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1.
Frontiers in microbiology ; 14, 2023.
Article in English | EuropePMC | ID: covidwho-2280173

ABSTRACT

The real-time polymerase chain reaction (PCR), commonly known as quantitative PCR (qPCR), is increasingly common in environmental microbiology applications. During the COVID-19 pandemic, qPCR combined with reverse transcription (RT-qPCR) has been used to detect and quantify SARS-CoV-2 in clinical diagnoses and wastewater monitoring of local trends. Estimation of concentrations using qPCR often features a log-linear standard curve model calibrating quantification cycle (Cq) values obtained from underlying fluorescence measurements to standard concentrations. This process works well at high concentrations within a linear dynamic range but has diminishing reliability at low concentrations because it cannot explain "non-standard” data such as Cq values reflecting increasing variability at low concentrations or non-detects that do not yield Cq values at all. Here, fundamental probabilistic modeling concepts from classical quantitative microbiology were integrated into standard curve modeling approaches by reflecting well-understood mechanisms for random error in microbial data. This work showed that data diverging from the log-linear regression model at low concentrations as well as non-detects can be seamlessly integrated into enhanced standard curve analysis. The newly developed model provides improved representation of standard curve data at low concentrations while converging asymptotically upon conventional log-linear regression at high concentrations and adding no fitting parameters. Such modeling facilitates exploration of the effects of various random error mechanisms in experiments generating standard curve data, enables quantification of uncertainty in standard curve parameters, and is an important step toward quantifying uncertainty in qPCR-based concentration estimates. Improving understanding of the random error in qPCR data and standard curve modeling is especially important when low concentrations are of particular interest and inappropriate analysis can unduly affect interpretation, conclusions regarding lab performance, reported concentration estimates, and associated decision-making.

2.
Paediatr Int Child Health ; : 1-11, 2023 Mar 01.
Article in English | MEDLINE | ID: covidwho-2264860

ABSTRACT

Vitamin D plays an active role beyond mineral metabolism and skeletal health, including regulation of the immune system. Vitamin D deficiency is widely prevalent, and observational studies link low vitamin D status to a risk of infections and auto-immune disorders. Reports indicate an inverse relationship between vitamin D status and such conditions. This review details vitamin D signalling interactions with the immune system and provides experimental and clinical evidence evaluating vitamin D status, vitamin D supplementation and host susceptibility to infections, inflammation and auto-immunity. The published literature including related reviews, systematic reviews, meta-analyses, randomised controlled trials (RCTs), observational studies and basic science reports have been synthesised. Meta-analyses of observational studies have demonstrated a link between low vitamin D status and risk of acute respiratory infections, COVID-19 disorders, multiple sclerosis, type 1 diabetes (T1DM), inflammatory bowel disease (IBD), systemic lupus erythematosus and other auto-immune disorders. Observational studies suggest that vitamin D supplementation may protect against several infectious and auto-immune conditions. Meta-analyses of RCTs had mixed results, demonstrating a small protective role for vitamin D supplementation against acute respiratory infections, especially in those with vitamin D deficiency and children, and providing modest benefits for the management of T1DM and IBD. Vitamin D status is inversely associated with the incidence of several infectious and auto-immune conditions. Supplementation is recommended for those with vitamin D deficiency or at high risk of deficiency, and it might provide additional benefit in acute respiratory infections and certain auto-immune conditions.

3.
J Patient Rep Outcomes ; 7(1): 31, 2023 03 21.
Article in English | MEDLINE | ID: covidwho-2283318

ABSTRACT

OBJECTIVE: The novel Coronavirus (COVID-19) has continued to present a significant burden to global public health efforts. The purpose of this study was to estimate the health-related quality of life, disability, and health status of individuals with self-reported long COVID at various lengths of recovery. METHODS: We conducted a cross-sectional online survey of individuals with self-reported long COVID. Participants were asked to complete the five-item EuroQOL EQ-5D-5L and EQ visual analog scale, the 12-item World Health Organization Disability Assessment Schedule (WHODAS) 2.0 and the 10-item Patient Reported Outcome Measurement Information System (PROMIS) Global Health v1.2 short form. Descriptive and inferential statistics were used to characterize the responses and differences across groups. RESULTS: Eighty-two participants from 13 countries completed the EQ-5D-5L, 73 completed the WHODAS 2.0 and 80 participants completed the PROMIS. The mean EQ-5D-5L utility score was 0.51. The mean WHODAS score was 49.0. In the previous 30 days, participants reported their symptoms affected them for a mean of 24 days, they were totally unable to carry out usual activities for 15 days, and they cut back or reduced activities for 26 days. The mean PROMIS physical health and mental health scores were 10.7 and 8.6, respectively, corresponding to below-average health. No significant differences were detected across time or according to severity of acute infection. CONCLUSIONS: Long COVID presents a significant chronic health burden to adults in the US and abroad. This health burden may persist for many months post-acute infection.


