Diversity Of Coronaviruses Research Articles

Potent and broadly neutralizing antibodies against sarbecoviruses induced by sequential COVID-19 vaccination

The current SARS-CoV-2 variants strikingly evade all authorized monoclonal antibodies and threaten the efficacy of serum-neutralizing activity elicited by vaccination or prior infection, urging the need to develop antivirals against SARS-CoV-2 and related sarbecoviruses. Here, we identified both potent and broadly neutralizing antibodies from a five-dose vaccinated donor who exhibited cross-reactive serum-neutralizing activity against diverse coronaviruses. Through single B-cell sorting and sequencing followed by a tailor-made computational pipeline, we successfully selected 86 antibodies with potential cross-neutralizing ability from 684 antibody sequences. Among them, PW5-570 potently neutralized all SARS-CoV-2 variants that arose prior to Omicron BA.5, and the other three could broadly neutralize all current SARS-CoV-2 variants of concern, SARS-CoV and their related sarbecoviruses (Pangolin-GD, RaTG13, WIV-1, and SHC014). Cryo-EM analysis demonstrates that these antibodies have diverse neutralization mechanisms, such as disassembling spike trimers, or binding to RBM or SD1 to affect ACE2 binding. In addition, prophylactic administration of these antibodies significantly protects nasal turbinate and lung infections against BA.1, XBB.1, and SARS-CoV viral challenge in golden Syrian hamsters, respectively. Importantly, post-exposure treatment with PW5-5 and PW5-535 also markedly protects against XBB.1 challenge in these models. This study reveals the potential utility of computational process to assist screening cross-reactive antibodies, as well as the potency of vaccine-induced broadly neutralizing antibodies against current SARS-CoV-2 variants and related sarbecoviruses, offering promising avenues for the development of broad therapeutic antibody drugs.

Unilateral Lung Parenchymal Infiltrates with GGO & Evolving Consolidation as Presenting Feature of Sporadic COVID-19 Pneumonia in Post Pandemic Era in a Patient with Acute Febrile Respiratory Illness

Sporadic COVID-19 cases will be predicted to occur in coming few years ahead as observed in previously known influenza virus related pandemics. Herd immunity due to natural infection and hybrid immunity after COVID-19 vaccination has played crucial role in waning of this pandemic. COVID-19 pneumonia has a very ‘typical’ radiological presentations, observed globally; classified as GGO and consolidations involving peripheral parts of lung, bilateral disease, predominantly pleural based areas initially and involves central portions as disease process advances. Such radiological presentations are never documented in history before this pandemic, which has helped in suspecting COVID-19 illness in cases with negative microbiological results initially and such illness were classified as SARI (severe acute respiratory illness). Cases with typical radiological features for COVID-19 with RT PCR positive results were defined as case of COVID-19 illness. Both the clinical scenarios were managed with similar protocol during hospitalization. COVID-19 case burden has significantly decreased in last one year since declaration of end of pandemic by WHO and now we are in post pandemic phase. Since beginnings of pandemic, many corona virus variants were emerged with variable infectivity, virulence, pathogenesis, mortality and morbidity. As pandemic is over, cases are rarely observed with lung involvement, COVID RT PCR testing, HRCT reporting’s in line with pandemic protocol and requirement of resources to treat these cases are less required and utilized today. In present case report, 32-year male, presented in outdoor unit with history of acute febrile respiratory illness with dry cough, high grade fever and chest tightness and chest discomfort of acute onset. HRCT thorax documented Pleural based, peripheral, unifocal or solitary opacity with predominant GGOs in right lower lobe with normal left lung. He is treated in indoor unit in line with community acquired pneumonia protocol and observed clinical worsening with four-fold raised in inflammatory markers. Oxygenation is worsened and raised IL-6, CRP and LDH has given clue to think towards COVID-19 etiology. Thorat swab for COVID-19 RT PCR is positive and managed according to protocol for COVID-19 illness. This is the only observed COVID-19 pneumonia case in last six months, in which; clinical-radiological patters were typical of pandemic illness of second wave of COVID-19 illness due to delta variant. Our case is the sporadic case reported with all clinical features of pandemic illness. We have suspected COVID-19 etiology in spite of ‘atypical unilateral lung involvement’ due to worsened clinical features and abnormally raised inflammatory markers with poor response to standard treatment protocol for community acquired pneumonia. High index of suspicion is must, and; timely interventions with use of rational treatment including remdesivir, heparin & steroids combination during hospitalization has documented successful outcome. We recommend COVID-19 RT PCR testing in all community acquired cases nonresponding to standard guidelines to have timely diagnosis and treatment. Sporadic cases rare to occur, and they do occur for few years ahead of this end of pandemic due to virus variant, and we must quote ‘rare things are not rare to happen’.

