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Efforts are being made worldwide to understand the immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for the coronavirus disease 2019 (COVID-19) pandemic, including the impact of T cell immunity and cross-recognition with seasonal coronaviruses. Screening of SARS-CoV-2 peptide pools revealed that the nucleocapsid (N) protein induced an immunodominant response in HLA-B7+ COVID-19-recovered individuals that was also detectable in unexposed donors. A single N-encoded epitope that was highly conserved across circulating coronaviruses drove this immunodominant response. In vitro peptide stimulation and crystal structure analyses revealed T cell-mediated cross-reactivity toward circulating OC43 and HKU-1 betacoronaviruses but not 229E or NL63 alphacoronaviruses because of different peptide conformations. T cell receptor (TCR) sequencing indicated that cross-reactivity was driven by private TCR repertoires with a bias for TRBV27 and a long CDR3ß loop. Our findings demonstrate the basis of selective T cell cross-reactivity for an immunodominant SARS-CoV-2 epitope and its homologs from seasonal coronaviruses, suggesting long-lasting protective immunity.
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Linfocitos T CD8-positivos/inmunología , COVID-19/inmunología , Proteínas de la Nucleocápside de Coronavirus/inmunología , Epítopos Inmunodominantes/inmunología , SARS-CoV-2/inmunología , Secuencia de Aminoácidos , Coronavirus/clasificación , Coronavirus/inmunología , Proteínas de la Nucleocápside de Coronavirus/química , Reacciones Cruzadas , Epítopos de Linfocito T/química , Epítopos de Linfocito T/inmunología , Antígeno HLA-B7/química , Antígeno HLA-B7/genética , Antígeno HLA-B7/inmunología , Humanos , Epítopos Inmunodominantes/química , Memoria Inmunológica , Modelos Moleculares , Péptidos/química , Péptidos/inmunología , Receptores de Antígenos de Linfocitos T/química , Receptores de Antígenos de Linfocitos T/genética , Receptores de Antígenos de Linfocitos T/inmunologíaRESUMEN
Adoptive T-cell immunotherapy has provided promising results in the treatment of viral complications in humans, particularly in the context of immunocompromised patients who have exhausted all other clinical options. The capacity to expand T cells from healthy immune individuals is providing a new approach to anti-viral immunotherapy, offering rapid off-the-shelf treatment with tailor-made human leukocyte antigen (HLA)-matched T cells. While most of this research has focused on the treatment of latent viral infections, emerging evidence that SARS-CoV-2-specific T cells play an important role in protection against COVID-19 suggests that the transfer of HLA-matched allogeneic off-the-shelf virus-specific T cells could provide a treatment option for patients with active COVID-19 or at risk of developing COVID-19. We initially screened 60 convalescent individuals and based on HLA typing and T-cell response profile, 12 individuals were selected for the development of a SARS-CoV-2-specific T-cell bank. We demonstrate that these T cells are specific for up to four SARS-CoV-2 antigens presented by a broad range of both HLA class I and class II alleles. These T cells show consistent functional and phenotypic properties, display cytotoxic potential against HLA-matched targets and can recognize HLA-matched cells infected with different SARS-CoV-2 variants. These observations demonstrate a robust approach for the production of SARS-CoV-2-specific T cells and provide the impetus for the development of a T-cell repository for clinical assessment.
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Antígenos HLA/inmunología , Inmunoterapia Adoptiva , SARS-CoV-2/inmunología , Linfocitos T/inmunología , Adulto , Epítopos de Linfocito T , Femenino , Células HEK293 , Humanos , Inmunofenotipificación , Masculino , Persona de Mediana Edad , Adulto JovenRESUMEN
Node localization is critical for accessing diverse nodes that provide services in remote places. Single-anchor localization techniques suffer co-linearity, performing poorly. The reliable multiple anchor node selection method is computationally intensive and requires a lot of processing power and time to identify suitable anchor nodes. Node localization in wireless sensor networks (WSNs) is challenging due to the number and placement of anchors, as well as their communication capabilities. These senor nodes possess limited energy resources, which is a big concern in localization. In addition to convention optimization in WSNs, researchers have employed nature-inspired algorithms to localize unknown nodes in WSN. However, these methods take longer, require lots of processing power, and have higher localization error, with a greater number of beacon nodes and sensitivity to parameter selection affecting localization. This research employed a nature-inspired crow search algorithm (an improvement over other nature-inspired algorithms) for selecting the suitable number of anchor nodes from the population, reducing errors in localizing unknown nodes. Additionally, the weighted centroid method was proposed for identifying the exact location of an unknown node. This made the crow search weighted centroid localization (CS-WCL) algorithm a more trustworthy and efficient method for node localization in WSNs, with reduced average localization error (ALE) and energy consumption. CS-WCL outperformed WCL and distance vector (DV)-Hop, with a reduced ALE of 15% (from 32%) and varying communication radii from 20 m to 45 m. Also, the ALE against scalability was validated for CS-WCL against WCL and DV-Hop for a varying number of beacon nodes (from 3 to 2), reducing ALE to 2.59% (from 28.75%). Lastly, CS-WCL resulted in reduced energy consumption (from 120 mJ to 45 mJ) for varying network nodes from 30 to 300 against WCL and DV-Hop. Thus, CS-WCL outperformed other nature-inspired algorithms in node localization. These have been validated using MATLAB 2022b.
