When False-Positives Arise: Troubleshooting a SARS-Coronavirus-2 (SARS-CoV-2) Detection Assay on a Semi-Automated Platform

BACKGROUND

During the COVID-19 pandemic, many molecular diagnostic laboratories performed high-throughput SARS-CoV-2 testing often with implementation of automated workflows. In parallel, vaccination campaigns resulted increasingly in specimens from fully vaccinated patients, with resultant clinical inquiries regarding positive results in this patient population. This prompted a quality improvement initiative to investigate the semi-automated testing workflow for false-positive results. The troubleshooting workflow is described and procedural improvements are outlined that serve as a resource for other molecular diagnostic laboratories that need to overcome testing anomalies in a semi-automated environment.

METHODS

This workflow utilized the MagMax-96 Viral RNA kit and the CDC 2019-nCoV RT-qPCR Panel on the Agilent Bravo Liquid-Handler (Bravo). Screening of the environment, personnel, and the mechanical performance of instrumentation using low Ct checkerboard challenges was executed to identify sources of cross-contamination. Evaluation of the assay and reporting design was conducted.

RESULTS

Specimen contamination was observed during the viral extraction process on the Bravo. Changes to the program reduced plate contamination by 50% and importantly revealed consistent hallmarks of contaminated samples. We adjusted the reporting algorithm using these indicators of false positives. False positives that were identified made up 0.11% of the 45 000+ tests conducted over the following 8 months.

CONCLUSIONS

These adjustments provided confident and quality results while maintaining turnaround time for patients and pandemic-related public health initiatives. This corrected false-positive rate is concordant with previously published studies from diagnostic laboratories utilizing automated systems and may be considered a laboratory performance standard for this type of testing.

The influence of clinic care on perceptions and knowledge of non-communicable diseases and physical activity from a low-resourced community: a mixed-method study

Background

Health promotion for the management of risk factors for non-communicable diseases (NCDs) is an integral part of standard care in South Africa. Most persons presenting with NCDs utilise public primary health care centres for disease management. This mixed-methods study aimed at expanding current understanding of the the influence of standard clinic care (usual care) on perceptions and knowledge of risk factors for NCDs and physical activity (PA) among persons from a low-resourced community. Qualitatively the perceptions of women from a low-resourced community about risk factors for NCDs and PA were explored throughout 24-weeks of standard clinic care. Parallel quantitative data was collected to describe changes in risk factors for NCDs and trends in self-reported knowledge about risk factors of NCDs and PA.

Method

A convergent-parallel mixed-methods research design was used. The study was carried out in a public primary health care setting, in the North West Province, South Africa. From a convenience sample of 100 participants, 77 African women aged between 34 and 79 years were recruited for the study. Data were collected at three time-points including baseline, 12 weeks, and 24 weeks of a standard clinic care health-promotion programme. The qualitative data was collected during focus group discussions, and the quantitative data included questionnaires on knowledge of physical activity and risk factors for NCDs as well as anthropometric and biological measurements. Qualitative and quantitative data were analysed independently for each phase and then consolidated for interpretation. All data was collected in the same setting.

Results

Participants' initial understanding and perceptions of NCD risk factors were poor. Qualitative findings showed that participants knew little about the specific physical activity they could engage in and the role of PA in NCD management. Participants preferred low-intensity activities. Heart-disease knowledge improved significantly at 12 weeks intervention compared to baseline MD = -3.655, p < 0.001. There were improvements in PA knowledge at 12 weeks from baseline MD = -0.625 p = 0.02. There were significant weight (MD = 1.420, p = 0.002) and waist circumference reductions (MD = 0.621, p = 0.02) from baseline to 24 weeks.

Conclusion

Standard clinic care improved knowledge of physical activity and risk factors for NCDs, but perceptions of risk factors for NCDs and PA were unchanged. This study offers insight into the perceptions held by women from a low-resource setting and how future interventions to manage and prevent NCDs should be structured.

Trial registration

PACTR201609001771813.

CT coronary angiography in Selected Group of patients with Chest pain of new onset predicts and prevents hospital admissions & Outpatient Clinic referrals

Funding Acknowledgements

Type of funding sources: None.

Introduction

NICE (National Institute of Clinical Excellence) guidelines currently recommend the use of CT coronary Angiogram (CTCA) as the initial test to investigate coronary artery disease in patients with new onset of chest pain.

