bluuebunny/crossref_metadata_2025_split huggingface dataset:
The human IGHD3-22 encoded motif contributes to broad reactivity of anti-SARS-CoV-2 antibodies
Authors: Liu Hejun , Wilson Ian A 
Published: January 2023

Abstract
The continuous evolution of SARS-CoV-2 coronavirus, the etiological agent of COVID-19, has resulted in the accumulation of mutations that may either escape from host immunity or increase its transmissibility. Cross-neutralizing antibodies targeting highly conserved sites of sarbecoviruses are critical to combat these SARS-CoV-2 variants and other related sarbecoviruses. However, these antibodies are apparently less frequently isolated, although robust antibody responses have been observed in many COVID-19 patients and vaccinees. Here, we describe a structural motif encoded by the human IGHD3-22 gene that targets a functionally conserved surface on the spike protein across sarbecoviruses. We compared antibody structures binding to this conserved site and found a recurrent YYDRxG motif within cross-neutralizing antibodies that mediates strong polar and hydrophobic interactions to the receptor-binding domain of SARS-CoV-2. A computational search using the YYDRxG pattern with publicly available antibody sequences yield over 100 such antibodies with many that broadly neutralize SARS-CoV-2 variants of concern, as well as other sarbecoviruses. Our analysis revealed a common convergent solution to counteract sarbecoviruses, but which seems to be elicited less frequently than other responses by the human humoral immune system. Nevertheless, statistical analysis shows that these YYDRxG sequences are commonly elicited in COVID-19 patients and vaccinees, providing a promising strategy that could be implemented in broad anti-sarbecovirus antibody identification and for pan-sarbecovirus vaccine development.
SARS-CoV-2 vaccination induces T cell memory responses able to cross-recognize ongoing SARS-CoV-2 variants including omicron.
Authors: Grifoni Alba , Tarke Alison , Dan Jennifer , Coelho Camila , Zhang Zeli , Weiskopf Daniela , Da Silva Antunes Ricardo , Crotty Shane , Sette Alessandro 
Published: January 2023

Abstract
The emergence of SARS-CoV-2 variants raises concerns about the efficacy of COVID-19 vaccines to induce an immune response capable of recognizing upcoming variants. While there are multiple studies detailing the impact of SARS-CoV-2 variants on neutralizing antibodies, there is relatively little information on the effect of variant mutations on CD4 and CD8 T cell recognition. We will present the results of our ongoing study on the effects on T cell reactivity to a comprehensive panel of variants circulating globally (B.1.617.2 [delta], P.1 [gamma], B.1.617.1 [kappa], C.37 [lambda], R.1, B.1.1.7 [alpha], B.1.351 [beta], B.1.1.519, B.1.525 [eta], B.1.526 [iota], B.1.427/9 [epsilon], B.1.526.1 and B.1.621 [mu] comparing it with the most recent B.1.1.529 [omicron] variant. The results will span from bioinformatics analyses addressing the effect of SARS-CoV-2 mutations of known epitopes in the Immune Epitope Database (IEDB, https://www.iedb.org/) to the experimental evaluation of the T cell responses specific to each SARS-CoV-2 Spike variant in individuals immunized with several vaccine platforms and at multiple timepoints after vaccination. Parallel experiments will also determine the epitope repertoire in specific donors and dissect the impact of SARS-CoV-2 variant associated mutations on the recognition of each CD4 and CD8 T cell epitope. Finally, the capability of T cell cross-recognition will be compared with breakthrough infection and with or without booster vaccination.
This project has been funded in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. 75N93021C00016 to A.S. and Contract No. 75N9301900065 to A.S, D.W.
Galectin-9 protects humanized-ACE2 immunocompetent mice from SARS-CoV-2 Infection
Authors: Yeung Stephen T , Premeaux Thomas A , Niki Toshiro , Pillai Satish K , Khanna Kamal M , Ndhlovu Lishomwa C 
Published: January 2023

