COVID-19 Patient Samples Research Articles

No sign of Rotavirus co-infection in COVID-19 patients with gastrointestinal symptoms.

The main goal of the present study is to investigate the incidence of Rotavirus co-infection in COVID-19 patients. Fecal samples of COVID-19 patients with gastrointestinal symptoms which had positive PCR- were collected from Abadan's hospital, Iran during the period December 2020 to January 2021. Samples were analyzed by RT-PCR to determine the presence of Rotavirus. Finally, the total samples size of 37 were included in this study. The mean age of patients was 48.22 years. Abdominal pain alone was detected in 48.65% of the patients. At least one gastrointestinal symptom was detected in all of the patients. Diarrhea and fever were seen in 13.51% and 59.46% of patients, respectively. Nausea and vomiting were seen in 5.41% of the patients. RT-PCR showed no infection of Rotavirus among the patients. Gastrointestinal symptoms related to COVID-19 are common. More studies is need among these patients groups for investigate co-infection with other fecal viral shedding carries, due to a worse prognosis and its association with disease severity.

Prevalence and predictors of outcomes among ESRD patients with COVID-19

Background End-stage renal disease patients on hemodialysis (ESRD) patients are at high risk for contracting COVID-19. In this propensity matched cohort study, we examined the prevalence of COVID-19 in emergency room (ER) patients and examined whether clinical outcomes varied by ESRD status.MethodsPatients who visited George Washington University Hospital ER from April 2020 to April 2021 were reviewed for COVID-19 and ESRD status. Among COVID-positive ER patients, the propensity for ESRD was calculated using a logistic regression model to create a propensity-matched sample of ESRD vs non-ESRD COVID-19 patients. A multivariable model examined whether ESRD was an independent predictor of death and other outcomes in COVID-19 patients.ResultsAmong the 27,106 ER patients, 2689 of whom were COVID-positive (9.9%). The odds of testing positive for COVID-19 were 0.97 ([95% CI: 0.78–1.20], p = 0.76) in ESRD vs non-ESRD patients after adjusting for age, sex, and race. There were 2414 COVID-positive individuals with non-missing data, of which 98 were ESRD patients. In this COVID-positive sample, ESRD patients experienced a higher incidence of stroke, sepsis, and pneumonia than non-ESRD individuals. Significant independent predictors of death included age, race, sex, insurance status, and diabetes mellitus. Those with no insurance had odds of death that was 212% higher than those with private insurance (3.124 [1.695–5.759], p < 0.001). ESRD status was not an independent predictor of death (1.215 [0.623–2.370], p = 0.57). After propensity-matching in the COVID-positive patients, there were 95 ESRD patients matched with 283 non-ESRD individuals. In this sample, insurance status continued to be an independent predictor of mortality, while ESRD status was not. ESRD patients were more likely to have lactic acidosis (36% vs 15%) and length of hospital stay ≥ 7 days (48% vs 31%), but no increase in odds for any studied adverse outcomes.ConclusionsIn ER patients, ESRD status was not associated with higher odds for testing positive for COVID-19. Among ER patients who were COVID positive, ESRD was not associated with mortality. However, insurance status had a strong and independent association with death among ER patients with COVID-19.

Towards real-time monitoring of COVID-19 nosocomial clusters using SARS-CoV-2 genomes in a university hospital of the French Alps

ObjectivesExperience of Nextstrain [1,2] and its approach adapted to the local context encouraged us to carry out real-time monitoring of COVID-19 nosocomial clusters in our establishment, the Grenoble Alpes University Hospital. Patients and methods, ResultsThrough identification from electronic health records of nosocomial pathways and clusters and calculation of genetic distances from sequenced samples of COVID-19 patients, we were able to identify potential nosocomial clusters in very close to real time with a significant time saving compared to classical epidemiological surveillance, and to better understand and characterize nosocomial clusters. ConclusionThrough early detection and characterization of clusters, we may prevent infection of our patients by further implementing the appropriate measures.

