SARS-CoV-2 と COVID-19 に関する備忘録 Vol.30

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SARS-CoV-2 と COVID-19 に関するメモ・備忘録

◆Enhanced immune evasion of SARS-CoV-2 variants KP.3.1.1 and XEC through N-terminal domain mutations【THE LANCET　2024年11月22日】

KP.3, a subvariant of JN.1, has rapidly emerged as the dominant strain of SARS-CoV-2 in several countries, and has been designated as a Variant Under Monitoring. Previous studies indicate that the unique Q493E substitution in KP.3 Spike glycoprotein enhances its receptor ACE2-binding affinity and immune evasion, enabling it to outcompete KP.2. Notably, KP.3.1.1, which only carries one additional S31 deletion compared to KP.3, has surpassed KP.3 to become the new dominant strain globally (figure A; appendix p 4). Meanwhile, XEC, a recombinant variant of KS.1.1 and KP.3.3, shows strong potential to become the next dominant strain, rapidly expanding across Europe and North America. Compared with KP.3, XEC has only two additional spike mutations, F59S and T22N (appendix p 4). Both S31del and T22N introduce potential glycosylation on the N-terminal domain. Consequently, there is an imperative need to characterise the antigenicity and infectivity of KP.3.1.1 and XEC.

Here we first used surface plasmon resonance to assess the binding affinity between human ACE2 and the Spike of JN.1, KP.3, KP.3.1.1, and XEC. We found KP.3, KP.3.1.1, and XEC showed a significant increase in ACE2-Spike binding affinity compared with JN.1; however, we did not observe significant changes in the receptor binding of KP.3.1.1 and XEC relative to KP.3, despite the N-terminal domain glycosylation mutations (figure B). We then evaluated the infectivity of KP.3.1.1 and XEC using vesicular stomatitis virus-based pseudoviruses in Vero cells. We found that although the pseudovirus infectivity of KP.3, KP.3.1.1, and XEC increased compared with JN.1, no significant differences were observed among KP.3, KP.3.1.1, and XEC (figure C), which is consistent with another recent study.

With the vesicular stomatitis virus-based pseudovirus system, in our study we assessed the neutralisation of convalescent plasma against KP.3.1.1 and XEC, involving plasma samples from two cohorts. Participants in both cohorts received two or three doses of inactivated SARS-CoV-2 vaccines and had breakthrough infections with BA.5 or BF.7. One cohort (n=29) was reinfected by JN.1, and the other (n=21) by JN.1 or XDV with F456L (appendix p11). The specific variant causing reinfections was inferred from local prevalence (>90%) at the sampling timepoint (appendix p6). Of note, XDV shares the same Spike sequence as JN.1. We found that KP.3.1.1 and XEC showed significantly enhanced immune evasion capabilities compared with KP.3 (figure D). Compared with KP.3, the 50% neutralisation titre values against KP.3.1.1 decreased by 1·2-fold in the JN.1 group and 1·5-fold in the JN.1 or XDV with F456L group, whereas against XEC values decreased by 1·8-fold in the JN.1 group and 2·1-fold in the JN.1 or XDV with F456L group. Notably, the JN.1 or XDV with F456L group showed significant plasma neutralisation improvement against KP.2 only, with no differences observed against KP.3, KP.3.1.1, and XEC (appendix p7).

Since KP.3.1.1 and XEC do not have additional receptor-binding domain mutations compared with KP.3, and most neutralising antibodies should target the receptor-binding domain instead of the N-terminal domain, we hypothesised the unexpected strong evasion mediated by the N-terminal domain glycosylation mutations could be attributed to potential effects on the neutralising activity of receptor-binding domain-targeting neutralising antibodies through allosteric effects. Indeed, compared with KP.3, KP.3.1.1 and XEC showed enhanced escape capabilities against neutralising antibodies targeting various epitopes on the receptor-binding domain in Vero cells, especially those competing with ACE2 (figure E; appendix p 8). The inhibition efficiency of soluble ACE2 against KP.3.1.1 and XEC also showed a slight reduction. This enhanced antibody escape capability indicates that the glycosylation mutations on the N-terminal domain of KP.3.1.1 and XEC, located away from the epitopes on the receptor-binding domain, potentially reduce receptor-binding domain-targeting neutralising antibody activity via allostery.

