Aging shapes infection profiles of influenza A virus and SARS-CoV-2 in human lung slices (preprint)

The recent coronavirus disease 2019 (COVID-19) outbreak revealed the susceptibility of elderly patients to respiratory virus infections, showing cell senescence or subclinical persistent inflammatory profiles and favouring the development of severe pneumonia. In our study, we evaluated the potential influence of lung aging on the efficiency of replication of influenza A virus (IAV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV 2), as well as determined the pro-inflammatory and antiviral responses of the distal lung tissue. Using precision-cut lung slices (PCLS) from donors of different ages, we found that pandemic H1N1 and avian H5N1 IAV replicated in the lung parenchyma with high efficacy. In contrast to these IAV strains, SARS-CoV-2 early isolate and Delta variant of concern (VOC) replicated less efficiently in PCLS. Interestingly, both viruses showed reduced replication in PCLS from older compared to younger donors, suggesting that aged lung tissue represents a sub optimal environment for viral replication. Regardless of the age-dependent viral loads, PCLS responded to infection with both viruses by an induction of IL-6 and IP-10/CXCL10 mRNAs, being highest for H5N1. Finally, while SARS-CoV-2 infection was not causing detectable cell death, IAV infection caused significant cytotoxicity and induced significant early interferon responses. In summary, our findings suggest that aged lung tissue might not favour viral dissemination, pointing to a determinant role of dysregulated immune mechanisms in the development of severe disease.

Molecular epidemiology of invasive Group A Streptococcal infections before and after the COVID-19 pandemic in Switzerland (preprint)

Group A Streptococcus (GAS, aka Streptococcus pyogenes) poses a significant public health concern, causing a diverse spectrum of infections with high mortality rates. Following the COVID-19 pandemic, a resurgence of invasive GAS (iGAS) infections has been documented, necessitating efficient outbreak detection methods. Whole genome sequencing (WGS) serves as the gold standard for GAS molecular typing, albeit constrained by time and costs. This study aimed to characterize the postpandemic increased prevalence of iGAS on the molecular epidemiological level in order to assess whether new, more virulent variants have emerged, as well as to assess the performance of the rapid and cost-effective Fourier-transform infrared (FTIR) spectroscopy as an alternative to WGS for detecting and characterizing GAS transmission routes. A total of 66 iGAS strains isolated from nine Swiss hospitals during the COVID-19 post-pandemic increased GAS prevalence were evaluated and compared to 15 strains collected before and 12 during the COVID-19 pandemic. FT-IR measurements and WGS were conducted for network analysis. Demographic, clinical, and epidemiological data were collected. Skin and soft tissue infection was the most common diagnosis, followed by primary bacteremia and pneumonia. Viral co-infections were found in 25% of cases and were significantly associated with more severe disease requiring intensive care unit admission. WGS analysis did not reveal emerging GAS genetic distinct variants after the COVID-19 pandemic, indicating the absence of a pandemic-induced shift. FT-IR spectroscopy exhibited limitations in differentiating genetically distant GAS strains, yielding poor overlap with WGS-derived clusters. The emm1/ST28 gebotype was predominant in our cohort and was associated with five of the seven deaths recorded, in accordance with the molecular epidemiological data before the pandemic. Additionally, no notable shift in antibiotic susceptibility patterns was observed. Our data suggest that mainly non-pathogen related factors contributed to the recent increased prevalence of iGAS.

The inflammatory microenvironment of the lung at the time of infection governs innate control of SARS-CoV-2 replication (preprint)