Urokinase System in Pathogenesis of Pulmonary Fibrosis: A Hidden Threat of COVID-19

Pulmonary fibrosis is a common and threatening post-COVID-19 complication with poorly resolved molecular mechanisms and no established treatment. The plasminogen activator system, including urokinase (uPA) and urokinase receptor (uPAR), is involved in the pathogenesis of COVID-19 and contributes to the development of lung injury and post-COVID-19 pulmonary fibrosis, although their cellular and molecular underpinnings still remain obscure. The aim of the current study was to assess the role of uPA and uPAR in the pathogenesis of pulmonary fibrosis. We analyzed uPA and uPAR expression in human lung tissues from COVID-19 patients with pulmonary fibrosis using single-cell RNA-seq and immunohistochemistry. We modeled lung fibrosis in Plau-/- and Plaur-/- mice upon bleomycin instillation and explored the effect of uPAR downregulation in A549 and BEAS-2B lung epithelial cells. We found that uPAR expression drastically decreased in the epithelial airway basal cells and monocyte/macrophage cells, whereas uPA accumulation significantly increased in tissue samples of COVID-19 patients. Lung injury and fibrosis in Plaur-/- vs. WT mice upon bleomycin instillation revealed that uPAR deficiency resulted in pro-fibrogenic uPA accumulation, IL-6 and ACE2 upregulation in lung tissues and was associated with severe fibrosis, weight loss and poor survival. uPAR downregulation in A549 and BEAS-2B was linked to an increased N-cadherin expression, indicating the onset of epithelial-mesenchymal transition and potentially contributing to pulmonary fibrosis. Here for the first time, we demonstrate that plasminogen treatment reversed lung fibrosis in Plaur-/- mice: the intravenous injection of 1 mg of plasminogen on the 21st day of bleomycin-induced fibrosis resulted in a more than a two-fold decrease in the area of lung fibrosis as compared to non-treated mice as evaluated by the 42nd day. The expression and function of the plasminogen activator system are dysregulated upon COVID-19 infection, leading to excessive pulmonary fibrosis and worsening the prognosis. The potential of plasminogen as a life-saving treatment for non-resolving post-COVID-19 pulmonary fibrosis warrants further investigation.

Immunothrombosis and Complement Activation Contribute to Disease Severity and Adverse Outcome in COVID-19

Severe COVID-19 is characterized by systemic inflammation and multiple organ dysfunction syndrome (MODS). Arterial and venous thrombosis are involved in the pathogenesis of MODS and fatality in COVID-19. There is evidence that complement and neutrophil activation in the form of neutrophil extracellular traps are main drivers for development of microvascular complications in COVID-19. Plasma and serum samples were collected from 83 patients infected by SARS-CoV-2 during the two first waves of COVID-19, before the availability of SARS-CoV-2 vaccination. Samples were collected at enrollment, day 11, and day 28; and patients had differing severity of disease. In this comprehensive study, we measured cell-free DNA, neutrophil activation, deoxyribonuclease I activity, complement activation, and D-dimers in longitudinal samples of COVID-19 patients. We show that all the above markers, except deoxyribonuclease I activity, increased with disease severity. Moreover, we provide evidence that in severe disease there is continued neutrophil and complement activation, as well as D-dimer formation and nucleosome release, whereas in mild and moderate disease all these markers decrease over time. These findings suggest that neutrophil and complement activation are important drivers of microvascular complications and that they reflect immunothrombosis in these patients. Neutrophil activation, complement activation, cell-free DNA, and D-dimer levels have the potential to serve as reliable biomarkers for disease severity and fatality in COVID-19. They might also serve as suitable markers with which to monitor the efficacy of therapeutic interventions in COVID-19.