Abstract
The COVID19 pandemic caused by SARS CoV 2 remains a global health crisis even with vaccines and sparse FDA approved therapies. To limit mortality and morbidity, therapeutics are critical. Galectin 9 (gal9) is a b-galactoside binding protein, modulating cell-cell and cell-matrix interactions. It has been shown circulating gal9 levels are elevated in response to infection in patient sera with moderate to severe disease. One report gal9 unexpectedly competitively binds the ACE2 receptor on host cells, impeding viral entry. Therefore, we hypothesize early recombinant gal9 (rgal9) treatment post infection (pi) may prevent binding of the virus to prone host cells yielding a decreased severity of SARS CoV 2 related disease. To determine the potential of gal9 for treating COVID19, we infected and treated K18 hACE2 mice with a single dose of human rgal9 (rhgal9) or PBS i.p. and monitored 12 days for morbidity. Subgroups of mice were humanely euthanized at 2 and 5 dpi for viral plaque assay, flow cytometry, and protein analysis from lung tissue and BALF. We found that mice treated with rhgal9 during acute phase of infection have improved survival compared to PBS control. At 5 dpi, rhgal9 mice had enhanced viral clearance in the BALF and not in the lung parenchyma. We noted increased CD8 T cell and decreased neutrophil frequencies in the lung at 5 dpi. Finally, BALF had elevated levels of Type 1 IFN at 2 dpi and increased proinflammatory cytokines at 5 dpi. This suggests rhgal9 treatment may be therapeutic for acute COVID19, as rhgal9 with other anti-inflammatory mediator treatments cut associated harmful inflammation. Further studies are required to determine the optimal time, combination and duration of treatment pi to effectively target the gal9 pathway.
Endogenous interferon-lambda signaling restricts virus replication and disease severity in a murine model of SARS-CoV-2 infection
Authors: Solstad Abigail , Kenney Adam D , Zani Ashley , Yount Jacob S , Hemann Emily A 
Published: January 2023

Abstract
Interferon-lambda (IFN-λ) is currently being investigated in a phase III clinical trial as a therapeutic against COVID-19. Exogenous IFN-λ restricts SARS-CoV-2 in vitro and in Balb/c and C57Bl/6 (WT) murine models of infection. However, roles of endogenously produced IFN-λ in SARS-CoV-2 pathogenesis are not currently known, and the overall mechanisms by which IFN-λ modulates the induction of protective immune responses in SARS-CoV-2 infections remains to be elucidated. We find that IFN-λ receptor deficient mice (Ifnlr1−/−) infected with mouse-adapted SARS-CoV-2 lose significantly more weight and have increased SARS-CoV-2 viral replication compared to WT through day 5 post infection. Intriguingly, Ifit3 and Ifitm3 are increased in the lungs of Ifnlr1−/− mice compared to WT following infection, despite similar IFN-α/β and IFN-λ mRNA levels, suggesting compensatory increases in type I IFN signaling are not driving the increased weight loss or ISG induction observed in Ifnlr1−/− mice. Global transcriptomics revealed induction of a suppressive immunoregulatory signature with increased IL-10 as a hallmark in Ifnlr1−/− lungs, suggesting IFN-λ is critically involved in regulating appropriate immune activation to limit SARS-CoV-2 pathogenesis. Histological analysis revealed a significant increase in CD45+ cells (but not neutrophils) in the lungs of Ifnlr1−/− mice compared to WT on day 5 post infection, and we identified increases in pathways associated with myeloid cell function and T cell activation in Ifnlr1−/− by comparative transcriptomics. Overall, broadening the understanding of how IFN-λ regulates SARS-CoV-2 infection, pathogenesis, and immunity will inform the utilization of IFN-λ as an immunotherapy and adjuvant.
Supported by NIH Award K22 AI146141 to EAH.
Analysis of SARS-CoV-2 pathogenicity in COVID-19 cynomolgus macaque model reflecting human COVID-19 pathological conditions
Authors: Urano Emiko , Okamura Tomotaka , Yasutomi Yasuhiro 
Published: January 2023

Abstract
The pandemic of SARS-CoV-2 is still raging worldwide. Although rapid vaccination has been progressing in the world as a countermeasure against COVID-19, there are many issues regarding this disease including the emergence of variants and of their virulence that need to be elucidated, and a useful animal model is still necessary.
We have established COVID-19 cynomolgus macaque (CM) model using healthy young CMs and CMs of advanced age (23 – 30 years of age, equivalent to 69 – 90 years of age in humans) with underlying diseases including diabetes and hyperlipidemia. There were differences between the pathological conditions in young macaques and elderly macaques of advanced age similar to observed in humans. In this study, we analyzed the virulence and pathology of SARS-CoV-2 variants of concern (VOCs) using COVID-19 CM model.
Elucidation of how adaptive immunity in patients is induced by SARS-CoV-2 natural infection is critical for establishing a vaccine strategy, serologic therapies, public health control and prediction of infection. Therefore, we conducted the prolonged rechallenge analysis using COVID-19 CM model reinoculated with either the same or a different strain of SARS-CoV-2 that was used for the initial infection. Protective immunity against rechallenge of SARS-CoV-2 is under consideration, but in one elderly monkey reinfection showed transient pneumonia with increased levels of various serum cytokines and chemokines without detecting viruses in swab samples.
Overall, the SARS-CoV-2-infected CM models reflected the pathology in humans, and studies using COVID-19 CM models should contribute to the elucidation of the complicated pathophysiology of COVID-19.
Supported by grants from AMED (JP20fk0108414) and JSPS (21K19395)
Immune responses to SARS-Cov-2 variants in adult and elderly mRNA vaccine recipients
Authors: Jergovic Mladen , Uhrlaub Jennifer , Watanabe Makiko , Coplen Christopher P , Nikolich-Zugich Janko 
Published: January 2023

