Middle East Respiratory Syndrome Research Articles

Predicting drug-Protein interaction with deep learning framework for molecular graphs and sequences: Potential candidates against SAR-CoV-2.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the COVID-19 disease, which represents a new life-threatening disaster. Regarding viral infection, many therapeutics have been investigated to alleviate the epidemiology such as vaccines and receptor decoys. However, the continuous mutating coronavirus, especially the variants of Delta and Omicron, are tended to invalidate the therapeutic biological product. Thus, it is necessary to develop molecular entities as broad-spectrum antiviral drugs. Coronavirus replication is controlled by the viral 3-chymotrypsin-like cysteine protease (3CLpro) enzyme, which is required for the virus's life cycle. In the cases of severe acute respiratory syndrome coronavirus (SARS-CoV) and middle east respiratory syndrome coronavirus (MERS-CoV), 3CLpro has been shown to be a promising therapeutic development target. Here we proposed an attention-based deep learning framework for molecular graphs and sequences, training from the BindingDB 3CLpro dataset (114,555 compounds). After construction of such model, we conducted large-scale screening the in vivo/vitro dataset (276,003 compounds) from Zinc Database and visualize the candidate compounds with attention score. geometric-based affinity prediction was employed for validation. Finally, we established a 3CLpro-specific deep learning framework, namely GraphDPI-3CL (AUROC: 0.958) achieved superior performance beyond the existing state of the art model and discovered 10 molecules with a high binding affinity of 3CLpro and superior binding mode.

Quantitative assay to analyze neutralization and inhibition of authentic Middle East respiratory syndrome coronavirus

To date, there is no licensed vaccine for Middle East respiratory syndrome coronavirus (MERS-CoV). Therefore, MERS-CoV is one of the diseases targeted by the Coalition for Epidemic Preparedness Innovations (CEPI) vaccine development programs and has been classified as a priority disease by the World Health Organization (WHO). An important measure of vaccine immunogenicity and antibody functionality is the detection of virus-neutralizing antibodies. We have developed and optimized a microneutralization assay (MNA) using authentic MERS-CoV and standardized automatic counting of virus foci. Compared to our standard virus neutralization assay, the MNA showed improved sensitivity when analyzing 30 human sera with good correlation of results (Spearman’s correlation coefficient r = 0.8917, p value < 0.0001). It is important to use standardized materials, such as the WHO international standard (IS) for anti-MERS-CoV immunoglobulin G, to compare the results from clinical trials worldwide. Therefore, in addition to the neutralizing titers (NT50 = 1384, NT80 = 384), we determined the IC50 and IC80 of WHO IS in our MNA to be 0.67 IU/ml and 2.6 IU/ml, respectively. Overall, the established MNA is well suited to reliably quantify vaccine-induced neutralizing antibodies with high sensitivity.

Rational Design of 3D Polymer Corona Interfaces of Single-Walled Carbon Nanotubes for Receptor-Free Virus Recognition.

Facing the escalating threat of viruses worldwide, the development of efficient sensor elements for rapid virus detection has never been more critical. Traditional point-of-care (POC) sensors struggle due to their reliance on fragile biological receptors and limited adaptability to viral strains. In this study, we introduce a nanosensor design for receptor-free virus recognitions using near-infrared (NIR) fluorescent single-walled carbon nanotubes (SWCNTs) functionalized with a poly(ethylene glycol) (PEG)-phospholipid (PEG-lipid) array. Three-dimensional (3D) corona interfaces of the nanosensor array enable selective and sensitive detection of diverse viruses, including Ebola, Lassa, H3N2, H1N1, Middle East respiratory syndrome (MERS), severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1), and SARS-CoV-2, even without any biological receptors. The PEG-lipid components, designed considering chain length, fatty acid saturation, molecular weight, and end-group moieties, allow for precise quantification of viral recognition abilities. High-throughput automated screening of the array demonstrates how the physicochemical properties of the PEG-lipid/SWCNT 3D corona interfaces correlate with viral detection efficiency. Utilizing molecular dynamics and AutoDock simulations, we investigated the impact of PEG-lipid components on 3D corona interface formation, such as surface coverage and hydrodynamic radius and specific molecular interactions based on chemical potentials. Our findings not only enhance detection specificity across various antigens but also accelerate the development of sensor materials for promptly identifying and responding to emerging antigen threats.

