SARS-CoV-2 recombinase polymerase amplification assay with lateral flow readout and duplexed full process internal control

Nucleic acid amplification tests for the detection of SARS-CoV-2 have been an important testing mechanism for the COVID-19 pandemic. While these traditional nucleic acid diagnostic methods are highly sensitive and selective, they are not suited to home or clinic-based uses. Comparatively, rapid antigen tests are cost-effective and user friendly but lack in sensitivity and specificity. Here we report on the development of a one-pot, duplexed reverse transcriptase recombinase polymerase amplification SARS-CoV-2 assay with MS2 bacteriophage as a full process control. Detection is carried out with either real-time fluorescence or lateral flow readout with an analytical sensitivity of 50 copies per reaction. Unlike previously published assays, the RNA-based MS2 bacteriophage control reports on successful operation of lysis, reverse transcription, and amplification. This SARS-CoV-2 assay features highly sensitive detection, visual readout through an LFA strip, results in less than 25 minutes, minimal instrumentation, and a useful process internal control to rule out false negative test results.

REverSe TRanscrIptase chain termination (RESTRICT) for selective measurement of nucleotide analogs used in HIV care and prevention

Sufficient drug concentrations are required for efficacy of antiretroviral drugs used in HIV care and prevention. Measurement of nucleotide analogs, included in most HIV medication regimens, enables monitoring of short- and long-term adherence and the risk of treatment failure. The REverSe TRanscrIptase Chain Termination (RESTRICT) assay rapidly infers the concentration of intracellular nucleotide analogs based on the inhibition of DNA synthesis by HIV reverse transcriptase enzyme. Here, we introduce a probabilistic model for RESTRICT and demonstrate selective measurement of multiple nucleotide analogs using DNA templates designed according to the chemical structure of each drug. We measure clinically relevant concentrations of tenofovir diphosphate, emtricitabine triphosphate, lamivudine triphosphate, and azidothymidine triphosphate with agreement between experiment and theory. RESTRICT represents a new class of activity-based assays for therapeutic drug monitoring in HIV care and could be extended to other diseases treated with nucleotide analogs.

Rapid detection of hepatitis C virus using recombinase polymerase amplification

Over 71 million people are infected with hepatitis C virus (HCV) worldwide, and approximately 400,000 global deaths result from complications of untreated chronic HCV. Pan-genomic direct-acting antivirals (DAAs) have recently become widely available and feature high cure rates in less than 12 weeks of treatment. The rollout of DAAs is reliant on diagnostic tests for HCV RNA to identify eligible patients with viremic HCV infections. Current PCR-based HCV RNA assays are restricted to well-resourced central laboratories, and there remains a prevailing clinical need for expanded access to decentralized HCV RNA testing to provide rapid chronic HCV diagnosis and linkage to DAAs in outpatient clinics. This paper reports a rapid, highly accurate, and minimally instrumented assay for HCV RNA detection using reverse transcription recombinase polymerase amplification (RT-RPA). The assay detects all HCV genotypes with a limit of detection of 25 copies per reaction for genotype 1, the most prevalent in the United States and worldwide. The clinical sensitivity and specificity of the RT-RPA assay were both 100% when evaluated using 78 diverse clinical serum specimens. The accuracy, short runtime, and low heating demands of RT-RPA may enable implementation in a point-of-care HCV test to expand global access to effective treatment via rapid chronic HCV diagnosis.

