Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study

Bacterial co-infection in COVID-19: a call to stay vigilant

Co-infection with diverse bacteria is commonly seen in patients infected with the novel coronavirus, SARS-CoV-2. This type of co-infection significantly impacts the occurrence and development of novel coronavirus infection. Bacterial co-pathogens are typically identified in the respiratory system and blood culture, which complicates the diagnosis, treatment, and prognosis of COVID-19, and even exacerbates the severity of disease symptoms and increases mortality rates. However, the status and impact of bacterial co-infections during the COVID-19 pandemic have not been properly studied. Recently, the amount of literature on the co-infection of SARS-CoV-2 and bacteria has gradually increased, enabling a comprehensive discussion on this type of co-infection. In this study, we focus on bacterial infections in the respiratory system and blood of patients with COVID-19 because these infection types significantly affect the severity and mortality of COVID-19. Furthermore, the progression of COVID-19 has markedly elevated the antimicrobial resistance among specific bacteria, such as Klebsiella pneumoniae, in clinical settings including intensive care units (ICUs). Grasping these resistance patterns is pivotal for the optimal utilization and stewardship of antibiotics, including fluoroquinolones. Our study offers insights into these aspects and serves as a fundamental basis for devising effective therapeutic strategies. We primarily sourced our articles from PubMed, ScienceDirect, Scopus, and Google Scholar. We queried these databases using specific search terms related to COVID-19 and its co-infections with bacteria or fungi, and selectively chose relevant articles for inclusion in our review.

Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic

Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Seafood Wholesale Market. Here, we analyze environmental qPCR and sequencing data collected in the Huanan market in early 2020. We demonstrate that market-linked severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity is consistent with market emergence and find increased SARS-CoV-2 positivity near and within a wildlife stall. We identify wildlife DNA in all SARS-CoV-2-positive samples from this stall, including species such as civets, bamboo rats, and raccoon dogs, previously identified as possible intermediate hosts. We also detect animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them with those from farms and other markets. This analysis provides the genetic basis for a shortlist of potential intermediate hosts of SARS-CoV-2 to prioritize for serological and viral sampling.

COVID-19 AND MANIA: A CASE WITH A ONE-YEAR FOLLOW UP

COVID-19 may affect central nervous system. The symptoms related to the CNS may occur through the direct neuroinvasion of the virus, inflammation, autoimmunity, psychosocial stressors and treatment side effects. COVID-19 can increase the severity of existing mental illnesses and also trigger the onset of a new mental illness. In this case report, we present a 52-year-old male patient with no previous psychiatric history as well as no family history of mental illness. The patient's manic symptoms began while he was hospitalized due to severe COVID-19 pneumonia. The patient, who self-discharged himself from the hospital was brought to the emergency department involuntarily by his relatives 14 days later and was admitted to the psychiatry service. In this case report, possible etiological factors were discussed and the treatment course during the hospitalization and one year follow-up were presented. Our aim is to contribute to the literature by discussing possible etiological factors and management of mania that started during the treatment of COVID-19. COVID-19 can affect the central nervous system and be associated with psychiatric symptoms. Keywords: COVID-19, Mania, Bipolar Disorder, Central Nervous System.

Immunogenicity of an Inactivated COVID-19 Vaccine in People Living with HIV in Guangxi, China: A Prospective Cohort Study

The inactivated COVID-19 vaccine has demonstrated high efficacy in the general population through extensive clinical and real-world studies. However, its effectiveness in immunocompromised individuals, particularly those living with HIV (PLWH), remains limited. In this study, 20 PLWH and 15 HIV-seronegative individuals were recruited to evaluate the immunogenicity of an inactivated COVID-19 vaccine in PLWH through a prospective cohort study. The median age of the 20 PLWH and 15 HIV-seronegative individuals was 42 years and 31 years, respectively. Of the PLWH, nine had been on ART for over five years. The median anti-SARS-CoV-2 S-RBD IgG antibody level on d224 was higher than that on d42 (8188.7 ng/mL vs. 3200.9 ng/mL, P < 0.05). Following COVID-19 infection, the antibody level increased to 29,872.5 ng/mL on dre+90, 12.19 times higher than that on d300. Compared with HIV-seronegative individuals, the antibody level in PLWH was lower on d210 (183.3 ng/mL vs. 509.3 ng/mL, P < 0.01), while there was no difference after d224. The symptoms of COVID-19 infection in PLWH were comparable to those in HIV-seronegative individuals. In this study, the inactivated COVID-19 vaccine demonstrated good immunogenicity in PLWH. The protective benefit of booster vaccinations for PLWH cannot be ignored. Implementing a booster vaccination policy for PLWH is an effective approach to providing better protection against the COVID-19 pandemic.

Clinical efficacy of Fufang Yinhua Jiedu (FFYH) granules in mild COVID-19 and its anti-SARS-CoV-2 mechanism by blocking autophagy through inhibiting the AKT/mTOR signaling pathway

Background

Fufang Yinhua Jiedu (FFYH) granules are recommended for treating coronavirus pneumonia (COVID-19) in China. However, its anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) activity and clinical efficacy against COVID-19 remain to be confirmed.

Aims

Our study aimed to investigate the anti-SARS-CoV-2 effect and potential mechanism of FFYH.

Materials and Methods

The activity of FFYH against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was evaluated via cell pathogenic effects, immunoblotting, immunofluorescence staining, and qRT-PCR. The potential mechanism of FFYH against SARS-CoV-2 was investigated by immunoblotting. One head-to-head randomized controlled trial was designed to evaluate the clinical efficacy of FFYH in mild COVID-19. Two hundred patients were randomly recruited to receive either FFYH or LHQW (Lianhua Qingwen) granules.

Results

The in vitro results indicated that FFYH effectively inhibited SARS-CoV-2 replication by suppressing CPE and decreasing viral RNA and protein expression. A time-of-drug-addition assay confirmed that FFYH mainly targeted the binding and replication stages of the SARS-CoV-2 life cycle. Mechanistic studies revealed that blocking SARS-CoV-2-triggered autophagy may be the primary mechanism by which FFYH protects against SARS-CoV-2 infection by regulating the phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) signaling pathway. Clinical results confirmed that FFYH effectively shortened the recovery time of clinical symptoms and viral nucleic acid negativity, improved abnormal hematology parameters, and controlled excessive cytokine responses in mild COVID-19 patients. Subgroup analysis revealed that FFYH improved the recovery time of clinical symptoms, improved hematological parameters, and controlled excessive cytokine storms to a greater extent in the mild COVID-19 male subgroup, abnormal hematology subgroup, and 32-42-year-old subgroup than in the corresponding LHQW subgroup (P < 0.05). No patients progressed to severe or critical cases.

Conclusion

Our results indicate that FFYH not only has good anti-viral activity against SARS-CoV-2 but also has significant efficacy against COVID-19, indicating that FFYH may be a novel complementary option for treating COVID-19.

Liver ultrasound evaluation of acutely increased liver function tests of COVID-19 hospitalized patients

BACKGROUND

The incidence of hepatic abnormalities has been notably higher following the coronavirus disease 2019 (COVID-19) infection, attributed to the virus's entry into cells via angiotensin-converting enzyme 2 (ACE2) surface expression. The gastrointestinal tract's significant ACE2 expression, alongside a lesser degree in the biliary epithelium, has been implicated in gastrointestinal symptoms and liver injury.

PURPOSE

The aim of this study was to determine whether specific ultrasonographic findings in the liver correlate with acute increases in liver function tests (LFTs) among hospitalized patients.

METHODS

A retrospective analysis was conducted on hospitalized COVID-19 patients at Hazem Mebaireek General Hospital in Qatar, from March 1, 2020, to June 30, 2020. The study focused on patients who experienced acute increases in LFTs, excluding those with chronic liver disease. Ultrasound imaging and patient records were reviewed to gather data.

RESULTS

Out of 223 ultrasound studies of COVID-19 patients, 158 met the inclusion criteria. The majority were male, with a mean age of 47.76 ± 13.76 years. Ultrasound results showed 43.7% normal liver parenchyma, while 56.3% exhibited nonspecific abnormalities such as diffuse liver hyperechogenicity (39.2%), enlargement with diffuse hyperechogenicity (12.7%), and other findings (4.4%). The biliary tree was predominantly normal (96.2%), with 3.8% showing abnormalities, including intrahepatic (2.5%) and extrahepatic (1.3%) dilatation. Gallbladder evaluations were normal in 60.1% of cases, with 39.9% showing abnormalities like stones (6.3%), stones with sludge (13.3%), polyps (6.3%), wall thickening (1.9%), and other conditions (12%). A significant correlation was found between abnormal liver parenchyma findings and elevated levels of bilirubin (total and direct) and alkaline phosphatase, with p-values < 0.05. Only aspartate aminotransferase levels showed a significant correlation with biliary tree abnormalities.

CONCLUSION

The most common ultrasonographic finding associated with acute increases in LFTs among hospitalized COVID-19 patients was diffuse liver hyperechogenicity, with or without enlargement. These findings suggest a nonspecific yet significant association with liver function anomalies in the context of COVID-19.

Detection of SARS-CoV-2 on the environmental surfaces and its implications for pandemic preparedness

Even though death due to COVID-19 is no longer a public health emergency, less virulent but highly transmissible forms of SARS-CoV-2 continue to spread in many countries leading to outbreaks and rise in hospitalizations in the affected regions. Lessons learned during the pandemic must be put into action to protect the world's population from another catastrophe like COVID-19. Novel approaches that were developed for tracking the spread of SARS-CoV-2 included analysis of wastewater, air samples, and various environmental surfaces. We conducted a study in Kuwait during the peak of COVID-19 pandemic to examine if SARS-CoV-2 could be detected in swabs taken from frequently touched environmental surfaces. We selected 12 Cooperative Society Stores-two from each governorate of Kuwait-for collection of surface samples. The Cooperative Society Stores are widely distributed across the whole country and cater to daily household needs including groceries and other essential items. These stores operated even during the "lockdown" imposed at the height of the pandemic. We collected swabs from high-touch surfaces including the handles of the shopping carts and freezers, the elevators, the keypads of the point-of-service terminals of cash counters, and the automated teller machines. All the surfaces tested showed a variable presence of SARS-CoV-2 by reverse transcriptase quantitative PCR, showing the validity of the proof-of-concept study. Monitoring of the presence of SARS-CoV-2 by surface sampling thus offers a cheap but effective means of environmental surveillance for coronaviruses. We therefore strongly recommend the addition of surface environmental sampling as a strategy for pandemic preparedness everywhere.