In summary, we found that KP.3.1.1 and especially XEC showed enhanced humoral immune evasion and receptor-binding domain-targeting antibody escape capabilities, supporting the foreseeable dominance of the XEC variant of SARS-CoV-2. However, the mechanisms by which T22N and S31del enhance antibody escape from receptor-binding domain-targeting antibodies remain unclear and require further exploration. The potential mechanisms could involve kinetic changes in receptor-binding domain conformational dynamics induced by additional N-terminal domain glycosylation or effect on membrane fusion efficiency. Further studies are necessary to elucidate the mechanism.

◆Enhanced immune evasion of SARS-CoV-2 variants KP.3.1.1 and XEC through N-terminal domain mutations【nature Pediatric Research　2024年11月27日】

Abstract

Background

Many children suffer from lingering symptoms after COVID-19, known as long COVID syndrome (LCS), otherwise called Post COVID-19 Condition (PCC). Despite extensive research, the prevalence of symptoms, its impact on quality of life, and underlying mechanisms still need to be fully understood. As neutrophilic granulocytes play an essential role in COVID-19, and their prolonged disruption was found to cause immunological diseases, we hypothesized their ongoing disturbed functionality in LCS.

Methods

We studied 129 children with LCS, 32 convalescent children (CG+), and 8 uninfected children (CG−). Online questionnaires and in-person examinations assessed symptoms, quality of life, and functioning (QoL-F). Effector functions of neutrophilic granulocytes obtained from the venous blood of 29 LCS and 17 CG+ children were also investigated.

Results

Persistent fatigue was the most common symptom in children with LCS, while both control groups complained about anxiety most frequently. LCS children experienced significantly more symptoms, impairing their QoL-F compared to CG+. Neutrophilic granulocyte dysfunction was found in LCS children, with decreased superoxide-producing activity and phagocytosis compared to CG+. The number of complaints of children with LCS correlated significantly with altered neutrophil effector functions.

Conclusion

Neutrophil dysfunction in children with LCS may be part of the disease pathogenesis or a predisposing factor.

Impact

  • Using online questionnaires validated during in-person medical examinations and including two different control groups, our study compellingly supports and adds to previous clinical observations in the field.
  • Our study provides valuable insights into the prevalence and characteristics of pediatric LCS, highlighting the significant quality of life and functioning impairment compared to control groups.
  • By detecting neutrophilic granulocyte dysfunction in children with LCS, we shed light on a previously overlooked pathophysiological component of the condition.
  • We demonstrate a significant correlation between clinical symptoms and superoxide production, further enhancing our understanding of the underlying mechanisms of pediatric LCS.

◆Cross-Section of Neurological Manifestations Among SARS-CoV-2 Omicron Subvariants—Single-Center Study【MDPI　2024年11月20日】

Abstract

Background/Objectives: The Omicron variant of SARS-CoV-2 is undergoing constant mutation. New strains vary in neuropathogenicity and the neurological spectrum of disease. The aim of this study was to assess the frequency and clinical characteristics of neurological manifestations during the Omicron dominance among hospitalized patients, including the differences between three subsequent periods.
Methods: This retrospective single-center study included 426 hospitalized adults with confirmed COVID-19 divided into three periods (O1, O2, and O3) dependent on the dominance of Omicron subvariants in Poland. Demographic and clinical data, in particular neurological manifestations, were collected and compared. Results: The median age of the group was 74, older in subsequent (later) periods. The number of patients with a history of previous SARS-CoV-2 infection or vaccination increased with the duration of the pandemic. The severity of COVID-19 became lower in successive periods. Neurological manifestations were observed in 55.4% of patients, and the most frequent were delirium, headache, myalgia, dizziness, cerebrovascular diseases, and encephalopathy. In subsequent periods of Omicron dominance, a higher frequency of neurological manifestations such as delirium, transient ischemic attack (TIA), and encephalopathy was observed. Headache or myalgia was related to a shorter hospitalization while delirium, cerebrovascular diseases, and ischemic stroke were linked with an increased risk of death. Conclusions: The Omicron variant of SARS-CoV-2 presents a wide spectrum of neurological manifestations. Although there is an improvement in the survival rate of patients with COVID-19, the frequency of neurological manifestations increases. The occurrence of delirium, cerebrovascular diseases, and ischemic stroke results in higher mortality.