Human coronavirus OC43 nanobody neutralizes virus and protects mice from infection.

The pandemic potential presented by coronaviruses has been demonstrated by the ongoing COVID-19 pandemic and previous epidemics caused by severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus. Outside of these major pathogenic coronaviruses, there are four endemic coronaviruses that infect humans: hCoV-OC43, hCoV-229E, hCoV-HKU1, and hCoV-NL63. We identified a collection of nanobodies against human coronavirus OC43 (hCoV-OC43) and found that two high-affinity nanobodies potently neutralized hCoV-OC43 at low nanomolar concentrations. Prophylactic administration of one neutralizing nanobody reduced viral loads in mice infected with hCoV-OC43, showing the potential for nanobody-based therapies for hCoV-OC43 infections.

Role of mushrooms as a novel antiviral agents–lesson learnt from SARS-COV-2 infection

Coronavirus, SARS-CoV-2, producing the disease COVID-19 is a virus that aim at mostly the human respiratory system and other organs. SARS-CoV-2 is a novel strain that has not been earlier recognized in human beings, however, there have been earlier outbreaks of various versions of the coronavirus including severe acute respiratory syndrome (SARS-CoV1) and Middle East respiratory syndrome (MERS-CoV) which have been acclaimed as major pathogens that are an immense warning to public health and world-wide economies. Presently, no exact cure for SARS-CoV-2 infection has been recognized; however, certain medicines have shown noticeable effectiveness in viral inhibition of the disease. Natural substances such as herbs and mushrooms have earlier established immense antiviral and anti-inflammatory activity. Thus, the potential of natural substances as effectual treatments against COVID-19 may seem hopeful. One of the would-be candidates against the SARS-CoV-2 virus may be different types of mushrooms many of these are widely used as a raw material in various medical conditions. In this overview, we have evaluated mushrooms which are natural products with many biological activities in terms of the antiviral and anti-inflammatory effects. Keywords: Coronavirus; SARS-CoV-2, Herbs, Mushrooms, Antiviral agents, COVID-19 Infection antiviral sources, Pneumonia.

Antibody-dependent enhancement (ADE) of SARS-CoV-2 in patients exposed to MERS-CoV and SARS-CoV-2 antigens.

This study evaluated the potential for antibody-dependent enhancement (ADE) in serum samples from patients exposed to Middle East respiratory syndrome coronavirus (MERS-CoV). Furthermore, we evaluated the effect of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination on ADE in individuals with a MERS infection history. We performed ADE assay in sera from MERS recovered and SARS-CoV-2-vaccinated individuals using BHK cells expressing FcgRIIa, SARS-CoV-2, and MERS-CoV pseudoviruses (PVs). Further, we analyzed the association of ADE to serum IgG levels and neutralization. Out of 16 MERS patients, nine demonstrated ADE against SARS-CoV-2 PV, however, none of the samples demonstrated ADE against MERS-CoV PV. Furthermore, out of the seven patients exposed to SARS-CoV-2 vaccination after MERS-CoV infection, only one patient (acutely infected with MERS-CoV) showed ADE for SARS-CoV-2 PV. Further analysis indicated that IgG1, IgG2, and IgG3 against SARS-CoV-2 S1 and RBD subunits, IgG1 and IgG2 against the MERS-CoV S1 subunit, and serum neutralizing activity were low in ADE-positive samples. In summary, samples from MERS-CoV-infected patients exhibited ADE against SARS-CoV-2 and was significantly associated with low levels of neutralizing antibodies. Subsequent exposure to SARS-CoV-2 vaccination resulted in diminished ADE activity while the PV neutralization assay demonstrated a broadly reactive antibody response in some patient samples.

