The SARS-CoV-2 virus, which is a major threat to human health, has undergone many mutations during the replication process due to errors in the replication steps and modifications in the structure of viral proteins. The XBB variant was identified for the first time in Singapore in the fall of 2022. It was then detected in other countries, including the United States, Canada, and the United Kingdom. We study the impact of sequence changes on Spike protein structure on the subvariants of XBB with particular attention to the velocity of variant diffusion and virus activity w.r.t. its diffusion. We examine the structural and functional distinctions of the variants in 3 different conformations: (i) Spike glycoprotein in complex with ACE2 (1-up state), (ii) Spike glycoprotein (closed-1 state) and (iii) S protein (open-1 state). We also estimate the transmissibility of the affinity binding between Spike proteins and ACE2. The market binding affinity observed in specific variants raises questions about the efficacy of current vaccines in controlling the spread of these variants. This work may be useful in devising strategies to manage the ongoing COVID-19 pandemic. To stay ahead of the virus evolution, further research and surveillance should be carried out to adjust public health measures accordingly.

Metabolomics has been increasingly utilized in studying host response to infections and under-standing the progression of multi-system disorders such as COVID-19. The analysis of metabo-lites in response to SARS-CoV-2 infection provides a snapshot of the endogenous host metabo-lism and its role in shaping the interaction with SARS-CoV-2. The current study investigated the metabolic signatures of mortality and severity in COVID-19 patients using a targeted metabo-lomics approach. Blood plasma concentrations were quantified through LC-MS using MxP Quant 500 kit. We utilized Kaplan-Meier survival analysis to investigate the correlation between various metabolic markers and patient outcomes. A comparison of survival rates between individuals with high levels of various metabolites and those with low levels showed statistically significant differences in survival outcomes. We further used four metabolic markers to develop a COVID-19 mortality risk model through the application of multiple machine learning methods. These metabolic predictors can be further validated as potential biomarkers to identify patients at risk of poor outcomes. Finally, integrating machine learning models in metabolome analysis of COVID-19 patients can improve our understanding of disease mortality by providing insight into the relationship between metabolites and survival probability, which can lead to the development of potential therapeutics and clinical risk models.

Title: Interstitial Lung Diseases and COVID19 Pneumonia

A document by Asma Albtoosh. Click on the document to view its contents.

Rationale. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) can provide precise analysis of a protein’s conformational dynamics across varied states, such as heat-denatured vs. native protein structures, localizing regions that are specifically affected by such conditional changes. Maximizing protein sequence coverage provides high confidence that regions of interest were located by HDX-MS, but one challenge for complete sequence coverage is N-glycosylation sites. The deuteration of peptides post-translationally modified by asparagine-bound glycans (glycopeptides) has not always been identified in previous reports of HDX-MS analyses, causing significant sequence coverage gaps in heavily glycosylated proteins and uncertainty in structural dynamics in many regions throughout a glycoprotein. Methods. We detected deuterated glycopeptides with a Tribrid Orbitrap Eclipse mass spectrometer performing data-dependent acquisition. An MS scan was used to identify precursor ions, if high-energy collision-induced dissociation (HCD) MS/MS of the precursor indicated oxonium ions diagnostic for complex glycans then electron transfer low-energy collision-induced dissociation (EThcD) MS/MS scans of the precursor identified the modified asparagine residue and the glycan’s mass. As in traditional HDX-MS the identified glycopeptides were then analyzed at the MS level in samples labeled with D 2O. Results. We report HDX-MS analysis of the SARS-CoV-2 spike protein ectodomain in its trimeric pre-fusion form, which has 22 predicted N-glycosylation sites per monomer, with and without heat treatment. We identified glycopeptides and calculated their average isotopic mass shifts from deuteration. Inclusion of the deuterated glycopeptides increased sequence coverage of spike ectodomain from 76% to 84%, demonstrated that glycopeptides had been deuterated, and improved confidence in results localizing structural re-arrangements. Conclusion. Inclusion of deuterated glycopeptides improves the analysis of the conformational dynamics of glycoproteins such as viral surface antigens and cellular receptors.