◆SARS-CoV-2 infection of human pluripotent stem cell-derived vascular cells reveals smooth muscle cells as key mediators of vascular pathology during infection【bioRxiv　2024年11月26日】

Abstract

Although respiratory symptoms are the most prevalent disease manifestation of infection by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), nearly 20% of hospitalized patients are at risk for thromboembolic events. This prothrombotic state is considered a key factor in the increased risk of stroke, which is observed clinically during both acute infection and long after symptoms clear. Here we develop a model of SARS-CoV-2 infection using human-induced pluripotent stem cell-derived endothelial cells (ECs), pericytes (PCs), and smooth muscle cells (SMCs) to recapitulate the vascular pathology associated with SARS-CoV-2 exposure. Our results demonstrate that perivascular cells, particularly SMCs, are a susceptible vascular target for SARS-CoV-2 infection. Utilizing RNA sequencing, we characterize the transcriptomic changes accompanying SARS-CoV-2 infection of SMCs, PCs, and ECs. We observe that infected SMCs shift to a pro-inflammatory state and increase the expression of key mediators of the coagulation cascade. Further, we show human ECs exposed to the secretome of infected SMCs produce hemostatic factors that contribute to vascular dysfunction, despite not being susceptible to direct infection. The findings here recapitulate observations from patient sera in human COVID-19 patients and provide mechanistic insight into the unique vascular implications of SARS-CoV-2 infection at a cellular level.

◆The identification of a SARs-CoV2 S1 protein derived peptide with super-antigen-like stimulatory properties on T-cells【bioRxiv　2024年11月27日】

Abstract

Severe COVID-19 can trigger a cytokine storm, leading to acute respiratory distress syndrome (ARDS) with similarities to superantigen-induced toxic shock syndrome. An outstanding question is whether SARS-CoV-2 protein sequences can directly induce inflammatory responses. In this study, we identify a region in the SARS-CoV-2 S1 spike protein with sequence homology to bacterial super-antigens (termed P3). Computational modeling predicts P3 binding to sites on MHC class I/II and the TCR that partially overlap with sites for the binding of staphylococcal enterotoxins B and H. Like SEB and SEH peptides, P3 stimulated 25-40% of human CD4+ and CD8+ T cells, increasing IFN-γ and granzyme B production. viSNE and SPADE profiling identified overlapping and distinct IFN-γ and GZMB subsets. The super-antigenic properties of P3 were further evident by its selective expansion of T cells expressing specific TCR Vα and Vβ chain repertoires. In vivo experiments in mice revealed that the administration of P3 led to a significant upregulation of proinflammatory cytokines IL-1β, IL-6, and TNF-α. While the clinical significance of P3 in COVID-19 remains unclear, its homology to other mammalian proteins suggests a potential role for this peptide family in human inflammation and autoimmunity.

◆Endothelial inflammation in COVID-19【Science　2024年11月28日】

Abstract

The vascular endothelium forms a crucial interface between tissues and the blood stream and maintains normal blood flow (1). In its homeostatic state, the endothelium resists blood clotting, vasoconstriction, and inflammation and maintains selective barrier functions. This tightly regulated suite of properties can shift rapidly to unleash a series of functions vital to stanch blood loss from wounds or mobilize innate and adaptive immune defenses to repair injury and fight pathogenic microorganisms. But these defensive actions of endothelial cells can, if overexuberant, aggravate disease. Infection with severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) has highlighted how altered endothelial functions contribute to multiorgan health effects during the acute phase of COVID-19 and potentially to the longer-term consequences associated with Long Covid.

◆Healthcare utilisation of 282,080 individuals with long COVID over two years: a multiple matched control, longitudinal cohort analysis【SageJournals　2024年11月27日】

Abstract

Objectives

To investigate healthcare utilisation and cost in individuals with long COVID (LC) at population level.

Design

Case–control cohort analysis with multiple age-, sex-, ethnicity-, deprivation-, region- and comorbidity-matched control groups: (1) COVID only, no LC; (2) pre-pandemic; (3) contemporary non-COVID; and (4) pre-LC (self-controlled, pre-COVID pandemic).

