A deficient immune response to SARS-CoV-2 in the nasopharynx is associated with severe COVID-19 pneumonia.

OBJECTIVES: We analyzed the expression of inflammatory and antiviral genes in the nasopharynx of SARS-CoV-2 infected patients and their association with the severity of COVID-19 pneumonia. METHODS: We conducted a cross-sectional study on 223 SARS-CoV-2 infected patients. Clinical data were collected from medical records, and nasopharyngeal samples were collected in the first 24 hours after admission to the emergency room. The gene expression of eight proinflammatory/antiviral genes (plasminogen activator urokinase receptor [PLAUR], interleukin [IL]-6, IL-8, interferon [IFN]-ß, IFN-stimulated gene 15 [ISG15], retinoic acid-inducible gene I [RIG-I], C-C motif ligand 5 [CCL5], and chemokine C-X-C motif ligand 10 [CXCL10]) were quantified by real-time polymerase chain reaction. Outcome variables were: (i) pneumonia; (ii) severe pneumonia or acute respiratory distress syndrome. Statistical analysis was performed using multivariate logistic regression analyses. RESULTS: We enrolled 84 mild, 88 moderate, and 51 severe/critical cases. High expression of PLAUR (adjusted odds ratio [aOR] = 1.25; P = 0.032, risk factor) and low expression of CXCL10 (aOR = 0.89; P = 0.048, protective factor) were associated with pneumonia. Furthermore, lower values of ISG15 (aOR = 0.88, P = 0.021), RIG-I (aOR = 0.87, P = 0.034), CCL5 (aOR = 0.73, P <0.001), and CXCL10 (aOR = 0.84, P = 0.002) were risk factors for severe pneumonia/acute respiratory distress syndrome. CONCLUSION: An unbalanced early innate immune response to SARS-CoV-2 in the nasopharynx, characterized by high expression of PLAUR and low expression of antiviral genes (ISG15 and RIG-I), and chemokines (CCL5 and CXCL10), was associated with COVID-19 severity.

Metabolic Profiling at COVID-19 Onset Shows Disease Severity and Sex-Specific Dysregulation.

Background: metabolic changes through SARS-CoV-2 infection has been reported but not fully comprehended. This metabolic dysregulation affects multiple organs during COVID-19 and its early detection can be used as a prognosis marker of severity. Therefore, we aimed to characterize metabolic and cytokine profile at COVID-19 onset and its relationship with disease severity to identify metabolic profiles predicting disease progression. Material and Methods: we performed a retrospective cross-sectional study in 123 COVID-19 patients which were stratified as asymptomatic/mild, moderate and severe according to the highest COVID-19 severity status, and a group of healthy controls. We performed an untargeted plasma metabolic profiling (gas chromatography and capillary electrophoresis-mass spectrometry (GC and CE-MS)) and cytokine evaluation. Results: After data filtering and identification we observed 105 metabolites dysregulated (66 GC-MS and 40 CE-MS) which shown different expression patterns for each COVID-19 severity status. These metabolites belonged to different metabolic pathways including amino acid, energy, and nitrogen metabolism among others. Severity-specific metabolic dysregulation was observed, as an increased transformation of L-tryptophan into L-kynurenine. Thus, metabolic profiling at hospital admission differentiate between severe and moderate patients in the later phase of worse evolution. Several plasma pro-inflammatory biomarkers showed significant correlation with deregulated metabolites, specially with L-kynurenine and L-tryptophan. Finally, we describe a strong sex-related dysregulation of metabolites, cytokines and chemokines between severe and moderate patients. In conclusion, metabolic profiling of COVID-19 patients at disease onset is a powerful tool to unravel the SARS-CoV-2 molecular pathogenesis. Conclusions: This technique makes it possible to identify metabolic phenoconversion that predicts disease progression and explains the pronounced pathogenesis differences between sexes.

High Seroprevalence Against SARS-CoV-2 Among Faculty of Medicine and Health Sciences Personnel and Students of the University of Alcalá, Spain: Contributing Factors.

