Table 4_Temporal TCR dynamics and epitope diversity mark recovery in severe COVID-19 patients.xlsx

IntroductionSevere COVID-19 is characterized by immune dysregulation, with T cells playing a central role in disease progression and recovery. However, the longitudinal dynamics of the T cell receptor (TCR) repertoire during the course of severe illness remain unclear.
MethodsTo investigate temporal changes in adaptive immunity, we analyzed peripheral blood samples from the ICU-admitted severe COVID-19 patients (n = 36) collected at three time points: Day 1 (T1), Day 4 (T2), and Day 7 (T3). Bulk RNA-sequencing was performed to extract TCR repertoires, and cytokine profiles were assessed in parallel. TCR clonotypes were annotated using VDJdb and TCRex to infer potential epitope specificities.
ResultsBy T3, we observed a 2.3-fold expansion in TCR clonotypes along with increased TCR-β (TRB) chain usage, indicating the emergence of a broad polyclonal T cell response. In contrast, TCR-γ (TRG) chain prevalence declined. Pro-inflammatory cytokines, including IL-1β and IL-6, were reduced over time, marking a shift toward immune resolution. Changes in CDR3 motifs and preferential TRBV gene segment usage were detected, suggesting repertoire adaptation. Additionally, annotated TCR clonotypes at T3 mapped to SARS-CoV-2 and other pathogen-associated epitopes (e.g., CMV, Plasmodium), reflecting possible cross-reactivity or memory T cell recruitment.
DiscussionThese findings suggest a coordinated transition from immune dysfunction to recovery in severe COVID-19, marked by expanding TCR diversity, reduced inflammation, and predicted broadening of antigen recognition. The integrated analysis of TCR repertoire dynamics and cytokine profiles provides insights into the adaptive immune mechanisms underlying viral clearance and immune stabilization.

引言
重症新型冠状病毒肺炎（COVID-19）以免疫失调为特征，T细胞在疾病进展与转归中发挥核心作用。然而，重症病程中T细胞受体（T cell receptor, TCR）库的纵向动态变化仍不明确。

方法
为探究适应性免疫的时序变化，本研究对收入重症监护病房（intensive care unit, ICU）的36例重症COVID-19患者的外周血样本进行分析，样本采集于三个时间点：第1天（T1）、第4天（T2）及第7天（T3）。通过批量RNA测序（bulk RNA-sequencing）提取TCR库，并同步评估细胞因子谱。研究采用VDJdb与TCRex对TCR克隆型进行注释，以推断潜在的表位特异性。

结果
至T3时，我们观察到TCR克隆型扩增2.3倍，同时TCR-β（TRB）链的使用频率升高，提示出现广泛的多克隆T细胞应答。与之相反，TCR-γ（TRG）链的占比有所下降。包括白细胞介素-1β（IL-1β）、白细胞介素-6（IL-6）在内的促炎细胞因子随时间推移水平降低，标志着向免疫稳态恢复的转变。研究还检测到CDR3基序的变化以及TRBV基因片段的偏好性使用，提示TCR库发生适应性重塑。此外，T3时注释得到的TCR克隆型可匹配新型冠状病毒（SARS-CoV-2）及其他病原体相关表位（如巨细胞病毒（cytomegalovirus, CMV）、疟原虫（Plasmodium）），反映了潜在的交叉反应或记忆T细胞招募现象。

讨论
上述研究结果表明，重症COVID-19患者体内存在从免疫功能失调到恢复的协同转变，其特征为TCR多样性增加、炎症水平降低以及抗原识别范围的预期拓宽。本研究对TCR库动态变化与细胞因子谱的整合分析，为阐明病毒清除与免疫稳态维持背后的适应性免疫机制提供了新见解。