Detection of specific antibodies against SARS-CoV-2 spike protein via ultra-sensitive bio-functionalized carbonnitride-reduced graphene oxide electrochemical immunosensing platform in real samples

Ultrasensitive immunosensing device based on bio-functionalized C3N4/RGO nanocomposite allows for exact differentiation between positive and negative real COVID-19 patient samples.

The association between different blood group systems and susceptibility to COVID-19: a single center cross-sectional study from Saudi Arabia.

Since the beginning of COVID-19 pandemic, many associated factors have been investigated to clarify the susceptibility and severity among the affected individuals. Biological markers can play an important role in identification of individual susceptibility to such pandemic. Growing evidence suggest the influence of different blood group systems on susceptibility to COVID-19 virus, with a particular blood type conferring selection advantage. The study aimed to determine the association of ABO, Rhesus (D) and P1 blood groups with COVID-19 susceptibility in Taif city, Western Saudi Arabia. ABO, D and P1 blood antigens were determined in 104 blood samples of COVID-19 patients versus 100 control samples using either automated immunohematology analyser or test tube method. Statistical differences between patients and control samples were calculated based on p-value where results of ≤ 0.05 were considered significant. O+ve blood group constituted the predominant type among the studied samples. Determination of P1 antigen showed significant association where Anti-P1 was positive in 76.9% of patients compared to 61.0% of controls with a P value of 0.01 conferring the susceptibility of P1+ve patients to COVID-19. Although our study showed no significant association between ABO and D, and susceptibility to COVID-19, there was a significant association between P1+ve and COVID-19. P1+ve participants were 2.131 times more associated with the risk of COVID-19 infection than those with Anti P1-ve. Thus, P1 antigen can be used as a biological marker for identification of individuals susceptibility to COVID-19. It is strongly advised that such individuals should consider extra protective measures. Further studies on other contributing factors should also be considered for more scientific clarity.

1044. Identification and Characterization of an Unconventional NK Subset in COVID-19

Abstract Background Coronavirus Disease 2019 (COVID-19) caused by the SARS-CoV-2 virus is associated with dysregulation in the innate immune response including NK cells. NK cells are integral in the innate immune response against viral infections. Canonical NK cells are classified as CD56dim CD16+ and CD56bright CD16-. An unconventional subset of CD56dim CD16- NK cells has previously been identified in COVID-19 that is not present in other viral infections. Here we characterize phenotypic changes in the NK cells of patients with severe COVID-19 as work towards determining the functional status of this unconventional subset. Methods Peripheral blood mononuclear cells (PBMCs) and plasma were isolated from healthy donors (n=5) and patients with severe COVID-19 on Extra Corporeal Membrane Oxygenation (ECMO) (n=15). Primary NK cells were stimulated in vitro with plasma from patients with severe COVID-19 or healthy donors. Flow cytometry was used to phenotype the NK cells. A separate cohort of PBMC samples (n=7) from patients requiring hospitalization for COVID-19 underwent Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq) analysis. Results The CD56bright CD16- NK subset was expanded in PBMCs from patients with severe COVID-19 as compared to healthy controls. CITE-Seq demonstrated that NK cells without surface CD16 clustered separately based on transcriptional profiling and did express FCGR3A at the translational level. Stimulation with COVID-19 plasma recapitulated the loss of CD16 from primary human NK cells and led to increased activity of Caspase 3/7. Figure 1.NK cells shift from the CD56dim CD16+ subset to the CD56dim CD16-subset in patients with severe COVID-19. a) Representative gating of NK cell subsets by Flow Cytometry in healthy and COVID-19 patient peripheral blood mononuclear cells (PBMCs). b) Percentage of total NK cells belonging to a particular cell subset compared between healthy donor samples (n=4) and COVID-19 patient samples (n=8). Data points represent an individual patient sample. Error bars represent the standard deviation of the mean. Differences between groups was analyzed using a two tailed t-test. *: p&amp;lt; 0.05, ns: not significant Figure 2.NK cells shift from the CD56dim CD16+ subset to the CD56dim CD16-subset after stimulation with COVID-19 plasma in vitro a) Representative gating of NK cell subsets by Flow Cytometry analysis in healthy donor NK cells stimulated by healthy plasma and COVID-19 patient plasma. b)Relative change in percentage of total NK cells belonging to a particular cell subset compared between healthy donor plasma (n=6)and COVID-19 patient plasma (n=15) stimulation conditions. Error bars represent the standard deviation of the mean and the difference between groups was analyzed using a two-tailed T-test. **: p&amp;lt; 0.01, ***: p&amp;lt; 0.001, ns: not significant. Conclusion We demonstrate and characterize a nonclassical population of CD56dim CD16- NK cells that are present in patients with severe COVID-19 and replicate this phenotype in vitro. Reproduction of this in vivo phenotype in an in vitro system will allow for additional studies on the functional state of NK cell subsets in COVID-19. The presence of this NK cell population may reflect a dysregulated innate immune response and immunopathogenesis of COVID-19. Disclosures All Authors: No reported disclosures.