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Forest fire monitoring is very much needed for protecting the forest from any kind of disaster or anomaly leading to the destruction of the forest. Now, with the advent of Internet of Things (IoT), a good amount of research has been done on energy consumption, coverage, and other issues. These works did not focus on forest fire management. The IoT-enabled environment is made up of low power lossy networks (LLNs). For improving the performance of routing protocol in forest fire management, energy-efficient routing protocol for low power lossy networks (E-RPL) was developed where residual power was used as an objective function towards calculating the rank of the parent node to form the destination-oriented directed acyclic graph (DODAG). The challenge in E-RPL is the scalability of the network resulting in a long end-to-end delay and less packet delivery. Additionally, the energy of sensor nodes increased with different transmission range. So, for obviating the above-mentioned drawbacks in E-RPL, compressed data aggregation and energy-based RPL routing (CAA-ERPL) is proposed. The CAA-ERPL is compared with E-RPL, and the performance is analyzed resulting in reduced packet transfer delay, less energy consumption, and increased packet delivery ratio for 10, 20, 30, 40, and 50 nodes. This has been evaluated using a Contiki Cooja simulator.
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Redes de Comunicación de Computadores , Compresión de Datos , Bosques , Tecnología InalámbricaRESUMEN
Vaccines have curtailed the devastation wrought by COVID-19. Nevertheless, emerging variants result in a high incidence of breakthrough infections. Here we assess the impact of vaccination and breakthrough infection on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) T cell immunity. We demonstrate that COVID-19 vaccination induces robust spike-specific T cell responses that, within the CD4+ compartment, display comparable IFN-γ responses to SARS-CoV-2 infection without vaccination. Vaccine-induced CD8+ IFN-γ responses however, were significantly greater than those primed by SARS-CoV-2 infection alone. This increased responsiveness is associated with induction of novel HLA-restricted CD8+ T cell epitopes not primed by infection alone (without vaccination). Despite these augmented responses, breakthrough infection still induced de novo T cell responses against additional SARS-CoV-2 CD8+ epitopes that display HLA-associated immunodominance hierarchies consistent with those in unvaccinated COVID-19 convalescent individuals. This study demonstrates the unique modulation of anti-viral T cell responses against multiple viral antigens following consecutive yet distinct priming events in COVID-19 vaccination and breakthrough infection.
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Understanding the immune response to severe acute respiratory syndrome coronavirus (SARS-CoV-2) is critical to overcome the current coronavirus disease (COVID-19) pandemic. Efforts are being made to understand the potential cross-protective immunity of memory T cells, induced by prior encounters with seasonal coronaviruses, in providing protection against severe COVID-19. In this study we assessed T-cell responses directed against highly conserved regions of SARS-CoV-2. Epitope mapping revealed 16 CD8+ T-cell epitopes across the nucleocapsid (N), spike (S), and open reading frame (ORF)3a proteins of SARS-CoV-2 and five CD8+ T-cell epitopes encoded within the highly conserved regions of the ORF1ab polyprotein of SARS-CoV-2. Comparative sequence analysis showed high conservation of SARS-CoV-2 ORF1ab T-cell epitopes in seasonal coronaviruses. Paradoxically, the immune responses directed against the conserved ORF1ab epitopes were infrequent and subdominant in both convalescent and unexposed participants. This subdominant immune response was consistent with a low abundance of ORF1ab encoded proteins in SARS-CoV-2 infected cells. Overall, these observations suggest that while cross-reactive CD8+ T cells likely exist in unexposed individuals, they are not common and therefore are unlikely to play a significant role in providing broad preexisting immunity in the community. IMPORTANCE T cells play a critical role in protection against SARS-CoV-2. Despite being highly topical, the protective role of preexisting memory CD8+ T cells, induced by prior exposure to circulating common coronavirus strains, remains less clear. In this study, we established a robust approach to specifically assess T cell responses to highly conserved regions within SARS-CoV-2. Consistent with recent observations we demonstrate that recognition of these highly conserved regions is associated with an increased likelihood of milder disease. However, extending these observations we observed that recognition of these conserved regions is rare in both exposed and unexposed volunteers, which we believe is associated with the low abundance of these proteins in SARS-CoV-2 infected cells. These observations have important implications for the likely role preexisting immunity plays in controlling severe disease, further emphasizing the importance of vaccination to generate the immunodominant T cells required for immune protection.