Outcomes of COVID-19 in patients with obinutuzumab compared with patients with rituximab: a retrospective cohort study

BACKGROUND

Patients treated with anti-CD20 monoclonal antibodies could have a higher risk of adverse outcomes of coronavirus disease 2019 (COVID-19). The novel anti-CD20 monoclonal antibody obinutuzumab has shown greater B-cell depletion and superior in vitro efficacy than rituximab. We aimed to assess whether obinutuzumab would result in worse COVID-19 outcomes than rituximab.

METHODS

We retrospectively reviewed 124 patients with B-cell lymphoma, 106 of whom received rituximab treatment and 18 of whom received obinutuzumab treatment. The adverse outcomes of COVID-19 were compared between patients in the two cohorts.

RESULTS

The proportions of patients who were hospitalized (55.6% vs. 20.8%, p = 0.005), experienced prolonged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (38.9% vs. 2.9%, p < 0.001), and developed severe COVID-19 (33.3% vs. 4.7%, p < 0.001) were higher in patients with obinutuzumab than in those with rituximab. Multivariate analyses showed that obinuzumab treatment was associated with higher incidences of prolonged SARS-CoV-2 infection (OR 27.05, 95% CI 3.75-195.22, p = 0.001) and severe COVID-19(OR 15.07, 95% CI 2.58-91.72, p = 0.003).

CONCLUSIONS

Our study suggested that patients treated with obinutuzumab had a higher risk of prolonged SARS-CoV-2 infection and severe COVID-19 than those treated with rituximab.

Investigating the relationship between lymphocyte cells apoptosis and DNA damage and oxidative stress and therapeutic and clinical outcomes of COVID-19 elderly patients

BACKGROUND

While COVID-19 has been controlled and deaths have decreased, the long-term consequences of COVID-19 remain a challenge we face today. This study was conducted to determine the relationship between the apoptosis of lymphocyte cells with DNA damage and oxidative stress and the therapeutic and clinical outcomes of elderly patients with COVID-19.

METHODS

This study was conducted from April 2020 to May 2021 (the period of severe attacks of the epidemic peak of COVID-19) and September 2022 (the post-COVID-19 period). The study groups included elderly patients with COVID-19 hospitalized in the ICU and normal wards of the hospital as well as elderly patients with influenza. A polymerase chain reaction was used to check the validity of the studied diseases. The Annexin V/Propidium Iodide method was used to evaluate the level of apoptosis. Genotoxic effects and DNA damage were assessed by the comet assay method. Total antioxidant status (TAS), total oxidant status (TOS), and myeloperoxidase activity (MPO) were measured by photometric methods.

RESULTS

The highest level of apoptosis in peripheral blood lymphocytes and the highest level of DNA damage were observed at both times in the intubated-ICU and non-intubated-ICU groups. In all groups, there was a significant increase in peripheral blood lymphocyte apoptosis levels and DNA damage levels compared to the healthy control group (p < 0.01). The level of apoptosis and DNA damage decreased significantly in the post-COVID-19 period (p < 0.01). In the investigation of oxidative stress biomarkers, the oxidative stress index, including TOS and MPO levels, increased in patients (p < 0.01), and the TAS level decreased (p < 0.01).

CONCLUSION

It shows that the apoptosis of lymphocyte cells, DNA damage, and oxidative stress can be effective in prognostic decisions and is a suitable predictor for diagnosing the condition of patients with viral infections such as COVID-19 and influenza.

Risk assessment and clinical implications of COVID-19 in multiple myeloma patients: A systematic review and meta-analysis

INTRODUCTION

Patients with multiple myeloma (MM) face heightened infection susceptibility, particularly severe risks from COVID-19. This study, the first systematic review in its domain, seeks to assess the impacts of COVID-19 on MM patients.

METHOD

Adhering to PRISMA guidelines and PROSPERO registration (ID: CRD42023407784), this study conducted an exhaustive literature search from January 1, 2020, to April 12, 2024, using specified search terms in major databases (PubMed, EMBASE, and Web of Science). Quality assessment utilized the JBI Critical checklist, while publication bias was assessed using Egger's test and funnel plot. The leave-one-out sensitivity analyses were performed to assess the robustness of the results by excluding one study at a time to identify studies with a high risk of bias or those that significantly influenced the overall effect size. Data synthesis involved fitting a random-effects model and estimating meta-regression coefficients.

RESULTS

A total of 14 studies, encompassing a sample size of 3214 yielded pooled estimates indicating a hospitalization rate of 53% (95% CI: 40.81, 65.93) with considerable heterogeneity across studies (I2 = 99%). The ICU admission rate was 17% (95% CI: 11.74, 21.37), also with significant heterogeneity (I2 = 94%). The pooled mortality rate was 22% (95% CI: 15.33, 28.93), showing high heterogeneity (I2 = 97%). The pooled survival rate stood at 78% (95% CI: 71.07, 84.67), again exhibiting substantial heterogeneity (I2 = 97%). Subgroup analysis and meta-regression highlighted that study types, demographic factors, and patient comorbidities significantly contributed to the observed outcome heterogeneity, revealing distinct patterns. Mortality rates increased by 15% for participants with a median age above 67 years. ICU admission rates were positively correlated with obesity, with a 20% increase for groups with at least 19% obesity. Mortality rates rose by 33% for the group of patients with at least 19% obesity, while survival rates decreased by 33% in the same group.

CONCLUSION

Our meta-analysis sheds light on diverse COVID-19 outcomes in multiple myeloma. Heterogeneity underscores complexities, and study types, demographics, and co-morbidities significantly influence results, emphasizing the nuanced interplay of factors.

De novo design of SARS-CoV-2 main protease inhibitors with characteristic binding modes

The coronavirus disease 2019 (COVID-19) is caused by a novel coronavirus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which spreads rapidly all over the world. The main protease (Mpro) is significant to the replication and transcription of viruses, making it an attractive drug target against coronaviruses. Here, we introduce a series of novel inhibitors which are designed de novo through structure-based drug design approach that have great potential to inhibit SARS-CoV-2 Mproin vitro. High-resolution structures show that these inhibitors form covalent bonds with the catalytic cysteine through the novel dibromomethyl ketone (DBMK) as a reactive warhead. At the same time, the designed phenyl group beside the DBMK warhead inserts into the cleft between H41 and C145 through π-π stacking interaction, splitting the catalytic dyad and disrupting proton transfer. This unique binding model provides novel clues for the cysteine protease inhibitor development of SARS-CoV-2 as well as other pathogens.

ƩS COVID-19 is a rapid high throughput and sensitive one-step quadruplex real-time RT-PCR assay

Real-time reverse transcription polymerase chain reaction (RT-PCR), a standard method recommended for the diagnosis of coronavirus disease 2019 (COVID-19) requires 2-4 h to get the result. Although antigen test kit (ATK) is used for COVID-19 screening within 15-30 min, the drawback is its limited sensitivity. Hence, a rapid one-step quadruplex real-time RT-PCR assay: termed ƩS COVID-19 targeting ORF1ab, ORF3a, and N genes of SARS-CoV-2; and Avocado sunblotch viroid (ASBVd) as an internal control was developed. Based on strategies including designing high melting temperature primers with short amplicons, applying a fast ramp rate, minimizing hold time, and reducing the range between denaturation and annealing/extension temperatures; the assay could be accomplished within 25 min. The limit of detection of ORF1ab, ORF3a, and N genes were 1.835, 1.310, and 1 copy/reaction, respectively. Validation was performed in 205 combined nasopharyngeal and oropharyngeal swabs. The sensitivity, specificity, positive predictive value, and negative predictive value were 92.8%, 100%, 100%, and 97.1%, respectively with 96.7% accuracy. Cohen's Kappa was 0.93. The newly developed rapid real-time RT-PCR assay was highly sensitive, specific, and fast, making it suitable for use as an alternative method to support laboratory diagnosis of COVID-19 in outpatient and emergency departments.

Angiotensin-(1-7) infusion in COVID-19 patients admitted to the ICU: a seamless phase 1-2 randomized clinical trial

BACKGROUND

The coronavirus-related disease (COVID-19) is mainly characterized by a respiratory involvement. The renin-angiotensin system (RAS) has a relevant role in the pathogenesis of COVID-19, as the virus enters host's cells via the angiotensin-converting enzyme 2 (ACE2).

METHODS

This investigator-initiated, seamless phase 1-2 randomized clinical trial was conceived to test the safety and efficacy of continuous short-term (up to 7 days) intravenous administration of Angiotensin-(1-7) in COVID-19 patients admitted to two intensive care units (ICU). In addition to standard of care, intravenous administration of Angiotensin-(1-7) was started at 5 mcg/Kg day and increased to 10 mcg/Kg day after 24 h (Phase 1; open label trial) or given at 10 mcg/Kg day and continued for a maximum of 7 days or until ICU discharge (Phase 2; double-blind randomized controlled trial). The rate of serious adverse events (SAEs) served as the primary outcome of the study for Phase 1, and the number of oxygen free days (OFDs) by day 28 for Phase 2.