Clinical characteristics of 13 cases of Coronavirus infection complicated with severe central nervous system lesions in Shanxi children’s hospital

BackgroundThe new coronavirus Omicron variant strain spread rapidly worldwide and is currently the primary mutant strain prevalent in the world.ObjectiveTo explore the clinical features of severe central nervous system lesions in children infected with novel coronavirus Omicron mutant strain, so as to provide a reference for clinical diagnosis and treatment.Materials and methodsThe clinical data of 13 children diagnosed with novel coronavirus Omicron variant strain complicated with severe central nervous system infection from December 13, 2022, to January 31, 2023, in the Children’s Intensive Care Medicine Department of Shanxi Children’s Hospital were retrospectively analyzed.ResultsAmong the 13 children, there were 9 males (69%) and 4 females (31%); the ages ranged from 1-year-old 16 days to 13 years old, with a median age of 9 years old, and most of them were school-age children (84.6%). The 13 children were usually healthy, but this time they were all positive for the new coronavirus nucleic acid test. The 13 children had obvious signs of the abnormal nervous system when they were admitted to the hospital, among which 12 cases (92.3%) showed convulsions, 11 children had obvious disturbance of consciousness (84.6%) when they were admitted to the hospital, and 5 children had circulatory disorders (38.4%). Among the 13 children, 2 were cured (15.3%), 5 children had serious sequelae (38.4%) when they were discharged from the hospital, and 6 children died of severe illness (46.3%).ConclusionThis study illuminates the clinical characteristics of severe central nervous system complications in children with coronavirus variant infection, highlighting rapid onset, swift progression, relatively poor prognosis, and notable symptoms such as high fever, convulsions, altered consciousness, elevated interleukin-6 levels, increased cerebrospinal fluid lactate levels, and early imaging changes.

Pregnancy-Related Complications During the COVID-19 Pandemic in Iran.

The COVID-19 pandemic has profoundly affected healthcare systems worldwide, with significant collateral damage to vulnerable populations, including the perinatal population. This study sought to compare pregnancy-related complications before and during the COVID-19 pandemic in Iran. This retrospective data analysis was performed from February 20 to August 20, 2019 (prior to the onset of the COVID-19 pandemic) and from February 20 to August 20, 2020 (during the pandemic), encompassing the initial wave of the pandemic and the subsequent lockdown. To collect data, we utilized the medical records of 168,358 women obtained from the Iranian Maternal and Neonatal Network, which is a comprehensive electronic health record database management system specifically designed to store information pertaining to maternal and neonatal health. A total of 168,358 medical records were analyzed, with 87388 (51.9%) and 80970 (48.1%) before and during the pandemic, respectively. The occurrence of pregnancy complications was found to be significantly more frequent during the pandemic compared to the pre-pandemic period. Notably, there was a higher likelihood of experiencing preeclampsia (odds ratio [OR]=1.14, 95% confidence interval [CI]: 1.07‒1.22, P=0.0001) and gestational diabetes (OR=1.14, 95% CI: 1.09‒1.19, P=0.0001) during the pandemic. Furthermore, cesarean section (CS) became more prevalent during the pandemic in comparison to vaginal delivery (OR=1.19, 95% CI: 1.17‒-1.22, P=0.0001). Our findings demonstrated a significant association between the COVID-19 pandemic and an escalation in adverse pregnancy outcomes, notably preeclampsia, gestational diabetes, and CS deliveries. However, further research is warranted to gain a richer understanding of the intricate interplay between the COVID-19 pandemic and pregnancy complications. This is particularly crucial in light of the evolving landscape of new coronavirus variants.

