Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India

Uttar Pradesh is the densely populated state of India and is the sixth highest COVID-19 affected state with 22,904 deaths recorded on November 12, 2021. Whole-genome sequencing (WGS) is being used as a potential approach to investigate genomic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. In this study, a total of 87 SARS-CoV-2 genomes−49 genomes from the first wave (March 2020 to February 2021) and 38 genomes from the second wave (March 2021 to July 2021) from Eastern Uttar Pradesh (E-UP) were sequenced and analyzed to understand its evolutionary pattern and variants against publicaly available sequences. The complete genome analysis of SARS-CoV-2 during the first wave in E-UP largely reported transmission of G, GR, and GH clades with specific mutations. In contrast, variants of concerns (VOCs) such as Delta (71.0%) followed by Delta AY.1 (21.05%) and Kappa (7.9%) lineages belong to G clade with prominent signature amino acids were introduced in the second wave. Signature substitution at positions S:L452R, S:P681R, and S:D614G were commonly detected in the Delta, Delta AY.1, and Kappa variants whereas S:T19R and S:T478K were confined to Delta and Delta AY.1 variants only. Vaccine breakthrough infections showed unique mutational changes at position S:D574Y in the case of the Delta variant, whereas position S:T95 was conserved among Kappa variants compared to the Wuhan isolate. During the transition from the first to second waves, a shift in the predominant clade from GH to G clade was observed. The identified spike protein mutations in the SARS-CoV-2 genome could be used as the potential target for vaccine and drug development to combat the effects of the COVID-19 disease.

Did Sgr cause the vertical waves in the solar neighbourhood?

ABSTRACT The vertical distribution of stars in the solar neighbourhood is not in equilibrium but contains a wave signature in both density and velocity space originating from a perturbation. With the discovery of the phase-space spiral in Gaia data release (DR) 2, determining the origin of this perturbation has become even more urgent. We develop and test a fast method for calculating the perturbation from a passing satellite on the vertical component of a part of a disc galaxy. This fast method allows us to test a large variety of possible perturbations to the vertical disc very quickly. We apply our method to the range of possible perturbations to the solar neighbourhood stemming from the recent passage of the Sagittarius dwarf galaxy (Sgr), varying its mass, mass profile, and present-day position within their observational uncertainties, and its orbit within different realistic models for the Milky Way’s gravitational potential. We find that we are unable to reproduce the observed asymmetry in the vertical number counts and its concomitant breathing mode in velocity space for any plausible combination of Sgr and Milky Way properties. In all cases, either the amplitude or the perturbation wavelength of the number-count asymmetry and of the oscillations in the mean vertical velocity produced by the passage of Sgr are in large disagreement with the observations from Gaia DR2. We conclude that Sgr cannot have caused the observed oscillations in the vertical disc or the Gaia phase-space spiral.

Impact of quark deconfinement in neutron star mergers and hybrid star mergers

We describe an unambiguous gravitational-wave signature to identify the occurrence of a strong phase transition from hadronic matter to deconfined quark matter in neutron star mergers. Such a phase transition leads to a strong softening of the equation of state and hence to more compact merger remnants compared to purely hadronic models. If a phase transition takes place during merging, this results in a characteristic increase of the dominant postmerger gravitational-wave frequency relative to the tidal deformability characterizing the inspiral phase. By comparing results from different purely hadronic and hybrid models we show that a strong phase transition can be identified from a single, simultaneous measurement of pre- and postmerger gravitational waves. Furthermore, we present new results for hybrid star mergers, which contain quark matter already during the inspiral stage. Also for these systems we find that the postmerger GW frequency is increased compared to purely hadronic models. We thus conclude that also hybrid star mergers with an onset of the hadron-quark phase transition at relatively low densities may lead to the very same characteristic signature of quark deconfinement in the postmerger GW signal as systems undergoing the phase transition during merging.

Spin characterization of systematics in CMB surveys – a comprehensive formalism

ABSTRACT The CMB B-mode polarization signal – both the primordial gravitational wave signature and the signal sourced by lensing – is subject to many contaminants from systematic effects. Of particular concern are systematics that result in mixing of signals of different ‘spin’, particularly leakage from the much larger spin-0 intensity signal to the spin-2 polarization signal. We present a general formalism, which can be applied to arbitrary focal plane setups, that characterizes signals in terms of their spin. We provide general expressions to describe how spin-coupled signals observed by the detectors manifest at map-level, in the harmonic domain, and in the power spectra, focusing on the polarization spectra – the signals of interest for upcoming CMB surveys. We demonstrate the presence of a previously unidentified cross-term between the systematic and the intrinsic sky signal in the power spectrum, which in some cases can be the dominant source of contamination. The formalism is not restricted to intensity to polarization leakage but provides a complete elucidation of all leakage including polarization mixing, and applies to both full and partial (masked) sky surveys, thus covering space-based, balloon-borne, and ground-based experiments. Using a pair-differenced setup, we demonstrate the formalism by using it to completely characterize the effects of differential gain and pointing systematics, incorporating both intensity leakage and polarization mixing. We validate our results with full time ordered data simulations. Finally, we show in an Appendix that an extension of simple binning map-making to include additional spin information is capable of removing spin-coupled systematics during the map-making process.