Our aim was to evaluate the relationship between the CT coronary angiogram findings on index presentation, and hospital admissions and re-referral to outpatient clinics in following 2 years.

Method

Data was accrued via a retrospective analysis of electronic medical records at Sunderland Royal Hospital pertaining to patients who presented to the Rapid Access Chest Pain Clinic (RACPC) and underwent CTCA in 2017.Data included:

Presentation – Typical & atypical angina

Risk factors profile

Investigations including ECG, ECHO, CTCA, perfusion scan and invasive coronary angiography

Severity of coronary artery lesion on CTCA

Hospital admissions or re-referral to outpatient clinics in 2 year follow up

Results

In the 235 patients studied, mean age was 56 years with 130 (55.5%) men and 195 (82.9%) presented with atypical angina as shown in table.

Out of 195 patients with atypical chest pain only 17 (8.7%) were diabetics and most of them 178 (91%) had Coronary Calcium score of 1-400. Most patients (184) underwent CT coronary angiogram with 39 (21%) having normal coronary arteries, 126 (68%) with mild to moderate coronary artery disease and 19 (11%) with severe coronary artery disease. Subsequent assessments with invasive coronary angiography, myocardial perfusion scan and Treadmill exercise did not reveal significant disease warranting coronary revascularization.

Patients with normal or mild -moderate CAD on CTCA 24 (15%) represented with acute chest pain (only one needed PCI) and 6 (3.5%) were referred to outpatient clinics over 2 years follow up. In patients with severe CAD on CTCA, 6 (32%) presented with acute chest pain and 4 (21%) needed PCI. Almost all patients were treated with statins and antiplatelets following CTCA results.

Conclusion

CT coronary angiography is sensitive and specific in assessment of hemodynamically significant coronary artery disease in non-diabetic patients presenting with angina in outpatient setting.

CTCA in patients with normal or mild to moderate CAD also gives confidence to the clinician and prevents further un-necessary investigation and hospital admissions/outpatient referrals.

935 Stridor in Multiple System Atrophy: An Otolaryngologist Perspective

Background

Bilateral vocal cord paralysis is a rare emergency presentation for Parkinson's disease (PD) but an acknowledged complication of an atypical rarer form of PD called Multi system atrophy ( MSA). MSA is a neurodegenerative disorder comprising of autononic failure, cerebellar ataxia and parkinsonism. An early occurence of stridor can indicate a shorten survival and quality of life remains uncertain. Airway definitive management of this patient group can pose a dilemma for the Otolaryngologist who may be asked to provide a specialist opinion.

Case: We present a case of a 73 year old female who developed mild stridor, hours after an emergency right sided hemiarthroplasty. On day 23 of her admission, there was a sudden airway deteoriation. The otolaryngology and anasthetic emergency team stablised her conservatively with an option of non invasive ventilation. Bilateral vocal cord palsy was observed on nasendoscopy On day 27, she was eventually diagnosed with MSA and showed partial response to a trial of madopar. Both options of a tracheostomy and laser cordotomy were avoided. She was safely discharged with follow up.

Conclusions

There remains gaps in the literature towards an unaminous consensus on stridor management in MSA patients. However, raising awareness of this patient groups will strenghten decision making processes.

Relationships between type of hoof lesion and behavioral signs of lameness in Holstein cows housed in Canadian tiestall facilities

