Review of COVID-19 testing and diagnostic methods

More than six billion tests for COVID-19 has been already performed in the world. The testing for SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) virus and corresponding human antibodies is essential not only for diagnostics and treatment of the infection by medical institutions, but also as a pre-requisite for major semi-normal economic and social activities such as international flights, off line work and study in offices, access to malls, sport and social events. Accuracy, sensitivity, specificity, time to results and cost per test are essential parameters of those tests and even minimal improvement in any of them may have noticeable impact on life in the many countries of the world. We described, analyzed and compared methods of COVID-19 detection, while representing their parameters in 22 tables. Also, we compared test performance of some FDA approved test kits with clinical performance of some non-FDA approved methods just described in scientific literature. RT-PCR still remains a golden standard in detection of the virus, but a pressing need for alternative less expensive, more rapid, point of care methods is evident. Those methods that may eventually get developed to satisfy this need are explained, discussed, quantitatively compared. The review has a bioanalytical chemistry prospective, but it may be interesting for a broader circle of readers who are interested in understanding and improvement of COVID-19 testing, helping eventually to leave COVID-19 pandemic in the past.

Molecular specificity of L2 monoclonal antibodies that bind to carbohydrate determinants of neural cell adhesion molecules and their resemblance to other monoclonal antibodies recognizing the myelin-associated glycoprotein

L2 monoclonal antibodies and HNK-1 have been shown to bind to related carbohydrate determinants in the myelin-associated glycoprotein (MAG) and several adhesion molecules of the nervous system including neural cell adhesion molecule (N-CAM), L1 and J1. It is shown here that MAG is the principal component in human white matter binding the L2 antibodies, but the most prominent antigens with the L2 epitopes in human gray matter are of higher Mr. It is also shown that the L2 antibodies resemble HNK-1 in binding to some 19-28 kDa glycoproteins and some sulfated, glucuronic acid-containing sphingoglycolipids of the peripheral nervous system (PNS). In addition, monoclonal and polyclonal antibodies raised to human MAG are shown to cross react with bovine N-CAM due to the presence of common carbohydrate constituents. The results further emphasize the shared antigenicity between MAG, N-CAM and other adhesion molecules. In addition, they demonstrate that the L2 antibodies belong to a family of monoclonal antibodies (including HNK-1, human IgM paraproteins associated with neuropathy, and others) that are characterized by reactivity against carbohydrate determinants shared by human MAG, the 19-28 kDa glycoproteins of the PNS and the sulfated, glucuronic acid-containing sphingoglycolipids of the PNS.

SERS immuno- and apta-assays in biosensing/bio-detection: Performance comparison, clinical applications, challenges

Surface Enhanced Raman Spectroscopy is increasingly used as a sensitive bioanalytical tool for detection of variety of analytes ranging from viruses and bacteria to cancer biomarkers and toxins, etc. This comprehensive review describes principles of operation and compares the performance of immunoassays and aptamer assays with Surface Enhanced Raman scattering (SERS) detection to each other and to some other bioassay methods, including ELISA and fluorescence assays. Both immuno- and aptamer-based assays are categorized into assay on solid substrates, assays with magnetic nanoparticles and assays in laminar flow or/and strip assays. The best performing and recent examples of assays in each category are described in the text and illustrated in the figures. The average performance, particularly, limit of detection (LOD) for each of those methods reflected in 9 tables of the manuscript and average LODs are calculated and compared. We found out that, on average, there is some advantage in terms of LOD for SERS immunoassays (0.5 pM median LOD of 88 papers) vs SERS aptamer-based assays (1.7 pM median LOD of 51 papers). We also tabulated and analyzed the clinical performance of SERS immune and aptamer assays, where selectivity, specificity, and accuracy are reported, we summarized the best examples. We also reviewed challenges to SERS bioassay performance and real-life application, including non-specific protein binding, nanoparticle aggregation, limited nanotag stability, sometimes, relatively long time to results, etc. The proposed solutions to those challenges are also discussed in the review. Overall, this review may be interesting not only to bioanalytical chemist, but to medical and life science researchers who are interested in improvement of bioanalyte detection and diagnostics.

