Evidence from whole genome sequencing of aerosol transmission of SARS-CoV-2 almost 5 hours after hospital room turnover.

Experimental evidence suggests that Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) remains viable within aerosols with a half-life of approximately 3 hours; however, it remains unclear how long airborne SARS-CoV-2 can transmit infection. Whole genome sequencing during an outbreak suggested in-room transmission of SARS-CoV-2 to two patients admitted nearly 2 and 5 hours, respectively, after discharge of an asymptomatic infected patient. These findings suggest that airborne SARS-CoV-2 may transmit infection for over 4 hours, even in a hospital setting.

Trends in antibiotic prescribing in primary care out-of-hours doctors' services in Ireland.

Background: Infections are a common reason for patient consultation in out-of-hours (OOH) doctors' services. Surveillance of antibiotic prescribing in OOH settings is important to develop tailored antimicrobial stewardship (AMS) interventions. Objectives: To evaluate antibiotic prescribing patterns in OOH services in the Cork Kerry region, Ireland to inform future AMS interventions. Methods: A retrospective, observational cohort study was conducted of all oral antibiotic prescriptions in OOH doctors' consultations between 1 December 2019 and 31 December 2021 in the region. Data were gathered on age, gender, date and time of consultation, consultation method (in person, remote), antibiotic and its indication. Data were analysed using Microsoft Excel v.2018 and SPSS v.28. Results: Overall, 17% (69 017 of 406 812) of the OOH doctors' consultations resulted in an antibiotic prescription during the study period. This varied from 31% of OOH consultations in December 2019 to less than 2% of OOH consultations in April 2020. Of the antibiotics prescribed, 21% were for children under 6 years old. Respiratory tract infections (RTIs) were the most common indication for antibiotics (59%). Amoxicillin was the most commonly prescribed antibiotic (40% of all prescriptions). Red (reserved) antibiotics accounted for 19% of all prescriptions. During the COVID-19 pandemic period of the study, 66% of 49 421 of antibiotic prescriptions were issued from remote consultations. Conclusions: Low antibiotic prescribing levels during the early stages of the pandemic were not sustained. Antibiotic prescriptions from remote consultations were common. A key opportunity for AMS is addressing the volume of antibiotic prescribing for RTIs, particularly in children.

Correlation of a commercial platform's results with post-vaccination SARS-CoV-2 neutralizing antibody response and clinical host factors.

INTRODUCTION: The objective of this study was to describe the correlation between the commercially available assay for anti-S1/RBD IgG and protective serum neutralizing antibodies (nAb) against SARS-CoV-2 in an adult population after SARS-CoV-2 vaccination, and determine if clinical variables impact this correlation. METHODS: We measured IgG anti-S1/RBD using the IgG-II CMIA assay and nAb IC50 values against SARS-CoV-2 WA-1 in sera serially collected post-mRNA vaccination in veterans and healthcare workers of the Veterans Affairs Connecticut Healthcare System (VACHS) between December 2020 and January 2022. The correlation between IgG and IC50 was measured using Pearson correlation. Clinical variables (age, sex, race, ethnicity, prior COVID infection defined by RT-PCR, history of malignancy, estimated glomerular filtration rate (GFR calculated using CKD-EPI equation) were collected by manual chart review. The impact of these clinical variables on the IgG-nAb correlation was analyzed first with univariable regression. Variables with a significance of p < 0.15 were analyzed with forward stepwise regression analysis. RESULTS: From 127 sera samples in 100 unique subjects (age 20-93 years; mean 63.83; SD 15.63; 29% female; 67% White), we found a robust correlation between IgG anti-S1/RBD and nAb IC50 (R2 = 0.83, R2adj = 0.70, p < 0.0001). Race, ethnicity, and a history of malignancy were not significant on univariable analysis. GFR (p < 0.05) and prior COVID infection (p < 0.001) had a significant impact on the correlation between IgG anti-S1/RBD and nAb IC50. Age (p = 0.06) and sex (p = 0.07) trended towards significance on univariable analysis, but were not significant on multivariable regression. CONCLUSIONS: There was a strong correlation between IgG anti-S1/RBD and nAb IC50 after SARS-CoV-2 vaccination. Clinical comorbidities, such as prior COVID infection and renal function, impacted this correlation. These results may assist the prediction of post-vaccination immune protection in clinical settings using cost-effective commercial platforms.

