John Cunningham Virus (JCV) and BK Virus (BKV) are the most extensively studied Human Polyomaviruses (HPyVs), primarily associated with Progressive Multifocal Leukoencephalopathy (PML) and BKV Nephropathy (BKVN), respectively. While co-infection with these viruses has been documented in the same disease, simultaneous manifestation in distinct pathologies has not been previously reported. We present the first documented case of concurrent PML and Polyomavirus Nephropathy (PVN) due to reactivation of two different HPyVs, offering new insights into the clinical spectrum of HPyV-related diseases.

This longitudinal study investigated the differential composition of the nasopharyngeal microbiome in patients presenting different COVID-19 infectious phenotypes and its evolution during convalescence, with a focus on post-acute sequelae of SARS-CoV-2 (PASC) and its potential microbiome-related mechanisms. Microbiota composition was assessed for a cohort of healthy participants (n = 25), influenza patients (n = 24), and patients with moderate (n = 50) and severe (n = 57) COVID-19. Samples were collected at two time points: during the acute infection phase and at approximately 3-month follow-up. From collected nasopharyngeal swab samples, metagenomics using shotgun sequencing was performed and the microbiota composition was analyzed. Alpha and beta diversity analyses revealed no significant differences in overall community diversity between patient groups across visits. However, differential abundance testing identified specific species, such as Dolosigranulum pigrum and various Corynebacterium species, whose profiles correlated with PASC development. Furthermore, the analysis of microbial co-associations identifies commensal species, including D. pigrum and Corynebacterium species, which are less abundant in patients who develop PASC, consistent with a potential protective role suggested by experimental studies but not proven by our observational data. Antibiotic use was associated with lower levels of key protective taxa, which may increase susceptibility to PASC in case of superinfection. These findings highlight the potential importance of the nasopharyngeal microbiome in acute COVID-19 disease outcomes and suggest that preserving or restoring a balanced respiratory microbiome could mitigate the risk of COVID-19 persistent symptoms and PASC development. Our results may set the stage for future clinical interventions involving probiotics or microbial-derived metabolites to promote respiratory health post-COVID-19.IMPORTANCEThis study highlights the importance of bacteria naturally found in the upper respiratory tract, particularly the nasopharynx (the nasopharyngeal microbiome), in shaping how severely COVID-19 affects patients and whether they experience persistent symptoms, also called long-COVID or post-acute sequelae of SARS-CoV-2 (PASC). By examining microbiome samples from healthy people, influenza patients, and individuals with COVID-19 during acute and convalescent phases, we found that certain commensal bacteria, namely, Dolosigranulum pigrum and Corynebacterium species, were less abundant in individuals who developed long-COVID and more abundant in those who fully recovered. We also observed that antibiotic treatment was associated with lower abundances of these commensal taxa, in turn coinciding with a higher frequency of PASC. These findings suggest that the composition of the nasopharyngeal microbiome is associated with recovery trajectories after COVID-19 and motivate future research into treatments aimed toward the microbiome to improve respiratory health following infection.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT05557539.

