Standardization of SARS-CoV-2 Cycle Threshold Values: Multisite Investigation Evaluating Viral Quantitation across Multiple Commercial COVID-19 Detection Platforms

The demand for testing during the coronavirus disease 2019 (COVID-19) pandemic has resulted in the production of several different commercial platforms and laboratory-developed assays for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This has created several challenges, including, but not limited to, the standardization of diagnostic testing, utilization of cycle threshold (CT) values for quantitation and clinical interpretation, and data harmonization. Using reference standards consisting of a linear range of SARS-CoV-2 concentrations quantitated by viral culture-based methods and droplet digital PCR, we investigated the commutability and standardization of SARS-CoV-2 quantitation across different laboratories in the United States. We assessed SARS-CoV-2 CT values generated on multiple reverse transcription-PCR (RT-PCR) platforms and analyzed PCR efficiencies, linearity, gene targets, and CT value agreement. Our results demonstrate the inappropriateness of using SARS-CoV-2 CT values without established standards for viral quantitation. Further, we emphasize the importance of using reference standards and controls validated to independent assays, to compare results across different testing platforms and move toward better harmonization of COVID-19 quantitative test results. IMPORTANCE From the onset of the COVID-19 pandemic, the demand for SARS-CoV-2 testing has resulted in an explosion of analytical tests with very different approaches and designs. The variability in testing modalities, compounded by the lack of available commercial reference materials for standardization early in the pandemic, has led to several challenges regarding data harmonization for viral quantitation. In this study, we assessed multiple commercially available RT-PCR platforms across different laboratories within the United States using standardized reference materials characterized by viral culture methods and droplet digital PCR. We observed variability in the results generated by different instruments and laboratories, further emphasizing the importance of utilizing validated reference standards for quantitation, to better harmonize SARS-CoV-2 test results.

Evaluation of potential COVID-19 recurrence in patients with late repeat positive SARS-CoV-2 testing

BACKGROUND

SARS-CoV-2 reinfection and reactivation has mostly been described in case reports. We therefore investigated the epidemiology of recurrent COVID-19 SARS-CoV-2.

METHODS

Among patients testing positive for SARS-CoV-2 between March 11 and July 31, 2020 within an integrated healthcare system, we identified patients with a recurrent positive SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) assay ≥60 days after an initial positive test. To assign an overall likelihood of COVID-19 recurrence, we combined quantitative data from initial and recurrent positive RT-PCR cycle thresholds-a value inversely correlated with viral RNA burden- with a clinical recurrence likelihood assigned based on independent, standardized case review by two physicians. "Probable" or "possible" recurrence by clinical assessment was confirmed as the final recurrence likelihood only if a cycle threshold value obtained ≥60 days after initial testing was lower than its preceding cycle threshold or if the patient had an interval negative RT-PCR.

RESULTS

Among 23,176 patients testing positive for SARS-CoV-2, 1,301 (5.6%) had at least one additional SARS-CoV-2 RT-PCRs assay ≥60 days later. Of 122 testing positive, 114 had sufficient data for evaluation. The median interval to the recurrent positive RT-PCR was 85.5 (IQR 74-107) days. After combining clinical and RT-PCR cycle threshold data, four patients (3.5%) met criteria for probable COVID-19 recurrence. All four exhibited symptoms at recurrence and three required a higher level of medical care compared to their initial diagnosis. After including six additional patients (5.3%) with possible recurrence, recurrence incidence was 4.3 (95% CI 2.1-7.9) cases per 10,000 COVID-19 patients.

CONCLUSIONS

Only 0.04% of all COVID-19 patients in our health system experienced probable or possible recurrence; 90% of repeat positive SARS-CoV-2 RT-PCRs were not consistent with true recurrence. Our pragmatic approach combining clinical and quantitative RT-PCR data could aid assessment of COVID-19 reinfection or reactivation by clinicians and public health personnel.