Immunogenicity of vaccine encoding spike protein against Middle East respiratory syndrome coronavirus in mammalian model.

Immunogenicity of vaccine encoding spike protein against Middle East respiratory syndrome coronavirus in mammalian model.

Design and Application of Biosafe Coronavirus Engineering Systems without Virulence

In the last twenty years, three deadly zoonotic coronaviruses (CoVs)—namely, severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and SARS-CoV-2—have emerged. They are considered highly pathogenic for humans, particularly SARS-CoV-2, which caused the 2019 CoV disease pandemic (COVID-19), endangering the lives and health of people globally and causing unpredictable economic losses. Experiments on wild-type viruses require biosafety level 3 or 4 laboratories (BSL-3 or BSL-4), which significantly hinders basic virological research. Therefore, the development of various biosafe CoV systems without virulence is urgently needed to meet the requirements of different research fields, such as antiviral and vaccine evaluation. This review aimed to comprehensively summarize the biosafety of CoV engineering systems. These systems combine virological foundations with synthetic genomics techniques, enabling the development of efficient tools for attenuated or non-virulent vaccines, the screening of antiviral drugs, and the investigation of the pathogenic mechanisms of novel microorganisms.

GS-441524-Diphosphate-Ribose Derivatives as Nanomolar Binders and Fluorescence Polarization Tracers for SARS-CoV-2 and Other Viral Macrodomains.

Viral macrodomains that can bind to or hydrolyze protein adenosine diphosphate ribosylation (ADP-ribosylation) have emerged as promising targets for antiviral drug development. Many inhibitor development efforts have been directed against the severe acute respiratory syndrome coronavirus 2 macrodomain 1 (SARS-CoV-2 Mac1). However, potent inhibitors for viral macrodomains are still lacking, with the best inhibitors still in the micromolar range. Based on GS-441524, a remdesivir precursor, and our previous studies, we have designed and synthesized potent binders of SARS-CoV-2 Mac1 and other viral macrodomains including those of Middle East respiratory syndrome coronavirus (MERS-CoV), Venezuelan equine encephalitis virus (VEEV), and Chikungunya virus (CHIKV). We show that the 1'-CN group of GS-441524 promotes binding to all four viral macrodomains tested while capping the 1″-OH of GS-441524-diphosphate-ribose with a simple phenyl ring further contributes to binding. Incorporating these two structural features, the best binders show 20- to 6000-fold increases in binding affinity over ADP-ribose for SARS-CoV-2, MERS-CoV, VEEV, and CHIKV macrodomains. Moreover, building on these potent binders, we have developed two highly sensitive fluorescence polarization tracers that only require nanomolar proteins and can effectively resolve the binding affinities of nanomolar inhibitors. Our findings and probes described here will facilitate future development of more potent viral macrodomain inhibitors.

A tale of endurance: bats, viruses and immune dynamics.

The emergence of highly zoonotic viral infections has propelled bat research forward. The viral outbreaks including Hendra virus, Nipah virus, Marburg virus, Ebola virus, Rabies virus, Middle East respiratory syndrome coronavirus, SARS-CoV and the latest SARS-CoV-2 have been epidemiologically linked to various bat species. Bats possess unique immunological characteristics that allow them to serve as a potential viral reservoir. Bats are also known to protect themselves against viruses and maintain their immunity. Therefore, there is a need for in-depth understanding into bat-virus biology to unravel the major factors contributing to the coexistence and spread of viruses.

Inactivated Split MERS-CoV Antigen Prevents Lethal Middle East Respiratory Syndrome Coronavirus Infections in Mice.