Search of a genomic sequence database for potential novel blood group antigens: Investigation into why some amino acid substitutions are not immunogenic.

BACKGROUND: Polypeptide blood group antigens are typically identified through investigation of the antibodies they induce. Human genome sequence databases are a new tool to identify AA substitutions that potentially create blood group antigens. STUDY DESIGN AND METHODS: The Erythrogene genomic sequence database was searched for missense mutations not known to be blood group antigens in the extracellular domains of selected RBC proteins in European populations. Any mutations found with prevalence of 1%-90% and not known to have induced antibodies in transfusion practice were analyzed using protein structural analysis and epitope prediction programs to determine why they apparently lack immunogenicity. RESULTS: Thirteen missense mutations not known to create blood group antigens were identified in the extracellular domains of Kell, BCAM, and RhD proteins, but not in RhCE, Urea Transporter 1 (Kidd), Atypical Chemokine Receptor 1 (Duffy), glycophorin A or glycophorin B. While 11 of the 13 mutations had low prevalence (<1%), a Kell Ser726Pro substitution and a BCAM Val196Ile substitution had predicted phenotype prevalences of 43.2% and 5.7%, respectively. Ser726Pro had multiple properties of a linear B-cell epitope, but possible suboptimal protein location for B-cell receptor binding and limited T-cell epitope possibilities. Val196Ile was not predicted to be in a linear B-cell epitope. CONCLUSION: Multiple potential new blood group antigens of low prevalence were identified. Whether they are antigenic remains to be determined. Two higher prevalence variants in Kell and BCAM are unlikely antigens, otherwise their antibodies presumably would already have been identified. Possible reasons for their poor immunogenicity were identified.

Relationship between B-cell epitope structural properties and the immunogenicity of blood group antigens: Outlier properties of the Kell K1 antigen.

BACKGROUND: The immunogenicities of polypeptide blood group antigens vary, despite most being created by single amino acid (AA) substitutions. To study the basis of these differences, we employed an immunoinformatics approach to determine whether AA substitution sites of blood group antigens have structural features typical of B-cell epitopes and whether the extent of B-cell epitope properties is positively related to immunogenicity. STUDY DESIGN AND METHODS: Fifteen structural property prediction programs were used to determine the likelihood of ß-turns, surface accessibility, flexibility, hydrophilicity, particular AA composition and AA pairs, and other B-cell epitope properties at AA substitution sites of polypeptide blood group antigens. RESULTS: AA substitution sites of Lua , Jka , E, c, M, Fya , C, and S were each located in regions with at least two structural features typical of B-cell epitopes. The substitution site of K, the most immunogenic non-ABO/D antigen, scored the lowest for most B-cell epitope properties and was the only one not predicted to be part of a linear B-cell epitope. The most immunogenic antigens studied (K, Jka , Lua , E) had B-cell epitope structural properties determined by the fewest programs; the least immunogenic antigens (e.g., Fya , S, C, c) had B-cell epitope properties according to the most programs. DISCUSSION: Counter to prediction, the immunogenicity of polypeptide blood group antigens was not positively related to B-cell epitope structural features present at their AA-substitution sites. Instead, it tended to be negatively related. The AA-substitution site of the most immunogenic non-ABO/D antigen, K, had the least B-cell epitope features.

Clinical and virologic factors associated with outcomes of COVID-19 before and after vaccination among Veterans: Retrospective analysis from six New England states.