Although foot pain can affect gait, the presence of a hoof lesion may or may not cause the cow to show visible changes in their gait. This can be dependent on the type and severity of the lesion; for example, the presence of a sole ulcer (SU) has been associated with increased gait scores, whereas digital dermatitis (DD) and sole hemorrhage (SH) have not. In tiestall facilities, gait scoring can be difficult to perform. An alternative method, known as stall lameness scoring (SLS), allows observers to assess cattle for lameness while they remain in their stall. Lameness is determined based on behavioral changes in weight bearing and foot positioning, which include: shifting weight, resting a foot, standing on the edge of the stall, and uneven weight bearing when stepping side to side. The aim of this study was to examine relationships between hoof lesions and these behavioral indicators. A total of 557 observations of SLS and corresponding hoof trimming records, collected during routine trimming events on 7 tiestall herds, were obtained. Trimming was performed by 2 trained hoof trimmers with good agreement on lesion identification, based on quizzes taken at the beginning and mid-way through the study. To ensure trimming had no effect on the behavioral indicators observed, SLS was always performed by a trained observer before trimming. Behavioral indicators focused on the hind limbs only; therefore, the analysis was confined to hind limb lesions using logistic regression to detect the presence of hoof lesion based on observations made during SLS. Seventy-five percent of observed cows had no SLS behavioral indicators, whereas, 11, 12, and 1% had 1, 2, and 3 behavioral indicators, respectively. At least one hind limb lesion was noted during trimming in 19% of cows, with the most common lesions being DD (7%), SU (6%), and SH (4%). A cow that was observed resting one foot and bearing weight unevenly when moving side to side had higher odds of having a hind limb hoof lesion than a cow not displaying these behaviors. When looking at specific hoof lesions, a cow observed resting one limb and bearing weight unevenly had higher odds of having a SU compared with those not displaying these behaviors. A cow observed shifting their weight from one foot to another had higher odds of having SH, and a cow observed bearing weight unevenly had higher odds of DD. Behavioral indicators in weight bearing and foot positioning can help identify cows in tiestalls with hind limb hoof lesions. Producers could routinely observe their cattle for these indicators to assist in the identification of cows that may require treatment. This could help reduce the duration of clinical lameness through earlier intervention.

Analysis of the frequency of bacteraemia of dental origin implicated in infective endocarditis in patients requiring valve surgery

Understanding the frequency of bacteraemia of dental origin that is implicated in severe infective endocarditis (IE) will further our understanding of the disease's pathoaetiology and help us take steps to reduce its prevalence. A total of 78 patients from the Royal Papworth Hospital, Cambridge, who had valve surgery due to IE (as confirmed by the Modified Duke Criteria) were included. Case notes were retrospectively reviewed for microorganisms that were implicated in the bacteraemia and IE. Associated factors were also recorded to determine whether they were different if a dental or non-dental pathogen was inoculated. A dental pathogen was implicated in 24 of the patients with IE; 20 had non-dental pathogens, and 30 were culture negative. This was not deemed statistically significant (p=0.54). Of the associated factors, only smoking was statistically significant with a greater proportion of non-smokers having bacteraemia of dental origin (p=0.03). No other associated factor was appreciably different based on the aetiology of the microorganism. Our results indicate that dental pathogens are not more likely to cause severe IE. We therefore advocate the stance adopted by the current national guidance on the judicious prescription of antibiotic prophylaxis for IE with regard to dental procedures.

Development and implementation of a risk assessment and management program for enzootic bovine leukosis in Atlantic Canada

Over the past 30 yr, the prevalence of bovine leukemia virus (BLV) infection has increased in North America, including Atlantic Canada, at both the herd and individual cow levels. This has occurred despite increased awareness of the disease and its deleterious effects and despite implementation of management practices aimed at reducing disease transmission. Our objectives were to identify risk factors associated with the within-herd prevalence of BLV-infected cows by using a risk assessment and management program workbook, as well as to determine the current level of BLV prevalence in the Atlantic Canada region. We hypothesized that previously established risk factors, including management practices associated with calf rearing and fly control, would affect within-herd BLV prevalence. Bulk tank milk (BTM) samples were collected in January and April of 2016 and again during the same months in 2017 and 2018 from all dairy farms shipping milk in the region. Samples were tested with ELISA for levels of anti-BLV antibodies to estimate within-herd prevalence. Regional BLV prevalence at the herd level was 88.39% of dairy herds infected in 2016 and 89.30% in 2018. All dairy farms shipping milk and who had BTM samples collected in 2017 (n = 605) were eligible to participate in the risk assessment and management program questionnaire (RAMP), which was developed and distributed to all bovine veterinarians in Atlantic Canada. One hundred and six RAMP were returned, with representation from all 4 provinces. The RAMP results were combined with the mean BTM ELISA results, and univariable logistic regression followed by multivariable logistic regression was performed to investigate the association between RAMP risk factors and the estimated within-herd BLV prevalence. Factors in the multivariable model significantly associated with the odds of a herd being classified as >25% estimated within-herd prevalence included history of diagnosis of clinical BLV and calves receiving colostrum from cows with unknown BLV status. Differences in within-herd prevalence were not associated with hypodermic needle and injection practices, rectal sleeve practices, or using bulls for natural breeding, based on these 106 dairy farms.