Abstract Background Post-acute sequelae of COVID-19 (PASC) is clinically heterogeneous and mechanistically unresolved, and single-analyte studies have struggled to explain it. Methods We profiled matched plasma proteomics, metabolomics and whole-blood transcriptomics at acute infection and convalescence (mean 86 days later) in a Belgian cohort, using linear mixed models, multi-omic gene-set enrichment, and a degree-matched differential-correlation approach to quantify how each node’s interactions were rewired between patients who developed PASC and those who recovered; seven axis proteins were additionally quantified by multiplex immunoassay as orthogonal validation. Findings Single-omic testing yielded few FDR-significant features, yet multi-omic enrichment showed sustained complement-cascade involvement from acute illness to follow-up in PASC. Correlation networks re-organised topologically toward C3 and lost the immunoglobulin V-gene co-expression seen in recovery. The most rewired nodes — heparin cofactor II (SERPIND1), alpha-1 antitrypsin (SERPINA1), complement factor H-related 5 (CFHR5), prothrombin/thrombin (F2) and immunoglobulin V-gene transcripts (notably IGLV3-21) — changed in their co-expression structure rather than in abundance. In multiplex validation, acute CRP was elevated in patients who developed PASC (FDR = 0.012), whereas the directly measured abundances of the network-nominated proteins were unchanged. Interpretation These trajectory-aware, cross-omic networks nominate a thrombo-inflammatory axis in which complement and coagulation regulation remain dysregulated in PASC at the level of wiring rather than abundance, providing a systems framework for validation and for exploring interventions at the complement–coagulation–platelet interface. Funding Sofina COVID Solidarity Fund (King Baudouin Foundation), Fondation Saint-Luc and the FNRS. Research in context Evidence before this study Persistent complement activation, coagulation abnormalities and endothelial dysfunction have been reported in post-acute sequelae of COVID-19 (PASC), and earlier multi-omic studies linked complement and coagulation to persistent symptoms. Most of this evidence, however, rests on differences in the abundance of individual molecules, is cross-sectional or limited in omic breadth, and reports only small effects in convalescent plasma, leaving unclear how these systems are jointly reorganised over time. Added value of this study Using matched proteomic, metabolomic and transcriptomic profiling of the same plasma at acute infection and convalescence, we quantified how the interaction structure of the complement–coagulation network is rewired between patients who develop PASC and those who recover. This trajectory-aware, network-rewiring readout identified coordinated changes in complement and coagulation regulators (heparin cofactor II, alpha-1 antitrypsin, complement factor H-related 5, prothrombin/thrombin) and immunoglobulin V-gene transcripts that were invisible to single-analyte testing, and a targeted multiplex assay confirmed elevated acute CRP in patients who later developed PASC while showing that the network-nominated proteins did not differ in abundance. Implications of all the available evidence PASC may be characterised less by large shifts in individual molecules than by a reorganisation of how complement, coagulation and humoral components co-vary. A network-rewiring approach can nominate mechanistically coherent, testable targets at the complement–coagulation–platelet interface and points to the intensity of acute inflammation as a marker of later risk. These hypotheses require confirmation in larger, independent cohorts with orthogonal, quantitative assays before any clinical application.

The indication for treatment of viral hepatitis B and C depends on the degree of deterioration of liver function and secondarily viral load. APRI and MELD scores are WHO-validated tests for the assessment of liver fibrosis. They are inexpensive and non-invasive. Many patients suffer from viral hepatitis B or C in the Democratic Republic of Congo. These scores are an asset in the medical management of these patients. The objective of this study was to compare APRI and MELD scores in the prediction of fibrosis in patients with chronic viral hepatitis B in Lubumbashi. It included infected patients followed in the gastroenterology departments of the hospitals of Lubumbashi and the Center of Excellence and Expertise for Viral Hepatitis and other Pathologies (CEEHP). Biological parameters of patient samples were evaluated to calculate APRI and MELD scores. Analytical performance of APRI and MELD scores was evaluated by using liver biopsy as gold standard.The APRI and MELD scores had a sensitivity of 100% and a specificity of 93.5 and 88.6%, respectively. In the fibrosis group of patients infected with HBV, the mean APRI score was of 1.89 whereas the mean MELD score was of 12.4 Incorporating these scores in routine clinical practice could reduce the morbidity rate, the costs related to the practice of liver biopsy and thus improve the routine management of viral hepatitis in Lubumbashi.