SARS-CoV-2 infection leads to vastly divergent clinical outcomes ranging from asymptomatic infection to fatal disease. Co-morbidities, sex, age, host genetics and vaccine status are known to affect disease severity. Yet, how the inflammatory milieu of the lung at the time of SARS-CoV-2 exposure impacts the control of viral replication remains poorly understood. We demonstrate here that immune events in the mouse lung closely preceding SARS-CoV-2 infection significantly impact viral control and we identify key innate immune pathways required to limit viral replication. A diverse set of pulmonary inflammatory stimuli, including resolved antecedent respiratory infections with S. aureus or influenza, ongoing pulmonary M. tuberculosis infection, ovalbumin/alum-induced asthma or airway administration of defined TLR ligands and recombinant cytokines, all establish an antiviral state in the lung that restricts SARS-CoV-2 replication upon infection. In addition to antiviral type I interferons, the broadly inducible inflammatory cytokines TNF and IL-1 precondition the lung for enhanced viral control. Collectively, our work shows that SARS-CoV-2 may benefit from an immunologically quiescent lung microenvironment and suggests that heterogeneity in pulmonary inflammation that precedes or accompanies SARS-CoV-2 exposure may be a significant factor contributing to the population-wide variability in COVID-19 disease outcomes.

SARS-CoV-2 infected human ACE2 transgenic pigs develop severe COVID-19-like pathology. (preprint)

COVID-19 continues to cause significant morbidity and mortality, with emerging strains rapidly spreading despite substantial immunity through vaccination and previous exposure. Animal models that accurately reflect COVID-19 are vital for testing mechanisms of disease, enabling development of improved vaccines and therapeutics. We have developed human ACE2 transgenic pigs that are highly susceptible to SARS-CoV-2 and display clinical signs, disease progression, and lung inflammation that faithfully replicate severe COVID-19 in humans.

Molecular mechanisms of Thalidomide effectiveness on COVID-19 patients explained: ACE2 is a new ΔNp63α target gene (preprint)

COVID-19 pandemics is caused by the SARS-CoV-2 virus, whose internalization and infection are mediated by the Angiotensin Converting Enzyme 2 (ACE2). The identification of novel approaches to tackle this step is instrumental for the development of therapies for the management of COVID-19 and other diseases with a similar mechanism of infection. Thalidomide, a drug sadly known for its teratogenic effects, has potent immunomodulatory and anti-inflammatory properties. Treatment with this drug has been shown to improve the immune functions of COVID-19 patients and proposed for the management of COVID-19 in clinical practice through drug repositioning. Here, we investigated the molecular details linking Thalidomide to ACE2 and COVID-19, showing that in conditions mimicking SARS-CoV-2 associated cytokine storm, the transcription factor p63 and ACE2 are stabilized and IL-8 production is increased. In such conditions, we found p63 to bind to and regulate the expression of the ACE2gene. We previously showed that p63 is degraded upon Thalidomide treatment, and now found that treatment with this drug—or with its analogue Lenalidomide—downregulates ACE2 through p63 degradation. Finally, we found that Thalidomide treatment reduce in vitro infection by pseudo-SARS-CoV-2, a baculovirus pseudotyped with the SARS-CoV-2 spike protein. Overall, we propose the dual effect of Thalidomide in reducing SARS-CoV-2 viral re-entry and inflammation through p63 degradation to weaken SARS-CoV-2 entry into host cells and mitigate lung inflammation, making it a valuable option in clinical management of COVID-19.

The Dysregulation of the Monocyte-Dendritic Cell Interplay Is Associated with In-Hospital Mortality in COVID-19 Pneumonia (preprint)

Background: The monocyte-phagocyte system (MPS), including monocytes/macrophages and dendritic cells (DCs), plays a key role in anti-viral immunity. We aimed to analyze the prognostic value of the MPS components on in-hospital mortality in a cohort of 58 patients (M/F ; mean ageSD years) with COVID-19 pneumonia and 22 age- and sex-matched healthy controls. Methods: We measured frequencies and absolute numbers of peripheral blood CD169+ monocytes, conventional CD1c+ and CD141+ (namely cDC2 and cDC1), and plasmacytoid CD303+ DCs by means of multi-parametric flow cytometry. A gene profile analysis of 770 immune-inflammatory related human genes and 20 SARS-CoV-2 genes was also performed. Results: Median frequencies and absolute counts of CD169-expressing monocytes were significantly higher in COVID-19 patients than in controls (p 0.04 and p 0.01, respectively). Conversely, percentages and absolute numbers of all DC subsets were markedly depleted in patients (p

