Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

Background The first epidemic wave of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Scotland resulted in high case numbers and mortality in care homes. In Lothian, over one-third of care homes reported an outbreak, while there was limited testing of hospital patients discharged to care homes. Aim To investigate patients discharged from hospitals as a source of SARS-CoV-2 introduction into care homes during the first epidemic wave. Methods A clinical review was performed for all patients discharges from hospitals to care homes from 1st March 2020 to 31st May 2020. Episodes were ruled out based on coronavirus disease 2019 (COVID-19) test history, clinical assessment at discharge, whole-genome sequencing (WGS) data and an infectious period of 14 days. Clinical samples were processed for WGS, and consensus genomes generated were used for analysis using Cluster Investigation and Virus Epidemiological Tool software. Patient timelines were obtained using electronic hospital records. Findings In total, 787 patients discharged from hospitals to care homes were identified. Of these, 776 (99%) were ruled out for subsequent introduction of SARS-CoV-2 into care homes. However, for 10 episodes, the results were inconclusive as there was low genomic diversity in consensus genomes or no sequencing data were available. Only one discharge episode had a genomic, time and location link to positive cases during hospital admission, leading to 10 positive cases in their care home. Conclusion The majority of patients discharged from hospitals were ruled out for introduction of SARS-CoV-2 into care homes, highlighting the importance of screening all new admissions when faced with a novel emerging virus and no available vaccine

Passive seismic source localization via common-reflection-surface attributes

The common-reflection-surface (CRS) stack can be viewed as a physically justified extension of the classical common-midpoint (CMP) stack, utilizing redundant information not only in a single, but in several neighboring CMP gathers. The zero-offset CRS moveout is parameterized in terms of kinematic attributes, which utilize reciprocity and raypath symmetries to describe the two-way process of the actual wave propagation in active seismic experiments by the propagation of auxiliary one-way wavefronts. For the diffraction case, only the attributes of a single one-way wavefront, originating from the diffractor are sufficient to explain the traveltime differences observed at the surface. While paraxial ray theory gives rise to a second-order approximation of the CRS traveltime, many higher-order approximations were subsequently introduced either by squaring the second-order expression or by employing principles of optics and geometry. It was recently discovered that all of these higher-order operators can be formulated either for the optical projection or in an auxiliary medium of a constant effective velocity. Utilizing this duality and the one-way nature of the CRS parameters, we present a simple data-driven stacking scheme that allows for the estimation of the a priori unknown excitation time of a passive seismic source. In addition, we demonstrate with a simple data example that the output of the suggested workflow can directly be used for subsequent focusing-based normal-incidence-point (NIP) tomography, leading to a reliable localization in depth