Association of serum ADMA, SDMA and L-NMMA concentrations with disease progression in COVID-19 patients.

This study determines and compares the concentrations of arginine and methylated arginine products ((asymmetric dimethylarginine (ADMA), symmetric dimethylarginine (SDMA), n-monomethyl-1-arginine (L-NMMA) and homoarginine (HA)) for assessment of their association with disease severity in serum samples of COVID-19 patients. Serum arginine and methylated arginine products of 57 mild-moderate and 29 severe (N = 86) COVID-19 patients and 21 controls were determined by tandem mass spectrometry. Moreover, the concentrations of some of the routine clinical laboratory parameters -neutrophil lymphocyte ratio (NLR), C-reactive protein, ferritin, D-dimer, and fibrinogen measured during COVID-19 follow-up were also taken into consideration and compared with the concentrations of arginine and methylated arginine products. Serum ADMA, SDMA and L-NMMA were found to be significantly higher in severe COVID-19 patients, than in both mild-moderate patients and the control group (P < 0.001 for each). In addition, multiple logistic regression analysis indicated L-NMMA (cut-off =120 nmol/L OR = 34, 95% confidence interval (CI) = 3.5-302.0, P= 0.002), CRP (cut-off = 32 mg/L, OR = 37, 95% CI = 4.8-287.0, P < 0.001), and NLR (cut-off = 7, OR = 22, 95% CI = 1.4-335.0, P = 0.020) as independent risk factors for identification of severe patients. The concentration of methylated arginine metabolites are significantly altered in COVID-19 disease. The results of this study indicate a significant correlation between the severity of COVID-19 disease and concentrations of CRP, NLR and L-NMMA.

New insights into extracellular and intracellular redox status in COVID-19 patients

BackgroundThe imbalance of redox homeostasis induces hyper-inflammation in viral infections. In this study, we explored the redox system signature in response to SARS-COV-2 infection and examined the status of these extracellular and intracellular signatures in COVID-19 patients. MethodThe multi-level network was constructed using multi-level data of oxidative stress-related biological processes, protein-protein interactions, transcription factors, and co-expression coefficients obtained from GSE164805, which included gene expression profiles of peripheral blood mononuclear cells (PBMCs) from COVID-19 patients and healthy controls. Top genes were designated based on the degree and closeness centralities. The expression of high-ranked genes was evaluated in PBMCs and nasopharyngeal (NP) samples of 30 COVID-19 patients and 30 healthy controls. The intracellular levels of GSH and ROS/O2• − and extracellular oxidative stress markers were assayed in PBMCs and plasma samples by flow cytometry and ELISA. ELISA results were applied to construct a classification model using logistic regression to differentiate COVID-19 patients from healthy controls. ResultsCAT, NFE2L2, SOD1, SOD2 and CYBB were 5 top genes in the network analysis. The expression of these genes and intracellular levels of ROS/O2• − were increased in PBMCs of COVID-19 patients while the GSH level decreased. The expression of high-ranked genes was lower in NP samples of COVID-19 patients compared to control group. The activity of extracellular enzymes CAT and SOD, and the total oxidant status (TOS) level were increased in plasma samples of COVID-19 patients. Also, the 2-marker panel of CAT and TOS and 3-marker panel showed the best performance. ConclusionSARS-COV-2 disrupts the redox equilibrium in immune cells and the upper respiratory tract, leading to exacerbated inflammation and increased replication and entrance of SARS-COV-2 into host cells. Furthermore, utilizing markers of oxidative stress as a complementary validation to discriminate COVID-19 from healthy controls, seems promising.

