Genome Characterization of a Novel Wastewater Bacteroides fragilis Bacteriophage (vB_BfrS_23) and its Host GB124

Bacteroides spp. are part of the human intestinal microbiota but can under some circumstances become clinical pathogens. Phages are a potentially valuable therapeutic treatment option for many pathogens, but phage therapy for pathogenic Bacteroides spp. including Bacteroides fragilis is currently limited to three genome-sequenced phages. Here we describe the isolation from sewage wastewater and genome of a lytic phage, vB_BfrS_23, that infects and kills B. fragilis strain GB124. Transmission electron microscopy identified this phage as a member of the Siphoviridae family. The phage is stable when held at temperatures of 4 and 60°C for 1 h. It has a very narrow host range, only infecting one host from a panel of B. fragilis strains (n = 8). Whole-genome sequence analyses of vB_BfrS_23 determined it is double-stranded DNA phage and is circularly permuted, with a genome of 48,011 bp. The genome encodes 73 putative open reading frames. We also sequenced the host bacterium, B. fragilis GB124 (5.1 Mb), which has two plasmids of 43,923 and 4,138 bp. Although this phage is host specific, its isolation together with the detailed characterization of the host B. fragilis GB124 featured in this study represent a useful starting point from which to facilitate the future development of highly specific therapeutic agents. Furthermore, the phage could be a novel tool in determining water (and water reuse) treatment efficacy, and for identifying human fecal transmission pathways within contaminated environmental waters and foodstuffs

Multispacecraft current estimates at swarm

During the first several months of the three-spacecraft Swarm mission all three spacecraft camerepeatedly into close alignment, providing an ideal opportunity for validating the proposed dual-spacecraftmethod for estimating current density from the Swarm magnetic field data. Two of the Swarm spacecraftregularly fly side-by-side in closely similar orbits, while the third at times approaches the other two. Thisprovides a data set which under certain assumptions of stationarity of the magnetic field can produce 2, 3, 4,5 (or more) point measurements, which can be cross compared. We find that at low Earth orbit the use oftime-shifted positions allow stable estimates of current density to be made and can verify temporal effects aswell as validating the interpretation of the current components as arising predominantly from field-alignedcurrents. In the case of four-spacecraft configurations we can resolve the full vector current and therefore cancheck the perpendicular as well as parallel current density components directly, together with the qualityfactor for the estimates directly (for the first time in situ at low Earth orbit)

Identification and Characterization of Two Novel Viruses in Ocular Infections in Reindeer

A thorough understanding of virus diversity in wildlife provides epidemiological baseline information about pathogens. In this study, eye swab samples were obtained from semi-domesticated reindeer (Rangifer tarandus tarandus) in Norway during an outbreak of infectious eye disease, possibly a very early stage of infectious keratoconjunctivitis (IKC). Large scale molecular virus screening, based on host nucleic acid depletion, sequence-independen

Robotic Ultrasound Guidance by B-scan Plane Positioning Control

AbstractUltrasound is indispensable imaging modality for clinical diagnosis such as fetus assessment and heart assessment. Moreover, many ultrasound applications for image guided procedures have been proposed and attempted because US is less invasive, less cost, and high portability. However, to obtain US images, a US imaging probe has to be held manually and contacted with a patient body. To address the issue, we have proposed a robotic system for automatic probe scanning. The system consists of a probe scanning robot, navigation software, an optical tracking device, and an ultrasound imaging device. The robot, that is six degrees of freedom, is composed of a frame mechanism and a probe holding mechanism. The frame mechanism has six pneumatic actuators to reduce its weight, and the probe holding mechanism has one DC motor. The probe holding mechanism is connected with the pneumatic actuators using wires. Moreover, the robot can control the position and orientation of the B-scan plane based on the transformation between an optical tracker attached to the US probe and the B-scan plane. The navigation system, which is connected with the tracking device and an US imaging device via a VGA cable, computes the relative position between the positions of a therapeutic tool and the B-scan plane, and sends it to the robot. Then the position of the B-scan plane can be controlled based on the tool position. Also, the navigation system displays the plane with a texture of an actual echogram and a tool model three-dimensionally to monitor the relative position of the tool and the B-scan plane. To validate the basic system performance, phantom tests were conducted. The phantom was made of gelatin and poly(ethylene glycol). In the tests, the needle was inserted into the phantom, and the B-scan plane was controlled to contain a tracked needle in real-time. From the results, the needle was continuously visualized during needle insertion. Therefore, it is confirmed that the system has a great potential for automatic US image guided procedures

