Efficacy and Safety of a Protein-Based SARS-CoV-2 Vaccine: A Randomized Clinical Trial.

Importance: The protein-based SARS-CoV-2 vaccines FINLAY-FR-2 (Soberana 02) and FINLAY-FR-1A (Soberana Plus) showed good safety and immunogenicity in phase 1 and 2 trials, but the clinical efficacy of the vaccine remains unknown. Objective: To evaluate the efficacy and safety of a 2-dose regimen of FINLAY-FR-2 (cohort 1) and a 3-dose regimen of FINLAY-FR-2 with FINLAY-FR-1A (cohort 2) in Iranian adults. Design, Setting, and Participants: A multicenter, randomized, double-blind, placebo-controlled, phase 3 trial was conducted at 6 cities in cohort 1 and 2 cities in cohort 2. Participants included individuals aged 18 to 80 years without uncontrolled comorbidities, coagulation disorders, pregnancy or breastfeeding, recent immunoglobulin or immunosuppressive therapy, and clinical presentation or laboratory-confirmed COVID-19 on enrollment. The study was conducted from April 26 to September 25, 2021. Interventions: In cohort 1, 2 doses of FINLAY-FR-2 (n = 13 857) or placebo (n = 3462) were administered 28 days apart. In cohort 2, 2 doses of FINLAY-FR-2 plus 1 dose of FINLAY-FR-1A (n = 4340) or 3 placebo doses (n = 1081) were administered 28 days apart. Vaccinations were administered via intramuscular injection. Main Outcomes and Measures: The primary outcome was polymerase chain reaction-confirmed symptomatic COVID-19 infection at least 14 days after vaccination completion. Other outcomes were adverse events and severe COVID-19. Intention-to-treat analysis was performed. Results: In cohort 1 a total 17 319 individuals received 2 doses and in cohort 2 5521 received 3 doses of the vaccine or placebo. Cohort 1 comprised 60.1% men in the vaccine group and 59.1% men in the placebo group; cohort 2 included 59.8% men in the vaccine group and 59.9% in the placebo group. The mean (SD) age was 39.3 (11.9) years in cohort 1 and 39.7 (12.0) years in cohort 2, with no significant difference between the vaccine and placebo groups. The median follow-up time in cohort 1 was 100 (IQR, 96-106) days and, in cohort 2, 142 (137-148) days. In cohort 1, 461 (3.2%) cases of COVID-19 occurred in the vaccine group and 221 (6.1%) in the placebo group (vaccine efficacy: 49.7%; 95% CI, 40.8%-57.3%) vs 75 (1.6%) and 51 (4.3%) in cohort 2 (vaccine efficacy: 64.9%; 95% CI, 49.7%-59.5%). The incidence of serious adverse events was lower than 0.1%, with no vaccine-related deaths. Conclusions and Relevance: In this multicenter, randomized, double-blind, placebo-controlled, phase 3 trial of the efficacy and safety of FINLAY-FR-2 and FINLAY-FR-1A, 2 doses of FINLAY-FR-2 plus the third dose of FINLAY-FR-1A showed acceptable vaccine efficacy against symptomatic COVID-19 as well as COVID-19-related severe infections. Vaccination was generally safe and well tolerated. Therefore, Soberana may have utility as an option for mass vaccination of the population, especially in resource-limited settings, because of its storage condition and affordable price. Trial Registration: isrctn.org Identifier: IRCT20210303050558N1.

The quantity and quality of anti-SARS-CoV-2 antibodies show contrariwise association with COVID-19 severity: lessons learned from IgG avidity.

