Deep immunoglobulin repertoire sequencing depicts a comprehensive atlas of spike-specific antibody lineages shared among COVID-19 convalescents.

Neutralizing antibodies are a key component in protective humoral immunity against SARS-CoV-2. Currently, available technologies cannot track epitope-specific antibodies in global antibody repertoires. Thus, the comprehensive repertoire of spike-specific neutralizing antibodies elicited by SARS-CoV-2 infection is not fully understood. We therefore combined high-throughput immunoglobulin heavy chain (IgH) repertoire sequencing, and structural and bioinformatics analysis to establish an antibodyomics pipeline, which enables tracking spike-specific antibody lineages that target certain neutralizing epitopes. We mapped the neutralizing epitopes on the spike and determined the epitope-preferential antibody lineages. This analysis also revealed numerous overlaps between immunodominant neutralizing antibody-binding sites and mutation hotspots on spikes as observed so far in SARS-CoV-2 variants. By clustering 2677 spike-specific antibodies with 360 million IgH sequences that we sequenced, a total of 329 shared spike-specific antibody clonotypes were identified from 33 COVID-19 convalescents and 24 SARS-CoV-2-naïve individuals. Epitope mapping showed that the shared antibody responses target not only neutralizing epitopes on RBD and NTD but also non-neutralizing epitopes on S2. The immunodominance of neutralizing antibody response is determined by the occurrence of specific precursors in human naïve B-cell repertoires. We identified that only 28 out of the 329 shared spike-specific antibody clonotypes persisted for at least 12 months. Among them, long-lived IGHV3-53 antibodies are likely to evolve cross-reactivity to Omicron variants through accumulating somatic hypermutations. Altogether, we created a comprehensive atlas of spike-targeting antibody lineages in COVID-19 convalescents and antibody precursors in human naïve B cell repertoires, providing a valuable reference for future vaccine design and evaluation.

Immune response and severity of Omicron BA.5 reinfection among individuals previously infected with different SARS-CoV-2 variants.

Introduction: COVID-19 continues to spread worldwide, with an increasing number of individuals experiencing reinfection after recovering from their primary infection. However, the nature and progression of this infection remain poorly understood. We aimed to investigate the immune response, severity and outcomes of Omicron BA.5 reinfection among individuals previously infected with different SARS-CoV-2 variants. Methods: We enrolled 432 COVID-19 cases who had experienced prior infection with the ancestral SARS-CoV-2 virus, Delta variant or Omicron BA.2 variant between January 2020 and May 2022 in Guangzhou, China. All cases underwent follow-up from March to April, 2023 through telephone questionnaires and clinical visits. Nasal lavage fluid and peripheral blood were collected to assess anti-RBD IgA, anti-RBD IgG and virus-specific IFN-γ secreting T cells. Results: Our study shows that 73.1%, 56.7% and 12.5% of individuals with a prior infection of the ancestral virus, Delta or Omicron BA.2 variant experienced reinfection with the BA.5 variant, respectively. Fever, cough and sore throat were the most common symptoms of BA.5 reinfection, with most improving within one week and none progressing to a critical condition. Compared with individuals without reinfection, reinfected patients with a prior Delta infection exhibited elevated levels of nasal anti-RBD IgA, serum anti-RBD IgG and IFN-γ secreting T cells, whereas there was no noticeable change in reinfected individuals with a prior BA.2 infection. Conclusion: These results suggest that BA.5 reinfection is common but severe outcomes are relatively rare. Reinfection with a novel SARS-CoV-2 variant different from the prior infection may induce a more robust immune protection, which should be taken into account during vaccine development.

Shared IGHV1-69-encoded neutralizing antibodies contribute to the emergence of L452R substitution in SARS-CoV-2 variants.

SARS-CoV-2 variants continue to emerge facing established herd immunity. L452R, previously featured in the Delta variant, quickly emerged in Omicron subvariants, including BA.4/BA.5, implying a continued selection pressure on this residue. The underlying links between spike mutations and their selective pressures remain incompletely understood. Here, by analyzing 221 structurally characterized antibodies, we found that IGHV1-69-encoded antibodies preferentially contact L452 using germline-encoded hydrophobic residues at the tip of HCDR2 loop. Whereas somatic hypermutations or VDJ rearrangements are required to acquire L452-contacting hydrophobic residues for non-IGHV1-69 encoded antibodies. Antibody repertoire analysis revealed that IGHV1-69 L452-contacting antibody lineages are commonly induced among COVID-19 convalescents but non-IGHV1-69 encoded antibodies exhibit limited prevalence. In addition, we experimentally demonstrated that L452R renders most published IGHV1-69 antibodies ineffective. Furthermore, we found that IGHV1-69 L452-contacting antibodies are enriched in convalescents experienced Omicron BA.1 (without L452R) breakthrough infections but rarely found in Delta (with L452R) breakthrough infections. Taken together, these findings support that IGHV1-69 population antibodies contribute to selection pressure for L452 substitution. This study thus provides a better understanding of SARS-CoV-2 variant genesis and immune evasion.

