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APOBEC3 enzymes are innate immune effectors that introduce mutations into viral genomes. These enzymes are cytidine deaminases which transform cytosine into uracil. They preferentially mutate cytidine preceded by thymidine making the 5'TC motif their favored target. Viruses have evolved different strategies to evade APOBEC3 restriction. Certain viruses actively encode viral proteins antagonizing the APOBEC3s, others passively face the APOBEC3 selection pressure thanks to a depleted genome for APOBEC3-targeted motifs. Hence, the APOBEC3s left on the genome of certain viruses an evolutionary footprint. The aim of our study is the identification of these viruses having a genome shaped by the APOBEC3s. We analyzed the genome of 33,400 human viruses for the depletion of APOBEC3-favored motifs. We demonstrate that the APOBEC3 selection pressure impacts at least 22% of all currently annotated human viral species. The papillomaviridae and polyomaviridae are the most intensively footprinted families; evidencing a selection pressure acting genome-wide and on both strands. Members of the parvoviridae family are differentially targeted in term of both magnitude and localization of the footprint. Interestingly, a massive APOBEC3 footprint is present on both strands of the B19 erythroparvovirus; making this viral genome one of the most cleaned sequences for APOBEC3-favored motifs. We also identified the endemic coronaviridae as significantly footprinted. Interestingly, no such footprint has been detected on the zoonotic MERS-CoV, SARS-CoV-1 and SARS-CoV-2 coronaviruses. In addition to viruses that are footprinted genome-wide, certain viruses are footprinted only on very short sections of their genome. That is the case for the gamma-herpesviridae and adenoviridae where the footprint is localized on the lytic origins of replication. A mild footprint can also be detected on the negative strand of the reverse transcribing HIV-1, HIV-2, HTLV-1 and HBV viruses. Together, our data illustrate the extent of the APOBEC3 selection pressure on the human viruses and identify new putatively APOBEC3-targeted viruses.

Controversy exists regarding the association of bovine leukemia virus (BLV) and breast cancer. PCR-based experimental evidence indicates that BLV DNA is present in breast tissue and that as many as 37% of cancer cases may be attributable to viral exposure. Since this association might have major consequences for human health, we evaluated 51 whole genomes of breast cancer samples for the presence of BLV DNA. Among 32 billion sequencing reads retrieved from the NCBI database of genotype and phenotype, none mapped on different strains of the BLV genome. Controls for sequence divergence and proviral loads further validated the approach. This unbiased analysis thus excludes a clonal insertion of BLV in breast tumor cells and strongly argues against an association between BLV and breast cancer.

Human adenoviruses (HAdVs) are a large family of DNA viruses counting more than a hundred strains divided into seven species (A to G). HAdVs induce respiratory tract infections, gastroenteritis and conjunctivitis. APOBEC3B is a cytidine deaminase that restricts several DNA viruses. APOBEC3B is also implicated in numerous cancers where it is responsible for the introduction of clustered mutations into the cellular genome. In this study, we demonstrate that APOBEC3B is an adenovirus restriction factor acting through a deaminase-dependent mechanism. APOBEC3B introduces C-to-T clustered mutations into the adenovirus genome. APOBEC3B reduces the propagation of adenoviruses by limiting viral genome replication, progression to late phase, and production of infectious virions. APOBEC3B restriction efficiency varies between adenoviral strains, the A12 strain being more sensitive to APOBEC3B than the B3 or C2 strains. In A12-infected cells, APOBEC3B clusters in the viral replication centers. Importantly, we show that adenovirus infection leads to a reduction of the quantity and/or enzymatic activity of the APOBEC3B protein depending on the strains. The A12 strain seems less able to resist APOBEC3B than the B3 or C2 strains, a characteristic which could explain the strong depletion of the APOBEC3-targeted motifs in the A12 genome. These findings suggest that adenoviruses evolved different mechanisms to antagonize APOBEC3B. Elucidating these mechanisms could benefit the design of cancer treatments. This study also identifies adenoviruses as triggers of the APOBEC3B-mediated innate response. The involvement of certain adenoviral strains in the genesis of the APOBEC3 mutational signature observed in tumors deserves further study.