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COVID-19/inmunología , Epítopos de Linfocito T/inmunología , SARS-CoV-2/inmunología , Secuencia de Aminoácidos , Linfocitos T CD8-positivos/inmunología , COVID-19/genética , COVID-19/virología , Secuencia Conservada , Coronavirus/química , Coronavirus/clasificación , Coronavirus/genética , Coronavirus/inmunología , Infecciones por Coronavirus/genética , Infecciones por Coronavirus/inmunología , Infecciones por Coronavirus/virología , Reacciones Cruzadas , Mapeo Epitopo , Epítopos de Linfocito T/química , Epítopos de Linfocito T/genética , Humanos , Células T de Memoria/inmunología , SARS-CoV-2/química , SARS-CoV-2/genética , SARS-CoV-2/fisiología , Alineación de Secuencia , Glicoproteína de la Espiga del Coronavirus/química , Glicoproteína de la Espiga del Coronavirus/genética , Glicoproteína de la Espiga del Coronavirus/inmunologíaRESUMEN
The emergence of the SARS-CoV-2 Omicron variant has raised concerns of escape from vaccine-induced immunity. A number of studies have demonstrated a reduction in antibody-mediated neutralization of the Omicron variant in vaccinated individuals. Preliminary observations have suggested that T cells are less likely to be affected by changes in Omicron. However, the complexity of human leukocyte antigen genetics and its impact upon immunodominant T cell epitope selection suggests that the maintenance of T cell immunity may not be universal. In this study, we describe the impact that changes in Omicron BA.1, BA.2 and BA.3 have on recognition by spike-specific T cells. These T cells constitute the immunodominant CD8+ T cell response in HLA-A*29:02+ COVID-19 convalescent and vaccinated individuals; however, they fail to recognize the Omicron-encoded sequence. These observations demonstrate that in addition to evasion of antibody-mediated immunity, changes in Omicron variants can also lead to evasion of recognition by immunodominant T cell responses.
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COVID-19 , Epítopos Inmunodominantes , Humanos , SARS-CoV-2/genética , Linfocitos T CD8-positivos , Anticuerpos Antivirales , Anticuerpos Neutralizantes , Glicoproteína de la Espiga del Coronavirus/genéticaRESUMEN
OBJECTIVES: With the ongoing emergence of SARS-CoV-2 variants and potential to evade vaccine-induced neutralisation, understanding the magnitude and breadth of vaccine-induced T-cell immunity will be critical for the ongoing optimisation of vaccine approaches. Strategies that provide a rapid and easily translatable means of assessing virus-specific T-cell responses provide an opportunity to monitor the impact of vaccine rollouts in the community. In this study, we assessed whether our recently developed SARS-CoV-2 whole-blood assay could be used effectively to analyse T-cell responses following vaccination. METHODS: Following a median of 15 days after the first dose of the ChAdOx1-S (AstraZeneca®) vaccine, peripheral blood was isolated from 58 participants. Blood was incubated overnight with an overlapping set of spike protein peptides and assessed for cytokine production using a cytometric bead array. RESULTS: The majority of vaccine recipients (51/58) generated a T helper 1 response (IFN-γ and/or IL-2) following a single dose of ChAdOx1-S. The magnitude of the IFN-γ and IL-2 response strongly correlated in vaccine recipients. While the production of other cytokines was evident in individuals who did not generate IFN-γ and IL-2, they showed no correlation in magnitude, nor did we see a correlation between sex or age and the magnitude of the response. CONCLUSIONS: The whole-blood cytokine assay provides a rapid approach to assessing T-cell immunity against SARS-CoV-2 in vaccine recipients. While the majority of participants generated a robust SARS-CoV-2-specific T-cell response following their first dose, some did not, demonstrating the likely importance of the booster dose in improving T-cell immunity.
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OBJECTIVES: There is emerging evidence that SARS-CoV-2-specific memory T-cell responses are likely to provide critical long-term protection against COVID-19. Strategies to rapidly assess T-cell responses are therefore likely to be important for assessing immunity in the global population. METHODS: Here, we have developed a rapid immune-monitoring strategy to assess virus-specific memory T-cell responses in the peripheral blood of COVID-19 convalescent individuals. We validated SARS-CoV-2-specific memory T-cell responses detected in whole blood using in vitro expansion with SARS-CoV-2 proteins. RESULTS: T-cell immunity characterised by the production of IFN-γ and IL-2 could be consistently detected in the whole blood of recovered participants. T cells predominantly recognised structural SARS-CoV-2 proteins. In vitro expansion demonstrated that while CD8+ T cells recognised nucleocapsid protein, spike protein and ORF3a, CD4+ T cells more broadly targeted multiple SARS-CoV-2 proteins. CONCLUSION: These observations provide a timely monitoring approach for identifying SARS-CoV-2 cellular immunity and may serve as a diagnostic for the stratification of risk in immunocompromised and other at-risk individuals.