Quantitative isothermal amplification on paper membranes using amplification nucleation site analysis

Quantitative nucleic acid amplification tests (qNAATs) are critical in treating infectious diseases, such as in HIV viral load monitoring or SARS-CoV-2 testing, in which viral load indicates viral suppression or infectivity. Quantitative PCR is the gold standard tool for qNAATs; however, there is a need to develop point-of-care (POC) qNAATs to manage infectious diseases in outpatient clinics, low- and middle-income countries, and the home. Isothermal amplification methods are an emerging tool for POC NAATs as an alternative to traditional PCR-based workflows. Previous works have focused on relating isothermal amplification bulk fluorescence signals to input copies of target nucleic acids for sample quantification with limited success. In this work, we show that recombinase polymerase amplification (RPA) reactions on paper membranes exhibit discrete fluorescent amplification nucleation sites. We demonstrate that the number of nucleation sites can be used to quantify HIV-1 DNA and viral RNA in less than 20 minutes. An image-analysis algorithm quantifies nucleation sites and determines the input nucleic acid copies in the range of 67-3000 copies per reaction. We demonstrate a mobile phone-based system for image capture and onboard processing, illustrating that this method may be used at the point-of-care for qNAATs with minimal instrumentation.

HIV pre-exposure prophylaxis adherence test using reverse transcription isothermal amplification inhibition assay

Current HIV antiretroviral therapy (ART) or pre-exposure prophylaxis (PrEP) therapy adherence monitoring relies on either patient self-reported adherence or monitored drug dispensing, which are not reliable. We report a proof-of-concept adherence monitoring assay which directly measures nucleotide reverse transcriptase inhibitor (NRTI) concentration using a reverse transcription isothermal amplification inhibition assay. We measure the concentration of Tenofovir diphosphate (TFV-DP) - an NRTI that functions as a deoxyadenosine triphosphate (dATP) analog and long-term adherence marker for PrEP - by measuring the inhibition of the reverse transcription of an RNA template. The completion or inhibition of reverse transcription is evaluated by recombinase polymerase amplification (RPA), an isothermal nucleic acid amplification assay commonly used for point-of-care diagnostics. We present and validate a model that predicts the amplification probability as a function of dATP and TFV-DP concentrations, nucleotide insertion sites on the RNA template, and RNA template concentration. The model can be used to rationally design and optimize the assay to operate at clinically relevant TFV-DP concentrations. We provide statistical analysis that demonstrates how the assay may be used as a qualitative or semi-quantitative tool for measuring adherence to NRTI drugs and used to support patient compliance. Due to its simple instrumentation and short runtime (<1 hour), this assay has the potential for implementation in low-complexity laboratories or point-of-care settings, which may improve access to ART and PrEP adherence monitoring.

Quantitative Isothermal Amplification on Paper Membranes using Amplification Nucleation Site Analysis

Quantitative nucleic acid amplification tests (qNAATs) are critical in treating infectious diseases, such as in HIV viral load monitoring or SARS-CoV-2 testing, in which viral load indicates viral suppression or infectivity. Quantitative PCR is the gold standard tool for qNAATs; however, there is a need to develop point-of-care (POC) qNAATs to manage infectious diseases in outpatient clinics, low- and middle-income countries, and the home. Isothermal amplification methods are an emerging tool for POC NAATs as an alternative to traditional PCR-based workflows. Previous works have focused on relating isothermal amplification bulk fluorescence signals to input copies of target nucleic acids for sample quantification with limited success. In this work, we show that recombinase polymerase amplification (RPA) reactions on paper membranes exhibit discrete fluorescent amplification nucleation sites. We demonstrate that the number of nucleation sites can be used to quantify HIV-1 DNA and RNA in less than 20 minutes. An image-analysis algorithm quantifies nucleation sites and determines the input nucleic acid copies in the range of 67-3,000 copies per reaction. We demonstrate a mobile phone-based system for image capture and onboard processing, illustrating that this method may be used at the point-of-care for qNAATs with minimal instrumentation.

