Structural basis of biased T cell receptor recognition of an immunodominant HLA-A2 epitope of the SARS-CoV-2 spike protein

CD8+ T cells play an important role in vaccination and immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Although numerous SARS-CoV-2 CD8+ T cell epitopes have been identified, the molecular basis underpinning T cell receptor (TCR) recognition of SARS-CoV-2-specific T cells remains unknown. The T cell response directed toward SARS-CoV-2 spike protein–derived S269–277 peptide presented by the human leukocyte antigen (HLA)-A∗02:01 allomorph (hereafter the HLA-A2S269–277 epitope) is, to date, the most immunodominant SARS-CoV-2 epitope found in individuals bearing this allele. As HLA-A2S269–277-specific CD8+ T cells utilize biased TRAV12 gene usage within the TCR α-chain, we sought to understand the molecular basis underpinning this TRAV12 dominance. We expressed four TRAV12+ TCRs which bound the HLA-A2S269–277 complex with low micromolar affinity and determined the crystal structure of the HLA-A2S269–277 binary complex, and subsequently a ternary structure of the TRAV12+ TCR complexed to HLA-A2S269–277. We found that the TCR made extensive contacts along the entire length of the S269–277 peptide, suggesting that the TRAV12+ TCRs would be sensitive to sequence variation within this epitope. To examine this, we investigated cross-reactivity toward analogous peptides from existing SARS-CoV-2 variants and closely related coronaviruses. We show via surface plasmon resonance and tetramer studies that the TRAV12+ T cell repertoire cross-reacts poorly with these analogous epitopes. Overall, we defined the structural basis underpinning biased TCR recognition of CD8+ T cells directed at an immunodominant epitope and provide a framework for understanding TCR cross-reactivity toward viral variants within the S269–277 peptide

Pacific Ocean–wide profile of CYP1A1 expression, stable carbon and nitrogen isotope ratios, and organic contaminant burden in sperm whale skin biopsies

This paper is not subject to U.S. copyright. The definitive version was published in Environmental Health Perspectives 119 (2011): 337-343, doi:10.1289/ehp.0901809.Background: Ocean pollution affects marine organisms and ecosystems as well as humans. The International Oceanographic Commission recommends ocean health monitoring programs to investigate the presence of marine contaminants and the health of threatened species and the use of multiple and early-warning biomarker approaches. Objective: We explored the hypothesis that biomarker and contaminant analyses in skin biopsies of the threatened sperm whale (Physeter macrocephalus) could reveal geographical trends in exposure on an oceanwide scale. Methods: We analyzed cytochrome P450 1A1 (CYP1A1) expression (by immunohistochemistry), stable nitrogen and carbon isotope ratios (as general indicators of trophic position and latitude, respectively), and contaminant burdens in skin biopsies to explore regional trends in the Pacific Ocean. Results: Biomarker analyses revealed significant regional differences within the Pacific Ocean. CYP1A1 expression was highest in whales from the Galapagos, a United Nations Educational, Scientific, and Cultural Organization World Heritage marine reserve, and was lowest in the sampling sites farthest away from continents. We examined the possible influence of the whales’ sex, diet, or range and other parameters on regional variation in CYP1A1 expression, but data were inconclusive. In general, CYP1A1 expression was not significantly correlated with contaminant burdens in blubber. However, small sample sizes precluded detailed chemical analyses, and power to detect significant associations was limited. Conclusions: Our large-scale monitoring study was successful at identifying regional differences in CYP1A1 expression, providing a baseline for this known biomarker of exposure to aryl hydrocarbon receptor agonists. However, we could not identify factors that explained this variation. Future oceanwide CYP1A1 expression profiles in cetacean skin biopsies are warranted and could reveal whether globally distributed chemicals occur at biochemically relevant concentrations on a global basis, which may provide a measure of ocean integrity.Funding was provided by National Institute of Environmental Health Sciences grant P42-ES-0469, Superfund Basic Research Program grant P42ES007381, NOAA Sea Grant NA86RG0075 R/B-162, and the Ocean Alliance