Middle East respiratory syndrome coronavirus (MERS-CoV) causes fatal infections, with about 36% mortality in humans, and is endemic to the Middle East. MERS-CoV uses human dipeptidyl peptidase 4 (hDPP4) as a receptor for infection. Despite continued research efforts, no licensed vaccine is available for protection against this disease in humans. Therefore, this study sought to develop an inactivated fragmented MERS-CoV vaccine grown in Vero cells in an hDPP4-transgenic mouse model. Two-dose immunisation in mice with 15, 20, or 25 μg of spike proteins of inactivated split MERS-CoV antigens induced neutralising antibodies, with titres ranging from NT 80 to 1280. In addition, all immunised mice were completely protected, with no virus detection in tissues, weight loss, or mortality. The immunised splenocytes produced more cytokines that stimulate immune response (IFN-γ and TNF-α) than those that regulate it (IL-4 and IL-10). Taken together, the inactivated fragmented MERS-CoV vaccine is effective for the protection of mice against lethal MERS-CoV. Thus, the inactivated fragmented MERS-CoV vaccine warrants further testing in other hosts.

NS7a of SADS-CoV promotes viral infection via inducing apoptosis to suppress type III interferon production.

Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a newly discovered swine coronavirus with potential cross-species transmission risk. Although SADS-CoV-induced host cell apoptosis and innate immunity antagonization has been revealed, underlying signaling pathways remain obscure. Here, we demonstrated that infection of SADS-CoV induced apoptosis in vivo and in vitro, and that viral protein NS7a is mainly responsible for SADS-CoV-induced apoptosis in host cells. Furthermore, we found that NS7a interacted with apoptosis-inducing factor mitochondria associated 1 (AIFM1) to activate caspase-3 via caspase-6 in SADS-CoV-infected cells, and enhanced SADS-CoV replication. Importantly, NS7a suppressed poly(I:C)-induced expression of type III interferon (IFN-λ) via activating caspase-3 to cleave interferon regulatory factor 3 (IRF3), and caspase-3 inhibitor protects piglets against SADS-CoV infection in vivo. These findings reveal how SADS-CoV induced apoptosis to inhibit innate immunity and provide a valuable clue to the development of effective drugs for the clinical control of SADS-CoV infection.IMPORTANCEOver the last 20 years, multiple animal-originated coronaviruses, including severe acute respiratory syndrome coronavirus (SARS-CoV), middle east respiratory syndrome coronavirus (MERS-CoV), and SARS-CoV-2, have caused millions of deaths, seriously jeopardized human health, and hindered social development, indicating that the study of animal-originated coronaviruses with potential for cross-species transmission is particularly important. Bat-originated swine acute diarrhea syndrome coronavirus (SADS-CoV), discovered in 2017, can not only cause fatal diarrhea in piglets, but also infect multiple human cells, with a potential risk of cross-species transmission, but its pathogenesis is unclear. In this study, we demonstrated that NS7a of SADS-CoV suppresses IFN-λ production via apoptosis-inducing factor mitochondria associated 1 (AIFM1)-caspase-6-caspase-3-interferon regulatory factor 3 (IRF3) pathway, and caspase-3 inhibitor (Z-DEVD-FMK) can effectively inhibit SADS-CoV replication and protect infected piglets. Our findings in this study contribute to a better understanding of SADS-CoV-host interactions as a part of the coronaviruses pathogenesis and using apoptosis-inhibitor as a drug as potential therapeutic approaches for prevention and control of SADS-CoV infection.

COVID-19 drug discovery and treatment options.

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused substantial morbidity and mortality, and serious social and economic disruptions worldwide. Unvaccinated or incompletely vaccinated older individuals with underlying diseases are especially prone to severe disease. In patients with non-fatal disease, long COVID affecting multiple body systems may persist for months. Unlike SARS-CoV and Middle East respiratory syndrome coronavirus, which have either been mitigated or remained geographically restricted, SARS-CoV-2 has disseminated globally and is likely to continue circulating in humans with possible emergence of new variants that may render vaccines less effective. Thus, safe, effective and readily available COVID-19 therapeutics are urgently needed. In this Review, we summarize the major drug discovery approaches, preclinical antiviral evaluation models, representative virus-targeting and host-targeting therapeutic options, and key therapeutics currently in clinical use for COVID-19. Preparedness against future coronavirus pandemics relies not only on effective vaccines but also on broad-spectrum antivirals targeting conserved viral components or universal host targets, and new therapeutics that can precisely modulate the immune response during infection.