Differentiating Immune Checkpoint Inhibitor-Related Pneumonitis From COVID-19 Pneumonia Using a CT-based Radiomics Nomogram (preprint)

Objectives This study aimed to develop and validate a radiomics nomogram that effectively distinguishes between immune checkpoint inhibitor-related pneumonitis (CIP) and COVID-19 pneumonia using radiographic imaging features. Methods We included 97 patients in this study, identifying 269 pneumonia lesions—159 from COVID-19 and 110 from CIP. The dataset was randomly divided into a training set (70% of the data) and a validation set (30%). We extracted radiomics features from corticomedullary and nephrographic phase-contrast computed tomography (CT) images, constructed a radiomics signature, and calculated a radiomics score (Rad-score). Using these features, we built models with three classifiers and assessed demographics and CT findings to create a clinical factors model. We then constructed a radiomics nomogram that combines the Rad-score with independent clinical factors and evaluated its performance in terms of calibration, discrimination, and clinical usefulness. Results In constructing the radiomics signature, 33 features were critical for differentiating between CIP and COVID-19 pneumonia. The support vector machine classifier was the most accurate of the three classifiers used. The Rad-score, gender, lesion location, radiological features, and lesion borders were included in the nomogram. The nomogram demonstrated superior predictive performance, significantly outperforming the clinical factors model in the training set (AUC comparison, p = 0.02638). Calibration curves indicated good fit in both training and validation sets, and the nomogram displayed greater net benefit compared to the clinical model. Conclusion The radiomics nomogram emerges as a noninvasive, quantitative tool with significant potential to differentiate between CIP and COVID-19 pneumonia. It enhances diagnostic accuracy and supports radiologists, especially in overburdened medical systems, through the use of machine learning predictions.

Prognostic value of SOFA combined with chest CT severity score in patients with critical COVID-19 pneumonia: a retrospective study (preprint)

Background: Either sequential organ failure assessment (SOFA) score or chest CT severity score (CT-SS) is often used alone to evaluate the prognosis of patients with critical coronavirus disease 2019 (COVID-19), but each of them has intrinsic deficiency. Herein, we attempted to investigate the predictive value of the combination of SOFA and CT-SS for the prognosis of COVID-19. Materials and Methods: A single-center retrospective study was performed in the Second Affiliated Hospital of Zhejiang University School of Medicine from December 2022 to January 2023. Patients with critical COVID-19 pneumonia were divided into two groups of survival or non-survival of hospitalization. The data including clinical characteristics, CT-SS, SOFA score, laboratory results on admission day were collected and analyzed. In addition, the predictive value of SOFAscore, chest CT-SS, or their combination for in-hospital mortality of COVID-19 pneumonia were compared by receiver operating characteristic (ROC) curve. Results: A total of 424 patients with a mean age of 75.46 years and a major proportion of male (69.10%) were finally enrolled, and the total in-hospital mortality was 43.40% (184/424). In comparison with survival group, significant higher proportions of older age (>75 years), comorbidities including obesity, diabetes, and cerebrovascular disease, more needs of mechanical ventilation and continuous renal replacement therapy (CRRT) were observed in the non-survival group (all P﹤0.05). In addition, non-survival patients had a higher value of creatinine, procalcitonin, C-reactive protein, interleukin-6 , SOFA score , CT-SS  (all P﹤0.05) on admission day. Multivariate logistic regression analysis further showed that older age, obesity, diabetes, SOFA score, CT-SS, mechanical ventilation, and lymphocytopenia (all P﹤0.05) were independently related with in-hospital mortality. Moreover, the area under the curve (AUC) of combination of SOFA score and chest CT-SS became significant higher than their respective alone (P＜0.01). Conclusion: A simple combination of SOFA scorewith chest CT-SS on admission elicits a better predictive value for in-hospital mortality of critical COVID-19 patients, which could also serve as a promising indicator for prognosis prediction of other severe lung diseases like severe pneumonia and acute lung injury.

