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Clinical observations indicate that COVID-19 is a systemic disease. An investigation of the viral distribution within the human body and its correlation with tissue damage can aid in understanding the pathophysiology of SARS-CoV-2 infection. We present a detailed mapping of the viral RNA in 61 tissues and organs of 11 deceased patients with COVID-19. The autopsies were performed within the early postmortem interval (between 1.5 and 15 hr, mean: 5.6 hr) to minimize the bias due to viral RNA and tissue degradation. Very high viral loads (>10 4 copies/ml) were detected in most patients' lungs, and the presence of intact viral particles in the lung tissue could be verified by transmission electron microscopy. Interestingly, viral RNA was detected throughout various extrapulmonary tissues and organs without visible tissue damage. The dissemination of SARS-CoV-2-RNA throughout the body supports the hypothesis that there is a maladaptive host response with viremia and multiorgan dysfunction. Since the discovery of the new coronavirus that causes COVID-19, scientists have been scrambling to understand the different features of the virus. While a lot more is now known about SARS-CoV-2, several key questions have proved more difficult to answer. For example, it remained unclear where the virus travels to in the body and causes the most harm. To help answer this question, Deinhardt-Emmer, Wittschieber et al. performed postmortem examinations on 11 patients who had recently died of COVID-19. After sampling 61 different organs and tissues from each patient, several tests were used to detect traces of SARS-CoV-2. The experiments showed that the largest pool of SARS-CoV-2 was present in the lungs, where it had caused severe damage to the alveolae, the delicate air sacs at the end of the lungs’ main air tubes. Small amounts of the virus were also detected in other organs and tissues, but no severe tissue damage was seen. In addition, Deinhardt-Emmer, Wittschieber et al. found that each patient had increased levels of some of the proteins involved in inflammation and blood clotting circulating their bloodstream. This suggests that the inflammation caused by SARS-CoV-2 leads to an excessive immune reaction throughout the entire body. This research provides important new insights into which areas of the body are most impacted by SARS-CoV-2. These findings may help to design more effective drug treatments that target the places SARS-CoV-2 is most likely to accumulate and help patients fight off the infection at these regions.

The telomerase RNA component (Terc) constitutes a non-coding RNA critical for telomerase function, commonly associated with aging and pivotal in immunomodulation during inflammation. Our study unveils heightened susceptibility to pneumonia caused by Staphylococcus aureus (S. aureus ) in Terc knockout ( Terc ko/ko ) mice compared to both young and old infected counterparts. The exacerbated infection in Terc ko/ko mice correlates with heightened inflammation, manifested by elevated interleukin-1β (IL-1β) levels and activation of the NLR family pyrin domain containing 3 (NLRP3) inflammasome within the lung. Employing mRNA sequencing methods alongside in vitro analysis of alveolar macrophages (AMs) and T cells, our study elucidates a compelling correlation between Terc ko/ko , inflammation, and impaired T cell functionality. Terc deletion results in compromised T cell function, characterized by dysregulation of the T cell receptor and absence of CD247, potentially compromising the host’s capacity to mount an effective immune response against S. aureus . This investigation provides insights into the intricate mechanisms governing increased vulnerability to severe pneumonia in the context of Terc deficiency, which might also contribute to aging-related pathologies, while also highlighting the influence of Terc on T cell function.

