Hybrid Immunization In COVID-19: Time Matters (preprint)

Purpose: SARS-CoV-2 reinfections have been frequent, even among those vaccinated. The aim of this study is to know if hybrid immunity (infection+vaccination) is affected by the moment of vaccination and the number of doses received. Methods: We conducted a retrospective study in 745 patients with a history of COVID-19 reinfection and recovered the dates of infection and reinfection and vaccination status (date and number of doses). To assess differences in the time to reinfection(tRI) between unvaccinated, vaccinated before 6 months and later, and comparing one, two or three doses(incomplete, complete and booster regime) we performed  the log-rank test of the cumulative incidence calculated as 1 minus the Kaplan-Meier estimator. Results: The tRI was significantly higher in those vaccinated vs. non-vaccinated (q<0.001). However, an early incomplete regime(1 dose) protects similar time than not receiving a vaccine. Vaccination before 6 months after infection showed a lower tRI compared to those vaccinated later with the same regime(q<0.001). Actually, early vaccination with complete(2 doses) and booster regimes(3 doses) provided lower length of protection compared to vaccinating later with incomplete(1 dose) and complete regime(2 doses), respectively.  Vaccination with complete and booster regimes significantly increases the tRI(q<0.001). Conclusion: Vaccination increases the time it takes for a person to become reinfected with SARS-CoV-2. Increasing the time from infection to vaccination increases the time in which a person could be reinfected. Booster doses increase the time to reinfection. Those results emphasize the role of vaccines and boosters during the pandemic and can guide strategies on future vaccination policy.

Unbiased spectral cytometry immunome characterization predicts COVID-19 mRNA vaccine failure in older adults and patients with lymphoid malignancies. (preprint)

COVID-19 affects the population unequally with a higher impact on aged and immunosuppressed people. Hence, we assessed the effect of SARS-CoV-2 vaccination in immune compromised patients (older adults and oncohematologic patients), compared with healthy counterparts. While the acquired humoral and cellular memory did not predict subsequent infection 18 months after full immunization, spectral and computational cytometry revealed several subsets within the CD8+ T-cells, B-cells, NK cells, monocytes and CD45RA+CCR7- T{gamma}{delta} cells differentially expressed in further infected and non-infected individuals not just following immunization, but also prior to that. Of note up to 7 subsets were found within the CD45RA+CCR7- T{gamma}{delta} population with some of them being expanded and other decreased in subsequently infected individuals. Moreover, some of these subsets also predicted COVID-induced hospitalization in oncohematologic patients. Therefore, we hereby have identified several cellular subsets that, even before vaccination, strongly related to COVID-19 vulnerability as opposed to the acquisition of cellular and/or humoral memory following vaccination with SARS-CoV-2 mRNA vaccines.

Antigenemia Is Associated to Viral Sepsis and Mortality in COVID-19 (preprint)

Background: Severe COVID-19 has been proposed to represent a form of viral sepsis. The prevalence of sepsis due to this disease has not been evaluated. Some patients with severe COVID-19 present SARS-CoV-2 antigenemia. Whether antigenemia constitutes a factor associated to viral sepsis and fatal outcome in these patients is unknown. Methods: This study recruited 400 patients hospitalized with COVID-19. Prevalence of sepsis in the first 24 hours following hospitalization was determined using the SEPSIS-3 criteria. Prevalence and concentration of SARS-CoV-2 N-antigenemia was determined in plasma at hospitalization using the Panbio® COVID-19 Ag Rapid Test from Abbott and the COV-QUANTO® ELISA from AAZ. Findings: The prevalence of sepsis due to SARS-CoV-2 infection at hospitalization was of 54%, affecting mostly to the respiratory, renal and coagulation function. Antigenemia was present in the 53% of the patients, and constituted an independent risk factor of sepsis in the multivariate analysis (OR [CI95%], p): presence of N-antigenemia (Panbio®): (1·6 [1·1 - 2·5],0·023); concentration of N-antigen >575 pg/mL (COV-QUANTO®): (1·9 [1·0 - 3·5], 0·043). Antigenemia was associated with a reduction in the survival mean time of 9·42 and 9·33 days in the 90 first days following hospitalization, based on the PANBIO® and the COV-QUANTO® tests respectively. Interpretation: Half of the COVID-19 patients needing of hospitalization fulfill the criteria of sepsis. Antigenemia is strongly linked to the presence of this condition, and confers a higher risk of mortality. Monitoring the presence of antigenemia at the earlier moments of COVID-19 could help to identify those patients at risk of deterioration. Clinical Trial Registration Details: This was a sub-study of the CIBERES-UCI-COVID project, registered at Clinicaltrials.gov with the identification NCT04457505. Funding Information: Instituto de Salud Carlos III (COV20/00110; CP20/00041; FI20/00278), Fundació La Marató de TV3 (473/C/2021).Declaration of Interests: AT, JME, FB, RA and JFBM have a patent application on SARS-CoV-2 antigenemia. The remainder authors declare no conflicts of interest regarding this work.Ethics Approval Statement: Written or oral informed consent was obtained directly from all patients, or their legal representative, before enrolment. Scientific and ethical approval of the study protocol was obtained from the respective scientific committees for clinical research of the participant hospitals.