RESULTS

Between August 2020 and July 2021, when the study was prematurely stopped due to low recruitment rate, 28 patients were included in Phase 1 and 79 patients in Phase 2. Of those, 78 were included in the intention to treat analysis, and the primary outcome was available for 77 patients. During Phase 1, one SAE (i.e., bradycardia) was considered possibly related to the infusion, justifying its discontinuation. In Phase 2, OFDs did not differ between groups (median 19 [0-21] vs. 14 [0-18] days; p = 0.15). When patients from both phases were analyzed in a pooled intention to treat approach (Phase 1-2 trial), OFDs were significantly higher in treated patients, when compared to controls (19 [0-21] vs. 14 [0-18] days; absolute difference -5 days, 95% CI [0-7] p = 0.04).

CONCLUSIONS

The main findings of our study indicate that continuous intravenous infusion of Angiotensin-(1-7) at 10 mcg/Kg day in COVID-19 patients admitted to the ICU with severe pneumonia is safe. In Phase II intention to treat analysis, there was no significant difference in OFD between groups. Trial Registration ClinicalTrials.gov Identifier: NCT04633772-Registro Brasileiro de Ensaios Clínicos, UTN number: U1111-1255-7167.

Increased 90-Day Morbidity and Mortality Among Patients With Hip Fracture During the COVID-19 Pandemic

BACKGROUND

When coronavirus disease 2019 (COVID-19) first spread to the United States, our institution was at the outbreak's epicenter. Despite limited understanding of COVID-19's long-term effects, we continued performing surgical fixation of geriatric hip fractures under strict guidelines. This study examined the outcomes of these patients during the pandemic compared with those of patients treated pre-pandemic.

MATERIALS AND METHODS

We conducted a retrospective cohort study of patients with hip fractures between December 2019 and June 2020, the peak of the pandemic in our region. Outcomes of patients treated with surgical fixation (2020 cohort) were compared with those of a historical control group (2019 cohort). The primary outcome was 90-day mortality, with secondary outcomes including pneumonia, thromboembolic events, emergency department visits, readmission, and cardiac events.

RESULTS

The 2020 cohort (n=64) and 2019 cohort (n=78) had similar baseline characteristics. The 2020 cohort had a 4.27 times higher risk (95% CI, 1.30-13.98) of developing pneumonia compared with the pre-pandemic cohort but had no other differences in 90-day complications. Patients with COVID-19 in the 2020 cohort had a 5.09 times higher risk (95% CI, 1.35-19.20) of developing pneumonia and a 5.38 times higher risk (95% CI, 1.13-25.64) of postoperative mortality. There was no increased risk for thromboembolism between the 2020 and 2019 cohorts, even among COVID-19 cases, as all patients received anticoagulation with heparin.

CONCLUSION

Our study demonstrates that hip fracture surgery remained safe during the peak of the US COVID-19 pandemic, with an expected increase in pneumonia and mortality risk for patients with hip fracture with COVID-19. [Orthopedics. 202x;4x(x):xx-xx.].

The Prevalence and Clinical Features of Co-Infection with SARS-CoV-2 and Influenza Virus during the COVID-19 Pandemic in Semnan, Iran

Background

COVID-19 and influenza are both contagious respiratory diseases. Influenza virus can increase the severity of COVID-19 infection in the cold months of the year through damage to respiratory ciliated cells, which may cause an increase in hospitalization, disease symptoms and mortality rate. Therefore, the purpose of this study was to ascertain the frequency of co-infection with the influenza virus and SARS-CoV-2, as well as the impact of co-infection on clinical outcomes in hospitalized patients suffering from respiratory problems within Semnan City, Iran.

Methods

In this cross-sectional descriptive study, we investigated 1267 hospitalized patients with respiratory problems between September 2021 and March 2022. Two nasopharyngeal and oropharyngeal throat swab samples were collected from each patient and tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A, and influenza B viruses using real-time reverse-transcriptase- polymerase-chain-reaction (RT-PCR). The collected data were analyzed with χ² test, ANOVA, paired Student's t-test, and Pearson's correlation coefficient test in different groups. Analyzes were done with SPSS 26.0 software.

Results

In total, 29.6% (n = 375) of patients had confirmed positive results for SARS-CoV-2, and their median age was 55.4 ± 24.63 years. It was found that 1.9% (n = 7) and 0.5% (n = 2) of COVID-19 patients had co-infections with influenza viruses A and B, respectively. In 2.4% of the cases, co-infection with COVID-19 and influenza was found. 8 out of 9 patients (88.8%) recovered, while one patient (11.1%) died. Co-infection did not significantly correlate with cancer (P = 0.588), diabetes (P = 0.202), hypertension (P = 0.530), or any other illness. Also, Associations of death and co-infection with diabetes, cardiovascular disease, or CKD showed that a statistically significant correlation was present only between diabetes and death. Based on the ANOVA test to look at associations of death and co-infection with diabetes, cardiovascular disease, or CKD, it showed that there was no significant association of co-infection with diabetes (P = 0.202), hypertension (P = 0.530), cancer (P = 0.588), and other diseases.

Conclusion

Although a low proportion of COVID-19 patients have influenza co-infection, the importance of such co-infection, especially in high-risk individuals and the elderly, cannot be ignored. Given the prevalence of influenza co-infection, increased coverage of flu vaccination is encouraged to mitigate the transmission of the influenza virus during the ongoing COVID-19 pandemic and reduce the risk of severe outcomes and mortality.

Promoting Collaborative Scholarship During the COVID-19 Pandemic Through an Innovative COVID-19 Data Explorer and Repository at Yale School of Medicine: Development and Usability Study

BACKGROUND

The COVID-19 pandemic sparked a surge of research publications spanning epidemiology, basic science, and clinical science. Thanks to the digital revolution, large data sets are now accessible, which also enables real-time epidemic tracking. However, despite this, academic faculty and their trainees have been struggling to access comprehensive clinical data. To tackle this issue, we have devised a clinical data repository that streamlines research processes and promotes interdisciplinary collaboration.

OBJECTIVE

This study aimed to present an easily accessible up-to-date database that promotes access to local COVID-19 clinical data, thereby increasing efficiency, streamlining, and democratizing the research enterprise. By providing a robust database, a broad range of researchers (faculty and trainees) and clinicians from different areas of medicine are encouraged to explore and collaborate on novel clinically relevant research questions.

METHODS

A research platform, called the Yale Department of Medicine COVID-19 Explorer and Repository (DOM-CovX), was constructed to house cleaned, highly granular, deidentified, and continually updated data from over 18,000 patients hospitalized with COVID-19 from January 2020 to January 2023, across the Yale New Haven Health System. Data across several key domains were extracted including demographics, past medical history, laboratory values during hospitalization, vital signs, medications, imaging, procedures, and outcomes. Given the time-varying nature of several data domains, summary statistics were constructed to limit the computational size of the database and provide a reasonable data file that the broader research community could use for basic statistical analyses. The initiative also included a front-end user interface, the DOM-CovX Explorer, for simple data visualization of aggregate data. The detailed clinical data sets were made available for researchers after a review board process.

RESULTS

As of January 2023, the DOM-CovX Explorer has received 38 requests from different groups of scientists at Yale and the repository has expanded research capability to a diverse group of stakeholders including clinical and research-based faculty and trainees within 15 different surgical and nonsurgical specialties. A dedicated DOM-CovX team guides access and use of the database, which has enhanced interdepartmental collaborations, resulting in the publication of 16 peer-reviewed papers, 2 projects available in preprint servers, and 8 presentations in scientific conferences. Currently, the DOM-CovX Explorer continues to expand and improve its interface. The repository includes up to 3997 variables across 7 different clinical domains, with continued growth in response to researchers' requests and data availability.

CONCLUSIONS

The DOM-CovX Data Explorer and Repository is a user-friendly tool for analyzing data and accessing a consistently updated, standardized, and large-scale database. Its innovative approach fosters collaboration, diversity of scholarly pursuits, and expands medical education. In addition, it can be applied to other diseases beyond COVID-19.

Investigation of risk factors for invasive pulmonary aspergillosis among patients with COVID-19

COVID-19 associated pulmonary aspergillosis (CAPA) had been reported, and raised concern about this secondary infection due to the high mortality. This study aimed to investigate the risk factors for CAPA. The enrolled 114 COVID-19 patients were further divided into CAPA group and non-CAPA group. Demographic characteristics, underlying diseases, laboratory parameters and therapeutic schedule between the two groups were compared to identify the independent risk factors for CAPA by univariate analysis and multivariable logistic regression analysis. Sensitivity and specificity of independent risk factors were confirmed by receiver operating characteristic (ROC) curve analysis. Univariate analysis showed that renal transplant, IL-6 and CRP levels, decreased CD4 + T cell and CD8 + T cell, duration of antibiotics therapy, and prolonged mechanical ventilation were risk factors for development of CAPA. These factors were further analyzed by multivariable logistic regression analysis and the results indicated that elevated IL-6 level, decreased CD4 + T cell and prolonged mechanical ventilation could be recognized as independent risk factors for CAPA in COVID-19 patients. Identification of these risk factors is essential to initiate antifungal therapy as soon as possible to improve outcome of patients with CAPA.

Prevalence, incidence and associated factors of musculoskeletal disorders before and during the Covid-19 pandemic in faculty members: a comparative cross-sectional study

BACKGROUND

The COVID-19 pandemic has led to the broad acceptance of distance education (DE), with university professors and students conducting the teaching-learning process remotely from their homes. The propose of this study to investigate the prevalence of musculoskeletal disorders (MSDs) before and during the COVID-19 pandemic and identify risk factors associated with DE that may contribute to an increased incidence of these disorders among university professors.

METHODS

This cross-sectional analytical study took a comparative approach and involved 310 university professors in Iran. Data were gathered using an online questionnaire. Initially, demographic and occupational information of the professors, hours of physical activity, and hours spent using electronic devices were recorded. Participants were then asked to report MSDs in various body areas throughout the previous year and the previous seven days. Finally, MSDs risk factors such as workstation ergonomics during computer, laptop, smartphone, and tablet use, as well as working postures during online teaching or offline content development during the COVID-19 pandemic, were examined.