Clinical evaluation of the acuitas® AMR gene panel for rapid detection of bacteria and genotypic antibiotic resistance determinants

Urinary tract infections are leading causes of hospital admissions. Accurate and timely diagnosis is important due to increasing morbidity and mortality from antimicrobial resistance. We evaluated a polymerase chain reaction test (Acuitas AMR Gene Panel with the Acuitas Lighthouse Software) for detection of 5 common uropathogens (Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa, Enterococcus faecalis) and antibiotic resistance genes directly from urine for prediction of phenotypic resistance. Overall percent agreement was 97% for semiquantitative detection of uropathogens versus urine culture using a cut-off of 10⁴ colony forming units per mL urine. Overall accuracy was 91% to 93% for genotypic prediction of common antibiotic resistance harbored by E. coli, K. pneumoniae, and P. mirabilis.

A consensus-based practical and daily guide for the treatment of acne patients

BACKGROUND

Many current guidelines provide detailed evidence-based recommendations for acne treatment.

OBJECTIVE

To create consensus-based, simple, easy-to-use algorithms for clinical acne treatment in daily office-based practice and to provide checklists to assist in determining why a patient may not have responded to treatment and what action to take.

METHODS

Existing treatment guidelines and consensus papers were reviewed. The information in them was extracted and simplified according to daily clinical practice needs using a consensus-based approach and based on the authors' clinical expertise.

RESULTS

As outcomes, separate simple algorithms are presented for the treatment of predominant comedonal, predominant papulopustular and nodular/conglobate acne. Patients with predominant comedonal acne should initially be treated with a topical retinoid, azelaic acid or salicylic acid. Fixed combination topicals are recommended for patients with predominant papulopustular acne with treatment tailored according to the severity of disease. Treatment recommendations for nodular/conglobate acne include oral isotretinoin or fixed combinations plus oral antibiotics in men, and these options may be supplemented with oral anti-androgenic hormonal therapy in women. Further decisions regarding treatment responses should be evaluated 8 weeks after treatment initiation in patients with predominant comedonal or papulopustular acne and 12 weeks after in those with nodular/conglobate acne. Maintenance therapy with a topical retinoid or azelaic acid should be commenced once a patient is clear or almost clear of their acne to prevent the disease from recurring. The principal explanations for lack of treatment response fall into 5 main categories: disease progression, non-drug-related reasons, drug-related reasons, poor adherence, and adverse events.

CONCLUSION

This practical guide provides dermatologists with treatment algorithms adapted to different clinical features of acne which are simple and easy to use in daily clinical practice. The checklists to establish the causes for a lack of treatment response and subsequent action to take will facilitate successful acne management.

Photonic wire biosensor microarray chip and instrumentation with application to serotyping of Escherichia coli isolates

A complete photonic wire molecular biosensor microarray chip architecture and supporting instrumentation is described. Chip layouts with 16 and 128 independent sensors have been fabricated and tested, where each sensor can provide an independent molecular binding curve. Each sensor is 50 μm in diameter, and consists of a millimeter long silicon photonic wire waveguide folded into a spiral ring resonator. An array of 128 sensors occupies a 2 × 2 mm2 area on a 6 × 9 mm2 chip. Microfluidic sample delivery channels are fabricated monolithically on the chip. The size and layout of the sensor array is fully compatible with commercial spotting tools designed to independently functionalize fluorescence based biochips. The sensor chips are interrogated using an instrument that delivers sample fluid to the chip and is capable of acquiring up to 128 optical sensor outputs simultaneously and in real time. Coupling light from the sensor chip is accomplished through arrays of sub-wavelength surface grating couplers, and the signals are collected by a fixed two-dimensional detector array. The chip and instrument are designed so that connection of the fluid delivery system and optical alignment are automated, and can be completed in a few seconds with no active user input. This microarray system is used to demonstrate a multiplexed assay for serotyping E. coli bacteria using serospecific polyclonal antibody probe molecules.