SARS-CoV-2 Delta and Omicron variants evade population antibody response by mutations in a single spike epitope.

Population antibody response is thought to be important in selection of virus variants. We report that SARS-CoV-2 infection elicits a population immune response that is mediated by a lineage of VH1-69 germline antibodies. A representative antibody R1-32 from this lineage was isolated. By cryo-EM, we show that it targets a semi-cryptic epitope in the spike receptor-binding domain. Binding to this non-ACE2 competing epitope results in spike destruction, thereby inhibiting virus entry. On the basis of epitope location, neutralization mechanism and analysis of antibody binding to spike variants, we propose that recurrent substitutions at 452 and 490 are associated with immune evasion of the identified population antibody response. These substitutions, including L452R (present in the Delta variant), disrupt interactions mediated by the VH1-69-specific hydrophobic HCDR2 to impair antibody-antigen association, enabling variants to escape. The first Omicron variants were sensitive to antibody R1-32 but subvariants that harbour L452R quickly emerged and spread. Our results provide insights into how SARS-CoV-2 variants emerge and evade host immune responses.

A Class of Shark-Derived Single-Domain Antibodies can Broadly Neutralize SARS-Related Coronaviruses and the Structural Basis of Neutralization and Omicron Escape.

The identification of a novel class of shark-derived single domain antibodies, named vnarbodies that show picomolar affinities binding to the receptor binding domain (RBD) of Wuhan and Alpha, Beta, Kappa, Delta, Delta-plus, and Lambda variants, is reported. Vnarbody 20G6 and 17F6 have broad neutralizing activities against all these SARS-CoV-2 viruses as well as other sarbecoviruses, including Pangolin coronavirus and Bat coronavirus. Intranasal administration of 20G6 effectively protects mice from the challenges of SARS-CoV-2 Wuhan and Beta variants. 20G6 and 17F6 contain a unique "WXGY" motif in the complementary determining region 3 that binds to a hidden epitope on RBD, which is highly conserved in sarbecoviruses through a novel ß-sheet interaction. It is found that the S375F mutation on Omicron RBD disrupts the structure of ß-strand, thus impair the binding with 20G6. The study demonstrates that shark-derived vnarbodies offer a prophylactic and therapeutic option against most SARS-CoV-2 variants and provide insights into antibody evasion by the Omicron variant.

Analysis of B Cell Receptor Repertoires Reveals Key Signatures of the Systemic B Cell Response after SARS-CoV-2 Infection.

A comprehensive study of the B cell response against SARS-CoV-2 could be significant for understanding the immune response and developing therapeutical antibodies and vaccines. To define the dynamics and characteristics of the antibody repertoire following SARS-CoV-2 infection, we analyzed the mRNA transcripts of immunoglobulin heavy chain (IgH) repertoires of 24 peripheral blood samples collected between 3 and 111 days after symptom onset from 10 COVID-19 patients. Massive clonal expansion of naive B cells with limited somatic hypermutation (SHM) was observed in the second week after symptom onset. The proportion of low-SHM IgG clones strongly correlated with spike-specific IgG antibody titers, highlighting the significant activation of naive B cells in response to a novel virus infection. The antibody isotype switching landscape showed a transient IgA surge in the first week after symptom onset, followed by a sustained IgG elevation that lasted for at least 3 months. SARS-CoV-2 infection elicited poly-germ line reactive antibody responses. Interestingly, 17 different IGHV germ line genes recombined with IGHJ6 showed significant clonal expansion. By comparing the IgH repertoires that we sequenced with the 774 reported SARS-CoV-2-reactive monoclonal antibodies (MAbs), 13 shared spike-specific IgH clusters were found. These shared spike-specific IgH clusters are derived from the same lineage of several recently published neutralizing MAbs, including CC12.1, CC12.3, C102, REGN10977, and 4A8. Furthermore, identical spike-specific IgH sequences were found in different COVID-19 patients, suggesting a highly convergent antibody response to SARS-CoV-2. Our analysis based on sequencing antibody repertoires from different individuals revealed key signatures of the systemic B cell response induced by SARS-CoV-2 infection. IMPORTANCE Although the canonical delineation of serum antibody responses following SARS-CoV-2 infection has been well established, the dynamics of antibody repertoire at the mRNA transcriptional level has not been well understood, especially the correlation between serum antibody titers and the antibody mRNA transcripts. In this study, we analyzed the IgH transcripts and characterized the B cell clonal expansion and differentiation, isotype switching, and somatic hypermutation in COVID-19 patients. This study provided insights at the repertoire level for the B cell response after SARS-CoV-2 infection.

