MHC class II proteins mediate cross-species entry of bat influenza viruses.

Zoonotic influenza A viruses of avian origin can cause severe disease in individuals, or even global pandemics, and thus pose a threat to human populations. Waterfowl and shorebirds are believed to be the reservoir for all influenza A viruses, but this has recently been challenged by the identification of novel influenza A viruses in bats1,2. The major bat influenza A virus envelope glycoprotein, haemagglutinin, does not bind the canonical influenza A virus receptor, sialic acid or any other glycan1,3,4, despite its high sequence and structural homology with conventional haemagglutinins. This functionally uncharacterized plasticity of the bat influenza A virus haemagglutinin means the tropism and zoonotic potential of these viruses has not been fully determined. Here we show, using transcriptomic profiling of susceptible versus non-susceptible cells in combination with genome-wide CRISPR-Cas9 screening, that the major histocompatibility complex class II (MHC-II) human leukocyte antigen DR isotype (HLA-DR) is an essential entry determinant for bat influenza A viruses. Genetic ablation of the HLA-DR α-chain rendered cells resistant to infection by bat influenza A virus, whereas ectopic expression of the HLA-DR complex in non-susceptible cells conferred susceptibility. Expression of MHC-II from different bat species, pigs, mice or chickens also conferred susceptibility to infection. Notably, the infection of mice with bat influenza A virus resulted in robust virus replication in the upper respiratory tract, whereas mice deficient for MHC-II were resistant. Collectively, our data identify MHC-II as a crucial entry mediator for bat influenza A viruses in multiple species, which permits a broad vertebrate tropism.

A perfect X-ray beam splitter and its applications to time-domain interferometry and quantum optics exploiting free-electron lasers.

X-ray free-electron lasers (FELs) deliver ultrabright X-ray pulses, but not the sequences of phase-coherent pulses required for time-domain interferometry and control of quantum states. For conventional split-and-delay schemes to produce such sequences, the challenge stems from extreme stability requirements when splitting Ångstrom wavelength beams, where the tiniest path-length differences introduce phase jitter. We describe an FEL mode based on selective electron-bunch degradation and transverse beam shaping in the accelerator, combined with a self-seeded photon emission scheme. Instead of splitting the photon pulses after their generation by the FEL, we split the electron bunch in the accelerator, prior to photon generation, to obtain phase-locked X-ray pulses with subfemtosecond duration. Time-domain interferometry becomes possible, enabling the concomitant program of classical and quantum optics experiments with X-rays. The scheme leads to scientific benefits of cutting-edge FELs with attosecond and/or high-repetition rate capabilities, ranging from the X-ray analog of Fourier transform infrared spectroscopy to damage-free measurements.

Enhanced X-ray free-electron laser performance with optical klystron and helical undulators.

This article presents a demonstration of the improved performance of an X-ray free-electron laser (FEL) using the optical klystron mechanism and helical undulator configuration, in comparison with the common planar undulator configuration without optical klystron. The demonstration was carried out at Athos, the soft X-ray beamline of SwissFEL. Athos has variable-polarization undulators, and small magnetic chicanes placed between every two undulators to fully exploit the optical klystron. It was found that, for wavelengths of 1.24 nm and 3.10 nm, the required length to achieve FEL saturation is reduced by about 35% when using both the optical klystron and helical undulators, with each effect accounting for about half of the improvement. Moreover, it is shown that a helical undulator configuration provides a 20% to 50% higher pulse energy than planar undulators. This work represents an important step towards more compact and high-power FELs, rendering this key technology more efficient, affordable and accessible to the scientific community.

Millijoule Femtosecond X-Ray Pulses from an Efficient Fresh-Slice Multistage Free-Electron Laser.

We present the generation of x-ray pulses with average pulse energies up to one millijoule and rms pulse durations down to the femtosecond level. We have produced these intense and short pulses by employing the fresh-slice multistage amplification scheme with a transversely tilted electron beam in a free-electron laser. In this scheme, a short pulse is produced in the first stage and later amplified by fresh parts of the electron bunch in up to a total of four stages of amplification. Our implementation is efficient, since practically the full electron beam contributes to produce the x-ray pulse. Our implementation is also compact, utilizing only 32 m of undulator. The demonstration was done at Athos, the soft x-ray beamline of SwissFEL, which was designed with high flexibility to take full advantage of the multistage amplification scheme. It opens the door for scientific opportunities following ultrafast dynamics using nonlinear x-ray spectroscopy techniques or avoiding electronic damage when capturing structures with a single intense pulse via single-particle imaging.