The Microstructure of High Strength Cement Pastes

The microstructures of high strength pastes of OPC and high alumina cements prepared by the high shear mixing of a low water/cement ratio paste with water soluble polymers have been studied by transmission electron microscopy. In the case of high strength OPC, the usual hydration products are present, however, the CSH gel lacks the fibrillar morphology often observed in conventional cements. Pastes based on high alumina cement do not contain the normal crystalline calcium aluminate hydrates but a small quantity of gel containing the organic polymer forms a continuous network structure bonding clinker grains. Microanalysis of the polymer phase in high alumina cement revealed the presence of Ca and Al while Ca-rich interstitial gel material was found in OPC pastes.

Guideline on the management of psoriasis in South Africa

BACKGROUND; Psoriasis vulgaris is a chronic, relapsing, immune-mediated, potentially devastating disease, influenced by genetic and environmental factors, that can cause substantial morbidity and psychological stress and have a profound negative impact on patient quality of life.

OBJECTIVE

These guidelines for the management of psoriasis have been developed in an attempt to improve the outcomes of treatment of this condition in South Africa. Psoriasis has a major impact on the quality of life of sufferers, and it is expected that these guidelines, if implemented, will play a role in achieving improved outcome.

SCOPE

These guidelines were developed to address the diagnosis and treatment of psoriasis, of differing degrees of severity and in patients of all ages, by all health care professionals involved with its management.

RECOMMENDATIONS

All health care workers involved in the management of psoriasis should take note of these guidelines and try to implement them in clinical practice as far as possible. All treatment methods and procedures not substantiated by evidence from the literature should be discontinued and avoided to decrease the financial burden of psoriasis treatment.

VALIDATION

These guidelines were developed through general consensus by a group of 8 South African dermatologists (the 'Working Group') sanctioned by the Dermatological Society of South Africa (DSSA), by adaptation for the South African situation of the current guidelines used in the USA, the UK, Germany, Canada and Finland. Draft documents were made available for comment to the dermatological community as a whole via the official website of the DSSA, and the guidelines were presented and discussed at the annual congress of the DSSA in 2008. All input from these sources, where appropriate, were then incorporated into these guidelines. GUIDELINES SPONSOR: Schering-Plough initiated the project and sponsored the meetings of the working group and all costs generated by these meetings. PLANS FOR GUIDELINE REVISION: The field of biologicals and cytokine modulators is in a rapid phase of development, and revision of the scope and content of these guidelines will be ongoing as longer-term data emerge.

Silicon-on-insulator guided mode resonant grating for evanescent field molecular sensing

We present experimental and theoretical results of label-free molecular sensing using the transverse magnetic mode of a 0.22 mum thick silicon slab waveguide with a surface grating implemented in a guided mode resonance configuration. Due to the strong overlap of the evanescent field of the waveguide mode with a molecular layer attached to the surface, these sensors exhibit high sensitivity, while their fabrication and packaging requirements are modest. Experimentally, we demonstrate a resonance wavelength shift of approximately 1 nm when a monolayer of the protein streptavidin is attached to the surface, in good agreement with calculations based on rigorous coupled wave analysis. In our current optical setup this shift corresponds to an estimated limit of detection of 0.2% of a monolayer of streptavidin.

A community change in the algal endosymbionts of a scleractinian coral following a natural bleaching event: field evidence of acclimatization

The symbiosis between reef-building corals and their algal endosymbionts (zooxanthellae of the genus Symbiodinium) is highly sensitive to temperature stress, which makes coral reefs vulnerable to climate change. Thermal tolerance in corals is known to be substantially linked to the type of zooxanthellae they harbour and, when multiple types are present, the relative abundance of types can be experimentally manipulated to increase the thermal limits of individual corals. Although the potential exists for this to translate into substantial thermal acclimatization of coral communities, to date there is no evidence to show that this takes place under natural conditions. In this study, we show field evidence of a dramatic change in the symbiont community of Acropora millepora, a common and widespread Indo-Pacific hard coral species, after a natural bleaching event in early 2006 in the Keppel Islands (Great Barrier Reef). Before bleaching, 93.5% (n=460) of the randomly sampled and tagged colonies predominantly harboured the thermally sensitive Symbiodinium type C2, while the remainder harboured a tolerant Symbiodinium type belonging to clade D or mixtures of C2 and D. After bleaching, 71% of the surviving tagged colonies that were initially C2 predominant changed to D or C1 predominance. Colonies that were originally C2 predominant suffered high mortality (37%) compared with D-predominant colonies (8%). We estimate that just over 18% of the original A. millepora population survived unchanged leaving 29% of the population C2 and 71% D or C1 predominant six months after the bleaching event. This change in the symbiont community structure, while it persists, is likely to have substantially increased the thermal tolerance of this coral population. Understanding the processes that underpin the temporal changes in symbiont communities is key to assessing the acclimatization potential of reef corals.

