BACKGROUND AND AIMS:Cirrhosis favours infections that can lead to liver decompensation and death. Some of these infections can be prevented by vaccination. This study aimed to evaluate the immune response after HBV, pneumococcal, diphtheria, and tetanus vaccination in cirrhotic patients. METHODS:Patients with cirrhosis were prescribed 3 doses of hepatitis B vaccine, a tetanus-diphtheria booster and/or a 13-valent pneumococcal conjugate vaccine followed by a 23-valent polysaccharide vaccine. HBs seroconversion was assessed 6 months after the last booster dose. Antibody concentrations for seven pneumococcal serotypes, tetanus and diphtheria were measured by ELISA before (V0) and 4 to 6 months after vaccination (V1). RESULTS:Of the 125 patients enrolled, 83 were analysed for HBs seroconversion, 119 for pneumococcal vaccine response and 117 for tetanus and diphtheria vaccine response. The anti-HBs seroconversion rate was 31%. A doubling of the antibody was observed in 19% of cases for tetanus and in 26% of cases for diphtheria. For the pneumococcal vaccine, the global protection (at least 5 antibodies with a concentration ≥ 1.3 mg/L against the 7 serotypes of pneumococcus tested) increased from 39% before vaccination to 80% after vaccination. However, only 48% of patients had a 2-fold increase in IgG antibody for at least five of the seven serotypes tested. CONCLUSION:Our study highlights a weak response to the hepatitis B, tetanus, and diphtheria vaccines and an acceptable immunological response to the pneumococcal vaccine, although lower than in healthy subjects. There is a real need to optimise vaccination in cirrhotics.

Hepatitis E virus (HEV) exhibits genetic diversity associated with distinct public health outcomes and circulation patterns across interconnected human and environmental reservoirs. Most studies have focused on genome-wide diversity, revealing relationships between genotype, virulence, and dissemination routes. However, the role of localized mutations in the capsid protein (ORF2), which may influence the extracellular fate and ecology of HEV through changes in surface biological and physicochemical properties of virions, received limited attention. Here, we combined large-scale analysis of European HEV sequences, structural modeling, and physicochemical characterization to investigate such variations in ORF2. Analysis of ORF2 sequences on a genomic segment highly reported in GenBank, derived from patients and the environment, revealed recurrent mutation motifs (single H354Y and triple H354Y-G357S-V364I motifs) located in a conserved capsid hinge region connecting the middle (M) and protruding (P) domains of the protein. These motifs displayed distinct frequency patterns according to sequence sources and were associated with genotypes 3 and 1, respectively. AlphaFold-based modeling identified this region as a flexible interface between the M and P domains and indicated that mutations reduce predicted alignment error of the P domain relative to the overall protein model, consistent with altered exposure at the virion surface. In vitro analyses of synthetic peptides encompassing this critical region revealed increased hydrophobicity and structural rearrangements, supporting local modulation of capsid surface properties. Together, these results identify a structurally and physicochemically sensitive hinge region in the HEV capsid, suggesting a link between ORF2 sequence variations, genotype, virion surface properties, and environmental circulation.IMPORTANCEHepatitis E virus (HEV) is a major cause of viral hepatitis worldwide, which is transmitted through complex, genotype-linked dissemination routes between humans, animals, and environmental waters. Understanding the circulation dynamics of HEV virions is essential for improving environmental surveillance, risk assessment, and public health strategies within a One Health approach. By combining genetic, structural, and physicochemical analyses, this study highlights specific mutation motifs in a hinge region of the ORF2 capsid protein likely to link distinct distribution patterns of HEV across environmental reservoirs to potential changes in virion surface properties. Such mutation motifs may serve as molecular signatures for exploring virus persistence and dissemination in environmental contexts. Overall, this work provides a new framework for connecting viral genetic variation to environmental behavior beyond traditional genotype classification.

