A Multiplexed Cas13-Based Assay with Point-of-Care Attributes for Simultaneous COVID-19 Diagnosis and Variant Surveillance.

Point-of-care (POC) nucleic acid detection technologies are poised to aid gold-standard technologies in controlling the COVID-19 pandemic, yet shortcomings in the capability to perform critically needed complex detection-such as multiplexed detection for viral variant surveillance-may limit their widespread adoption. Herein, we developed a robust multiplexed clustered regularly interspaced short palindromic repeats (CRISPR)-based detection using LwaCas13a and PsmCas13b to simultaneously diagnose severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and pinpoint the causative SARS-CoV-2 variant of concern (VOC)-including globally dominant VOCs Delta (B.1.617.2) and Omicron (B.1.1.529)-all the while maintaining high levels of accuracy upon the detection of multiple SARS-CoV-2 gene targets. The platform has several attributes suitable for POC use: premixed, freeze-dried reagents for easy use and storage; convenient direct-to-eye or smartphone-based readouts; and a one-pot variant of the multiplexed detection. To reduce reliance on proprietary reagents and enable sustainable use of such a technology in low- and middle-income countries, we locally produced and formulated our own recombinase polymerase amplification reaction and demonstrated its equivalent efficiency to commercial counterparts. Our tool-CRISPR-based detection for simultaneous COVID-19 diagnosis and variant surveillance that can be locally manufactured-may enable sustainable use of CRISPR diagnostics technologies for COVID-19 and other diseases in POC settings.

Mammalian retrovirus-like protein PEG10 packages its own mRNA and can be pseudotyped for mRNA delivery.

Eukaryotic genomes contain domesticated genes from integrating viruses and mobile genetic elements. Among these are homologs of the capsid protein (known as Gag) of long terminal repeat (LTR) retrotransposons and retroviruses. We identified several mammalian Gag homologs that form virus-like particles and one LTR retrotransposon homolog, PEG10, that preferentially binds and facilitates vesicular secretion of its own messenger RNA (mRNA). We showed that the mRNA cargo of PEG10 can be reprogrammed by flanking genes of interest with Peg10's untranslated regions. Taking advantage of this reprogrammability, we developed selective endogenous encapsidation for cellular delivery (SEND) by engineering both mouse and human PEG10 to package, secrete, and deliver specific RNAs. Together, these results demonstrate that SEND is a modular platform suited for development as an efficient therapeutic delivery modality.

Dual modes of CRISPR-associated transposon homing.

Tn7-like transposons have co-opted CRISPR systems, including class 1 type I-F, I-B, and class 2 type V-K. Intriguingly, although these CRISPR-associated transposases (CASTs) undergo robust CRISPR RNA (crRNA)-guided transposition, they are almost never found in sites targeted by the crRNAs encoded by the cognate CRISPR array. To understand this paradox, we investigated CAST V-K and I-B systems and found two distinct modes of transposition: (1) crRNA-guided transposition and (2) CRISPR array-independent homing. We show distinct CAST systems utilize different molecular mechanisms to target their homing site. Type V-K CAST systems use a short, delocalized crRNA for RNA-guided homing, whereas type I-B CAST systems, which contain two distinct target selector proteins, use TniQ for RNA-guided DNA transposition and TnsD for homing to an attachment site. These observations illuminate a key step in the life cycle of CAST systems and highlight the diversity of molecular mechanisms mediating transposon homing.

Rapid SARS-CoV-2 testing in primary material based on a novel multiplex RT-LAMP assay.