Audience engagement in outrage factors embedded in COVID‐19 news: A content analysis of South Korean news articles and reader comments

AbstractThe risk perception of lay people is believed to be guided by qualitative characteristics of risk they perceive. Outrage factors refer to perceived characteristics of risk that arouse emotional responses and thereby influence risk perception. Conducting a content analysis of coronavirus disease 2019 online news coverage, we identified outrage factors embedded in news stories to determine how those factors are associated with audience engagement, measured by counting news consumer comments and clicks on emotional expressions on each news story. As a result, the average outrage score for a news story was significantly associated with the number of clicks on emotional expressions and comments. When it comes to individual outrage factors, a news story covering a case of violation against social distancing or other governmental guidelines was found to be accompanied by more comments and more emotional expressions, indicating the strongest power of moral nature. The outrage factor of voluntariness, human origin, accident history and controllability were also associated with one or both types of the audience responses. The news stories of business owners who involuntarily shut down their businesses or those comparing the current pandemic to Middle East respiratory syndrome that broke out in 2015 in the nation showed a similar pattern of audience engagement. Furthermore, liberal media were more likely to convey outrage factors than media with a less liberal orientation, which was manifested in the outrage score for each story. We discuss the potential of outrage factors as a new content‐based factor for audience engagement in online risk communication.

Impact of COVID-19 on Pediatric Inflammatory Bowel Diseases-From Expectations to Reality.

Viral infections have always been considered a threat to global health, with numerous outbreaks across time. Despite the relative recent experience with coronavirus-associated diseases such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), severe acute respiratory syndrome-2's (SARS-CoV-2) continuous evolution displays a different behavior. With a tropism for both respiratory and digestive mucosa, coronavirus disease 2019 (COVID-19) and inflammatory bowel disease (IBD) seem to share a particular common background. Current literature offers evidence that viral alteration of the immune system, inflammatory intestinal tissue damage, increased intestinal permeability, incomplete viral clearance with viral antigen persistence, and intestinal dysbiosis, might explain SARS-CoV-2-IBD relationship in terms of etiopathogenesis and evolution. The hyperinflammatory state that both entities have in common explains the lack of success of current IBD therapy, raising the need for new personalized therapeutic options, with better outcomes for IBD and COVID-19 as well. This review aims to summarize the current available data on pediatric IBD evolution, management, and outcomes in the post-COVID period, with an emphasis on the particular aspects of the SARS-CoV-2-IBD relationship in children.

SARS-CoV-2 nsp15 endoribonuclease antagonizes dsRNA-induced antiviral signaling

Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 has caused millions of deaths since its emergence in 2019. Innate immune antagonism by lethal CoVs such as SARS-CoV-2 is crucial for optimal replication and pathogenesis. The conserved nonstructural protein 15 (nsp15) endoribonuclease (EndoU) limits activation of double-stranded (ds)RNA-induced pathways, including interferon (IFN) signaling, protein kinase R (PKR), and oligoadenylate synthetase/ribonuclease L (OAS/RNase L) during diverse CoV infections including murine coronavirus and Middle East respiratory syndrome (MERS)-CoV. To determine how nsp15 functions during SARS-CoV-2 infection, we constructed a recombinant SARS-CoV-2 (nsp15mut) expressing catalytically inactivated nsp15, which we show promoted increased dsRNA accumulation. Infection with SARS-CoV-2 nsp15mut led to increased activation of the IFN signaling and PKR pathways in lung-derived epithelial cell lines and primary nasal epithelial air-liquid interface (ALI) cultures as well as significant attenuation of replication in ALI cultures compared to wild-type virus. This replication defect was rescued when IFN signaling was inhibited with the Janus activated kinase (JAK) inhibitor ruxolitinib. Finally, to assess nsp15 function in the context of minimal (MERS-CoV) or moderate (SARS-CoV-2) innate immune induction, we compared infections with SARS-CoV-2 nsp15mut and previously described MERS-CoV nsp15 mutants. Inactivation of nsp15 had a more dramatic impact on MERS-CoV replication than SARS-CoV-2 in both Calu3 cells and nasal ALI cultures suggesting that SARS-CoV-2 can better tolerate innate immune responses. Taken together, SARS-CoV-2 nsp15 is a potent inhibitor of dsRNA-induced innate immune response and its antagonism of IFN signaling is necessary for optimal viral replication in primary nasal ALI cultures.