Improving the therapeutic management of HIV-positive persons is a major public health issue and includes better detection of drug resistance mutations (DRMs). The aim of this study was (i) to explore DRMs in HIV-1-positive persons presenting a blood viral load (VL) < 1000 genomes copies (gc)/mL, including the analyze of cerebrospinal fluid (CSF) and HIV-DNA from peripheral blood mononuclear cells using ultradeep sequencing (UDS) and (ii), to evaluate how these DRMs could influence the clinical practices. For each patient (n = 12), including five low-VL patients (i.e., <1000 gc/mL), HIV-1 UDS targeting the protease, reverse transcriptase and integrase genes was performed on plasma, proviral DNA, and CSF when available. Sequencing discordances or failures were mostly found in samples from low-VL patients. A 5% UDS cut-off allowed to increase the sensitivity to detect DRMs in different compartments, excepted in CSF. Patients with the highest viral quasispecies heterogeneity were naïve of treatment or presented a medical history suggesting low selection pressure or virological failures. When analyzing compartmentalization and following-up patients: low-frequency variants (LFVs) were responsible for 47% (n = 8) and 76% (n = 13) of changes in drug resistance interpretation, respectively. In such cases, we conclude that UDS is a robust technique, which still could be improved by increase the RNA and/or DNA extraction in low-VL samples to detect LFVs. Further studies are needed to define the impact of LFVs on antiretroviral treatments. At last, when considering a DRM, the use of mutational load would probably be more suitable than frequencies.

ObjectivesCalculations of SARS-CoV-2 transmission networks at a population level have been limited. Networks that estimate infections between individuals and whether this results in a mutation, can be a way to evaluate fitness of a mutational clone by how much it expands in number as well as determining the likelihood a transmission results in a new variant.MethodsAustralian Delta and Omicron SARS-CoV-2 sequences were downloaded from GISAID. Transmission networks of infection between individuals were estimated using a novel mathematical method.ResultsMany of the sequences were identical, with clone sizes following power law distributions driven by negative binomial probability distributions for both the number of infections per individual and the number of mutations per transmission (median 0.74 nucleotide changes for Delta and 0.71 for Omicron). Using these distributions, an agent-based model was able to replicate the observed clonal network structure, providing a basis for more detailed COVID-19 modelling. Possible recombination events, tracked by insertion/deletion (indel) patterns, were identified for each variant in these outbreaks.ConclusionsThis modelling approach reveals key transmission characteristics of SARS-CoV-2 and may complement traditional contact tracing. This methodology can also be applied to other diseases as genetic sequencing of viruses becomes more commonplace.

Hepatitis E virus (HEV) is considered as an emerging zoonotic pathogen circulating in a wide range of animals. In recent decades, the genus Paslahepevirus frequently isolated in pigs were the most involved in human clinical practice. In addition, the genus Rocahepevirus have been isolated in rodents, and transmission to humans is increasingly reported worldwide, although gaps remain regarding the exposure factors. In this study, the presence of HEV was investigated in urban wastewater, swine slaughterhouse wastewater and river waters, in a geographical area where its circulation had previously been reported. In addition to the expected detection of Paslahepevirus in almost all waters samples collected, Rocahepevirus strains were detected with the same frequencies in urban and river waters, at concentrations up to 40-fold higher. No Rocahepeviruses were detected in swine slaughterhouse wastewater. This is the first study demonstrating the presence of Rocahepevirus in French wastewater. Although no evidence of transmission was reported among patients followed for a suspected HEV infection in the same area between April 2019 and October 2023 (i.e. 135/3078 serological tests positive for anti-HEV IgM detection; 46/822 blood samples positive for Paslahepevirus genome detection but none for Rocahepevirus), the circulation of Rocahepevirus in waters in such concentrations raises the question of the possible zoonotic transmission to human. Indeed, the waterborne transmission of HEV is now well documented in industrialized countries, and the exploration of the growing number of human infections in Europe involving Rocahepevirus has not until now made it possible to clarify the transmission routes.

