[COVID-19 To overcome its severity and sequelae.]

COVID-19パンデミックから3年が経過したが,いまだにCOVID-19は社会的活動に大きな影響を与えている.mRNAワクチンの普及とウイルス自身の変異(オミクロン株の流行)により,その重症化率は下がったが,2022年12月時点で感染者数自体は増加傾向にあり,関連死者数も増加している.さらに,COVID-19罹患後も一部の患者では後遺症に長く苦しむこととなり,ポストコロナ時代にはこれらが課題となっている.本特集ではこれまでに明らかになった免疫学的知見について整理することで,これらの課題について解決の糸口となることを願う.(著者抄録)

Single-cell analyses and host genetics highlight the role of innate immune cells in COVID-19 severity.

Mechanisms underpinning the dysfunctional immune response in severe acute respiratory syndrome coronavirus 2 infection are elusive. We analyzed single-cell transcriptomes and T and B cell receptors (BCR) of >895,000 peripheral blood mononuclear cells from 73 coronavirus disease 2019 (COVID-19) patients and 75 healthy controls of Japanese ancestry with host genetic data. COVID-19 patients showed a low fraction of nonclassical monocytes (ncMono). We report downregulated cell transitions from classical monocytes to ncMono in COVID-19 with reduced CXCL10 expression in ncMono in severe disease. Cell-cell communication analysis inferred decreased cellular interactions involving ncMono in severe COVID-19. Clonal expansions of BCR were evident in the plasmablasts of patients. Putative disease genes identified by COVID-19 genome-wide association study showed cell type-specific expressions in monocytes and dendritic cells. A COVID-19-associated risk variant at the IFNAR2 locus (rs13050728) had context-specific and monocyte-specific expression quantitative trait loci effects. Our study highlights biological and host genetic involvement of innate immune cells in COVID-19 severity.

A sex-biased imbalance between Tfr, Tph, and atypical B cells determines antibody responses in COVID-19 patients.

Sex-biased humoral immune responses to COVID-19 patients have been observed, but the cellular basis for this is not understood. Using single-cell proteomics by mass cytometry, we find disrupted regulation of humoral immunity in COVID-19 patients, with a sex-biased loss of circulating follicular regulatory T cells (cTfr) at a significantly greater rate in male patients. In addition, a male sex-associated cellular network of T-peripheral helper, plasma blasts, proliferating and extrafollicular/atypical CD11c+ memory B cells was strongly positively correlated with neutralizing antibody concentrations and negatively correlated with cTfr frequency. These results suggest that sex-specific differences to the balance of cTfr and a network of extrafollicular antibody production-associated cell types may be a key factor in the altered humoral immune responses between male and female COVID-19 patients.

Secondary subcutaneous abscess due to mixed infections by Peptoniphilus olsenii and Gleimia europaea after COVID-19.

This report described a rare case of subcutaneous anaerobic bacterial abscess due to Peptoniphilus olsenii and Gleimia europaea after COVID-19. The patient received incision and drainage of the abscess and antibiotics, thereby achieving recovery. Immunodeficiency related to COVID-19 and its treatment might contribute to secondary skin and subcutaneous bacterial infections.

Efficacy and risk of mRNA vaccination in patients with autoimmune inflammatory rheumatic diseases.

Coronavirus disease 2019 (COVID-19), which spread worldwide from Wuhan, China, in 2019, appeared for a time to be overcome by the remarkable efficacy of mRNA vaccines; however, new variants of severe acute respiratory syndrome coronavirus 2 have emerged and remain rampant. The involvement of the virus in the emergence of variant strains and the relationship between vaccine efficacy and immunosuppressive drugs have attracted significant attention, particularly with regard to patients with autoimmune inflammatory rheumatic disease (AIRD) who take immunosuppressive drugs. This review outlines the relationship between mRNA vaccines, one of the key strategies against COVID-19, and AIRD and discusses the immune response elicited by mRNA vaccines. Furthermore, the impact of immunosuppressive agents on the mRNA vaccine-induced immune response in patients with AIRD and side effects of the vaccine, such as exacerbation of the underlying disease, is outlined.