Preparation of antiviral multispray with cationic antimicrobial dialkyldimethyl ammonium salt and sulfobetaine against new coronaviruses (SARS-CoV-2).

The novel sudden acute respiratory syndrome coronavirus 2 is an enveloped virus currently causing severe illness and death worldwide. Common antiseptics such as alcohol have some efficacy in disinfecting everyday surroundings, but development of more effective disinfectants is imperative. A series of studies focusing on cationic antimicrobials resulted in the development of a safe and effective novel coronavirus disinfectant, DEA-171, which provides ≥99.98 % inhibition of all novel coronavirus variants within 1 min.

Antiviral activity of pyrazole derivatives bearing a hydroxyquinoline scaffold against SARS-CoV-2, HCoV-229E, MERS-CoV, and IBV propagation.

The ongoing global threat posed by coronaviruses necessitates the urgent development of effective antiviral agents. In this study, we investigated the potential of hydroxyquinoline-pyrazole candidates as antiviral agents against a range of coronaviruses, including SARS-CoV-2, MERS-CoV, and HCoV-229E. Molecular docking studies were conducted to assess the binding affinity of the synthesized compounds to key viral proteins. The compounds were prepared via condensation reactions of a pyrazolylhydrazide derivative with 2-chloro-3-formylquinoline, yielding hydrazone and pyrrolone derivatives. The cytotoxicity of compounds was evaluated using Vero E6 cells, and their antiviral activity was assessed via plaque reduction assays and viral inhibition assays using hydroxychloroquine as a positive control antiviral drug. The results revealed promising antiviral activity of the synthesized compounds against all tested coronaviruses, with selectivity indices indicating their potential as selective antiviral agents. Notably, the compounds exhibited potent inhibition of SARS-CoV-2 at lower concentrations, highlighting their promise as therapeutic candidates against this highly pathogenic virus. Likewise, the modeling pharmacokinetics approach showed its appropriate drug-likeness and bioavailability assets. These findings underscore the importance of hydroxyquinoline-pyrazole derivatives as potential antiviral agents against diverse coronaviruses, providing valuable insights for further therapeutic development.

Synthesis of some ribonucleosides derivatives and molecular docking analysis against variant corona virus omicrone

In this work, ribonucleoside products have been prepared by employing stannic tetrachloride (SnCl4) and natural phosphate as catalysts. The obtained result suggests that this catalyst facilitates the reactions of ribonucleoside-like products in a stereo-controlled manner, exhibiting β-selectivity when reacting with trimethylsilyl uracil, the ribonucleosides derivatives were obtained in suitable yields. In addition, we have performed the molecular docking analysis, demonstrated that the synthesized compounds have potential for antiviral activity against the omicron variant of coronavirus, and the D3, D4, E and F products have a higher binding energy than the molnupiravir drug, indicating that these products may be a probable drugs for the omicron variant.

Detection of SARS-CoV-2-Specific Cells Utilizing Whole Proteins and/or Peptides in Human PBMCs Using IFN-ƴ ELISPOT Assay.

SARS-CoV-2 continues to threaten global public health, making COVID-19 immunity studies of utmost importance. Waning of antibody responses postinfection and/or vaccination and the emergence of immune escape variants have been ongoing challenges in mitigating SARS-CoV-2 morbidity and mortality. While a tremendous amount of work has been done to characterize humoral immune responses to SARS-CoV-2 virus and vaccines, cellular immunity, mediated by T cells, is critical for efficient viral control and protection and demonstrates high durability and cross-reactivity to coronavirus variants. Thus, ELISPOT, a standard assay for antigen-specific cellular immune response assessment, allows us to evaluate SARS-CoV-2-specific T-cell response by quantifying the frequency of SARS-CoV-2-specific cytokine-secreting cells in vitro. We have outlined a detailed procedure to study T-cell recall responses to SARS-CoV-2 in human peripheral blood mononuclear cells (PBMCs) following infection and/or vaccination using an optimized IFN-γ ELISPOT assay. Our methodologies can be adapted to assess other cytokines and are a useful tool for studying other viral pathogen and/or peptide-specific T-cell responses.