Gaining more appreciation on the protective/damaging aspects of anti-SARS-CoV-2 immunity associated with disease severity is of great importance. This study aimed to evaluate the avidity of serum IgG antibodies against SARS-CoV-2 spike (S) and nucleocapsid (N) in hospitalized symptomatic COVID-19 patients and asymptomatic RT-PCR-confirmed SARS-CoV-2 carriers as well as to compare antibody avidities with respect to vaccination status, vaccination dose and reinfection status. Serum levels of anti-S and anti-N IgG were determined using specific ELISA kits. Antibody avidity was determined by urea dissociation assay and expressed as avidity index (AI) value. Despite higher IgG levels in the symptomatic group, AI values of both anti-S and anti-N IgG were significantly lower in this group compared to asymptomatic individuals. In both groups, anti-S AI values were elevated in one-dose and two-dose vaccinees versus unvaccinated subjects, although significant differences were only detected in the symptomatic group. However, anti-N avidity showed no significant difference between the vaccinated and unvaccinated subgroups. Almost all vaccinated patients of different subgroups (based on vaccine type) had higher anti-S IgG avidity, while the statistical significance was detected only between those receiving Sinopharm compared to the unvaccinated subgroup. Also, statistically significant differences in antibody AIs were only found between primarily infected individuals of the two groups. Our findings indicate a key role for anti-SARS-CoV-2 IgG avidity in protection from symptomatic COVID-19 and calls for the incorporation of antibody avidity measurement into the current diagnostic tests to predict effective immunity toward SARS-CoV-2 infection or even for prognostic purposes.

Investigation of antimicrobial resistance patterns and molecular typing of Pseudomonas aeruginosa isolates among Coronavirus disease-19 patients.

BACKGROUND: Pseudomonas aeruginosa is a common co-infecting pathogen recognized among COVID-19 patients. We aimed to investigate the antimicrobial resistance patterns and molecular typing of Pseudomonas aeruginosa isolates among Coronavirus disease-19 patients. METHODS: Between December 2020 and July 2021, 15 Pseudomonas aeruginosa were isolated from COVID-19 patients in the intensive care unit at Sina Hospital in Hamadan, west of Iran. The antimicrobial resistance of the isolates was determined by disk diffusion and broth microdilution methods. The double-disk synergy method, Modified Hodge test, and polymerase chain reaction were utilized to detect Pseudomonas aeruginosa extended spectrum beta-lactamase and carbapenemase producers. Microtiter plate assay was performed to evaluate the biofilm formation ability of the isolates. The isolates phylogenetic relatedness was revealed using the multilocus variable-number tandem-repeat analysis method. RESULTS: The results showed Pseudomonas aeruginosa isolates had the most elevated resistance to imipenem (93.3%), trimethoprim-sulfamethoxazole (93.3%), ceftriaxone (80%), ceftazidime (80%), gentamicin (60%), levofloxacin (60%), ciprofloxacin (60%), and cefepime (60%). In the broth microdilution method, 100%, 100%, 20%, and 13.3% of isolates showed resistance to imipenem, meropenem, polymyxin B, and colistin, respectively. Ten (66.6%) isolates were identified as multiple drug resistance. Carbapenemase enzymes and extended spectrum beta-lactamases were identified in 66.6% and 20% of the isolates, respectively and the biofilm formation was detected in 100% of the isolates. The blaOXA-48, blaTEM, blaIMP, blaSPM, blaPER, blaVEB, blaNDM, blaSHV, and blaCTX-M genes were detected in 100%, 86.6%, 86.6%, 40%, 20%, 20%, 13.3%, 6.6%, and 6.6% of the isolates, respectively. The blaVIM, blaGIM, blaGES, and blaMCR-1 genes were not identified in any of the isolates. The MLVA typing technique showed 11 types and seven main clusters and most isolates belong to cluster I, V and VII. CONCLUSION: Due to the high rate of antimicrobial resistance, as well as the genetic diversity of Pseudomonas aeruginosa isolates from COVID-19 patients, it is indispensable to monitor the antimicrobial resistance pattern and epidemiology of the isolates on a regular basis.

Comparison of the efficacy of equivalent doses of dexamethasone, methylprednisolone, and hydrocortisone for treatment of COVID-19-related acute respiratory distress syndrome: a prospective three-arm randomized clinical trial.

