Mapping SARS-CoV-2 antigenic relationships and serological responses

Vaccination has greatly reduced the disease burden of SARS-CoV-2. However, since late 2020, variants have emerged that are able to escape immunity from vaccination and previous infections, including B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta), and B.1.1.529 (Omicron and its descendants). In combination with vaccination, infections with different variants form the basis of current population immunity against SARS-CoV-2

Protocol to isolate nuclei from Chlamydomonas reinhardtii for ATAC sequencing.

The isolation of sufficient amounts of intact nuclei is essential to obtain high-resolution maps of chromatin accessibility via assay for transposase-accessible chromatin using sequencing (ATAC-seq). Here, we present a protocol for tag-free isolation of nuclei from both cell walled and cell wall-deficient strains of the green model alga Chlamydomonas reinhardtii at a suitable quality for ATAC-seq. We describe steps for nuclei isolation, quantification, and downstream ATAC-seq. This protocol is optimized to shorten the time of isolation and quantification of nuclei

Protocol to isolate nuclei from Chlamydomonas reinhardtii for ATAC sequencing

Summary: The isolation of sufficient amounts of intact nuclei is essential to obtain high-resolution maps of chromatin accessibility via assay for transposase-accessible chromatin using sequencing (ATAC-seq). Here, we present a protocol for tag-free isolation of nuclei from both cell walled and cell wall-deficient strains of the green model alga Chlamydomonas reinhardtii at a suitable quality for ATAC-seq. We describe steps for nuclei isolation, quantification, and downstream ATAC-seq. This protocol is optimized to shorten the time of isolation and quantification of nuclei. : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics

Journal of Leukocyte Biology / Diminished secretion and function of IL29 is associated with impaired IFN response of neonatal plasmacytoid dendritic cells

Plasmacytoid dendritic cells (pDCs) are key players in the antiviral immune response and type III IFNs such as IL29 appear to play a pivotal role in pDC function. Pronounced susceptibility to viral infections in neonates is partly resulting from diminished antiviral immune mechanisms. Accordingly, the aim of the present study was to investigate the impact of IL29 in the altered immune response of neonatal pDCs. PBMCs of adult and term newborns were stimulated with CpGODN2216 in the presence or absence of IL29 and assessed for IFN production, downstreamsignaling, and activation marker expression. A significantly lower IL29 production after TLR9specific stimulation was demonstrated in neonatal pDCs. IL29 enhanced the IFN production of pDCs in adults compared to newborns. Newborn pDCs displayed a significantly lower surface expression of IL10 and IL28R receptor resulting in diminished STAT1 and IRF7 activation. Interestingly, concomitant stimulation with CpGODN2216/IL29 had no impact on the expression of surface activation and maturation markers of pDCs in neither population. The diminished antiviral immune response of neonatal pDCs is associated with reduced production and cellular responses toward IL29. Potential therapeutic agents enhancing the IL29 response in neonatal pDCs possibly augment viral protection in newborns.(VLID)510290

Characterizing SARS-CoV-2 neutralization profiles after bivalent boosting using antigenic cartography