SARS-CoV-2 ORF8 accessory protein is a virulence factor

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encodes six accessory proteins (3a, 6, 7a, 7b, 8, and 9b) for which limited information is available on their role in pathogenesis. We showed that the deletion of open reading frames (ORFs) 6, 7a, or 7b individually did not significantly impact viral pathogenicity in humanized K18-hACE2 transgenic mice. In contrast, the deletion of ORF8 partially attenuated SARS-CoV-2, resulting in reduced lung pathology and 40% less mortality, indicating that ORF8 is a critical determinant of SARS-CoV-2 pathogenesis. Attenuation of SARS-CoV-2-∆8 was not associated with a significant decrease in replication either in the lungs of mice or in organoid-derived human airway cells. An increase in the interferon signaling at early times post-infection (1 dpi) in the lungs of mice and a decrease in the pro-inflammatory and interferon response at late times post-infection, both in the lungs of mice (6 dpi) and in organoid-derived human airway cells [72 hours post-infection (hpi)], were observed. The early, but not prolonged, interferon response along with the lower inflammatory response could explain the partial attenuation of SARS-CoV-∆8. The presence of ORF8 in SARS-CoV-2 was associated with an increase in the number of macrophages in the lungs of mice. In addition, the supernatant of SARS-CoV-2-WT (wild-type)-infected organoid-derived cells enhanced the activation of macrophages as compared to SARS-CoV-2-∆8-infected cells. These results show that ORF8 is a virulence factor involved in inflammation that could be targeted in COVID-19 therapies. IMPORTANCE The relevance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ORF8 in the pathogenesis of COVID-19 is unclear. Virus natural isolates with deletions in ORF8 were associated with wild milder disease, suggesting that ORF8 might contribute to SARS-CoV-2 virulence. This manuscript shows that ORF8 is involved in inflammation and in the activation of macrophages in two experimental systems: humanized K18-hACE2 transgenic mice and organoid-derived human airway cells. These results identify ORF8 protein as a potential target for COVID-19 therapies.</p

SARS-CoV-2 ORF8 accessory protein is a virulence factor

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encodes six accessory proteins (3a, 6, 7a, 7b, 8, and 9b) for which limited information is available on their role in pathogenesis. We showed that the deletion of open reading frames (ORFs) 6, 7a, or 7b individually did not significantly impact viral pathogenicity in humanized K18-hACE2 transgenic mice. In contrast, the deletion of ORF8 partially attenuated SARS-CoV-2, resulting in reduced lung pathology and 40% less mortality, indicating that ORF8 is a critical determinant of SARS-CoV-2 pathogenesis. Attenuation of SARS-CoV-2-∆8 was not associated with a significant decrease in replication either in the lungs of mice or in organoid-derived human airway cells. An increase in the interferon signaling at early times post-infection (1 dpi) in the lungs of mice and a decrease in the pro-inflammatory and interferon response at late times post-infection, both in the lungs of mice (6 dpi) and in organoid-derived human airway cells [72 hours post-infection (hpi)], were observed. The early, but not prolonged, interferon response along with the lower inflammatory response could explain the partial attenuation of SARS-CoV-∆8. The presence of ORF8 in SARS-CoV-2 was associated with an increase in the number of macrophages in the lungs of mice. In addition, the supernatant of SARS-CoV-2-WT (wild-type)-infected organoid-derived cells enhanced the activation of macrophages as compared to SARS-CoV-2-∆8-infected cells. These results show that ORF8 is a virulence factor involved in inflammation that could be targeted in COVID-19 therapies. IMPORTANCE The relevance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ORF8 in the pathogenesis of COVID-19 is unclear. Virus natural isolates with deletions in ORF8 were associated with wild milder disease, suggesting that ORF8 might contribute to SARS-CoV-2 virulence. This manuscript shows that ORF8 is involved in inflammation and in the activation of macrophages in two experimental systems: humanized K18-hACE2 transgenic mice and organoid-derived human airway cells. These results identify ORF8 protein as a potential target for COVID-19 therapies.</p

Specific serology for emerging human coronaviruses by protein microarray

We present a serological assay for the specific detection of IgM and IgG antibodies against the emerging human coronavirus hCoV-EMC and the SARS-CoV based on protein microarray technology. The assay uses the S1 receptor-binding subunit of the spike protein of hCoV-EMC and SARS-CoV as antigens. The assay has been validated extensively using putative cross-reacting sera of patient cohorts exposed to the four common hCoVs and sera from convalescent patients infected with hCoV-EMC or SARS-CoV