Monitoring cognitive and psychological alterations in COVID-19 patients: A longitudinal neuropsychological study

BackgroundSARS-COV-2 infection has been associated to long-lasting neuropsychiatric sequelae, including cognitive deficits, that persist after one year. However, longitudinal monitoring has been scarcely performed. Here, in a sample of COVID-19 patients, we monitor cognitive, psychological and quality of life-related profiles up to 22 months from resolution of respiratory disease. MethodsOut of 657 COVID-19 patients screened at Manzoni Hospital (Lecco, Italy), 22 underwent neuropsychological testing because of subjective cognitive disturbances at 6 months, 16 months, and 22 months. Tests of memory, attention, and executive functions were administered, along with questionnaires for depressive and Post-traumatic stress disorder (PTSD) symptoms, psychological well-being and quality of life. Cross-sectional descriptives, correlational, as well as longitudinal analyses considering COVID19-severity were carried out. A preliminary comparison with a sample of obstructive sleep apneas patients was also performed. ResultsAround 50% of COVID-19 patients presented with cognitive deficits at t0. The most affected domain was verbal memory. Pathological scores diminished over time, but a high rate of borderline scores was still observable. Longitudinal analyses highlighted improvements in verbal and non-verbal long term memory, as well as attention, and executive functioning. Depression and PTSD-related symptoms were present in 30% of patients. The latter decreased over time and were associated to attentional-executive performance. ConclusionsCognitive dysfunctions in COVID-19 patients may extend over 1 year, yet showing a significant recovery in several cases. Cognitive alterations are accompanied by a significant psychological distress. Many patients displaying borderline scores, especially those at higher risk of dementia, deserve clinical monitoring.

Subpopulation composition of peripheral blood lymphocytes in COVID-19

The pathogenesis of severe coronavirus infection COVID-19 is associated with activation of immune system, cytokine storm, impaired blood clotting, microvascular thrombosis, organ ischemia and multiple organ dysfunction syndrome. The role of various lymphocyte subpopulations in COVID-19 is still debated. The aim of our study was to analyze the subpopulational profile of peripheral blood lymphocytes in COVID-19 patients as compared with healthy donors.The study included 20 COVID-19 patients (11 males and 9 females,) and 26 healthy donors. Average age of the patients was 52 and 56 years, respectively. Clinical examinations were performed by standard laboratory methods. Peripheral blood lymphocytes were isolated in the Ficoll gradient. The cells were stained with antibodies to specific antigens of main lymphocyte populations, endothelial cells, and apoptotic cell markers. The analysis was performed by flow cytometry. The results showed that all patients had elevated C-reactive protein (14- to 35-fold), ferritin (1.2- to 13-fold), D-dimers (1.2- to 90-fold). 55% of men had a decrease in the absolute number of lymphocytes, in women this index was at the low normal limit. Cytometric analysis showed that, among peripheral blood lymphocytes, the proportion of functional cells expressing the CD45 marker ranged from 2 to 12% in 70% of patients, as compared with 80-99% among the donors. The proportion of CD45+ lymphocytes significantly correlated with the level of hemoglobin, but not with the levels of inflammatory biochemical markers. Among the functional lymphocytes of patients, there was a decrease in the proportion of CD3+, CD4+, CD8+T cells, increased proportion of natural killer CD56+ and the apoptotic (AnnexinV+) cell contents, but the proportion of CD19 and HLA-DR+B cells was not changed. Analysis of the lymphocyte (LC) subpopulations that did not express CD45 marker showed that this fraction contained different lymphocyte subsets with reduced expression of CD4, CD8, CD19, CD56 etc. in the blood of patients and donors. Higher percentage of endothelial cells expressing CD62P marker made the difference between patients and donors.Laboratory determination of lymphocyte subsets in blood samples of COVID-19 patients does not reflect the real severity pattern of the disease, thus requiring studies of the CD45-expressing functional cell populations.