A Retrospective Study Comparing Mortality Rates between Vaccinated and Unvaccinated Kidney Transplant Recipients

Background: With the emergence of vaccines for COVID-19, mortality and severity of disease have decreased. However, patients with certain comorbidities, such as immunosuppression, CKD, and renal transplant, still have higher mortality rates as compared to the general population. Current data suggests that the risk of developing COVID-19 among transplant patients was reported to be about 5%, which is significantly higher than the risk rate of 0.3% in the general population. Studies utilizing larger sample sizes (i.e., multiple cohorts, sites, hospitals) comparing COVID-19 outcomes among renal transplant patients with a control group are lacking. background: Coronaviruses belong to a family of Viruses that can cause range of illnesses ranging from the common cold, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) (1,2). In 2019 a new Coronavirus was identified and was named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Severe Acute Respiratory Syndrome Coronavirus-2 (SARSCoV-2) which belongs to the genus beta-CoV which also includes Severe Acute Respiratory Syndrome CoV (SARS-CoV), and Middle Eastern Respiratory Syndrome CoV (MERS-CoV) (2). World Health Organization (WHO) later announced an alternative name for the disease caused by SARS-CoV-2: CoV disease (COVID-19) (2). As of May 25, 2022 an estimated 524,339,768 cases of COVID-19 were reported to World health organization including 6,281,260 deaths related to COVID globally. However, the disease affects patients with certain risk factors disproportionally. Recent data has shown chronic comorbidities, such as acute kidney injury, COPD, diabetes, hypertension, CVD, cancer, increased D-dimer, along with demographic variables such as male gender, older age, current smoker, and obesity are clinical risk factors for a fatal outcome associated with coronavirus [3]. With the emergence of COVID-19 vaccines, severity and mortality of the disease decreased and has contributed in controlling the pandemic that has claimed so many lives across the globe (4). Even with the emergence of vaccine, the disease continued to claim a disproportionate number of lives, particularly among immunocompromised individuals Objective: The purpose of this descriptive study was to compare the mortality rate between vaccinated and unvaccinated kidney transplant recipients. objective: The purpose of this study is to provide a descriptive overview of clinical outcomes between vaccinated and unvaccinated kidney transplant recipients in a single transplant center in West Texas Methods: Participants were recruited at a community-based transplant clinic in West Texas. Results Among the group of participants who tested positive for COVID-19 between 2020 and 2022, higher mortality rates and longer hospital stays were noted among those unvaccinated (72% unvaccinated had greater than 5-day length of stay vs. 33% vaccinated). method: Retrospective Data was collected from Kidney Transplant Clinic at a Medical Center located in El Paso, Texas. Data was gathered between January 2020 and January 2022 from the transplant database. Data was extrapolated for demographics including age, race, gender. Other data included vaccinated vs. unvaccinated status, comorbidities, immunosuppression status, outcomes such as length of stay in the hospital and mortality rate. A total of 38 patients were included in the study between the year 2020 and 2022. In cases where the patient died, missing data was collected from the next of kin. Inclusion criteria included aged 18 and older, being a kidney transplant recipient (deceased and living) and had a current functioning transplanted kidney. We included all patients who tested positive for COVID-19 during January 2020 to December 2022. Patient whose data could not be obtained since they were deceased and/or did not have next of kin were excluded from the study. Patients were also excluded from the study if their missing data could not be obtained or validated by patient or next of kin. Conclusion: Our study suggests that vaccination against COVID-19 decreases mortality rates in kidney transplant recipients. result: Among the 38 patients included in the data set 94.7% identified as Hispanic vs 5.2% were non-Hispanics and 71% were male vs 28.9% were females. The majority of the patients were vaccinated (71% vs 28.9% non-vaccinated). The data also showed higher rates of death in Unvaccinated population as opposed to vaccinated patients (90.9% vs 14.8%). 72% of unvaccinated transplant recipients had a length of stay greater than 5 days compared to 33% of vaccinated patients. All of the patients evaluated in the cohort had two or more comorbidities such as HTN, atrial fibrillation and DM2 (100%). Among patients included in the cohort 84.2% were deceased renal transplant recipients while 15.7% living renal transplant recipients. Furthermore, increased mortality rates were seen among patients treated with higher induction doses (greater than 350mg). A total of 20 patients in the cohort received greater than 350 mg of induction doses out of which 9 were unvaccinated (45%) and 12 were vaccinated (60%). Out of the 9 unvaccinated patients 8 patients died (88%) while 1 patient survived (11.1). Respiratory failure was the main cause of death among patients that passed away, regardless of vaccine status (90.9% Vaccinated vs 14.8% unvaccinated). conclusion: Large phase 3 clinical trials are still currently underway worldwide to study the effects of vaccine on transplant patient. Our study suggests that vaccination against COVID 19 decreases mortality rates in Kidney Transplant recipient. Our retrospective study compared mortality rates between vaccinated and unvaccinated Kidney transplant recipients in a small clinic setting. It is important to have a large prospective double-blind study on the use of vaccinations in renal transplant recipients would be useful to study the effectiveness on this population.