Acceptance and Attitudes towards Covid-19 Vaccines: A Cross-Sectional Study from India

ABSTRACT: COVID-19 is a pandemic caused by SARS-CoV-2 – 2 that caused a devastating impact and has affected human population globally. The mitigation measures to impede and contain the spread of the COVID-19 disease included lockdowns, social distancing, and use of masks, hand sanitization & other basic hygiene practices. Administration of vaccines was considered the most effective strategy to reduce the risk of the disease. Several vaccines developed against multiple variants of Coronavirus to combat the dreadful disease. The project was taken with the objective to know the perceptions of people about the COVID-19 vaccines and was intended to evaluate the awareness, attitude, and factors determining their acceptance or hesitancy towards the vaccine among the Indian population. This study was conducted using a snowball sampling technique employing a cross-sectional and web-based online survey. A self-administered questionnaire was prepared and circulated among the general Indian population and feedback was collected and analyzed on knowledge and awareness, attitudes, and perceptions about COVID-19 vaccines. A total of 1,507 respondents from different states of India have participated in the survey. A considerable percentage of the population approximately 90% was fully vaccinated due to concerted efforts of Government authorities and health officials. The majority of the people were hesitant and unsure to administer booster doses of vaccines. The results suggested that the majority of the Indian population had good knowledge and awareness about Covid 19 vaccines and had a very positive attitude and acceptance towards vaccines but showed a lack of interest towards booster doses. Hence, various strategies need to be formulated to update the information to the public through awareness programs and their effective implementation.

Cyclosporine A micellar nasal spray characterization and antiviral action against SARS-CoV-2

The upper airways represent the point of entrance from where Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection spreads to the lungs. In the present work, α-tocopheryl-polyethylene-glycol succinate (TPGS) micelles loaded with cyclosporine A (CSA) were developed for nasal administration to prevent or treat the viral infection in the very first phases. The behavior of the micelles in presence of simulated nasal mucus was investigated in terms of stability and mucopenetration rate, evidencing long-term stability and fast diffusion across the glycoproteins matrix. Moreover, the spray characteristics of the micellar formulation and deposition profile in a silicon nasal model were studied using three nasal spray devices. Results allowed to identify the nasal spray pump (BiVax, Aptar) able to provide the wider and uniform deposition of the nasal cavity. The cyclosporine A micelles antiviral activity against SARS-CoV-2 was tested on the Omicron BA.1 variant using Vero E6 cells with protocols simulating treatment before, during and after the infection of the upper airways. Complete viral inactivation was observed for the cyclosporine-loaded micelles while a very low activity was evidenced for the non-formulated drug, suggesting a synergistic activity of the drug and the formulation. In conclusion, this work showed that the developed cyclosporine A-loaded micellar formulations have the potential to be clinically effective against a wide spectrum of coronavirus variants.

Overview of Nucleocapsid-Targeting Vaccines against COVID-19.

The new SARS-CoV-2 coronavirus, which emerged in late 2019, is a highly variable causative agent of COVID-19, a contagious respiratory disease with potentially severe complications. Vaccination is considered the most effective measure to prevent the spread and complications of this infection. Spike (S) protein-based vaccines were very successful in preventing COVID-19 caused by the ancestral SARS-CoV-2 strain; however, their efficacy was significantly reduced when coronavirus variants antigenically different from the original strain emerged in circulation. This is due to the high variability of this major viral antigen caused by escape from the immunity caused by the infection or vaccination with spike-targeting vaccines. The nucleocapsid protein (N) is a much more conserved SARS-CoV-2 antigen than the spike protein and has therefore attracted the attention of scientists as a promising target for broad-spectrum vaccine development. Here, we summarized the current data on various N-based COVID-19 vaccines that have been tested in animal challenge models or clinical trials. Despite the high conservatism of the N protein, escape mutations gradually occurring in the N sequence can affect its protective properties. During the three years of the pandemic, at least 12 mutations have arisen in the N sequence, affecting more than 40 known immunogenic T-cell epitopes, so the antigenicity of the N protein of recent SARS-CoV-2 variants may be altered. This fact should be taken into account as a limitation in the development of cross-reactive vaccines based on N-protein.

