Cohort Profile of the Chilean COVID-19 Biorepository: a Multicentric initiative for multi-omics research on COVID-19 and LONG-COVID in a Latin American population. (preprint)

PurposeMolecular mechanisms underlying COVID-19 susceptibility and severity are still poorly understood. The presence of genetic risk factors associated with ethnic background has been suggested, highlighting non-European ancestry as a risk factor for hospitalization in the United States. However, the representation of non-European populations in genomic case-control and cohort studies remains insufficient, and Latin American populations have been significantly understudied. Addressing this gap, we established The Chilean COVID-19 Biorepository, a multicentric endeavor comprising high-quality biological samples and associated data collected throughout Chile under stringent biobanking standards that ensure high quality, reproducibility, and interoperability. ParticipantsThe Chilean COVID-19 Biorepository was established by a network of nine nodes distributed in five macro-zones nationwide. The study enrolled adult participants living in Chile who had tested positive for SARS-CoV-2 infection and provided broad written informed consent. Blood samples were collected with EDTA and processed to store blood, plasma, buffy-coat, and DNA. Quality control measures, such as Standard Preanalytical Code (SPREC), incident reporting, DNA concentration, and absorbance ratio (260/280), were implemented to ensure the reliability and quality of the collected samples. Sociodemographic data, habits, clinical information, use of medications, and preexisting pathologies were registered. A weekly iterative workflow was implemented to ensure the quality and integrity of specimens and data. Findings to dateBetween October 2020 and February 2021, 2262 participants were recruited, pseudonymized, and categorized by disease severity into six categories, from asymptomatic to lethal. Notably, the Biorepository exhibited high compliance rates (>90%) across all quality control assessed items, reflecting high adherence to biobanking standards. A noteworthy feature of this cohort is the self-identification of 279 participants (12.3%) into thirteen different ethnic groups. Amerindian ancestry from genome-wide genetic data was 44.0%[SD15.5%] and increased to 61.2%[SD19.5%] when considering participants who identified as Native South Americans. As a data-contributor partner of the COVID-19 Host Genetics Initiative, the Chilean COVID-19 Biorepository has contributed to the publication of a second updated genome-wide association study, further enhancing our knowledge of the role of host genetics in susceptibility and severity to SARS-CoV-2. Future plansThe Chilean COVID-19 Biorepository, under the leadership of Latin American researchers from a Latin American country, substantially adds to the integration of Latin American populations in the global collections landscape. Just as ocurred with the COVID-19 Host Genetics Initiative, we expect that this repository will attract global network collaborations for comparative studies on the effects of COVID-19 across diverse populations, including exploring potential genetic advantages or disadvantages in the context of SARS-CoV-2 infection. Researchers involved in establishing this biorepository are currently associated within a collaborative initiative known as COVID-19 Genomics Network (C19-GenoNet), aimed to accelerate the identification of genetic factors in both hosts and pathogens that influence the short and long-term outcomes of SARS-CoV-2 infection. The broad informed consent utilized enables longitudinal cohort follow-up, thereby allowing for investigating the long-term consequences of SARS-CoV-2 infection, particularly concerning long-COVID. Thus, participants of this cohort were re-contacted to assess the development of long-COVID through a survey-based approach. The re-contact and recruitment procedures yielded a high response rate (82.11%), demonstrating strong participant engagement. In this case as well, this cohort has been leveraged by collaboration with the COVID-19 Host Genetics Initiative for the forthcoming publication of a genome-wide association study on long-COVID. The concerted endeavors invested in this Chilean initiative have led to the establishment and consolidation of C19-GenoNet as both a research network and a biobanking network. A comprehensive catalog of the C19-GenoNet biobank network has been created and is accessible online at https://redcovid.uchile.cl/. STRENGHT AND LIMITATIONS OF THIS STUDYO_LIThis study is one of the largest cohorts of COVID-19 patients with associated Biobank reported so far in Latin America. C_LIO_LIThe studys design and rigorous weekly monitoring ensured effective collection of high-quality simples and maximized the quality and completeness of data, with the ability to re-contact participants in case of problematic information. C_LIO_LIThere were no control or reliable information about the time between the infection and the sampling, which may hamper the comparison of some parameters among cases due to transcriptional dynamics after SARS-CoV-2 infection. C_LIO_LIThe study is based on a self-reported survey, which may represent a bias when analyzing specific clinical phenotypes. C_LI

