The impact of viral mutations on recognition by SARS-CoV-2 specific T cells.

We identify amino acid variants within dominant SARS-CoV-2 T cell epitopes by interrogating global sequence data. Several variants within nucleocapsid and ORF3a epitopes have arisen independently in multiple lineages and result in loss of recognition by epitope-specific T cells assessed by IFN-γ and cytotoxic killing assays. Complete loss of T cell responsiveness was seen due to Q213K in the A∗01:01-restricted CD8+ ORF3a epitope FTSDYYQLY207-215; due to P13L, P13S, and P13T in the B∗27:05-restricted CD8+ nucleocapsid epitope QRNAPRITF9-17; and due to T362I and P365S in the A∗03:01/A∗11:01-restricted CD8+ nucleocapsid epitope KTFPPTEPK361-369. CD8+ T cell lines unable to recognize variant epitopes have diverse T cell receptor repertoires. These data demonstrate the potential for T cell evasion and highlight the need for ongoing surveillance for variants capable of escaping T cell as well as humoral immunity.This work is supported by the UK Medical Research Council (MRC); Chinese Academy of Medical Sciences(CAMS) Innovation Fund for Medical Sciences (CIFMS), China; National Institute for Health Research (NIHR)Oxford Biomedical Research Centre, and UK Researchand Innovation (UKRI)/NIHR through the UK Coro-navirus Immunology Consortium (UK-CIC). Sequencing of SARS-CoV-2 samples and collation of data wasundertaken by the COG-UK CONSORTIUM. COG-UK is supported by funding from the Medical ResearchCouncil (MRC) part of UK Research & Innovation (UKRI),the National Institute of Health Research (NIHR),and Genome Research Limited, operating as the Wellcome Sanger Institute. T.I.d.S. is supported by a Well-come Trust Intermediate Clinical Fellowship (110058/Z/15/Z). L.T. is supported by the Wellcome Trust(grant number 205228/Z/16/Z) and by theUniversity of Liverpool Centre for Excellence in Infectious DiseaseResearch (CEIDR). S.D. is funded by an NIHR GlobalResearch Professorship (NIHR300791). L.T. and S.C.M.are also supported by the U.S. Food and Drug Administration Medical Countermeasures Initiative contract75F40120C00085 and the National Institute for Health Research Health Protection Research Unit (HPRU) inEmerging and Zoonotic Infections (NIHR200907) at University of Liverpool inpartnership with Public HealthEngland (PHE), in collaboration with Liverpool School of Tropical Medicine and the University of Oxford.L.T. is based at the University of Liverpool. M.D.P. is funded by the NIHR Sheffield Biomedical ResearchCentre (BRC – IS-BRC-1215-20017). ISARIC4C is supported by the MRC (grant no MC_PC_19059). J.C.K.is a Wellcome Investigator (WT204969/Z/16/Z) and supported by NIHR Oxford Biomedical Research Centreand CIFMS. The views expressed are those of the authors and not necessarily those of the NIHR or MRC

Sequential extraction of polycyclic aromatic hydrocarbons using subcritical water

A rapid sequential subcritical (superheated) water extraction method for polycyclic aromatic hydrocarbons (PAHs) in contaminated soil and sediment is presented. Decreasing the polarity of water by successive increase of the extraction temperature from 50 °C to 200 °C at the moderate pressure (10.3 MPa) enabled selective, non-exhaustive extractions to be performed. Concurrent with increasing temperatures to 150 °C there was an increase in PAH extraction efficiencies. For the majority of determinations no significant differences between extractions at 150 °C and 200 °C were observed. Varied extraction efficiencies of PAHs at the same extraction conditions reflected dissimilarities between environmental matrices investigated. Selective subcritical water extraction of PAHs was proportional to their octanol-water partition coefficients. This technique may be applicable in evaluation of risks associated with PAH contaminated sites and in assessments of their bioremediation potential

Beyond contaminated land assessment: On costs and benefits of bioaccessibility prediction