Background:Hepatitis E virus (HEV) is the commonest cause of acute viral hepatitis in Western countries. Immunocompromised patients may develop chronic hepatitis. This study aims at determining the seroprevalence and the prevalence of chronic HEV infections in a single tertiary center in Belgium. Methods:From May 2022 to April 2023, we prospectively screened for HEV [immunoglobulin G (IgG), immunoglobulin M (IgM), and polymerase chain reaction (PCR)] all patients transplanted from a solid organ transplantation (SOT) and patients suffering from a lymphoma or followed for a bone marrow transplantation. Results:A total of 740 patients were included: 335 followed for a kidney transplantation (KT), 136 for a heart transplantation (HT), 200 for a liver transplantation (LT), and 69 for a hematological disease (HD). The HEV seroprevalence of the total population is 9.9%. In subgroup analysis, the HEV seroprevalence is 11% for the HT patients, 8.4% for the KT patients, 14% for the LT patients, and 2.9% for the patients followed for HD. There was a significant difference for HEV seroprevalence between HDs and HT group (P=0.046) and between HD and LT group (P=0.01). The identified risk factors for HEV seropositivity were age and being liver transplanted. In the total population, we identified 5 patients with chronic HEV (0.6%), all of them were kidney transplanted patients. HEV clearance was not achieved after decreasing immunosuppression, and a ribavirin treatment was initiated. Conclusions:HEV IgG seroprevalence in our immunosuppressed population is 9.9%. Chronic HEV was found in 0.6% of the patients, all kidney transplanted and having required ribavirin treatment.

CMV infection remains a well-recognized threat in immunocompromised patients and is a major cause of congenital infection. If plasma and whole blood are routinely used as clinical samples for detection of CMV infection and disease, CMV laboratory testing in non-blood samples is becoming more and more relevant to support the diagnosis, prognosis and management of CMV infection. Accurate CMV viral load assessment in various body fluids is therefore essential. We evaluated the performance of the Alinity m CMV assay for detecting and quantifying CMV in plasma, amniotic fluid, bronchoalveolar lavage, cerebrospinal fluid, saliva and urine. Using a commercially available CMV reference panel and CMV culture supernatant, we assessed the linearity and accuracy of the Alinity m CMV assay across the different sample types. Excellent linear correlations (r values > 0.98) and a good accuracy (bias < ± 0.50 Log10 IU/mL and SD < 0.23) were observed. In conclusion, the Alinity m CMV assay is suitable to detect and quantify CMV DNA in plasma but also in all non-plasma samples tested. Random and continuous access capabilities of the Alinity m enable rapid and efficient laboratory detection and quantification of CMV DNA.

(1) Background: Group A Streptococcal (GAS) pharyngitis is common, resulting in numerous ambulatory visits. Accurate diagnosis is challenging. This study evaluated the clinical utility, cost, and performance of a nucleic acid amplification test (NAAT) for GAS detection, comparing it to a rapid antigen detection test (RADT) and throat culture. Additionally, we assessed the diagnostic stewardship related to these testing methods to ensure appropriate antibiotic use in clinical practice. Methods: Between November 2022 and February 2023, 82 throat swabs were analyzed, with McIsaac clinical scores calculated for each. The Abbott ID NOW STREP A 2 NAAT and Sekisui Diagnostics’ OSOM® STREP A RADT were performed, followed by bacterial culture. Diagnostic performance was compared using culture as the gold standard. Results: Of the 82 samples, 28 (34.14%) tested positive for pathogenic germs, primarily Streptococcus pyogenes (92.85%). RADTs showed a sensitivity of 80.76% and a specificity of 100%, while NAATs demonstrated a sensitivity of 100% and specificity of 96.42%. Cost analysis indicated the need for reimbursement adjustments to optimize NAAT’s economic benefits. Clinical data indicated that symptoms alone were insufficient for reliable diagnosis. Conclusions: This study confirmed the superior sensitivity of Abbott’s Strep A2 NAAT over RADT. Given the Belgian guidelines against routine antibiotic treatment for pharyngitis and considering local treatment recommendations and cost, implementing NAAT for GAS detection in Belgian laboratories is less beneficial. However, the role of NAAT in supporting antimicrobial stewardship by ensuring appropriate antibiotic use remains significant.