HIV detection from human serum with paper-based isotachophoretic RNA extraction and reverse transcription recombinase polymerase amplification

The number of people living with HIV continues to increase with the current total near 38 million, of which about 26 million are receiving antiretroviral therapy (ART). These treatment regimens are highly effective when properly managed, requiring routine viral load monitoring to assess successful viral suppression. Efforts to expand access by decentralizing HIV nucleic acid testing in low- and middle-income countries (LMICs) has been hampered by the cost and complexity of current tests. Sample preparation of blood samples has traditionally relied on cumbersome RNA extraction methods, and it continues to be a key bottleneck for developing low-cost POC nucleic acid tests. We present a microfluidic paper-based analytical device (μPAD) for extracting RNA and detecting HIV in serum, leveraging low-cost materials, simple buffers, and an electric field. We detect HIV virions and MS2 bacteriophage internal control in human serum using a novel lysis and RNase inactivation method, paper-based isotachophoresis (ITP) for RNA extraction, and duplexed reverse transcription recombinase polymerase amplification (RT-RPA) for nucleic acid amplification. We design a specialized ITP system to extract and concentrate RNA, while excluding harsh reagents used for lysis and RNase inactivation. We found the ITP μPAD can extract and purify 5000 HIV RNA copies per mL of serum. We then demonstrate detection of HIV virions and MS2 bacteriophage in human serum within 45-minutes.

Pilot evaluation of an enzymatic assay for rapid measurement of antiretroviral drug concentrations

Objective

Maintaining adequate drug adherence is crucial to ensure the HIV prevention benefits of pre-exposure prophylaxis (PrEP). We developed an enzymatic assay for rapidly measuring tenofovir-diphosphate (TFV-DP) concentrations—a metabolite that indicates long-term PrEP adherence.

Setting

The study was conducted at the Madison HIV Clinic at Harborview Medical Center in Seattle.

Methods

We enrolled adults receiving standard oral PrEP, and individuals not receiving any antiretrovirals. We measured TFV-DP concentrations in diluted whole blood using our novel REverSe TRanscrIptase Chain Termination (RESTRICT) assay, based on inhibition of HIV reverse transcriptase (RT) enzyme. Blood samples were diluted in water, DNA templates, nucleotides, RT, and intercalating dye added, and results measured with a fluorescence reader—stronger fluorescence indicated higher RT activity. We compared RESTRICT assay results to TFV-DP concentrations from matched dried blood spot samples measured by liquid chromatography tandem mass spectrometry (LC–MS/MS) using ≥ 700 fmol/punch TFV-DP as a threshold for adequate adherence (≥ 4 doses/week).

Results

Among 18 adults enrolled, 4 of 7 participants receiving PrEP had TFV-DP levels ≥ 700 fmol/punch by LC–MS/MS. RESTRICT fluorescence correlated with LC–MS/MS measurements (r = − 0.845, p < 0.0001). Median fluorescence was 93.3 (95% confidence interval [CI] 90.9 to 114) for samples < 700 fmol/punch and 54.4 (CI 38.0 to 72.0) for samples ≥ 700 fmol/punch. When calibrated to an a priori defined threshold of 82.7, RESTRICT distinguished both groups with 100% sensitivity and 92.9% specificity.

Conclusions

This novel enzymatic assay for measuring HIV reverse transcriptase activity may be suitable for distinguishing TFV-DP concentrations in blood that correspond to protective PrEP adherence.

Nucleic acid sample preparation from whole blood in a paper microfluidic device using isotachophoresis

Nucleic acid amplification tests (NAATs) are a crucial diagnostic and monitoring tool for infectious diseases. A key procedural step for NAATs is sample preparation: separating and purifying target nucleic acids from crude biological samples prior to nucleic acid amplification and detection. Traditionally, sample preparation has been performed with liquid- or solid-phase extraction, both of which require multiple trained user steps and significant laboratory equipment. The challenges associated with sample preparation have limited the dissemination of NAAT point-of-care diagnostics in low resource environments, including low- and middle-income countries. We report on a paper-based device for purification of nucleic acids from whole blood using isotachophoresis (ITP) for point-of-care NAATs. We show successful extraction and purification of target nucleic acids from large volumes (33 µL) of whole human blood samples with no moving parts and few user steps. Our device utilizes paper-based buffer reservoirs to fully contain the liquid ITP buffers and does not require complex filling procedures, instead relying on the natural wicking of integrated paper membranes. We perform on-device blood fractionation via filtration to remove leukocytes and erythrocytes from our sample, followed by integrated on-paper proteolytic digestion of endogenous plasma proteins to allow for successful isotachophoretic extraction. Paper-based isotachophoresis purifies and concentrates target nucleic acids that are added directly to recombinase polymerase amplification (RPA) reactions. We show consistent amplification of input copy concentrations of as low as 3 × 10³ copies nucleic acid per mL input blood with extraction and purification taking only 30 min. By employing a paper architecture, we are able to incorporate these processes in a single, robust, low-cost design, enabling the direct processing of large volumes of blood, with the only intermediate user steps being the removal and addition of tape. Our device represents a step towards a simple, fully integrated sample preparation system for nucleic acid amplification tests at the point-of-care.

