Temporal transcriptomic analysis using TrendCatcher identifies early and persistent neutrophil activation in severe COVID-19

The immune response to SARS-CoV-2 in COVID-19 as a recall response susceptible to immune imprinting: A prospective cohort study

The antibody response to SARS-CoV-2 does not follow the immunoglobulin isotype pattern of primary responses, conflicting with the current interpretation of COVID-19.

METHODS

Prospective cohort study of 191 SARS-CoV-2 infection cases and 44 controls from the second wave of COVID-19. The study stratified patients by severity and analyzed the trajectories of SARS-CoV-2 antibodies and multiple immune variables.

RESULTS

Isotype-specific antibody time course profiles to SARS-CoV-2 revealed a pattern of recall response in 94.2 % of cases. The time course profiles of plasmablasts, B cells, cTfh high-resolution subsets, and cytokines indicated a secondary response. The transcriptomic data showed that this cohort is strictly comparable to contemporary cohorts.

CONCLUSIONS

In most cases, the immune response to SARS-CoV-2 is a recall response. This constitutes a favorable scenario for most COVID-19 cases to be subjected to immune imprinting by endemic coronavirus, which, in turn, can influence the immune response to SARS-CoV-2.

Metacell-based differential expression analysis identifies cell type specific temporal gene response programs in COVID-19 patient PBMCs

By profiling gene expression in individual cells, single-cell RNA-sequencing (scRNA-seq) can resolve cellular heterogeneity and cell-type gene expression dynamics. Its application to time-series samples can identify temporal gene programs active in different cell types, for example, immune cells' responses to viral infection. However, current scRNA-seq analysis has limitations. One is the low number of genes detected per cell. The second is insufficient replicates (often 1-2) due to high experimental cost. The third lies in the data analysis-treating individual cells as independent measurements leads to inflated statistics. To address these, we explore a new computational framework, specifically whether "metacells" constructed to maintain cellular heterogeneity within individual cell types (or clusters) can be used as "replicates" for increasing statistical rigor. Toward this, we applied SEACells to a time-series scRNA-seq dataset from peripheral blood mononuclear cells (PBMCs) after SARS-CoV-2 infection to construct metacells, and used them in maSigPro for quadratic regression to find significantly differentially expressed genes (DEGs) over time, followed by clustering expression velocity trends. We showed that such metacells retained greater expression variances and produced more biologically meaningful DEGs compared to either metacells generated randomly or from simple pseudobulk methods. More specifically, this approach correctly identified the known ISG15 interferon response program in almost all PBMC cell types and many DEGs enriched in the previously defined SARS-CoV-2 infection response pathway. It also uncovered additional and more cell type-specific temporal gene expression programs. Overall, our results demonstrate that the metacell-pseudoreplicate strategy could potentially overcome the limitation of 1-2 replicates.

Immune mechanisms underlying COVID-19 pathology and post-acute sequelae of SARS-CoV-2 infection (PASC)

With a global tally of more than 500 million cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections to date, there are growing concerns about the post-acute sequelae of SARS-CoV-2 infection (PASC), also known as long COVID. Recent studies suggest that exaggerated immune responses are key determinants of the severity and outcomes of the initial SARS-CoV-2 infection as well as subsequent PASC. The complexity of the innate and adaptive immune responses in the acute and post-acute period requires in-depth mechanistic analyses to identify specific molecular signals as well as specific immune cell populations which promote PASC pathogenesis. In this review, we examine the current literature on mechanisms of immune dysregulation in severe COVID-19 and the limited emerging data on the immunopathology of PASC. While the acute and post-acute phases may share some parallel mechanisms of immunopathology, it is likely that PASC immunopathology is quite distinct and heterogeneous, thus requiring large-scale longitudinal analyses in patients with and without PASC after an acute SARS-CoV-2 infection. By outlining the knowledge gaps in the immunopathology of PASC, we hope to provide avenues for novel research directions that will ultimately lead to precision therapies which restore healthy immune function in PASC patients.

Evaluating chest pain in patients with post COVID conditions permission to think outside of the box

Chest pain is among the most common symptoms of post-COVID-19 Conditions (PCC) that prompts medical attention. Because the SARS-CoV-2 virus has proclivity for many organs and organ systems in the chest, ranging from the heart, lungs, great vessels, lymphatics, and peripheral nerves, clinicians evaluating patients with chest pain must consider a broad differential diagnosis and take a comprehensive approach to management.