BACKGROUND: This prospective controlled clinical trial aimed to compare the efficacy of methylprednisolone, dexamethasone, and hydrocortisone at equivalent doses in patients with severe COVID-19. METHODS: In total, 106 patients with mild to moderate COVID-19-related acute respiratory distress syndrome (ARDS) were randomized to receive either dexamethasone (6 mg once a day), methylprednisolone (16 mg twice a day), or hydrocortisone (50 mg thrice a day) for up to 10 days. All participants received a standard of care for COVID-19. The primary and secondary efficacy outcomes included all-cause 28-day mortality, clinical status on day 28 assessed using the World Health Organization (WHO) eight-category ordinal clinical scale, number of patients requiring mechanical ventilation and intensive care unit (ICU) care, number of ventilator-free days, length of hospital and ICU stay, change in PaO2:FiO2 ratios during the first 5 days after treatment, and incidence of serious adverse events. P-values below 0.008 based on Bonferroni's multiple-testing correction method were considered statistically significant. RESULTS: According to the obtained results, there was a trend toward more favorable clinical outcomes in terms of needing mechanical ventilation and ICU care, number of ventilator-free days, change in PaO2:FiO2 ratios during the first 5 days after treatment, clinical status score at day 28, length of ICU and hospital stay, and overall 28-day mortality in patients receiving dexamethasone compared to those receiving methylprednisolone or hydrocortisone; however, likely due to the study's small sample size, the difference between groups reached a significant level only in the case of clinical status score on day 28 (p-value = 0.003). There was no significant difference in the incidence of serious adverse events between the study groups. CONCLUSION: Based on the results, severe cases of COVID-19 treated with dexamethasone might have a better clinical status at 28-day follow-up compared to methylprednisolone and hydrocortisone at an equivalent dose. Larger multicenter trials are required to confirm our findings.

Effect of Convalescent Plasma Therapy on Clinical Improvement of COVID-19 Patients: A Randomized Clinical Trial.

Background: Due to the critical condition of COVID-19, it is necessary to evaluate the efficacy of administrating convalescent plasma to COVID-19 patients. Therefore, we decided to design a clinical trial to investigate the effect of convalescent plasma of patients recovered from COVID-19 on the treatment outcome of COVID-19-infected patients. Materials and Methods: In this parallel randomized controlled clinical trial, patients in the intervention group received standard treatment plus convalescent plasma of patients recovered from COVID-19. We allocated 60 patients to each treatment group through balanced block randomization. Then, COVID-19 outcomes, vital signs, and biochemical parameters were compared between the two treatment groups by the independent t test and ANCOVA. Results: The mean age (SD) of the patients in the intervention and standard treatment groups was 52.84 (15.77) and 55.15 (14.34) years, respectively. Although patients in the intervention group reported more hospitalization days (11.45±5.86 vs. 10.42±6.79), death rates (26.67% vs. 18.13%), ICU admission (45 vs. 41.67%), and ARDS (11.67% vs. 3.33%), these differences were not statistically significant (P>0.05). Moreover, the two groups were homogenous in vital signs and biochemical parameters before and after treatment (P>0.05). Conclusion: The present study indicated that convalescent plasma therapy has no significant effect on the survival, hospitalization, and ICU admission of COVID-19 patients.

Identification of Risk Factors for COVID-19-related Death using Machine Learning Methods.

Background: Unknown cases of pneumonia appeared in late 2019 in Wuhan, China. Following the worldwide spread of the disease, the World Health Organization declared it a pandemic on March 11, 2020. The total number of infected people worldwide as of December 16, 2020, was more than 74 million, more than one million and six hundred thousand of whom died from Coronavirus Disease 2019 (COVID-19). This study aimed to identify the risk factors for the mortality of COVID-19 in Hamadan, west of Iran. Materials and Methods: This cross-sectional study used the information of all patients with COVID-19 admitted to Shahid Beheshti and Sina hospitals in Hamadan during January 2020-November 2020. Logistic regression model, decision tree, and random forest were used to assess risk factors for death due to COVID-19. Results: This study was conducted on 1853 people with COVID-19. Blood urea nitrogen change, SPO2 at admission, the duration of hospitalization, age, neutrophil count, lymphocyte count, number of breaths, complete blood count, systolic blood pressure, hemoglobin, and sodium were effective predictors in both methods of decision tree and random forest. Conclusion: The risk factors identified in the present study may serve as surrogate indicators to identify the risk of death due to COVID-19. The proper model to predict COVID-19-related mortality is random forest based on sensitivity.

The effects of nutrition bio-shield superfood powder on immune system function: A clinical trial study among patients with COVID-19.