Modified streptavidin–biotin based lateral flow test strip for rapid detection of SARS-CoV-2 S1 antigen in saliva samples

Compared to other infectious diseases, for which LFT development can take years, SARS-CoV-2 antigen LFTS were developed and deployed within months. LFTS for antigen detection were adopted on an unprecedented scale during the COVID-19 pandemic, but many of them lack the sensitivity especially for samples with low viral load. In our previous work, we developed an enhanced signal strip for detection of SARS CoV-2 SI antigens in saliva. Here we introduce some modification to improve the sensitivity, and specificity, and to lower the cost of the strip, by using biotin streptavidin (BS) system. In the modified BS strip, gold-streptavidin and biotinylated Nanobodies (Nbs) against S1 antigen were externally mixed with the tested samples (saliva or nasopharyngeal swab) before their application on the sample pad of the test strip containing angiotensin converting enzyme (ACE-2), as the capturing probe. The study included 320 individuals, with 180 being positively confirmed by RT-PCR and 140 confirmed negative, as well as, 45 health care workers, who were responsible for screening and handling of surgical cases in General Surgery Department and COVID clinic of TBRI. Our results proved that modified BS strip improved the overall sensitivity and specificity of S1antigen detection in saliva samples (95.21% and 99.29% respectively) compared to our previously developed enhanced LFTS (91.66% and 98.57% respectively). Also, the sensitivity of cases with Ct ≤ 30, Ct ≤\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\le$$\\end{document} 35, and Ct ≤\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\le$$\\end{document} 40 using the modified BS strip showed higher values (98.54%, 95.38%, and 88.89% respectively), compared to the corresponding results of our previously developed enhanced LFTS (95.86%, 92.31%, and 82.22% respectively). There were no cross-reactions with either Middle East respiratory syndrome corona virus MERS-CoV or SARS-CoV antigens. Furthermore, we found that the lower viral detection limit (LVD) of BS strip was obviously lower than our previous LVD limit of the enhanced LFTS (0.2 × 104 copies/ml vs. 0.4 × 104 copies/ml, respectively). Our developed BS strip showed that saliva samples gave better results than nasopharyngeal swabs of the same patients. The fact of using smaller amounts of Nbs, and ACE2, as well as the dispensing off of conjugate pad when applying BS strip modifications, justified the expected reduction in the costs of the strip. The implementation of BS strips on saliva samples of 45 health co-workers, who were tested 4 and 6 days after exposure to infection, showed an increase in the sensitivity, starting from the 4th day and reaching its highest level on the 6th day in both high risk and paramedic groups (90.9%, and 80.0%, respectively). This study provides evidence that employment of the modified BS system could increase the sensitivity of the strips, lower their cost, and render them an effective screening tool for early detection of the virus in saliva of suspected Covid-19 patients.

