Model design for nonparametric phylodynamic inference and applications to pathogen surveillance

Inference of effective population size from genomic data can provide unique information about demographic history and, when applied to pathogen genetic data, can also provide insights into epidemiological dynamics. The combination of nonparametric models for population dynamics with molecular clock models which relate genetic data to time has enabled phylodynamic inference based on large sets of time-stamped genetic sequence data. The methodology for nonparametric inference of effective population size is well-developed in the Bayesian setting, but here we develop a frequentist approach based on nonparametric latent process models of population size dynamics. We appeal to statistical principles based on out-of-sample prediction accuracy in order to optimize parameters that control shape and smoothness of the population size over time. Our methodology is implemented in a new R package entitled mlesky. We demonstrate the flexibility and speed of this approach in a series of simulation experiments and apply the methodology to a dataset of HIV-1 in the USA. We also estimate the impact of non-pharmaceutical interventions for COVID-19 in England using thousands of SARS-CoV-2 sequences. By incorporating a measure of the strength of these interventions over time within the phylodynamic model, we estimate the impact of the first national lockdown in the UK on the epidemic reproduction number.

Pacemaker endocarditis caused by Propionibacterium acnes in an adult patient with Ebstein's anomaly: a report of a rare case

We report a rare case of a Brazilian adult woman with Ebstein's Anomaly who presented with pacemaker endocarditis caused by Propionibacterium acnes. Ebstein's Anomaly is a rare congenital malformation of the heart. Infective endocarditis is defined as an infection of heart valves, of the mural endocardium, of a septal defect, or of a cardiac electronic implantable device. Propionibacterium acnes is a skin commensal bacterium, that is usually considered as a contaminant, but can, on rare occasions, cause serious infections including endocarditis of prosthetic valves, native valves and cardiac electronic implantable devices. Diagnosis was made after nearly two years of investigation by identification of the organism by the MALDI-TOF technique and transoesophageal echocardiogram. The patient was successfully treated with daptomycin and device removal. She remains free of endocarditis after 32 months of follow-up.

Expression and secretion of Bluetongue virus serotype 8 (BTV-8)VP2 outer capsid protein by mammalian cells

VP2 is the outermost Bluetongue virus (BTV) antigenic protein, forming triskelion motifs on the virion surface. Although VP2 has been expressed successfully through many systems, its paracrine expression as a soluble form by mammalian cells represents a difficult task. In the present paper two fragments of VP2 have been expressed successfully into the medium of transiently transfected mammalian cells through a fusion peptides strategy. The crude conditioned medium containing the secreted peptide could be employed for immunodiagnostic assay development or vaccine purposes.

Double immunization strategy with a BoHV-4-vectorialized secreted chimeric peptide BVDV-E2/BoHV-1-gD

A bovine herpesvirus 4 was isolated from the milk cell fraction of a healthy cow and his full genome cloned as a bacterial artificial chromosome. So cloned viral genome was used as a vector platform to deliver in vitro and in vivo an optimized secreted chimeric peptide obtained by the fusion of the bovine viral diarrhoea virus glycoprotein E2 ectodomain with the bovine herpesvirus 1 glycoprotein D ectodomain. Recombinant virus infected cells robustly expressed and secreted the chimeric peptide into the culture medium and inoculated animals with the recombinant virus successfully responded toward antigens, gE2 and gD. Thus, this work has implications for the development of safe and effective polyvalent vaccines.

Specialized phloem parenchyma cells in Norway spruce (Pinaceae) bark are an important site of defense reactions

The bark anatomy of Norway spruce clones that were resistant or susceptible to Ceratocystis polonica, a bark-beetle-vectored fungal pathogen, was compared. The major difference concerned the axial parenchyma cells, called polyphenolic parenchyma (PP cells) because of their vacuolar deposits. The phenolic nature of the deposits was indicated by autofluorescence under blue light, and immunocytochemical studies demonstrating PP cells are enriched in phenylalanine ammonia lyase (EC 4.3.1.5), a key enzyme in phenolic synthesis. Susceptible-clone PP cells occurred as single rows filled with dense deposits. The resistant clone had 40% more PP cells, which occurred in rows two cells thick plus as individual cells scattered among the sieve cells and had lighter deposits. Trees inoculated with fungus were analyzed but a distinct fungal response could not be separated from the general wound response. In the resistant clone, phenolic bodies were reduced in size and density or disappeared completely 12 d after wounding, and PP cell size increased. The susceptible-clone phenolics and cell size changed only slightly. These data show that PP cells are active in synthesis, storage, and modification of phenolics in response to wounding, providing an important site of constitutive and inducible defenses.