease Control Arbovirus Reference Collection revealed that this same virus, now named Bangui virus, was first isolated in 1970 from an individual in the Central African Republic. Time-scaled phylogenetic analyses of Bangui with the related Anopheles and Tanga serogroup complexes indicate that this virus emerged nearly 10,000 years ago. Pervasive and episodic models further suggest that this virus is under purifying selection and that only distant common ancestors were subject to positive selection events. This study represents only the second identification of a Bangui virus infection in over 50 years. The presumed rarity of Bangui virus infections in humans can be explained by its constraint to an avian host and insect vector, precluding efficient transmission into the human population. Our results demonstrate that molecular phylogenetic analyses can provide insights into the threat posed by novel or re-emergent viruses identified by mNGS.