Persistence of SARS-CoV-2 neutralizing antibodies and anti-Omicron IgG induced by BNT162b2 mRNA vaccine in patients with autoimmune inflammatory rheumatic disease: an explanatory study in Japan.

Background: Autoimmune inflammatory rheumatic disease (AIRD) patients are at high risk of the coronavirus disease 2019 (COVID-19), but the medium-term effects of immunosuppressants on vaccine efficacy are unknown. We investigated the duration of humoral responses against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) wild-type and Omicron variant in AIRD patients administered with two doses of the BNT162b2 (Pfizer-BioNTech) vaccine. Methods: Serum-neutralizing antibody (NAb) and anti-receptor-binding domain (RBD)/spike antibody levels were measured. Short- and medium-term effects of immunosuppressants were analyzed pre-vaccination (Term 1) and 14-42 days (Term 2) and 100-200 days (Term 3) after the second vaccination. Findings: From Feb 1, 2021, to Feb 28, 2022, 439 AIRD patients and 146 healthy controls were investigated. The seropositivity rate and log10-NAb titers were significantly lower in AIRD patients than in controls at Terms 2 and 3. In rheumatoid arthritis patients, tumor necrosis factor-α inhibitors (TNFis) at Term 3, and older age, glucocorticoids, and abatacept at Terms 2 and 3 were risk factors for reduced responses. Anti-Omicron RBD/spike IgG levels strongly correlated with NAb titers. Interpretation: Glucocorticoids, TNFis, and abatacept treatments negatively affect the longevity of humoral responses to SARS-CoV-2, including Omicron, after two vaccine doses. These findings may inform the timing of additional vaccination for AIRD patients. Funding: Cloud Funding of Peace Winds Japan; Center of Innovation Program from the Ministry of Education, Culture, Sports, Science and Technology of Japan; Japan Society for the Promotion of Science KAKENHI; Japan Agency for Medical Research and Development; Kansai Economic Federation; Mitsubishi Zaidan; and Research Grant from Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology.

Next-generation proteomics of serum extracellular vesicles combined with single-cell RNA sequencing identifies MACROH2A1 associated with refractory COVID-19.

BACKGROUND: The coronavirus disease 2019 (COVID-19) pandemic is widespread; however, accurate predictors of refractory cases have not yet been established. Circulating extracellular vesicles, involved in many pathological processes, are ideal resources for biomarker exploration. METHODS: To identify potential serum biomarkers and examine the proteins associated with the pathogenesis of refractory COVID-19, we conducted high-coverage proteomics on serum extracellular vesicles collected from 12 patients with COVID-19 at different disease severity levels and 4 healthy controls. Furthermore, single-cell RNA sequencing of peripheral blood mononuclear cells collected from 10 patients with COVID-19 and 5 healthy controls was performed. RESULTS: Among the 3046 extracellular vesicle proteins that were identified, expression of MACROH2A1 was significantly elevated in refractory cases compared to non-refractory cases; moreover, its expression was increased according to disease severity. In single-cell RNA sequencing of peripheral blood mononuclear cells, the expression of MACROH2A1 was localized to monocytes and elevated in critical cases. Consistently, single-nucleus RNA sequencing of lung tissues revealed that MACROH2A1 was highly expressed in monocytes and macrophages and was significantly elevated in fatal COVID-19. Moreover, molecular network analysis showed that pathways such as "estrogen signaling pathway," "p160 steroid receptor coactivator (SRC) signaling pathway," and "transcriptional regulation by STAT" were enriched in the transcriptome of monocytes in the peripheral blood mononuclear cells and lungs, and they were also commonly enriched in extracellular vesicle proteomics. CONCLUSIONS: Our findings highlight that MACROH2A1 in extracellular vesicles is a potential biomarker of refractory COVID-19 and may reflect the pathogenesis of COVID-19 in monocytes.

Consecutive BNT162b2 mRNA vaccination induces short-term epigenetic memory in innate immune cells.