Acknowledgements: We thank Albert Falch, Verena Pittl, Maria Huber, Anna Sauerwein, Anne Heberle, and Toni Rabensteiner for excellent technical and organizational support. We thank Prof. Florian Krammer and Prof. Viviana Simon for sharing their Delta isolate and Prof. Oliver T. Keppler and Dr. Marcel Stern for sharing their Gamma isolate with us. The European Union’s Horizon 2020 research and innovation program under grant agreement No. 101016174 and the Austrian Science Fund (FWF) with project number P35159-B supported J.K. The NIH NIAID Centers of Excellence for Influenza Research and Response (CEIRR) contract 75N93021C00014 as part of the SAVE program supported J.K., D.S., and A.N. A.N. was supported by the Gates Cambridge Trust.Funder: European Union’s Horizon 2020 research and innovation program under grant agreement No. 101016174 NIH NIAID Centers of Excellence for Influenza Research and Response (CEIRR) contract 75N93021C00014 as part of the SAVE programFunder: Gates Cambridge Trust; doi: https://doi.org/10.13039/501100005370Since emergence of the initial SARS-CoV-2 BA.1, BA.2 and BA.5 variants, Omicron has diversified substantially. Antigenic characterization of these new variants is important to analyze their potential immune escape from population immunity and implications for future vaccine composition. Here, we describe an antigenic map based on human single-exposure sera and live-virus isolates that includes a broad selection of recently emerged Omicron variants such as BA.2.75, BF.7, BQ, XBB and XBF variants. Recent Omicron variants clustered around BA.1 and BA.5 with some variants further extending the antigenic space. Based on this antigenic map we constructed antibody landscapes to describe neutralization profiles after booster immunization with bivalent mRNA vaccines based on ancestral virus and either BA.1 or BA.4/5. Immune escape of BA.2.75, BQ, XBB and XBF variants was also evident in bivalently boosted individuals, however, cross-neutralization was improved for those with hybrid immunity. Our results indicate that future vaccine updates are needed to induce cross-neutralizing antibodies against currently circulating variants

Characterizing SARS-CoV-2 neutralization profiles after bivalent boosting using antigenic cartography

Abstract Since emergence of the initial SARS-CoV-2 BA.1, BA.2 and BA.5 variants, Omicron has diversified substantially. Antigenic characterization of these new variants is important to analyze their potential immune escape from population immunity and implications for future vaccine composition. Here, we describe an antigenic map based on human single-exposure sera and live-virus isolates that includes a broad selection of recently emerged Omicron variants such as BA.2.75, BF.7, BQ, XBB and XBF variants. Recent Omicron variants clustered around BA.1 and BA.5 with some variants further extending the antigenic space. Based on this antigenic map we constructed antibody landscapes to describe neutralization profiles after booster immunization with bivalent mRNA vaccines based on ancestral virus and either BA.1 or BA.4/5. Immune escape of BA.2.75, BQ, XBB and XBF variants was also evident in bivalently boosted individuals, however, cross-neutralization was improved for those with hybrid immunity. Our results indicate that future vaccine updates are needed to induce cross-neutralizing antibodies against currently circulating variants

Characterizing SARS-CoV-2 neutralization profiles after bivalent boosting using antigenic cartography.

Since emergence of the initial SARS-CoV-2 BA.1, BA.2 and BA.5 variants, Omicron has diversified substantially. Antigenic characterization of these new variants is important to analyze their potential immune escape from population immunity and implications for future vaccine composition. Here, we describe an antigenic map based on human single-exposure sera and live-virus isolates that includes a broad selection of recently emerged Omicron variants such as BA.2.75, BF.7, BQ, XBB and XBF variants. Recent Omicron variants clustered around BA.1 and BA.5 with some variants further extending the antigenic space. Based on this antigenic map we constructed antibody landscapes to describe neutralization profiles after booster immunization with bivalent mRNA vaccines based on ancestral virus and either BA.1 or BA.4/5. Immune escape of BA.2.75, BQ, XBB and XBF variants was also evident in bivalently boosted individuals, however, cross-neutralization was improved for those with hybrid immunity. Our results indicate that future vaccine updates are needed to induce cross-neutralizing antibodies against currently circulating variants

Characterizing SARS-CoV-2 neutralization profiles after bivalent boosting using antigenic cartography.

