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

Citizen science records describe the distribution and migratory behaviour of a piscivorous predator, Pomatomus saltatrix

Understanding the processes driving species distributions is a key question in ecology, yet obtaining pertinent data for many species can be challenging. Tag-recapture data from voluntary recreational fisheries programmes is an undervalued citizen science data resource and can provide valuable observation records for data-poor species. Here, we highlight the utility of such data by compiling four tag-recapture datasets (n = 20 878 tags) to describe the movements and distribution of a piscivorous predator, tailor Pomatomus saltatrix, with respect to their environment. We compared species distribution models that explored a trade-off between temporal duration and spatial extent. Both models revealed sea surface temperature (SST) was an important factor in describing the distribution and density of tailor. However, the model with broader spatial extent indicated a non-linear response to SST, peaking at 21.5°C, while the model with temporal longevity showed a linear SST response. This disjunct showcases the importance of building models across an adequate geographic extent to ensure covariate responses are not truncated. This is the first study to comprehensively describe the distribution and migrations of adult tailor across their eastern Australian distribution. The results are discussed in light of ocean warming along eastern Australia, and the subsequent implications for using tag-recapture data in fisheries management

Reasons to Be Skeptical about Sentience and Pain in Fishes and Aquatic Invertebrates

The welfare of fishes and aquatic invertebrates is important, and several jurisdictions have included these taxa under welfare regulation in recent years. Regulation of welfare requires use of scientifically validated welfare criteria. This is why applying Mertonian skepticism toward claims for sentience and pain in fishes and aquatic invertebrates is scientifically sound and prudent, particularly when those claims are used to justify legislation regulating the welfare of these taxa. Enacting welfare legislation for these taxa without strong scientific evidence is a societal and political choice that risks creating scientific and interpretational problems as well as major policy challenges, including the potential to generate significant unintended consequences. In contrast, a more rigorous science-based approach to the welfare of aquatic organisms that is based on verified, validated and measurable endpoints is more likely to result in “win-win” scenarios that minimize the risk of unintended negative impacts for all stakeholders, including fish and aquatic invertebrates. The authors identify as supporters of animal welfare, and emphasize that this issue is not about choosing between welfare and no welfare for fish and aquatic invertebrates, but rather to ensure that important decisions about their welfare are based on scientifically robust evidence. These ten reasons are delivered in the spirit of organized skepticism to orient legislators, decision makers and the scientific community, and alert them to the need to maintain a high scientific evidential bar for any operational welfare indicators used for aquatic animals, particularly those mandated by legislation. Moving forward, maintaining the highest scientific standards is vitally important, in order to protect not only aquatic animal welfare, but also global food security and the welfare of humans.</p