Physiological, biochemical, and metabolic changes in diploid and triploid watermelon leaves during flooding

Background

Flooding is a major stress factor impacting watermelon growth and production globally. Metabolites play a crucial role in coping with both biotic and abiotic stresses.

Methods

In this study, diploid (2X) and triploid (3X) watermelons were investigated to determine their flooding tolerance mechanisms by examining physiological, biochemical, and metabolic changes at different stages. Metabolite quantification was done using UPLC-ESI-MS/MS and a total of 682 metabolites were detected.

Results

The results showed that 2X watermelon leaves had lower chlorophyll content and fresh weights compared to 3X. The activities of antioxidants, such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), were higher in 3X than in 2X. 3X watermelon leaves showed lower O2 production rates, MDA, and hydrogen peroxide (H2O2) levels in response to flooding, while higher ethylene production was observed. 3X had higher levels of dehydrogenase activity (DHA) and ascorbic acid + dehydrogenase (AsA + DHA), but both 2X and 3X showed a significant decline in the AsA/DHA ratio at later stages of flooding. Among them, 4-guanidinobutyric acid (mws0567), an organic acid, may be a candidate metabolite responsible for flooding tolerance in watermelon and had higher expression levels in 3X watermelon, suggesting that triploid watermelon is more tolerant to flooding.

Conclusion

This study provides insights into the response of 2X and 3X watermelon to flooding and the physiological, biochemical, and metabolic changes involved. It will serve as a foundation for future in-depth molecular and genetic studies on flooding response in watermelon.

Prior Vaccination Exceeds Prior Infection in Eliciting Innate and Humoral Immune Responses in Omicron Infected Outpatients

Antibody response following Omicron infection is reported to be less robust than that to other variants. Here we investigated how prior vaccination and/or prior infection modulates that response. Disease severity, antibody responses and immune transcriptomes were characterized in four groups of Omicron-infected outpatients (n=83): unvaccinated/no prior infection, vaccinated/no prior infection, unvaccinated/prior infection and vaccinated/prior infection. The percentage of patients with asymptomatic or mild disease was highest in the vaccinated/no prior infection group (87%) and lowest in the unvaccinated/no prior infection group (47%). Significant anti-Omicron spike antibody levels and neutralizing activity were detected in the vaccinated group immediately after infection but were not present in the unvaccinated/no prior infection group. Within two weeks, antibody levels against Omicron, increased. Omicron neutralizing activity in the vaccinated group exceeded that of the prior infection group. No increase in neutralizing activity in the unvaccinated/no prior infection group was seen. The unvaccinated/prior infection group showed an intermediate response. We then investigated the early transcriptomic response following Omicron infection in these outpatient populations and compared it to that found in unvaccinated hospitalized patients with Alpha infection. Omicron infected patients showed a gradient of transcriptional response dependent upon whether or not they were previously vaccinated or infected. Vaccinated patients showed a significantly blunted interferon response as compared to both unvaccinated Omicron infected outpatients and unvaccinated Alpha infected hospitalized patients typified by the response of specific gene classes such as OAS and IFIT that control anti-viral responses and IFI27, a predictor of disease outcome.

Timeline Kinetics of Systemic and Airway Immune Mediator Storm for Comprehensive Analysis of Disease Outcome in Critically Ill COVID-19 Patients

In the present study, the levels of serum and airway soluble chemokines, pro-inflammatory/regulatory cytokines, and growth factors were quantified in critically ill COVID-19 patients (total n=286) at distinct time points (D0, D2-6, D7, D8-13 and D>14-36) upon Intensive Care Unit (ICU) admission. Augmented levels of soluble mediators were observed in serum from COVID-19 patients who progress to death. An opposite profile was observed in tracheal aspirate samples, indicating that systemic and airway microenvironment diverge in their inflammatory milieu. While a bimodal distribution was observed in the serum samples, a unimodal peak around D7 was found for most soluble mediators in tracheal aspirate samples. Systems biology tools further demonstrated that COVID-19 display distinct eccentric soluble mediator networks as compared to controls, with opposite profiles in serum and tracheal aspirates. Regardless the systemic-compartmentalized microenvironment, networks from patients progressing to death were linked to a pro-inflammatory/growth factor-rich, highly integrated center. Conversely, patients evolving to discharge exhibited networks of weak central architecture, with lower number of neighborhood connections and clusters of pro-inflammatory and regulatory cytokines. All in all, this investigation with robust sample size landed a comprehensive snapshot of the systemic and local divergencies composed of distinct immune responses driven by SARS-CoV-2 early on severe COVID-19.