The surface hydrophobicity of native or engineered non-enveloped viruses and virus-like particles (VLPs) is a key parameter regulating their fate in living and artificial aqueous systems. Its modulation is mainly depending on the structure and environment of particles. Nevertheless, unexplained variations have been reported between structurally similar viruses and with pH. This indicates that some modulating factors of their hydrophobicity remain to be identified. Herein we investigate the potential involvement of RNA cargo in the MS2 phage used as non-enveloped RNA virus model, by examining the SDS-induced electrophoretic mobility shift (SEMS) determined for native MS2 virions and corresponding RNA-free VLPs at various pH. Interestingly, the SEMS of VLPs was larger and more variable from pH 5 to 9 compared to native virions. These observations are discussed in term of RNA-dependent changes in surface hydrophobicity, suggesting that RNA cargo may be a major modulator/ regulator of this viral parameter.

Severe COVID-19 damages alveolar lung cells that lack the angiotensin-converting enzyme 2 (ACE2) but express the lipolysis-stimulated lipoprotein receptor (LSR). Here we show that LSR enabled SARS-CoV-2 to produce infectious progenies and cause cell death. LSR-mediated cytolysis resulted from cathepsin L cleavage of the spike protein and occurred when the viral load reached a critical threshold. Monoclonal antibodies targeting the ACE2 binding domain did not attenuate LSR-mediated cytolysis. Human IgG induced by COVID-19 and two out of five monoclonals lowered tenfold SARS-CoV-2 cytolytic threshold. Antibody-enhanced cytolysis persisted with variant escaping their ACE2 neutralizing effect. A recombinant decoy of the LSR binding domain (LBDx) selectively suppressed LSR-mediated replication, neutralized cytolysis caused by six variants, and protected primary human pneumocytes from SARS-CoV-2 cytopathic effects. LBDx treatments starting days after a lethal SARS-CoV-2 infection improved K18-hACE2 mouse survival. These findings open novel strategies to tackle severe COVID-19 and investigate post-acute sequelae.

Since the beginning of the COVID-19 pandemic, counting infected people has underestimated asymptomatic cases. This literature scoping review assessed the seroprevalence progression in general populations worldwide over the first year of the pandemic. Seroprevalence studies were searched in PubMed, Web of Science and medRxiv databases up to early April 2021. Inclusion criteria were a general population of all ages or blood donors as a proxy. All articles were screened for the title and abstract by two readers, and data were extracted from selected articles. Discrepancies were resolved with a third reader. From 139 articles (including 6 reviews), the seroprevalence estimated in 41 countries ranged from 0 to 69%, with a heterogenous increase over time and continents, unevenly distributed among countries (differences up to 69%) and sometimes among regions within a country (up to 10%). The seroprevalence of asymptomatic cases ranged from 0% to 31.5%. Seropositivity risk factors included low income, low education, low smoking frequency, deprived area residency, high number of children, densely populated centres, and presence of a case in a household. This review of seroprevalence studies over the first year of the pandemic documented the progression of this virus across the world in time and space and the risk factors that influenced its spread.

The continuous emergence of SARS-CoV-2 variants favors potential co-infections and/or viral mutation events, leading to possible new biological properties. The aim of this work was to characterize SARS-CoV-2 genetic variability during the Delta–Omicron shift in patients and in a neighboring wastewater treatment plant (WWTP) in the same urban area. The surveillance of SARS-CoV-2 was performed by routine screening of positive samples by single nucleotide polymorphism analysis within the S gene. Moreover, additionally to national systematic whole genome sequencing (WGS) once a week in SARS-CoV-2-positive patients, WGS was also applied when mutational profiles were difficult to interpret by routine screening. Thus, WGS was performed on 414 respiratory samples and on four wastewater samples, northeastern France. This allowed us to report (i) the temporally concordant Delta to Omicron viral shift in patients and wastewaters; (ii) the characterization of 21J (Delta) and 21K (Omicron)/BA.1-21L (Omicron)/BA.2-BA.4 mixtures from humans or environmental samples; (iii) the mapping of composite mutations and the predicted impact on immune properties in the viral Spike protein.