SARS-CoV-2 severity classification from plasma sample using confocal Raman spectroscopy.

The world is on the brink of facing coronavirus's (COVID-19) fourth wave as the mutant forms of viruses are escaping neutralizing antibodies in spite of being vaccinated. As we have already witnessed that it has encumbered our health system, with hospitals swamped with infected patients observed during the viral outbreak. Rapid triage of patients infected with SARS-CoV-2 is required during hospitalization to prioritize and provide the best point of care. Traditional diagnostics techniques such as RT-PCR and clinical parameters such as symptoms, comorbidities, sex and age are not enough to identify the severity of patients. Here, we investigated the potential of confocal Raman microspectroscopy as a powerful tool to generate an expeditious blood-based test for the classification of COVID-19 disease severity using 65 patients plasma samples from cohorts infected with SARS-CoV-2. We designed an easy manageable blood test where we used a small volume (8μl) of inactivated whole plasma samples from infected patients without any extra solvent usage in plasma processing. Raman spectra of plasma samples were acquired and multivariate exploratory analysis PC-LDA (principal component based linear discriminant analysis) was used to build a model, which segregated the severe from the non-severe COVID-19 group with a sensitivity of 83.87%, specificity of 70.60% and classification efficiency of 76.92%. Among the bands expressed in both the cohorts, the study led to the identification of Raman fingerprint regions corresponding to lipids (1661, 1742), proteins amide I and amide III (1555, 1247), proteins (Phe) (1006, 1034), and nucleic acids (760) to be differentially expressed in severe COVID-19 patient's samples. In summary, the current study exhibits the potential of confocal Raman to generate simple, rapid, and less expensive blood tests to triage the severity of patients infected with SARS-CoV-2.

Association of Clinical Features with Spike Glycoprotein Mutations in Iranian COVID-19 Patients.

Mutations in spike glycoprotein, a critical protein of SARS-CoV-2, could directly impact pathogenicity and virulence. The D614G mutation, a non-synonymous mutation at position 614 of the spike glycoprotein, is a predominant variant circulating worldwide. This study investigated the occurrence of mutations in the crucial zone of the spike gene and the association of clinical symptoms with spike mutations in isolated viruses from Iranian patients infected with SARS-CoV-2 during the second and third waves of the COVID-19 epidemic in Isfahan, the third-largest city in Iran. The extracted RNA from 60 nasopharyngeal samples of COVID-19 patients were subjected to cDNA synthesis and RT-PCR (in three overlapping fragments). Each patient's reverse transcriptase polymerase chain reaction (RT-PCR) products were assembled and sequenced. Information and clinical features of all sixty patients were collected, summarized, and analyzed using the GENMOD procedure of SAS 9.4. Analysis of 60 assembled sequences identified nine nonsynonymous mutations. The D614G mutation has the highest frequency among the amino acid changes. In our study, in 31 patients (51.66%), D614G mutation was determined. For all the studied symptoms, no significant relationship was observed with the incidence of D614G mutation. D614G, a common mutation among several of the variants of SARS-CoV-2, had the highest frequency among the studied sequences and its frequency increased significantly in the samples of the third wave compared to the samples of the second wave of the disease.