Enzymatic and Chemical-Based Methods to Inactivate Endogenous Blood Ribonucleases for Nucleic Acid Diagnostics

There are ongoing research efforts into simple and low-cost point-of-care nucleic acid amplification tests (NATs) addressing widespread diagnostic needs in resource-limited clinical settings. Nucleic acid testing for RNA targets in blood specimens typically requires sample preparation that inactivates robust blood ribonucleases (RNases) that can rapidly degrade exogenous RNA. Most NATs rely on decades-old methods that lyse pathogens and inactivate RNases with high concentrations of guanidinium salts. Herein, we investigate alternatives to standard guanidinium-based methods for RNase inactivation using an activity assay with an RNA substrate that fluoresces when cleaved. The effects of proteinase K, nonionic surfactants, SDS, dithiothreitol, and other additives on RNase activity in human serum are reported. Although proteinase K has been widely used in protocols for nuclease inactivation, it was found that high concentrations of proteinase K are unable to eliminate RNase activity in serum, unless used in concert with denaturing concentrations of SDS. It was observed that SDS must be combined with proteinase K, dithiothreitol, or both for irreversible and complete RNase inactivation in serum. This work provides an alternative chemistry for inactivating endogenous RNases for use in simple, low-cost point-of-care NATs for blood-borne pathogens.

Enzymatic Assay for Rapid Measurement of Antiretroviral Drug Levels

Poor adherence to pre-exposure prophylaxis (PrEP) and antiretroviral therapy (ART) can lead to human immunodeficiency virus (HIV) acquisition and emergence of drug-resistant infections, respectively. Measurement of antiviral drug levels provides objective adherence information that may help prevent adverse health outcomes. Gold-standard drug-level measurement by liquid chromatography/mass spectrometry is centralized, heavily instrumented, and expensive and is thus unsuitable and unavailable for routine use in clinical settings. We developed the REverSe TRanscrIptase Chain Termination (RESTRICT) assay as a rapid and accessible measurement of drug levels indicative of long-term adherence to PrEP and ART. The assay uses designer single-stranded DNA templates and intercalating fluorescent dyes to measure complementary DNA (cDNA) formation by reverse transcriptase in the presence of nucleotide reverse transcriptase inhibitor drugs. We optimized the RESTRICT assay using aqueous solutions of tenofovir diphosphate (TFV-DP), a metabolite that indicates long-term adherence to ART and PrEP, at concentrations over 2 orders of magnitude above and below the clinically relevant range. We used dilution in water as a simple sample preparation strategy to detect TFV-DP spiked into whole blood and accurately distinguished TFV-DP drug levels corresponding to low and high PrEP adherences. The RESTRICT assay is a fast and accessible test that could be useful for patients and clinicians to measure and improve ART and PrEP adherence.

