Importance: Recent reports have highlighted an intense influenza activity related to the circulation of the influenza A(H3N2) subclade k variant. There is no data available on the impact of the emergence of H3N2 subclade k on the severity of the 2025/2026 epidemic or on the clinical phenotype of patients requiring admission to the intensive care unit (ICU). Objective: To compare the clinical presentation, hospital mortality and virological characteristics of patients with laboratory-confirmed influenza infection included in French intensive care units during the 2025/2026 epidemic season with those of patients admitted during the 2024/2025 season. We also aimed at measuring the impact of the A(H3N2) subtype on hospital mortality during the 2025/2026 season. Design: Prospective, multicenter, observational SEVARVIR cohort study including patients admitted during the 2024/2025 and 2025/2026 influenza seasons. Setting: Forty-two French ICUs Participants: Adult patients with laboratory-confirmed influenza infection Interventions: none Main Outcomes and Measures: The primary outcome measure was in-hospital mortality. Results: Patients admitted in intensive care units for influenza in 2024/2025 (n=360) and 2025/2026 (n=325) were included in the French nationwide prospective multicentre SEVARVIR study. There was no significant difference in day28 mortality between the seasons (12.7%, n=45/355 vs 16.5% n=28/170; p=0.28). In the 2025-26 season, 49% had the A(H1N1) subtype and 51% the A(H3N2) subtype (k subclade: 77%). The univariable Cox analysis revealed that patients infected with A(H3N2) viruses were at greater risk of death over time. Multivariable Cox analysis revealed that during the 2025-2026 season, age (adjusted hazard ratio, aHR=1.05 [1.00;1.11]; p=0.046) and the clinical frailty scale (aHR=1.82 [1.26;2.72]; p=0.001) were associated with an increased risk of death. The A(H3N2) subtype was not associated with an increased risk of death (aHR=1.13 [0.32;4.51]; p=0.85). Phylogenetic analyses from our ICU cohort together with 300 contextual sequences from community-acquired influenza cases collected during the same period showed no clustering according to severity. Conclusions and Relevance: This French national prospective observational study, found that the emergence of the influenza A(H3N2) subclade K was associated with an increased risk of death in univariable but not multivariable analysis, adjusting for host-related factors. ### Competing Interest Statement Slim Fourati has served as a speaker for GlaxoSmithKline, AstraZeneca, MSD, Pfeizer, Cepheid and Moderna, SANOFI. Jean-Michel Pawlotsky has served as an advisor or speaker for Abbvie, Arbutus, Assembly Biosciences, Gilead and Merck. Etienne Audureau has received fees for lectures from Alexion, Sanofi, Gilead and Pfizer. His hospital has received research grant from Pfizer, MSD and Alexion. Remi COUDROY received fees and reimbursement for travel expenses from Fisher and Paykel Healthcare. Sylvie LARRAT received reimbursement for travel expenses from GILEAD and Biomerieux. All others authors have nothing to disclose. ### Clinical Protocols ### Funding Statement The SEVARVIR study has been funded by the EMERGEN consortium ANRS Maladies Infectieuses Emergentes (ANRS0153). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study was approved by the Comite de Protection des Personnes Sud-Mediterranee I (Number EudraCT/ID-RCB: 2021-A02914-37). Informed consent was obtained from all patients or their relatives. The study was conducted in accordance with the 1964 Helsinki Declaration and subsequent amendments. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes the clinical datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request