Physiological homeostasis for ecological success of Typha (Typha domingensis Pers.) populations in saline soils

The natural capacity of plants to endure salt stress is largely regulated by multifaceted structural and physio-biochemical modulations. Salt toxicity endurance mechanism of six ecotypes of Typha domingensis Pers. was evaluated by analyzing photosynthesis, ionic homeostasis, and stomatal physiology under different levels of salinity (0, 100, 200 and 300 mM NaCl). Typha populations were collected across different areas of Punjab, an eastern province in Pakistan. All studied attributes among ecotypes presented differential changes as compared to control. Different salt treatments not only affected gas exchange attributes but also shown significant modifications in stomatal anatomical changes. As compared to control, net photosynthetic rate, transpiration rate, total chlorophyll contents and carotenoids were increased by 111%, 64%, 103% and 171% respectively, in Sahianwala ecotype among all other ecotypes. Similarly, maximum water use efficiency (WUE), sub stomatal CO2 concentration, sodium (Na+) and chloride (Cl-) contents were observed in Sahianwala (191%, 93%, 168%, 158%) and Knotti (162%, 75%, 146%, 182%) respectively, as compared to the others ecotypes. Adaxial and abaxial stomatal areas remained stable in Sahianwala and Knotti. The highest abaxial stomatal density was observed in Gatwala ecotype (42 mm2) and maximum adaxial stomatal density was recorded in Sahianwala ecotype (43 mm2) at 300 mM NaCl salinity. The current study showed that Typha ecotypes responded varyingly to salinity in terms of photosynthesis attributes to avoid damages due to salinity. Overall, differential photosynthetic activity, WUE, and changes in stomatal attributes of Sahianwala and Knotti ecotypes contributed more prominently in tolerating salinity stress. Therefore, Typha domingensis is a potential species to be used to rehabilitate salt affected lands for agriculture and aquatic habitat.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-00963-x.

SERS for Detection of Proteinuria: A Comparison of Gold, Silver, Al Tape, and Silicon Substrates for Identification of Elevated Protein Concentration in Urine

Excessive protein excretion in human urine is an early and sensitive marker of diabetic nephropathy and primary and secondary renal disease. Kidney problems, particularly chronic kidney disease, remain among the few growing causes of mortality in the world. Therefore, it is important to develop an efficient, expressive, and low-cost method for protein determination. Surface enhanced Raman spectroscopy (SERS) methods are potential candidates to achieve these criteria. In this paper, a SERS method was developed to distinguish patients with proteinuria from the healthy group. Commercial gold nanoparticles (AuNPs) with diameters of 60 nm and 100 nm, and silver nanoparticles (AgNPs) with a diameter of 100 nm were tested on the surface of four different substrates including silver and gold films, silicon, and aluminum tape. SERS spectra were acquired from 111 unique human urine samples prepared and measured for each of the seven different nanoparticle plus substrate combinations. Data analysis by the PCA-LDA algorithm and the ROC curves gave results for the diagnostic figures of merits. The best sensitivity, specificity, accuracy, and AUC were 0.91, 0.84, 0.88, and 0.94 for the set with 100 nm Au NPs on the silver substrate, respectively. Among the three metal substrates, the substrate with AuNPs and Al tape performed slightly worse than the other three substrates, and 100 nm gold nanoparticles on average produced better results than 60 nm gold nanoparticles. The 60 nm diameter AuNPs and silicon, which is about one order of magnitude more cost-effective than AuNPs and gold film, showed a relative performance close to the performance of 60 nm AuNPs and Au film (average AUC 0.88 (Si) vs. 0.89 (Au)). This is likely the first reported application of unmodified silicon in SERS substrates applied for direct detection of proteins in any biofluid, particularly in urine. These results position silicon and AuNPs@Si in particular as a perspective SERS substrate for direct urine analysis, including clinical diagnostics of proteinuria.

Ruptured Intracranial Aneurysms Treated with the Pipeline Embolization Device: A Systematic Review and Pooled Analysis of Individual Patient Data

BACKGROUND

The Pipeline Embolization Device (PED) is a flow-diverting stent for the treatment of intracranial aneurysms and is used off-label for a subset of ruptured aneurysms not amenable to traditional treatment.

PURPOSE

Our aim was to evaluate the safety and efficacy of the PED for treatment of ruptured intracranial aneurysms.

DATA SOURCES

A systematic review of the MEDLINE, EMBASE, and Scopus data bases from January 2011 to March 2020 was performed for articles reporting treatment of ruptured intracranial aneurysms with the PED.

STUDY SELECTION

A total of 12 studies comprising 145 patients with 145 treated aneurysms were included for analysis.

