Dynamics of Whole Transcriptome Analysis (WTA) and Surface markers expression (AbSeq) in Immune Cells of COVID-19 Patients and Recovered captured through Single Cell Genomics

Introduction

Single-cell multi-omics studies, such as multidimensional transcriptomics (whole transcriptomic analysis, WTA), and surface marker analysis (antibody sequencing, AbSeq), have turned out to be valuable techniques that offer inaccessible possibilities for single-cell profiling of mRNA, lncRNA, and proteins.

Methods

We used this technique to understand the dynamics of mRNA and protein-level differences in healthy, COVID-19-infected and recovered individuals using peripheral blood mononuclear cells (PBMCs). Our results demonstrate that compared to mRNA expression, protein abundance is a better indicator of the disease state.

Results

We demonstrate that compared to mRNA expression, protein abundance is a better indicator of the disease state. We observed high levels of cell identity and regulatory markers, CD3E, CD4, CD8A, CD5, CD7, GITR, and KLRB1 in healthy individuals, whereas markers related to cell activation, CD38, CD28, CD69, CD62L, CD14, and CD16 elevated in the SARS-CoV-2 infected patients at both WTA and AbSeq levels. Curiously, in recovered individuals, there was a high expression of cytokine and chemokine receptors (CCR5, CCR7, CCR4, CXCR3, and PTGRD2). We also observed variations in the expression of markers within cell populations under different states.

Discussion

Furthermore, our study emphasizes the significance of employing an oligo-based method (AbSeq) that can help in diagnosis, prognosis, and protection from disease/s by identifying cell surface markers that are unique to different cell types or states. It also allows simultaneous study of a vast array of markers, surpassing the constraints of techniques like FACS to query the vast repertoire of proteins.

Memory impairment among recovered COVID-19 patients: The prevalence and risk factors, a retrospective cohort study

The aim of this study is to demonstrate the prevalence of the long-term side effects of COVID-19, namely memory impairment among recovered patients, and obtaining the associated factors that link with memory impairment. It is a cross-sectional retrospective cohort study, that has been conducted from September to November 2022 in Iraq. People who were previously infected with COVID-19 were included. The study was performed by asking people to complete a questionnaire platform by either online or face-to-face interview. The Memory Assessment Clinic-Q (MAC-Q) test was utilized, scores that are equal or higher than 25 are indicative of memory decline. Thousand two hundred and eighty-seven participated in this study. However, only 1157 were included in the final analysis. Three hundred ninety-nine (34.49%) have memory impairment after COVID-19 recovery. Female gender, older age group, repeated exposure to COVID-19 infections, severe diseases, and exposure to multiple SARS-CoV-2 variants were independent risk factors of memory deficit in post-COVID-19 survivors with a p-value of 0.0001, 0.02, 0.0001, 0.001, 0.0001 respectively. It is crucial to pay particular attention to psychosocial rehabilitation of such risky groups. COVID-19 vaccine administrations with booster shots are necessary steps to decrease the disease incidence and avoid subsequent post-COVID-19 symptoms.

Experiences, life changes, and support systems of recovered COVID-19 patients from practitioners’ perspectives: A qualitative study

The spread of COVID-19 brought a worldwide pandemic that interrupted daily life and activities. By the end of 2020, there were more than 83 million diagnosed cases and 1.8 million deaths worldwide (World Health Organization, 2020). In Wuhan, China, more than 7 million individuals were quarantined at the beginning of the pandemic. Despite the widespread impact of the pandemic, limited studies have focused on recovered COVID-19 patients’ experiences. Therefore, this qualitative study was conducted to better understand the shared experiences of recovered COVID-19 patients in Wuhan, through the lens of social work practitioners working with them. A thematic analysis of 14 individual interviews resulted in three main themes: trauma, long-term perspective change, and support systems. Recovered patients commonly reported rejection, discrimination, stigma, and self-blame as a result of having had COVID-19. Although some reported receiving social support from family members, neighbors, or employers, others reported severe rejection and maltreatment. Experiences also influenced whether patients had a more positive or negative outlook toward the future. Findings call for health care practitioners and service providers to better support COVID-19 patients using a culturally sensitive, trauma-informed approach. Neighborhood-level factors and interventions are also discussed.

Threats to the dignity of COVID-19 patients: A qualititative study

Background: Dignity is a fundamental concept that has been threatened by the COVID-19 pandemic. Several factors threaten the dignity of COVID-19 patients, whether in palliative care departments, medical or surgery wards, intensive care units, or long-term care facilities. This threat is exacerbated by the increasing number of affected patients, the high transmission of the virus and problems such as limited resources, shortage of workforce, and ineffective communication. Recognizing the threats and challenges that currently affect the patients' dignity and managing them can help maintain the patients' dignity and increase their satisfaction. Research objective: This study seeks to explain the threats to the dignity of hospitalized COVID-19 patients. Research design: This qualitative study was conducted using conventional content analysis. Data were collected through in-depth, semi-structured, face-to-face interviews with 21 COVID-19 patients with maximum variation. Data were analyzed using Graneheim and Lundman's conventional content analysis and encoded with MAXQDA-10 software. The participants had already recovered from COVID-19 when the interviews were held. Ethical considerations: The study protocol was approved by the Research Ethics Committee of medical universities in northwestern Iran (IR.UMSU.REC.1399.345). Ethical principles were observed during the study. Findings: The analysis of the interviews revealed three main categories and 11 subcategories for the threats to the dignity of COVID-19 patients. The main categories included facing imposed conditions (five subcategories), facing unprofessional performance (four subcategories), and ineffective communication (two subcategories). Conclusion: The findings of the present study can help health officials and policymakers in taking positive steps to maintain patients' dignity by designing and implementing beneficial programs.