Bartonella quintana is rarely associated with neurological manifestations. This report describes a rare case of endocarditis complicated by a cerebral stroke caused by B. quintana. We also briefly reviewed the neurological clinical spectrum of B. quintana disease described in the literature. Serology tests were performed using the VIRCLIA®-system (chemiluminescence assay, Vircell, Spain) and immunofluorescence assay (IFA; Focus Diagnostics, USA). Cerebrospinal fluid (CSF) was tested using the BioFire-CSF-FilmArray-Meningitis/Encephalitis Panel (bioMérieux, France). CSF, plasma, and biopsy samples were tested using Bartonella-qPCR combined with Sanger-sequencing. A 23-year-old male Afghan refugee residing in Belgium presented with persistent fatigue and cough. A calcified aortic bicuspid with severe insufficiency and moderately associated stenosis was diagnosed. A transesophageal echocardiogram revealed a shrinking valve and a mobile mass attached to the calcification of the free edge at the aorta. He developed fever, a moderate inflammatory syndrome with normocytic anemia, and renal failure with hematuria and proteinuria, indicating probable glomerulonephritis. He met the Duke criteria for infective endocarditis, though blood cultures were initially negative. Bartonella serology later returned positive. He developed a fever and intense headache. CSF showed moderate pleiocytosis, but a negative-FilmArray. Neurovascular MR-angiography revealed a multifocal ischemic stroke. His aortic valve was replaced (Ross procedure). The biopsy showed nodular and degenerative fibro-calcified rearrangements. B.  quintana presence was confirmed in CSF, blood, and mitral valve samples. Our report underlines that B. quintana is a rare but a possible cause of endocarditis and neurological damage, and emphasizes the need for effective healthcare access, which is often limited in the countries of origin of migrants and even for migrants residing in high-resource countries.

Plasma proteomics is a precious tool in human disease research but requires extensive sample preparation in order to perform in-depth analysis and biomarker discovery using traditional data-dependent acquisition (DDA). Here, we highlight the efficacy of combining moderate plasma prefractionation and data-independent acquisition (DIA) to significantly improve proteome coverage and depth while remaining cost-efficient. Using human plasma collected from a 20-patient COVID-19 cohort, our method utilizes commonly available solutions for depletion, sample preparation, and fractionation, followed by 3 liquid chromatography-mass spectrometry/MS (LC-MS/MS) injections for a 360 min total DIA run time. We detect 1321 proteins on average per patient and 2031 unique proteins across the cohort. Differential analysis further demonstrates the applicability of this method for plasma proteomic research and clinical biomarker identification, identifying hundreds of differentially abundant proteins at biological concentrations as low as 47 ng/L in human plasma. Data are available via ProteomeXchange with the identifier PXD047901. In summary, this study introduces a streamlined, cost-effective approach to deep plasma proteome analysis, expanding its utility beyond classical research environments and enabling larger-scale multiomics investigations in clinical settings. Our comparative analysis revealed that fractionation, whether the samples were pooled or separate postfractionation, significantly improved the number of proteins quantified. This underscores the value of fractionation in enhancing the depth of plasma proteome analysis, thereby offering a more comprehensive landscape for biomarker discovery in diseases such as COVID-19.

Ixodes ricinus is a vector of several pathogens of public health interest. While forests are the primary habitat for I. ricinus, its abundance and infection prevalence are expected to vary within forest stands. This study assesses the spatio-temporal variations in tick abundance and infection prevalence with three pathogens in and around a peri-urban forest where human exposure is high. Ticks were sampled multiple times in 2016 and 2018 in multiple locations with a diversity of undergrowth, using the consecutive drags method. Three zoonotic pathogens were screened for, Borrelia burgdorferi s.l., Coxiella burnetii, and Francisella tularensis. The influence of season, type of site and micro-environmental factors on tick abundance were assessed with negative binomial generalized linear mixed-effects models. We collected 1642 nymphs and 181 adult ticks. Ticks were most abundant in the spring, in warmer temperatures, and where undergrowth was higher. Sites with vegetation unaffected by human presence had higher abundance of ticks. Forest undergrowth type and height were significant predictors of the level of tick abundance in a forest. The consecutive drags method is expected to provide more precise estimates of tick abundance, presumably through more varied contacts with foliage. Borrelia burgdorferi s.l. prevalence was estimated from pooled ticks at 5.33%, C. burnetii was detected in six pools and F. tularensis was not detected. Borrelia afzelii was the dominant B. burgdorferi genospecies. Tick abundance and B. burgdorferi s.l. infection prevalence were lower than other estimates in Belgian forests.