Respiratory syncytial virus is associated with lower respiratory tract infections. As several types and genotypes can circulate at the same time, genomic characterisation is important for timely epidemiological control and treatment measures. In the last 6 seasons (2017-2023), 191236 nasopharyngeal swabs were processed for respiratory viruses. The incidence of RSV reached 7% in the pre-pandemic season. RSV was most frequent in children under 5 years of age (12.6%), but was also significant in those over 70 years of age (5.63%). The measures taken to control SARS-Cov2 infection were useful for RSV control and the incidence decreased to 1.8%, but caused a change in the types. Pre-pandemic, the majority circulating types were RSV-B/RSV-B/RSV-A and in pandemic it was RSV-B/RSV-B. In the last season, RSV-B and RSV-A were detected in the same proportion. Genetic characterization showed three new clades. This has been taken into account in order to take the correct measures.

Background: There has been an increase in the number of patients with lung cancer who had previously contracted SARS-CoV-2 and currently require surgery. This study was to share the early postoperative outcomes in patients who underwent radical lung cancer surgery after early recovery of COVID-19 infection. Methods We retrospectively collected data for 99 patients who had undergone lung cancer surgery in our hospital during January 2022 and January 2023 (including the peak of the COVID-19 crisis）. The patients were divided into two groups according to the inclusion criteria and exclusion criteria. One of these included individuals with a history of SARS-CoV-2 infection. Perioperative and follow-up data at 30-day and 90-day were recorded. Results There were no statistical differences between groups (p > 0.05) in terms of their postoperative complications or 30-day and 90-day postoperative readmission rates. However, there were significant differences between groups (p < 0.05) in terms of their tumor sizes, pathological stages, total drainage volumes, drainage diversion times, and hospital stays. Conclusions The results of the present trial suggested that it is safe to implement radical curative lung cancer surgery in patients without pulmonary impairment and in the early stages (2–4 weeks) of recovery from SARS-CoV-2 infection.

The information on the microbiome’s human pathways and active members that can affect SARS-CoV-2 susceptibility and pathogenesis in the salivary proteome is very scarce. Here, we studied samples collected from April to June 2020 from unvaccinated patients. We compared 10 infected and hospitalized patients with severe (n=5) and moderate (n=5) Coronavirus Disease (COVID-19) with 10 uninfected individuals, including Non-COVID but susceptible individuals (n=5) and Non-COVID and non-susceptible healthcare workers with repeated high-risk exposures (n=5). By performing high-throughput proteomic profiling in saliva samples, we detected 226 unique differentially expressed (DE) human proteins between groups (q-value ≤0.05) out of 2721 unambiguously identified proteins (false discovery rate ≤1%). Major differences were observed between the Non-COVID vs the non-susceptible groups. Bioinformatics analysis of DE proteins revealed human proteomic signatures related to inflammatory responses, central cellular processes, and antiviral activity associated with saliva of SARS-CoV-2 infected patients (p-value ≤0.0004). Discriminatory biomarker signatures from human saliva include cystatins, protective molecules present in the oral cavity, calprotectins, involved in cell cycle progression, and histones, related to nucleosome functions. The expression level of two human proteins related to protein transport in the cytoplasm, named DYNC1 (p-value, 0.0021) and MAPRE1 (p-value, 0.047), correlated with angiotensin-converting enzyme 2 (ACE2) plasma activity. Finally, the proteomes of microorganisms present in the saliva samples showed 4 main microbial functional features related to ribosome functioning that are overrepresented in the infected group. Our study explores potential candidates involved in pathways implicated in SARS-CoV-2 susceptibility although further studies in larger cohorts will be necessary.

