Browsing by Author "Daniell, Xiaoju"
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Item Open Access Mapping SARS-CoV-2 antigenic relationships and serological responses.(Science (New York, N.Y.), 2023-10) Wilks, Samuel H; Mühlemann, Barbara; Shen, Xiaoying; Türeli, Sina; LeGresley, Eric B; Netzl, Antonia; Caniza, Miguela A; Chacaltana-Huarcaya, Jesus N; Corman, Victor M; Daniell, Xiaoju; Datto, Michael B; Dawood, Fatimah S; Denny, Thomas N; Drosten, Christian; Fouchier, Ron AM; Garcia, Patricia J; Halfmann, Peter J; Jassem, Agatha; Jeworowski, Lara M; Jones, Terry C; Kawaoka, Yoshihiro; Krammer, Florian; McDanal, Charlene; Pajon, Rolando; Simon, Viviana; Stockwell, Melissa S; Tang, Haili; van Bakel, Harm; Veguilla, Vic; Webby, Richard; Montefiori, David C; Smith, Derek JDuring the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, multiple variants escaping preexisting immunity emerged, causing reinfections of previously exposed individuals. Here, we used antigenic cartography to analyze patterns of cross-reactivity among 21 variants and 15 groups of human sera obtained after primary infection with 10 different variants or after messenger RNA (mRNA)-1273 or mRNA-1273.351 vaccination. We found antigenic differences among pre-Omicron variants caused by substitutions at spike-protein positions 417, 452, 484, and 501. Quantifying changes in response breadth over time and with additional vaccine doses, our results show the largest increase between 4 weeks and >3 months after a second dose. We found changes in immunodominance of different spike regions, depending on the variant an individual was first exposed to, with implications for variant risk assessment and vaccine-strain selection.Item Open Access Mapping SARS-CoV-2 antigenic relationships and serological responses.(bioRxiv, 2022-07-13) Wilks, Samuel H; Mühlemann, Barbara; Shen, Xiaoying; Türeli, Sina; LeGresley, Eric B; Netzl, Antonia; Caniza, Miguela A; Chacaltana-Huarcaya, Jesus N; Corman, Victor M; Daniell, Xiaoju; Datto, Michael B; Dawood, Fatimah S; Denny, Thomas N; Drosten, Christian; Fouchier, Ron AM; Garcia, Patricia J; Halfmann, Peter J; Jassem, Agatha; Jeworowski, Lara M; Jones, Terry C; Kawaoka, Yoshihiro; Krammer, Florian; McDanal, Charlene; Pajon, Rolando; Simon, Viviana; Stockwell, Melissa S; Tang, Haili; van Bakel, Harm; Veguilla, Vic; Webby, Richard; Montefiori, David C; Smith, Derek JDuring the SARS-CoV-2 pandemic, multiple variants with differing amounts of escape from pre-existing immunity have emerged, causing concerns about continued protection. Here, we use antigenic cartography to quantify and visualize the antigenic relationships among 16 SARS-CoV-2 variants titrated against serum samples taken post-vaccination and post-infection with seven different variants. We find major antigenic differences caused by substitutions at spike positions 417, 452, 484, and possibly 501. B.1.1.529 (Omicron BA.1) showed the highest escape from all sera tested. Visualization of serological responses as antibody landscapes shows how reactivity clusters in different regions of antigenic space. We find changes in immunodominance of different spike regions depending on the variant an individual was exposed to, with implications for variant risk assessment and vaccine strain selection. One sentence summary: Antigenic Cartography of SARS-CoV-2 variants reveals amino acid substitutions governing immune escape and immunodominance patterns.Item Unknown Optimization and validation of a neutralizing antibody assay for HIV-1 in A3R5 cells.(Journal of immunological methods, 2014-07) Sarzotti-Kelsoe, Marcella; Daniell, Xiaoju; Todd, Christopher A; Bilska, Miroslawa; Martelli, Amanda; LaBranche, Celia; Perez, Lautaro G; Ochsenbauer, Christina; Kappes, John C; Rountree, Wes; Denny, Thomas N; Montefiori, David CA3R5 is a human CD4(+) lymphoblastoid cell line that was engineered to express CCR5 and is useful for the detection of weak neutralizing antibody responses against tier 2 strains of HIV-1. Here we describe the optimization and validation of the HIV-1 neutralizing antibody assay that utilizes A3R5 cells, performed in compliance with Good Clinical Laboratory Practice (GCLP) guidelines. The assay utilizes Renilla luciferase-expressing replication competent infectious molecular clones (IMC) encoding heterologous env genes from different HIV-1 clades. Key assay validation parameters tested included specificity, accuracy, precision, limit of detection and quantitation, specificity, linearity and range, and robustness. Plasma samples demonstrated higher non-specific activity than serum samples in the A3R5 assay. This assay can tolerate a wide range of virus input but is more sensitive to cell concentration. The higher sensitivity of the A3R5 assay in neutralization responses to tier 2 strains of HIV-1 makes it complementary to, but not a substitute for the TZM-bl assay. The validated A3R5 assay is employed as an endpoint immunogenicity test for vaccine-elicited neutralizing antibodies against tier 2 strains of HIV-1, and to identify correlates of protection in HIV-1 vaccine trials conducted globally.