Identification of SARS-CoV-2 Main Protease (Mpro) Cleavage Sites Using Two-Dimensional Electrophoresis and In Silico Cleavage Site Prediction.

The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a crucial role in its life cycle. The Mpro-mediated limited proteolysis of the viral polyproteins is necessary for the replication of the virus, and cleavage of the host proteins of the infected cells may also contribute to viral pathogenesis, such as evading the immune responses or triggering cell toxicity. Therefore, the identification of host substrates of the viral protease is of special interest. To identify cleavage sites in cellular substrates of SARS-CoV-2 Mpro, we determined changes in the HEK293T cellular proteome upon expression of the Mpro using two-dimensional gel electrophoresis. The candidate cellular substrates of Mpro were identified by mass spectrometry, and then potential cleavage sites were predicted in silico using NetCorona 1.0 and 3CLP web servers. The existence of the predicted cleavage sites was investigated by in vitro cleavage reactions using recombinant protein substrates containing the candidate target sequences, followed by the determination of cleavage positions using mass spectrometry. Unknown and previously described SARS-CoV-2 Mpro cleavage sites and cellular substrates were also identified. Identification of target sequences is important to understand the specificity of the enzyme, as well as aiding the improvement and development of computational methods for cleavage site prediction.

Characterization of Casirivimab Plus Imdevimab, Sotrovimab, and Bamlanivimab Plus Etesevimab-Derived Interference in Serum Protein Electrophoresis and Immunofixation Electrophoresis.

BACKGROUND: Therapeutic monoclonal antibodies can be a source of assay interference in clinical serum protein electrophoresis (SPEP) and immunofixation electrophoresis (IFE), producing monoclonal bands that can be misinterpreted as a monoclonal gammopathy related to a B-cell or plasma cell neoplasm. The extent to which new anti-COVID-19 monoclonal antibodies produce this interference is unknown. METHODS: Casirivimab plus imdevimab, sotrovimab, and bamlanivimab plus etesevimab were spiked into patient serum samples to evaluate for SPEP/IFE interference, to characterize the position of therapy-derived bands relative to a reference band (either combined beta band or beta 1 band, depending on instrument platform), and to confirm heavy and light chain utilization of each medication. Serum samples from patients who had recently received casirivimab plus imdevimab or sotrovimab were also evaluated for comparison. RESULTS: When spiked into serum samples, all tested anti-COVID-19 monoclonal antibodies generated interference in SPEP/IFE. Importantly, the patterns of interference differed between spiked serum samples and serum from patients who had recently received casirivimab plus imdevimab or sotrovimab. CONCLUSIONS: Imdevimab can be added to the growing list of therapeutic monoclonal antibodies that produce sustained interference in SPEP/IFE. Although casirivimab and sotrovimab also produce assay interference in vitro, these antibodies are not reliably detected in serum from recently infused patients. The value of relative band position in recognizing bands that may represent therapeutic monoclonal antibodies is also emphasized. Clinicians and laboratorians should consider therapeutic monoclonal antibody interference in diagnostic SPEP/IFE and review a patient's medication list when new or transient monoclonal bands are identified.

Rapid and sensitive detection of viral particles by coupling redox cycling and electrophoretic enrichment.

The COVID-19 pandemic has highlighted the need for rapid, low-cost, and sensitive virus detection platforms to monitor and mitigate widespread outbreaks. Electrochemical sensors are a viable choice to fill this role but still require improvements to the signal magnitude, especially for early detection and low viral loads. Herein, finite element analysis of a novel biosensor concept for single virion counting using a generator-collector microelectrode design is presented. The proposed design combines a redox-cycling amplified electrochemical current with electrophoresis-driven electrode-particle collision for rapid virus detection. The effects of experimental (e.g. scan rate, collector bias) and geometric factors are studied to optimize the sensor design. Two generator-collector configurations are explored: a ring-disk configuration to analyze sessile droplets and an interdigitated electrode (IDE) design housed in a microchannel. For the ring-disk configuration, we calculate an amplification factor of ∼5 and collector efficiency of ∼0.8 for a generator-collector spacing of 600 nm. For the IDE, the collector efficiency is even larger, approaching unity. The dual-electrode mode is critical for increasing the current and electric field strength. As a result, the current steps upon virus capture are more than an order of magnitude larger compared to single-mode. Additionally, single virus capture times are reduced from over 700 s down to ∼20 s. Overall, the frequency of virus capture and magnitude of the electrochemical current steps depend on the virus properties and electrode configuration, with the IDE capable of single virus detection within seconds owing to better particle confinement in the microchannel.

