Simplified Cas13-based assays for the fast identification of SARS-CoV-2 and its variants.

The widespread transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) call for rapid nucleic acid diagnostics that are easy to use outside of centralized clinical laboratories. Here we report the development and performance benchmarking of Cas13-based nucleic acid assays leveraging lyophilised reagents and fast sample inactivation at ambient temperature. The assays, which we named SHINEv.2 (for 'streamlined highlighting of infections to navigate epidemics, version 2'), simplify the previously reported RNA-extraction-free SHINEv.1 technology by eliminating heating steps and the need for cold storage of the reagents. SHINEv.2 detected SARS-CoV-2 in nasopharyngeal samples with 90.5% sensitivity and 100% specificity (benchmarked against the reverse transcription quantitative polymerase chain reaction) in less than 90 min, using lateral-flow technology and incubation in a heat block at 37 °C. SHINEv.2 also allows for the visual discrimination of the Alpha, Beta, Gamma, Delta and Omicron SARS-CoV-2 variants, and can be run without performance losses by using body heat. Accurate, easy-to-use and equipment-free nucleic acid assays could facilitate wider testing for SARS-CoV-2 and other pathogens in point-of-care and at-home settings.

Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants.

The coronavirus disease 2019 (COVID-19) pandemic has demonstrated a clear need for high-throughput, multiplexed and sensitive assays for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses and their emerging variants. Here, we present a cost-effective virus and variant detection platform, called microfluidic Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (mCARMEN), which combines CRISPR-based diagnostics and microfluidics with a streamlined workflow for clinical use. We developed the mCARMEN respiratory virus panel to test for up to 21 viruses, including SARS-CoV-2, other coronaviruses and both influenza strains, and demonstrated its diagnostic-grade performance on 525 patient specimens in an academic setting and 166 specimens in a clinical setting. We further developed an mCARMEN panel to enable the identification of 6 SARS-CoV-2 variant lineages, including Delta and Omicron, and evaluated it on 2,088 patient specimens with near-perfect concordance to sequencing-based variant classification. Lastly, we implemented a combined Cas13 and Cas12 approach that enables quantitative measurement of SARS-CoV-2 and influenza A viral copies in samples. The mCARMEN platform enables high-throughput surveillance of multiple viruses and variants simultaneously, enabling rapid detection of SARS-CoV-2 variants.

Re-Examining the Race to Send Ventilators to Low-Resource Settings.

COVID-19 is devastating health systems globally and causing severe ventilator shortages. Since the beginning of the outbreak, the provision and use of ventilators has been a key focus of public discourse. Scientists and engineers from leading universities and companies have rushed to develop low-cost ventilators in hopes of supporting critically ill patients in developing countries. Philanthropists have invested millions in shipping ventilators to low-resource settings, and agencies such as the World Health Organization and the World Bank are prioritizing the purchase of ventilators. While we recognize the humanitarian nature of these efforts, merely shipping ventilators to low-resource environments may not improve outcomes of patients and could potentially cause harm. An ecosystem of considerable technological and human resources is required to support the usage of ventilators within intensive care settings. Medical-grade oxygen supplies, reliable electricity, bioengineering support, and consumables are all needed for ventilators to save lives. However, most ICUs in resource-poor settings do not have access to these resources. Patients on ventilators require continuous monitoring from physicians, nurses, and respiratory therapists skilled in critical care. Health care workers in many low-resource settings are already exceedingly overburdened, and pulling these essential human resources away from other critical patient needs could reduce the overall quality of patient care. When deploying medical devices, it is vital to align the technological intervention with the clinical reality. Low-income settings often will not benefit from resource-intensive equipment, but rather from contextually appropriate devices that meet the unique needs of their health systems.