Postmortem Lung Biopsy in a Sample of COVID-19 Patients in Iraq

Background: The entire world was affected by the outbreak of novel coronavirus 2 (SARS-CoV-2), which influenced daily life worldwide and affected the medical, social, and economic prospects of all nations. This virus occurs clinically in four variants: asymptomatic; mild upper respiratory tract infection (URTI); anosmia and/ or ageusia as the only symptoms; and severe systemic disease, such as bilateral interstitial pneumonia. Approximately 20% of the population develops the severe course associated with cytokine release syndrome (CRS). Those who develop lung injury and dyspnea have higher mortality. An autopsy can reveal the pathogenesis and determine the cause of death. Objectives: To understand the pathophysiological changes in lung tissue in COVID-19-affected individuals. Patients and Methods: This is a case series of post-mortem lung histopathology examinations of deceased COVID-19-positive patients. Samples were collected from postmortem models acquired from six diseased individuals who tested positive for SARS-CoV-2 by reverse transcriptase polymerase chain (PCR) reaction and subsequently passed away in the tertiary hospital between July and September 2020 because of COVID-19. Their slides and paraffin-embedded blocks of lung biopsies, as well as their reports, were collected and sent to two pathologists for further evaluation of COVID-19-related changes in the lungs. Results: Only two of the six patients confirmed features of diffuse alveolar injury with hyaline layer and fibrin thrombi in pulmonary arteries, small vessel congestion, and pulmonary infarction. Two patients demonstrated diffuse alveolar fibrosis (organizing pneumonia), severe inflammation, and foci of squamous metaplasia, in addition to the deposition of carbon particles. One case had diffuse pulmonary fibrosis with pulmonary artery thrombosis without an inflammatory background. In another case, there were atypical large cells, ischemic necrosis, and severe inflammation with macrophages and pneumocyte hyperplasia inside the alveoli. Conclusion: the thromboembolic events suggest a role for COVID-19-induced coagulopathy. Molecular mechanisms and clinical features of COVID -19 should be studied. Atypical alterations need to be investigated to confirm their relation to COVID-19 infection.

Detection of unusual high molecular form of albumin in blood serum of COVID-19 patients

Blood sera of 12 severe Covid-19 patients and 14 healthy human donors were subjected to original TCA-extraction/acetone-precipitation followed by SDS-PAAG electrophoresis and mass-spectrometry. 76 kDa protein was detected as one of the differentially expressed proteins in the samples of Covid-19 patients. This 76 kDa protein was identified with mass-spectrometry as human serum albumin. Such molecular form of albumin was absent in blood serum of healthy human donors. The potential ways of generation of the unusual form of human serum albumin and its probable diagnostic value were discussed. Keywords: acetone-precipitation, biomarker proteins, COVID-19, electrophoresis, mass-spectrometry, TCA-extraction, unusual form of human serum albumin

Neutralization effect of plasma from vaccinated COVID-19 convalescents on SARS-CoV-2 Omicron variants.

BackgroundCOVID-19 has caused a global pandemic and the death toll is increasing. With the coronavirus continuously mutating, Omicron has replaced Delta as the most widely reported variant in the world. Studies have shown that the plasma of some vaccinated people does not neutralize the Omicron variant. However, further studies are needed to determine whether plasma neutralizes Omicron after one- or two-dose vaccine in patients who have recovered from infection with the original strain.MethodsThe pseudovirus neutralization assays were performed on 64 plasma samples of convalescent COVID-19 patients, which were divided into pre-vaccination group, one-dose vaccinated group and two-dose vaccinated group.ResultsIn the three groups, there were significant reductions of sera neutralizing activity from WT to Delta variant (B.1.617.2), and from WT to Omicron variant (B.1.1.529) (ps<0.001), but the difference between Delta and Omicron variants were not significant (p>0.05). The average neutralization of the Omicron variant showed a significant difference between pre-vaccination and two-dose vaccinated convalescent individuals (p<0.01).ConclusionsAmong the 64 plasma samples of COVID-19 convalescents, whether vaccinated or not, Omicron (B.1.1.529) escaped the neutralizing antibodies, with a significantly decreased neutralization activity compared to WT. And two-dose of vaccine could significantly raise the average neutralization of Omicron in convalescent individuals.