BACKGROUND: Rapid and extensive testing of large parts of the population and specific subgroups is crucial for proper management of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and decision-making in times of a pandemic outbreak. However, point-of-care (POC) testing in places such as emergency units, outpatient clinics, airport security points or the entrance of any public building is a major challenge. The need for thermal cycling and nucleic acid isolation hampers the use of standard PCR-based methods for this purpose. METHODS: To avoid these obstacles, we tested PCR-independent methods for the detection of SARS-CoV-2 RNA from primary material (nasopharyngeal swabs) including reverse transcription loop-mediated isothermal amplification (RT-LAMP) and specific high-sensitivity enzymatic reporter unlocking (SHERLOCK). RESULTS: Whilst specificity of standard RT-LAMP assays appears to be satisfactory, sensitivity does not reach the current gold-standard quantitative real-time polymerase chain reaction (qPCR) assays yet. We describe a novel multiplexed RT-LAMP approach and validate its sensitivity on primary samples. This approach allows for fast and reliable identification of infected individuals. Primer optimization and multiplexing helps to increase sensitivity significantly. In addition, we directly compare and combine our novel RT-LAMP assays with SHERLOCK. CONCLUSION: In summary, this approach reveals one-step multiplexed RT-LAMP assays as a prime-option for the development of easy and cheap POC test kits.

Clinical validation of a Cas13-based assay for the detection of SARS-CoV-2 RNA.

Nucleic acid detection by isothermal amplification and the collateral cleavage of reporter molecules by CRISPR-associated enzymes is a promising alternative to quantitative PCR. Here, we report the clinical validation of the specific high-sensitivity enzymatic reporter unlocking (SHERLOCK) assay using the enzyme Cas13a from Leptotrichia wadei for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-the virus that causes coronavirus disease 2019 (COVID-19)-in 154 nasopharyngeal and throat swab samples collected at Siriraj Hospital, Thailand. Within a detection limit of 42 RNA copies per reaction, SHERLOCK was 100% specific and 100% sensitive with a fluorescence readout, and 100% specific and 97% sensitive with a lateral-flow readout. For the full range of viral load in the clinical samples, the fluorescence readout was 100% specific and 96% sensitive. For 380 SARS-CoV-2-negative pre-operative samples from patients undergoing surgery, SHERLOCK was in 100% agreement with quantitative PCR with reverse transcription. The assay, which we show is amenable to multiplexed detection in a single lateral-flow strip incorporating an internal control for ribonuclease contamination, should facilitate SARS-CoV-2 detection in settings with limited resources.

Point-of-care testing for COVID-19 using SHERLOCK diagnostics.

The recent outbreak of the novel coronavirus SARS-CoV-2, which causes COVID-19, can be diagnosed using RT-qPCR, but inadequate access to reagents and equipment has slowed disease detection and impeded efforts to mitigate viral spread. Alternative approaches based on combinations of isothermal amplification and CRISPR-mediated detection, such as the SHERLOCK (Specific High Sensitivity Enzymatic Reporter UnLOCKing) technique, offer reduced dependence on RT-qPCR equipment, but previously reported methods required multiple fluid handling steps, complicating their deployment outside clinical labs. Here we developed a simple test chemistry called STOP (SHERLOCK Testing in One Pot) for detecting SARS-CoV-2 in one hour that is suitable for point-of-care use. This simplified test, STOPCovid, provides sensitivity comparable to RT-qPCR-based SARS-CoV-2 tests and has a limit of detection of 100 copies of viral genome input in saliva or nasopharyngeal swabs per reaction. Using lateral flow readout, the test returns result in 70 minutes, and using fluorescence readout, the test returns result in 40 minutes. Moreover, we validated STOPCovid using nasopharyngeal swabs from COVID-19 patients and were able to correctly diagnose 12 positive and 5 negative patients out of 3 replicates. We envision that implementation of STOPCovid will significantly aid "test-trace-isolate" efforts, especially in low-resource settings, which will be critical for long-term public health safety and effective reopening of the society.

Response to Comment on "RNA-guided DNA insertion with CRISPR-associated transposases".