Relatively few studies have investigated HIV-1 persistence in tissues, especially in healthy people-living-with-HIV-1 (PLWH) on a successful antiretroviral regimen containing second generation integrase inhibitors. In the ANRS EP64 DOLUVOIR, we explore HIV-1 persistence in five accessible anatomical sites in 20 PLWH on an efficient first-line ART regimen containing dolutegravir with virological load <50 copies/mL: PBMCs, rectum, adipose tissue, lymph node and sperm. We quantify total HIV-DNA and cell-associated HIV-1 RNA in different compartments. We sequence HIV-1 DNA for searching drug resistance mutations (DRM) (in RT and INT) and for studying HIV diversity within tissues (ENV). Intact proviral DNA is estimated in PBMCs with an adapted IPDA assay. Broad ranges of total HIV-DNA and transcripts levels are detected in lymph nodes, PBMCs, adipose tissue and rectum with the highest levels being found in lymph nodes (2.77 log copies HIV-1-DNA/106 cells and 1.50 log copies of HIV-1 cell-associated-RNA/µg RNA). HIV-1 DNA is undetected in all sperm samples (n = 19) except for one (1.52 log copies HIV-1-DNA/106 cells). No difference is noted between the diversity in the four compartments. DRMs to the current regimen are found archived in compartments of six participants. Only two major DRMs to dolutegravir (G118R and R263K) are found archived in two participants. They are the results of APOBEC hypermutations. Despite ongoing transcriptional activity, persistence of HIV-1 in deep tissues is not associated with the selection of DRMs to dolutegravir on intact proviruses. Our results suggest that the detectable transcriptional activity stems predominantly from defective proviral DNA. The main obstacle for the eradication of Human immunodeficiency Virus (HIV-1) is that the virus persists deep in the human body. In this present study, we explore this persistence by measuring the level of infection and expression of viral genes in five parts of the body: blood, rectum, lymph nodes, sperm and fat. We look in 20 People-living-with-HIV-1 on successful treatment with a combination of medicines including one called Dolutegravir. We demonstrate that the levels of infection are highest in lymph nodes. By testing HIV-1 DNA for drug resistance, we show that this persistence in the body does not lead to major resistance to Dolutegravir. Mchantaf et al. explore HIV-1 persistence in five anatomical compartments in people living with HIV on successful Dolutegravir therapy. They find the highest levels of infection and viral transcription in lymph nodes, and that persistence is not associated with the selection of drug resistance mutations to Dolutegravir.

In the context of viral epidemic surveillance, generating accurate consensus viral genomes from sequencing data is critical for tracking the emergence of mutations of concern, evaluating the genomic diversity of circulating viruses, and anticipating which viral strains could become most prevalent. However, this task is made difficult by the presence of Deletion-containing Viral Genomes (DelVGs), which contain truncated (or rearranged) and potentially mutated versions of the full length virus genome. Because these DelVGs can outnumber the full genome in terms of coverage, potential DelVG specific mutations may be erroneously incorporated into the final consensus, thereby compromising its accuracy. Automatic detection of these DelVGs and of the genomic positions that may harbor DelVG specific mutations is therefore crucial. Here, we present DIPScan, a new method able to (i) accurately and efficiently detect DelVGs in short read datasets, and (ii) mask or correct positions in the consensus genome that may be affected by DelVG-specific mutations. DIPScan achieves this through tailored metrics for breakpoint characterization and selection, linear modeling to estimate DelVG relative abundance from well-defined region and junction coverage, and efficient heuristic algorithms for reliable consensus sequence correction. Using several hundreds of simulated and real patient-derived NGS datasets from the National Reference Center (NRC) for respiratory viruses at Institut Pasteur, we demonstrate the capacity of DIPScan to accurately and efficiently detect DelVGs and to correctly adjust the consensus sequences. DIPScan is implemented as a Nextflow workflow, making it highly flexible, scalable, and reproducible, and is now used routinely at the NRC.