RESULTS

The majority of the participants were male (66.13%), with a PhD (46.77%) and a faculty member position (74.2%). On average, the use of computers and laptops increased by 2.67 h and 2.72 h, respectively, during the pandemic compared to before the pandemic. This increase was statistically significant (P < 0.001). MSDs incidence increased significantly before and during the COVID pandemic was observed in the areas of the neck, shoulders, lower and upper back, arms, forearms, wrists and fingers (P < 0.05). The highest cumulative incidence (Cin) of MSDs was related to the neck (Cin = 24.20%), upper back (Cin = 21.29%), low back (Cin = 18.06%) and fingers (Cin = 16.13%). The prevalence of MSDs during the COVID pandemic was significantly associated with employment status (P = 0.042), work experience (P = 0.016), age (P = 0.027), increase in the use of computers/ laptops (P < 0.001), decrease of the smartphone/tablet distance from the body (P = 0.047), workstation (smartphone-tablet, computer, laptop) (P < 0.05), head position (smartphone-tablet) (P = 0.029), display height (computer/laptop) (P = 0.045) and physical activity (P = 0.006).

CONCLUSIONS

It appears that the increased duration of smartphone, computer, and laptop use, combined with decreased physical activity and detrimental changes in ergonomic conditions of workstations during the quarantine period caused by the COVID-19 pandemic, has resulted in a shift from dynamic to static tasks and an increase in the prevalence and incidence of MSDs among university professors.

Acute severe hepatitis and COVID-19: case report

COVID-19, caused by SARS-CoV-2, has been declared an international public health emergency. Patients with COVID-19, even without a history of liver disease, frequently present with liver test disturbances. Due to the multisystemic involvement of COVID-19, the pathogenesis of liver injury is likely to be multifactorial, involving systemic inflammation, small vessel thrombosis, hepatic hypoxia, and potential drug toxicity, ruling out direct infection of hepatocytes by SARS-CoV-2. COVID-19 can cause severe acute hepatitis. We report the case of a 25-year-old man admitted to emergency with abdominal pain who presented with acute severe liver failure before respiratory signs.

Chronic disease patients have fewer social contacts: A pilot survey with implications for transmission dynamics

Non-communicable diseases (NCD) are the most important cause of death in the world. The socio-economic costs associated with NCDs makes it imperative to prevent and control them in the 21st century. The severe toll that the COVID-19 pandemic has taken worldwide is an unfortunate illustration of our limited insight into the infectious risk for the global population. Co-incidence between NCD and infection offers an underexplored opportunity to design preventive policies. In a pilot survey, we observed that the NCD population displays a substantial reduction in their social contacting behavior as compared to the general population. This indicates that existing mathematical models based on contact surveys in the general population are not applicable to the NCD population and that the risk of acquiring an infection following a contact is probably underestimated. Our demonstration of reduced social mixing in several chronic conditions, raises the question to what extent the social mixing is influenced by the burden of disease. We advocate the design of disease-specific contact surveys to address how the burden of disease associates with social contact behavior and the risk of infection. The SARS-CoV-2 pandemic offers an unprecedented opportunity to gain insight into the importance of infection in the NCD population and to find ways to improve healthcare procedures.

SARS-CoV-2 co-detection with other respiratory pathogens-descriptive epidemiological study

BACKGROUND

Co-detection of respiratory pathogens with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is poorly understood. This descriptive epidemiological study aimed to determine the effect of the interaction of different respiratory pathogens on clinical variables.

METHODS

We retrospectively reviewed the results of comprehensive multiplex polymerase chain reaction (PCR) testing from November 2020 to March 2023 to estimate respiratory pathogen co-detection rates in Shinjuku, Tokyo. We evaluated the interactions of respiratory pathogens, particularly SARS-CoV-2, between observed and expected co-detection. We estimated the trend of co-detection with SARS-CoV-2 in terms of age and sex and applied a multiple logistic regression model adjusted for age, testing period, and sex to identify influencing factors between co-detection and single detection for each pathogen.

RESULTS

Among 57,746 patients who underwent multiplex PCR testing, 10,516 (18.2%) had positive for at least one of the 22 pathogens. Additionally, 881 (1.5%) patients were confirmed to have a co-detection. SARS-CoV-2 exhibited negative interactions with adenovirus, coronavirus, human metapneumovirus, parainfluenza virus, respiratory syncytial virus, and rhino/enterovirus. SARS-CoV-2 co-detection with other pathogens occurred most frequently in patients of the youngest age group (0-4 years). A multiple logistic regression model indicated that younger age was the most influential factor for SARS-CoV-2 co-detection with other respiratory pathogens.

CONCLUSION

The study highlights the prevalence of SARS-CoV-2 co-detection with other respiratory pathogens in younger age groups, necessitating further exploration of the clinical implications and severity of SARS-CoV-2 co-detection.

A brief overview of SARS-CoV-2 infection and its management strategies: a recent update

The COVID-19 pandemic has become a global health crisis, inflicting substantial morbidity and mortality worldwide. A diverse range of symptoms, including fever, cough, dyspnea, and fatigue, characterizes COVID-19. A cytokine surge can exacerbate the disease's severity. This phenomenon involves an increased immune response, marked by the excessive release of inflammatory cytokines like IL-6, IL-8, TNF-α, and IFNγ, leading to tissue damage and organ dysfunction. Efforts to reduce the cytokine surge and its associated complications have garnered significant attention. Standardized management protocols have incorporated treatment strategies, with corticosteroids, chloroquine, and intravenous immunoglobulin taking the forefront. The recent therapeutic intervention has also assisted in novel strategies like repurposing existing medications and the utilization of in vitro drug screening methods to choose effective molecules against viral infections. Beyond acute management, the significance of comprehensive post-COVID-19 management strategies, like remedial measures including nutritional guidance, multidisciplinary care, and follow-up, has become increasingly evident. As the understanding of COVID-19 pathogenesis deepens, it is becoming increasingly evident that a tailored approach to therapy is imperative. This review focuses on effective treatment measures aimed at mitigating COVID-19 severity and highlights the significance of comprehensive COVID-19 management strategies that show promise in the battle against COVID-19.

A clinical study of rhino-orbital-cerebral mucormycosis during the COVID-19 pandemic in western Maharashtra

Background

The aim of the study was to describe the epidemiology and study the risk factors, clinical presentation, management, and outcome of rhino-orbital-cerebral mucormycosis (ROCM) in terms of mortality, exenteration, eye salvage, and vision salvage.

Methods

This retrospective, observational study was carried out over a period of two months. A detailed history was noted, and an ophthalmological examination was done. The diagnosis was done by Potassium hydroxide (KOH) mount and fungal culture. Magnetic resonance imaging (MRI) of the orbit, brain, and paranasal sinuses were performed. Medical (intravenous amphotericin B, posaconazole), surgical (retrobulbar amphotericin B injection, exenteration, Functional Endoscopic Sinus Surgery (FESS)), or combined management was evaluated, and clinical outcomes was noted.

Results

The mean age of patients was 54.2 years and the male-to-female ratio was 1.77/1. The most common underlying risk factor for ROCM was uncontrolled diabetes mellitus (70%), followed by the use of corticosteroids for the management of coronavirus disease 2019 (COVID-19) infection in 68% of patients. The most common clinical presentation was diminution of vision followed by eschar, ptosis, and proptosis. Medical and FESS were done in all patients; exenteration was done in 12% of patients. Sixty-six percent of patients were alive with regression of ROCM, 20% of patients were alive with residual, 8% of patients were alive with the progression of ROCM, and 6% of patients had expired. Among the ones who are alive, the ocular outcome was orbital exenteration in 12.76%, the eye was salvaged in 25.53 and vision salvage was achieved in 61.70%.

Conclusion

ROCM affects older males. Immunosuppression due to COVID-19 infection, diabetes mellitus, and corticosteroid use in the management of COVID-19 are the main risk factors for the development of ROCM. Antifungal therapy along with surgical debridement decreases mortality.

Association Between COVID-19 and Neurological Diseases: Evidence from Large-Scale Mendelian Randomization Analysis and Single-Cell RNA Sequencing Analysis

Observational studies have suggested that SARS-CoV-2 infection increases the risk of neurological diseases, but it remains unclear whether the association is causal. The present study aims to evaluate the causal relationships between SARS-CoV-2 infections and neurological diseases and analyzes the potential routes of SARS-CoV-2 entry at the cellular level. We performed Mendelian randomization (MR) analysis with CAUSE method to investigate causal relationship of SARS-CoV-2 infections with neurological diseases. Then, we conducted single-cell RNA sequencing (scRNA-seq) analysis to obtain evidence of potential neuroinvasion routes by measuring SARS-CoV-2 receptor expression in specific cell subtypes. Fast gene set enrichment analysis (fGSEA) was further performed to assess the pathogenesis of related diseases. The results showed that the COVID-19 is causally associated with manic (delta_elpd, - 0.1300, Z-score: - 2.4; P = 0.0082) and epilepsy (delta_elpd: - 2.20, Z-score: - 1.80; P = 0.038). However, no significant effects were observed for COVID-19 on other traits. Moreover, there are 23 cell subtypes identified through the scRNA-seq transcriptomics data of epilepsy, and SARS-CoV-2 receptor TTYH2 was found to be specifically expressed in oligodendrocyte and astrocyte cell subtypes. Furthermore, fGSEA analysis showed that the cell subtypes with receptor-specific expression was related to methylation of lysine 27 on histone H3 (H3K27ME3), neuronal system, aging brain, neurogenesis, and neuron projection. In summary, this study shows causal links between SARS-CoV-2 infections and neurological disorders such as epilepsy and manic, supported by MR and scRNA-seq analysis. These results should be considered in further studies and public health measures on COVID-19 and neurological diseases.