Accelerated brain age in young to early middle-aged adults after mild to moderate COVID-19 infection (preprint)

Cognitive decline is a common adverse effect of the Coronavirus Disease of 2019 (COVID-19), particularly in the post-acute disease phase. The mechanisms of cognitive impairment after COVID-19 (COGVID) remain unclear, but neuroimaging studies provide evidence of brain changes, many that are associated with aging. Therefore, we calculated Brain Age Gap (BAG), which is the difference between brain age and chronological age, in a cohort of 25 mild to moderate COVID-19 survivors (did not experience breathlessness, pneumonia, or respiratory/organ failure) and 24 non-infected controls (mean age = 30 +/- 8) using magnetic resonance imaging (MRI). BAG was significantly higher in the COVID-19 group (F = 4.22, p = 0.046) by 2.65 years. Additionally, 80% of the COVID-19 group demonstrated an accelerated BAG compared to 13% in the control group (X2 = 20.0, p < 0.001). Accelerated BAG was significantly correlated with lower cognitive function (p < 0.041). Females in the COVID-19 group demonstrated a 99% decreased risk of accelerated BAG compared to males (OR = 0.015, 95% CI: 0.001 to 0.300). There was also a small (1.4%) but significant decrease in risk for accelerated BAG associated with longer time since COVID-19 diagnosis (OR = 0.986, 95% CI: 0.977 to 0.995). Our findings provide a novel biomarker of COGVID and point to accelerated brain aging as a potential mechanism of this adverse effect. Our results also offer further insight regarding gender-related disparities in cognitive morbidity associated with COVID-19.

MORTALITY-ASSOCIATED SARS-COV-2 GENOMIC VARIANTS FROM PATIENTS HOSPITALIZED FOR SEVERE PNEUMONIA IN AGUASCALIENTES, MEXICO FROM 2020 TO 2023 (preprint)

The SARS-CoV-2 virus has caused a global health crisis, resulting in a significant loss of human lives. It is essential to report disease and mutation associations to provide ideas for public health interventions and preventive measures. In this study, to determine the association between genomic variants and the severity of pneumonia caused by SARS-CoV-2, a sequencing analysis of 150 patient samples with confirmed COVID-19 was conducted. These samples were collected between 2021 and 2023 and isolated in Aguascalientes, Mexico. The patient cohort had males and females ranging from 0 to 91 years old. Males accounted for 66% of the population analyzed. The Delta variant was the most prevalent lineage associated with deaths in 2021-2022, while the B.1.1.529 lineages emerged in mid-2022. Currently, the XBB lineage is the most commonly identified in Mexico. New mutations L95M and L46M in ORF 8 and ORF 9 were discovered in 30% and 20% of the sequences and are uniquely present in the studied population. These mutations are positively associated with patient death. This study provides valuable data to aid in understanding the evolution of SARS-CoV-2 in specific populations and explores the severity of the disease and mutation correlations.

Cause-Specific Excess Mortality in the US During the COVID-19 Pandemic (preprint)

The COVID-19 pandemic was a significant shock to United States mortality, and it is important to understand how the pandemic impacted other causes of death. We estimated monthly excess mortality in the US by cause of death, age, and sex, for official deaths at ages 15 and older. Data come from the CDC Wonder Multiple Cause of Death database. We used a compositionally robust Generalized Additive Model (GAM) to estimate expected mortality counts in March 2020-December 2022 for eight causes of death: accidents, cardiovascular diseases, cancer, diabetes, influenza and pneumonia, substance-related (drugs and alcohol), suicide, and residual (including COVID-19 related deaths). Analyses were stratified by sex and 15-year age groups from 15-29 to 75+. Excess mortality was calculated as observed deaths minus expected deaths. From March 2020 to December 2022, we estimated 1 298 763 total excess deaths (95% CI: 1 226 542 to 1 370 804). While there were fewer deaths than expected due to some causes like flu/pneumonia and suicide, the largest number of excess deaths, excluding COVID-19, were attributed to cardiovascular diseases (115 765 deaths, 95% CI:  98 697 to 133 783) and substance use (86 637 deaths, 95% CI: 79 273 to 93 690). Percent excess substance-related mortality was high across all ages, while percent excess from cardiovascular diseases was highest at midlife ages. Some of these excess cardiovascular deaths were likely due to undercounted COVID-19 deaths, but others may reflect indirect impacts of the pandemic on healthcare utilization or longer-term effects of COVID-19 infections.

