Characterization of SARS-CoV-2 nucleocapsid protein reveals multiple functional consequences of the C-terminal domain

Nucleocapsid (N) encoded by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays key roles in the replication cycle and is a critical serological marker. Here, we characterize essential biochemical properties of N and describe the utility of these insights in serological studies. We define N domains important for oligomerization and RNA binding and show that N oligomerization provides a high-affinity RNA-binding platform. We also map the RNA-binding interface, showing protection in the N-terminal domain and linker region. In addition, phosphorylation causes reduction of RNA binding and redistribution of N from liquid droplets to loose coils, showing how N-RNA accessibility and assembly may be regulated by phosphorylation. Finally, we find that the C-terminal domain of N is the most immunogenic, based on antibody binding to patient samples. Together, we provide a biochemical description of SARS-CoV-2 N and highlight the value of using N domains as highly specific and sensitive diagnostic markers

Real-time observation of antigen¿antibody association using a low-cost biosensing system based on photonic bandgap structures

This paper was published in OPTICS LETTERS and is made available as an electronic reprint with the permission of OSA. The paper can be found at the following URL on the OSA website: http://dx.doi.org/10.1364/OL.37.003684. Systematic or multiple reproduction or distribution to multiple locations via electronic or other means is prohibited and is subject to penalties under law[EN] In this letter, we present experimental results of antibody detection using a biosensor based on photonic bandgap structures, which are interrogated using a power-based readout technique. This interrogation method allows a realtime monitoring of the association process between the antigen probes and the target antibodies, allowing the instantaneous observation of any interaction event between molecules. because etunable lasers and optical spectrum analyzers are avoided for the readout, a drastic reduction of the final cost of the platform is obtained. Furthermore, the performance of the biosensing system is significantly enhanced due to the large number of data values obtained per second.This work was partially funded by the European Commission under contract FP7-295043-BELERA, from the Spanish Ministerio de Ciencia e Innovacion (MICINN) under contracts TEC2008-06333 and CTQ2010-15943 (subprogram BQU), and from Generalitat Valenciana through the PROMETEO grants 2010-008 and 2012-087.García Castelló, J.; Toccafondo, V.; Escorihuela Fuentes, J.; Bañuls Polo, MJ.; Maquieira Catala, Á.; García-Rupérez, J. (2012). Real-time observation of antigen¿antibody association using a low-cost biosensing system based on photonic bandgap structures. Optics Letters. 37(17):3684-3686. https://doi.org/10.1364/OL.37.003684S368436863717Luchansky, M. S., & Bailey, R. C. (2011). High-Q Optical Sensors for Chemical and Biological Analysis. Analytical Chemistry, 84(2), 793-821. doi:10.1021/ac2029024Qavi, A. J., & Bailey, R. C. (2010). Multiplexed Detection and Label-Free Quantitation of MicroRNAs Using Arrays of Silicon Photonic Microring Resonators. Angewandte Chemie International Edition, 49(27), 4608-4611. doi:10.1002/anie.201001712García-Rupérez, J., Toccafondo, V., Bañuls, M. J., Castelló, J. G., Griol, A., Peransi-Llopis, S., & Maquieira, Á. (2010). Label-free antibody detection using band edge fringes in SOI planar photonic crystal waveguides in the slow-light regime. Optics Express, 18(23), 24276. doi:10.1364/oe.18.024276Toccafondo, V., García-Rupérez, J., Bañuls, M. J., Griol, A., Castelló, J. G., Peransi-Llopis, S., & Maquieira, A. (2010). Single-strand DNA detection using a planar photonic-crystal-waveguide-based sensor. Optics Letters, 35(21), 3673. doi:10.1364/ol.35.003673Claes, T., Molera, J. G., De Vos, K., Schacht, E., Baets, R., & Bienstman, P. (2009). Label-Free Biosensing With a Slot-Waveguide-Based Ring Resonator in Silicon on Insulator. IEEE Photonics Journal, 1(3), 197-204. doi:10.1109/jphot.2009.2031596Scullion, M. G., Di Falco, A., & Krauss, T. F. (2011). Slotted photonic crystal cavities with integrated microfluidics for biosensing applications. Biosensors and Bioelectronics, 27(1), 101-105. doi:10.1016/j.bios.2011.06.023Zlatanovic, S., Mirkarimi, L. W., Sigalas, M. M., Bynum, M. A., Chow, E., Robotti, K. M., … Grot, A. (2009). Photonic crystal microcavity sensor for ultracompact monitoring of reaction kinetics and protein concentration. Sensors and Actuators B: Chemical, 141(1), 13-19. doi:10.1016/j.snb.2009.06.007Sepúlveda, B., Río, J. S. del, Moreno, M., Blanco, F. J., Mayora, K., Domínguez, C., & Lechuga, L. M. (2006). Optical biosensor microsystems based on the integration of highly sensitive Mach–Zehnder interferometer devices. Journal of Optics A: Pure and Applied Optics, 8(7), S561-S566. doi:10.1088/1464-4258/8/7/s41Claes, T., Bogaerts, W., & Bienstman, P. (2011). Vernier-cascade label-free biosensor with integrated arrayed waveguide grating for wavelength interrogation with low-cost broadband source. Optics Letters, 36(17), 3320. doi:10.1364/ol.36.003320Zinoviev, K. E., Gonzalez-Guerrero, A. B., Dominguez, C., & Lechuga, L. M. (2011). Integrated Bimodal Waveguide Interferometric Biosensor for Label-Free Analysis. Journal of Lightwave Technology, 29(13), 1926-1930. doi:10.1109/jlt.2011.2150734Densmore, A., Vachon, M., Xu, D.-X., Janz, S., Ma, R., Li, Y.-H., … Schmid, J. H. (2009). Silicon photonic wire biosensor array for multiplexed real-time and label-free molecular detection. Optics Letters, 34(23), 3598. doi:10.1364/ol.34.003598Castelló, J. G., Toccafondo, V., Pérez-Millán, P., Losilla, N. S., Cruz, J. L., Andrés, M. V., & García-Rupérez, J. (2011). Real-time and low-cost sensing technique based on photonic bandgap structures. Optics Letters, 36(14), 2707. doi:10.1364/ol.36.002707Krishnamoorthy, G., Bianca Beusink, J., & Schasfoort, R. B. M. (2010). High-throughput surface plasmon resonance imaging-based biomolecular kinetic screening analysis. Analytical Methods, 2(8), 1020. doi:10.1039/c0ay00112

