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Background 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 cytidine deaminase activity. Methods By using a sensitive PCR (3D-PCR) method allowing differential amplification of AT-rich DNA, we analyzed the level of APOBEC3-induced MPXV editing in infected cells and in patients. Results 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. 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 epidemic. Conclusions 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.

Bioinformatics is a field known for the numerous standards and formats that have been developed over the years. This plethora of formats, sometimes complementary, and often redundant, poses many challenges to bioinformatics data analysts. They constantly need to find the best tool to convert their data into the suitable format, which is often a complex, technical and time consuming task. Moreover, these small yet important tasks are often difficult to make reproducible. To over-come these difficulties, we initiatedBioConvert, a collaborative project to facilitate the conversion of life science data from one format to another.BioConvertaggregates existing software within a single framework and complemented them with original code when needed. It provides a common interface to make the user experience more streamlined instead of having to learn tens of them. Currently,BioConvertsupports about 50 formats and 100 direct conversions in areas such as alignment, sequencing, phylogeny, and variant calling. In addition to being useful for end-users,BioConvertcan also be utilized by developers as a universal benchmarking framework for evaluating and comparing numerous conversion tools. Additionally, we provide a web server implementing an online user-friendly interface toBioConvert, hence allowing direct use for the community.

The bootstrap method is based on resampling alignments and re-estimating trees. Felsenstein’s bootstrap proportions (FBP) is 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 tends to return low supports 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 {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, without inducing falsely supported branches. Nonetheless, it has been argued that TBE must be used with care due to sampling issues, especially in datasets with 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 depth, using empirical datasets. Our results show that the main critic 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.

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 ofAPOBEC3Fgene exposes the MPXV genome to a broad spectrum of mutations that may be modeling the mutational landscape after multiple cycles of viral replication.

Aim To reduce the delay in defibrillation of out-of-hospital cardiac arrest (OHCA) patients, recent publications have shown that drones equipped with an automatic external defibrillator (AED) appear to be effective in sparsely populated areas. To study the effectiveness of AED-drones in high-density urban areas, we developed an algorithm based on emergency dispatch parameters for the rate and detection speed of cardiac arrests and technical and meteorological parameters. Methods We ran a numerical simulation to compare the actual time required by the Basic Life Support team (BLSt) for OHCA patients in Greater Paris in 2017 to the time required by an AED-drone. Endpoints were the proportion of patients with “AED-drone first” and the defibrillation time gained. We built an open-source website ( https://airborne-aed.org/ ) to allow modelling by modifying one or more parameters and to help other teams model their own OHCA data. Results Of 3014 OHCA patients, 72.2 ± 0.7% were in the “no drone flight” group, 25.8 ± 0.2% in the “AED-drone first” group, and 2.1 ± 0.2% in the “BLSt-drone first” group. When a drone flight was authorized, it arrived an average 190 s before BLSt in 93% of cases. The possibility of flying the drone during the aeronautical night improved the results of the “AED-drone first” group the most (+60%). Conclusions In our very high-density urban model, at most 26% of OHCA patients received an AED from an AED-drone before BLSt. The flexible parameters of our website model allows evaluation of the impact of each choice and concrete implementation of the AED-drone.

Integrons are genetic elements found exclusively in bacteria. They are well known for their role in disseminating antibiotic resistance genes among pathogens and more generally for enabling bacteria to rapidly adapt to changing environmental conditions. Integrons constitute a natural system to capture, stockpile, shuffle, express and disseminate genes embedded in cassettes. All these events are governed by the integron integrase through site-specific recombination between integron att sites (attC and attI sites). Here, we demonstrate that integron integrase can efficiently catalyze the insertion of cassettes in bacterial genomes, outside the att sites carried by the integron system. Surprisingly, analysis of more than 5 × 10 to the power of 5 independent clones revealed that the genome recombination sites differ greatly, in terms of sequence and structure, from both classical attC and attI recombination sites. We named theses new sites attG. Notably, among these a few are driving integration at very high rates. We also showed that, once inserted in genomes, cassettes can be expressed if located near a bacterial promoter. Moreover, even if occurring at low frequency, genome inserted cassettes can be excised precisely or imprecisely, inducing in this latter case, chromosomal modifications. These results unveil a new route for antibiotic resistance dissemination and expand the role of integrons in bacterial genome evolution.

Les traitements de données sont au cœur de nombreux domaines de la Bioinformatique. Ils consistent en l’enchaînement d’un grand nombre d’outils bioinformatiques et manipulent des données massives et diverses. Ce chapitre décrit les difficultés d’implémentation et d’exécution de ces traitements, introduit les systèmes de gestion de workflows comme élément de solution et souligne les problèmes de recherche encore ouverts.

