Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing.

The rapid identification and isolation of infected individuals remains a key strategy for controlling the spread of SARS-CoV-2. Frequent testing of populations to detect infection early in asymptomatic or presymptomatic individuals can be a powerful tool for intercepting transmission, especially when the viral prevalence is low. However, RT-PCR testing-the gold standard of SARS-CoV-2 diagnosis-is expensive, making regular testing of every individual unfeasible. Sample pooling is one approach to lowering costs. By combining samples and testing them in groups the number of tests required is reduced, substantially lowering costs. Here we report on the implementation of pooling strategies using 3-d and 4-d hypercubes to test a professional sports team in South Africa. We have shown that infected samples can be reliably detected in groups of 27 and 81, with minimal loss of assay sensitivity for samples with individual Ct values of up to 32. We report on the automation of sample pooling, using a liquid-handling robot and an automated web interface to identify positive samples. We conclude that hypercube pooling allows for the reliable RT-PCR detection of SARS-CoV-2 infection, at significantly lower costs than lateral flow antigen (LFA) tests.

A pooled testing strategy for identifying SARS-CoV-2 at low prevalence.

Suppressing infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) will probably require the rapid identification and isolation of individuals infected with the virus on an ongoing basis. Reverse-transcription polymerase chain reaction (RT-PCR) tests are accurate but costly, which makes the regular testing of every individual expensive. These costs are a challenge for all countries around the world, but particularly for low-to-middle-income countries. Cost reductions can be achieved by pooling (or combining) subsamples and testing them in groups1-7. A balance must be struck between increasing the group size and retaining test sensitivity, as sample dilution increases the likelihood of false-negative test results for individuals with a low viral load in the sampled region at the time of the test8. Similarly, minimizing the number of tests to reduce costs must be balanced against minimizing the time that testing takes, to reduce the spread of the infection. Here we propose an algorithm for pooling subsamples based on the geometry of a hypercube that, at low prevalence, accurately identifies individuals infected with SARS-CoV-2 in a small number of tests and few rounds of testing. We discuss the optimal group size and explain why, given the highly infectious nature of the disease, largely parallel searches are preferred. We report proof-of-concept experiments in which a positive subsample was detected even when diluted 100-fold with negative subsamples (compared with 30-48-fold dilutions described in previous studies9-11). We quantify the loss of sensitivity due to dilution and discuss how it may be mitigated by the frequent re-testing of groups, for example. With the use of these methods, the cost of mass testing could be reduced by a large factor. At low prevalence, the costs decrease in rough proportion to the prevalence. Field trials of our approach are under way in Rwanda and South Africa. The use of group testing on a massive scale to monitor infection rates closely and continually in a population, along with the rapid and effective isolation of people with SARS-CoV-2 infections, provides a promising pathway towards the long-term control of coronavirus disease 2019 (COVID-19).

CPT-Symmetric Universe.

We propose that the state of the Universe does not spontaneously violate CPT. Instead, the Universe after the big bang is the CPT image of the Universe before it, both classically and quantum mechanically. The pre- and postbang epochs comprise a universe-antiuniverse pair, emerging from nothing directly into a hot, radiation-dominated era. CPT symmetry selects a unique QFT vacuum state on such a spacetime, providing a new interpretation of the cosmological baryon asymmetry, as well as a remarkably economical explanation for the cosmological dark matter. Requiring only the standard three-generation model of particle physics (with right-handed neutrinos), a Z_{2} symmetry suffices to render one of the right-handed neutrinos stable. We calculate its abundance from first principles: matching the observed dark matter density requires its mass to be 4.8×10^{8} GeV. Several other testable predictions follow: (i) the three light neutrinos are Majorana particles and allow neutrinoless double ß decay; (ii) the lightest neutrino is massless; and (iii) there are no primordial long-wavelength gravitational waves. We mention connections to the strong CP problem and the arrow of time.

No Smooth Beginning for Spacetime.

We identify a fundamental obstruction to any theory of the beginning of the Universe, formulated as a semiclassical path integral. The Hartle-Hawking no boundary proposal and Vilenkin's tunneling proposal are examples of such theories. Each may be formulated as the quantum amplitude for obtaining a final 3-geometry by integrating over 4-geometries. We introduce a new mathematical tool-Picard-Lefschetz theory-for defining the semiclassical path integral for gravity. The Lorentzian path integral for quantum cosmology with a positive cosmological constant is mathematically meaningful in this approach, but the Euclidean version is not. The Lorentzian-Picard-Lefschetz formulation yields unambiguous predictions. Unfortunately, the outcome is that primordial tensor (gravitational wave) fluctuations are unsuppressed. We prove a general theorem to this effect, in a wide class of theories.

Two- and Three-Dimensional Probes of Parity in Primordial Gravity Waves.

