Comparison of systemic inflammatory profiles in COVID-19 and community-acquired pneumonia patients: a prospective cohort study

Integrating Interpretability in Machine Learning and Deep Neural Networks: A Novel Approach to Feature Importance and Outlier Detection in COVID-19 Symptomatology and Vaccine Efficacy

In this study, we introduce a novel approach that integrates interpretability techniques from both traditional machine learning (ML) and deep neural networks (DNN) to quantify feature importance using global and local interpretation methods. Our method bridges the gap between interpretable ML models and powerful deep learning (DL) architectures, providing comprehensive insights into the key drivers behind model predictions, especially in detecting outliers within medical data. We applied this method to analyze COVID-19 pandemic data from 2020, yielding intriguing insights. We used a dataset consisting of individuals who were tested for COVID-19 during the early stages of the pandemic in 2020. The dataset included self-reported symptoms and test results from a wide demographic, and our goal was to identify the most important symptoms that could help predict COVID-19 infection accurately. By applying interpretability techniques to both machine learning and deep learning models, we aimed to improve understanding of symptomatology and enhance early detection of COVID-19 cases. Notably, even though less than 1% of our cohort reported having a sore throat, this symptom emerged as a significant indicator of active COVID-19 infection, appearing 7 out of 9 times in the top four most important features across all methodologies. This suggests its potential as an early symptom marker. Studies have shown that individuals reporting sore throat may have a compromised immune system, where antibody generation is not functioning correctly. This aligns with our data, which indicates that 5% of patients with sore throats required hospitalization. Our analysis also revealed a concerning trend of diminished immune response post-COVID infection, increasing the likelihood of severe cases requiring hospitalization. This finding underscores the importance of monitoring patients post-recovery for potential complications and tailoring medical interventions accordingly. Our study also raises critical questions about the efficacy of COVID-19 vaccines in individuals presenting with sore throat as a symptom. The results suggest that booster shots might be necessary for this population to ensure adequate immunity, given the observed immune response patterns. The proposed method not only enhances our understanding of COVID-19 symptomatology but also demonstrates its broader utility in medical outlier detection. This research contributes valuable insights to ongoing efforts in creating interpretable models for COVID-19 management and vaccine optimization strategies. By leveraging feature importance and interpretability, these models empower physicians, healthcare workers, and researchers to understand complex relationships within medical data, facilitating more informed decision-making for patient care and public health initiatives.

Evaluation of molecular mechanisms of riboflavin anti-COVID-19 action reveals anti-inflammatory efficacy rather than antiviral activity

BACKGROUND

Riboflavin (vitamin B2) is one of the most important water-soluble vitamins and a coenzyme involved in many biochemical processes. It has previously been shown that adjuvant therapy with flavin mononucleotide (a water-soluble form of riboflavin) correlates with normalization of clinically relevant immune markers in patients with COVID-19, but the mechanism of this effect remains unclear. Here, the antiviral and anti-inflammatory effects of riboflavin were investigated to elucidate the molecular mechanisms underlying the riboflavin-induced effects.

METHODS

Riboflavin was evaluated for recombinant SARS-CoV-2 PLpro inhibition in an enzyme kinetic assay and for direct inhibition of SARS-CoV-2 replication in Vero E6 cells, as well as for anti-inflammatory activity in polysaccharide-induced inflammation models, including endothelial cells in vitro and acute lung inflammation in vivo.

RESULTS

For the first time, the ability of riboflavin at high concentrations (above 50 μM) to inhibit SARS-CoV-2 PLpro protease in vitro was demonstrated; however, no inhibition of viral replication in Vero E6 cells in vitro was found. At the same time, riboflavin exerted a pronounced anti-inflammatory effect in the polysaccharide-induced inflammation model, both in vitro, preventing polysaccharide-induced cell death, and in vivo, reducing inflammatory markers (IL-1β, IL-6, and TNF-α) and normalizing lung histology.

CONCLUSIONS

It is concluded that riboflavin reveals anti-inflammatory rather than antiviral activity for SARS-CoV-2 infection.

GENERAL SIGNIFICANCE

Riboflavin could be suggested as a promising compound for the therapy of inflammatory diseases of broad origin.

Low pre-existing endemic human coronavirus (HCoV-NL63)-specific T cell frequencies are associated with impaired SARS-CoV-2-specific T cell responses in people living with HIV

Background

Understanding how HIV affects SARS-CoV-2 immunity is crucial for managing COVID-19 in sub-Saharan populations due to frequent coinfections. Our previous research showed that unsuppressed HIV is associated with weaker immune responses to SARS-CoV-2, but the underlying mechanisms are unclear. We investigated how pre-existing T cell immunity against an endemic human coronavirus HCoV-NL63 impacts SARS-CoV-2 T cell responses in people living with HIV (PLWH) compared to uninfected individuals, and how HIV-related T cell dysfunction influences responses to SARS-CoV-2 variants.

Methods

We used flow cytometry to measure T cell responses following PBMC stimulation with peptide pools representing beta, delta, wild-type, and HCoV-NL63 spike proteins. Luminex bead assay was used to measure circulating plasma chemokine and cytokine levels. ELISA and MSD V-PLEX COVID-19 Serology and ACE2 Neutralization assays were used to measure humoral responses.

Results

Regardless of HIV status, we found a strong positive correlation between responses to HCoV-NL63 and SARS-CoV-2. However, PLWH exhibited weaker CD4+ T cell responses to both HCoV-NL63 and SARS-CoV-2 than HIV-uninfected individuals. PLWH also had higher proportions of functionally exhausted (PD-1high) CD4+ T cells producing fewer proinflammatory cytokines (IFNγ and TNFα) and had elevated plasma IL-2 and IL-12(p70) levels compared to HIV-uninfected individuals. HIV status didn't significantly affect IgG antibody levels against SARS-CoV-2 antigens or ACE2 binding inhibition activity.

Conclusion

Our results indicate that the decrease in SARS-CoV-2 specific T cell responses in PLWH may be attributable to reduced frequencies of pre-existing cross-reactive responses. However, HIV infection minimally affected the quality and magnitude of humoral responses, and this could explain why the risk of severe COVID-19 in PLWH is highly heterogeneous.

Targeting CMV Reactivation to Optimize Care for Critically Ill COVID-19 Patients: A Review on the Therapeutic Potential of Antiviral Treatment

Cytomegalovirus (CMV) reactivation has been linked to adverse clinical outcomes in critically ill patients, with emerging evidence suggesting a potential connection with severe COVID-19. Mechanisms driving this association may include primary lung injury, amplification of systemic inflammation, and secondary immunosuppression. Diagnostic challenges in detecting and assessing CMV reactivation necessitate a comprehensive approach to improve accuracy and inform treatment decisions. Currently, there is limited evidence on the efficacy and safety of CMV pharmacotherapy in critically ill COVID-19 patients. Although insights from non-COVID-19 critical illness studies suggest a potential role for antiviral treatment or prophylaxis, the risks and benefits must be carefully balanced in this vulnerable patient population. Understanding the pathophysiological role of CMV in the context of COVID-19 and exploring the advantages of antiviral treatment are crucial for optimizing care in critically ill patients. This review provides a comprehensive synthesis of available evidence, emphasizing the need for additional investigation to establish the role of CMV treatment or prophylaxis in the management of severe COVID-19 and to develop a framework for future research on this topic.