Background Alveolar macrophages (AMs) are crucial innate immune cells that play important roles during infection with severe acute respiratory syndrome coronavirus type 2 (SARS‐CoV‐2). Ex vivo human precision‐cut lung slices (PCLSs) are well‐suited models to study immune reactions and biochemical changes within host cells as well as to follow functional macrophage phenotype plasticity within complex tissue environment. Raman spectroscopy emerged in recent years as a powerful method for label‐free cell characterization. Methods Human PCLSs from one donor were infected with either the SARS‐CoV‐2 delta or omicron variant. Immunofluorescence microscopy localized AMs and virus particles. Cytokine levels of interferon‐gamma (IFN‐γ) and interleukin 18 (IL‐18) were quantified. The lung slice model was optimized for label‐free Raman spectroscopic imaging and for the characterization of single AMs within the three‐dimensional structure of the PCLS model. Results Fluorescence microscopy confirmed the location of AMs and virus particles within the PCLS model. Raman spectroscopic imaging generated false‐colour images, revealing distinct spectroscopic differences between AMs in the uninfected control PCLS model and those in PCLS models infected with SARS‐CoV‐2. These differences included variations in intracellular RNA, carotenoid, triacyl glyceride, and glucose levels, consistent in interpretation with cytokine quantification data. A linear discriminant analysis (LDA) classification model achieved an 83% accuracy in distinguishing cells from infected lung slices from those of the uninfected controls. The LDA loadings pointed to spectral bands that had been previously identified in an in vitro stimulation study of macrophages. Conclusions Raman spectroscopy can characterize the cellular immune response and phenotype plasticity of AMs to infection with SARS‐CoV‐2 within a PCLS model in a label‐free and non‐invasive manner. The ability to distinguish cells from infected PCLSs from cells of the uninfected control PCLS based on intracellular biochemical changes highlights the potential of Raman spectroscopy as a powerful diagnostic tool in immunology and clinical diagnostics. Label‐free Raman spectroscopy is utilized for an in‐depth characterization of alveolar macrophages directly within intact precision‐cut human lung slices. Characteristic biochemical changes in individual alveolar macrophages upon ex vivo infection with SARS‐CoV‐2 virus are revealed and enable a reliable statistical differentiation of single macrophages from SARS‐CoV2 infected tissue slices from those of uninfected controls.

Obesity is a globally increasing health problem, entailing diverse comorbidities such as infectious diseases. An obese weight status has marked effects on lung function that can be attributed to mechanical dysfunctions. Moreover, the alterations of adipocyte-derived signal mediators strongly influence the regulation of inflammation, resulting in chronic low-grade inflammation. Our review summarizes the known effects regarding pulmonary bacterial and viral infections. For this, we discuss model systems that allow mechanistic investigation of the interplay between obesity and lung infections. Overall, obesity gives rise to a higher susceptibility to infectious pathogens, but the pathogenetic process is not clearly defined. Whereas, viral infections often show a more severe course in obese patients, the same patients seem to have a survival benefit during bacterial infections. In particular, we summarize the main mechanical impairments in the pulmonary tract caused by obesity. Moreover, we outline the main secretory changes within the expanded adipose tissue mass, resulting in chronic low-grade inflammation. Finally, we connect these altered host factors to the influence of obesity on the development of lung infection by summarizing observations from clinical and experimental data.

Neutrophil granulocytes represent an important part of the innate immune response, involved in combatting viral pathogens.2 The detection technology based on Raman spectroscopy (RS) has been applied in virus detection.3 High throughput screening RS (HTS-RS) represents an innovative strategy for direct and non-destructive detection of changes in the composition and phenotype of the white blood cells.4–7 The principle of this technique is to irradiate a cell with laser light for a few seconds and record the inelastically scattered light as a spectrum.4 Compared to traditional flow cytometry, this spectrum displays the sample's label-free molecular signature, which is susceptible to change due to biological stimulations.5–7 Machine learning approaches are applied to transfer the spectral into meaningful biological information.8 It is well-established that neutrophil granulocytes require pre-stimulation to induce their inflammatory capacity.1 In our study, we are using RS to examine the cell response of non-activated, tumor necrosis factor-alpha (TNF-α)- and LPS-activated neutrophils to SARS-CoV-2 infection. Main contributions are assigned to the Amide I band around 1660 cm−1 and the Amide III band around 1240 cm−1.9 The functional amino acid tryptophan typically contributes to the signal around 1550 cm−1.9 The quite intense signal around 1450 cm−1 is due to the CH2 deformation vibration shared by lipids and proteins.9 The region 1200–1300 cm−1 is characterized by highly mixed vibrational bands involving the amide III, contributions from the amino acid phenylalanine and tyrosine and nucleic acids.9 The C-N stretch vibration of proteins appears at 1130 cm−1.9 To verify a successful infection, we determined the production of inflammatory cytokines after 3 h (Figure 2C, blue bars) and 24 h (Figure 2C, red bars) virus-cell interaction in the supernatant of the cell culture. The increased neutrophil count has been observed in patients with severe COVID-19.1 The neutrophil response to SARS-CoV-2 infection occurs through immune activation and results in various phenotypic changes like degranulation and the release of pro-inflammatory cytokines.1,2 Variations associated with the SARS-CoV-2 - neutrophil interaction are pronounced in the wavenumber region of the Amide I band and between 1550 and 1580 cm−1, which gives an indication of changes in the tryptophan homeostasis of the neutrophils. The tryptophan metabolism pathway plays a crucial role in inflammation and immune tolerance captured in Raman spectra.7 Our findings indicate a respond of neutrophil granulocytes to SARS-CoV-2 by producing antiviral and inflammatory substances, including IP-10 and IL-6, identified as an independent predictor for disease progression.1,2 In addition, pre-stimulation by TNF- α and LPS results in increased expression of the measured cytokines. Since LPS is a strong stimulant in neutrophil granulocytes, it was used as a positive control.1 Neutrophile number and activation have beneficial and detrimental effects during viral infection.1 In our study, phenotypic change of neutrophil granulocytes was detectable in response to pre-stimuli accompanied by SARS-CoV-2 infection using HTS RS.