We show that three-dimensional information is critical to discerning the effects of parity violation in the primordial gravity-wave background. If present, helical gravity waves induce parity-violating correlations in the cosmic microwave background (CMB) between parity-odd polarization B modes and parity-even temperature anisotropies (T) or polarization E modes. Unfortunately, EB correlations are much weaker than would be naively expected, which we show is due to an approximate symmetry resulting from the two-dimensional nature of the CMB. The detectability of parity-violating correlations is exacerbated by the fact that the handedness of individual modes cannot be discerned in the two-dimensional CMB, leading to a noise contribution from scalar matter perturbations. In contrast, the tidal imprints of primordial gravity waves fossilized into the large-scale structure of the Universe are a three-dimensional probe of parity violation. Using such fossils the handedness of gravity waves may be determined on a mode-by-mode basis, permitting future surveys to probe helicity at the percent level if the amplitude of primordial gravity waves is near current observational upper limits.

Shocks in the Early Universe.

We point out a surprising consequence of the usually assumed initial conditions for cosmological perturbations. Namely, a spectrum of Gaussian, linear, adiabatic, scalar, growing mode perturbations not only creates acoustic oscillations of the kind observed on very large scales today, it also leads to the production of shocks in the radiation fluid of the very early Universe. Shocks cause departures from local thermal equilibrium as well as create vorticity and gravitational waves. For a scale-invariant spectrum and standard model physics, shocks form for temperatures 1 GeV

Perfect Quantum Cosmological Bounce.

We study quantum cosmology with conformal matter comprising a perfect radiation fluid and a number of conformally coupled scalar fields. Focusing initially on the collective coordinates (minisuperspace) associated with homogeneous, isotropic backgrounds, we are able to perform the quantum gravity path integral exactly. The evolution describes a "perfect bounce", in which the Universe passes smoothly through the singularity. We extend the analysis to spatially flat, anisotropic universes, treated exactly, and to generic inhomogeneous, anisotropic perturbations treated at linear and nonlinear order. This picture provides a natural, unitary description of quantum mechanical evolution across a cosmological bounce. We provide evidence for a semiclassical description in which all fields pass "around" the cosmological singularity along complex classical paths.

The origins of the universe: why is there something rather than nothing?

Perhaps the greatest mystery is why the universe exists in the first place. How is it possible for something to emerge from nothing, or has a universe in some form always existed? This question of origins-both of the universe as a whole and of the fundamental laws of physics-raises profound scientific, philosophical, and religious questions, culminating in the most basic existential question of all: Why are we here? Discussion of this and related questions is presented in this paper.

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.

Naturalness of CP violation in the standard model.

We construct a natural measure on the space of Cabibbo-Kobayashi-Maskawa matrices in the standard model, assuming the fermion mass matrices are randomly selected from a distribution which incorporates the observed quark mass hierarchy. This measure allows us to assess the likelihood of Jarlskog's CP violation parameter J taking its observed value J approximately 3 x 10(-5). We find that the observed value, while well below the mathematically allowed maximum, is in fact typical once the observed quark masses are assumed.

Why the cosmological constant is small and positive.

Within conventional big bang cosmology, it has proven to be very difficult to understand why today's cosmological constant is so small. In this paper, we show that a cyclic model of the universe can naturally incorporate a dynamical mechanism that automatically relaxes the value of the cosmological constant, including contributions to the vacuum density at all energy scales. Because the relaxation time grows exponentially as the vacuum density decreases, nearly every volume of space spends an overwhelming majority of the time at the stage when the cosmological constant is small and positive, as observed today.

Inflationary predictions for scalar and tensor fluctuations reconsidered.

We reconsider the predictions of inflation for the spectral index of scalar (energy density) fluctuations (ns) and the tensor/scalar ratio (r) using a discrete, model-independent measure of the degree of fine-tuning required to obtain a given combination of (ns, r ). We find that, except for cases with numerous unnecessary degrees of fine-tuning, ns is less than 0.98, measurably different from exact Harrison-Zel'dovich. Furthermore, if ns >or= 0.95, in accord with current measurements, the tensor/scalar ratio satisfies r >or= 10(-2), a range that should be detectable in proposed cosmic microwave background polarization experiments and direct gravitational wave searches.

Designing cyclic universe models.

The phenomenological constraints on the scalar field potential in cyclic models of the Universe are presented. We show that cyclic models require a comparable degree of tuning to that needed for inflationary models. The constraints are reduced to a set of simple design rules including "fast-roll" parameters analogous to the "slow-roll" parameters in inflation.

Inflation versus cyclic predictions for spectral tilt.

We present a nearly model-independent estimate that yields the predictions of a class of simple inflationary and ekpyrotic or cyclic models for the spectral tilt of the primordial density inhomogeneities that enables us to compare the two scenarios. Remarkably, we find that the two produce an identical result, n(s) approximately 0.95. For inflation, the same estimate predicts a ratio of tensor to scalar contributions to the low l multipoles of the microwave background anisotropy of T/S approximately 20%; the tensor contribution is negligible for ekpyrotic or cyclic models, as shown in earlier papers.

A cyclic model of the universe.

We propose a cosmological model in which the universe undergoes an endless sequence of cosmic epochs that begin with a "bang" and end in a "crunch." Temperature and density at the transition remain finite. Instead of having an inflationary epoch, each cycle includes a period of slow accelerated expansion (as recently observed) followed by contraction that produces the homogeneity, flatness, and energy needed to begin the next cycle.