Versatile modulators for laser-based FEL seeding at SwissFEL.

The Paul Scherrer Institute is implementing laser-based seeding in the soft X-ray beamline (Athos) of its free-electron laser, SwissFEL, to enhance the temporal and spectral properties of the delivered photon pulses. This technique requires, among other components, two identical modulators for coupling the electron beam with an external laser with a wavelength range between 260 and 1600 nm. The design, magnetic measurements results, alignment, operation and also details of the novel and exotic magnetic configuration of the prototype are described.

Anti-platelet factor 4 antibodies causing VITT do not cross-react with SARS-CoV-2 spike protein.

Vaccine-induced immune thrombotic thrombocytopenia (VITT) is a severe adverse effect of ChAdOx1 nCoV-19 COVID-19 vaccine (Vaxzevria) and Janssen Ad26.COV2.S COVID-19 vaccine, and it is associated with unusual thrombosis. VITT is caused by anti-platelet factor 4 (PF4) antibodies activating platelets through their FcγRIIa receptors. Antibodies that activate platelets through FcγRIIa receptors have also been identified in patients with COVID-19. These findings raise concern that vaccination-induced antibodies against anti-SARS-CoV-2 spike protein cause thrombosis by cross-reacting with PF4. Immunogenic epitopes of PF4 and SARS-CoV-2 spike protein were compared using in silico prediction tools and 3D modeling. The SARS-CoV-2 spike protein and PF4 share at least 1 similar epitope. Reactivity of purified anti-PF4 antibodies from patients with VITT was tested against recombinant SARS-CoV-2 spike protein. However, none of the affinity-purified anti-PF4 antibodies from 14 patients with VITT cross-reacted with SARS-CoV-2 spike protein. Sera from 222 polymerase chain reaction-confirmed patients with COVID-19 from 5 European centers were tested by PF4-heparin enzyme-linked immunosorbent assays and PF4-dependent platelet activation assays. We found anti-PF4 antibodies in sera from 19 (8.6%) of 222 patients with COVID-19. However, only 4 showed weak to moderate platelet activation in the presence of PF4, and none of those patients developed thrombotic complications. Among 10 (4.5%) of 222 patients who had COVID-19 with thrombosis, none showed PF4-dependent platelet-activating antibodies. In conclusion, antibodies against PF4 induced by vaccination do not cross-react with the SARS-CoV-2 spike protein, indicating that the intended vaccine-induced immune response against SARS-CoV-2 spike protein is not the trigger of VITT. PF4-reactive antibodies found in patients with COVID-19 in this study were not associated with thrombotic complications.

Airborne Disinfection by Dry Fogging Efficiently Inactivates Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Mycobacteria, and Bacterial Spores and Shows Limitations of Commercial Spore Carriers.

Airborne disinfection of high-containment facilities before maintenance or between animal studies is crucial. Commercial spore carriers (CSC) coated with 106 spores of Geobacillus stearothermophilus are often used to assess the efficacy of disinfection. We used quantitative carrier testing (QCT) procedures to compare the sensitivity of CSC with that of surrogates for nonenveloped and enveloped viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), mycobacteria, and spores, to an aerosolized mixture of peroxyacetic acid and hydrogen peroxide (aPAA-HP). We then used the QCT methodology to determine relevant process parameters to develop and validate effective disinfection protocols (≥4-log10 reduction) in various large and complex facilities. Our results demonstrate that aPAA-HP is a highly efficient procedure for airborne room disinfection. Relevant process parameters such as temperature and relative humidity can be wirelessly monitored. Furthermore, we found striking differences in inactivation efficacies against some of the tested microorganisms. Overall, we conclude that dry fogging a mixture of aPAA-HP is highly effective against a broad range of microorganisms as well as material compatible with relevant concentrations. Furthermore, CSC are artificial bioindicators with lower resistance and thus should not be used for validating airborne disinfection when microorganisms other than viruses have to be inactivated.IMPORTANCE Airborne disinfection is not only of crucial importance for the safe operation of laboratories and animal rooms where infectious agents are handled but also can be used in public health emergencies such as the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. We show that dry fogging an aerosolized mixture of peroxyacetic acid and hydrogen peroxide (aPAA-HP) is highly microbicidal, efficient, fast, robust, environmentally neutral, and a suitable airborne disinfection method. In addition, the low concentration of dispersed disinfectant, particularly for enveloped viral pathogens such as SARS-CoV-2, entails high material compatibility. For these reasons and due to the relative simplicity of the procedure, it is an ideal disinfection method for hospital wards, ambulances, public conveyances, and indoor community areas. Thus, we conclude that this method is an excellent choice for control of the current SARS-CoV-2 pandemic.