Although the respiratory tract is the main target of SARS-CoV-2, other tissues and organs are permissive to the infection. In this report, we investigated this wide-spectrum tropism by studying the SARS-CoV-2 genetic intra-host variability in multiple tissues. The virological and histological investigation of multiple specimens from a post-mortem COVID-19 patient was performed. SARS-CoV-2 genome was detected in several tissues, including the lower respiratory system, cardio-vascular biopsies, stomach, pancreas, adrenal gland, mediastinal ganglion and testicles. Subgenomic RNA transcripts were also detected, in favor of an active viral replication, especially in testicles. Ultra-deep sequencing allowed us to highlight several SARS-CoV-2 mutations according to tissue distribution. More specifically, mutations of the spike protein, i.e., V341A (18.3%), E654 (44%) and H655R (30.8%), were detected in the inferior vena cava. SARS-CoV-2 variability can contribute to heterogeneous distributions of viral quasispecies, which may affect the COVID-19 pathogeny.

Background: Exposure of healthcare workers (HCW) to SARS-CoV-2 is a public health concern. Not only are HCWs particularly exposed to SARS-CoV-2, but their contamina-tion can also weaken the healthcare system.Methods: We analyzed exposure of French University Hospital HCWs to SARS-CoV-2 through his-tory of positive RT-PCR test and SARS-CoV-2 seroprevalence. Potential risk factors, such as age, BMI, having children or not, working in a COVID-19 unit, or smoking were explored.Results: From May to June 2020, among the 8960 employees of the University Hospital of Nancy, a serological test was performed in 4696 HCWs. The average (SD) age was 40.4 (11.4) years, and the sample included 3926 women (83.6%). Of the 4696 HCWs, 1050 were smokers (22.4%). Among them, 2231 HCWs had a history of COVID-19 symptoms and/or flu-like syn-drome (47.5%) and 238 were seropositive (5.1%). Neither gender, sex, BMI, nor having children were associated with a history of positive RT-PCR test or seropositive status. Previous work in a COVID-19 unit was associated with a history of positive RT-PCR test (p = 0.045), but not with seroprevalence (p = 0.215). As expected, history of COVID-19 clinical manifestations was more frequent in HCWs with positive serology than in HCWs with negative serology (adjusted OR = 1.9, 95%CI [1.4-2.5], p < 0.001). Less expected, smoking was associated with a reduced risk of seropositivity among HCWs (adjusted OR = 0.6, 95%CI [0.4-0.9], p = 0.019).

The aim of the present study was to develop a simple, sensitive, and specific approach to quantifying the SARS-CoV-2 genome in wastewater and to evaluate this approach as a means of epidemiological surveillance. Twelve wastewater samples were collected from a metropolitan area in north-eastern France during April and May 2020. In addition to the quantification of the SARS-CoV-2 genome, F-specific RNA phages of genogroup II (FRNAPH GGII), naturally present in wastewater, were used as an internal process control for the viral concentration and processing of RT-PCR inhibitors. A concentration method was required to allow the quantification of the SARS-CoV-2 genome over the longest possible period. A procedure combining ultrafiltration, phenol-chloroform-isoamyl alcohol purification, and the additional purification of the RNA extracts was chosen for the quantification of the SARS-CoV-2 genome in 100-mL wastewater samples. At the same time, the COVID-19 outbreak was evaluated through patients from the neighbouring University Hospital of Nancy, France. A regular decrease in the concentration of the SARS-CoV-2 genome from ~104 gc/L to ~102 gc/L of wastewater was observed over the eight weeks of the study, during which the population was placed under lockdown. The SARS-CoV-2 genome was even undetectable during one week in the second half of May and present but non-quantifiable in the last sample (28 May). A concordant circulation in the human community was highlighted by virological diagnosis using respiratory samples, which showed a decrease in the number of COVID-19 cases from 677 to 52 per week over the same period. The environmental surveillance of COVID-19 using a reliable viral quantification procedure to test wastewater is a key approach. The real-time detection of viral genomes can allow us to predict and monitor the circulation of SARS-CoV-2 in clinical settings and survey the entire urban human population.