Serological Profile Of Specific Antibodies Against Dominant Antigens Of SARS-CoV-2 In Chilean COVID-19 Patients. (preprint)

Coronavirus disease 2019 (COVID-19) is caused by SARS-CoV-2 and has been a pandemic since March 2020. Currently, the virus has infected more than 50 million people worldwide and more than half a million in Chile. For many coronaviruses, Spike (S) and Nucleocapsid (N) proteins are described as major antigenic molecules, inducing seroconversion and production of neutralizing antibodies. In this work, we evaluated the presence in serum of IgM, IgA and IgG antibodies against N and S proteins of SARS-CoV-2 using western blot, and developed an ELISA test for the qualitative characterization of COVID-19 patients. Patients with an active infection or who have recovered from COVID-19 showed specific immunoblotting patterns for the recombinants S protein and its domains S1 and S2, as well as for the N protein of SARS-CoV-2. Anti-N antibodies were more frequently detected than anti-S or anti-S1-RBD antibodies. People who were never exposed to SARS-CoV-2 did not show reactivity. Finally, indirect ELISA assays using N and S1-RBD proteins, alone or in combination, were established with variable sensitivity and specificity depending on the antigen bound to the solid phase. Overall, Spike showed higher specificity than the nucleocapsid, and comparable sensitivity for both antigens. Both approaches confirmed the seroconversion after infection and allowed us to implement the analysis of antibodies in blood for research purposes in a local facility.

Convalescent Plasma in COVID-19. Mortality-Safety First Results of the Prospective Multicenter FALP 001-2020 Trial (preprint)

BackgroundThe use of convalescent plasma (CP) to treat COVID-19 has shown promising results; however, its effectiveness remains uncertain. The purpose of this study was to determine the safety and mortality of CP among patients hospitalized with COVID-19. Study Design and MethodsThis multicenter, open-label, uncontrolled clinical trial is currently being conducted at nine hospitals in Chile. Patients hospitalized due to COVID-19 who were still within 14 days since symptom onset were classified into four groups: Patients with cancer and severe COVID-19. Patients with cancer and non-severe COVID-19. Patients with severe COVID-19 and patients with non-severe COVID-19 only. The intervention involved two 200-cc. CP transfusions with anti-SARS-CoV-2 IgG titers [≥] 1:320 collected from COVID-19-recovered donors. Results192 patients hospitalized for COVID-19 received CP transfusions. At the first transfusion, 90.6% fulfilled the criteria for severity, and 41.1% required mechanical ventilation. 11.5% of the patients had cancer. Overall 7-day and 30-day mortality since the first CP transfusion was 5.7% and 16.1% respectively. There were no differences at either time point in mortality between the four groups. Patients on mechanical ventilation when receiving CP had higher mortality rates than those who were not (22.8% vs. 11.5%; p = 0.037). Overall 30-day mortality was higher in patients over 65 than in younger patients (p = 0.019). Severe adverse events were reported in four patients (2.1%) with an overall transfusion-related lung injury rate of 1.56%. No CP-related deaths occurred. DiscussionCP is safe when used in patients with COVID-19 even when also presenting severity criteria or risk factors. Our mortality rate is comparable to reports from larger studies. Controlled clinical trials are required to determine efficacy. RegistrationNCT04384588

Discovery of SARS-CoV-2 antiviral synergy between remdesivir and approved drugs in human lung cells (preprint)