Establishment of a human organoid-based evaluation system for assessing interspecies infection risk of animal-borne coronaviruses

ABSTRACT The COVID-19 pandemic presents a major threat to global public health. Several lines of evidence have shown that the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), along with two other highly pathogenic coronaviruses, SARS-CoV and Middle East Respiratory Syndrome (MERS-CoV) originated from bats. To prevent and control future coronavirus outbreaks, it is necessary to investigate the interspecies infection and pathogenicity risks of animal-related coronaviruses. Currently used infection models, including in vitro cell lines and in vivo animal models, fail to fully mimic the primary infection in human tissues. Here, we employed organoid technology as a promising new model for studying emerging pathogens and their pathogenic mechanisms. We investigated the key host-virus interaction patterns of five human coronaviruses (SARS-CoV-2 original strain, Omicron BA.1, MERS-CoV, HCoV-229E, and HCoV-OC43) in different human respiratory organoids. Five indicators, including cell tropism, invasion preference, replication activity, host response and virus-induced cell death, were developed to establish a comprehensive evaluation system to predict coronavirus interspecies infection and pathogenicity risks. Using this system, we further examined the pathogenicity and interspecies infection risks of three SARS-related coronaviruses (SARSr-CoV), including WIV1 and rRsSHC014S from bats, and MpCoV-GX from pangolins. Moreover, we found that cannabidiol, a non-psychoactive plant extract, exhibits significant inhibitory effects on various coronaviruses in human lung organoid. Cannabidiol significantly enhanced interferon-stimulated gene expression but reduced levels of inflammatory cytokines. In summary, our study established a reliable comprehensive evaluation system to analyse infection and pathogenicity patterns of zoonotic coronaviruses, which could aid in prevention and control of potentially emerging coronavirus diseases.

Cytopathological study of pleural effusion in SARS-CoV2 RTPCR positive subjects during pandemic at tertiary care hospital

Introduction and Aim: Respiratory system is the most common system affected by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).Review of literature reveals that pleural effusion were seen in one third of cases with Middle East Respiratory Syndrome(MERS) but were rarely reported in SARS –CoV2.This study aims to study the cytomorphological changes in Pleural effusion seen in SARS CoV-2 positive cases, to correlate the cytological findings with radiological CT COVID-19 Reporting and Data System(CORADS)scorings and to categorize pleural effusion as isolated cause of SARS CoV-2 or aggravation of underlying other etiologies.   Materials and Methods: Pleural fluid samples of SARS CoV-2 RT PCR positive cases, obtained from patients of all age groups were included in the study. The samples were predominantly from Covid19 wave 1 (March 2020- February 2021) and few from Covid wave 2(March 2021-April 2021). Biochemical analysis, hematological parameters, cytomorphology and associated comorbidity was recorded, and analysis done.   Results: Male predominance was observed. Most common cytological and biochemical finding in pleural fluid analysis was Exudative pleural effusion. Predominant cytological features showed lymphocytic effusion. Radiology showed maximum left sided pleural effusion (42%). CORADS score was 6 in majority of cases and effusion as an isolated cause was seen in few cases.   Conclusion: Pleural effusion is a rare finding in SARS COV-2 induced bronchopneumonia. Effusion is seen with a high CORADS score, and they carry a high risk of mortality. This study suggests having SARS CoV-2 infection as a differential diagnostic entity when we find the mentioned morphological and biochemical findings as discussed in the present study.