Background: Neuromuscular blocking agents (NMBAs) are muscle relaxants used to assist mechanical ventilation but lead in 1 per 10,000 anesthesia cases to severe acute hypersensitivity reactions-that is, anaphylaxis. Incidences vary between types of NMBAs. Rocuronium, a widely used nondepolarizing aminosteroid NMBA, induces among the highest anaphylaxis rates. Rocuronium-induced anaphylaxis is proposed to rely on preexisting rocuronium-binding antibodies, but no such antibodies have ever been identified. Objectives: We sought to identify rocuronium-specific antibody repertoires from plasma cells or plasmablasts of rocuroniumimmunized mice to determine the affinities, structures, and anaphylactogenic potential of these antibodies for rocuronium. Methods: We engrafted rocuronium onto carrier proteins allowing immunization of mice against rocuronium, screening for rocuronium-specific antibody responses, and sorting of rocuronium-specific plasma cells using droplet microfluids coupled to single-cell antibody gene (variable heavy chain [VH] and variable light chain [VL]) sequencing. Results: The 2 different repertoires of >500 VH-VL pairs were oligoclonal, comprised 3 major clonal families, and displayed convergence. Expressed as human IgG1, these antibodies demonstrated subnanomolar affinities for rocuronium with families either monospecific for rocuronium or cross-reactive only for closely related NMBAs. Expressed as human IgE, they triggered human mast cell and basophil activation, and severe passive systemic anaphylaxis in mice humanized for the IgE receptor Fc epsilon RI. Cocrystal structures between rocuronium and antibody representatives of 3 different VH-VL families revealed distinct interaction modes, with the ammonium group involved systematically in the binding interface. Conclusions: This work identifies the epitopes of antibody reactivity to rocuronium, demonstrates anaphylactogenic potential of anti-rocuronium IgE, and establishes the first mouse model of NMBA anaphylaxis.

Felsenstein's bootstrap is the most commonly used method to measure branch support in phylogenetics. Current sequencing technologies can result in massive sampling of taxa (e.g. SARS-CoV-2). In this case, the sequences are very similar, the trees are short, and the branches correspond to a small number of mutations (possibly 0). Nevertheless, these trees contain a strong signal, with unresolved parts but a low rate of false branches. With such data, Felsenstein's bootstrap is not satisfactory. Due to the frequentist nature of bootstrap sampling, the expected support of a branch corresponding to a single mutation is ∼63%, even though it is highly likely to be correct. Here, we propose a Bayesian version of the phylogenetic bootstrap in which sites are assigned uninformative prior probabilities. The branch support can then be interpreted as a posterior probability. We do not view the alignment as a small subsample of a large sample of sites, but rather as containing all available information (e.g. as with complete viral genomes, which are becoming routine). We give formulas for expected supports under the assumption of perfect phylogeny, in both the frequentist and Bayesian frameworks, where a branch corresponding to a single mutation now has an expected support of ∼90%. Simulations show that these theoretical results are robust to realistic data. Analyses on low-homoplasy viral and nonviral datasets show that Bayesian bootstrap support is easier to interpret, with high supports for branches very likely to be correct. As homoplasy increases, the two supports become closer and strongly correlated.

Background: First-generation anti-SARS-CoV-2 monoclonal antibodies (mAbs) used for prophylaxis or therapeutic purposes in immunocompromised patients have been withdrawn because of the emergence of resistant Omicron variants. In 2024, 2 novel mAbs, VYD222/Pemivibart and AZD3152/Sipavibart, were approved by health authorities, but their activity against contemporary JN.1 sublineages is poorly characterized. Methods: We isolated authentic JN.1.1, KP.1.1, LB.1, and KP.3.3 viruses and evaluated their sensitivity to neutralization by these mAbs in 2 target cell lines. Results: Compared to ancestral strains, VYD222/Pemivibart remained moderately active against JN.1 subvariants, with a strong increase of 50% Inhibitory Concentration (IC50), reaching up to 3 to 15 µg/mL for KP.3.3. AZD3152/Sipavibart neutralized JN.1.1 but lost antiviral efficacy against KP.1.1, LB.1, and KP.3.3. Conclusions: Our results highlight the need for a close clinical monitoring of VYD222/Pemivibart and raise concerns about the clinical efficacy of AZD3152/Sipavibart.