What Happens to the Immune System after Vaccination or Recovery from COVID-19?

Due to its leading role in fighting infections, the human immune system has been the focus of many studies in the context of Coronavirus disease 2019 (COVID-19). In a worldwide effort, the scientific community has transitioned from reporting about the effects of the novel coronavirus on the human body in the early days of the pandemic to exploring the body's many immunopathological and immunoprotecting properties that have improved disease treatment and enabled the development of vaccines. The aim of this review is to explain what happens to the immune system after recovery from COVID-19 and/or vaccination against SARS-CoV-2, the virus that causes the disease. We detail the way in which the immune system responds to a SARS-CoV-2 infection, including innate and adaptive measures. Then, we describe the role of vaccination, the main types of COVID-19 vaccines and how they protect us. Further, we explain the reason why immunity after COVID-19 infection plus a vaccination appears to induce a stronger response compared with virus exposure alone. Additionally, this review reports some correlates of protection from SARS-CoV-2 infection. In conclusion, we reinforce that vaccination is safe and important in achieving herd immunity.

Potent and Persistent Antibody Response in COVID-19 Recovered Patients

SARS-CoV-2 has caused a global pandemic with millions infected and numerous fatalities. Virus-specific antibodies can be detected in infected patients approximately two weeks after symptom onset. In this study, we set up ELISA technology coating with purified SARS-CoV-2 S and N proteins to study the antibody response of 484 serum samples. We established a surrogate viral inhibition assay using SARS-CoV-2 S protein pseudovirus system to determine the neutralization potency of collected serum samples. Here, we report robust antibody responses to SARS-CoV-2 in 484 recovered patients varying from 154 to 193 days, with 92% of recovered patients displaying a positive virus-specific spike glycoprotein IgG (s-IgG) response, while the ratio of positive spike glycoprotein IgM (s-IgM) reached 63%. Furthermore, moderate to potent neutralization activities were also observed in 62% of patients, correlating significantly with s-IgG response. This study strongly supports the long-term presence of antibodies in recovered patients against SARS-CoV-2, although all serum samples were collected from individuals with mild or moderate symptoms.

Clinical characteristics, cause analysis and infectivity of COVID-19 nucleic acid repositive patients: A literature review

Coronavirus disease 2019 (COVID-19) poses a serious threat to human health and lives. The virus is still spreading throughout the world, and the cumulative number of confirmed cases is increasing. After patients with COVID-19 are treated and discharged, some have repeated clinical symptoms and become positive for nucleic acid tests a second time. Through analysis and review of the existing literature, the proportion of repositive patients in the discharged patient population and their clinical characteristics were systematically described for the first time. Furthermore, an in-depth analysis of the causes of repositive nucleic acid tests and the potential transmission of the disease provides the basis for the management and protection of discharged patients with COVID-19.

Positive SARS-CoV-2 RNA recurs repeatedly in a case recovered from COVID-19: dynamic results from 108 days of follow-up

The evidence of long-term clinical dynamic on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) RNA re-positive case are less. We performed a 108 days follow-up on dynamic clinical presentations in a case, who hospitalized three times due to the positive recurrence of SARS-CoV-2 RNA after discharge, to understand the prognosis of the 2019-Coronavirus disease (COVID-19). In this case, positive SARS-CoV-2 recurred even after apparent recovery (normal CT imaging, no clinical symptoms, negative SARS-CoV-2 on stool sample and negative serum IgM test) from COVID-19, viral shedding duration lasted for 65 days, the time from symptom onset to disappearance was up to 95 days. Erythrocyte-associated indicators, liver function and serum lipid metabolism presented abnormal throughout during the observation period. Awareness of atypical presentations such as this one is important to prompt the improvement of the management of COVID-19.

Prealbumin as a Predictor of Prognosis in Patients With Coronavirus Disease 2019

Background: The predictive value of prealbumin for the prognosis of coronavirus disease 2019 (COVID-19) has not been extensively investigated.

Methods: A total of 1,115 patients with laboratory-confirmed COVID-19 were enrolled at Tongji hospital from February to April 2020 and classified into fatal (n = 129) and recovered (n = 986) groups according to the patient's outcome. Prealbumin and other routine laboratory indicators were measured simultaneously.

Results: The level of prealbumin on admission was significantly lower in fatal patients than in recovered patients. For predicting the prognosis of COVID-19, the performance of prealbumin was better than most routine laboratory indicators, such as albumin, lymphocyte count, neutrophil count, hypersensitive C-reactive protein, d-dimer, lactate dehydrogenase, creatinine, and hypersensitive cardiac troponin I. When a threshold of 126 mg/L was used to discriminate between fatal and recovered patients, the sensitivity and specificity of prealbumin were, respectively, 78.29 and 90.06%. Furthermore, a model based on the combination of nine indexes showed an improved performance in predicting the death of patients with COVID-19. Using a cut-off value of 0.19, the prediction model was able to distinguish between fatal and recovered individuals with a sensitivity of 86.82% and a specificity of 90.37%.

Conclusions: A lower level of prealbumin on admission may indicate a worse outcome of COVID-19. Immune and nutritional status may be vital factors for predicting disease progression in the early stage of COVID-19.