We aimed to characterize clinical and demographic factors affecting clinical outcomes of COVID-19 and describe viral epidemiology among unvaccinated Veterans in New England. Veterans infected with COVID-19 in Veterans Administration healthcare systems in six New England states from April 8, 2020, to September 2, 2021, were correlated with outcomes of 30-day mortality, nonpsychiatric hospitalization, and intensive care unit admission (ICU-care). We sequenced 827 viral genomes. Of 3950 Veterans with COVID-19 before full vaccination, 81% were White, 8% were women, and the mean age was 60 years. Overall, 19% of Veterans required hospitalization, 2.8% required ICU care, and 4.9% died. In this largely male and older cohort, poor outcomes correlated with increasing age. Most New England Veterans (>97%) were infected with B.1 sublineages with the D614G mutation in 2020 and early 2021. B.1.617.2 lineage (68%) predominated after July 2021.

Selective Delivery of Clinically Approved Tubulin Binding Agents through Covalent Conjugation to an Active Targeting Moiety.

The efficacy and tolerability of tubulin binding agents are hampered by their low specificity for cancer cells like most clinically used anticancer agents. To improve specificity, tubulin binding agents have been covalently conjugated to agents that target cancer cells to give actively targeted drug conjugates. These conjugates are designed to increase uptake of the drug by cancer cells while having limited uptake by normal cells, thereby improving efficacy and tolerability. Approaches used include an attachment to small molecules, polysaccharides, peptides, proteins, and antibodies that exploit the overexpression of receptors for these substances. Antibody targeted strategies have been the most successful to date, with six such examples having gained clinical approval. Many other conjugate types, especially those targeting the folate receptor, have shown promising efficacy and toxicity profiles in pre-clinical models and in early-stage clinical studies. Presented herein is a discussion of the success or otherwise of the recent strategies used to form these actively targeted conjugates.

Career destinations of graduates from a medical school with an 18-week longitudinal integrated clerkship in general practice: a survey of alumni 6 to 8 years after graduation.

BACKGROUND: There is a worldwide recruitment and retention crisis in general practice. Workforce planning has identified the need to train more general practitioners as an urgent priority. Exposure of medical students to general practice as part of the formal and hidden curriculum, the use of longitudinal integrated clerkships, and positive experiences and role models in general practice are all thought to be contributing factors to doctors choosing careers in general practice. AIM: The aim of this study was to identify career destinations of medical school graduates in a medical school with an 18-week longitudinal integrated clerkship in general practice. DESIGN AND SETTING: This study was conducted in a single graduate entry medical school at the University of Limerick, Ireland. PARTICIPANTS: Medical school alumni 6-8 years after graduation. METHOD: A survey of graduating cohorts of the medical school from 2011 to 2013 was conducted through email and telephone. RESULTS: There were a total of 175 alumni for the period 2011 to 2013. Data was collected on 92% (161/175) through an online survey, follow-up email and telephone interview, and was triangulated with searches of professional registration databases and information from key informants. Between 6 and 8 years after graduation, a total of 43% of alumni were engaged in general practice as a career. CONCLUSION: The reform of the delivery of general practice within medical school curricula should be considered by medical schools, curriculum designers and policy-makers as part of an overall strategy to address the recruitment and retention of general practitioners as part of the global healthcare workforce.

SARS-CoV-2 detection in setting of viral swabs scarcity: Are MRSA swabs and viral swabs equivalent?

BACKGROUND: The global pandemic of Severe Acute Respiratory Syndrome-Related Coronavirus 2 (SARS-CoV2) has resulted in unprecedented challenges for healthcare systems. One barrier to widespread testing has been a paucity of traditional respiratory viral swab collection kits relative to the demand. Whether other sample collection kits, such as widely available MRSA nasal swabs can be used to detect SARS-CoV-2 is unknown. METHODS: We compared simultaneous nasal MRSA swabs (COPAN ESwabs ® 480C flocked nasal swab in 1mL of liquid Amies medium) and virals wabs (BD H192(07) flexible mini-tip flocked nasopharyngeal swabs in 3mL Universal Transport Medium) for SARS-CoV-2 PCR testing using Simplexa COVID-19 Direct assay on patients over a 4-day period. When the results were discordant, the viral swab sample was run again on the Cepheid Xpert Xpress ® SARS-CoV-2 assay. RESULTS: Of the 81 included samples, there were 19 positives and 62 negatives in viral media and 18 positives and 63 negative in the MRSA swabs. Amongst all included samples, there was concordance between the COPAN ESwabs ® 480C and the viral swabs in 78 (96.3%). CONCLUSION: We found a high rate of concordance in test results between COPAN ESwabs ® 480C in Amies solution and BD H192(07) nasopharyngeal swabs in in 3 mL of Universal Viral Transport medium viral media. Clinicians and laboratories should feel better informed and assured using COPAN ESwabs ® 480C to help in the diagnosis of COVID-19.