Subject(s)
COVID-19 , Quality of Life , Adult , Humans , Quality of Life/psychology , Post-Acute COVID-19 Syndrome , Self Report , Cross-Sectional Studies , COVID-19/epidemiology , Health Status
4.
Front Microbiol ; 14: 1048661, 2023.
Article in English | MEDLINE | ID: covidwho-2280174

ABSTRACT

The real-time polymerase chain reaction (PCR), commonly known as quantitative PCR (qPCR), is increasingly common in environmental microbiology applications. During the COVID-19 pandemic, qPCR combined with reverse transcription (RT-qPCR) has been used to detect and quantify SARS-CoV-2 in clinical diagnoses and wastewater monitoring of local trends. Estimation of concentrations using qPCR often features a log-linear standard curve model calibrating quantification cycle (Cq) values obtained from underlying fluorescence measurements to standard concentrations. This process works well at high concentrations within a linear dynamic range but has diminishing reliability at low concentrations because it cannot explain "non-standard" data such as Cq values reflecting increasing variability at low concentrations or non-detects that do not yield Cq values at all. Here, fundamental probabilistic modeling concepts from classical quantitative microbiology were integrated into standard curve modeling approaches by reflecting well-understood mechanisms for random error in microbial data. This work showed that data diverging from the log-linear regression model at low concentrations as well as non-detects can be seamlessly integrated into enhanced standard curve analysis. The newly developed model provides improved representation of standard curve data at low concentrations while converging asymptotically upon conventional log-linear regression at high concentrations and adding no fitting parameters. Such modeling facilitates exploration of the effects of various random error mechanisms in experiments generating standard curve data, enables quantification of uncertainty in standard curve parameters, and is an important step toward quantifying uncertainty in qPCR-based concentration estimates. Improving understanding of the random error in qPCR data and standard curve modeling is especially important when low concentrations are of particular interest and inappropriate analysis can unduly affect interpretation, conclusions regarding lab performance, reported concentration estimates, and associated decision-making.

5.
J Med Virol ; 95(2): e28442, 2023 02.
Article in English | MEDLINE | ID: covidwho-2248007

ABSTRACT

Wastewater-based SARS-CoV-2 surveillance enables unbiased and comprehensive monitoring of defined sewersheds. We performed real-time monitoring of hospital wastewater that differentiated Delta and Omicron variants within total SARS-CoV-2-RNA, enabling correlation to COVID-19 cases from three tertiary-care facilities with >2100 inpatient beds in Calgary, Canada. RNA was extracted from hospital wastewater between August/2021 and January/2022, and SARS-CoV-2 quantified using RT-qPCR. Assays targeting R203M and R203K/G204R established the proportional abundance of Delta and Omicron, respectively. Total and variant-specific SARS-CoV-2 in wastewater was compared to data for variant specific COVID-19 hospitalizations, hospital-acquired infections, and outbreaks. Ninety-six percent (188/196) of wastewater samples were SARS-CoV-2 positive. Total SARS-CoV-2 RNA levels in wastewater increased in tandem with total prevalent cases (Delta plus Omicron). Variant-specific assessments showed this increase to be mainly driven by Omicron. Hospital-acquired cases of COVID-19 were associated with large spikes in wastewater SARS-CoV-2 and levels were significantly increased during outbreaks relative to nonoutbreak periods for total SARS-CoV2, Delta and Omicron. SARS-CoV-2 in hospital wastewater was significantly higher during the Omicron-wave irrespective of outbreaks. Wastewater-based monitoring of SARS-CoV-2 and its variants represents a novel tool for passive COVID-19 infection surveillance, case identification, containment, and potentially to mitigate viral spread in hospitals.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , RNA, Viral , Wastewater , Tertiary Care Centers , Disease Outbreaks
7.
Catalysts ; 12(9):943, 2022.
Article in English | MDPI | ID: covidwho-2005944