Rice et al suggest that the CRISPR-associated transposase ShCAST system could lead to additional insertion products beyond simple integration of the donor. We clarify the outcomes of ShCAST-mediated insertions in Escherichia coli, which consist of both simple insertions and integration of the donor plasmid. This latter outcome can be avoided by use of a 5' nicked DNA donor.

iPSC-Derived Endothelial Cells Affect Vascular Function in a Tissue-Engineered Blood Vessel Model of Hutchinson-Gilford Progeria Syndrome.

Hutchinson-Gilford progeria syndrome (HGPS) is a rare disorder caused by a point mutation in the Lamin A gene that produces the protein progerin. Progerin toxicity leads to accelerated aging and death from cardiovascular disease. To elucidate the effects of progerin on endothelial cells, we prepared tissue-engineered blood vessels (viTEBVs) using induced pluripotent stem cell-derived smooth muscle cells (viSMCs) and endothelial cells (viECs) from HGPS patients. HGPS viECs aligned with flow but exhibited reduced flow-responsive gene expression and altered NOS3 levels. Relative to viTEBVs with healthy cells, HGPS viTEBVs showed reduced function and exhibited markers of cardiovascular disease associated with endothelium. HGPS viTEBVs exhibited a reduction in both vasoconstriction and vasodilation. Preparing viTEBVs with HGPS viECs and healthy viSMCs only reduced vasodilation. Furthermore, HGPS viECs produced VCAM1 and E-selectin protein in TEBVs with healthy or HGPS viSMCs. In summary, the viTEBV model has identified a role of the endothelium in HGPS.

A cytosine deaminase for programmable single-base RNA editing.

Programmable RNA editing enables reversible recoding of RNA information for research and disease treatment. Previously, we developed a programmable adenosine-to-inosine (A-to-I) RNA editing approach by fusing catalytically inactivate RNA-targeting CRISPR-Cas13 (dCas13) with the adenine deaminase domain of ADAR2. Here, we report a cytidine-to-uridine (C-to-U) RNA editor, referred to as RNA Editing for Specific C-to-U Exchange (RESCUE), by directly evolving ADAR2 into a cytidine deaminase. RESCUE doubles the number of mutations targetable by RNA editing and enables modulation of phosphosignaling-relevant residues. We apply RESCUE to drive ß-catenin activation and cellular growth. Furthermore, RESCUE retains A-to-I editing activity, enabling multiplexed C-to-U and A-to-I editing through the use of tailored guide RNAs.

RNA-guided DNA insertion with CRISPR-associated transposases.

CRISPR-Cas nucleases are powerful tools for manipulating nucleic acids; however, targeted insertion of DNA remains a challenge, as it requires host cell repair machinery. Here we characterize a CRISPR-associated transposase from cyanobacteria Scytonema hofmanni (ShCAST) that consists of Tn7-like transposase subunits and the type V-K CRISPR effector (Cas12k). ShCAST catalyzes RNA-guided DNA transposition by unidirectionally inserting segments of DNA 60 to 66 base pairs downstream of the protospacer. ShCAST integrates DNA into targeted sites in the Escherichia coli genome with frequencies of up to 80% without positive selection. This work expands our understanding of the functional diversity of CRISPR-Cas systems and establishes a paradigm for precision DNA insertion.

Cost effectiveness of a clinical pharmacist on a neurosurgical team.

OBJECTIVE: In 1999, the Society of Critical Care Medicine formally recognized that pharmacists were essential for the provision of high quality care to the critically ill population. This study is a brief quantitative analysis of the benefit provided by a clinical pharmacist in a multidisciplinary neurosurgical setting. METHODS: Patients admitted to the neurosurgical service in the 2 years before and 2 years after the implementation of dedicated neurosurgical pharmacy services were retrospectively reviewed. The clinical pharmacist was responsible for monitoring and evaluating all adult patients on the service and rounding with the team 6 days a week. RESULTS: A total of 2156 patients were admitted during the study period. No significant differences were noted among severity of illness scores between the 2 groups. During this time, 11 250 interventions were recorded by the pharmacist. The average pharmacy and intravenous therapy cost per patient between the pre- and postimplementation groups decreased from $4833 to $3239, resulting in a total savings of $1,718,260 over the duration of the study period. The average hospital stay decreased from 8.56 to 7.24 days (P = 0.003). Early hospital mortality also decreased from 3.34% to 1.95% (P = 0.06). For those patients who were discharged from the hospital, there was a significant decrease in readmission rates between the 2 groups (P < 0.05) CONCLUSION: Having a dedicated clinical pharmacist with critical care training rounding routinely with a neurosurgical team significantly reduced hospital stay, readmission rates, and pharmacy costs. Clinical pharmacists can have a significant effect on clinical and economic measures in the intensive care unit, and their participation on a multidisciplinary critical care team should be a standard of care.