ß-Glucan extracts from the same edible shiitake mushroom Lentinus edodes produce differential in-vitro immunomodulatory and pulmonary cytoprotective effects - Implications for coronavirus disease (COVID-19) immunotherapies.

Coronavirus pneumonia is accompanied by rapid virus replication, where a large number of inflammatory cell infiltration and cytokine storm may lead to acute lung injury, acute respiratory distress syndrome (ARDS) and death. The uncontrolled release of pro-inflammatory cytokines, including interleukin (IL)-1ß and IL-6, is associated with ARDS. This constituted the first study to report on the variability in physicochemical properties of ß-glucans extracts from the same edible mushroom Lentinus edodes on the reduction of these pro-inflammatory cytokines and oxidative stress. Specifically, the impact on the immunomodulatory and cytoprotective properties of our novel in 'house' (IH-Lentinan, IHL) and a commercial (Carbosynth-Lentinan, CL) Lentinan extract were investigated using in vitro models of lung injury and macrophage phagocytosis. CL comprised higher amounts of α-glucans and correspondingly less ß-glucans. The two lentinan extracts demonstrated varying immunomodulatory activities. Both Lentinan extracts reduced cytokine-induced NF-κB activation in human alveolar epithelial A549 cells, with the IHL extract proving more effective at lower doses. In contrast, in activated THP-1 derived macrophages, the CL extract more effectively attenuated pro-inflammatory cytokine production (TNF-α, IL-8, IL-2, IL-6, IL-22) as well as TGF-ß and IL-10. The CL extract attenuated oxidative stress-induced early apoptosis, while the IHL extract attenuated late apoptosis. Our findings demonstrate significant physicochemical differences between Lentinan extracts, which produce differential in vitro immunomodulatory and pulmonary cytoprotective effects that may also have positive relevance to candidate COVID-19 therapeutics targeting cytokine storm.

More than coffee - a World Café to explore enablers of pharmacy practice research.

BACKGROUND: Pharmacists are in demand now more than ever to provide high-quality expertise about the effectiveness, safety and use of medications. Amidst an increasingly complex and costly healthcare system, policy makers need robust evidence to justify public spending on pharmacy services. Research on the impact of existing and emerging pharmacy practices is required. OBJECTIVE: To explore barriers and opportunities to enhance research among pharmacists in Ireland utilising a World Café methodology. METHODS: A pharmacy research discussion day was held in November 2018, open to all pharmacists in Ireland. A World Café methodology was utilised as a mechanism to facilitate group discussions about pharmacy practice research. RESULTS: Discussions with 63 attendees identified four themes and seventeen subthemes. The four themes were challenges undertaking research, research motivations, leadership and training. Subthemes included robust evidence, clinical, economic and societal outcomes, alignment with national and international health system priorities, need for incentives from professional training bodies, competitive business model and embed within schools of pharmacy. CONCLUSIONS: The most commonly discussed barriers inhibiting research were workload, technology limitations and financial considerations. Organisational leadership to prioritise and coordinate research efforts, training to build research capacity, building on existing examples of excellence and initiation of bottom-up community-based research projects were identified in our study as opportunities to enhance pharmacist involvement in research and ultimately patient health outcomes.

The University of Limerick Education and Research Network for General Practice (ULEARN-GP): practice characteristics and general practitioner perspectives.