Clinical characteristics and initial C-reactive protein (CRP) levels associated with COVID-19 pneumonia in hospitalized patients at Huataphan Hospital, a primary care setting in Thailand (preprint)

Background Rapid diagnosis of pneumonia in COVID-19 infection patients is crucial for early effective management to reduce mortality. A challenge exists for the few radiologists in community hospitals in primary care settings in Thailand, in that general practitioners usually read chest X-rays themselves and may misdiagnosed COVID-19 pneumonia.Objective To evaluate the initial clinical characteristics and initial CRP values associated with COVID-19 pneumonia, confirmed by two radiologists, in proven COVID-19 hospitalized patients.Methods A retrospective cohort study was conducted between 1 July 2021 and 31 October 2021 at Huataphan Hospital in a primary care setting in Thailand. 412 hospitalized COVID-19 patients, 51% female with a median age of 34 (IQR 24, 46) years and 15.8% of them had at least one comorbidity were evaluated. The results showed that prevalence of chest X-rays (CXR) revealed COVID-19 pneumonias were diagnosed and confirmed by two radiologists was 63%. Female sex, older age patients, and pre-existing comorbidities were more common in COVID-19 pneumonia than those without COVID-19 pneumonia. C-reactive protein (CRP) values were statistically significantly higher in COVID-19 pneumonia compared to those without COVID-19 pneumonia (median CRP 10.8 vs. 2.3 mg/dL, p < 0.001). CRP cut-off value of 4 mg/dL was associated with radiographically confirmed COVID-19 pneumonia with the area under the curve (AUC) 66.8% (95% CI, 62.0%-71.5%), sensitivity 66.7% (95% CI, 60.6%-72.4%) and specificity 66.9% (95% CI, 58.8%-74.3%). Every 1 mg/dL increase in CRP was associated with a 4% increase in presentation of COVID-19 pneumonia (aOR 1.04, 95%CI 1.02–1.06, p = 0.001).Conclusions Initial CRP value in hospitalized COVID-19 infections can be used in the primary care hospital setting in combination with clinical assessment and chest X-ray for early diagnosis of COVID-19 pneumonia.

Healthcare-associated infections and antimicrobial use in acute care hospitals: a point prevalence survey in Lombardy, Italy, in 2022 (preprint)

Background: Healthcare-Associated Infections (HAIs) are a global public health issue, representing a significant burden of disease that leads to prolonged hospital stays, inappropriate use of antimicrobial drugs, intricately linked to the development of resistant microorganisms, and higher costs for healthcare systems. The study aimed to measure the prevalence of HAIs, the use of antimicrobials, and assess healthcare- and patient-related risk factors, to help identify key intervention points for effectively reducing the burden of HAIs.Methods: A total of 28 acute care hospitals in the Lombardy region, Northern Italy, participated in the third European Point Prevalence Survey (PPS-3) coordinated by ECDC for the surveillance of HAIs in acute care hospitals (Protocol 6.0).Results: HAIs were detected in 1,259 (10.1%, 95% CI 9.6–10.7%) out of 12,412 enrolled patients. 1,385 HAIs were reported (1.1 HAIs per patient on average). The most common types of HAIs were bloodstream infections (262 cases, 18.9%), urinary tract infections (237, 17.1%), SARS-CoV-2 infections (236, 17.0%), pneumonia and lower respiratory tract infections (231, 16.7%), and surgical site infections (152, 11.0%). Excluding SARS-CoV-2 infections, the overall prevalence of HAIs was 8.4% (95% CI 7.9–8.9%).