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Hepatitis E virus is the main cause of acute hepatitis worldwide. The dichotomy between waterborne human-restricted genotypes 1 and 2 circulating in developing countries and zoonotic genotypes 3 and 4 infecting human through consumption of contaminated meat in industrialized countries is currently discussed, with the detection of HEV in waters of industrialized nations. Chronic infections are described in immunocomprommised patients, as well as extra hepatic syndromes. In vivo and in vitro data have shown that HEV genetic variability can impact the bioclinical relevance of the infection, by highlighting mutations associated with severity. Genetic variability has also to be considered when exploring transmission ways, with the description of new animal reservoirs and new strains able to infect humans. HEV genetic variability is one of the keys to better control its transmission and to adapt diagnostic tools and strategies, with the aim to protect vulnerable populations.

Hepatitis E virus (HEV) usually causes self‐limited liver diseases but can also result in severe cases. Genotypes 1 (G1) and 2 circulate in developing countries are human‐restricted and waterborne, while zoonotic G3 and G4 circulating in industrialized countries preferentially infect human through consumption of contaminated meat. Our aims were to identify amino acid patterns in HEV variants that could be involved in pathogenicity or in transmission modes, related to their impact on antigenicity and viral surface hydrophobicity. HEV sequences from human (n = 37) and environmental origins (wild boar [n = 3], pig slaughterhouse effluent [n = 6] and urban wastewater [n = 2]) were collected for the characterization of quasispecies using ultra‐deep sequencing (ORF2/ORF3 overlap). Predictive and functional assays were carried out to investigate viral particle antigenicity and hydrophobicity. Most quasispecies showed a major variant while a mixture was observed in urban wastewater and in one chronically infected patient. Amino acid signatures were identified, as a rabbit‐linked HEV pattern in two infected patients, or the S68L (ORF2) / H81C (ORF3) residue mostly identified in wild boars. By comparison with environmental strains, molecular patterns less likely represented in humans were identified. Patterns impacting viral hydrophobicity and/or antigenicity were also observed, and the higher hydrophobicity of HEV naked particles compared with the enveloped forms was demonstrated. HEV variants isolated from human and environment present molecular patterns that could impact their surface properties as well as their transmission. These molecular patterns may concern only one minor variant of a quasispecies and could emerge under selective pressure.

The World Health Organisation recommends monitoring the circulation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We investigated anti–SARS-CoV-2 total immunoglobulin (IgT) antibody seroprevalence and in vitro sero-neutralization in Nancy, France, in spring 2020. Individuals were randomly sampled from electoral lists and invited with household members over 5 years old to be tested for anti–SARS-CoV-2 (IgT, i.e., IgA/IgG/IgM) antibodies by ELISA (Bio-rad); the sero-neutralization activity was evaluated on Vero CCL-81 cells. Among 2006 individuals, the raw seroprevalence was 2.1% (95% confidence interval 1.5 to 2.9), was highest for 20- to 34-year-old participants (4.7% (2.3 to 8.4)), within than out of socially deprived area (2.5% vs. 1%, p = 0.02) and with than without intra-family infection (p < 10−6). Moreover, 25% of participants presented at least one COVID-19 symptom associated with SARS-CoV-2 positivity (p < 10−13), with highly discriminant anosmia or ageusia (odds ratio 27.8 [13.9 to 54.5]); 16.3% (6.8 to 30.7) of seropositive individuals were asymptomatic. Positive sero-neutralization was demonstrated in vitro for 31/43 seropositive subjects. Regarding the very low seroprevalence, a preventive effect of the lockdown in March 2020 can be assumed for the summer, but a second COVID-19 wave, as expected, could be subsequently observed in this poorly immunized population.