Setting

National, population-based, linked UK electronic health records (British Heart Foundation/NHS England Secure Data Environment).

Participants

Adults aged ≥18 years with LC between January 2020 and January 2023.

Main outcome measures

Healthcare utilisation (number of consultations/visits per person: primary care (general practitioner [GP]), secondary care (outpatient [OP], inpatient [IP] and emergency department [ED], investigations and procedures) and inflation-adjusted cost (£) for LC and control populations per month, calendar year and pandemic year for each category.

Results

A total of 282,080 individuals with LC were included between January 2020 and January 2023. The control groups were COVID only, no LC (n = 1,112,370), pre-pandemic (n = 1,031,285), contemporary non-COVID (n = 1,118,360) and pre-LC (n = 282,080). Healthcare utilisation per person (per month/year) was higher in LC than controls across GP, OP and ED. For IP, LC had higher healthcare utilisation than pre-LC and contemporary non-COVID (all p < 0.0001). Healthcare utilisation of the LC group increased progressively between 2020 and 2023, compared with controls. Median cost per patient/year was also higher in individuals with LC than all control groups. Conclusions

LC has been associated with substantial, persistent healthcare utilisation and cost over the last three years. Future funding, resources and staff for LC prevention, treatment and research must be prioritised to reduce sustained primary and secondary healthcare utilisation and costs.

◆Persistence of spike protein at the skull-meninges-brain axis may contribute to the neurological sequelae of COVID-19【Cell host & Microbe　2024年11月29日】

Summary

SARS-CoV-2 infection is associated with long-lasting neurological symptoms, although the underlying mechanisms remain unclear. Using optical clearing and imaging, we observed the accumulation of SARS-CoV-2 spike protein in the skull-meninges-brain axis of human COVID-19 patients, persisting long after viral clearance. Further, biomarkers of neurodegeneration were elevated in the cerebrospinal fluid from long COVID patients, and proteomic analysis of human skull, meninges, and brain samples revealed dysregulated inflammatory pathways and neurodegeneration-associated changes. Similar distribution patterns of the spike protein were observed in SARS-CoV-2-infected mice. Injection of spike protein alone was sufficient to induce neuroinflammation, proteome changes in the skull-meninges-brain axis, anxiety-like behavior, and exacerbated outcomes in mouse models of stroke and traumatic brain injury. Vaccination reduced but did not eliminate spike protein accumulation after infection in mice. Our findings suggest persistent spike protein at the brain borders may contribute to lasting neurological sequelae of COVID-19.

◆Endothelial Glycocalyx Anomalies and Ocular Manifestations in Patients with Post-Acute COVID-19【MDPI　2024年11月29日】

Summary

Objectives: To report ophthalmological and microvascular findings in patients with post-acute COVID-19.
Methods: In this prospective, monocentric cohort study, we included patients with post-acute COVID-19 who presented with ophthalmological symptoms. All patients underwent indocyanine green angiography (ICGA), OCT, OCT-angiography, adaptive optics, and GlycoCheck assessments.
Results: We included 44 patients, predominantly female (81.8%), with a mean age of 47.5 ± 11.5 years. Key ICGA findings revealed hyperreflective dots in 32 eyes (36.4%) and hemangioma-like lesions in 7 eyes (8.0%). Capillary non-perfusion in the superficial capillary plexus (SCP) and deep capillary plexus (DCP) was observed in 42 eyes (47.7%) and 21 eyes (23.9%), respectively. Eyes with hyperreflective dots exhibited a lower perfused boundary region (PBR), while those with superficial punctate keratitis showed a higher PBR (p = 0.02 and p = 0.002, respectively). Eyes with capillary non-perfusion in the SCP displayed lower capillary densities (CD4, CD5, and CD4-6; p = 0.001, 0.03, and 0.03, respectively), and eyes with non-perfusion in the DCP had lower CD4 (p = 0.03). A negative correlation was identified between capillary density and the wall-to-lumen ratio. Conclusions: Patients with post-acute COVID-19 demonstrate both retinal and choroidal vascular anomalies. Ocular pathology was associated with reduced capillary density. These injuries appear to stem more from microvascular disruptions than from persistent glycocalyx abnormalities.