In vitro generated antibodies guide thermostable ADDomer nanoparticle design for nasal vaccination and passive immunization against SARS-CoV-2.

Background: Due to COVID-19, pandemic preparedness emerges as a key imperative, necessitating new approaches to accelerate development of reagents against infectious pathogens. Methods: Here, we developed an integrated approach combining synthetic, computational and structural methods with in vitro antibody selection and in vivo immunization to design, produce and validate nature-inspired nanoparticle-based reagents against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Results: Our approach resulted in two innovations: (i) a thermostable nasal vaccine called ADDoCoV, displaying multiple copies of a SARS-CoV-2 receptor binding motif derived epitope and (ii) a multivalent nanoparticle superbinder, called Gigabody, against SARS-CoV-2 including immune-evasive variants of concern (VOCs). In vitro generated neutralizing nanobodies and electron cryo-microscopy established authenticity and accessibility of epitopes displayed by ADDoCoV. Gigabody comprising multimerized nanobodies prevented SARS-CoV-2 virion attachment with picomolar EC50. Vaccinating mice resulted in antibodies cross-reacting with VOCs including Delta and Omicron. Conclusion: Our study elucidates Adenovirus-derived dodecamer (ADDomer)-based nanoparticles for use in active and passive immunization and provides a blueprint for crafting reagents to combat respiratory viral infections.

Development and evaluation of low-volume tests to detect and characterize antibodies to SARS-CoV-2.

Low-volume antibody assays can be used to track SARS-CoV-2 infection rates in settings where active testing for virus is limited and remote sampling is optimal. We developed 12 ELISAs detecting total or antibody isotypes to SARS-CoV-2 nucleocapsid, spike protein or its receptor binding domain (RBD), 3 anti-RBD isotype specific luciferase immunoprecipitation system (LIPS) assays and a novel Spike-RBD bridging LIPS total-antibody assay. We utilized pre-pandemic (n=984) and confirmed/suspected recent COVID-19 sera taken pre-vaccination rollout in 2020 (n=269). Assays measuring total antibody discriminated best between pre-pandemic and COVID-19 sera and were selected for diagnostic evaluation. In the blind evaluation, two of these assays (Spike Pan ELISA and Spike-RBD Bridging LIPS assay) demonstrated >97% specificity and >92% sensitivity for samples from COVID-19 patients taken >21 days post symptom onset or PCR test. These assays offered better sensitivity for the detection of COVID-19 cases than a commercial assay which requires 100-fold larger serum volumes. This study demonstrates that low-volume in-house antibody assays can provide good diagnostic performance, and highlights the importance of using well-characterized samples and controls for all stages of assay development and evaluation. These cost-effective assays may be particularly useful for seroprevalence studies in low and middle-income countries.

CD8+ T-cell specificity is compromised at a defined MHCI/CD8 affinity threshold.

The CD8 co-receptor engages peptide-major histocompatibility complex class I (pMHCI) molecules at a largely invariant site distinct from the T-cell receptor (TCR)-binding platform and enhances the sensitivity of antigen-driven activation to promote effective CD8+ T-cell immunity. A small increase in the strength of the pMHCI/CD8 interaction (~1.5-fold) can disproportionately amplify this effect, boosting antigen sensitivity by up to two orders of magnitude. However, recognition specificity is lost altogether with more substantial increases in pMHCI/CD8 affinity (~10-fold). In this study, we used a panel of MHCI mutants with altered CD8-binding properties to show that TCR-mediated antigen specificity is delimited by a pMHCI/CD8 affinity threshold. Our findings suggest that CD8 can be engineered within certain biophysical parameters to enhance the therapeutic efficacy of adoptive T-cell transfer irrespective of antigen specificity.

The use of yellow fluorescent hybrids to indicate mating in Trypanosoma brucei.

