Pithoviruses Are Invaded by Repeats That Contribute to Their Evolution and Divergence from Cedratviruses.

Pithoviridae are amoeba-infecting giant viruses possessing the largest viral particles known so far. Since the discovery of Pithovirus sibericum, recovered from a 30,000-yr-old permafrost sample, other pithoviruses, and related cedratviruses, were isolated from various terrestrial and aquatic samples. Here, we report the isolation and genome sequencing of 2 Pithoviridae from soil samples, in addition to 3 other recent isolates. Using the 12 available genome sequences, we conducted a thorough comparative genomic study of the Pithoviridae family to decipher the organization and evolution of their genomes. Our study reveals a nonuniform genome organization in 2 main regions: 1 concentrating core genes and another gene duplications. We also found that Pithoviridae genomes are more conservative than other families of giant viruses, with a low and stable proportion (5% to 7%) of genes originating from horizontal transfers. Genome size variation within the family is mainly due to variations in gene duplication rates (from 14% to 28%) and massive invasion by inverted repeats. While these repeated elements are absent from cedratviruses, repeat-rich regions cover as much as a quarter of the pithoviruses genomes. These regions, identified using a dedicated pipeline, are hotspots of mutations, gene capture events, and genomic rearrangements that contribute to their evolution.

Airway management during a respiratory arrest in a clinical simulation scenario. Experience at a pediatric residency program. / Manejo de la vía aérea ante un caso de paro respiratorio en un escenario clínico simulado. Experiencia en una residencia de pediatría.

Introduction. Respiratory failure is the most common cause of cardiac arrest in pediatrics. Recognizing and managing it adequately is critical. Simulation is used to improve medical skills. The objective of this study was to establish the proportion of pediatric residents who recognized a respiratory arrest in a child at a simulation center. Methods. This was an observational study in 77 residents. A simulation of a patient with respiratory distress that progressed to respiratory arrest was used. Results. Among the 77 participants, 48 recognized respiratory arrest (62.3%). The mean time to recognize respiratory arrest was 38.16 seconds. Conclusion. Respiratory arrest was recognized by 62.3% of participants. Among those who did so, the average time was 38.16 seconds. Severe failures were noted in some of the expected interventions.

Introducción. La insuficiencia respiratoria es la causa más común de paro cardíaco en pediatría; su reconocimiento y el manejo adecuado son cruciales. La simulación se utiliza para mejorar las habilidades médicas. El objetivo del trabajo fue determinar la proporción de residentes de pediatría que reconocieron un paro respiratorio (PR) pediátrico en un centro de simulación. Métodos. Se realizó un estudio observacional con 77 médicos residentes. Se utilizó un caso simulado de un paciente con dificultad respiratoria que progresa a PR. Resultados. De los 77 participantes, 48 reconocieron el paro respiratorio (62,3 %). El tiempo medio para reconocer el PR fue de 38,16 segundos. Conclusión. El 62,3 % de los participantes logró reconocer el paro respiratorio. Entre aquellos que lo identificaron, el tiempo promedio fue de 38,16 segundos. Se observaron graves deficiencias en algunas de las intervenciones esperadas.

Past and present giant viruses diversity explored through permafrost metagenomics.

Giant viruses are abundant in aquatic environments and ecologically important through the metabolic reprogramming of their hosts. Less is known about giant viruses from soil even though two of them, belonging to two different viral families, were reactivated from 30,000-y-old permafrost samples. This suggests an untapped diversity of Nucleocytoviricota in this environment. Through permafrost metagenomics we reveal a unique diversity pattern and a high heterogeneity in the abundance of giant viruses, representing up to 12% of the sum of sequence coverage in one sample. Pithoviridae and Orpheoviridae-like viruses were the most important contributors. A complete 1.6 Mb Pithoviridae-like circular genome was also assembled from a 42,000-y-old sample. The annotation of the permafrost viral sequences revealed a patchwork of predicted functions amidst a larger reservoir of genes of unknown functions. Finally, the phylogenetic reconstructions not only revealed gene transfers between cells and viruses, but also between viruses from different families.

Metagenomic survey of the microbiome of ancient Siberian permafrost and modern Kamchatkan cryosols.

