Enabling laboratory readiness and preparedness for the evaluation of suspected viral hemorrhagic fevers: development of a laboratory toolkit.

PURPOSE: Viral hemorrhagic fevers (VHFs), such as Ebola virus disease, Marburg virus disease, and Lassa fever, are associated with significant morbidity and mortality and the potential for person-to-person transmission. While most individuals in whom VHF is suspected will ultimately be diagnosed with a non-VHF illness, such patients may present to any United States healthcare facility (HCF) for initial evaluation; therefore, all HCFs must be prepared to evaluate and initiate care for suspect VHF patients, especially if they are acutely ill. Included within this evaluation is the ability to perform basic routine laboratory testing before VHF-specific diagnostic test results are available, as well as rapid malaria testing to assess for a common, dangerous "VHF mimic." OBJECTIVE: To improve laboratory preparedness and readiness in the initial care of suspect VHF patients who may present to acute care hospitals. DESIGN: Plan-Do-Study-Act quality improvement model. SETTING: Frontline healthcare facilities and their clinical laboratories. METHODS: We describe the development of a laboratory testing toolkit for a suspect VHF patient that can assist frontline HCFs in providing basic laboratory testing required for the care of these patients. RESULTS: The toolkit provides guidance on infection prevention and control, waste management, occupational health, laboratory test collection, processing, and resulting, in the context of suspect VHF patient evaluation. CONCLUSIONS: The toolkit is designed to be readily adapted by any frontline HCF in the US. With the guidance provided, facilities will be able to support safer initial evaluation of VHF suspects and ensure high-quality patient care.

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.