Since emergence of the initial SARS-CoV-2 BA.1, BA.2 and BA.5 variants, Omicron has diversified substantially. Antigenic characterization of these new variants is important to analyze their potential immune escape from population immunity and implications for future vaccine composition. Here, we describe an antigenic map based on human single-exposure sera and live-virus isolates that includes a broad selection of recently emerged Omicron variants such as BA.2.75, BF.7, BQ, XBB and XBF variants. Recent Omicron variants clustered around BA.1 and BA.5 with some variants further extending the antigenic space. Based on this antigenic map we constructed antibody landscapes to describe neutralization profiles after booster immunization with bivalent mRNA vaccines based on ancestral virus and either BA.1 or BA.4/5. Immune escape of BA.2.75, BQ, XBB and XBF variants was also evident in bivalently boosted individuals, however, cross-neutralization was improved for those with hybrid immunity. Our results indicate that future vaccine updates are needed to induce cross-neutralizing antibodies against currently circulating variants

Characterizing SARS-CoV-2 neutralization profiles after bivalent boosting using antigenic cartography

Acknowledgements: We thank Albert Falch, Verena Pittl, Maria Huber, Anna Sauerwein, Anne Heberle, and Toni Rabensteiner for excellent technical and organizational support. We thank Prof. Florian Krammer and Prof. Viviana Simon for sharing their Delta isolate and Prof. Oliver T. Keppler and Dr. Marcel Stern for sharing their Gamma isolate with us. The European Union’s Horizon 2020 research and innovation program under grant agreement No. 101016174 and the Austrian Science Fund (FWF) with project number P35159-B supported J.K. The NIH NIAID Centers of Excellence for Influenza Research and Response (CEIRR) contract 75N93021C00014 as part of the SAVE program supported J.K., D.S., and A.N. A.N. was supported by the Gates Cambridge Trust.Funder: European Union’s Horizon 2020 research and innovation program under grant agreement No. 101016174 NIH NIAID Centers of Excellence for Influenza Research and Response (CEIRR) contract 75N93021C00014 as part of the SAVE programFunder: Gates Cambridge Trust; doi: https://doi.org/10.13039/501100005370Since emergence of the initial SARS-CoV-2 BA.1, BA.2 and BA.5 variants, Omicron has diversified substantially. Antigenic characterization of these new variants is important to analyze their potential immune escape from population immunity and implications for future vaccine composition. Here, we describe an antigenic map based on human single-exposure sera and live-virus isolates that includes a broad selection of recently emerged Omicron variants such as BA.2.75, BF.7, BQ, XBB and XBF variants. Recent Omicron variants clustered around BA.1 and BA.5 with some variants further extending the antigenic space. Based on this antigenic map we constructed antibody landscapes to describe neutralization profiles after booster immunization with bivalent mRNA vaccines based on ancestral virus and either BA.1 or BA.4/5. Immune escape of BA.2.75, BQ, XBB and XBF variants was also evident in bivalently boosted individuals, however, cross-neutralization was improved for those with hybrid immunity. Our results indicate that future vaccine updates are needed to induce cross-neutralizing antibodies against currently circulating variants

Direct comparison of SARS-CoV-2 variant specific neutralizing antibodies in human and hamster sera

Acknowledgements: We thank Albert Falch and Verena Pittl for their excellent technical support. The NIH NIAID Centers of Excellence for Influenza Research and Response (CEIRR) contract 75N93021C00014 as part of the SAVE program supported JK, DJS, BLH, AN, SHW, and ST. AN was supported by the Gates Cambridge Trust. The European Union’s Horizon 2020 research and innovation program under grant agreement No. 101016174 and the Austrian Science Fund (FWF) with the project number P35159-B supported JK.Funder: Gates Cambridge Trust; doi: https://doi.org/10.13039/501100005370AbstractAntigenic characterization of newly emerging SARS-CoV-2 variants is important to assess their immune escape and judge the need for future vaccine updates. To bridge data obtained from animal sera with human sera, we analyzed neutralizing antibody titers in human and hamster single infection sera in a highly controlled setting using the same authentic virus neutralization assay performed in one laboratory. Using a Bayesian framework, we found that titer fold changes in hamster sera corresponded well to human sera and that hamster sera generally exhibited higher reactivity.</jats:p