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SARS-CoV-2 Omicron XBB infections boost cross-variant neutralizing antibodies, potentially explaining the observed delay of the JN.1 wave in some Brazilian regions.
IJID Reg
March 2025
Laboratory of Respiratory Viruses, Exanthematous and Enteroviruses and Viral Emergencies, Oswaldo Cruz Institute, Rio de Janeiro, Brazil.
Unlabelled: The SARS-CoV-2 JN.1 lineage emerged in late 2023 and quickly replaced the XBB lineages, becoming the predominant Omicron variant worldwide in 2024. We estimate the epidemiologic impact of this SARS-CoV-2 lineage replacement in Brazil and we further assessed the cross-reactive neutralizing antibody (NAb) responses in a cohort of convalescent Brazilian patients infected during 2023.
View Article and Find Full Text PDFBroad-spectrum affinity chromatography of SARS-CoV-2 and Omicron vaccines from ligand screening to purification.
J Chromatogr A
January 2025
Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China. Electronic address:
Emerging variants of SARS-CoV-2 pose great technological and regulatory challenges to vaccine manufacturing, especially in downstream processing. To address this dilemma, the development of broad-spectrum affinity chromatography for the purification of wild-type SARS-CoV-2 and its variants is crucial. We propose a comprehensive strategy to achieve this goal via the identification of high-affinity peptides by affinity selection of phage display and next-generation sequencing (NGS) and the evaluation of chromatographic performance.
View Article and Find Full Text PDFEmergence of SARS-CoV-2 subgenomic RNAs that enhance viral fitness and immune evasion.
PLoS Biol
January 2025
RNA Virus Replication Laboratory, The Francis Crick Institute, London, United Kingdom.
Coronaviruses express their structural and accessory genes via a set of subgenomic RNAs, whose synthesis is directed by transcription regulatory sequences (TRSs) in the 5' genomic leader and upstream of each body open reading frame. In SARS-CoV-2, the TRS has the consensus AAACGAAC; upon searching for emergence of this motif in the global SARS-CoV-2 sequences, we find that it evolves frequently, especially in the 3' end of the genome. We show well-supported examples upstream of the Spike gene-within the nsp16 coding region of ORF1b-which is expressed during human infection, and upstream of the canonical Envelope gene TRS, both of which have evolved convergently in multiple lineages.
View Article and Find Full Text PDFSingle-cell transcriptome atlas of peripheral immune features to Omicron breakthrough infection under booster vaccination strategies.
Front Immunol
January 2025
School of Public Health and Health Management, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China.
Introduction: The high percentage of Omicron breakthrough infection in vaccinees is an emerging problem, of which we have a limited understanding of the phenomenon.
Methods: We performed single-cell transcriptome coupled with T-cell/B-cell receptor (TCR/BCR) sequencing in 15 peripheral blood mononuclear cell (PBMC) samples from Omicron infection and naïve with booster vaccination.
Results: We found that after breakthrough infection, multiple cell clusters showed activation of the type I IFN pathway and widespread expression of Interferon-stimulated genes (ISGs); T and B lymphocytes exhibited antiviral and proinflammatory-related differentiation features with pseudo-time trajectories; and large TCR clonal expansions were concentrated in effector CD8 T cells, and clonal expansions of BCRs showed a preference for IGHV3.
Variants and vaccines impact nasal immunity over three waves of SARS-CoV-2.
Nat Immunol
January 2025
Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA.
Viral variant and host vaccination status impact infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), yet how these factors shift cellular responses in the human nasal mucosa remains uncharacterized. We performed single-cell RNA sequencing (scRNA-seq) on nasopharyngeal swabs from vaccinated and unvaccinated adults with acute Delta and Omicron SARS-CoV-2 infections and integrated with data from acute infections with ancestral SARS-CoV-2. Patients with Delta and Omicron exhibited greater similarity in nasal cell composition driven by myeloid, T cell and SARS-CoV-2 cell subsets, which was distinct from that of ancestral cases.
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