Integrons are genetic elements involved in bacterial adaptation which capture, shuffle and express genes encoding adaptive functions embedded in cassettes. These events are governed by the integron integrase through site-specific recombination between attC and attI integron sites. Using computational and molecular genetic approaches, here we demonstrate that the integrase also catalyses cassette integration into bacterial genomes outside of its known att sites. Once integrated, these cassettes can be expressed if located near bacterial promoters and can be excised at the integration point or outside, inducing chromosomal modifications in the latter case. Analysis of more than 5 × 10 5 independent integration events revealed a very large genomic integration landscape. We identified consensus recombination sequences, named attG sites, which differ greatly in sequence and structure from classical att sites. These results unveil an alternative route for dissemination of adaptive functions in bacteria and expand the role of integrons in bacterial evolution.

Chapter 9 Measures of Branch Support in Phylogenetics Olivier GASCUEL, Olivier GASCUEL ISYEB, CNRS, MNHN, Sorbonne Université, EPHE, UA, Paris, FranceSearch for more papers by this authorFrédéric LEMOINE, Frédéric LEMOINE Unité de bioinformatique évolutive, Hub de bioinformatique et biostatistiques, Institut Pasteur, Université Paris Cité, FranceSearch for more papers by this author Olivier GASCUEL, Olivier GASCUEL ISYEB, CNRS, MNHN, Sorbonne Université, EPHE, UA, Paris, FranceSearch for more papers by this authorFrédéric LEMOINE, Frédéric LEMOINE Unité de bioinformatique évolutive, Hub de bioinformatique et biostatistiques, Institut Pasteur, Université Paris Cité, FranceSearch for more papers by this author Gilles Didier, Gilles DidierSearch for more papers by this authorStéphane Guindon, Stéphane GuindonSearch for more papers by this author Book Author(s):Gilles Didier, Gilles DidierSearch for more papers by this authorStéphane Guindon, Stéphane GuindonSearch for more papers by this author First published: 12 April 2024 https://doi.org/10.1002/9781394284252.ch9 AboutPDFPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShareShare a linkShare onEmailFacebookTwitterLinkedInRedditWechat Summary The first step in phylogeny is to construct a tree from data. The inferred tree comprises internal nodes or "ancestral nodes", leaves bijectively associated with taxa, and branch lengths measured in expected number of substitutions per site. The reconstruction of a tree from sequences is a form of statistical inference. This chapter introduces fast local methods; the Felsenstein bootstrap and a new version based on the transfer distance, particularly suited to large datasets with little phylogenetic signal; and the posterior probabilities used in a Bayesian framework, including a fast local approach. The transfer bootstrap indicates whether there are a large or small number of taxa that are unstable concerning the branch in question and allow to identify the most unstable taxa. Bayesian supports give the posterior probability of the branch under study, which depends on the amount of information contained in the data in favor of this branch. References Anisimova , M. and Gascuel , O. ( 2006 ). 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Bioinformatics workflows are increasingly used for sharing analyses, serving as a cornerstone for enhancing the reproducibility and shareability of bioinformatics analyses. In particular, Nextflow is a commonly used workflow system, permitting the creation of large workflows while offering substantial flexibility. An increasing number of Nextflow workflows are being shared on repositories such as GitHub. However, this tremendous opportunity to reuse existing code remains largely underutilized. In cause, the increasing complexity of workflows constitute a major obstacle to code reuse. Consequently, there is a rising need for tools that can help bioinformaticians extract valuable information from their own and others' workflows. To facilitate workflow inspection and reuse, we developed BioFlow-Insight to automatically analyze the code of Nextflow workflows and generate useful information, particularly in the form of visual graphs depicting the workflow's structure and representing its individual analysis steps. BioFlow-Insight is an open-source tool, available as both a command-line interface and a web service. It is accessible at https://pypi.org/project/bioflow-insight/ and https://bioflow-insight.pasteur.cloud/.