BACKGROUND: A well-functioning general practice sector that has a strong research component is recognised as a key foundation of any modern health system. General practitioners (GPs) are more likely to collaborate in research if they are part of an established research network. The primary aims of this study are to describe Ireland's newest general practice-based research network and to analyse the perspectives of the network's members on research engagement. METHOD: A survey was sent to all GPs participating in the network in order to document practice characteristics so that this research network's profile could be compared to other national profiles of Irish general practice. In depth interviews were then conducted and analysed thematically to explore the experiences and views of a selection of these GPs on research engagement. RESULTS: All 134 GPs responded to the survey. Practices have similar characteristics to the national profile in terms of location, size, computerisation, type of premises and out of hours arrangements. Twenty-two GPs were interviewed and the resulting data was categorised into subthemes and four related overarching themes: GPs described catalysts for research in their practices, the need for coherence in how research is understood in this context, systems failures, whereby the current health system design is prohibitive of GP participation and aspirations for a better future. CONCLUSION: This study has demonstrated that the research network under examination is representative of current trends in Irish general practice. It has elucidated a better understanding of factors that need to be addressed in order to encourage more GPs to engage in the research process.

Relationship of epitope glycosylation and other properties of blood group proteins to the immunogenicity of blood group antigens.

BACKGROUND: The intrinsic properties of polypeptide blood group antigens that determine their relative immunogenicities are unknown. Because size, composition, charge, dose, and epitope glycosylation affect the immunogenicity of other polypeptides, we examined whether similar properties were related to the immunogenicity of blood group antigens. STUDY DESIGN AND METHODS: Amino acid (AA) sequences of antithetical blood group antigens were searched for N- and O-glycosylation sites. Regression analysis was carried out to determine whether blood group protein properties, including total and ectodomain size, red blood cell (RBC) antigen site density, number of mismatched AAs between an antigen and its closest homolog, and differences in mass, charge, and hydrophobicity of the mismatched AAs, were related to immunogenicity. RESULTS: The immunogenicities of non-RhD polypeptide antigens were directly related to the total and ectodomain sizes of their carrier proteins. A negative power relationship existed between RBC antigen site density and immunogenicity, such that the most immunogenic antigens had the lowest site density. The strong immunogenicity of RhD was related to the number of AA mismatches between RhD and RhCE, to their cumulative hydrophobicity and electrostatic mismatch scores, and the cumulative AA mass difference. No N- or O-glycosylation differences were predicted for antithetical or homologous antigens, other than a previously known N-glycosylation difference between K and k. CONCLUSION: Epitope glycosylation appeared not to be a determinant of immunogenicity for blood group antigens, except possibly for K. The immunogenicity of blood group antigens was positively related to total and ectodomain sizes of blood group proteins and negatively related to antigen site density. Such findings should be considered hypothesis generating for future, more definitive studies.

Structural and functional impacts of amino acid substitutions that create blood group antigens: implications for immunogenicity.

BACKGROUND: The immunogenicities of polypeptide blood group antigens vary widely. One possible determinant of immunogenicity is antigenic foreignness. The goal was to employ alternative ways of assessing foreignness and determine whether foreignness was related to immunogenicity. STUDY DESIGN AND METHODS: Foreignness was assessed as the extent of protein functional disruption caused by the exofacial amino acid (AA) substitutions that create blood group antigens, using AA substitution prediction algorithms such as Meta-SNP and according to whether those substitutions were radical or conservative. RESULTS: AA substitutions that create the most immunogenic antigens had the highest Meta-SNP scores, predictive of greater protein structure and function changes. Four of the 11 exofacial AAs that distinguish the most immunogenic antigen, RhD, from RhCE, and substitutions creating four of the five next most immunogenic antigens had the highest Meta-SNP scores (0.293-0.649). Excluding the outlier Jka , the mean Meta-SNP score of the four most immunogenic non-RhD antigens (K, Lua , E, c) was 3.7-fold higher than the mean of the four least immunogenic (M, Fya , C, S), 0.459 versus 0.123 (p = 0.0026). Regression analysis revealed a relationship between immunogenicity and Meta-SNP score (R2 = 0.953). Actual protein functional disruption was predicted for the AA substitution creating the E antigen. An AA cluster at Positions 350, 353, and 354 of RhD was unique, containing radical substitutions according to two classification schemes and relatively high Meta-SNP scores (0.351-0.432). CONCLUSION: The immunogenicity of blood group antigens was related to the functional disruption caused by the AA substitutions that create the antigens, as measured by Meta-SNP score.