Abstract
Aging is associated with a reduced magnitude of primary immune responses to vaccination and constriction of immune receptor repertoire diversity. Clinical trials demonstrate high efficacy of mRNA based SARS-CoV-2 vaccines in the elderly but concerns about virus variant escape have not been well addressed. Recently, we have conducted an in-depth analysis of humoral and cellular immunity against the early-pandemic virus strain as well as the P.1./Gamma, B.1.617/Delta and B.1.595 SARS-CoV-2 variants in adult and elderly mRNA vaccine recipients. As others have reported, robust immunity required the second dose of vaccine. Older vaccine recipients exhibited an expected 3–5x reduction (but not a complete loss) in neutralizing antibody titers against P.1./Gamma and B.1.595 that did not statistically differ from that measured in adults. Moreover, older vaccinees manifest robust cellular immunity against SARS-CoV-2, including to variants, that remained statistically comparable to the adult group. While the duration of these immune responses remains to be determined over longer periods of time, these results provide reasons for optimism regarding vaccine protection of older adults against SARS-CoV-2 variants. Experiments are currently in progress to determine cellular immunity in adult and older adult mRNA vaccine recipients to Omicron (B.1.1.529), the newest variant of concern. We will present results on T cell polyfunction and production of cytokines in response to Spike protein peptide pool from Omicron variant in a large cohort of convalescents and adult and elderly mRNA vaccine recipients.
Repurposed antibiotic and antiviral drugs inhibit the immune evasive endoribonuclease of SARS-CoV-2 and restrict coronavirus infection in vitro
Authors: von Beck Troy Alexander , Hernandez Luis Mena , Zhou Hongyi , Skolnick Jeffrey , Jacob Joshy 
Published: January 2023

Abstract
Despite the success of SARS-CoV-2 vaccines in curbing viral transmission and severe disease, infections in unvaccinated and immune deficient patients continue to drive significant morbidity and mortality globally. To address the needs of this patient population, multiple antiviral drugs must be developed to expand on the protection currently offered by convalescent plasma, monoclonal antibodies, remdesivir, and other next generation SARS-CoV-2 antivirals which may be contraindicated for some patient groups. To this end, we employed a machine-learning based virtual ligand screening algorithm, FRAGSITE, to screen a library of FDA approved compounds for binding to the SARS-CoV-2 endoribonuclease (nsp15), a structurally conserved and demonstrated coronavirus virulence factor in SARS-CoV-1, HCoV-229E, IBV, MHV, and PEDV. Using recombinant SARS-CoV-2 nsp15, we identified the inhibition of nuclease activity by 11 drugs in vitro; 6 also restrict infection by the related human OC43 coronavirus in human A549 airway epithelial cells as measured by a focus forming assay. Among these 6 candidates, pibrentasvir remained active against HCoV-OC43 at the lowest concentration (IC50 &lt; 0.625μM). Consistent with previous findings, HCoV-OC43 infection of A549 cells did not provoke an innate response to the viral dsRNA as quantified by IFNB1 mRNA production, antiviral stress granule formation, or RNase L activation. Our preliminary results suggest that antiviral stress granule formation is partially restored by nsp15 inhibitor treatment in HCoV-OC43 infected cells, although IFNβ production and RNase L activation remain unchanged.
Supported by grants from the Emory School of Medicine
SARS-CoV-2 epitope-specific CD8+ clonotypes persist 8 month post-infection despite reduced clonality.
Authors: Zornikova Ksenia V , Khmelevskaya Alexandra , Sheetikov Savely , Shcherbakova Olga V , Kirukhin Dmitry , Titov Aleksei , Zvyagin Ivan V , Efimov Grigory A 
Published: January 2023