DATA ANALYSIS

Individual patient data were collected. Nonparametric tests were used to compare differences among patients. Logistic regression was used to determine an association with outcome variables.

DATA SYNTHESIS

Mean aneurysm size was 5.9 mm, and most were blister (51.0%) or dissecting (26.9%) in morphology. Three (2.1%) aneurysms reruptured following PED placement. Univariate logistic regression identified larger aneurysm size as a significant predictor of aneurysm rerupture (P = .008). Of patients with radiographic follow-up, 87.5% had complete aneurysm occlusion. Symptomatic neurologic complications occurred in 16.5%.

LIMITATIONS

Analysis was limited by the quality of the included data, most of which were from small case series representing class III medical evidence. No study assessed outcome in a blinded or independently adjudicated manner.

CONCLUSIONS

Most ruptured aneurysms treated with the PED were blister or dissecting aneurysms. Treatment was associated with a rerupture rate of 2.1% and a complete occlusion rate of 87.5%.

Trends in Application of SERS Substrates beyond Ag and Au, and Their Role in Bioanalysis

This article compares the applications of traditional gold and silver-based SERS substrates and less conventional (Pd/Pt, Cu, Al, Si-based) SERS substrates, focusing on sensing, biosensing, and clinical analysis. In recent decades plethora of new biosensing and clinical SERS applications have fueled the search for more cost-effective, scalable, and stable substrates since traditional gold and silver-based substrates are quite expensive, prone to corrosion, contamination and non-specific binding, particularly by S-containing compounds. Following that, we briefly described our experimental experience with Si and Al-based SERS substrates and systematically analyzed the literature on SERS on substrate materials such as Pd/Pt, Cu, Al, and Si. We tabulated and discussed figures of merit such as enhancement factor (EF) and limit of detection (LOD) from analytical applications of these substrates. The results of the comparison showed that Pd/Pt substrates are not practical due to their high cost; Cu-based substrates are less stable and produce lower signal enhancement. Si and Al-based substrates showed promising results, particularly in combination with gold and silver nanostructures since they could produce comparable EFs and LODs as conventional substrates. In addition, their stability and relatively low cost make them viable alternatives for gold and silver-based substrates. Finally, this review highlighted and compared the clinical performance of non-traditional SERS substrates and traditional gold and silver SERS substrates. We discovered that if we take the average sensitivity, specificity, and accuracy of clinical SERS assays reported in the literature, those parameters, particularly accuracy (93-94%), are similar for SERS bioassays on AgNP@Al, Si-based, Au-based, and Ag-based substrates. We hope that this review will encourage research into SERS biosensing on aluminum, silicon, and some other substrates. These Al and Si based substrates may respond efficiently to the major challenges to the SERS practical application. For instance, they may be not only less expensive, e.g., Al foil, but also in some cases more selective and sometimes more reproducible, when compared to gold-only or silver-only based SERS substrates. Overall, it may result in a greater diversity of applicable SERS substrates, allowing for better optimization and selection of the SERS substrate for a specific sensing/biosensing or clinical application.

Stenotrophomonas maltophilia Meningitis - A Case Series and Review of the Literature

Stenotrophomonas maltophilia is an infrequent cause of acute bacterial meningitis and only a few cases have been reported in the literature. Infection is associated with morbidity and mortality, and its optimal management remains ill-defined. The aim of the current study is to review the management of S. maltophilia meningitis.

We described two cases of S. maltophilia meningitis following neurosurgical procedures. The first patient was a 60-year-old female. She was admitted to the hospital with a left basal ganglia bleed and underwent placement of an external ventricular drain for the treatment of hydrocephalus. She developed S. maltophilia meningitis 20 days after surgery. She was successfully treated with a combination of trimethoprim-sulfamethoxazole and intravenous colistin and the removal of the drain. She successfully underwent a ventriculoperitoneal (VP) shunt placement at the therapeutic midway point. The second patient was a 35-year-old male with a history of intracranial aneurysm bleeding. He had undergone a craniotomy and placement of a ventriculoperitoneal shunt two years previously. His shunt was replaced twice due to blockage. The last replacement had occurred 15 days prior to the development of meningitis. He was treated with a combination of trimethoprim-sulfamethoxazole and ceftazidime (as well as undergoing another shunt replacement) and experienced an excellent recovery.