Ethanol, errors, and the speed-accuracy trade-off

Ethanol has been shown to have a relatively greater effect on error rates in speeded tasks than temazepam, and this may be due to a differential effect on the speed-accuracy trade-off (SATO). This study used different instruction sets to influence the SATO. Forty-nine healthy volunteers (24 males, aged 18-41 years) were allocated at random to one of three instruction conditions--emphasising accuracy, neutral, and emphasising speed. After familiarisation, they took part in two sessions spaced at least 4 days apart in which they received either ethanol (0.8 g/kg, max 60 g males, 50 g females) or placebo in randomised order. Tests were administered starting at 30 and 75 min postdrug. Instructions significantly affected performance. In two maze tasks, one on paper, the other on a pen computer, the pattern of instruction effects was as expected. A significant increase in errors with ethanol was seen for both maze tasks, and there was a tendency to speed up with ethanol (significant only for the pen computer task). Responses to fixed stimulus sequences on the Four-Choice Reaction Test also showed a tendency to speed up and an increase in errors with ethanol, while all other tests showed both slowing and increases in errors with ethanol compared to placebo. Error scores are consistently increased by ethanol in all test situations, while the effects of ethanol on speed are variable across tests.

Validity and sensitivity of a pen computer battery of performance tests

This study compared administration of performance tests and visual analogue scales (VAS) using a newly developed pen computer (PenC) battery with established tests using either pencil-and-paper (PP) or conventional computer. The performance of 47 subjects (23 male, age 18-45 years, weight 51-112 kg) was compared on the two systems after a dose of ethanol (0.8 g/kg up to a maximum of 60 g for males, 50 g for females) or placebo in a double-blind two-period randomized crossover study. Mean (SD) blood ethanol concentrations (breathalyser) were 94.5 mg/100 ml (21.9) at the start of the test battery (30 min post-drink) and 80.2 (13.0) at the end of the battery (75 min post-drink). Ethanol effects were found in all tests, with most outcome measures showing significant slowing or loss of accuracy. Results from the Rapid Visual Information Processing, Sentence Verification and Continuous Attention tasks show that the ethanol-placebo difference and the statistical significance of this difference are in close correspondence for the two modes of administration. The pen computer versions of these tasks may therefore be used as direct replacements for the previous versions. Digit-Symbol and maze tasks did not correspond so closely both showing differences in the speed-accuracy trade-off between the two modes. These tests, however, are sensitive to the effects of ethanol, and may be useful in their own right. Principal component analysis suggested that VAS may be grouped into two factors: (1) 'functional integrity', including measures of alertness and perceived proficiency, and (2) 'mood', including happiness and sociability. Factor 1 showed substantial effects of ethanol, while factor 2 was unchanged. There was close agreement between the results from PP and PenC for both factors as well as for the Sober-Drunk scale, which showed the expected effects of ethanol. Thus pen computer VAS perform in a similar way to the PP versions.

