Using molecular tools to compare various concentration protocols prior to detecting SARS-CoV-2 RNA in wastewater. (Special Issue: Chemistry and global challenges (part A).)

Background: Reports showed presence of SARS-CoV-2 genetic material in wastewater. Wastewater concentration methods are optimized for detection of non-enveloped viruses so need to be adopted for enveloped viruses and their genetic material. Methods: Conventional (cRT-PCR) and quantitative real time RT-PCR (qRT-PCR) were used as readouts to compare 4 water concentration methods namely, (A) filtration on negatively charged membrane followed by extracting RNA from it, (B) adsorbtion-elution method, (C) flocculation with skimmed milk and (D) polyethylene glycol precipitation, to detect SARS-CoV-2 RNA and 229E human coronavirus (229E-HCoV) as a model for spike-containing enveloped virus from fresh and wastewater. Results: On using cRT-PCR: recovery rate of SARS-CoV-2 RNA was better using method A then B for fresh water and method B then D for wastewater. 229E-HCoV recovery from fresh water was better using method C then A and methods B then D for wastewater. On using qRT-PCR, both methods A and B were better for SARS-CoV-2 RNA recovery from both fresh and wastewater. For the 229E-HCoV methods A was the most efficient for fresh water and method B for wastewater. Conclusion: Method B is recommended for SARS-CoV-2 RNA or whole 229E-HCoV recovery from wastewater.

The Infant Transcriptome in Meningococcal Septic Shock: A Force in Precision Cellular Dysfunction Suggesting a Cytokine Storm?

BACKGROUND AND AIM: The ideal biomarker(s) to track evolution and the underlying basis of sepsis remain elusive. We hypothesized that assessing differential mRNA gene expression may aid in tracking sepsis pathogenesis in infants with meningococcal septic shock (MSS). METHOD(S): Temporal paediatric gene expression datasets from Meningococcal Group B sepsis studies in the United Kingdom (MSS1, 29 samples) and Holland (MSS2, 41 samples) underwent Principal Component Analysis (PCA) and Gene Set Enrichment Analysis (GSEA). RESULT(S): Gene-expression clustering algorithm for both datasets demonstrated a baseline state on admission, an intermediate state, and a final state. Additionally, PCA plots suggested a gene-expression trajectory. The MSS1 study showed that 410 genes differentiated survivors from a nonsurvivor, including the ICAM-3 gene. Moreover GSEA t-Test identified apoptosis to be significantly differently (p = 0.02 and q = 0.15) associated with the fatal case compared to the four survivors in MSS1. Also in MSS1, we identified a genesignature for cytokine production which included 5 genes (CLC, HFE, HLA-F, NLRP3, TNFRSF1B) from the cytokine GSEA gene panel. The genes NLRP3 and TNFRSF1B have been noted in the cytokine storm of Coronavirus infection. Also Transcript Time Course Analysis (TTCA) confirmed differential gene function associated with Coronavirus. CONCLUSION(S): Transcriptomic analysis in two independent datasets in infants with MSS identified a trajectorial pattern. Further, the transcriptome expression differed between survivors and non-survivors, suggesting differences in cytokine signalling. Including the existence of genes associated with the cytokine storm of SARS-CoV2. The exploitability of transcriptome analysis to guide therapy and prognosis requires further investigation. (Figure Presented).

In-Vitro and in-Vivovascular Endothelial Growth Factor Subtypes a & B in Severe Acute Respiratory Syndrome Pathogenesis

BACKGROUND AND AIM: Increased Vascular Endothelial Growth Factor (VEGFA) Gene Expression (GE) has been documented in SARS-CoV2 infection. We wished to understand the relationship of VEGFA and VEGF B GE in both Murine SARS-CoV and Human SARS-CoV-2 in-vitro models of infection. METHOD(S): Secondary analysis of datasets from mice given nasal installation of SARS-CoV (MA15), MS1 (GSE33266MCV-1) and MS2 (GSE68820) from pulmonary tissues was undertaken. This allowed viral dose and temporal response analysis, respectively. Also studied were In-vitro Human hACE2 cells infected with SARS-CoV2 (dataset INV, GSE169158). Gene expression (GE) VEGF sub-types were analysed using Qlucore Omics Explorer (QOE) and gene enrichment functional profiling through the g:Profiler online platform. RESULT(S): For Murine studies, MA15 instillation compared to controls in MS1, lead to down-regulation of both VEGFB (MA15 10

Clinical Profile of Mortality and Treatment Profile of Survival in Patients with COVID-19 Pneumonia Admitted to Dubai Hospital