In the present era, healthcare systems grapple with substan- tial volumes of medical data. However, a significant portion of this data is marked by incompleteness, inconsistency, er- rors, and unsuitability for training Machine Learning (ML) or Deep Learning (DL) algorithms. This necessitates preprocess- ing the data to render it amenable to utilization by ML/DL al- gorithms. Medical datasets predominantly feature two types of attributes: numerical and categorical values. The conver- sion of categorical features into numerical vectors is a crucial step in preparing the data for ML/DL algorithms, known as Feature Engineering (FE) based categorical encoding. Con- ventional and straightforward encoding of categorical fea- tures, termed one-hot encoding, generates multiple columns, thereby transforming data from a lower-dimensional to a higher- dimensional space. This approach poses challenges, includ- ing increased memory requirements due to the proliferation of columns. Considering these issues, this research proposes an encoding technique named “Weight of Evidence with En- tity Embedding” (WoEEE). The WoEEE approach bolsters the predictive capabilities of ML/DL algorithms by calculating the weight of evidence and concurrently mitigates dimension- ality issues. To empirically validate the proposed method, it is tested on six diverse datasets: Breast Cancer, Hospital Readmission, Vadu, Covid-19, Stroke, and Heartstatlog. Four distinct ML/DL algorithms—Decision Tree (DT), Random For- est (RF), Logistic Regression (LR), and a simple Feed-forward Neural Network (NN)— are employed for testing. The re- sults obtained demonstrate that the WoEEE approach yields an average improvement of 11.18%, 10.37%, 5.83%, 7.58%, 7.83%, and 6.83% across all combinations of datasets, classi- fiers, and encoding methods. Furthermore, an Anova test is performed to confirm the effectiveness of WoEEE in encod- ing categorical data, especially for tasks involving binary clas- sification. This enhances the treatment of categorical data in ML and data analytics scenarios. Overall, WoEEE shows po- tential as a valuable approach for categorical data encoding, making a positive contribution to the creation of effective techniques for handling this type of data in real-world appli- cations.

A document by Hatem Alahwal. Click on the document to view its contents.

Nonpharmaceutical interventions (NPIs) against coronavirus disease 2019 (COVID-19) reduced the prevalence of coronavirus among children and influenced the transmission of other viruses. This study investigates the impact of NPIs on human enterovirus (HEV) among children in Hangzhou, China. We collected and analyzed the laboratory results and clinical data of children diagnosed with hand, foot, and mouth disease (HFMD) or herpangina (HA) during the following periods: pre-COVID-19 (January 2019 to December 2019), COVID-19 pandemic (January 2020 to December 2022), and post-COVID-19 (January to August 2023). A total of 38,582 specimens that met the inclusion criteria were enrolled, of which 1,777 (5.58%) tested positive for enterovirus. In comparison to the pre-COVID-19 period, which had 695 (5.63%) HEV-positive specimens, the numbers dramatically decreased to 69 (1.19%), 398 (5.12%), and 112 (1.58%) in 2020, 2021, and 2022, respectively, but significantly increased to 503 (9.00%) in 2023. Seasonal peaks of infections occurred between May and August each year, with positive rates of 10.58%, 25.27%, 31.74%, and 10.97%, respectively. Notably, June and July accounted for half of all cases, with a rate of 57.01%. The difference in the positive rates of HEV infection between males and females was statistically significant (P<0.005), with 5.12% (1,084/21,176) and 4.43% (693/15,629) testing positive, respectively, resulting in a male to female ratio of 1.56:1. Among the same age groups, children aged 3-5 years and 5-7 years had the highest positive rates at 11.03% (342/3,102) and 10.03% (205/2,024), respectively, after synthesizing five years of data. The detection rate of HEV-positive cases increased with age, but after the age of 7, the rate declined. The detected types of HEV indicated that enterovirus 71 (EV-A71) and coxsackievirus A16 (CV-A16) are no longer the two common pathogens causing HFMD and HA. In conclusion, NPIs for COVID-19 are highly effective in reducing the transmission of HEV. However, the relaxation of NPIs results in a resurgence of HEVs, surpassing prepandemic levels. Active awareness and surveillance of the epidemiological characteristics of HEV are essential for preventing, controlling, and managing the development of HFMD and HA, as well as contributing to the development of a multivalent HFMD vaccine.

An extensive arterial thrombosis with lower limb ischemia in a COVID-19 patient: a case report.Johary Andriamamonjisoa Andriamizanaka1, Etienne Rakotomijoro2, Volatiana Andriananja3, Mihaja Raberahona4, Radonirina Lazasoa Andrianasolo5, Rivonirina Andry Rakotoarivelo6, Jean de Dieu Randria Mamy7

A document by Roshan Bhandari. Click on the document to view its contents.

Left Ventricular Thrombus Formation in aCOVID-19 Patient with a Complex Course of Pericarditis and Myocardial Infarction.