Monoclonal antibodies specific for the hemagglutinin-neuraminidase protein define neutralizing epitopes specific for Newcastle disease virus genotype 2.VII from Egypt.

BACKGROUND: Newcastle disease is a devastating disease in poultry caused by virulent Newcastle disease virus (NDV), a paramyxovirus endemic in many regions of the world despite intensive vaccination. Phylogenetic analyses reveal ongoing evolution of the predominant circulating genotype 2.VII, and the relevance of potential antigenic drift is under discussion. To investigate variation within neutralization-sensitive epitopes within the protein responsible for receptor binding, i.e. the Hemagglutinin-Neuraminidase (HN) spike protein, we were interested in establishing genotype-specific monoclonal antibodies (MAbs). METHODS: An HN-enriched fraction of a gradient-purified NDV genotype 2.VII was prepared and successfully employed to induce antibodies in BalbC mice that recognize conformationally intact sites reactive by haemagglutination inhibition (HI). For subsequent screening of mouse hybridoma cultures, an NDV-ELISA was established that utilizes Concanavalin A (ConA-ELISA) coupled glycoproteins proven to present conformation-dependent epitopes. RESULTS: Six out of nine selected MAbs were able to block receptor binding as demonstrated by HI activity. One MAb recognized an epitope only present in the homologue virus, while four other MAbs showed weak reactivity to selected other genotypes. On the other hand, one broadly cross-reacting MAb reacted with all genotypes tested and resembled the reactivity profile of genotype-specific polyclonal antibody preparations that point to minor antigenic differences between tested NDV genotpyes. CONCLUSIONS: These results point to the concurrent presence of variable and conserved epitopes within the HN molecule of NDV. The described protocol should help to generate MAbs against a variety of NDV strains and to enable in depth analysis of the antigenic profiles of different genotypes.

Performance of a SARS CoV-2 antibody ELISA based on simultaneous measurement of antibodies against the viral nucleoprotein and receptor-binding domain.

SARS CoV-2 antibody assays measure antibodies against the viral nucleoprotein (NP) or spike protein. The study examined if testing of antibodies against both antigens increases the diagnostic sensitivity. Sera (N=98) from infected individuals were tested with ELISAs based on the NP, receptor-binding domain (RBD), or both proteins. The AUROCs were 0.958 (NP), 0.991 (RBD), and 0.992 (NP/RBD). The RBD- and NP/RBD-based ELISAs showed better performance than the NP-based assay. Simultaneous testing for antibodies against NP and RBD increased the number of true and false positives. If maximum diagnostic sensitivity is required, the NP/RBD-based ELISA is preferable. Otherwise, the RBD-based ELISA is sufficient.

Demonstration of Large Bandwidth Hard X-Ray Free-Electron Laser Pulses at SwissFEL.

We have produced hard x-ray free-electron laser (FEL) radiation with unprecedented large bandwidth tunable up to 2%. The experiments have been carried out at SwissFEL, the x-ray FEL facility at the Paul Scherrer Institute in Switzerland. The bandwidth is enhanced by maximizing the energy chirp of the electron beam, which is accomplished by optimizing the compression setup. We demonstrate continuous tunability of the bandwidth with a simple method only requiring a quadrupole magnet. The generation of such broadband FEL pulses will improve the efficiency of many techniques such as x-ray crystallography and spectroscopy, opening the door to significant progress in photon science. It has already been demonstrated that the broadband pulses of SwissFEL are beneficial to enhance the performance of crystallography, and further SwissFEL users plan to exploit this large bandwidth radiation to improve the efficiency of their measurement techniques.

Isolation and characterization of new Puumala orthohantavirus strains from Germany.