Understanding the Potential Impact of Different Drug Properties On SARS-CoV-2 Transmission and Disease Burden: A Modelling Analysis

Background The public health impact of the COVID-19 pandemic has motivated a rapid search for potential therapeutics, with some key successes. However, the potential impact of different treatments, and consequently research and procurement priorities, have not been clear. Methods Using a mathematical model of SARS-CoV-2 transmission, COVID-19 disease and clinical care, we explore the public-health impact of different potential therapeutics, under a range of scenarios varying healthcare capacity, epidemic trajectories; and drug efficacy in the absence of supportive care. Results The impact of drugs like dexamethasone (delivered to the most critically-ill in hospital and whose therapeutic benefit is expected to depend on the availability of supportive care such as oxygen and mechanical ventilation) is likely to be limited in settings where healthcare capacity is lowest or where uncontrolled epidemics result in hospitals being overwhelmed. As such, it may avert 22% of deaths in high-income countries but only 8% in low-income countries (assuming R=1.35). Therapeutics for different patient populations (those not in hospital, early in the course of infection) and types of benefit (reducing disease severity or infectiousness, preventing hospitalisation) could have much greater benefits, particularly in resource-poor settings facing large epidemics. Conclusions Advances in the treatment of COVID-19 to date have been focussed on hospitalised-patients and predicated on an assumption of adequate access to supportive care. Therapeutics delivered earlier in the course of infection that reduce the need for healthcare or reduce infectiousness could have significant impact, and research into their efficacy and means of delivery should be a priority