Abstract
Memory T cells play a crucial role in acceleration of immune response during reinfection with the same pathogen. Since the beginning of the COVID-19 pandemic, attention has been focused on determining the epitopes of SARS-CoV-2 that give rise to long-lived memory T cells.
We examined the immune response to 12 immunogenic CD8+ epitopes in 26 COVID-19 convalescent patients. Paired blood samples were collected shortly after infection and approximately 8 months after. Using ex vivo T cell expansions with a subsequent MHC-tetramer+ cell-sorting and T cell receptor beta-chain (TCRβ) sequencing we studied the epitope-specific CD8+ response on the clonal level. In total in both time points we identified 756 epitope-specific TCRβ sequences. Nine epitopes were immunodominant while five immunogenic epitopes (YLQ, KCY, LLY, KTF and ALW) yielded response in 100% of tested individuals. This coincided with a high number of clones per individual specific to these epitopes (median = 16.5).
Despite the very low frequency of specific cells in the total repertoire most (75.4%) of responses were retained at 8-month post-infection. The median number of clones for the top five most immunogenic epitopes dropped to 6. The TCRβ repertoires of T cells specific to the studied epitopes were characterized by different degrees of CDR3 homology. LLY and YLQ-specific TCRβ had the highest degree of mutual similarity while KCY and KTF-specific TCRβ were the most diverse.
Our data demonstrates that despite the overall decrease of T cell reactivity and clonality most epitopes are still recognized due to the ability of memory SARS-CoV-2-specific CD8+ cells to survive over prolonged periods of time.
The work was supported by the Russian Science Foundation grant 20-15-00395.
A Longitudinal Study of Humoral Immune Responses to SARS-CoV-2 Spike Proteins in Gamma-Interferon-inducible Lysosomal Thiol Reductase Deficient Mice
Authors: He Xiao , Guo Li , Dai Hu , Jensen Peter E 
Published: January 2023

Abstract
The disulfide (S-S) bonds located in the receptor binding domain (RBD) of Spike (S) proteins of SARS-CoV-2 are critical for structural folding and viral entry. Once entered cells, S proteins, like other exogenous Ag, can be transported into endo/lysosomes, where gamma-interferon-inducible lysosomal thiol reductase (GILT) is the only thiol reductase located, which can reduce S-S bonds. GILT mediated S-S bond reduction in APC is critical in unfolding of native S-S bonds containing Ag, subsequently processing/presenting Ag, and, finally, triggering CD4 T cell responses. Recently, we also find GILT plays a role in Ab responses. Whether GILT mediates anti-SARSCoV-2 host defense responses remains unknown. We hypothesized that GILT is important in eliciting host humoral immune responses against SARS-CoV-2 by reducing S-S bonds and exposing Ag epitopes. To address this, we used 3 different types of S protein derived Ag to immunize GILT KO or B6 control mice and measured the specific Ab responses in a longitudinal study. GILT KO or B6 wildtype mice were given RBD, S1 region and the full length of extracellular domain of S proteins with CFA initially, and boosted at week 3 with the same Ag in IFA. Sera were collected at weeks 3 and 5, months 3, 4 and 5 for quantification of specific anti-RBD, S1 and S Ab. At all timepoints examined, GILT KO mice generated lower specific Ab titers to the immunogens, as compared to B6. Furthermore, decay of anti-specific Ab in GILT KO was faster than that in controls after immunization. Our preliminary findings showed an important role of GILT in humoral immune responses against SARS-CoV-2, suggesting unfolding S-S bonds is critical in this process. Recombinant GILT as a therapeutic might benefit patients with COVID-19.
Supported by Seed Grant, Univ. of Utah
Epitope-specific T cell response to SARS-CoV-2 infection and vaccination
Authors: Minervina Anastasia , Pogorelyy Mikhail , Kirk Allison M , Chou Ching-Heng , Allen E Kaitlynn , Crawford Jeremy Chase , McGargill Maureen Ann , Thomas Paul G 
Published: January 2023