Consecutive mRNA vaccinations against SARS-CoV-2 reinforced both innate and adaptive immune responses. However, it remains unclear whether the enhanced innate immune responses are mediated by epigenetic regulation and, if so, whether these effects persist. Using mass cytometry, RNA-seq, and ATAC-seq, we show that BNT162b2 mRNA vaccination upregulated antiviral and IFN-stimulated gene expression in monocytes with greater effects after the second vaccination than those after the first vaccination. Transcription factor-binding motif analysis also revealed enriched IFN regulatory factors and PU.1 motifs in accessible chromatin regions. Importantly, although consecutive BNT162b2 mRNA vaccinations boosted innate immune responses and caused epigenetic changes in isolated monocytes, we showed that these effects occur only transiently and disappear 4 weeks after the second vaccination. Furthermore, single-cell RNA sequencing analysis revealed that a similar gene signature was impaired in the monocytes of unvaccinated COVID-19 patients with acute respiratory distress syndrome. These results reinforce the importance of the innate immune response in the determination of COVID-19 severity but indicate that, unlike adaptive immunity, innate immunity is not unexpectedly sustained even after consecutive vaccination. This study, which focuses on innate immmune memory, may provide novel insights into the vaccine development against infectious diseases.

Duration of SARS-CoV-2 RNA positivity from various specimens and clinical characteristics in patients with COVID-19: a systematic review and meta-analysis.

BACKGROUND: The duration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA positivity will be important to prevent the spread of coronavirus disease 2019 (COVID-19). A systematic review and meta-analysis were conducted following PRISMA to determine the duration from several parts of the body and clinical characteristics affecting it. MAIN TEXT: PubMed, Web of Science, Scopus, and CENTRAL were searched for original studies reporting the duration from COVID-19 onset to the disappearance of viral RNA. Of the 1682 studies identified, 100 met the selection criteria and 13,431 patients were included in this study. The duration of SARS-CoV-2 RNA positivity was 18.29 [95% confidence interval: 17.00-19.89] days in the upper respiratory tract samples, 23.79 [20.43-27.16] days in the sputum, 14.60 [12.16-17.05] days in the blood, and 22.38 [18.40-26.35] days in the stool. Sensitivity analysis revealed that the duration was positively correlated with age, comorbidities, severity, and usage of glucocorticoid. Subgroup analysis indicated that the presence or absence of complications had the greatest impact on the difference in DSRP. CONCLUSIONS: The duration of SARS-CoV-2 RNA positivity was 18.29 days in the upper respiratory tract samples. The duration in the sputum and the stool was longer, while that in the blood was shorter. The duration in the upper respiratory tract samples was longer in older, with any comorbidities, severer, and treated with glucocorticoid. These results provide the basic data for the duration of SARS-CoV-2 RNA positivity, and in the future, the effect of vaccination against SARS-CoV-2 and the SARS-CoV-2 variants on the duration of RNA positivity should be assessed.

Longitudinal alterations of the gut mycobiota and microbiota on COVID-19 severity.

BACKGROUND: The impact of SARS-CoV-2 infection on the gut fungal (mycobiota) and bacterial (microbiota) communities has been elucidated individually. This study analyzed both gut mycobiota and microbiota and their correlation in the COVID-19 patients with severe and mild conditions and follow-up to monitor their alterations after recovery. METHODS: We analyzed the gut mycobiota and microbiota by bacterial 16S and fungal ITS1 metagenomic sequencing of 40 severe patients, 38 mild patients, and 30 healthy individuals and reanalyzed those of 10 patients with severe COVID-19 approximately 6 months after discharge. RESULTS: The mycobiota of the severe and mild groups showed lower diversity than the healthy group, and in some, characteristic patterns dominated by a single fungal species, Candida albicans, were detected. Lower microbial diversity in the severe group was observed, but no differences in its diversity or community structure were detected between the mild and healthy groups. The microbiota of the severe group was characterized by an increase in Enterococcus and Lactobacillus, and a decrease in Faecalibacterium and Bacteroides. The abundance of Candida was positively correlated with that of Enterococcus in patients with COVID-19. After the recovery of severe patients, alteration of the microbiota remained, but the mycobiota recovered its diversity comparable to that of mild and healthy groups. CONCLUSION: In mild cases, the microbiota is stable during SARS-CoV-2 infection, but in severe cases, alterations persist for 6 months after recovery.

Case report: Acute exacerbation of interstitial pneumonia related to messenger RNA COVID-19 vaccination.