The present study aimed to evaluate the effects of Nutrition Bio-shield Superfood (NBS) powder on the immune system function and clinical manifestations in patients with COVID-19. We compare the effects of NBS powder on the immune system function and clinical manifestations among two different groups: 1) intervention group receiving standard treatment scheduled according to treatment guidelines plus NBS powder, and 2) control group receiving only the same standard treatment. The serum levels of IL-2, IL-6, IL-17, IFNγ, and TNFα were determined after four weeks of treatment by specific ELISA kits according to the manufacturer's instructions. Finally, the level of immune system stimulation and inflammatory markers were compared at baseline and after intervention in both groups. Data were analyzed using SPSS (version 22). A p-value of ≤ 0.05 was set as significant. A total of 47 patients with COVID-19 (24 patients in the intervention group and 23 patients in the control group) were included in this study. Results showed that the differences in the mean decrease of IL-2, IL-6, and TNF-α in the intervention group in comparison to the control group were 0.93, 10.28, and 8.11 pg/ml, respectively (P<0.001). On the other hand, there was no difference in IL-17, IFNγ, monocytes, eosinophil, and other inflammatory indices between the intervention and control groups. Although NBS powder was able to significantly decrease the levels of some proinflammatory cytokines in patients with COVID-19, however, it is noteworthy that the course of the disease was to large part unaffected by NBS power and there was a reduction independent of treatment. The present study indicates that NBS powder could provide a beneficial anti-inflammatory effect in patients with COVID-19. Hence, NBS in treating patients with COVID-19 shows promise as an adjuvant to the current standard antiviral treatment of such patients. Clinical Trial Registration: https://www.irct.ir, identifier IRCT20200426047206N1.

Susceptibility and Severity of COVID-19 Are Both Associated With Lower Overall Viral-Peptide Binding Repertoire of HLA Class I Molecules, Especially in Younger People.

An important number of studies have been conducted on the potential association between human leukocyte antigen (HLA) genes and COVID-19 susceptibility and severity since the beginning of the pandemic. However, case-control and peptide-binding prediction methods tended to provide inconsistent conclusions on risk and protective HLA alleles, whereas some researchers suggested the importance of considering the overall capacity of an individual's HLA Class I molecules to present SARS-CoV-2-derived peptides. To close the gap between these approaches, we explored the distributions of HLA-A, -B, -C, and -DRB1 1st-field alleles in 142 Iranian patients with COVID-19 and 143 ethnically matched healthy controls, and applied in silico predictions of bound viral peptides for each individual's HLA molecules. Frequency comparison revealed the possible predisposing roles of HLA-A*03, B*35, and DRB1*16 alleles and the protective effect of HLA-A*32, B*58, B*55, and DRB1*14 alleles in the viral infection. None of these results remained significant after multiple testing corrections, except HLA-A*03, and no allele was associated with severity, either. Compared to peptide repertoires of individual HLA molecules that are more likely population-specific, the overall coverage of virus-derived peptides by one's HLA Class I molecules seemed to be a more prominent factor associated with both COVID-19 susceptibility and severity, which was independent of affinity index and threshold chosen, especially for people under 60 years old. Our results highlight the effect of the binding capacity of different HLA Class I molecules as a whole, and the more essential role of HLA-A compared to HLA-B and -C genes in immune responses against SARS-CoV-2 infection.

Transmission of COVID-19 and its Determinants among Close Contacts of COVID-19 Patients Running title.

BACKGROUND: This study aimed to determine the secondary attack rate (SAR) and its determinants to describe the clinical features and epidemiological aspects of patients and determine the risk factors of COVID-19 among household contacts in Hamadan Province, west of Iran. STUDY DESIGN: A cohort study. METHODS: In this cohort study, a total of 323 index cases and 989 related close contacts ages more than 15 years old (family members, relatives, and co-workers) were enrolled using a manual contact tracing approach, and all participants were tested by reverse transcription polymerase chain reaction test. In this research, the frequency of symptoms was assessed, the SAR among contacts of index cases was calculated, and the risk factors of COVID-19 were evaluated by the logistic regression model. RESULTS: The secondary attack rate for total household members of index cases was estimated at 31.7% (95% CI: 28.8-34.7). It was found that among household contacts, the highest SARs were related to spouses 47.1% (95% CI: 38.7-55.7) and grandparents/parents 39.3% (95% CI: 29.4, 49.9) of index cases, who had also higher risks to become secondary cases (adjusted odds ratio [OR]=2.98, 95% CI: 1.31-6.75 and adjusted OR=2.76, 95% CI: 1.18-6.44, respectively). Considering the occupation of contacts, unemployed and retired people and housewives were most susceptible for transmission of COVID-19. It was revealed that cough was the most prevalent symptom among index and secondary cases. CONCLUSION: Our findings indicated that spouses and grandparents/parents of index cases were the most susceptible individuals for COVID-19 transmission. Prolonged exposure with index case before COVID-19 diagnosis raised the chance of infection among secondary cases.