Knowledge, attitude, and adherence to coronavirus preventive measures among residents of the Kingdom of Saudi Arabia.

Since the SARS-CoV-2 virus, the virus that causes COVID-19, has been spreading globally, variants have emerged and been identified in many countries around the world. This descriptive cross-sectional study aimed to explore the level of knowledge, attitude, and adherence to coronavirus variant preventive measures among residents of the Kingdom of Saudi Arabia. This is a cross-sectional online survey that was conducted between April and November 2020 and involved the residents of the Kingdom of Saudi Arabia. An electronic invitation for participation was sent to prospective participants, including the link to the research instrument, using social media websites. A total of 780 participants responded to a 4-part online survey developed by the investigators. The findings revealed that 72.9% of the participants (95% CI: 69.6%-75.9%) had a high level of knowledge about COVID-19; 78.2% said they supported all precautionary measures put in place by health authorities; only 29% wore face masks; and 93% wash their hands at least 5 times a day. Furthermore, 69% of the residents were always covering their mouth and nose when coughing or sneezing with a piece of tissue paper, while 71% were observing physical distancing. Participants showed a positive attitude towards supporting all the precautionary measures being put in place by the health authorities and the efforts made by healthcare workers in the kingdom. Residents in Saudi Arabia showed a high level of knowledge of COVID-19 variants. Higher levels of education, being employed, and higher income were factors that influenced participants' knowledge positively (P < .05). Females and younger age were predictors of a better attitude towards COVID-19 (P < .01).The majority of the residents were afraid of the spread and mutation of the coronavirus. This study highlights the value of continuing community service learning programs for raising knowledge retention and adherence to coronavirus variant prevention strategies.

Mucosal recombinant BCG vaccine induces lung-resident memory macrophages and enhances trained immunity via mTORC2/HK1-mediated metabolic rewiring

Bacillus Calmette–Guérin (BCG) vaccination induces a type of immune memory known as “trained immunity”, characterized by the immunometabolic and epigenetic changes in innate immune cells. However, the molecular mechanism underlying the strategies for inducing and/or boosting trained immunity in alveolar macrophages remains unknown. Here, we found that mucosal vaccination with the recombinant strain rBCGPPE27 significantly augmented the trained immune response in mice, facilitating a superior protective response against Mycobacterium tuberculosis and non-related bacterial reinfection in mice when compared to BCG. Mucosal immunization with rBCGPPE27 enhanced innate cytokine production by alveolar macrophages associated with promoted glycolytic metabolism, typical of trained immunity. Deficiency of the mammalian target of rapamycin complex 2 and hexokinase 1 abolished the immunometabolic and epigenetic rewiring in mouse alveolar macrophages after mucosal rBCGPPE27 vaccination. Most noteworthy, utilizing rBCGPPE27’s higher-up trained effects: The single mucosal immunization with rBCGPPE27-adjuvanted coronavirus disease (CoV-2) vaccine raised the rapid development of virus-specific immunoglobulin G antibodies, boosted pseudovirus neutralizing antibodies, and augmented T helper type 1-biased cytokine release by vaccine-specific T cells, compared to BCG/CoV-2 vaccine. These findings revealed that mucosal recombinant BCG vaccine induces lung-resident memory macrophages and enhances trained immunity via reprogramming mTORC2- and HK-1-mediated aerobic glycolysis, providing new vaccine strategies for improving tuberculosis (TB) or coronavirus variant vaccinations, and targeting innate immunity via mucosal surfaces.