Calcium in gravitropism. A re-examination

For more than a decade it has been assumed that there is a strong relationship between Ca2+ and gravitropism. There is evidence to suggest that the movement of Ca2+ in the wall might regulate extension growth and that free intracellular Ca2+ might mediate signalling in statocytes. However, it is unlikely that changes in either wall Ca2+ or the concentration of free intracellular calcium, [Ca2+]i, act independently of each other. This results in ambiguity in both experimentation and interpretation of experimental information. It is also uncertain that the observed redistributions of wall Ca2+ are sufficient to induce bending and there is at present no direct evidence from measurement or imaging that changes in [Ca2+]i initiate or transduce gravitropic signals. The evidence relating Ca2+ to gravitropism is therefore substantial but still circumstantial. The involvement of free intracellular Ca2+ might best be tested using the new technologies of transgenic aequorin targeted to columella cells and thus resolve this important question. New information which relates control or orientation of tip-growing cells, such as pollen tubes, to cytosolic Ca2+ manipulation is presented. This information may be directly applicable to a gravitropic model system studied for many years, the Chara rhizoid.

Calcium in gravitropism. A re-examination

For more than a decade it has been assumed that there is a strong relationship between Ca2+ and gravitropism. There is evidence to suggest that the movement of Ca2+ in the wall might regulate extension growth and that free intracellular Ca2+ might mediate signalling in statocytes. However, it is unlikely that changes in either wall Ca2+ or the concentration of free intracellular calcium, [Ca2+]i, act independently of each other. This results in ambiguity in both experimentation and interpretation of experimental information. It is also uncertain that the observed redistributions of wall Ca2+ are sufficient to induce bending and there is at present no direct evidence from measurement or imaging that changes in [Ca2+]i initiate or transduce gravitropic signals. The evidence relating Ca2+ to gravitropism is therefore substantial but still circumstantial. The involvement of free intracellular Ca2+ might best be tested using the new technologies of transgenic aequorin targeted to columella cells and thus resolve this important question. New information which relates control or orientation of tip-growing cells, such as pollen tubes, to cytosolic Ca2+ manipulation is presented. This information may be directly applicable to a gravitropic model system studied for many years, the Chara rhizoid.

The role of calmodulin in the gravitropic response of the Arabidopsis thaliana agr-3 mutant

Calmodulin, a primary plant calcium receptor, is known to be intimately involved with gravitropic sensing and transduction. Using the calmodulin-binding inhibitors trifluoperazine, W7 and calmidazolium, gravitropic curvature of Arabidopsis thaliana (L.) Heynh, ecotype Landsberg, roots was separable into two phases. Phase I was detected at very low concentrations (0.01 microM) of trifluoperazine and calmidazolium, did not involve growth changes, accounted for about half the total curvature of the root and may represent the specific contribution of the cap to gravity sensing. Phase II commenced around 1.0 microM and involved inhibition of both growth and curvature. The agr-3 mutant exhibited a reduced gravitropic response and was found to lack phase I curvature, suggesting that the mutation alters either use or expression of calmodulin. The sequences of wild-type and agr-3 calmodulin (CaM-1) cDNAs, which are root specific were completely determined and found to be identical. Upon gravitropic stimulation, wild-type Arabidopsis seedlings increased calmodulin mRNA levels by threefold in 0.5 h. On the other hand, gravitropic stimulation of agr-3 decreased calmodulin mRNA accumulation. The possible basis of the two phases of curvature is discussed and it is concluded that agr-3 has a lesion located in a general gravity transmission sequence, present in many root cells, which involves calmodulin mRNA accumulation.

Effects of nitrous oxide on psychological performance. A dose-response study using inhalation of concentrations up to 15%

In this six-period randomised double-blind study, 12 healthy volunteers inhaled mixtures of nitrous oxide at concentrations of 0% (placebo); 3%, 5%, 7%, 10%, and 15% in oxygen. Each concentration was inhaled for 55 min, each period being on a separate day. The order of treatments was randomised using a Latin-Square design. The effects of nitrous oxide were assessed using a battery of performance tests which included measures of attention, psychomotor function, memory and cognition. Mood was assessed using visual analogue scales. Measures of attention and psychomotor performance showed impairment at 15% nitrous oxide, and subjective measures showed sedation at this dose. The Buschke Selective Reminding Task showed impairment to long-term recall at all doses of nitrous oxide compared to placebo, while short-term recall was impaired only at 15%. These results suggest that consolidation of memory may be particularly sensitive to disruption as a result of CNS depression.