Background: Most COVID-19 studies conclude old age and coexisting illnesses as mortality determinants owing to different populations or methodologies, or omitting factors affecting outcomes. Methods: We analyzed COVID-19 patients' data (N = 391) of Dubai Hospital between January 1, 2020 and June 30, 2020. Results: Only 19 patients (4.8%) were UAE nationals, while 372 (95.2%) were expatriates. Median age was 48 (interquartile range, 40-56) years;22% were <40 years, and only 16.6% were female. Cough was the most common symptom (78.7%), fever was 77.4%, and gastrointestinal symptoms were least common (13.8%). Approximately 95% had elevated C-reactive protein (CRP) and D-dimers (79%), lymphocytopenia 47.3%, and thrombocytopenia 13.8%. Mortality was 30% for the total sample and 50% in ICU patients. ICU patients were older than non-ICU (age;49.6 +/- 10.9 vs. 46.7 +/- 12.7 years, p = 0.04). Eighty-five percent of ICU patients required invasive mechanical ventilation, 78% vasopressors, 88% sedation, 84% muscle paralysis, while none require any of these in the medical group. Survivors had fewer patients with sedatives (p = 0.01). The median length of stay in the hospital was 19 days, ICU stays 14 days, and ventilator 11 days. The Mann-Whitney test showed that survivors spent more days in the ICU (median [IQR] 18 [6.5-29.5] vs. 11 [4-18], p value 0.003) and the hospital (32 [14.5-49.5] vs. 14 [7-21], p value 0.001) than nonsurvivors. Ferritin and D-dimers were higher in nonsurvivors, but CRP was lower in nonsurvivors (ferritin (ng/mL) median (IQR) 1,434 (661.5-2206.5) versus 1,362 (630-2,094), p value = 0.017, CRP (mg/L) 118.7 (53.4-184) versus 134.9 (66.5-203.2), p value 0.001 and D-dimer (mu g/mL) 1.54 (0-3.13) versus 1.09 (0-2.51), p value = 0.001). Multiple logistic regression analysis determined age, fever on admission, use of oxygen, mechanical ventilation, and steroids as predictors of survival. Conclusions: COVID-19 patients were young males with pre-existing conditions. Ferritin, CRP, and D-dimers were higher in nonsurvivors. Treatment with chloroquine, antivirals, and anticoagulation was not different between survivors and nonsurvivors. Steroid use was a survival predictor.

Radical Trachelectomy for the Treatment of Early-Stage Cervical Cancer: A Systematic Review.

OBJECTIVE: To assess surgical, oncologic, and pregnancy outcomes in patients undergoing radical vaginal, abdominal, or laparoscopic trachelectomy for the treatment of early-stage cervical cancer, using a methodic review of published literature. DATA SOURCES: PubMed, EMBASE, and Cochrane Library sources, including ClinicalTrials.gov, were searched from 1990-2019 with terms "cervical cancer" and "(vaginal, abdominal, open, minimally invasive, or laparoscopic) radical trachelectomy." Grey literature and unpublished data were omitted. METHODS OF STUDY SELECTION: After removal of duplicates from a combined EndNote library of results, 490 articles were reviewed using Covidence software. Two reviewers screened titles and abstracts, and then screened full texts. Selection criteria included articles that reported radical trachelectomy with lymph node assessment as primary therapy for cervical carcinoma, with stated follow-up intervals and recurrences. TABULATION, INTEGRATION, AND RESULTS: Variables of interest were manually extracted into an electronic database. A total 47 articles that reported on 2,566 women met inclusion criteria. Most tumors were of squamous histology (68.5%), stage IB1 (74.8%), 2 cm or less (69.2%), and without lymphovascular invasion (68.8%). Of planned trachelectomies, 9% were converted intraoperatively to hysterectomy. Separated by route of trachelectomy, 58.1%, 37.2%, and 4.7% were performed using radical vaginal, abdominal, and laparoscopic approaches, respectively. With median follow-up of 48 months (range 2-202 months) across studies, median recurrence rate was 3.3% (range 0-25%); median time to recurrence was 26 months (range 8-44 months). Median 5-year recurrence-free and overall survival were 94.6% (range 88-97.3%) and 97.4% (range 95-99%), respectively. The posttrachelectomy pregnancy rate was 23.9%, with a live-birth rate of 75.1%. CONCLUSION: Radical trachelectomy for fertility-preserving treatment of cervical cancer is widely reported in the literature, though publications are mainly limited to case reports and case series. Reported follow-up periods infrequently meet standard oncologic parameters but show encouraging recurrence-free and overall survival rates and pregnancy outcomes. Higher-level evidence needed for meta-analysis is lacking. SYSTEMATIC REVIEW REGISTRATION: PROSPERO, CRD42019132443.