Acceleration of N-nitrosation reactions by electrophiles

Selected mechanisms by which electrophiles can facilitate N-nitrosamine formation are reviewed. Special attention is given to a recently discovered reaction in which nitrogen in its lowest (ammonia) oxidation state is efficiently converted to N-nitroso compounds by oxidation in the presence of secondary amines; an electrophilic transition metal centre (E+) makes this reaction possible by initially N-coordinating the ammonia (E+ + NH3----E-NH3+). Other mechanisms considered include: the conversion of nitrite under nonacidic conditions via nitro complexes to nitrosatively active transition metal nitrosyl intermediates (E+ + NO(2-)----E-NO(2-)----E-NO2+); catalysis of N-nitrosamine formation in nitrite-amine mixtures by electrophilic carbon centres that initiate the reaction by attack on the amine (E+ + R2NH----E-NR2); and coordination of nitrite by carbon electrophiles to form activated O-bound species (E+ + ONO(-)----E-O-NO) capable of performing the required N-nitrosation. The findings suggest that acceleration of N-nitrosamine-forming reactions by electrophiles may be a critical factor to consider in attempting to rationalize, predict and control the distribution of carcinogenic N-nitroso compounds in vivo and in the environment.

The costoclavicular ligament revisited: a functional and anatomical study

INTRODUCTION

The sternoclavicular joint is of clinical importance. However, there is scant information in the literature regarding one ligament of this area, the costoclavicular ligament (CCL).

MATERIAL AND METHODS

In order to further elucidate this structure, 10 adult formalin-fixed cadavers (17 sides) underwent dissection of the CCL. Once the CCL was identified, measurements were made of its dimensions and observations made of its anatomy. Next, ranges of motion were performed of the upper extremity and the CCL observed for tension or laxity.

RESULTS

Of the 17 sternoclavicular regions examined 16 (94%) were found to possess a CCL. The average medial and lateral lengths, width and thickness were 1, 2, 1.2, 0.340 cm, respectively. The width of the CCL was statistically smaller in women that in men. The majority of ligaments were single structures traveling from the inferior surface of the medial clavicle just lateral and sometimes-fused (12.5%) to the lateral edge of the sternoclavicular joint. These fibers then terminated on the medial end of the first rib and first costal cartilage (75%) or exclusively onto the first costal cartilage (25%). Most ligaments were single and not composed of two parts. Arm abduction resulted in tautness of the ligament and increased as the degree of abduction increased. Internal rotation of the arm translated into medial shift of the clavicle, raising the clavicle away from the first rib creating tension on the CCL. Moderate degrees of external rotation were required before the CCL became taut and even began to pull the first rib laterally. Small amounts of protraction and retraction of the scapula both put the CCL under tension.

CONCLUSIONS

The CCL is a constant structure found just lateral to the sternoclavicular joint. This ligament was a single band in the majority of our specimens and limited most ranges of motion of the proximal upper limb thus stabilizing the sternoclavicular region.

Surface plasmon resonance investigations of human epidermal growth factor receptor 2

This investigation utilizes surface plasmon resonance (SPR) spectroscopy to detect and quantify human epidermal growth factor receptor 2 (HER-2), an oncogene product that is over-expressed in some aggressive forms of breast cancer. Specifically, the HER-2 trans-membrane protein p185 and its extra cellular fragment p105 are analytes targeted in this work by using a gold-based biosensor slide on which an anti-HER-2 antibody has been immobilized by attachment to Protein G that is fixed to the gold film. A detection limit of > or =11 ng/mL for p185 resulted when trastuzumab was used as the anti-HER-2 antibody on the biosensor slide. Experiments with semi-purified p105 revealed that it binds weakly and reversibly to trastuzumab, therefore complicating its detection and quantification. Results of studies that reacted a 13-amino-acid peptide (PP13) from the HER-2 kinase domain with its specific antibody were critically different than p185 and p105 studies. Spectral analysis of the reflectivity at constant bulk buffer refractive index revealed a progressive negative SPR shift over time. A negative shift suggests that a loss of protein mass from the anti-PP13 antibody-Protein G biosensor is occurring. Several possibilities that may explain these negative SPR shifts are discussed.