Background Understanding the cellular host factors that promote and inhibit viral entry is important for identifying viral countermeasures. CRISPR whole genome screens can be used to rapidly discover host factors that contribute to or impair viral entry. However, when using the live viruses and cellular lethality for selection, these screens can identify an overwhelming number of genes without specificity for the stage of the viral infection cycle. New screening methods are needed to identify host machinery contributing to specific steps of viral infection. Here, we developed a CRISPR whole genome screen and counter screen strategy based on a pseudoviral platform that allowed identification of genes specific to SARS-CoV-2 spike and vesicular stomatitis virus glycoprotein VSV-G mediated entry. Methods To focus the screen onto the entry step, we used non-lytic fluorescent reporters in combination with a comparative counter screen strategy to distinguish host genes affecting the pseudoviral reporter from those unique to envelope-mediated entry. Screening of SARS-CoV-2 spike and VSV-G on the same lentiviral pseudovirus allowed identification of entry-specific genes relative to genes associated with retro-transcription, integration, and reporter expression from the lentiviral pseudovirus. Second, a Cre-Gag fusion protein in the pseudovirus was used to bypass retro-transcription and integration by directly activating a floxed GFP reporter upon entry to reduce the number of gene hits and increase specificity for viral entry. Results Our approach correctly identified SARS-CoV-2 and VSV-G receptors ACE2 and LDLR, respectively and distinguished genes associated with retroviral reporter expression from envelope-mediated entry. Moreover, the CRE-Gag fusion/flox reporter increased the screen specificity for viral entry associated genes. Validation of a few hits demonstrates that this approach distinguishes envelope-specific host factors from genes affecting reporter expression. Conclusion Overall, this approach provides a new strategy for identifying host genes influencing viral entry without the confounding complexity of live-viral screens which produce long gene lists associated with all aspects of viral pathogenesis and replication. This approach provides a pathway for increasing the specificity of CRISPR whole genome screens for identifying host genes contributing to specific steps in viral infection.

Background: While risk of infection with SARS-CoV-2 is low to pregnant women and the fetus, there is increased risk of preterm birth and admission into ICU. The fetus is relatively protected against infection, with cases of vertical transmission being rare. Various receptors and accessory molecules which are known to regulate SARS-CoV-2 viral entry into host cells have soluble versions which could act as decoy traps. Following on from our previous findings regarding the abundance of some of these molecules in breast milk and amniotic fluid, we show the maternal-fetal interface is also rich in these molecules and how systemically they can be differentially expressed between males, non-pregnant females, pregnant females, and neonates. Methods: Archived placental samples from before the pandemic, and blood from participants in late 2020 who had not tested positive for COVID-19 were analysed for the presence of receptors by ELISA, immunohistochemistry, immunoblotting and flow cytometry. Results: We have confirmed that the placenta and membranes are particularly rich in CD26 and CD147 and gone on to consider if it is possible that shedding of these molecules into the maternal and fetal circulation occurs. However, except for sCD147 in umbilical cord plasma compared to all groups and sNRP-1 in pregnant women in comparison to men and neonates, the expression of soluble forms of these molecules is primarily consistent between the groups studied here. Conclusion: The maternal-fetal interface has potential mechanisms to protect the fetus from contracting SARS-CoV-2 by being rich with soluble versions of receptors involved in host cell entry of the virus, thereby limiting infection of host cells.

Purpose Although monoclonal antibodies specific to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are known, information about the B-cell receptor (BCR) repertoire and its change in patients during COVID-19 disease progression is underreported. Methods We used immunoglobulin heavy chain (IGH) variable region (IGHV) spectratyping and next-generation sequencing of peripheral blood B-cell genomic DNA collected at multiple time points during disease evolution to study B-cell response to SARS-CoV-2 infection in 14 individuals with acute COVID-19. Results We found a broad distribution of responding B-cell clones. The IGH gene usage was not significantly skewed but frequencies of individual IGH genes changed repeatedly. We found predominant usage of unmutated and low mutation-loaded IGHV rearrangements characterizing naïve and extrafollicular B-cells among the majority of expanded peripheral B-cell clonal lineages at most tested time points in most patients. IGH rearrangement usage showed no apparent relation to anti-SARS-CoV-2 antibody titers. Some patients demonstrated mono/oligoclonal populations carrying highly mutated IGHV rearrangements indicating antigen experience at some of the time points tested, including even before anti-SARS-CoV-2 antibodies were detected. Conclusion We present evidence demonstrating that the B-cell response to SARS-CoV-2 is individual and includes different lineages of B-cells at various time points during COVID-19 progression.