The unceasing circulation of SARS-CoV-2 leads to the continuous emergence of novel viral sublineages. Here, we isolate and characterize XBB.1, XBB.1.5, XBB.1.9.1, XBB.1.16.1, EG.5.1.1, EG.5.1.3, XBF, BA.2.86.1 and JN.1 variants, representing >80% of circulating variants in January 2024. The XBB subvariants carry few but recurrent mutations in the spike, whereas BA.2.86.1 and JN.1 harbor >30 additional changes. These variants replicate in IGROV-1 but no longer in Vero E6 and are not markedly fusogenic. They potently infect nasal epithelial cells, with EG.5.1.3 exhibiting the highest fitness. Antivirals remain active. Neutralizing antibody (NAb) responses from vaccinees and BA.1/BA.2-infected individuals are markedly lower compared to BA.1, without major differences between variants. An XBB breakthrough infection enhances NAb responses against both XBB and BA.2.86 variants. JN.1 displays lower affinity to ACE2 and higher immune evasion properties compared to BA.2.86.1. Thus, while distinct, the evolutionary trajectory of these variants combines increased fitness and antibody evasion.

Evolutionary convergences are observed at all levels, from phenotype to DNA and protein sequences, and changes at these different levels tend to be correlated. Notably, convergent mutations can lead to convergent changes in phenotype, such as changes in metabolism, drug resistance, and other adaptations to changing environments. We propose a two-component approach to detect mutations subject to convergent evolution in protein alignments. The "Emergence" component selects mutations that emerge more often than expected, while the "Correlation" component selects mutations that correlate with the convergent phenotype under study. With regard to Emergence, a phylogeny deduced from the alignment is provided by the user and is used to simulate the evolution of each alignment position. These simulations allow us to estimate the expected number of mutations in a neutral model, which is compared to the observed number of mutations in the data studied. In Correlation, a comparative phylogenetic approach, is used to measure whether the presence of each of the observed mutations is correlated with the convergent phenotype. Each component can be used on its own, for example Emergence when no phenotype is available. Our method is implemented in a standalone workflow and a webserver, called ConDor. We evaluate the properties of ConDor using simulated data, and we apply it to three real datasets: sedge PEPC proteins, HIV reverse transcriptase, and fish rhodopsin. The results show that the two components of ConDor complement each other, with an overall accuracy that compares favorably to other available tools, especially on large datasets.

The bootstrap method is based on resampling sequence alignments and re-estimating trees. Felsenstein’s bootstrap proportions (FBP) are the most common approach to assess the reliability and robustness of sequence-based phylogenies. However, when increasing taxon sampling (i.e., the number of sequences) to hundreds or thousands of taxa, FBP tend to return low support for deep branches. The transfer bootstrap expectation (TBE) has been recently suggested as an alternative to FBP. TBE is measured using a continuous transfer index in [0,1] for each bootstrap tree, instead of the binary {0,1} index used in FBP to measure the presence/absence of the branch of interest. TBE has been shown to yield higher and more informative supports while inducing a very low number of falsely supported branches. Nonetheless, it has been argued that TBE must be used with care due to sampling issues, especially in datasets with a high number of closely related taxa. In this study, we conduct multiple experiments by varying taxon sampling and comparing FBP and TBE support values on different phylogenetic depths, using empirical datasets. Our results show that the main critique of TBE stands in extreme cases with shallow branches and highly unbalanced sampling among clades, but that TBE is still robust in most cases, while FBP is inescapably negatively impacted by high taxon sampling. We suggest guidelines and good practices in TBE (and FBP) computing and interpretation.