459. Characteristics and Presentations of Hospitalized Children due to three predominate COVID-19 variants within a healthcare network

Abstract Background Variants of SARS-CoV-2 caused three major waves of infections in NJ. Children and young adults were hospitalized with varying symptoms and severity of illness depending on the variant. The objectives of this study are to describe differences in the demographic and clinical characteristics, severity of illness and outcomes in pediatric patients during the different SARS-CoV-2 waves in our hospital network. Methods We conducted a retrospective study of pediatric patients admitted to one of our three network hospitals with SARS-CoV-2 infection or with post-COVID-19 inflammatory conditions such as Multisystem Inflammatory Syndrome in Children (MIS-C) during the different waves of infection. Patients who were asymptomatic but incidentally tested positive for SARS-CoV-2 and were hospitalized for unrelated indications were excluded. We defined the timelines as follows: Wave 1 occurred between March 1, 2020 and May 31, 2020; wave 2 occurred between November 1, 2020-January 31, 2021; and wave 3 occurred between December 1, 2021-February 28, 2022. Demographic characteristics, clinical features, and outcomes were recorded and compared with respect to the different variants. Results Of 351 total patients included in this study, 74 were admitted during wave 1, 94 during wave 2, and 181 during wave 3. The median age of patients decreased from wave 1 (11.5 years) to wave 3 (3 years) (p=0.0034). 87.7% of the patients were unvaccinated. The overall incidence of admissions related to COVID-19 pneumonia decreased in wave 3 compared to wave 1 and 2. COVID-19 bronchiolitis or croup admissions occurred mostly in wave 3. No significant difference in intensive care admissions was observed in any wave. Length of stay decreased across the waves (p&amp;lt; 0.0001). Treatments required did not vary between the waves except for a decrease in antibiotic use with each subsequent wave (p&amp;lt; 0.0001). Conclusion The impact of COVID-19 on the pediatric population differs from the adult population, and the overall numbers of hospitalized children has mirrored the peak in cases observed during each infection wave. Our study illustrates the changes in clinical presentation and severity observed with the different coronavirus variants. Disclosures Tara Lozy, MA in Data Science, Eli Lilly &amp; Company: Stocks/Bonds

Low-sugar universal mRNA vaccine against coronavirus variants with deletion of glycosites in the S2 or stem of SARS-CoV-2 spike messenger RNA (mRNA).

Since the outbreak of Severe Acute Respiratory Syndrome Virus-2 (SARS-CoV-2) in 2019, more than 15 million spike protein sequences have been identified, raising a new challenge for the development of a broadly protective vaccine against the various emerging variants. We found that the virus, like most other human viruses, depends on host-made glycans to shield the conserved epitopes on spike protein from immune response and demonstrated that deletion of the glycan shields exposed highly conserved epitopes and elicited broadly protective immune responses. In this study, we identified 17 conserved epitopes from 14 million spike protein sequences and 11 of the conserved epitopes are in the S2 domain, including the six most conserved epitopes in the stem region. We also demonstrated that deletion of the glycosites in the spike messenger RNA (mRNA) S2 domain or the stem region exposed the highly conserved epitopes and elicited broadly protective immune responses, particularly CD-8+ T cell response against various SARS-CoV-2 variants, and other human coronaviruses including MERS, SARS viruses, and those causing common cold.

1348. Identification of GB-0669, a Novel S-2 Targeted Spike Monoclonal Antibody in Development for SARS-CoV-2 Prophylaxis