Abstract
SARS-CoV-2 mRNA vaccines are effective for COVID-19 prevention, eliciting both robust antibody responses in naive individuals and boosting antibody levels in convalescent donors. However, the effect of repeated antigen exposures, such as vaccination following infection or breakthrough infections, on the magnitude, repertoire, and phenotype of pre-existing memory T cells, is still poorly understood. Thus, we compared epitope-specific CD8 T cells elicited after SARS-CoV-2 infection, vaccination of both naive and recovered individuals, and breakthrough infection cases. We used pools of 18 DNA-barcoded MHC-class I multimers, combined with scRNAseq and scTCRseq, to characterize T cell responses as defined by magnitude, specificity, T cell receptor (TCR) repertoire, and gene expression profile to both spike-derived and non-spike derived epitopes. In-depth analysis of over 4000 unique epitope-specific TCR sequences demonstrates that both vaccination and infection, including breakthrough cases, elicit identical repertoires as measured by dominant TCR motifs and repertoire diversity, indicating that BNT162b2 vaccination largely recapitulates spike-specific T cell repertoire generation by infection. Importantly, in COVID-19-recovered individuals receiving the vaccine, pre-existing spike-specific memory cells showed both clonal expansion and a phenotypic shift towards more differentiated CCR7-CD45RA+ effector cells, demonstrating the potency of this vaccine to recall spike-specific CD8 memory T cells. Importantly, in breakthrough infections, we observed a high proportion of T cells targeting non-spike epitopes, showing that new immune memory could be formed during SARS-CoV-2 infection after vaccination.
The work was funded by 75N93019C00052, HHSN272201400006C, 3U01AI144616-02S1, R01AI136514
Metabolic syndrome enhances viral disease severity and reduces vaccine efficacy in mice
Authors: Geerling Elizabeth , Carpenter Danielle H , Schwetye Katherine E , DeBosch Brian , Pinto Amelia 
Published: January 2023

Abstract
Metabolic syndrome (MetS) is a cluster of conditions linked by chronic inflammation that increase the risk for comorbidities. Currently, 1/3 of United States adults have MetS. Globally, obesity rates have tripled since 1975, which is notable since it is a criterium used to diagnose MetS. MetS patients show higher mortality post-SARS-CoV-2 infection and poor vaccination outcomes following influenza virus vaccination when compared to metabolically healthy humans. However, the mechanisms driving MetS-induced immune dysfunction are unknown. Based on previously published work, we hypothesize that MetS-associated chronic inflammation alters programming of adaptive immune cells critical for viral control, thus enhancing disease severity and reducing vaccine efficacy. To challenge this, we use West Nile virus and SARS-CoV-2 in MetS murine models. By infecting or vaccinating chow fed wild type (WT) and high fat diet induced MetS mice, we compared immune responses over time. Our results indicate that MetS mice have higher mortality post infection, heightened viral titers, severe organ pathology, dysfunctional T and B cell responses and reduced neutralizing antibody efficacy when compared to WT mice. Further, MetS alters antibody and T cell responses post-vaccination, rendering vaccination insufficient for protecting against severe viral disease. Our results imply that MetS enhances viral disease severity and reduces vaccine efficacy. Ongoing studies in our lab are focused on determining the mechanism by which MetS alters adaptive immune cell function, with our data implicating chronic inflammation as an inducer of immune cell epigenetic changes that alter their differentiation landscapes and consequently effector functions.
Supported by grants from NIH (R01 12781495) and DoD (USAMRDCPR192269).
ADAM-17 protease promotes inflammation and mortality while decreasing viral burden in a COVID-19 mouse model
Authors: Hedges Jodi F , Snyder Deann T , Robison Amanda , Walk Heather , Havlak Karlin , Shepardson Kelly , Kominsky Douglas , Rynda-Apple Agnieszka , Walcheck Bruce , Jutila Mark A 
Published: January 2023

Abstract
Angiotensin Converting Enzyme 2 (ACE2) is the primary cell entry receptor for SARS-CoV-1 and SARS-CoV-2 viruses. A disintegrin and metalloproteinase 17 (ADAM-17) is a protease located in the cell membrane of most cells that, upon cellular activation, cleaves ectodomains of transmembrane proteins, including that of ACE2, from cell surfaces. We hypothesized that blockade of ADAM-17 activity would alter COVID-19 pathogenesis. To assess this pathway, we blocked the function of ADAM-17 using a monoclonal antibody in the K18 human ACE2 Tg mouse model of COVID-19. Antibody-treated mice were healthier, less moribund, and had significantly less lung inflammation than saline treated mice. However, the viral burden in the lungs of anti-ADAM17 Ab-treated mice was significantly greater. ADAM17 also cleaves TNF-a and its blockade decreased lung TNF-a production induced by intratracheal LPS delivery. We are currently testing this possibility in the COVID-19 mouse model. Thus, ADAM-17 appears to have a critical anti-viral role, but also promotes damaging inflammation following SARS-CoV-2 infection. Since the inflammatory cascade is ultimately the reason for the adverse outcomes in COVID-19 patients, there may be a therapeutic application for the anti-ADAM-17 antibody.