Résumé L’état d’urgence sanitaire est levé en France le 10 juillet 2020. A cette date, la Brigade de sapeurs-pompiers de Paris (BSPP) a déjà réalisé 11 737 interventions en lien direct avec l’épidémie. Au paroxysme de cette crise sanitaire, la Brigade a répondu à plus de 2 600 appels quotidiens et réalisé presque 600 interventions COVID-19 par jour, sans ne jamais avoir à dégrader la qualité de sa réponse contre les incendies. Cet article rapporte l’expérience de la BSPP et les enseignements issus de la crise COVID-19. Il décrit la cinétique de sa montée en puissance progressive ainsi que les actions diverses menées au profit de la population défendue ainsi que de ses propres personnels.

Resume Les feux d’habitation en milieu urbain confrontent les equipes medicales a la prise en charge de nombreuses victimes d’âges differents. Les equipes medicales non specialisees en pediatrie doivent se preparer a la prise en charge de victimes pediatriques. Les particularites anatomiques physiologiques et comportementales de l’enfant le rendent plus vulnerable que l’adulte aux fumees d’incendies. Les enfants ne sont pas des petits adultes. Ces victimes pediatriques peuvent etre intoxiquees aux fumees d’incendie, brulees ou traumatisees severes. Les deces de victimes pediatriques lors des incendies sont plus dus aux inhalations de fumees qu’aux brulures. Le tri des victimes s’effectue au poste medical avance ou il faut anticiper l’arrivee d’enfants en detresse vitale. Les principaux traitements inities consistent a l’administration d’oxygene et d’antidotes (hydroxocobalamine) en cas d’intoxication par les fumees d’incendie. L’evolution du sinistre et donc du nombre de victimes potentielles sont imprevisibles. Il est par consequent important d’anticiper la demande de renforts pediatriques, si ceux si sont disponibles. L’anticipation, l’organisation et les differents maillons de la chaine de secours sont primordiaux.

G-quadruplexes (G4s) are four-stranded nucleic acid structures formed by the stacking of G-tetrads. Here we investigated their formation and function during HIV-1 infection. Using bioinformatics and biophysics analyses we first searched for evolutionary conserved G4-forming sequences in HIV-1 genome. We identified 10 G4s with conservation rates higher than those of HIV-1 regulatory sequences such as RRE and TAR. We then used porphyrin-based G4-binders to probe the formation of the G4s during infection of human cells by native HIV-1. The G4-binders efficiently inhibited HIV-1 infectivity, which is attributed to the formation of G4 structures during HIV-1 replication. Using a qRT-PCR approach, we showed that the formation of viral G4s occurs during the first 2 h post-infection and their stabilization by the G4-binders prevents initiation of reverse transcription. We also used a G4-RNA pull-down approach, based on a G4-specific biotinylated probe, to allow the direct detection and identification of viral G4-RNA in infected cells. Most of the detected G4-RNAs contain crucial regulatory elements such as the PPT and cPPT sequences as well as the U3 region. Hence, these G4s would function in the early stages of infection when the viral RNA genome is being processed for the reverse transcription step.

During 2015-2016, Cape Verde, an island nation off the coast of West Africa, experienced a Zika virus (ZIKV) outbreak involving 7,580 suspected Zika cases and 18 microcephaly cases. Analysis of the complete genomes of 3 ZIKV isolates from the outbreak indicated the strain was of the Asian (not African) lineage. The Cape Verde ZIKV sequences formed a distinct monophylogenetic group and possessed 1-2 (T659A, I756V) unique amino acid changes in the envelope protein. Phylogeographic and serologic evidence support earlier introduction of this lineage into Cape Verde, possibly from northeast Brazil, between June 2014 and August 2015, suggesting cryptic circulation of the virus before the initial wave of cases were detected in October 2015. These findings underscore the utility of genomic-scale epidemiology for outbreak investigations. ispartof: EMERGING INFECTIOUS DISEASES vol:26 issue:6 pages:1084-1090 ispartof: location:United States status: published