Abstract Background The clinical benefit of anti-spike mAbs for prophylaxis and treatment of SARS-CoV-2 is now well established (Baum 2020, Loo 2022, Westendorf 2022, Jones 2021, Kreuzberger 2021, Cathcart 2021, Hirsch 2022, Shi 2020); However, the evolution of SARS CoV-2 due to immune pressure has compromised the utility of all previously approved mAbs which target the variable, immune dominant receptor binding domain of the Spike protein. Despite the success of vaccination protecting the general population, the immunocompromised and elderly remain at high risk of serious disease and mortality from SARS CoV-2 infection. Therefore, there is a need to develop mAbs that remain active across current and emergent SARS CoV-2 variants for such populations. Methods The Generate Platform uses machine learning (ML) models to generate therapeutics with desirable properties. We used this platform to explore the amino acid sequence landscape compatible with the binding conformation and breadth of neutralization for mAbs targeting the conserved S-2 stem helix of Spike. While S-2 directed antibodies can broadly neutralize diverse coronaviruses, they are generally limited by potency. We employed an iterative computation- experimentation loop to design antibodies that bind to the S-2 stem helix, optimizing for potency, breadth and developability. Results The Generate Platform was employed to identify S-2 targeted Spike antibodies with high potency and breadth of neutralization resulting in GB-0669. GB-0669 exhibits sub-nM neutralization against all SARS-CoV-2 variants and Omicron sublineages including the highly immune evasive strain XBB. GB-0669 also displays sub-nM neutralization against sarbecoviruses associated with previous epidemics (SARS-CoV-1) and those of pandemic potential (WIV1, bat SARS-like coronavirus). The GB 0669 epitope was mapped by co-crystallization and is consistent with the observed breadth; all key interactions are &amp;gt;99% conserved with no evidence of immune escape. Conclusion GB-0669, a novel mAB targeting the conserved S-2 region of Spike, is hypothesized to be effective for prophylaxis of COVID-19 across all Omicron sublineages and future variants as well as CoVs with pandemic potential. Disclosures Francesco Borriello, MD PhD, Generate Biomedicines: Employee Gevorg Grigoryan, PhD, Generate Biomedicines: Chief Technology Officer|Generate Biomedicines: Ownership Interest|Generate Biomedicines: Stocks/Bonds Daria Hazuda, PhD, Generate Biomedicines: Employee|Generate Biomedicines: Stocks/Bonds|Merck and Co: Employee|Merck and Co: Stocks/Bonds Nathan H. Joh, PhD, Generate Biomedicines: Employee at Generate Biomedicines

A phenothiazine urea derivative broadly inhibits coronavirus replication via viral protease inhibition

Coronavirus (CoV) replication requires efficient cleavage of viral polyproteins into an array of non-structural proteins involved in viral replication, organelle formation, viral RNA synthesis, and host shutoff. Human CoVs (HCoVs) encode two viral cysteine proteases, main protease (Mpro) and papain-like protease (PLpro), that mediate polyprotein cleavage. Using a structure-guided approach, a phenothiazine urea derivative that inhibits both SARS-CoV-2 Mpro and PLpro protease activity was identified. In silico docking studies also predicted the binding of the phenothiazine urea to the active sites of structurally similar Mpro and PLpro proteases from distantly related alphacoronavirus, HCoV-229 E (229 E), and the betacoronavirus, HCoV-OC43 (OC43). The lead phenothiazine urea derivative displayed broad antiviral activity against all three HCoVs tested in cellulo. It was further demonstrated that the compound inhibited 229 E and OC43 at an early stage of viral replication, with diminished formation of viral replication organelles, and the RNAs that are made within them, as expected following viral protease inhibition. These observations suggest that the phenothiazine urea derivative readily inhibits viral replication and may broadly inhibit proteases of diverse coronaviruses.

A Longitudinal Evaluation of Coronavirus Disease 2019 and Its Effects on Spinal Decompressions With or Without Fusion.

Retrospective cohort. The objectives were to (1) compare the safety of spine surgery before and after the emergence of coronavirus disease 2019 (COVID-19) and (2) determine whether patients with a history of COVID-19 were at increased risk of adverse events. The COVID-19 pandemic had a tremendous impact on several health care services. In spine surgery, elective cases were canceled and patients received delayed care due to the uncertainty of disease transmission and surgical outcomes. As new coronavirus variants arise, health care systems require guidance on how to provide optimal patient care to all those in need of our services. A retrospective review of patients undergoing spine surgery between January 1, 2019 and June 30, 2021 was performed. Patients were split into pre-COVID or post-COVID cohorts based on local government guidelines. Inpatient complications, 90-day readmission, and 90-day mortality were compared between groups. Secondary analysis included multiple logistic regression to determine independent predictors of each outcome. A total of 2976 patients were included for analysis with 1701 patients designated as pre-COVID and 1275 as post-COVID. The pre-COVID cohort had fewer patients undergoing revision surgery (16.8% vs 21.9%, P < 0.001) and a lower home discharge rate (84.5% vs 88.2%, P = 0.008). Inpatient complication (9.9% vs 9.2%, P = 0.562), inpatient mortality (0.1% vs 0.2%, P = 0.193), 90-day readmission (3.4% vs 3.2%, P = 0.828), and 90-day mortality rates (0.8% vs 0.8%, P = 0.902) were similar between groups. Patients with positive COVID-19 tests before surgery had similar complication rates (7.7% vs 6.1%, P = 1.000) as those without a positive test documented. After the emergence of COVID-19, patients undergoing spine surgery had a greater number of medical comorbidities, but similar rates of inpatient complications, readmission, and mortality. Prior COVID-19 infection was not associated with an increased risk of postsurgical complications or mortality. Level III.