Messenger RNA (mRNA) vaccines that protect against COVID-19 are widely used in many countries owing to their high efficacy and safety profiles. Recently, few severe adverse events, such as anaphylaxis and myocarditis, were reported in healthy individuals. The safety of mRNA COVID-19 vaccines has not been adequately studied in patients with interstitial lung disease. We report 2 cases of acute exacerbation of preexisting interstitial pneumonia associated with mRNA COVID-19 vaccination. In both cases, lung disease was stable before the vaccination. Initial responses to steroid therapy were unfavorable, and intravenous cyclophosphamide was administered in both cases. Both patients were diagnosed with vaccine-related exacerbation of interstitial pneumonia based on laboratory results, radiologic features, and the observed clinical course, which lacked other causative events. We suggest that clinicians should note the possibility of acute exacerbation of pneumonia after mRNA COVID-19 vaccination and carefully monitor patients with interstitial lung disease.

Marked increase of interferon-ß after BNT162b2 mRNA vaccination: a case of polyarthritis with pleurisy.

Exacerbation of rheumatic disease after vaccination against SARS-CoV-2 is being reported. However, there are only a few cases of new-onset rheumatic diseases. We present two cases of new-onset persistent polyarthritis that developed in patients after receiving the mRNA vaccine against SARS-CoV-2. One patient had bilateral pleural effusions with markedly elevated serum interferon (IFN)-ß, while the other had no effusion, with serum IFN-ß comparable with that in healthy subjects. Other cytokines were unaltered in association with effusion. Both patients responded well to treatment with 20 mg prednisolone. Although more investigations are needed, the marked increase in serum IFN-ß levels observed in the case with pleural effusion may reflect an excessive response from the innate immune system to mRNA vaccines.

COVID-19 in a human T-cell lymphotropic virus type-1 carrier.

This is the first report of COVID-19 in a human T-cell lymphotropic virus type-1 (HTLV-1) carrier. HTLV-1 infection can cause immune dysfunction even in asymptomatic carriers. This case highlights the need for guidance on management of COVID-19-HTLV-1 coinfection, specifically on the appropriate use of corticosteroid treatment while considering secondary infection.

Longer Prehospitalization and Preintubation Periods in Intubated Non-survivors and ECMO Patients With COVID-19: A Systematic Review and Meta-Analysis.

Purpose: There is no clear consensus on the clinical course of critical COVID-19 patients. We examined the clinical course among intubated survivors, non-survivors, and extracorporeal membrane oxygenation (ECMO) patients to reveal the standard clinical course and the difference among critical COVID-19 patients. Methods: In this systematic review and meta-analysis, we searched PubMed, Web of Science, and Scopus for original studies published until December 11, 2020, including case accumulation and clinical course reporting. Pregnant patients and children were excluded. We followed PRISMA guidelines and registered them with PROSPERO (CRD42021235534). Results: Of the 11,716 studies identified, 94 met the selection criteria, and 2,549 cases were included in this meta-analysis. The times from intubation to extubation and death were 12.07 days (95% confidence interval 9.80-14.33 days) and 10.14 days (8.18-12.10 days), respectively, and the ECMO duration was 14.72 days (10.57-18.87 days). The time from symptom onset to hospitalization (prehospitalization period) of intubated survivors, non-survivors, and ECMO patients was 6.15 (4.61-7.69 days), 6.45 (4.55-8.34 days), and 7.15 days (6.48-7.81 days), and that from symptom onset to intubation (preintubation period) was 8.58 (7.36-9.80 days), 9.14 (7.26-11.01 days), and 10.54 days (9.18-11.90 days), respectively. Sensitivity analysis showed that the time from intubation to extubation and death was longer in the US and Europe than in East Asia. Conclusion: For COVID-19, we hypothesize that prehospitalization and preintubation periods are longer in intubated non-survivors and ECMO patients than in intubated survivors. These periods may serve as a predictor of disease severity or death and support therapeutic strategy determination.

Prolonged corticosteroid therapy and cytomegalovirus infection in patients with severe COVID-19.