The Earth’s magnetic field displays variations on a broad range of time scales, from years to hundreds of millions of years. The last two decades of global and continuous satellite geomagnetic field monitoring have considerably enriched the knowledge on the rapid physical processes taking place in the Earth’s outer core. Identification of axisymmetric torsional Alfvén waves with subdecadal periods from observatory and satellite data has given access to an averaged intensity of the magnetic field in the Earth’s core interior. A significant part of the rapid signal, however, resides in nonaxisymmetric motions. Their origin has remained elusive, as previous studies of magnetohydrodynamic waves in the Earth’s core mainly focused on their possible signature on centennial time scales. Here, we identify nonaxisymmetric wavelike patterns in the equatorial region of the core surface from the observed geomagnetic variations. These wavelike features have large spatial scales, interannual periods in the vicinity of 7 y, amplitudes reaching 3 km/y, and coherent westward drift at phase speeds of about 1,500 km/y.We interpret and model these flows as the signature of Magneto–Coriolis (MC) eigenmodes. Their identification offers a way to probe the cylindrical radial component of the magnetic field inside Earth’s core. It follows from our work that there is no need for a stratified layer at the top of the core to account for the rapid geomagnetic field changes.

The regulation of proviral latency is a central problem in retrovirology. We postulate that the genomic integration site of human T lymphotropic virus type 1 (HTLV-1) determines the pattern of expression of the provirus, which in turn determines the abundance and pathogenic potential of infected T cell clones in vivo. We recently developed a high-throughput method for the genome-wide amplification, identification and quantification of proviral integration sites. Here, we used this protocol to test two hypotheses. First, that binding sites for transcription factors and chromatin remodelling factors in the genome flanking the proviral integration site of HTLV-1 are associated with integration targeting, spontaneous proviral expression, and in vivo clonal abundance. Second, that the transcriptional orientation of the HTLV-1 provirus relative to that of the nearest host gene determines spontaneous proviral expression and in vivo clonal abundance. Integration targeting was strongly associated with the presence of a binding site for specific host transcription factors, especially STAT1 and p53. The presence of the chromatin remodelling factors BRG1 and INI1 and certain host transcription factors either upstream or downstream of the provirus was associated respectively with silencing or spontaneous expression of the provirus. Cells expressing HTLV-1 Tax protein were significantly more frequent in clones of low abundance in vivo. We conclude that transcriptional interference and chromatin remodelling are critical determinants of proviral latency in natural HTLV-1 infection.

Non-coding RNAs play a significant role in viral infection cycles, with recent attention focused on circular RNAs (circRNAs) originating from various viral families. Notably, these circRNAs have been associated with oncogenesis and alterations in viral fitness. However, identifying their expression has proven more challenging than initially anticipated due to unique viral characteristics. This challenge has the potential to impede progress in our understanding of viral circRNAs. Key hurdles in working with viral genomes include: (1) the presence of repetitive regions that can lead to misalignment of sequencing reads, and (2) unconventional splicing mechanisms that deviate from conserved eukaryotic patterns. To address these challenges, we developed vCircTrappist, a bioinformatic pipeline tailored to identify backsplicing events and pinpoint loci expressing circRNAs in RNA sequencing data. Applying this pipeline, we obtained novel insights from both new and existing datasets encompassing a range of animal and human pathogens belonging to Herpesviridae, Retroviridae, Adenoviridae, Flaviviridae and Orthomyxoviridae families. Subsequent RT-PCR and Sanger sequencings validated the accuracy of the developed bioinformatic tool for a selection of new candidate virus-derived circRNAs. These findings demonstrate that vCircTrappist is an open and unbiased approach for comprehensive identification of virus-derived circRNAs.

Retroviruses are not expected to encode miRNAs because of the potential problem of self-cleavage of their genomic RNAs. This assumption has recently been challenged by experiments showing that bovine leukemia virus (BLV) encodes miRNAs from intragenomic Pol III promoters. The BLV miRNAs are abundantly expressed in B-cell tumors in the absence of significant levels of genomic and subgenomic viral RNAs. Using deep RNA sequencing and functional reporter assays, we show that miRNAs mediate the expression of genes involved in cell signaling, cancer and immunity. We further demonstrate that BLV miRNAs are essential to induce B-cell tumors in an experimental model and to promote efficient viral replication in the natural host.