Understanding the potential impact of different drug properties on SARS-CoV-2 transmission and disease burden : a modelling analysis

Q1Q1Background The unprecedented public health impact of the COVID-19 pandemic has motivated a rapid search for potential therapeutics, with some key successes. However, the potential impact of different treatments, and consequently research and procurement priorities, have not been clear. Methods and Findings develop a mathematical model of SARS-CoV-2 transmission, COVID-19 disease and clinical care to explore the potential public-health impact of a range of different potential therapeutics, under a range of different scenarios varying: i) healthcare capacity, ii) epidemic trajectories; and iii) drug efficacy in the absence of supportive care. In each case, the outcome of interest was the number of COVID-19 deaths averted in scenarios with the therapeutic compared to scenarios without. We find the impact of drugs like dexamethasone (which are delivered to the most critically-ill in hospital and whose therapeutic benefit is expected to depend on the availability of supportive care such as oxygen and mechanical ventilation) is likely to be limited in settings where healthcare capacity is lowest or where uncontrolled epidemics result in hospitals being overwhelmed. As such, it may avert 22% of deaths in highincome countries but only 8% in low-income countries (assuming R=1.35). Therapeutics for different patient populations (those not in hospital, early in the course of infection) and types of benefit (reducing disease severity or infectiousness, preventing hospitalisation) could have much greater benefits, particularly in resource-poor settings facing large epidemics. Conclusions There is a global asymmetry in who is likely to benefit from advances in the treatment of COVID-19 to date, which have been focussed on hospitalised-patients and predicated on an assumption of adequate access to supportive care. Therapeutics that can feasibly be delivered to those earlier in the course of infection that reduce the need for healthcare or reduce infectiousness could have significant impact, and research into their efficacy and means of delivery should be a priorityRevista Internacional - Indexad

Patient portal functionalities and patient outcomes among patients with diabetes: systematic review (Preprint)

Background: Patient portal use could help improve diabetes patients’ care and health outcomes due to the features such as appointment booking, e-messaging, repeat prescription ordering that enable patient-centred care and improved patient self-management of the disease. Objective: To assess health and healthcare quality outcomes associated with the use of tethered (portals that are connected to the electronic healthcare record) patient portals by adult patients (18 years or older) with diabetes. Methods: We searched the databases including Medline, Embase and Scopus and reported the review methodology using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Three independent reviewers screened titles and abstracts, and two reviewers assessed full-texts of relevant studies and performed data extraction and quality assessments of the included studies. We used the Cochrane Collaboration Risk of Bias Tool and the National Heart, Lung and Blood Institute (NIH) Study Quality Assessment Tools to assess the risk of bias of the included studies. Data were summarised through narrative synthesis. Results: Twelve studies were included in this review. Nine studies reported outcomes related to glycaemic control and most of them found statistically significant associations between using a patient portal and glycaemic control. Some studies also found an inverse association or no association between patient portal use and blood pressure, LDL cholesterol or BMI. Studies reported mixed outcomes regarding the use of patient portals and healthcare utilisation measures such as office visits, emergency department visits and hospitalisations. Few studies reported overall improved quality of care for diabetes patients who used patient portals. Conclusions: Studies mostly reported improved health outcomes for diabetes patients who used patient portals. However, the limitations of studying the effects of patient portals exist that do not guarantee whether the outcomes reported were completely a result of patient portal use or if confounding factors exist. Randomised controlled trials and mixed-methods studies could help understand the mechanisms involved in diabetes patient health outcome improvements and patient portal use. Clinical Trial: The protocol of this systematic review was registered in PROSPERO (registration number: CRD42019141131)