Prevalence and Timing of Tracheostomy and Its Impact on Clinical Outcomes in COVID-19 Pneumonia Patients in Dubai Hospital

Introduction: Coronavirus has caused more than a million deaths as of October 2020. Hospitals consider tracheostomy after the patient is virus negative, usually after 3 weeks. Prevalence and timing of tracheostomy and its impact on survival among COVID patients are unknown. Methods: A retrospective, single-center study of all patients with COVID-19 ARDS who underwent tracheostomy was conducted. Patients with age <18 and patients treated with ECMO were excluded. Duration of ventilation before tracheostomy was recorded. Clinical variables, outcome variables, and confounding variables were recorded and compared between patients with tracheostomy and without tracheostomy. The aim was to determine prevalence and timing of tracheostomy and its impact on clinical outcomes. Results: We found that tracheostomies were performed only in 21 out of 196 patients (10.8%). Tracheostomies were performed after 3 weeks on average (22.1 ± 7.5 days). Survival was significantly higher in patients who underwent tracheostomy (85.7 vs. 42.5%, p = 0.001). LOSICU was longer for tracheostomy patients than patients without tracheostomy (median [IQR]: 35 [23-47] vs. 15 [9-21], p = 0.001). Patients who underwent tracheostomy had a higher proportion of treatment with continuous renal replacement therapy (CRRT) (52 vs. 30%, p = 0.04), more COVID-19 swab testing (6.5 [4.5-8.5] vs. 5 [3-7], p = 0.002), more days on mechanical ventilation (34.5 [24-45] vs. 11 [5.5-16.5], p = 0.001), and more length of stay in the hospital (54 [38-70] vs. 20 [10.5-29.5], p = 0.001). All other factors were not statistically different between the 2 groups. Approximately 29% of patients had possible false-negative testing as their swab became positive after being negative. Conclusion: Tracheostomy was performed only in 10% of our patients with COVID-19 ARDS. Time to tracheostomy was after 3 weeks on average. Survival was better in patients with tracheostomy, but tracheostomized patients stayed longer in the ICU and hospital and utilized more days of mechanical ventilation and CRRT.

Prediction of Cytokine Storm and Mortality in Patients with COVID-19 Admitted to ICU: Do Markers Tell the Story?

Introduction: COVID-19 has caused approximately one million deaths worldwide as of November 24, 2020. Markers of disease activity like ferritin, C-reactive protein (CRP), and D-dimers are frequently monitored to detect the best opportunity for intensive treatment. Methods: All patients of >18 years of age were included. The primary variables of interest, ferritin, CRP, and D-dimers, for each patient throughout hospitalization were recorded. Primary clinical outcomes of length of stay in ICU and survival were recorded. Demographics: age, gender, BMI, and nationality. Ferritin, CRP, and D-dimers were recorded daily if available for the whole ICU stay, and all other variables were recorded on admission day to ICU. Results: The sample includes 235 records. More than 95% of patients have all markers on the day of admission to ICU were ferritin (median 1,278;IQR 1,424), D-dimer 1.21 (3.4), and CRP 129.5 (121). Daily average levels of markers were different from their admission day level: ferritin 1,395 (1,331), D-dimer 3.11 (5.52), and CRP 107 (75.8). Multiple logistic regression analysis determined that average CRP during the stay was the only predictor of survival. Discussion: Data on markers utilization to detect the acute phase of inflammation help clinicians focus on the opportunity window for intensive treatment. Conclusion: Average CRP during the stay in ICU is higher than CRP on admission. Average CRP is the only factor that predicts survival.

Service delivery during COVID-19 pandemic in orthopedic surgery mayo hospital, lahore

Aim: To explain our experience of service delivery at Orthopedic surgery during pandemic severe acute respiratory syndrome coronavirus (SARS VoV-19). Methods: We studied a retrospective cohort-based on a manual medical record of the Department of Orthopedic Surgery and Traumatology Unit-I, King Edward Medical University, Mayo Hospital, Lahore, from March to July 2020. The medical record of admission operated cases in accident & emergency, indoor, and all patients attended in the out-patient department were stated. We continued the delivery of our service in an emergency, indoor, elective operation theater, and an out-patient department (OPD). The experience of running the services in the emergency, indoor, and OPD was gathered to present for best practices in future perspective. Results: Out of the total of 4660 patients treated, there were 2831(60.75%) males, and 1885(40.4%) were female. The mean age of the patients was 32.8±10.14-year. Amongst the total 4660, 1906(40.9%) patients were operated, and 2754(59.1%) were attended in the OPD. Out of these operated patients, 1839 (96.5%) were trauma patients, 58(3.04%) follow up surgery, 05(0.26%) tumor surgeries, 3(0.16%) arthroplasties, and 01 arthroscopies. Amongst the total of 1839 operated patients in an emergency, 1177(64%) were minor procedures, and 662(36%) were major procedures. Total Admissions in the COVID-19 pandemic were 769 (16.5%), out of which 715(92.98%) were admitted through accident and emergency. Conclusion: There was limitation to elective surgery, with risk to manage the emergency in orthopedic trauma patient. Emergency and tumor surgeries poses real challenge for safety during COVID-19 pandemic.