In the context of global warming, the melting of Arctic permafrost raises the threat of a reemergence of microorganisms some of which were shown to remain viable in ancient frozen soils for up to half a million years. In order to evaluate this risk, it is of interest to acquire a better knowledge of the composition of the microbial communities found in this understudied environment. Here, we present a metagenomic analysis of 12 soil samples from Russian Arctic and subarctic pristine areas: Chukotka, Yakutia and Kamchatka, including nine permafrost samples collected at various depths. These large datasets (9.2 × 1011 total bp) were assembled (525 313 contigs > 5 kb), their encoded protein contents predicted, and then used to perform taxonomical assignments of bacterial, archaeal and eukaryotic organisms, as well as DNA viruses. The various samples exhibited variable DNA contents and highly diverse taxonomic profiles showing no obvious relationship with their locations, depths or deposit ages. Bacteria represented the largely dominant DNA fraction (95%) in all samples, followed by archaea (3.2%), surprisingly little eukaryotes (0.5%), and viruses (0.4%). Although no common taxonomic pattern was identified, the samples shared unexpected high frequencies of ß-lactamase genes, almost 0.9 copy/bacterial genome. In addition to known environmental threats, the particularly intense warming of the Arctic might thus enhance the spread of bacterial antibiotic resistances, today's major challenge in public health. ß-Lactamases were also observed at high frequency in other types of soils, suggesting their general role in the regulation of bacterial populations.

Comparative Analysis of the Circular and Highly Asymmetrical Marseilleviridae Genomes.

Marseilleviridae members are large dsDNA viruses with icosahedral particles 250 nm in diameter infecting Acanthamoeba. Their 340 to 390 kb genomes encode 450 to 550 protein-coding genes. Since the discovery of marseillevirus (the prototype of the family) in 2009, several strains were isolated from various locations, among which 13 are now fully sequenced. This allows the organization of their genomes to be deciphered through comparative genomics. Here, we first experimentally demonstrate that the Marseilleviridae genomes are circular. We then acknowledge a strong bias in sequence conservation, revealing two distinct genomic regions. One gathers most Marseilleviridae paralogs and has undergone genomic rearrangements, while the other, enriched in core genes, exhibits the opposite pattern. Most of the genes whose protein products compose the viral particles are located in the conserved region. They are also strongly biased toward a late gene expression pattern. We finally discuss the potential advantages of Marseilleviridae having a circular genome, and the possible link between the biased distribution of their genes and the transcription as well as DNA replication mechanisms that remain to be characterized.

The DNA methylation landscape of giant viruses.

DNA methylation is an important epigenetic mark that contributes to various regulations in all domains of life. Giant viruses are widespread dsDNA viruses with gene contents overlapping the cellular world that also encode DNA methyltransferases. Yet, virtually nothing is known about the methylation of their DNA. Here, we use single-molecule real-time sequencing to study the complete methylome of a large spectrum of giant viruses. We show that DNA methylation is widespread, affecting 2/3 of the tested families, although unevenly distributed. We also identify the corresponding viral methyltransferases and show that they are subject to intricate gene transfers between bacteria, viruses and their eukaryotic host. Most methyltransferases are conserved, functional and under purifying selection, suggesting that they increase the viruses' fitness. Some virally encoded methyltransferases are also paired with restriction endonucleases forming Restriction-Modification systems. Our data suggest that giant viruses' methyltransferases are involved in diverse forms of virus-pathogens interactions during coinfections.

Manejo de la vía aérea ante un caso de paro respiratorio en un escenario clínico simulado. Experiencia en una residencia de pediatría / Airway management during a respiratory arrest in a clinical simulation scenario. Experience at a pediatric residency program

Introducción. La insuficiencia respiratoria es la causa más común de paro cardíaco en pediatría; su reconocimiento y el manejo adecuado son cruciales. La simulación se utiliza para mejorar las habilidades médicas. El objetivo del trabajo fue determinar la proporción de residentes de pediatría que reconocieron un paro respiratorio (PR) pediátrico en un centro de simulación. Métodos. Se realizó un estudio observacional con 77 médicos residentes. Se utilizó un caso simulado de un paciente con dificultad respiratoria que progresa a PR. Resultados. De los 77 participantes, 48 reconocieron el paro respiratorio (62,3 %). El tiempo medio para reconocer el PR fue de 34,43 segundos. Conclusión. El 62,3 % de los participantes logró reconocer el paro respiratorio. Entre aquellos que lo identificaron, el tiempo promedio fue de 34,43 segundos. Se observaron graves deficiencias en algunas de las intervenciones esperadas.

Introduction. Respiratory failure is the most common cause of cardiac arrest in pediatrics. Recognizing and managing it adequately is critical. Simulation is used to improve medical skills. The objective of this study was to establish the proportion of pediatric residents who recognized a respiratory arrest in a child at a simulation center. Methods. This was an observational study in 77 residents. A simulation of a patient with respiratory distress that progressed to respiratory arrest was used. Results. Among the 77 participants, 48 recognized respiratory arrest (62.3%). The mean time to recognize respiratory arrest was 34.43 seconds. Conclusion. Respiratory arrest was recognized by 62.3% of participants. Among those who did so, the average time was 34.43 seconds. Severe failures were noted in some of the expected interventions.