Neutrophil-to-Lymphocyte Ratio as a Prognostic Indicator in COVID-19: Evidence from a Northern Tanzanian Cohort (preprint)

Background: COVID-19 caused a profound global impact, resulting in significant cases and deaths. The progression of COVID-19 clinical manifestations is influenced by a dysregulated inflammatory response. Early identification of the subclinical progression is crucial for timely intervention and improved patient outcomes. While there are various biomarkers to predict disease severity and outcomes, their accessibility and affordability pose challenges in resource-limited settings. We explored the potentiality of the neutrophil-to-lymphocyte ratio (NLR) as a cost-effective inflammatory marker to predict disease severity, clinical deterioration, and mortality in affected patients. Methodology: A hospital-based retrospective cohort study was conducted at KCMC Hospital among COVID-19 patients followed from admission to discharge between 1st March 2020 and 31st March 2022. NLR was calculated as the absolute neutrophil count in µL divided by the absolute lymphocyte count in μL. The NLR cut-off value was determined using Receiver Operating Characteristic (ROC) analysis and assessed its predictive ability at admission for in-hospital mortality. The Chi-square test compared the proportion of NLR by patient characteristics. The association of NLR with disease severity and mortality was analyzed using the modified Poisson and Cox regression models, respectively. Results: The study included 504 patients, with a median age of 64 years, 57.1% were males, and 68.3% had severe COVID-19. The in-hospital COVID-19 mortality rate was 37.7%. An NLR cutoff value of 6.1 or higher had a sensitivity of 92.1% (95% CI 89.2%–94.0%) and a specificity of 92.0% (95% CI 89.7%–94.4%). Additionally, 39.5% of patients with an NLR value of 6.1 or higher had increased risk of severe disease, subsequent clinical deterioration, and mortality. Conclusion and recommendation: An NLR value of 6.1 or higher at the time of hospital admission associated with severe disease, clinical deterioration, and mortality in patients with COVID-19. Integration of NLR as a prognostic parameter in COVID-19 prognosis scales could improve risk assessment and guide appropriate management strategies for COVID-19 patients, as well as for potential future viral-related pneumonias. Further prospective studies are necessary to validate these findings and evaluate the clinical utility of NLR in larger cohorts of patients.

Neuroleptic malignant syndrome in a patient with COVID-19 and the possible role of SARS-CoV-2 in its manifestation. Case report and overview of published cases (preprint)

Background: The manifestationof severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is more complex than that of pulmonary infection, and neuropsychiatric symptoms play a role in this complexity. In this paper, we present the case of a 29-year-old schizophrenic patient who suffered from neuroleptic malignant syndrome (NMS) that developed during coronavirus disease 2019 (COVID-19) infection, with an emphasis on the possible connection between these two conditions. Additionally, we provide an overview of published NMS cases in patients with COVID-19 or after vaccination against SARS-CoV-2. Case presentation: A 29-year-old patient treated for schizophrenia was admitted to the hospital for agitation and aggressivity; shortly after arrival at the hospital, laryngospasm and hypoxia occurred. The patient tested positive for SARS-CoV-2, and later, he developed pneumonia. After continuing restlessness, haloperidol was administered, and a few days later, neuroleptic malignant syndrome occurred. He was treated with bromocriptine and recovered. Conclusions: As SARS-CoV-2 is known to interact with angiotensin-converting enzyme 2 and DOPA-decarboxylase is known to be coexpressed with this receptor, we hypothesized that COVID-19 infection might playa substantial role in the development of NMS.

Biological Effects of Corticosteroids on Pneumococcal Pneumonia in Mice and Humans (preprint)