Orthohantaviruses are re-emerging rodent-borne pathogens distributed all over the world. Here, we report the isolation of a Puumala orthohantavirus (PUUV) strain from bank voles caught in a highly endemic region around the city Osnabrück, north-west Germany. Coding and non-coding sequences of all three segments (S, M, and L) were determined from original lung tissue, after isolation and after additional passaging in VeroE6 cells and a bank vole-derived kidney cell line. Different single amino acid substitutions were observed in the RNA-dependent RNA polymerase (RdRP) of the two stable PUUV isolates. The PUUV strain from VeroE6 cells showed a lower titer when propagated on bank vole cells compared to VeroE6 cells. Additionally, glycoprotein precursor (GPC)-derived virus-like particles of a German PUUV sequence allowed the generation of monoclonal antibodies that allowed the reliable detection of the isolated PUUV strain in the immunofluorescence assay. In conclusion, this is the first isolation of a PUUV strain from Central Europe and the generation of glycoprotein-specific monoclonal antibodies for this PUUV isolate. The obtained virus isolate and GPC-specific antibodies are instrumental tools for future reservoir host studies.

A simple and compact scheme to enhance the brightness of self-amplified spontaneous emission free-electron-lasers.

A simple and compact scheme that enhances the brightness of self-amplified spontaneous-emission (SASE) free-electron lasers is presented. The method combines the high-brightness SASE scheme and the optical klystron concept to increase the temporal coherence of the produced radiation and to reduce the required length of the undulator beamline at the same time. The scheme is very simple and only requires compact chicanes between the modules of the undulator beamline. Simulations show that, in comparison with SASE, the brightness can be improved by up to a factor of ten and the required length to achieve saturation can be reduced by 20% or more.

The SwissFEL soft X-ray free-electron laser beamline: Athos.

The SwissFEL soft X-ray free-electron laser (FEL) beamline Athos will be ready for user operation in 2021. Its design includes a novel layout of alternating magnetic chicanes and short undulator segments. Together with the APPLE X architecture of undulators, the Athos branch can be operated in different modes producing FEL beams with unique characteristics ranging from attosecond pulse length to high-power modes. Further space has been reserved for upgrades including modulators and an external seeding laser for better timing control. All of these schemes rely on state-of-the-art technologies described in this overview. The optical transport line distributing the FEL beam to the experimental stations was designed with the whole range of beam parameters in mind. Currently two experimental stations, one for condensed matter and quantum materials research and a second one for atomic, molecular and optical physics, chemical sciences and ultrafast single-particle imaging, are being laid out such that they can profit from the unique soft X-ray pulses produced in the Athos branch in an optimal way.

Compact coherence enhancement by subharmonic self-seeding in X-ray free-electron laser facilities.

X-ray free-electron lasers (FELs) are cutting-edge scientific tools able to generate transversely coherent radiation with very high power and ultra-short pulse durations. The self-seeding mechanism has been proven to increase the longitudinal coherence of the FEL radiation but its efficiency could be significantly improved, especially for soft X-rays. This paper proposes the enhancement of the performance of self-seeding by combining it with the harmonic generation mechanism. In particular, by starting the process with a subharmonic of the wavelength of interest, the coherence of the produced radiation is improved, the undulator beamline becomes more compact, and the monochromator realization is simplified. Numerical simulations for SwissFEL are presented showing that the method can be employed, within a given space, to increase the spectral brightness by one order of magnitude or more with respect to standard self-seeding. This coherence enhancement will be fundamental for many photon science applications and techniques such as resonant inelastic X-ray scattering.

High seroprevalence of dengue virus indicates that dengue virus infections are frequent in central and eastern Sudan.

OBJECTIVES: To determine the seroprevalence of dengue in central and eastern Sudan and the breadth of neutralising antibody responses. METHODS: Blood was drawn from 483 patients with fever who visited outpatient clinics in Port Sudan, Red Sea state, in three towns in Kassala state and in El Obeid, North Kordofan, in December 2012 and January 2013. Sera were tested for dengue virus IgG and IgM by ELISA (Panbio) and sera without serologic evidence of acute infection (IgM negative) were used for the analysis of the seroprevalence. DENV neutralisation tests were performed to determine the specificity of the ELISA and to examine the degree of cross-neutralisation of multiple DENV serotypes. RESULTS: Sixty-seven per cent (302 of 448) of the sera were dengue virus IgG-positive. The seroprevalence in Port Sudan was 89% (106 of 119 sera), in Kassala 61% (128 of 209) and in North Kordofan 56.7% (68 of 120). Thirty-one of 32 ELISA-positive sera neutralised dengue viruses indicating that the ELISA was highly specific. The majority of the sera broadly neutralised all four dengue virus serotypes indicating multiple infections. CONCLUSIONS: The majority of the population in central and eastern Sudan has been infected with dengue viruses, many people repeatedly. The high seroprevalence underscores the need for extended dengue surveillance in Sudan, broad disease awareness in medical institutions and in the population and diagnostic capacity building for severe dengue infections.