A diverse bacterial community colonizes the respiratory system, including commensals such as Staphylococcus epidermidis (S. epidermidis) and Streptococcus salivarius (S. salivarius), as well as facultative pathogens like Staphylococcus aureus (S. aureus). This study aimed to establish a colonized cell culture model to investigate the impact of these bacteria on influenza A virus (IAV) infection. Respiratory epithelial cells were exposed to S. epidermidis, S. salivarius, or S. aureus, using either live or heat-inactivated bacteria, followed by IAV infection. Cell integrity was assessed microscopically, cytotoxicity was measured via LDH assay, and inflammatory responses were analyzed through cytokine expression. Additionally, macrophage function was examined in response to bacterial colonization and IAV infection. While commensals maintained epithelial integrity for 48 h, S. aureus induced severe cell damage and death. The most pronounced epithelial destruction was caused by coinfection with S. aureus and IAV. Notably, commensals did not confer protection against IAV but instead enhanced epithelial inflammation. These effects were dependent on live bacteria, as inactivated bacteria had no impact. However, prior exposure to S. epidermidis and S. salivarius improved macrophage-mediated immune responses against IAV. These findings suggest that while individual commensals do not directly protect epithelial cells, they may contribute to immune training and enhance lung defense mechanisms.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global health problem. Although the respiratory system is the main impaired organ, conjunctivitis is one of its common findings. However, it is not yet understood if SARS-CoV-2 can infect the eye and if the ocular surface can be a potential route of SARS-CoV-2 transmissions. Our review focuses on the viral entry mechanisms to give a better understanding of the interaction between SARS-CoV-2 and the eye. We highlighted findings that give evidence for multiple potential receptors of SARS-CoV-2 on the ocular surface. Additionally, we focused on data concerning the detection of viral RNA and its spike protein in the various ocular tissues from patients. However, the expression level seemed to be relatively low compared to the respiratory tissues as a result of a unique environment surrounding the ocular surface and the innate immune response of SARS-CoV-2. Nevertheless, our review suggests the ocular surface as a potential route for SARS-CoV-2 transmission, and as a result of this study we strongly recommend the protection of the eyes for ophthalmologists and patients at risk.

Background The prevalence of Staphylococcus aureus isolates carrying the Panton-Valentine leukocidin (PVL) gene is higher in Africa (≈50%) compared to Europe (< 5%). The study aimed to measure anti-PVL-antibodies in Africans and Germans in a multi-center study and to test whether detected antibodies can neutralize the cytotoxic effect of PVL on polymorphonuclear leukocytes (PMNs). Methods Sera from asymptomatic Africans ( n  = 22, Nigeria, Gabon) and Caucasians ( n  = 22, Germany) were used to quantify antibody titers against PVL and α-hemolysin (in arbitrary units [AU]) by ELISA. PMNs from one African and German donor were exposed to 5 nM recombinant PVL to measure the neutralizing effect of serial dilutions of pooled sera from African and Caucasian participants, or donor sera at 0.625 and 2.5% (v/v). Results Anti-PVL-antibodies were significantly higher in Africans than in Germans (1.9 vs. 0.7 AU, p  < 0.0001). The pooled sera from the study participants neutralized the cytotoxic effect of PVL on African and German PMNs in a dose dependent manner. Also, neutralization of PVL on PMNs from the African and German donors had a stronger effect with African sera (half-maximal inhibitory concentration (IC 50 ) = 0.27 and 0.47%, respectively) compared to Caucasian sera (IC 50  = 3.51 and 3.59% respectively). Conclusion Africans have higher levels of neutralizing anti-PVL-antibodies. It remains unclear if or at what level these antibodies protect against PVL-related diseases.