S. maltophilia is a rare but important cause of nosocomial meningitis. It is strongly associated with prior hospitalization and neurosurgical intervention, which is also found in our case series. The management of S. maltophilia meningitis is a therapeutic challenge due to its high resistance to multiple antibiotics. Optimal therapy is based on antimicrobial sensitivity, and the trimethoprim-sulfamethoxazole-based combination has been shown to be successful. The duration of therapy is debatable, but like most gram-negative meningitis infections, therapy lasting up to three weeks appears to be adequate.

Effects of substrate induced respiration on the stability of bottom ash in landfill cover environment

The municipal solid waste incineration bottom ash is being increasingly used to construct landfill covers in Sweden. In post-closure, owing to increased cover infiltration, the percolating water can add external organic matter to bottom ash. The addition and subsequent degradation of this external organic matter can affect metal mobility through complexation and change in redox conditions. However, the impacts of such external organic matter addition on bottom ash stability have not been fully evaluated yet. Therefore, the objective of this study was to evaluate the impact of external organic matter on bottom ash respiration and metal leaching. The samples of weathered bottom ash were mixed with oven dried and digested wastewater sludge (1%-5% by weight). The aerobic respiration activity (AT4), as well as the leaching of metals, was tested with the help of respiration and batch leaching tests. The respiration and heavy metal leaching increased linearly with the external organic matter addition. Based on the results, it was concluded that the external organic matter addition would negatively affect the quality of landfill cover drainage.

Residual organic matter and microbial respiration in bottom ash: Effects on metal leaching and eco-toxicity

A common assumption regarding the residual organic matter, in bottom ash, is that it does not represent a significant pool of organic carbon and, beyond metal-ion complexation process, it is of little consequence to evolution of ash/leachate chemistry. This article evaluates the effect of residual organic matter and associated microbial respiratory processes on leaching of toxic metals (i.e. arsenic, copper, chromium, molybdenum, nickel, lead, antimony and zinc), eco-toxicity of ash leachates. Microbial respiration was quantified with help of a respirometric test equipment OXITOP control system. The effect of microbial respiration on metal/residual organic matter leaching and eco-toxicity was quantified with the help of batch leaching tests and an eco-toxicity assay - Daphnia magna. In general, the microbial respiration process decreased the leachate pH and eco-toxicity, indicating modification of bioavailability of metal species. Furthermore, the leaching of critical metals, such as copper and chromium, decreased after the respiration in both ash types (fresh and weathered). It was concluded that microbial respiration, if harnessed properly, could enhance the stability of fresh bottom ash and may promote its reuse.

Ex-vivo antihypertensive and calcium channel blocking activity of Androsace foliosa n-hexane leaves fraction on isolated rabbit aorta

Hypertension is persistent elevation in blood pressure for 3-4 weeks. Estimated global prevalence of hypertension suggested that by the Year 2025 (29%) of adult worldwide are suffering from hypertension (1.56 billion). Hypertension complications are hemorrhage, atherosclerosis, renal artery stenosis, angina pectoris end organ damage, cardiomyopathy, myocardial infarction and retinopathy. Along with other drug class Calcium channel blocker are also used for the treatment of hypertension. In this study the possible action of the n-hexane leaves fraction of the Androsace foliosa on isolated rabbit aorta was examined. Antihypertensive activity was examined in the existence of standard agonist like phenylephrine and antagonist like Verapamil. Phenylephrine (PE 1μM) high K⁺ was used to steady the tissue materials. Additionally to observe the calcium channel blocking effect the tissues were treated with n-hexane segment of A. foliosa leaves. Aortic tissues were treated 4-5intervals with Ca^+2- free preparation earlier to control calcium reaction curve (CRCs). Verapamil is utilized as standard calcium channel inhibitory mediator and is used as an antagonist. The Af. n-hexane leaves fraction completely inhibited the precontractions induced by Phenylephrine (1μM) and K⁺ (80 mM) precontractions, with EC₅₀ standards of 1.0mM (0.3-1.0mg/mL) and 4.90mM (1-3mg/mL), respectively. Androsace foliosa n-hexane leaves fraction was tested for calcium channel inhibitory effect on isolated rabbit aorta. A. foliosa n- hexane leaves segment at the dosage of 1mg/mL block the calcium channel approximately (35±5%). Consequence indicates that A. foliosa n-hexane leaves segment block calcium channel in the similar manner as compared to the standard calcium channel blocker drug (verapamil).