In vivo validation of the release rate and palatability of remoxipride-modified release suspension

Remoxipride, a D2-dopamine receptor antagonist, is well tolerated and completely absorbed after oral administration. Because of its extremely bitter taste, an oral palatable suspension was developed by using a taste-masking microencapsulation. The bioavailability of remoxipride was investigated in two studies in healthy volunteers after administration of a 100-mg dose in suspension. The first study used a capsule as reference, and the second study a plain solution. Taste assessment was carried out in the second study. The extent of bioavailability was the same when comparing the oral suspension to a capsule and to a plain solution. However, the rate of absorption is delayed, and Tmax was 3.0 hr after the suspension, 1.0 hr after the oral solution, and 1.6 hr after the capsule. The release rate in vitro from the suspension was determined by applying the USP-paddle method. By using numerical convolution and deconvolution, the release rates in vivo and in vitro were shown to be similar when using water with 0.5% sodium lauryl sulfate as dissolution liquid. The taste-masked oral suspension is suitable for full-scale production, with good control of the encapsulation process and of the preparation of a suspension.

Lymphangioleiomyomatosis presenting in a postmenopausal woman

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Orienting behaviour during aerial and underwater visual discrimination by the mink (Mustela vison schreber)

Orienting responses by mink during aerial and underwater visual discrimination tests were most frequent when the grating lines subtended angles at the eye near the visual threshold angle. Factorial analysis showed that in air and in water at ranges from 10 to 90 cm most responses occurred at 30 cm discrimination distance and more occurred to marginally supra-threshold than to marginally sub-threshold stimuli. Between media, more responses occurred in air than in water. At longer ranges the mink oriented less readily than at 30 cm but if orienting occurred better discrimination followed than if the mink did not orient.

Comparative aerial and underwater visual acuity of the mink, Mustela vison schreber, as a function of discrimination distance and stimulus luminance

The aerial threshold visual angle of mink rose from 15.4 min at 10 cm stimulus distance to 19.1 min at 90 cm and the underwater angle varied from 32.7 min at 10 cm to 46.6 min at 90 cm, all at 34 mL luminance. At constant 30 cm stimulus distance, the aerial angle rose from 15 min at 34 mL to 51.7 min at 0.012 mL, the underwater angle from 31.4 min at 34 mL to 95 min at 0.012 mL, the aerial and underwater data forming similar curves. If mink hunt in water at somewhat higher light levels than in air they can obtain equal acuities in the two media.

The formation, isolation and importance of isopeptides in heated proteins

The separation and resolution of the isopeptides Nepsilon (gamma-L-glutamyl)-L-lysine and Nepsilon (beta-aspertyl)-L-lysine, formed in heated proteins, has been successfully achieved. The method demands a well characterised ion-exchange column and the use of pH 3.40 lithium citrate buffer (O.2N Li+). Due to variations in particle size and percentage crosslinkages in the ion-exchange resin a computer assisted buffer gradient system has been developed. This system affects resolution of both isopeptides in 7h. The use of leucyl-glycine as an internal standard facilitates quantitative estimation of the isopeptides. This separative method has been used to analyse a series of heated protein samples and to estimate the quantities of isopeptides formed. The ability of a protein to form isopeptides links is discussed as well as the implication of such links on the reactivity and digestibility of proteins.

Ultrastructural Studies Relating to the Surface Morphology of Cultured Cells

Scanning electron microscopy and a surface-replica technique for transmission electron microscopy have been used to study the ultrastructural features of cultured-cell surfaces The presence of microvilli measuring 0.1-0.2 µm in diameter by up to 5 µm in length has been noted as a regular feature of Landschütz ascites, ‘fibroblastic’ HeLa, and canine kidney, cells. The surfaces of chick mesenchyme cells were notably almost devoid of microvilli. The presence of microvilli at the cell surface is discussed briefly.