PURPOSE: Seroprevalence against SARS-CoV-2 within university systems is poorly studied, making evidence-based discussions of educational system reopening difficult. Moreover, few studies evaluate how antibodies against SARS-CoV-2 are maintained over time. We assessed serological response against the SARS-CoV-2 virus among our university students and staff. PATIENTS AND METHODS: In this prospective cohort study, seroprevalence was determined in 705 randomly selected volunteers, members of the Faculty of Medicine and Health Sciences of the University of Alcalá, using a chemiluminescent Siemens' SARS-CoV-2 immunoassay for total antibodies. Positive samples were tested for IgG and IgM/IgA using VIRCLIA® MONOTEST (Vircell). A first analysis took place during June 2020, and in those testing positive, a determination of secondary outcomes was performed in November 2020. RESULTS: A total of 130 subjects showed anti-SARS-CoV-2 antibodies (18.5%, 95% CI, 15.8-21.5%). Of these, IgM/IgA was positive in 27 and indeterminate in 19; IgG was positive in 118, indeterminate in 1. After 23 weeks, among 102 volunteers remeasured, IgG became undetectable in 6. Presence of antibodies was associated, in multivariable logistic regression, with exposure to infected patients (31.3%) [OR 1.84, 95% CI, 1.14-2.96; P = 0.012], presence of COVID-19 symptoms (52.4%) [OR 6.88, 95% CI, 4.28-11.06; P < 0.001], and confirmed earlier infection (82.9%) [OR 11.87, 95% CI, 4.26-33.07; P < 0.001]. CONCLUSIONS: The faculty of medicine and health sciences personnel and students of our university showed a high infection rate for SARS-CoV-2 during 2020 associated with providing clinical care to infected patients. This emphasizes the importance of the performance of continuous surveillance methods of the most exposed health personnel, including health science students.

High SARS-CoV-2 Viral Load and Low CCL5 Expression Levels in the Upper Respiratory Tract Are Associated With COVID-19 Severity.

Mucosal immune response in the upper respiratory tract is crucial for initial control of viral replication, clearance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and progression of coronavirus disease 2019 (COVID-19). We analyzed SARS-CoV-2 RNA load and expression of selected immune genes in the upper respiratory tract (nasopharynx) of 255 SARS-CoV-2-infected patients and evaluated their association with severe COVID-19. SARS-CoV-2 replication in nasopharyngeal mucosa induces expression of several innate immune genes. High SARS-CoV-2 viral load and low CCL5 expression levels were associated with intensive care unit admission or death, although CCL5 was the best predictor of COVID-19 severity.

Age-Adjusted Endothelial Activation and Stress Index for Coronavirus Disease 2019 at Admission Is a Reliable Predictor for 28-Day Mortality in Hospitalized Patients With Coronavirus Disease 2019.

Background: Endothelial Activation and Stress Index (EASIX) predict death in patients undergoing allogeneic hematopoietic stem cell transplantation who develop endothelial complications. Because coronavirus disease 2019 (COVID-19) patients also have coagulopathy and endotheliitis, we aimed to assess whether EASIX predicts death within 28 days in hospitalized COVID-19 patients. Methods: We performed a retrospective study on COVID-19 patients from two different cohorts [derivation (n = 1,200 patients) and validation (n = 1,830 patients)]. The endpoint was death within 28 days. The main factors were EASIX [(lactate dehydrogenase * creatinine)/thrombocytes] and aEASIX-COVID (EASIX * age), which were log2-transformed for analysis. Results: Log2-EASIX and log2-aEASIX-COVID were independently associated with an increased risk of death in both cohorts (p < 0.001). Log2-aEASIX-COVID showed a good predictive performance for 28-day mortality both in the derivation cohort (area under the receiver-operating characteristic = 0.827) and in the validation cohort (area under the receiver-operating characteristic = 0.820), with better predictive performance than log2-EASIX (p < 0.001). For log2 aEASIX-COVID, patients with low/moderate risk (<6) had a 28-day mortality probability of 5.3% [95% confidence interval (95% CI) = 4-6.5%], high (6-7) of 17.2% (95% CI = 14.7-19.6%), and very high (>7) of 47.6% (95% CI = 44.2-50.9%). The cutoff of log2 aEASIX-COVID = 6 showed a positive predictive value of 31.7% and negative predictive value of 94.7%, and log2 aEASIX-COVID = 7 showed a positive predictive value of 47.6% and negative predictive value of 89.8%. Conclusion: Both EASIX and aEASIX-COVID were associated with death within 28 days in hospitalized COVID-19 patients. However, aEASIX-COVID had significantly better predictive performance than EASIX, particularly for discarding death. Thus, aEASIX-COVID could be a reliable predictor of death that could help to manage COVID-19 patients.

Comparative evaluation of Panbio and SD Biosensor antigen rapid diagnostic tests for COVID-19 diagnosis.