Two-color operation of a free-electron laser with a tilted beam.

With the successful operation of free-electron lasers (FELs) as user facilities there has been a growing demand for experiments with two photon pulses with variable photon energy and time separation. A configuration of an undulator with variable-gap control and a delaying chicane in the middle of the beamline is proposed. An injected electron beam with a transverse tilt will only yield FEL radiation for the parts which are close to the undulator axis. This allows, after re-aligning and delaying the electron beam, a different part of the bunch to be used to produce a second FEL pulse. This method offers independent control in photon energy and delay. For the parameters of the soft X-ray beamline Athos at the SwissFEL facility the photon energy tuning range is a factor of five with an adjustable delay between the two pulses from -50 to 950 fs.

Generation of ultra-large-bandwidth X-ray free-electron-laser pulses with a transverse-gradient undulator.

A new and simple method to generate X-ray free-electron-laser radiation with unprecedented spectral bandwidth above the 10% level is presented. The broad bandwidth is achieved by sending a transversely tilted beam through a transverse-gradient undulator. The extent of the bandwidth can easily be controlled by variation of the beam tilt or the undulator gradient. Numerical simulations confirm the validity and feasibility of this method.

Undulator beamline optimization with integrated chicanes for X-ray free-electron-laser facilities.

An optimization of the undulator layout of X-ray free-electron-laser (FEL) facilities based on placing small chicanes between the undulator modules is presented. The installation of magnetic chicanes offers the following benefits with respect to state-of-the-art FEL facilities: reduction of the required undulator length to achieve FEL saturation, improvement of the longitudinal coherence of the FEL pulses, and the ability to produce shorter FEL pulses with higher power levels. Numerical simulations performed for the soft X-ray beamline of the SwissFEL facility show that optimizing the advantages of the layout requires shorter undulator modules than the standard ones. This proposal allows a very compact undulator beamline that produces fully coherent FEL pulses and it makes possible new kinds of experiments that require very short and high-power FEL pulses.

Expression of immunogenic structural proteins of cyprinid herpesvirus 3 in vitro assessed using immunofluorescence.

Cyprinid herpesvirus 3 (CyHV-3), also called koi herpesvirus (KHV), is the aetiological agent of a fatal disease in carp and koi (Cyprinus carpio L.), referred to as koi herpesvirus disease. The virus contains at least 40 structural proteins, of which few have been characterised with respect to their immunogenicity. Indirect immunofluorescence assays (IFAs) using two epitope-specific monoclonal antibodies (MAbs) were used to examine the expression kinetics of two potentially immunogenic and diagnostically relevant viral antigens, an envelope glycoprotein and a capsid-associated protein. The rate of expression of these antigens was determined following a time-course of infection in two CyHV-3 susceptible cell lines. The results were quantified using an IFA, performed in microtitre plates, and image analysis was used to analyse confocal micrographs, enabling measurement of differential virus-associated fluorescence and nucleus-associated fluorescence from stacks of captured scans. An 8-tenfold increase in capsid-associated protein expression was observed during the first 5 days post-infection compared to a ≤ 2-fold increase in glycoprotein expression. A dominant protein of ~100 kDa reacted with the capsid-associated MAb (20F10) in western blot analysis. This band was also recognised by sera obtained from carp infected with CyHV-3, indicating that this capsid-associated protein is produced in abundance during infection in vitro and is immunogenic to carp. Mass spectrometry carried out on this protein identified it as a previously uncharacterised product of open reading frame 84. This abundantly expressed and immunogenic capsid-associated antigen may be a useful candidate for KHV serological diagnostics.

Simple Method to Generate Terawatt-Attosecond X-Ray Free-Electron-Laser Pulses.

X-ray free-electron lasers (XFELs) are cutting-edge research tools that produce almost fully coherent radiation with high power and short-pulse length with applications in multiple science fields. There is a strong demand to achieve even shorter pulses and higher radiation powers than the ones obtained at state-of-the-art XFEL facilities. In this context we propose a novel method to generate terawatt-attosecond XFEL pulses, where an XFEL pulse is pushed through several short good-beam regions of the electron bunch. In addition to the elements of conventional XFEL facilities, the method uses only a multiple-slotted foil and small electron delays between undulator sections. Our scheme is thus simple, compact, and easy to implement both in already operating as well as future XFEL projects. We present numerical simulations that confirm the feasibility and validity of our proposal.