Systemic corticosteroid therapy is frequently used to treat coronavirus disease 2019 (COVID-19). However, its maximum duration without secondary infections remains unclear. We aimed to evaluate the utility of monitoring cytomegalovirus (CMV) infection in patients with COVID-19 and estimate the maximum duration of systemic corticosteroid therapy without secondary infections. We included 59 patients with severe COVID-19 without CMV infection on admission to the intensive care unit (ICU). All patients received systemic corticosteroid therapy under invasive mechanical ventilation, with examination for plasma CMV-deoxyribonucleic acid (DNA) levels during the ICU stay. We analyzed the correlations among patient characteristics, CMV infection, diseases, and patient mortality. CMV infections were newly identified in 15 (25.4%) patients; moreover, anti-CMV treatment was administered to six (10.2%) patients during the ICU stay. Four (6.8%) patients had secondary infection-related mortality. The cumulative incidences of CMV infection and anti-CMV treatment during the ICU stay were 26.8% (95% confidence interval [CI], 15.8%-39.0%) and 12.3% (95% CI, 4.8%-23.4%), respectively. Furthermore, the median duration of systemic corticosteroid therapy without CMV infection was 15 days (95% CI, 13-16 days). The presence of CMV infection was associated with mortality during the ICU stay (p = 0.003). Monitoring plasma CMV-DNA levels could facilitate the detection of secondary CMV infection due to prolonged systemic corticosteroid therapy. The duration of systemic corticosteroid therapy for COVID-19 should be limited.

Identification of conserved SARS-CoV-2 spike epitopes that expand public cTfh clonotypes in mild COVID-19 patients.

Adaptive immunity is a fundamental component in controlling COVID-19. In this process, follicular helper T (Tfh) cells are a subset of CD4+ T cells that mediate the production of protective antibodies; however, the SARS-CoV-2 epitopes activating Tfh cells are not well characterized. Here, we identified and crystallized TCRs of public circulating Tfh (cTfh) clonotypes that are expanded in patients who have recovered from mild symptoms. These public clonotypes recognized the SARS-CoV-2 spike (S) epitopes conserved across emerging variants. The epitope of the most prevalent cTfh clonotype, S864-882, was presented by multiple HLAs and activated T cells in most healthy donors, suggesting that this S region is a universal T cell epitope useful for booster antigen. SARS-CoV-2-specific public cTfh clonotypes also cross-reacted with specific commensal bacteria. In this study, we identified conserved SARS-CoV-2 S epitopes that activate public cTfh clonotypes associated with mild symptoms.

COVID-19 in a patient with sporadic lymphangioleiomyomatosis awaiting lung transplantation.

Coronavirus disease 2019 (COVID-19) is an emerging viral disease with a mortality that depends on the individual's condition. Underlying comorbidities are major risk factors for COVID-19-related morbidity and mortality. However, information regarding the clinical course of COVID-19 in patients with rare respiratory system diseases is lacking. Here, we present a case of severe COVID-19 in a patient with advanced sporadic lymphangioleiomyomatosis (LAM) who was awaiting lung transplantation. She experienced a marked worsening of her respiratory status despite the limited size of the infiltrations seen on chest computed tomography. She responded to treatment with dexamethasone and remdesivir, and did not require mechanical ventilation. She recovered her pre-COVID-19 respiratory function. This case illustrates that patients with severe lung parenchymal destruction due to advanced LAM are at risk of worsening hypoxemia, but may not have a bad outcome if managed appropriately. Prevention and early diagnosis of COVID-19 are crucial in patients with advanced LAM. Future studies are needed to improve understanding of the clinical features and optimal treatment of COVID-19 in patients with LAM.

Fatal cytomegalovirus pneumonia in a critically ill patient with COVID-19.

Coronavirus disease 2019 (COVID-19) can cause severe lymphopenia and respiratory failure requiring prolonged invasive mechanical ventilation (MV). COVID-19 patients with severe lymphopenia or respiratory failure are at risk of developing secondary infections. Here, we present the needle autopsy findings of a critically ill patient with COVID-19 who required reintubation and prolonged MV, and eventually died of secondary cytomegalovirus (CMV) pneumonia. This case highlights the potential risk of long-term steroid use and the need for routine monitoring for CMV infection in critically ill patients with COVID-19.