Background: Streptococcus pneumoniae is the most common bacterial cause of community acquired pneumonia and the acute respiratory distress syndrome (ARDS). Some clinical trials have demonstrated a beneficial effect of corticosteroid therapy in community acquired pneumonia, COVID-19, and ARDS, but the mechanisms of this benefit remain unclear. The objective of this study was to investigate the effects of corticosteroids on the pulmonary biology of pneumococcal pneumonia in an observational cohort of mechanically ventilated patients and in a mouse model of bacterial pneumonia with Streptococcus pneumoniae. Methods: We studied gene expression with lower respiratory tract transcriptomes from a cohort of mechanically ventilated patients and in mice. We also carried out comprehensive physiologic, biochemical, and histological analyses in mice to identify the mechanisms of lung injury in Streptococcus pneumoniae with and without adjunctive steroid therapy. Results: Transcriptomic analysis identified pleiotropic effects of steroid therapy on the lower respiratory tract in critically ill patients with pneumococcal pneumonia, findings that were reproducible in mice. In mice with pneumonia, dexamethasone in combination with ceftriaxone reduced (1) pulmonary edema formation, (2) alveolar protein permeability, (3) proinflammatory cytokine release, (4) histopathologic lung injury score, and (5) hypoxemia but did not increase bacterial burden. Conclusions: The gene expression studies in patients and in the mice support the clinical relevance of the mouse studies, which replicate several features of pneumococcal pneumonia and steroid therapy in humans. In combination with appropriate antibiotic therapy in mice, treatment of pneumococcal pneumonia with steroid therapy reduced hypoxemia, pulmonary edema, lung permeability, and histologic criteria of lung injury, and also altered inflammatory responses at the protein and gene expression level. The results from these studies provide evidence for the mechanisms that may explain the beneficial effects of glucocorticoid therapy in patients with community acquired pneumonia from Streptococcus Pneumoniae.

Signature Inflammatory Cytokine panel: IL-10, IL-6, VEGF and IL-8 in Covid-19 (preprint)

Objective We aimed to assess a battery of inflammatory cytokines in SARS-CoV-2 patients to determine the cytokines of prognostic and/ predictive relevance in Covid-19.Methods In a cohort of total 100 SARS-CoV-2 patients (RT-PCR confirmed) hospitalized in associated SMHS hospital of GMC Srinagar, Kashmir (North India), the level of a battery of cytokines IL-6, IL-8, IL-10, IL-1α and VEGF, TNF-α and ferritin, were estimated by Enzyme Linked Immunosorbent Assay ( ELISA) on Multimode Microplate reader.Result The deranged levels of these cytokines were mostly found in patients > 60 years of age with cough and pneumonia as the most common symptoms. Correlation analysis revealed significant association between interleukin's IL-6, IL-8 and disease severity (p = 0.002) (p = 0.007) and poor disease outcome (p = 0.04), (p = 0.009) respectively. Similar association was also found between decreased levels of VEGF and poor disease outcome (p = 0.02). Further ROC analysis, univariant and multivariant (after adjusting for age, gender and other inflammatory markers), revealed increased IL-10 (AUC = 0.72) and IL-6 (AUC = 0.70) as independent markers of both disease severity(p = 0.02) (p = 0.01) and disease outcome (P = 0.03) (p = 0.02) and decreased VEGF (AUC = 0.69) as independent marker of disease outcome only (p = 0.03). Significant association of cough with IL-8 levels (p = 0.01) and of diabetes with raised ferritin levels (p = 0.01) with very high ferritin levels (> 1500ng/ml) as indicator of those that are likely to develop hyperinflammatory phenotype was found in SARS-CoV-2 patients.Conclusion We conclude ‘IL-6, IL10, VEGF and IL-8’ as the signature inflammatory cytokine panel in Covid-19. An increased IL-10, IL-6 levels proved to be equally significant independent prognosticators of Covid − 19 severity and predictors of poor disease outcome and decreased VEGF level as predictors of poor disease outcome in SARS-CoV-2 patients. Testing of the signature inflammatory cytokine panel is, therefore, recommended for optimal clinical decision making in Covid-19.

Genomic epidemiology and evolution of rhinovirus in western Washington State, 2021-22 (preprint)