International audience; Phylogenetics is nowadays at the center of numerous studies in many fields, ranging from comparative genomics to molecular epidemiology. However, phylogenetic analysis workflows are usually complex and difficult to implement, as they are often composed of many small, reccuring, but important data manipulations steps. Among these, we can find file reformatting, sequence renaming, tree re-rooting, tree comparison, bootstrap support computation, etc. These are often performed by custom scripts or by several heterogeneous tools, which may be error prone, uneasy to maintain and produce results that are challenging to reproduce. For all these reasons, the development and reuse of phylogenetic workflows is often a complex task. We identified many operations that are part of most phylogenetic analyses, and implemented them in a toolkit called Gotree/Goalign. The Gotree/Goalign toolkit implements more than 120 user-friendly commands and an API dedicated to multiple sequence alignment and phylogenetic tree manipulations. It is developed in Go, which makes executables easily installable, integrable in workflow environments, and parallelizable when possible. Moreover, Go is a compiled language, which accelerates computations compared to interpreted languages. This toolkit is freely available on most platforms (Linux, MacOS and Windows) and most architectures (amd64, i386) on GitHub at https://github.com/evolbioinfo/gotree, Bioconda and DockerHub.

Evolutionary convergences are observed at all levels, from phenotype to DNA and protein sequences, and the changes observed at these different levels tend to be strongly correlated. Here we propose a simulation-based method to detect positions under convergent evolution in large protein alignments, without prior knowledge on the phenotype and environmental constraints. A phylogeny is inferred from the data and used in simulations to estimate the expected number of amino-acid changes in stable evolutionary constraints (null model) for each position. Similarly, we count the number of mutations towards the same amino acid in the data and test if they are occurring more often than expected. We applied our method to two real datasets: HIV reverse transcriptase and fish rhodopsin, and to HIV-like simulated data. On the latter, with known convergent events and substitution model, we detected on average two third of these events, with a low fraction of false positives. With HIV data, one knows that drug resistance mutations (DRMs) are convergent. Even without any knowledge of patient treatment status, we retrieved more than 70% of positions corresponding to known DRMs. On the rhodopsin dataset, four substitutions are supposed to be convergent, as they change the maximum wavelength absorption of the photoreceptor and occurred several times independently during evolution. We detected three of them. These results demonstrate the potential of the method to target specific mutations to be further studied experimentally or, for example, using a nonsynonymous/synonymous rate ratio approach. Our software named ConDor is available at http://condor.pasteur.cloud.

Background In 2016-2017, 68 women in Southern Vietnam had RT-PCR confirmed Zika virus (ZIKV) infection during pregnancy. We report here the outcomes of the pregnancies and the virological analyses related to this outbreak. Methods We collected clinical and epidemiological information from the women who were enrolled in the study. Medical records related to the pregnancy in 2016–2017 were retrieved for those who were not able to be enrolled in the study. Children born to women with ZIKV infection during pregnancy were also enrolled. Serum samples were evaluated for presence of ZIKV antibodies. Phylogenetic analyses were performed on Zika virus genomes sequenced from the 2016–2017 serum samples. Findings Of the 68 pregnancies, 58 were livebirths and 10 were medically terminated. Four of the medical records from cases of fetal demise were able to be retrieved, of which one was consistent with congenital ZIKV infection. Of the 58 women with a livebirth, 21 participated in the follow-up investigation. All but two women had serologic evidence of ZIKV infection. Of the 21 children included in the study (mean age: 30.3 months), 3 had microcephaly at birth. No other clinical abnormalities were reported and no differences in neurodevelopment were observed compared to a control group. Phylogenetic analysis revealed a clade within the ZIKV Asian lineage and branch at the root of samples from the 2013–2014 French Polynesian outbreak. The prM S139N mutation was not observed. Interpretation We have been able to demonstrate a clade within the ZIKV Asian lineage implicated in adverse pregnancy outcomes in Southern Vietnam. Funding INCEPTION project (PIA/ANR-16-CONV-0005) and a grant received from BNP Paribas Simplidon.

Blood transfusion is a mainstay of therapy for trauma-induced coagulopathy, but the optimal modalities for plasma transfusion in the prehospital setting remain to be defined.To determine whether lyophilized plasma transfusion can reduce the incidence of trauma-induced coagulopathy compared with standard care consisting of normal saline infusion.This randomized clinical trial was performed at multiple centers in France involving prehospital medical teams. Participants included 150 adults with trauma who were at risk for hemorrhagic shock and associated coagulopathy between April 1, 2016, and September 30, 2019, with a 28-day follow-up. Data were analyzed from November 1, 2019, to July 1, 2020.Patients were randomized in a 1:1 ratio to receive either plasma or standard care with normal saline infusion (control).The primary outcome was the international normalized ratio (INR) on arrival at the hospital. Secondary outcomes included the need for massive transfusion and 30-day survival. As a safety outcome, prespecified adverse events included thrombosis, transfusion-related acute lung injury, and transfusion-associated circulatory overload.Among 150 randomized patients, 134 were included in the analysis (median age, 34 [IQR, 26-49] years; 110 men [82.1%]), with 68 in the plasma group and 66 in the control group. Median INR values were 1.21 (IQR, 1.12-1.49) in the plasma group and 1.20 (IQR, 1.10-1.39) in the control group (median difference, -0.01 [IQR, -0.09 to 0.08]; P = .88). The groups did not differ significantly in the need for massive transfusion (7 [10.3%] vs 4 [6.1%]; relative risk, 1.78 [95% CI, 0.42-8.68]; P = .37) or 30-day survival (hazard ratio for death, 1.07 [95% CI, 0.44-2.61]; P = .89). In the full intention-to-treat population (n = 150), the groups did not differ in the rates of any of the prespecified adverse events.In this randomized clinical trial including severely injured patients at risk for hemorrhagic shock and associated coagulopathy, prehospital transfusion of lyophilized plasma was not associated with significant differences in INR values vs standard care with normal saline infusion. Nevertheless, these findings show that lyophilized plasma transfusion is a feasible and safe procedure for this patient population.ClinicalTrials.gov Identifier: NCT02736812.