Plasma proteomic is a precious tool in human disease research, but requires extensive sample preparation in order to perform in-depth analysis and biomarker discovery using traditional Data-Dependent Acquisition (DDA). Here, we highlight the efficacy of combining moderate plasma prefractionation and Data-Independent Acquisition (DIA) to significantly improve proteome coverage and depth, while remaining cost- and time-efficient.Using human plasma collected from a 20-patient COVID-19 cohort, our method utilises commonly available solutions for depletion, sample preparation, and fractionation, followed by 3 LC-MS/MS injections for a 360-minutes DIA run time. DIA-NN software was then used for precursor identification, and the QFeatures R package was used for protein aggregation.We detect 1,321 proteins on average per patient, and 2,031 unique proteins across the cohort. Filtering precursors present in under 25% of patients, we still detect 1,230 average proteins and 1,590 unique proteins, indicating robust protein identification. Differential analysis further demonstrates the applicability of this method for plasma proteomic research and clinical biomarker identification.In summary, this study introduces a streamlined, cost- and time-effective approach to deep plasma proteome analysis, expanding its utility beyond classical research environments and enabling larger-scale multi-omics investigations in clinical settings.### Competing Interest StatementThe authors have declared no competing interest.* DDA : Data-dependent acquisition DIA : Data-independent acquisition LC-MS/MS : Liquid chromatography tandem mass spectrometry COVID-19 : Novel coronavirus disease 2019 LC : Liquid chromatography MS : mass spectrometry LC-MS : Liquid chromatography mass spectrometry RT : Room temperature RPM : Rotations per minute TEAB : triethylammonium bicarbonate ACN : Acetonitrile TFA : Trifluoroacetic acid APD : Advanced peak detection HPLC : High-performance liquid chromatography FWHM : Full width at half-maximum resolution HCD : Higher energy collisional dissociation AGC : Automatic gain control FDR : False discovery rate HYGIEIA : Hypothesizing the genesis of infectious diseases and epidemics through an integrated systems biology approach AUC : Area under the curve PCA : Principal component analysis PC : Principal component QC : Quality control SDS : Sodium dodecyl-sulfate logFC : Log fold change NLM : National library of medicine

Objectives: In recent years, commercial molecular tools for diagnosis of invasive aspergillosis have emerged, requiring evaluation to ensure quality. Here we assessed the specificity of Aspergillus spp.-ELITe MGB Assay a commercial assay tergeting 18S gene of Aspergillus spp. Design and methods: As part of a method validation, we evaluate the specificity of the Aspergillus spp.-ELITe MGB Assay by testing fourteen culture based samples of sequenced non-Aspergillus fungal species. The benefits of a pre-lysis treatment was evaluated in parallel on serial dilutions of an Aspergillus fumigatus strain. Results: Our findings revealed cross-reactivity in five strains using the 50 copies/mL cut-off recommended by the manufacturer, suggesting potential diagnostic errors and inappropriate management of patients. Pre-lysis treatment does not affect the limit of detection at serial dilution. Conclusions: In conclusion, the Aspergillus spp. ELITe MGB Assay exhibits limited specificity in culture-based samples, underscoring the importance of careful utilization in laboratories. Further studies are warranted to better comprehend of the impact of this cross-reactivity on clinical samples.