Inferring hospital admissions from SARS-CoV-2 virus loads in wastewater in The Netherlands, August 2020 – February 2022

Wastewater-based surveillance enables tracking of SARS-CoV-2 circulation at a local scale in near-real time. Here we investigate the relation between virus loads and the number of hospital admissions in the Netherlands. Inferred virus loads from August 2020 until February 2022 in each of the 344 Dutch municipalities are analysed in a Bayesian multilevel Poisson regression to relate virus loads to daily age-stratified (in groups of 20 years) hospital admissions. Covariates include municipal vaccination coverages stratified by age and dose (first, second, and booster) and prevalence of the circulating coronavirus variants (wildtype, Alpha, Delta, and Omicron (BA.1 and BA.2)). Our model captures the relation between hospital admissions and virus loads well. Estimated hospitalisation rates per 1,000,000 persons per day at a virus load of 1013 particles range from 0.18 (95 % Prediction Interval (PI): 0.046–0.48) in children (0–19 years) to 20.1 (95 % PI: 9.46–36.8) in the oldest age group (80 years and older) in an unvaccinated population with only wildtype SARS-CoV-2 circulation. The analyses indicate a nearly twofold (1.92 (95 % PI: 1.78–2.05)) decrease in the expected number of hospitalisations at a given virus load between the Alpha and the Omicron variant. Our analyses show that virus load estimates in wastewater are closely related to the expected number of hospitalisations and provide an attractive tool to detect increased SARS-CoV-2 circulation at a local scale, even when there are few hospital admissions. Our analyses enable integration of data at the municipality level into meaningful conversion rates to translate virus loads at a local level into expected numbers of hospital admissions, which would allow for a better interpretation of virus loads detected in wastewater.

Physics-Based Signal Analysis of Genome Sequences: An Overview of GenomeBits.

A comprehensive overview of the recent physics-inspired genome analysis tool, GenomeBits, is presented. This is based on traditional signal processing methods such as discrete Fourier transform (DFT). GenomeBits can be used to extract underlying genomics features from the distribution of nucleotides, and can be further used to analyze the mutation patterns in viral genomes. Examples of the main GenomeBits findings outlining the intrinsic signal organization of genomics sequences for different SARS-CoV-2 variants along the pandemic years 2020-2022 and Monkeypox cases in 2021 are presented to show the usefulness of GenomeBits. GenomeBits results for DFT of SARS-CoV-2 genomes in different geographical regions are discussed, together with the GenomeBits analysis of complete genome sequences for the first coronavirus variants reported: Alpha, Beta, Gamma, Epsilon and Eta. Interesting features of the Delta and Omicron variants in the form of a unique 'order-disorder' transition are uncovered from these samples, as well as from their cumulative distribution function and scatter plots. This class of transitions might reveal the cumulative outcome of mutations on the spike protein. A salient feature of GenomeBits is the mapping of the nucleotide bases (A,T,C,G) into an alternating spin-like numerical sequence via a series having binary (0,1) indicators for each A,T,C,G. This leads to the derivation of a set of statistical distribution curves. Furthermore, the quantum-based extension of the GenomeBits model to an analogous probability measure is shown to identify properties of genome sequences as wavefunctions via a superposition of states. An association of the integral of the GenomeBits coding and a binding-like energy can, in principle, also be established. The relevance of these different results in bioinformatics is analyzed.