The impact of COVID-19 on routine patient care from a laboratory perspective.

BACKGROUND: Globally, few studies have examined the effect of the COVID-19 pandemic on routine patient care and follow-up. OBJECTIVES: To evaluate the effect of the COVID-19 response on biochemical test requests received from outpatient departments (OPDs) and peripheral clinics serviced by the National Health Laboratory Service Chemical Pathology Laboratory at Tygerberg Hospital, Cape Town, South Africa (SA). Request volumes were used as a measure of the routine care of patients, as clinical information was not readily available. METHODS: A retrospective audit was conducted. The numbers of requests received from OPDs and peripheral clinics for creatinine, glycated haemoglobin (HbA1c), lipid profiles, thyroid-stimulating hormone (TSH), free thyroxine, free tri-iodothyronine (fT3), serum and urine protein electrophoresis, serum free light chains and neonatal total serum bilirubin were obtained from 1 March to 30 June for 2017, 2018, 2019 and 2020. RESULTS: The biggest impact was seen on lipids, creatinine, HbA1c, TSH and fT3. The percentage reduction between 1 March and 30 June 2019 and between 1 March and 30 June 2020 was 59% for lipids, 64% for creatinine and HbA1c, 80% for TSH and 81% for fT3. There was a noteworthy decrease in overall analyte testing from March to April 2020, coinciding with initiation of level 5 lockdown. Although an increase in testing was observed during June 2020, the number of requests was still lower than in June 2019. CONCLUSIONS: This study, focusing on the short-term consequences of the SA response to the COVID-19 pandemic, found that routine follow-up of patients with communicable and non-communicable diseases was affected. Future studies are necessary to evaluate the long-term consequences of the pandemic for these patient groups.

Hydroxychloroquine Exhibits a Strong Complex Interaction with DNA: Unraveling the Mechanism of Action.

In the past months, the use of the drug hydroxychloroquine has considerably increased in many countries, associated with a proposed treatment for the COVID-19 disease. Although there is no conclusive evidence about the efficacy of the drug for this purpose, surprisingly there are no conclusive studies in the literature concerning its mechanism of action inside cells, which is related to its interaction with nucleic acids. Here, we performed a robust characterization of the interaction between hydroxychloroquine and double-stranded DNA using single-molecule force spectroscopy and gel electrophoresis. Two different binding modes were identified, namely, minor groove binding for low drug concentrations and intercalation for high drug concentrations, and the sets of binding parameters were determined for each of these modes. Such results have unraveled in detail the molecular mechanism of action of the drug as a DNA ligand.

Physicochemical properties of SARS-CoV-2 for drug targeting, virus inactivation and attenuation, vaccine formulation and quality control.

The material properties of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its proteins are discussed. We review the viral structure, size, rigidity, lipophilicity, isoelectric point, buoyant density and centrifugation conditions, stability against pH, temperature, UV light, gamma radiation, and susceptibility to various chemical agents including solvents and detergents. Possible inactivation, downstream, and formulation conditions are given including suitable buffers and some first ideas for quality-control methods. This information supports vaccine development and discussion with competent authorities during vaccine approval and is certainly related to drug-targeting strategies and hygienics. Several instructive tables are given, including the pI and grand average of hydropathicity (GRAVY) of SARS-CoV-1 and -2 proteins in comparison. SARS-CoV-1 and SARS-CoV-2 are similar in many regards, so information can often be derived. Both are unusually stable, but sensitive at their lipophilic membranes. However, since seemingly small differences can have strong effects, for example, on immunologically relevant epitope settings, unevaluated knowledge transfer from SARS-CoV-1 to SARS-CoV-2 cannot be advised. Published knowledge regarding downstream processes, formulations and quality assuring methods is, as yet, limited. However, standard approaches employed for other viruses and vaccines seem to be feasible including virus inactivation, centrifugation conditions, and the use of adjuvants.