The SARS coronavirus 2 (SARS-CoV-2) has caused an ongoing global pandemic with currently 29 million confirmed cases and close to a million deaths. At this time, there are no FDA-approved vaccines or therapeutics for COVID-19, but Emergency Use Authorization has been granted for remdesivir, a broad-spectrum antiviral nucleoside analog. However, remdesivir is only moderately efficacious against SARS-CoV-2 in the clinic, and improved treatment strategies are urgently needed. To accomplish this goal, we devised a strategy to identify compounds that act synergistically with remdesivir in preventing SARS-CoV-2 replication. We conducted combinatorial high-throughput screening in the presence of submaximal remdesivir concentrations, using a human lung epithelial cell line infected with a clinical isolate of SARS-CoV-2. We identified 20 approved drugs that act synergistically with remdesivir, many with favorable pharmacokinetic and safety profiles. Strongest effects were observed with established antivirals, Hepatitis C virus nonstructural protein 5 A (HCV NS5A) inhibitors velpatasvir and elbasvir. Combination with their partner drugs sofosbuvir and grazoprevir further increased efficacy, increasing remdesivir's apparent potency 25-fold. We therefore suggest that the FDA-approved Hepatitis C therapeutics Epclusa (velpatasvir/sofosbuvir) and Zepatier (elbasvir/grazoprevir) should be fast-tracked for clinical evaluation in combination with remdesivir to improve treatment of acute SARS-CoV-2 infections.

Early Anti-SARS-CoV-2 Convalescent Plasma in Patients Admitted for COVID-19: A Randomized Phase II Clinical Trial (preprint)

Background: Convalescent plasma (CP), despite limited evidence on its efficacy, is being widely used as a compassionate therapy for hospitalized patients with COVID-19. We aimed to evaluate the efficacy and safety of early CP therapy in COVID-19 progression. Methods: Open-label, single-center, randomized clinical trial performed in an academic center in Santiago, Chile from May 10, 2020, to July 18, 2020, with final follow-up August 17, 2020. The trial included patients hospitalized within the first 7 days of COVID-19 symptoms onset, presenting risk factors for illness progression and not on mechanical ventilation. The intervention consisted in immediate CP (early plasma group) versus no CP unless developing pre-specified criteria of deterioration (deferred plasma group). Additional standard treatment was allowed in both arms. The primary outcome was a composite of mechanical ventilation, hospitalization for >14 days or death. Key secondary outcomes included: time to respiratory failure, days of mechanical ventilation, hospital length-of-stay, mortality at 30 days, and SARS-CoV-2 RT-PCR clearance rate. Results: Of 58 randomized patients (mean age, 65.8 years, 50% male), 57 (98.3%) completed the trial. A total of 13 (43.3%) participants from the deferred group received plasma based on clinical aggravation. We found no benefit in the primary outcome (32.1% vs 33.3%, OR 0.95, 95% CI 0.32-2.84, p>0.99) in the early versus deferred CP group. In-hospital mortality rate was 17.9% vs 6.7% (OR 3.04, 95% CI 0.54-17.2, p=0.25), mechanical ventilation 17.9% vs 6.7% (OR 3.04, 95% CI 0.54-17.2, p=0.25), and prolonged hospitalization 21.4% vs 30% (OR 0.64, 95%CI, 0.19-2.1, p=0.55) in early versus deferred CP group, respectively. Viral clearance rate on day 3 (26% vs 8%, p=0.20) and day 7 (38% vs 19%, p=0.37) did not differ between groups. Two patients experienced serious adverse events within 6 or less hours after plasma transfusion. Conclusion: Immediate addition of CP therapy in early stages of COVID-19 -compared to its use only in case of patient deterioration- did not confer benefits in mortality, length of hospitalization or mechanical ventilation requirement.

The COVID-19 immune landscape is dynamically and reversibly correlated with disease severity (preprint)

Despite a rapidly growing body of literature on COVID-19, our understanding of the immune correlates of disease severity, course and outcome remains poor. Using mass cytometry, we assessed the immune landscape in longitudinal whole blood specimens from 59 patients presenting with acute COVID-19, and classified based on maximal disease severity. Hospitalized patients negative for SARS-CoV-2 were used as controls. We found that the immune landscape in COVID-19 forms three dominant clusters, which correlate with disease severity. Longitudinal analysis identified a pattern of productive innate and adaptive immune responses in individuals who have a moderate disease course, whereas those with severe disease have features suggestive of a protracted and dysregulated immune response. Further, we identified coordinate immune alterations accompanying clinical improvement and decline that were also seen in patients who received IL-6 pathway blockade. The hospitalized COVID-19 negative cohort allowed us to identify immune alterations that were shared between severe COVID-19 and other critically ill patients. Collectively, our findings indicate that selection of immune interventions should be based in part on disease presentation and early disease trajectory due to the profound differences in the immune response in those with mild to moderate disease and those with the most severe disease.