The continued epidemic threat of SARS-CoV-2 and implications for the future of global public health

A new coronavirus (CoV) called SARS-CoV-2 emerged in Wuhan, China in December 2019 as the etiological agent of a viral pneumonia called COVID-19. The global spread of SARS-CoV-2 has been so extensive that the WHO declared COVID-19 a pandemic on March 11, 2020. Below, we discuss the emergence of SARS-CoV-2 and provide the historical context, which strongly suggests emerging CoVs provide an immediate threat to global public health and will continue to do so in the future

Evidence Supporting a Zoonotic Origin of Human Coronavirus Strain NL63

The relationship between bats and coronaviruses (CoVs) has received considerable attention since the severe acute respiratory syndrome (SARS)-like CoV was identified in the Chinese horseshoe bat (Rhinolophidae) in 2005. Since then, several bats throughout the world have been shown to shed CoV sequences, and presumably CoVs, in the feces; however, no bat CoVs have been isolated from nature. Moreover, there are very few bat cell lines or reagents available for investigating CoV replication in bat cells or for isolating bat CoVs adapted to specific bat species. Here, we show by molecular clock analysis that alphacoronavirus (α-CoV) sequences derived from the North American tricolored bat (Perimyotis subflavus) are predicted to share common ancestry with human CoV (HCoV)-NL63, with the most recent common ancestor between these viruses occurring approximately 563 to 822 years ago. Further, we developed immortalized bat cell lines from the lungs of this bat species to determine if these cells were capable of supporting infection with HCoVs. While SARS-CoV, mouse-adapted SARS-CoV (MA15), and chimeric SARS-CoVs bearing the spike genes of early human strains replicated inefficiently, HCoV-NL63 replicated for multiple passages in the immortalized lung cells from this bat species. These observations support the hypothesis that human CoVs are capable of establishing zoonotic-reverse zoonotic transmission cycles that may allow some CoVs to readily circulate and exchange genetic material between strains found in bats and other mammals, including humans

The dark energy spectrometer - A potential multi-fiber instrument for the Blanco 4-meter telescope

We describe the preliminary design of the Dark Energy Spectrometer (DESpec), a fiber-fed spectroscopic instrument concept for the Blanco 4-meter telescope at Cerro Tololo Inter-American Observatory (CTIO). DESpec would take advantage of the infrastructure recently deployed for the Dark Energy Camera (DECam). DESpec would be mounted in the new DECam prime focus cage, would be interchangeable with DECam, would share the DECam optical corrector, and would feature a focal plane with ∼4000 robotically positioned optical fibers feeding multiple high-throughput spectrometers. The instrument would have a field of view of 3.8 square degrees, a wavelength range of approximately 500<λ<1000 nm, and a spectral resolution of R∼3000. DESpec would provide a powerful spectroscopic follow-up system for sources in the Southern hemisphere discovered by the Dark Energy Survey and LSST

Properties of Type Ia supernovae inside rich galaxy clusters

We used the Gaussian Mixture Brightest Cluster Galaxy catalogue and Sloan Digital Sky Survey-II supernovae data with redshifts measured by the Baryon Oscillation Spectroscopic Survey to identify 48 Type Ia supernovae (SNe Ia) residing in rich galaxy clusters and compare their properties with 1015 SNe Ia in the field. Their light curves were parametrized by the SALT2 model and the significance of the observed differences was assessed by a resampling technique. To test our samples and methods, we first looked for known differences between SNe Ia residing in active and passive galaxies. We confirm that passive galaxies host SNe Ia with smaller stretch, weaker colour–luminosity relation [β of 2.54(22) against 3.35(14)], and that are ∼0.1 mag more luminous after stretch and colour corrections. We show that only 0.02 per cent of random samples drawn from our set of SNe Ia in active galaxies can reach these values. Reported differences in the Hubble residuals scatter could not be detected, possibly due to the exclusion of outliers. We then show that, while most field and cluster SNe Ia properties are compatible at the current level, their stretch distributions are different (∼3σ): besides having a higher concentration of passive galaxies than the field, the cluster’s passive galaxies host SNe Ia with an average stretch even smaller than those in field passive galaxies (at 95 per cent confidence).We argue that the older age of passive galaxies in clusters is responsible for this effect since, as we show, old passive galaxies host SNe Ia with smaller stretch than young passive galaxies (∼4σ).Web of Scienc