Background: CFTR-Related Metabolic Syndrome/ Cystic Fibrosis Screen Positive, Inconclusive Diagnosis (CRMS/CFSPID) is the diagnosis in infants who have a positive Cystic Fibrosis (CF) newborn screen (NBS), 2 CF-causing mutations, and borderline or normal sweat test. NY State implemented a new CF NBS algorithm (IRT-DNA-SEQ) in December 2017 with significant improvement in positive predictive value. This algorithm also resulted in detection of more CRMS cases. For these infants repeat sweat testing is recommended at 6, 12, and 18 months to monitor for risk of rising sweat chloride over time and 6-48% of infants with CRMS develop clinical features suggestive of CF. Infants with CRMS and sweat test results in the normal range are often lost to follow and parents were unwilling to return for recommended repeat sweat testing during the statewide lockdown during the peak of COVID-19 pandemic. We recognized the practice gap exacerbated during the pandemic and underscore the importance of establishing a medical home in a CF Center for longitudinal care. Methods: Retrospective analysis of infants with CRMS from December 2017 to December 2020 were collected by 10 NY CF Centers and the NBS program with NYU as the data collection and statistical analysis site. Infants with CRMS without repeat sweat chloride testing at 6 months of age were considered lost to follow up, and their parents were contacted via mail or telephone. Families completed a questionnaire that was developed with the assistance of CF Voice to evaluate parental understanding of CRMS and the recommendation for repeat sweat chloride testing. Primary care providers (PCPs) caring for infants with CRMS were also contacted and provided educational materials about CRMS. A subcommittee of CF Center Directors met to develop a statewide approach for the management of infants with CRMS. Results: Of 350 infants diagnosed with CRMS, 179 (51.1%) infants were lost to follow up. As an outcome of this QI effort 31 (17.3%) were scheduled for repeat sweat tests and follow up at CF Centers. This QI effort explored the knowledge and practice gap among PCPs with limited understanding of the implications of a CRMS diagnosis. CF Center Directors subcommittee issued a consensus statement regarding evaluation and follow up for infants with CRMS in NY. Conclusions: This QI effort effectively recaptured infants with CRMS previously lost to follow up. Consensus recommendations for CRMS include annual visits until 2-6 years of age for repeat sweat testing and in adolescence to educate the patient about clinical and reproductive implications of CRMS.

Background: Accurate prediction of SARS-CoV-2 severity remains a challenge. Torque Teno Virus (TTV), recognized as a surrogate marker for cellular immunity in solid organ transplant recipients, holds potential for assessing infection outcomes. Objectives: We investigated whether quantifying TTV in nasopharyngeal samples upon emergency ward (ED) admission could serve as an early predictor of SARS-CoV-2 severity. Study design: Retrospective single-center study in the ED of Saint-Louis Hospital in Paris, France. TTV DNA was quantified in nasopharyngeal swab samples collected for SARS-CoV-2 testing. Results: Among 295 SARS-CoV-2 infected patients, 92 returned home, 160 were admitted to medical wards, and 43 to the intensive care unit. Among 295 SARS-CoV-2 patients, 92 were discharged, 160 hospitalized, and 43 admitted to the intensive care unit (ICU). Elevated TTV loads were observed in ICU patients (Median: 3.02 log copies/mL, interquartile range [IQR]: 2.215-3.825), exceeding those in discharged (2.215, [0; 2.962]) or hospitalized patients (2.24, [0; 3.29]) (p=0.006). Multivariate analysis identified diabetes, obesity, hepatitis, fever, dyspnea, oxygen requirement, and TTV load as predictors of ICU admission. A 2.91 log 10 copies/mL TTV threshold independently predicted ICU admission. Conclusion: Nasopharyngeal TTV quantification in SARS-CoV-2 infected patients is linked to the likelihood of ICU admission and might reflect respiratory immunosuppression.