ABSTRACT

Visible-light-driven photocatalysts have gained increasing attention in the past few decades in treating emerging contaminants in water and wastewater. In this work, the photocatalytic activity of the coupled graphitic carbon nitride (GCN) and silver chromate (Ag2CrO4), herein denoted as GCN/Ag2CrO4, nanocomposites was evaluated for degrading organic pollutants and inactivating microorganisms under visible light irradiation using a royal blue light-emitting diode (LED). The organic pollutants studied were 2,4-dichlorophenoxyacetic acid (2,4-D) and methyl chlorophenoxy propionic acid (MCPP or Mecoprop-P) present in KillexR, a commercially available herbicide, bovine serum albumin (BSA) protein, and SARS-CoV-2 spike protein. The disinfection experiments were conducted on wastewater secondary effluent. The results showed that over 85% degradation was achieved for both 2,4-D and Mecoprop-P in 120 min while 100% of BSA protein and 77.5% of SARS-CoV-2 protein were degraded in 20 min and 30 min, respectively. Additionally, GCN/Ag2CrO4 nanocomposites led to over one log reduction of cellular ATP (cATP), total coliforms, and E. coli in wastewater treatment plant (WWTP) secondary effluent after 60 min of royal blue LED irradiation. It was observed that the degradation performance of a photocatalyst under light irradiation is contaminant-specific. The binding affinity of the released metal ions from GCN/Ag2CrO4 with protein and ATP functional groups was responsible for the degradation of proteins and the reduction of cATP, while the generated ROS was responsible for the disinfection of total coliforms and E. coli. Overall, the results indicate that GCN/Ag2CrO4 nanocomposite is a promising photocatalyst in degrading organic pollutants and disinfecting microorganisms under visible light irradiation within a reasonable time.

8.
Emerg Infect Dis ; 28(9): 1770-1776, 2022 09.
Article in English | MEDLINE | ID: covidwho-1963355

ABSTRACT

Wastewater monitoring of SARS-CoV-2 enables early detection and monitoring of the COVID-19 disease burden in communities and can track specific variants of concern. We determined proportions of the Omicron and Delta variants across 30 municipalities covering >75% of the province of Alberta (population 4.5 million), Canada, during November 2021-January 2022. Larger cities Calgary and Edmonton exhibited more rapid emergence of Omicron than did smaller and more remote municipalities. Notable exceptions were Banff, a small international resort town, and Fort McMurray, a medium-sized northern community that has many workers who fly in and out regularly. The integrated wastewater signal revealed that the Omicron variant represented close to 100% of SARS-CoV-2 burden by late December, before the peak in newly diagnosed clinical cases throughout Alberta in mid-January. These findings demonstrate that wastewater monitoring offers early and reliable population-level results for establishing the extent and spread of SARS-CoV-2 variants.


Subject(s)
COVID-19 , SARS-CoV-2 , Alberta/epidemiology , COVID-19/epidemiology , Humans , SARS-CoV-2/genetics , Wastewater
10.
ATS Sch ; 3(2): 270-284, 2022 Jun.
Article in English | MEDLINE | ID: covidwho-1929098

ABSTRACT

Background: Evidence shows poor adherence to strategies for reducing morbidity and mortality in intensive care unit (ICU) patients receiving mechanical ventilation globally. Best practice management relies on training all members of the interprofessional ICU team, each with complementary roles in patient management. Objectives: To develop and evaluate a novel two-phase, train-the-trainer, interprofessional and multicultural "Best Practice Management of the Ventilated ICU Patient" multimodality, simulation-enhanced curriculum for Thai education leaders in critical care. Methods: In phase 1 (Oregon Health and Science University cohort), two groups of nine ICU nurses and one critical care physician representing experts in critical care and education from a large hospital system in Thailand participated in a weeklong, immersive course consisting of didactic, simulation, and in situ immersive sessions focused on best practice management of mechanically ventilated ICU patients, as well as training in our educational techniques. Outcomes were assessed with pre- and postcourse knowledge assessments and overall course evaluation. In phase 2 (Thai cohort), participants from phase 1 returned to Thailand and implemented a lower fidelity curriculum in two hospitals, using the same pre- and posttest knowledge assessment in 41 participants, before the onset of the coronavirus disease (COVID-19) 6 pandemic. Results: In the Oregon Health and Science University cohort, the mean pretest knowledge score was 58.4 ± 13.2%, with a mean improvement to 82.5 ± 11.6% after completion of the course (P , 0.05). The greatest improvements were seen in respiratory physiology and advanced/disease-specific concepts, which demonstrated absolute improvements of 30.4% and 30.6%, respectively (P < 0.05). Participants had a high degree of satisfaction, with 90% rating the course as "excellent" and .90% reporting that the course "greatly improved" their understanding of best practices and comfort in managing mechanical ventilation. The Thai cohort had a mean baseline score of 45.4 ± 15.0% and a mean improvement to 70.3 ± 19.1% after training (P < 0.05). This cohort also saw the greatest improvement in respiratory physiology and advanced/disease-specific concepts, with 26.2% and 26.3% absolute improvements, respectively (P < 0.05). Conclusion: A novel, two-phase, interprofessional, multicultural, simulation-enhanced train-the-trainer curriculum was feasible and effective in improving education in best practice management of mechanically ventilated patients and may be a useful model for improving the care of ICU patients across the world.