Description of a Novel Fameshifting Site in the 5'UTR of SARS-CoV-2 as a Potential Drug Target (preprint)

SARS-CoV-2 is an enveloped positive-sense single-stranded RNA coronavirus that causes COVID-19 whose present outbreak has cost a high number of casualties throughout the world. The aim of this work was to scan the SARS-CoV-2 genome in search for new therapeutic targets. We found a sequence in the 5'UTR (NC 045512:74-130), consisting of a typical heptamer next to a structured region that may cause frameshifting. The potential biological value of this region is shown by its similarity with other coronaviruses related with SARS-CoV and its sequence conservation within isolates from SARS-CoV-2. We have predicted the secondary structure of the region by means of different bioinformatic tools. We have chosen a probable secondary structure to proceed with a 3D reconstruction of the structured segment. We carried out virtual docking on the 3D structure to look for a binding site and then for drug ligands from a database of lead compounds. Several molecules that would probably administered as oral drugs show promising binding affinity within the structured region and so it would be possible interfere the potential regulatory role of our sequence of interest.

Absent or insufficient anti-SARS-CoV-2 S antibodies at ICU admission are associated to higher viral loads in plasma, antigenemia and mortality in COVID-19 patients (preprint)

Purposeto evaluate the association between anti-SARS-CoV-2 S IgM and IgG antibodies with viral RNA load in plasma, the frequency of antigenemia and with the risk of mortality in critically ill patients with COVID-19. Methodsanti-SARS-CoV-2 S antibodies levels, viral RNA load and antigenemia were profiled in plasma of 92 adult patients in the first 24 hours following ICU admission. The impact of these variables on 30-day mortality was assessed by using Kaplan-Meier curves and multivariate Cox regression analysis. Resultsnon survivors showed more frequently absence of anti-SARS-CoV-2 S IgG and IgM antibodies than survivors (26.3% vs 5.6% for IgM and 18.4% vs 5.6% for IgG), and a higher frequency of antigenemia (47.4% vs 22.2%) (p <0.05). Non survivors showed lower concentrations of anti-S IgG and IgM and higher viral RNA loads in plasma, which were associated to increased 30-day mortality and decreased survival mean time. [Adjusted HR (CI95%), p]: [S IgM (AUC [≥]60): 0.48 (0.24; 0.97), 0.040]; [S IgG (AUC [≥]237): 0.47 (0.23; 0.97), 0.042]; [Antigenemia (+): 2.45 (1.27; 4.71), 0.007]; [N1 viral load ([≥] 2.156 copies/mL): 2.21 (1.11; 4.39),0.024]; [N2 viral load ([≥] 3.035 copies/mL): 2.32 (1.16; 4.63), 0.017]. Frequency of antigenemia was >2.5-fold higher in patients with absence of antibodies. Levels of anti-SARS-CoV-2 S antibodies correlated inversely with viral RNA load. Conclusionabsence / insufficient levels of anti-SARS-CoV-2 S antibodies following ICU admission is associated to poor viral control, evidenced by increased viral RNA loads in plasma, higher frequency of antigenemia, and also to increased 30-day mortality. Take-home messageabsent or low levels of antibodies against the S protein of SARS-CoV- 2 at ICU admission is associated to an increased risk of mortality, higher frequency of antigenemia and higher viral RNA loads in plasma. Profiling anti-SARS-CoV-2 s antibodies at ICU admission could help to predict outcome and to better identify those patients potentially deserving replacement treatment with monoclonal or polyclonal antibodies.

SARS-CoV-2-RNA viremia is associated to hypercytokinemia and critical illness in COVID-19 (preprint)

BackgroundSevere COVID-19 is characterized by clinical and biological manifestations typically observed in sepsis. SARS-CoV-2 RNA is commonly detected in nasopharyngeal swabs, however viral RNA can be found also in peripheral blood and other tissues. Whether systemic spreading of the virus or viral components plays a role in the pathogenesis of the sepsis-like disease observed in severe COVID-19 is currently unknown. MethodsWe determined the association of plasma SARS-CoV-2 RNA with the biological responses and the clinical severity of patients with COVID-19. 250 patients with confirmed COVID-19 infection were recruited (50 outpatients, 100 hospitalised ward patients, and 100 critically ill). The association between plasma SARS-CoV-2 RNA and laboratory parameters was evaluated using multivariate GLM with a gamma distribution. The association between plasma SARS-CoV-2 RNA and severity was evaluated using multivariate ordinal logistic regression analysis and Generalized Linear Model (GLM) analysis with a binomial distribution. ResultsThe presence of SARS-CoV-2-RNA viremia was independently associated with a number of features consistently identified in sepsis: 1) high levels of cytokines (including CXCL10, CCL-2, IL-10, IL-1ra, IL-15, and G-CSF); 2) higher levels of ferritin and LDH; 3) low lymphocyte and monocyte counts 4) and low platelet counts. In hospitalised patients, the presence of SARS-CoV-2-RNA viremia was independently associated with critical illness: (adjusted OR= 8.30 [CI95%=4.21 - 16.34], p < 0.001). CXCL10 was the most accurate identifier of SARS-CoV-2-RNA viremia in plasma (area under the curve (AUC), [CI95%], p) = 0.85 [0.80 - 0.89), <0.001]), suggesting its potential role as a surrogate biomarker of viremia. The cytokine IL-15 most accurately differentiated clinical ward patients from ICU patients (AUC: 0.82 [0.76 - 0.88], <0.001). Conclusionssystemic dissemination of genomic material of SARS-CoV-2 is associated with a sepsis-like biological response and critical illness in patients with COVID-19. RNA viremia could represent an important link between SARS-CoV-2 infection, host response dysfunction and the transition from moderate illness to severe, sepsis-like COVID-19 disease.