Untargeted plasma metabolomic fingerprinting highlights several biomarkers for the diagnosis and prognosis of coronavirus disease 19.

ObjectivesThe COVID-19 pandemic has been a serious worldwide public health crisis since 2020 and is still challenging healthcare systems. New tools for the prognosis and diagnosis of COVID-19 patients remain important issues.DesignHere, we studied the metabolome of plasma samples of COVID-19 patients for the identification of prognosis biomarkers.PatientsPlasma samples of eighty-six SARS-CoV-2-infected subjects and 24 healthy controls were collected during the first peak of the COVID-19 pandemic in France in 2020.Main resultsPlasma metabolome fingerprinting allowed the successful discrimination of healthy controls, mild SARS-CoV-2 subjects, and moderate and severe COVID-19 patients at hospital admission. We found a strong effect of SARS-CoV-2 infection on the plasma metabolome in mild cases. Our results revealed that plasma lipids and alterations in their saturation level are important biomarkers for the detection of the infection. We also identified deoxy-fructosyl-amino acids as new putative plasma biomarkers for SARS-CoV-2 infection and COVID-19 severity. Finally, our results highlight a key role for plasma levels of tryptophan and kynurenine in the symptoms of COVID-19 patients.ConclusionOur results showed that plasma metabolome profiling is an efficient tool for the diagnosis and prognosis of SARS-CoV-2 infection.

Study of the immunological and biochemical changes of COVID-19 patients and the gene expression of their Nrf2 gene in southren Iraq

This study was to determine the effect of the Coronavirus in samples (blood and serum) and its association with biochemical and immunological parameters and some factors including age, gender, clinical symptoms, and chronic diseases. 100 samples of COVID-19 patients (male and female) were collected in southern Iraq for 3 months (March 1 - 1 June). The results of this study showed (84% severe state and 16% critical state). High levels of ferritin in the severe case of COVID-19 patients, while D-dimer high levels in the critical cases of COVID-19 patients. CRP and WBC are at high levels in critical cases for COVID-19 patients. While the platelet levels of COVID-19 patients were low in critical cases.RT-PCR examined NRF2 gene expression to determine gene expression levels 5'- A/GTGACNNNGC, its relationship with COVID-19, and biochemical and immunological parameters. High levels of gene expression in severe cases and we did not find any effect of gender or age on gene expression levels NRF2. Parameter levels were not affected by the gender of the patient when infected with COVID-19. While platelet levels were high in females, due to some physiological factors.

Deep mutational scanning identifies SARS-CoV-2 Nucleocapsid escape mutations of currently available rapid antigen tests

The effects of mutations in continuously emerging variants of SARS-CoV-2 are a major concern for the performance of rapid antigen tests. To evaluate the impact of mutations on 17 antibodies used in 11 commercially available antigen tests with emergency use authorization, we measured antibody binding for all possible Nucleocapsid point mutations using a mammalian surface-display platform and deep mutational scanning. The results provide a complete map of the antibodies’ epitopes and their susceptibility to mutational escape. Our data predict no vulnerabilities for detection of mutations found in variants of concern. We confirm this using the commercial tests and sequence-confirmed COVID-19 patient samples. The antibody escape mutational profiles generated here serve as a valuable resource for predicting the performance of rapid antigen tests against past, current, as well as any possible future variants of SARS-CoV-2, establishing the direct clinical and public health utility of our system.