11.
Pediatr Pulmonol ; 57(7): 1814-1817, 2022 07.
Article in English | MEDLINE | ID: covidwho-1913872

ABSTRACT

This pilot study successfully implemented a standardized protocol for tablet-based ototoxicity screening in pediatric cystic fibrosis (CF) patients exposed to aminoglycosides. Further studies are needed to assess the impact of implementation in a larger number of patients, as well as to determine barriers that may exist at centers with variation in available resources. This method of ototoxicity screening represents an accessible alternative to traditional audiology testing, and given the continued improvements in expected life span for people with CF, it is imperative that patients have regular access to this type of screening to allow for early identification of medication-related toxicities.


Subject(s)
Audiology , Cystic Fibrosis , Ototoxicity , Aminoglycosides/adverse effects , Anti-Bacterial Agents/adverse effects , Child , Cystic Fibrosis/drug therapy , Humans , Pharmacists , Pilot Projects
12.
J Am Coll Health ; : 1-5, 2022 Jun 03.
Article in English | MEDLINE | ID: covidwho-1878609

ABSTRACT

Objective: To investigate demographics, sport type, athletic identity, and COVID-19 sport season cancelation in relation to alcohol consumption among college student athletes shortly after the pandemic emerged. Participants: College student athletes recruited from U.S. athletic departments. Methods: Survey data were collected from 5,915 college student athletes in April/May 2020. Results: Being female, Latinx, and in a relationship were associated with lower alcohol consumption. Among males, team sport participation was related to greater alcohol consumption. Among females, athletic identity was inversely related to drinking, which was moderated by sport type, such that alcohol consumption was lower as athletic identity strengthened in individual (vs. team) sport athletes. However, we did not find a relationship of COVID-19 sport season cancelation with drinking. Conclusions: Our gender-specific findings are novel and generalizable based on a large, national sample of college student athletes, and may inform strategies for alcohol consumption education among college team sport athletes.

13.
Water Res ; 220: 118611, 2022 Jul 15.
Article in English | MEDLINE | ID: covidwho-1852230

ABSTRACT

Wastewater-based epidemiology (WBE) is an emerging surveillance tool that has been used to monitor the ongoing COVID-19 pandemic by tracking SARS-CoV-2 RNA shed into wastewater. WBE was performed to monitor the occurrence and spread of SARS-CoV-2 from three wastewater treatment plants (WWTP) and six neighborhoods in the city of Calgary, Canada (population 1.44 million). A total of 222 WWTP and 192 neighborhood samples were collected from June 2020 to May 2021, encompassing the end of the first-wave (June 2020), the second-wave (November end to December 2020) and the third-wave of the COVID-19 pandemic (mid-April to May 2021). Flow-weighted 24-hour composite samples were processed to extract RNA that was then analyzed for two SARS-CoV-2-specific regions of the nucleocapsid gene, N1 and N2, using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Using this approach SARS-CoV-2 RNA was detected in 98.06% (406/414) of wastewater samples. SARS-CoV-2 RNA abundance was compared to clinically diagnosed COVID-19 cases organized by the three-digit postal code of affected individuals' primary residences, enabling correlation analysis at neighborhood, WWTP and city-wide scales. Strong correlations were observed between N1 & N2 gene signals in wastewater and new daily cases for WWTPs and neighborhoods. Similarly, when flow rates at Calgary's three WWTPs were used to normalize observed concentrations of SARS-CoV-2 RNA and combine them into a city-wide signal, this was strongly correlated with regionally diagnosed COVID-19 cases and clinical test percent positivity rate. Linked census data demonstrated disproportionate SARS-CoV-2 in wastewater from areas of the city with lower socioeconomic status and more racialized communities. WBE across a range of urban scales was demonstrated to be an effective mechanism of COVID-19 surveillance.