The aim of our study was to evaluate the diagnostic performance of two antigen rapid diagnostic tests (Ag-RDTs) to diagnose severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We evaluated Panbio and SD-Biosensor Ag-RDTs. We employed 186 polymerase chain reaction (PCR) negative samples to evaluate the specificity and 170 PCR positive samples to assess the sensitivity. We evaluated their sensitivity according to Cycle threshold (C t ) values and days post onset of symptoms (d.p.o.). Tests were compared using the McNemar's test. Agreement was evaluated using the kappa score. Specificity was 100% for Panbio and 97.3% for SD-Biosensor. Sensitivity for samples with C t ≤ 20 was 100% for both assays and for samples with C t = 20-25 was 93.0% (Panbio) and 95.3% (SD-Biosensor) (p = 1.000). Sensitivity decreased for samples wit C t = 25-30 (Panbio: 41.3%, SD-Biosensor: 52.2%, p = 0.125) and samples with C t ≥ 30 (Panbio: 5.0%, SD-Biosensor: 17.5%, p = 0.063). Sensitivity within seven d.p.o. was 87.7% for Panbio and 90.4% for SD-Biosensor and notably decreased after seven d.p.o. Agreement with PCR was excellent for high viral load samples (C t ≤ 25): Panbio, 98.9%, kappa = 0.974; SD-Biosensor, 97.4%, kappa = 0.940. Agreement between Ag-RDTs was excellent (94.9%, kappa = 0.882). Panbio and SD-Biosensor Ag-RDTs showed excellent agreement and diagnostic performance results for samples with high viral loads (C t ≤ 25) or samples within seven d.p.o.

Diagnostic performance of CerTest and Panbio antigen rapid diagnostic tests to diagnose SARS-CoV-2 infection.

OBJECTIVES: Antigen rapid diagnostic tests (Ag-RDT) have been developed as reliable tools to control the SARS-CoV-2 pandemic. The objective of our study was to evaluate the diagnostic performance of two Ag-RDTs. METHODS: We evaluated CerTest SARS-CoV-2 Ag One Step Card Test and Panbio COVID-19 Ag Rapid Test Device Ag-RDTs. We included 320 nasopharyngeal samples: 150 PCR negative samples to assess the specificity and 170 PCR positive samples to evaluate the sensitivity. We also evaluated their sensitivity according to cycle threshold (Ct) values and the time from the onset of symptoms. Tests were compared using the McNemar's test and agreement was evaluated using the kappa score (k). RESULTS: Both Ag-RDTs showed a specificity of 100 %. Overall sensitivity was 53.5 % for CerTest and 60.0 % for Panbio. For samples with Ct≤ 25, sensitivity was 94.0 % for CerTest and 96.4 % for Panbio (p = 0.500). Regarding samples with Ct>25, sensitivity was 14.0 % for CerTest and 24.4 % for Panbio (p = 0.004). Sensitivity for samples within the first 5 days after the onset of symptoms were 84.8 % for CerTest and 91.3 % for Panbio (p = 0.250) and notably decreased for samples taken after the fifth day. Both Ag-RDTs showed an excellent agreement between them (agreement = 96.7 %, k = 0.920). Agreement with PCR was also excellent for high viral load samples (Ct<25) for CerTest (98.0 %, k = 0.954) and Panbio (98.8 %, k = 0.973). CONCLUSIONS: CerTest SARS-CoV-2 and Panbio COVID-19 Ag showed excellent performance and agreement results for samples with high viral loads (Ct ≤ 25) or samples taken within the first 5 days after the onset of symptoms.

Comparative evaluation of six immunoassays for the detection of antibodies against SARS-CoV-2.

OBJECTIVES: Serologic techniques can serve as a complement to diagnose SARS-CoV-2 infection. The objective of our study was to compare the diagnostic performance of six immunoassays to detect antibodies against SARS-CoV-2: three lateral flow immunoassays (LFAs), one ELISA and two chemiluminescence assays (CLIAs). METHODS: We evaluated three LFAs (Alltest, One Step and SeroFlash), one ELISA (Dia.Pro) and two CLIAs (Elecsys and COV2T). To assess the specificity, 60 pre-pandemic sera were used. To evaluate the sensitivity, we used 80 serum samples from patients with positive PCR for SARS-CoV-2. Agreement between techniques was evaluated using the kappa score (k). RESULTS: All immunoassays showed a specificity of 100 % except for SeroFlash (96.7 %). Overall sensitivity was 61.3 %, 73.8 %, 67.5 %, 85.9 %, 88.0 % and 92.0 % for Alltest, One Step, SeroFlash, Dia.Pro, Elecsys and COV2T, respectively. Sensitivity increased throughout the first two weeks from the onset of symptoms, reaching sensitivities over 85 % from 14 days for all LFAs, being One Step the most sensitive (97.6 %), followed by SeroFlash (95.1 %). Dia.Pro, Elecsys and COV2T showed sensitivities over 97 % from 14 days, being 100 % for COV2T. One Step showed the best agreement results among LFAs, showing excellent agreement with Dia.Pro (agreement = 94.2 %, k = 0.884), COV2T (99.1 %, k = 0.981) and Elecsys (97.3 %, k = 0.943). Dia.Pro, COV2T and Elecsys also showed excellent agreement between them. CONCLUSIONS: One Step, Dia.Pro, Elecsys and COV2T obtained the best diagnostic performance results. All these techniques showed a specificity of 100 % and sensitivities over 97 % from 14 days after the onset of symptoms, as well as excellent levels of agreement.

Severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection among hospital workers in a severely affected institution in Madrid, Spain: A surveillance cross-sectional study.

OBJECTIVE: To analyze the impact of the coronavirus disease 2019 (COVID-19) pandemic in workers of a hospital located in one of the most affected areas in Spain. DESIGN, SETTINGS, AND PATIENTS: Cross-sectional study performed between March and May 2020 over all workers of a secondary hospital in Madrid, Spain. METHODS: We employed polymerase chain reaction (PCR, for symptomatic individuals) and serology (for both PCR-negative symptomatic workers and asymptomatic workers) as diagnostic tests for severe acute respiratory coronavirus virus 2 (SARS-CoV-2). We analyzed the prevalence of the virus in healthcare workers (HCWs) and nonhealthcare workers (nHCWs). We also collected information about the use of personal protective equipment (PPEs) and possible contacts prior to infection. RESULTS: In total, 2,963 workers were included: 1,092 were symptomatic, and of these, 539 were positive by PCR (49.4% of symptomatic workers). From the remaining symptomatic workers, 197 (35.6%) were positive by serology. Regarding asymptomatic workers, 345 were positive by serology (31.9% of infected workers). In total, 1,081 (36.5%) presented a positive diagnostic test for SARS-CoV-2. Infection rates were different between HCWs (37.4%) and nHCWs (29.8%) (P = .006). In the multivariate logistic regression analysis, the use of PPE (protective: OR, 0.56; 95% CI, 0.44-0.72; P < .001) and previous contact with COVID-19 patients (risk factor: OR, 1.69; 95% CI, 1.28-2.24; P < .001) were independent factors that were associated with SAS-CoV-2 infection. CONCLUSIONS: Overall, >36% of our workers became infected with SARS-CoV-2, and the rate of asymptomatic infections accounted for almost 32% of all SARS-CoV-2 infections. We detected differences in the rates of infection between HCWs and nHCWs. The use of PPE and previous contact with COVID-19 patients were associated with SARS-CoV-2 infection.

Alltest rapid lateral flow immunoassays is reliable in diagnosing SARS-CoV-2 infection from 14 days after symptom onset: A prospective single-center study.

OBJECTIVES: SARS-CoV-2 infection diagnosis is challenging in patients from 2 to 3 weeks after the onset of symptoms, due to the low positivity rate of the PCR. Serologic tests could be complementary to PCR in these situations. The aim of our study was to analyze the diagnostic performance of one serologic rapid test in COVID-19 patients. METHODS: We evaluated a lateral flow immunoassay (AllTest COVID-19 IgG/IgM) which detects IgG and IgM antibodies. We validated the serologic test using serum samples from 100 negative patients (group 1) and 90 patients with COVID-19 confirmed by PCR (group 2). Then, we prospectively evaluated the test in 61 patients with clinical diagnosis of pneumonia of unknown etiology that were negative for SARS-CoV-2 by PCR (group 3). RESULTS: All 100 patients from group 1 were negative for the serologic test (specificity = 100 %). Regarding group 2 (PCR-positive), the median time from their symptom onset until testing was 17 days. For these 90 group-2 patients, the test was positive for either IgM or IgG in 58 (overall sensitivity = 64.4 %), and in patients tested 14 days or more after the onset of symptoms, the sensitivity was 88.0 %. Regarding the 61 group-3 patients, median time after symptom onset was also 17 days, and the test was positive in 54 (88.5 % positivity). CONCLUSIONS: Our study shows that Alltest lateral flow immunoassay is reliable as a complement of PCR to diagnose SARS-CoV-2 infection after 14 days from the onset of symptoms and in patients with pneumonia and negative PCR for SARS-CoV-2.