Aim: The influence of human factors on safety in healthcare settings is well established, with targeted interventions reducing risk and enhancing team performance. In experimental and early phase clinical research participant safety is paramount and safeguarded by guidelines, protocolised care and staff training, however the real-world interaction and implementation of these risk-mitigating measures has never been subjected to formal system-based assessment. Methods: Independent structured observations, systematic review of study documents, and interviews and focus groups were used to collate data on three key tasks undertaken in a Clinical Research Facilty (CRF) during a SARS CoV-2 controlled human infection model (CHIM) study. The Systems Engineering Initiative for Patient Safety (SEIPS) was employed to analyse and categorise findings, and develop recommendations for safety interventions. Results: High levels of team functioning and a clear focus on participant safety were evident throughout the study. Despite this, latent risks in both study-specific and CRF work systems were identified in all four SEIPS domains (people, environment, tasks and tools). 14 actionable recommendations were generated collaboratively. These included inter-organisation and inter-study standardisation, optimised checklists for safety critical tasks, and use of simulation for team training and exploration of work systems. Conclusion: This pioneering application of human factors techniques to analyse work systems during the conduct of research in a CRF revealed risks unidentified by routine review and appraisal, and despite international guideline adherence. SEIPS may aid categorisation of system problems and the formulation of recommendations that reduce risk and mitigate potential harm applicable across a trials portfolio

A document by hai hong Lin. Click on the document to view its contents.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) enters the host cell by binding to angiotensin-converting enzyme 2 (ACE2). While evolutionarily conserved, ACE2 glycoproteins differ across various species and differential interactions with Spike (S) glycoproteins of SARS-CoV-2 viruses impact species specificity. Reverse zoonoses led to SARS-CoV-2 outbreaks on multiple American mink ( Mustela vison) farms during the pandemic and gave rise to mink-associated S substitutions known for transmissibility between mink and zoonotic transmission to humans. In this study, we used bio-layer interferometry (BLI) to discern the differences in binding affinity between multiple human and mink-derived S glycoproteins of SARS-CoV-2 and their respective ACE2 glycoproteins. Further, we conducted a structural analysis of a mink variant S glycoprotein and American mink ACE2 (mvACE2) using cryo-electron microscopy (cryo-EM), revealing four distinct conformations. We discovered a novel intermediary conformation where the mvACE2 glycoprotein is bound to the receptor-binding domain (RBD) of the S glycoprotein in a “down” position, approximately 34° lower than previously reported “up” RBD. Finally, we compared residue interactions in the S-ACE2 complex interface of S glycoprotein conformations with varying RBD orientations. These findings provide valuable insights into the molecular mechanisms of SARS-CoV-2 entry.

A document by Harkesh Arora. Click on the document to view its contents.

Background: A proportion of the convalescent SARS-CoV-2 pediatric population presents nonspecific symptoms, mental health problems and a reduction in quality of life similar to myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and long COVID-19 symptomatic. However, data regarding its clinical manifestation and immune mechanisms are currently scarce. Methods: In this study, we perform a comprehensive clinical and immunological profiling of 17 convalescent COVID-19 children with post-acute COVID-19 sequelae (PASC) manifestation and 13 convalescent children without PASC manifestation. A detailed medical history, blood and instrumental tests and physical examination were obtained from all patients. SARS-CoV-2 reactive T cell response was analyzed via multiparametric flowcytometry and the humoral immunity was addressed via pseudovirus neutralization and ELISA assay. Results: The most common PASC symptoms were shortness of breath/exercise intolerance, paresthesia, smell/taste disturbance, chest pain, dyspnea, headache and lack of concentration. Blood count and clinical chemistry showed no statistical differences among the study groups. We detected higher frequencies of spike (S) reactive CD4+ and CD8+ T cells among the PASC study group, characterized by TNFα and IFNγ production and low functional avidity. CRP levels are positively correlated with IFNγ producing reactive CD8+ T cells. Conclusions: Our data might indicate a possible involvement of a persistent cellular inflammatory response triggered by SARS-CoV-2 in the development of the observed sequelae in pediatric PASC. These results may have implications on future therapeutic and prevention strategies.