A Comparison of Whole Genome Sequencing of SARS-CoV-2 Using Amplicon-Based Sequencing, Random Hexamers, and Bait Capture.

Genome sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is increasingly important to monitor the transmission and adaptive evolution of the virus. The accessibility of high-throughput methods and polymerase chain reaction (PCR) has facilitated a growing ecosystem of protocols. Two differing protocols are tiling multiplex PCR and bait capture enrichment. Each method has advantages and disadvantages but a direct comparison with different viral RNA concentrations has not been performed to assess the performance of these approaches. Here we compare Liverpool amplification, ARTIC amplification, and bait capture using clinical diagnostics samples. All libraries were sequenced using an Illumina MiniSeq with data analyzed using a standardized bioinformatics workflow (SARS-CoV-2 Illumina GeNome Assembly Line; SIGNAL). One sample showed poor SARS-CoV-2 genome coverage and consensus, reflective of low viral RNA concentration. In contrast, the second sample had a higher viral RNA concentration, which yielded good genome coverage and consensus. ARTIC amplification showed the highest depth of coverage results for both samples, suggesting this protocol is effective for low concentrations. Liverpool amplification provided a more even read coverage of the SARS-CoV-2 genome, but at a lower depth of coverage. Bait capture enrichment of SARS-CoV-2 cDNA provided results on par with amplification. While only two clinical samples were examined in this comparative analysis, both the Liverpool and ARTIC amplification methods showed differing efficacy for high and low concentration samples. In addition, amplification-free bait capture enriched sequencing of cDNA is a viable method for generating a SARS-CoV-2 genome sequence and for identification of amplification artifacts.

Transverse Velocities with the Moving Lens Effect.

Gravitational potentials that change in time induce fluctuations in the observed cosmic microwave background (CMB) temperature. Cosmological structure moving transverse to our line of sight provides a specific example known as the moving lens effect. Here, we explore how the observed CMB temperature fluctuations, combined with the observed matter overdensity, can be used to infer the transverse velocity of cosmological structures on large scales. We show that near-future CMB surveys and galaxy surveys will have the statistical power to make a first detection of the moving lens effect, and we discuss applications for the reconstructed transverse velocity.

Detecting Patchy Reionization in the Cosmic Microwave Background.

Upcoming cosmic microwave background (CMB) experiments will measure temperature fluctuations on small angular scales with unprecedented precision. Small-scale CMB fluctuations are a mixture of late-time effects: gravitational lensing, Doppler shifting of CMB photons by moving electrons [the kinematic Sunyaev-Zel'dovich (KSZ) effect], and residual foregrounds. We propose a new statistic which separates the KSZ signal from the others, and also allows the KSZ signal to be decomposed in redshift bins. The decomposition extends to high redshift and does not require external data sets such as galaxy surveys. In particular, the high-redshift signal from patchy reionization can be cleanly isolated, enabling future CMB experiments to make high-significance and qualitatively new measurements of the reionization era.

Quantifying the BICEP2-Planck tension over gravitational waves.

The recent BICEP2 measurement of B-mode polarization in the cosmic microwave background (r = 0.2(-0.05)(+0.07)), a possible indication of primordial gravity waves, appears to be in tension with the upper limit from WMAP (r < 0.13 at 95% C.L.) and Planck (r < 0.11 at 95% C.L.). We carefully quantify the level of tension and show that it is very significant (around 0.1% unlikely) when the observed deficit of large-scale temperature power is taken into account. We show that measurements of TE and EE power spectra in the near future will discriminate between the hypotheses that this tension is either a statistical fluke or a sign of new physics. We also discuss extensions of the standard cosmological model that relieve the tension and some novel ways to constrain them.

Universal bound on N-point correlations from inflation.

Models of inflation in which non-Gaussianity is generated outside the horizon, such as curvaton models, generate distinctive higher-order correlation functions in the cosmic microwave background and other cosmological observables. Testing for violation of the Suyama-Yamaguchi inequality τ(NL) ≥ (6/5f (NL))(2), where f(NL) and f(NL) denote the amplitude of the three-point and four-point functions in certain limits, has been proposed as a way to distinguish qualitative classes of models. This inequality has been proved for a wide range of models, but only weaker versions have been proved in general. In this Letter, we give a proof that the Suyama-Yamaguchi inequality is always satisfied. We discuss scenarios in which the inequality may appear to be violated in an experiment such as Planck and how this apparent violation should be interpreted.