Detection rate of blood group alloimmunization based on real-world testing practices and kinetics of antibody induction and evanescence.

BACKGROUND: Failure to detect non-ABO blood group alloantibodies places patients at risk for hemolytic reactions. Suboptimal alloantibody detection could result from posttransfusion testing performed too early, too late, or not at all. Testing performed too early may precede antibody induction, while testing performed too late could miss antibodies that have evanesced. Taking these factors into account, our goal was to determine the percentage of alloantibodies detected with real-world testing practices. STUDY DESIGN AND METHODS: The alloantibody detection rate in a general hospital setting was determined based on the frequency and timing of antibody testing after red blood cell (RBC) transfusions and rates of antibody induction and evanescence. Intervals to follow up testing after RBC transfusions (n = 561 RBC units in 100 random patients) were determined retrospectively. Best-fit lines and equations for antibody induction and evanescence were computed on previously published data. RESULTS: Nearly half (271/561; 48.3%) of RBC infusions had either no follow-up antibody screen or testing too soon (<30 days) after transfusion to detect alloimmunization. Of the remaining RBC units, 10.3% (58/561) had follow-up testing 30 to 112 days posttransfusion, 28.7% (161/561) were followed up at more than 112 days, and 12.7% (71/561) were tested at both 30 to 112 days and more than 112 days. By inputting these timing data into best-fit line equations for antibody induction and evanescence, we calculated an alloantibody detection rate of 31.6%. CONCLUSION: Posttransfusion antibody testing was inadequately timed for optimal alloantibody detection. Real-world compatibility testing was predicted to detect less than one-third of non-ABO antibodies, thereby exposing patients to risks of mismatched transfusion.

Warfarin Pharmacogenetics Reevaluated: Subgroup Analysis Reveals a Likely Underestimation of the Maximum Pharmacogenetic Benefit by Clinical Trials.

OBJECTIVES: Various patient subgroups were examined to determine which ones obtain the largest pharmacogenetic improvements in warfarin dose accuracy. Subgrouping schemes of recent clinical trials were analyzed for comparison. METHODS: The accuracy of a pharmacogenetic dose algorithm was determined retrospectively in comparison to that of a clinical algorithm in subgroups of the International Warfarin Pharmacogenetics Consortium (IWPC) patient database (n = 2,274) and of newly studied clinic patients (n = 146). RESULTS: White patients with low-dose genotypes (*1*3/AA, *2*2/AA, *2*3/GA, *2*3/AA, *3*3/GG, *3*3/GA, and *3*3/AA) achieved the largest pharmacogenetic improvements in warfarin dose accuracy. Mean absolute dosing error (MAE) in this subgroup of IWPC and newly studied patients was reduced 75.7% and 89.7%, respectively. White IWPC patients with >2 variants or ≥2 mg/day absolute difference between pharmacogenetic and clinical dose predictions obtained MAE reductions of 71.1% and 65.3%, respectively. By comparison, unstratified populations and subgroups of a major clinical trial, when replicated in IWPC patients, obtained smaller MAE reductions of 31.8% to 48.2%. Blacks and Asians obtained substantially smaller dose accuracy improvements overall than whites. CONCLUSIONS: Patient subgroups were identified that obtained the largest pharmacogenetic improvements in warfarin dose accuracy. These subgroups have not been analyzed in clinical trials to date, likely resulting in underestimation of the pharmacogenetic benefit.