The Characteristics of Coronary Artery Lesions in COVID-19 Infected Patients With Coronary Artery Disease: An Optical Coherence Tomography Study

COVID-19 may predispose patients to cardiac injuries but whether COVID-19 infection affects the morphological features of coronary plaques to potentially influence the outcome of patients with coronary artery disease (CAD) remains unknown. By using optical coherence tomography (OCT), this study compared the characteristics of coronary plaque in patients with CAD with/without COVID-19 infection. The 206 patients were divided into 2 groups. The COVID-19 group had 113 patients between December 7, 2022, and March 31, 2023, who received OCT assessment after China decided to lift the restriction on COVID-19 and had a history of COVID-19 infection. The non-COVID-19 group had 93 patients without COVID-19 infection who underwent OCT before December 7, 2022. The COVID-19 group demonstrated a higher incidence of plaque ruptures (53.1% vs 38.7%, p = 0.039), erosions (28.3% vs 11.8%, p = 0.004), fibrous (96.5% vs 89.2%, p = 0.041) and diffuse lesions (73.5% vs 50.5%, p <0.001) compared with the non-COVID-19 group, whereas non-COVID-19 group exhibited a higher frequency of cholesterol crystals (83.9% vs 70.8%, p = 0.027), deep calcifications (65.6% vs 51.3%, p = 0.039) and solitary lesions (57.0% vs 34.5%, p = 0.001). Kaplan-Meier survival analysis revealed a significantly lower major adverse cardiac events-free probability in the COVID-19 group (91.6% vs 95.5%, p = 0.006) than in the non-COVID-19 group. In conclusion, OCT demonstrated that COVID-19 infection is associated with coronary pathological changes such as more plaque ruptures, erosions, fibrosis, and diffuse lesions. Further, COVID-19 infection is associated with a higher propensity for acute coronary events and a higher risk of major adverse cardiac events in patients with CAD.

Identification of novel small-molecule inhibitors of SARS-CoV-2 by chemical genetics

There are only eight approved small molecule antiviral drugs for treating COVID-19. Among them, four are nucleotide analogues (remdesivir, JT001, molnupiravir, and azvudine), while the other four are protease inhibitors (nirmatrelvir, ensitrelvir, leritrelvir, and simnotrelvir-ritonavir). Antiviral resistance, unfavourable drug‒drug interaction, and toxicity have been reported in previous studies. Thus there is a dearth of new treatment options for SARS-CoV-2. In this work, a three-tier cell-based screening was employed to identify novel compounds with anti-SARS-CoV-2 activity. One compound, designated 172, demonstrated broad-spectrum antiviral activity against multiple human pathogenic coronaviruses and different SARS-CoV-2 variants of concern. Mechanistic studies validated by reverse genetics showed that compound 172 inhibits the 3-chymotrypsin-like protease (3CLpro) by binding to an allosteric site and reduces 3CLpro dimerization. A drug synergistic checkerboard assay demonstrated that compound 172 can achieve drug synergy with nirmatrelvir in vitro. In vivo studies confirmed the antiviral activity of compound 172 in both Golden Syrian Hamsters and K18 humanized ACE2 mice. Overall, this study identified an alternative druggable site on the SARS-CoV-2 3CLpro, proposed a potential combination therapy with nirmatrelvir to reduce the risk of antiviral resistance and shed light on the development of allosteric protease inhibitors for treating a range of coronavirus diseases.

Clinical characteristics and risk factors for bacterial co-infections in COVID-19 patients: A retrospective study

OBJECTIVE

This study aimed to analyse the bacterial composition, distribution, drug sensitivity, and clinical characteristics of patients with coronavirus disease 2019 (COVID-19) who develop bacterial co-infections.

METHODS

We conducted a retrospective study of 184 patients with COVID-19 admitted between December 2022 and January 2023. Data on gender, age, length of hospital stay, pneumonia classification, underlying diseases, invasive surgery, hormone therapy, inflammation indicators, and other relevant information were collected. Samples of sputum, bronchoscopy sputum, alveolar lavage fluid, middle urine, puncture fluid, wound secretions, and blood were collected for pathogen isolation, identification, and drug sensitivity testing.

RESULTS

The majority of patients with COVID-19 with bacterial co-infection were elderly and had underlying diseases. Invasive surgery and hormone therapy were identified as risk factors for co-infections. Laboratory analysis showed reduced lymphocyte counts and elevated levels of C-reactive protein and procalcitonin. The most common pathogens in co-infections were Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa. The detection rate of drug-resistant strains, including methicillin-resistant S. aureus, carbapenem-resistant K. pneumoniae, carbapenem-resistant A. baumannii, carbapenem-resistant P. aeruginosa, and carbapenem-resistant E. coli, increased with the severity of pneumonia.

CONCLUSION

Respiratory tract infections were the most common site of bacterial co-infection in patients with COVID-19. Severe cases were more susceptible to multidrug-resistant pathogens, leading to a higher mortality rate. Timely control and prevention of co-infection are crucial for improving the prognosis of patients with COVID-19.

Unveiling coagulation dysfunction in patients with COVID-19: a retrospective analysis

Coagulation dysfunction has emerged as a significant aspect of COVID-19 pathophysiology, with abnormal coagulation parameters observed in severe cases. This study aimed to investigate the predictive value of coagulation parameters, including prothrombin time (PT), activated partial thromboplastin time (PTT), and international normalized ratio (INR) for mortality in patients with COVID-19. A retrospective analysis was conducted on a cohort of patients diagnosed with COVID-19. Coagulation parameters, including PT, PTT, and INR, were measured upon admission. Receiver operating characteristic (ROC) curve analysis was performed to evaluate the predictive performance of these parameters. Sensitivity and specificity were calculated, and the area under the curve (AUC) values were determined. The analysis included 156 patients diagnosed with COVID-19. The t-test revealed a significant difference (P < 0.05) in PTT, PT, and INR. PTT demonstrated the highest predictive performance, with an AUC value of 0.68, indicating superior discrimination compared with PT and INR. PTT exhibited a sensitivity of 83% and a specificity of 46% for identifying deceased patients. These findings suggest that PTT may serve as a valuable prognostic marker of mortality risk in patients with COVID-19. Coagulation indicators, particularly PTT, predicted COVID-19 mortality. Monitoring coagulation markers may help stratify the risk and guide treatment. Further research and validation studies are needed to corroborate these findings and to establish the clinical importance of coagulation markers in COVID-19 therapy. COVID-19 coagulation dysfunction mechanisms must be understood in order to design targeted therapies to reduce thrombotic consequences.

Investigating the pathogenesis of vitreous in postmortem COVID patients via untargeted metabolomics based bioinformatics model

SARS-CoV-2 virus has become a worldwide pandemic causing millions of death. This severe disaster lead to a immense panic and stress all over the world. Several studies were dedicated to understand its mechanism, pathogenesis and spreading characteristics. By this way, scientists try to develop different therapy and diagnose strategies. For these reasons, several metabolomics, proteomics and genomics studies were also carried out to improve knowledge in this newly identified virus. In this study, we are aimed to explain the pathogenesis of SARS-CoV-2 exposure on postmortem COVID (+) patients via untargeted metabolomics analysis. To carry out this study, a Data Independent Acquisition SWATH method is optimized and performed. Vitreous samples were analyzed in both MS1 and MS2 ESI(+) mode. An orthogonal Partial Least Square Discriminant Analysis were performed for classification. It was observed that lipid metabolism, several amino acids and oxidative stress biomarkers were strongly affected due to high inflammation and possible cytokine storm.

A novel deterioration prediction system for mild COVID-19 patients in Korea: a retrospective study

The ongoing coronavirus disease 2019 (COVID-19) pandemic presents serious public health threats. Omicron, the current most prevalent strain of COVID-19, has a low fatality rate and very high transmissibility, so the number of patients with mild symptoms of COVID-19 is rapidly increasing. This change of pandemic challenges medical systems worldwide in many aspects, including sharp increases in demands for hospital infrastructure, critical shortages in medical equipment, and medical staff. Predicting deterioration in mild patients could alleviate these problems. A novel scoring system was proposed for predicting the deterioration of patients whose condition may worsen rapidly and those who all still mild or asymptomatic. Retrospective cohorts of 954 and 2,035 patients that quarantined in the Residential Treatment Center were assembled for derivation and external validation of mild COVID-19, respectively. Deterioration was defined as transfer to a local hospital due to worsening condition of the patients during the 2-week isolation period. A total of 15 variables: sex, age, seven pre-existing conditions (diabetes, hypertension, cardiovascular disease, respiratory disease, liver disease, kidney disease, and organ transplant), and five vital signs (systolic blood pressure (SBP), diastolic blood pressure (DBP), heart rate (HR), body temperature, and oxygen saturation (SpO2)) were collected. A scoring system was developed using seven variables (age, pulse rate, SpO2, SBP, DBP, temperature, and hypertension) with significant differences between the transfer and not transfer groups in logistic regression. The proposed system was compared with existing scoring systems that assess the severity of patient conditions. The performance of the proposed scoring system to predict deterioration in patients with mild COVID-19 showed an area under the receiver operating characteristic (AUC) of 0.868. This is a statistically significant improvement compared to the performance of the previous patient condition assessment scoring systems. During external validation, the proposed system showed the best and most robust predictive performance (AUC = 0.768; accuracy = 0.899). In conclusion, we proposed a novel scoring system for predicting patients with mild COVID-19 who will experience deterioration which could predict the deterioration of the patient's condition early with high predictive performance. Furthermore, because the scoring system does not require special calculations, it can be easily measured to predict the deterioration of a patients' condition. This system can be used as effective tool for early detection of deterioration in mild COVID-19 patients.

