Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)

In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV

Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)

55 Pág.In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.This work was supported in part through the Laulima Government Solutions, LLC, prime contract with the U.S. National Institute of Allergy and Infec tious Diseases (NIAID) under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC, under Contract No. HHSN272201800013C. U.J.B. was supported by the Division of Intramural Resarch, NIAID. This work was also funded in part by Contract No. HSHQDC15-C-00064 awarded by DHS S and T for the management and operation of The National Biodefense Analysis and Countermeasures Centre, a federally funded research and development centre operated by the Battelle National Biodefense Institute (V.W.); and NIH contract HHSN272201000040I/HHSN27200004/D04 and grant R24AI120942 (N.V., R.B.T.). S.S. acknowl edges support from the Mississippi Agricultural and Forestry Experiment Station (MAFES), USDA-ARS project 58-6066-9-033 and the National Institute of Food and Agriculture, U.S. Department of Agriculture, Hatch Project, under Accession Number 1021494. The funders had no role in the design of the study; in the collection, analysis, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the U.S. Department of the Army, the U.S. Department of Defence, the U.S. Department of Health and Human Services, including the Centres for Disease Control and Prevention, the U.S. Department of Homeland Security (DHS) Science and Technology Directorate (S and T), or of the institutions and companies affiliated with the authors. In no event shall any of these entities have any responsibility or liability for any use, misuse, inability to use, or reliance upon the information contained herein. The U.S. departments do not endorse any products or commercial services mentioned in this publication. The U.S. Government retains and the publisher, by accepting the article for publication, acknowledges that the U.S.Government retains a non-exclusive, paid up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for U.S. Government purposes.Peer reviewe

Isolating the effect of confounding from the observed survival benefit of screening participants — a methodological approach illustrated by data from the German mammography screening programme

Abstract Background Mammography screening programmes (MSP) aim to reduce breast cancer mortality by shifting diagnoses to earlier stages. However, it is difficult to evaluate the effectiveness of current MSP because analyses can only rely on observational data, comparing women who participate in screening with women who do not. These comparisons are subject to several biases: one of the most important is self-selection into the MSP, which introduces confounding and is difficult to control for. Here, we propose an approach to quantify confounding based on breast cancer survival analyses using readily available routine data sources. Methods Using data from the Cancer Registry of North Rhine-Westphalia, Germany, we estimate the relative contribution of confounding to the observed survival benefit of participants of the German MSP. This is accomplished by comparing non-participants, participants with screen-detected and participants with interval breast cancers for the endpoints “death from breast cancer” and “death from all causes other than breast cancer” — the latter being assumed to be unrelated to any MSP effect. By using different contrasts, we eliminate the effects of stage shift, lead and length time bias. The association of breast cancer detection mode with survival is analysed using Cox models in 68,230 women, aged 50–69 years, with breast cancer diagnosed in 2006–2014 and followed up until 2018. Results The hazard of dying from breast cancer was lower in participants with screen-detected cancer than in non-participants (HR = 0.21, 95% CI: 0.20–0.22), but biased by lead and length time bias, and confounding. When comparing participants with interval cancers and non-participants, the survival advantage was considerably smaller (HR = 0.62, 95% CI: 0.58–0.66), due to the elimination of stage shift and lead time bias. Finally, considering only mortality from causes other than breast cancer in the latter comparison, length time bias was minimised, but a survival advantage was still present (HR = 0.63, 95% CI: 0.56–0.70), which we attribute to confounding. Conclusions This study shows that, in addition to stage shift, lead and length time bias, confounding is an essential component when comparing the survival of MSP participants and non-participants. We further show that the confounding effect can be quantified without explicit knowledge of potential confounders by using a negative control outcome

Phenotype.

<p>Phenotype.</p

Surface analysis of infected valves.

<p>For surface analysis using scanning electron microscopy (SEM), infected native (A-C; patient 3) and prosthetic (D-F; patient 7) heart valve tissues were cut into small pieces and fixed. After pretreatment and exposure to osmium tetroxide, tissues were dehydrated and mounted on standard SEM stubs with carbon tape. The cured samples were finally sputter-coated with a platinum layer and evaluated with a scanning electron microscope. (A-C) SEM images of the surface of an infected native valve. (A) Overview. (B) Epithelial cell boundaries are discernable. Inset: note that few bacteria are attached to the smooth surface and that these seem to be often damaged (arrow). (C) At higher magnification scattered bacteria showing apparently intact morphology (arrow) can also be found. (D-F) Ultrastructure images of infected biological prosthetic valve. (D) Overview. (E) The surface is characterized by deep holes and cracks where microbes may be concealed; the surface appears rough. Inset: note that the few bacteria attached to the outside often seem to be damaged (arrow). (F) At higher magnification a number of apparently intact bacteria (arrows) showing different morphologies can be found; note the fibrous structure of the substrate, providing ideal adhesion sites.</p

Ultrastructural features of infective endocarditis.

<p>Using focused ion beam scanning electron microscopy (FIB-SEM), 3D reconstructions of infected phagocytic cells were generated. (A) Transversal cut through a native infected valve (patient 3). Cells cluttered with numerous viable bacteria showed evidence of a process of intracellular bacterial survival. Nuclei of human cells are indicated by n (black or white). Note some cells carrying a large number of bacteria that nearly fill the cytoplasmic space. Survival of these cells would be unlikely. Inset: a further example from another area. (B) Transverse cut through a biological prosthesis infected with <i>Staphylococcus aureus</i> (patient 5). Monocytes cluttered with numerous viable bacteria show evidence of a process in which bacteria escape from a phagocytic vacuole into the cytoplasm; the plasma membrane of some cells is partially disrupted (white arrows), indicating cell death and release of bacterial cargo. Nuclei of monocytes showing intact plasma membrane are indicated by n (black), and the nucleus of a heavily damaged immune cell is indicated by n (white); arrowheads denote phagosomes with intact (black) and disrupted membranes (white); white arrows indicate disrupted plasma membranes. Insets: further examples from another area. (C-E, patient 3) 3View-SEM 3D-reconstruction of a 11.2 μm x 13.3 μm x 3.2 μm (xyz) block at 10 nm x 10 nm x 50 nm (xyz) resolution showing two cells cluttered with numerous viable bacteria (yellow); yellow = bacteria, green = cell membrane. (F-H, patient 5) 3View-SEM 3D-reconstruction of a 24.6 μm x 19.2 μm x 5.7 μm (xyz) block at 10 nm x 10 nm x 50 nm (xyz) resolution showing a monocyte cluttered with numerous viable bacteria (yellow); note that the plasma membrane is partially disrupted (arrows), indicating death of the cell. In addition, several bacteria are located within the extracellular space (red); yellow = bacteria, green = cell membrane, blue = nucleus. (I-K, patient 5) High resolution (2.5 nm x 2.5 nm x 5 nm (xyz)); (F) the nucleus of the cell is highly fragmented as is typical for neutrophilic granulocytes.</p

Clinical characteristics.

<p>Clinical characteristics.</p