Patient portal functionalities and patient outcomes among diabetes patients: a systematic review

Background: Patient portal use could help improve diabetes patients’ care and health outcomes due to the functionalities such as appointment booking, e-messaging, repeat prescription ordering that enables patient-centred care and improve the patient’s self-management of the disease. Objective: To summarise the evidence regarding the use of patient portal (portals that are connected to the electronic healthcare record) or patient portal functionality (e.g. appointment booking or e-messages) and their reported associations with health and healthcare quality outcomes among adult diabetes patients. Methods: We searched the databases Medline, Embase and Scopus and reported the review methodology using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Three independent reviewers screened titles and abstracts, and two reviewers assessed full-texts of relevant studies and performed data extraction and quality assessments of the included studies. We used the Cochrane Collaboration Risk of Bias Tool and the National Heart, Lung and Blood Institute (NHLBI) Study Quality Assessment Tools to assess the risk of bias of the included studies. Data was summarised through narrative synthesis. Results: Twelve studies were included in this review. Five studies reported overall patient portal use and its association with diabetes health and healthcare quality outcomes. Six studies reported E-messaging or email use associated outcomes and two studies reported prescription refill associated outcomes. Reported associations included the association between patient portal use and blood pressure, LDL cholesterol or BMI. Few studies reported outcomes regarding the use of patient portals and healthcare utilisation measures such as office visits, emergency department visits and hospitalisations. Limited number of studies reported overall quality of care for diabetes patients who used patient portals. Conclusions: The included studies mostly reported improved glycaemic control outcomes for diabetes patients who used patient portals. However, limitations of studying the effects of patient portals exist that do not guarantee whether the outcomes reported were completely a result of patient portal use or if confounding factors exist. Randomised controlled trials and mixed-methods studies could help understand the mechanisms involved in diabetes patient health outcome improvements and patient portal use

The ADVANCE trial: Phase 3, randomised comparison of TAF/FTC plus DTG, TDF/FTC plus DTG or TDF/FTC/EFV for first-line treatment of HIV-1 infection

Background: In low- and middle-income countries, most treatment-naïve people living with HIV (PLWH) take tenofovir disoproxil fumarate (TDF) with FTC (or 3TC) and efavirenz (EFV). Dolutegravir (DTG) and tenofovir alafenamide fumarate (TAF) are recommended in international guidelines, but clinical experience with these ARVs in sub-Saharan Africa is limited. In South Africa, over 10% of patients have transmitted NNRTI drug resistance. Methods: We conducted a 96-week, open-label randomised trial in South Africa, comparing TAF/FTC/DTG, TDF/FTC/DTG and TDF/FTC/EFV. Inclusion criteria included age ≥12 years, no prior ART >30 days, creatinine clearance >60 mL/min (>80 mL/min if 500 copies/mL. Pregnancy and tuberculosis (TB) were exclusion criteria. There was no screening for baseline drug resistance, consistent with South African treatment guidelines. The primary treatment failure endpoint was 48-week HIV-1 RNA >50 copies/mL, discontinuation or missing data (Intent-to-treat population, non-inferiority margin -10%, significance level p=0.017, adjusted for multiple comparisons). We report 48-week efficacy and safety data. Results: We randomised 1053 PLWH between February 2017 and May 2018: 99% black, 59% female, mean age 32 years, with mean CD4 336 cells/uL. At week 48, the percentage of participants with HIV RNA 50 copies/mL re-supressed after adherence counselling and re-testing. Overall, 136/185 (74%) of treatment failures were from discontinuation. Clinical adverse events and laboratory abnormalities were similar between treatment arms. Conclusions: In the ADVANCE study, TAF/FTC/DTG and TDF/FTC/DTG demonstrated non-inferior efficacy versus TDF/FTC/EFV, with low rates of virologic failure in all three arms despite country-level background NRTI/NNRTI resistance. There were more discontinuations for adverse events in the TDF/FTC/EFV arm. â€