Subject(s)
COVID-19 , Humans , Pandemics , RNA, Viral , SARS-CoV-2 , Urban Population , Wastewater
14.
British Journal of Surgery ; 109(SUPPL 2):ii6, 2022.
Article in English | EMBASE | ID: covidwho-1778892

ABSTRACT

Aim: The Covid-19 pandemic encouraged prompt modification to clinical practice to minimise hospital attendances in an aim to minimize exposure and protection of the NHS whilst maintaining the standards of patient care. Current literature advocates that Four-Dimensional Computerised Tomography (4DCT) has equal diagnostic value as ultrasound alone or a combination of ultrasound and Sestamibi scan in the identification of abnormal parathyroid glands in the work up for surgical management of hyperparathyroidism. In response to the evolving pandemic at Addenbrookes we modified our practice and escalated 4DCT as our first line imaging. In light of this we had a unique opportunity to evaluate the diagnostic value of the currently used imaging modalities. Methods: This is a retrospective study of 270 parathyroidectomies who underwent pre-operative 4DCT (n=270), ultrasound (n= 254) and sestamibi scan (n=253). Subsequently, we assessed the accuracy of these three modalities with the of intra-operative findings, histology, postoperative calcium and PTH. Results: The sensitivity of the 4DCT was 77% in comparison to 43% sensitivity of the ultrasound alone. (p.0.05). The combined sensitivity of ultrasound and Sestamibi scan was found to be 69%. Conclusion: The implementation of 4DCT as a single modality diagnostic imaging can be considered equally effective and accurate in the diagnosis of parathyroid abnormality. Implementing this would reduce the number of diagnostic tests improving the likelihood of successful operative planning and reduce financial cost.

15.
Probation Journal ; 2021.
Article in English | Scopus | ID: covidwho-1503716

ABSTRACT

In this paper, we draw on data from a recent study of how Covid-19 and related restrictions impacted on vulnerable and/or marginalised populations in Scotland (Armstrong and Pickering, 2020), including justice-affected people (i.e. people in prison and under supervision, their families and those that work with them;see Gormley et al., 2020). Focusing here mainly on interviews with people released from prison and others under community-based criminal justice supervision, we explore how the pandemic impacted on their experiences. Reflecting upon and refining previous analyses of how supervision is experienced as ‘pervasive punishment’ (McNeill, 2019), we suggest that both the pandemic and public health measures associated with its suppression have changed the ‘pains’ and ‘gains’ of supervision (Hayes, 2015), in particular, by exacerbating the ‘suspension’ associated with it. We conclude by discussing the implications of our findings for the pursuit of justice in the recovery from Covid-19. © The Author(s) 2021.

16.
Journal of the American Academy of Child & Adolescent Psychiatry ; 60(10):S237-S237, 2021.
Article in English | Academic Search Complete | ID: covidwho-1461214
17.
Journal of Cystic Fibrosis ; 20:S76-S76, 2021.
Article in English | Academic Search Complete | ID: covidwho-1454661
18.
In Practice ; 43(4):229-232, 2021.
Article in English | Web of Science | ID: covidwho-1237417

ABSTRACT

Exceptional leadership is key to the long-term sustainability of the veterinary sector, yet there is still little understanding of the skills and behaviours required for effective leadership within the profession. The increasing levels of burnout, stress and depression within the profession combined with the effects of the Covid-19 pandemic and the challenges thrown up by today's volatile, uncertain, complex and ambiguous world means that many veterinary businesses are left with a toxic cocktail of issues to overcome. This article, the second in a series on leadership, highlights what is required of successful leaders in the veterinary profession.

19.
European Urology Open Science ; 20:S21, 2020.
Article in English | EMBASE | ID: covidwho-1108859

ABSTRACT

Introduction: Ireland has the one of the lowest urologist per population ratios in Europe1. Out-patient department (OPD) visits are time consuming, costly and frequently patients cannot be reviewed in the intended timeframe2. With the COVID-19 crisis innovative virtual models of care are essential. Methods: Patients for OPD review were assessed by a Consultant in a “virtual” clinic using electronic records (letters, imaging, blood results) and chart review if required. Patients were either discharged, discharged for GP testing with specified re-referral criteria, phone/letter follow up by a LUTS clinical nurse specialist, investigated and reviewed by phone/letter, or returned for face-to-face consultation. Results: 400 patients were assessed. The majority were seen previously by SHO or junior registrar. 160 (40%) patients were discharged directly via letter and advice. 121 (30%) required further imaging and could be contacted by phone with the results. 79 (20%) could be contacted by the LUTS clinical nurse specialist for phone/written review. 40 (10%) necessitated face-to-face OPD review for clinical assessment or investigation review. In 47 patients there was insufficient information available in the electronic platforms, thus requiring formal chart review. Overall, 360 patients could be managed via “virtual” means. The potential out-patient cost savings were estimated at €27,000. Conclusion: With this COVID-19 pandemic, innovative models of care are necessitated. Introduction of a “virtual” OPD clinic allows reliable review of patients with reduced face-to-face follow-up attendances. Further study of staff training and patient satisfaction is required.

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