Direct observations indicate that the magnitude of the Earth’s magnetic axial dipole has decreased over the past 175 years; it is now 9% weaker than it was in 1840. Here we show how the rate of dipole decay may be controlled by a planetary-scale gyre in the liquid metal outer core. The gyre’s meridional limbs on average transport normal polarity magnetic flux equatorward and reverse polarity flux poleward. Asymmetry in the geomagnetic field, due to the South Atlantic Anomaly, is essential to the proposed mechanism. We find that meridional flux advection accounts for the majority of the dipole decay since 1840, especially during times of rapid decline, with magnetic diffusion making an almost steady contribution generally of smaller magnitude. Based on the morphology of the present field, and the persistent nature of the gyre, the current episode of dipole decay looks set to continue, at least for the next few decades. The magnitude of the Earth’s magnetic dipole has decreased by 9% over the past 175 years. Here, the authors suggest that the rate of dipole decay is controlled by a huge gyre in the liquid metal outer core acting on a field asymmetry, and that decay is set to continue for the next few decades.

Estimation of immunological and microbiological diversity is vital to our understanding of infection and the immune response. For instance, what is the diversity of the T cell repertoire? These questions are partially addressed by high-throughput sequencing techniques that enable identification of immunological and microbiological \"species\" in a sample. Estimators of the number of unseen species are needed to estimate population diversity from sample diversity. Here we test five widely used non-parametric estimators, and develop and validate a novel method, DivE, to estimate species richness and distribution. We used three independent datasets: (i) viral populations from subjects infected with human T-lymphotropic virus type 1; (ii) T cell antigen receptor clonotype repertoires; and (iii) microbial data from infant faecal samples. When applied to datasets with rarefaction curves that did not plateau, existing estimators systematically increased with sample size. In contrast, DivE consistently and accurately estimated diversity for all datasets. We identify conditions that limit the application of DivE. We also show that DivE can be used to accurately estimate the underlying population frequency distribution. We have developed a novel method that is significantly more accurate than commonly used biodiversity estimators in microbiological and immunological populations.

We use more than 2 years of magnetic data from the Swarm mission, and monthly means from 160 ground observatories as available in March 2016, to update the CHAOS time-dependent geomagnetic field model. The new model, CHAOS-6, provides information on time variations of the core-generated part of the Earth’s magnetic field between 1999.0 and 2016.5. We present details of the secular variation (SV) and secular acceleration (SA) from CHAOS-6 at Earth’s surface and downward continued to the core surface. At Earth’s surface, we find evidence for positive acceleration of the field intensity in 2015 over a broad area around longitude 90°E that is also seen at ground observatories such as Novosibirsk. At the core surface, we are able to map the SV up to at least degree 16. The radial field SA at the core surface in 2015 is found to be largest at low latitudes under the India–South-East Asia region, under the region of northern South America, and at high northern latitudes under Alaska and Siberia. Surprisingly, there is also evidence for significant SA in the central Pacific region, for example near Hawaii where radial field SA is observed on either side of a jerk in 2014. On the other hand, little SV or SA has occurred over the past 17 years in the southern polar region. Inverting for a quasi-geostrophic core flow that accounts for this SV, we obtain a prominent planetary-scale, anti-cyclonic, gyre centred on the Atlantic hemisphere. We also find oscillations of non-axisymmetric, azimuthal, jets at low latitudes, for example close to 40°W, that may be responsible for localized SA oscillations. In addition to scalar data from Ørsted, CHAMP, SAC-C and Swarm , and vector data from Ørsted, CHAMP and Swarm , CHAOS-6 benefits from the inclusion of along-track differences of scalar and vector field data from both CHAMP and the three Swarm satellites, as well as east–west differences between the lower pair of Swarm satellites, Alpha and Charlie . Moreover, ground observatory SV estimates are fit to a Huber-weighted rms level of 3.1 nT/year for the eastward components and 3.8 and 3.7 nT/year for the vertical and southward components. We also present an update of the CHAOS high-degree lithospheric field, making use of along-track differences of CHAMP scalar and vector field data to produce a new static field model that agrees well with the MF7 field model out to degree 110.