Advances towards sustainable land management necessitate application of a broader portfolio of decision-support tools that improve evaluation of contaminated land. Over the last decade regulators have directed concerted effort towards rationalization of risk-based contaminated land policies recognizing bioavailability and bioaccessibility as concepts to be incorporated into risk assessments. The desire for a precise and rapid method to inform consideration of bioavailability and bioaccessibility to support risk assessment of contaminated land has never been greater. This study presents a comprehensive appraisal of both emerging non-exhaustive extraction techniques (subcritical water extraction and Brij 700 extraction) developed to reflect polycyclic aromatic hydrocarbon (PAH) bioaccessibility to microorganisms as well as formerly demonstrated methodologies (the use of cyclodextrins and butanol extraction). Application of unified evaluation criteria across different techniques enabled comparison not only from the bioaccessibility prediction perspective but also analysis of economical (cost of extraction) and practical (such as extraction time) measures. Whilst the use of cyclodextrins was the best predictor of the bioaccessible fraction for the majority of compounds, other methods appeared more cost- and time-effective. Juxtaposition of the techniques presented in this study assists establishing cost-benefit trade-offs of different non-exhaustive extraction techniques and contributes to tailoring information on contaminant bioaccessibility to support risk evaluation on contaminated sites

Environmentally friendly assessment of organic compound bioaccessibility using sub-critical water

The evaluation of microbial availability of contaminants is of high importance for better reflecting the processes governing contaminant fate in soil and for establishing the risk associated with contaminated sites. A sub-critical water extraction technique was assessed for its potential to determine the microbially degradable fraction of [14C]phenanthrene-associated activity in two dissimilar soils at three different ageing times (14, 28 and 49 days). For the majority of determinations, no significant (p > 0.05) difference between sub-critical water-extracted 14C-activity at 160 °C and the fraction mineralized by catabolically active Pseudomonas sp. was observed. Collectively, the results suggested that the sub-critical water extraction technique was an appropriate technique for predicting the biodegradable fraction of phenanthrene-associated 14C-activity in dissimilar soils following increasing soil-contaminant contact time. Sub-critical water extraction reflects phenanthrene bioaccessibility in the soil

Bringing bioavailability into contaminated land decision making: The way forward?

Beyond the current regulatory regime there is ongoing research into the environmental fate of pollutants that could potentially be integrated into contaminated land decision making. In an era of great demand for decision support tools it is increasingly urgent for scientists to develop reliable methodology assisting sustainable land management and for policy makers to adopt these developments. This is true notably for widespread land contamination with polycyclic aromatic hydrocarbons. Recently published research on bioavailability offers complementary approach into contaminated land evaluation as well as the assistance in the development of remediation strategies. We review these studies and critically discuss the implementation of bioavailability across different disciplines within contaminated land management. We identify scientific gaps and recommend transdisciplinary research confronting key normative questions facing regulators. Discussion is presented with reference to the United Kingdom's contaminated land regime. This regime is risk based and as a consequence the general principles, concerns, and chemistry behind bioavailability processes discussed in this review are applicable to risk-based approaches elsewhere

Bioavailability and Bioaccessibility of Hydrophobic Organic Contaminants in Soil and Associated Desorption-Based Measurements

Many publications on contaminant bioavailability in soils often state that the use of total contaminant concentrations in risk assessment is an overly conservative approach. Such conservatism makes traditional risk assessment approaches and contaminated land decision-making expensive. The risk-based approach to contaminated land management strives to identify and manage the potential risks of significant harm being caused to humans and ecological receptors, following exposure to contaminated land. Risk-based approaches are more cost-effective than the traditional approaches from the perspective of contaminated land management. Contaminant bioavailability or bioaccessibility is one of the critical concepts that underpins risk-based approaches to contaminated land management. Bioavailability describes the fraction of the total contaminant concentration that desorbs from soil and is immediately available to cause harm to a living organism, after passing through the organism’s membrane. Bioaccessibility describes what is available and potentially available under natural environmental conditions and during realistic timeframes. The reliable measurements of either contaminant bioavailability or bioaccessibility is therefore critical; in this regard, a thorough understanding of contaminant sequestration and desorption behaviour is required. This chapter discusses the fate of HOCs in soils, bioavailability and bioaccessibility of organic contaminants and their associated desorption-based measurements