Germline IGHV3-53-encoded RBD-targeting neutralizing antibodies are commonly present in the antibody repertoires of COVID-19 patients.

Monoclonal antibodies (mAbs) encoded by IGHV3-53 (VH3-53) targeting the spike receptor-binding domain (RBD) have been isolated from different COVID-19 patients. However, the existence and prevalence of shared VH3-53-encoded antibodies in the antibody repertoires is not clear. Using antibody repertoire sequencing, we found that the usage of VH3-53 increased after SARS-CoV-2 infection. A highly shared VH3-53-J6 clonotype was identified in 9 out of 13 COVID-19 patients. This clonotype was derived from convergent gene rearrangements with few somatic hypermutations and was evolutionary conserved. We synthesized 34 repertoire-deduced novel VH3-53-J6 heavy chains and paired with a common IGKV1-9 light chain to produce recombinant mAbs. Most of these recombinant mAbs (23/34) possess RBD binding and virus-neutralizing activities, and recognize ACE2 binding site via the same molecular interface. Our computational analysis, validated by laboratory experiments, revealed that VH3-53 antibodies targeting RBD are commonly present in COVID-19 patients' antibody repertoires, indicating many people have germline-like precursor sequences to rapidly generate SARS-CoV-2 neutralizing antibodies. Moreover, antigen-specific mAbs can be digitally obtained through antibody repertoire sequencing and computational analysis.

Correlation between GPR, MHR and elderly essential hypertension with unstable angina pectoris. / GPR、MHRä¸Žè€å¹´åŽŸå‘æ€§é«˜è¡€åŽ‹åˆå¹¶ä¸ç¨³å®šåž‹å¿ƒç»žç—›çš„ç›¸å ³æ€§.

OBJECTIVES: To investigate the level and significance of serum γ-glutamyl transferase-to-platelet ratio (GPR) and monocyte count to high-density lipoprotein ratio (MHR) in patients with essential hypertension (EH) and unstable angina (UA). METHODS: A total of 218 patients with coronary angiography aged ≥60 years, who were admitted to the EH hospital of the Department of Cardiac Medicine, Affiliated Hospital of Chengde Medical College, were selected from September 2018 to September 2019. They were divided into an EH+UA group (n=113) and an EH group (n=105). In addition, 106 patients with normal coronary angiography who were diagnosed with coronary heart disease were selected as a control group. The general data, blood biochemical indicators, GPR and MHR in each group were compared, and partial correlation analysis and receiver operator characteristic (ROC) curve analysis were performed. RESULTS: Compared with the control group, patients in the EH+UA group and the EH group had higher body mass index (BMI), tyiglyceride (TG), GPR, and MHR, and lower high-density lipoprotein-cholesterol (HDL-C) (all P<0.05); and patients in the EH+UA group had higher white blood cell counts, alanine aminotransferase (ALT), and uric acid (all P<0.05). Compared with the EH group, patients in the EH+UA group had higher GPR and MHR (both P<0.05). Partial correlation analysis showed that after controlling the antihypertensive drugs and lipid-lowering drugs, GPR was found to be positively correlated with BMI, white blood cell count, ALT, TG, and uric acid (r=0.160, 0.111, 0.205, 0.250, 0.154, respectively, all P<0.05), which was negatively correlated with HDL-C (r=-0.238, P<0.05); MHR was positively correlated with BMI, ALT, TG, uric acid, and GPR (r=0.186, 0.307, 0.157, 0.141, 0.223, respectively, all P<0.05), and negatively correlated with HDL-C (r=-0.610, P<0.001). ROC curve analysis showed that GPR had higher specificity and positive predictive value, while MHR had higher sensitivity. When the two indicators were combined, the sensitivity and positive predictive value were higher. CONCLUSIONS: There is a correlation between GPR, MHR and EH combined with UA pectoris, and the combined detection of the two indicators has adjuvant diagnostic value for elderly EH combined with UA.

IL-34 and coronary heart disease complicated with diabetes mellitus. / IL-34ä¸Žå† å¿ƒç— åˆå¹¶ç³–å°¿ç— .

Coronary heart disease and diabetes mellitus are closely related to chronic low-grade inflammation. Interleukin-34 (IL-34) is a new member of the interleukin family discovered in recent years. It is involved in the pathophysiological process of mononuclear phagocyte system mainly via binding to colony stimulating factor-1 receptor, and it is closely related to inflammatory and autoimmune diseases. IL-34 is highly expressed in patients with coronary heart disease or diabetes mellitus. IL-34 induces atherosclerosis and insulin resistance through multiple pro-inflammatory actions, ultimately leading to the occurrence and development of coronary heart disease, type 2 diabetes, and their comorbidities.