Sediment metal enrichment and ecological risk assessment of ten ports and estuaries in the World Harbours Project

Ten global harbours were assessed for sediment quality by quantifying the magnitude of anthropogenic change and ecological risk. Anthropogenic change (enrichment) was high for Derwent River and Sydney estuary, moderate for Santander Harbour, Rio de Janeiro and Dublin Port, slight for Hong Kong, minimal for Darwin. All 10 enrichment indices used showed similar results. Derwent River sediment was rated at high ecological risk, followed by Sydney and Santander estuaries with moderate risk. Auckland and Darwin sediments exhibited minimal ecological risk and sediment in the remaining harbours (Dublin, Hong Kong, Ravenna, Ria de Vigo and Rio de Janeiro) were assessed at slight ecological risk. The extraordinary variety of environments and types/quantities/qualities of data investigated resulted in as much a critique and development of methodology, as an assessment of human impact, including unique techniques for elemental normalisation and contaminant classification. Recommendations for an improved technical framework for sediment quality assessment are provided.

Quality of life, physical activity and cardiorespiratory fitness in black African women: B-Healthy project

PURPOSE

To study the associations between physical activity (PA), cardiorespiratory fitness (CRF), and health-related quality of life (HRQoL) in black African women from a low socioeconomic community in South Africa.

METHODS

Black African women (n = 146) aged 35-75 years from a low socioeconomic community in South Africa participated in this study. We measured PA levels via ActiHeart® accelerometers, and CRF by measuring peak oxygen consumption (V̇O₂ peak). HRQoL was assessed once with the SF-8 Health Survey (SF-8). Participants were classified into groups based on age, moderate to vigorous PA (MVPA), and V̇O₂ peak. Logistic regressions were used to compare the odds of having total HRQoL component scores above reported norms across PA and fitness groups. Two multiple linear regression models were developed using physical component summary (PCS) and mental component summary (MCS) as response variables respectively.

RESULTS

V̇O₂ peak and MVPA varied considerably across the sample and declined with increasing age. Participants in higher quartiles of MVPA and CRF showed trends to higher PCS scores. For CRF these trends were statistically significant, and persisted after adjustment for age and other possible confounders (p = 0.036). PCS was significantly associated with age, relative V̇O₂ peak, and income (all p < 0.05), while MCS was associated with income (p = 0.028).

CONCLUSIONS

CRF is the most significant predictor, together with age and income, on the PCS of the HRQoL among black African women. We recommend that when seeking improvements in HRQoL, interventions should focus on improving CRF, particularly V̇O₂ peak.

Prevalence of hock, knee, and neck skin lesions and associated risk factors in dairy herds in the Maritime Provinces of Canada

Skin lesions are commonly seen in dairy herds and have been associated with animal-, environmental-, and management factors. These lesions are not only a welfare concern, but they also affect profitability. Three areas on the cattle were examined for skin lesions: the hock, knee, and neck. Previous Canadian studies estimating the prevalence of lesions and the risk factors associated with them have not included the Maritime Provinces. In this study, 73 herds in the Maritime Provinces were chosen voluntarily to participate, with both tiestalls (n = 33) and freestalls (n = 40) represented. Within each herd, 67 to 90% of the lactating cows were selected and assessed for potential animal-, environmental-, and management-based risk factors. If producers were aware of the potential risk factors, this could help them reduce the prevalence in their herd. Leg lesions were scored on a 4-point scale (0-3) based on hair loss, swelling, and scabs, with a lesion defined as a score of 2 or 3 on at least 1 hock or knee. Necks were scored on a 3-point scale (0-2), with a lesion defined as score 2. For freestalls, the prevalence (95% confidence interval) of hock lesions was 39% (29-49%), knee lesions was 14% (11-18%), and neck lesions was 1% (<1-2%). Similarly, for tiestalls the prevalence (95% confidence interval) of hock lesions was 39% (33-46%), knee lesions was 17% (13-22%), and neck lesions was 5% (3-8%). Due to differences in management and methods of assessment between facility types, tiestalls and freestalls were analyzed separately. Due to dichotomization of cows as having a skin lesion or not, random-effects multivariable logistic regression was used to determine the risk factors for each lesion and facility type. Several environmental-based measurements, such as the stall base, type and dryness of bedding, and type of milking parlor, were associated with leg lesions. An environmental-based measurement that was associated with neck lesions was the design of the feed rail barrier in freestalls and the dimensions of the tie rail in tiestalls. Animal-based risk factors, such as stage of lactation, parity, and body condition, were also associated with all 3 types of lesions. This study showed that lesions to the hock, knee, and neck were common in the Maritime Provinces of Canada. Although differences were seen between facility types, in general, the results suggest that improving stall design and management and feed bunk design would help producers reduce the number of skin lesions seen in dairy cattle.