Background: Human rhinoviruses (RV) primarily cause the common cold, but infection outcomes vary from subclinical to severe cases, including asthma exacerbations and fatal pneumonia in immunocompromised individuals. To date, therapeutic strategies have been hindered by the high diversity of serotypes. Global surveillance efforts have traditionally focused on sequencing VP1 or VP2/VP4 genetic regions, leaving gaps in understanding RV true genomic diversity. Methods: We sequenced 1,003 RV genomes from nasal swabs of symptomatic and asymptomatic individuals to explore viral evolution during two epidemiologically distinct periods in Washington State: when the COVID 19 pandemic affected the circulation of other seasonal respiratory viruses except for RV (from February to July 2021), and when the seasonal viruses reemerged with the severe RSV and influenza outbreak (November and December 2022). We constructed maximum likelihood and BEAST phylodynamic trees to characterize intra-genotype evolution. Results: We detected 100 of 168 known genotypes, identified two new genotypes (A111 and C59), and observed inter-genotypic recombination and genotype cluster swapping from 2021 to 2022. We found a significant association between the presence of symptoms and viral load, but not with RV species or genotype. Phylodynamic trees, polyprotein selection pressure, and Shannon diversity revealed co-circulation of divergent clades within genotypes with high amino acid constraints throughout polyprotein. Discussion: Our study underscores the dynamic nature of RV genomic epidemiology within a localized geographic region, as more than 20% of existing genotypes within each RV species co-circulated each month. Our findings also emphasize the importance of investigating correlations between rhinovirus genotypes and serotypes to understand long-term immunity and cross-protection.

Could SP-A and SP-D Serum Levels Predict COVID-19 Severity? (preprint)

Given the various clinical manifestations that characterize COVID-19, the scientific community is constantly searching for biomarkers with prognostic value. SP-A and SP-D collectins play a crucial role in ensuring proper alveolar function and an alteration of their serum levels have been reported in several pulmonary diseases characterized by ARDS and pulmonary fibrosis. Considering that such clinical manifestations can also occur during SARS-CoV-2 infection, we wondered if these collectins could act as prognostic markers. In this regard, serum levels of SP-A and SP-D were measured by enzyme immunoassay in patients with SARS-CoV-2 infection (n=51) at admission (T0) and after 7 days (T1) and compared with healthy donors (n=11). SP-D increased in COVID-19 patients compared to healthy controls during the early phases of infection, while a significant reduction was observed at T1. Stratifying SARS-CoV-2 patients according to disease severity, increased serum SP-D levels were observed in severe compared to mild patients. In the light of these results SP-D, but not SP-A, seems to be an eligible marker of COVID-19 pneumonia and the early detection of SP-D serum levels could be crucial for a preventive clinical management

Pulmonary fibrosis in critically ill patients with COVID-19: A multi-center retrospective cohort study in South Korea (preprint)

Background: Pulmonary fibrosis persists long after recovering from coronavirus disease 2019 (COVID-19) infection, thereby reducing quality of life and lung function. We aimed to evaluate the prevalence and risk factors for pulmonary fibrosis in patients with severe COVID-19 pneumonia requiring mechanical ventilation, a high-risk group for developing pulmonary fibrosis. Methods: Clinical data and chest computed tomography (CT) scans of patients with severe COVID-19 pneumonia requiring mechanical ventilation were retrospectively collected from nine hospitals in South Korea. Fibrotic-like changes on chest CT were visually assessed. Results: We included 125 patients with a mean age of 68.5 years, 60.8% men and 7.2% having underlying lung disease. Based on follow-up chest CT (the median interval: 38.0 days, interquartile range: 24.0–68.0 days), 94 (75.2%) patients exhibited fibrotic-like changes, with traction bronchiectasis and/or bronchiolectasis being the most common change (60.8%). Adjusted Cox regression analysis revealed as association between hemoglobin levels ≤9 g/dL and an increased risk of pulmonary fibrosis development (HR: 3.182, 95% Cl: 1.203–8.415, P=0.025). Among all patients, 17.6% died during hospitalization and 71.2% experienced complications, including intubation-related airway injury (12.8%), ventilator-associated pneumonia (44.8%), lung injury (11.2%), and hemodynamic disturbance (33.4%). In-hospital mortality (16.1% vs. 18.1%) and complications (67.7% vs. 72.3%) were similar between patients with and without fibrotic-like changes. Conclusion: Our study demonstrated that in patients with severe COVID-19 pneumonia requiring mechanical ventilation, chest CT revealed fibrotic-like changes in approximately three-fourths of patients. Low hemoglobin levels might be associated with pulmonary fibrosis in severe COVID-19 pneumonia.