The unceasing circulation of SARS-CoV-2 leads to the continuous emergence of novel viral sublineages. Here, we isolated and characterized XBB.1, XBB.1.5, XBB.1.9.1, XBB.1.16.1, EG.5.1.1, EG.5.1.3, XBF, BA.2.86.1 and JN.1 variants, representing >80% of circulating variants in January 2024. The XBB subvariants carry few but recurrent mutations in the spike, whereas BA.2.86.1 and JN.1 harbor >30 additional changes. These variants replicated in IGROV-1 but no longer in Vero E6 and were not markedly fusogenic. They potently infected nasal epithelial cells, with EG.5.1.3 exhibiting the highest fitness. Antivirals remained active. Neutralizing antibody (NAb) responses from vaccinees and BA.1/BA.2-infected individuals were markedly lower compared to BA.1, without major differences between variants. An XBB breakthrough infection enhanced NAb responses against both XBB and BA.2.86 variants. JN.1 displayed lower affinity to ACE2 and higher immune evasion properties compared to BA.2.86.1. Thus, while distinct, the evolutionary trajectory of these variants combines increased fitness and antibody evasion.

The landscape of SARS-CoV-2 variants dramatically diversified with the simultaneous appearance of multiple subvariants originating from BA.2, BA.4, and BA.5 Omicron sub-lineages. They harbor a specific set of mutations in the spike that can make them more evasive to therapeutic monoclonal antibodies. In this study, we compared the neutralizing potential of monoclonal antibodies against the Omicron BA.2.75.2, BQ.1, BQ.1.1, and XBB variants, with a pre-Omicron Delta variant as a reference. Sotrovimab retains some activity against BA.2.75.2, BQ.1, and XBB as it did against BA.2/BA.5, but is less active against BQ.1.1. Within the Evusheld/AZD7442 cocktail, Cilgavimab lost all activity against all subvariants studied, resulting in loss of Evusheld activity. Finally, Bebtelovimab, while still active against BA.2.75, also lost all neutralizing activity against BQ.1, BQ.1.1, and XBB variants.

On May 6, 2022, a powerful outbreak of monkeypox virus (MPXV) had been reported outside of Africa, with many continuing new cases being reported around the world. Analysis of mutations among the two different lineages present in the 2021 and 2022 outbreaks revealed the presence of G->A mutations occurring in the 5’GpA context, indicative of APOBEC3 cytosine deaminase activity. By using a sensitive PCR (3D-PCR) method allowing differential amplification of AT-rich DNA, we demonstrate that G->A hypermutated MPXV genomes can be recovered experimentally from APOBEC3 transfection followed by MPXV infection. Here, among the 7 human APOBEC3 cytidine deaminases (A3A-A3C, A3DE, A3F-A3H), only APOBEC3F was capable of extensively deaminating cytidine residues in MPXV genomes. Hyperedited genomes were also recovered in ~42% of analyzed patients, indicating that editing is part of the natural cycle of MPXV infection. Moreover, we demonstrate that substantial repair of these mutations occurs. Upon selection, corrected G->A mutations escaping drift loss contribute to the MPXV evolution observed in the current epidemics. Thus, stochastic or transient overexpression of APOBEC3F gene exposes the MPXV genome to a broad spectrum of mutations that may be modeling the mutational landscape after multiple cycles of viral replication.

Integrons are genetic elements involved in bacterial adaptation. They can capture, shuffle and express adaptive functions embedded in cassettes. These events are governed by the integron integrase through site-specific recombination between attC and attI integron sites. Here, we demonstrated that the integrase can efficiently catalyze insertion of cassettes in bacterial genomes, outside the att sites. We showed that, once inserted in genomes, cassettes can be expressed, if located near bacterial promoters, and can be excised at the insertion point and even outside, inducing chromosomal modifications in the latter case. Analysis of more than 5 × 10 5 independent insertion events revealed a very large genomic insertion landscape with recombination sites greatly different, in terms of sequence and structure, from classical att sites. We named these new sites attG . These results unveil a new efficient route for dissemination of adaptive functions and expand the role of integrons in bacterial evolution.

Most people living with HIV need antiretroviral therapy to control their infection and experience viral relapse in case of treatment interruption, because of viral reservoir (proviruses) persistence. Knowing that proviruses are very diverse and most of them are defective in treated individuals, we aimed to characterize the HIV blood reservoirs of posttreatment controllers (PTCs), rare models of drug-free remission, in comparison with spontaneous controllers and treated individuals.