Prevalence of lameness and associated risk factors on dairy farms in the Maritime Provinces of Canada

Lameness in dairy cattle is a major issue for the industry due to the effects on the welfare of the animal, the economic impact, and consumer perception. The aim of this study was to determine the prevalence of lameness and explore potential risk factors in the Maritime Provinces of Canada. Cows were scored for lameness and potential risk factors and were assessed in 46 freestall herds and 33 tiestall herds in Nova Scotia, New Brunswick, and Prince Edward Island. In freestall herds, lameness was assessed using the most common method, locomotion scoring. A cow with a gait score of ≥3 out of 5 was considered to be lame. In tiestall herds, lameness was assessed using an alternative method known as stall lameness scoring. This assessment consisted of observation of the cow for 4 behavioral changes: standing on the edge of the stall, shifting weight, resting a limb, and uneven weight bearing when moved side to side. A cow displaying 2 or more of these behaviors was considered to be lame. At the time of the assessment, other animal-, environmental-, and management-based measurements were collected. These measurements were used in multivariable logistic regression analysis to determine risk factors that were associated with lameness for both freestalls and tiestalls independently. The prevalence of lameness was 21% for freestall-housed cattle and 15% for tiestall-housed cattle. Of the 1,488 tiestall-housed cows that were assessed, 68% showed no behavioral changes, whereas 15, 15, 2, and <1% showed 1, 2, 3, or 4 changes, respectively. In freestalls, higher odds of lameness were seen when cows spent ≥3 h/d in the holding area for milking compared with those that spent <3 h/d. In tiestall herds, higher odds of lameness were seen when bedding material was wet compared with when it was dry. For both lactating cow facility types, housing the dry cows and heifers on a deep bedded pack compared with tiestalls or freestalls was associated with a decreased odds of lameness. There were also many cow-level variables associated with lameness, including parity, daily milk production, stage of production, body condition, and width at the tuber coxae (hook bones). If producers become aware of the risk factors associated with lameness, they can make informed decisions on where to implement changes to help reduce the level of lameness in their herd.

Aspects of digestive function in sheep related to phenotypic variation in methane emissions

Ruminant livestock contribute to atmospheric methane (CH4) from enteric microbial fermentation of feed in the reticulo-rumen. Our research aimed to increase understanding of how digestive characteristics and rumen anatomy of the host animal contribute to variation in CH4 emissions between individual sheep. In total, 64 ewes were used in an incomplete block experiment with four experimental test periods (blocks). Ewes were chosen to represent the diversity of phenotypic variation in CH4 emissions: there were at least 10 offspring from each of four sires and a range of liveweights. Throughout the experiment, the ewes were fed equal parts of lucerne and oaten chaff, twice daily, at 1.5 times the maintenance requirements. Daily CH4 emission (g/day) increased significantly (P &lt; 0.001) with an increasing dry-matter intake (DMI) and reticulo-rumen volume (P &lt; 0.001). Lower methane yield (g CH4/kg DMI) was associated with shorter mean retention times of liquid (r = 0.59; P &lt; 0.05) and particle (r = 0.63; P &lt; 0.05) phases of the digesta in the rumen. Significant between sire variation was observed in CH4 emissions and in rumen volume (P = 0.02), the masses of liquids (P = 0.009) and particles (P &lt; 0.03) in the rumen and the proportion of gas in the dorsal sac of the rumen (P = 0.008). The best predictors of variation in CH4 emissions due to the host were DMI, CO2 emissions, rumen volume, liveweight, mean retention time of particles in the rumen, dorsal papillae density and the proportion of liquid in the contents of the rumen compartments.