During the COVID-19 pandemic crisis, many measures were taken around the world to limit the SARS-CoV-2 transmission that disrupted people's day-to-day lives in many ways. Unfortunately, most of these measures had detrimental consequences, such as isolation, misinformation, fear, and violence, inducing a loss of wellbeing for many people. One of the most vulnerable groups to these pandemic consequences was children. We conducted a study to assess children and staff wellbeing in French-speaking primary schools in Belgium after the COVID-19 pandemic crisis. A 37-question questionnaire based on the Revised Children's Manifest Anxiety Scale (RCMAS) was used for each child and a 14-question questionnaire based on the Hospital Anxiety and Depression scale (HAD) was used for each staff to assess their wellbeing. The three-drawing method was used to assess children's representation of wellbeing before, during, and after the COVID-19 pandemic, respectively. A total of 282 children and 33 staff answered the wellbeing questionnaire. 63% of children (174/276) had symptoms of anxiety, and 38% (104/282) had a definite state of anxiety. 65% of children (178/276) had symptoms of social desirability, and 55% (151/276) had a definite state of social desirability. The wellbeing representation was impacted by the COVID-19 pandemic during and after the pandemic. Very few staff accepted to participate in the study. A total of 102 children created drawings. The representation of children's wellbeing in their drawings showed that the pandemic had had an impact on their life, which was reflected in different ways in the drawings during the pandemic, such as isolation, negative content, negative facial expressions, or sadness. After the COVID-19 pandemic crisis, the wellbeing of children remained affected; anxiety was still as high as it was during the COVID-19 pandemic crisis. Particular attention must be devoted to children as a vulnerable group, to avoid consequences in the long term.

BACKGROUND Occult hepatitis B infection (OBI) is a globally prevalent infection, with its frequency being influenced by the prevalence of hepatitis B virus (HBV) infection in a particular geographic region, including Africa. OBI can be transmitted through blood transfusions and organ transplants and has been linked to the development of hepatocellular carcinoma (HCC). The associated HBV genotype influences the infection. AIM To highlight the genetic diversity and prevalence of OBI in Africa. METHODS This systematic review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines and involved a comprehensive search on PubMed, Google Scholar, Science Direct, and African Journals Online for published studies on the prevalence and genetic diversity of OBI in Africa. RESULTS The synthesis included 83 articles, revealing that the prevalence of OBI varied between countries and population groups, with the highest prevalence being 90.9% in patients with hepatitis C virus infection and 38% in blood donors, indicating an increased risk of HBV transmission through blood transfusions. Cases of OBI reactivation have been reported following chemotherapy. Genotype D is the predominant, followed by genotypes A and E. CONCLUSION This review highlights the prevalence of OBI in Africa, which varies across countries and population groups. The study also demonstrates that genotype D is the most prevalent.

BACKGROUND:Between 2018 and 2022, a Belgian tertiary care hospital faced a growing issue with acquiring carbapenemase-producing organisms (CPO), mainly VIM-producing P. aeruginosa (PA-VIM) and NDM-producing Enterobacterales (CPE-NDM) among hospitalized patients in the adult intensive care unit (ICU). AIM:To investigate this ICU long-term CPO outbreak involving multiple species and a persistent environmental reservoir. METHODS:Active case finding, environmental sampling, whole-genome sequencing (WGS) analysis of patient and environmental strains, and implemented control strategies were described in this study. FINDINGS:From 2018 to 2022, 37 patients became colonized or infected with PA-VIM and/or CPE-NDM during their ICU stay. WGS confirmed the epidemiological link between clinical and environmental strains collected from the sink drains with clonal strain dissemination and horizontal gene transfer mediated by plasmid conjugation and/or transposon jumps. Environmental disinfection by quaternary ammonium-based disinfectant and replacement of contaminated equipment failed to eradicate environmental sources. Interestingly, efflux pump genes conferring resistance to quaternary ammonium compounds were widespread in the isolates. As removing sinks was not feasible, a combination of a foaming product degrading the biofilm and foaming disinfectant based on peracetic acid and hydrogen peroxide has been evaluated and has so far prevented recolonization of the proximal sink drain by CPO. CONCLUSION:The persistence in the hospital environment of antibiotic- and disinfectant-resistant bacteria with the ability to transfer mobile genetic elements poses a serious threat to ICU patients with a risk of shifting towards an endemicity scenario. Innovative strategies are needed to address persistent environmental reservoirs and prevent CPO transmission.