Conversion from continuous insulin infusions to subcutaneous insulin in critically ill patients.

BACKGROUND: Continuous insulin infusions have become a standard of care in many intensive care units (ICUs); however, methods for transitioning patients from continuous infusions to other insulin therapies have not been extensively evaluated. OBJECTIVE: To determine the most effective method for transitioning ICU patients from continuous insulin infusions to subcutaneous insulin therapy. METHODS: A searchable pharmacy database at the University of North Carolina Hospitals was used to retrospectively identify adults admitted to the neurosurgery ICU and prescribed a continuous insulin infusion between May 2007 and February 2008. All patients were transitioned to subcutaneous insulin upon floor transfer. Patients were stratified according to the dose of subcutaneous insulin as a percentage of their prior 24-hour continuous insulin requirement and then analyzed on the rate of achievement of goal blood glucose values (80-150 mg/dL) within the first 48 hours after transition. RESULTS: A total of 769 blood glucose values from 79 patients were recorded during the study. Data analysis demonstrated significantly lower median blood glucose values with the use of subcutaneous insulin doses that were 60-70% of insulin infusion requirements when compared with all other groups. For patients without a history of diabetes mellitus, the use of a subcutaneous dose that was 60-70% of the insulin infusion requirement resulted in a significantly greater percentage of patients within the target range compared with other groups (78%; p < 0.05). For those with a history of diabetes, subcutaneous doses higher than 70% of the insulin infusion requirement yielded the most frequent achievement of target values, although there was substantial variability within this group. No significant difference was noted in the incidence of hypoglycemia (blood glucose <80 mg/dL) between groups, although the frequency of hypoglycemia was almost twice as high in the group with diabetes as in those without it (4.2% vs 2.2%). CONCLUSIONS: Methods currently used to transition patients off insulin infusions vary widely. Initial data suggest that utilizing 60-70% of the 24-hour insulin infusion requirement as a subcutaneous dose would result in blood glucose values of 80-150 mg/dL 70% of the time. Further study is necessary to adequately assess the optimal insulin infusion transition protocol for critically ill patients to ensure both safety and efficacy.

Guidelines for the initial management of metastatic brain tumors: role of surgery, radiosurgery, and radiation therapy.

Brain metastases are an increasingly important determinant of survival and quality of life in patients with cancer. Current approaches to the management of brain metastases are driven by prognostic factors, including the Karnofsky Performance Status, tumor histology, number of metastases, patient age, and status of systemic disease. Most brain metastases are treated with radiosurgery, computer-assisted surgery, or whole brain radiation therapy. Remarkable advances in computer-assisted neuronavigation have made neurosurgical removal of metastases safer, even in eloquent areas of the brain. Computerization also enhances the efficacy and safety of conformal radiosurgery planning using various modern stereotactic radiosurgery (SRS) technologies, including newer frameless-based systems. Controversial issues include whether to defer whole brain radiotherapy (WBRT) in patients undergoing SRS or image-guided surgery and when to use SRS "boost" in a patient undergoing WBRT. The determination of how best to apply these treatments for individual patients cannot be standardized to a single paradigm, but data from well-controlled studies help physicians make informed decisions about the benefits and risks of each approach.