Gas-phase detection of trinitrotoluene utilizing a solid-phase antibody immobilized on a gold film by means of surface plasmon resonance spectroscopy

A multilayered biosensor was constructed and found to detect trinitrotoluene (TNT) in ppb concentrations in air both prior to and after detonation of TNT without use of a liquid phosphate buffered saline (PBS) superstrate. The biosensor surface was fabricated from a monoclonal antibody for TNT covalently bound to an 11,11'-dithio-bis(succinimidoylundecanoate) (DSU) self-assembled monolayer immobilized on a thin gold film bonded to a BK7 glass slide. The binding between the immobilized antibody and TNT antigen was detected using surface plasmon resonance spectroscopy (SPRS). Biosensor specificity for TNT was demonstrated with chemical homologues as well as against an unrelated explosive, RDX.

Electrocatalytic reduction of nitrate in water

Nitrate (NO(3)(-)) contamination of groundwater is a common problem throughout intensive agricultural areas (nonpoint source pollution). Current processes (e.g., ion exchange, membrane separation) for NO(3)(-) removal have various disadvantages. The objective of this study was to evaluate an electrocatalytic reduction process to selectively remove NO(3)(-) from groundwater associated with small agricultural communities. A commercially available ELAT (E-Tek Inc., Natick, MA) carbon cloth with a 30% surface coated Rh (rhodium) (1microg x cm(-1)) was tested at an applied potential of -1.5 V versus standard calomel electrode (SCE) with a Pt auxiliary electrode. Electrocatalytic reduction process (electrolysis) of NO(3)(-) was tested with cyclic voltammetry (CV) in samples containing NO(3)(-) and 0.1M NaClO(4)(-). Nitrate and NO(2)(-) concentrations in test solutions and groundwater samples were analyzed by ion chromatography (IC). The presence of Rh on the carbon cloth surface resulted in current increase of 36% over uncoated carbon cloths. The electrocatalysis experiments using Rh coated carbon cloth resulted in reduction of NO(3)(-) and NO(2)(-) on a timescale of minutes. Nitrite is produced as a product, but is rapidly consumed upon further electrolysis. Field groundwater samples subjected to electrocatalysis experiments, without the addition of NaClO(4)(-) electrolyte, also exhibited removal of NO(3)(-) on a timescale of minutes. Overall, results suggest that at an applied potential of -1.5 V with respect to SCE, Rh coated carbon cloth can reduce NO(3)(-) concentrations in field groundwater samples from 73 to 39 mg/L (16.58 to 8.82 mg/L as N) on a timescale range of 40-60 min. The electrocatalytic reduction process described in this study may prove useful for removing NO(3)(-) and NO(2)(-) from groundwater associated with nonpoint source pollution.

Threshold models applied to Holstein conformation traits

Threshold animal models were applied to five conformation traits of Canadian Holsteins. The estimated breeding values for sires from the threshold model allowed the calculation of predicted percentages of daughters in the desirable categories. Results were compared with those from a linear animal model in terms of their ability to predict future percentages of daughters in the desirable categories using an independent set of data. There was no advantage in a threshold model compared with a conventional linear animal model in its ability to predict future daughter performance. This was likely due to the 18 categories used in the classification of major type traits in Canada and the nearly normal distribution of observations across categories.

Use of Chenopodium hybridum facilitates isolation of brome mosaic virus RNA recombinants

Three mutant brome mosaic virus (BMV) RNA-2 transcripts bearing two alterations in the pseudoknot region and one in arm C of the 3' tRNA region, previously characterized as being deficient in tRNA-like functions, have been assayed for their ability to infect and replicate (in the presence of wild-type RNAs-1 and -3) in Chenopodium hybridum plants. Although the introduced mutations have been shown to incapacitate the replication of RNA-2 in barley protoplasts, C. hybridum plants inoculated with these mutants developed local lesions indistinguishable in appearance and morphology from control inoculations containing wild-type RNA-2. Sequence analysis of progeny RNA-2 from two single lesion isolates for each mutant inoculum revealed that the input mutations were restored to functional sequences by homologous recombination within the 3'tRNA-like region. These results, which reflect the ease with which progeny RNA can be characterized from single lesions, exemplify the value of C. hybridum for studying recombination among viral RNAs.