Type Ia Supernova Properties as a Function of the Distance to the Host Galaxy in the SDSS-II SN Survey

We use type-Ia supernovae (SNe Ia) discovered by the SDSS-II SN Survey to search for dependencies between SN Ia properties and the projected distance to the host galaxy center, using the distance as a proxy for local galaxy properties (local star-formation rate, local metallicity, etc.). The sample consists of almost 200 spectroscopically or photometrically confirmed SNe Ia at redshifts below 0.25. The sample is split into two groups depending on the morphology of the host galaxy. We fit light-curves using both MLCS2k2 and SALT2, and determine color (AV, c) and light-curve shape (delta, x1) parameters for each SN Ia, as well as its residual in the Hubble diagram. We then correlate these parameters with both the physical and the normalized distances to the center of the host galaxy and look for trends in the mean values and scatters of these parameters with increasing distance. The most significant (at the 4-sigma level) finding is that the average fitted AV from MLCS2k2 and c from SALT2 decrease with the projected distance for SNe Ia in spiral galaxies. We also find indications that SNe in elliptical galaxies tend to have narrower light-curves if they explode at larger distances, although this may be due to selection effects in our sample. We do not find strong correlations between the residuals of the distance moduli with respect to the Hubble flow and the galactocentric distances, which indicates a limited correlation between SN magnitudes after standardization and local host metallicity.Comment: Accepted for publication in The Astrophysical Journal (33 pages, 5 figures, 8 tables

Escape from human monoclonal antibody neutralization affects in vitro and in vivo fitness of severe acute respiratory syndrome coronavirus

Background. Severe acute respiratory syndrome (SARS) emerged as a human disease in 2002. Detailed phylogenetic analysis and epidemiologic studies have suggested that the SARS Coronavirus (SARS-CoV) originated from animals. The spike (S) glycoprotein has been identified as a major target of protective immunity and contains ≥3 regions that are targeted by neutralizing antibodies in the S1 and S2 domains. We previously characterized a panel of neutralizing human monoclonal antibodies (MAbs), but the majority of epitopes recognized by the MAbs remain unknown. Methods. In the present study, we generated neutralization escape mutants and studied the effect of these neutralization escape mutations on human and animal receptor usage as well as on in vitro and in vivo fitness. Results. Distinct but partially overlapping sets of amino acids were identified that are critical to the binding of MAbs with differential neutralization profiles. We also identified possible interactions between the S1 and S2 domains of the SARS-CoV S glycoprotein. Finally, we showed that escape from neutralization usually attenuates SARS-CoV infection. Conclusions. These data provide a mechanism for overcoming neutralization escape by use of broadly crossreactive cocktails of cross-neutralizing MAbs that recognize residues within the receptor-binding domain that are critical for virus replication and virulence