The characteristics and risk factors of in-stent restenosis in patients with percutaneous coronary intervention: what can we do.

BACKGROUND: Percutaneous coronary intervention (PCI) is a common treatment for patients with coronary heart disease, and intra-stent restenosis (ISR) is a serious complication after PCI. It's necessary to identify the potential risk factors to provide evidence for the prevention of ISR. METHODS: The patients who underwent coronary angiography 1 year after PCI in our hospital from January 2017 to May 2019 were selected. The characteristics and results of clinical examination of ISR and no-ISR patients were compared, Multivariate logistic regression analyses were performed to identify the risk factors. RESULTS: A total of 209 patients were included, the incidence of ISR after PCI was 30.62%. There were significant differences on the hypertension, diabetes, number of coronary artery lesions, reasons for stent implantation, the diameter of stent, the length of stent and stent position between ISR group and no-ISR patients (all p < 0.05). The LDL-C in ISR groups was significantly higher than that of no-ISR group (p = 0.048), there were no significant differences between two groups in FPG, TG, TC, HDL-C, Apo A1, Apo B, LP-a and glycated haemoglobin (all p > 0.05). The hypertension (OR 4.30, 95% CI 1.12-9.34), diabetes (OR 5.29, 95% CI 1.25-9.01), number of coronary artery lesions ≥ 2 (OR 4.84, 95% CI 1.21-9.55), LDL-C ≥ 1.9 mmol/L (OR 5.93, 95% CI 2.29-10.01), unstable angina (OR 2.92, 95% CI 1.20-4.55), left anterior descending artery (OR 4.01, 95% CI 1.73-7.58), diameter of stent ≥ 3 mm (OR 5.42, 95% CI 1.24-10.84), the length of stent > 20 mm (OR 3.06, 95% CI 1.19-5.22) were the independent risk factor for ISR (all p < 0.05). CONCLUSION: It is necessary to take preventive measures against these risk factors to reduce ISR, and studies with larger sample size and longer follow-up on this issue are needed in the future.

Meta-analysis of safety of the coadministration of statin with fenofibrate in patients with combined hyperlipidemia.

Addition of fenofibrate to statin therapy might represent a viable treatment option for patients whose high risk for coronary heart disease is not controlled by a statin alone. However, safety of coadministration of statin with fenofibrate has been a great concern. The present study tested the safety of coadministration of statin with fenofibrate. We systematically searched the literature to identify randomized controlled trials examining safety of coadministration of statin with fenofibrate. A meta-analysis was performed to estimate safety of coadministration of statin with fenofibrate using fixed-effects models. There were 1,628 subjects in the identified 6 studies. Discontinuation attributed to any adverse events (4.5% vs 3.1%, p = 0.20), any adverse events (42% vs 41%, p = 0.82), adverse events related to study drug (10.9% vs 11.0%, p = 0.95), and serious adverse events (2.0% vs 1.5%, p = 0.71) were not significantly different in the 2 arms. Incidence of alanine aminotransferase and/or aspartate aminotransferase ≥3 times upper limit of normal in the combination therapy arm was significantly higher than in the statin monotherapy arm (3.1% vs 0.2%, p = 0.0009). In the 6 trials with 1,628 subjects no case of myopathy or rhabdomyolysis was reported. In conclusion, statin-fenofibrate combination therapy was tolerated as well as statin monotherapy. Physicians should consider statin-fenofibrate combination therapy to treat patients with mixed dyslipidemia.

[Association of QT dispersion, ST/heart rate slope and ST-segment depression in exercise test to evaluate restenosis after percutaneous coronary intervention].

OBJECTIVE: To evaluate the sensitivity and specificity of QT dispersion (QTd) and ST/heart rate slope (ST/HRs) at the end of ECG exercise test plus ST-segment depression on diagnosing restenosis after percutaneous coronary intervention (PCI). METHODS: Between November 2001 and December 2003, 129 patients underwent PCI successfully, and they were examined 3-6 months later. At the end of treadmill exercise, QTd and ST/HRs were measured. All patients also accepted coronary angiography to ascertain whether he/she had restenosis. The results of QTd and ST/HRs plus ST-segment depression were then evaluated. RESULTS: The sensitivity and specificity of QTd and ST/HRs plus ST-segment depression were 84.6% and 80.4% respectively. Both of them were significantly higher than conventional ST-segment depression standard (sensitivity was 53.3% and specificity was 66.7%, P<0.05). CONCLUSION: Measuring QTd and ST/HRs at the end of ECG treadmill exercise test plus ST-segment depression can be used for the diagnosis of restenosis after PCI.