On the potential of the EChO mission to characterise gas giant atmospheres

Space telescopes such as EChO (Exoplanet Characterisation Observatory) and JWST (James Webb Space Telescope) will be important for the future study of extrasolar planet atmospheres. Both of these missions are capable of performing high sensitivity spectroscopic measurements at moderate resolutions in the visible and infrared, which will allow the characterisation of atmospheric properties using primary and secondary transit spectroscopy. We use the NEMESIS radiative transfer and retrieval tool (Irwin et al. 2008, Lee et al. 2012) to explore the potential of the proposed EChO mission to solve the retrieval problem for a range of H2-He planets orbiting different stars. We find that EChO should be capable of retrieving temperature structure to ~200 K precision and detecting H2O, CO2 and CH4 from a single eclipse measurement for a hot Jupiter orbiting a Sun-like star and a hot Neptune orbiting an M star, also providing upper limits on CO and NH3. We provide a table of retrieval precisions for these quantities in each test case. We expect around 30 Jupiter-sized planets to be observable by EChO; hot Neptunes orbiting M dwarfs are rarer, but we anticipate observations of at least one similar planet.Comment: 22 pages, 30 figures, 4 tables. Accepted for publication in MNRA

Exoplanet atmospheres with EChO: spectral retrievals using EChOSim

We demonstrate the effectiveness of the Exoplanet Characterisation Observatory mission concept for constraining the atmospheric properties of hot and warm gas giants and super Earths. Synthetic primary and secondary transit spectra for a range of planets are passed through EChOSim (Waldmann & Pascale 2014) to obtain the expected level of noise for different observational scenarios; these are then used as inputs for the NEMESIS atmospheric retrieval code and the retrieved atmospheric properties (temperature structure, composition and cloud properties) compared with the known input values, following the method of Barstow et al. (2013a). To correctly retrieve the temperature structure and composition of the atmosphere to within 2 {\sigma}, we find that we require: a single transit or eclipse of a hot Jupiter orbiting a sun-like (G2) star at 35 pc to constrain the terminator and dayside atmospheres; 20 transits or eclipses of a warm Jupiter orbiting a similar star; 10 transits/eclipses of a hot Neptune orbiting an M dwarf at 6 pc; and 30 transits or eclipses of a GJ1214b-like planet.Comment: 13 pages, 15 figures, 1 table. Accepted by Experimental Astronomy. The final publication will shortly be available at Springer via http://dx.doi.org/10.1007/s10686-014-9397-

From spectra to atmospheres: solving the underconstrained retrieval problem for exoplanets

Spectroscopic observations of transiting exoplanets have provided the first indications of their atmospheric structure and composition. Optimal estimation retrievals have been successfully applied to solar system planets to determine the temperature, composition and aerosol properties of their atmospheres, and have recently been applied to exoplanets. We show the effectiveness of the technique when combined with simulated observations from the proposed space telescope EChO, and also discuss the difficulty of constraining a complex system with sparse data and large uncertainties, using the super-Earth GJ 1214b as an exampl

Understanding and Mitigating Biases when Studying Inhomogeneous Emission Spectra with JWST

Exoplanet emission spectra are often modelled assuming that the hemisphere observed is well represented by a horizontally homogenised atmosphere. However this approximation will likely fail for planets with a large temperature contrast in the James Webb Space Telescope (JWST) era, potentially leading to erroneous interpretations of spectra. We first develop an analytic formulation to quantify the signal-to-noise ratio and wavelength coverage necessary to disentangle temperature inhomogeneities from a hemispherically averaged spectrum. We find that for a given signal-to-noise ratio, observations at shorter wavelengths are better at detecting the presence of inhomogeneities. We then determine why the presence of an inhomogeneous thermal structure can lead to spurious molecular detections when assuming a fully homogenised planet in the retrieval process. Finally, we quantify more precisely the potential biases by modelling a suite of hot Jupiter spectra, varying the spatial contributions of a hot and a cold region, as would be observed by the different instruments of JWST/NIRSpec. We then retrieve the abundances and temperature profiles from the synthetic observations. We find that in most cases, assuming a homogeneous thermal structure when retrieving the atmospheric chemistry leads to biased results, and spurious molecular detection. Explicitly modelling the data using two profiles avoids these biases, and is statistically supported provided the wavelength coverage is wide enough, and crucially also spanning shorter wavelengths. For the high contrast used here, a single profile with a dilution factor performs as well as the two-profile case, with only one additional parameter compared to the 1-D approach.Comment: Accepted for publication by MNRA

How Does Thermal Scattering Shape the Infrared Spectra of Cloudy Exoplanets? A Theoretical Framework and Consequences for Atmospheric Retrievals in the JWST era

Observational studies of exoplanets are suggestive of a ubiquitous presence of clouds. The current modelling techniques used in emission to account for the clouds tend to require prior knowledge of the cloud condensing species and often do not consider the scattering effects of the cloud. We explore the effects that thermal scattering has on the emission spectra by modelling a suite of hot Jupiter atmospheres with varying cloud single-scattering albedos (SSAs) and temperature profiles. We examine cases ranging from simple isothermal conditions to more complex structures and physically driven cloud modelling. We show that scattering from nightside clouds would lead to brightness temperatures that are cooler than the real atmospheric temperature if scattering is unaccounted for. We show that scattering can produce spectral signatures in the emission spectrum even for isothermal atmospheres. We identify the retrieval degeneracies and biases that arise in the context of simulated JWST spectra when the scattering from the clouds dominates the spectral shape. Finally, we propose a novel method of fitting the SSA spectrum of the cloud in emission retrievals, using a technique that does not require any prior knowledge of the cloud chemical or physical properties.Comment: Accepted to MNRA

The Transit Spectra of Earth and Jupiter

In recent years, a number of observations have been made of the transits of 'Hot Jupiters', such as HD 189733b, which have been modelled to derive atmospheric structure and composition. As measurement techniques improve, the transit spectra of 'Super-Earths' such as GJ 1214b are becoming better constrained, allowing model atmospheres to be fitted for this class of planet also. While it is not yet possible to constrain the atmospheric states of small planets such as the Earth or cold planets like Jupiter, this may become practical in the coming decades and if so, it is of interest to determine what we might infer from such measurements. Here we have constructed atmospheric models of the Solar System planets from 0.4 - 15.5 microns that are consistent with ground-based and satellite observations and from these calculate the primary transit and secondary eclipse spectra (with respect to the Sun and typical M-dwarfs) that would be observed by a 'remote observer', many light years away. From these spectra we test what current retrieval models might infer about their atmospheres and compare these with the 'ground truths' in order to assess: a) the inherent uncertainties in transit spectra observations; b) the relative merits of primary transit and secondary eclipse spectra; and c) the advantages of directly imaged spectra. We find that secondary eclipses would not give sufficient information, but that primary transits give much better determination. We find that a single transit of Jupiter in front of the Sun could potentially be used to determine temperature and stratospheric composition, but for the Earth the mean atmospheric composition could only be determined if it were orbiting an M-dwarf. For both planets we note that direct imaging with sufficient nulling of the light from the parent star provides the best method of determining the atmospheric properties of such planets

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

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

AbstractUnderstanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.</jats:p