Regulation viral RNA transcription and replication by higher-order RNA structures within the nsp1 coding region of MERS coronavirus

Coronavirus (CoV) possesses numerous functional cis-acting elements in its positive-strand genomic RNA. Although most of these RNA structures participate in viral replication, the functions of RNA structures in the genomic RNA of CoV in viral replication remain unclear. In this study, we investigated the functions of the higher-order RNA stem-loop (SL) structures SL5B, SL5C, and SL5D in the ORF1a coding region of Middle East respiratory syndrome coronavirus (MERS-CoV) in viral replication. Our approach, using reverse genetics of a bacterial artificial chromosome system, revealed that SL5B and SL5C play essential roles in the discontinuous transcription of MERS-CoV. In silico analyses predicted that SL5C interacts with a bulged stem-loop (BSL) in the 3' untranslated region, suggesting that the RNA structure of SL5C is important for viral RNA transcription. Conversely, SL5D did not affect transcription, but mediated the synthesis of positive-strand genomic RNA. Additionally, the RNA secondary structure of SL5 in the revertant virus of the SL5D mutant was similar to that of the wild-type, indicating that the RNA structure of SL5D can finely tune RNA replication in MERS-CoV. Our data indicate novel regulatory mechanisms of viral RNA transcription and replication by higher-order RNA structures in the MERS-CoV genomic RNA.

Immunogenicity and Protective Efficacy of Dose-Sparing Epigraph Vaccine against H3 Swine Influenza A Virus

Swine influenza A virus (IAV-S) is a highly prevalent and transmissible pathogen infecting worldwide swine populations. Our previous work has shown that the computationally derived vaccine platform, Epigraph, can induce broadly cross-reactive and durable immunity against H3 IAV-S in mice and swine. Therefore, in this study, we assess the immunogenicity and protective efficacy of the Epigraph vaccine at increasingly lower doses to determine the minimum dose required to maintain protective immunity against three genetically divergent H3 IAV-S. We assessed both antibody and T cell responses and then challenged with three H3N2 IAV-S derived from either Cluster IV(A), Cluster I, or the 2010.1 "human-like" cluster and assessed protection through reduced pathology, reduced viral load in the lungs, and reduced viral shedding from nasal swabs. Overall, we observed a dose-dependent effect where the highest dose of Epigraph protected against all three challenges, the middle dose of Epigraph protected against more genetically similar IAV-S, and the lowest dose of Epigraph only protected against genetically similar IAV-S. The results of these studies can be used to continue developing a broadly protective and low-dose vaccine against H3 IAV-S.

Non-Covalent Inhibitors of SARS-CoV-2 Papain-Like Protease (PLpro): In Vitro and In Vivo Antiviral Activity

The SARS-CoV-2 papain-like protease (PLpro), essential for viral processing and immune response disruption, is a promising target for treating acute infection of SARS-CoV-2. To date, there have been no reports of PLpro inhibitors with both submicromolar potency and animal model efficacy. To address the challenge of PLpro's featureless active site, a noncovalent inhibitor library with over 50 new analogs was developed, targeting the PLpro active site by modulating the BL2-loop and engaging the BL2-groove. Notably, compounds 42 and 10 exhibited strong antiviral effects and were further analyzed pharmacokinetically. 10, in particular, showed a significant lung accumulation, up to 12.9-fold greater than plasma exposure, and was effective in a mouse model of SARS-CoV-2 infection, as well as against several SARS-CoV-2 variants. These findings highlight the potential of 10 as an in vivo chemical probe for studying PLpro inhibition in SARS-CoV-2 infection.

Factors affecting COVID-19 vaccine uptake in populations with higher education: insights from a cross-sectional study among university students in Malawi

BACKGROUND

The Coronavirus disease-2019 (COVID-19) vaccines were rolled out in many countries; however, sub-optimal COVID-19 vaccine uptake remains a major public health concern globally. This study aimed at assessing the factors that affected the uptake, hesitancy, and resistance of the COVID-19 vaccine among university undergraduate students in Malawi, a least developed country in Africa.

METHODS

A descriptive cross-sectional study design was conducted using an online semi-structured questionnaire. A total of 343 University undergraduate students in Blantyre participated in this study after obtaining ethical clearance. Data was exported from Survey Monkey to Microsoft Excel version-21 for cleaning and was analysed using SPSS version-29. Descriptive statistics, including percentages, were performed to define the sample characteristics. Pearson Chi-square and Fisher's exact test were performed to identify significant relationships between vaccine uptake and demographics. A 95% confidence interval was set, and a p-value of < 0.05 was considered statistically significant.

RESULTS

Of the 343 participants, 43% were vaccinated. Among the vaccinated, the majority (47.3%, n = 69/146) received Johnson & Johnson vaccine followed by AstraZeneca (46.6%, n = 68/146). The commonly reported reason for vaccine acceptance was 'to protect me against getting COVID-19' (49%); whereas vaccine hesitancy was attributed to 'lack of knowledge (34%), and concerns about vaccine safety (25%).

CONCLUSIONS

This study found that adequate knowledge about benefits and safety of COVID-19 vaccine could potentially increase uptake. Lack of credible information or misinformation contributed to vaccine hesitancy. The findings provide insights for design of strategies to increase future vaccine uptake and reduce determinants of vaccine hesitancy. To reduce vaccination hesitancy in any population with or without higher education, we recommend that institutions entrusted with vaccine management must optimise health messaging, and reduce mis-information and dis-information.

Severe COVID-19 infection: An institutional review and literature overview

BACKGROUND

Our study aimed to describe the group of severe COVID-19 patients at an institutional level, and determine factors associated with different outcomes.

METHODS

A retrospective chart review of patients admitted with severe acute hypoxic respiratory failure due to COVID-19 infection. Based on outcomes, we categorized 3 groups of severe COVID-19: (1) Favorable outcome: progressive care unit admission and discharge (2) Intermediate outcome: ICU care (3) Poor outcome: in-hospital mortality.

RESULTS

Eighty-nine patients met our inclusion criteria; 42.7% were female. The average age was 59.7 (standard deviation (SD):13.7). Most of the population were Caucasian (95.5%) and non-Hispanic (91.0%). Age, sex, race, and ethnicity were similar between outcome groups. Medicare and Medicaid patients accounted for 62.9%. The average BMI was 33.5 (SD:8.2). Moderate comorbidity was observed, with an average Charlson Comorbidity index (CCI) of 3.8 (SD:2.6). There were no differences in the average CCI between groups(p = 0.291). Many patients (67.4%) had hypertension, diabetes (42.7%) and chronic lung disease (32.6%). A statistical difference was found when chronic lung disease was evaluated; p = 0.002. The prevalence of chronic lung disease was 19.6%, 27.8%, and 40% in the favorable, intermediate, and poor outcome groups, respectively. Smoking history was associated with poor outcomes (p = 0.04). Only 7.9% were fully vaccinated. Almost half (46.1%) were intubated and mechanically ventilated. Patients spent an average of 12.1 days ventilated (SD:8.5), with an average of 6.0 days from admission to ventilation (SD:5.1). The intermediate group had a shorter average interval from admission to ventilator (77.2 hours, SD:67.6), than the poor group (212.8 hours, SD:126.8); (p = 0.001). The presence of bacterial pneumonia was greatest in the intermediate group (72.2%), compared to the favorable group (17.4%), and the poor group (56%); this was significant (p<0.0001). In-hospital mortality was seen in 28.1%.

CONCLUSION

Most patients were male, obese, had moderate-level comorbidity, a history of tobacco abuse, and government-funded insurance. Nearly 50% required mechanical ventilation, and about 28% died during hospitalization. Bacterial pneumonia was most prevalent in intubated groups. Patients who were intubated with a good outcome were intubated earlier during their hospital course, with an average difference of 135.6 hours. A history of cigarette smoking and chronic lung disease were associated with poor outcomes.

Microbial infection among SARS-COV-2-infected patients in a COVID-19-dedicated tertiary care hospital of Bangladesh: a cross-sectional study

Objectives. This study aimed to determine patterns of respiratory, blood-borne and uropathogenic microbial pathogens among SARS-CoV-2-infected patients in a COVID-19-(coronavirus disease 2019) dedicated tertiary care hospital in Dhaka, Bangladesh. Design.This was a cross-sectional study. Setting. In a COVID-19-dedicated tertiary care hospital in Dhaka, Bangladesh, conducted from March to June 2021. Participants. Hospitalized individuals with COVID-19 infection regardless of age or sex. Primary and secondary outcome measures. The percentage of co-infected COVID-19 patients and the characterization of the micro-organisms responsible for co-infection served as the primary outcome measures. Finding any associations between co-infection and age, co-infection and sex and co-infection and comorbidity was the secondary outcome variable. Interventions. Not applicable. Results.Out of 79 patients, 61 % were male, and the mean age was 49.53 years. Co-infection was seen in 7.7 % of patients, out of which 5.1 % of isolates were from urine samples, followed by 2.6 % from blood. Bacteria isolated from urine were Enterococcus (2.6 %), coagulase-negative Staphylococcus (CONS) (1.3 %) and Enterobacter spp. (1.3 %). Pseudomonas spp. was the only organism isolated from blood sample. Mixed growth was found in nasopharyngeal and throat swabs, with the predominant species being Staphylococcus aureus and Streptococcus spp. At the time of data collection, 55.7 % of patients had been given antimicrobials, and 30.4 % of patients had been given a single antimicrobial. HBsAg was positive in 1.3 % of patients and none were anti-hepatitis C or dengue NS1Ag positive. Conclusion. Microbial infection has been seen to be associated with SARS-CoV-2 infections and is of great value in prescribing antimicrobials and reducing fatal outcomes of hospitalized patients.

Protracted exercise tolerance post-coronavirus disease 2019 in endurance athletes: A survey

Background

The global coronavirus disease 2019 (COVID-19) pandemic irrevocably influenced our lives, yet research in a diversity of countries is lacking. Cardiorespiratory fitness may be impaired for up to a year post-COVID-19 infection.

Objectives

Our study aimed to compare acute and exertional symptoms, fatigue, and exercise performance in masters-age endurance athletes according to their return-to-sport status.

Method

A cross-sectional survey-based observational study of long-distance runners and cyclists was conducted. Data were stratified into two groups: those who returned to their pre-illness level of sport and those who did not and were compared statistically.

