Multi-omic characteristics of longitudinal immune profiling in subjects with breakthrough infection caused by Omicron BA.5 sublineages

Background Omicron sub-variants have led to millions of coronavirus disease 2019 (COVID-19) cases worldwide. Although Omicron breakthrough infections (BTIs) exhibit lower hospitalization rates than previous variants, concerns about post-COVID-19 conditions (PCC) persist. More importantly, the immune response dynamics, lymphocyte subsets, and immune repertoire features following BA.5 sublineages BTI remain poorly understood. Methods In a longitudinal cohort, we monitored the recovery dynamics in patients with BTI at various time points. We employed single-cell transcriptomics, T cell receptor (TCR)/BCR sequencing, and antibody mass spectrometry to sequentially assess the immune response following BA.5.2 or BF.7 BTI. Findings Serological analysis revealed active cellular and humoral immunity 2-week post-BTI, with significant increases in cytokines (CKs) like IFN-γ, TNFβ, IL-2, and neutralizing antibodies. CK levels reverted to pre-infection levels, while broadly neutralizing antibodies remained high 1-month post-infection. Single-cell sequencing demonstrated robust immune activation and antiviral responses in NK, T, and B lymphocytes within 1-month post-BTI. Interestingly, the immune system maintained its strength to combat viral infection at 2-week post-BTI, transitioning toward repair and tissue damage elimination at 1-month. Imbalance between activated and inhibitory immune responses, and tissue repair may contribute to the development of PCC. TCR/BCR library analysis revealed a higher clonal type in the BTI_2w group, mainly in NKT, memory T or B, and plasma cells, crucial for immune memory and antigen clearance. The BTI_1m group exhibited more IgG and IgA-type BCRs, with higher somatic hypermutation indicating greater maturity. Biological function verification of IgG and IgA-type monoclonal antibodies corresponding to amplified BCRs revealed antigen-specific and broad-spectrum antibodies. Interpretation Our study elucidated the dynamic immune profiling of individuals two weeks and one month after Omicron BA.5 sublineages BTI. This provided essential insights into pathogenicity, sequential immune status, recovery mechanisms of Omicron sublineage BTI, and novel concepts for broad-spectrum antibody development.