Variation in methane production over time and physiological state in sheep

Livestock produce 10% of the total CO2-equivalent greenhouse gases in Australia, predominantly as methane from rumen fermentation. Genetic selection has the potential to reduce emissions and be adopted in Australian grazing systems. Developing a breeding objective for reduced methane emissions requires information about heritability, genetic relationships, when best to measure the trait and knowledge of the annual production of methane. Among- and within-animal variation in methane production, methane yield and associated traits were investigated, so as to determine the optimal time of measurement and the relationship between that measurement and the total production of methane. The present study measured 96 ewes for methane production, liveweight, feed intake, rumen volume and components, and volatile fatty acid (VFA) production and composition. Measurements were recorded at three ages and different physiological states, including growing (12 months), dry and pregnant (21 months) and dry (non-pregnant, non-lactating; 28 months of age). The single biggest determinant of methane production was feed intake, but there were additional effects of age, proportion of propionate to (acetate+butyrate) in rumen VFA, total VFA concentration and CO2 flux. Rumen volume and pregnancy status also significantly affected methane production. Methane production, CO2 flux, liveweight, feed intake and rumen volume had high repeatability (&gt;65%), but repeatability of methane yield and VFA traits were low (&lt;20%). There were no interactions between sire and age (or pregnancy status) for methane traits. This suggests that methane could be measured at any time in the production cycle. However, because MY is reduced during pregnancy, it might be best to measure methane traits in dry ewes (neither pregnant nor lactating).

Using serum and plasma samples to assess failure of transfer of passive immunity in dairy calves

The objectives of this study were (1) to determine the differences in IgG and total protein (TP) content of serum and plasma samples collected from the same calves; (2) to evaluate the correlation between calf serum and plasma IgG levels, Brix scores, and TP concentrations; (3) to determine whether different cut-off values should be used for plasma and serum to assess failure of transfer of passive immunity (FTPI) in dairy calves; and (4) to evaluate the level of agreement between results obtained from using serum and plasma samples of the same calves to assess FTPI using optimal cut-off values. Blood samples (n = 217) were collected from Holstein calves at 3 to 10 d of age on 30 commercial dairy farms in Nova Scotia and Newfoundland, Canada. Paired serum and plasma samples were analyzed for IgG concentration by the reference radial immunodiffusion assay, transmission infrared (TIR) spectroscopy, digital and optical Brix refractometers, and optical TP refractometer. The IgG concentrations measured by RID and TIR spectroscopy in serum were similar to those in plasma. However, the Brix and TP refractometer readings were significantly higher in plasma than in serum. The prevalence of FTPI in serum and plasma samples based on a RID-IgG concentration <10 g/L was 43.3 and 46.5%, respectively. The RID-IgG concentration was correlated with TIR-IgG (r = 0.92 and 0.89), digital Brix (r = 0.80 and 0.80), optical Brix (r = 0.77 and 0.77), and optical TP (r = 0.75 and 0.77) refractometers in serum and plasma, respectively. The correlations between paired serum and plasma IgG content were 0.85 by TIR spectroscopy, 0.80 by digital Brix, 0.77 by optical Brix, and 0.79 by optical TP refractometer. The optimal cut-off values for TIR spectroscopy, digital Brix, optical Brix, and TP refractometers to assess FTPI using serum were 13.1 g/L, 8.7% Brix, 8.4% Brix and 5.1 g/dL, respectively; and the optimal cut-off values with plasma were 13.4 g/L, 9.4% Brix, 9.3% Brix and 5.8 g/dL, respectively. When using these optimal cut-off values, the level of agreement (88.1%) between results derived from testing serum and plasma by TIR spectroscopy was substantial, with a kappa (κ) value of 0.76. The results derived from testing serum and plasma by digital Brix refractometer showed substantial agreement (83.4%), with a κ value of 0.65, which is higher than the agreement and κ value (74.7% and 0.51) reported for the optical Brix refractometer. Substantial agreement (81.6%) between serum and plasma TP was also obtained when using the optical TP refractometer, with a κ value of 0.63. In conclusion, serum or plasma samples can be used interchangeably for measuring IgG concentrations and assessing FTPI in dairy calves. However, different cut-offs must be used to assess FTPI depending on the sample matrix. Furthermore, results obtained from serum samples showed higher agreement with the reference RID assay than those obtained from plasma samples.