Results

A total of 308 survey responses were included in the analysis. The mean age of the athletes was 44.9 + 10.2 years, with 55.2% being male. The group that did not return to their pre-illness level of sport (31.5%) had more post-COVID sequelae, worse illness severity, with a higher frequency of resting and exertional symptoms, notably fatigue and dyspnoea. Decreased exercise capacity was correlated with increased physical fatigue scores.

Conclusion

Almost one-third of endurance athletes suffered protracted exercise tolerance post-COVID-19. Long-term symptoms may be more consequential in this athlete population.

Clinical Implications

Symptoms that may indicate cardiopulmonary consequences in recreational athletes should be investigated in order to facilitate return to sport and the important mental and physical benefits thereof. This will augment outcomes after respiratory tract infections and management of return to sport and expectations of endurance athletes.

A Retrospective Study: Evaluating the Impact of the COVID-19 Pandemic on Inflammatory Markers in Hospitalized Patients

BACKGROUND

The COVID-19 pandemic has had a significant impact globally, and understanding the relationship between inflammatory markers and disease progression is crucial for effective management. This retrospective study aimed to examine the association between various inflammatory markers, such as C-reactive protein (CRP), the erythrocyte sedimentation rate (ESR), lactate dehydrogenase (LDH), D-dimer, ferritin, and procalcitonin (PCT), and the characteristics of disease progression and outcomes in individuals affected by COVID-19.

METHODS

This study collected raw data from 470 patients who tested positive for SARS-CoV-2 using RT-PCR.

RESULTS

The logistic regression analysis revealed that elevated LDH levels were associated with male gender, ICU admission, low oxygen saturation (O2 < 93%), the need for mechanical ventilation, death, and the presence of lung infiltrates. Higher D-dimer levels were associated with older age, diabetes mellitus, cardiac disease, and low oxygen saturation. Ferritin levels were significantly associated with older age, ICU admission, low oxygen saturation, mechanical ventilation, and lung infiltrates. In contrast, CRP was only significant regarding lung infiltrates and procalcitonin levels were not significantly associated with any of the examined factors.

CONCLUSION

This study highlights the importance of monitoring key inflammatory markers, such as LDH, D-dimer, and ferritin, as they are significantly associated with the severity of COVID-19 illness. These findings can inform clinical decision-making and guide the development of targeted interventions to improve patient outcomes.

Impact of the COVID-19 pandemic on risk of sarcopenia: From lockdown and infection perspectives: A systematic review and meta-analysis

BACKGROUND

During the new coronavirus disease 2019 (COVID-19) pandemic, there are numerous symptoms in the skeletal muscular system, such as decreased skeletal muscle mass, strength, and muscle function, which are the main manifestations of sarcopenia. To investigate the impact of the COVID-19 pandemic on sarcopenia from the perspectives of COVID-19 pandemic lockdown and COVID-19 infection, we conducted this study.

METHODS

We searched for literature related to COVID-19 and sarcopenia published in PubMed, Embase, Cochrane Library, and Web of Science. Two researchers independently searched and screened the articles, extracted data, and assessed the quality of the final included literature. RevMan 5.4 was used for meta-analysis.

RESULTS

A total of 8 articles with a total of 1145 patients were included. There was a significant difference in SARC-F scores (MD = 0.67, 95%CI = [0.41, 0.93], Z = 5.00, P < .00001), handgrip (MD = -1.57, 95%CI = [-2.41, -0.73], Z = 3.66, P = .0002), body weight (MD = -1.87, 95%CI = [-3.69, -0.05], Z = 2.01, P = .04), and skeletal muscle mass index (MD = -0.28, 95%CI = [-0.54, -0.02], Z = 2.13, P = .03) between the time before the COVID-19 pandemic and during the COVID-19 pandemic. However, the results showed that there was no significant difference in muscle mass between the 2 groups (MD = -1.72, 95%CI = [-4.39, 0.94], Z = 1.27, P = .21).

CONCLUSION

The COVID-19 pandemic has had an impact on sarcopenia. Both infection with COVID-19 and lockdown during the COVID-19 pandemic increase the risk of sarcopenia. Research should pay more attention to this disease during the COVID-19 pandemic and adopt effective interventions to minimize adverse outcomes.

P-selectin Facilitates SARS-CoV-2 Spike 1 Subunit Attachment to Vesicular Endothelium and Platelets

SARS-CoV-2 infection starts from the association of its spike 1 (S1) subunit with sensitive cells. Vesicular endothelial cells and platelets are among the cell types that bind SARS-CoV-2, but the effectors that mediate viral attachment on the cell membrane have not been fully elucidated. Herein, we show that P-selectin (SELP), a biomarker for endothelial dysfunction and platelet activation, can facilitate the attachment of SARS-CoV-2 S1. Since we observe colocalization of SELP with S1 in the lung tissues of COVID-19 patients, we perform molecular biology experiments on human umbilical vein endothelial cells (HUVECs) to confirm the intermolecular interaction between SELP and S1. SELP overexpression increases S1 recruitment to HUVECs and enhances SARS-CoV-2 spike pseudovirion infection. The opposite results are determined after SELP downregulation. As S1 causes endothelial inflammatory responses in a dose-dependent manner, by activating the interleukin (IL)-17 signaling pathway, SELP-induced S1 recruitment may contribute to the development of a "cytokine storm" after viral infection. Furthermore, SELP also promotes the attachment of S1 to the platelet membrane. Employment of PSI-697, a small inhibitor of SELP, markedly decreases S1 adhesion to both HUVECs and platelets. In addition to the role of membrane SELP in facilitating S1 attachment, we also discover that soluble SELP is a prognostic factor for severe COVID-19 through a meta-analysis. In this study, we identify SELP as an adhesive site for the SARS-CoV-2 S1, thus providing a potential drug target for COVID-19 treatment.

An Epidemiological Assessment of SARS-CoV-2 in the Sewage System of a Higher Education Institution

Background: The World Health Organization declared the end of the COVID-19 pandemic in May 2023, three years after the adoption of global emergency measures. Monitoring of SARS-CoV-2 in sewage underscores its importance due to its effectiveness and cost-effectiveness, highlighting the need to prioritize research on water resources and sanitation. Objectives: The aim of this study was to conduct an epidemiological assessment of SARS-CoV-2 in the sewage system of a higher education institution located in Vitória Espírito Santo State, Maruípe campus. Methods: Over a period of 66 days, from February 6 to April 12, 2023, 15 samples were collected. Each sample consisted of 1 L, collected in 1 hour, with 250 mL collected every 15 minutes. The samples were characterized by assessing their appearance, and pH was measured using a Horiba U-50 multiparameter probe. The extracted RNA was subjected to RT-qPCR using the Allplex™ 2019-nCovAssay Seegene kit. Results: The samples exhibited a cloudy appearance with impurities, and the pH ranged from 6.35 to 8.17. Among the evaluated samples, SARS-CoV-2 RNA was detected in two, and, by comparing this with the epidemiological bulletin issued by the State Health Department, an increase in cases in the state was observed during the collection period of these samples. Conclusions: Sewage monitoring proved to be an important tool in this post-pandemic period, serving as an alert and prevention mechanism for the population in relation to new outbreaks. Furthermore, it represents a low-cost mapping strategy and extensive testing of a population, aligning with the studies presented at the beginning of the pandemic. We recommend specific adjustments considering distinct populations.

Clinical characteristics and outcomes of patients with candidemia during the COVID-19 pandemic: Insights from experience in the Omicron era

BACKGROUND

In Taiwan, COVID-19 outbreaks caused by the Omicron variant occurred in 2022. We investigated the incidence of candidemia during COVID-19 pandemic and the mortality of candidemia patients with COVID-19 in Taiwan.

METHODS

The incidence of candidemia and fluconazole susceptibility of Candida species before (2015-2019) and during COVID-19 pandemic (2020-2023) at Kaohsiung Chang Gung Memorial Hospital were investigated. The associated factors with mortality in candidemia patients during COVID-19 pandemic were analyzed. Candidemia patients who had COVID-19 within the prior 90 days (case group, n = 34) were propensity-score matched for age, ICU admission, and abdominal surgery in a 1:4 ratio with candidemia patients without COVID-19 (control group, n = 136).

RESULTS

Age (adjusted odds ratio [AOR] = 1.02, 95% CI: 1.01-1.03), ICU stay (AOR = 1.84, 95% CI: 1.29-2.62), higher Charlson comorbidity index (AOR = 1.08, 95% CI: 1.03-1.13), corticosteroid use (AOR = 1.50, 95% CI: 1.04-2.17) were associated with increased risk of mortality; abdominal surgery (AOR = 0.47, 95% CI: 0.29-0.74) and infected by Candida parapsilosis (AOR = 0.61, 95% CI: 0.38-0.98) were associated with decreased risk of mortality. After matching, there was no significant difference in mortality rates between the case and control groups. The incidence of candidemia increased from 196 to 278 patients/100,000 admissions during COVID-19 pandemic, while the causative species of candidemia and fluconazole susceptibility rates were similar.

CONCLUSION

While the incidence of candidemia increased during COVID-19 pandemic, there was no significant difference in mortality between candidemia patients with and without COVID-19 in the Omicron era.

Investigating the Potential Impact of CCR5-Δ32 Variant on COVID-19 Outcome: A Case-Control Study in Iranian Population

Background

The impact of CCR5-Δ32 on COVID-19 outcomes has been the focus of much research. This genetic variant may protect against SARS-CoV-2 infection, while others have produced conflicting results. Given the controversial results of previous research on different populations, we aimed to investigate the possible association between the CCR5-Δ32 variant and COVID-19 severity in an Iranian population.

Methods

This case-control study was conducted between 25th of April till 10th of October 2021 at Rasoul Akram Hospital of Iran University of Medical Sciences, Tehran, Iran. We investigated the association between CCR5-Δ32 genotype and COVID-19 severity in 200 unrelated Iranian patients. The patients were divided into 2 groups: 100 patients with severe COVID-19 (case group) and 100 patients with mild COVID-19 (control group). Genotyping of CCR5-Δ32 was performed using the polymerase chain reaction (PCR) technique.