A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses

ABSTRACT Several biosafety level 3 and/or 4 (BSL-3/4) pathogens are high-consequence, single-stranded RNA viruses, and their genomes, when introduced into permissive cells, are infectious. Moreover, many of these viruses are select agents (SAs), and their genomes are also considered SAs. For this reason, cDNAs and/or their derivatives must be tested to ensure the absence of infectious virus and/or viral RNA before transfer out of the BSL-3/4 and/or SA laboratory. This tremendously limits the capacity to conduct viral genomic research, particularly the application of next-generation sequencing (NGS). Here, we present a sequence-independent method to rapidly amplify viral genomic RNA while simultaneously abolishing both viral and genomic RNA infectivity across multiple single-stranded positive-sense RNA (ssRNA+) virus families. The process generates barcoded DNA amplicons that range in length from 300 to 1,000 bp, which cannot be used to rescue a virus and are stable to transport at room temperature. Our barcoding approach allows for up to 288 barcoded samples to be pooled into a single library and run across various NGS platforms without potential reconstitution of the viral genome. Our data demonstrate that this approach provides full-length genomic sequence information not only from high-titer virion preparations but it can also recover specific viral sequence from samples with limited starting material in the background of cellular RNA, and it can be used to identify pathogens from unknown samples. In summary, we describe a rapid, universal standard operating procedure that generates high-quality NGS libraries free of infectious virus and infectious viral RNA. IMPORTANCE This report establishes and validates a standard operating procedure (SOP) for select agents (SAs) and other biosafety level 3 and/or 4 (BSL-3/4) RNA viruses to rapidly generate noninfectious, barcoded cDNA amenable for next-generation sequencing (NGS). This eliminates the burden of testing all processed samples derived from high-consequence pathogens prior to transfer from high-containment laboratories to lower-containment facilities for sequencing. Our established protocol can be scaled up for high-throughput sequencing of hundreds of samples simultaneously, which can dramatically reduce the cost and effort required for NGS library construction. NGS data from this SOP can provide complete genome coverage from viral stocks and can also detect virus-specific reads from limited starting material. Our data suggest that the procedure can be implemented and easily validated by institutional biosafety committees across research laboratories

The WiggleZ Dark Energy Survey: Survey Design and First Data Release

The WiggleZ Dark Energy Survey is a survey of 240,000 emission line galaxies in the distant universe, measured with the AAOmega spectrograph on the 3.9-m Anglo-Australian Telescope (AAT). The target galaxies are selected using ultraviolet photometry from the GALEX satellite, with a flux limit of NUV<22.8 mag. The redshift range containing 90% of the galaxies is 0.2<z<1.0. The primary aim of the survey is to precisely measure the scale of baryon acoustic oscillations (BAO) imprinted on the spatial distribution of these galaxies at look-back times of 4-8 Gyrs. Detailed forecasts indicate the survey will measure the BAO scale to better than 2% and the tangential and radial acoustic wave scales to approximately 3% and 5%, respectively. This paper provides a detailed description of the survey and its design, as well as the spectroscopic observations, data reduction, and redshift measurement techniques employed. It also presents an analysis of the properties of the target galaxies, including emission line diagnostics which show that they are mostly extreme starburst galaxies, and Hubble Space Telescope images, which show they contain a high fraction of interacting or distorted systems. In conjunction with this paper, we make a public data release of data for the first 100,000 galaxies measured for the project.Comment: Accepted by MNRAS; this has some figures in low resolution format. Full resolution PDF version (7MB) available at http://www.physics.uq.edu.au/people/mjd/pub/wigglez1.pdf The WiggleZ home page is at http://wigglez.swin.edu.au

The Sloan Digital Sky Survey Quasar Catalog I. Early Data Release

We present the first edition of the Sloan Digital Sky Survey (SDSS) Quasar Catalog. The catalog consists of the 3814 objects (3000 discovered by the SDSS) in the initial SDSS public data release that have at least one emission line with a full width at half maximum larger than 1000 km/s, luminosities brighter than M_i^* = -23, and highly reliable redshifts. The area covered by the catalog is 494 square degrees; the majority of the objects were found in SDSS commissioning data using a multicolor selection technique. The quasar redshifts range from 0.15 to 5.03. For each object the catalog presents positions accurate to better than 0.2" rms per coordinate, five band (ugriz) CCD-based photometry with typical accuracy of 0.05 mag, radio and X-ray emission properties, and information on the morphology and selection method. Calibrated spectra of all objects in the catalog, covering the wavelength region 3800 to 9200 Angstroms at a spectral resolution of 1800-2100, are also available. Since the quasars were selected during the commissioning period, a time when the quasar selection algorithm was undergoing frequent revisions, the sample is not homogeneous and is not intended for statistical analysis.Comment: 27 pages, 4 figures, 4 tables, accepted by A