Abstract Objectives The detection of SARS-CoV-2 in infected people is a key tool to help in controlling COVID-19 pandemic. Like rapid antigenic tests, automated antigen tests, that present the advantage of a higher throughput flow, may be of interest. The LIAISON® SARS-CoV-2 Ag test was evaluated for the quantification of SARS-CoV-2 nucleocapsid antigen in nasopharyngeal swabs by comparison to RT-PCR. Methods The study involved 378 nasopharyngeal samples (UTM® and FLOQSwab™, Copan Diagnostics), including 46 swabs positive for SARS-CoV-2 by RT-PCR. These samples came from asymptomatic (n=99, 26.2%) or symptomatic people (n=279, 73.8%), at different times from symptom onset. The samples were analyzed on LIAISON® XL. Results The overall specificity was 99.4% (CI95% [98.6–100]). The negative predictive value reached 100% in asymptomatic people. Among the 46 positive samples, the overall sensitivity was 84.8% (CI95% [74.4–95.2]), reached 91.9% (CI95% [83.1–100]) in the first fourth days after symptoms onset and was 100% for Cq values ≤25. Antigen was not detected in samples with Cq values >25. Similar results were observed on nasopharyngeal swabs coming from patients infected with the 20I/501Y.V1 variant or the 20H/501Y.V2 variant. Conclusions According to technical performances, the LIAISON® SARS-CoV-2 Ag test may be a useful tool for COVID-19 diagnosis, especially during the first four days of symptoms.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is genetically variable, allowing it to adapt to various hosts including humans. Indeed, SARS-CoV-2 has accumulated around two mutations per genome each month. The first relevant event in this context was the occurrence of the mutant D614G in the Spike gene. Moreover, several variants have emerged, including the well-characterized 20I/501Y.V1, 20H/501Y.V2, and 20J/501Y.V3 strains, in addition to those that have been detected within clusters, such as 19B/501Y or 20C/655Y in France. Mutants have also emerged in animals, including a variant transmitted to humans, namely, the Mink variant detected in Denmark. The emergence of these variants has affected the transmissibility of the virus (for example, 20I/501Y.V1, which was up to 82% more transmissible than other preexisting variants), its severity, and its ability to escape natural, adaptive, vaccine, and therapeutic immunity. In this respect, we review the literature on variants that have currently emerged, and their effect on vaccines and therapies, and, in particular, monoclonal antibodies (mAbs). The emergence of SARS-CoV-2 variants must be examined to allow effective preventive and curative control strategies to be developed.

AbstractBackgroundThe World Health Organisation recommends monitoring the circulation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We aimed to estimate anti–SARS-CoV-2 total immunoglobulin (IgT) antibody seroprevalence and describe symptom profiles and in vitro seroneutralization in Nancy, France, in spring 2020.MethodsIndividuals were randomly sampled from electoral lists and invited with household members over 5 years old to be tested for anti–SARS-CoV-2 (IgT, i.e. IgA/IgG/IgM) antibodies by ELISA (Bio-rad). Serum samples were classified according to seroneutralization activity >50% (NT50) on Vero CCL-81 cells. Age- and sex-adjusted seroprevalence was estimated. Subgroups were compared by chi-square or Fisher exact test and logistic regression.ResultsAmong 2006 individuals, 43 were SARS-CoV-2–positive; the raw seroprevalence was 2.1% (95% confidence interval 1.5 to 2.9), with adjusted metropolitan and national standardized seroprevalence 2.5% (1.8 to 3.3) and 2.3% (1.7 to 3.1). Seroprevalence was highest for 20-to 34-year-old participants (4.7% [2.3 to 8.4]), within than out of socially deprived area (2.5% vs 1%, P=0.02) and with than without intra-family infection (p<10−6). Moreover, 25% (23 to 27) of participants presented at least one COVID-19 symptom associated with SARS-CoV-2 positivity (p<10−13), with anosmia or ageusia highly discriminant (odds ratio 27.8 [13.9 to 54.5]), associated with dyspnea and fever. Among the SARS-CoV-2-positives, 16.3% (6.8 to 30.7) were asymptomatic. For 31 of these individuals, positive seroneutralization was demonstrated in vitro.ConclusionsIn this population of very low anti-SARS-CoV-2 antibody seroprevalence, a beneficial effect of the lockdown can be assumed, with frequent SARS-CoV-2 seroneutralization among IgT-positive patients.Key MessagesTotal immunoglobulin antibody (IgT) measurement is an accurate tool to monitor the circulation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and a key biological feature to assume the spread of COVID-19 later after the appearance of symptoms.IgT seroprevalence was 2.1% in the Grand Nancy Metropolitan area, France; was highest for young adults; in socially deprived area, but this was not confirmed at the individual level; and was associated with high intra-family viral transmission.About two thirds of IgT-positive individuals exhibited SARS-CoV-2–positive seroneutralization.Trial registrationNCT04448769