Results

The frequency of CCR5-Δ32 allele was 11 in the case group and 16 in the control group. However, no significant association was found between this genetic variant and the clinical outcomes of COVID-19.

Conclusion

The CCR5-Δ32 variant cannot serve as a reliable predictive factor for identifying individuals prone to developing severe COVID-19 in Iranian population. Additionally, targeting CCR5 would not be a viable treatment approach for COVID-19 in Iranians.

Serum 25-hydroxyvitamin D levels and health outcomes of hospitalization owing to COVID-19: a retrospective cross-sectional study

OBJECTIVE

We investigated the role of serum 25(OH)D (25-hydroxyvitamin D) in COVID-related health outcomes.

METHODS

We conducted a retrospective cross-sectional study using data of the National Center of Disease Control and Public Health, Georgia. We extracted patient data including length of hospital stay, transfer to the intensive care unit, requirement for oxygen therapy, treatment with glucocorticoids, and symptoms. After obtaining written informed consent, 384 individuals were enrolled. We divided participants into three groups according to 25(OH)D levels: group 1 = 25(OH)D <12 ng/mL (n = 83), group 2 = 25(OH)D 12-20 ng/mL (n = 141), and group 3 = 25(OH)D >20 ng/mL (n = 160).

RESULTS

The odds ratio (OR) for hospitalization in group 1 versus group 2 was 8.7 (95% confidence interval [CI] 3.6-21.3) and 5.6 for group 1 versus 3 (95% CI 2.7-11.9). Regarding oxygen therapy, OR = 28.41 for group 1 versus 2 (95% CI 3.7-220.5) and OR = 5.2 for group 1 versus 3 (95% CI 1.9-14.1). Regarding treatment with glucocorticoids, OR = 3.7 for group 1 versus 2 (95% CI 1.1-12.5) and OR = 8.4 for group 1 versus 3 (95% CI 1.8-40.7).

CONCLUSION

COVID-19-related morbidity was associated with decreased serum 25(OH)D levels. Future studies should investigate the potential role of vitamin D sufficiency in preventing SARS-CoV-2 infection and mortality.

A study on the correlation between lung injury severity and cardiac function through a closed-loop model

OBJECTIVE

Numerous clinical and pathological studies have confirmed that lung injury can cause cardiovascular disease, but there is no explanation for the mechanism by which the degree of lung injury affects cardiac function. We attempt to reveal this mechanism of influence by simulating a cyclic model.

METHOD

This study established a closed-loop cardiovascular model with a series of electrical parameters. Including the heart, lungs, arteries, veins, etc., each part of the cardiovascular system is modeled using centralized parameters. Adjusting these lung resistances to alter the degree of lung injury is aimed at reflecting the impact of different degrees of lung injury on cardiac function. Finally, analyze and compare the changes in blood pressure, aortic flow, atrioventricular volume, and atrioventricular pressure among different lung injuries to obtain the changes in cardiac function.

RESULTS

In this model, the peak aortic flow decreased, the earlier the trough appeared, and the total aortic flow decreased. Left atrial blood pressure decreased from 6.5 mmHg to around 5.5 mmHg, left ventricular blood pressure decreased from 100 mmHg to around 50 mmHg, and aortic blood pressure also decreased from 100 mmHg to around 50 mmHg. The blood pressure in the pulmonary artery, right atrium, and right ventricle increases. The right ventricular blood pressure decreased from 20 mmHg to around 40 mmHg, while the right atrial blood pressure slightly increased. It can be seen that the increase in impedance has a greater impact on ventricular blood pressure than on atrium. Pulmonary arterial pressure significantly increases, rising from 20 mmHg to around 50 mmHg, forming pulmonary hypertension. The left ventricular end-systolic potential energy, filling energy, stroke work, stroke output, left ventricular filling period, maximum blood pressure during ventricular ejection period, and stroke energy efficiency decrease.

CONCLUSION

We established a closed-loop cardiovascular model that reveals that the more severe lung injury, the higher blood pressure in the pulmonary artery, right atrium, and right ventricle, while the lower blood pressure in the left atrium, left ventricle, and aorta. The increase in pulmonary impedance leads to abnormalities in myocardial contraction, diastolic function, and cardiac reserve capacity, leading to a decrease in cardiac function. This closed-loop model provides a method for pre assessment of cardiovascular disease after lung injury.

Screening of Potential Inhibitors Targeting the Main Protease Structure of SARS-CoV-2 via Molecular Docking, and Approach with Molecular Dynamics, RMSD, RMSF, H-Bond, SASA and MMGBSA

Severe Acute Respiratory Syndrome caused by a coronavirus is a recent viral infection. There is no scientific evidence or clinical trials to indicate that possible therapies have demonstrated results in suspected or confirmed patients. This work aims to perform a virtual screening of 1430 ligands through molecular docking and to evaluate the possible inhibitory capacity of these drugs about the Mpro protease of Covid-19. The selected drugs were registered with the FDA and available in the virtual drug library, widely used by the population. The simulation was performed using the MolAiCalD algorithm, with a Lamarckian genetic model (GA) combined with energy estimation based on rigid and flexible conformation grids. In addition, molecular dynamics studies were also performed to verify the stability of the receptor-ligand complexes formed through analyses of RMSD, RMSF, H-Bond, SASA, and MMGBSA. Compared to the binding energy of the synthetic redocking coupling (-6.8 kcal/mol/RMSD of 1.34 Å), which was considerably higher, it was then decided to analyze the parameters of only three ligands: ergotamine (-9.9 kcal/mol/RMSD of 2.0 Å), dihydroergotamine (-9.8 kcal/mol/RMSD of 1.46 Å) and olysio (-9.5 kcal/mol/RMSD of 1.5 Å). It can be stated that ergotamine showed the best interactions with the Mpro protease of Covid-19 in the in silico study, showing itself as a promising candidate for treating Covid-19.

Cytokine and chemokine profiles in the sera of COVID-19 patients with different stages of severity

INTRODUCTION

COVID-19 is a viral infection that disturbs the host's immune system and causes an overproduction of cytokines leading to a cytokine storm. The present study aimed to evaluate the serum levels of 27 protein biomarkers to determine their association with COVID-19 disease severity.

METHODS

The serum levels of 89 patients with different degrees of COVID-19 disease severity [asymptomatic (n = 14), moderate (n = 14), severe (n = 30), and critical (n = 31)] and 14 healthy individuals were tested for a panel of 27 cytokines and chemokines using Luminex assay (27 Bio‑Plex Pro Human Cytokine, Bio-rad™).

RESULTS

IL-12, IL-2 and IL-13, as well as IL-17 and GM-CSF were clearly undetectable in asymptomatic patients. IL-8 levels were higher in asymptomatic compared with other groups. Very high levels of IL-6, IL-10 and the chemokines MIP-1α, MCP-1 and IP10 were associated with disease progression, while IL-4 tends to decrease with disease severity.

CONCLUSION

Our study provides more evidence that excessive cytokine synthesis is linked to the disease progression.

RNAseq-based transcriptomics of treatment-naïve multi-inflammatory syndrome in children (MIS-C) demonstrates predominant activation of matrisome, innate and humoral immune pathways

MIS-C is a rare, highly inflammatory state resembling incomplete Kawasaki disease, temporarily associated with COVID-19. The pathogenesis is not completely known. RNAseq was carried out on whole blood of six treatment-naïve MIS-C patients. This was compared against RNAseq transcriptomics data of five healthy controls (HC), four Kawasaki Disease (KD) and seven systemic Juvenile Idiopathic Arthritis (sJIA). Using PCA, MIS-C clustered separately from HC, KD and sJIA. Amongst the top 50 significant genes in the three comparisons with HC, KD, and sJIA, common genes were: TMCC2, ITGA2B, DMTN, GFI1B, PF4, QSER1, GRAP2, TUBB1. DSEA revealed that maximum number of hits for overexpressed pathways was for NABA matrisome activation when MIS-C was compared against HC. Cytokine stimulated cellular activation pathways, specifically IL-10 were downregulated. MIS-C had more activated pathways of neutrophil degranulation and acquired immune activation but less of coagulation system or heat-shock system involvement as compared to KD. As compared to sJIA, humoral immune response and complements were activated. Matrisome activation was higher, with increased cell-cell interaction and ECM signalling. This analysis revealed novel insights into the pathogenesis of MIS-C, including the potential role of matrisomes, humoral immune system and down-regulated interleukin-10 pathways.

SARS-CoV-2: Prediction of critical ionic amino acid mutations

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), that caused coronavirus disease 2019 (COVID-19), has been studied thoroughly, and several variants are revealed across the world with their corresponding mutations. Studies and vaccines development focus on the genetic mutations of the S protein due to its vital role in allowing the virus attach and fuse with the membrane of a host cell. In this perspective, we study the effects of all ionic amino acid mutations of the SARS-CoV-2 viral spike protein S1 when bound to Antibody CC12.1 within the SARS-CoV-2:CC12.1 complex model. Binding free energy calculations between SARS-CoV-2 and antibody CC12.1 are based on the Analysis of Electrostatic Similarities of Proteins (AESOP) framework, where the electrostatic potentials are calculated using Adaptive Poisson-Boltzmann Solver (APBS). The atomic radii and charges that feed into the APBS calculations are calculated using the PDB2PQR software. Our results are the first to propose in silico potential life-threatening mutations of SARS-CoV-2 beyond the present mutations found in the five common variants worldwide. We find each of the following mutations: K378A, R408A, K424A, R454A, R457A, K458A, and K462A, to play significant roles in the binding to Antibody CC12.1, since they are turned into strong inhibitors on both chains of the S1 protein, whereas the mutations D405A, D420A, and D427A, show to play important roles in this binding, as they are turned into mild inhibitors on both chains of the S1 protein.