A point-of-care lateral flow assay for neutralising antibodies against SARS-CoV-2

Background: As vaccines against SARS-CoV-2 are now being rolled out, a better understanding of immunity to the virus, whether from infection, or passive or active immunisation, and the durability of this protection is required. This will benefit from the ability to measure antibody-based protection to SARS-CoV-2, ideally with rapid turnaround and without the need for laboratory-based testing. Methods: We have developed a lateral flow POC test that can measure levels of RBD-ACE2 neutralising antibody (NAb) from whole blood, with a result that can be determined by eye or quantitatively on a small instrument. We compared our lateral flow test with the gold-standard microneutralisation assay, using samples from convalescent and vaccinated donors, as well as immunised macaques. Findings: We show a high correlation between our lateral flow test with conventional neutralisation and that this test is applicable with animal samples. We also show that this assay is readily adaptable to test for protection to newly emerging SARS-CoV-2 variants, including the beta variant which revealed a marked reduction in NAb activity. Lastly, using a cohort of vaccinated humans, we demonstrate that our whole-blood test correlates closely with microneutralisation assay data (specificity 100% and sensitivity 96% at a microneutralisation cutoff of 1:40) and that fingerprick whole blood samples are sufficient for this test. Interpretation: Taken together, the COVID-19 NAb-testTM device described here provides a rapid readout of NAb based protection to SARS-CoV-2 at the point of care

Robust and prototypical immune responses towards COVID-19 BNT162b2 vaccines in Indigenous people

SARS-CoV-2 has led to >270 million infections and >5 million deaths globally. Indigenous people are disproportionately affected by infectious diseases, therefore also more susceptible to the COVID-19 pandemic. There are an estimated 476 million indigenous people globally, including an estimated 798,365 Aboriginal and Torres Strait Islander in Australia. With the high vulnerability to COVID-19, this knowledge is urgently needed to better protect indigenous populations. We evaluated a breadth of immune responses in indigenous (n=57) and non-indigenous (n=49) individuals after COVID-19 vaccination. We tested RBD antibodies, spike/RBD-probe-specific B cells, peptide stimulations with activation-induced marker (AIM) assay and intracellular cytokine staining. We found 22% and 34% seroconversion rates after 1st dose of BNT162b2 vaccine for Indigenous and non-indigenous individuals, respectively, which increased to 100% at 1-mth after 2nd dose for both groups. RBD-specific IgG levels in indigenous individuals at 1-mth after 2nd dose positively correlated with their body mass index. At 1-mth after the 2nd COVID-19 vaccination, CD4+ and CD8+ T cell responses via AIM expression and IFN-γ+TNF+ production was comparable between indigenous and non-indigenous individuals. We are also going to assess the longevity of antibodies and T cells. Therefore, COVID-19 vaccination induced similar immune responses in indigenous and non-indigenous individuals

Circulating effector γδ T cell populations are associated with acute coronavirus disease 19 in unvaccinated individuals

Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection causes severe coronavirus disease 2019 (COVID‐19) in a small proportion of infected individuals. The immune system plays an important role in the defense against SARS‐CoV‐2, but our understanding of the cellular immune parameters that contribute to severe COVID‐19 disease is incomplete. Here, we show that populations of effector γδ T cells are associated with COVID‐19 in unvaccinated patients with acute disease. We found that circulating CD27negCD45RA+CX3CR1+ Vδ1effector cells expressing Granzymes (Gzms) were enriched in COVID‐19 patients with acute disease. Moreover, higher frequencies of GzmB+ Vδ2+ T cells were observed in acute COVID‐19 patients. SARS‐CoV‐2 infection did not alter the γδ T cell receptor repertoire of either Vδ1+ or Vδ2+ subsets. Our work demonstrates an association between effector populations of γδ T cells and acute COVID‐19 in unvaccinated individuals