Predictors of death in patients with COVID-19: A cross-sectional study in West of Iran.

Background: Coronavirus disease 2019 (COVID-19) is a contagious disease caused by a newly identified coronavirus. Our knowledge about the survival rate and prognostic factors of the disease is not established well. The purpose of this study was to evaluate the predictors of COVID-19 mortality in Hamadan province in western Iran. Methods: In this study, we included all laboratory-confirmed COVID-19 cases with known treatment outcomes in Hamadan province, Iran, between 20, 2020, to May 10, 2020. Demographic, clinical, laboratory data, and treatment outcomes were obtained from computerized medical records and compared between survived cases and patients with death outcomes. Univariable and multivariable logistic regression models were used to determine the predictors of death. Results: From 749 investigated patients, 77 patients (10.28%) died during the treatment. The Mean age of patients was 53.97±19.04 years. Multivariable logistic regression showed that males had 2.07 (95% CI: 1.73, 2.54) fold higher odds of death. Those with 60 years old and more had 6.49 (95% CI: 4.53, 7.93) fold higher odds of death. Patients with an underlying disease had 7.14 (95% CI: 6.94, 7.38) fold higher odds of death, and patients who were hospitalized in the ICU ward had 2.24 (95% CI: 1.75, 2.90) times higher odds of COVID-19 related mortality. Conclusion: The potential predictors of death in COVID-19 cases, including the male gender, older age, and having an underlying disease could help physicians to identify patients with poor prognoses at an early stage and better management of them.

Concise Update on Genomics of COVID-19: Approach to Its latest Mutations, Escalated Contagiousness, and Vaccine Resistance.

The novel coronavirus disease 2019 (COVID-19) that started to invade the world from the Chinese fish market, causes an acute respiratory distress syndrome. COVID-19 is a dreadful infectious disease that surfaced only less than 8 months ago and caused the deadly COVID-19 pandemic. In this new species with a positive, single-strand RNA genome and a huge size, from the proteomics point view, there are no changes in sequences of amino acids in NSP7, 13, matrix, or envelope or other proteins including 8b and p6 and excluding NSP2 and NSP3. P6 is a multifunctional golgi-endoplasmic reticulum membrane-associated protein. This complex has a key duty to increase the replication rate of the virus and also causes intrinsic immune system responses by suppressing the signal transducer and activator of transcription factor 1 (STAT 1) translocated to the nucleus. Palmitoylated proteins elevate hydrophobicity which helps in membrane connection. Inside the N-linked glycosylation, moieties oligosaccharide is adhering to Asn-X-Ser/Thr canonical sequence. This helps for exact enfolding and carrying viral proteins by industriously using host's chaperon proteins including calreticulin and calnexin. 2B proteins encourage the internalization of major histocompatibility complex, class-I (MHC-I) protein and meanwhile inhibit their transfer to the surface of the cell as a recognition side. The deubiquitination of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has precise modification apparatus in the posttranslational stage. In this article, we outlined the recent and up-to-date data on genomic and molecular structures, epidemiology, vaccine development, and, last but not least, the clinical features, diagnostics, and treatment of the novel coronavirus.

SARS-CoV-2;from vaccine development to drug discovery and prevention guidelines

All species of coronavirus may cause infections in birds which is known to us since the 60s, but recently, from Nov 2019, the disease emerged in humans from the seafood market in Wuhan city. The previous viral outbreaks like SARS-CoV and MERS-CoV have also shown a greater mortality rate when transmitted to humans than other animals. An emerging concern in the 2019 novel coronavirus (SARS-CoV-2) is in terms of developing vaccine or discovery of new drugs to overcome the current viral pandemic. In this rapid-review, we aim to update the available data on coronavirus with the latest findings and achievements. So far, great steps have been taken such as hrsACE2 by a Swedish team from Karolinska Institute. Monash University announced the efficacy of Ivermectin to overcome COVID-19. The CRISPR/Cas13d as a new innovative therapeutics based might overcome the challenge of COVID-19. those strains of virus which lacking E protein-encoding regions are the perfect choice for vaccine development.