BACKGROUND: Trypanosoma brucei undergoes genetic exchange in its insect vector, the tsetse fly, by an unknown mechanism. The difficulties of working with this experimental system of genetic exchange have hampered investigation, particularly because the trypanosome life cycle stages involved cannot be cultured in vitro and therefore must be examined in the insect. Searching for small numbers of hybrid trypanosomes directly in the fly has become possible through the incorporation of fluorescent reporter genes, and we have previously carried out a successful cross using a reporter-repressor strategy. However, we could not be certain that all fluorescent trypanosomes observed in that cross were hybrids, due to mutations of the repressor leading to spontaneous fluorescence, and we have therefore developed an alternative strategy. RESULTS: To visualize the production of hybrids in the fly, parental trypanosome clones were transfected with a gene encoding Green Fluorescent Protein (GFP) or Red Fluorescent Protein (RFP). Co-infection of flies with red and green fluorescent parental trypanosomes produced yellow fluorescent hybrids, which were easily visualized in the fly salivary glands. Yellow trypanosomes were not seen in midgut or proventricular samples and first appeared in the glands as epimastigotes as early as 13 days after fly infection. Cloned progeny originating from individual salivary glands had yellow, red, green or no fluorescence and were confirmed as hybrids by microsatellite, molecular karyotype and kinetoplast (mitochondrial) DNA analyses. Hybrid clones showed biparental inheritance of both nuclear and kinetoplast genomes. While segregation and reassortment of the reporter genes and microsatellite alleles were consistent with Mendelian inheritance, flow cytometry measurement of DNA content revealed both diploid and polyploid trypanosomes among the hybrid progeny clones. CONCLUSION: The strategy of using production of yellow hybrids to indicate mating in trypanosomes provides a robust and unequivocal system for analysis of genetic exchange. Mating occurred with high frequency in these experimental crosses, limited only by the ability of both parental trypanosomes to invade the salivary glands. Yellow hybrids appeared as soon as trypanosomes invaded the salivary glands, implicating the short, unattached epimastigote as the sexual stage. The recovery of diploid, triploid and tetraploid hybrids in these crosses was surprising as genetic markers appeared to have been inherited according to Mendelian rules. As the polyploid hybrids could have been produced from fusion of unreduced gametes, there is no fundamental conflict with a model of genetic exchange involving meiosis.

Smoking influences the immunological architecture of the human larynx.

Little is known about the effects of demographic and lifestyle factors on laryngeal mucosal immunology. Pinch biopsies of laryngeal mucosa were studied from 63 patients without laryngeal disease. Areas of positive staining for HLA-DR, HLA-DQ, HLA-DP, CD45, CD45RA, CD45RO, CD4, CD8, and CD79 were calculated. Patients were stratified according to gender and smoking status. Analysis of covariance showed current cigarette smokers had increased numbers of CD4+ T cells and there was an association between older age and greater CD4+ T cell numbers in both epithelium and lamina propria. Older age and female gender were associated with decreased lamina propria CD4+ CD45RO+ T cells and an increase in CD4+ CD45RO- T cells. T cell populations in the larynx may therefore be influenced by smoking, age and gender. We hypothesize that smoking induces changes in normal immunological function of the larynx, which may contribute to the etiology of inflammatory disease and cancer.

The level of non-citation of articles within a journal as a measure of quality: a comparison to the impact factor.

BACKGROUND: Current methods of measuring the quality of journals assume that citations of articles within journals are normally distributed. Furthermore using journal impact factors to measure the quality of individual articles is flawed if citations are not uniformly spread between articles. The aim of this study was to assess the distribution of citations to articles and use the level of non-citation of articles within a journal as a measure of quality. This ranking method is compared with the impact factor, as calculated by ISI(R). METHODS: Total citations gained by October 2003, for every original article and review published in current immunology (13125 articles; 105 journals) and surgical (17083 articles; 120 journals) fields during 2001 were collected using ISI(R) Web of Science. RESULTS: The distribution of citation of articles within an individual journal is mainly non-parametric throughout the literature. One sixth (16.7%; IQR 13.6-19.2) of articles in a journal accrue half the total number of citations to that journal. There was a broader distribution of citation to articles in higher impact journals and in the field of immunology compared to surgery. 23.7% (IQR 14.6-42.4) of articles had not yet been cited. Levels of non-citation varied between journals and subject fields. There was a significant negative correlation between the proportion of articles never cited and a journal's impact factor for both immunology (rho = -0.854) and surgery journals (rho = -0.924). CONCLUSION: Ranking journals by impact factor and non-citation produces similar results. Using a non-citation rate is advantageous as it creates a clear distinction between how citation analysis is used to determine the quality of a journal (low level of non-citation) and an individual article (citation counting). Non-citation levels should therefore be made available for all journals.