Background Alterations in the gut microbiom can significantly impact various regions in the human body, including the pulmonary tract. This study investigates alterations in the gut microbiome during a high-fat diet (HFD), particularly short-chain fatty acids (SCFAs), and how these metabolites affect lung infection caused by Influenza A virus (IAV). Methods We used a HFD-mouse model to evaluate gut microbiota composition, SCFA levels, and pulmonary outcomes following IAV infection. Microbial changes were analyzed via taxonomic and functional profiling and SCFA levels were measured from non-obese and obese serum donors. Ultimately, acetate’s effects were tested ex vivo in human precision-cut lung slices (PCLS) and in vitro in pulmonary epithelial cells. Mechanistic studies investigated the involvement of the SCFA receptor free fatty acid receptor 2 (FFAR2) and intracellular antiviral pathways. Results Our data indicates an increased Firmicutes/Bacteroidetes ratio of the gut microbiome and an altered carbohydrate metabolism, leading to reduced SCFA production. Infected HFD mice showed increased IAV titers and sustained microbial alterations. Interestingly, acetate demonstrated antiviral effects in both the human PCLS model and pulmonary cells with an reduced viral replication. These effects depended on FFAR2, which also acts as an IAV co-receptor, as acetate treatment led to FFAR2 internalization and influenced host cell metabolism in our in vitro data. Conclusion HFD alters the SCFA production, reducing acetate levels in the gut microbiome. This reduction may lead to higher viral loads and worsened disease in HFD mice infected with IAV. Our findings indicate that acetate has antiviral effects during IAV infection in both a human ex vivo lung model and pulmonary epithelial cells. Here, acetate prevents viral entry and affects the cellular metabolic state and antiviral response. Understanding these mechanisms could provide new targets for preventing and treating viral infections in individuals with diet-related health issues. Graphical Abstract

Background It is essential to avoid admission of patients with undetected corona virus disease 2019 (COVID-19) to hospitals’ general wards. Even repeated negative reverse transcription polymerase chain reaction (RT-PCR) results do not rule-out COVID-19 with certainty. The study aimed to evaluate a rule-out strategy for COVID-19 using chest computed tomography (CT) in adults being admitted to the emergency department and suspected of COVID-19. Methods In this prospective, single centre, diagnostic accuracy cohort study, consecutive adults (≥ 18 years) presenting with symptoms consistent with COVID-19 or previous contact to infected individuals, admitted to the emergency department and supposed to be referred to general ward were included in March and April 2020. All participants underwent low-dose chest CT. RT-PCR- and specific antibody tests were used as reference standard. Main outcome measures were sensitivity and specificity of chest CT. Predictive values were calculated based on the theorem of Bayes using Fagan’s nomogram. Results Of 165 participants (56.4% male, 71 ± 16 years) included in the study, the diagnosis of COVID-19 was confirmed with RT-PCR and AB tests in 13 participants (prevalence 7.9%). Sensitivity and specificity of chest CT were 84.6% (95% confidence interval [CI], 54.6–98.1) and 94.7% (95% CI, 89.9–97.7), respectively. Positive and negative likelihood ratio of chest CT were 16.1 (95% CI, 7.9–32.8) and 0.16 (95% CI, 0.05–0.58) and positive and negative predictive value were 57.9% (95% CI, 40.3–73.7) and 98.6% (95% CI, 95.3–99.6), respectively. Conclusion At a low prevalence of COVID-19, chest CT could be used as a complement to repeated RT-PCR testing for early COVID-19 exclusion in adults with suspected infection before referral to hospital’s general wards. Trial registration ClinicalTrials.gov: NCT04357938 April 22, 2020.