Widely applicable, accurate and fast inference methods in phylodynamics are needed to fully profit from the richness of genetic data in uncovering the dynamics of epidemics. Standard methods, including maximum-likelihood and Bayesian approaches, generally rely on complex mathematical formulae and approximations, and do not scale with dataset size. We develop a likelihood-free, simulation-based approach, which combines deep learning with (1) a large set of summary statistics measured on phylogenies or (2) a complete and compact representation of trees, which avoids potential limitations of summary statistics and applies to any phylodynamics model. Our method enables both model selection and estimation of epidemiological parameters from very large phylogenies. We demonstrate its speed and accuracy on simulated data, where it performs better than the state-of-the-art methods. To illustrate its applicability, we assess the dynamics induced by superspreading individuals in an HIV dataset of men-having-sex-with-men in Zurich. Our tool PhyloDeep is available ongithub.com/evolbioinfo/phylodeep.

Although the global response to COVID-19 has not been entirely unified, the opportunity arises to assess the impact of regional public health interventions and to classify strategies according to their outcome. Analysis of genetic sequence data gathered over the course of the pandemic allows us to link the dynamics associated with networks of connected individuals with specific interventions. In this study, clusters of transmission were inferred from a phylogenetic tree representing the relationships of patient sequences sampled from December 30, 2019 to April 17, 2020. Metadata comprising sampling time and location were used to define the global behavior of transmission over this earlier sampling period, but also the involvement of individual regions in transmission cluster dynamics. Results demonstrate a positive impact of international travel restrictions and nationwide lockdowns on global cluster dynamics. However, residual, localized clusters displayed a wide range of estimated initial secondary infection rates, for which uniform public health interventions are unlikely to have sustainable effects. Our findings highlight the presence of so-called “super-spreaders”, with the propensity to infect a larger-than-average number of people, in countries, such as the USA, for which additional mitigation efforts targeting events surrounding this type of spread are urgently needed to curb further dissemination of SARS-CoV-2.

SARS-CoV-2 is the virus responsible for the global COVID19 pandemic. We review what is known about the origin of this virus, detected in China at the end of December 2019. The genome of this virus mainly evolves under the effect of point mutations. These are generally neutral and have no impact on virulence and severity, but some appear to influence infectivity, notably the D614G mutation of the Spike protein. To date (30/09/2020) no recombination of the virus has been documented in the human host, and very few insertions and deletions. The worldwide spread of the virus was the subject of controversies that we summarize, before proposing a new approach free from the limitations of previous methods. The results show a complex scenario with, for example, numerous introductions to the USA and returns of the virus from the USA to certain countries including France.Le SARS-CoV-2 est le virus responsable de la pandémie mondiale de COVID19. On dresse ici un bilan de ce qui est connu sur l’origine de ce virus, détecté en Chine fin décembre 2019. Le génome de ce virus évolue sous l’effet de mutations ponctuelles. Celles-ci sont généralement neutres et sans impact sur la virulence et la sévérité, mais certaines semblent influer sur l’infectiosité, notamment la mutation D614G de la protéine Spike. A l’inverse, on n’a à ce jour (30/09/2020) documenté aucune recombinaison du virus chez l’hôte humain, et très peu d’insertions et de délétions. La propagation mondiale du virus a fait l’objet de polémiques sur lesquelles nous revenons, avant de proposer une nouvelle approche débarrassée des limites des méthodes précédentes. Les résultats montrent une propagation complexe avec, par exemple, de très nombreuses introductions aux USA et des retours du virus depuis les USA vers certains pays dont la France.